Align anthranilate synthase (subunit 2/2) (EC 4.1.3.27) (characterized)
to candidate WP_232203923.1 CPAR_RS01885 isochorismate synthase
Query= BRENDA::Q06128 (421 letters) >NCBI__GCF_000020505.1:WP_232203923.1 Length = 461 Score = 107 bits (266), Expect = 1e-27 Identities = 75/242 (30%), Positives = 130/242 (53%), Gaps = 7/242 (2%) Query: 174 GYIFQVVLSRFYRYIFSGDPLRIYYNLRRINP--SPYMFYLKFDEKY-LIGSSPELLFRV 230 G + +V+L+R FSG I + L P + Y FY + E + + +PE L+R Sbjct: 212 GGLDKVILARQTELSFSGKVPAIRFLLDYPYPENAAYRFYFEPIEGHAFVSFTPERLYRR 271 Query: 231 QDNIVETYPIAGTRPRGADQEEDLKLELELMNSEKDKAEHLMLVDLARNDLGKVCVPGTV 290 ++++T +AGT + + +D L+ SEKD EH + D +L VC + Sbjct: 272 DGDLLQTEALAGTVTKEKVKADDHTASKLLLASEKDVREHRFVKDTIYRELQPVC--SEI 329 Query: 291 KVPELMYVEKYSHVQHIVSKVIGTLKKKY-NALNVLSATFPAGTVSGAPKPMAMNIIETL 349 + E + V + + + H+ ++ L+ ++ N VL P V G P+ AM +I ++ Sbjct: 330 DMQEEVGVLQLNRLAHLYARCRARLRPEFRNDSTVLRQLHPTPAVGGVPREEAMELILSV 389 Query: 350 EEYKRGPYAGAVGFISADGNAEFAIAIRTAFLNKELLRIHAGAGIVYDSNPESEYFETEH 409 E + RG YA VG++S D AEFA+ IR+A + ++ + +++GAG+V S+PESE+ E + Sbjct: 390 EPFCRGWYAAPVGWLSRDA-AEFAVGIRSALIFEDKVYLYSGAGLVRGSDPESEWEEVDQ 448 Query: 410 KL 411 K+ Sbjct: 449 KI 450 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: 388 Number of extensions: 14 Number of successful extensions: 3 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: 461 Length adjustment: 32 Effective length of query: 389 Effective length of database: 429 Effective search space: 166881 Effective search space used: 166881 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 Apr 09 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