Align candidate 209406 DVU0470 (tryptophan synthase, beta subunit)
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.14988.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.2e-180 584.2 0.0 7e-180 584.1 0.0 1.0 1 lcl|MicrobesOnline__882:209406 DVU0470 tryptophan synthase, bet Domain annotation for each sequence (and alignments): >> lcl|MicrobesOnline__882:209406 DVU0470 tryptophan synthase, beta subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 584.1 0.0 7e-180 7e-180 1 384 [. 4 386 .. 4 387 .. 0.99 Alignments for each domain: == domain 1 score: 584.1 bits; conditional E-value: 7e-180 TIGR00263 1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiylkredllhtG 79 g+fg+fGG++vpe l++ l e+e+a +++ ++f++el++ll+++agr+tplt +++ls++lg + ++lkredllhtG lcl|MicrobesOnline__882:209406 4 GYFGDFGGRFVPELLMPPLMEIEAAMRDIMPTQAFRHELDDLLHNFAGRETPLTRCDTLSRELG-CTLWLKREDLLHTG 81 79*************************************************************8.************** PP TIGR00263 80 ahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqklnvfrmellgakvvpvtsGs 158 ahk+nn+lgqalla+r+Gk+r++aetGaGqhGvata+aaa+lgl+c v+mGa dverq+ nv+rm+llga+vvpv+sG+ lcl|MicrobesOnline__882:209406 82 AHKVNNTLGQALLARRMGKTRLVAETGAGQHGVATAAAAARLGLSCIVFMGAVDVERQSANVMRMKLLGAEVVPVESGT 160 ******************************************************************************* PP TIGR00263 159 ktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeevkeqilekegrlPdaviacvGGGsnaiGifa 237 +tlkda+ne+lr W+++ +thy+ G+a+GphPfP++vr+fq+vig+e+++q+le+ g lPd+v+acvGGGsnaiG+f+ lcl|MicrobesOnline__882:209406 161 RTLKDAINETLRYWIAEQGSTHYCFGTAAGPHPFPTLVRDFQAVIGHETRRQMLERTGALPDMVVACVGGGSNAIGMFH 239 ******************************************************************************* PP TIGR00263 238 afiedeeveligveagGkGidtekhaatlskGkeGvlhGaktkllqdedGqieeahsvsaGldypgvgPehaalaetgr 316 af++d +v+++gvea+G+G ++a ++ G++GvlhG++t+llqd dGqi ++hsvsaGldypgvgPeha+l tgr lcl|MicrobesOnline__882:209406 240 AFVDDADVRIVGVEAAGTGEPGCYNSAPINLGSPGVLHGNRTMLLQDGDGQILPSHSVSAGLDYPGVGPEHAHLGATGR 318 ******************************************************************************* PP TIGR00263 317 aeyeaitdeealealkllskeeGiipalesshalaaleklapklkkdeivvvnlsGrGdkdletvaka 384 + y +td++al+a+k+l++ eGiipalessha+a + + l++ vvvnlsGrGdkd++ v+++ lcl|MicrobesOnline__882:209406 319 VVYGMVTDTQALAAFKALTRAEGIIPALESSHAVAWVLENPHLLPQGGNVVVNLSGRGDKDMDIVREH 386 ****************************************************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (395 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 9.25 // [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