Align cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized)
to candidate RR42_RS26910 RR42_RS26910 isovaleryl-CoA dehydrogenase
Query= BRENDA::Q39QF5 (380 letters) >FitnessBrowser__Cup4G11:RR42_RS26910 Length = 393 Score = 246 bits (629), Expect = 6e-70 Identities = 152/382 (39%), Positives = 214/382 (56%), Gaps = 10/382 (2%) Query: 3 HLTEEQKLTLDMVRDVATREIAPRALELDEKSLFPEYARDLFAKLGLLNPLLPAAYGGTE 62 HL E+ + + VR+ A E+APRA E+D FP A LG+L + YGG Sbjct: 10 HLGEDIDMLRETVRNWAQAELAPRAAEIDRTDQFPMDAWKKMGDLGVLGITVAEEYGGAN 69 Query: 63 MGVLTLALILEELGRVCASTALLLIAQTDGMLPIIH-GGSPELKERYLRRFAGESTLLTA 121 MG L + +EE+ R AS L A ++ + IH G+ K RYL + + A Sbjct: 70 MGYLAHMIAMEEISRASASVGLSYGAHSNLCVNQIHRNGTAAQKARYLPKLVS-GDWIGA 128 Query: 122 LAATEPAAGSDLLAMKTRAVRQGDKYVINGQKCFITNGSVADVIVVYAYTDPEKGSKGIS 181 LA +EP AGSD+++MK RA +GD YV+NG K +ITNG DV+VVYA T+P+ G++G++ Sbjct: 129 LAMSEPNAGSDVVSMKLRADFKGDHYVLNGTKMWITNGPDCDVLVVYAKTEPDLGARGMT 188 Query: 182 AFVVEKGTPGLVYGRNESKMGMRGSINSELFFENMEVPAENIIGAEGTGFANLMQTLSTN 241 AF+VEKG G + K+GMRGS EL F+++EVP ENI+G E G LM L Sbjct: 189 AFIVEKGMKGFSVAQKLDKLGMRGSHTGELVFQDVEVPVENILGGENLGAKVLMSGLDYE 248 Query: 242 RVFCAAQAVGIAQGALDIAVRHTQDRVQFGKPIAHLAPVQFMVADMATAVEASRLLTRKA 301 R + VGI Q +D+ + DR QFG+ I +Q VADM T ++A+R Sbjct: 249 RAVLSGGPVGIMQACMDVITPYIHDRKQFGQSIGEFQLIQGKVADMYTTLQAARSYLYTV 308 Query: 302 AELLDDGDKKAVLYGSMAKTMA------SDTAMRVTTDAVQVLGGSGYMKENGVERMMRD 355 + LD K V + K A ++ A + ++VQ+LGG+GY+ E V R+ RD Sbjct: 309 GKNLDSLGKDHV--RQVRKDCAAVILYTAEKATWMAGESVQILGGNGYINEYPVGRLWRD 366 Query: 356 AKLTQIYTGTNQITRMVTGRAL 377 AKL +I GT++I RM+ GR L Sbjct: 367 AKLYEIGAGTSEIRRMLIGREL 388 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: 337 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: 380 Length of database: 393 Length adjustment: 30 Effective length of query: 350 Effective length of database: 363 Effective search space: 127050 Effective search space used: 127050 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 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