Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate BPHYT_RS33865 BPHYT_RS33865 tryptophan synthase alpha chain
Query= uniprot:H0BV16 (269 letters) >FitnessBrowser__BFirm:BPHYT_RS33865 Length = 270 Score = 307 bits (786), Expect = 2e-88 Identities = 155/269 (57%), Positives = 200/269 (74%), Gaps = 4/269 (1%) Query: 1 MSRIASTFSALQAQGRKALIPYVTAGFPFADITPALMHGMVEAGADVIELGVPFSDPMAD 60 MSRI +TF+AL AQG+K LIP++TAG P T MH + GADVIELGVPFSDPMAD Sbjct: 1 MSRIKNTFAALSAQGKKGLIPFMTAGDPDPARTVEFMHALAAGGADVIELGVPFSDPMAD 60 Query: 61 GPVIQKAGEKALSLGIGMVQVLDHVREFRKRNNTTPVVLMGYANPVERYDQKHGEGAFVR 120 GPVIQ++ E+AL+ G+ + V+ V+ FR+ N+TTPVVLMGYANP+ER G AF + Sbjct: 61 GPVIQQSSERALAHGVSLRHVIADVKRFRETNDTTPVVLMGYANPIERM----GTEAFAK 116 Query: 121 DSAAAGVDGVLIVDYPPEECEAFAASLRAHGMDLIFLLAPTSTDERMAEVARVASGYVYY 180 + AGVDGVL+VDYPPEEC FA +++ G+D IFLLAPTSTDER+AEV ++ASGYVYY Sbjct: 117 AAKEAGVDGVLVVDYPPEECANFAEQMQSAGIDPIFLLAPTSTDERIAEVGKIASGYVYY 176 Query: 181 VSLKGVTGSGALDTAAVEQMLPRIRQHVTIPVGVGFGIRDAATAQAIGKVADAVVIGSRI 240 VSLKGVTG+ LD +++ +P I+ V +PVGVGFGIRDA TA+++ +V+DAVVIGSRI Sbjct: 177 VSLKGVTGAANLDVSSIASKIPAIKSRVPLPVGVGFGIRDAQTARSVAEVSDAVVIGSRI 236 Query: 241 IQLIEDQEHAKVVPLTIDFLRGIRKALDA 269 +QL+E F+ +R+ALD+ Sbjct: 237 VQLLEQAAPEAAAETLTRFVAEVREALDS 265 Lambda K H 0.321 0.137 0.389 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 261 Number of extensions: 8 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 269 Length of database: 270 Length adjustment: 25 Effective length of query: 244 Effective length of database: 245 Effective search space: 59780 Effective search space used: 59780 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 47 (22.7 bits)
Align candidate BPHYT_RS33865 BPHYT_RS33865 (tryptophan synthase alpha chain)
to HMM TIGR00262 (trpA: tryptophan synthase, alpha 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/TIGR00262.hmm # target sequence database: /tmp/gapView.28737.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00262 [M=256] Accession: TIGR00262 Description: trpA: tryptophan synthase, alpha 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-79 252.7 0.2 1.5e-79 252.5 0.2 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS33865 BPHYT_RS33865 tryptophan synthas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS33865 BPHYT_RS33865 tryptophan synthase alpha chain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 252.5 0.2 1.5e-79 1.5e-79 1 255 [. 8 259 .. 8 260 .. 0.98 Alignments for each domain: == domain 1 score: 252.5 bits; conditional E-value: 1.5e-79 TIGR00262 1 fetlkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagvk 70 f++l ++++k ++pF+tagdPd ++++e+++ l+ Gad++ElGvpfsDP+aDGp+iq+++ RAl++gv+ lcl|FitnessBrowser__BFirm:BPHYT_RS33865 8 FAALSAQGKKGLIPFMTAGDPDPARTVEFMHALAAGGADVIELGVPFSDPMADGPVIQQSSERALAHGVS 77 67889999************************************************************** PP TIGR00262 71 vekalellkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakkhg 140 ++++++ +k++re++ + P+vl+ y+n+i ++g+e+F + akeagvdgvlv+D P ee +++ e+ ++ g lcl|FitnessBrowser__BFirm:BPHYT_RS33865 78 LRHVIADVKRFRETNDTTPVVLMGYANPIERMGTEAFAKAAKEAGVDGVLVVDYPPEECANFAEQMQSAG 147 ********************************************************************** PP TIGR00262 141 vkqiflvaPtaeeerlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkalskkPvlvGFGiskk 210 +++ifl aPt+ +er+ ++ + ++G+vY vs Gvtga + +++ + i +k+ Pv vGFGi + lcl|FitnessBrowser__BFirm:BPHYT_RS33865 148 IDPIFLLAPTSTDERIAEVGKIASGYVYYVSLKGVTGAANLDVSSIASKIPAIKSRVPLPVGVGFGIRDA 217 ****************************************999999************************ PP TIGR00262 211 eqvkelkelgadgvivGsAlvkiieeklddeekaleeleefvkel 255 + ++++ e+ +d+v++Gs +v+++e+ +e+a e l fv e+ lcl|FitnessBrowser__BFirm:BPHYT_RS33865 218 QTARSVAEV-SDAVVIGSRIVQLLEQA--APEAAAETLTRFVAEV 259 *********.889*************9..7899999999999875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (256 nodes) Target sequences: 1 (270 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 10.07 // [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