Align 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized)
to candidate WP_057507563.1 ABB28_RS04915 acyl-CoA dehydrogenase
Query= reanno::pseudo3_N2E3:AO353_25680 (375 letters) >NCBI__GCF_001431535.1:WP_057507563.1 Length = 388 Score = 305 bits (782), Expect = 1e-87 Identities = 170/372 (45%), Positives = 234/372 (62%), Gaps = 3/372 (0%) Query: 5 DEQLQISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTGY 64 + Q +AAR FAQ L P AA WD E FP+EAI + ELGF G+ + + GG Sbjct: 11 EAQQAYREAARDFAQAELAPHAARWDAEGIFPREAIAKAGELGFCGLYMDPEVGGSGLSR 70 Query: 65 LAYAMALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAFALT 124 L A+ +EE+A D + + +S+HN + + +G + + LA+G L ++ LT Sbjct: 71 LDAAVVIEELANVDPSTAAYVSIHNMASWM-VSTWGQQALRAAWGADLAAGIRLASYCLT 129 Query: 125 EPQAGSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFIV 184 EP AGSDA+SLKT A +GD YVLNG K FI SG A ++V AG GISA V Sbjct: 130 EPGAGSDAASLKTTAVRDGDDYVLNGSKAFI-SGAGATELLVVMARTGGAGAGGISAIAV 188 Query: 185 PTDSPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGEEGEGYKIALANLEGGRVGI 244 P D PG R E+K+G ++ T I FE+V+VPV N LGEEG G+K+A+ L+GGR+ I Sbjct: 189 PADLPGISYGRKEEKMGWNSQPTRGITFENVRVPVGNLLGEEGGGFKLAMKGLDGGRINI 248 Query: 245 ASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALR 304 A+ S+G A+ A +AAR Y ER FGK + E QA+ F+LADMA ++ ARQMVH AA Sbjct: 249 AACSLGAAQGALDAARRYMGERRQFGKALAEFQALQFKLADMAIELVAARQMVHTAARKL 308 Query: 305 DSG-KPALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIYEGT 363 D+G A V +MAK FA++ +C+ ALQ GGYGY+ ++P+ER+ RD RV QI EGT Sbjct: 309 DAGASDANVWCAMAKRFATDAGFTICNEALQIHGGYGYIREYPIERLLRDSRVHQILEGT 368 Query: 364 SDIQRMVISRNL 375 ++I R++++R+L Sbjct: 369 NEIMRVIVARHL 380 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: 361 Number of extensions: 17 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 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