Align D-arginine dehydrogenase (EC 1.4.99.6) (characterized)
to candidate WP_057507894.1 ABB28_RS06665 D-amino acid dehydrogenase small subunit
Query= BRENDA::Q9HTQ0 (432 letters) >NCBI__GCF_001431535.1:WP_057507894.1 Length = 428 Score = 634 bits (1634), Expect = 0.0 Identities = 315/426 (73%), Positives = 358/426 (84%), Gaps = 1/426 (0%) Query: 1 MRVLVLGSGVIGTASAYYLARAGFEVVVVDRQDGPALETSFANAGQVSPGYASPWAAPGI 60 MRVL+LGSGVIGT SA+YL +AGFEV V+DRQ GPALETSFANAGQ+S GY SPWAAPG+ Sbjct: 1 MRVLILGSGVIGTTSAWYLRQAGFEVTVLDRQPGPALETSFANAGQLSFGYTSPWAAPGV 60 Query: 61 PLKAMKWLLEKHAPLAIKLTSDPSQYAWMLQMLRNCTAERYAVNKERMVRLSEYSRDCLD 120 P KA+ WL EKHAPLAI+ D +QY W+ QMLRNCT ERYA+NK RMVR+SEYSRDCL+ Sbjct: 61 PKKAIGWLFEKHAPLAIRPGMDLAQYRWLWQMLRNCTQERYAINKARMVRMSEYSRDCLN 120 Query: 121 ELRAETGIAYEGRTLGTTQLFRTQAQLDAAGKDIAVLERSGVPYEVLDRDGIARVEPALA 180 +LRAETGI YEGR LGTTQLFRTQ QLDA+ +DI VL + GVPYEVLDR GI EPALA Sbjct: 121 QLRAETGIDYEGRDLGTTQLFRTQQQLDASAQDIEVLAQYGVPYEVLDRAGIVAAEPALA 180 Query: 181 KVADKLVGALRLPNDQTGDCQLFTTRLAEMAKGLGVEFRFGQNIERLDFAGDRINGVLVN 240 V D LVGALRLP DQTGDCQLFT RLA MA GVEFR+ +I ++ GDRI GV V+ Sbjct: 181 HV-DGLVGALRLPRDQTGDCQLFTRRLAAMAAEAGVEFRYDVDIAGVEREGDRITGVRVD 239 Query: 241 GELLTADHYVLALGSYSPQLLKPLGIKAPVYPLKGYSLTVPITNPEMAPTSTILDETYKV 300 G+L TADHYV+ALGSYSP L+ PLG+ PVYPLKGYSLT+PIT+P MAPTSTILDE+YKV Sbjct: 240 GKLETADHYVVALGSYSPALVAPLGLDLPVYPLKGYSLTLPITDPAMAPTSTILDESYKV 299 Query: 301 AITRFDQRIRVGGMAEIAGFDLSLNPRRRETLEMITTDLYPEGGDISQATFWTGLRPATP 360 A+TRFD RIRVGGMAE+AGFDLSL+ RRR+TLE + DLYP+GGD+S+A FWTGLRPATP Sbjct: 300 AVTRFDNRIRVGGMAEVAGFDLSLSARRRQTLERVVRDLYPKGGDLSRAEFWTGLRPATP 359 Query: 361 DGTPIVGATRYRNLFLNTGHGTLGWTMACGSGRYLADLMAKKRPQISTEGLDISRYSNSP 420 DGTP++GAT RNLFLNTGHGTLGWTMACGSGRYLADLM+ ++PQISTEGLDI RY Sbjct: 360 DGTPVIGATPLRNLFLNTGHGTLGWTMACGSGRYLADLMSARQPQISTEGLDIFRYGGKG 419 Query: 421 ENAKNA 426 A +A Sbjct: 420 AVAAHA 425 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: 627 Number of extensions: 16 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: 428 Length adjustment: 32 Effective length of query: 400 Effective length of database: 396 Effective search space: 158400 Effective search space used: 158400 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 24 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