Align D-amino acid dehydrogenase; D-alanine dehydrogenase; EC 1.4.99.- (characterized)
to candidate RR42_RS04585 RR42_RS04585 amino acid dehydrogenase
Query= SwissProt::O30745 (432 letters) >FitnessBrowser__Cup4G11:RR42_RS04585 Length = 434 Score = 588 bits (1515), Expect = e-172 Identities = 292/431 (67%), Positives = 340/431 (78%), Gaps = 5/431 (1%) Query: 1 MRVVILGSGVFGVASAWYLSQAGHDVTVIDRQPGPAEETSAANAGQISPGYAAPWAAPGV 60 MRV++LGSGV GV SAWYL++AGH+VTVIDR+ PA TS ANAGQISPGYA+PWAAPGV Sbjct: 1 MRVLVLGSGVIGVTSAWYLARAGHEVTVIDREAAPALGTSFANAGQISPGYASPWAAPGV 60 Query: 61 PLKAIKWMFQRHAPLAIGLDGTSFQLKWMWQMLRNCDTRHYMENKGRMVRLAEYSRDCLK 120 PLKAIKWMFQ HAPL+I DGT FQL+WMWQML NC Y NK RMVRLAEYSRDC+ Sbjct: 61 PLKAIKWMFQEHAPLSIKPDGTLFQLQWMWQMLMNCSAERYAVNKERMVRLAEYSRDCIV 120 Query: 121 ALRDTTGIQYEGRQGGTLQLFRTAKQYENATRDIAVLEDAGVPYQLLEAKRLAEVEPALA 180 ALR TGI YEGRQ GTLQLFRTA+Q + A +DIAVLE AGVPYQLL + LA EPALA Sbjct: 121 ALRADTGIAYEGRQQGTLQLFRTAEQLDGAAKDIAVLEQAGVPYQLLSREELAASEPALA 180 Query: 181 EVSHKLTGGLRLPNDETGDCQLFTTRLAAMADQAGVTFRFNTAVDALLHEGDRIAGVKCG 240 VSHKLTGGLRLPNDETGDCQLFT +LAAMA+ GV F++N ++D LL +GD I G G Sbjct: 181 AVSHKLTGGLRLPNDETGDCQLFTGQLAAMAEGLGVQFQYNRSIDGLLTKGDAITGAMVG 240 Query: 241 MRIIKGDAYVMAFGSYSTAMLK----GLVDIPVYPLKGYSLTIPIAQEDGAPVSTILDVT 296 + D V+A GS+ST +K GL ++PVYPLKG+SLT+P+ D +PVST+LD T Sbjct: 241 GEPVMADLVVVALGSWSTPFVKNFLPGLSNLPVYPLKGFSLTVPMTNADRSPVSTVLDET 300 Query: 297 YTIAITRFDQRIRVGGMAEIVGFNKTLLQPRRETLEMVVRDLFPRGGHVEQATFWTGLRP 356 + +AITRFD RIRVGGMA+IVG+++TL +R TLE VV DLFP G V +A+FWTGLRP Sbjct: 301 FKVAITRFDDRIRVGGMAQIVGYDRTLDPAKRRTLEHVVTDLFPGAGDVSRASFWTGLRP 360 Query: 357 MTPDGTPVVGRTAYKNLWLNTGHGTLGWTMACGSGQLISDLISGRTPAIPYDDLAVARY- 415 MTPDGTP+VG T K LWLNTGHGTLGWTMACGSG+L+SDL+SG +PAI DDL+VARY Sbjct: 361 MTPDGTPIVGPTQVKGLWLNTGHGTLGWTMACGSGKLLSDLVSGTSPAIRADDLSVARYL 420 Query: 416 SPGFTPARPQH 426 P T A P+H Sbjct: 421 KPARTHAAPRH 431 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: 669 Number of extensions: 20 Number of successful extensions: 2 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: 434 Length adjustment: 32 Effective length of query: 400 Effective length of database: 402 Effective search space: 160800 Effective search space used: 160800 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