Align D-amino acid dehydrogenase; D-alanine dehydrogenase; EC 1.4.99.- (characterized)
to candidate HSERO_RS08375 HSERO_RS08375 D-amino acid dehydrogenase small subunit
Query= SwissProt::P0A6J5 (432 letters) >FitnessBrowser__HerbieS:HSERO_RS08375 Length = 433 Score = 601 bits (1550), Expect = e-176 Identities = 296/432 (68%), Positives = 345/432 (79%), Gaps = 7/432 (1%) Query: 1 MRVVILGSGVVGVASAWYLNQAGHEVTVIDREPGAALETSAANAGQISPGYAAPWAAPGV 60 MRVVILGSGV+GV SAWYL +AGH+VTV+DR+PG ALETS NAGQISPGYA+PWAAPG+ Sbjct: 1 MRVVILGSGVIGVTSAWYLARAGHDVTVLDRQPGPALETSFGNAGQISPGYASPWAAPGI 60 Query: 61 PLKAIKWMFQRHAPLAVRLDGTQFQLKWMWQMLRNCDTSHYMENKGRMVRLAEYSRDCLK 120 PLKAIKWMFQ HAPLA+RLDG+ QL+WMWQMLRNC+ Y NK RMVRLAEYSRDCL+ Sbjct: 61 PLKAIKWMFQEHAPLAIRLDGSFNQLRWMWQMLRNCNAERYAVNKERMVRLAEYSRDCLR 120 Query: 121 ALRAETNIQYEGRQGGTLQLFRTEQQYENATRDIAVLEDAGVPYQLLESSRLAEVEPALA 180 LRA+ I YEGRQ GTLQLFR+++Q E A +DIAVL++AGVP++LL +L EPALA Sbjct: 121 DLRADVGIPYEGRQQGTLQLFRSQEQLEGAAKDIAVLKEAGVPFELLTPDQLGNAEPALA 180 Query: 181 EVAHKLTGGLQLPNDETGDCQLFTQNLARMAEQAGVKFRFNTPVDQLLCDGEQIYGVKCG 240 +V KLTGGL+LPNDETGDCQLFT LA MAEQ GVKFR+ +D L G +I GV CG Sbjct: 181 KVRDKLTGGLRLPNDETGDCQLFTTRLATMAEQIGVKFRYGVDIDALAMAGGKIAGVVCG 240 Query: 241 DEVIKADAYVMAFGSYSTAML---KGIVDIPVYPLKGYSLTIPIAQEDGAPVSTILDETY 297 E+++AD+YV+A GSYS +L G+ IPVYPLKGYS+T+PI APVSTILDETY Sbjct: 241 KELVQADSYVVALGSYSPQLLGEVPGLPAIPVYPLKGYSITVPITDASAAPVSTILDETY 300 Query: 298 KIAITRFDNRIRVGGMAEIVGFNTELLQPRRETLEMVVRDLYPRGGHVEQATFWTGLRPM 357 KIA+TRFD+RIRVGGMAEIVG++T L RR TLE+VV DL+P G QA+FWTGLRPM Sbjct: 301 KIAVTRFDDRIRVGGMAEIVGYDTALKAKRRATLELVVNDLFPGAGDTAQASFWTGLRPM 360 Query: 358 TPDGTPVVGRTRFKNLWLNTGHGTLGWTMACGSGQLLSDLLSGRTPAIPYEDLSVARY-- 415 TPDGTPVVG T NL++NTGHGTLGWTM+CGSGQLL+DL+SGR PAI +EDLSV RY Sbjct: 361 TPDGTPVVGATPVSNLYINTGHGTLGWTMSCGSGQLLADLISGRRPAIAHEDLSVERYLS 420 Query: 416 --SRGFTPSRPG 425 R TP G Sbjct: 421 SGGRAQTPRLAG 432 Lambda K H 0.319 0.136 0.415 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: 668 Number of extensions: 27 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 432 Length of database: 433 Length adjustment: 32 Effective length of query: 400 Effective length of database: 401 Effective search space: 160400 Effective search space used: 160400 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 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