Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_069663039.1 BCR25_RS07700 tryptophan synthase subunit alpha
Query= uniprot:H0BV16 (269 letters) >NCBI__GCF_001730305.1:WP_069663039.1 Length = 257 Score = 140 bits (352), Expect = 4e-38 Identities = 84/252 (33%), Positives = 133/252 (52%), Gaps = 7/252 (2%) Query: 1 MSRIASTFSALQAQGRKALIPYVTAGFPFADITPALMHGMVEAGADVIELGVPFSDPMAD 60 M + + Q +PY+ AG D A + + +AGA IELG+PFSDP+AD Sbjct: 1 MKTLTEQLTKKQQANETIFVPYIMAGAQGLDQLEAEITLLCDAGASAIELGIPFSDPVAD 60 Query: 61 GPVIQKAGEKALSLGIGMVQVLDHVREFRKRNNTTPVVLMGYANPVERYDQKHGEGAFVR 120 GPVIQ AG +AL + + +++D + +K + TP++LM Y NP+ Y G V+ Sbjct: 61 GPVIQAAGLRALENDVSLEKIID---QLKKISTKTPLILMTYFNPIFHY----GLEQLVQ 113 Query: 121 DSAAAGVDGVLIVDYPPEECEAFAASLRAHGMDLIFLLAPTSTDERMAEVARVASGYVYY 180 + A V G++I D P E L + LI L+A T+ +R+AE+ G++Y Sbjct: 114 ELAETNVKGLIIPDLPYEHQHLLTPLLENSDIALIPLIALTTPKDRIAELVEAGEGFIYA 173 Query: 181 VSLKGVTGSGALDTAAVEQMLPRIRQHVTIPVGVGFGIRDAATAQAIGKVADAVVIGSRI 240 V++ GVTG G A++++ L I++ PV GFGI K V++GS+I Sbjct: 174 VAVNGVTGVGREYQASLDEHLAYIQKISDKPVLAGFGISSKDHVARFRKNCAGVIVGSKI 233 Query: 241 IQLIEDQEHAKV 252 + L+ + + A+V Sbjct: 234 VDLLSEGKQAEV 245 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: 184 Number of extensions: 11 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: 269 Length of database: 257 Length adjustment: 25 Effective length of query: 244 Effective length of database: 232 Effective search space: 56608 Effective search space used: 56608 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_069663039.1 BCR25_RS07700 (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.3089429.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.1e-72 227.6 0.1 7.4e-72 227.3 0.1 1.0 1 NCBI__GCF_001730305.1:WP_069663039.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001730305.1:WP_069663039.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 227.3 0.1 7.4e-72 7.4e-72 4 241 .. 11 244 .. 8 256 .. 0.94 Alignments for each domain: == domain 1 score: 227.3 bits; conditional E-value: 7.4e-72 TIGR00262 4 lkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagvkvekale 76 ++++e+ fvp++ ag l++ i+ l++aGa+a+ElG+pfsDP+aDGp+iqaa lRAl++ v++ek+++ NCBI__GCF_001730305.1:WP_069663039.1 11 KQQANETIFVPYIMAGAQGLDQLEAEITLLCDAGASAIELGIPFSDPVADGPVIQAAGLRALENDVSLEKIID 83 57899*****************************************************************777 PP TIGR00262 77 llkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakkhgvkqiflvaP 149 lkk+ k P++l+ty+n+if++g+e+ +++++e+ v+g++++DlP+e ++ l+ ++ +++ i l+a NCBI__GCF_001730305.1:WP_069663039.1 84 QLKKISTK---TPLILMTYFNPIFHYGLEQLVQELAETNVKGLIIPDLPYEHQHLLTPLLENSDIALIPLIAL 153 77777666...9************************************************************* PP TIGR00262 150 taeeerlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkalskkPvlvGFGiskkeqvkelkelgad 222 t++++r+ ++ e +eGf+Y+v+v Gvtg+ ++ +++++e ++ ++++s+kPvl GFGis k++v + ++ + NCBI__GCF_001730305.1:WP_069663039.1 154 TTPKDRIAELVEAGEGFIYAVAVNGVTGVGREYQASLDEHLAYIQKISDKPVLAGFGISSKDHVARFRKN-CA 225 ********************************************************************99.67 PP TIGR00262 223 gvivGsAlvkiieekldde 241 gvivGs +v++++e ++ e NCBI__GCF_001730305.1:WP_069663039.1 226 GVIVGSKIVDLLSEGKQAE 244 8***********9996632 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (256 nodes) Target sequences: 1 (257 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: 19.38 // [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