Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_017600181.1 D471_RS0119590 tryptophan synthase subunit alpha
Query= uniprot:H0BV16 (269 letters) >NCBI__GCF_000341125.1:WP_017600181.1 Length = 271 Score = 155 bits (391), Expect = 1e-42 Identities = 94/246 (38%), Positives = 133/246 (54%), Gaps = 9/246 (3%) Query: 4 IASTFSALQAQGRKALIPYVTAGFPFADITPALMHGMVEAGADVIELGVPFSDPMADGPV 63 +++ +A + + R ALI + AGFP + ++ MVE G DVIE+G+P+SDPM DGP Sbjct: 6 LSTALAAAREEDRAALIGSLPAGFPDVASSIRVIEAMVEGGCDVIEVGLPYSDPMMDGPT 65 Query: 64 IQKAGEKALSLGIGMVQVLDHVREFRKRNNTTPVVLMGYANPVERYDQKHGEGAFVRDSA 123 IQ+A ++AL+ G V V V+M Y NP+ERY G G F A Sbjct: 66 IQRAADRALAAGTTTDDVFRVVEATAATG--AAAVVMSYWNPIERY----GVGRFAEGLA 119 Query: 124 AAGVDGVLIVDYPPEECEAFAASLRAHGMDLIFLLAPTSTDERMAEVARVASGYVYYVSL 183 AG GV+ D PEE + + A+ A G+D IFL+AP+STD R+A +G+VY SL Sbjct: 120 KAGGAGVITPDLIPEEADEWIAASDAAGLDRIFLVAPSSTDRRLALTTATCTGFVYAASL 179 Query: 184 KGVTGSGALDTAAVEQMLPRIRQHV---TIPVGVGFGIRDAATAQAIGKVADAVVIGSRI 240 GVTG+ E ++ R R+ +PV VG GI A A + AD V++G+ Sbjct: 180 MGVTGTRVQVADTAETLVRRTREVTRASALPVCVGLGISTGAQAAEVAGYADGVIVGAGF 239 Query: 241 IQLIED 246 Q + D Sbjct: 240 CQRVLD 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: 201 Number of extensions: 8 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: 271 Length adjustment: 25 Effective length of query: 244 Effective length of database: 246 Effective search space: 60024 Effective search space used: 60024 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_017600181.1 D471_RS0119590 (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.11478.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.3e-62 195.7 0.0 3.8e-62 195.5 0.0 1.0 1 lcl|NCBI__GCF_000341125.1:WP_017600181.1 D471_RS0119590 tryptophan syntha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000341125.1:WP_017600181.1 D471_RS0119590 tryptophan synthase subunit alpha # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 195.5 0.0 3.8e-62 3.8e-62 4 255 .. 13 263 .. 10 264 .. 0.94 Alignments for each domain: == domain 1 score: 195.5 bits; conditional E-value: 3.8e-62 TIGR00262 4 lkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagvkve 72 ++++ a++ + ag Pd++ s+++i+ +v+ G d++E+G+p+sDP+ DGptiq+a+ RAl+ag++++ lcl|NCBI__GCF_000341125.1:WP_017600181.1 13 AREEDRAALIGSLPAGFPDVASSIRVIEAMVEGGCDVIEVGLPYSDPMMDGPTIQRAADRALAAGTTTD 81 6788899************************************************************** PP TIGR00262 73 kalellkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakkhgv 141 ++++++++ ++ + v+++y n+i ++gv F + +++ag gv+ +Dl eead+ + a+ g+ lcl|NCBI__GCF_000341125.1:WP_017600181.1 82 DVFRVVEATAAT--GAAAVVMSYWNPIERYGVGRFAEGLAKAGGAGVITPDLIPEEADEWIAASDAAGL 148 *******99887..777899************************************************* PP TIGR00262 142 kqiflvaPtaeeerlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkal...skkPvlvGFGi 207 + iflvaP++ + rl + +++GfvY+ s +Gvtg+r +v++++++l+++ +++ s+ Pv+vG Gi lcl|NCBI__GCF_000341125.1:WP_017600181.1 149 DRIFLVAPSSTDRRLALTTATCTGFVYAASLMGVTGTRVQVADTAETLVRRTREVtraSALPVCVGLGI 217 **************************************************99887222578******** PP TIGR00262 208 skkeqvkelkelgadgvivGsAlvkiieeklddeekaleeleefvkel 255 s q+ e+ adgvivG+ + +++ + d e l ++++f++el lcl|NCBI__GCF_000341125.1:WP_017600181.1 218 STGAQAAEVAGY-ADGVIVGAGFCQRVLDA-PDLETGLIAVRSFAEEL 263 ***********9.9**********999888.45888888899888876 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: 10.72 // [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