Align isochorismate lyase (EC 4.2.99.21); isochorismate synthase (EC 5.4.4.2) (characterized)
to candidate PP_0417 PP_0417 Anthranilate synthase component 1
Query= BRENDA::P9WFX1 (450 letters) >FitnessBrowser__Putida:PP_0417 Length = 493 Score = 134 bits (337), Expect = 7e-36 Identities = 96/310 (30%), Positives = 146/310 (47%), Gaps = 16/310 (5%) Query: 141 IMVSEKEIRLFDAGIRHREAIDRLLATGVREVPQSRSVDVSDDPSG---FRRRVAVAVDE 197 ++V E + F+ G + + LL T + + R +D+S + FR E Sbjct: 171 VLVDPAEDQAFEQG---QARLQGLLETLRQPITPRRGLDLSGPQAAEPAFRSSYTREDYE 227 Query: 198 IAAGRYHKVILSR-CVEVP----FAIDFPLT----YRLGRRHNTPVRSFLLQLGGIRALG 248 A GR + IL+ C++V +IDF YR R N + G +G Sbjct: 228 NAVGRIKEYILAGDCMQVVPSQRMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVG 287 Query: 249 YSPELVTAVRADGVVITEPLAGTRALGRGPAIDRLARDDLESNSKEIVEHAISVRSSLEE 308 SPE++ V D +V P+AGTR G DR DDL S+ KEI EH + + + Sbjct: 288 SSPEVLVRVE-DNLVTVRPIAGTRPRGATEEADRALEDDLLSDDKEIAEHLMLIDLGRND 346 Query: 309 ITDIAEPGSAAVIDFMTVRERGSVQHLGSTIRARLDPSSDRMAALEALFPAVTASGIPKA 368 + ++ GS + + M + +V H+ S + +L M AL A+ PA T SG PK Sbjct: 347 VGRVSSTGSVRLTEKMVIERYSNVMHIVSNVTGQLREGLTAMDALRAILPAGTLSGAPKI 406 Query: 369 AGVEAIFRLDECPRGLYSGAVVMLSADGGLDAALTLRAAYQVGGRTWLRAGAGIIEESEP 428 +E I L+ RG+Y GAV + +G +D A+ +R A G ++AG GI+ +S P Sbjct: 407 RAMEIIDELEPVKRGVYGGAVGYFAWNGNMDTAIAIRTAVIKDGELHVQAGGGIVADSVP 466 Query: 429 EREFEETCEK 438 E+EET K Sbjct: 467 ALEWEETINK 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: 449 Number of extensions: 27 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