Align candidate WP_010438046.1 G7G_RS0102665 (tryptophan synthase subunit beta)
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.1887029.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.1e-202 656.9 0.0 5.8e-202 656.7 0.0 1.0 1 NCBI__GCF_000192475.1:WP_010438046.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000192475.1:WP_010438046.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 656.7 0.0 5.8e-202 5.8e-202 1 384 [. 17 401 .. 17 402 .. 0.99 Alignments for each domain: == domain 1 score: 656.7 bits; conditional E-value: 5.8e-202 TIGR00263 1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiylkre 73 g+fg fGG++v+e+l++ + le++y+kak+d++f++e+++l+ +y+grp+pl++a++l+++lggakiylkr+ NCBI__GCF_000192475.1:WP_010438046.1 17 GRFGIFGGRFVSETLMPLILSLEEEYNKAKDDPTFWAEMDDLWANYVGRPSPLYYAERLTEHLGGAKIYLKRD 89 78*********************************************************************** PP TIGR00263 74 dllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqklnvfrmel 146 +l+htGahkinn+lgq++la+r+Gk+riiaetGaGqhGvatat++a++gl+c vymGa+dv+rq++nvfrm+l NCBI__GCF_000192475.1:WP_010438046.1 90 ELNHTGAHKINNVLGQIILARRMGKTRIIAETGAGQHGVATATVCAKFGLKCIVYMGAHDVQRQAPNVFRMRL 162 ************************************************************************* PP TIGR00263 147 lgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeevkeqilekegrlP 219 lga+v+pvtsG+ tlkda+n+alrdWvt+v+dt+y++G+++GphP+P++vr+fqs+ig+e+keq++++egrlP NCBI__GCF_000192475.1:WP_010438046.1 163 LGAEVIPVTSGRGTLKDAMNDALRDWVTNVRDTFYCIGTVAGPHPYPAMVRDFQSIIGKEAKEQMHKAEGRLP 235 ************************************************************************* PP TIGR00263 220 daviacvGGGsnaiGifaafiedeeveligveagGkGidt.ekhaatlskGkeGvlhGaktkllqdedGqiee 291 d++ia++GGGsna+G+f++f++d+ev++igveagGkG+++ ++h+a+l+ G++GvlhG++t+llqd+dGqi e NCBI__GCF_000192475.1:WP_010438046.1 236 DTIIAAIGGGSNAMGLFYPFLDDKEVNIIGVEAGGKGVNEkMEHCASLTGGRPGVLHGNRTYLLQDDDGQILE 308 **************************************98689****************************** PP TIGR00263 292 ahsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGiipalesshalaaleklapklkkde 364 +s+saGldypg+gPeh++l+++gra+y++itd+ealea++l++ +eGiipale shala+++k+ap+l+kd+ NCBI__GCF_000192475.1:WP_010438046.1 309 GYSISAGLDYPGIGPEHSWLNDIGRANYVSITDKEALEAFQLCCATEGIIPALEPSHALAHVMKIAPDLPKDH 381 ************************************************************************* PP TIGR00263 365 ivvvnlsGrGdkdletvaka 384 ++ +n++GrGdkd++tva++ NCBI__GCF_000192475.1:WP_010438046.1 382 LICMNMCGRGDKDVQTVAQY 401 *****************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (415 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 16.48 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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