Align isochorismate lyase (EC 4.2.99.21); isochorismate synthase (EC 5.4.4.2) (characterized)
to candidate RR42_RS18295 RR42_RS18295 anthranilate synthase component I
Query= BRENDA::P9WFX1 (450 letters) >FitnessBrowser__Cup4G11:RR42_RS18295 Length = 505 Score = 137 bits (344), Expect = 1e-36 Identities = 98/311 (31%), Positives = 148/311 (47%), Gaps = 17/311 (5%) Query: 137 PRTRIMVSEKEIRLFDAGIRHREAIDRLLATGVREVPQSRSVDVSDDPSGFRRRVAVAVD 196 P T + RL + ++ R+ +D + + + R + +D + V A + Sbjct: 178 PTTPEAYARARQRLRELRMKLRQPVDVPITSPSVQTDVYREFEKAD----YLAAVHKAKE 233 Query: 197 EIAAGRYHKVILSRCVEVPFAIDFPLT-YRLGRRHNTPVRSFLLQLGGIRALGYSPELVT 255 I AG +V + + + P+ D PLT YR R N + G + +G SPE++ Sbjct: 234 YIMAGDMMQVQIGQRLVKPYR-DSPLTLYRALRSLNPSPYMYFYNFGDFQIVGASPEILV 292 Query: 256 AV-----------RADGVVITEPLAGTRALGRGPAIDRLARDDLESNSKEIVEHAISVRS 304 R D +V PLAGTRA G P D +L ++ KEI EH + + Sbjct: 293 RQETRRVGSNGDQREDHIVTIRPLAGTRARGNTPEKDAQLATELLNDPKEIAEHVMLIDL 352 Query: 305 SLEEITDIAEPGSAAVIDFMTVRERGSVQHLGSTIRARLDPSSDRMAALEALFPAVTASG 364 + +I IAE GS V D M + + VQH+ S++ L P + L A FPA T SG Sbjct: 353 ARNDIGRIAEIGSVKVTDQMVIEKYSHVQHIVSSVEGTLKPGMSNLDVLRATFPAGTLSG 412 Query: 365 IPKAAGVEAIFRLDECPRGLYSGAVVMLSADGGLDAALTLRAAYQVGGRTWLRAGAGIIE 424 PK +E I L+ RG+Y GAV LS G +D A+ +R G +++A AGI+ Sbjct: 413 APKVHAMEIIDELEPRKRGIYGGAVGYLSFGGEMDLAIAIRTGIVKDGNLYVQAAAGIVA 472 Query: 425 ESEPEREFEET 435 +S+PE E+ ET Sbjct: 473 DSDPEAEWRET 483 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: 484 Number of extensions: 20 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: 505 Length adjustment: 33 Effective length of query: 417 Effective length of database: 472 Effective search space: 196824 Effective search space used: 196824 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