Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 3/3) (EC 1.3.1.109); short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate N515DRAFT_0941 N515DRAFT_0941 isovaleryl-CoA dehydrogenase
Query= BRENDA::Q18AQ1 (378 letters) >FitnessBrowser__Dyella79:N515DRAFT_0941 Length = 385 Score = 278 bits (712), Expect = 1e-79 Identities = 144/373 (38%), Positives = 232/373 (62%), Gaps = 2/373 (0%) Query: 6 KKYQMLKELYVSFAENEVKPLATELDEEERFPYETVEKMAKAGMMGIPYPKEYGGEGGDT 65 ++ +L+E +FAE E+ P AT++D + FP + K + G++G+ P+ YGG G Sbjct: 8 EELDLLRESVHAFAEKEIAPRATQIDHDNVFPADLWRKFGEMGLLGMTIPEAYGGTGLGY 67 Query: 66 VGYIMAVEELSRVCGTTGVILSAHTSLGSWPIYQYGNEEQKQKFLRPLASGEKLGAFGLT 125 + +++A+EE+SR G+ G+ AH++L ++ GNEEQ++K++ L SGE +GA ++ Sbjct: 68 LAHMVAMEEISRASGSVGLSYGAHSNLCVQNLFHNGNEEQRRKYIPRLCSGEYVGALAMS 127 Query: 126 EPNAGTDASGQQTT-AVLDGDEYILNGSKIFITNAIAGDIYVV-MAMTDKSKGNKGISAF 183 EP AG+D G + A L GD ++ NG+K++ITN D+ +V M + G++ ++AF Sbjct: 128 EPGAGSDVVGSMSCKAELRGDVWVANGTKMWITNGPDADVLLVYMRTAPRPAGSRCMTAF 187 Query: 184 IVEKGTPGFSFGVKEKKMGIRGSATSELIFEDCRIPKENLLGKEGQGFKIAMSTLDGGRI 243 I+EKG GFS K K+G+RGS T EL+FEDC IP N++G+ +G ++ MS LD R+ Sbjct: 188 IIEKGMKGFSTAQKLDKLGMRGSNTCELVFEDCEIPAANIVGEVNEGVRVLMSGLDTERL 247 Query: 244 GIAAQALGLAQGALDETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVYQAAI 303 ++ LGL Q A+D + YV+ER QF P+ F Q ++ADM +Q++R Y A Sbjct: 248 VLSGGPLGLMQAAMDLVLPYVRERKQFNAPIGTFGMMQAKVADMYTALQSSRGFAYMVAR 307 Query: 304 NKDLGKPYGVEAAMAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITEIYEG 363 D G ++ A L A++ A++V +A+Q GG GY ++P R++RDAK+ EI G Sbjct: 308 EFDQGSKSRIDPAACLLNASQNAVKVALEAIQALGGNGYINEFPAGRLLRDAKLYEIGAG 367 Query: 364 TSEVQRMVISGKL 376 T+E++RM+I +L Sbjct: 368 TNEIRRMLIGREL 380 Lambda K H 0.315 0.133 0.373 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: 360 Number of extensions: 16 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: 378 Length of database: 385 Length adjustment: 30 Effective length of query: 348 Effective length of database: 355 Effective search space: 123540 Effective search space used: 123540 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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