Align isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate GFF1029 HP15_1008 acyl-CoA dehydrogenase domain protein
Query= BRENDA::P26440 (426 letters) >FitnessBrowser__Marino:GFF1029 Length = 383 Score = 249 bits (636), Expect = 1e-70 Identities = 144/375 (38%), Positives = 214/375 (57%), Gaps = 5/375 (1%) Query: 47 EEQRQLRQTMAKFLQEHLAPKAQEIDRSNEFKNLREFWKQLGNLGVLGITAPVQYGGSGL 106 EE R ++ K L++ + P + ++S RE W LGN G+L + P ++GG G Sbjct: 8 EELAMFRDSVIKVLEKEVTPHYEAWEKSGLVP--RELWNTLGNAGMLCVDVPEEWGGIGA 65 Query: 107 GYLEHVLVMEEISRAS-GAVGLSYGAHSNLCINQLVRNGNEAQKEKYLPKLISGEYIGAL 165 + V+V EE++R GA+ + HS++ L GNE Q++++LPKL+SGE +GA+ Sbjct: 66 PFQFSVVVGEELARMGFGALSTNVMVHSDIVAPYLSHMGNEEQRQQWLPKLVSGEAVGAI 125 Query: 166 AMSEPNAGSDVVSMKLKAEKKGNHYILNGNKFWITNGPDADVLIVYAKTDLAAVPASRGI 225 AM+EP AGSD+ +++ A K G+ YILNG+K +ITNG AD++IV AKTD A +RGI Sbjct: 126 AMTEPGAGSDLQAIRTSAVKDGDEYILNGSKTFITNGQHADMVIVAAKTDPKA--GARGI 183 Query: 226 TAFIVEKGMPGFSTSKKLDKLGMRGSNTCELIFEDCKIPAANILGHENKGVYVLMSGLDL 285 + F+V+ +PGFS + LDK+G +T EL F D +IPA+ +LG E +G LM L Sbjct: 184 SLFLVDTSLPGFSKGRNLDKIGQHSGDTSELFFSDMRIPASALLGEEGQGFVYLMKELPR 243 Query: 286 ERLVLAGGPLGLMQAVLDHTIPYLHVREAFGQKIGHFQLMQGKMADMYTRLMACRQYVYN 345 ERLV+ + + LD TI Y RE FGQK+ Q + ++A M T + +V Sbjct: 244 ERLVIGALGVAAARGSLDLTIAYAQERELFGQKLAQLQNTRFEIARMETDYRVNKAFVDQ 303 Query: 346 VAKACDEGHCTAKDCAGVILYSAECATQVALDGIQCFGGNGYINDFPMGRFLRDAKLYEI 405 D G A + + E +VA +Q FGG GY ++P+ R DA++ I Sbjct: 304 CIDQYDLGELDAPTASMAKYSATEMQCRVADGCLQLFGGYGYTTEYPISRAFIDARVQRI 363 Query: 406 GAGTSEVRRLVIGRA 420 GTSEV + +I R+ Sbjct: 364 YGGTSEVMKEIIARS 378 Lambda K H 0.321 0.137 0.410 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: 377 Number of extensions: 20 Number of successful extensions: 3 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: 426 Length of database: 383 Length adjustment: 31 Effective length of query: 395 Effective length of database: 352 Effective search space: 139040 Effective search space used: 139040 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