Align isochorismate lyase (EC 4.2.99.21); isochorismate synthase (EC 5.4.4.2) (characterized)
to candidate WP_027457669.1 K420_RS0108445 anthranilate synthase component I
Query= BRENDA::P9WFX1 (450 letters) >NCBI__GCF_000519045.1:WP_027457669.1 Length = 491 Score = 130 bits (328), Expect = 7e-35 Identities = 82/254 (32%), Positives = 123/254 (48%), Gaps = 1/254 (0%) Query: 185 SGFRRRVAVAVDEIAAGRYHKVILSRCVEVPFAIDFPLTYRLGRRHNTPVRSFLLQLGGI 244 + F++ V A I G +V+LS+ + PF YR R N F Sbjct: 219 AAFKQAVLKAKRYITEGDIMQVVLSQRMTKPFMASPLALYRTLRSLNPSPYMFYFDFEDY 278 Query: 245 RALGYSPELVTAVRADGVVITEPLAGTRALGRGPAIDRLARDDLESNSKEIVEHAISVRS 304 +G SPE++ + + V + P+AGTR G P D +L ++ KE EH + Sbjct: 279 HVVGASPEILVRLEGERVTV-RPIAGTRKRGASPEEDAALAVELLADEKERAEHTQLLDL 337 Query: 305 SLEEITDIAEPGSAAVIDFMTVRERGSVQHLGSTIRARLDPSSDRMAALEALFPAVTASG 364 + +A+ GS V + M V V H+ S + RL P D + L A FPA T SG Sbjct: 338 GRNDCGRVAKVGSVKVTENMIVERYSHVMHIVSNVEGRLQPGLDALDVLRATFPAGTVSG 397 Query: 365 IPKAAGVEAIFRLDECPRGLYSGAVVMLSADGGLDAALTLRAAYQVGGRTWLRAGAGIIE 424 PK +E I L+ RG+Y+G+V LS +G +D A+ +R + ++AGAGI+ Sbjct: 398 APKVRAMEIIDELEPVKRGIYAGSVGYLSFNGDMDVAIAIRTGVIKDKKLHVQAGAGIVA 457 Query: 425 ESEPEREFEETCEK 438 +S PE E++ET K Sbjct: 458 DSNPESEWQETQNK 471 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: 458 Number of extensions: 24 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: 491 Length adjustment: 33 Effective length of query: 417 Effective length of database: 458 Effective search space: 190986 Effective search space used: 190986 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