Align D-arginine dehydrogenase (EC 1.4.99.6) (characterized)
to candidate PP_4311 PP_4311 putative D-amino acid dehydrogenase 2 small subunit
Query= BRENDA::Q9HTQ0 (432 letters) >FitnessBrowser__Putida:PP_4311 Length = 397 Score = 245 bits (625), Expect = 2e-69 Identities = 144/400 (36%), Positives = 217/400 (54%), Gaps = 9/400 (2%) Query: 2 RVLVLGSGVIGTASAYYLARAGFEVVVVDRQDGPALETSFANAGQVSPGYASPWAAPGIP 61 RV V+G GV+G A+AY L R G+ V +++ +D A TSFAN GQ+S Y +P A G+P Sbjct: 4 RVTVIGGGVVGLATAYALVREGWSVDLIEARDSLASATSFANGGQLSYRYVAPLADAGVP 63 Query: 62 LKAMKWLLEKHAPLAIKLTSDPSQYAWMLQMLRNCTAERYAVNKERMVRLSEYSRDCLDE 121 +A+ WLL +PL ++L DP+Q+ W+L C N +++ L+ S+ L + Sbjct: 64 WQALGWLLRGESPLRLRLRMDPAQWRWLLAFTLACRRSVNRRNAGQLLELALCSQAVLAQ 123 Query: 122 LRAETGIAYEG-RTLGTTQLFRTQAQLDAAGKDIAVLERSGVPYEVLDRDGIARVEPALA 180 R + + G R G FR++ A G++ S +VL + +EPAL Sbjct: 124 WREDHNLGDFGWRRNGKLVAFRSERAF-AQGREQLTDPAS---QQVLAAAELRGLEPALD 179 Query: 181 KVADKLVGALRLPNDQTGDCQLFTTRLAEMAKGLG-VEFRFGQNIERLDFAGDRINGVLV 239 VG + ++ GDC +F RL + + G F G+ + +L ++ + + Sbjct: 180 GAP--FVGGVFTAGEEVGDCHVFCLRLEALLRASGQCRFLLGRPVTQLVQRQGQVVALQL 237 Query: 240 NGELLTADHYVLALGSYSPQLLKPLGIKAPVYPLKGYSLTVPITNPEMAPTSTILDETYK 299 + L + VL G P L P G++ PVYPLKGYSLT PI+ + P ++ D K Sbjct: 238 GDQQLDVEQLVLCAGHRGPGLALP-GVQIPVYPLKGYSLTAPISAGHLPPEVSLTDYERK 296 Query: 300 VAITRFDQRIRVGGMAEIAGFDLSLNPRRRETLEMITTDLYPEGGDISQATFWTGLRPAT 359 + R Q++RV M +I GFD S++ RR +++ + + P D QA W G+RPAT Sbjct: 297 IVYARLGQQLRVAAMVDIVGFDESVDMRRLQSMRRLALETLPRAADYGQAVEWAGMRPAT 356 Query: 360 PDGTPIVGATRYRNLFLNTGHGTLGWTMACGSGRYLADLM 399 P G PI+G T YRNL+LN GHG LG+T+ACGS + LA +M Sbjct: 357 PTGVPIIGGTVYRNLWLNLGHGALGFTLACGSAQRLARMM 396 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: 444 Number of extensions: 17 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: 397 Length adjustment: 31 Effective length of query: 401 Effective length of database: 366 Effective search space: 146766 Effective search space used: 146766 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