Align isochorismate lyase (EC 4.2.99.21); isochorismate synthase (EC 5.4.4.2) (characterized)
to candidate PfGW456L13_1217 Anthranilate synthase, aminase component (EC 4.1.3.27)
Query= BRENDA::P9WFX1 (450 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1217 Length = 493 Score = 129 bits (323), Expect = 3e-34 Identities = 83/266 (31%), Positives = 126/266 (47%), Gaps = 4/266 (1%) Query: 173 PQSRSVDVSDDPSGFRRRVAVAVDEIAAGRYHKVILSRCVEVPFAIDFPLTYRLGRRHNT 232 P RS DD + + V + I AG +V+ S+ + + F YR R N Sbjct: 215 PVFRSSFTQDD---YEKAVDTIKEYILAGDCMQVVPSQRMSIDFKAAPIDLYRALRCFNP 271 Query: 233 PVRSFLLQLGGIRALGYSPELVTAVRADGVVITEPLAGTRALGRGPAIDRLARDDLESNS 292 + G +G SPE++ V D ++ P+AGTR G D +DL S+ Sbjct: 272 TPYMYFFNFGDFHVVGSSPEVLVRVE-DNLITVRPIAGTRPRGANEEADLALEEDLLSDD 330 Query: 293 KEIVEHAISVRSSLEEITDIAEPGSAAVIDFMTVRERGSVQHLGSTIRARLDPSSDRMAA 352 KEI EH + + + ++E GS + + M + +V H+ S + +L M A Sbjct: 331 KEIAEHLMLIDLGRNDTGRVSEIGSVKLTEKMVIERYSNVMHIVSNVTGQLKSGLTAMDA 390 Query: 353 LEALFPAVTASGIPKAAGVEAIFRLDECPRGLYSGAVVMLSADGGLDAALTLRAAYQVGG 412 L A+ PA T SG PK +E I L+ RG+Y GAV + +G +D A+ +R A G Sbjct: 391 LRAILPAGTLSGAPKIRAMEIIDELEPVKRGVYGGAVGYFAWNGNMDTAIAIRTAVIKNG 450 Query: 413 RTWLRAGAGIIEESEPEREFEETCEK 438 ++AG GI+ +S P E+EET K Sbjct: 451 ELHVQAGGGIVADSVPALEWEETLNK 476 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: 469 Number of extensions: 23 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: 493 Length adjustment: 33 Effective length of query: 417 Effective length of database: 460 Effective search space: 191820 Effective search space used: 191820 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