Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate CCNA_03838 CCNA_03838 gluconate 2-dehydrogenase/glyoxylate reductase/hydroxypyruvate reductase
Query= BRENDA::Q9I530 (329 letters) >FitnessBrowser__Caulo:CCNA_03838 Length = 328 Score = 138 bits (347), Expect = 2e-37 Identities = 101/312 (32%), Positives = 158/312 (50%), Gaps = 27/312 (8%) Query: 26 ELHFQQAHLQADTAVLAQG-FEVVCAFVNDDLSRPVLERLAAGGTRLVALRSAGYNHVDL 84 EL+ + AD V A +V+ + D + +L R + +L+A AG +++D+ Sbjct: 29 ELNVSDKPMTADELVDAMSRADVLVPTITDRIDSRLLSR-SGDRLKLIANFGAGVDNIDV 87 Query: 85 AAAEALGLPVVHVPAYSPHAVAEHAVGLILTLNRRLHRAYNRTREGDFSLHG-----LTG 139 A A A G+ V + P A+ + LI+ +RR+ + G F HG + G Sbjct: 88 ATANARGIIVTNTPGVLTEDTADLTMTLIMAASRRIVEGAEVVKAGGF--HGWSPTWMMG 145 Query: 140 FDLHGKRVGVIGTGQIGETFARIMAGFGCELLAYDPYP-NPRI-QALGGRYL-ALDALLA 196 L GKR+G+IG G+IG+ AR FG ++ ++ P +PRI + LG Y +LD +LA Sbjct: 146 RRLWGKRLGIIGMGRIGQAVARRAKAFGMQVHYHNRKPVSPRIAEELGCTYWESLDQMLA 205 Query: 197 ESDIVSLHCPLTADTRHLIDAQRLATMKPGAMLINTGRGALVNAAALIEALKSGQLGYLG 256 D VS++CP T T HL+ A+RL ++P A+++NT RG +++ AL L G++ G Sbjct: 206 RMDFVSVNCPHTPATYHLLSARRLKLLRPHAVVVNTARGEVIDEGALANMLAKGEIAGAG 265 Query: 257 LDVYEEEADIFFEDRSDQPLQDDVLARLLSFPNVVVTAHQAFLTREALAAIADTTLDNIA 316 LDVYE E I +LL PNVV+ H T E + + + N+ Sbjct: 266 LDVYEHEPAI--------------NPKLLKLPNVVLLPHMGSATVEGRIDMGEKVIVNVK 311 Query: 317 AWQDG-TPRNRV 327 + DG P +RV Sbjct: 312 TFMDGHRPPDRV 323 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: 232 Number of extensions: 11 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: 329 Length of database: 328 Length adjustment: 28 Effective length of query: 301 Effective length of database: 300 Effective search space: 90300 Effective search space used: 90300 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: 49 (23.5 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