Align 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase; EC 1.1.1.368 (characterized)
to candidate WP_043744206.1 AMB_RS10835 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
Query= SwissProt::O87871 (368 letters) >NCBI__GCF_000009985.1:WP_043744206.1 Length = 358 Score = 483 bits (1244), Expect = e-141 Identities = 232/356 (65%), Positives = 280/356 (78%), Gaps = 1/356 (0%) Query: 14 MSSNPHRWMMTSPGAPMVRAEFEIGELSADQVVVAVAGCGVCHTDLGYYYDSVRTNHALP 73 MS + +RWMMT G PMV+ EI A +V+V VAGCGVCHTDL YYY+ VRTNHALP Sbjct: 1 MSISAYRWMMTGVGQPMVKEAMEIAAPGAGEVLVEVAGCGVCHTDLDYYYNGVRTNHALP 60 Query: 74 LALGHEISGRVVQAGANAAQWLGRAVIVPAVMPCGTCELCTSGHGTICRDQVMPGNDIQG 133 LALGHEISGRV+QAGA A W+G+AVI+ AV+PCG C+LC G GTICR Q MPGND+QG Sbjct: 61 LALGHEISGRVIQAGAGAESWVGKAVIISAVIPCGQCDLCKRGKGTICRSQKMPGNDLQG 120 Query: 134 GFASHVVVPARGLCPVDEARLAAAGLQLADVSVVADAVTTPYQAVLQAGVEPGDVAVVIG 193 GFA+H+ VPA GLC VDEARL AAGL+L++VSVVADA+TTPYQA +QAG+ GD+ +VIG Sbjct: 121 GFATHITVPANGLCAVDEARLKAAGLELSEVSVVADALTTPYQAAVQAGIGQGDLVIVIG 180 Query: 194 VGGVGGYAVQIANAFGASVVAIDVDPAKLEMMSKHGAALTLNAREI-SGRDLKKAIEAHA 252 GGVGGY+VQ+A+A GA+VVA+D+DP KLE + GA LTLN ++ S R++KK I A A Sbjct: 181 CGGVGGYSVQVASAMGATVVALDIDPVKLEAVKAAGAKLTLNPKDFPSTREIKKEIGAFA 240 Query: 253 KANGLRLTRWKIFECSGTGAGQTSAYGLLTHGATLAVVGFTMDKVEVRLSNLMAFHARAL 312 KA GLR T W I ECSG+ GQ SA+ L+ HG T+ VVG+TM+K E RLSNLMAFHARAL Sbjct: 241 KAQGLRSTEWIIMECSGSVPGQQSAFDLMVHGCTICVVGYTMNKAEFRLSNLMAFHARAL 300 Query: 313 GNWGCLPEYYPAALDLVLDKKIDLASFIERHPLDQIGEVFAAAHAHKLTRRAILTP 368 GNWGC P+ YP ALDLVL KI++ +F+ER PLD I + FAA H HKL+RRA+L P Sbjct: 301 GNWGCPPDLYPGALDLVLSGKINVKNFVERRPLDSINDTFAAVHDHKLSRRAVLCP 356 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: 397 Number of extensions: 13 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: 358 Length adjustment: 29 Effective length of query: 339 Effective length of database: 329 Effective search space: 111531 Effective search space used: 111531 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