Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_012674347.1 SULAZ_RS04145 tryptophan synthase subunit beta
Query= uniprot:P50383 (425 letters) >NCBI__GCF_000021545.1:WP_012674347.1 Length = 415 Score = 143 bits (360), Expect = 1e-38 Identities = 112/359 (31%), Positives = 181/359 (50%), Gaps = 34/359 (9%) Query: 73 GRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAKEEGIEHVVTETG 132 GRPTPL+ A RL + + A+IY K E TG+HKIN + Q K G + ++ ETG Sbjct: 58 GRPTPLYFASRLTQVVGG-AKIYLKREDLLHTGAHKINNTLGQVLLTKRLGKKRIIAETG 116 Query: 133 AGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYASPTNLTEYGRKIL 192 AGQ G + A AA+++ ++ TI+M + E++ + M+L GA V + + G + L Sbjct: 117 AGQHGVSTATAAALFGLECTIYMGEEDAERQALNVFRMKLLGAKV-----EIVKSGSRTL 171 Query: 193 ETNPQHPGSLGIAMSEAIEYALKN--EFRYLVGSVLD------VVLLHQSVIGQETITQ- 243 + A++EA+ + N Y++GS L +V QSVIG+E Q Sbjct: 172 KD----------AVNEALRDWVTNVRTTHYIIGSALGPHPFPMIVRDFQSVIGEEVKNQI 221 Query: 244 LDLLGEDADILIGCVGGGSNFGGFTYPFIGNKKGKRYIAVSSAEIPKFSKGEYKYDFPDS 303 L++ G+ D+++ CVGGGSN G YPFI +++ K + V + + S Sbjct: 222 LEIEGKLPDVIVACVGGGSNAIGIFYPFIEDEEVK-LVGVEAGGYGLETGMHAASIVGGS 280 Query: 304 AGLLPLVKMITLGKDY---VPPPIYAGGLRYHGVAPTLSLLTKEGIVEWREYNEREIFEA 360 G+L +K L + + GL Y GV P + L + G + + E E Sbjct: 281 VGVLHGMKSYFLQDQWGQIETTHSISAGLDYPGVGPEHAYLKESGRATYITATDEEALEG 340 Query: 361 AKIFIENQGIVPAPESAHAIRAVVDEAIEARKN-NERKVIVFNLSGHGLLDLSNYESMM 418 + +GI+PA ES+HA V +A+E KN ++ + +V NLSG G D+ + ++++ Sbjct: 341 FLLLSRTEGIIPALESSHA----VIKAVEIAKNLDKHQSVVINLSGRGDKDVQSVKNLL 395 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: 450 Number of extensions: 28 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: 415 Length adjustment: 32 Effective length of query: 393 Effective length of database: 383 Effective search space: 150519 Effective search space used: 150519 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_012674347.1 SULAZ_RS04145 (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.1230204.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.5e-197 640.4 0.3 6.3e-197 640.2 0.3 1.0 1 NCBI__GCF_000021545.1:WP_012674347.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000021545.1:WP_012674347.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 640.2 0.3 6.3e-197 6.3e-197 1 383 [. 11 393 .. 11 395 .. 0.99 Alignments for each domain: == domain 1 score: 640.2 bits; conditional E-value: 6.3e-197 TIGR00263 1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiylkre 73 g++g+fGG+y+pe+l++aleele++y k+k+d +fk++l ++l eyagrptpl+fa++l++ +ggakiylkre NCBI__GCF_000021545.1:WP_012674347.1 11 GYYGQFGGKYLPETLIPALEELEQQYLKIKNDGDFKRQLLYYLTEYAGRPTPLYFASRLTQVVGGAKIYLKRE 83 79*********************************************************************** PP TIGR00263 74 dllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqklnvfrmel 146 dllhtGahkinn+lgq+ll+krlGkkriiaetGaGqhGv+tataaal+glec++ymG+ed erq+lnvfrm+l NCBI__GCF_000021545.1:WP_012674347.1 84 DLLHTGAHKINNTLGQVLLTKRLGKKRIIAETGAGQHGVSTATAAALFGLECTIYMGEEDAERQALNVFRMKL 156 ************************************************************************* PP TIGR00263 147 lgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeevkeqilekegrlP 219 lgakv v+sGs+tlkdavnealrdWvt+v++thy++Gsa+GphPfP ivr+fqsvigeevk+qile eg+lP NCBI__GCF_000021545.1:WP_012674347.1 157 LGAKVEIVKSGSRTLKDAVNEALRDWVTNVRTTHYIIGSALGPHPFPMIVRDFQSVIGEEVKNQILEIEGKLP 229 ************************************************************************* PP TIGR00263 220 daviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhGaktkllqdedGqieea 292 d+++acvGGGsnaiGif++fiedeev+l+gveagG G++t +haa++ G++GvlhG+k+++lqd+ Gqie++ NCBI__GCF_000021545.1:WP_012674347.1 230 DVIVACVGGGSNAIGIFYPFIEDEEVKLVGVEAGGYGLETGMHAASIVGGSVGVLHGMKSYFLQDQWGQIETT 302 ************************************************************************* PP TIGR00263 293 hsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGiipalesshalaaleklapklkkdei 365 hs+saGldypgvgPeha+l+e+gra+y ++tdeeale++ lls++eGiipalessha+ ++++a++l+k++ NCBI__GCF_000021545.1:WP_012674347.1 303 HSISAGLDYPGVGPEHAYLKESGRATYITATDEEALEGFLLLSRTEGIIPALESSHAVIKAVEIAKNLDKHQS 375 ************************************************************************* PP TIGR00263 366 vvvnlsGrGdkdletvak 383 vv+nlsGrGdkd+++v++ NCBI__GCF_000021545.1:WP_012674347.1 376 VVINLSGRGDKDVQSVKN 393 **************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (415 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 27.68 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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