Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate H281DRAFT_06067 H281DRAFT_06067 tryptophan synthase, beta chain
Query= uniprot:P50383 (425 letters) >FitnessBrowser__Burk376:H281DRAFT_06067 Length = 397 Score = 124 bits (312), Expect = 4e-33 Identities = 115/381 (30%), Positives = 171/381 (44%), Gaps = 54/381 (14%) Query: 56 ERYIKIPEEV----RDRYLSIGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINT 111 E++ K PE V R+ +GRP+P++ A+R E L A+I+ K E TG+HKIN Sbjct: 35 EKFQKDPEFVAEYERELKYFVGRPSPIYHAQRWSELLGG-AQIFLKREDLNHTGAHKINN 93 Query: 112 AIPQAYFAKEEGIEHVVTETGAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQ 171 I QA AK G V+ ETGAGQ G A A A+ + M+ ++M ++ M+ Sbjct: 94 VIGQALLAKRMGKPRVIAETGAGQHGVATATIAARFGMECVVYMGAEDVRRQAANVYRMK 153 Query: 172 LYGANVYASPTNLTEYGRKILETNPQHPGSLGIAMSEAIEYALKNEFRYLVGSVLD---- 227 L GA+V E G + L+ +L AM + + ++N F Y++G+V Sbjct: 154 LLGASVVP-----VESGSRTLK------DALNEAMRDWVT-NVENTF-YIIGTVAGPHPY 200 Query: 228 --VVLLHQSVIGQETITQL-DLLGEDADILIGCVGGGSNFGGFTYPFIGNK--------- 275 +V Q VIG E Q+ +L+G D +I CVGGGSN G YP+I + Sbjct: 201 PMMVRDFQRVIGDECKVQMPELIGRQPDAVIACVGGGSNAMGIFYPYIDDTAVELIGVEA 260 Query: 276 -----KGKRYIAVSSAEIPKFSKGEYKYDFPDSAGLLPLVKMITLGKDYVPPPIYAGGLR 330 + R+ A P G Y D G + I+ G D Sbjct: 261 AGDGIESGRHAASLIGGSPGVLHGNRTYLLQDENGQIIETHSISAGLD------------ 308 Query: 331 YHGVAPTLSLLTKEGIVEWREYNEREIFEAAKIFIENQGIVPAPESAHAIRAVVDEAIEA 390 Y GV P + L + ++ + E +A +GI+PA ES+HA+ A Sbjct: 309 YPGVGPEHAWLKEINRAQYVGITDEEALKAFHDCCRIEGIIPALESSHALAYATKLAPTL 368 Query: 391 RKNNERKVIVFNLSGHGLLDL 411 K+ K ++ NLSG G D+ Sbjct: 369 PKD---KHLLVNLSGRGDKDM 386 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: 372 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: 397 Length adjustment: 31 Effective length of query: 394 Effective length of database: 366 Effective search space: 144204 Effective search space used: 144204 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 H281DRAFT_06067 H281DRAFT_06067 (tryptophan synthase, beta chain)
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.26757.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.8e-197 640.6 0.1 5.4e-197 640.4 0.1 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_06067 H281DRAFT_06067 tryptophan synth Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_06067 H281DRAFT_06067 tryptophan synthase, beta chain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 640.4 0.1 5.4e-197 5.4e-197 1 384 [. 9 392 .. 9 393 .. 1.00 Alignments for each domain: == domain 1 score: 640.4 bits; conditional E-value: 5.4e-197 TIGR00263 1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklgga 66 g+fg+fGG +v+e+l++al+el++ayek++kd+ef++e+e+ lk ++grp+p+++a++ s+ lgga lcl|FitnessBrowser__Burk376:H281DRAFT_06067 9 GHFGQFGGVFVAETLVHALDELRAAYEKFQKDPEFVAEYERELKYFVGRPSPIYHAQRWSELLGGA 74 68**************************************************************** PP TIGR00263 67 kiylkredllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGae 132 +i+lkredl+htGahkinn++gqallakr+Gk r+iaetGaGqhGvatat+aa++g+ec+vymGae lcl|FitnessBrowser__Burk376:H281DRAFT_06067 75 QIFLKREDLNHTGAHKINNVIGQALLAKRMGKPRVIAETGAGQHGVATATIAARFGMECVVYMGAE 140 ****************************************************************** PP TIGR00263 133 dverqklnvfrmellgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivre 198 dv rq+ nv+rm+llga+vvpv+sGs+tlkda+nea+rdWvt+ve+t+y++G+++GphP+P +vr+ lcl|FitnessBrowser__Burk376:H281DRAFT_06067 141 DVRRQAANVYRMKLLGASVVPVESGSRTLKDALNEAMRDWVTNVENTFYIIGTVAGPHPYPMMVRD 206 ****************************************************************** PP TIGR00263 199 fqsvigeevkeqilekegrlPdaviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaa 264 fq+vig+e+k q+ e gr PdaviacvGGGsna+Gif+++i+d veligvea+G Gi++ +haa lcl|FitnessBrowser__Burk376:H281DRAFT_06067 207 FQRVIGDECKVQMPELIGRQPDAVIACVGGGSNAMGIFYPYIDDTAVELIGVEAAGDGIESGRHAA 272 ****************************************************************** PP TIGR00263 265 tlskGkeGvlhGaktkllqdedGqieeahsvsaGldypgvgPehaalaetgraeyeaitdeealea 330 +l G++GvlhG++t+llqde+Gqi e+hs+saGldypgvgPeha+l+e++ra+y+ itdeeal+a lcl|FitnessBrowser__Burk376:H281DRAFT_06067 273 SLIGGSPGVLHGNRTYLLQDENGQIIETHSISAGLDYPGVGPEHAWLKEINRAQYVGITDEEALKA 338 ****************************************************************** PP TIGR00263 331 lkllskeeGiipalesshalaaleklapklkkdeivvvnlsGrGdkdletvaka 384 ++ +++ eGiipalesshala+++klap+l+kd+ ++vnlsGrGdkd++tva++ lcl|FitnessBrowser__Burk376:H281DRAFT_06067 339 FHDCCRIEGIIPALESSHALAYATKLAPTLPKDKHLLVNLSGRGDKDMHTVAER 392 ***************************************************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (397 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: 10.99 // [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