Align D-arginine dehydrogenase (EC 1.4.99.6) (characterized)
to candidate SM_b20267 SM_b20267 D-amino acid dehydrogenase
Query= BRENDA::Q9HTQ0 (432 letters) >FitnessBrowser__Smeli:SM_b20267 Length = 413 Score = 162 bits (409), Expect = 2e-44 Identities = 127/425 (29%), Positives = 190/425 (44%), Gaps = 28/425 (6%) Query: 3 VLVLGSGVIGTASAYYLARAGFEVVVVDRQDGPALETSFANAGQVSPGYASPWAAPGIPL 62 V+V+G+GV+G +A +G V V+DR+ GPA S NAG + P A+PGI Sbjct: 6 VIVIGAGVVGLTAAIAAVASGLSVTVLDRE-GPAAGASAGNAGAFAFTDILPLASPGILK 64 Query: 63 KAMKWLLEKHAPLAIKLTSDPSQYA-----WMLQMLRNCTAERYAVNKERMVRLSEYSRD 117 KA KWLL+ PL + P YA WM + R C R A + L + S+ Sbjct: 65 KAPKWLLDPLGPLTV-----PPAYALKIAPWMFRFWRACQPGRVAHSTAAQTALMDLSKA 119 Query: 118 CLDELRAETGIAYEGRTLGTTQLFRTQAQLDAAGKDIAVLERSGVPYEVLDRDGIARVEP 177 L+ TG A R G Q++ +A+ A+ G+ + LD GIA ++P Sbjct: 120 ELEPFLGATGTASMLRKEGNLQVYEGEAEFKASLAGWKARADHGIEFRHLDAAGIAEIQP 179 Query: 178 ALAKVADKLVGALRLPN-DQTGDCQLFTTRLAEMAKGLGVEFRFGQNIERLDFAGDRING 236 LA + A P D +L+T LA+ + +G + + L + Sbjct: 180 GLAA---RFTHATFTPGWYSIADPKLYTLALADHFRTIGGVIERAE-VTALKPVDGGVEV 235 Query: 237 VLVNGELLTADHYVLALGSYSPQLLKPLGIKAPVYPLKGYSLTVPITNPEMAPTSTILDE 296 + +G A VL+ G++S ++ + LG P+ +GY+ T+P ++ T Sbjct: 236 LSADGRRRRAAQVVLSAGAFSHRVARTLGESIPLETERGYNTTLPADAFDLRTQITFGGH 295 Query: 297 TYKVAITRFDQRIRVGGMAEIAGFDLSLNPRRRETL----EMITTDLYPEGGDISQATFW 352 + +TR IRVGG E+ G DL N RR E + + L PEGG W Sbjct: 296 GF--VVTRLSTGIRVGGAVELGGLDLPPNFRRSEAMLKKAQAFLPGLKPEGG-----VQW 348 Query: 353 TGLRPATPDGTPIVGATRYR-NLFLNTGHGTLGWTMACGSGRYLADLMAKKRPQISTEGL 411 G RP+ PD P +G R + GHG LG T + G+ R +ADL+ + P I Sbjct: 349 MGFRPSLPDSLPAIGRARATPRVIFAFGHGHLGLTQSAGTARIVADLLTGRTPAIDIAPF 408 Query: 412 DISRY 416 R+ Sbjct: 409 SPQRF 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: 421 Number of extensions: 21 Number of successful extensions: 8 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