Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate GFF929 HP15_908 enoyl-CoA hydratase/isomerase
Query= BRENDA::Q1D5Y4 (258 letters) >FitnessBrowser__Marino:GFF929 Length = 259 Score = 155 bits (391), Expect = 1e-42 Identities = 98/258 (37%), Positives = 142/258 (55%), Gaps = 8/258 (3%) Query: 5 KVDARGPIEIWTIDGESRRNAISRAMLKELGELVTRVSSSRDVRAVVITGAGDKAFCAGA 64 +++ RG I + TI+ N ++ L L +V ++ RD+ A+V+TG G+K + AGA Sbjct: 6 QLEKRGHIAVLTINNPPA-NTWTKDSLIALTNIVKELNEDRDIFALVMTGQGEKFYSAGA 64 Query: 65 DLKERATMAE-DEVRAFLDG--LRRTFRAIEKSDCVFIAAINGAALGGGTELALACDLRV 121 DLK T A+ D+ RA G F +++ V IAA+NG A+GGG E A+ACD+R+ Sbjct: 65 DLK---TFADGDKARANEMGQLFGEAFSTLQRFRGVSIAAVNGYAMGGGLECAMACDIRI 121 Query: 122 AAPAAELGLTEVKLGIIPGGGGTQRLARLVGPGRAKDLILTARRINAAEAFSVGLANRLA 181 A A++ L E +G++P GGTQ L LVG G AK +IL R+ A A +GL + Sbjct: 122 AEEHAQMALPEAGVGLLPCAGGTQNLPWLVGEGWAKRMILCGERVKADTALRIGLVEEVV 181 Query: 182 PEGHLLAVAYGLAESVVENAPIAVATAKHAI-DEGTGLELDDALALELRKYEEILKTEDR 240 P G L A LAE + +P + A K + G DD +E + E+ TED+ Sbjct: 182 PSGQGLDKALELAEMACQQSPSSTARCKTLVMSARDGRSHDDGWRMERELFVELFSTEDQ 241 Query: 241 LEGLRAFAEKRAPVYKGR 258 EG+ AF EKR P +K R Sbjct: 242 KEGVNAFLEKRKPEWKNR 259 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: 143 Number of extensions: 6 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: 258 Length of database: 259 Length adjustment: 24 Effective length of query: 234 Effective length of database: 235 Effective search space: 54990 Effective search space used: 54990 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