Align Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized)
to candidate WP_011842447.1 RSPH17029_RS17990 enoyl-CoA hydratase/isomerase family protein
Query= SwissProt::Q0AVM1 (260 letters) >NCBI__GCF_000015985.1:WP_011842447.1 Length = 257 Score = 148 bits (374), Expect = 1e-40 Identities = 90/262 (34%), Positives = 143/262 (54%), Gaps = 7/262 (2%) Query: 1 MAYEN--IILEKEEKLAVLYINRPKAMNALNKDTLLEIKDAVTAVNDDPAVELLIITGSG 58 M YEN + + + LAV+ ++RP A NA++ + EI+ + +DPA+ + ++TG+G Sbjct: 1 MDYENRFVKVSVDRGLAVVTLDRPPA-NAVSLEVYDEIRRTFHRLGEDPAMRVAVLTGAG 59 Query: 59 DKSFVAGADIAFMQNLSAMEAREFGALGQKVFRLIEAMEKPVIAAVNGFALGGGCELAMC 118 K F G D+ +L A E+ A + F + PV+ A+NG A+G G LA Sbjct: 60 -KVFCGGNDVNDFVDLEFDRATEYLAHVRLTFNALYDCPIPVVGAINGAAVGTGIVLASL 118 Query: 119 CDFRIAASNAKFGQPEVGLGITPGFGGTQRLPRLVGPGMAKQLLYTADVINADEAFRIGL 178 CD RIA+ A F PE+ +G+ GG++ + RL G GM + ++YT + ADEA R + Sbjct: 119 CDIRIASERAVFALPEIDVGV---LGGSRHVMRLAGQGMTRWMMYTGRRVRADEALRARI 175 Query: 179 VNKVVQPEELLPEVKKIAGRILSKGQLAVRLSKAAANEGMQTDIDRAMSIEADAFGLCFA 238 V++VV PEE++P IA I SK A+RL+K N + ++ E Sbjct: 176 VDEVVPPEEVMPRAMAIAEEIASKSPPAIRLAKLGLNRTEEMNMKEGYEFECTLTAAVRR 235 Query: 239 TQDQKEGMTAFLEKRKANFISK 260 T + +EG AFLEKR+ ++ ++ Sbjct: 236 TPEAREGAMAFLEKRQPSYAAR 257 Lambda K H 0.319 0.136 0.378 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: 167 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: 260 Length of database: 257 Length adjustment: 24 Effective length of query: 236 Effective length of database: 233 Effective search space: 54988 Effective search space used: 54988 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 (21.8 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 10 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