Align cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized)
to candidate BPHYT_RS25400 BPHYT_RS25400 butyryl-CoA dehydrogenase
Query= BRENDA::Q39QF5 (380 letters) >FitnessBrowser__BFirm:BPHYT_RS25400 Length = 381 Score = 248 bits (633), Expect = 2e-70 Identities = 145/375 (38%), Positives = 211/375 (56%), Gaps = 4/375 (1%) Query: 4 LTEEQKLTLDMVRDVATREIAPRALELDEKSLFPEYARDLFAKLGLLNPLLPAAYGGTEM 63 LTE+Q L D R VA IAP A E D +S +P A+LG L L+P YGG+ Sbjct: 9 LTEQQTLIRDTARRVANEIIAPTAAERDLQSAWPRSELKALAELGFLGMLIPEQYGGSGA 68 Query: 64 GVLTLALILEELGRVCASTALLLIAQTDGMLPIIHGGSPELKERYLRRFA-GESTLLTAL 122 G+L + E V A A ++ L I+ G+ K+RYL A GES + A Sbjct: 69 GILDFCIAQHEFAAVDAGLATIMHVHNFTALTIVEHGTETQKQRYLPAMACGES--IGAF 126 Query: 123 AATEPAAGSDLLAMKTRAVRQGDKYVINGQKCFITNGSVADVIVVYAYTDPEKGSKGISA 182 TEP AGSD +++ A R+GD YV+NG K FI+NGS A V + +A TD G +G S Sbjct: 127 LLTEPHAGSDTASLRASARREGDHYVLNGTKQFISNGSEAGVGIAFAITDKAAGKRGAST 186 Query: 183 FVVEKGTPGLVYGRNESKMGMRGSINSELFFENMEVPAENIIGAEGTGFANLMQTLSTNR 242 F+++ PG R ESK+G + +++ E VPAEN++G EG G+ +M +S R Sbjct: 187 FIIDPNAPGYSVTRIESKLGQHTAHTAQIALEGYRVPAENLLGLEGDGYRTVMAGVSDGR 246 Query: 243 VFCAAQAVGIAQGALDIAVRHTQDRVQFGKPIAHLAPVQFMVADMATAVEASRLLTRKAA 302 + A + G+A+GALD AV++ ++R +G P+ L V F +ADMA V+ + AA Sbjct: 247 IGIAFISAGVARGALDAAVKYAREREAYGGPLTKLQAVAFDLADMAAQVDVAWQYCLHAA 306 Query: 303 ELLDDGDKKAVLYGSMAKTMASDTAMRVTTDAVQVLGGSGYMKENGVERMMRDAKLTQIY 362 L D G + S+AK AS+ A +V +DA+Q+ GG GY+ + VER +RD ++ +IY Sbjct: 307 RLRDAG-FDCIKEASIAKLFASEIAEKVCSDALQIHGGYGYLTDFPVERYLRDVRICKIY 365 Query: 363 TGTNQITRMVTGRAL 377 GT+ I +++ R L Sbjct: 366 EGTSHIQKLIISRNL 380 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: 330 Number of extensions: 11 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: 381 Length adjustment: 30 Effective length of query: 350 Effective length of database: 351 Effective search space: 122850 Effective search space used: 122850 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