Align 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase; EC 1.1.1.368 (characterized)
to candidate 3607669 Dshi_1078 Alcohol dehydrogenase zinc-binding domain protein (RefSeq)
Query= SwissProt::O87871 (368 letters) >FitnessBrowser__Dino:3607669 Length = 345 Score = 116 bits (291), Expect = 8e-31 Identities = 102/315 (32%), Positives = 146/315 (46%), Gaps = 40/315 (12%) Query: 43 DQVVVAVAGCGVCHTDL-GYYYDSVRTNHALPLALGHEISGRVVQAGANAAQWLGRAVIV 101 D VV+ V CGVC +D G+ + R GHE G V++AG AA G V+ Sbjct: 26 DGVVLKVLACGVCRSDWHGWVGEHPRVKPGQ--IGGHEYCGEVIEAGPRAAFKPGDRVVA 83 Query: 102 PAVMPCGTCELCTSGHGTICRDQVMPGNDIQGGFASHVVVP---ARGLCPVDEARLAAAG 158 P ++ CG+C C +G C +Q +PG G FA +V VP P + AAG Sbjct: 84 PFILACGSCPSCQAGAQNTCPNQRLPGFVEPGAFAEYVAVPFDHNLSRLPDSLSPTVAAG 143 Query: 159 LQLADVSVVADAVTTPYQAVL-QAGVEPGDVAVVIGVGGVGGYAVQIANAFGASVVAIDV 217 L VTT + A+ +A V+ + V G GG+G +V +ANA GA V+A+DV Sbjct: 144 L--------GCRVTTAWHALTGRAAVQGAEWVAVHGTGGIGLSSVILANALGARVIAVDV 195 Query: 218 DPAKLEMMSKHGAALTLNARE---------ISGRDLKKAIEAHAKANGLRLTRWKIFECS 268 KL ++HGA +TLNARE I+G AIE A G+ T EC Sbjct: 196 VDEKLTHAAQHGAEVTLNAREGDVAARIKQITGGGAHVAIE----ALGIPETVNASLECL 251 Query: 269 GTGAGQTSAYGLLT-HGATLAVVGFTMDKVEVRLSNLMAFHARALGNWGCLPEYYPAALD 327 G+ GL T H A + + + + NL + R + +W YP+ L Sbjct: 252 -RPLGRHVQVGLPTGHTARMEI-----NMSAIYQGNLAVYGTRGMPSW-----RYPSLLS 300 Query: 328 LVLDKKIDLASFIER 342 L+ ++D++ I R Sbjct: 301 LIETGRVDMSPLIAR 315 Lambda K H 0.320 0.134 0.406 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: 302 Number of extensions: 15 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: 368 Length of database: 345 Length adjustment: 29 Effective length of query: 339 Effective length of database: 316 Effective search space: 107124 Effective search space used: 107124 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: 49 (23.5 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