Align anthranilate synthase (subunit 2/2) (EC 4.1.3.27) (characterized)
to candidate 7026942 Shewana3_4071 isochorismate synthases (RefSeq)
Query= BRENDA::Q06128 (421 letters) >FitnessBrowser__ANA3:7026942 Length = 452 Score = 117 bits (294), Expect = 5e-31 Identities = 81/246 (32%), Positives = 125/246 (50%), Gaps = 10/246 (4%) Query: 178 QVVLSRFYRYIFSG--DPLRIYYNLRRINPSPYMFYLKFD-EKYLIGSSPELLFRVQDNI 234 +VVLSR + DP + + NP+ + F +F ++ I SPE LFR + Sbjct: 209 KVVLSRHTELEVNAQVDPWMVLACWQGRNPNSFQFGFQFSPDRTYISCSPERLFRRRQQE 268 Query: 235 VETYPIAGTRPRGADQEEDLKLELELMNSEKDKAEHLMLVDLARNDLGKVCVPGT--VKV 292 + T +AGT RG +QEED L L+ K+ E+ L R + + P + V Sbjct: 269 LFTEALAGTTVRGLNQEEDTALANALLEDNKNSVEN----QLVRRHIVSMLSPLSQHVGA 324 Query: 293 PELMYVEKYSHVQHIVSKVIGTLKKKYNALNVLSATFPAGTVSGAPKPMAMNIIETLEEY 352 E + K +H+QH+ + LK+ N +L A P V G P+ AM I E Y Sbjct: 325 EEAATIFKLNHIQHLHRAIRAELKQGVNDFQLLQALHPTPAVGGLPRESAMRFIREREGY 384 Query: 353 KRGPYAGAVGFISADGNAEFAIAIRTAFLNKELLRIHAGAGIVYDSNPESEYFETEHKLK 412 RG YAGA G+ + +EF++AIR+A + + + AGAGI+ S+PE+E+ E E+KL Sbjct: 385 MRGWYAGACGYFN-KFESEFSVAIRSALIEPGKINLFAGAGIIAGSDPEAEWQELENKLA 443 Query: 413 ALKTAI 418 + + + Sbjct: 444 TIMSIL 449 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: 395 Number of extensions: 12 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: 452 Length adjustment: 32 Effective length of query: 389 Effective length of database: 420 Effective search space: 163380 Effective search space used: 163380 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