Align isochorismate lyase (EC 4.2.99.21); isochorismate synthase (EC 5.4.4.2) (characterized)
to candidate GFF3346 HP15_3288 anthranilate synthase component I
Query= BRENDA::P9WFX1 (450 letters) >FitnessBrowser__Marino:GFF3346 Length = 513 Score = 135 bits (340), Expect = 3e-36 Identities = 92/287 (32%), Positives = 142/287 (49%), Gaps = 9/287 (3%) Query: 157 HREAIDRLLATGVREVPQSRSVDVSDDPSGFRR-RVAVAVDEIAA----GRYHKVILSRC 211 HR+ D A E + ++VD SD SGF + + AVD+I G + ++S+ Sbjct: 214 HRQTAD---APRTPEHLRGKAVDESDFISGFTQDKFEAAVDKIKGYVLDGDVMQTVISQR 270 Query: 212 VEVPFAIDFPLTYRLGRRHNTPVRSFLLQLGGIRALGYSPELVTAVRADGVVITEPLAGT 271 + +PF YR R N + L LG +G SPE++ V + V + P+AGT Sbjct: 271 MSIPFEAPPLNLYRSLRVLNPSPYMYFLDLGDFHIVGSSPEILARVEDEEVTV-RPIAGT 329 Query: 272 RALGRGPAIDRLARDDLESNSKEIVEHAISVRSSLEEITDIAEPGSAAVIDFMTVRERGS 331 R G A D+ +L ++ KEI EH + + + ++E G+ + D M V Sbjct: 330 RKRGATDAEDKALEAELLADPKEIAEHLMLIDLGRNDAGRVSETGTVRLTDKMIVERYSH 389 Query: 332 VQHLGSTIRARLDPSSDRMAALEALFPAVTASGIPKAAGVEAIFRLDECPRGLYSGAVVM 391 V H+ S + RL ++ + L A PA T SG PK +E I L+ RG+Y GAV Sbjct: 390 VMHIVSNVTGRLKDNTSCLDVLRATLPAGTLSGAPKIRAMEIIDELEPVKRGVYGGAVGY 449 Query: 392 LSADGGLDAALTLRAAYQVGGRTWLRAGAGIIEESEPEREFEETCEK 438 LS +G +D A+ +R A ++AGAG++ +S P E++ET K Sbjct: 450 LSFNGNMDTAIAIRTAVIKDNTLHIQAGAGVVADSVPRLEWKETMNK 496 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: 472 Number of extensions: 25 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: 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