Align isochorismate lyase (EC 4.2.99.21); isochorismate synthase (EC 5.4.4.2) (characterized)
to candidate 15384 b1264 anthranilate synthase component I (NCBI)
Query= BRENDA::P9WFX1 (450 letters) >FitnessBrowser__Keio:15384 Length = 520 Score = 97.1 bits (240), Expect = 1e-24 Identities = 77/251 (30%), Positives = 115/251 (45%), Gaps = 14/251 (5%) Query: 198 IAAGRYHKVILSRCVEVPFAIDFPLTYRLGRRHNTPVRSFLLQLGGIRALGYSPELVTAV 257 I AG +V+ SR +P Y L + + +P F +Q G SPE +++ Sbjct: 256 IRAGEIFQVVPSRRFSLPCPSPLAAYYVLKKSNPSPYM-FFMQDNDFTLFGASPE--SSL 312 Query: 258 RADGV---VITEPLAGTRALGRGPAIDRLARD-------DLESNSKEIVEHAISVRSSLE 307 + D + P+AGTR GR A L RD ++ ++ KE+ EH + V + Sbjct: 313 KYDATSRQIEIYPIAGTRPRGRR-ADGSLDRDLDSRIELEMRTDHKELSEHLMLVDLARN 371 Query: 308 EITDIAEPGSAAVIDFMTVRERGSVQHLGSTIRARLDPSSDRMAALEALFPAVTASGIPK 367 ++ I PGS V D V V HL S + L D + A A T SG PK Sbjct: 372 DLARICTPGSRYVADLTKVDRYSYVMHLVSRVVGELRHDLDALHAYRACMNMGTLSGAPK 431 Query: 368 AAGVEAIFRLDECPRGLYSGAVVMLSADGGLDAALTLRAAYQVGGRTWLRAGAGIIEESE 427 ++ I + RG Y GAV +A G LD + +R+A G ++AGAG++ +S Sbjct: 432 VRAMQLIAEAEGRRRGSYGGAVGYFTAHGDLDTCIVIRSALVENGIATVQAGAGVVLDSV 491 Query: 428 PEREFEETCEK 438 P+ E +ET K Sbjct: 492 PQSEADETRNK 502 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: 433 Number of extensions: 16 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: 520 Length adjustment: 34 Effective length of query: 416 Effective length of database: 486 Effective search space: 202176 Effective search space used: 202176 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: 52 (24.6 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