Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate Ac3H11_1535 Tryptophan synthase alpha chain (EC 4.2.1.20)
Query= uniprot:H0BV16 (269 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1535 Length = 269 Score = 498 bits (1283), Expect = e-146 Identities = 255/269 (94%), Positives = 261/269 (97%) Query: 1 MSRIASTFSALQAQGRKALIPYVTAGFPFADITPALMHGMVEAGADVIELGVPFSDPMAD 60 MSRI +TF L+AQGRKALIPYVTAGFPFADITPALMHGMVEAGADVIELGVPFSDPMAD Sbjct: 1 MSRIQTTFEQLKAQGRKALIPYVTAGFPFADITPALMHGMVEAGADVIELGVPFSDPMAD 60 Query: 61 GPVIQKAGEKALSLGIGMVQVLDHVREFRKRNNTTPVVLMGYANPVERYDQKHGEGAFVR 120 GPVIQKAGEKAL LG+GMVQVLDHVREFRKRN TTPVVLMGYANPVERYDQ HGEGAFVR Sbjct: 61 GPVIQKAGEKALGLGVGMVQVLDHVREFRKRNTTTPVVLMGYANPVERYDQVHGEGAFVR 120 Query: 121 DSAAAGVDGVLIVDYPPEECEAFAASLRAHGMDLIFLLAPTSTDERMAEVARVASGYVYY 180 DSA AGVDGVLIVDYPPEECEAFAASL+A+GMDLIFLLAPTSTDERMA+VARVASGYVYY Sbjct: 121 DSAEAGVDGVLIVDYPPEECEAFAASLQANGMDLIFLLAPTSTDERMAQVARVASGYVYY 180 Query: 181 VSLKGVTGSGALDTAAVEQMLPRIRQHVTIPVGVGFGIRDAATAQAIGKVADAVVIGSRI 240 VSLKGVTGSGALDTAAVEQMLPRIRQHV IPVGVGFGIRDAATAQAIGKVADAVVIGSRI Sbjct: 181 VSLKGVTGSGALDTAAVEQMLPRIRQHVHIPVGVGFGIRDAATAQAIGKVADAVVIGSRI 240 Query: 241 IQLIEDQEHAKVVPLTIDFLRGIRKALDA 269 IQLIEDQEHAKVVPLTIDFLRGIRKALDA Sbjct: 241 IQLIEDQEHAKVVPLTIDFLRGIRKALDA 269 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: 401 Number of extensions: 11 Number of successful extensions: 1 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: 269 Length adjustment: 25 Effective length of query: 244 Effective length of database: 244 Effective search space: 59536 Effective search space used: 59536 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 Ac3H11_1535 (Tryptophan synthase alpha chain (EC 4.2.1.20))
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.16687.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-71 226.0 0.2 2.1e-71 225.8 0.2 1.0 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1535 Tryptophan synthase alpha chain Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1535 Tryptophan synthase alpha chain (EC 4.2.1.20) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 225.8 0.2 2.1e-71 2.1e-71 1 238 [. 8 248 .. 8 263 .. 0.95 Alignments for each domain: == domain 1 score: 225.8 bits; conditional E-value: 2.1e-71 TIGR00262 1 fetlkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaael 62 fe+lk+++ ka++p+vtag P ++++ +++ +v+aGad++ElGvpfsDP+aDGp+iq+a lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1535 8 FEQLKAQGRKALIPYVTAGFPFADITPALMHGMVEAGADVIELGVPFSDPMADGPVIQKAGE 69 899*********************************************************** PP TIGR00262 63 RAlkagvkvekalellkkvrekasniPivlltyynlifkk....gveeFyakakeagvdgvl 120 +Al gv + ++l+ ++++r+++++ P+vl+ y+n++ ++ g+ +F++ +eagvdgvl lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1535 70 KALGLGVGMVQVLDHVREFRKRNTTTPVVLMGYANPVERYdqvhGEGAFVRDSAEAGVDGVL 131 *************************************65422338899************** PP TIGR00262 121 vaDlPleeaddlleaakkhgvkqiflvaPtaeeerlkkiaekseGfvYlvsvaGvtgarerv 182 ++D P ee + + + + +g++ ifl aPt+ +er+ ++a+ ++G+vY vs Gvtg lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1535 132 IVDYPPEECEAFAASLQANGMDLIFLLAPTSTDERMAQVARVASGYVYYVSLKGVTGSGALD 193 ************************************************************99 PP TIGR00262 183 eeevkelikkvkalskkPvlvGFGiskkeqvkelkelgadgvivGsAlvkiieekl 238 +++v++++ +++++ ++Pv vGFGi + ++++ ++ ad+v++Gs ++++ie++ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1535 194 TAAVEQMLPRIRQHVHIPVGVGFGIRDAATAQAIGKV-ADAVVIGSRIIQLIEDQE 248 9*************************99999988888.899************983 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (256 nodes) Target sequences: 1 (269 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: 00:00:00.00 # Mc/sec: 7.60 // [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