Align Putative enoyl-CoA hydratase protein; EC 4.2.1.17 (characterized, see rationale)
to candidate AZOBR_RS07775 AZOBR_RS07775 enoyl-CoA hydratase
Query= uniprot:Q92VJ6 (261 letters) >FitnessBrowser__azobra:AZOBR_RS07775 Length = 268 Score = 113 bits (282), Expect = 5e-30 Identities = 75/250 (30%), Positives = 118/250 (47%), Gaps = 4/250 (1%) Query: 11 DQRGVARVTLARSEKHNALSATMIGELTAVVGRLATDASIRAVILDAEGKSFCAGGDLDW 70 D+ GVA +TL R + NALS ++G L A + + D+++RAV+L G +FCAG DL Sbjct: 19 DRDGVATLTLNRPQARNALSVGLMGALQAELDTIHQDSTVRAVVLAGAGPAFCAGHDLKE 78 Query: 71 MRQQFSADRPTRIAEATRLAMMLKALNDLPKPLIARVHGNAFGGGVGLISVCDTVIAASG 130 MR + DR + + + ++ ++ + +P+IA+VHG A G L++ CD A Sbjct: 79 MRA--NPDRAAYESLFVQCSKLMLTVSRIRQPVIAKVHGIATAAGCQLVATCDLAYCADT 136 Query: 131 AQFGLTETRLGLIPATISPYVIARTGEARARPLFMSARVFGAEEAKVAGFVTTVVDGTML 190 A+F +GL +T + G A + + + GAEEA G V V L Sbjct: 137 ARFATPGVNIGLFCSTPMVALSRAVGRKAAMEMLLLGDLIGAEEAVRIGLVNRAVPADRL 196 Query: 191 DGAVEAAVTAYLVAAPGAAGRAKR-LARSLGLPITDAVIAATIEQLADTWETDEAREGVS 249 D V A +P K R + L + +A A + + +A EG+ Sbjct: 197 DAVVTEAAGKIAAKSPLTLAIGKEAFYRQIELDVEEA-YAYAARVMTENMLARDAEEGID 255 Query: 250 AFFERRNPSW 259 AF ++R P W Sbjct: 256 AFLQKRPPVW 265 Lambda K H 0.321 0.133 0.383 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: 178 Number of extensions: 7 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: 261 Length of database: 268 Length adjustment: 25 Effective length of query: 236 Effective length of database: 243 Effective search space: 57348 Effective search space used: 57348 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