Align D-alanine dehydrogenase (EC 1.4.99.-) (characterized)
to candidate Pf6N2E2_3402 D-amino acid dehydrogenase small subunit (EC 1.4.99.1)
Query= reanno::acidovorax_3H11:Ac3H11_4848 (445 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3402 Length = 410 Score = 244 bits (624), Expect = 3e-69 Identities = 151/422 (35%), Positives = 214/422 (50%), Gaps = 16/422 (3%) Query: 1 MKTIVLGAGIIGISTAWHLLERGHEVIVIDRQPDAALETSFANAAQISVSYCEPWANREA 60 M+ V+GAGI+G+S+AW L + GH V VIDR +A + S AN AQ+S SY +P A+ Sbjct: 1 MEICVVGAGIVGLSSAWFLHKAGHTVTVIDRAGEAGMGASAANGAQLSYSYVQPLADPSL 60 Query: 61 PLKALKWMFDKEAPLLFRPQMDWQQWRWGLQFLAQCNDTAFERNVQQIVALGAYSHAALK 120 K + ++ PL F PQ +QWRW ++FLA C + + +++ L S AL Sbjct: 61 LPGIPKMLLERNGPLKFSPQWSLEQWRWCVEFLAACRTSVSRQTTVELLELAHESRLALD 120 Query: 121 DLVGTTGIEYNRLERGIAHFYTDQKSFDAAGHAVELMRKHGV-QRRLVSRDELLQIEPAF 179 + ++ + G Y D +S AG V+ G Q+++VS E L IEPA Sbjct: 121 AFISQEKVQCDFARTGKLVLYPDAESLRKAGDQVKFQAAQGARQQKIVSPAEALSIEPAL 180 Query: 180 RAYGDKITGGTYTSTDESGDARVFTQELARRCIARGAQFLYGHDVLRLNKIGNAIDSVAV 239 Y G +T ++ + D R QELAR +G +FL+ +V + I ++ + Sbjct: 181 EGYKKAFHGAIHTDSECAVDGRKLCQELARLLSTQGVRFLFDSEVAAFRRERGRITALEI 240 Query: 240 MARQPGGGGKKDFILKADAVVVACGSYSAPLLRSVGVDLPIYPGKGYSATFPLLRPEGAP 299 G G +L AVV+A G+YSA LL + GV +P+YP KGYS T P+ AP Sbjct: 241 HHAIEGPG-----LLGTQAVVLAAGAYSAGLLSAFGVRMPVYPLKGYSITLPITDSMNAP 295 Query: 300 MVSTIDDGKKIAMSRLGNHLRVAGTIELNGWDLTLDSSLARARCHMLSRRIEAILPGVCD 359 VS D +K +R+G+ LRVAG +EL G LD+S+ R L +A+ Sbjct: 296 TVSVTDMRRKTVFARIGDRLRVAGMVELCG----LDASIPVKRIEQLKASTQALF----- 346 Query: 360 TRTPEEGGDPQYWTGLRPATPTNIPFIGRTRVGKLWVNAGHGTLGWTHGAGSGKALAELI 419 D Q WTG RPATPT P + + L+VN G G LG T GS + L LI Sbjct: 347 -GLEWNADDCQPWTGWRPATPTGRPILAVSGCDNLYVNCGQGALGMTLAFGSAQRLVRLI 405 Query: 420 SG 421 G Sbjct: 406 GG 407 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: 438 Number of extensions: 20 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: 410 Length adjustment: 32 Effective length of query: 413 Effective length of database: 378 Effective search space: 156114 Effective search space used: 156114 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