Align 3-methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate WP_086510402.1 BZY95_RS13290 enoyl-CoA hydratase
Query= metacyc::MONOMER-16071 (271 letters) >NCBI__GCF_002151265.1:WP_086510402.1 Length = 277 Score = 242 bits (618), Expect = 6e-69 Identities = 133/261 (50%), Positives = 172/261 (65%), Gaps = 5/261 (1%) Query: 4 FSTLEVIRDPRGFATLWLSREDKNNAFNAQMIRELIVAIDQL---AEDASLRFVLLRGRG 60 FS L + D RG A L L+R D +NAF+ +I EL +D+L A +R V+L G Sbjct: 7 FSQLSI--DERGVARLTLNRPDVHNAFDDSLIAELNEHLDKLHDAARHGEVRVVVLGSEG 64 Query: 61 RHFSAGADLAWMQQSAQLDFNTNLDDAHELGELMYALHRLKAPTLAVVQGAAFGGALGLI 120 + FSAGADL WM++ + DF NL D+ +L +LM+ L L PT+ VQGAAFGGA+GL Sbjct: 65 KSFSAGADLGWMKRMVEYDFEGNLADSRKLSQLMHGLDTLPCPTVCRVQGAAFGGAVGLA 124 Query: 121 SCCDMAIGAEDAQLCLSEVRIGLAPAVISPFVVKAIGERAARRYALTAERFTGVRARELG 180 +CCD+ I +E A+ CLSEV+IGL+PAVISP+V +A+G R RRYALTAE +A ELG Sbjct: 125 ACCDIVIASEKAKFCLSEVKIGLSPAVISPYVQRALGSRQMRRYALTAEVIDADKALELG 184 Query: 181 LLAEVYPASELDDHVEAWVSNLLQNSPQALRATKDLLREVDDGELSPALRRYCENTIARI 240 L ++ +D+ VEA ++ LL SPQA RATK LL EV S A R + I+ + Sbjct: 185 LAHQIVGHDHIDEAVEAMIATLLAGSPQAQRATKSLLAEVARDSDSKATREHTCRVISEL 244 Query: 241 RVSAEGQEGLRAFLEKRRPAW 261 RVSAEGQEGL +F EKRRPAW Sbjct: 245 RVSAEGQEGLTSFFEKRRPAW 265 Lambda K H 0.321 0.135 0.394 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: 211 Number of extensions: 7 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: 271 Length of database: 277 Length adjustment: 25 Effective length of query: 246 Effective length of database: 252 Effective search space: 61992 Effective search space used: 61992 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