Align D-arginine dehydrogenase (EC 1.4.99.6) (characterized)
to candidate PfGW456L13_1040 D-amino acid dehydrogenase small subunit (EC 1.4.99.1)
Query= BRENDA::Q9HTQ0 (432 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1040 Length = 413 Score = 303 bits (775), Expect = 8e-87 Identities = 165/411 (40%), Positives = 243/411 (59%), Gaps = 9/411 (2%) Query: 2 RVLVLGSGVIGTASAYYLARAGFEVVVVDRQDGPALETSFANAGQVSPGYASPWAAPGIP 61 RV ++G GVIG A+AY L R GFEV VV+ +D ETSFAN GQ+S Y +P A G+P Sbjct: 4 RVCIIGGGVIGLATAYALVRDGFEVTVVEARDSLGSETSFANGGQLSYRYVAPLADAGVP 63 Query: 62 LKAMKWLLEKHAPLAIKLTSDPSQYAWMLQMLRNCTAERYAVNKERMVRLSEYSRDCLDE 121 L+A+ W+L +PL ++ DP+Q+ WM L C N ++RL+ +S+D L Sbjct: 64 LQAIGWMLRGDSPLKLRPRFDPAQWRWMASFLGACRRSVNRENAAHLLRLALFSQDTLKS 123 Query: 122 LRAETGIA-YEGRTLGTTQLFRTQAQLDAAGKDIAVLERSGVPYEVLDRDGIARVEPALA 180 R + G+A ++ R G FR + + A + +A ++ +VL A++EPAL Sbjct: 124 WREDDGLAGFQWRRNGKLVTFRQNSSFEHARQGLADPQQQ----QVLSPAECAQLEPAL- 178 Query: 181 KVADKLVGALRLPNDQTGDCQLFTTRLAEMAKGLG-VEFRFGQNIERLDFAGDRINGVLV 239 + VGA+ P+++ GDC F +LA + G EFR GQ + + + +N + + Sbjct: 179 -IDAPFVGAIYTPDEEVGDCHGFCQQLAARLQASGRCEFRLGQAVTGIRHSNGSVNAIEL 237 Query: 240 NGELLTADHYVLALGSYSPQLLKPLGIKAPVYPLKGYSLTVPITNPEMAPTSTILDETYK 299 G+LL+ D V+A G SP L P G++ P+YPLKGYSLTVPI AP +I D K Sbjct: 238 GGQLLSVDQLVIAAGHRSPLLALP-GLQLPLYPLKGYSLTVPIGAGHRAPDVSITDYDRK 296 Query: 300 VAITRFDQRIRVGGMAEIAGFDLSLNPRRRETLEMITTDLYPEGGDISQATFWTGLRPAT 359 + R +++RV M +I GFD +L+P+R ++ D +P G +A W G+RPAT Sbjct: 297 IVYARIGKQLRVAAMVDIVGFDPALDPKRLALIKRQARDTFPNAGAYDEAVEWAGMRPAT 356 Query: 360 PDGTPIVGATRYRNLFLNTGHGTLGWTMACGSGRYLADLMAKKRPQISTEG 410 P G P++GAT YRNL+LN GHG LG+T+ACGSGR L++L+ ++R I +G Sbjct: 357 PSGVPLLGATAYRNLWLNLGHGALGFTLACGSGRLLSELIGERRLSIDLQG 407 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: 477 Number of extensions: 22 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: 413 Length adjustment: 32 Effective length of query: 400 Effective length of database: 381 Effective search space: 152400 Effective search space used: 152400 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: 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