Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate 17613 b3553 putative dehydrogenase (VIMSS)
Query= curated2:O27051 (525 letters) >FitnessBrowser__Keio:17613 Length = 324 Score = 184 bits (468), Expect = 3e-51 Identities = 107/273 (39%), Positives = 153/273 (56%), Gaps = 5/273 (1%) Query: 51 SRTKVTREVIEAAPRLKIIARAGVGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLM 110 S V ++E P+L+ + VG DN DV A T R I++++ P + TVA+ + L+ Sbjct: 52 SNENVNAALLEKMPKLRATSTISVGYDNFDVDALTARKILLMHTPTVLTETVADTLMALV 111 Query: 111 LALARKIAIADRSVKEGKWEKN---RFMGIELNGKTLGIIGMGRIGSQVVVRTK-AFGMD 166 L+ AR++ VK G+W + + G +++ KTLGI+GMGRIG + R F M Sbjct: 112 LSTARRVVEVAERVKAGEWTASIGPDWYGTDVHHKTLGIVGMGRIGMALAQRAHFGFNMP 171 Query: 167 IMVYDPYISKEAAEEMGVTVTDLETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAF 226 I+ KEA E DL+TLL+ESD V + +PLT ET HL ++F MK +A Sbjct: 172 ILYNARRHHKEAEERFNARYCDLDTLLQESDFVCLILPLTDETHHLFGAEQFAKMKSSAI 231 Query: 227 IVNCARGGIIDEDALYRALKDGEIAGAALDVFEEEP-PEGSPLLELENVVLTPHIGASTS 285 +N RG ++DE+AL AL+ GEI A LDVFE+EP SPLL + NVV PHIG++T Sbjct: 232 FINAGRGPVVDENALIAALQKGEIHAAGLDVFEQEPLSVDSPLLSMANVVAVPHIGSATH 291 Query: 286 EAQRDAAIIVANEIKTVFQGGAPRNVLNMPVMD 318 E + A + + QG +N +N V D Sbjct: 292 ETRYGMAACAVDNLIDALQGKVEKNCVNPHVAD 324 Lambda K H 0.316 0.135 0.366 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: 315 Number of extensions: 15 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: 525 Length of database: 324 Length adjustment: 31 Effective length of query: 494 Effective length of database: 293 Effective search space: 144742 Effective search space used: 144742 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 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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