Align anthranilate synthase (subunit 2/2) (EC 4.1.3.27) (characterized)
to candidate AO353_24000 AO353_24000 isochorismate synthase
Query= BRENDA::Q06128 (421 letters) >FitnessBrowser__pseudo3_N2E3:AO353_24000 Length = 391 Score = 114 bits (284), Expect = 7e-30 Identities = 82/269 (30%), Positives = 133/269 (49%), Gaps = 6/269 (2%) Query: 156 NKNSYERIVSESLEYIRSGYIFQVVLSRFYRYIFSGDPL--RIYYNLRRINPSPYMFYLK 213 ++ ++R V ++ R + + VLS +F+ D + NLR N S Y F + Sbjct: 123 DEQGFKRAVEHAIVNFRHSDVRKAVLSVQRELVFAQDVDVGAMQNNLRAQNQSGYHFRVP 182 Query: 214 F-DEKYLIGSSPELLFRVQDNIVETYPIAGTRPRGADQEEDLKLELELMNSEKDKAEHLM 272 D LIG SPELL + P+AG+ R +D + D + L SEKD EH + Sbjct: 183 MPDGATLIGVSPELLVHKDGLNFVSNPLAGSAKRMSDPQADRRNADWLSASEKDHYEHRL 242 Query: 273 LVDLARNDLGKVCVPGTVKVPELMYVEKYSHVQHIVSKVIGTLKKK-YNALNVLSATFPA 331 + + LG++C + VP+ + + H+ +++ GTL +AL + P Sbjct: 243 VTEDIATQLGELCTQ--LDVPQRPSLISTPALWHLSTRIEGTLADPTVSALQLACRLHPT 300 Query: 332 GTVSGAPKPMAMNIIETLEEYKRGPYAGAVGFISADGNAEFAIAIRTAFLNKELLRIHAG 391 V G P A +I +E ++RG + G VG+ A GN E+ + IR + + +R+ AG Sbjct: 301 PAVCGFPTERARRLIRFVEPFERGLFTGMVGWCDAQGNGEWVVTIRCGTVKRNRVRLFAG 360 Query: 392 AGIVYDSNPESEYFETEHKLKALKTAIGV 420 AGIV S+P+SE+ E + KL + A G+ Sbjct: 361 AGIVEASSPDSEWTEVQTKLGTMLRACGL 389 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: 327 Number of extensions: 14 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: 391 Length adjustment: 31 Effective length of query: 390 Effective length of database: 360 Effective search space: 140400 Effective search space used: 140400 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: 50 (23.9 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