Align D-alanine dehydrogenase (EC 1.4.99.-) (characterized)
to candidate WP_086511526.1 BZY95_RS19365 D-amino acid dehydrogenase
Query= reanno::acidovorax_3H11:Ac3H11_4848 (445 letters) >NCBI__GCF_002151265.1:WP_086511526.1 Length = 411 Score = 219 bits (559), Expect = 1e-61 Identities = 151/420 (35%), Positives = 210/420 (50%), Gaps = 31/420 (7%) Query: 5 VLGAGIIGISTAWHLLERGHEVIVIDRQPDAALETSFANAAQISVSYCEPWANREAPLKA 64 V+G GI G++TA LL+RG +V + +R AA+ETSFAN Q+S S E W + LK Sbjct: 6 VIGGGITGVTTAHALLKRGLDVTLYERNRYAAMETSFANGGQLSASNAEVWTHWPTVLKG 65 Query: 65 LKWMFDKEAPLLFRPQMDWQQWRWGLQFLAQCNDTAFERNVQQIVALGAYSHAALKDLVG 124 L+WM +APLL P+ W + W +F+A A +A+ A H L Sbjct: 66 LRWMLRADAPLLVNPRPSWHKLSWFAEFMAAIPRYADNTTETACLAIAARDH--LYRWAR 123 Query: 125 TTGIEYNRLERGIAHFYTDQKSFDAAGHAVELMRKHGVQRRLVSRDELLQIEPAFRAYGD 184 IE++ RGI H Y D++SF A EL+ K G+ RR V+ E+ +EP GD Sbjct: 124 EENIEFDLERRGILHIYRDRRSFAHAEKVSELLAKGGLARRAVTPQEMRALEP--NLAGD 181 Query: 185 KITGGTYTSTDESGDARVFTQELARRCIARGAQFLYGHDVLRLNKIGNAIDSVAVMARQP 244 GG +T +D +GD FTQ LA RG YG +V +G D V+ + Sbjct: 182 -YYGGFFTESDATGDIHKFTQGLAAAIERRGVTTRYGMEV---RDVGADADGAWVVTEE- 236 Query: 245 GGGGKKDFILKADAVVVACGSYSAPLLRSVGVDLPIYPGKGYSATFPL---LRPEGAPMV 301 G++ + D +VV G S L +G + +YP KGYS T L E APMV Sbjct: 237 ---GREAY----DGLVVCAGVGSRGLAARLGDRVNVYPVKGYSITVHLDDRASREAAPMV 289 Query: 302 STIDDGKKIAMSRLG-NHLRVAGTIELNGWDLTLDSSLARARCHMLSRRIEAILPGVCDT 360 S +DD K+ SRLG + RVAGT E NG ++ + R L +E PGV Sbjct: 290 SLLDDEAKLVTSRLGADRFRVAGTAEFNG----INRDIRHDRIRPLIDWVEQCFPGVGTR 345 Query: 361 RTPEEGGDPQYWTGLRPATPTNIPFIGRTRVGKLWVNAGHGTLGWTHGAGSGKALAELIS 420 R W GLRP P +P +GR R+ ++ N GHG LGWT A + + +A+ ++ Sbjct: 346 RVVP-------WAGLRPMLPDMMPRVGRGRLPSVFYNTGHGHLGWTLSAITAELVADAVT 398 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: 489 Number of extensions: 29 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: 411 Length adjustment: 32 Effective length of query: 413 Effective length of database: 379 Effective search space: 156527 Effective search space used: 156527 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 24 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