Align D-lactate dehydrogenase; EC 1.1.1.28 (characterized)
to candidate CA265_RS09010 CA265_RS09010 3-phosphoglycerate dehydrogenase
Query= CharProtDB::CH_091801 (331 letters) >FitnessBrowser__Pedo557:CA265_RS09010 Length = 315 Score = 122 bits (306), Expect = 1e-32 Identities = 85/290 (29%), Positives = 140/290 (48%), Gaps = 34/290 (11%) Query: 31 TQELLTPETAKLAEGSDSAVVYQQLDYTRETLTALANVGVTNLSLRNVGTDNIDFDAARE 90 T+ + + A+ + D+ V +E + A+ N+ + + VG DNID + AR Sbjct: 26 TETVPQDQLAEALKNYDAITVRSATKVRKELIDAVPNIKL--IGRGGVGMDNIDVEYARS 83 Query: 91 FNFNISNVPVYSPNAIAEHSMLQLSRLLR------RTKALDAKIAKRDLRWAPTTGREMR 144 N+ N P S ++AE L +R R ++ +L+ A G E+ Sbjct: 84 QGINVVNTPAASSLSVAELVFSHLFTGIRFLQDANRKMPVEGSTQFNNLKKAYAKGTELS 143 Query: 145 MQTVGVIGTGHIGRVAINILKGFGAKVIAYDKYPNAE---LQAEG-------LYVDTLDE 194 +T+G+IG G IGR + G G V+AYD YP+ L+ +G + +LDE Sbjct: 144 GKTIGIIGFGRIGRATAKVALGLGMNVLAYDLYPSESEITLEFQGGKSVSIPIKTVSLDE 203 Query: 195 LYAQADAISLYVPGVPENHHLINADAIAKMKDGVVIMNAARGNLMDIDAIIDGLNSGKIS 254 + +D SL+ P + ++ A+ AKMK+GV I+N +RG +D A+ID LNSGK+S Sbjct: 204 VITGSDFFSLHTPFADKP--ILGAEEFAKMKNGVGIVNCSRGGTIDELALIDALNSGKVS 261 Query: 255 DFGMDVYENEVACSMKIGLVKNSPDAKIADLIARENVMITPHTAFYTTKA 304 G+DV++NE +A+++ + +TPH T +A Sbjct: 262 FAGLDVFDNE--------------PTPLAEILTHPKISLTPHIGASTNEA 297 Lambda K H 0.317 0.133 0.374 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: 255 Number of extensions: 11 Number of successful extensions: 3 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: 331 Length of database: 315 Length adjustment: 28 Effective length of query: 303 Effective length of database: 287 Effective search space: 86961 Effective search space used: 86961 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: 48 (23.1 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