Align D-alanine dehydrogenase (EC 1.4.99.-) (characterized)
to candidate RR42_RS04385 RR42_RS04385 amino acid dehydrogenase
Query= reanno::azobra:AZOBR_RS08020 (436 letters) >FitnessBrowser__Cup4G11:RR42_RS04385 Length = 420 Score = 295 bits (754), Expect = 2e-84 Identities = 165/411 (40%), Positives = 231/411 (56%), Gaps = 4/411 (0%) Query: 1 MRVIVLGSGVIGVSTAYFLAKAGHEVTVVDRQPGPALETSYANAGEVSPGYSAPWAAPGL 60 M+V+++G+GVIG+S A+ LA GHEVTV++R+ GP ETS+AN G++S Y AP A PG+ Sbjct: 1 MKVVIVGAGVIGMSAAWRLAGDGHEVTVLERRDGPGEETSFANGGQLSYSYVAPLAGPGV 60 Query: 61 MAKAVKWMLMKHSPLVIRPKMDPAMWSWCLKLLANANERSYEINKGRMVRLAEYSRDCLR 120 +AK W+L SP+ RP DPA W W N + E +++RLA YSRD ++ Sbjct: 61 LAKVPGWLLRADSPMRFRPSADPAQWRWLAAFARACNASASEAATRKLLRLAFYSRDLMQ 120 Query: 121 VLRDETGIRYDERAKGTLQVFRTQKQVDAAATDMAVLDRFKVPYSLLDVEGCAAVEPALR 180 D + +G L V R AA + LD + C A+EPAL Sbjct: 121 AFVDSQPADFGFARRGKLIVHRDAASFAAACRLLDYQASLGCEQQALDGDACVALEPALA 180 Query: 181 LVKEKIVGGLLLPGDETGDCFRFTNALAAMATEL-GVEFRYNTGIRKLESDGRRVTGVVT 239 ++ I G + P +E DC RF ALA + + GV R+ T + +E +G RV+GV T Sbjct: 181 GIRGAIAGAIHTPSEEVADCHRFCLALAQLLHDRPGVSLRFGTSVLGIEREGDRVSGVRT 240 Query: 240 DAGTLTADSYVVAMGSYSPTLVKPFGLDLPVYPVKGYSLTLPIVDAAGAPESTVMDETHK 299 DAG AD+ VVA G S L+KP G+ P++P+KGYS+T+PI D AP ++ D K Sbjct: 241 DAGIERADAVVVAGGIGSVALLKPLGVQAPLWPLKGYSITVPIRDGERAPHISITDAARK 300 Query: 300 IAVTRLGDRIRVGGTAELTGFDLTLRPGRRGPLDHVVSDLF---PTGGDLSKAEFWTGLR 356 I R+G+ +RV G A+L D + R L LF G + + + W GLR Sbjct: 301 IVYARIGNTLRVAGMADLVRADTNIDRARIATLACETRTLFGGMAPGMEPEQLQPWAGLR 360 Query: 357 PNTPDGTPIVGPTPVRNLFLNTGHGTLGWTMAAGSGRVVADVVGGRQTEID 407 P TP G P+VG + VR L+LN GHG LG+T+A GS ++AD + GR+ ID Sbjct: 361 PATPTGLPMVGRSGVRGLWLNIGHGALGFTLAMGSAGLLADGLAGRKPAID 411 Lambda K H 0.319 0.136 0.408 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: 486 Number of extensions: 19 Number of successful extensions: 4 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: 436 Length of database: 420 Length adjustment: 32 Effective length of query: 404 Effective length of database: 388 Effective search space: 156752 Effective search space used: 156752 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 (21.7 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