Align candidate PP_0083 PP_0083 (tryptophan synthase beta chain)
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.15843.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.2e-197 640.0 0.1 8.2e-197 639.8 0.1 1.0 1 lcl|FitnessBrowser__Putida:PP_0083 PP_0083 tryptophan synthase beta Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_0083 PP_0083 tryptophan synthase beta chain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 639.8 0.1 8.2e-197 8.2e-197 1 384 [. 14 397 .. 14 398 .. 0.99 Alignments for each domain: == domain 1 score: 639.8 bits; conditional E-value: 8.2e-197 TIGR00263 1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiylkredl 75 g fg+fGG+yv+e+l++ + +l ++ye ak+d++f +el ++ ++y grp pl+fa++l+++ ggaki++kre+l lcl|FitnessBrowser__Putida:PP_0083 14 GLFGSFGGRYVAETLMPLVLDLAREYEAAKADPKFLEELAYFQRDYIGRPNPLYFAERLTEHCGGAKIFFKREEL 88 67************************************************************************* PP TIGR00263 76 lhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqklnvfrmellgak 150 +htGahk+nn +gq+llakr+Gkkr+iaetGaG hGvatat+aa++gl c++ymGa+d+erq+ nvfrm+llga+ lcl|FitnessBrowser__Putida:PP_0083 89 NHTGAHKVNNCIGQVLLAKRMGKKRLIAETGAGMHGVATATVAARFGLPCVIYMGATDIERQQANVFRMKLLGAE 163 *************************************************************************** PP TIGR00263 151 vvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeevkeqilekegrlPdaviac 225 +vpvt G+ tlkda+nealrdWvt+vedt+y++G+++GphP+P++vr+fqs+ig+e+++q++ekegrlPd ++ac lcl|FitnessBrowser__Putida:PP_0083 164 IVPVTAGTGTLKDAMNEALRDWVTNVEDTFYLIGTVAGPHPYPAMVRDFQSIIGKETRAQLQEKEGRLPDSLVAC 238 *************************************************************************** PP TIGR00263 226 vGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhGaktkllqdedGqieeahsvsaGld 300 vGGGsna+G+f++f+e+++v++igveagG+G++t+khaa+l+ G +GvlhG++t+llqd+dGqi++ahs+saGld lcl|FitnessBrowser__Putida:PP_0083 239 VGGGSNAMGLFHEFLEEPSVQIIGVEAGGHGVHTDKHAASLNGGVPGVLHGNRTYLLQDQDGQITDAHSISAGLD 313 *************************************************************************** PP TIGR00263 301 ypgvgPehaalaetgraeyeaitdeealealkllskeeGiipalesshalaaleklapklkkdeivvvnlsGrGd 375 ypg+gPeha+l+e +r+ey++itd+eal+a+++ ++ eGiipalesshala ++k apkl+kd+++vv lsGrGd lcl|FitnessBrowser__Putida:PP_0083 314 YPGIGPEHAYLHEVKRVEYVSITDDEALDAFHATCRLEGIIPALESSHALAEAIKRAPKLPKDHLMVVCLSGRGD 388 *************************************************************************** PP TIGR00263 376 kdletvaka 384 kd++tv+++ lcl|FitnessBrowser__Putida:PP_0083 389 KDMQTVMNH 397 ******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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 12.47 // [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