Align Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized)
to candidate WP_061535300.1 CAter10_RS11365 crotonase/enoyl-CoA hydratase family protein
Query= reanno::psRCH2:GFF2389 (257 letters) >NCBI__GCF_001584165.1:WP_061535300.1 Length = 260 Score = 119 bits (297), Expect = 8e-32 Identities = 87/250 (34%), Positives = 125/250 (50%), Gaps = 10/250 (4%) Query: 4 ETLLVDIQERVALITLNRPQALNALNGQLISELNQALGQLEADPQIGCIVLTGSAKAFAA 63 +T+L D + ITLN+P NA++ + ++L+ A + EAD + +LTG+ F Sbjct: 2 QTVLFDTDASICTITLNKPHKRNAVDRAMAADLHAAFERFEADASLRVAILTGAGDHFCG 61 Query: 64 GADIKEMAELTYPQIY--LDDFFADADRIATRR----KPLIAAVAGYALGGGCELALLCD 117 GAD+ + + P + LD + + R KPLIAAV GYA+ GG ELALL D Sbjct: 62 GADLSAIGD---PDLRNELDAEGGGSGPMGPTRMALSKPLIAAVNGYAVAGGLELALLAD 118 Query: 118 MIFAADNARFGQPEVNLGVLPGIGGTQRLTRAVGKAKAMDMCLTGRQMDAAEAERAGLVA 177 + A ++A FG GV GGT RL R +G A+A+DM LTGR + A EA GLV Sbjct: 119 LRVADEDAVFGVFCRRWGVPLIDGGTVRLPRIIGMARALDMILTGRPVSATEAFEMGLVN 178 Query: 178 RVFPAESLLEETLKAARVIAEKSLPATMMIKESVNRAFETTLAEGIRFERRVFHAVFATA 237 R+ E + A IA + + S ++ L E +R E + A Sbjct: 179 RLTRVGGAPAEAQELAHQIASFPQQCMLTDRRSAYEQWDLPLGEALRHEGKQ-GVPIVLA 237 Query: 238 DQKEGMAAFS 247 + KEG A F+ Sbjct: 238 EGKEGAARFT 247 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: 157 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: 260 Length adjustment: 24 Effective length of query: 233 Effective length of database: 236 Effective search space: 54988 Effective search space used: 54988 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