Align Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale)
to candidate GFF3051 Psest_3109 Enoyl-CoA hydratase/carnithine racemase
Query= uniprot:A0A2Z5MCI7 (262 letters) >FitnessBrowser__psRCH2:GFF3051 Length = 272 Score = 108 bits (270), Expect = 1e-28 Identities = 80/251 (31%), Positives = 128/251 (50%), Gaps = 11/251 (4%) Query: 16 TLVLTLSNPGARNALHPDMYAAGIEALDSVERDPSIRAVVITG-ADNFFCAGGNLNRLLE 74 T ++T+++P A N + + ++ + D I A+VI+G + FF AG +L + Sbjct: 27 TALITINHPPA-NTWDRESLIGLKQVVEHLNHDDDIYALVISGQGEKFFSAGADLKLFAD 85 Query: 75 ---NRAKDPSVQAQSIDLLAEWISALRLSSKPVIAAVDGAAAGAGFSLALACDLIVAADD 131 NRA++ + + E ALR IAA++G A G G ALACDL +A Sbjct: 86 GDRNRAREMARR------FGEAFEALRDFRGVSIAAINGFALGGGLECALACDLRIAEQQ 139 Query: 132 AKFVMSYARVGLTPDGGGSWFLAQALPRQLATEVLIEGKPIGAARLHELGVVNKLTKPGT 191 A+ + A VGL P GG+ LA + A +++ G+ I A +G++ ++ +PG Sbjct: 140 AQMGLPEASVGLLPCAGGTQALAWLVGEGWAKRMILCGERITAETALRIGLIEQVVEPGQ 199 Query: 192 ARDAAVAWADELGKISPNSVARIKTLVCAAGTQPLSEHLVAERDNFVASLHHREGLEGIS 251 AR A+ A + + SP +V IK L+ A + AER+ FV + LEG++ Sbjct: 200 ARGHALLLAARIARQSPVAVRAIKPLIDGARQRLPHTFGAAEREAFVELFEAEDTLEGVN 259 Query: 252 AFLEKRAPVYK 262 AFLEKR P ++ Sbjct: 260 AFLEKRDPRWR 270 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: 140 Number of extensions: 5 Number of successful extensions: 1 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: 272 Length adjustment: 25 Effective length of query: 237 Effective length of database: 247 Effective search space: 58539 Effective search space used: 58539 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