Align 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized)
to candidate 5209191 Shew_1669 butyryl-CoA dehydrogenase (RefSeq)
Query= reanno::pseudo3_N2E3:AO353_25680 (375 letters) >FitnessBrowser__PV4:5209191 Length = 385 Score = 326 bits (836), Expect = 6e-94 Identities = 170/372 (45%), Positives = 242/372 (65%), Gaps = 3/372 (0%) Query: 5 DEQLQISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTGY 64 ++Q Q ++ A QFAQE L PFAA+WD EH FPK+ I + ELGF + PE GG Sbjct: 7 EDQRQFAELATQFAQEELAPFAAKWDEEHHFPKDVIQKAGELGFCSLYSPESEGGMGLSR 66 Query: 65 LAYAMALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAFALT 124 L ++ E++A G A + ++++HN + + FG+ ++ + + L +G L ++ LT Sbjct: 67 LDSSIIFEQLAMGCTATTAMLTIHNMATWM-VTSFGSQTLRDEWSEALTTGNKLASYCLT 125 Query: 125 EPQAGSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFIV 184 E AGSDA+SLKT+A GD YV++G K FI+ + +++V T AG +GISA + Sbjct: 126 EAGAGSDAASLKTKAVREGDEYVISGAKMFISGAGSTELLVVMCRTG-DAGPKGISAIAI 184 Query: 185 PTDSPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGEEGEGYKIALANLEGGRVGI 244 P D+ G + EDK+G +A T +I F+ V+VPV N LGEEG+G+ A+ L+GGR+ I Sbjct: 185 PADAAGISYGKAEDKMGWNAQPTREITFDKVRVPVTNLLGEEGQGFTFAMKGLDGGRINI 244 Query: 245 ASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALR 304 A+ SVG A+AA E A+ Y ER+ FGKPI QA+ F+LADMAT++ ARQMV AA Sbjct: 245 ATCSVGTAQAALERAQQYMNERQQFGKPIAAFQALQFKLADMATELVAARQMVRLAAFKL 304 Query: 305 DSGKP-ALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIYEGT 363 DSG P A +MAK FA+++ VC +ALQ GGYGY+ ++PLER +RDVRV QI EGT Sbjct: 305 DSGDPEATAYCAMAKRFATDVGFNVCDSALQLHGGYGYIREYPLERHFRDVRVHQILEGT 364 Query: 364 SDIQRMVISRNL 375 ++I R++I+R L Sbjct: 365 NEIMRLIIARRL 376 Lambda K H 0.319 0.134 0.389 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: 381 Number of extensions: 12 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: 375 Length of database: 385 Length adjustment: 30 Effective length of query: 345 Effective length of database: 355 Effective search space: 122475 Effective search space used: 122475 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 (21.8 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