Align candidate PfGW456L13_566 (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.4303.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-197 642.5 0.0 1.5e-197 642.2 0.0 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_566 Tryptophan synthase beta chain ( Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_566 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 ! 642.2 0.0 1.5e-197 1.5e-197 1 384 [. 14 397 .. 14 398 .. 0.99 Alignments for each domain: == domain 1 score: 642.2 bits; conditional E-value: 1.5e-197 TIGR00263 1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfa 56 g fg+fGG+yv+e+l++ + +l ++ye ak+d++fk+el ++ ++y+grp+pl+fa lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_566 14 GLFGAFGGRYVAETLMPLILDLAREYELAKEDPAFKEELAYFQRDYVGRPSPLYFA 69 67****************************************************** PP TIGR00263 57 knlskklggakiylkredllhtGahkinnalgqallakrlGkkriiaetGaGqhGv 112 ++l++ ggakiylkre+l+htGahkinn +gq+lla+r+GkkriiaetGaG hGv lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_566 70 ERLTEFCGGAKIYLKREELNHTGAHKINNCIGQILLARRMGKKRIIAETGAGMHGV 125 ******************************************************** PP TIGR00263 113 atataaallglecevymGaedverqklnvfrmellgakvvpvtsGsktlkdavnea 168 atat+aa++gl+c++ymG++d+erq+ nvfrm+llga+v+pv G+ tlkda+nea lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_566 126 ATATVAARFGLDCVIYMGTTDIERQQANVFRMKLLGAEVIPVVAGTGTLKDAMNEA 181 ******************************************************** PP TIGR00263 169 lrdWvtsvedthyvlGsavGphPfPeivrefqsvigeevkeqilekegrlPdavia 224 lrdWvt+v++t+y++G+++GphP+P++vr+fq+vig+e++eq++++egrlPd ++a lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_566 182 LRDWVTNVDSTFYLIGTVAGPHPYPAMVRDFQAVIGKETREQLQAQEGRLPDSLVA 237 ******************************************************** PP TIGR00263 225 cvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhGaktk 280 c+GGGsna+G+f++f++d++ve+igvea+G Gi+t khaa+l+ G +GvlhG++t lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_566 238 CIGGGSNAMGLFHPFLDDKSVEIIGVEAAGYGIETGKHAASLNGGVPGVLHGNRTF 293 ******************************************************** PP TIGR00263 281 llqdedGqieeahsvsaGldypgvgPehaalaetgraeyeaitdeealealkllsk 336 llqd+dGqi +ahs+saGldypg+gPeha+l+++gr++y+++td+eal+a++++++ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_566 294 LLQDDDGQIIDAHSISAGLDYPGIGPEHAWLHDIGRVQYTSVTDDEALAAFHQCCR 349 ******************************************************** PP TIGR00263 337 eeGiipalesshalaaleklapklkkdeivvvnlsGrGdkdletvaka 384 eGiipales+hala + k ap+l+kd+++vvnlsGrGdkd++tv+++ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_566 350 LEGIIPALESAHALAEVFKRAPTLPKDHLMVVNLSGRGDKDMQTVMHH 397 *********************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (406 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: 00:00:00.02 # Mc/sec: 7.54 // [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