Align D-alanine dehydrogenase (EC 1.4.99.-) (characterized)
to candidate GFF2666 HP15_2610 D-amino acid dehydrogenase small subunit
Query= reanno::acidovorax_3H11:Ac3H11_4848 (445 letters) >FitnessBrowser__Marino:GFF2666 Length = 427 Score = 402 bits (1033), Expect = e-116 Identities = 202/435 (46%), Positives = 277/435 (63%), Gaps = 20/435 (4%) Query: 1 MKTIVLGAGIIGISTAWHLLERGHEVIVIDRQPDAALETSFANAAQISVSYCEPWANREA 60 M +VLGAG++G +TAW+L ++GH+V V+DRQ A LETS+AN QISVS+ EPWAN A Sbjct: 11 MHILVLGAGVVGTTTAWYLQKQGHQVTVVDRQNQAGLETSYANGGQISVSHAEPWANPSA 70 Query: 61 PLKALKWMFDKEAPLLFRPQMDWQQWRWGLQFLAQCNDTAFERNVQQIVALGAYSHAALK 120 PLK +KW+F +APLLFRP++D QWRW L FL QC N++Q+V LG YS + L+ Sbjct: 71 PLKVMKWLFQPDAPLLFRPRLDPAQWRWALSFLGQCTLARAAHNIRQMVNLGTYSCSQLQ 130 Query: 121 DLVGTTGIEYNRLERGIAHFYTDQKSFDAAGHAVELMRKHGVQRRLVSRDELLQIEPAFR 180 L GIEYN LE+GI HFYT+ FD A +M+ G R+++ D +++EPA + Sbjct: 131 ALREEAGIEYNHLEKGILHFYTNPAEFDGAMEPTRIMQDLGCDRQIIDADRAVELEPALK 190 Query: 181 AYGDKITGGTYTSTDESGDARVFTQELARRCIARGAQFLYGHDVLRLNKIGNAIDSVAVM 240 ++I G TYTS DESGDAR+FTQ LA+RC G +F YG ++L + G + + + Sbjct: 191 PIRNRIAGATYTSEDESGDARMFTQNLAKRCAEAGVEFRYGTEILSFERAGERVLGIQTL 250 Query: 241 ARQPGGGGKKDFILKADAVVVACGSYSAPLLRSVGVDLPIYPGKGYSATFPLLRPEGAPM 300 G + L+ADA V++ GS+SA L +G+ L IYP KGYS T P+ E A Sbjct: 251 R-----DGHHE-TLRADAYVLSMGSFSAALASQLGIFLNIYPAKGYSITVPVKNEEAAFN 304 Query: 301 VSTIDDGKKIAMSRLGNHLRVAGTIELNGWDLTLDSSLARARCHMLSRRIEAILPGVCDT 360 VS DD K+ SRLG+ +RVAGT ELNG+ L+ + RC + RR ++ Sbjct: 305 VSLTDDEYKLVYSRLGDRMRVAGTAELNGYSRKLNYT----RCRAIVRRTAEVM------ 354 Query: 361 RTPEEG--GDPQYWTGLRPATPTNIPFIGRTRVGKLWVNAGHGTLGWTHGAGSGKALAEL 418 PE G ++WTGLRPATP+N+P+IG++ L++N GHGTLGWTH GS ALA++ Sbjct: 355 --PEAGYWDQAEFWTGLRPATPSNVPYIGKSHFANLYLNTGHGTLGWTHSCGSAAALADI 412 Query: 419 ISGQVPAMNFGFCGM 433 I G+ P ++F F G+ Sbjct: 413 IDGRKPEVDFTFSGL 427 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: 536 Number of extensions: 18 Number of successful extensions: 3 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: 427 Length adjustment: 32 Effective length of query: 413 Effective length of database: 395 Effective search space: 163135 Effective search space used: 163135 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