Align Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized)
to candidate WP_047094365.1 AAV99_RS12275 enoyl-CoA hydratase/isomerase family protein
Query= reanno::psRCH2:GFF2389 (257 letters) >NCBI__GCF_001013305.1:WP_047094365.1 Length = 252 Score = 103 bits (258), Expect = 3e-27 Identities = 85/259 (32%), Positives = 121/259 (46%), Gaps = 21/259 (8%) Query: 6 LLVDIQERVALITLNRPQALNALNGQLISELNQALGQLEADPQIGCIVLTGSAKA--FAA 63 L ++ VA + ++R NA N + + L Q ADP + +V+ + F A Sbjct: 3 LRLEFDGPVAHLLIDRLDKRNAFNMAMWEAMPGLLEQARADPAVRTLVIRSAQPGGVFCA 62 Query: 64 GADIKEM-------AELTYPQIYLDDFFADADRIATRRKPLIAAVAGYALGGGCELALLC 116 GADIKEM A L Q ++ D R+ P +A V G +GGGC +A+ C Sbjct: 63 GADIKEMLLHKDDGAWLAANQAAINRVQHDLARLTL---PTVAFVEGDCVGGGCGIAIAC 119 Query: 117 DMIFAADNARFGQPEVNLGVLPGIGGTQRLTRAVGKAKAMDMCLTGRQMDAAEAERAGLV 176 D+ A D ARFG LG++ + + LT VG +A M TG +DAAEA+R GLV Sbjct: 120 DLRVATDKARFGITPGKLGIVYPLHDVKLLTDLVGPGQAKRMLFTGGLLDAAEAQRIGLV 179 Query: 177 ARVFPA-ESLLEETLKAARVIAEKSLPATMMIKESVNRAFETTLAEGIRFERRVFHAVFA 235 + + LL + L A S + IK V R + + + +F F Sbjct: 180 EMIADSPRGLLNDILSA-------SPHSIREIKMFVRRVLDGQTGDDDQ-TLAIFTDAFM 231 Query: 236 TADQKEGMAAFSEKRKPEF 254 D EG AAF+ KRKP+F Sbjct: 232 RGDFAEGAAAFAGKRKPDF 250 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: 130 Number of extensions: 7 Number of successful extensions: 3 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: 252 Length adjustment: 24 Effective length of query: 233 Effective length of database: 228 Effective search space: 53124 Effective search space used: 53124 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 24 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