Align candidate GFF1870 HP15_1827 (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.29422.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-194 632.4 0.2 1.6e-194 632.2 0.2 1.0 1 lcl|FitnessBrowser__Marino:GFF1870 HP15_1827 tryptophan synthase, b Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF1870 HP15_1827 tryptophan synthase, beta subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 632.2 0.2 1.6e-194 1.6e-194 1 383 [. 18 400 .. 18 402 .. 1.00 Alignments for each domain: == domain 1 score: 632.2 bits; conditional E-value: 1.6e-194 TIGR00263 1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiylkredl 75 g+fg+fGG++v+e+l+ +l lek+y ++kkd+ef++ +++ l +y+grptpl+fa++ls+++gga+i+lkredl lcl|FitnessBrowser__Marino:GFF1870 18 GHFGAFGGRFVSETLMDSLMTLEKEYARLKKDPEFQARFDKELADYVGRPTPLYFAERLSRETGGAQIWLKREDL 92 68************************************************************************* PP TIGR00263 76 lhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqklnvfrmellgak 150 htGahk+nn++gqalla lGkkriiaetGaGqhGvatat++a+lglec+v+mGaedv+rq+lnvfrm+llga+ lcl|FitnessBrowser__Marino:GFF1870 93 CHTGAHKVNNTIGQALLASFLGKKRIIAETGAGQHGVATATVCARLGLECHVFMGAEDVQRQSLNVFRMKLLGAT 167 *************************************************************************** PP TIGR00263 151 vvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeevkeqilekegrlPdaviac 225 v++v+ G+ktlkda+n+a+rdWv++v+dt+y++G+++GphP+P +vr+fqsvig+e+++q lek g+lPda++ac lcl|FitnessBrowser__Marino:GFF1870 168 VHAVQGGTKTLKDAMNDAMRDWVAHVDDTFYIIGTVAGPHPYPLLVRDFQSVIGRETRRQALEKTGKLPDALVAC 242 *************************************************************************** PP TIGR00263 226 vGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhGaktkllqdedGqieeahsvsaGld 300 vGGGsnaiG+f++f++de+v+l+gveagG+Gidt khaa l +G++GvlhG++t+l+ de+Gqi +hsvsaGld lcl|FitnessBrowser__Marino:GFF1870 243 VGGGSNAIGMFYPFLSDESVQLYGVEAGGLGIDTGKHAAPLCAGRPGVLHGNRTYLMEDENGQIAGTHSVSAGLD 317 *************************************************************************** PP TIGR00263 301 ypgvgPehaalaetgraeyeaitdeealealkllskeeGiipalesshalaaleklapklkkdeivvvnlsGrGd 375 ypgvgPeh++l+++gra+y+++td+ea+e++++l++ eGi+pale++ha+a+++kla++++kd++vv+n+sGrGd lcl|FitnessBrowser__Marino:GFF1870 318 YPGVGPEHSWLKDIGRANYVSVTDDEAMEGFRKLTRVEGIMPALETAHAVAYAIKLAATMDKDQTVVINVSGRGD 392 *************************************************************************** PP TIGR00263 376 kdletvak 383 kd++tvak lcl|FitnessBrowser__Marino:GFF1870 393 KDINTVAK 400 ******98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (406 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: 00:00:00.02 # Mc/sec: 7.63 // [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