Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate H281DRAFT_06065 H281DRAFT_06065 tryptophan synthase, alpha chain
Query= uniprot:H0BV16 (269 letters) >FitnessBrowser__Burk376:H281DRAFT_06065 Length = 288 Score = 307 bits (786), Expect = 2e-88 Identities = 156/269 (57%), Positives = 198/269 (73%), Gaps = 4/269 (1%) Query: 1 MSRIASTFSALQAQGRKALIPYVTAGFPFADITPALMHGMVEAGADVIELGVPFSDPMAD 60 MSRI +TF AL AQG+K LIP++TAG P T MH + GADVIELGVPFSDPMAD Sbjct: 19 MSRIKNTFDALSAQGKKGLIPFMTAGDPDPARTVEFMHALAAGGADVIELGVPFSDPMAD 78 Query: 61 GPVIQKAGEKALSLGIGMVQVLDHVREFRKRNNTTPVVLMGYANPVERYDQKHGEGAFVR 120 GPVIQ++ E+AL+ G+ + V+ V+ FR+ N+TTPVVLMGYANP+ER G AF + Sbjct: 79 GPVIQQSSERALAHGVSLRHVIADVKRFRETNDTTPVVLMGYANPIERM----GAEAFAK 134 Query: 121 DSAAAGVDGVLIVDYPPEECEAFAASLRAHGMDLIFLLAPTSTDERMAEVARVASGYVYY 180 + AGVDGVL+VDYPPEEC FA +R+ G+D IFLLAPTSTDER+AEV ++ASGYVYY Sbjct: 135 AAKEAGVDGVLVVDYPPEECANFAEKMRSAGIDPIFLLAPTSTDERIAEVGKIASGYVYY 194 Query: 181 VSLKGVTGSGALDTAAVEQMLPRIRQHVTIPVGVGFGIRDAATAQAIGKVADAVVIGSRI 240 VSLKGVTG+ LD +++ +P I+ V +PVGVGFGIRDA TA+ + +V+DAVVIGSRI Sbjct: 195 VSLKGVTGAANLDVSSIASKIPAIKSRVPLPVGVGFGIRDAETARLVAEVSDAVVIGSRI 254 Query: 241 IQLIEDQEHAKVVPLTIDFLRGIRKALDA 269 +QL+E F+ +R+ALD+ Sbjct: 255 VQLLEQTAPEAAAGTLTRFVAEVREALDS 283 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: 275 Number of extensions: 9 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: 288 Length adjustment: 25 Effective length of query: 244 Effective length of database: 263 Effective search space: 64172 Effective search space used: 64172 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 H281DRAFT_06065 H281DRAFT_06065 (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.17075.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.6e-79 250.2 0.1 9.2e-79 249.9 0.1 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_06065 H281DRAFT_06065 tryptophan synth Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_06065 H281DRAFT_06065 tryptophan synthase, alpha chain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 249.9 0.1 9.2e-79 9.2e-79 1 254 [. 26 276 .. 26 278 .. 0.97 Alignments for each domain: == domain 1 score: 249.9 bits; conditional E-value: 9.2e-79 TIGR00262 1 fetlkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlk 66 f++l ++++k ++pF+tagdPd ++++e+++ l+ Gad++ElGvpfsDP+aDGp+iq+++ RAl+ lcl|FitnessBrowser__Burk376:H281DRAFT_06065 26 FDALSAQGKKGLIPFMTAGDPDPARTVEFMHALAAGGADVIELGVPFSDPMADGPVIQQSSERALA 91 67889999********************************************************** PP TIGR00262 67 agvkvekalellkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddl 132 +gv+++++++ +k++re++ + P+vl+ y+n+i ++g e+F + akeagvdgvlv+D P ee +++ lcl|FitnessBrowser__Burk376:H281DRAFT_06065 92 HGVSLRHVIADVKRFRETNDTTPVVLMGYANPIERMGAEAFAKAAKEAGVDGVLVVDYPPEECANF 157 ****************************************************************** PP TIGR00262 133 leaakkhgvkqiflvaPtaeeerlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkalsk 198 e+ ++ g+++ifl aPt+ +er+ ++ + ++G+vY vs Gvtga + +++ + i +k+ lcl|FitnessBrowser__Burk376:H281DRAFT_06065 158 AEKMRSAGIDPIFLLAPTSTDERIAEVGKIASGYVYYVSLKGVTGAANLDVSSIASKIPAIKSRVP 223 ************************************************999999************ PP TIGR00262 199 kPvlvGFGiskkeqvkelkelgadgvivGsAlvkiieeklddeekaleeleefvke 254 Pv vGFGi +e ++ + e+ +d+v++Gs +v+++e++ +e+a l fv e lcl|FitnessBrowser__Burk376:H281DRAFT_06065 224 LPVGVGFGIRDAETARLVAEV-SDAVVIGSRIVQLLEQT--APEAAAGTLTRFVAE 276 ********************9.889*************9..678888888888876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (256 nodes) Target sequences: 1 (288 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: 00:00:00.00 # Mc/sec: 7.97 // [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