Align cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized)
to candidate GFF1026 HP15_1005 acyl-CoA dehydrogenase domain protein
Query= BRENDA::Q39QF5 (380 letters) >FitnessBrowser__Marino:GFF1026 Length = 389 Score = 243 bits (621), Expect = 5e-69 Identities = 145/373 (38%), Positives = 216/373 (57%), Gaps = 8/373 (2%) Query: 11 TLDMVRD----VATREIAPRALELDEKSLFPEYARDLFAKLGLLNPLLPAAYGGTEMGVL 66 TLDM+R+ A EIAPRA E+D + FP +GLL + YGG++MG L Sbjct: 15 TLDMLREQINGFAASEIAPRAEEIDRNNEFPMDLWRKMGDMGLLGITVSEEYGGSDMGYL 74 Query: 67 TLALILEELGRVCASTALLLIAQTDGMLPIIH-GGSPELKERYLRRF-AGESTLLTALAA 124 + +EE+ R AS L A ++ + IH G+ E K++YL + +GE + ALA Sbjct: 75 AHVIAMEEISRASASVGLSYGAHSNLCVNQIHRNGTEEQKQKYLPKLVSGEH--IGALAM 132 Query: 125 TEPAAGSDLLAMKTRAVRQGDKYVINGQKCFITNGSVADVIVVYAYTDPEKGSKGISAFV 184 +EP AGSD+++MK A +GD Y++NG K +ITNG A+ V+YA TD GS+G++AF+ Sbjct: 133 SEPNAGSDVISMKLTAKDEGDHYLLNGNKMWITNGPDANTYVIYAKTDTSAGSRGVTAFI 192 Query: 185 VEKGTPGLVYGRNESKMGMRGSINSELFFENMEVPAENIIGAEGTGFANLMQTLSTNRVF 244 VE+ PG + K+GMRGS EL F++ +VP EN++G G G LM L R+ Sbjct: 193 VERDAPGFSRHQKLDKLGMRGSNTCELVFQDCKVPKENVLGGVGNGAKVLMSGLDYERLV 252 Query: 245 CAAQAVGIAQGALDIAVRHTQDRVQFGKPIAHLAPVQFMVADMATAVEASRLLTRKAAEL 304 + +GI Q A+D+ V + ++R QFG+ I VQ VADM T + ++ A Sbjct: 253 LSGGPLGIMQAAMDVVVPYIRERKQFGQAIGEFELVQGKVADMYTWMNTAKSYVYMVAMS 312 Query: 305 LDDGDKKAVLYGSMAKTMASDTAMRVTTDAVQVLGGSGYMKENGVERMMRDAKLTQIYTG 364 D G + + A +++ A ++ DA+Q+LGG+GY+ E R++RDAKL +I G Sbjct: 313 ADRGAETTRKDAAGAILYSAEMATKIALDAIQLLGGNGYINEYPTGRLLRDAKLYEIGAG 372 Query: 365 TNQITRMVTGRAL 377 T++I RM+ GR L Sbjct: 373 TSEIRRMLIGREL 385 Lambda K H 0.319 0.134 0.371 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: 345 Number of extensions: 9 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 380 Length of database: 389 Length adjustment: 30 Effective length of query: 350 Effective length of database: 359 Effective search space: 125650 Effective search space used: 125650 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 (21.7 bits) S2: 50 (23.9 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