Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate 5209803 Shew_2256 tryptophan synthase subunit alpha (RefSeq)
Query= uniprot:H0BV16 (269 letters) >FitnessBrowser__PV4:5209803 Length = 267 Score = 150 bits (379), Expect = 3e-41 Identities = 90/248 (36%), Positives = 136/248 (54%), Gaps = 5/248 (2%) Query: 2 SRIASTFSALQAQGRKALIPYVTAGFPFADITPALMHGMVEAGADVIELGVPFSDPMADG 61 +R + F+AL A GR A +P+VT G P +++ ++ +VE GAD +ELG PFSDP+ADG Sbjct: 3 NRYQAAFAALNASGRGAFVPFVTIGDPNRELSLKIIETLVENGADALELGFPFSDPLADG 62 Query: 62 PVIQKAGEKALSLGIGMVQVLDHVREFRKRNNTTPVVLMGYANPVERYDQKHGEGAFVRD 121 PVIQ A +AL+ G + + R + P+ L+ YAN V +G AF Sbjct: 63 PVIQGANLRALAAGTTPGGCFEIITAVRAKYPELPIGLLLYANLV----YANGVEAFYAK 118 Query: 122 SAAAGVDGVLIVDYPPEECEAFAASLRAHGMDLIFLLAPTSTDERMAEVARVASGYVYYV 181 + AAGVD VLI D P EE F A+ +AH + IF+ P E + +VA GY Y + Sbjct: 119 AKAAGVDSVLIADVPVEEAAPFIAAAKAHEVAPIFIAPPNGDAETLRQVAEQGQGYTYLL 178 Query: 182 SLKGVTGSGALDTAAVEQMLPRIRQHVTIPVGVGFGIRDAATAQ-AIGKVADAVVIGSRI 240 S GVTG+ + ++ +L +++ P +GFGI + + AI A + GS + Sbjct: 179 SRAGVTGTESKAGMPLDDILAQLKAFDAPPPLLGFGIAEPDQVKAAIDSGAAGAISGSAV 238 Query: 241 IQLIEDQE 248 +++IE + Sbjct: 239 VKIIETHQ 246 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: 193 Number of extensions: 10 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: 267 Length adjustment: 25 Effective length of query: 244 Effective length of database: 242 Effective search space: 59048 Effective search space used: 59048 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 5209803 Shew_2256 (tryptophan synthase subunit alpha (RefSeq))
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.23619.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.4e-104 333.3 0.0 3.8e-104 333.1 0.0 1.0 1 lcl|FitnessBrowser__PV4:5209803 Shew_2256 tryptophan synthase su Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PV4:5209803 Shew_2256 tryptophan synthase subunit alpha (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 333.1 0.0 3.8e-104 3.8e-104 1 256 [] 9 264 .. 9 264 .. 0.99 Alignments for each domain: == domain 1 score: 333.1 bits; conditional E-value: 3.8e-104 TIGR00262 1 fetlkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagvkvekalell 78 f++l++++ afvpFvt gdP+ e sl+ii+tlv++GadalElG+pfsDPlaDGp+iq a+lRAl+ag+++ ++e++ lcl|FitnessBrowser__PV4:5209803 9 FAALNASGRGAFVPFVTIGDPNRELSLKIIETLVENGADALELGFPFSDPLADGPVIQGANLRALAAGTTPGGCFEII 86 678999999********************************************************************* PP TIGR00262 79 kkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakkhgvkqiflvaPtaeeerl 156 +vr+k+++ Pi+ll+y+nl++++gve+Fyakak+agvd+vl+aD+P+eea+ ++ aak h+v++if+++P+ + e+l lcl|FitnessBrowser__PV4:5209803 87 TAVRAKYPELPIGLLLYANLVYANGVEAFYAKAKAAGVDSVLIADVPVEEAAPFIAAAKAHEVAPIFIAPPNGDAETL 164 ****************************************************************************** PP TIGR00262 157 kkiaekseGfvYlvsvaGvtgarerveeevkelikkvkalskkPvlvGFGiskkeqvkelkelgadgvivGsAlvkii 234 +++ae+++G++Yl+s+aGvtg+++++ ++++++++ka+ + P l+GFGi++++qvk++++ ga+g+i+GsA+vkii lcl|FitnessBrowser__PV4:5209803 165 RQVAEQGQGYTYLLSRAGVTGTESKAGMPLDDILAQLKAFDAPPPLLGFGIAEPDQVKAAIDSGAAGAISGSAVVKII 242 ****************************************************************************** PP TIGR00262 235 eeklddeekaleeleefvkelk 256 e + dde+++l +l +f++e+k lcl|FitnessBrowser__PV4:5209803 243 ETHQDDEQALLSALGQFTREMK 264 *******************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (256 nodes) Target sequences: 1 (267 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: 00:00:00.01 # Mc/sec: 6.38 // [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