Align cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized)
to candidate PfGW456L13_2983 Butyryl-CoA dehydrogenase (EC 1.3.99.2)
Query= BRENDA::Q39QF5 (380 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2983 Length = 375 Score = 268 bits (686), Expect = 1e-76 Identities = 154/373 (41%), Positives = 220/373 (58%), Gaps = 3/373 (0%) Query: 6 EEQKLTLDMVRDVATREIAPRALELDEKSLFPEYARDLFAKLGLLNPLLPAAYGGTEMGV 65 ++Q+ DM RD A + P A E D + FP+ A A LG L+P +GG + G Sbjct: 5 DDQQQIRDMARDFAQERLKPFAAEWDREHRFPKEAIGEMAGLGFFGMLVPEQWGGCDTGY 64 Query: 66 LTLALILEELGRVC-ASTALLLIAQTDGMLPIIHGGSPELKERYLRRFAGESTLLTALAA 124 L A+ LEE+ A + ++ + + G +PI++ G+ E KER+L+ A +L A A Sbjct: 65 LAYAMALEEIAAGDGACSTIMSVHNSVGCVPILNYGTDEQKERFLKPLAS-GAMLGAFAL 123 Query: 125 TEPAAGSDLLAMKTRAVRQGDKYVINGQKCFITNGSVADVIVVYAYTDPEKGSKGISAFV 184 TEP AGSD +KTRA +GD YV+NG K FIT+G A V++V+A TDP G +GISAF+ Sbjct: 124 TEPQAGSDASGLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFI 183 Query: 185 VEKGTPGLVYGRNESKMGMRGSINSELFFENMEVPAENIIGAEGTGFANLMQTLSTNRVF 244 V +PG R E K+G S ++ FE+++VP N +G EG G+ + L RV Sbjct: 184 VPTDSPGYKVARVEDKLGQHASDTCQILFEDVKVPLANRLGEEGEGYRIALANLEGGRVG 243 Query: 245 CAAQAVGIAQGALDIAVRHTQDRVQFGKPIAHLAPVQFMVADMATAVEASRLLTRKAAEL 304 A+Q+VG+A+ A + A + ++R FGKPI V F +ADMAT + +R + AA L Sbjct: 244 IASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAAL 303 Query: 305 LDDGDKKAVLYGSMAKTMASDTAMRVTTDAVQVLGGSGYMKENGVERMMRDAKLTQIYTG 364 D G K A++ SMAK AS+ A +V + A+Q LGG GY+ + VER+ RD ++ QIY G Sbjct: 304 RDSG-KPALVEASMAKLFASEMAEKVCSSALQTLGGYGYLNDFPVERIYRDVRVCQIYEG 362 Query: 365 TNQITRMVTGRAL 377 T+ I RMV R L Sbjct: 363 TSDIQRMVISRNL 375 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: 302 Number of extensions: 15 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: 380 Length of database: 375 Length adjustment: 30 Effective length of query: 350 Effective length of database: 345 Effective search space: 120750 Effective search space used: 120750 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