Align D-alanine dehydrogenase (EC 1.4.99.-) (characterized)
to candidate H281DRAFT_02794 H281DRAFT_02794 D-amino acid dehydrogenase small subunit (EC 1.4.99.1)
Query= reanno::acidovorax_3H11:Ac3H11_4848 (445 letters) >FitnessBrowser__Burk376:H281DRAFT_02794 Length = 403 Score = 228 bits (580), Expect = 3e-64 Identities = 149/419 (35%), Positives = 215/419 (51%), Gaps = 26/419 (6%) Query: 5 VLGAGIIGISTAWHLLERGHEVIVIDRQPDAALETSFANAAQISVSYCEPWANREAPLKA 64 ++GAGI G++TA L + GH V V +R AA+ETSFAN Q+S S E W + LK Sbjct: 6 IIGAGITGVTTAHALAQCGHHVTVFERHRYAAMETSFANGGQLSASNAEVWNSMATVLKG 65 Query: 65 LKWMFDKEAPLLFRPQMDWQQWRWGLQFLAQCNDTAFERNVQQIVALGAYSHAALKDLVG 124 L+WMF ++APLL P W ++ W +FL Q + N + V L + L + Sbjct: 66 LRWMFMRDAPLLLNPVPTWHKYSWMGEFLRQI--PHYRANTVETVRLAIAAREHLFSIAE 123 Query: 125 TTGIEYNRLERGIAHFYTDQKSFDAAGHAVELMRKHGVQRRLVSRDELLQIEPAFRAYGD 184 GI+++ RGI H Y +K FDAA +L+R+ G++R V+ E+ +IEP +GD Sbjct: 124 QEGIDFDLERRGILHVYKTRKEFDAAAKVNDLLREGGLERSAVTASEVQRIEPTL--HGD 181 Query: 185 KITGGTYTSTDESGDARVFTQELARRCIARGAQFLYGHDVLRLNKIGNAIDSVAVMARQP 244 GG +T +D +GD FT+ LA C+ G QF Y +++ + + A ++ A Sbjct: 182 -FYGGFFTPSDSTGDIHKFTRGLADACVRHGVQFHYDAEIMSIEQ--PAEGRFSLTAHLE 238 Query: 245 GGGGKKDFILKADAVVVACGSYSAPLLRSVGVDLPIYPGKGYSATFPL---LRPEGAPMV 301 G + F + +VV G S +G + +YP KGYS T L + AP V Sbjct: 239 GETQRFGF----ERIVVCAGVKSRDFAAMLGDHVNVYPVKGYSITVCLDDATSRQRAPWV 294 Query: 302 STIDDGKKIAMSRLG-NHLRVAGTIELNGWDLTLDSSLARARCHMLSRRIEAILPGVCDT 360 S +DD KI SRLG + RVAGT E+NG++ + S AR L P V Sbjct: 295 SLLDDSAKIVTSRLGADRFRVAGTAEINGFNRDIRS----ARIAPLVDWTRRHFPEVSTA 350 Query: 361 RTPEEGGDPQYWTGLRPATPTNIPFIGRTRVGKLWVNAGHGTLGWTHGAGSGKALAELI 419 R W GLRP P+ +P +GR + ++ N GHG LGWT A + +A+A I Sbjct: 351 RVIP-------WAGLRPMLPSMLPKVGRGKRRGVFYNTGHGHLGWTLSAATAQAVARAI 402 Lambda K H 0.321 0.137 0.424 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: 466 Number of extensions: 22 Number of successful extensions: 7 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: 445 Length of database: 403 Length adjustment: 32 Effective length of query: 413 Effective length of database: 371 Effective search space: 153223 Effective search space used: 153223 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: 51 (24.3 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