Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate N515DRAFT_0941 N515DRAFT_0941 isovaleryl-CoA dehydrogenase
Query= reanno::pseudo3_N2E3:AO353_20350 (387 letters) >FitnessBrowser__Dyella79:N515DRAFT_0941 Length = 385 Score = 500 bits (1288), Expect = e-146 Identities = 246/379 (64%), Positives = 302/379 (79%), Gaps = 2/379 (0%) Query: 8 FALGETIDMLRDQVRAFVSKEIAPRAAQIDIDNLFPADLWRKFGDMGLLGITVPEEYGGA 67 F+LGE +D+LR+ V AF KEIAPRA QID DN+FPADLWRKFG+MGLLG+T+PE YGG Sbjct: 4 FSLGEELDLLRESVHAFAEKEIAPRATQIDHDNVFPADLWRKFGEMGLLGMTIPEAYGGT 63 Query: 68 GLGYLAHVVAMEEISRGSASVALSYGAHSNLCVNQINRNGTHEQKAKYLPKLISGEHIGA 127 GLGYLAH+VAMEEISR S SV LSYGAHSNLCV + NG EQ+ KY+P+L SGE++GA Sbjct: 64 GLGYLAHMVAMEEISRASGSVGLSYGAHSNLCVQNLFHNGNEEQRRKYIPRLCSGEYVGA 123 Query: 128 LAMSEPNAGSDVV-SMKLRADKRGDHYVLNGSKTWITNGPDANTYVIYAKT-DLEKGPHG 185 LAMSEP AGSDVV SM +A+ RGD +V NG+K WITNGPDA+ ++Y +T G Sbjct: 124 LAMSEPGAGSDVVGSMSCKAELRGDVWVANGTKMWITNGPDADVLLVYMRTAPRPAGSRC 183 Query: 186 ITAFIVERDWKGFSRSNKFDKLGMRGSNTCELFFDDVEVPEENILGVLNGGVKVLMSGLD 245 +TAFI+E+ KGFS + K DKLGMRGSNTCEL F+D E+P NI+G +N GV+VLMSGLD Sbjct: 184 MTAFIIEKGMKGFSTAQKLDKLGMRGSNTCELVFEDCEIPAANIVGEVNEGVRVLMSGLD 243 Query: 246 YERVVLSGGPTGIMQACMDLIVPYIHDRKQFGQSIGEFQLIQGKVADMYTQLNASRAYLY 305 ER+VLSGGP G+MQA MDL++PY+ +RKQF IG F ++Q KVADMYT L +SR + Y Sbjct: 244 TERLVLSGGPLGLMQAAMDLVLPYVRERKQFNAPIGTFGMMQAKVADMYTALQSSRGFAY 303 Query: 306 AVAQACERGETTRKDAAGVILYSAERATQMALDAIQILGGNGYINEFPAGRLLRDAKLYE 365 VA+ ++G +R D A +L +++ A ++AL+AIQ LGGNGYINEFPAGRLLRDAKLYE Sbjct: 304 MVAREFDQGSKSRIDPAACLLNASQNAVKVALEAIQALGGNGYINEFPAGRLLRDAKLYE 363 Query: 366 IGAGTSEIRRMLIGRELFN 384 IGAGT+EIRRMLIGREL++ Sbjct: 364 IGAGTNEIRRMLIGRELYH 382 Lambda K H 0.319 0.137 0.400 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: 509 Number of extensions: 18 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: 387 Length of database: 385 Length adjustment: 30 Effective length of query: 357 Effective length of database: 355 Effective search space: 126735 Effective search space used: 126735 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 (21.7 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