Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate CCNA_01794 CCNA_01794 enoyl-CoA hydratase/isomerase family
Query= BRENDA::Q1D5Y4 (258 letters) >FitnessBrowser__Caulo:CCNA_01794 Length = 256 Score = 140 bits (354), Expect = 2e-38 Identities = 94/259 (36%), Positives = 139/259 (53%), Gaps = 14/259 (5%) Query: 6 VDARGPIEIWTIDGESRRNAISRAMLKELGELVTRVSSSRDVRAVVITGAGDKAFCAGAD 65 ++ RG I I T++ NA+S+A+ L + + ++ DV V++TGAGD+AF AG D Sbjct: 4 IERRGAIAIVTLNRPEAMNALSKALRLALHDAIVQLDQDPDVSVVILTGAGDRAFTAGLD 63 Query: 66 LKER----ATM--AEDEVRAFLDGLRRTFRAIEKSDCVFIAAINGAALGGGTELALACDL 119 LKE A M A D+ D RA+E I AING A+ GG ELALACD+ Sbjct: 64 LKELGGDPAAMGAANDQ-----DARSNPVRAVETCRKPVIGAINGVAITGGFELALACDV 118 Query: 120 RVAAPAAELGLTEVKLGIIPGGGGTQRLARLVGPGRAKDLILTARRINAAEAFSVGLANR 179 +A+ A T ++GI+PG G +Q+L+RL+GP RAK+L LT ++A A GL NR Sbjct: 119 LLASENARFADTHARVGIMPGWGLSQKLSRLIGPYRAKELSLTGNFLDARTAADWGLVNR 178 Query: 180 LAPEGHLLAVAYGLAESVVENAPIAVATAKHAIDEGTGLELDDALALELRKYEEILKTED 239 + LL A +A+ + A++ K ID+G + + LALE +E Sbjct: 179 VTTASELLPTALRMAQDMASIPVEALSFYKSLIDDGYAVAFGEGLALE---HERSSAHNR 235 Query: 240 RLEGLRAFAEKRAPVYKGR 258 + R A++R + +GR Sbjct: 236 TVTPERVEAQRRQVMERGR 254 Lambda K H 0.319 0.136 0.380 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: 135 Number of extensions: 5 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: 258 Length of database: 256 Length adjustment: 24 Effective length of query: 234 Effective length of database: 232 Effective search space: 54288 Effective search space used: 54288 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 (21.7 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