Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate 350680 BT1152 D-3-phosphoglycerate dehydrogenase (NCBI ptt file)
Query= BRENDA::Q9I530 (329 letters) >FitnessBrowser__Btheta:350680 Length = 306 Score = 107 bits (267), Expect = 4e-28 Identities = 76/229 (33%), Positives = 123/229 (53%), Gaps = 21/229 (9%) Query: 24 GFELHFQQAHLQADTAVLAQGFEVVCAFV--NDDLSRPVLERLAAGGTRLVALRSAGYNH 81 G+EL + + D A L + A + +D + VL+ AA ++V AGY++ Sbjct: 27 GYELALLEKY--TDKAQLLDAVKDANAIIIRSDIIDAEVLD--AAKELKIVVRAGAGYDN 82 Query: 82 VDLAAAEALGLPVVHVPAYSPHAVAEHAVGLILTLNRRLHRAYNRTREGDFSLHGLTGFD 141 VDLAAA A + V++ P + +AVAE A+G+++ R + +G +G + Sbjct: 83 VDLAAATAHNVCVMNTPGQNSNAVAELALGMMVYAVRNFY-------------NGTSGTE 129 Query: 142 LHGKRVGVIGTGQIGETFARIMAGFGCELLAYDPY-PNPRIQALGGRYL-ALDALLAESD 199 L GK++G+ G +G AR+ GFG E+ AYD + P I+ G + L + + L Sbjct: 130 LMGKKLGIHAYGNVGRNVARVAKGFGMEVYAYDAFCPKEVIEKDGVKALDSAEELYKTCQ 189 Query: 200 IVSLHCPLTADTRHLIDAQRLATMKPGAMLINTGRGALVNAAALIEALK 248 +VSLH P TA+T++ I+ L M GAML+NT R ++N A LI+ ++ Sbjct: 190 VVSLHIPATAETKNSINYALLKDMPKGAMLVNTARKEVINEAELIKLME 238 Lambda K H 0.323 0.137 0.402 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: 225 Number of extensions: 10 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: 329 Length of database: 306 Length adjustment: 27 Effective length of query: 302 Effective length of database: 279 Effective search space: 84258 Effective search space used: 84258 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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