Align Branched-chain acyl-CoA dehydrogenase (EC 1.3.99.12) (characterized)
to candidate GFF928 HP15_907 acyl-CoA dehydrogenase domain protein
Query= reanno::ANA3:7025618 (385 letters) >FitnessBrowser__Marino:GFF928 Length = 388 Score = 540 bits (1391), Expect = e-158 Identities = 261/387 (67%), Positives = 319/387 (82%), Gaps = 2/387 (0%) Query: 1 MDFNFNEDQRQFADLARQFAADELAPFAAKWDEEHHFPKDVIQKAGELGFCSLYSPESEG 60 MDFN EDQ F + AR FA +AP AAKWD EH FP D++++AGE+GF +Y+PE+ G Sbjct: 1 MDFNLTEDQLAFREAARAFAEKSMAPHAAKWDNEHIFPVDMMKEAGEMGFMGMYTPEALG 60 Query: 61 GMGLSRLDASIIFEELSKGCTATTAMLTIHNMATWMVTTWGTDTLRQAWSEPLTTGQMLA 120 GMGLSRLD S+I EEL+ C +T A +TIHNMATWMV ++ +D L+Q L +G+ LA Sbjct: 61 GMGLSRLDTSVIVEELAAACPSTAAFITIHNMATWMVASFASDDLKQEIVPKLASGEWLA 120 Query: 121 SYCLTEPGAGSDAASLQTKAVREGDEYVVSGSKMFISGAGSTELLVVMCRTG--QAGPKG 178 SYCLTEPGAGSDAASL+TKAVR+GD YV++GSK+FISGAG+T++LV+M RTG +G KG Sbjct: 121 SYCLTEPGAGSDAASLRTKAVRDGDSYVINGSKVFISGAGATDILVLMARTGAPDSGYKG 180 Query: 179 ISAIAIPADSEGIIYGKAEDKMGWNAQPTRLVTFDNVRVPVANLLGEEGQGFTFAMKGLD 238 IS IPAD++GI YGK E+KMGW++QPTR+++ +NVR+P +N +G+EG GF AMKGLD Sbjct: 181 ISTFVIPADADGISYGKNEEKMGWHSQPTRMISLENVRIPASNRVGDEGDGFAIAMKGLD 240 Query: 239 GGRINIATCSVGTAQAALERATQYMNERQQFGKPLAAFQALQFKLADMATELVAARQMVR 298 GGR+NIATCS+G AQAAL RA YM+ER+QFGKPLAAFQALQFKLADMAT LVAARQMVR Sbjct: 241 GGRLNIATCSLGGAQAALLRARNYMHEREQFGKPLAAFQALQFKLADMATNLVAARQMVR 300 Query: 299 LAAFKLDSGDPEATAYCAMAKRFATDVGFQVCDAALQIHGGYGYIREYPLERHFRDVRVH 358 L AFKLD+ DPEAT +CAMAKRFATD F+V + ALQ+HGGYGYIREYPLER+ RD+RVH Sbjct: 301 LGAFKLDNADPEATLHCAMAKRFATDACFEVVNEALQLHGGYGYIREYPLERYLRDLRVH 360 Query: 359 QILEGTNEIMRLIIARRLLDENAGQIL 385 QILEGTNEIMRLI+ARRLLD+ + + Sbjct: 361 QILEGTNEIMRLIVARRLLDDGVAEAI 387 Lambda K H 0.320 0.134 0.396 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: 10 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: 385 Length of database: 388 Length adjustment: 30 Effective length of query: 355 Effective length of database: 358 Effective search space: 127090 Effective search space used: 127090 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