Align D-alanine dehydrogenase (EC 1.4.99.-) (characterized)
to candidate Ga0059261_3351 Ga0059261_3351 Glycine/D-amino acid oxidases (deaminating)
Query= reanno::azobra:AZOBR_RS08020 (436 letters) >FitnessBrowser__Korea:Ga0059261_3351 Length = 405 Score = 229 bits (585), Expect = 9e-65 Identities = 140/401 (34%), Positives = 205/401 (51%), Gaps = 6/401 (1%) Query: 3 VIVLGSGVIGVSTAYFLAKAGHEVTVVDRQPGPALETSYANAGEVSPGYSAPWAAPGLMA 62 +IVLG+GV+G++TA LA GH VTVVD GP L TS+AN ++S Y+ A+P ++ Sbjct: 7 IIVLGAGVVGMATALTLAGRGHRVTVVDGAGGPGLGTSFANGAQLSYAYTDALASPSVLR 66 Query: 63 KAVKWMLMKHSPLVIRPKMDPAMWSWCLKLLANANERSYEINKGRMVRLAEYSRDCLRVL 122 + +L L +P +DP W + L N S+ N + LA SR L L Sbjct: 67 QIPHILLGLDPALRFQPHLDPDFLRWSIAFLRNCGAGSFRRNTLAGLALAARSRLALDQL 126 Query: 123 RDETGIRYDERAKGTLQVFRTQKQVDAAATDMAVLDRFKVPYSLLDVEGCAAVEPALRLV 182 + + Y + G + ++RT AA +A+ + +LLD + A+EP L V Sbjct: 127 TERHALEYGQSVPGKIHIYRTAASFAAAEAMVALKRANGITQTLLDPDAAVALEPMLAPV 186 Query: 183 KEKIVGGLLLPGDETGDCFRFTNALAAMATELGVEFRYNTGIRKLESDGRRVTGVVTDAG 242 +++I G L PG+ GD RF + G ++ + ++E+ G + +VT G Sbjct: 187 RDEIAGALHTPGEAVGDPHRFCSGAHDALIRAGGSSMFDLPVERIETQGSQ-PAIVTRCG 245 Query: 243 T-LTADSYVVAMGSYSPTLVKPFGLDLPVYPVKGYSLTLPIVDAAGAPESTVMDETHKIA 301 T + AD V+A G +P L + G+ LPV P+KGYS+T P A AP +++ D +++ Sbjct: 246 TRVPADRIVLAAGPGAPRLARSLGVYLPVQPMKGYSITAP--TGAAAPRASITDVANRVV 303 Query: 302 VTRLGDRIRVGGTAELTGFDLTLRPGRRGPLDHVVSDLFPTGGDLSKAE-FWTGLRPNTP 360 RLG+R+R+ G AE+ D + P R L P D E W GLRP TP Sbjct: 304 FARLGNRMRIAGLAEVGRRDTRVEPDRLRALTDSARAALPQAADYDNIESSWAGLRPMTP 363 Query: 361 DGTPIVGPTPVRNLFLNTGHGTLGWTMAAGSGRVVADVVGG 401 D PI T + NTGHG LGWT AAGS VA ++ G Sbjct: 364 DSLPIT-RTIAPGVIANTGHGGLGWTYAAGSAERVAQIIEG 403 Lambda K H 0.319 0.136 0.408 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: 424 Number of extensions: 16 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: 436 Length of database: 405 Length adjustment: 32 Effective length of query: 404 Effective length of database: 373 Effective search space: 150692 Effective search space used: 150692 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 (21.7 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