Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate CA265_RS23175 CA265_RS23175 phosphoglycerate dehydrogenase
Query= BRENDA::Q9I530 (329 letters) >FitnessBrowser__Pedo557:CA265_RS23175 Length = 309 Score = 135 bits (341), Expect = 1e-36 Identities = 81/252 (32%), Positives = 138/252 (54%), Gaps = 8/252 (3%) Query: 65 AAGGTRLVALRSAGYNHVDLAAAEALGLPVVHVPAYSPHAVAEHAVGLILTLNRRLHRAY 124 AA + VA AG +++D A + +++ P + AV EHA GL+L+L RA Sbjct: 61 AAPNLKFVARAGAGLDNIDDKIAFERNIELINAPEGNCDAVGEHATGLLLSLMNNFRRAD 120 Query: 125 NRTREGDFSLHGLTGFDLHGKRVGVIGTGQIGETFARIMAGFGCELLAYDPYPNPRIQAL 184 R G + G G++L GK+VG+IG G +G++FA+ +AGF +++AYD Y A Sbjct: 121 IEIRNGVWDREGNRGYELKGKKVGIIGYGFMGQSFAKKLAGFEVDVMAYDKYKTGFSDAF 180 Query: 185 GGRYLALDALLAESDIVSLHCPLTADTRHLIDAQRLATMKPGAMLINTGRGALVNAAALI 244 R ++++ ++ SD++SLH PLTA+T+ ++D + K INT RG +VN A++ Sbjct: 181 -AREVSMEEIVKHSDVLSLHIPLTAETKQMVDDEYFYHFKKPIFFINTARGEIVNTPAVL 239 Query: 245 EALKSGQLGYLGLDVYEEEADIFFEDRSDQPLQDDVLARLLSFPNVVVTAHQAFLTREAL 304 A+KSG++ GLDV + E F +Q ++ L + V++T H T ++ Sbjct: 240 NAIKSGKILGAGLDVLQTEK---FPALGEQAWYNE----LKNNDKVILTPHVGGWTFDSY 292 Query: 305 AAIADTTLDNIA 316 I++ + ++ Sbjct: 293 RKISEVLAEKLS 304 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: 264 Number of extensions: 11 Number of successful extensions: 2 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: 309 Length adjustment: 28 Effective length of query: 301 Effective length of database: 281 Effective search space: 84581 Effective search space used: 84581 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 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