Align D-arginine dehydrogenase (EC 1.4.99.6) (characterized)
to candidate GFF5186 PS417_26560 amino acid dehydrogenase
Query= BRENDA::Q9HTQ0 (432 letters) >FitnessBrowser__WCS417:GFF5186 Length = 407 Score = 285 bits (729), Expect = 2e-81 Identities = 161/412 (39%), Positives = 230/412 (55%), Gaps = 14/412 (3%) Query: 3 VLVLGSGVIGTASAYYLARAGFEVVVVDRQDGPALETSFANAGQVSPGYASPWAAPGIPL 62 V ++G GVIG ASAY L RAG EV ++D ++ ETSFAN GQ+S Y +P A G+PL Sbjct: 2 VCIIGGGVIGLASAYALVRAGHEVTLIDARETLGSETSFANGGQLSYRYVAPLADAGVPL 61 Query: 63 KAMKWLLEKHAPLAIKLTSDPSQYAWMLQMLRNCTAERYAVNKERMVRLSEYSRDCLDEL 122 +A+ WLL +PL ++ DP Q+ WM L C N ++RL+ S+D L Sbjct: 62 QAIGWLLRGDSPLKLRPRLDPQQWRWMAAFLGACRGSVNKRNAAHLLRLASLSQDTLQVW 121 Query: 123 RAETGI-AYEGRTLGTTQLFRTQAQLDAA-GKDIAVLERSGVPYEVLDRDGIARVEPALA 180 R + ++ R G FR + A GK +L++ +VL AR+EPALA Sbjct: 122 RDLDRLDGFDWRRNGKLVTFRNANAFERARGKVTDILQQ-----QVLSTADCARLEPALA 176 Query: 181 KVADKLVGALRLPNDQTGDCQLFTTRLAEMAKGLG-VEFRFGQNIERLDFAGDRINGVLV 239 VG + PN++ DC F RLA + G F G+ + + A R+ + + Sbjct: 177 DGG--FVGGIYTPNEEVADCHAFCQRLAARLEASGRCRFMLGRKVTGIRHAKGRVQAIEL 234 Query: 240 NGELLTADHYVLALGSYSPQLLKPLGIKAPVYPLKGYSLTVPITNPEMAPTSTILDETYK 299 E++ +H VLA G S +L G+ P+YPLKGYSL+VPI AP +I D K Sbjct: 235 GDEVMPVEHLVLAAGYRSAEL----GVPLPLYPLKGYSLSVPIGAQHQAPNVSITDYDRK 290 Query: 300 VAITRFDQRIRVGGMAEIAGFDLSLNPRRRETLEMITTDLYPEGGDISQATFWTGLRPAT 359 + R +++RV M +I GFD L P+R ++ +++P GD QA W G+RPAT Sbjct: 291 IVYARIGEQLRVAAMVDIVGFDARLEPKRLALMKRQALEIFPLAGDYDQAVEWAGMRPAT 350 Query: 360 PDGTPIVGATRYRNLFLNTGHGTLGWTMACGSGRYLADLMAKKRPQISTEGL 411 P G P++GA+ YRNL+LN GHG LG+T+ACGSG+ LA+L+ + P I +GL Sbjct: 351 PTGVPLIGASVYRNLWLNLGHGALGFTLACGSGQLLAELIGQHAPSIDMQGL 402 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: 483 Number of extensions: 23 Number of successful extensions: 3 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: 407 Length adjustment: 32 Effective length of query: 400 Effective length of database: 375 Effective search space: 150000 Effective search space used: 150000 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