Align candidate BWI76_RS11845 BWI76_RS11845 (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.14548.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-192 625.4 0.0 2.3e-192 625.2 0.0 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS11845 BWI76_RS11845 tryptophan synthas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS11845 BWI76_RS11845 tryptophan synthase subunit beta # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 625.2 0.0 2.3e-192 2.3e-192 2 383 .. 8 389 .. 7 391 .. 0.99 Alignments for each domain: == domain 1 score: 625.2 bits; conditional E-value: 2.3e-192 TIGR00263 2 kfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiylkr 72 +fgefGG yvp++l++al++le+a+ +a+kd++f++e+++llk+yagrpt+lt ++nl++ + + +ylkr lcl|FitnessBrowser__Koxy:BWI76_RS11845 8 YFGEFGGMYVPQILMPALRQLEEAFVSAQKDPAFQAEFTDLLKNYAGRPTALTKCRNLTEGTR-TTLYLKR 77 7************************************************************97.9****** PP TIGR00263 73 edllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqklnvfr 143 edllh+Gahk+n++lgqallakr+Gk++iiaetGaGqhGva+a+a+allgl+c++ymGa+d+erq++nvfr lcl|FitnessBrowser__Koxy:BWI76_RS11845 78 EDLLHGGAHKTNQVLGQALLAKRMGKTEIIAETGAGQHGVASALASALLGLKCRIYMGAKDIERQSPNVFR 148 *********************************************************************** PP TIGR00263 144 mellgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeevkeqilek 214 m+l+ga+v+pv+sGs+tlkda+nealrdW++s+e++hy+lG+a+GphPfP+ivrefq++igee+k+qilek lcl|FitnessBrowser__Koxy:BWI76_RS11845 149 MRLMGAEVIPVHSGSSTLKDACNEALRDWSGSYETAHYMLGTAAGPHPFPTIVREFQRMIGEETKAQILEK 219 *********************************************************************** PP TIGR00263 215 egrlPdaviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhGaktkllqde 285 egrlPdaviacvGGGsnaiG+fa+fi++ +v ligve++G+Gi++ +h+a l++G++G+ +G+k+ ++q+e lcl|FitnessBrowser__Koxy:BWI76_RS11845 220 EGRLPDAVIACVGGGSNAIGMFADFIDETTVGLIGVEPAGHGIESGEHGAPLKHGRVGIYFGMKSPMMQTE 290 *********************************************************************** PP TIGR00263 286 dGqieeahsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGiipalesshalaalekl 356 +Gqiee++s+saGld+p+vgP+ha+l+ +gra y++itd+eal+a+k ls++eGiipalesshala++ k+ lcl|FitnessBrowser__Koxy:BWI76_RS11845 291 EGQIEESYSISAGLDFPSVGPQHAYLNSIGRADYVSITDDEALDAFKELSRHEGIIPALESSHALAHALKM 361 ********************************************************************999 PP TIGR00263 357 apklk.kdeivvvnlsGrGdkdletvak 383 + + + k++++vvnlsGrGdkd++tv++ lcl|FitnessBrowser__Koxy:BWI76_RS11845 362 MRENPeKEQLLVVNLSGRGDKDIFTVHD 389 8876659******************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (397 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: 8.44 // [ok]
This GapMind analysis is from Apr 09 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