Align Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized)
to candidate BWI76_RS13115 BWI76_RS13115 2,3-dehydroadipyl-CoA hydratase
Query= reanno::psRCH2:GFF2389 (257 letters) >FitnessBrowser__Koxy:BWI76_RS13115 Length = 255 Score = 211 bits (537), Expect = 1e-59 Identities = 121/253 (47%), Positives = 157/253 (62%), Gaps = 2/253 (0%) Query: 6 LLVDIQERVALITLNRPQALNALNGQLISELNQALGQLEADPQIGCIVLTGSAKAFAAGA 65 L + RV +TLNRPQA NALN L+ ++ L DP +G V++G+ + FAAGA Sbjct: 4 LFIARHARVLQLTLNRPQARNALNNALLMQIADVLDAAALDPTVGVCVISGNERFFAAGA 63 Query: 66 DIKEMAELTYPQIYLDDFFADA-DRIATRRKPLIAAVAGYALGGGCELALLCDMIFAADN 124 D+ EMAE P LDD RI KPLIA+V GYALG GCELAL+CD+I A DN Sbjct: 64 DLNEMAENDLPAT-LDDIRPRLWARIDAFSKPLIASVNGYALGAGCELALICDLIVAGDN 122 Query: 125 ARFGQPEVNLGVLPGIGGTQRLTRAVGKAKAMDMCLTGRQMDAAEAERAGLVARVFPAES 184 ARFG PE+ LG++PG GGTQRL R+VGKA A M L+G +DA +A RAGLV+ V+P Sbjct: 123 ARFGLPEITLGMMPGAGGTQRLIRSVGKALASRMVLSGESIDAHQALRAGLVSEVYPPAL 182 Query: 185 LLEETLKAARVIAEKSLPATMMIKESVNRAFETTLAEGIRFERRVFHAVFATADQKEGMA 244 E L A +A S A K+S+ + E +L G++ ER++F + AT D++EG+ Sbjct: 183 TDEYALSLAATVARHSPLALRAAKQSLRLSQEVSLQAGLQQERQLFTLLSATEDRREGID 242 Query: 245 AFSEKRKPEFTNR 257 AF KR EF R Sbjct: 243 AFLHKRTAEFKGR 255 Lambda K H 0.321 0.135 0.375 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: 144 Number of extensions: 6 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: 257 Length of database: 255 Length adjustment: 24 Effective length of query: 233 Effective length of database: 231 Effective search space: 53823 Effective search space used: 53823 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 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