Align D-alanine dehydrogenase (EC 1.4.99.-) (characterized)
to candidate Ac3H11_416 D-amino acid dehydrogenase small subunit (EC 1.4.99.1)
Query= reanno::psRCH2:GFF3724 (432 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_416 Length = 410 Score = 244 bits (622), Expect = 5e-69 Identities = 150/416 (36%), Positives = 231/416 (55%), Gaps = 16/416 (3%) Query: 1 MRVLVLGSGVVGTASAYYLARAGFEVVVVDRQPAVAMETSFANAGQVSPGYASPWAAPGV 60 M++ ++G+G+VG +AY LA G EV V +++ A A E SFA AG ++P +PWA PG Sbjct: 1 MKIAIVGAGIVGVTTAYELASDGHEVTVFEQRSAAAEEASFATAGLLAPHLLTPWAVPGF 60 Query: 61 PLKAMKWLLQRHAPLAIKLTGDVDQ--YLWMAQMLRNCTAARYAVNKERMVRLSEYSRDC 118 A++ L+ HA L +L+G + + + W+++ R+ T A A + RL++YS+ Sbjct: 61 G-HALR-LMGPHATL--RLSGGLSRANWAWLSRW-RSATHASSAP-AAALERLAQYSQSR 114 Query: 119 LDELRAETGIAYEGRQLGTTQLFRTQAQLDAAAKDIAVLERSGVPYELLDRAAIGRVEPA 178 L L + +E Q G L RT+ + + VL SGV +D ++EP Sbjct: 115 LQALAQRHELDFEASQ-GRLVLLRTEQERAQLQPALQVLRDSGVALREVDADIARQIEPG 173 Query: 179 LAKVAHKLSGALRLPNDQTGDCQMFTSRLAEMALALGVEFRFGQNIQRLEHAGDRIAGVW 238 L+ A L+GA+ LP+ + G+C++F L + GV F F I R+ G GV Sbjct: 174 LSPEA-PLAGAIHLPDARAGNCRLFAQLLRQGTQGSGVHFAFNTRIDRI---GTTPVGVV 229 Query: 239 IDGK--LETADRYVLALGSYSPQMLKPLGIRAPVYPLKGYSLTVPISDPAMAPQSTVLDE 296 + G+ L D VL G+ S +L LG+R P+ + GYS++ P+ + APQ++V+D Sbjct: 230 VQGESDLRRFDAVVLCAGTASAALLPALGMRLPMAAVYGYSVSAPLRESTHAPQASVVDA 289 Query: 297 TYKVAITRFDQRIRVGGMAEIAGHDLSLNPRRRETLEMVVGDLYPQGGDPAEAV-FWTGL 355 +++ITR QR+R+ G AE+AG D + + L + D +P G + V W G Sbjct: 290 AQQISITRLGQRVRIAGGAELAGADAEHHAATLQRLYRTLNDWFPGGAQLSSGVQVWRGA 349 Query: 356 RPATPDGTPIIGATAYRNLYLNTGHGTLGWTMACGSGRVLADLLASKRPQISTDGL 411 RP PDG P++GA+ L+LNTGHG GW +ACGS R LADL+A + P++ DGL Sbjct: 350 RPLLPDGAPVVGASGVPGLWLNTGHGAGGWALACGSARALADLMAQRVPEVPLDGL 405 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: 508 Number of extensions: 31 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: 432 Length of database: 410 Length adjustment: 32 Effective length of query: 400 Effective length of database: 378 Effective search space: 151200 Effective search space used: 151200 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