Align candidate WP_028486900.1 B076_RS0108340 (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.13252.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-197 642.4 0.3 1.5e-197 642.2 0.3 1.0 1 lcl|NCBI__GCF_000483485.1:WP_028486900.1 B076_RS0108340 tryptophan syntha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000483485.1:WP_028486900.1 B076_RS0108340 tryptophan synthase subunit beta # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 642.2 0.3 1.5e-197 1.5e-197 1 383 [. 13 395 .. 13 397 .. 1.00 Alignments for each domain: == domain 1 score: 642.2 bits; conditional E-value: 1.5e-197 TIGR00263 1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiy 69 g+fg +GG + pe+l++ale+l+++y+++k+d++f +el++ l++y+grptpl++a++ s++lggakiy lcl|NCBI__GCF_000483485.1:WP_028486900.1 13 GHFGPYGGIFAPETLMAALEQLNQEYQSLKNDSAFLSELSDDLRDYVGRPTPLYYAQRWSESLGGAKIY 81 68******************************************************************* PP TIGR00263 70 lkredllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqk 138 lkredl+htGahk+nn++gqallakrlGk+riiaetGaGqhGva+at+aa+lglec+vymGa+dv rq+ lcl|NCBI__GCF_000483485.1:WP_028486900.1 82 LKREDLNHTGAHKVNNTIGQALLAKRLGKTRIIAETGAGQHGVASATVAARLGLECVVYMGADDVVRQA 150 ********************************************************************* PP TIGR00263 139 lnvfrmellgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeev 207 +nv rm++lgakvv+v+sG++tlkda+nea+rdWvt+v+dt+y++G+++GphP+P++vr+fq+vig+e+ lcl|NCBI__GCF_000483485.1:WP_028486900.1 151 PNVARMKMLGAKVVAVESGTRTLKDALNEAMRDWVTNVDDTFYIIGTVAGPHPYPAMVRDFQAVIGREA 219 ********************************************************************* PP TIGR00263 208 keqilekegrlPdaviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhG 276 ++q+lekeg+lPda+iacvGGGsnaiG+f++f+ de v+++gvea+G+G++t +haa l +G++GvlhG lcl|NCBI__GCF_000483485.1:WP_028486900.1 220 RQQVLEKEGKLPDALIACVGGGSNAIGLFHEFLPDEGVAIYGVEAAGHGLETGQHAAPLCAGTPGVLHG 288 ********************************************************************* PP TIGR00263 277 aktkllqdedGqieeahsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGiipale 345 ++t+l+qd++Gqi +hs+saGldypgvgPeha+l+++gra+y+ai+deeal++++ l+k eGiipale lcl|NCBI__GCF_000483485.1:WP_028486900.1 289 NRTYLMQDKNGQIIGTHSISAGLDYPGVGPEHAWLKDIGRANYVAIDDEEALQGFRDLTKYEGIIPALE 357 ********************************************************************* PP TIGR00263 346 sshalaaleklapklkkdeivvvnlsGrGdkdletvak 383 +sha+a+++klap+++kd++++vnlsGrGdkd++t+a+ lcl|NCBI__GCF_000483485.1:WP_028486900.1 358 TSHAIAYATKLAPTMDKDQVIIVNLSGRGDKDMNTIAQ 395 ************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (401 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: 9.18 // [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