Align tryptophan synthase subunit α (EC 4.1.2.8) (characterized)
to candidate WP_051941042.1 BS73_RS29030 tryptophan synthase subunit alpha
Query= metacyc::MONOMER-3561 (251 letters) >NCBI__GCF_000744815.1:WP_051941042.1 Length = 280 Score = 169 bits (429), Expect = 4e-47 Identities = 102/254 (40%), Positives = 152/254 (59%), Gaps = 9/254 (3%) Query: 4 KGSLIPYLTAGDPSVEKTLEFLLAV-EEFAGLIELGIPFSDPMADGKTIQESHYRALRNG 62 + +L+ YL AG P+V+ + + A+ E +E+G+P SDP+ DG TIQ + ALR G Sbjct: 27 RAALVGYLPAGFPTVDGGIAAVKALLEGGCDAVEIGLPHSDPVLDGATIQTADDIALRAG 86 Query: 63 FKLDDTFRILREFRR-HSSTPVILMTYYNPVFRTGVKKFLGEAKASGADGILVVDLPVSH 121 + D R +RE PV++MTY+NPV R GV +F + +G G+++ DLPV Sbjct: 87 VRTKDVLRTVREVASAFPQAPVLVMTYWNPVDRYGVDRFAADLAEAGGAGVILPDLPVEE 146 Query: 122 AGEFLDAAKEEGLKTVFLAAPNTPDERLREIDKASTGFVYLISLYGTTGARDRLPETAFE 181 AG +L AA+ GL TVF+ AP++ DERLR + A TGFVY ++ G TG R+++ + A + Sbjct: 147 AGPWLAAAERLGLDTVFVVAPSSRDERLRLVTAAGTGFVYAAAVMGVTGTREQVGDLAED 206 Query: 182 FVRRARKICNNKLAVGFGVSRREQVEELLKAG-ADGVVVGSALIELISRSENPVEE---- 236 V+R R + + + VG GVS +Q E+ AG ADGV+VGSA ++ I S + +E Sbjct: 207 LVKRTRAVTDLPVCVGIGVSNEKQAAEV--AGFADGVIVGSAFVKRILESGDDLESGLAG 264 Query: 237 LRRKVAELSGYSRA 250 +R A L+ RA Sbjct: 265 IRETAAALARGVRA 278 Lambda K H 0.319 0.138 0.386 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: 206 Number of extensions: 7 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: 251 Length of database: 280 Length adjustment: 25 Effective length of query: 226 Effective length of database: 255 Effective search space: 57630 Effective search space used: 57630 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 (21.7 bits) S2: 47 (22.7 bits)
Align candidate WP_051941042.1 BS73_RS29030 (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.2891643.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-74 236.1 0.0 1.8e-74 235.9 0.0 1.0 1 NCBI__GCF_000744815.1:WP_051941042.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000744815.1:WP_051941042.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 235.9 0.0 1.8e-74 1.8e-74 4 255 .. 22 272 .. 19 273 .. 0.98 Alignments for each domain: == domain 1 score: 235.9 bits; conditional E-value: 1.8e-74 TIGR00262 4 lkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagvkvekale 76 ++++ a+v ++ ag P+++ + ++k l + G da+E+G+p+sDP++DG tiq+a+ Al+agv+++++l+ NCBI__GCF_000744815.1:WP_051941042.1 22 ARAEGRAALVGYLPAGFPTVDGGIAAVKALLEGGCDAVEIGLPHSDPVLDGATIQTADDIALRAGVRTKDVLR 94 5677889****************************************************************** PP TIGR00262 77 llkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakkhgvkqiflvaP 149 +++v + +++P+ ++ty n++ ++gv+ F a ++eag gv+++DlP+eea+ l aa++ g++++f+vaP NCBI__GCF_000744815.1:WP_051941042.1 95 TVREVASAFPQAPVLVMTYWNPVDRYGVDRFAADLAEAGGAGVILPDLPVEEAGPWLAAAERLGLDTVFVVAP 167 ************************************************************************* PP TIGR00262 150 taeeerlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkalskkPvlvGFGiskkeqvkelkelgad 222 ++ +erl+ ++ ++GfvY+ +v+Gvtg+re+v + +++l+k+ +a+++ Pv+vG G+s++ q+ e+ + ad NCBI__GCF_000744815.1:WP_051941042.1 168 SSRDERLRLVTAAGTGFVYAAAVMGVTGTREQVGDLAEDLVKRTRAVTDLPVCVGIGVSNEKQAAEVAGF-AD 239 *********************************************************************9.9* PP TIGR00262 223 gvivGsAlvkiieeklddeekaleeleefvkel 255 gvivGsA+vk+i e+ dd e l+ ++e + +l NCBI__GCF_000744815.1:WP_051941042.1 240 GVIVGSAFVKRILESGDDLESGLAGIRETAAAL 272 ***************9********999987765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (256 nodes) Target sequences: 1 (280 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: 16.96 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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