Align isochorismate lyase (EC 4.2.99.21); isochorismate synthase (EC 5.4.4.2) (characterized)
to candidate CCNA_03048 CCNA_03048 para-aminobenzoate synthetase component I
Query= BRENDA::P9WFX1 (450 letters) >FitnessBrowser__Caulo:CCNA_03048 Length = 524 Score = 112 bits (280), Expect = 3e-29 Identities = 83/270 (30%), Positives = 126/270 (46%), Gaps = 9/270 (3%) Query: 180 VSDDPSGFRRRVAVAVDEIAAGRYHKVILSRCVEVPFAID---FPLTYRLGRRHNTPVRS 236 V+ DP+ + VA V I G + ++R A F L RL + P + Sbjct: 251 VASDPATYETAVAQVVARIVGGEIFQANIARAWTGRLAAGVDPFDLFVRLRAQSPAPFSA 310 Query: 237 FLLQLGGIRALGYSPELVTAVRADGVVITEPLAGTRALGRGPAIDRLARDDLESNSKEIV 296 + +L G + SPE + A G + T+P+ GTR GR P DR +L ++ K+ Sbjct: 311 YW-RLPGRALVSNSPERFLKLDAAGAIQTQPIKGTRPRGRDPVEDRALAAELLASDKDRA 369 Query: 297 EHAISVRSSLEEITDIAEPGSAAVIDFMTVRERGSVQHLGSTIRARLDPSSDRMAALEAL 356 E+ + V ++ ++ GS + V +V HL ST+ ARL P L A Sbjct: 370 ENLMIVDLMRNDLARVSPAGSVRAPELFKVESFANVHHLVSTVTARLAPGRGVADLLRAS 429 Query: 357 FPAVTASGIPKAAGVEAIFRLDECPRGLYSGAVVMLSADGGLDAALTLRAAYQV----GG 412 FP + +G PK ++ I L E PRG Y G++ DG D+++ +R V G Sbjct: 430 FPPGSITGAPKVQAMKVIAEL-EPPRGPYCGSLFWAGVDGAFDSSVLIRTVGLVQDGAGW 488 Query: 413 RTWLRAGAGIIEESEPEREFEETCEKLSTL 442 R RAGAGI+ +S+P E ET K++ L Sbjct: 489 RLEARAGAGIVADSDPRGERLETEAKIAAL 518 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: 554 Number of extensions: 33 Number of successful extensions: 3 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: 524 Length adjustment: 34 Effective length of query: 416 Effective length of database: 490 Effective search space: 203840 Effective search space used: 203840 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: 52 (24.6 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