Align D-amino acid dehydrogenase; D-alanine dehydrogenase; EC 1.4.99.- (characterized)
to candidate GFF3476 HP15_3418 D-amino acid dehydrogenase small subunit
Query= SwissProt::P0A6J5 (432 letters) >FitnessBrowser__Marino:GFF3476 Length = 423 Score = 281 bits (719), Expect = 3e-80 Identities = 144/422 (34%), Positives = 239/422 (56%), Gaps = 8/422 (1%) Query: 1 MRVVILGSGVVGVASAWYLNQAGHEVTVIDREPGAALETSAANAGQISPGYAAPWAAPGV 60 M + ++G GVVG+ +A+ LN+ GH+VTV++R A ETS ANA Q S G PWA P + Sbjct: 1 MHIAVVGGGVVGMTTAYELNRRGHQVTVLERHSMAGNETSKANAAQRSYGVVYPWADPAI 60 Query: 61 PLKAIKWMFQRHAPLAVRLDGTQFQLKWMWQMLRNC-DTSHYMENKGRMVRLAEYSRDCL 119 KAI W+ ++ PL +R + LK+M+ LR + N+ M+RL +SR+ Sbjct: 61 VFKAIPWILKQDGPLKLRFPPSVETLKFMFATLRYAWSPGLFGLNRRAMLRLGIHSRERF 120 Query: 120 KALRAETNIQYEGRQGGTLQLFRTEQQYENATRDIAVLEDAGVPYQLLESSRLAEVEPAL 179 AL E ++ ++G G L L T + E +L + G+P +LL ++ + EP + Sbjct: 121 MALEKELDLSFDGDHQGLLHLASTPEALEGYRTTHELLNELGIPSRLLTPEQVRDAEPGM 180 Query: 180 AEVAHKLTGGLQLPNDETGDCQLFTQNLARMAEQAGVKFRFNTPVDQLLCDGEQIYGVKC 239 L G L D TGDC F++ LA++ E G+ R+N ++L+ D +++ + Sbjct: 181 VGNG-PLYGALSYDTDGTGDCHKFSRELAKVCEAKGIVVRYNVEAEKLIADDQRVSAISV 239 Query: 240 GD-----EVIKADAYVMAFGSYSTAMLKGI-VDIPVYPLKGYSLTIPIAQEDGAPVSTIL 293 + E ++ DA V++ G +S +++ + +++P+YP+KGYSLT+P+ + P STI Sbjct: 240 RNSDGVMEALEVDAVVISAGCWSNHLVQPLGLELPIYPVKGYSLTVPMKDPEQGPASTIH 299 Query: 294 DETYKIAITRFDNRIRVGGMAEIVGFNTELLQPRRETLEMVVRDLYPRGGHVEQATFWTG 353 D+ +K+ TR +R+R G E+ FN ++ + R T+ V +P ++ A WTG Sbjct: 300 DDNFKVVSTRLGDRLRATGFVELADFNRDIPEARLATIRKSVESRFPGCADLDAAETWTG 359 Query: 354 LRPMTPDGTPVVGRTRFKNLWLNTGHGTLGWTMACGSGQLLSDLLSGRTPAIPYEDLSVA 413 RPMTPDG ++GR +NL+LNTGHGT GWT++ GS +++ ++ G P++ + Sbjct: 360 FRPMTPDGPAIIGRGPRENLYLNTGHGTFGWTLSAGSADVIAQVIEGEEPSVCLDAFRPG 419 Query: 414 RY 415 R+ Sbjct: 420 RF 421 Lambda K H 0.319 0.136 0.415 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: 459 Number of extensions: 24 Number of successful extensions: 4 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: 432 Length of database: 423 Length adjustment: 32 Effective length of query: 400 Effective length of database: 391 Effective search space: 156400 Effective search space used: 156400 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