Align 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase; EC 1.1.1.368 (characterized)
to candidate Pf6N2E2_1522 Alcohol dehydrogenase (EC 1.1.1.1)
Query= SwissProt::O87871 (368 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1522 Length = 327 Score = 87.0 bits (214), Expect = 6e-22 Identities = 62/190 (32%), Positives = 87/190 (45%), Gaps = 11/190 (5%) Query: 27 GAPMVRAEFEIGELSADQVVVAVAGCGVCHTDLGYYYDSVRTNHALPLALGHEISGRVVQ 86 G P+ E +A Q+++ V CGVC TDL + +D LP GHEI G V Sbjct: 10 GQPLQLEERPQPTPAAGQLLIKVQACGVCRTDL-HLFDGELPQARLPRVPGHEIVGEVTA 68 Query: 87 AGANAA-QWLGRAVIVPAV-MPCGTCELCTSGHGTICRDQVMPGNDIQGGFASHVVVPAR 144 GA A W+GR V VP + CG CE C SG +C + G + GG+A + V AR Sbjct: 69 VGAQVAPDWIGRRVGVPWLGWTCGVCEFCRSGRENLCDQALFTGCQLDGGYADYTVADAR 128 Query: 145 GLCPVDEARLAAAGLQLADVSVVADAVTTPYQAVLQAGVEPGDVAVVIGVGGVGGYAVQI 204 P+ + L+ A+ + + A ++A+ A P + G G A+QI Sbjct: 129 FCFPLPDT------LEAAEAAPLLCAGLIGFRALQMAQNAPH--LGLYGFGAAAHLAIQI 180 Query: 205 ANAFGASVVA 214 A G V A Sbjct: 181 AVGRGQQVYA 190 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: 271 Number of extensions: 17 Number of successful extensions: 2 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: 327 Length adjustment: 29 Effective length of query: 339 Effective length of database: 298 Effective search space: 101022 Effective search space used: 101022 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