Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_086511467.1 BZY95_RS19070 tryptophan synthase subunit alpha
Query= uniprot:M4NLA4 (266 letters) >NCBI__GCF_002151265.1:WP_086511467.1 Length = 273 Score = 227 bits (579), Expect = 2e-64 Identities = 121/242 (50%), Positives = 160/242 (66%), Gaps = 1/242 (0%) Query: 2 SRIDRRFAALKAANRTGLIPFVTAGDPSPEHMVALMHALVDAGADLIELGVPFSDPMADG 61 +R+D FAALKA R L+ +VTAGDP E + ++ L AGAD+IE+G+PFSDPMADG Sbjct: 5 TRLDECFAALKAEQRPALVTYVTAGDPDFETSLKILQGLPAAGADVIEIGMPFSDPMADG 64 Query: 62 PVIQHASERAIAKGVGLADVLGWVAAFRQHDADTPIVLMGYLNPIETHGYARFAGEAVQA 121 P IQ A+ RA+ G + L V AFRQ D+ TP+VLMGY NPI +G ARF +A +A Sbjct: 65 PTIQKAALRALGSGQTMTRTLELVHAFRQQDSQTPLVLMGYYNPIHRYGVARFLADAARA 124 Query: 122 GVDGVLLVDCPLE-ESAVLQPLRDAGLQRILLAAPTTEPSRMAQLCGSAEGFLYYVSFAG 180 GVDG+++VD P E + + P R+ G+ I LA PTT+ R+ ++ +A GFLY V G Sbjct: 125 GVDGLIVVDLPPEHDDELCLPAREHGIAFIRLATPTTDAKRLPRVLNNASGFLYCVLVNG 184 Query: 181 ITGAAHLSTGDIAARVADVRARAKAPVAVGFGIRDAASAKAIAGFADAVVIGSALVDRLA 240 ITG + D+ V +R R++ PVAVGFGIR AA A AI F+DAVV+GSALV+ + Sbjct: 185 ITGGSAPPPQDVERMVGQLRERSRLPVAVGFGIRTAAQAAAIGRFSDAVVVGSALVEAIE 244 Query: 241 GA 242 A Sbjct: 245 SA 246 Lambda K H 0.322 0.136 0.394 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: 212 Number of extensions: 8 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: 266 Length of database: 273 Length adjustment: 25 Effective length of query: 241 Effective length of database: 248 Effective search space: 59768 Effective search space used: 59768 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 (21.9 bits) S2: 47 (22.7 bits)
Align candidate WP_086511467.1 BZY95_RS19070 (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.11352.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.8e-81 257.7 0.0 4.3e-81 257.5 0.0 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086511467.1 BZY95_RS19070 tryptophan synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086511467.1 BZY95_RS19070 tryptophan synthase subunit alpha # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 257.5 0.0 4.3e-81 4.3e-81 1 255 [. 11 263 .. 11 264 .. 0.98 Alignments for each domain: == domain 1 score: 257.5 bits; conditional E-value: 4.3e-81 TIGR00262 1 fetlkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagv 69 f++lk+++ a+v++vtagdPd+e+sl+i++ l aGad++E+G+pfsDP+aDGptiq+a+lRAl +g lcl|NCBI__GCF_002151265.1:WP_086511467.1 11 FAALKAEQRPALVTYVTAGDPDFETSLKILQGLPAAGADVIEIGMPFSDPMADGPTIQKAALRALGSGQ 79 78999**************************************************************** PP TIGR00262 70 kvekalellkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakk 138 +++++lel++++r++ s+ P+vl+ yyn+i+++gv F+a a+ agvdg++v+DlP e d+l a++ lcl|NCBI__GCF_002151265.1:WP_086511467.1 80 TMTRTLELVHAFRQQDSQTPLVLMGYYNPIHRYGVARFLADAARAGVDGLIVVDLPPEHDDELCLPARE 148 ********************************************************************* PP TIGR00262 139 hgvkqiflvaPtaeeerlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkalskkPvlvGFGi 207 hg++ i l++Pt++ +rl ++ ++++Gf Y+v v G+tg + ++v++++ ++++ s+ Pv+vGFGi lcl|NCBI__GCF_002151265.1:WP_086511467.1 149 HGIAFIRLATPTTDAKRLPRVLNNASGFLYCVLVNGITGGSAPPPQDVERMVGQLRERSRLPVAVGFGI 217 ********************************************************************* PP TIGR00262 208 skkeqvkelkelgadgvivGsAlvkiieeklddeekaleeleefvkel 255 + q+ ++ + +d+v+vGsAlv+ ie ++++ a+e+++ +v+el lcl|NCBI__GCF_002151265.1:WP_086511467.1 218 RTAAQAAAIGRF-SDAVVVGSALVEAIESA-ETRHGAVEAVHGLVREL 263 ******999999.899************99.89999******999987 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6.44 // [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