Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_086511466.1 BZY95_RS19065 tryptophan synthase subunit beta
Query= uniprot:P50383 (425 letters) >NCBI__GCF_002151265.1:WP_086511466.1 Length = 401 Score = 135 bits (339), Expect = 3e-36 Identities = 114/363 (31%), Positives = 166/363 (45%), Gaps = 54/363 (14%) Query: 72 IGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAKEEGIEHVVTET 131 +GRP+PL+ A+RL E+ ARIY K E TG+HKIN I Q AK G ++ ET Sbjct: 58 VGRPSPLYFAERLTEHFGG-ARIYLKREELNHTGAHKINNCIGQILLAKRMGKTRIIAET 116 Query: 132 GAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYASPTNLTEYGRKI 191 GAG G A A A+ + M ++M E++ M+L GA V T Sbjct: 117 GAGMHGVATATVAARFGMPCVVYMGSADIERQQPNVFRMKLLGAEVIPVTTG-------- 168 Query: 192 LETNPQHPGSLGIAMSEAIEYALKN--EFRYLVGSVLD------VVLLHQSVIGQETITQ 243 G+L AM+EA+ + N + Y++G+V +V Q+VIG+ET TQ Sbjct: 169 -------TGTLKDAMNEALRDWVTNVEDTFYIIGTVAGPHPYPAMVRDFQAVIGRETRTQ 221 Query: 244 -LDLLGEDADILIGCVGGGSNFGGFTYPF--------IGNKKGKR------YIAVSSAEI 288 L+ G D L+ C+GGGSN G +PF IG + G + + A + Sbjct: 222 ILEKEGRLPDSLVACIGGGSNAMGLFHPFLADETVQMIGVEAGGKGVDTGLHAASLTGGE 281 Query: 289 PKFSKGEYKYDFPDSAGLLPLVKMITLGKDYVPPPIYAGGLRYHGVAPTLSLLTKEGIVE 348 P G Y D G + + + GL Y G+ P + L + G VE Sbjct: 282 PGVLHGNRTYLLQDEDGQI------------IDAHSISAGLDYPGIGPEHAWLHERGRVE 329 Query: 349 WREYNEREIFEAAKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHGL 408 + + E A + +GI+PA ESAHA+ V A +++ ++V NLSG G Sbjct: 330 YVSITDDEALAAFQCCCRLEGIIPALESAHALAEVAKRAPSLPRDH---LMVVNLSGRGD 386 Query: 409 LDL 411 D+ Sbjct: 387 KDM 389 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: 377 Number of extensions: 19 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: 401 Length adjustment: 31 Effective length of query: 394 Effective length of database: 370 Effective search space: 145780 Effective search space used: 145780 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_086511466.1 BZY95_RS19065 (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.25314.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-200 651.7 0.0 2.3e-200 651.5 0.0 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086511466.1 BZY95_RS19065 tryptophan synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086511466.1 BZY95_RS19065 tryptophan synthase subunit beta # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 651.5 0.0 2.3e-200 2.3e-200 1 384 [. 12 395 .. 12 396 .. 1.00 Alignments for each domain: == domain 1 score: 651.5 bits; conditional E-value: 2.3e-200 TIGR00263 1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiy 69 g+fg+fGG++vpe+l++ ++el+++y+ a++d+ef+++l ++ ++y+grp+pl+fa++l+++ gga+iy lcl|NCBI__GCF_002151265.1:WP_086511466.1 12 GMFGRFGGRFVPETLMPLITELQSEYDAARQDTEFQRQLAYFQRDYVGRPSPLYFAERLTEHFGGARIY 80 79******************************************************************* PP TIGR00263 70 lkredllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqk 138 lkre+l+htGahkinn +gq+llakr+Gk+riiaetGaG hGvatat+aa++g+ c+vymG+ d+erq+ lcl|NCBI__GCF_002151265.1:WP_086511466.1 81 LKREELNHTGAHKINNCIGQILLAKRMGKTRIIAETGAGMHGVATATVAARFGMPCVVYMGSADIERQQ 149 ********************************************************************* PP TIGR00263 139 lnvfrmellgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeev 207 +nvfrm+llga+v+pvt+G+ tlkda+nealrdWvt+vedt+y++G+++GphP+P++vr+fq+vig+e+ lcl|NCBI__GCF_002151265.1:WP_086511466.1 150 PNVFRMKLLGAEVIPVTTGTGTLKDAMNEALRDWVTNVEDTFYIIGTVAGPHPYPAMVRDFQAVIGRET 218 ********************************************************************* PP TIGR00263 208 keqilekegrlPdaviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhG 276 ++qilekegrlPd ++ac+GGGsna+G+f++f+ de+v++igveagGkG+dt haa+l+ G++GvlhG lcl|NCBI__GCF_002151265.1:WP_086511466.1 219 RTQILEKEGRLPDSLVACIGGGSNAMGLFHPFLADETVQMIGVEAGGKGVDTGLHAASLTGGEPGVLHG 287 ********************************************************************* PP TIGR00263 277 aktkllqdedGqieeahsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGiipale 345 ++t+llqdedGqi +ahs+saGldypg+gPeha+l+e+gr+ey++itd+eal+a++ +++ eGiipale lcl|NCBI__GCF_002151265.1:WP_086511466.1 288 NRTYLLQDEDGQIIDAHSISAGLDYPGIGPEHAWLHERGRVEYVSITDDEALAAFQCCCRLEGIIPALE 356 ********************************************************************* PP TIGR00263 346 sshalaaleklapklkkdeivvvnlsGrGdkdletvaka 384 s+hala + k ap+l++d+++vvnlsGrGdkd+ +va++ lcl|NCBI__GCF_002151265.1:WP_086511466.1 357 SAHALAEVAKRAPSLPRDHLMVVNLSGRGDKDMMSVAQH 395 ***********************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (401 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 7.14 // [ok]
This GapMind analysis is from Apr 10 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