Align candidate WP_028989187.1 G579_RS0104270 (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.11644.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-192 625.5 0.1 2e-192 625.3 0.1 1.0 1 lcl|NCBI__GCF_000423825.1:WP_028989187.1 G579_RS0104270 tryptophan syntha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000423825.1:WP_028989187.1 G579_RS0104270 tryptophan synthase subunit beta # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 625.3 0.1 2e-192 2e-192 1 384 [. 11 394 .. 11 395 .. 1.00 Alignments for each domain: == domain 1 score: 625.3 bits; conditional E-value: 2e-192 TIGR00263 1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiy 69 g+fg +GG + +e+l++ l+el++ay a+ d++f++el+ l +++grp pl++a++ls++lgga+iy lcl|NCBI__GCF_000423825.1:WP_028989187.1 11 GHFGPYGGVFAAETLMAPLQELTRAYAAAQVDPAFQAELKADLAQFVGRPNPLYHAARLSRQLGGAQIY 79 68******************************************************************* PP TIGR00263 70 lkredllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqk 138 lkredl+htGahkinn++gqalla+r+Gk+r+iaetGaGqhGvatat+aa+ g+ec+vymG+edv rq+ lcl|NCBI__GCF_000423825.1:WP_028989187.1 80 LKREDLNHTGAHKINNTVGQALLARRMGKRRVIAETGAGQHGVATATVAARYGMECVVYMGEEDVRRQS 148 ********************************************************************* PP TIGR00263 139 lnvfrmellgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeev 207 +nvfrm+llga+v pv+sGs+tlkda+nea+rdWvt+v+dt+y++G+++GphP+P +vr+f +vigee+ lcl|NCBI__GCF_000423825.1:WP_028989187.1 149 INVFRMRLLGAEVRPVSSGSRTLKDALNEAMRDWVTNVDDTFYIIGTVAGPHPYPMMVRDFHKVIGEEA 217 ********************************************************************* PP TIGR00263 208 keqilekegrlPdaviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhG 276 ++q e+ grlPd+ +acvGGGsnaiG+f++fiede v+l+gvea+G+G+++ +haa l++G++GvlhG lcl|NCBI__GCF_000423825.1:WP_028989187.1 218 RAQCVEQTGRLPDVCVACVGGGSNAIGLFYPFIEDEGVRLVGVEAAGSGVASGRHAAPLTAGRPGVLHG 286 ********************************************************************* PP TIGR00263 277 aktkllqdedGqieeahsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGiipale 345 ++t+l+ d dGqi e+hs+saGldypgvgPeha+l+++graey+a+tdeeal+a++ll+++eGi+pale lcl|NCBI__GCF_000423825.1:WP_028989187.1 287 NRTYLMEDADGQIIETHSISAGLDYPGVGPEHAYLKDIGRAEYVAMTDEEALAAFHLLTRTEGIMPALE 355 ********************************************************************* PP TIGR00263 346 sshalaaleklapklkkdeivvvnlsGrGdkdletvaka 384 ++hala++ +lap+l+ ++ +vv+lsGrGdkd++tva++ lcl|NCBI__GCF_000423825.1:WP_028989187.1 356 TAHALAYAFQLAPTLRPEQSIVVSLSGRGDKDIHTVAEY 394 ************************************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 0.00s 00:00:00.01 Elapsed: 00:00:00.02 # Mc/sec: 6.86 // [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