parse_signalproteins.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import numpy as np\n",
    "import subprocess\n",
    "import sys\n",
    "sys.path.append(\"..\")\n",
    "from src.useful import read3line_tmbed\n",
    "from src.useful import fasta2df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>sequence</th>\n",
       "      <th>predicted_type</th>\n",
       "      <th>predicted_cleavage</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>MKNVGWLCRVCLIFLAGIILSLLEHTTWAQGPADPGELGPCAVSSQ...</td>\n",
       "      <td>SP</td>\n",
       "      <td>MKNVGWLCRVCLIFLAGIILSLLEHTTWA</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>MKRRSKGFSFAIAILLIACITLFFIWGAQNHFYETVLVDTDENPRE...</td>\n",
       "      <td>NO_SP</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>MKKALLLLILSILCVLVYSQVYEIGHTTITFNDPSRSRDIETEIYY...</td>\n",
       "      <td>NO_SP</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>MKTRGNGTDTQPAARPLRWPLLLCALLLGLLPAACGSDDDSAPGSP...</td>\n",
       "      <td>LIPO</td>\n",
       "      <td>MKTRGNGTDTQPAARPLRWPLLLCALLLGLLPAA</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>MRRAILSWLLLLAVGLGRFIPPDRPGPCAVETGRLSVTTEGGRLPV...</td>\n",
       "      <td>SP</td>\n",
       "      <td>MRRAILSWLLLLAVGLGRFIPP</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                            sequence predicted_type  \\\n",
       "0  MKNVGWLCRVCLIFLAGIILSLLEHTTWAQGPADPGELGPCAVSSQ...             SP   \n",
       "1  MKRRSKGFSFAIAILLIACITLFFIWGAQNHFYETVLVDTDENPRE...          NO_SP   \n",
       "2  MKKALLLLILSILCVLVYSQVYEIGHTTITFNDPSRSRDIETEIYY...          NO_SP   \n",
       "3  MKTRGNGTDTQPAARPLRWPLLLCALLLGLLPAACGSDDDSAPGSP...           LIPO   \n",
       "4  MRRAILSWLLLLAVGLGRFIPPDRPGPCAVETGRLSVTTEGGRLPV...             SP   \n",
       "\n",
       "                   predicted_cleavage  \n",
       "0       MKNVGWLCRVCLIFLAGIILSLLEHTTWA  \n",
       "1                                 NaN  \n",
       "2                                 NaN  \n",
       "3  MKTRGNGTDTQPAARPLRWPLLLCALLLGLLPAA  \n",
       "4              MRRAILSWLLLLAVGLGRFIPP  "
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "usp = pd.read_csv('PETases_uniquephyla_12152023_predictedSPs_results.csv', header=0)\n",
    "usp.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>ProteinID</th>\n",
       "      <th>aa_sequence</th>\n",
       "      <th>TMBed_prediction</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>D4993_C5_H1_Bin_524_scaffold_590470_15</td>\n",
       "      <td>MKNVGWLCRVCLIFLAGIILSLLEHTTWAQGPADPGELGPCAVSSQ...</td>\n",
       "      <td>SSSSSSSSSSSSSSSSSSSSSSSSSSSSSooooooooooooooooo...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>D4993_C5_H4_Bin_238_scaffold_20386_9</td>\n",
       "      <td>MKRRSKGFSFAIAILLIACITLFFIWGAQNHFYETVLVDTDENPRE...</td>\n",
       "      <td>SSSSSSSSSSSSSSSSSSiHHHHHoooooooooooooooooooooo...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>D4993_C5_H1_Bin_313_scaffold_691639_41</td>\n",
       "      <td>MKKALLLLILSILCVLVYSQVYEIGHTTITFNDPSRSRDIETEIYY...</td>\n",
       "      <td>SSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooo...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>D4993_C5_H1_Bin_289_scaffold_436608_7</td>\n",
       "      <td>MKTRGNGTDTQPAARPLRWPLLLCALLLGLLPAACGSDDDSAPGSP...</td>\n",
       "      <td>SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSooooooooooo...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>D4993_C5_H4_Bin_164_scaffold_52205_2</td>\n",
       "      <td>MRRAILSWLLLLAVGLGRFIPPDRPGPCAVETGRLSVTTEGGRLPV...</td>\n",
       "      <td>SSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooo...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                ProteinID  \\\n",
       "0  D4993_C5_H1_Bin_524_scaffold_590470_15   \n",
       "1    D4993_C5_H4_Bin_238_scaffold_20386_9   \n",
       "2  D4993_C5_H1_Bin_313_scaffold_691639_41   \n",
       "3   D4993_C5_H1_Bin_289_scaffold_436608_7   \n",
       "4    D4993_C5_H4_Bin_164_scaffold_52205_2   \n",
       "\n",
       "                                         aa_sequence  \\\n",
       "0  MKNVGWLCRVCLIFLAGIILSLLEHTTWAQGPADPGELGPCAVSSQ...   \n",
       "1  MKRRSKGFSFAIAILLIACITLFFIWGAQNHFYETVLVDTDENPRE...   \n",
       "2  MKKALLLLILSILCVLVYSQVYEIGHTTITFNDPSRSRDIETEIYY...   \n",
       "3  MKTRGNGTDTQPAARPLRWPLLLCALLLGLLPAACGSDDDSAPGSP...   \n",
       "4  MRRAILSWLLLLAVGLGRFIPPDRPGPCAVETGRLSVTTEGGRLPV...   \n",
       "\n",
       "                                    TMBed_prediction  \n",
       "0  SSSSSSSSSSSSSSSSSSSSSSSSSSSSSooooooooooooooooo...  \n",
       "1  SSSSSSSSSSSSSSSSSSiHHHHHoooooooooooooooooooooo...  \n",
       "2  SSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooo...  \n",
       "3  SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSooooooooooo...  \n",
       "4  SSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooo...  "
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "tmbed = read3line_tmbed('PETHits_uniquephyla_Guaymas2020_ALLBINS_12152023.fasta.tmbed.3lines')\n",
    "tmbed.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>ProteinID</th>\n",
       "      <th>aa_sequence</th>\n",
       "      <th>TMBed_prediction</th>\n",
       "      <th>sig_prot</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>D4993_C5_H1_Bin_524_scaffold_590470_15</td>\n",
       "      <td>MKNVGWLCRVCLIFLAGIILSLLEHTTWAQGPADPGELGPCAVSSQ...</td>\n",
       "      <td>SSSSSSSSSSSSSSSSSSSSSSSSSSSSSooooooooooooooooo...</td>\n",
       "      <td>29</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>D4993_C5_H4_Bin_238_scaffold_20386_9</td>\n",
       "      <td>MKRRSKGFSFAIAILLIACITLFFIWGAQNHFYETVLVDTDENPRE...</td>\n",
       "      <td>SSSSSSSSSSSSSSSSSSiHHHHHoooooooooooooooooooooo...</td>\n",
       "      <td>18</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>D4993_C5_H1_Bin_313_scaffold_691639_41</td>\n",
       "      <td>MKKALLLLILSILCVLVYSQVYEIGHTTITFNDPSRSRDIETEIYY...</td>\n",
       "      <td>SSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooo...</td>\n",
       "      <td>19</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>D4993_C5_H1_Bin_289_scaffold_436608_7</td>\n",
       "      <td>MKTRGNGTDTQPAARPLRWPLLLCALLLGLLPAACGSDDDSAPGSP...</td>\n",
       "      <td>SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSooooooooooo...</td>\n",
       "      <td>35</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>D4993_C5_H4_Bin_164_scaffold_52205_2</td>\n",
       "      <td>MRRAILSWLLLLAVGLGRFIPPDRPGPCAVETGRLSVTTEGGRLPV...</td>\n",
       "      <td>SSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooo...</td>\n",
       "      <td>17</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                ProteinID  \\\n",
       "0  D4993_C5_H1_Bin_524_scaffold_590470_15   \n",
       "1    D4993_C5_H4_Bin_238_scaffold_20386_9   \n",
       "2  D4993_C5_H1_Bin_313_scaffold_691639_41   \n",
       "3   D4993_C5_H1_Bin_289_scaffold_436608_7   \n",
       "4    D4993_C5_H4_Bin_164_scaffold_52205_2   \n",
       "\n",
       "                                         aa_sequence  \\\n",
