Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_011386364.1 AMB_RS20300 tryptophan synthase subunit alpha
Query= uniprot:H0BV16 (269 letters) >NCBI__GCF_000009985.1:WP_011386364.1 Length = 269 Score = 233 bits (593), Expect = 4e-66 Identities = 126/271 (46%), Positives = 173/271 (63%), Gaps = 9/271 (3%) Query: 1 MSRIASTFSALQAQGRKALIPYVTAGFPFADITPALMHGMVEAGADVIELGVPFSDPMAD 60 MSRIA F+ L+A+ R AL+ ++TAG P + AL+ GM AGAD+IELG+PF+DPMAD Sbjct: 1 MSRIAKRFAKLKAENRAALVTFITAGDPDHATSQALLDGMPAAGADIIELGMPFTDPMAD 60 Query: 61 GPVIQKAGEKALSLGIGMVQVLDHVREFRKRNNTTPVVLMGYANPVERYDQKHGEGAFVR 120 GP IQ A +AL+ G + Q L+ V FRK + TP++LMGY NPV + G F Sbjct: 61 GPAIQLAAGRALAAGGSLRQTLEMVEAFRKTDAETPIILMGYYNPVYAW----GAEKFAA 116 Query: 121 DSAAAGVDGVLIVDYPPEECEAFAASLRAHGMDLIFLLAPTSTDERMAEVARVASGYVYY 180 D+A AGVDG++IVD PPEE + LR G+D I L PTS D R+ V ASG+VYY Sbjct: 117 DAAKAGVDGLIIVDLPPEEADELVPFLRQAGIDFIVLTTPTSDDARLPVVLANASGFVYY 176 Query: 181 VSLKGVTGSGALDTAAVEQMLPRIRQHVTIPVGVGFGIRDAATAQAIGKVADAVVIGSRI 240 VS+ G+TG+ + +A+++ + RIR+H +PV VGFGI+D A A + +VAD V+GS I Sbjct: 177 VSIAGITGTASAAQSAIDEAVARIRRHTGLPVCVGFGIKDPAQAAEVARVADGAVVGSAI 236 Query: 241 IQLIED---QEHAKVVPLTI--DFLRGIRKA 266 + ++ D + A PL + D G+R A Sbjct: 237 VSVLADNIGKPGAVSAPLALVKDLAAGVRGA 267 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: 239 Number of extensions: 12 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: 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 WP_011386364.1 AMB_RS20300 (tryptophan synthase subunit alpha)
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.24818.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-80 255.7 0.1 1.9e-80 255.5 0.1 1.0 1 lcl|NCBI__GCF_000009985.1:WP_011386364.1 AMB_RS20300 tryptophan synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_011386364.1 AMB_RS20300 tryptophan synthase subunit alpha # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 255.5 0.1 1.9e-80 1.9e-80 1 244 [. 8 250 .. 8 261 .. 0.97 Alignments for each domain: == domain 1 score: 255.5 bits; conditional E-value: 1.9e-80 TIGR00262 1 fetlkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagv 69 f++lk+++ a+v+F+tagdPd ++s +++ + aGad++ElG+pf DP+aDGp+iq a+ RAl+ag lcl|NCBI__GCF_000009985.1:WP_011386364.1 8 FAKLKAENRAALVTFITAGDPDHATSQALLDGMPAAGADIIELGMPFTDPMADGPAIQLAAGRALAAGG 76 7899***************************************************************** PP TIGR00262 70 kvekalellkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakk 138 +++++le+++++r++ + Pi+l+ yyn++++ g e+F a a++agvdg++++DlP eead+l+ ++ lcl|NCBI__GCF_000009985.1:WP_011386364.1 77 SLRQTLEMVEAFRKTDAETPIILMGYYNPVYAWGAEKFAADAAKAGVDGLIIVDLPPEEADELVPFLRQ 145 ********************************************************************* PP TIGR00262 139 hgvkqiflvaPtaeeerlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkalskkPvlvGFGi 207 g++ i+l +Pt+++ rl + +++GfvY vs aG+tg+ + ++++++e+++++++++ Pv+vGFGi lcl|NCBI__GCF_000009985.1:WP_011386364.1 146 AGIDFIVLTTPTSDDARLPVVLANASGFVYYVSIAGITGTASAAQSAIDEAVARIRRHTGLPVCVGFGI 214 ********************************************************************* PP TIGR00262 208 skkeqvkelkelgadgvivGsAlvkiieeklddeeka 244 + q+ e+ + adg++vGsA+v +++++++++ ++ lcl|NCBI__GCF_000009985.1:WP_011386364.1 215 KDPAQAAEVARV-ADGAVVGSAIVSVLADNIGKPGAV 250 ***********9.99***************9976554 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 7.59 // [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