Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate WP_010441027.1 G7G_RS0110000 acyl-CoA dehydrogenase
Query= SwissProt::Q2LQN9 (414 letters) >NCBI__GCF_000192475.1:WP_010441027.1 Length = 385 Score = 192 bits (488), Expect = 1e-53 Identities = 130/384 (33%), Positives = 198/384 (51%), Gaps = 21/384 (5%) Query: 37 LTEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLF---ADLGLLSPLVPVEYGG 93 +T+E ++ EM + P + E+ V RD + GL++ + EYGG Sbjct: 11 VTDEHRMFAEMAGRFMDDALVPNTEKWAEDG---VVDRDFWLQAGQTGLMAGSIAEEYGG 67 Query: 94 TGMDITTFAMVLEEIGKVCASTALMLLAQADGMLSIILD-----GSPALKEKYLPRFGEK 148 G + ++ L E TA G+ SI+ GS K K+LP+ Sbjct: 68 VGGGMGFDSVTLYE------QTARGDAGWGYGIQSIVTHYITTYGSEDQKHKWLPKLAS- 120 Query: 149 STLMTAFAATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSK 208 ++ A A TEPG GSD+ A+KT A K G+ Y + G K FITNG AD++ V A TD S Sbjct: 121 GEMIGALAMTEPGTGSDVQAVKTTAEKDGNSYRLKGSKIFITNGQSADLVIVAAKTDKSL 180 Query: 209 GAKGMSTFVVE-RGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVG-EEGKGFAY 266 GAKG+S VE GT G G N +K+GM+G +ELFFED++VP NL+G EEG+GF Sbjct: 181 GAKGVSLIAVETEGTEGFRRGRNLEKLGMKGNDTAELFFEDVKVPMTNLLGPEEGQGFYQ 240 Query: 267 LMGALSINRVFCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEA 326 LM L R+ A+G A+ +++ +ER+ FG+ + +F +A+ T+ E Sbjct: 241 LMKQLPWERLTIGIMALGAIDFAISETVKYVQERKAFGQRVMDFQNTRFKLAECKTKAEV 300 Query: 327 ARLLVRKATTLLDAKDKRGPLIGGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMM 386 R V L+A + M K + S+ ++ + +Q+ GG G+M EY + R+ Sbjct: 301 LRSFVNDCIGKLEA-GELDAATASMVKYWGSEVQNEIMHECLQLFGGYGFMMEYPIARLY 359 Query: 387 REAKLTQIYTGTNQITRMVTGRSL 410 +A++ IY GTN++ + + RSL Sbjct: 360 ADARVQMIYGGTNEVMKELIARSL 383 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: 332 Number of extensions: 19 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: 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 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