Read

TMKit supports reading biological sequences from FASTA, PDB (both RCSB and PDBTM), and XML files from PDBTM through the tmk.seq module.

Since residues in FASTA sequences may not perfectly align with those in PDB structures—due to discontinuities in experimentally resolved residues caused by crystallization challenges (refer to [1^])—TMKit provides a mapping and conversion system to align FASTA IDs with PDB IDs.

While the sequence remains unchanged in both formats, this mapping ensures that each residue’s exact position in the PDB structure can be accurately referenced in relation to its FASTA sequence.

[1^]: Pao, KC., Wood, N.T., Knebel, A. et al. Activity-based E3 ligase profiling uncovers an E3 ligase with esterification activity. Nature 556, 381–385 (2018). https://doi.org/10.1038/s41586-018-0026-1

Reminder of data

Please make sure that the build-in example dataset has been downloaded before you walk through the tutorial.

Sequence from a Fasta file

We can read a sequence from a Fasta file by putting the following code. We can use protein 1xqf chain A (./data/fasta/1xqfA.fasta).

Label1

import tmkit as tmk

sequence = tmk.seq.read_from_fasta(
    fasta_fpn='./data/fasta/1xqfA.fasta'
)

Attributes

Attribute	Description
fasta_fpn	path to a Fasta file

Please see here for better understanding the file-naming system.

Output

AVADKADNAFMMICTALVLFMTIPGIALFYGGLIRGKNVLSMLTQVTVTFALVCILWVVYGYSLAFGEGNNFFGNINWLMLKNIELTAVMGSIYQYIHVAFQGSFACITVGLIVGALAERIRFSAVLIFVVVWLTLSYIPIAHMVWGGGLLASHGALDFAGGTVVHINAAIAGLVGAYLPHNLPMVFTGTAILYIGWFGFNAGSAGTANEIAALAFVNTVVATAAAILGWIFGEWALRGKPSLLGACSGAIAGLVGVTPACGYIGVGGALIIGVVAGLAGLWGVTMPCDVFGVHGVCGIVGCIMTGIFAASSLGGVGFAEGVTMGHQLLVQLESIAITIVWSGVVAFIGYKLADLTVGLRVP

Sequence from a PDB file

We can read a sequence from a Fasta file by putting the following code. We can use protein 1xqf chain A (./data/pdb/1xqfA.pdb).

Label1

import tmkit as tmk

sequence = tmk.seq.read_from_pdb(
    pdb_fp='./data/pdb/',
    prot_name='1xqf',
    seq_chain='A',
    file_chain='A',
)

Attributes

Attribute	Description
pdb_fp	path where a target PDB file is placed
prot_name	name of a protein in the prefix of a PDB file name (e.g., 1xqf in 1xqfA.pdb)
seq_chain	chain of a protein in the prefix of a PDB file name (e.g., A in 1xqfA.pdb) (biological purpose)
file_chain	chain of a protein in the prefix of a PDB file name (e.g., A in 1xqfA.pdb) (technical purpose)

Please see here for better understanding the file-naming system.

Output

AVADKADNAFMMICTALVLFMTIPGIALFYGGLIRGKNVLSMLTQVTVTFALVCILWVVYGYSLAFGEGNNFFGNINWLMLKNIELTAVMGSIYQYIHVAFQGSFACITVGLIVGALAERIRFSAVLIFVVVWLTLSYIPIAHMVWGGGLLASHGALDFAGGTVVHINAAIAGLVGAYLPHNLPMVFTGTAILYIGWFGFNAGSAGTANEIAALAFVNTVVATAAAILGWIFGEWALRGKPSLLGACSGAIAGLVGVTPACGYIGVGGALIIGVVAGLAGLWGVTMPCDVFGVHGVCGIVGCIMTGIFAASSLGGVGFAEGVTMGHQLLVQLESIAITIVWSGVVAFIGYKLADLTVGLRVP

Sequence from an XML file

We can read a sequence from a Fasta file by putting the following code. We can use protein 1xqf chain A (./data/xml/1xqf.xml).

