Align candidate WP_011802417.1 PNAP_RS15235 (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.8088.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-196 637.9 0.7 3.5e-196 637.7 0.7 1.0 1 lcl|NCBI__GCF_000015505.1:WP_011802417.1 PNAP_RS15235 tryptophan synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015505.1:WP_011802417.1 PNAP_RS15235 tryptophan synthase subunit beta # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 637.7 0.7 3.5e-196 3.5e-196 1 383 [. 11 394 .. 11 396 .. 0.99 Alignments for each domain: == domain 1 score: 637.7 bits; conditional E-value: 3.5e-196 TIGR00263 1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiy 69 g+fg +GG +v+e+l +a++el++ay ++++d++f +e+++ lk+++grp+p+++a+++s+++gga+iy lcl|NCBI__GCF_000015505.1:WP_011802417.1 11 GHFGIYGGSFVSETLTHAINELKDAYARYQNDPKFLAEFNYELKHFVGRPSPIYHAARMSREQGGAQIY 79 68******************************************************************* PP TIGR00263 70 lkredllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqk 138 lkredl+htGahkinn++gqa+la+r+Gk+riiaetGaGqhGvatat++a+ glec+vymG+edv+rq+ lcl|NCBI__GCF_000015505.1:WP_011802417.1 80 LKREDLNHTGAHKINNTIGQAMLARRMGKQRIIAETGAGQHGVATATICARYGLECVVYMGSEDVKRQS 148 ********************************************************************* PP TIGR00263 139 lnvfrmellgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeev 207 +nv+rm+llga+vvpv+sGsktlkda+nea+rdWv++v++t+y++G+++GphP+P +vr+fqsvig+e+ lcl|NCBI__GCF_000015505.1:WP_011802417.1 149 PNVYRMNLLGATVVPVESGSKTLKDALNEAMRDWVANVDNTFYIIGTVAGPHPYPMMVRDFQSVIGTEC 217 ********************************************************************* PP TIGR00263 208 keqileke.grlPdaviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlh 275 +q+ e++ gr Pdav+acvGGGsna+Gif+++i +e+ +ligvea+G+G+d+ kh+a+l++G +Gvlh lcl|NCBI__GCF_000015505.1:WP_011802417.1 218 LSQMPEMNaGRQPDAVVACVGGGSNAMGIFHPYIAHENTRLIGVEAAGEGLDSGKHSASLQRGLPGVLH 286 ******999************************************************************ PP TIGR00263 276 GaktkllqdedGqieeahsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGiipal 344 G++t++lq++dGq++e+hs+saGldypgvgPeha+l+++graey+ itd+eal+a+++l+++eGiipal lcl|NCBI__GCF_000015505.1:WP_011802417.1 287 GNRTYVLQNDDGQVTETHSISAGLDYPGVGPEHAYLKDIGRAEYVGITDTEALQAFHYLCRTEGIIPAL 355 ********************************************************************* PP TIGR00263 345 esshalaaleklapklkkdeivvvnlsGrGdkdletvak 383 es+ha+a+++kla++++ d+ ++vnlsGrGdkd+ tva+ lcl|NCBI__GCF_000015505.1:WP_011802417.1 356 ESAHAVAYAMKLAKTMRSDQSILVNLSGRGDKDIGTVAD 394 ************************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (434 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: 7.24 // [ok]
This GapMind analysis is from Apr 10 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