Align candidate 8501004 DvMF_1741 (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.10673.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-183 594.8 0.0 4.3e-183 594.6 0.0 1.0 1 lcl|FitnessBrowser__Miya:8501004 DvMF_1741 tryptophan synthase su Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Miya:8501004 DvMF_1741 tryptophan synthase subunit beta (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 594.6 0.0 4.3e-183 4.3e-183 1 383 [. 4 385 .. 4 387 .. 0.99 Alignments for each domain: == domain 1 score: 594.6 bits; conditional E-value: 4.3e-183 TIGR00263 1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiylkredllh 77 g+fgefGGq+vpe l++ l+ele+a +++ ++f++el++ll+++agr+tplt +++ls +lg ++++lkredllh lcl|FitnessBrowser__Miya:8501004 4 GYFGEFGGQFVPELLMPPLRELEAAMRDILPSDKFRAELDDLLRNFAGRETPLTACPTLSAELG-VHLWLKREDLLH 79 79*************************************************************8.************ PP TIGR00263 78 tGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqklnvfrmellgakvvpv 154 tGahk+nn+lgqallak++Gk+ ++aetGaGqhGvata+aaa+lg+ec++ymGa+dv rq++nv+rm+llgakvvpv lcl|FitnessBrowser__Miya:8501004 80 TGAHKVNNTLGQALLAKYMGKTALVAETGAGQHGVATAAAAARLGMECVIYMGATDVVRQAPNVMRMKLLGAKVVPV 156 ***************************************************************************** PP TIGR00263 155 tsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeevkeqilekegrlPdaviacvGGGsn 231 +sG+ktlkda+nealr W+++ ++thy+ G+a+GphPfP++vr++qsvig+e ++q+le+ grlPd+v+acvGGGsn lcl|FitnessBrowser__Miya:8501004 157 QSGTKTLKDAINEALRYWIAQQDSTHYCFGTAAGPHPFPTLVRDLQSVIGRESRAQMLERVGRLPDMVVACVGGGSN 233 ***************************************************************************** PP TIGR00263 232 aiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhGaktkllqdedGqieeahsvsaGldypgvgPeh 308 aiG+f++fi+d +v+++gvea+G+G ++a ++ G++GvlhG++t+llqd dGqie++hsvsaGldypgvgPeh lcl|FitnessBrowser__Miya:8501004 234 AIGMFHPFIDDASVRIVGVEAAGTGEPGCYNSAPINLGRPGVLHGQMTMLLQDADGQIEPSHSVSAGLDYPGVGPEH 310 ***************************************************************************** PP TIGR00263 309 aalaetgraeyeaitdeealealkllskeeGiipalesshalaaleklapklkkdeivvvnlsGrGdkdletvak 383 a+l +gra y +td++alea+++l+++eGiipalesshala + + kl+ vvvnlsGrGdkd+e v++ lcl|FitnessBrowser__Miya:8501004 311 AHLGAIGRAAYGMATDSQALEAFQALTRREGIIPALESSHALAWVLNNRDKLPAGGHVVVNLSGRGDKDMEIVRE 385 ***********************************************************************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (394 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: 8.66 // [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