Align BadK (characterized)
to candidate AO356_30355 AO356_30355 enoyl-CoA hydratase
Query= metacyc::MONOMER-943 (258 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_30355 Length = 264 Score = 145 bits (367), Expect = 6e-40 Identities = 91/254 (35%), Positives = 139/254 (54%), Gaps = 8/254 (3%) Query: 10 TQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGNTRAFAAGADIAS 69 T GRV + LNRP+ NAL+++++D+L ALLA D +D IG VI G AF +G D+ Sbjct: 8 TVGRVMVAKLNRPEKKNALSESMLDSLRTALLAADENDDIGCFVITGAGDAFCSGGDLGR 67 Query: 70 MAAWSYSD--------VYGSNFITRNWETIRQIRKPVLAAVAGLAYGGGCELALACDIVI 121 AA S + + I KP++AAV G A G G +L+L CD+ Sbjct: 68 RAAESAEGDPTPLERKIRLQKVTHQVALAIENFEKPLIAAVNGAAVGAGMDLSLQCDMRF 127 Query: 122 AGRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRVV 181 A SA+FA I++GL+PG GG LPR +G AKA+++ + ++AEEA G+V+RV Sbjct: 128 ASESARFAEAYIRVGLIPGNGGCYLLPRIVGTAKALELLWTGDFVSAEEALALGIVNRVF 187 Query: 182 DDDRLRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASADAR 241 DD L +T+ AT +A ++K+ L ++ + L + ++ ++ D + Sbjct: 188 SDDELMQQTLDFATRLADGPPIQQRSIKKLLYQSLRTDLRTSLESVAAQMAVVQSTDDYK 247 Query: 242 EGIQAFLEKRAPCF 255 E I+A+ EKR P F Sbjct: 248 EAIKAYKEKRKPRF 261 Lambda K H 0.321 0.135 0.389 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: 102 Number of extensions: 4 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: 258 Length of database: 264 Length adjustment: 25 Effective length of query: 233 Effective length of database: 239 Effective search space: 55687 Effective search space used: 55687 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 (21.9 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
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