Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_011802418.1 PNAP_RS15240 tryptophan synthase subunit alpha
Query= uniprot:H0BV16 (269 letters) >NCBI__GCF_000015505.1:WP_011802418.1 Length = 272 Score = 417 bits (1071), Expect = e-121 Identities = 213/272 (78%), Positives = 238/272 (87%), Gaps = 4/272 (1%) Query: 1 MSRIASTFSALQAQGRKALIPYVTAGFPFADITPALMHGMVEAGADVIELGVPFSDPMAD 60 MSRI STFS+L+ QGRKALIPYVTAGFPFAD+TP LMHGMV GADVIELG+PFSDP AD Sbjct: 1 MSRIESTFSSLKTQGRKALIPYVTAGFPFADVTPELMHGMVAGGADVIELGMPFSDPSAD 60 Query: 61 GPVIQKAGEKALSLGIGMVQVLDHVREFRKRNNTTPVVLMGYANPVERYDQKHGEGA--- 117 GPVIQKAGEKALS GIG+VQVL+ VR FR +++TTPVVLMGYANPVERYD KHG GA Sbjct: 61 GPVIQKAGEKALSFGIGLVQVLEMVRIFRTKDHTTPVVLMGYANPVERYDIKHGAGASES 120 Query: 118 -FVRDSAAAGVDGVLIVDYPPEECEAFAASLRAHGMDLIFLLAPTSTDERMAEVARVASG 176 F+RD+AAAGVDG+LIVDYPPEEC F+A L+AHGMDLIFLLAPTSTD RMA+VA+VASG Sbjct: 121 AFIRDAAAAGVDGMLIVDYPPEECVEFSARLKAHGMDLIFLLAPTSTDARMAQVAQVASG 180 Query: 177 YVYYVSLKGVTGSGALDTAAVEQMLPRIRQHVTIPVGVGFGIRDAATAQAIGKVADAVVI 236 YVYYVSLKGVTG+G LD AVE MLPRIR+HV +PVGVGFGIRDAATA+AIGKVADAVVI Sbjct: 181 YVYYVSLKGVTGAGTLDVDAVEAMLPRIRRHVNVPVGVGFGIRDAATAKAIGKVADAVVI 240 Query: 237 GSRIIQLIEDQEHAKVVPLTIDFLRGIRKALD 268 GS+IIQLIE+Q +V + DFL+ IR ALD Sbjct: 241 GSKIIQLIENQPRDRVAAVAHDFLKEIRSALD 272 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: 321 Number of extensions: 10 Number of successful extensions: 2 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: 272 Length adjustment: 25 Effective length of query: 244 Effective length of database: 247 Effective search space: 60268 Effective search space used: 60268 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_011802418.1 PNAP_RS15240 (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.28275.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.9e-69 218.0 0.1 6e-69 217.7 0.1 1.0 1 lcl|NCBI__GCF_000015505.1:WP_011802418.1 PNAP_RS15240 tryptophan synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015505.1:WP_011802418.1 PNAP_RS15240 tryptophan synthase subunit alpha # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 217.7 0.1 6e-69 6e-69 1 251 [. 8 263 .. 8 269 .. 0.92 Alignments for each domain: == domain 1 score: 217.7 bits; conditional E-value: 6e-69 TIGR00262 1 fetlkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagv 69 f lk+++ ka++p+vtag P ++++ e+++ +v Gad++ElG+pfsDP aDGp+iq+a +Al+ g+ lcl|NCBI__GCF_000015505.1:WP_011802418.1 8 FSSLKTQGRKALIPYVTAGFPFADVTPELMHGMVAGGADVIELGMPFSDPSADGPVIQKAGEKALSFGI 76 678999*************************************************************** PP TIGR00262 70 kvekalellkkvrekasniPivlltyynlifkkgv........eeFyakakeagvdgvlvaDlPleead 130 + ++le+++ +r k ++ P+vl+ y+n++ ++++ +F++ a++agvdg+l++D P ee lcl|NCBI__GCF_000015505.1:WP_011802418.1 77 GLVQVLEMVRIFRTKDHTTPVVLMGYANPVERYDIkhgagaseSAFIRDAAAAGVDGMLIVDYPPEECV 145 ******************************776431111222257************************ PP TIGR00262 131 dlleaakkhgvkqiflvaPtaeeerlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkalskk 199 ++ k hg++ ifl aPt+ + r+ ++a+ ++G+vY vs Gvtga + ++v++++ +++++ ++ lcl|NCBI__GCF_000015505.1:WP_011802418.1 146 EFSARLKAHGMDLIFLLAPTSTDARMAQVAQVASGYVYYVSLKGVTGAGTLDVDAVEAMLPRIRRHVNV 214 ********************************************************************* PP TIGR00262 200 PvlvGFGiskkeqvkelkelgadgvivGsAlvkiieeklddeekaleeleef 251 Pv vGFGi + +k++ ++ ad+v++Gs ++++ie++ ++++ + ++f lcl|NCBI__GCF_000015505.1:WP_011802418.1 215 PVGVGFGIRDAATAKAIGKV-ADAVVIGSKIIQLIENQP--RDRVAAVAHDF 263 ***********999999998.899************994..44444444555 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (256 nodes) Target sequences: 1 (272 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: 11.00 // [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