Label1

import tmkit as tmk

sequence = tmk.seq.read_from_xml(
    xml_fp='./data/xml/',
    xml_name='1xqf',
    seq_chain='A',
)

Attributes

Attribute	Description
xml_fp	path where a target XML file is placed
xml_name	name of the XML file
seq_chain	chain of a protein

Please see here for better understanding the file-naming system.

Output

APAVADKADNAFMMICTALVLFMTIPGIALFYGGLIRGKNVLSMLTQVTVTFALVCILWVVYGYSLAFGEGNNFFGNINWLMLKNIELTAVMGSIYQYIHVAFQGSFACITVGLIVGALAERIRFSAVLIFVVVWLTLSYIPIAHMVWGGGLLASHGALDFAGGTVVHINAAIAGLVGAYLIGKRVGFGKEAFKPHNLPMVFTGTAILYIGWFGFNAGSAGTANEIAALAFVNTVVATAAAILGWIFGEWALRGKPSLLGACSGAIAGLVGVTPACGYIGVGGALIIGVVAGLAGLWGVTMLKRLLRVDDPCDVFGVHGVCGIVGCIMTGIFAASSLGGVGFAEGVTMGHQLLVQLESIAITIVWSGVVAFIGYKLADLTVGLRVPEEQEREGLDVNSHGENAYNADQAQQPAQADLE

Get residue IDs from a FASTA file

We can still use the Fasta file (protein 1xqf chain A) to extract IDs of residues (./data/fasta/1xqf.fasta).

Label1

import tmkit as tmk

seq_fasta_ids = tmk.seq.fasid(
    fasta_fpn='./data/fasta/1xqfA.fasta',
)

Attributes

Attribute	Description
fasta_fpn	path to a Fasta file

Please see here for better understanding the file-naming system.

