Align candidate WP_057687222.1 ABB28_RS15200 (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.19259.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.9e-190 616.8 0.3 9e-190 616.6 0.3 1.0 1 lcl|NCBI__GCF_001431535.1:WP_057687222.1 ABB28_RS15200 tryptophan synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001431535.1:WP_057687222.1 ABB28_RS15200 tryptophan synthase subunit beta # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 616.6 0.3 9e-190 9e-190 1 383 [. 17 399 .. 17 401 .. 0.99 Alignments for each domain: == domain 1 score: 616.6 bits; conditional E-value: 9e-190 TIGR00263 1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiy 69 g+fg++GG +v+e+l+ l+el +ay++a+kd++f +e+++ l +y+grp+p+++a++ls ++gga+i lcl|NCBI__GCF_001431535.1:WP_057687222.1 17 GHFGRYGGSFVAETLVGPLQELAAAYDQARKDPAFIAEYDHDLAHYVGRPSPIYHARRLSDHVGGAQIL 85 68******************************************************************* PP TIGR00263 70 lkredllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqk 138 lkredl+htGahkinn++gqalla r+GkkriiaetGaGqhGva+at+aa+lglec+vymGa+d+erqk lcl|NCBI__GCF_001431535.1:WP_057687222.1 86 LKREDLNHTGAHKINNTIGQALLASRMGKKRIIAETGAGQHGVASATVAARLGLECVVYMGATDIERQK 154 ********************************************************************* PP TIGR00263 139 lnvfrmellgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeev 207 +nv+rm+llga+vvpvtsGs+tlkda+nea+rdWvt+v+dt+y++G+++Gp+P+P++vr+f +++g+e+ lcl|NCBI__GCF_001431535.1:WP_057687222.1 155 INVYRMKLLGATVVPVTSGSATLKDALNEAMRDWVTNVQDTFYIIGTVAGPDPYPRMVRDFNAIVGREA 223 ********************************************************************* PP TIGR00263 208 keqilekegrlPdaviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhG 276 +eq+l + grlPda+ acvGGGsnaiG+f+af++d ev+++g ea+G Gi+t +haa++++G++GvlhG lcl|NCBI__GCF_001431535.1:WP_057687222.1 224 REQMLLEYGRLPDAITACVGGGSNAIGLFHAFLNDREVQIFGAEAAGDGIETGRHAASIAAGRPGVLHG 292 ******99************************************************************* PP TIGR00263 277 aktkllqdedGqieeahsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGiipale 345 ++t++l d+dGqi e+hsvsaGldypgvgPeha+la++gra+y itdeeal+a++lls++eGi++ale lcl|NCBI__GCF_001431535.1:WP_057687222.1 293 NRTYVLCDDDGQIIETHSVSAGLDYPGVGPEHAFLADSGRATYLGITDEEALQAFHLLSRTEGILAALE 361 ********************************************************************* PP TIGR00263 346 sshalaaleklapklkkdeivvvnlsGrGdkdletvak 383 sshala+++kla + ++d++v++nlsGrGdkd++t+a lcl|NCBI__GCF_001431535.1:WP_057687222.1 362 SSHALAQAIKLARERPRDQLVLCNLSGRGDKDVHTIAA 399 ***********************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (405 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: 9.30 // [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