Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate 3606773 Dshi_0204 acyl-CoA dehydrogenase domain protein (RefSeq)
Query= reanno::pseudo6_N2E2:Pf6N2E2_1146 (375 letters) >FitnessBrowser__Dino:3606773 Length = 564 Score = 205 bits (521), Expect = 3e-57 Identities = 128/384 (33%), Positives = 207/384 (53%), Gaps = 15/384 (3%) Query: 5 EEQTQIRDMARQFAEERLKPFAAEWD-REHRFPREAIDEMAELGFFGMLVPEQWGGCDTG 63 +E IR+ R+F+ ++++P A EW ++ P E I+E+AE+G FG+ +PE++GG Sbjct: 181 DELEMIREQFRRFSVDKVEPHAHEWHLKDELIPMEIIEELAEMGVFGLTIPEEYGGFGLS 240 Query: 64 YLAYAMTLEEIAAGDGACSTIMSVHNSVGCVPILKFGNDEQKAKFLTPLASGAMLGAFAL 123 + + EE++ G ++ + + I+ G +EQK K+L LAS L Sbjct: 241 KASMCVVSEELSRGYIGVGSL-GTRSEIAAELIICGGTEEQKQKWLPRLASAETLPTAVF 299 Query: 124 TEPQAGSDASSLKTRA-RLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDP-SAGKRGISA 181 TEP GSD +L+TRA + E + + G K +IT V+ + A T P + RG+S Sbjct: 300 TEPNTGSDLGALRTRAVQDENGDWKVTGNKTWITHAARTHVMTLLARTKPDTTDHRGLSM 359 Query: 182 FIV---------PTDSPGYSVARVEDKLGQHASDTCQILFEDLKVPVGNRLG-EEGEGYK 231 F+ P + G + +E LG ++ F++ V N LG EEG+G+K Sbjct: 360 FLAEKTPGTDEAPFPTEGMTGGEIE-VLGYRGMKEYELAFDNFHVKGENLLGGEEGKGFK 418 Query: 232 IALANLEGGRVGIAAQAVGMARAAFEAARDYARERSSFGKPIIEHQAVAFRLADMATQIA 291 + E R+ AA+A+G+A++A + + YA +R FGK +I V+ +LA MA +I Sbjct: 419 QLMETFESARIQTAARAIGVAQSALDVSMQYAIDRKQFGKSLINFPRVSGKLAMMAVEIM 478 Query: 292 VARQMVHYAAALRDSGQPALVEASMAKLFASEMAEKVCSMALQTLGGYGYLNDFPLERIY 351 VARQ+ +++A +D G+ VEA MAKL + +A LQ GG G+ ++ + RI Sbjct: 479 VARQLTYFSAFEKDEGRRCDVEAGMAKLLGARVAWAAADNGLQIHGGNGFALEYGISRIL 538 Query: 352 RDVRVCQIYEGTSDIQRMVISRNL 375 D R+ I+EG ++IQ VI+R L Sbjct: 539 CDARILNIFEGAAEIQAQVIARRL 562 Score = 26.2 bits (56), Expect = 0.002 Identities = 16/44 (36%), Positives = 22/44 (50%) Query: 270 GKPIIEHQAVAFRLADMATQIAVARQMVHYAAALRDSGQPALVE 313 G + EHQ + LA +AT RQM +A L+ G+ VE Sbjct: 55 GALVEEHQTASHGLAWLATYAQSLRQMQKWAETLQADGKFGEVE 98 Lambda K H 0.320 0.134 0.388 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: 450 Number of extensions: 25 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 375 Length of database: 564 Length adjustment: 33 Effective length of query: 342 Effective length of database: 531 Effective search space: 181602 Effective search space used: 181602 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: 51 (24.3 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