Align Methylglutaconyl-CoA hydratase, mitochondrial; AU-specific RNA-binding enoyl-CoA hydratase; AU-binding enoyl-CoA hydratase; muAUH; Itaconyl-CoA hydratase; EC 4.2.1.18; EC 4.2.1.56 (characterized)
to candidate PP_2217 PP_2217 enoyl-CoA hydratase
Query= SwissProt::Q9JLZ3 (314 letters) >FitnessBrowser__Putida:PP_2217 Length = 257 Score = 153 bits (386), Expect = 5e-42 Identities = 88/247 (35%), Positives = 145/247 (58%), Gaps = 7/247 (2%) Query: 66 VLGINRAYGKNALSKNLLKMLSKAVDALKSDKKVRTIIIRSEVPGIFCAGADLKERAKMH 125 ++ +NR NAL+ ++ +++A+D L+ D + +++ F AGAD+KE A++ Sbjct: 16 LITLNRPQALNALNAQIVGEINQALDQLERDPNIGCVVLTGSAKA-FAAGADIKEMAELQ 74 Query: 126 SSEVGPFVSKIRSVINDIANLPVPTIAAIDGLALGGGLELALACDIRVAASSAKMGLVET 185 ++ +V + S + IAN P IAA+ G ALGGG ELA+ CD +AA +AK G E Sbjct: 75 YPQI--YVDDLFSDADRIANRRKPIIAAVSGFALGGGCELAMMCDFILAADNAKFGQPEI 132 Query: 186 KLAIIPGGGGTQRLPRAIGMSLAKELIFSARVLDGQEAKAVGLISHVLEQNQEGDAAYRK 245 L ++PG GGTQRL RA+G + A EL + R++ +EA+ GL++ ++ Q + + A + Sbjct: 133 NLGVLPGMGGTQRLTRAVGKAKAMELCLTGRLMGAEEAERAGLVARIVPQAELVEEALKV 192 Query: 246 ALDLAREFLPQGPVAMRVAKLAINQGMEVDLVTGLAIEEACYAQTISTKDRLEGLLAFKE 305 A +A + + PV+M V K ++N+ EV L G+ E + ST+D+ EG+ AF Sbjct: 193 AATIASKSI---PVSMMV-KESVNRAFEVTLSEGVRFERRVFHAAFSTEDQKEGMAAFIA 248 Query: 306 KRPPRYK 312 KR ++K Sbjct: 249 KREAQFK 255 Lambda K H 0.318 0.135 0.377 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: 149 Number of extensions: 9 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: 314 Length of database: 257 Length adjustment: 26 Effective length of query: 288 Effective length of database: 231 Effective search space: 66528 Effective search space used: 66528 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