       "0  MKNVGWLCRVCLIFLAGIILSLLEHTTWAQGPADPGELGPCAVSSQ...   \n",
       "1  MKRRSKGFSFAIAILLIACITLFFIWGAQNHFYETVLVDTDENPRE...   \n",
       "2  MKKALLLLILSILCVLVYSQVYEIGHTTITFNDPSRSRDIETEIYY...   \n",
       "3  MKTRGNGTDTQPAARPLRWPLLLCALLLGLLPAACGSDDDSAPGSP...   \n",
       "4  MRRAILSWLLLLAVGLGRFIPPDRPGPCAVETGRLSVTTEGGRLPV...   \n",
       "\n",
       "                                    TMBed_prediction  sig_prot  \n",
       "0  SSSSSSSSSSSSSSSSSSSSSSSSSSSSSooooooooooooooooo...        29  \n",
       "1  SSSSSSSSSSSSSSSSSSiHHHHHoooooooooooooooooooooo...        18  \n",
       "2  SSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooo...        19  \n",
       "3  SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSooooooooooo...        35  \n",
       "4  SSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooo...        17  "
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#Count number of instances of 'S' in each row of the TMBed_prediction column\n",
    "tmbed['sig_prot'] = tmbed['TMBed_prediction'].str.count('S')\n",
    "tmbed.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>ID</th>\n",
       "      <th>Prediction</th>\n",
       "      <th>OTHER</th>\n",
       "      <th>SP(Sec/SPI)</th>\n",
       "      <th>LIPO(Sec/SPII)</th>\n",
       "      <th>TAT(Tat/SPI)</th>\n",
       "      <th>TATLIPO(Sec/SPII)</th>\n",
       "      <th>PILIN(Sec/SPIII)</th>\n",
       "      <th>CS Position</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>D4993_C5_H1_Bin_524_scaffold_590470_15</td>\n",
       "      <td>SP</td>\n",
       "      <td>0.000215</td>\n",
       "      <td>0.999186</td>\n",
       "      <td>0.000154</td>\n",
       "      <td>0.000147</td>\n",
       "      <td>0.000133</td>\n",
       "      <td>0.000128</td>\n",
       "      <td>CS pos: 29-30. Pr: 0.9771</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>D4993_C5_H4_Bin_238_scaffold_20386_9</td>\n",
       "      <td>LIPO</td>\n",
       "      <td>0.399009</td>\n",
       "      <td>0.013556</td>\n",
       "      <td>0.585253</td>\n",
       "      <td>0.000097</td>\n",
       "      <td>0.000069</td>\n",
       "      <td>0.002018</td>\n",
       "      <td>CS pos: 25-26. Pr: 0.0801</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>D4993_C5_H1_Bin_313_scaffold_691639_41</td>\n",
       "      <td>SP</td>\n",
       "      <td>0.000218</td>\n",
       "      <td>0.999172</td>\n",
       "      <td>0.000153</td>\n",
       "      <td>0.000156</td>\n",
       "      <td>0.000139</td>\n",
       "      <td>0.000138</td>\n",
       "      <td>CS pos: 19-20. Pr: 0.9803</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>D4993_C5_H1_Bin_289_scaffold_436608_7</td>\n",
       "      <td>LIPO</td>\n",
       "      <td>0.000702</td>\n",
       "      <td>0.396399</td>\n",
       "      <td>0.602234</td>\n",
       "      <td>0.000205</td>\n",
       "      <td>0.000265</td>\n",
       "      <td>0.000176</td>\n",
       "      <td>CS pos: 34-35. Pr: 0.5705</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>D4993_C5_H4_Bin_164_scaffold_52205_2</td>\n",
       "      <td>SP</td>\n",
       "      <td>0.135076</td>\n",
       "      <td>0.853162</td>\n",
       "      <td>0.010856</td>\n",
       "      <td>0.000293</td>\n",
       "      <td>0.000268</td>\n",
       "      <td>0.000303</td>\n",
       "      <td>CS pos: 25-26. Pr: 0.5599</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                       ID Prediction     OTHER  SP(Sec/SPI)  \\\n",
       "0  D4993_C5_H1_Bin_524_scaffold_590470_15         SP  0.000215     0.999186   \n",
       "1    D4993_C5_H4_Bin_238_scaffold_20386_9       LIPO  0.399009     0.013556   \n",
       "2  D4993_C5_H1_Bin_313_scaffold_691639_41         SP  0.000218     0.999172   \n",
       "3   D4993_C5_H1_Bin_289_scaffold_436608_7       LIPO  0.000702     0.396399   \n",
       "4    D4993_C5_H4_Bin_164_scaffold_52205_2         SP  0.135076     0.853162   \n",
       "\n",
       "   LIPO(Sec/SPII)  TAT(Tat/SPI)  TATLIPO(Sec/SPII)  PILIN(Sec/SPIII)  \\\n",
       "0        0.000154      0.000147           0.000133          0.000128   \n",
       "1        0.585253      0.000097           0.000069          0.002018   \n",
       "2        0.000153      0.000156           0.000139          0.000138   \n",
       "3        0.602234      0.000205           0.000265          0.000176   \n",
       "4        0.010856      0.000293           0.000268          0.000303   \n",
       "\n",
       "                 CS Position  \n",
       "0  CS pos: 29-30. Pr: 0.9771  \n",
       "1  CS pos: 25-26. Pr: 0.0801  \n",
       "2  CS pos: 19-20. Pr: 0.9803  \n",
       "3  CS pos: 34-35. Pr: 0.5705  \n",
       "4  CS pos: 25-26. Pr: 0.5599  "
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#Read in the SP6 data\n",
    "sp6 = pd.read_csv('SP6_PETHITs_prediction_results.txt', skiprows=1, header=0, sep='\\t')\n",
    "sp6.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>ProteinID</th>\n",
       "      <th>aa_sequence</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>D4993_C5_H1_Bin_524_scaffold_590470_15</td>\n",
       "      <td>QGPADPGELGPCAVSSQIVDIDGTLTTHFYYPTDNTCDSHTAPYPG...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>D4993_C5_H4_Bin_238_scaffold_20386_9</td>\n",
       "      <td>WGAQNHFYETVLVDTDENPRETHLVGQIDGVFTDENYGEYEVTIYY...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>D4993_C5_H1_Bin_313_scaffold_691639_41</td>\n",
       "      <td>QVYEIGHTTITFNDPSRSRDIETEIYYPADVAGENVAVSTGTFPVC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>D4993_C5_H1_Bin_289_scaffold_436608_7</td>\n",
       "      <td>CGSDDDSAPGSPAGNEPFYAPDELGPFAVGRSTFTIVDADRGDREL...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>D4993_C5_H4_Bin_164_scaffold_52205_2</td>\n",
       "      <td>GPCAVETGRLSVTTEGGRLPVLIYRPRPPGRLKEQAAVVFGHGLLA...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                ProteinID  \\\n",
       "0  D4993_C5_H1_Bin_524_scaffold_590470_15   \n",
       "1    D4993_C5_H4_Bin_238_scaffold_20386_9   \n",
       "2  D4993_C5_H1_Bin_313_scaffold_691639_41   \n",
       "3   D4993_C5_H1_Bin_289_scaffold_436608_7   \n",
       "4    D4993_C5_H4_Bin_164_scaffold_52205_2   \n",
       "\n",
       "                                         aa_sequence  \n",
       "0  QGPADPGELGPCAVSSQIVDIDGTLTTHFYYPTDNTCDSHTAPYPG...  \n",
       "1  WGAQNHFYETVLVDTDENPRETHLVGQIDGVFTDENYGEYEVTIYY...  \n",
       "2  QVYEIGHTTITFNDPSRSRDIETEIYYPADVAGENVAVSTGTFPVC...  \n",
       "3  CGSDDDSAPGSPAGNEPFYAPDELGPFAVGRSTFTIVDADRGDREL...  \n",
       "4  GPCAVETGRLSVTTEGGRLPVLIYRPRPPGRLKEQAAVVFGHGLLA...  "
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "sp6_pro = fasta2df('SP6_PETHitsprocessed_entries.fasta.txt')\n",
    "sp6_pro.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "#rename column\n",
    "sp6_pro.rename(columns={'aa_sequence': 'sp6_aa'}, inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>sequence</th>\n",
       "      <th>predicted_type</th>\n",
       "      <th>predicted_cleavage</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>MKNVGWLCRVCLIFLAGIILSLLEHTTWAQGPADPGELGPCAVSSQ...</td>\n",
