Align Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale)
to candidate AZOBR_RS29210 AZOBR_RS29210 enoyl-CoA hydratase
Query= uniprot:A0A2Z5MCI7 (262 letters) >FitnessBrowser__azobra:AZOBR_RS29210 Length = 266 Score = 122 bits (307), Expect = 6e-33 Identities = 86/255 (33%), Positives = 130/255 (50%), Gaps = 9/255 (3%) Query: 14 ESTLVLTLSNPGARNALH-PDMYAAGIEALDSVERDPSIRAVVITGADNFFCAGGNLNRL 72 + + LT++ P RN + PDM A +EALD ++RD SIR ++TG F +GGNL + Sbjct: 11 DGIVTLTINRPETRNPISDPDMIEAMLEALDRIDRDLSIRTAILTGTGTSFSSGGNLKTM 70 Query: 73 LENRAKDPSVQAQSIDLLAEWISALRLSSK----PVIAAVDGAAAGAGFSLALACDLIVA 128 E + + AQ+ I L L+ + P+IAAV+G A GAG LA CDL +A Sbjct: 71 GEQGGINDPLPAQTRRNYKFGIQRLPLAFEALEVPIIAAVNGPAIGAGCDLACMCDLRIA 130 Query: 129 ADDAKFVMSYARVGLTPDGGGSWFLAQALPRQLATEVLIEGKPIGAARLHELGVVNKLTK 188 A+ A F S+ +VG+ P GG+W L + + A E+ + G PI AA G+V+K+ Sbjct: 131 AERAVFAESFVKVGIVPGDGGAWLLPRVVGFSKACEMALTGDPIDAAEALACGLVSKVVP 190 Query: 189 PGTARDAAVAWADELGKISPNSVARIKTLVCAAGTQPLSEHLVAERDNFVASLHH--REG 246 A A + P++V K L+ G +HL+ E + +L H + Sbjct: 191 NDELLAEARKLAMRIAANPPHAVRMTKRLL-REGRNATLDHLL-ELSAAMQALAHATADH 248 Query: 247 LEGISAFLEKRAPVY 261 E ++A L KR P + Sbjct: 249 KEAVAALLGKRPPSF 263 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: 162 Number of extensions: 9 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: 266 Length adjustment: 25 Effective length of query: 237 Effective length of database: 241 Effective search space: 57117 Effective search space used: 57117 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 Apr 09 2024. 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