Output

{1: 'A', 2: 'V', 3: 'A', 4: 'D', 5: 'K', 6: 'A', 7: 'D', 8: 'N', 9: 'A', 10: 'F', 11: 'M', 12: 'M', 13: 'I', 14: 'C', 15: 'T', 16: 'A', 17: 'L', 18: 'V', 19: 'L', 20: 'F', 21: 'M', 22: 'T', 23: 'I', 24: 'P', 25: 'G', 26: 'I', 27: 'A', 28: 'L', 29: 'F', 30: 'Y', 31: 'G', 32: 'G', 33: 'L', 34: 'I', 35: 'R', 36: 'G', 37: 'K', 38: 'N', 39: 'V', 40: 'L', 41: 'S', 42: 'M', 43: 'L', 44: 'T', 45: 'Q', 46: 'V', 47: 'T', 48: 'V', 49: 'T', 50: 'F', 51: 'A', 52: 'L', 53: 'V', 54: 'C', 55: 'I', 56: 'L', 57: 'W', 58: 'V', 59: 'V', 60: 'Y', 61: 'G', 62: 'Y', 63: 'S', 64: 'L', 65: 'A', 66: 'F', 67: 'G', 68: 'E', 69: 'G', 70: 'N', 71: 'N', 72: 'F', 73: 'F', 74: 'G', 75: 'N', 76: 'I', 77: 'N', 78: 'W', 79: 'L', 80: 'M', 81: 'L', 82: 'K', 83: 'N', 84: 'I', 85: 'E', 86: 'L', 87: 'T', 88: 'A', 89: 'V', 90: 'M', 91: 'G', 92: 'S', 93: 'I', 94: 'Y', 95: 'Q', 96: 'Y', 97: 'I', 98: 'H', 99: 'V', 100: 'A', 101: 'F', 102: 'Q', 103: 'G', 104: 'S', 105: 'F', 106: 'A', 107: 'C', 108: 'I', 109: 'T', 110: 'V', 111: 'G', 112: 'L', 113: 'I', 114: 'V', 115: 'G', 116: 'A', 117: 'L', 118: 'A', 119: 'E', 120: 'R', 121: 'I', 122: 'R', 123: 'F', 124: 'S', 125: 'A', 126: 'V', 127: 'L', 128: 'I', 129: 'F', 130: 'V', 131: 'V', 132: 'V', 133: 'W', 134: 'L', 135: 'T', 136: 'L', 137: 'S', 138: 'Y', 139: 'I', 140: 'P', 141: 'I', 142: 'A', 143: 'H', 144: 'M', 145: 'V', 146: 'W', 147: 'G', 148: 'G', 149: 'G', 150: 'L', 151: 'L', 152: 'A', 153: 'S', 154: 'H', 155: 'G', 156: 'A', 157: 'L', 158: 'D', 159: 'F', 160: 'A', 161: 'G', 162: 'G', 163: 'T', 164: 'V', 165: 'V', 166: 'H', 167: 'I', 168: 'N', 169: 'A', 170: 'A', 171: 'I', 172: 'A', 173: 'G', 174: 'L', 175: 'V', 176: 'G', 177: 'A', 178: 'Y', 179: 'L', 180: 'P', 181: 'H', 182: 'N', 183: 'L', 184: 'P', 185: 'M', 186: 'V', 187: 'F', 188: 'T', 189: 'G', 190: 'T', 191: 'A', 192: 'I', 193: 'L', 194: 'Y', 195: 'I', 196: 'G', 197: 'W', 198: 'F', 199: 'G', 200: 'F', 201: 'N', 202: 'A', 203: 'G', 204: 'S', 205: 'A', 206: 'G', 207: 'T', 208: 'A', 209: 'N', 210: 'E', 211: 'I', 212: 'A', 213: 'A', 214: 'L', 215: 'A', 216: 'F', 217: 'V', 218: 'N', 219: 'T', 220: 'V', 221: 'V', 222: 'A', 223: 'T', 224: 'A', 225: 'A', 226: 'A', 227: 'I', 228: 'L', 229: 'G', 230: 'W', 231: 'I', 232: 'F', 233: 'G', 234: 'E', 235: 'W', 236: 'A', 237: 'L', 238: 'R', 239: 'G', 240: 'K', 241: 'P', 242: 'S', 243: 'L', 244: 'L', 245: 'G', 246: 'A', 247: 'C', 248: 'S', 249: 'G', 250: 'A', 251: 'I', 252: 'A', 253: 'G', 254: 'L', 255: 'V', 256: 'G', 257: 'V', 258: 'T', 259: 'P', 260: 'A', 261: 'C', 262: 'G', 263: 'Y', 264: 'I', 265: 'G', 266: 'V', 267: 'G', 268: 'G', 269: 'A', 270: 'L', 271: 'I', 272: 'I', 273: 'G', 274: 'V', 275: 'V', 276: 'A', 277: 'G', 278: 'L', 279: 'A', 280: 'G', 281: 'L', 282: 'W', 283: 'G', 284: 'V', 285: 'T', 286: 'M', 287: 'P', 288: 'C', 289: 'D', 290: 'V', 291: 'F', 292: 'G', 293: 'V', 294: 'H', 295: 'G', 296: 'V', 297: 'C', 298: 'G', 299: 'I', 300: 'V', 301: 'G', 302: 'C', 303: 'I', 304: 'M', 305: 'T', 306: 'G', 307: 'I', 308: 'F', 309: 'A', 310: 'A', 311: 'S', 312: 'S', 313: 'L', 314: 'G', 315: 'G', 316: 'V', 317: 'G', 318: 'F', 319: 'A', 320: 'E', 321: 'G', 322: 'V', 323: 'T', 324: 'M', 325: 'G', 326: 'H', 327: 'Q', 328: 'L', 329: 'L', 330: 'V', 331: 'Q', 332: 'L', 333: 'E', 334: 'S', 335: 'I', 336: 'A', 337: 'I', 338: 'T', 339: 'I', 340: 'V', 341: 'W', 342: 'S', 343: 'G', 344: 'V', 345: 'V', 346: 'A', 347: 'F', 348: 'I', 349: 'G', 350: 'Y', 351: 'K', 352: 'L', 353: 'A', 354: 'D', 355: 'L', 356: 'T', 357: 'V', 358: 'G', 359: 'L', 360: 'R', 361: 'V', 362: 'P'}

Get residue IDs from a FASTA file

TMKit allows for extracting structure-derived IDs of residues from a PDB protein file. For example, we can still use protein 1xqf chain A for this (./data/pdb/1xqf.pdb).

