Align isochorismate lyase (EC 4.2.99.21); isochorismate synthase (EC 5.4.4.2) (characterized)
to candidate WP_014026579.1 PYRFU_RS05145 anthranilate synthase component I
Query= BRENDA::P9WFX1 (450 letters) >NCBI__GCF_000223395.1:WP_014026579.1 Length = 437 Score = 127 bits (319), Expect = 7e-34 Identities = 111/343 (32%), Positives = 164/343 (47%), Gaps = 24/343 (6%) Query: 107 FGWVAFEF--GVHRYGLQQRLAPHT-PLARVFSPRTRIMVSEKEIRLF----DAGIRHRE 159 FG V++E GV + L +L HT P+ RVF P ++ R + DA + E Sbjct: 99 FGVVSYEAVAGVEPW-LAPKLRRHTWPVVRVFEPEVLVVYDRLTGRAYVCPGDADLGEAE 157 Query: 160 AIDRLLATG-VREVPQSRSVDVSDDPSGFRRRVAVAVDEIAAGRYHKVILSRCVEVPF-A 217 + A G V E P+ F V A I G + +++LSR + Sbjct: 158 IGGFVQARGPVYETPREE----------FEAWVREAKRLIEEGEFFQIVLSRVERYEYNG 207 Query: 218 IDFPLTYRLGRRHNTPVRSFLLQLGGIRALGYSPELVTAVRADGVVITEPLAGTRALGRG 277 L RL + +P F L++G +G SPEL+ + G T P+AGTR G+ Sbjct: 208 SPLALYERLAGGNPSPYM-FYLRMGDHWIVGTSPELLVKMSL-GRAETHPIAGTRPRGKT 265 Query: 278 PAIDRLARDDLESNSKEIVEHAISVRSSLEEITDIAEPGSAAVIDFMTVRERGSVQHLGS 337 P D +++ + KE EH + V + ++ IA PG+ V M V + VQHL S Sbjct: 266 PEEDVALEEEMLRDEKERAEHMMLVDLARNDLGRIAVPGTVRVTALMDVEKYSHVQHLVS 325 Query: 338 TIRARLDPSSDRMAALEALFPAVTASGIPKAAGVEAIFRLDECPRGLYSGAVVMLSADGG 397 + A + P + L A FPA T SG PK +E I L++ PRG Y+GAV + + G Sbjct: 326 RVEALVKPKTLYSDVLAATFPAGTVSGAPKTRAMEYIAVLEDEPRGPYAGAVGVYAERAG 385 Query: 398 LDAALTLRAAYQV-GGRTWLRAGAGIIEESEPEREFEETCEKL 439 + A+ +R+ + G RAGAGI+ +S PERE+ ET K+ Sbjct: 386 -ETAIVIRSVWSYEDGIVEARAGAGIVYDSVPEREYMETVHKI 427 Lambda K H 0.319 0.135 0.386 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: 448 Number of extensions: 30 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: 450 Length of database: 437 Length adjustment: 32 Effective length of query: 418 Effective length of database: 405 Effective search space: 169290 Effective search space used: 169290 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 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 10 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