       "      <td>SP</td>\n",
       "      <td>MKNVGWLCRVCLIFLAGIILSLLEHTTWA</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>MKRRSKGFSFAIAILLIACITLFFIWGAQNHFYETVLVDTDENPRE...</td>\n",
       "      <td>NO_SP</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>MKKALLLLILSILCVLVYSQVYEIGHTTITFNDPSRSRDIETEIYY...</td>\n",
       "      <td>NO_SP</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>MKTRGNGTDTQPAARPLRWPLLLCALLLGLLPAACGSDDDSAPGSP...</td>\n",
       "      <td>LIPO</td>\n",
       "      <td>MKTRGNGTDTQPAARPLRWPLLLCALLLGLLPAA</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>MRRAILSWLLLLAVGLGRFIPPDRPGPCAVETGRLSVTTEGGRLPV...</td>\n",
       "      <td>SP</td>\n",
       "      <td>MRRAILSWLLLLAVGLGRFIPP</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                            sequence predicted_type  \\\n",
       "0  MKNVGWLCRVCLIFLAGIILSLLEHTTWAQGPADPGELGPCAVSSQ...             SP   \n",
       "1  MKRRSKGFSFAIAILLIACITLFFIWGAQNHFYETVLVDTDENPRE...          NO_SP   \n",
       "2  MKKALLLLILSILCVLVYSQVYEIGHTTITFNDPSRSRDIETEIYY...          NO_SP   \n",
       "3  MKTRGNGTDTQPAARPLRWPLLLCALLLGLLPAACGSDDDSAPGSP...           LIPO   \n",
       "4  MRRAILSWLLLLAVGLGRFIPPDRPGPCAVETGRLSVTTEGGRLPV...             SP   \n",
       "\n",
       "                   predicted_cleavage  \n",
       "0       MKNVGWLCRVCLIFLAGIILSLLEHTTWA  \n",
       "1                                 NaN  \n",
       "2                                 NaN  \n",
       "3  MKTRGNGTDTQPAARPLRWPLLLCALLLGLLPAA  \n",
       "4              MRRAILSWLLLLAVGLGRFIPP  "
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "usp.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [],
   "source": [
    "def trim_prot_usp(row):\n",
    "    snippet = row['predicted_cleavage']\n",
    "    sequence = row['sequence']\n",
    "    if snippet in sequence: \n",
    "        dropped = sequence.replace(snippet, '')\n",
    "    return dropped "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>sequence</th>\n",
       "      <th>predicted_type</th>\n",
       "      <th>predicted_cleavage</th>\n",
       "      <th>usp_aa</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>MKNVGWLCRVCLIFLAGIILSLLEHTTWAQGPADPGELGPCAVSSQ...</td>\n",
       "      <td>SP</td>\n",
       "      <td>MKNVGWLCRVCLIFLAGIILSLLEHTTWA</td>\n",
       "      <td>QGPADPGELGPCAVSSQIVDIDGTLTTHFYYPTDNTCDSHTAPYPG...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>MKTRGNGTDTQPAARPLRWPLLLCALLLGLLPAACGSDDDSAPGSP...</td>\n",
       "      <td>LIPO</td>\n",
       "      <td>MKTRGNGTDTQPAARPLRWPLLLCALLLGLLPAA</td>\n",
       "      <td>CGSDDDSAPGSPAGNEPFYAPDELGPFAVGRSTFTIVDADRGDREL...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>MRRAILSWLLLLAVGLGRFIPPDRPGPCAVETGRLSVTTEGGRLPV...</td>\n",
       "      <td>SP</td>\n",
       "      <td>MRRAILSWLLLLAVGLGRFIPP</td>\n",
       "      <td>DRPGPCAVETGRLSVTTEGGRLPVLIYRPRPPGRLKEQAAVVFGHG...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>MRFISLISILLLFNLSMAVEIHDLHFYNRYNHTVAATIYLPENLNN...</td>\n",
       "      <td>SP</td>\n",
       "      <td>MRFISLISILLLFNLSMA</td>\n",
       "      <td>VEIHDLHFYNRYNHTVAATIYLPENLNNSPAVIFCGGWLSSREMYS...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>MKKTAIYITYILTICTISIFAQSYEMGHRSEIYIDPSRGDRAIPTE...</td>\n",
       "      <td>SP</td>\n",
       "      <td>MKKTAIYITYILTICTISIFA</td>\n",
       "      <td>QSYEMGHRSEIYIDPSRGDRAIPTEIYYPSLTAGDDVPVADPPTGG...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                            sequence predicted_type  \\\n",
       "0  MKNVGWLCRVCLIFLAGIILSLLEHTTWAQGPADPGELGPCAVSSQ...             SP   \n",
       "3  MKTRGNGTDTQPAARPLRWPLLLCALLLGLLPAACGSDDDSAPGSP...           LIPO   \n",
       "4  MRRAILSWLLLLAVGLGRFIPPDRPGPCAVETGRLSVTTEGGRLPV...             SP   \n",
       "5  MRFISLISILLLFNLSMAVEIHDLHFYNRYNHTVAATIYLPENLNN...             SP   \n",
       "6  MKKTAIYITYILTICTISIFAQSYEMGHRSEIYIDPSRGDRAIPTE...             SP   \n",
       "\n",
       "                   predicted_cleavage  \\\n",
       "0       MKNVGWLCRVCLIFLAGIILSLLEHTTWA   \n",
       "3  MKTRGNGTDTQPAARPLRWPLLLCALLLGLLPAA   \n",
       "4              MRRAILSWLLLLAVGLGRFIPP   \n",
       "5                  MRFISLISILLLFNLSMA   \n",
       "6               MKKTAIYITYILTICTISIFA   \n",
       "\n",
       "                                              usp_aa  \n",
       "0  QGPADPGELGPCAVSSQIVDIDGTLTTHFYYPTDNTCDSHTAPYPG...  \n",
       "3  CGSDDDSAPGSPAGNEPFYAPDELGPFAVGRSTFTIVDADRGDREL...  \n",
       "4  DRPGPCAVETGRLSVTTEGGRLPVLIYRPRPPGRLKEQAAVVFGHG...  \n",
       "5  VEIHDLHFYNRYNHTVAATIYLPENLNNSPAVIFCGGWLSSREMYS...  \n",
       "6  QSYEMGHRSEIYIDPSRGDRAIPTEIYYPSLTAGDDVPVADPPTGG...  "
      ]
     },
     "execution_count": 27,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#subtract the predicted_cleavage column from the sequence column to get the protein without signal peptide\n",
    "usp.dropna(subset=['predicted_cleavage'], inplace=True)\n",
    "usp['usp_aa'] = usp.apply(lambda x: trim_prot_usp(x), axis=1)\n",
    "usp.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 44,
   "metadata": {},
   "outputs": [],
   "source": [
    "#FIrst need to create the suggested tmbed sequences\n",
    "def trim_prot_tmbed(row):\n",
    "    num_sig = row['TMBed_prediction'].count('S')\n",
    "    sequence = row['aa_sequence']\n",
    "    if num_sig == 0:\n",
    "        return None\n",
    "    else:\n",
    "        return sequence[num_sig:]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 45,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>ProteinID</th>\n",
       "      <th>aa_sequence</th>\n",
       "      <th>TMBed_prediction</th>\n",
       "      <th>sig_prot</th>\n",
       "      <th>tmbed_aa</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>D4993_C5_H1_Bin_524_scaffold_590470_15</td>\n",
       "      <td>MKNVGWLCRVCLIFLAGIILSLLEHTTWAQGPADPGELGPCAVSSQ...</td>\n",
       "      <td>SSSSSSSSSSSSSSSSSSSSSSSSSSSSSooooooooooooooooo...</td>\n",
       "      <td>29</td>\n",
       "      <td>QGPADPGELGPCAVSSQIVDIDGTLTTHFYYPTDNTCDSHTAPYPG...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>D4993_C5_H4_Bin_238_scaffold_20386_9</td>\n",
       "      <td>MKRRSKGFSFAIAILLIACITLFFIWGAQNHFYETVLVDTDENPRE...</td>\n",
       "      <td>SSSSSSSSSSSSSSSSSSiHHHHHoooooooooooooooooooooo...</td>\n",
       "      <td>18</td>\n",
       "      <td>CITLFFIWGAQNHFYETVLVDTDENPRETHLVGQIDGVFTDENYGE...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>D4993_C5_H1_Bin_313_scaffold_691639_41</td>\n",
       "      <td>MKKALLLLILSILCVLVYSQVYEIGHTTITFNDPSRSRDIETEIYY...</td>\n",
       "      <td>SSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooo...</td>\n",
       "      <td>19</td>\n",
       "      <td>QVYEIGHTTITFNDPSRSRDIETEIYYPADVAGENVAVSTGTFPVC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>D4993_C5_H1_Bin_289_scaffold_436608_7</td>\n",
       "      <td>MKTRGNGTDTQPAARPLRWPLLLCALLLGLLPAACGSDDDSAPGSP...</td>\n",
       "      <td>SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSooooooooooo...</td>\n",
