Align 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized)
to candidate HSERO_RS12750 HSERO_RS12750 acyl-CoA dehydrogenase
Query= reanno::pseudo3_N2E3:AO353_25680 (375 letters) >FitnessBrowser__HerbieS:HSERO_RS12750 Length = 386 Score = 315 bits (806), Expect = 2e-90 Identities = 165/371 (44%), Positives = 238/371 (64%), Gaps = 3/371 (0%) Query: 6 EQLQISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTGYL 65 +QL +AR FA + PFAA+WD E FP + I + ELGF G+ PE GG L Sbjct: 8 DQLAFQQSARDFAAGEMAPFAAKWDEEAHFPLDVIAKAGELGFCGLYTPEADGGLGLSRL 67 Query: 66 AYAMALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAFALTE 125 + EE+A + + +++HN V + I +G K ++ + LA+G +G++ LTE Sbjct: 68 DATVVFEELARACTSTAAYLTIHNMVSWM-IASWGQPSLKAQWCEQLAAGRKIGSYCLTE 126 Query: 126 PQAGSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFIVP 185 P +GSDA+SLKT ARL HYVLNG K FI+ + V++V A T G RG+SA +VP Sbjct: 127 PGSGSDAASLKTTARLEDGHYVLNGSKAFISGAGSTDVLVVMARTG-GEGARGVSAIVVP 185 Query: 186 TDSPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGEEGEGYKIALANLEGGRVGIA 245 ++PG + E K+G ++ T I F++V+VP + LG+EG+G+ A+ L+GGR+ IA Sbjct: 186 GNAPGVSYGKKESKMGWNSQPTRTISFDNVKVPADHLLGQEGQGFIFAMKGLDGGRINIA 245 Query: 246 SQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALRD 305 + SVG A+AA +AA Y +ER+ FG+PI + QA+ F+LADM T++ ARQMV AA D Sbjct: 246 TCSVGAAQAALDAAHAYMKERKQFGRPIADFQALQFKLADMQTELVAARQMVRLAATKLD 305 Query: 306 SGKP-ALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIYEGTS 364 +G P A +MAK A+++ +VC+ ALQ GGYGY+ ++PLER +RDVRV QI EGT+ Sbjct: 306 AGSPEATTYCAMAKRLATDLGFRVCNEALQLHGGYGYIREYPLERYFRDVRVHQILEGTN 365 Query: 365 DIQRMVISRNL 375 +I R++ISR L Sbjct: 366 EIMRVIISRKL 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: 375 Number of extensions: 18 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: 386 Length adjustment: 30 Effective length of query: 345 Effective length of database: 356 Effective search space: 122820 Effective search space used: 122820 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