Align candidate WP_011188872.1 DP_RS08280 (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.302739.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-184 599.9 0.0 1.2e-184 599.8 0.0 1.0 1 NCBI__GCF_000025945.1:WP_011188872.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000025945.1:WP_011188872.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 599.8 0.0 1.2e-184 1.2e-184 1 383 [. 5 389 .. 5 391 .. 0.99 Alignments for each domain: == domain 1 score: 599.8 bits; conditional E-value: 1.2e-184 TIGR00263 1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiylkre 73 g+fg++GG y+pe+l e+++ le+ay++a++d++f++e+ +l+++y+ rptplt+a+nlsk+ gga+iy+kre NCBI__GCF_000025945.1:WP_011188872.1 5 GFFGNWGGVYLPEILRETFDRLEEAYQQARNDPSFWQEYLQLMSTYSCRPTPLTYAENLSKHFGGAQIYIKRE 77 68*********************************************************************** PP TIGR00263 74 dllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqklnvfrmel 146 dl+htGahk nn++gq ll+kr+Gkkr+iaetGaGqhGvatat+aa++glec++ymG+ dv+rq++nvf+me NCBI__GCF_000025945.1:WP_011188872.1 78 DLNHTGAHKANNVMGQGLLVKRMGKKRVIAETGAGQHGVATATMAAKFGLECTIYMGEVDVQRQRPNVFWMEK 150 ************************************************************************* PP TIGR00263 147 lgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeevkeqilekegrlP 219 +ga+vvpv++Gs+tlkda+nea+rdWv++++dthyvlG+a+Gp+PfPe+v++fqs+ig+e++eqi++ +gr P NCBI__GCF_000025945.1:WP_011188872.1 151 MGATVVPVKDGSRTLKDAINEAFRDWVSNIDDTHYVLGTACGPAPFPEMVSWFQSIIGTEAREQIERYHGRPP 223 ************************************************************************* PP TIGR00263 220 daviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGk..eGvlhGaktkllqdedGqie 290 v+acvGGGsna+Gif+ f+ed+++el+gveagG G++t +haa+l+ G +Gv +G+kt++lq++dGq++ NCBI__GCF_000025945.1:WP_011188872.1 224 KRVYACVGGGSNAMGIFQGFLEDKKIELVGVEAGGDGLETGRHAARLAGGDasPGVAQGYKTMFLQNDDGQMR 296 ************************************************996559******************* PP TIGR00263 291 eahsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGiipalesshalaaleklapklkkd 363 e+hsv+aGldy+gv+P +++l e+gr+++ea+td+e+l+al+l +k+eGiipales+ha a++ k a++l+ + NCBI__GCF_000025945.1:WP_011188872.1 297 ETHSVAAGLDYVGVSPILSHLWEEGRVRFEAATDTEVLAALELTMKKEGIIPALESAHAFAQAFKEASDLSPE 369 ************************************************************************* PP TIGR00263 364 eivvvnlsGrGdkdletvak 383 + +v+n+sGrGdkd++tva+ NCBI__GCF_000025945.1:WP_011188872.1 370 DAIVINMSGRGDKDIFTVAH 389 *****************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (410 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: 00:00:00.00 # Mc/sec: 17.36 // [ok]
This GapMind analysis is from Jul 25 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