Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (uncharacterized)
to candidate AZOBR_RS19065 AZOBR_RS19065 anthranilate phosphoribosyltransferase
Query= curated2:Q5WGS4 (341 letters) >FitnessBrowser__azobra:AZOBR_RS19065 Length = 496 Score = 64.7 bits (156), Expect = 5e-15 Identities = 64/207 (30%), Positives = 91/207 (43%), Gaps = 6/207 (2%) Query: 12 GESLSVQEAEQVMEQIMSGRATASQVASLITMMRVRGETAEEILGFAKGMRAY-ARKFPA 70 G L+ +EAE+ M I+ G A QV +L+ MMR+RG TA E+ G + MRA+ A Sbjct: 175 GRPLTAEEAEEAMTIILEGEADPVQVGALLGMMRMRGSTAPELAGLVRAMRAHVAAGLGR 234 Query: 71 VIEGTID-TCGTGGDGLGTFNISTASALVLASLGVPVAKHGNRSVSSKSGSAD-VLEELG 128 I+ ID C T + A+ LV A G V HG S+ SG + + +G Sbjct: 235 TIQADIDWPCFTSPNYHNPPWFFHAARLV-AQAGHRVLLHGGTGCSAASGRYEFIAPTVG 293 Query: 129 INIQASVEEACQMLETTNLCFL-FAPLYHQSMRHVAGPRKEIGFRTIFNLLGPLTNPAGA 187 I + A+ E L + + A L Q R + R +F + L PA A Sbjct: 294 IPVCANAREIAAALAAQRIAYAPLAALSPQIYRLIGLHRLTQTRSAVFEAV-HLLKPAKA 352 Query: 188 RYQLLGVYDEAAALKMGEALRQLGSEH 214 + LLG +A R LG +H Sbjct: 353 KTSLLGAAKPTYRELHRDAARILGWKH 379 Lambda K H 0.318 0.133 0.377 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: 356 Number of extensions: 17 Number of successful extensions: 1 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: 341 Length of database: 496 Length adjustment: 31 Effective length of query: 310 Effective length of database: 465 Effective search space: 144150 Effective search space used: 144150 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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