Align isochorismate lyase (EC 4.2.99.21); isochorismate synthase (EC 5.4.4.2) (characterized)
to candidate WP_013841403.1 DESRU_RS06925 anthranilate synthase component I
Query= BRENDA::P9WFX1 (450 letters) >NCBI__GCF_000215085.1:WP_013841403.1 Length = 507 Score = 145 bits (366), Expect = 3e-39 Identities = 91/263 (34%), Positives = 138/263 (52%), Gaps = 3/263 (1%) Query: 187 FRRRVAVAVDEIAAGRYHKVILSRCVEVPFAID-FPLTYRLGRRHNTPVRSFLLQLGGIR 245 F V A+D I AG +V+LS+ +PF D F L RL + +P ++ G + Sbjct: 233 FEEAVTRALDYIRAGDIFQVVLSQRFSLPFTGDPFDLYRRLRSINPSPYLTYF-NFGDLV 291 Query: 246 ALGYSPELVTAVRADGVVITEPLAGTRALGRGPAIDRLARDDLESNSKEIVEHAISVRSS 305 +G SPE++ V +G V T P+AGTR G+ D L ++ ++ KE EH + V Sbjct: 292 LVGASPEMLVRVE-EGKVFTRPIAGTRPRGKDETEDDLLAAEMLADEKERAEHLMLVDLG 350 Query: 306 LEEITDIAEPGSAAVIDFMTVRERGSVQHLGSTIRARLDPSSDRMAALEALFPAVTASGI 365 ++ +A PG+ V +M V V HL S + L+ D + AL A FPA T SG Sbjct: 351 RNDVGRVAVPGTVEVPQYMQVERYSHVMHLVSEAKGILEEGKDHLDALGACFPAGTVSGA 410 Query: 366 PKAAGVEAIFRLDECPRGLYSGAVVMLSADGGLDAALTLRAAYQVGGRTWLRAGAGIIEE 425 PK +E I L+ RG Y+GAV + G +D A+T+R A G + ++GAGI+ + Sbjct: 411 PKIRAMEIIEELEPLHRGPYAGAVGYVDFAGNMDTAITIRTAVVHRGSAYFQSGAGIVAD 470 Query: 426 SEPEREFEETCEKLSTLTPYLVA 448 S+P +E+EET K + ++A Sbjct: 471 SDPAKEYEETLHKARAMATAVMA 493 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: 21 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: 507 Length adjustment: 34 Effective length of query: 416 Effective length of database: 473 Effective search space: 196768 Effective search space used: 196768 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