Align candidate 202145 SO3023 (tryptophan synthase, beta subunit (NCBI ptt file))
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.26099.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-197 642.0 0.0 2.1e-197 641.8 0.0 1.0 1 lcl|FitnessBrowser__MR1:202145 SO3023 tryptophan synthase, beta Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__MR1:202145 SO3023 tryptophan synthase, beta subunit (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 641.8 0.0 2.1e-197 2.1e-197 2 383 .. 9 389 .. 8 391 .. 0.99 Alignments for each domain: == domain 1 score: 641.8 bits; conditional E-value: 2.1e-197 TIGR00263 2 kfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiylkredllhtGa 80 +fge+GG yvp++l++al++le+a+ +a++de+f++e+++llk+yagrpt+lt ++nls + +kiylkredllh+Ga lcl|FitnessBrowser__MR1:202145 9 YFGEYGGMYVPQILVPALKQLESAFVEAQTDESFQAEFTDLLKNYAGRPTALTLTRNLSPNPM-VKIYLKREDLLHGGA 86 7***********************************************************996.*************** PP TIGR00263 81 hkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqklnvfrmellgakvvpvtsGsk 159 hk+n++lgqallakr+Gkk+iiaetGaGqhGvata+a+allgl+c+vymGa+dv+rq++nvfrm+l+ga+v+pvtsGs+ lcl|FitnessBrowser__MR1:202145 87 HKTNQVLGQALLAKRMGKKEIIAETGAGQHGVATALACALLGLKCKVYMGAKDVARQSPNVFRMRLMGAEVIPVTSGSA 165 ******************************************************************************* PP TIGR00263 160 tlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeevkeqilekegrlPdaviacvGGGsnaiGifaa 238 tlkda+nea+rdW++s+e++hy+lG+a+GphPfP+ivrefq++igee+k+qile+egrlPdaviacvGGGsnaiG+fa+ lcl|FitnessBrowser__MR1:202145 166 TLKDACNEAMRDWSGSYEKAHYLLGTAAGPHPFPTIVREFQRIIGEETKKQILEREGRLPDAVIACVGGGSNAIGMFAD 244 ******************************************************************************* PP TIGR00263 239 fiedeeveligveagGkGidtekhaatlskGkeGvlhGaktkllqdedGqieeahsvsaGldypgvgPehaalaetgra 317 fi++ +veligve++GkGidt++h+a l++Gk+G+++G+k+ l+qd +Gqiee++s+saGld+p+vgP+ha+l+ +gra lcl|FitnessBrowser__MR1:202145 245 FIDETNVELIGVEPAGKGIDTHMHGAPLKHGKTGIFFGMKAPLMQDSEGQIEESYSISAGLDFPSVGPQHAHLNAIGRA 323 ******************************************************************************* PP TIGR00263 318 eyeaitdeealealkllskeeGiipalesshalaaleklapklkkdeivvvnlsGrGdkdletvak 383 +ye++td+ealea++ll+++eGiipales+hala++ +la++ +k++i+vvnlsGrGdkd++tv + lcl|FitnessBrowser__MR1:202145 324 RYESATDDEALEAFQLLARCEGIIPALESAHALAYALRLAKECTKETILVVNLSGRGDKDIFTVSD 389 ***************************************************************976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (396 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: 7.92 // [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