Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate WP_084199172.1 C0029_RS09065 acyl-CoA dehydrogenase
Query= reanno::psRCH2:GFF2397 (379 letters) >NCBI__GCF_002869505.1:WP_084199172.1 Length = 378 Score = 269 bits (687), Expect = 1e-76 Identities = 143/377 (37%), Positives = 216/377 (57%), Gaps = 1/377 (0%) Query: 2 LPNEDQNAIAEMARQFAQERLKPFAEQWSREHRYPAEAIGEMAALGFFGMLVPEQWGGSD 61 + NE+ +MAR+ ++ ++P E W +H P E + A G +PE +GG+ Sbjct: 1 MDNEELTLFRDMARRAYEQEIEPHYEGWEEQHLVPRELWNTLGAAGLLCPDMPEAYGGAG 60 Query: 62 TGYLAYAMALEEIAA-GDGACSTIMSVHNSVGCVPILRFGNEQQKSDFLTPLARGEQIGA 120 T +EE++ G G ++ +H+++ I FG E+QK +L + GE +GA Sbjct: 61 TSPRVCLAMIEEMSRMGFGGLASGYGIHSNIVAPYINHFGTEEQKQQWLPKMITGEAVGA 120 Query: 121 FALTEPQAGSDASSLRTRARRDGDHYVLNGAKQFITSGKHAGTVIVFAVTDPDAGKGGIS 180 A+TEP AGSD +RT A RDG+ +VLNG+K FIT+G HA VIV A+TDP G G S Sbjct: 121 LAMTEPGAGSDVQGIRTTAVRDGEEWVLNGSKIFITNGIHADLVIVAAITDPGKGAKGTS 180 Query: 181 AFIVPTDSPGYQVVRVEDKLGQHASDTCQIAFEDLRVPVANRLGEEGEGYRIALANLEGG 240 F+V PG++ +K+GQHASDT ++ F+D+R+P + LGEE +G+ I + L Sbjct: 181 LFLVDASLPGFEKGNKIEKIGQHASDTAELFFQDVRLPASALLGEENKGFVIMMTELPRE 240 Query: 241 RIGIAAQAVGMARAAFEAARDYARDRETFGKPIIEHQAVAFRLADMATQIAVARQMVHHA 300 R+GIAAQAV A A + DY +R+ FG+ + Q F LA++ T+IA+ R + Sbjct: 241 RLGIAAQAVAAAEGAMDITVDYVLERKAFGQTVASFQNTRFTLAEVKTEIALNRALYEKC 300 Query: 301 AALREVGRPALVEASMAKLFASEMAEKVCSAAIQTLGGYGYLADFPVERIYRDVRVCQIY 360 A G +A+M K +EM +Q GGYGY A++P+ R Y D R+ +IY Sbjct: 301 ADDYARGELTADDAAMLKYANTEMQCSTIDQCLQLFGGYGYTAEYPISRYYTDARIQRIY 360 Query: 361 EGTSDIQRLVISRNLGG 377 GTS+I R +++R++ G Sbjct: 361 GGTSEIMRELVARSILG 377 Lambda K H 0.320 0.135 0.391 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: 379 Number of extensions: 15 Number of successful extensions: 2 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: 379 Length of database: 378 Length adjustment: 30 Effective length of query: 349 Effective length of database: 348 Effective search space: 121452 Effective search space used: 121452 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 24 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