Align candidate WP_028486151.1 B076_RS0103880 (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.31153.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.1e-161 522.0 0.0 5.7e-161 521.8 0.0 1.0 1 lcl|NCBI__GCF_000483485.1:WP_028486151.1 B076_RS0103880 tryptophan syntha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000483485.1:WP_028486151.1 B076_RS0103880 tryptophan synthase subunit beta # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 521.8 0.0 5.7e-161 5.7e-161 1 383 [. 12 392 .. 12 394 .. 0.99 Alignments for each domain: == domain 1 score: 521.8 bits; conditional E-value: 5.7e-161 TIGR00263 1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiy 69 g+fg+fGG+++p +l++++ee+++ay ++ + +f +el+++ k+y grptp+++a+nlskk g a+iy lcl|NCBI__GCF_000483485.1:WP_028486151.1 12 GYFGDFGGAFLPPELIPHFEEINQAYLELGRSADFLNELKYIRKHYQGRPTPVYYAHNLSKKFG-AHIY 79 79*************************************************************8.**** PP TIGR00263 70 lkredllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqk 138 lkredl+h+Gahk+n ++ allak++Gk+++iaetGaGqhGva ataaa++glece++mG+ d+++ + lcl|NCBI__GCF_000483485.1:WP_028486151.1 80 LKREDLNHSGAHKLNHCMAEALLAKHMGKTKLIAETGAGQHGVALATAAAYFGLECEIHMGEIDIAKEA 148 ********************************************************************* PP TIGR00263 139 lnvfrmellgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeev 207 +nv rm+l+ga+vvpv+ G ++lk+av++a++ +v + +++ + +Gs+vGphPfP++vr+fqsv+g+e+ lcl|NCBI__GCF_000483485.1:WP_028486151.1 149 PNVTRMKLMGANVVPVSFGGRSLKEAVDSAFQSYVPQADTALFAIGSVVGPHPFPQMVRNFQSVVGHEA 217 ********************************************************************* PP TIGR00263 208 keqilekegrlPdaviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhG 276 +eq le+ g+lPd+v acvGGGsna+G+fa fi+de v l gve+ G+G + +h+at++ Gk+G++hG lcl|NCBI__GCF_000483485.1:WP_028486151.1 218 REQFLEMTGELPDQVGACVGGGSNAMGMFAGFIDDEGVGLNGVEPLGRGTELGEHSATMTYGKPGMIHG 286 ********************************************************************* PP TIGR00263 277 aktkllqdedGqieeahsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGiipale 345 +k ll d +G+ ++hs+++GldypgvgPeh++l+ +g+++y+a+td+e+l+a+ +l++ eGiipale lcl|NCBI__GCF_000483485.1:WP_028486151.1 287 FKCLLLEDAEGNPAPVHSIASGLDYPGVGPEHSYLKTIGKVNYHAVTDDETLDAFYQLCRLEGIIPALE 355 ********************************************************************* PP TIGR00263 346 sshalaaleklapklkkdeivvvnlsGrGdkdletvak 383 ssha+a ++k a+ + +++++nlsGrGdkd++ v++ lcl|NCBI__GCF_000483485.1:WP_028486151.1 356 SSHAVAWAMKHAQ-ANPGSTILINLSGRGDKDIDYVVD 392 **********998.56678999************9976 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: 8.19 // [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