       "      <td>35</td>\n",
       "      <td>GSDDDSAPGSPAGNEPFYAPDELGPFAVGRSTFTIVDADRGDRELP...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>D4993_C5_H4_Bin_164_scaffold_52205_2</td>\n",
       "      <td>MRRAILSWLLLLAVGLGRFIPPDRPGPCAVETGRLSVTTEGGRLPV...</td>\n",
       "      <td>SSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooo...</td>\n",
       "      <td>17</td>\n",
       "      <td>RFIPPDRPGPCAVETGRLSVTTEGGRLPVLIYRPRPPGRLKEQAAV...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                ProteinID  \\\n",
       "0  D4993_C5_H1_Bin_524_scaffold_590470_15   \n",
       "1    D4993_C5_H4_Bin_238_scaffold_20386_9   \n",
       "2  D4993_C5_H1_Bin_313_scaffold_691639_41   \n",
       "3   D4993_C5_H1_Bin_289_scaffold_436608_7   \n",
       "4    D4993_C5_H4_Bin_164_scaffold_52205_2   \n",
       "\n",
       "                                         aa_sequence  \\\n",
       "0  MKNVGWLCRVCLIFLAGIILSLLEHTTWAQGPADPGELGPCAVSSQ...   \n",
       "1  MKRRSKGFSFAIAILLIACITLFFIWGAQNHFYETVLVDTDENPRE...   \n",
       "2  MKKALLLLILSILCVLVYSQVYEIGHTTITFNDPSRSRDIETEIYY...   \n",
       "3  MKTRGNGTDTQPAARPLRWPLLLCALLLGLLPAACGSDDDSAPGSP...   \n",
       "4  MRRAILSWLLLLAVGLGRFIPPDRPGPCAVETGRLSVTTEGGRLPV...   \n",
       "\n",
       "                                    TMBed_prediction  sig_prot  \\\n",
       "0  SSSSSSSSSSSSSSSSSSSSSSSSSSSSSooooooooooooooooo...        29   \n",
       "1  SSSSSSSSSSSSSSSSSSiHHHHHoooooooooooooooooooooo...        18   \n",
       "2  SSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooo...        19   \n",
       "3  SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSooooooooooo...        35   \n",
       "4  SSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooo...        17   \n",
       "\n",
       "                                            tmbed_aa  \n",
       "0  QGPADPGELGPCAVSSQIVDIDGTLTTHFYYPTDNTCDSHTAPYPG...  \n",
       "1  CITLFFIWGAQNHFYETVLVDTDENPRETHLVGQIDGVFTDENYGE...  \n",
       "2  QVYEIGHTTITFNDPSRSRDIETEIYYPADVAGENVAVSTGTFPVC...  \n",
       "3  GSDDDSAPGSPAGNEPFYAPDELGPFAVGRSTFTIVDADRGDRELP...  \n",
       "4  RFIPPDRPGPCAVETGRLSVTTEGGRLPVLIYRPRPPGRLKEQAAV...  "
      ]
     },
     "execution_count": 45,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "tmbed['tmbed_aa'] = tmbed.apply(lambda x: trim_prot_tmbed(x), axis=1)\n",
    "tmbed.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 46,
   "metadata": {},
   "outputs": [],
   "source": [
    "#Join on sp6_pro with usp and tmbed\n",
    "tmbed_sp6 = tmbed.merge(sp6_pro, how='left', on='ProteinID')\n",
    "tmbed_sp6_usp = tmbed_sp6.merge(usp, how='left', left_on='aa_sequence', right_on='sequence')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 47,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>ProteinID</th>\n",
       "      <th>aa_sequence</th>\n",
       "      <th>TMBed_prediction</th>\n",
       "      <th>sig_prot</th>\n",
       "      <th>tmbed_aa</th>\n",
       "      <th>sp6_aa</th>\n",
       "      <th>sequence</th>\n",
       "      <th>predicted_type</th>\n",
       "      <th>predicted_cleavage</th>\n",
       "      <th>usp_aa</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>D4993_C5_H1_Bin_524_scaffold_590470_15</td>\n",
       "      <td>MKNVGWLCRVCLIFLAGIILSLLEHTTWAQGPADPGELGPCAVSSQ...</td>\n",
       "      <td>SSSSSSSSSSSSSSSSSSSSSSSSSSSSSooooooooooooooooo...</td>\n",
       "      <td>29</td>\n",
       "      <td>QGPADPGELGPCAVSSQIVDIDGTLTTHFYYPTDNTCDSHTAPYPG...</td>\n",
       "      <td>QGPADPGELGPCAVSSQIVDIDGTLTTHFYYPTDNTCDSHTAPYPG...</td>\n",
       "      <td>MKNVGWLCRVCLIFLAGIILSLLEHTTWAQGPADPGELGPCAVSSQ...</td>\n",
       "      <td>SP</td>\n",
       "      <td>MKNVGWLCRVCLIFLAGIILSLLEHTTWA</td>\n",
       "      <td>QGPADPGELGPCAVSSQIVDIDGTLTTHFYYPTDNTCDSHTAPYPG...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>D4993_C5_H4_Bin_238_scaffold_20386_9</td>\n",
       "      <td>MKRRSKGFSFAIAILLIACITLFFIWGAQNHFYETVLVDTDENPRE...</td>\n",
       "      <td>SSSSSSSSSSSSSSSSSSiHHHHHoooooooooooooooooooooo...</td>\n",
       "      <td>18</td>\n",
       "      <td>CITLFFIWGAQNHFYETVLVDTDENPRETHLVGQIDGVFTDENYGE...</td>\n",
       "      <td>WGAQNHFYETVLVDTDENPRETHLVGQIDGVFTDENYGEYEVTIYY...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>D4993_C5_H1_Bin_313_scaffold_691639_41</td>\n",
       "      <td>MKKALLLLILSILCVLVYSQVYEIGHTTITFNDPSRSRDIETEIYY...</td>\n",
       "      <td>SSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooo...</td>\n",
       "      <td>19</td>\n",
       "      <td>QVYEIGHTTITFNDPSRSRDIETEIYYPADVAGENVAVSTGTFPVC...</td>\n",
       "      <td>QVYEIGHTTITFNDPSRSRDIETEIYYPADVAGENVAVSTGTFPVC...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>D4993_C5_H1_Bin_289_scaffold_436608_7</td>\n",
       "      <td>MKTRGNGTDTQPAARPLRWPLLLCALLLGLLPAACGSDDDSAPGSP...</td>\n",
       "      <td>SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSooooooooooo...</td>\n",
       "      <td>35</td>\n",
       "      <td>GSDDDSAPGSPAGNEPFYAPDELGPFAVGRSTFTIVDADRGDRELP...</td>\n",
       "      <td>CGSDDDSAPGSPAGNEPFYAPDELGPFAVGRSTFTIVDADRGDREL...</td>\n",
       "      <td>MKTRGNGTDTQPAARPLRWPLLLCALLLGLLPAACGSDDDSAPGSP...</td>\n",
       "      <td>LIPO</td>\n",
       "      <td>MKTRGNGTDTQPAARPLRWPLLLCALLLGLLPAA</td>\n",
       "      <td>CGSDDDSAPGSPAGNEPFYAPDELGPFAVGRSTFTIVDADRGDREL...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>D4993_C5_H4_Bin_164_scaffold_52205_2</td>\n",
       "      <td>MRRAILSWLLLLAVGLGRFIPPDRPGPCAVETGRLSVTTEGGRLPV...</td>\n",
       "      <td>SSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooo...</td>\n",
       "      <td>17</td>\n",
       "      <td>RFIPPDRPGPCAVETGRLSVTTEGGRLPVLIYRPRPPGRLKEQAAV...</td>\n",
       "      <td>GPCAVETGRLSVTTEGGRLPVLIYRPRPPGRLKEQAAVVFGHGLLA...</td>\n",
       "      <td>MRRAILSWLLLLAVGLGRFIPPDRPGPCAVETGRLSVTTEGGRLPV...</td>\n",
       "      <td>SP</td>\n",
       "      <td>MRRAILSWLLLLAVGLGRFIPP</td>\n",
       "      <td>DRPGPCAVETGRLSVTTEGGRLPVLIYRPRPPGRLKEQAAVVFGHG...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                ProteinID  \\\n",
       "0  D4993_C5_H1_Bin_524_scaffold_590470_15   \n",
       "1    D4993_C5_H4_Bin_238_scaffold_20386_9   \n",
       "2  D4993_C5_H1_Bin_313_scaffold_691639_41   \n",
       "3   D4993_C5_H1_Bin_289_scaffold_436608_7   \n",
       "4    D4993_C5_H4_Bin_164_scaffold_52205_2   \n",
       "\n",
       "                                         aa_sequence  \\\n",
       "0  MKNVGWLCRVCLIFLAGIILSLLEHTTWAQGPADPGELGPCAVSSQ...   \n",
       "1  MKRRSKGFSFAIAILLIACITLFFIWGAQNHFYETVLVDTDENPRE...   \n",
       "2  MKKALLLLILSILCVLVYSQVYEIGHTTITFNDPSRSRDIETEIYY...   \n",
       "3  MKTRGNGTDTQPAARPLRWPLLLCALLLGLLPAACGSDDDSAPGSP...   \n",
       "4  MRRAILSWLLLLAVGLGRFIPPDRPGPCAVETGRLSVTTEGGRLPV...   \n",
       "\n",
       "                                    TMBed_prediction  sig_prot  \\\n",
       "0  SSSSSSSSSSSSSSSSSSSSSSSSSSSSSooooooooooooooooo...        29   \n",
       "1  SSSSSSSSSSSSSSSSSSiHHHHHoooooooooooooooooooooo...        18   \n",
