Align candidate GFF476 PGA1_c04870 (tryptophan synthase beta chain)
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.11906.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-202 657.9 0.0 3e-202 657.7 0.0 1.0 1 lcl|FitnessBrowser__Phaeo:GFF476 PGA1_c04870 tryptophan synthase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Phaeo:GFF476 PGA1_c04870 tryptophan synthase beta chain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 657.7 0.0 3e-202 3e-202 1 384 [. 17 403 .. 17 404 .. 0.99 Alignments for each domain: == domain 1 score: 657.7 bits; conditional E-value: 3e-202 TIGR00263 1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiylkredllh 77 g+fg fGG++v+e+l++ + le++y++ak+d++f++e+++l+k+y+grp+pl+fa++l+++lggakiylkr++l+h lcl|FitnessBrowser__Phaeo:GFF476 17 GRFGIFGGRFVSETLMPLILSLEEEYDRAKDDPSFWAEMDDLWKNYVGRPSPLYFAERLTEHLGGAKIYLKRDELNH 93 78*************************************************************************** PP TIGR00263 78 tGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqklnvfrmellgakvvpv 154 tGahkinn+lgq+lla+r+Gk+riiaetGaGqhGvatat++a++gl+c+vymGa+dv+rq++nvfrm+llga+v+pv lcl|FitnessBrowser__Phaeo:GFF476 94 TGAHKINNVLGQILLARRMGKDRIIAETGAGQHGVATATVCAKFGLKCVVYMGAHDVQRQAPNVFRMRLLGAEVIPV 170 ***************************************************************************** PP TIGR00263 155 tsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeevkeqileke..grlPdaviacvGGG 229 tsG+ tlkda+n+alrdWvt+v+dt+y++G+++GphP+P++vr+fqsvig+ev++q++e+e grlPd+via++GGG lcl|FitnessBrowser__Phaeo:GFF476 171 TSGRGTLKDAMNDALRDWVTNVHDTFYCIGTVAGPHPYPAMVRDFQSVIGKEVRWQLAEQEgeGRLPDTVIAAIGGG 247 *********************************************************9998779************* PP TIGR00263 230 snaiGifaafiedeeveligveagGkGidt.ekhaatlskGkeGvlhGaktkllqdedGqieeahsvsaGldypgvg 305 sna+G+f++f++d++v++igveagGkG+d+ ++h+a+l+ G++GvlhG++t+llqd+dGqi e +s+saGldypg+g lcl|FitnessBrowser__Phaeo:GFF476 248 SNAMGLFYPFLDDKSVNIIGVEAGGKGVDEkMQHCASLTGGRPGVLHGNRTYLLQDDDGQILEGFSISAGLDYPGIG 324 ****************************98689******************************************** PP TIGR00263 306 PehaalaetgraeyeaitdeealealkllskeeGiipalesshalaaleklapklkkdeivvvnlsGrGdkdletva 382 Peha+l+++gra y++itd+ealea++l + eGiipale shala+++k+ap+l+kd+i+v+n++GrGdkd++tva lcl|FitnessBrowser__Phaeo:GFF476 325 PEHAWLNDIGRADYVSITDKEALEAFQLSCAMEGIIPALEPSHALAHVMKIAPDLPKDHIIVMNMCGRGDKDIFTVA 401 ****************************************************************************9 PP TIGR00263 383 ka 384 ++ lcl|FitnessBrowser__Phaeo:GFF476 402 RH 403 76 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (417 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: 7.13 // [ok]
This GapMind analysis is from Apr 09 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