Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_011386363.1 AMB_RS20295 tryptophan synthase subunit beta
Query= uniprot:P50383 (425 letters) >NCBI__GCF_000009985.1:WP_011386363.1 Length = 407 Score = 125 bits (313), Expect = 3e-33 Identities = 108/363 (29%), Positives = 162/363 (44%), Gaps = 53/363 (14%) Query: 72 IGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAKEEGIEHVVTET 131 +GRP PL+ A RL + A+++ K E TG+HKIN I Q A+ G + ++ ET Sbjct: 61 VGRPNPLYFAPRLTQAFGG-AKVFLKREDLNHTGAHKINNCIGQILLARRMGKQRIIAET 119 Query: 132 GAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYASPTNLTEYGRKI 191 GAGQ G A A +++ M+ I+M E++ M+L GA V + Sbjct: 120 GAGQHGVATATVCALFGMQCVIYMGSTDIERQMPNVYRMKLLGAEVRPVTSG-------- 171 Query: 192 LETNPQHPGSLGIAMSEAIEYALKN--EFRYLVGSVLD------VVLLHQSVIGQETITQ 243 +L AM++A+ + N + YL+G+V +V QSVIG+E Q Sbjct: 172 -------AATLKDAMNDALRDWVSNVADTYYLIGTVAGPHPYPAMVRDFQSVIGEEAREQ 224 Query: 244 LDLL-GEDADILIGCVGGGSNFGGFTYPFI-------------GNKKGKRYIAVSSAEIP 289 + G D L+ C+GGGSN G +PF+ G+ K + A + P Sbjct: 225 MQAQEGRLPDSLVACIGGGSNAMGLFHPFLDDSSVRIIGVEAAGHGLDKLHAASLTGGKP 284 Query: 290 KFSKGEYKYDFPDSAGLLPLVKMITLGKDYVPPPIYAGGLRYHGVAPTLSLLTKEGIVEW 349 G Y D+ G + I+ G D Y G+ P S L + G VE+ Sbjct: 285 GVLHGNRTYLLQDADGQIAEAHSISAGLD------------YPGIGPEHSWLHESGRVEY 332 Query: 350 REYNEREIFEAAKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHGLL 409 + E A + +GI+PA ES+HAI A K++ ++V NLSG G Sbjct: 333 VSVTDDEAVAAFQQCTRLEGIIPALESSHAIAYASKIAPALPKDH---LMVVNLSGRGDK 389 Query: 410 DLS 412 D+S Sbjct: 390 DVS 392 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: 364 Number of extensions: 13 Number of successful extensions: 3 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: 407 Length adjustment: 31 Effective length of query: 394 Effective length of database: 376 Effective search space: 148144 Effective search space used: 148144 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_011386363.1 AMB_RS20295 (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.25988.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-199 648.8 0.0 1.8e-199 648.6 0.0 1.0 1 lcl|NCBI__GCF_000009985.1:WP_011386363.1 AMB_RS20295 tryptophan synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_011386363.1 AMB_RS20295 tryptophan synthase subunit beta # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 648.6 0.0 1.8e-199 1.8e-199 1 384 [. 15 397 .. 15 398 .. 0.99 Alignments for each domain: == domain 1 score: 648.6 bits; conditional E-value: 1.8e-199 TIGR00263 1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiy 69 g+fg fGG+yv+e+l++ + e+ekay ak+d++f++e+++ll++y+grp pl+fa++l+++ ggak++ lcl|NCBI__GCF_000009985.1:WP_011386363.1 15 GHFGIFGGRYVAETLMPLILEVEKAYAAAKADPAFQAEFRRLLSQYVGRPNPLYFAPRLTQAFGGAKVF 83 68******************************************************************* PP TIGR00263 70 lkredllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqk 138 lkredl+htGahkinn +gq+lla+r+Gk+riiaetGaGqhGvatat++al+g++c++ymG++d+erq lcl|NCBI__GCF_000009985.1:WP_011386363.1 84 LKREDLNHTGAHKINNCIGQILLARRMGKQRIIAETGAGQHGVATATVCALFGMQCVIYMGSTDIERQM 152 ********************************************************************* PP TIGR00263 139 lnvfrmellgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeev 207 +nv+rm+llga+v pvtsG +tlkda+n+alrdWv++v+dt+y++G+++GphP+P++vr+fqsvigee+ lcl|NCBI__GCF_000009985.1:WP_011386363.1 153 PNVYRMKLLGAEVRPVTSGAATLKDAMNDALRDWVSNVADTYYLIGTVAGPHPYPAMVRDFQSVIGEEA 221 ********************************************************************* PP TIGR00263 208 keqilekegrlPdaviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhG 276 +eq++++egrlPd ++ac+GGGsna+G+f++f++d++v++igvea+G+G+d+ haa+l+ Gk+GvlhG lcl|NCBI__GCF_000009985.1:WP_011386363.1 222 REQMQAQEGRLPDSLVACIGGGSNAMGLFHPFLDDSSVRIIGVEAAGHGLDK-LHAASLTGGKPGVLHG 289 **************************************************85.79************** PP TIGR00263 277 aktkllqdedGqieeahsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGiipale 345 ++t+llqd dGqi eahs+saGldypg+gPeh++l+e+gr+ey+++td+ea++a++++++ eGiipale lcl|NCBI__GCF_000009985.1:WP_011386363.1 290 NRTYLLQDADGQIAEAHSISAGLDYPGIGPEHSWLHESGRVEYVSVTDDEAVAAFQQCTRLEGIIPALE 358 ********************************************************************* PP TIGR00263 346 sshalaaleklapklkkdeivvvnlsGrGdkdletvaka 384 ssha+a+++k+ap+l+kd+++vvnlsGrGdkd++t+aka lcl|NCBI__GCF_000009985.1:WP_011386363.1 359 SSHAIAYASKIAPALPKDHLMVVNLSGRGDKDVSTIAKA 397 ************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (407 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 10.69 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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