Align isochorismate lyase (EC 4.2.99.21); isochorismate synthase (EC 5.4.4.2) (characterized)
to candidate WP_086511648.1 BZY95_RS19935 anthranilate synthase component I
Query= BRENDA::P9WFX1 (450 letters) >NCBI__GCF_002151265.1:WP_086511648.1 Length = 494 Score = 149 bits (375), Expect = 3e-40 Identities = 90/254 (35%), Positives = 129/254 (50%), Gaps = 1/254 (0%) Query: 185 SGFRRRVAVAVDEIAAGRYHKVILSRCVEVPFAIDFPLTYRLGRRHNTPVRSFLLQLGGI 244 +GF+ V + + AG + + S+ + +P+ YR R N F LG Sbjct: 224 AGFKAAVEKIKEYVLAGDVMQCVPSQRMSIPYRASPLDLYRALRSLNPSPYMFFFNLGDH 283 Query: 245 RALGYSPELVTAVRADGVVITEPLAGTRALGRGPAIDRLARDDLESNSKEIVEHAISVRS 304 +G SPE++T + DG V P+AGTR G+ DR +L ++ KEI EH + + Sbjct: 284 HVVGSSPEILTRLE-DGEVTVRPIAGTRVRGKTEEEDRALEAELLADPKEIAEHLMLIDL 342 Query: 305 SLEEITDIAEPGSAAVIDFMTVRERGSVQHLGSTIRARLDPSSDRMAALEALFPAVTASG 364 ++ I+E GS V D M V V H+ S + RL P M L A FPA T SG Sbjct: 343 GRNDVGRISETGSVQVTDQMAVERYSHVMHIVSNVTGRLKPGLSAMDVLRATFPAGTLSG 402 Query: 365 IPKAAGVEAIFRLDECPRGLYSGAVVMLSADGGLDAALTLRAAYQVGGRTWLRAGAGIIE 424 PK +E I L+ RG+YSGAV LS G +D A+ +R A G ++AGAG++ Sbjct: 403 APKIRAMEIIDELEPVKRGIYSGAVGYLSWHGNMDTAIAIRTAVIKDGELHVQAGAGVVA 462 Query: 425 ESEPEREFEETCEK 438 +S PE E++ET K Sbjct: 463 DSVPEMEWQETLNK 476 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: 481 Number of extensions: 29 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: 450 Length of database: 494 Length adjustment: 33 Effective length of query: 417 Effective length of database: 461 Effective search space: 192237 Effective search space used: 192237 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