Align candidate Pf1N1B4_1831 (Tryptophan synthase beta chain (EC 4.2.1.20))
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.21551.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.8e-198 644.2 0.0 4.4e-198 644.0 0.0 1.0 1 lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1831 Tryptophan synthase beta chain ( Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1831 Tryptophan synthase beta chain (EC 4.2.1.20) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 644.0 0.0 4.4e-198 4.4e-198 1 384 [. 14 397 .. 14 398 .. 0.99 Alignments for each domain: == domain 1 score: 644.0 bits; conditional E-value: 4.4e-198 TIGR00263 1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklg 64 g fg+fGG+yv+e+l++ + +l ++ye ak+d++fk+el ++ ++y+grp+pl+fa++l++ g lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1831 14 GLFGAFGGRYVAETLMPLILDLAREYEAAKEDPAFKEELAYFQRDYVGRPSPLYFAERLTEFCG 77 67************************************************************** PP TIGR00263 65 gakiylkredllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevy 128 gakiylkre+l+htGahkinn +gq+lla+r+GkkriiaetGaG hGvatat+aa++gl+c++y lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1831 78 GAKIYLKREELNHTGAHKINNCIGQILLARRMGKKRIIAETGAGMHGVATATVAARFGLDCVIY 141 **************************************************************** PP TIGR00263 129 mGaedverqklnvfrmellgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPf 192 mG++d+erq+ nvfrm+llga+v+pv G+ tlkda+nealrdWvt+v++t+y++G+++GphP+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1831 142 MGTTDIERQQANVFRMKLLGAEVIPVVAGTGTLKDAMNEALRDWVTNVDSTFYLIGTVAGPHPY 205 **************************************************************** PP TIGR00263 193 PeivrefqsvigeevkeqilekegrlPdaviacvGGGsnaiGifaafiedeeveligveagGkG 256 P++vr+fq+vig+e++eq++++egrlPd ++ac+GGGsna+G+f++f++d++ve+igvea+G G lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1831 206 PAMVRDFQAVIGKETREQLQAQEGRLPDSLVACIGGGSNAMGLFHPFLDDKSVEIIGVEAAGYG 269 **************************************************************** PP TIGR00263 257 idtekhaatlskGkeGvlhGaktkllqdedGqieeahsvsaGldypgvgPehaalaetgraeye 320 i+t khaa+l+ G +GvlhG++t llqdedGqi +ahs+saGldypg+gPeha+l+++gr++y+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1831 270 IETGKHAASLNGGVPGVLHGNRTFLLQDEDGQIIDAHSISAGLDYPGIGPEHAWLHDIGRVQYT 333 **************************************************************** PP TIGR00263 321 aitdeealealkllskeeGiipalesshalaaleklapklkkdeivvvnlsGrGdkdletvaka 384 ++td+eal+a++++++ eGiipales+hala + k ap+l+kd+++vvnlsGrGdkd++tv+++ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1831 334 SVTDDEALDAFHKCCRLEGIIPALESAHALAEVFKRAPTLPKDHLMVVNLSGRGDKDMQTVMHH 397 *************************************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (409 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: 10.82 // [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