Align candidate WP_026608185.1 METAC_RS0118720 (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.16599.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.6e-191 620.9 0.0 5.6e-191 620.6 0.0 1.1 1 lcl|NCBI__GCF_000427445.1:WP_026608185.1 METAC_RS0118720 tryptophan synth Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000427445.1:WP_026608185.1 METAC_RS0118720 tryptophan synthase subunit beta # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 620.6 0.0 5.6e-191 5.6e-191 1 384 [. 17 409 .. 17 410 .. 0.97 Alignments for each domain: == domain 1 score: 620.6 bits; conditional E-value: 5.6e-191 TIGR00263 1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskkl...... 63 g+fg fGG++v+e+l++ + +lek+ye akkd++fk+el++ll +y+grp+pl++a++l+++l lcl|NCBI__GCF_000427445.1:WP_026608185.1 17 GHFGIFGGRFVAETLMPLILDLEKHYEAAKKDPAFKAELDHLLTHYVGRPSPLYYAERLTEQLrqksae 85 68*********************************************************9986333333 PP TIGR00263 64 ....ggakiylkredllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevy 128 ggakiy+kre+l+htGahkinn+lgq+lla+r+Gk+riiaetGaGqhGvatata+a++glec vy lcl|NCBI__GCF_000427445.1:WP_026608185.1 86 tggrGGAKIYFKREELNHTGAHKINNVLGQILLARRMGKTRIIAETGAGQHGVATATACARFGLECIVY 154 3333578************************************************************** PP TIGR00263 129 mGaedverqklnvfrmellgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivr 197 mG+ dverqk+nvfrm++lgakvvpv+sG ktlkda+nealrdWvt+v+dt+y++G+a+GphP+P++vr lcl|NCBI__GCF_000427445.1:WP_026608185.1 155 MGSVDVERQKPNVFRMNMLGAKVVPVQSGAKTLKDAMNEALRDWVTNVDDTFYCIGTAAGPHPYPAMVR 223 ********************************************************************* PP TIGR00263 198 efqsvigeevkeqilekegrlPdaviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatl 266 +fq vig+e+++q++e egrlPd + ac+GGGsnaiG+f++f+++++ve++gvea+G G+d ++haa+l lcl|NCBI__GCF_000427445.1:WP_026608185.1 224 DFQCVIGDETRKQMQEIEGRLPDSLFACIGGGSNAIGLFHPFLDEPSVEIYGVEAAGYGLD-KQHAASL 291 ************************************************************8.589**** PP TIGR00263 267 skGkeGvlhGaktkllqdedGqieeahsvsaGldypgvgPehaalaetgraeyeaitdeealealklls 335 + G++GvlhG++t+ll d dGqiee hs+saGldypg+gPeha+l+etgr++y ++td+eal+a++l++ lcl|NCBI__GCF_000427445.1:WP_026608185.1 292 AGGRPGVLHGNRTYLLMDSDGQIEEGHSISAGLDYPGIGPEHAWLKETGRVTYLSATDAEALAAFQLCA 360 ********************************************************************* PP TIGR00263 336 keeGiipalesshalaaleklapklkkdeivvvnlsGrGdkdletvaka 384 k eGiipale +hala + ++ap++++d+++vvn+sGrGdkd++tva++ lcl|NCBI__GCF_000427445.1:WP_026608185.1 361 KLEGIIPALEPAHALAKVAEIAPQKQQDHLLVVNISGRGDKDIFTVADH 409 **********************************************976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (413 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: 00:00:00.02 # Mc/sec: 7.93 // [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