Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate 14185 b0039 crotonobetaine reductase subunit II, FAD-binding (NCBI)
Query= reanno::pseudo6_N2E2:Pf6N2E2_2191 (387 letters) >FitnessBrowser__Keio:14185 Length = 380 Score = 172 bits (435), Expect = 2e-47 Identities = 108/354 (30%), Positives = 171/354 (48%), Gaps = 3/354 (0%) Query: 34 AQIDIDNLFPADMWRKFGDMGLLGITVPEEYGGAGLGYLAHVVAMEEISRGSASVALSYG 93 A+ D D+++P + DMG+ + +PEE+GG G++ E+ R A + Y Sbjct: 30 AECDRDSVYPERFVKALADMGIDSLLIPEEHGGLDAGFVTLAAVWMELGRLGAPTYVLYQ 89 Query: 94 AHSNLCVNQINRNGNHEQKTKYLPKLISGEHIGALAMSEPNAGSDVVSMKLRADKRGDKY 153 N R G EQ K + +G+ + A++EP AGSDV S+K +R K Sbjct: 90 LPGGF--NTFLREGTQEQIDKIMAFRGTGKQMWNSAITEPGAGSDVGSLKTTYTRRNGKI 147 Query: 154 VLNGSKTWITNGPDANTYVIYAKTDLEKGPHGITAFIVERDWKGFSRSNKFDKLGMRGSN 213 LNGSK +IT+ V+ A+ T + V+ G + K +KLG+R + Sbjct: 148 YLNGSKCFITSSAYTPYIVVMARDGASPDKPVYTEWFVDMSKPGI-KVTKLEKLGLRMDS 206 Query: 214 TCELFFDDVEVPEDNILGALNGGVKVLMSGLDYERVVLSGGPTGIMQACMDLIVPYIHDR 273 CE+ FDDVE+ E ++ G G + D+ER +++ G + Y + R Sbjct: 207 CCEITFDDVELDEKDMFGREGNGFNRVKEEFDHERFLVALTNYGTAMCAFEDAARYANQR 266 Query: 274 KQFGQSIGEFQLIQGKVADMYTQLNASRAYLYAVAQACERGETTRKDAAGVILYSAERAT 333 QFG++IG FQLIQ K A M +LN+ + LY A + G T DAA + A A Sbjct: 267 VQFGEAIGRFQLIQEKFAHMAIKLNSMKNMLYEAAWKADNGTITSGDAAMCKYFCANAAF 326 Query: 334 QMALDAIQILGGNGYINEFPAGRLLRDAKLYEIGAGTSEIRRMLIGRELFNETR 387 ++ A+Q+LGG G R RD ++ + G+ E++ + +GR + + R Sbjct: 327 EVVDSAMQVLGGVGIAGNHRISRFWRDLRVDRVSGGSDEMQILTLGRAVLKQYR 380 Lambda K H 0.318 0.137 0.398 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: 370 Number of extensions: 16 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: 380 Length adjustment: 30 Effective length of query: 357 Effective length of database: 350 Effective search space: 124950 Effective search space used: 124950 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