Align candidate WP_072906560.1 BUB13_RS05600 (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.1320.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.8e-203 660.0 0.3 6.6e-203 659.9 0.3 1.0 1 lcl|NCBI__GCF_900142125.1:WP_072906560.1 BUB13_RS05600 tryptophan synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900142125.1:WP_072906560.1 BUB13_RS05600 tryptophan synthase subunit beta # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 659.9 0.3 6.6e-203 6.6e-203 1 384 [. 10 393 .. 10 394 .. 1.00 Alignments for each domain: == domain 1 score: 659.9 bits; conditional E-value: 6.6e-203 TIGR00263 1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiy 69 g+fge+GG+yv+e+l++al ele+ay+ +k+d+ f++e+e++lk+y+grp+pl+fa++l+++lggakiy lcl|NCBI__GCF_900142125.1:WP_072906560.1 10 GHFGEYGGRYVAETLMPALLELEEAYNAVKDDPCFREEFEYYLKNYVGRPSPLYFAQRLTEELGGAKIY 78 68******************************************************************* PP TIGR00263 70 lkredllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqk 138 lkredl+htGahk+nn++gq+lla+r+Gkk++iaetGaGqhGvatat+aal+g+ece++mG+ed+ rq+ lcl|NCBI__GCF_900142125.1:WP_072906560.1 79 LKREDLNHTGAHKVNNTVGQILLARRMGKKKVIAETGAGQHGVATATVAALFGMECEIFMGKEDIRRQA 147 ********************************************************************* PP TIGR00263 139 lnvfrmellgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeev 207 lnvfrm+llgakv+ tsG++tlkda+n+alr+Wvt+v+dt+yv+G+++GphP+P++vr+fqsvigee+ lcl|NCBI__GCF_900142125.1:WP_072906560.1 148 LNVFRMKLLGAKVHECTSGTATLKDAMNDALRHWVTHVRDTFYVIGTVAGPHPYPQLVRDFQSVIGEEA 216 ********************************************************************* PP TIGR00263 208 keqilekegrlPdaviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhG 276 k q++e+egrlPda iac+GGGsna+G+f++fi+d +v+ligvea+G+G+dt+khaa++s+G +GvlhG lcl|NCBI__GCF_900142125.1:WP_072906560.1 217 KVQLQEAEGRLPDAAIACIGGGSNAMGTFYPFIKDRSVRLIGVEAAGLGVDTDKHAASISAGAPGVLHG 285 ********************************************************************* PP TIGR00263 277 aktkllqdedGqieeahsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGiipale 345 +kt+llqdedGqi++ahs+saGldypgvgPeha+l+++graey++itd+ealea+++l++ eGiipale lcl|NCBI__GCF_900142125.1:WP_072906560.1 286 NKTYLLQDEDGQINHAHSISAGLDYPGVGPEHAHLQDIGRAEYVSITDDEALEAFQKLTRIEGIIPALE 354 ********************************************************************* PP TIGR00263 346 sshalaaleklapklkkdeivvvnlsGrGdkdletvaka 384 s+ha+a ++klap+l+k+++++v lsGrGdkd++tva+a lcl|NCBI__GCF_900142125.1:WP_072906560.1 355 SAHAIAEVMKLAPTLPKEQVLLVCLSGRGDKDIHTVADA 393 ************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (398 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: 8.77 // [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