Align isochorismate lyase (EC 4.2.99.21); isochorismate synthase (EC 5.4.4.2) (characterized)
to candidate CCNA_01972 CCNA_01972 anthranilate synthase component I
Query= BRENDA::P9WFX1 (450 letters) >FitnessBrowser__Caulo:CCNA_01972 Length = 513 Score = 122 bits (307), Expect = 2e-32 Identities = 85/269 (31%), Positives = 124/269 (46%), Gaps = 18/269 (6%) Query: 191 VAVAVDEIAAGRYHKVILSRCVEVPFAIDFPLTYRLGRRHNTPVRSFLLQLGGIRALGYS 250 VA A D IAAG +V+ S PF + YR RR N F L L G +G S Sbjct: 235 VAKAKDYIAAGDIFQVVASHRFRAPFDLPPFALYRSLRRTNPSPFLFFLNLDGFNLVGSS 294 Query: 251 PELVTAVRADGVVITEPLAGTRALGRGPAIDRLARDDLESNSKEIVEHAISVRSSLEEIT 310 PE++ +R DG + P+AGTR G P D +L ++ KE EH + + ++ Sbjct: 295 PEILVRLR-DGKITIRPIAGTRPRGATPEEDAALEAELLADPKERAEHLMLLDLGRNDVG 353 Query: 311 DIA----------------EPGSAAVIDFMTVRERGSVQHLGSTIRARLDPSSDRMAALE 354 +A + + V + T+ V H+ S + D + L Sbjct: 354 RVAMLNHHGRNAPPEQARPKGPNVRVTESFTIERYSHVMHIVSNVEGTAPEGVDPVDVLM 413 Query: 355 ALFPAVTASGIPKAAGVEAIFRLDECPRGL-YSGAVVMLSADGGLDAALTLRAAYQVGGR 413 A PA T SG PK +E I L+ RG+ Y+GAV ADG +D + LR A G Sbjct: 414 AALPAGTLSGAPKVRAMEIIDELEVEKRGISYAGAVGYFGADGAVDTCIVLRTALVKDGM 473 Query: 414 TWLRAGAGIIEESEPEREFEETCEKLSTL 442 +++AG GI+ +S+P+ E++ET K L Sbjct: 474 MYVQAGGGIVADSDPDAEYDETLHKSRAL 502 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: 520 Number of extensions: 30 Number of successful extensions: 4 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: 513 Length adjustment: 34 Effective length of query: 416 Effective length of database: 479 Effective search space: 199264 Effective search space used: 199264 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