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 WP_025763018.1 X939_RS0109475 enoyl-CoA hydratase
Query= SwissProt::Q9JLZ3 (314 letters) >NCBI__GCF_000566685.1:WP_025763018.1 Length = 259 Score = 130 bits (328), Expect = 3e-35 Identities = 82/261 (31%), Positives = 138/261 (52%), Gaps = 5/261 (1%) Query: 55 RHLEEENR-GIVVLGINRAYGKNALSKNLLKMLSKAVDALKSDKKVRTIIIRSEVPGIFC 113 +HL +N+ GIV + +NR + +AL+K L+K ++ A++ SD++VR +++ +E FC Sbjct: 3 QHLNFQNKEGIVRISLNRPHVHHALNKELIKEITLAIEVAASDEEVRAVLLTAEGDTAFC 62 Query: 114 AGADLKERAKMHSSEVGPFVSKIRSVINDIANLPVPTIAAIDGLALGGGLELALACDIRV 173 +GADLK+ +I I +LP P + ++GLA+G G LAL+CD+ V Sbjct: 63 SGADLKDTLDSKIDVDQTLREYYNPMIMAIRSLPKPVVCRLNGLAVGAGASLALSCDMVV 122 Query: 174 AASSAKMGLVETKLAIIPGGGGTQRLPRAIGMSLAKELIFSARVLDGQEAKAVGLISHVL 233 A SA + + ++ ++P G T LPR +G + A L + + + +EA+ +G+I+H + Sbjct: 123 ATESAYLAFMFVQIGLMPDAGATFILPRLVGSARAFALASTGQRVTAREAQHIGMIAHAV 182 Query: 234 EQNQEGDAAYRKALDLAREFLPQGPVAMRVAKLAINQGMEVDLVTGLAIEEACYAQTIST 293 + E D+ K L R Q AM K +NQ L L +E Q T Sbjct: 183 PAS-ELDSTVEKLLLYYRHAPTQAIAAM---KQVLNQSQHSSLEQMLDLERIHQHQLSKT 238 Query: 294 KDRLEGLLAFKEKRPPRYKGE 314 D G+ +F +K+ P Y+G+ Sbjct: 239 TDAKNGISSFLQKKKPDYQGK 259 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: 153 Number of extensions: 9 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: 314 Length of database: 259 Length adjustment: 26 Effective length of query: 288 Effective length of database: 233 Effective search space: 67104 Effective search space used: 67104 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 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