Align Probable enoyl-CoA hydratase; EC 4.2.1.17 (uncharacterized)
to candidate WP_092487896.1 BM299_RS18360 enoyl-CoA hydratase-related protein
Query= curated2:Q52995 (257 letters) >NCBI__GCF_900115975.1:WP_092487896.1 Length = 260 Score = 216 bits (549), Expect = 5e-61 Identities = 122/260 (46%), Positives = 165/260 (63%), Gaps = 3/260 (1%) Query: 1 MSYETLLVETQGRVGLITLNRPQALNALNAVLMRELDAALKAFDADRAVGAIVLAGS-EK 59 M + LL+E + + ++T+NRP+ LNALNA ++ELDAA+ D V I+L G+ EK Sbjct: 1 MGWNNLLLEKEAGIAVLTINRPKVLNALNAETLQELDAAMDQLGNDDEVRVIILTGAGEK 60 Query: 60 AFAAGADIKEMQGLDFVDGYLADFLGG--WEHVANARKPMIAAVSGFALGGGCELAMMCD 117 AF AGADI MQ L ++ LG + + N KP+IAA++GFALGGGCEL+M CD Sbjct: 61 AFVAGADIAFMQTLKPLEAKNFARLGQKVFSKIENLPKPVIAAINGFALGGGCELSMACD 120 Query: 118 FIIASETAKFGQPEITLGVIPGMGGSQRLTRAVGKAKAMDLILTGRMMDAAEAERSGLVS 177 IASE AK GQPE+ LG+I G GG+QRLTR V A +++ T M DA A R GLV+ Sbjct: 121 IRIASENAKLGQPEVNLGLIAGFGGTQRLTRLVNPGLAKEILFTADMYDAEAAHRIGLVN 180 Query: 178 RVVAPDRLLEEALGAAEKIASFSLPAAMMAKEAVNRSLELTLAEGLRFERRLFQSLFATE 237 VV L+ A++IA+ A ++K+AVN LE+ L + E LF +FATE Sbjct: 181 HVVPAGELMNFCKNMAKRIAARGPVAVQLSKQAVNDGLEMDLEKAFVHEADLFGLVFATE 240 Query: 238 DQKEGMAAFVAKRKAEFKHR 257 D++EG+AAF+ K+K EFK R Sbjct: 241 DREEGIAAFLGKKKPEFKGR 260 Lambda K H 0.321 0.134 0.371 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: 191 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 Apr 09 2024. 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