Align candidate WP_011190190.1 DP_RS14920 (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.807364.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.1e-187 607.1 0.1 8.2e-187 606.9 0.1 1.0 1 NCBI__GCF_000025945.1:WP_011190190.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000025945.1:WP_011190190.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 606.9 0.1 8.2e-187 8.2e-187 1 383 [. 8 390 .. 8 392 .. 0.99 Alignments for each domain: == domain 1 score: 606.9 bits; conditional E-value: 8.2e-187 TIGR00263 1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiylkre 73 g+fge+GGqyvpe+ll+ l+el ++y+k+k+d+ef++el++++k+++grptpl++++nls++lgga+iylkre NCBI__GCF_000025945.1:WP_011190190.1 8 GFFGEYGGQYVPEQLLPILNELAATYDKVKTDPEFRAELDYYMKKFSGRPTPLYHCSNLSRELGGAQIYLKRE 80 68*********************************************************************** PP TIGR00263 74 dllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqklnvfrmel 146 dl+h Gahk+nn+lgq+llakr+Gkk+iiaetGaGqhGva+a+ aal+g++c+vymG+ dverqklnvfrm++ NCBI__GCF_000025945.1:WP_011190190.1 81 DLNHLGAHKVNNTLGQILLAKRMGKKKIIAETGAGQHGVAAAATAALMGMKCTVYMGKVDVERQKLNVFRMRM 153 ************************************************************************* PP TIGR00263 147 lgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeevkeqilekegrlP 219 +ga+vv+ tsG++tlk+av+eal +W+++ e+ +y+lGsavGphP+P +vr+fqsvi++e++eq l g+lP NCBI__GCF_000025945.1:WP_011190190.1 154 MGAEVVTATSGQQTLKEAVDEALAAWMADAEESFYLLGSAVGPHPYPLMVRDFQSVISKEAREQFLTDTGKLP 226 ************************************************************************* PP TIGR00263 220 daviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhGaktkllqdedGqieea 292 d+ +ac+GGGsnaiG+fa+fi+d++v+ligve++G+G++ +haa+ls G++G+lhG+++++l+de G+ ++ NCBI__GCF_000025945.1:WP_011190190.1 227 DYCVACIGGGSNAIGMFANFIDDKDVQLIGVEPAGRGLKLGDHAASLSFGSPGILHGFNSYMLKDEAGDAAPV 299 ************************************************************************* PP TIGR00263 293 hsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGiipalesshalaaleklapklkkdei 365 +s+saGldyp+vgPeh++l+++gra+ye ++d+ea++a+ +ls++eGiipalesshala++ klap+l+ ++ NCBI__GCF_000025945.1:WP_011190190.1 300 YSISAGLDYPSVGPEHSYLKDIGRASYEYASDAEAVNAFFTLSQKEGIIPALESSHALAHVLKLAPTLSTEKS 372 ************************************************************************* PP TIGR00263 366 vvvnlsGrGdkdletvak 383 ++v lsGrGdkd+++va+ NCBI__GCF_000025945.1:WP_011190190.1 373 IIVCLSGRGDKDVAQVAE 390 ***************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (400 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: 13.14 // [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