Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate 200844 SO1679 acyl-CoA dehydrogenase family protein (NCBI ptt file)
Query= SwissProt::Q2LQN9 (414 letters) >lcl|FitnessBrowser__MR1:200844 SO1679 acyl-CoA dehydrogenase family protein (NCBI ptt file) Length = 385 Score = 262 bits (670), Expect = 1e-74 Identities = 144/373 (38%), Positives = 211/373 (56%), Gaps = 2/373 (0%) Query: 39 EEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTGMDI 98 E+Q+ E+ R A E+AP A + DE H FP +LG S P GG G+ Sbjct: 7 EDQRQFAELARQFATDELAPFAAKWDEEHHFPKDVIQKAGELGFCSLYSPESEGGMGLSR 66 Query: 99 TTFAMVLEEIGKVCASTALMLLAQADGMLSIILDGSPALKEKYLPRFGEKSTLMTAFAAT 158 +++ EE+ K C +T ML + G+ L++ + ++ ++ T Sbjct: 67 LDASIIFEELSKGCTATTAMLTIHNMATWMVTTWGTETLRQAWSEPL-TTGQMLASYCLT 125 Query: 159 EPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAKGMSTFVV 218 EPGAGSD +++T+AV GD+YV++G K FI+ ++L V T + G KG+S + Sbjct: 126 EPGAGSDAASLQTKAVPDGDEYVVSGSKMFISGAGSTELLVVMCRTGQA-GPKGISAIAI 184 Query: 219 ERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALSINRVFC 278 + G+IYG E KMG P + F+++ VP NL+GEEG+GF + M L R+ Sbjct: 185 PADSEGIIYGKAEDKMGWNAQPTRLVTFDNVRVPVANLLGEEGQGFTFAMKGLDGGRINI 244 Query: 279 ASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRKATTLL 338 A+ +VG AQ ALERA Q+ ER+QFGKP+A +QF +ADMATE+ AAR +VR A L Sbjct: 245 ATCSVGTAQAALERASQYMNERQQFGKPLAAFQALQFKLADMATELVAARQMVRLAAFKL 304 Query: 339 DAKDKRGPLIGGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLTQIYTGT 398 D+ D G MAK FA+D +V A+Q+ GG GY++EY +ER R+ ++ QI GT Sbjct: 305 DSGDPEGTAYCAMAKRFATDVGFQVCDAALQIHGGYGYIREYPLERHFRDVRVHQILEGT 364 Query: 399 NQITRMVTGRSLL 411 N+I R++ R LL Sbjct: 365 NEIMRLIIARRLL 377 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: 358 Number of extensions: 12 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: 414 Length of database: 385 Length adjustment: 31 Effective length of query: 383 Effective length of database: 354 Effective search space: 135582 Effective search space used: 135582 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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