       "2  SSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooo...        19   \n",
       "3  SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSooooooooooo...        35   \n",
       "4  SSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooo...        17   \n",
       "\n",
       "                                            tmbed_aa  \\\n",
       "0  QGPADPGELGPCAVSSQIVDIDGTLTTHFYYPTDNTCDSHTAPYPG...   \n",
       "1  CITLFFIWGAQNHFYETVLVDTDENPRETHLVGQIDGVFTDENYGE...   \n",
       "2  QVYEIGHTTITFNDPSRSRDIETEIYYPADVAGENVAVSTGTFPVC...   \n",
       "3  GSDDDSAPGSPAGNEPFYAPDELGPFAVGRSTFTIVDADRGDRELP...   \n",
       "4  RFIPPDRPGPCAVETGRLSVTTEGGRLPVLIYRPRPPGRLKEQAAV...   \n",
       "\n",
       "                                              sp6_aa  \\\n",
       "0  QGPADPGELGPCAVSSQIVDIDGTLTTHFYYPTDNTCDSHTAPYPG...   \n",
       "1  WGAQNHFYETVLVDTDENPRETHLVGQIDGVFTDENYGEYEVTIYY...   \n",
       "2  QVYEIGHTTITFNDPSRSRDIETEIYYPADVAGENVAVSTGTFPVC...   \n",
       "3  CGSDDDSAPGSPAGNEPFYAPDELGPFAVGRSTFTIVDADRGDREL...   \n",
       "4  GPCAVETGRLSVTTEGGRLPVLIYRPRPPGRLKEQAAVVFGHGLLA...   \n",
       "\n",
       "                                            sequence predicted_type  \\\n",
       "0  MKNVGWLCRVCLIFLAGIILSLLEHTTWAQGPADPGELGPCAVSSQ...             SP   \n",
       "1                                                NaN            NaN   \n",
       "2                                                NaN            NaN   \n",
       "3  MKTRGNGTDTQPAARPLRWPLLLCALLLGLLPAACGSDDDSAPGSP...           LIPO   \n",
       "4  MRRAILSWLLLLAVGLGRFIPPDRPGPCAVETGRLSVTTEGGRLPV...             SP   \n",
       "\n",
       "                   predicted_cleavage  \\\n",
       "0       MKNVGWLCRVCLIFLAGIILSLLEHTTWA   \n",
       "1                                 NaN   \n",
       "2                                 NaN   \n",
       "3  MKTRGNGTDTQPAARPLRWPLLLCALLLGLLPAA   \n",
       "4              MRRAILSWLLLLAVGLGRFIPP   \n",
       "\n",
       "                                              usp_aa  \n",
       "0  QGPADPGELGPCAVSSQIVDIDGTLTTHFYYPTDNTCDSHTAPYPG...  \n",
       "1                                                NaN  \n",
       "2                                                NaN  \n",
       "3  CGSDDDSAPGSPAGNEPFYAPDELGPFAVGRSTFTIVDADRGDREL...  \n",
       "4  DRPGPCAVETGRLSVTTEGGRLPVLIYRPRPPGRLKEQAAVVFGHG...  "
      ]
     },
     "execution_count": 47,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "tmbed_sp6_usp.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 48,
   "metadata": {},
   "outputs": [],
   "source": [
    "tmbed_sp6_usp.drop(columns=['sequence', 'predicted_cleavage', 'TMBed_prediction', 'sig_prot', 'predicted_cleavage', 'predicted_type'], inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 49,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>ProteinID</th>\n",
       "      <th>aa_sequence</th>\n",
       "      <th>tmbed_aa</th>\n",
       "      <th>sp6_aa</th>\n",
       "      <th>usp_aa</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>D4993_C5_H1_Bin_524_scaffold_590470_15</td>\n",
       "      <td>MKNVGWLCRVCLIFLAGIILSLLEHTTWAQGPADPGELGPCAVSSQ...</td>\n",
       "      <td>QGPADPGELGPCAVSSQIVDIDGTLTTHFYYPTDNTCDSHTAPYPG...</td>\n",
       "      <td>QGPADPGELGPCAVSSQIVDIDGTLTTHFYYPTDNTCDSHTAPYPG...</td>\n",
       "      <td>QGPADPGELGPCAVSSQIVDIDGTLTTHFYYPTDNTCDSHTAPYPG...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>D4993_C5_H4_Bin_238_scaffold_20386_9</td>\n",
       "      <td>MKRRSKGFSFAIAILLIACITLFFIWGAQNHFYETVLVDTDENPRE...</td>\n",
       "      <td>CITLFFIWGAQNHFYETVLVDTDENPRETHLVGQIDGVFTDENYGE...</td>\n",
       "      <td>WGAQNHFYETVLVDTDENPRETHLVGQIDGVFTDENYGEYEVTIYY...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>D4993_C5_H1_Bin_313_scaffold_691639_41</td>\n",
       "      <td>MKKALLLLILSILCVLVYSQVYEIGHTTITFNDPSRSRDIETEIYY...</td>\n",
       "      <td>QVYEIGHTTITFNDPSRSRDIETEIYYPADVAGENVAVSTGTFPVC...</td>\n",
       "      <td>QVYEIGHTTITFNDPSRSRDIETEIYYPADVAGENVAVSTGTFPVC...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>D4993_C5_H1_Bin_289_scaffold_436608_7</td>\n",
       "      <td>MKTRGNGTDTQPAARPLRWPLLLCALLLGLLPAACGSDDDSAPGSP...</td>\n",
       "      <td>GSDDDSAPGSPAGNEPFYAPDELGPFAVGRSTFTIVDADRGDRELP...</td>\n",
       "      <td>CGSDDDSAPGSPAGNEPFYAPDELGPFAVGRSTFTIVDADRGDREL...</td>\n",
       "      <td>CGSDDDSAPGSPAGNEPFYAPDELGPFAVGRSTFTIVDADRGDREL...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>D4993_C5_H4_Bin_164_scaffold_52205_2</td>\n",
       "      <td>MRRAILSWLLLLAVGLGRFIPPDRPGPCAVETGRLSVTTEGGRLPV...</td>\n",
       "      <td>RFIPPDRPGPCAVETGRLSVTTEGGRLPVLIYRPRPPGRLKEQAAV...</td>\n",
       "      <td>GPCAVETGRLSVTTEGGRLPVLIYRPRPPGRLKEQAAVVFGHGLLA...</td>\n",
       "      <td>DRPGPCAVETGRLSVTTEGGRLPVLIYRPRPPGRLKEQAAVVFGHG...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                ProteinID  \\\n",
       "0  D4993_C5_H1_Bin_524_scaffold_590470_15   \n",
       "1    D4993_C5_H4_Bin_238_scaffold_20386_9   \n",
       "2  D4993_C5_H1_Bin_313_scaffold_691639_41   \n",
       "3   D4993_C5_H1_Bin_289_scaffold_436608_7   \n",
       "4    D4993_C5_H4_Bin_164_scaffold_52205_2   \n",
       "\n",
       "                                         aa_sequence  \\\n",
       "0  MKNVGWLCRVCLIFLAGIILSLLEHTTWAQGPADPGELGPCAVSSQ...   \n",
       "1  MKRRSKGFSFAIAILLIACITLFFIWGAQNHFYETVLVDTDENPRE...   \n",
       "2  MKKALLLLILSILCVLVYSQVYEIGHTTITFNDPSRSRDIETEIYY...   \n",
       "3  MKTRGNGTDTQPAARPLRWPLLLCALLLGLLPAACGSDDDSAPGSP...   \n",
       "4  MRRAILSWLLLLAVGLGRFIPPDRPGPCAVETGRLSVTTEGGRLPV...   \n",
       "\n",
       "                                            tmbed_aa  \\\n",
       "0  QGPADPGELGPCAVSSQIVDIDGTLTTHFYYPTDNTCDSHTAPYPG...   \n",
       "1  CITLFFIWGAQNHFYETVLVDTDENPRETHLVGQIDGVFTDENYGE...   \n",
       "2  QVYEIGHTTITFNDPSRSRDIETEIYYPADVAGENVAVSTGTFPVC...   \n",
       "3  GSDDDSAPGSPAGNEPFYAPDELGPFAVGRSTFTIVDADRGDRELP...   \n",
       "4  RFIPPDRPGPCAVETGRLSVTTEGGRLPVLIYRPRPPGRLKEQAAV...   \n",
       "\n",
       "                                              sp6_aa  \\\n",
       "0  QGPADPGELGPCAVSSQIVDIDGTLTTHFYYPTDNTCDSHTAPYPG...   \n",
       "1  WGAQNHFYETVLVDTDENPRETHLVGQIDGVFTDENYGEYEVTIYY...   \n",
       "2  QVYEIGHTTITFNDPSRSRDIETEIYYPADVAGENVAVSTGTFPVC...   \n",
       "3  CGSDDDSAPGSPAGNEPFYAPDELGPFAVGRSTFTIVDADRGDREL...   \n",
       "4  GPCAVETGRLSVTTEGGRLPVLIYRPRPPGRLKEQAAVVFGHGLLA...   \n",
       "\n",
       "                                              usp_aa  \n",
       "0  QGPADPGELGPCAVSSQIVDIDGTLTTHFYYPTDNTCDSHTAPYPG...  \n",
       "1                                                NaN  \n",
       "2                                                NaN  \n",
       "3  CGSDDDSAPGSPAGNEPFYAPDELGPFAVGRSTFTIVDADRGDREL...  \n",
       "4  DRPGPCAVETGRLSVTTEGGRLPVLIYRPRPPGRLKEQAAVVFGHG...  "
      ]
     },
     "execution_count": 49,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "tmbed_sp6_usp.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "tmbed_sp6_usp.to_csv('PETases_uniquephyla_12152023_predictedSPs.csv', index=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 51,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>ProteinID</th>\n",
