Align D-alanine dehydrogenase (EC 1.4.99.-) (characterized)
to candidate Ac3H11_1644 D-amino acid dehydrogenase small subunit (EC 1.4.99.1)
Query= reanno::azobra:AZOBR_RS08020 (436 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1644 Length = 405 Score = 236 bits (601), Expect = 1e-66 Identities = 142/402 (35%), Positives = 202/402 (50%), Gaps = 4/402 (0%) Query: 1 MRVIVLGSGVIGVSTAYFLAKAGHEVTVVDRQPGPALETSYANAGEVSPGYSAPWAAPGL 60 M+V VLG+G++G++TAY L + G +VTV+D Q P S N ++S Y P A L Sbjct: 1 MQVCVLGAGIVGLATAYELHQRGMQVTVID-QAQPGTGASGGNGAQLSYSYVQPLANADL 59 Query: 61 MAKAVKWMLMKHSPLVIRPKMDPAMWSWCLKLLANANERSYEINKGRMVRLAEYSRDCLR 120 + + +L SPL +RP+ D W W L+ L N R+ E + +++ LA SR Sbjct: 60 WQQLPELLLSPRSPLKMRPQWDVHQWRWGLEFLRACNRRTSERSTEQLLALATLSRHGFE 119 Query: 121 VLRDETGIRYDERAKGTLQVFRTQKQVDAAATDMAVLDRFKVPYSLLDVEGCAAVEPALR 180 +R + D + G L ++ T + AA M + + + + C +EPAL+ Sbjct: 120 AMRQAEQLDCDFSSTGKLVLYSTPAGLAAAQRQMELQRAWGSEQESVSPQRCVEIEPALQ 179 Query: 181 LVKEKIVGGLLLPGDETGDCFRFTNALAAMATELGVEFRYNTGIRKLESDGRRVTGVVTD 240 + I G + P + DC L + GV F I +R+ V T Sbjct: 180 HYQSHIAGAIHTPSECAADCLAVCQGLHRILAARGVHFVLGARIEGFVRRAQRIAAVQTS 239 Query: 241 AGTLTADSYVVAMGSYSPTLVKPFGLDLPVYPVKGYSLTLPIVDAA-GAPESTVMDETHK 299 AG + A +V+A+GS S + G LPVYP+KGYS+TL DAA AP V D K Sbjct: 240 AGAIEAQQFVLALGSASHQAAQTLGFRLPVYPLKGYSITLDTTDAANAAPRVNVTDAARK 299 Query: 300 IAVTRLGDRIRVGGTAELTGFDLTLRPGRRGPLDHVVSDLFPTGGDLSKAEFWTGLRPNT 359 + R+G R+RV G AEL G + + P R L LFP D + WTG+RP T Sbjct: 300 VVFARIGQRLRVAGMAELVGHNHHIPPARIQSLREATRALFPGCSDFGELRPWTGMRPAT 359 Query: 360 PDGTPIVG--PTPVRNLFLNTGHGTLGWTMAAGSGRVVADVV 399 P G P+VG P NL LNTGHG LG+T+A G+ VA++V Sbjct: 360 PTGVPLVGRHPHAPDNLLLNTGHGALGFTLAFGTAAQVAELV 401 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: 395 Number of extensions: 17 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: 405 Length adjustment: 32 Effective length of query: 404 Effective length of database: 373 Effective search space: 150692 Effective search space used: 150692 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: 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