Align Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale)
to candidate Pf1N1B4_4788 Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17)
Query= uniprot:A0A2Z5MCI7 (262 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4788 Length = 257 Score = 111 bits (278), Expect = 1e-29 Identities = 78/240 (32%), Positives = 123/240 (51%), Gaps = 5/240 (2%) Query: 18 VLTLSNPGARNALHPDMYAAGIEALDSVERDPSIRAVVITGADNFFCAGGNLNRLLENRA 77 ++TL+ P A NAL+ + + ALD +E D +I +V+TG+ F AG ++ + E Sbjct: 16 LITLNRPQALNALNAQIVSELNHALDGLEADSNIGCIVLTGSKKAFAAGADIKEMAE--L 73 Query: 78 KDPSVQAQSIDLLAEWISALRLSSKPVIAAVDGAAAGAGFSLALACDLIVAADDAKFVMS 137 P + + ++ ++ R KP+IAAV+G A G G LAL CD I+A D+AKF Sbjct: 74 TYPQIYLDDLFSDSDRVANRR---KPIIAAVNGFALGGGCELALMCDFILAGDNAKFGQP 130 Query: 138 YARVGLTPDGGGSWFLAQALPRQLATEVLIEGKPIGAARLHELGVVNKLTKPGTARDAAV 197 +G+ P GG+ L +A+ + A E+ + G+ I A G+V ++ D A+ Sbjct: 131 EINLGVLPGMGGTQRLTRAVGKAKAMEMCLSGRLIDAVEAERCGIVARIVPADELVDEAL 190 Query: 198 AWADELGKISPNSVARIKTLVCAAGTQPLSEHLVAERDNFVASLHHREGLEGISAFLEKR 257 A + K S IK V A LSE + ER F A+ ++ EG++AF+ KR Sbjct: 191 KVAALIAKKSLPIAMMIKESVNRAFEVSLSEGVRFERRVFHAAFATQDQKEGMAAFIAKR 250 Lambda K H 0.317 0.132 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: 127 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: 262 Length of database: 257 Length adjustment: 24 Effective length of query: 238 Effective length of database: 233 Effective search space: 55454 Effective search space used: 55454 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