Align D-alanine dehydrogenase (EC 1.4.99.-) (characterized)
to candidate 3607136 Dshi_0558 D-amino-acid dehydrogenase (RefSeq)
Query= reanno::azobra:AZOBR_RS08020 (436 letters) >FitnessBrowser__Dino:3607136 Length = 419 Score = 506 bits (1304), Expect = e-148 Identities = 247/419 (58%), Positives = 306/419 (73%), Gaps = 1/419 (0%) Query: 1 MRVIVLGSGVIGVSTAYFLAKAGHEVTVVDRQPGPALETSYANAGEVSPGYSAPWAAPGL 60 M+V+++G+GVIGV+TAY+LAK G +V V+DRQ GP LETSYANAG++S G S+PWAAPG+ Sbjct: 1 MKVVIMGAGVIGVTTAYYLAKQGVKVVVIDRQTGPGLETSYANAGQLSYGMSSPWAAPGI 60 Query: 61 MAKAVKWMLMKHSPLVIRPKMDPAMWSWCLKLLANANERSYEINKGRMVRLAEYSRDCLR 120 KAVKWM MK PL I P + P MW WCL++L N N SY INKGRMVR++ YSRD + Sbjct: 61 PLKAVKWMFMKRRPLFIMPLLSPTMWKWCLQMLRNCNAESYAINKGRMVRVSSYSRDVMP 120 Query: 121 VLRDETGIRYDERAKGTLQVFRTQKQVDAAATDMAVLDRFKVPYSLLDVEGCAAVEPALR 180 L +TGI YD R GTLQ+FRT KQ+ A+ D AVL + PY +L + C VEPAL Sbjct: 121 DLIADTGIEYDGRQMGTLQLFRTAKQMKASKADQAVLAEYGSPYEVLGRDACIEVEPALA 180 Query: 181 LVKEKIVGGLLLPGDETGDCFRFTNALAAMATELGVEFRYNTGIRKLESDGRRVTGVVTD 240 V+ K VGGL L D TGDC FT AL E+GVEF+Y I+ + + +++GV T+ Sbjct: 181 EVRGKFVGGLRLTSDRTGDCRMFTIALTDKCIEMGVEFQYGQTIKAIAVENGKISGVDTE 240 Query: 241 -AGTLTADSYVVAMGSYSPTLVKPFGLDLPVYPVKGYSLTLPIVDAAGAPESTVMDETHK 299 AG ++ D+YV AMGSY+ ++ P G+ LPVYPVKGYS+TLP+ + A AP+ST+MDETHK Sbjct: 241 IAGRISGDAYVCAMGSYAVNVLNPIGIRLPVYPVKGYSVTLPVTNDAFAPQSTIMDETHK 300 Query: 300 IAVTRLGDRIRVGGTAELTGFDLTLRPGRRGPLDHVVSDLFPTGGDLSKAEFWTGLRPNT 359 +A+TRLGDRIRV G AE+ G+ L P + HV+ DLFP GGDLS+AE WTGLRP T Sbjct: 301 VAITRLGDRIRVAGQAEIVGYSNRLGPHATDTVRHVIGDLFPKGGDLSRAEGWTGLRPMT 360 Query: 360 PDGTPIVGPTPVRNLFLNTGHGTLGWTMAAGSGRVVADVVGGRQTEIDMDGLTVARYGR 418 PDGTP++GPT NLFLNTGHGTLGWTMA GSGR VADVV G+ EI M+GLT ARY R Sbjct: 361 PDGTPVLGPTRYENLFLNTGHGTLGWTMACGSGRAVADVVMGKPPEISMEGLTAARYAR 419 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: 552 Number of extensions: 18 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: 436 Length of database: 419 Length adjustment: 32 Effective length of query: 404 Effective length of database: 387 Effective search space: 156348 Effective search space used: 156348 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