Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_012853202.1 TCUR_RS14175 tryptophan synthase subunit alpha
Query= uniprot:H0BV16 (269 letters) >NCBI__GCF_000024385.1:WP_012853202.1 Length = 273 Score = 165 bits (417), Expect = 1e-45 Identities = 95/261 (36%), Positives = 144/261 (55%), Gaps = 15/261 (5%) Query: 8 FSALQAQGRKALIPYVTAGFPFADITPALMHGMVEAGADVIELGVPFSDPMADGPVIQKA 67 F +A+GR AL+ Y+ AGFP A MVEAG D+IE+G+P+SDP+ DGP IQ A Sbjct: 7 FEKAKAEGRAALVGYLPAGFPSHQGAIAAATAMVEAGCDIIEVGLPYSDPLMDGPTIQDA 66 Query: 68 GEKALSLGIGMVQVLDHVREFRKRNNTTPVVLMGYANPVERYDQKHGEGAFVRDSAAAGV 127 +AL+ G + VL V P ++M Y NP++RY G AF RD +AG Sbjct: 67 VHRALTGGTRVADVLRTVEAIAATG--APTLVMTYWNPIDRY----GVDAFARDLKSAGG 120 Query: 128 DGVLIVDYPPEECEAFAASLRAHGMDLIFLLAPTSTDERMAEVARVASGYVYYVSLKGVT 187 G++ D PEE E + A+ AH +D +FL+A TST+ER+ ++ V G+VY SL GVT Sbjct: 121 AGLITPDLTPEEAEPWLAASDAHDLDRVFLVALTSTEERLTKITNVCRGFVYAASLMGVT 180 Query: 188 GSGALDTAAVEQMLPRIRQHV--------TIPVGVGFGIRDAATAQAIGKVADAVVIGSR 239 G+ + ++ R R+ + +P+G+G G+ + A + AD V++GS Sbjct: 181 GTRSAVNTGAPGLVERTRKVLDRRPPEAPALPIGLGLGVSNGEQAAEVASFADGVIVGSA 240 Query: 240 II-QLIEDQEHAKVVPLTIDF 259 + +L++ + A V +F Sbjct: 241 FVRRLLDAPDEASAVRAVGEF 261 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: 213 Number of extensions: 14 Number of successful extensions: 4 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: 273 Length adjustment: 25 Effective length of query: 244 Effective length of database: 248 Effective search space: 60512 Effective search space used: 60512 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_012853202.1 TCUR_RS14175 (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.12571.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-64 203.2 0.0 1.9e-64 203.0 0.0 1.0 1 lcl|NCBI__GCF_000024385.1:WP_012853202.1 TCUR_RS14175 tryptophan synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000024385.1:WP_012853202.1 TCUR_RS14175 tryptophan synthase subunit alpha # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 203.0 0.0 1.9e-64 1.9e-64 1 255 [. 7 265 .. 7 266 .. 0.93 Alignments for each domain: == domain 1 score: 203.0 bits; conditional E-value: 1.9e-64 TIGR00262 1 fetlkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagv 69 fe+ k+++ a+v ++ ag P+ + ++ +++ +v+aG d++E+G+p+sDPl DGptiq+a RAl+ g+ lcl|NCBI__GCF_000024385.1:WP_012853202.1 7 FEKAKAEGRAALVGYLPAGFPSHQGAIAAATAMVEAGCDIIEVGLPYSDPLMDGPTIQDAVHRALTGGT 75 788999999************************************************************ PP TIGR00262 70 kvekalellkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakk 138 +v+++l+ ++++ ++ +P ++ty n+i ++gv++F + +k+ag g++ +Dl eea+ l a+ lcl|NCBI__GCF_000024385.1:WP_012853202.1 76 RVADVLRTVEAIAAT--GAPTLVMTYWNPIDRYGVDAFARDLKSAGGAGLITPDLTPEEAEPWLAASDA 142 ************988..99************************************************** PP TIGR00262 139 hgvkqiflvaPtaeeerlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkals........kk 199 h+++ +flva t+ eerl+ki++ ++GfvY+ s +Gvtg+r+ v++ + l+++ +++ + lcl|NCBI__GCF_000024385.1:WP_012853202.1 143 HDLDRVFLVALTSTEERLTKITNVCRGFVYAASLMGVTGTRSAVNTGAPGLVERTRKVLdrrppeapAL 211 *****************************************************9998752222222257 PP TIGR00262 200 PvlvGFGiskkeqvkelkelgadgvivGsAlvkiieeklddeekaleeleefvkel 255 P+ +G G+s+ eq+ e+ ++ adgvivGsA+v+++ + de a++++ ef+ el lcl|NCBI__GCF_000024385.1:WP_012853202.1 212 PIGLGLGVSNGEQAAEVASF-ADGVIVGSAFVRRLLDAP-DEASAVRAVGEFAAEL 265 999*****************.9***********999884.5778888888888766 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (256 nodes) Target sequences: 1 (273 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: 10.45 // [ok]
This GapMind analysis is from Apr 10 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