Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate CA265_RS02820 CA265_RS02820 acyl-CoA dehydrogenase
Query= SwissProt::Q2LQN9 (414 letters) >FitnessBrowser__Pedo557:CA265_RS02820 Length = 384 Score = 278 bits (711), Expect = 2e-79 Identities = 155/377 (41%), Positives = 224/377 (59%), Gaps = 7/377 (1%) Query: 38 TEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTGMD 97 TE Q+ + MVR+ A + I P +E DE FPV +LGL+ LVP EYGG+G+ Sbjct: 10 TETQQSVKAMVRDFAEKNIRPHIMEWDEAQHFPVELFKQLGELGLMGVLVPEEYGGSGLG 69 Query: 98 ITTFAMVLEEIGKVCASTALMLLAQADGMLSIILD-GSPALKEKYLPRFGEKSTLMTAFA 156 + V+ E+ +VC S L L A IL +P K+++LP+ + A+ Sbjct: 70 YQEYVDVIVEVARVCGSIGLSLAAHNSLCTGHILAFANPEQKQRWLPKLATAEWI-GAWG 128 Query: 157 ATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAKGMSTF 216 TE GSD L M T AV+ GD Y+ING K +IT+G DI V T +KG+S Sbjct: 129 LTEANTGSDALRMMTTAVEDGDDYIINGAKNWITHGKSGDIAVVMVRTGEQGSSKGISAI 188 Query: 217 VVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALSINRV 276 VVERGTPG G E K+GMR +E+ F++ VP NL+G G+GF M L R+ Sbjct: 189 VVERGTPGFTAGKKENKLGMRASETTEMIFDNCRVPKANLLGNVGEGFKQAMKVLDGGRI 248 Query: 277 FCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRKATT 336 A+ A+GIA+GA + A+ ++++R+QFG+PI+ I F +ADMATE+EAA LL+R+A Sbjct: 249 SIAALALGIAKGAFDAAVAYSKQRQQFGQPISSFQAISFKLADMATEIEAAELLIRQAA- 307 Query: 337 LLDAKDKRGPLI--GGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLTQI 394 D K++ P+ MAK FAS+ +++V TDAVQ+ GG GY +++ VE+ R++KL I Sbjct: 308 --DLKNRHLPMTKESAMAKYFASEVSVRVATDAVQIFGGYGYTKDFPVEKFYRDSKLCTI 365 Query: 395 YTGTNQITRMVTGRSLL 411 GT++I ++V R +L Sbjct: 366 GEGTSEIQKIVIAREVL 382 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: 338 Number of extensions: 15 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: 384 Length adjustment: 31 Effective length of query: 383 Effective length of database: 353 Effective search space: 135199 Effective search space used: 135199 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