Align isochorismate lyase (EC 4.2.99.21); isochorismate synthase (EC 5.4.4.2) (characterized)
to candidate WP_043768786.1 U743_RS12770 anthranilate synthase component I
Query= BRENDA::P9WFX1 (450 letters) >NCBI__GCF_000733765.1:WP_043768786.1 Length = 474 Score = 132 bits (333), Expect = 2e-35 Identities = 79/241 (32%), Positives = 121/241 (50%), Gaps = 1/241 (0%) Query: 198 IAAGRYHKVILSRCVEVPFAIDFPLTYRLGRRHNTPVRSFLLQLGGIRALGYSPELVTAV 257 I AG +V+ S+ + PF + YR RR N + L L +G SPE++ V Sbjct: 223 IRAGDVMQVVPSQRLSAPFTAEPLALYRAIRRLNPSPYLYCLNLDDHHVVGSSPEILVRV 282 Query: 258 RADGVVITEPLAGTRALGRGPAIDRLARDDLESNSKEIVEHAISVRSSLEEITDIAEPGS 317 D + PLAGTR G D ++L ++ KE+ EH + + ++ + E GS Sbjct: 283 E-DSEMHVRPLAGTRPRGATEEEDIRLAEELLADPKEVAEHLMLIDLGRNDVGRVCETGS 341 Query: 318 AAVIDFMTVRERGSVQHLGSTIRARLDPSSDRMAALEALFPAVTASGIPKAAGVEAIFRL 377 + + M + V H+ S + RL P + + AL A FP T SG PK +E I L Sbjct: 342 VKLTERMRIERYSHVMHIVSNVVGRLPPGTHALDALMAAFPTGTLSGAPKVRAMEIIEEL 401 Query: 378 DECPRGLYSGAVVMLSADGGLDAALTLRAAYQVGGRTWLRAGAGIIEESEPEREFEETCE 437 + RG+Y GAV + G LD A+ +R A GG+ +++GAG++ +S+P E+ ET Sbjct: 402 EPVRRGVYGGAVGYIGGSGNLDMAIAIRTAVIAGGQVHVQSGAGVVADSDPNAEWVETMN 461 Query: 438 K 438 K Sbjct: 462 K 462 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: 483 Number of extensions: 18 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: 474 Length adjustment: 33 Effective length of query: 417 Effective length of database: 441 Effective search space: 183897 Effective search space used: 183897 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 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