Align candidate 5209802 Shew_2255 (tryptophan synthase subunit beta (RefSeq))
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.31242.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.4e-197 640.2 0.0 7.4e-197 639.9 0.0 1.0 1 lcl|FitnessBrowser__PV4:5209802 Shew_2255 tryptophan synthase su Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PV4:5209802 Shew_2255 tryptophan synthase subunit beta (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 639.9 0.0 7.4e-197 7.4e-197 2 383 .. 8 388 .. 7 390 .. 0.99 Alignments for each domain: == domain 1 score: 639.9 bits; conditional E-value: 7.4e-197 TIGR00263 2 kfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiylkredllhtG 79 +fge+GG +vp++l++al++le+a+ +a++d++f++e+++llk+yagrpt+lt ++nls + +kiylkredllh+G lcl|FitnessBrowser__PV4:5209802 8 YFGEYGGMFVPQILMPALKQLEAAFVDAQNDPSFQAEFTDLLKNYAGRPTALTLTRNLSPNPL-VKIYLKREDLLHGG 84 7**********************************************************9996.************** PP TIGR00263 80 ahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqklnvfrmellgakvvpvtsG 157 ahk+n++lgqallakr+Gkk+iiaetGaGqhGvata+a+allgl+c+vymGa+dverq++nvfrm+l+ga+v+pvtsG lcl|FitnessBrowser__PV4:5209802 85 AHKTNQVLGQALLAKRMGKKEIIAETGAGQHGVATALACALLGLKCKVYMGAKDVERQSPNVFRMRLMGAEVIPVTSG 162 ****************************************************************************** PP TIGR00263 158 sktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeevkeqilekegrlPdaviacvGGGsnaiGi 235 s+tlkda+nea+rdW++s++++hy+lG+a+GphPfP+ivrefq++igee+k+qile+egrlPdaviacvGGGsnaiG+ lcl|FitnessBrowser__PV4:5209802 163 SATLKDACNEAMRDWSASYDKAHYLLGTAAGPHPFPTIVREFQRMIGEETKAQILEREGRLPDAVIACVGGGSNAIGM 240 ****************************************************************************** PP TIGR00263 236 faafiedeeveligveagGkGidtekhaatlskGkeGvlhGaktkllqdedGqieeahsvsaGldypgvgPehaalae 313 fa+fi++++v+ligve++G+Gidt kh+a l++Gk+G+++G+k+ l+qd++Gqiee++s+saGld+p+vgP+ha+la lcl|FitnessBrowser__PV4:5209802 241 FADFIDEPSVKLIGVEPAGLGIDTPKHGAPLKHGKTGIFFGMKAPLMQDKEGQIEESYSISAGLDFPSVGPQHAHLAA 318 ****************************************************************************** PP TIGR00263 314 tgraeyeaitdeealealkllskeeGiipalesshalaaleklapklkkdeivvvnlsGrGdkdletvak 383 tgra+ye++td+eal+a++ll+++eGiipales+hala+++kla++ ++++++vvnlsGrGdkd++tva+ lcl|FitnessBrowser__PV4:5209802 319 TGRATYESATDDEALAAFQLLARSEGIIPALESAHALAYAIKLAEAATEETLLVVNLSGRGDKDIFTVAD 388 *******************************************************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (403 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: 7.80 // [ok]
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.
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