Align D-lactate dehydrogenase; EC 1.1.1.28 (characterized)
to candidate CCNA_02230 CCNA_02230 gluconate 2-dehydrogenase
Query= CharProtDB::CH_091799 (329 letters) >FitnessBrowser__Caulo:CCNA_02230 Length = 319 Score = 97.4 bits (241), Expect = 4e-25 Identities = 81/271 (29%), Positives = 126/271 (46%), Gaps = 27/271 (9%) Query: 57 SRPVLEELKKHGVKYIALRCAGFNNVDLDAAKELGLKVVRVPAYDPEAVAEHAIGMMMTL 116 SR +L E+ + G+ IA G++ VD+ K G+ V + VA+HA+G+++ Sbjct: 63 SRDMLAEMPRLGL--IACVSVGYDGVDVPWCKAHGIAVTHSTGLNAADVADHAVGLVLAA 120 Query: 117 NRRIHRAYQRTRDANFS----LEGLTGFTMYGKTAGVIGTGKIGVAMLRILKGFGMRLLA 172 R I QR R ++S + G + G+ AGV+G G IG A+ LK F M++ Sbjct: 121 WRGIVEGDQRLRGGHWSHAERMAPRPG--LRGRKAGVVGLGHIGEAVAARLKAFDMKVAW 178 Query: 173 FDPYPSAAALELGVEYVD-LPTLFSESDVISLHCPLTPENYHLLNEAAFEQMKNGVMIVN 231 + P P E D L L +SDV+ + N HL+N+ E + +IVN Sbjct: 179 WAPRPK----ETDYPRADSLMALARDSDVLIVCARPDDSNRHLINKPVIEAVGAQGLIVN 234 Query: 232 TSRGALIDSQAAIEALKNQKIGSLGMDVYENERDLFFEDKSNDVIQDDVFRRLSACHNVL 291 +RG+LID A I+AL+ +G +DV+E E R + + Sbjct: 235 VARGSLIDEDALIQALRAGTLGMAALDVFEQE--------------PTPAARWADVPRTV 280 Query: 292 FTGHQAFLTAEALTSISQTTLQNLSNLEKGE 322 T H A T ++L ++ TL+NL GE Sbjct: 281 LTPHTAGATLDSLPAMVSLTLENLRRYFHGE 311 Lambda K H 0.320 0.136 0.388 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: 187 Number of extensions: 6 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: 319 Length adjustment: 28 Effective length of query: 301 Effective length of database: 291 Effective search space: 87591 Effective search space used: 87591 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 (21.8 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