Important

It is important to correctly mapping Fasta IDs of residues to their exact positions in a PDB structure as it may affect your biological analysis and result interpretation. You can see the output of the PDB IDs of residues of 1xqfA protein that do not agree to those from Fasta IDs. This tutorial offers a basic operation for this (please refer to [1]).

Label1

import tmkit as tmk

seq_fasta_ids = tmk.seq.fasid(
    fasta_fpn='./data/fasta/1xqfA.fasta',
)

Attributes

Attribute	Description
pdb_fp	path where a target PDB file is placed
prot_name	name of a protein in the prefix of a PDB file name (e.g., 1xqf in 1xqfA.pdb)
seq_chain	chain of a protein in the prefix of a PDB file name (e.g., A in 1xqfA.pdb) (biological purpose)
file_chain	chain of a protein in the prefix of a PDB file name (e.g., A in 1xqfA.pdb) (technical purpose)

Please see here for better understanding the file-naming system.

Output

{3: 'A', 4: 'V', 5: 'A', 6: 'D', 7: 'K', 8: 'A', 9: 'D', 10: 'N', 11: 'A', 12: 'F', 13: 'M', 14: 'M', 15: 'I', 16: 'C', 17: 'T', 18: 'A', 19: 'L', 20: 'V', 21: 'L', 22: 'F', 23: 'M', 24: 'T', 25: 'I', 26: 'P', 27: 'G', 28: 'I', 29: 'A', 30: 'L', 31: 'F', 32: 'Y', 33: 'G', 34: 'G', 35: 'L', 36: 'I', 37: 'R', 38: 'G', 39: 'K', 40: 'N', 41: 'V', 42: 'L', 43: 'S', 44: 'M', 45: 'L', 46: 'T', 47: 'Q', 48: 'V', 49: 'T', 50: 'V', 51: 'T', 52: 'F', 53: 'A', 54: 'L', 55: 'V', 56: 'C', 57: 'I', 58: 'L', 59: 'W', 60: 'V', 61: 'V', 62: 'Y', 63: 'G', 64: 'Y', 65: 'S', 66: 'L', 67: 'A', 68: 'F', 69: 'G', 70: 'E', 71: 'G', 72: 'N', 73: 'N', 74: 'F', 75: 'F', 76: 'G', 77: 'N', 78: 'I', 79: 'N', 80: 'W', 81: 'L', 82: 'M', 83: 'L', 84: 'K', 85: 'N', 86: 'I', 87: 'E', 88: 'L', 89: 'T', 90: 'A', 91: 'V', 92: 'M', 93: 'G', 94: 'S', 95: 'I', 96: 'Y', 97: 'Q', 98: 'Y', 99: 'I', 100: 'H', 101: 'V', 102: 'A', 103: 'F', 104: 'Q', 105: 'G', 106: 'S', 107: 'F', 108: 'A', 109: 'C', 110: 'I', 111: 'T', 112: 'V', 113: 'G', 114: 'L', 115: 'I', 116: 'V', 117: 'G', 118: 'A', 119: 'L', 120: 'A', 121: 'E', 122: 'R', 123: 'I', 124: 'R', 125: 'F', 126: 'S', 127: 'A', 128: 'V', 129: 'L', 130: 'I', 131: 'F', 132: 'V', 133: 'V', 134: 'V', 135: 'W', 136: 'L', 137: 'T', 138: 'L', 139: 'S', 140: 'Y', 141: 'I', 142: 'P', 143: 'I', 144: 'A', 145: 'H', 146: 'M', 147: 'V', 148: 'W', 149: 'G', 150: 'G', 151: 'G', 152: 'L', 153: 'L', 154: 'A', 155: 'S', 156: 'H', 157: 