Align 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized)
to candidate GFF928 HP15_907 acyl-CoA dehydrogenase domain protein
Query= reanno::pseudo3_N2E3:AO353_25680 (375 letters) >FitnessBrowser__Marino:GFF928 Length = 388 Score = 318 bits (816), Expect = 1e-91 Identities = 163/374 (43%), Positives = 244/374 (65%), Gaps = 3/374 (0%) Query: 4 TDEQLQISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTG 63 T++QL +AAR FA++ + P AA+WD EH FP + + E E+GF GM PE GG Sbjct: 6 TEDQLAFREAARAFAEKSMAPHAAKWDNEHIFPVDMMKEAGEMGFMGMYTPEALGGMGLS 65 Query: 64 YLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAFAL 123 L ++ +EE+AA + + +++HN + + F +DD K+ + LASG L ++ L Sbjct: 66 RLDTSVIVEELAAACPSTAAFITIHNMATWM-VASFASDDLKQEIVPKLASGEWLASYCL 124 Query: 124 TEPQAGSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTD-PSAGKRGISAF 182 TEP AGSDA+SL+T+A +GD YV+NG K FI+ ++++ A T P +G +GIS F Sbjct: 125 TEPGAGSDAASLRTKAVRDGDSYVINGSKVFISGAGATDILVLMARTGAPDSGYKGISTF 184 Query: 183 IVPTDSPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGEEGEGYKIALANLEGGRV 242 ++P D+ G + E+K+G H+ T I E+V++P +NR+G+EG+G+ IA+ L+GGR+ Sbjct: 185 VIPADADGISYGKNEEKMGWHSQPTRMISLENVRIPASNRVGDEGDGFAIAMKGLDGGRL 244 Query: 243 GIASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAA 302 IA+ S+G A+AA AR+Y ERE FGKP+ QA+ F+LADMAT + ARQMV A Sbjct: 245 NIATCSLGGAQAALLRARNYMHEREQFGKPLAAFQALQFKLADMATNLVAARQMVRLGAF 304 Query: 303 LRDSGKP-ALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIYE 361 D+ P A + +MAK FA++ +V + ALQ GGYGY+ ++PLER RD+RV QI E Sbjct: 305 KLDNADPEATLHCAMAKRFATDACFEVVNEALQLHGGYGYIREYPLERYLRDLRVHQILE 364 Query: 362 GTSDIQRMVISRNL 375 GT++I R++++R L Sbjct: 365 GTNEIMRLIVARRL 378 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: 366 Number of extensions: 11 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: 388 Length adjustment: 30 Effective length of query: 345 Effective length of database: 358 Effective search space: 123510 Effective search space used: 123510 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