Align 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized)
to candidate AZOBR_RS22300 AZOBR_RS22300 acyl-CoA dehydrogenase
Query= reanno::pseudo3_N2E3:AO353_25680 (375 letters) >FitnessBrowser__azobra:AZOBR_RS22300 Length = 377 Score = 526 bits (1356), Expect = e-154 Identities = 261/372 (70%), Positives = 313/372 (84%) Query: 4 TDEQLQISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTG 63 T+EQ + D AR FA ERL P AAE DR FPKE + EM LG GMLVPE++ G T Sbjct: 4 TEEQRMVRDMARDFAAERLAPTAAERDRTGAFPKEELAEMGRLGLMGMLVPEEFDGAGTD 63 Query: 64 YLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAFAL 123 ++AYA+A+EEIAAGDGA STIMSVHNSVGC+PILKFG+ +QKERFLKP+A G LG F L Sbjct: 64 HIAYALAIEEIAAGDGAISTIMSVHNSVGCMPILKFGSAEQKERFLKPMARGEQLGCFCL 123 Query: 124 TEPQAGSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFI 183 TEPQAGSDA+++KTRAR +G+H+VLNG KQFITSG+NA V IVFAV+DP AGK+GI+AF+ Sbjct: 124 TEPQAGSDAAAIKTRARRDGNHWVLNGTKQFITSGKNADVAIVFAVSDPEAGKKGITAFV 183 Query: 184 VPTDSPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGEEGEGYKIALANLEGGRVG 243 VPTD+PG++VARVE+KLGQ SDTCQI+ ED ++P LG EG GY++ALANLEGGR+G Sbjct: 184 VPTDTPGFQVARVEEKLGQSCSDTCQIVLEDCRIPADLMLGAEGGGYRVALANLEGGRIG 243 Query: 244 IASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAAL 303 IASQSVGMARAA + A YA+ER+S G PII+HQAVAFRLADMAT++ ARQ+V +AA+L Sbjct: 244 IASQSVGMARAALDHATRYAQERQSMGLPIIQHQAVAFRLADMATKVEAARQLVLHAASL 303 Query: 304 RDSGKPALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIYEGT 363 RD+G+P L EA+MAKLFASE+AE+VCS A+Q GGYGYL+DFP+ERIYRDVRVCQIYEGT Sbjct: 304 RDAGEPCLKEAAMAKLFASEIAERVCSDAIQIHGGYGYLNDFPVERIYRDVRVCQIYEGT 363 Query: 364 SDIQRMVISRNL 375 SDIQR+VISR L Sbjct: 364 SDIQRLVISRAL 375 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: 478 Number of extensions: 14 Number of successful extensions: 1 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: 377 Length adjustment: 30 Effective length of query: 345 Effective length of database: 347 Effective search space: 119715 Effective search space used: 119715 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