Align D-arginine dehydrogenase (EC 1.4.99.6) (characterized)
to candidate N515DRAFT_3723 N515DRAFT_3723 D-amino-acid dehydrogenase
Query= BRENDA::Q9HTQ0 (432 letters) >FitnessBrowser__Dyella79:N515DRAFT_3723 Length = 419 Score = 187 bits (474), Expect = 7e-52 Identities = 133/419 (31%), Positives = 203/419 (48%), Gaps = 17/419 (4%) Query: 3 VLVLGSGVIGTASAYYLARAGFEVVVVDRQDGPALETSFANAGQVSPGYASPWAAPGIPL 62 VL+LG GVIG ASAYYL RAG V V++ Q P +S N G ++P +A+P A PG+ Sbjct: 8 VLILGGGVIGLASAYYLLRAGATVRVLE-QGTPGCGSSHGNCGTITPSHAAPLAMPGMVS 66 Query: 63 KAMKWLLEKHAPLAIKLTSDPSQYAWMLQMLRNCTAERYAVNKERMVRLSEYSRDCLDEL 122 A++ + APL + DP + W+L R C + + + SR L+ L Sbjct: 67 VALRSMFRADAPLYLNPRPDPERLRWLLGFARRCNWRDFERATRARSAILQRSRGLLEAL 126 Query: 123 RAETGIAYEGRTLGTTQLFRTQAQLDAAGKDIA-VLERSGVPYEVLDRDGIARVEPALAK 181 + + E G ++RT+AQ++A + A VL+R G+ L D + +EPAL Sbjct: 127 VRDEALDCEFVAGGELYVYRTRAQMEADERHHAQVLDRLGIEVNRLRGDEVENLEPAL-- 184 Query: 182 VADKLVGALRLPNDQTGDCQLFTTRLAEMAKGLGVEFRFGQNIERLDFAGDRINGVLVNG 241 + G L P D + LA + LG G I++ RI+ V Sbjct: 185 -LPGVAGGLFHPGDAQLRPNRYAAELARRVRELGGVIESGARIDQFGLQDGRISHVRTTR 243 Query: 242 ELLTADHYVLALGSYSPQLLKPLGIKAPVYPLKGYSLTVPITNPEMAPTSTILDETYKVA 301 + + V+ALG++SP L + L ++ P+ P KGYS+T T P+ AP ++ V Sbjct: 244 GVFHGEQVVMALGAWSPLLGRLLDLRLPMQPGKGYSIT--YTRPQQAPRHALVLREAAVC 301 Query: 302 ITRFDQRIRVGGMAEIAGFDLSLNPRRRETLEMITTDLY--PEGGDISQATFWTGLRPAT 359 +T + R+G E +G+ LN R + L PEG ++ + W G RP + Sbjct: 302 VTTWGSGYRLGSTMEFSGYAEGLNRTRLDALRRGAAAALREPEGPEVLEE--WWGWRPMS 359 Query: 360 PDGTPIVG-ATRYRNLFLNTGHGTLGWTMACGSGRYLADLMAKKRPQISTEGLDISRYS 417 D PI+G +TR+ NL L T HG LG +M+ +G +A L + T LD + Y+ Sbjct: 360 MDEVPIIGPSTRWSNLLLATAHGMLGVSMSAATGELVAALAGR-----GTAALDPAPYA 413 Lambda K H 0.318 0.135 0.401 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: 472 Number of extensions: 26 Number of successful extensions: 7 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: 419 Length adjustment: 32 Effective length of query: 400 Effective length of database: 387 Effective search space: 154800 Effective search space used: 154800 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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