Align cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized)
to candidate AO356_01580 AO356_01580 isovaleryl-CoA dehydrogenase
Query= BRENDA::Q39QF5 (380 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_01580 Length = 387 Score = 246 bits (628), Expect = 8e-70 Identities = 153/379 (40%), Positives = 218/379 (57%), Gaps = 21/379 (5%) Query: 11 TLDMVRD----VATREIAPRALELDEKSLFPEYARDLFAKLGLLNPLLPAAYGGTEMGVL 66 T+DM+RD E+APRA ++D +LFP F +GLL +P YGG +G L Sbjct: 13 TIDMLRDQVQAFVKAELAPRAAQIDIDNLFPADMWRKFGDMGLLGITVPEEYGGAGLGYL 72 Query: 67 TLALILEELGRVCASTALLLIAQTDGMLPIIH-GGSPELKERYLRRF-AGESTLLTALAA 124 + +EE+ R AS AL A ++ + I+ G+ E K +YL + +GE + ALA Sbjct: 73 AHVVAMEEISRGSASVALSYGAHSNLCVNQINRNGNHEQKTKYLPKLISGEH--IGALAM 130 Query: 125 TEPAAGSDLLAMKTRAVRQGDKYVINGQKCFITNGSVADVIVVYAYTDPEKGSKGISAFV 184 +EP AGSD+++MK RA ++GD YV+NG K +ITNG A+ V+YA TD EKG GI+AF+ Sbjct: 131 SEPNAGSDVVSMKLRADKRGDHYVLNGSKTWITNGPDANTYVIYAKTDLEKGPHGITAFI 190 Query: 185 VEKGTPGLVYGRNESKMGMRGSINSELFFENMEVPAENIIGAEGTGFANLMQTLSTNRVF 244 VE+ G K+GMRGS ELFF+++EVP ENI+GA G LM L RV Sbjct: 191 VERDWKGFSRSNKFDKLGMRGSNTCELFFDDVEVPEENILGALNGGVKVLMSGLDYERVV 250 Query: 245 CAAQAVGIAQGALDIAVRHTQDRVQFGKPIAHLAPVQFMVADMATAVEASRLLTRKAAEL 304 + GI Q +D+ V + DR QFG+ I +Q VADM T + ASR A+ Sbjct: 251 LSGGPTGIMQACMDLIVPYIHDRKQFGQSIGEFQLIQGKVADMYTQLNASRAYLYAVAQA 310 Query: 305 LDDGDKK------AVLYGSMAKTMASDTAMRVTTDAVQVLGGSGYMKENGVERMMRDAKL 358 + G+ +LY +++ A ++ DA+Q+LGG+GY+ E R++RDAKL Sbjct: 311 CERGETTRKDAAGVILY-------SAERATQMALDAIQILGGNGYINEFPAGRLLRDAKL 363 Query: 359 TQIYTGTNQITRMVTGRAL 377 +I GT++I RM+ GR L Sbjct: 364 YEIGAGTSEIRRMLIGREL 382 Lambda K H 0.319 0.134 0.371 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: 329 Number of extensions: 10 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 380 Length of database: 387 Length adjustment: 30 Effective length of query: 350 Effective length of database: 357 Effective search space: 124950 Effective search space used: 124950 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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 Apr 09 2024. 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