Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_020177023.1 A3OQ_RS0118980 hypothetical protein
Query= BRENDA::P76082 (255 letters) >NCBI__GCF_000385335.1:WP_020177023.1 Length = 268 Score = 106 bits (265), Expect = 4e-28 Identities = 76/248 (30%), Positives = 124/248 (50%), Gaps = 8/248 (3%) Query: 12 VLLLTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITGNARFFAAGADLNEMAEK 71 + L+ LNR A RNA+++ LL L + A + ++ + G+ F AG DL + A K Sbjct: 17 IALIGLNRAAKRNAIDDDLLNALTEAIAKATKEAKAAI--LFGHGEHFCAGLDLAKHARK 74 Query: 72 DLAATLNDTRPQLW-ARLQAFNK---PLIAAVNGYALGAGCELALLCDVVVAGENARFGL 127 L +R W A + P IA ++G +G G ELA + +A E+A F L Sbjct: 75 TPVEALKTSRH--WHAAFDLIGRGDIPFIAVLHGGVIGGGLELAASAHIRIADESAFFAL 132 Query: 128 PEITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVSDVFPSDLTLEYA 187 PE + G+ G GG+ R+ R +G + + M+L+G ++A++ +A LV L A Sbjct: 133 PEGSRGLFVGGGGSVRVARLMGVARMTDMMLTGRLLSAREGCEANLVQYSVEKGQGLAKA 192 Query: 188 LQLASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQLFTLLAATEDRHEGISAFLQK 247 +LA++MA ++PL+ A AL + Q++A + GL E + + + I FL K Sbjct: 193 KELAARMAGNAPLSNFAILHALPRIQDMAQEDGLFVESLMSAFTQTSPEAKSRIEDFLNK 252 Query: 248 RTPDFKGR 255 R G+ Sbjct: 253 RVVPVSGK 260 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: 94 Number of extensions: 5 Number of successful extensions: 1 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: 268 Length adjustment: 25 Effective length of query: 230 Effective length of database: 243 Effective search space: 55890 Effective search space used: 55890 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 24 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