Align 3-methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate CCNA_02251 CCNA_02251 methylglutaconyl-CoA hydratase
Query= metacyc::MONOMER-16071 (271 letters) >FitnessBrowser__Caulo:CCNA_02251 Length = 279 Score = 183 bits (464), Expect = 4e-51 Identities = 102/250 (40%), Positives = 146/250 (58%), Gaps = 1/250 (0%) Query: 13 PRGFATLWLSREDKNNAFNAQMIRELIVAIDQLAEDASLRFVLLRGRGRHFSAGADLAWM 72 P G T+W++R DK NAF+A I L + L +R V LRG G FSAGADL+WM Sbjct: 28 PEGAVTVWINRPDKKNAFDAATIAALRQTFETLHGAEGVRIVFLRGVGGAFSAGADLSWM 87 Query: 73 QQSAQLDFNTNLDDAHELGELMYALHRLKAPTLAVVQGAAFGGALGLISCCDMAIGAEDA 132 + + D + N DA EL ++ ALH + A T+A+V+G AFGG GL++ CD A+ DA Sbjct: 88 ASAVEWDEDDNRQDALELAHMLKALHDIPALTVALVEGPAFGGGAGLVAACDHALALVDA 147 Query: 133 QLCLSEVRIGLAPAVISPFVVKAIGERAARRYALTAERFTGVRARELGLLAEVY-PASEL 191 + SEV++GL PA ISP+V++A+G R A+ T F A GL+ EV+ + L Sbjct: 148 KFAFSEVKLGLTPATISPYVIQALGPRTAKLLFATGRVFDADDAWGFGLVDEVFEDVASL 207 Query: 192 DDHVEAWVSNLLQNSPQALRATKDLLREVDDGELSPALRRYCENTIARIRVSAEGQEGLR 251 + +A ++ + +P A+ K L+ + +L L IAR RVS EGQEG+R Sbjct: 208 EGARDALIAEMAPCAPGAIGDAKALVNDFVGQKLDKGLIDESARRIARRRVSPEGQEGVR 267 Query: 252 AFLEKRRPAW 261 AFL +R+P+W Sbjct: 268 AFLARRKPSW 277 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: 226 Number of extensions: 12 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: 279 Length adjustment: 25 Effective length of query: 246 Effective length of database: 254 Effective search space: 62484 Effective search space used: 62484 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 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