Align isochorismate lyase (EC 4.2.99.21); isochorismate synthase (EC 5.4.4.2) (characterized)
to candidate Pf6N2E2_1717 Anthranilate synthase, aminase component (EC 4.1.3.27)
Query= BRENDA::P9WFX1 (450 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1717 Length = 489 Score = 132 bits (331), Expect = 3e-35 Identities = 83/260 (31%), Positives = 136/260 (52%), Gaps = 4/260 (1%) Query: 184 PSGFRRRVAVAVDEIAAGRYHKVILSRCVEVPFAIDFPLTYRLGRRHNTPVRSFLLQLGG 243 P F RV VA++ I AG +++ L + + + Y+ R N +L +GG Sbjct: 222 PEQFVERVEVAMEHIRAGDVYQIQLGHEIRIRSQVSPFDVYQNLRLRNPSPYMYLAHVGG 281 Query: 244 IRALGYSPELVTAVRADGVVITEPLAGTRALGRGPAIDRLARD-DLESNSKEIVEHAISV 302 I +G SPEL ++ D ++ P+AGT +G+ P +D +L + KE EH + + Sbjct: 282 IDLIGASPELFVRIK-DDLIEMRPIAGT--VGKKPGVDPTQLVLELTRSEKERAEHLMLI 338 Query: 303 RSSLEEITDIAEPGSAAVIDFMTVRERGSVQHLGSTIRARLDPSSDRMAALEALFPAVTA 362 +I + + GS V +FM V E + H+ S +R L P D ++A FPA T Sbjct: 339 DLCRNDIGRVCQAGSLEVDEFMLVEEYSHLYHMVSNVRGLLRPGLDAFDVIKASFPAGTM 398 Query: 363 SGIPKAAGVEAIFRLDECPRGLYSGAVVMLSADGGLDAALTLRAAYQVGGRTWLRAGAGI 422 SG PK +E I ++ RG+Y+GA+ ++ DG ++ AL +R+ G LRA AG+ Sbjct: 399 SGAPKVRAMELIEGMESNRRGIYAGALGLVGFDGSVNTALCIRSTVFDEGTYHLRASAGV 458 Query: 423 IEESEPEREFEETCEKLSTL 442 + +S PE E++ET K+ ++ Sbjct: 459 VADSVPELEWKETLYKMGSV 478 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: 428 Number of extensions: 19 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 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