Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate BWI76_RS13115 BWI76_RS13115 2,3-dehydroadipyl-CoA hydratase
Query= BRENDA::D3RXI0 (252 letters) >FitnessBrowser__Koxy:BWI76_RS13115 Length = 255 Score = 108 bits (270), Expect = 1e-28 Identities = 78/251 (31%), Positives = 126/251 (50%), Gaps = 7/251 (2%) Query: 8 VEKDERVARIKIANPPV-NVLDMETMKEIISAIDEVE---GVDVIVFSGEGKSFSAGAEI 63 + + RV ++ + P N L+ + +I +D V V V SG + F+AGA++ Sbjct: 6 IARHARVLQLTLNRPQARNALNNALLMQIADVLDAAALDPTVGVCVISGNERFFAAGADL 65 Query: 64 KEHFPDKAPEMIRWFT-QLIDKVLRCKAITVAAVKGFALGGGFELAIACDFVLASKNAKL 122 E + P + +L ++ +A+V G+ALG G ELA+ CD ++A NA+ Sbjct: 66 NEMAENDLPATLDDIRPRLWARIDAFSKPLIASVNGYALGAGCELALICDLIVAGDNARF 125 Query: 123 GVPEITLAHYPPV-AIALLPRMIGWKNAYELILTGEAITAERAFEIGLVNKVFEDENFEE 181 G+PEITL P L R +G A ++L+GE+I A +A GLV++V+ +E Sbjct: 126 GLPEITLGMMPGAGGTQRLIRSVGKALASRMVLSGESIDAHQALRAGLVSEVYPPALTDE 185 Query: 182 SVNDFVNSLLEKSSVALRLTKKALLFSTEKEYLSLFDVINDVYLSQLVKSEDAVEGLKAF 241 ++ S +ALR K++L S E + ++ + L +ED EG+ AF Sbjct: 186 YALSLAATVARHSPLALRAAKQSLRLSQEVSLQAGLQQERQLF-TLLSATEDRREGIDAF 244 Query: 242 LEKRKPEWKGR 252 L KR E+KGR Sbjct: 245 LHKRTAEFKGR 255 Lambda K H 0.318 0.136 0.382 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: 122 Number of extensions: 6 Number of successful extensions: 4 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: 252 Length of database: 255 Length adjustment: 24 Effective length of query: 228 Effective length of database: 231 Effective search space: 52668 Effective search space used: 52668 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 17 2021. 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