Align candidate WP_086510933.1 BZY95_RS16220 (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.27706.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.9e-169 547.7 0.0 9e-169 547.5 0.0 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086510933.1 BZY95_RS16220 tryptophan synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086510933.1 BZY95_RS16220 tryptophan synthase subunit beta # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 547.5 0.0 9e-169 9e-169 1 383 [. 14 396 .. 14 398 .. 0.99 Alignments for each domain: == domain 1 score: 547.5 bits; conditional E-value: 9e-169 TIGR00263 1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiy 69 g+fg+fGGq +p +l ++e+++aye+++ ++f++el el+ +y+grp+p+++a++ls++lgga+i+ lcl|NCBI__GCF_002151265.1:WP_086510933.1 14 GFFGRFGGQLIPPELKRVMDEIDAAYEEIRVRDDFQRELAELFADYVGRPSPIFYARRLSERLGGAQIH 82 68******************************************************************* PP TIGR00263 70 lkredllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqk 138 lkredl+htGahkin lg allak +Gk+++iaetGaGqhGva ata+al+g+ ce++mG+ d+e+ + lcl|NCBI__GCF_002151265.1:WP_086510933.1 83 LKREDLNHTGAHKINHCLGEALLAKFMGKTKVIAETGAGQHGVALATACALVGIPCEIHMGQVDIEKEH 151 ********************************************************************* PP TIGR00263 139 lnvfrmellgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeev 207 +nv +m++lg k+v+vt G++tlkdav++a+ ++ + ++ y +Gs+vGphPfP++vr+fqs+ig+e+ lcl|NCBI__GCF_002151265.1:WP_086510933.1 152 PNVTKMKILGCKLVAVTRGTATLKDAVDSAFEEYLKDPQNFLYAIGSVVGPHPFPKMVRDFQSIIGREA 220 ********************************************************************* PP TIGR00263 208 keqilekegrlPdaviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhG 276 +eq l+++grlPd+v acvGGGsnaiG+f+af++de v+l+gve++G+G+dt++h+atl+ Gk+G +hG lcl|NCBI__GCF_002151265.1:WP_086510933.1 221 REQFLARHGRLPDHVTACVGGGSNAIGMFTAFLDDEAVHLVGVEPAGEGLDTQRHSATLTLGKPGEIHG 289 ********************************************************************* PP TIGR00263 277 aktkllqdedGqieeahsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGiipale 345 + ++l de+G+ ++hs+++GldypgvgP+h++l+e gr+ ye++td+e+l+a+ +ls+ eGiipale lcl|NCBI__GCF_002151265.1:WP_086510933.1 290 MACYVLEDEQGNPMPVHSIASGLDYPGVGPQHSYLKELGRVDYETATDAECLDAFLTLSRVEGIIPALE 358 ********************************************************************* PP TIGR00263 346 sshalaaleklapklkkdeivvvnlsGrGdkdletvak 383 s+ha+a ++++ap+l+kd+ +++nlsGrGdkd + va+ lcl|NCBI__GCF_002151265.1:WP_086510933.1 359 SAHAVAWAMRIAPTLPKDRHILINLSGRGDKDADYVAD 396 *********************************99987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (400 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10.18 // [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