'G', 158: 'A', 159: 'L', 160: 'D', 161: 'F', 162: 'A', 163: 'G', 164: 'G', 165: 'T', 166: 'V', 167: 'V', 168: 'H', 169: 'I', 170: 'N', 171: 'A', 172: 'A', 173: 'I', 174: 'A', 175: 'G', 176: 'L', 177: 'V', 178: 'G', 179: 'A', 180: 'Y', 181: 'L', 195: 'P', 196: 'H', 197: 'N', 198: 'L', 199: 'P', 200: 'M', 201: 'V', 202: 'F', 203: 'T', 204: 'G', 205: 'T', 206: 'A', 207: 'I', 208: 'L', 209: 'Y', 210: 'I', 211: 'G', 212: 'W', 213: 'F', 214: 'G', 215: 'F', 216: 'N', 217: 'A', 218: 'G', 219: 'S', 220: 'A', 221: 'G', 222: 'T', 223: 'A', 224: 'N', 225: 'E', 226: 'I', 227: 'A', 228: 'A', 229: 'L', 230: 'A', 231: 'F', 232: 'V', 233: 'N', 234: 'T', 235: 'V', 236: 'V', 237: 'A', 238: 'T', 239: 'A', 240: 'A', 241: 'A', 242: 'I', 243: 'L', 244: 'G', 245: 'W', 246: 'I', 247: 'F', 248: 'G', 249: 'E', 250: 'W', 251: 'A', 252: 'L', 253: 'R', 254: 'G', 255: 'K', 256: 'P', 257: 'S', 258: 'L', 259: 'L', 260: 'G', 261: 'A', 262: 'C', 263: 'S', 264: 'G', 265: 'A', 266: 'I', 267: 'A', 268: 'G', 269: 'L', 270: 'V', 271: 'G', 272: 'V', 273: 'T', 274: 'P', 275: 'A', 276: 'C', 277: 'G', 278: 'Y', 279: 'I', 280: 'G', 281: 'V', 282: 'G', 283: 'G', 284: 'A', 285: 'L', 286: 'I', 287: 'I', 288: 'G', 289: 'V', 290: 'V', 291: 'A', 292: 'G', 293: 'L', 294: 'A', 295: 'G', 296: 'L', 297: 'W', 298: 'G', 299: 'V', 300: 'T', 301: 'M', 311: 'P', 312: 'C', 313: 'D', 314: 'V', 315: 'F', 316: 'G', 317: 'V', 318: 'H', 319: 'G', 320: 'V', 321: 'C', 322: 'G', 323: 'I', 324: 'V', 325: 'G', 326: 'C', 327: 'I', 328: 'M', 329: 'T', 330: 'G', 331: 'I', 332: 'F', 333: 'A', 334: 'A', 335: 'S', 336: 'S', 337: 'L', 338: 'G', 339: 'G', 340: 'V', 341: 'G', 342: 'F', 343: 'A', 344: 'E', 345: 'G', 346: 'V', 347: 'T', 348: 'M', 349: 'G', 350: 'H', 351: 'Q', 352: 'L', 353: 'L', 354: 'V', 355: 'Q', 356: 'L', 357: 'E', 358: 'S', 359: 'I', 360: 'A', 361: 'I', 362: 'T', 363: 'I', 364: 'V', 365: 'W', 366: 'S', 367: 'G', 368: 'V', 369: 'V', 370: 'A', 371: 'F', 372: 'I', 373: 'G', 374: 'Y', 375: 'K', 376: 'L', 377: 'A', 378: 'D', 379: 'L', 380: 'T', 381: 'V', 382: 'G', 383: 'L', 384: 'R', 385: 'V', 386: 'P'}

---

[1]

Citation Jianfeng Sun, Arulsamy Kulandaisamy, Jinlong Ru, M Michael Gromiha, Adam P Cribbs, TMKit: a Python interface for computational analysis of transmembrane proteins, Briefings in Bioinformatics, Volume 24, Issue 5, September 2023, bbad288, https://doi.org/10.1093/bib/bbad288