Align D-amino acid dehydrogenase; D-alanine dehydrogenase; EC 1.4.99.- (characterized)
to candidate H281DRAFT_00908 H281DRAFT_00908 D-amino-acid dehydrogenase
Query= SwissProt::O30745 (432 letters) >FitnessBrowser__Burk376:H281DRAFT_00908 Length = 432 Score = 187 bits (474), Expect = 7e-52 Identities = 132/436 (30%), Positives = 213/436 (48%), Gaps = 31/436 (7%) Query: 1 MRVVILGSGVFGVASAWYLSQAGHDVTVIDRQPGPAEETSAANAGQISPGYAAPWAAPGV 60 M V+++G G+ GVA+A+ L AGH V V++R A+ + + G + P W P Sbjct: 1 MDVIVIGGGIAGVATAYQLRAAGHRVCVVERHATVAQGATYGHGGTVLPTPLDVWFGP-- 58 Query: 61 PLKAIKWMFQRHAPLAIGLDGTSFQLKWMWQMLRNCDT--RHYMENKGRMVR-LAEYSRD 117 A + + G +G + Q L+ D R Y R++R L E SR+ Sbjct: 59 TFMANRQNAKNGVISKPGFNGPARQFVKKLAELQEPDEFGRQY-----RLLRPLVELSRE 113 Query: 118 CLKALRDTTGIQYEGRQGGTLQLFRTAKQYENATRDIAVLEDAGVPYQLLEAKRLAEVEP 177 + + G ++E + G L L R+A++++ + +L VP+ +L A E Sbjct: 114 AMADMEARFGFEFE-QASGLLHLVRSAQEWQQLQPALGLLALYEVPHHVLSPAECAAYEH 172 Query: 178 ALAEVSHKLTGGLRLPNDETGDCQLFTTRLAAMAD-QAGVTFRFNTAVDALLHEGDRIA- 235 ++ + GG+ ++ T +C LFT + D Q GV F V A+ +G R A Sbjct: 173 SV-RTEPEFAGGVLFEHERTANCPLFTKLIKQTLDTQGGVQFMLGCEVSAIRLDGQRAAV 231 Query: 236 ------GVKCGMR---IIKGDAYVMAFGSYSTAMLKGL-VDIPVYPLKGYSLTIPIAQED 285 G G R +I D V+A G S A+L+ L + +P++PL+ ++L PIA E+ Sbjct: 232 ELAPRPGAASGSREVDVIHADTIVVAGGYGSLALLERLGLALPLHPLRVHTLVAPIAHEE 291 Query: 286 GAPVSTILDVTYTIAITRFDQRIRVGGMAEIVGFN-------KTLLQPRRETLEMVVRDL 338 AP I+D I I+R + R+R+ G A + G N + L + L D Sbjct: 292 CAPHVAIVDAIKRIGISRMNHRLRIAGGAVLQGANLIDKPLGEALTKEALALLGQATHDW 351 Query: 339 FPRGGHVEQATFWTGLRPMTPDGTPVVGRTAYKNLWLNTGHGTLGWTMACGSGQLISDLI 398 P + A W G++ ++PDG PVVG + L++N GHG GW +ACG+G+LI+DL+ Sbjct: 352 IPGAARISAALPWEGIKLLSPDGLPVVGNALHPRLFVNVGHGPAGWGLACGAGKLIADLV 411 Query: 399 SGRTPAIPYDDLAVAR 414 +G+ P +P + LA R Sbjct: 412 AGQAPDLPDETLAALR 427 Lambda K H 0.321 0.137 0.422 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: 488 Number of extensions: 23 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: 432 Length adjustment: 32 Effective length of query: 400 Effective length of database: 400 Effective search space: 160000 Effective search space used: 160000 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