Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate RR42_RS14360 RR42_RS14360 tryptophan synthase subunit alpha
Query= uniprot:P50383 (425 letters) >FitnessBrowser__Cup4G11:RR42_RS14360 Length = 397 Score = 132 bits (332), Expect = 2e-35 Identities = 114/361 (31%), Positives = 165/361 (45%), Gaps = 50/361 (13%) Query: 72 IGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAKEEGIEHVVTET 131 +GRP+P++ A+R E L A+IY K E TG+HKIN I QA AK G V+ ET Sbjct: 55 VGRPSPIYHAQRWSEMLGG-AQIYLKREDLNHTGAHKINNVIGQALLAKRMGKPRVIAET 113 Query: 132 GAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYASPTNLTEYGRKI 191 GAGQ G A A A+ + M+ ++M +++ M+L GA V E G K Sbjct: 114 GAGQHGVATATIAARFGMECVVYMGSEDVKRQAANVYRMKLLGATVVP-----VESGSKT 168 Query: 192 LETNPQHPGSLGIAMSEAIEYALKNEFRYLVGSVLD------VVLLHQSVIGQETITQL- 244 L+ +L AM + + ++N F Y++G+V +V Q VIG+E Q+ Sbjct: 169 LK------DALNEAMRDWVT-NVENTF-YIIGTVAGPHPYPMMVRDFQCVIGEEAKVQMP 220 Query: 245 DLLGEDADILIGCVGGGSNFGGFTYPFIGNKKGK--------------RYIAVSSAEIPK 290 ++ G D +I CVGGGSN G YP+I +K + R+ A P Sbjct: 221 EMTGRQPDAVIACVGGGSNAMGIFYPYIEHKDVRLIGVEAAGDGLETGRHAAALIGGTPG 280 Query: 291 FSKGEYKYDFPDSAGLLPLVKMITLGKDYVPPPIYAGGLRYHGVAPTLSLLTKEGIVEWR 350 G Y D+ G + I+ G D Y GV P + L G E+ Sbjct: 281 VLHGNRTYLLQDANGQIIETHSISAGLD------------YPGVGPEHAWLKDIGRAEYV 328 Query: 351 EYNEREIFEAAKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHGLLD 410 + E +A +GI+PA ES+HAI A K+ K+++ NLSG G D Sbjct: 329 PITDEEALKAFHDCCRIEGIIPALESSHAIAYACKLAPTLPKD---KLLLVNLSGRGDKD 385 Query: 411 L 411 + Sbjct: 386 M 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: 369 Number of extensions: 18 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: 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 RR42_RS14360 RR42_RS14360 (tryptophan synthase subunit alpha)
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.5726.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.5e-197 641.0 0.0 3.9e-197 640.8 0.0 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS14360 RR42_RS14360 tryptophan synthase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS14360 RR42_RS14360 tryptophan synthase subunit alpha # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 640.8 0.0 3.9e-197 3.9e-197 1 384 [. 9 392 .. 9 393 .. 1.00 Alignments for each domain: == domain 1 score: 640.8 bits; conditional E-value: 3.9e-197 TIGR00263 1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiy 69 g+fg +GG +v+e+l++al+el++ay +++kd+ef +e+++ lk+++grp+p+++a++ s+ lgga+iy lcl|FitnessBrowser__Cup4G11:RR42_RS14360 9 GHFGPYGGSFVSETLVHALDELREAYAHFQKDPEFDAEYRRELKHFVGRPSPIYHAQRWSEMLGGAQIY 77 68******************************************************************* PP TIGR00263 70 lkredllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqk 138 lkredl+htGahkinn++gqallakr+Gk r+iaetGaGqhGvatat+aa++g+ec+vymG+edv+rq+ lcl|FitnessBrowser__Cup4G11:RR42_RS14360 78 LKREDLNHTGAHKINNVIGQALLAKRMGKPRVIAETGAGQHGVATATIAARFGMECVVYMGSEDVKRQA 146 ********************************************************************* PP TIGR00263 139 lnvfrmellgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeev 207 nv+rm+llga+vvpv+sGsktlkda+nea+rdWvt+ve+t+y++G+++GphP+P +vr+fq vigee+ lcl|FitnessBrowser__Cup4G11:RR42_RS14360 147 ANVYRMKLLGATVVPVESGSKTLKDALNEAMRDWVTNVENTFYIIGTVAGPHPYPMMVRDFQCVIGEEA 215 ********************************************************************* PP TIGR00263 208 keqilekegrlPdaviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhG 276 k q+ e+ gr PdaviacvGGGsna+Gif+++ie+++v+ligvea+G G++t +haa+l G++GvlhG lcl|FitnessBrowser__Cup4G11:RR42_RS14360 216 KVQMPEMTGRQPDAVIACVGGGSNAMGIFYPYIEHKDVRLIGVEAAGDGLETGRHAAALIGGTPGVLHG 284 ********************************************************************* PP TIGR00263 277 aktkllqdedGqieeahsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGiipale 345 ++t+llqd +Gqi e+hs+saGldypgvgPeha+l+++graey+ itdeeal+a++ +++ eGiipale lcl|FitnessBrowser__Cup4G11:RR42_RS14360 285 NRTYLLQDANGQIIETHSISAGLDYPGVGPEHAWLKDIGRAEYVPITDEEALKAFHDCCRIEGIIPALE 353 ********************************************************************* PP TIGR00263 346 sshalaaleklapklkkdeivvvnlsGrGdkdletvaka 384 ssha+a++ klap+l+kd++++vnlsGrGdkd++tva++ lcl|FitnessBrowser__Cup4G11:RR42_RS14360 354 SSHAIAYACKLAPTLPKDKLLLVNLSGRGDKDMHTVAER 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 8.54 // [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