Align D-alanine dehydrogenase (EC 1.4.99.-) (characterized)
to candidate GFF2076 Psest_2119 Glycine/D-amino acid oxidases (deaminating)
Query= reanno::psRCH2:GFF3724 (432 letters) >FitnessBrowser__psRCH2:GFF2076 Length = 414 Score = 287 bits (735), Expect = 4e-82 Identities = 169/419 (40%), Positives = 237/419 (56%), Gaps = 13/419 (3%) Query: 1 MRVLVLGSGVVGTASAYYLARAGFEVVVVDRQPAVAMETSFANAGQVSPGYASPWAAPGV 60 MRV V+G+GV+G A+AY L R G V +++R+ VA+ETSFAN GQ+S Y SP A GV Sbjct: 1 MRVAVIGAGVIGLATAYSLVRQGHSVELIERRDDVALETSFANGGQLSYRYVSPLADAGV 60 Query: 61 PLKAMKWLLQ-RHAPLAIKLTGDVDQYLWMAQMLRNCTAARYAVNKERMVRLSEYSRDCL 119 PL+A+ W+L+ APL + + Q+ W Q L C + N ++RL+ +S+ L Sbjct: 61 PLQAIGWMLRGADAPLRFRPQASLHQWRWCLQFLLACRRSVNRRNAAHLLRLALHSQQIL 120 Query: 120 DELRAETGI-AYEGRQLGTTQLFRTQAQLDAAAKDIAVLERSGVPYELLDRAAIGRVEPA 178 R + + + R G ++R Q L A A+ + SG LLD A VEPA Sbjct: 121 RSWREQDRLDGFAWRANGKLVIYRDQHSLHKGAA--AIDDDSG--QRLLDAAQCVDVEPA 176 Query: 179 LAKVAHKLSGALRLPNDQTGDCQMFTSRLAEMALALGVEFRF----GQNIQRLEHAGDRI 234 LA +A L G + P D+ DC +F + L + LG RF GQ++ L G R+ Sbjct: 177 LAPLAASLHGGIYSPGDEVADCHLFCTELLQR---LGASPRFRLHTGQSVSALRTEGKRV 233 Query: 235 AGVWIDGKLETADRYVLALGSYSPQMLKPLGIRAPVYPLKGYSLTVPISDPAMAPQSTVL 294 V + D V+A G+ S +LKPLGI P+YPLKGYSLTV ++D PQ+ V Sbjct: 234 RAVVLGRDDIAIDHLVVAAGTGSVGLLKPLGIDLPIYPLKGYSLTVGLADQDGVPQTNVT 293 Query: 295 DETYKVAITRFDQRIRVGGMAEIAGHDLSLNPRRRETLEMVVGDLYPQGGDPAEAVFWTG 354 D KV R D ++RV M +IAG D L+ +R TL+ + G +P GD A W G Sbjct: 294 DYDNKVVYARLDDQLRVAAMVDIAGWDAGLDQQRIATLQRLAGATFPGAGDYQRARQWAG 353 Query: 355 LRPATPDGTPIIGATAYRNLYLNTGHGTLGWTMACGSGRVLADLLASKRPQISTDGLDI 413 LRPATP GTP++G + + NL+LN GHG+LG+T+ACGS +L ++ P +S DGL + Sbjct: 354 LRPATPQGTPLLGRSGFDNLWLNVGHGSLGFTLACGSADLLTSVIGGSPPAVSLDGLSL 412 Lambda K H 0.320 0.135 0.405 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: 522 Number of extensions: 28 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: 414 Length adjustment: 32 Effective length of query: 400 Effective length of database: 382 Effective search space: 152800 Effective search space used: 152800 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: 50 (23.9 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