Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate H281DRAFT_01187 H281DRAFT_01187 short chain enoyl-CoA hydratase (EC 4.2.1.17)
Query= BRENDA::P76082 (255 letters) >FitnessBrowser__Burk376:H281DRAFT_01187 Length = 265 Score = 159 bits (403), Expect = 4e-44 Identities = 92/249 (36%), Positives = 139/249 (55%), Gaps = 10/249 (4%) Query: 12 VLLLTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITGNARFFAAGADLNEMAEK 71 V L+TLNRP +NAL+ A+ +L+ + + I V+TG F +GADL + + Sbjct: 22 VALVTLNRPEVKNALSRAMRRRLIAIFDEISARNDIRCAVLTGAGDTFCSGADLRDRPDP 81 Query: 72 DLAATLNDTRPQLWAR-----LQAFNKPLIAAVNGYALGAGCELALLCDVVVAGENARFG 126 D+ D W R ++ KP+IAAVNG ALGAG L CD++ A +NA F Sbjct: 82 DVPGDFLDHNR--WTRETGNAIKECVKPVIAAVNGAALGAGLGLMAACDIMYASDNAVFA 139 Query: 127 LPEITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVSDVFPSDLTLEY 186 +PEI +G+ AGG L G+S +M +G+ +TAQ + ++ DV P+D + Y Sbjct: 140 MPEINVGL---AGGASMLRTLFGRSTVRRMFFTGDKLTAQDLLRRNVLEDVLPADTLMPY 196 Query: 187 ALQLASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQLFTLLAATEDRHEGISAFLQ 246 ++LA ++AR SP+AL AK+A + ++ + E+ + +L+ TED E AFL+ Sbjct: 197 VMELARRIARKSPIALIEAKKAANFTDQMPQREAYRHEQDITMMLSRTEDAKEARMAFLE 256 Query: 247 KRTPDFKGR 255 KR P FKGR Sbjct: 257 KREPVFKGR 265 Lambda K H 0.318 0.130 0.356 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: 119 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: 255 Length of database: 265 Length adjustment: 24 Effective length of query: 231 Effective length of database: 241 Effective search space: 55671 Effective search space used: 55671 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 (21.8 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