Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_084058687.1 B9A12_RS13765 tryptophan synthase subunit beta
Query= uniprot:P50383 (425 letters) >NCBI__GCF_900176285.1:WP_084058687.1 Length = 397 Score = 149 bits (375), Expect = 2e-40 Identities = 129/408 (31%), Positives = 185/408 (45%), Gaps = 60/408 (14%) Query: 29 PQGAYFSRIDLLRSILP-KEVLRQQFTIERYIKIPEEVRDRYLSIGRPTPLFRAKRLEEY 87 P G + L+ ++L +E + T E + K ++ + Y GRPTPLF A+RL E Sbjct: 19 PYGGRYVAETLMPALLELEEAYLEVRTAESFQKEFRDLLEEYA--GRPTPLFHARRLSEA 76 Query: 88 LKTPARIYFKYEGATPTGSHKINTAIPQAYFAKEEGIEHVVTETGAGQWGTAVALAASMY 147 ARIY K E T TG+HKIN + Q A+ G V+ ETGAGQ G A A AA+++ Sbjct: 77 CGG-ARIYLKREDLTHTGAHKINNTLGQVLLARYMGKRKVIAETGAGQHGVATATAAALF 135 Query: 148 NMKSTIFMVKVSYEQKPMRRSIMQLYGANVYASPTNLTEYGRKILETNPQHPGSLGIAMS 207 M+ +FM ++ M+L GA V + G+L AM+ Sbjct: 136 GMECKVFMGTEDVRRQAPNVRRMELLGAQVVPVASG---------------TGTLKDAMN 180 Query: 208 EAIEY---ALKNEFRYLVGSVL------DVVLLHQSVIGQETITQ-LDLLGEDADILIGC 257 EA+ Y A+++ F Y++GSV +V Q VIG E Q L+ G D L+ C Sbjct: 181 EAMRYWVGAVRDTF-YVIGSVAGPHPYPQMVRDFQRVIGDEARRQILEREGRLPDALVAC 239 Query: 258 VGGGSNFGGFTYPFI--------------GNKKGKRYIAVSSAEIPKFSKGEYKYDFPDS 303 VGGGSN G +PF+ G GK + + + G Y D Sbjct: 240 VGGGSNAMGLFFPFLDDPVDLIGVEAAGEGVPTGKHAATLGAGSVGVL-HGSKSYVLQDE 298 Query: 304 AGLLPLVKMITLGKDYVPPPIYAGGLRYHGVAPTLSLLTKEGIVEWREYNEREIFEAAKI 363 G + I+ G D Y GV P + L + G + +RE EA + Sbjct: 299 NGQIREAHSISAGLD------------YPGVGPEHAWLKESGRAAYVSVTDREALEAFRR 346 Query: 364 FIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHGLLDL 411 +GI+PA ESAH AV +EA + + ++++ NLSG G DL Sbjct: 347 LSLLEGIIPALESAH---AVAHAMVEAARRDGHQILIVNLSGRGDKDL 391 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: 407 Number of extensions: 23 Number of successful extensions: 5 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 WP_084058687.1 B9A12_RS13765 (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.12896.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-193 629.3 0.0 1.5e-193 629.1 0.0 1.0 1 lcl|NCBI__GCF_900176285.1:WP_084058687.1 B9A12_RS13765 tryptophan synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900176285.1:WP_084058687.1 B9A12_RS13765 tryptophan synthase subunit beta # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 629.1 0.0 1.5e-193 1.5e-193 1 382 [. 15 395 .. 15 397 .] 0.99 Alignments for each domain: == domain 1 score: 629.1 bits; conditional E-value: 1.5e-193 TIGR00263 1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiy 69 g+fg +GG+yv+e+l++al ele+ay ++++ e+f+ke+++ll+eyagrptpl++a++ls++ gga+iy lcl|NCBI__GCF_900176285.1:WP_084058687.1 15 GHFGPYGGRYVAETLMPALLELEEAYLEVRTAESFQKEFRDLLEEYAGRPTPLFHARRLSEACGGARIY 83 68******************************************************************* PP TIGR00263 70 lkredllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqk 138 lkredl htGahkinn+lgq+lla+++Gk+++iaetGaGqhGvatataaal+g+ec+v+mG+edv rq+ lcl|NCBI__GCF_900176285.1:WP_084058687.1 84 LKREDLTHTGAHKINNTLGQVLLARYMGKRKVIAETGAGQHGVATATAAALFGMECKVFMGTEDVRRQA 152 ********************************************************************* PP TIGR00263 139 lnvfrmellgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeev 207 +nv rmellga+vvpv sG+ tlkda+nea+r Wv+ v+dt+yv+Gs++GphP+P++vr+fq+vig+e+ lcl|NCBI__GCF_900176285.1:WP_084058687.1 153 PNVRRMELLGAQVVPVASGTGTLKDAMNEAMRYWVGAVRDTFYVIGSVAGPHPYPQMVRDFQRVIGDEA 221 ********************************************************************* PP TIGR00263 208 keqilekegrlPdaviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhG 276 ++qile+egrlPda++acvGGGsna+G+f +f++d+ v+ligvea+G+G+ t khaatl +G++GvlhG lcl|NCBI__GCF_900176285.1:WP_084058687.1 222 RRQILEREGRLPDALVACVGGGSNAMGLFFPFLDDP-VDLIGVEAAGEGVPTGKHAATLGAGSVGVLHG 289 ***********************************9.******************************** PP TIGR00263 277 aktkllqdedGqieeahsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGiipale 345 +k+++lqde+Gqi+eahs+saGldypgvgPeha+l+e+gra y+++td+ealea+++ls eGiipale lcl|NCBI__GCF_900176285.1:WP_084058687.1 290 SKSYVLQDENGQIREAHSISAGLDYPGVGPEHAWLKESGRAAYVSVTDREALEAFRRLSLLEGIIPALE 358 ********************************************************************* PP TIGR00263 346 sshalaaleklapklkkdeivvvnlsGrGdkdletva 382 s+ha+a+++ a++ + ++i++vnlsGrGdkdl v lcl|NCBI__GCF_900176285.1:WP_084058687.1 359 SAHAVAHAMVEAARRDGHQILIVNLSGRGDKDLGIVF 395 ********************************98875 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: 00:00:00.02 # Mc/sec: 6.70 // [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