Align BadK (characterized)
to candidate H281DRAFT_03491 H281DRAFT_03491 short chain enoyl-CoA hydratase (EC 4.2.1.17)/Enoyl-CoA hydratase (EC 4.2.1.17)
Query= metacyc::MONOMER-943 (258 letters) >FitnessBrowser__Burk376:H281DRAFT_03491 Length = 266 Score = 137 bits (345), Expect = 2e-37 Identities = 100/270 (37%), Positives = 142/270 (52%), Gaps = 23/270 (8%) Query: 3 SNPILTETQGRVGIITLNRPDVLNALNDA-LMDALGGALLAFDADDGIGAIVIAGNTRAF 61 + P+L E G V ITLNRP+ NAL + ++DAL +L AD + AIV+ G AF Sbjct: 2 NEPVLYELDGGVATITLNRPETRNALTEMEVVDALVESLERAQADLNVRAIVLTGAGPAF 61 Query: 62 AAGADIASMAAWSYSDVYGSNF----------ITRNWETIRQIRKPVLAAVAGLAYGGGC 111 ++G +I M +G N I R ++ P +AAV G A+G GC Sbjct: 62 SSGGNIKHMR--DEVGTFGGNSAQIRENYRRGIQRIPRAFHELDLPCIAAVNGPAHGAGC 119 Query: 112 ELALACDIVIAGRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEA 171 +LAL CDI IA SA FA K+G++PG GG LPRA+G ++A +M + P++A+ A Sbjct: 120 DLALMCDIRIAAHSALFAESFAKIGIIPGDGGAWLLPRAVGLSRAAEMIFTGTPIDAQCA 179 Query: 172 DRYGLVSRVVDDDRLRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERREL 231 +GLVSRVV D L LA IA+ + P ++ + + L R + +L EL Sbjct: 180 LDWGLVSRVVPDAELLSTARELAARIAS-NPPNVLRMSKRLIREGQRMDLPSLL----EL 234 Query: 232 HARF-----ASADAREGIQAFLEKRAPCFS 256 A F +AD RE + A EKR P ++ Sbjct: 235 SAAFQGIVHRTADHREALAATFEKRTPNYT 264 Lambda K H 0.321 0.135 0.389 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: 129 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: 258 Length of database: 266 Length adjustment: 25 Effective length of query: 233 Effective length of database: 241 Effective search space: 56153 Effective search space used: 56153 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