Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate AZOBR_RS00520 AZOBR_RS00520 tryptophan synthase subunit alpha
Query= uniprot:M4NLA4 (266 letters) >FitnessBrowser__azobra:AZOBR_RS00520 Length = 271 Score = 238 bits (607), Expect = 1e-67 Identities = 128/244 (52%), Positives = 157/244 (64%), Gaps = 1/244 (0%) Query: 4 IDRRFAALKAANRTGLIPFVTAGDPSPEHMVALMHALVDAGADLIELGVPFSDPMADGPV 63 I RRFAALKA R GL+ F+TAGDP E A++H L AGADLIELG+PFSDPMADGP Sbjct: 1 IARRFAALKAEGRAGLVTFITAGDPDLETCRAVLHGLPAAGADLIELGLPFSDPMADGPA 60 Query: 64 IQHASERAIAKGVGLADVLGWVAAFRQHDADTPIVLMGYLNPIETHGYARFAGEAVQAGV 123 IQ AS RA+ G L V FR+ DADTP++LMGY NPI +G RF +A++AGV Sbjct: 61 IQAASLRALHAGTTARKTLDLVRGFRETDADTPVILMGYYNPIHAYGVDRFLADAIEAGV 120 Query: 124 DGVLLVDCPLEESAVL-QPLRDAGLQRILLAAPTTEPSRMAQLCGSAEGFLYYVSFAGIT 182 DG+++VD P EE L P AG+ I LA PTT+ R+ + + GF+YYVS AGIT Sbjct: 121 DGLIVVDLPPEEDEELCIPALKAGVNFIRLATPTTDDKRLPAVLQNTSGFVYYVSIAGIT 180 Query: 183 GAAHLSTGDIAARVADVRARAKAPVAVGFGIRDAASAKAIAGFADAVVIGSALVDRLAGA 242 GAA + A V ++ PVAVGFGI+ A +A ADA V+GSA+V RLAG Sbjct: 181 GAASADNAAVGAAVERLKRHTDLPVAVGFGIKTPEQAADVARVADAAVVGSAIVTRLAGG 240 Query: 243 TDAG 246 D G Sbjct: 241 LDGG 244 Lambda K H 0.322 0.136 0.394 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: 255 Number of extensions: 14 Number of successful extensions: 3 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: 266 Length of database: 271 Length adjustment: 25 Effective length of query: 241 Effective length of database: 246 Effective search space: 59286 Effective search space used: 59286 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 (21.9 bits) S2: 47 (22.7 bits)
Align candidate AZOBR_RS00520 AZOBR_RS00520 (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.16831.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.3e-82 260.8 0.0 4.9e-82 260.6 0.0 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS00520 AZOBR_RS00520 tryptophan synthas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS00520 AZOBR_RS00520 tryptophan synthase subunit alpha # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 260.6 0.0 4.9e-82 4.9e-82 1 240 [. 5 243 .. 5 263 .. 0.95 Alignments for each domain: == domain 1 score: 260.6 bits; conditional E-value: 4.9e-82 TIGR00262 1 fetlkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagv 69 f++lk+++ +v+F+tagdPdle+ +++ l aGad++ElG+pfsDP+aDGp+iqaa+lRAl+ag+ lcl|FitnessBrowser__azobra:AZOBR_RS00520 5 FAALKAEGRAGLVTFITAGDPDLETCRAVLHGLPAAGADLIELGLPFSDPMADGPAIQAASLRALHAGT 73 7889999999*********************************************************** PP TIGR00262 70 kvekalellkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakk 138 +++k+l+l++ +re+ + P++l+ yyn+i+++gv+ F+a a eagvdg++v+DlP ee ++l a k lcl|FitnessBrowser__azobra:AZOBR_RS00520 74 TARKTLDLVRGFRETDADTPVILMGYYNPIHAYGVDRFLADAIEAGVDGLIVVDLPPEEDEELCIPALK 142 ********************************************************************* PP TIGR00262 139 hgvkqiflvaPtaeeerlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkalskkPvlvGFGi 207 gv+ i l++Pt++++rl ++ ++++GfvY vs aG+tga + +++v ++++++k++++ Pv+vGFGi lcl|FitnessBrowser__azobra:AZOBR_RS00520 143 AGVNFIRLATPTTDDKRLPAVLQNTSGFVYYVSIAGITGAASADNAAVGAAVERLKRHTDLPVAVGFGI 211 ********************************************************************* PP TIGR00262 208 skkeqvkelkelgadgvivGsAlvkiieekldd 240 +eq+ ++ + ad+++vGsA+v +++ ld lcl|FitnessBrowser__azobra:AZOBR_RS00520 212 KTPEQAADVARV-ADAAVVGSAIVTRLAGGLDG 243 ***********9.889***********999983 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (256 nodes) Target sequences: 1 (271 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: 7.87 // [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