Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate Ac3H11_2359 Butyryl-CoA dehydrogenase (EC 1.3.99.2)
Query= SwissProt::Q2LQN9 (414 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2359 Length = 388 Score = 264 bits (674), Expect = 4e-75 Identities = 151/379 (39%), Positives = 215/379 (56%), Gaps = 6/379 (1%) Query: 36 ELTEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTG 95 ELTEEQ+ + R+ A E AP A DE FP A +LG P GG Sbjct: 4 ELTEEQRAFAQTARDFAQAEFAPHAAHWDEEGIFPKEAIAKAGELGFCGLYAPEAAGGLA 63 Query: 96 MDITTFAMVLEEIGKVCASTALMLLAQADGMLSIILDGSPALKEKYLPRF--GEKSTLMT 153 + +V EE+ V ST + + +PA+++ + P GEK + Sbjct: 64 LPRLDATLVFEEMAAVDPSTTAFITIHNMATWMLGTWATPAVRDHWGPLLTTGEK---LA 120 Query: 154 AFAATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYT-DPSKGAKG 212 ++ TEPGAGSD ++KTRA G++YVING K FI+ D+L + A T D GA G Sbjct: 121 SYCLTEPGAGSDAASLKTRAELVGNEYVINGAKAFISGAGSTDVLVLMARTGDAQSGASG 180 Query: 213 MSTFVVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALS 272 +S F V PG+ YG E+KMG P + F+++ +PA++L+G EG+GF M L Sbjct: 181 ISAFAVPADAPGISYGKKEQKMGWNSQPTRTISFDNVRIPADHLLGREGEGFKIAMKGLD 240 Query: 273 INRVFCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVR 332 R+ A+ +VG AQGAL A Q+ ++R+QFGKPIA +QF +ADMATE+ AAR +VR Sbjct: 241 GGRINIATCSVGAAQGALNAAQQYMQDRKQFGKPIASFQALQFKLADMATELVAARQMVR 300 Query: 333 KATTLLDAKDKRGPLIGGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLT 392 A + LDA + MAK FA+D V DA+Q+ GG GY++EY +ER++R+A++ Sbjct: 301 LAASKLDAGARDASTYCAMAKRFATDAGFTVINDALQLHGGYGYIREYPLERLLRDARVH 360 Query: 393 QIYTGTNQITRMVTGRSLL 411 QI GTN+I R++ R +L Sbjct: 361 QILEGTNEIMRVIIARRML 379 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: 342 Number of extensions: 7 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: 388 Length adjustment: 31 Effective length of query: 383 Effective length of database: 357 Effective search space: 136731 Effective search space used: 136731 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