Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate Dsui_0975 Dsui_0975 acyl-CoA dehydrogenase
Query= SwissProt::Q2LQN9 (414 letters) >FitnessBrowser__PS:Dsui_0975 Length = 390 Score = 252 bits (644), Expect = 1e-71 Identities = 150/375 (40%), Positives = 208/375 (55%), Gaps = 4/375 (1%) Query: 39 EEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTGMDI 98 E ++L + VR A +EIAPRA +ID ++ FP F DLGLL EYGGT M Sbjct: 12 ETIEMLRDTVRAFAAKEIAPRAAQIDRDNEFPADLWQKFGDLGLLGMTAEEEYGGTAMGY 71 Query: 99 TTFAMVLEEIGKVCASTALMLLAQADGMLSIIL-DGSPALKEKYLPRFGEKSTLMTAFAA 157 + +EEI + AS L A ++ ++ I +G+ A K KYLP T + A A Sbjct: 72 LAHIVAMEEISRASASVGLSYGAHSNLCVNQIRRNGTAAQKAKYLPGL-ISGTQVGALAM 130 Query: 158 TEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAKGMSTFV 217 +EP AGSD+++MK +A KKGD+YV+NG K +ITNG AD L V+A TD + GAKGM+ F+ Sbjct: 131 SEPNAGSDVVSMKLKAEKKGDRYVLNGSKMWITNGGDADTLVVYAKTDLNAGAKGMTAFI 190 Query: 218 VERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALSINRVF 277 VE+G G +G + K+GMRG LFF+D EVP EN++G G G LM L R Sbjct: 191 VEKGFKGFSHGTHLDKLGMRGSNTFPLFFDDCEVPEENVLGGVGNGAKVLMSGLDYERAV 250 Query: 278 CASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRKATTL 337 +GI ++ + + EREQFG I +Q +ADM + +A R V Sbjct: 251 LCGGPLGIMAACMDVVLPYLHEREQFGTAIGEFQLMQGKLADMYSTWQATRAYVYAVGQA 310 Query: 338 LDAKDKRGPLIGGMAKT--FASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLTQIY 395 D D L A ++++ A + DA+Q +GG GY EY R+ R+AKL +I Sbjct: 311 CDRADHARSLRKDAAGAILYSAEKATWMAGDAIQTLGGVGYTNEYPTGRLWRDAKLYEIG 370 Query: 396 TGTNQITRMVTGRSL 410 GT++I RM+ GR L Sbjct: 371 AGTSEIRRMLIGREL 385 Lambda K H 0.318 0.133 0.375 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: 403 Number of extensions: 16 Number of successful extensions: 4 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: 414 Length of database: 390 Length adjustment: 31 Effective length of query: 383 Effective length of database: 359 Effective search space: 137497 Effective search space used: 137497 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 (21.7 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