Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_013841408.1 DESRU_RS06950 tryptophan synthase subunit beta
Query= uniprot:P50383 (425 letters) >NCBI__GCF_000215085.1:WP_013841408.1 Length = 396 Score = 139 bits (349), Expect = 2e-37 Identities = 112/363 (30%), Positives = 169/363 (46%), Gaps = 54/363 (14%) Query: 72 IGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAKEEGIEHVVTET 131 +GRP+P++ A+ L E + ARI+ K E TG+HKIN + Q A+ G + ++ ET Sbjct: 53 VGRPSPVYLARGLSEKMGG-ARIWLKREDLNHTGAHKINNTLGQVLLARRMGKKRIIAET 111 Query: 132 GAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYASPTNLTEYGRKI 191 GAGQ G A A AA+M+ ++ ++M + ++ + M+L GA V + Sbjct: 112 GAGQHGVATATAAAMFGLQCVVYMGEEDIRRQSLNVFRMKLLGAEVVEVSSG-------- 163 Query: 192 LETNPQHPGSLGIAMSEAIEYALKN--EFRYLVGSVLD------VVLLHQSVIGQETITQ 243 G+L AM+EA+ + N Y++GSV +V Q +IGQE Q Sbjct: 164 -------TGTLKDAMNEAMRDWVTNVRNTYYIIGSVAGPHPYPMMVRDFQKIIGQEAREQ 216 Query: 244 -LDLLGEDADILIGCVGGGSNFGGFTYPFIGNKKGK--------------RYIAVSSAEI 288 L+ G ++ CVGGGSN G Y F+ +++ + R+ A +A Sbjct: 217 MLEQSGGLPHCVVACVGGGSNAMGAFYAFLEDREVELVGVEAGGLGLDTDRHAAPLTAGR 276 Query: 289 PKFSKGEYKYDFPDSAGLLPLVKMITLGKDYVPPPIYAGGLRYHGVAPTLSLLTKEGIVE 348 P G Y Y D G + V ++ G D Y GV P S L G V Sbjct: 277 PGVLHGSYSYLIQDGDGQVTPVHSVSAGLD------------YPGVGPEHSYLKDTGRVS 324 Query: 349 WREYNEREIFEAAKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHGL 408 + +RE A + +GI+PA ESAHA+ + A AR + ER ++V LSG G Sbjct: 325 YTVATDREALNAFHLLCRTEGIIPALESAHALAEAIKRA--ARMSKERSILVC-LSGRGD 381 Query: 409 LDL 411 D+ Sbjct: 382 KDV 384 Lambda K H 0.318 0.138 0.403 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 373 Number of extensions: 20 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 425 Length of database: 396 Length adjustment: 31 Effective length of query: 394 Effective length of database: 365 Effective search space: 143810 Effective search space used: 143810 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
Align candidate WP_013841408.1 DESRU_RS06950 (tryptophan synthase subunit beta)
to HMM TIGR00263 (trpB: tryptophan synthase, beta subunit (EC 4.2.1.20))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR00263.hmm # target sequence database: /tmp/gapView.3529828.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00263 [M=385] Accession: TIGR00263 Description: trpB: tryptophan synthase, beta subunit Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.3e-197 640.0 0.3 8.2e-197 639.8 0.3 1.0 1 NCBI__GCF_000215085.1:WP_013841408.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000215085.1:WP_013841408.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 639.8 0.3 8.2e-197 8.2e-197 1 384 [. 7 390 .. 7 391 .. 1.00 Alignments for each domain: == domain 1 score: 639.8 bits; conditional E-value: 8.2e-197 TIGR00263 1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiylkre 73 g+fg++GG +vpe+l++aleel+kay++a++d +f++e+e++lk+y+grp+p++ a+ ls+k+gga+i+lkre NCBI__GCF_000215085.1:WP_013841408.1 7 GYFGSYGGIFVPETLIPALEELTKAYQQAQQDGNFQREVEHYLKNYVGRPSPVYLARGLSEKMGGARIWLKRE 79 79*********************************************************************** PP TIGR00263 74 dllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqklnvfrmel 146 dl+htGahkinn+lgq+lla+r+GkkriiaetGaGqhGvatataaa++gl+c+vymG+ed+ rq+lnvfrm+l NCBI__GCF_000215085.1:WP_013841408.1 80 DLNHTGAHKINNTLGQVLLARRMGKKRIIAETGAGQHGVATATAAAMFGLQCVVYMGEEDIRRQSLNVFRMKL 152 ************************************************************************* PP TIGR00263 147 lgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeevkeqilekegrlP 219 lga+vv v+sG+ tlkda+nea+rdWvt+v++t+y++Gs++GphP+P +vr+fq++ig+e++eq+le+ g lP NCBI__GCF_000215085.1:WP_013841408.1 153 LGAEVVEVSSGTGTLKDAMNEAMRDWVTNVRNTYYIIGSVAGPHPYPMMVRDFQKIIGQEAREQMLEQSGGLP 225 ************************************************************************* PP TIGR00263 220 daviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhGaktkllqdedGqieea 292 v+acvGGGsna+G+f+af+ed evel+gveagG+G+dt++haa l++G++GvlhG++++l+qd dGq++++ NCBI__GCF_000215085.1:WP_013841408.1 226 HCVVACVGGGSNAMGAFYAFLEDREVELVGVEAGGLGLDTDRHAAPLTAGRPGVLHGSYSYLIQDGDGQVTPV 298 ************************************************************************* PP TIGR00263 293 hsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGiipalesshalaaleklapklkkdei 365 hsvsaGldypgvgPeh++l++tgr++y+ +td+eal+a++ll+++eGiipales+hala ++k a++++k++ NCBI__GCF_000215085.1:WP_013841408.1 299 HSVSAGLDYPGVGPEHSYLKDTGRVSYTVATDREALNAFHLLCRTEGIIPALESAHALAEAIKRAARMSKERS 371 ************************************************************************* PP TIGR00263 366 vvvnlsGrGdkdletvaka 384 ++v lsGrGdkd++tvak+ NCBI__GCF_000215085.1:WP_013841408.1 372 ILVCLSGRGDKDVHTVAKE 390 ****************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (396 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 27.62 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory