Align anthranilate synthase (subunit 2/2) (EC 4.1.3.27) (characterized)
to candidate WP_011319394.1 AVA_RS13325 isochorismate synthase MenF
Query= BRENDA::Q06128 (421 letters) >NCBI__GCF_000204075.1:WP_011319394.1 Length = 471 Score = 134 bits (338), Expect = 4e-36 Identities = 84/267 (31%), Positives = 148/267 (55%), Gaps = 8/267 (2%) Query: 156 NKNSYERIVSESLEYIRSGYIFQVVLSRFYRYIFSGDPLRIYY---NLRRINPSPYMFYL 212 N Y++ V+ +LE I+S + +VVL+ + S + + NLR+ +P+ Y+F Sbjct: 208 NGERYKKSVASALEKIQSKELSKVVLADILD-VSSNQHFNLLHSLNNLRKTHPNCYIFST 266 Query: 213 KFDE-KYLIGSSPELLFRVQDNIVETYPIAGTRPRGADQEEDLKLELELMNSEKDKAEHL 271 + + IG+SPE L + + + T +AG+ PRG ED L+NSEK++ EHL Sbjct: 267 SNGKGQNFIGASPERLITIHNQQLITDALAGSAPRGKTPAEDAANANRLLNSEKERHEHL 326 Query: 272 MLVDLARNDLGKVCVPGTVKVPELMYVEKYSHVQHIVSKVIGTLKKKYNALNVLSATFPA 331 +++D L ++ + V P L + S++QH+ + + + + L +++ P Sbjct: 327 LVMDFITQRLTQLGLLPQVLPPRL---RQLSNIQHLWTPINAIVPANVHPLKIIAQLHPT 383 Query: 332 GTVSGAPKPMAMNIIETLEEYKRGPYAGAVGFISADGNAEFAIAIRTAFLNKELLRIHAG 391 V+GA + +A I E ++RG YA +G+I + GN EF + IR+A ++ + R++AG Sbjct: 384 PAVAGAARDIACEEIRRYETFERGLYAAPLGWIDSQGNCEFIVGIRSALIDGDRARLYAG 443 Query: 392 AGIVYDSNPESEYFETEHKLKALKTAI 418 AGIV S+P+ E+ E + KL+AL A+ Sbjct: 444 AGIVAGSDPDREFAEVQLKLQALLKAL 470 Lambda K H 0.319 0.139 0.410 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: 396 Number of extensions: 23 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: 421 Length of database: 471 Length adjustment: 32 Effective length of query: 389 Effective length of database: 439 Effective search space: 170771 Effective search space used: 170771 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 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Jul 25 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