Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate 202146 SO3024 tryptophan synthase, alpha subunit (NCBI ptt file)
Query= uniprot:H0BV16 (269 letters) >FitnessBrowser__MR1:202146 Length = 278 Score = 162 bits (409), Expect = 9e-45 Identities = 96/268 (35%), Positives = 151/268 (56%), Gaps = 7/268 (2%) Query: 2 SRIASTFSALQAQGRKALIPYVTAGFPFADITPALMHGMVEAGADVIELGVPFSDPMADG 61 SR + FS L+A+GR A +P+VT G P +++ ++ +V+ GAD +ELG PFSDP+ADG Sbjct: 14 SRYQAAFSRLKAEGRGAFVPFVTLGDPSPELSLKIIDTLVQNGADALELGFPFSDPLADG 73 Query: 62 PVIQKAGEKALSLGIGMVQVLDHVREFRKRNNTTPVVLMGYANPVERYDQKHGEGAFVRD 121 PVIQ A +AL+ G + + + R + P+ L+ YAN V +G AF Sbjct: 74 PVIQGANLRALAAGTTPTACFELLAKIRAKYPELPIGLLLYANLV----FANGIDAFYAK 129 Query: 122 SAAAGVDGVLIVDYPPEECEAFAASLRAHGMDLIFLLAPTSTDERMAEVARVASGYVYYV 181 + AGVD VLI D P EE F + +AHG+ IF+ P + + +A+V++ GY Y + Sbjct: 130 AQQAGVDSVLIADVPVEEAAPFIQAAKAHGIAPIFIAPPNADSDTLAKVSQSGEGYTYLL 189 Query: 182 SLKGVTGSGALDTAAVEQMLPRIRQHVTIPVGVGFGIRDAATAQAIGKV-ADAVVIGSRI 240 S GVTG+ VE++L ++++ P +GFGI + A A K A + GS + Sbjct: 190 SRAGVTGADTKAGTPVEEILAKLQEFNAPPPLLGFGIAEPAQVSAAIKAGAAGAISGSAV 249 Query: 241 IQLIE--DQEHAKVVPLTIDFLRGIRKA 266 +++IE Q+ K++ +F R ++ A Sbjct: 250 VKIIETHQQDEVKLLAALGEFTRTMKAA 277 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: 216 Number of extensions: 14 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: 278 Length adjustment: 25 Effective length of query: 244 Effective length of database: 253 Effective search space: 61732 Effective search space used: 61732 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 202146 SO3024 (tryptophan synthase, alpha subunit (NCBI ptt file))
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.23507.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.4e-105 335.2 0.0 9.5e-105 335.1 0.0 1.0 1 lcl|FitnessBrowser__MR1:202146 SO3024 tryptophan synthase, alph Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__MR1:202146 SO3024 tryptophan synthase, alpha subunit (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 335.1 0.0 9.5e-105 9.5e-105 1 256 [] 20 275 .. 20 275 .. 0.99 Alignments for each domain: == domain 1 score: 335.1 bits; conditional E-value: 9.5e-105 TIGR00262 1 fetlkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagvkvekalellk 79 f lk+++ afvpFvt+gdP+ e sl+ii+tlv++GadalElG+pfsDPlaDGp+iq a+lRAl+ag++++ ++ell+ lcl|FitnessBrowser__MR1:202146 20 FSRLKAEGRGAFVPFVTLGDPSPELSLKIIDTLVQNGADALELGFPFSDPLADGPVIQGANLRALAAGTTPTACFELLA 98 6789999************************************************************************ PP TIGR00262 80 kvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakkhgvkqiflvaPtaeeerlkk 158 k+r+k+++ Pi+ll+y+nl+f++g+++Fyaka++agvd+vl+aD+P+eea+ +++aak hg+++if+++P+a++++l k lcl|FitnessBrowser__MR1:202146 99 KIRAKYPELPIGLLLYANLVFANGIDAFYAKAQQAGVDSVLIADVPVEEAAPFIQAAKAHGIAPIFIAPPNADSDTLAK 177 ******************************************************************************* PP TIGR00262 159 iaekseGfvYlvsvaGvtgarerveeevkelikkvkalskkPvlvGFGiskkeqvkelkelgadgvivGsAlvkiieek 237 +++++eG++Yl+s+aGvtga +++ + v+e+++k++++++ P l+GFGi+++ qv +++++ga+g+i+GsA+vkiie + lcl|FitnessBrowser__MR1:202146 178 VSQSGEGYTYLLSRAGVTGADTKAGTPVEEILAKLQEFNAPPPLLGFGIAEPAQVSAAIKAGAAGAISGSAVVKIIETH 256 ******************************************************************************* PP TIGR00262 238 lddeekaleeleefvkelk 256 +de k+l++l ef++++k lcl|FitnessBrowser__MR1:202146 257 QQDEVKLLAALGEFTRTMK 275 *****************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (256 nodes) Target sequences: 1 (278 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: 11.22 // [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