       "      <th>aa_sequence</th>\n",
       "      <th>tmbed_aa</th>\n",
       "      <th>sp6_aa</th>\n",
       "      <th>usp_aa</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>D4993_C5_H1_Bin_524_scaffold_590470_15</td>\n",
       "      <td>MKNVGWLCRVCLIFLAGIILSLLEHTTWAQGPADPGELGPCAVSSQ...</td>\n",
       "      <td>QGPADPGELGPCAVSSQIVDIDGTLTTHFYYPTDNTCDSHTAPYPG...</td>\n",
       "      <td>QGPADPGELGPCAVSSQIVDIDGTLTTHFYYPTDNTCDSHTAPYPG...</td>\n",
       "      <td>QGPADPGELGPCAVSSQIVDIDGTLTTHFYYPTDNTCDSHTAPYPG...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>D4993_C5_H4_Bin_238_scaffold_20386_9</td>\n",
       "      <td>MKRRSKGFSFAIAILLIACITLFFIWGAQNHFYETVLVDTDENPRE...</td>\n",
       "      <td>CITLFFIWGAQNHFYETVLVDTDENPRETHLVGQIDGVFTDENYGE...</td>\n",
       "      <td>WGAQNHFYETVLVDTDENPRETHLVGQIDGVFTDENYGEYEVTIYY...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>D4993_C5_H1_Bin_313_scaffold_691639_41</td>\n",
       "      <td>MKKALLLLILSILCVLVYSQVYEIGHTTITFNDPSRSRDIETEIYY...</td>\n",
       "      <td>QVYEIGHTTITFNDPSRSRDIETEIYYPADVAGENVAVSTGTFPVC...</td>\n",
       "      <td>QVYEIGHTTITFNDPSRSRDIETEIYYPADVAGENVAVSTGTFPVC...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>D4993_C5_H1_Bin_289_scaffold_436608_7</td>\n",
       "      <td>MKTRGNGTDTQPAARPLRWPLLLCALLLGLLPAACGSDDDSAPGSP...</td>\n",
       "      <td>GSDDDSAPGSPAGNEPFYAPDELGPFAVGRSTFTIVDADRGDRELP...</td>\n",
       "      <td>CGSDDDSAPGSPAGNEPFYAPDELGPFAVGRSTFTIVDADRGDREL...</td>\n",
       "      <td>CGSDDDSAPGSPAGNEPFYAPDELGPFAVGRSTFTIVDADRGDREL...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>D4993_C5_H4_Bin_164_scaffold_52205_2</td>\n",
       "      <td>MRRAILSWLLLLAVGLGRFIPPDRPGPCAVETGRLSVTTEGGRLPV...</td>\n",
       "      <td>RFIPPDRPGPCAVETGRLSVTTEGGRLPVLIYRPRPPGRLKEQAAV...</td>\n",
       "      <td>GPCAVETGRLSVTTEGGRLPVLIYRPRPPGRLKEQAAVVFGHGLLA...</td>\n",
       "      <td>DRPGPCAVETGRLSVTTEGGRLPVLIYRPRPPGRLKEQAAVVFGHG...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>D4993_C5_H3_Bin_233_scaffold_450023_15</td>\n",
       "      <td>MRFISLISILLLFNLSMAVEIHDLHFYNRYNHTVAATIYLPENLNN...</td>\n",
       "      <td>AVEIHDLHFYNRYNHTVAATIYLPENLNNSPAVIFCGGWLSSREMY...</td>\n",
       "      <td>VEIHDLHFYNRYNHTVAATIYLPENLNNSPAVIFCGGWLSSREMYS...</td>\n",
       "      <td>VEIHDLHFYNRYNHTVAATIYLPENLNNSPAVIFCGGWLSSREMYS...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>D4998_C1112_H2_Bin_16_scaffold_466487_1</td>\n",
       "      <td>MKKTAIYITYILTICTISIFAQSYEMGHRSEIYIDPSRGDRAIPTE...</td>\n",
       "      <td>QSYEMGHRSEIYIDPSRGDRAIPTEIYYPSLTAGDDVPVADPPTGG...</td>\n",
       "      <td>QSYEMGHRSEIYIDPSRGDRAIPTEIYYPSLTAGDDVPVADPPTGG...</td>\n",
       "      <td>QSYEMGHRSEIYIDPSRGDRAIPTEIYYPSLTAGDDVPVADPPTGG...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>D4993_C5_H1_Bin_231_scaffold_315435_5</td>\n",
       "      <td>MKFPQNHYLFVLILLLITLVPVSGCNDGSGGLEKTTELEPEDIYPL...</td>\n",
       "      <td>NDGSGGLEKTTELEPEDIYPLGDYYDPGKTGPYEVGVKTILLADNS...</td>\n",
       "      <td>CNDGSGGLEKTTELEPEDIYPLGDYYDPGKTGPYEVGVKTILLADN...</td>\n",
       "      <td>CNDGSGGLEKTTELEPEDIYPLGDYYDPGKTGPYEVGVKTILLADN...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>D4993_C5_H2_Bin_635_scaffold_53726_3</td>\n",
       "      <td>SRTRQILTEIYYPADTAGEEVPVAEPGAEGFPAVSFAHGRRMAWSA...</td>\n",
       "      <td>None</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>D4993_C5_H3_Bin_232_scaffold_209370_4</td>\n",
       "      <td>MEKWGVGAILLLGLGTCGSAGCGGGRVTPPDSPGEQMQAELAETLP...</td>\n",
       "      <td>CGGGRVTPPDSPGEQMQAELAETLPEGGGREGRESDVAEVDREGES...</td>\n",
       "      <td>CGGGRVTPPDSPGEQMQAELAETLPEGGGREGRESDVAEVDREGES...</td>\n",
       "      <td>GCGGGRVTPPDSPGEQMQAELAETLPEGGGREGRESDVAEVDREGE...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>D4994_C39_H2_Bin_234_scaffold_60347_1</td>\n",
       "      <td>MNSKLLFAILCMLITVVFAFGQNSANVQNEISYDVFDYAQHPMGTI...</td>\n",
       "      <td>QNSANVQNEISYDVFDYAQHPMGTIWGDPLPDAPALAARGEYMVGV...</td>\n",
       "      <td>QNSANVQNEISYDVFDYAQHPMGTIWGDPLPDAPALAARGEYMVGV...</td>\n",
       "      <td>FGQNSANVQNEISYDVFDYAQHPMGTIWGDPLPDAPALAARGEYMV...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>D4998_C1112_H2_Bin_486_scaffold_507122_1</td>\n",
       "      <td>VGTISFDLVDKERLELYGDKIGEERKFKAQMWYPSDDVTEGERAPW...</td>\n",
       "      <td>None</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>D4993_C5_H3_Bin_602_scaffold_375573_24</td>\n",
       "      <td>MMKDIAITFREGTIAARIYLPPPVHRAGEPHPGIIILHGYLAQQIQ...</td>\n",
       "      <td>None</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>D4998_C1112_H3_Bin_236_scaffold_103142_8</td>\n",
       "      <td>MEKPVVFENEGQQIVGMLHAPDGAEGLSPAVVMFHGFTGTKVEPHR...</td>\n",
       "      <td>None</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>D4993_C5_H1_Bin_410_scaffold_98646_2</td>\n",
       "      <td>MKFRFYAGILIIAVVLIAGCGKDGGIMTQDVEFTSDDGVLLKGTLY...</td>\n",
       "      <td>GKDGGIMTQDVEFTSDDGVLLKGTLYLPAGISEKLPGVTLAHMNMN...</td>\n",
       "      <td>CGKDGGIMTQDVEFTSDDGVLLKGTLYLPAGISEKLPGVTLAHMNM...</td>\n",
       "      <td>CGKDGGIMTQDVEFTSDDGVLLKGTLYLPAGISEKLPGVTLAHMNM...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>D4993_C5_LG_Bin_417_scaffold_264867_7</td>\n",
       "      <td>MTMAHHKPRFVLAVLLLCIAAALPAWSVEPLADPAKPGPYPVGVTT...</td>\n",
       "      <td>VEPLADPAKPGPYPVGVTTMLLVDHSRTDNALAGGPRSLMTEIWYP...</td>\n",
       "      <td>VEPLADPAKPGPYPVGVTTMLLVDHSRTDNALAGGPRSLMTEIWYP...</td>\n",
       "      <td>VEPLADPAKPGPYPVGVTTMLLVDHSRTDNALAGGPRSLMTEIWYP...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>D4993_C5_H1_Bin_371_scaffold_75545_3</td>\n",
       "      <td>MSLVITATMAVGLCGCTDNADTDGADGAEGSATEEGGTEESGKESG...</td>\n",
       "      <td>ADTDGADGAEGSATEEGGTEESGKESGEESKADLAALAAEVEEPGP...</td>\n",
       "      <td>CTDNADTDGADGAEGSATEEGGTEESGKESGEESKADLAALAAEVE...</td>\n",
       "      <td>CTDNADTDGADGAEGSATEEGGTEESGKESGEESKADLAALAAEVE...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>D4993_C5_H2_Bin_171_scaffold_197402_18</td>\n",
       "      <td>MSRAFSFASVAALLVFFAASIWLARLDKGGPPHTELMLEGEVPATL...</td>\n",
       "      <td>None</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>D4998_C1112_H1_Bin_364_scaffold_471436_3</td>\n",
       "      <td>MARLCRFTSGKTWHTVSVAALTLIILVFTSASALALEGNYEQREVD...</td>\n",
       "      <td>LEGNYEQREVDIWSDGTRLSGDLFYPSSIKEGQKLPAIVFCHGWGG...</td>\n",
       "      <td>LEGNYEQREVDIWSDGTRLSGDLFYPSSIKEGQKLPAIVFCHGWGG...</td>\n",
       "      <td>LALEGNYEQREVDIWSDGTRLSGDLFYPSSIKEGQKLPAIVFCHGW...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>D4998_C1112_H1_Bin_375_scaffold_86557_39</td>\n",
       "      <td>MRPFELLMLAGLVVHLVLFLQGREKNDTLRSVIAGLIALICLVHLF...</td>\n",
       "      <td>None</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>D4993_C5_H3_Bin_631_scaffold_202986_31</td>\n",
       "      <td>MSQYDPFLRGPFPAGVKTYEFEDTSRDRKLPIECWYPATSAYKGKD...</td>\n",
       "      <td>None</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>D4993_C5_H2_Bin_558_scaffold_155312_7</td>\n",
