Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate WP_050655857.1 C1M55_RS09530 acyl-CoA dehydrogenase
Query= SwissProt::Q2LQN9 (414 letters) >NCBI__GCF_002893965.1:WP_050655857.1 Length = 380 Score = 238 bits (608), Expect = 2e-67 Identities = 142/378 (37%), Positives = 213/378 (56%), Gaps = 13/378 (3%) Query: 38 TEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTGMD 97 ++E + L+E+ R++A + +AP+ E ++ +P GLLS P E+GG Sbjct: 9 SQEARDLIELTRDVADKVLAPKVNEYEKAEKYPDGVFPALGQAGLLSLPYPEEFGGGDQP 68 Query: 98 ITTFAMVLEEIGKVCASTALMLLAQADGMLSIILDGSPALKEKYLPRFGEKSTLMTAFAA 157 + VLEEI A+ A+ + + + G+ K ++LP +T+ A++ Sbjct: 69 YEVYLQVLEEIASRWAAVAVAVSVHSLSCFPLFTFGTDEQKNRWLPDMLGGNTI-GAYSL 127 Query: 158 TEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAKGMSTFV 217 +E AGSD A+ +A Y +NG K +ITNG AD ++A T G++G+S + Sbjct: 128 SEAQAGSDAAALSCKATPTDGGYRVNGSKAWITNGGKADFYNLFARTSDD-GSRGVSCLL 186 Query: 218 VERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALSINRVF 277 V++ GL +G E+KMG+R P + ++D +P E L+G+ G+G AL R+ Sbjct: 187 VDKDAEGLSFGKPEEKMGLRAVPTASANYDDAFIPEERLIGQRGQGLPIAFSALDSGRLG 246 Query: 278 CASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRKATTL 337 A+ AVGIAQGAL+ A+ + +ER+ FGK I + F++ADMA V++AR T Sbjct: 247 IAAVAVGIAQGALDDAVAYAKERKAFGKRIIDHQGLGFVLADMAAAVDSAR------ATY 300 Query: 338 LDAKDKRGPLI-----GGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLT 392 LDA +R + +AK A+D AMKVTTDAVQV GG GY Q++ VER MREAK+T Sbjct: 301 LDAARRRDAGVPYSRNASVAKLVATDAAMKVTTDAVQVFGGYGYTQDFPVERYMREAKIT 360 Query: 393 QIYTGTNQITRMVTGRSL 410 QI+ GTNQI R+V R L Sbjct: 361 QIFEGTNQIQRLVIARQL 378 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: 384 Number of extensions: 11 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: 380 Length adjustment: 31 Effective length of query: 383 Effective length of database: 349 Effective search space: 133667 Effective search space used: 133667 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 24 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