Align D-alanine dehydrogenase (EC 1.4.99.-) (characterized)
to candidate Dsui_0501 Dsui_0501 glycine/D-amino acid oxidase, deaminating
Query= reanno::acidovorax_3H11:Ac3H11_4848 (445 letters) >FitnessBrowser__PS:Dsui_0501 Length = 416 Score = 391 bits (1004), Expect = e-113 Identities = 213/432 (49%), Positives = 262/432 (60%), Gaps = 20/432 (4%) Query: 1 MKTIVLGAGIIGISTAWHLLERGHEVIVIDRQPDAALETSFANAAQISVSYCEPWANREA 60 M+ +VLGAG++G+++AW L E GHEV V+DRQP AALETSFAN QISV + EPWAN A Sbjct: 1 MRVLVLGAGVVGVTSAWFLAEAGHEVTVVDRQPGAALETSFANGGQISVCHAEPWANPRA 60 Query: 61 PLKALKWMFDKEAPLLFRPQMDWQQWRWGLQFLAQCNDTAFERNVQQIVALGAYSHAALK 120 P KAL+W+ ++APLLFR + D + W L+FLA C A RN++ I+AL YS L+ Sbjct: 61 PFKALEWLGKEDAPLLFRLRYDPALFAWSLRFLANCPPGATRRNIRDIIALALYSRQRLQ 120 Query: 121 DLVGTTGIEYNRLERGIAHFYTDQKSFDAAGHAVELMRKHGVQRRLVSRDELLQIEPAFR 180 L ++Y++ +GI H +T F+AA HA LMR+ GV R V + IEPA Sbjct: 121 ALRQALPLDYDQRCQGILHIFTQAAEFEAACHAAALMREFGVDREPVDAARCVAIEPALA 180 Query: 181 AYGDKITGGTYTSTDESGDARVFTQELARRCIARGAQFLYGHDVLRLNKIGNAIDSVAVM 240 A ++ GG YT +DESGDA FTQ LA ARG QF Y V ++ G + V Sbjct: 181 AVQGRLAGGDYTPSDESGDAHRFTQRLAEAAAARGVQFRYNCPVEKIASAGGRVAGVVA- 239 Query: 241 ARQPGGGGKKDFILKADAVVVACGSYSAPLLRSVGVDLPIYPGKGYSATFPLLRPEGAPM 300 GG +L ADA VVA GSYS LL+ GV +YPGKGYSAT L AP Sbjct: 240 ----GGD-----LLLADAYVVALGSYSPALLKPAGVKACVYPGKGYSATIALSPDSVAPS 290 Query: 301 VSTIDDGKKIAMSRLGNHLRVAGTIELNGWDLTLDSSLARARCHMLSRRIEAILPGVCDT 360 VS DD +KI MSRLGN LRVAGT E NG +L L RC L RR + P + Sbjct: 291 VSITDDERKIVMSRLGNRLRVAGTAEFNGHNL----DLTPVRCEALLRRALELFPQL--- 343 Query: 361 RTPEEGGDPQYWTGLRPATPTNIPFIGRTRVGKLWVNAGHGTLGWTHGAGSGKALAELIS 420 GDP YW GLRP TP+N+P IGRTR+ LW+N GHGTLGWT GS ALA+LIS Sbjct: 344 ---RPDGDPLYWCGLRPVTPSNVPLIGRTRLSNLWLNTGHGTLGWTLSCGSAAALADLIS 400 Query: 421 GQVPAMNFGFCG 432 G+ P +F F G Sbjct: 401 GRRPEPDFPFLG 412 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: 585 Number of extensions: 29 Number of successful extensions: 5 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: 416 Length adjustment: 32 Effective length of query: 413 Effective length of database: 384 Effective search space: 158592 Effective search space used: 158592 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