Align isochorismate lyase (EC 4.2.99.21); isochorismate synthase (EC 5.4.4.2) (characterized)
to candidate WP_068461603.1 APY04_RS08350 anthranilate synthase component I
Query= BRENDA::P9WFX1 (450 letters) >NCBI__GCF_001541235.1:WP_068461603.1 Length = 503 Score = 139 bits (350), Expect = 2e-37 Identities = 89/259 (34%), Positives = 129/259 (49%), Gaps = 1/259 (0%) Query: 184 PSGFRRRVAVAVDEIAAGRYHKVILSRCVEVPFAIDFPLTYRLGRRHNTPVRSFLLQLGG 243 P+ ++ V A + I AG +V+LS+ PF++ YR RR N F L G Sbjct: 231 PAEYKTMVERAKEYIVAGDIFQVVLSQRFSAPFSLPSFALYRALRRTNPSPFLFHLNFGA 290 Query: 244 IRALGYSPELVTAVRADGVVITEPLAGTRALGRGPAIDRLARDDLESNSKEIVEHAISVR 303 +G SPE++ VR +G V P+AGT G A D+ D L + KE EH + + Sbjct: 291 FALVGSSPEILVRVR-EGEVTIRPIAGTAPRGATEAEDQELADALLKDPKERAEHLMLLD 349 Query: 304 SSLEEITDIAEPGSAAVIDFMTVRERGSVQHLGSTIRARLDPSSDRMAALEALFPAVTAS 363 ++ +AE GS V + V H+ S + +LD D + AL A FPA T S Sbjct: 350 LGRNDVGRVAEVGSVTVTGRFFIERYSHVMHIVSNVIGKLDAKHDAVDALMAGFPAGTVS 409 Query: 364 GIPKAAGVEAIFRLDECPRGLYSGAVVMLSADGGLDAALTLRAAYQVGGRTWLRAGAGII 423 G PK +E I L++ RG Y+G V SA G +D+ + LR A G ++AGAG++ Sbjct: 410 GAPKVRAMEVIDELEKAKRGPYAGCVGYFSASGQMDSCIALRTAIIKDGVMHVQAGAGLV 469 Query: 424 EESEPEREFEETCEKLSTL 442 +S PE+E +E K L Sbjct: 470 HDSVPEKEQQECINKARAL 488 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: 440 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: 503 Length adjustment: 33 Effective length of query: 417 Effective length of database: 470 Effective search space: 195990 Effective search space used: 195990 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