Align candidate N515DRAFT_0115 N515DRAFT_0115 (tryptophan synthase beta chain)
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.10899.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.3e-193 626.8 0.7 8.3e-193 626.6 0.7 1.0 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_0115 N515DRAFT_0115 tryptophan syntha Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dyella79:N515DRAFT_0115 N515DRAFT_0115 tryptophan synthase beta chain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 626.6 0.7 8.3e-193 8.3e-193 1 383 [. 13 395 .. 13 397 .. 0.99 Alignments for each domain: == domain 1 score: 626.6 bits; conditional E-value: 8.3e-193 TIGR00263 1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklgga 66 g+fg+fGGqyv+e+l++ ++el++ay ++++d+ef +el++ lk y+grp+p+++a+ ls+++gga lcl|FitnessBrowser__Dyella79:N515DRAFT_0115 13 GRFGDFGGQYVAETLMAPIAELTEAYLRLREDPEFLAELDRDLKYYVGRPSPIYHAEGLSRHVGGA 78 78**************************************************************** PP TIGR00263 67 kiylkredllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGae 132 +i lkredl+htGahkinn++gqal+akr+Gk r+iaetGaGqhGva+at+aa++gl+c+vymGa lcl|FitnessBrowser__Dyella79:N515DRAFT_0115 79 QILLKREDLNHTGAHKINNTIGQALVAKRMGKPRVIAETGAGQHGVASATVAARFGLKCVVYMGAV 144 ****************************************************************** PP TIGR00263 133 dverqklnvfrmellgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivre 198 d+erqk+nv+rm+llga+vvpvtsGsktlkda+nea+rdWvt+v+dt+y++G+++GphP+P +vr+ lcl|FitnessBrowser__Dyella79:N515DRAFT_0115 145 DIERQKINVYRMKLLGAEVVPVTSGSKTLKDALNEAMRDWVTNVADTFYIIGTVAGPHPYPMMVRD 210 ****************************************************************** PP TIGR00263 199 fqsvigeevkeqilekegrlPdaviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaa 264 f +++g+e++eq+le+ grlPda+ acvGGGsnaiG+f+af++d +v+++g ea+G+Gi+t +haa lcl|FitnessBrowser__Dyella79:N515DRAFT_0115 211 FNAIVGREAREQMLEQYGRLPDAITACVGGGSNAIGLFHAFLNDANVRIVGAEAAGEGIATGHHAA 276 ****************************************************************** PP TIGR00263 265 tlskGkeGvlhGaktkllqdedGqieeahsvsaGldypgvgPehaalaetgraeyeaitdeealea 330 +l++G++GvlhG++t++l d++Gqi+e+hsvsaGldypgvgPeha+l++ graey+ itd+ealea lcl|FitnessBrowser__Dyella79:N515DRAFT_0115 277 SLAAGRPGVLHGNRTYVLCDDNGQITETHSVSAGLDYPGVGPEHAFLKDAGRAEYVGITDDEALEA 342 ****************************************************************** PP TIGR00263 331 lkllskeeGiipalesshalaaleklapklkkdeivvvnlsGrGdkdletvak 383 ++ll+++eGi++alessha+a+++kla +++kd++v++nlsGrGdkd++t+a lcl|FitnessBrowser__Dyella79:N515DRAFT_0115 343 FHLLARTEGILAALESSHAVAQAIKLAREMPKDQLVLCNLSGRGDKDVHTIAA 395 **************************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (401 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 7.04 // [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