Align isochorismate lyase (EC 4.2.99.21); isochorismate synthase (EC 5.4.4.2) (characterized)
to candidate WP_077277377.1 B1C78_RS01525 anthranilate synthase component I
Query= BRENDA::P9WFX1 (450 letters) >NCBI__GCF_002000365.1:WP_077277377.1 Length = 489 Score = 142 bits (358), Expect = 2e-38 Identities = 95/274 (34%), Positives = 137/274 (50%), Gaps = 3/274 (1%) Query: 166 ATG-VREVPQSRSVDVSDDPSGFRRRVAVAVDEIAAGRYHKVILSRCVEVPFAIDFPLTY 224 ATG R+V +S V + GF+ VA D I G +V+LS+ + +PFA Y Sbjct: 202 ATGDARKVHESDFVSGFTE-DGFKAAVARCKDYIVEGDVMQVVLSQRLSIPFAAPPVNLY 260 Query: 225 RLGRRHNTPVRSFLLQLGGIRALGYSPELVTAVRADGVVITEPLAGTRALGRGPAIDRLA 284 R R N F L L + +G SPE++ + D +V P+AGTR G A D Sbjct: 261 RALRSLNPSPYMFFLDLDDHQVVGSSPEILVRLE-DDIVTVRPIAGTRPRGATEAEDHAL 319 Query: 285 RDDLESNSKEIVEHAISVRSSLEEITDIAEPGSAAVIDFMTVRERGSVQHLGSTIRARLD 344 +L ++ KE EH + + + ++E GS + + M V V H+ S + RL Sbjct: 320 EAELLADPKERAEHLMLIDLGRNDAGRVSETGSVQLTEQMVVERYSHVMHIVSNVTGRLK 379 Query: 345 PSSDRMAALEALFPAVTASGIPKAAGVEAIFRLDECPRGLYSGAVVMLSADGGLDAALTL 404 M L A FPA T SG PK +E I L+ RG+Y+GAV LS G +D A+ + Sbjct: 380 AGMSAMDVLRATFPAGTVSGAPKIRAMEIIDELEPVKRGIYAGAVGYLSWAGNMDTAIAI 439 Query: 405 RAAYQVGGRTWLRAGAGIIEESEPEREFEETCEK 438 R A G+ ++AGAGI+ +S P+ E+ ET K Sbjct: 440 RTAVIKDGQLHIQAGAGIVHDSIPDNEWAETMNK 473 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: 494 Number of extensions: 26 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: 489 Length adjustment: 33 Effective length of query: 417 Effective length of database: 456 Effective search space: 190152 Effective search space used: 190152 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