Align Methylglutaconyl-CoA hydratase, mitochondrial; AU-specific RNA-binding enoyl-CoA hydratase; AU-binding enoyl-CoA hydratase; muAUH; Itaconyl-CoA hydratase; EC 4.2.1.18; EC 4.2.1.56 (characterized)
to candidate AO353_25675 AO353_25675 enoyl-CoA hydratase
Query= SwissProt::Q9JLZ3 (314 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25675 Length = 257 Score = 150 bits (379), Expect = 3e-41 Identities = 90/258 (34%), Positives = 152/258 (58%), Gaps = 8/258 (3%) Query: 57 LEEENRGIVVLGINRAYGKNALSKNLLKMLSKAVDALKSDKKVRTIIIRSEVPGIFCAGA 116 LE + R + ++ +NR NAL+ ++ L+ A+D L+++ ++ I++ F AGA Sbjct: 8 LEVQGR-VGLITLNRPQALNALNAQIVSELNHALDGLEANPEIGCIVLTGSKKA-FVAGA 65 Query: 117 DLKERAKMHSSEVGPFVSKIRSVINDIANLPVPTIAAIDGLALGGGLELALACDIRVAAS 176 D+KE A++ ++ ++ + S + +AN P IAA+ G ALGGG ELAL CD +A Sbjct: 66 DIKEMAELTYPQI--YLDDLFSDSDRVANRRKPVIAAVAGFALGGGCELALMCDFILAGD 123 Query: 177 SAKMGLVETKLAIIPGGGGTQRLPRAIGMSLAKELIFSARVLDGQEAKAVGLISHVLEQN 236 +AK G E L ++PG GGTQRL RA+G + A E+ S R++D EA+ G+++ ++ + Sbjct: 124 NAKFGQPEINLGVLPGMGGTQRLTRAVGKAKAMEMCLSGRLIDAVEAERCGIVARIVPVD 183 Query: 237 QEGDAAYRKALDLAREFLPQGPVAMRVAKLAINQGMEVDLVTGLAIEEACYAQTISTKDR 296 + D A + A +A++ L P+AM V K ++N+ EV L G+ E + +T+D+ Sbjct: 184 ELLDEALKVAALIAKKSL---PIAMMV-KESVNRAFEVSLSEGVRFERRVFHAAFATQDQ 239 Query: 297 LEGLLAFKEKRPPRYKGE 314 EG+ AF KR ++ G+ Sbjct: 240 KEGMAAFIAKREAQFVGK 257 Lambda K H 0.318 0.135 0.377 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: 142 Number of extensions: 9 Number of successful extensions: 4 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: 314 Length of database: 257 Length adjustment: 26 Effective length of query: 288 Effective length of database: 231 Effective search space: 66528 Effective search space used: 66528 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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