Align Enoyl-CoA hydratase (characterized, see rationale)
to candidate AZOBR_RS24105 AZOBR_RS24105 enoyl-CoA hydratase
Query= uniprot:A0A2Z5MEB0 (258 letters) >FitnessBrowser__azobra:AZOBR_RS24105 Length = 256 Score = 137 bits (346), Expect = 2e-37 Identities = 88/259 (33%), Positives = 137/259 (52%), Gaps = 13/259 (5%) Query: 2 VYENILVETRGRVGLVTLSRPKALNALNDALMDELGVALREFDADDAIGAIVLTGS-EKA 60 V++ IL E RG VG++TL+RP+ LNA N A+ DEL VA +F+ D + AI+LTG+ ++A Sbjct: 1 VFKFILTEVRGPVGIITLNRPEILNAWNAAMRDELVVAFDQFENQDGVRAIILTGAGDRA 60 Query: 61 FAAGADIGMMSTYSYMDVYKGDYITRNWE----TVRSIRKPIIAAVAGFALGGGCELAMM 116 F AG D+ T+ + + + WE +R++ KP+I A+ G A G ++A++ Sbjct: 61 FGAGQDLNETKTF---NADRAEEWVAEWERLYHRMRTLSKPLIIALNGVAAGSAFQVALL 117 Query: 117 CDMIFAADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGL 176 D + GQPEI GI G + + A+ MDL L+ R MDA E+ R GL Sbjct: 118 GDFRIGHAGVRMGQPEINSGI-ASTTGPWIMKEMIGLARTMDLTLSGRLMDAEESHRIGL 176 Query: 177 VSRVIPAASLIDESIAAGATIAEFPLPAVMMVK----ESVNRAYETTLAEGVHFERRLFH 232 ++R++P ++ ES+A +A P A+ + K E + LA GV +R + Sbjct: 177 INRIVPQDRVMAESLALAEELAAKPPVAMRLDKQRFREMTEAGFRDALAAGVRIQREAYA 236 Query: 233 SLFATEDQKEGMAAFVEKR 251 S +E +A KR Sbjct: 237 SGEPARMMEEFLAKRAAKR 255 Lambda K H 0.322 0.135 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: 147 Number of extensions: 9 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: 256 Length adjustment: 24 Effective length of query: 234 Effective length of database: 232 Effective search space: 54288 Effective search space used: 54288 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