       "      <td>MVMTFPGRNALLTLCLILLVALPAATEAPAGPYNVGYVIYDFPFVS...</td>\n",
       "      <td>EAPAGPYNVGYVIYDFPFVSPDGALQSLTTAVWYPTDAEPTPYTYG...</td>\n",
       "      <td>APAGPYNVGYVIYDFPFVSPDGALQSLTTAVWYPTDAEPTPYTYGD...</td>\n",
       "      <td>PAGPYNVGYVIYDFPFVSPDGALQSLTTAVWYPTDAEPTPYTYGDG...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>D4993_C5_H1_Bin_480_scaffold_706036_10</td>\n",
       "      <td>MRKSTYIAMFFAEFVFIIGAIVLFLPISQRPDHTGTYGIGIQAFHL...</td>\n",
       "      <td>AMFFAEFVFIIGAIVLFLPISQRPDHTGTYGIGIQAFHLIDENRKE...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>D4993_C5_H1_Bin_123_scaffold_530574_91</td>\n",
       "      <td>MTKVNFQNKEEKRIVGILSIPKGKGPYPAVIFCHGLGSSKESPLIK...</td>\n",
       "      <td>None</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>D4993_C5_H2_Bin_218_scaffold_547810_1</td>\n",
       "      <td>EPCKIDGDPELALAHELTSTGFVCIAPDAIGFGERTPPGAAPYHGA...</td>\n",
       "      <td>None</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>D4998_C1112_H1_Bin_5_scaffold_642509_4</td>\n",
       "      <td>MKKLSYIFILCILSLIFLPVFAHSQSYQIGHTSIIYYDANRSNREI...</td>\n",
       "      <td>QSYQIGHTSIIYYDANRSNREIPTEIYYPAENEGDNVPVADPYSDG...</td>\n",
       "      <td>QSYQIGHTSIIYYDANRSNREIPTEIYYPAENEGDNVPVADPYSDG...</td>\n",
       "      <td>HSQSYQIGHTSIIYYDANRSNREIPTEIYYPAENEGDNVPVADPYS...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>D4994_C39_H1_Bin_166_scaffold_728166_2</td>\n",
       "      <td>MKIIRSKVCCQRGKVKIQAIQYRPETNFAFPGVIILHGIEGFKAHH...</td>\n",
       "      <td>None</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27</th>\n",
       "      <td>D4994_C39_H2_Bin_42_scaffold_17674_10</td>\n",
       "      <td>MIEENIVLFDSVGRRIAGIIHRPEGRGPFPAVIIAHGFRSDKGRKR...</td>\n",
       "      <td>None</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28</th>\n",
       "      <td>D4993_C5_H3_Bin_14_scaffold_57130_4</td>\n",
       "      <td>MEIPVTFRNEGQQIIGIIHIPDGGGKFPGVILFHGCTGNKAEAHWI...</td>\n",
       "      <td>None</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29</th>\n",
       "      <td>D4998_C1112_H1_Bin_475_scaffold_637556_23</td>\n",
       "      <td>MKTEKITFLNQNGESLAAKLDSPENGDPQVFAIFVHCFTCGKDLVS...</td>\n",
       "      <td>None</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30</th>\n",
       "      <td>D4993_C5_H1_Bin_115_scaffold_205497_4</td>\n",
       "      <td>MTISFWKQIIILIIYSLSILSCAPANVQSQGSVQQADNKHINATSE...</td>\n",
       "      <td>QSQGSVQQADNKHINATSEREFRHVDIWSDGTRISGDLWYPKEFKG...</td>\n",
       "      <td>CAPANVQSQGSVQQADNKHINATSEREFRHVDIWSDGTRISGDLWY...</td>\n",
       "      <td>CAPANVQSQGSVQQADNKHINATSEREFRHVDIWSDGTRISGDLWY...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>31</th>\n",
       "      <td>D4993_C5_LG_Bin_348_scaffold_444466_6</td>\n",
       "      <td>KKLMFLSNRNDKRQIYRISLNRGEAEPLTKSKTSIRSFELSSDGKY...</td>\n",
       "      <td>None</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                    ProteinID  \\\n",
       "0      D4993_C5_H1_Bin_524_scaffold_590470_15   \n",
       "1        D4993_C5_H4_Bin_238_scaffold_20386_9   \n",
       "2      D4993_C5_H1_Bin_313_scaffold_691639_41   \n",
       "3       D4993_C5_H1_Bin_289_scaffold_436608_7   \n",
       "4        D4993_C5_H4_Bin_164_scaffold_52205_2   \n",
       "5      D4993_C5_H3_Bin_233_scaffold_450023_15   \n",
       "6     D4998_C1112_H2_Bin_16_scaffold_466487_1   \n",
       "7       D4993_C5_H1_Bin_231_scaffold_315435_5   \n",
       "8        D4993_C5_H2_Bin_635_scaffold_53726_3   \n",
       "9       D4993_C5_H3_Bin_232_scaffold_209370_4   \n",
       "10      D4994_C39_H2_Bin_234_scaffold_60347_1   \n",
       "11   D4998_C1112_H2_Bin_486_scaffold_507122_1   \n",
       "12     D4993_C5_H3_Bin_602_scaffold_375573_24   \n",
       "13   D4998_C1112_H3_Bin_236_scaffold_103142_8   \n",
       "14       D4993_C5_H1_Bin_410_scaffold_98646_2   \n",
       "15      D4993_C5_LG_Bin_417_scaffold_264867_7   \n",
       "16       D4993_C5_H1_Bin_371_scaffold_75545_3   \n",
       "17     D4993_C5_H2_Bin_171_scaffold_197402_18   \n",
       "18   D4998_C1112_H1_Bin_364_scaffold_471436_3   \n",
       "19   D4998_C1112_H1_Bin_375_scaffold_86557_39   \n",
       "20     D4993_C5_H3_Bin_631_scaffold_202986_31   \n",
       "21      D4993_C5_H2_Bin_558_scaffold_155312_7   \n",
       "22     D4993_C5_H1_Bin_480_scaffold_706036_10   \n",
       "23     D4993_C5_H1_Bin_123_scaffold_530574_91   \n",
       "24      D4993_C5_H2_Bin_218_scaffold_547810_1   \n",
       "25     D4998_C1112_H1_Bin_5_scaffold_642509_4   \n",
       "26     D4994_C39_H1_Bin_166_scaffold_728166_2   \n",
       "27      D4994_C39_H2_Bin_42_scaffold_17674_10   \n",
       "28        D4993_C5_H3_Bin_14_scaffold_57130_4   \n",
       "29  D4998_C1112_H1_Bin_475_scaffold_637556_23   \n",
       "30      D4993_C5_H1_Bin_115_scaffold_205497_4   \n",
       "31      D4993_C5_LG_Bin_348_scaffold_444466_6   \n",
       "\n",
       "                                          aa_sequence  \\\n",
       "0   MKNVGWLCRVCLIFLAGIILSLLEHTTWAQGPADPGELGPCAVSSQ...   \n",
       "1   MKRRSKGFSFAIAILLIACITLFFIWGAQNHFYETVLVDTDENPRE...   \n",
       "2   MKKALLLLILSILCVLVYSQVYEIGHTTITFNDPSRSRDIETEIYY...   \n",
       "3   MKTRGNGTDTQPAARPLRWPLLLCALLLGLLPAACGSDDDSAPGSP...   \n",
       "4   MRRAILSWLLLLAVGLGRFIPPDRPGPCAVETGRLSVTTEGGRLPV...   \n",
       "5   MRFISLISILLLFNLSMAVEIHDLHFYNRYNHTVAATIYLPENLNN...   \n",
       "6   MKKTAIYITYILTICTISIFAQSYEMGHRSEIYIDPSRGDRAIPTE...   \n",
       "7   MKFPQNHYLFVLILLLITLVPVSGCNDGSGGLEKTTELEPEDIYPL...   \n",
       "8   SRTRQILTEIYYPADTAGEEVPVAEPGAEGFPAVSFAHGRRMAWSA...   \n",
       "9   MEKWGVGAILLLGLGTCGSAGCGGGRVTPPDSPGEQMQAELAETLP...   \n",
       "10  MNSKLLFAILCMLITVVFAFGQNSANVQNEISYDVFDYAQHPMGTI...   \n",
       "11  VGTISFDLVDKERLELYGDKIGEERKFKAQMWYPSDDVTEGERAPW...   \n",
       "12  MMKDIAITFREGTIAARIYLPPPVHRAGEPHPGIIILHGYLAQQIQ...   \n",
       "13  MEKPVVFENEGQQIVGMLHAPDGAEGLSPAVVMFHGFTGTKVEPHR...   \n",
       "14  MKFRFYAGILIIAVVLIAGCGKDGGIMTQDVEFTSDDGVLLKGTLY...   \n",
       "15  MTMAHHKPRFVLAVLLLCIAAALPAWSVEPLADPAKPGPYPVGVTT...   \n",
       "16  MSLVITATMAVGLCGCTDNADTDGADGAEGSATEEGGTEESGKESG...   \n",
       "17  MSRAFSFASVAALLVFFAASIWLARLDKGGPPHTELMLEGEVPATL...   \n",
       "18  MARLCRFTSGKTWHTVSVAALTLIILVFTSASALALEGNYEQREVD...   \n",
       "19  MRPFELLMLAGLVVHLVLFLQGREKNDTLRSVIAGLIALICLVHLF...   \n",
       "20  MSQYDPFLRGPFPAGVKTYEFEDTSRDRKLPIECWYPATSAYKGKD...   \n",
       "21  MVMTFPGRNALLTLCLILLVALPAATEAPAGPYNVGYVIYDFPFVS...   \n",
       "22  MRKSTYIAMFFAEFVFIIGAIVLFLPISQRPDHTGTYGIGIQAFHL...   \n",
       "23  MTKVNFQNKEEKRIVGILSIPKGKGPYPAVIFCHGLGSSKESPLIK...   \n",
       "24  EPCKIDGDPELALAHELTSTGFVCIAPDAIGFGERTPPGAAPYHGA...   \n",
       "25  MKKLSYIFILCILSLIFLPVFAHSQSYQIGHTSIIYYDANRSNREI...   \n",
       "26  MKIIRSKVCCQRGKVKIQAIQYRPETNFAFPGVIILHGIEGFKAHH...   \n",
       "27  MIEENIVLFDSVGRRIAGIIHRPEGRGPFPAVIIAHGFRSDKGRKR...   \n",
       "28  MEIPVTFRNEGQQIIGIIHIPDGGGKFPGVILFHGCTGNKAEAHWI...   \n",
       "29  MKTEKITFLNQNGESLAAKLDSPENGDPQVFAIFVHCFTCGKDLVS...   \n",
