Align D-alanine dehydrogenase (EC 1.4.99.-) (characterized)
to candidate WP_041099259.1 SUTH_RS11035 D-amino acid dehydrogenase
Query= reanno::acidovorax_3H11:Ac3H11_4848 (445 letters) >NCBI__GCF_000828635.1:WP_041099259.1 Length = 417 Score = 382 bits (982), Expect = e-111 Identities = 209/430 (48%), Positives = 263/430 (61%), Gaps = 22/430 (5%) Query: 1 MKTIVLGAGIIGISTAWHLLERGHEVIVIDRQPDAALETSFANAAQISVSYCEPWANREA 60 M+ IVLGAG++G++TAW+L GHEV VI+RQP A ETSFAN QISVS+ EPWAN +A Sbjct: 1 MRVIVLGAGVVGVTTAWYLAADGHEVTVIERQPLPAQETSFANGGQISVSHAEPWANPQA 60 Query: 61 PLKALKWMFDKEAPLLFRPQMDWQQWRWGLQFLAQCNDTAFERNVQQIVALGAYSHAALK 120 P KALKWM ++APLL+R + D QW WGL+FL +C NV+ IV+LG S AAL+ Sbjct: 61 PWKALKWMGREDAPLLWRLRADPAQWAWGLRFLRECTAARARANVRAIVSLGLASRAALQ 120 Query: 121 DLVGTTGIEYNRLERGIAHFYTDQKSFDAAGHAVELMRKHGVQRRLVSRDELLQIEPAFR 180 L ++Y+ LERGI HFYTD F+ A LMR+ G +R + E L IEPA Sbjct: 121 SLRRELALDYDHLERGILHFYTDPAEFEHALPQAALMREFGCERVPKTAAECLAIEPALG 180 Query: 181 AYGDKITGGTYTSTDESGDARVFTQELARRCIARGAQFLYGHDVLRLNKIGNAIDSVAVM 240 + GGTYT++DESGDAR FT+ LAR + RG +F YG V L + G + V + Sbjct: 181 GSRVPVVGGTYTASDESGDARRFTETLARHAVGRGVRFRYGETVTALQREGGRVSGVRLA 240 Query: 241 ARQPGGGGKKDFILKADAVVVACGSYSAPLLRSVGVDLPIYPGKGYSATFPLLRPEGAPM 300 + + AD V+A GSYS LL+ +GV LP+YP KGYSAT L AP Sbjct: 241 SGETP---------CADMTVLALGSYSPLLLKPLGVRLPVYPAKGYSATLELAEGIAAPT 291 Query: 301 VSTIDDGKKIAMSRLGNHLRVAGTIELNGWDLTLDSSLARARCHMLSRRIEAILPGVCDT 360 VS DDG KI +SRLG LRVAGT E NG+ D+SL ARC L RI I P + Sbjct: 292 VSLTDDGHKIVISRLGQFLRVAGTAEFNGY----DTSLNAARCEALLHRIGEIFPALAAV 347 Query: 361 RTPEEGGDPQYWTGLRPATPTNIPFIG---RTRVGKLWVNAGHGTLGWTHGAGSGKALAE 417 G YW GLRPATP N+P IG + LW+N GHGTLGWT GS + LAE Sbjct: 348 ------GKVDYWAGLRPATPGNVPLIGDMAGAGLAGLWLNTGHGTLGWTLACGSARMLAE 401 Query: 418 LISGQVPAMN 427 +++G+ P ++ Sbjct: 402 MVAGRDPGLD 411 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: 592 Number of extensions: 26 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: 417 Length adjustment: 32 Effective length of query: 413 Effective length of database: 385 Effective search space: 159005 Effective search space used: 159005 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 Apr 09 2024. 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