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.20742.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: 10.08 // [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