       "30  MTISFWKQIIILIIYSLSILSCAPANVQSQGSVQQADNKHINATSE...   \n",
       "31  KKLMFLSNRNDKRQIYRISLNRGEAEPLTKSKTSIRSFELSSDGKY...   \n",
       "\n",
       "                                             tmbed_aa  \\\n",
       "0   QGPADPGELGPCAVSSQIVDIDGTLTTHFYYPTDNTCDSHTAPYPG...   \n",
       "1   CITLFFIWGAQNHFYETVLVDTDENPRETHLVGQIDGVFTDENYGE...   \n",
       "2   QVYEIGHTTITFNDPSRSRDIETEIYYPADVAGENVAVSTGTFPVC...   \n",
       "3   GSDDDSAPGSPAGNEPFYAPDELGPFAVGRSTFTIVDADRGDRELP...   \n",
       "4   RFIPPDRPGPCAVETGRLSVTTEGGRLPVLIYRPRPPGRLKEQAAV...   \n",
       "5   AVEIHDLHFYNRYNHTVAATIYLPENLNNSPAVIFCGGWLSSREMY...   \n",
       "6   QSYEMGHRSEIYIDPSRGDRAIPTEIYYPSLTAGDDVPVADPPTGG...   \n",
       "7   NDGSGGLEKTTELEPEDIYPLGDYYDPGKTGPYEVGVKTILLADNS...   \n",
       "8                                                None   \n",
       "9   CGGGRVTPPDSPGEQMQAELAETLPEGGGREGRESDVAEVDREGES...   \n",
       "10  QNSANVQNEISYDVFDYAQHPMGTIWGDPLPDAPALAARGEYMVGV...   \n",
       "11                                               None   \n",
       "12                                               None   \n",
       "13                                               None   \n",
       "14  GKDGGIMTQDVEFTSDDGVLLKGTLYLPAGISEKLPGVTLAHMNMN...   \n",
       "15  VEPLADPAKPGPYPVGVTTMLLVDHSRTDNALAGGPRSLMTEIWYP...   \n",
       "16  ADTDGADGAEGSATEEGGTEESGKESGEESKADLAALAAEVEEPGP...   \n",
       "17                                               None   \n",
       "18  LEGNYEQREVDIWSDGTRLSGDLFYPSSIKEGQKLPAIVFCHGWGG...   \n",
       "19                                               None   \n",
       "20                                               None   \n",
       "21  EAPAGPYNVGYVIYDFPFVSPDGALQSLTTAVWYPTDAEPTPYTYG...   \n",
       "22  AMFFAEFVFIIGAIVLFLPISQRPDHTGTYGIGIQAFHLIDENRKE...   \n",
       "23                                               None   \n",
       "24                                               None   \n",
       "25  QSYQIGHTSIIYYDANRSNREIPTEIYYPAENEGDNVPVADPYSDG...   \n",
       "26                                               None   \n",
       "27                                               None   \n",
       "28                                               None   \n",
       "29                                               None   \n",
       "30  QSQGSVQQADNKHINATSEREFRHVDIWSDGTRISGDLWYPKEFKG...   \n",
       "31                                               None   \n",
       "\n",
       "                                               sp6_aa  \\\n",
       "0   QGPADPGELGPCAVSSQIVDIDGTLTTHFYYPTDNTCDSHTAPYPG...   \n",
       "1   WGAQNHFYETVLVDTDENPRETHLVGQIDGVFTDENYGEYEVTIYY...   \n",
       "2   QVYEIGHTTITFNDPSRSRDIETEIYYPADVAGENVAVSTGTFPVC...   \n",
       "3   CGSDDDSAPGSPAGNEPFYAPDELGPFAVGRSTFTIVDADRGDREL...   \n",
       "4   GPCAVETGRLSVTTEGGRLPVLIYRPRPPGRLKEQAAVVFGHGLLA...   \n",
       "5   VEIHDLHFYNRYNHTVAATIYLPENLNNSPAVIFCGGWLSSREMYS...   \n",
       "6   QSYEMGHRSEIYIDPSRGDRAIPTEIYYPSLTAGDDVPVADPPTGG...   \n",
       "7   CNDGSGGLEKTTELEPEDIYPLGDYYDPGKTGPYEVGVKTILLADN...   \n",
       "8                                                 NaN   \n",
       "9   CGGGRVTPPDSPGEQMQAELAETLPEGGGREGRESDVAEVDREGES...   \n",
       "10  QNSANVQNEISYDVFDYAQHPMGTIWGDPLPDAPALAARGEYMVGV...   \n",
       "11                                                NaN   \n",
       "12                                                NaN   \n",
       "13                                                NaN   \n",
       "14  CGKDGGIMTQDVEFTSDDGVLLKGTLYLPAGISEKLPGVTLAHMNM...   \n",
       "15  VEPLADPAKPGPYPVGVTTMLLVDHSRTDNALAGGPRSLMTEIWYP...   \n",
       "16  CTDNADTDGADGAEGSATEEGGTEESGKESGEESKADLAALAAEVE...   \n",
       "17                                                NaN   \n",
       "18  LEGNYEQREVDIWSDGTRLSGDLFYPSSIKEGQKLPAIVFCHGWGG...   \n",
       "19                                                NaN   \n",
       "20                                                NaN   \n",
       "21  APAGPYNVGYVIYDFPFVSPDGALQSLTTAVWYPTDAEPTPYTYGD...   \n",
       "22                                                NaN   \n",
       "23                                                NaN   \n",
       "24                                                NaN   \n",
       "25  QSYQIGHTSIIYYDANRSNREIPTEIYYPAENEGDNVPVADPYSDG...   \n",
       "26                                                NaN   \n",
       "27                                                NaN   \n",
       "28                                                NaN   \n",
       "29                                                NaN   \n",
       "30  CAPANVQSQGSVQQADNKHINATSEREFRHVDIWSDGTRISGDLWY...   \n",
       "31                                                NaN   \n",
       "\n",
       "                                               usp_aa  \n",
       "0   QGPADPGELGPCAVSSQIVDIDGTLTTHFYYPTDNTCDSHTAPYPG...  \n",
       "1                                                 NaN  \n",
       "2                                                 NaN  \n",
       "3   CGSDDDSAPGSPAGNEPFYAPDELGPFAVGRSTFTIVDADRGDREL...  \n",
       "4   DRPGPCAVETGRLSVTTEGGRLPVLIYRPRPPGRLKEQAAVVFGHG...  \n",
       "5   VEIHDLHFYNRYNHTVAATIYLPENLNNSPAVIFCGGWLSSREMYS...  \n",
       "6   QSYEMGHRSEIYIDPSRGDRAIPTEIYYPSLTAGDDVPVADPPTGG...  \n",
       "7   CNDGSGGLEKTTELEPEDIYPLGDYYDPGKTGPYEVGVKTILLADN...  \n",
       "8                                                 NaN  \n",
       "9   GCGGGRVTPPDSPGEQMQAELAETLPEGGGREGRESDVAEVDREGE...  \n",
       "10  FGQNSANVQNEISYDVFDYAQHPMGTIWGDPLPDAPALAARGEYMV...  \n",
       "11                                                NaN  \n",
       "12                                                NaN  \n",
       "13                                                NaN  \n",
       "14  CGKDGGIMTQDVEFTSDDGVLLKGTLYLPAGISEKLPGVTLAHMNM...  \n",
       "15  VEPLADPAKPGPYPVGVTTMLLVDHSRTDNALAGGPRSLMTEIWYP...  \n",
       "16  CTDNADTDGADGAEGSATEEGGTEESGKESGEESKADLAALAAEVE...  \n",
       "17                                                NaN  \n",
       "18  LALEGNYEQREVDIWSDGTRLSGDLFYPSSIKEGQKLPAIVFCHGW...  \n",
       "19                                                NaN  \n",
       "20                                                NaN  \n",
       "21  PAGPYNVGYVIYDFPFVSPDGALQSLTTAVWYPTDAEPTPYTYGDG...  \n",
       "22                                                NaN  \n",
       "23                                                NaN  \n",
       "24                                                NaN  \n",
       "25  HSQSYQIGHTSIIYYDANRSNREIPTEIYYPAENEGDNVPVADPYS...  \n",
       "26                                                NaN  \n",
       "27                                                NaN  \n",
       "28                                                NaN  \n",
       "29                                                NaN  \n",
       "30  CAPANVQSQGSVQQADNKHINATSEREFRHVDIWSDGTRISGDLWY...  \n",
       "31                                                NaN  "
      ]
     },
     "execution_count": 51,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "tmbed_sp6_usp"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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