Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate PP_0762 PP_0762 Glycerate dehydrogenase
Query= BRENDA::C3SVM7 (410 letters) >FitnessBrowser__Putida:PP_0762 Length = 321 Score = 134 bits (337), Expect = 4e-36 Identities = 89/266 (33%), Positives = 135/266 (50%), Gaps = 12/266 (4%) Query: 45 EQLKESIRDAHFIGLRSRTHLTEDVINAAEKLVAIGCFCIGTNQVDLDAAAKRGIPVFNA 104 EQ+ E ++ A + + ++ L + A +L I GTN VDL AA +GI V N Sbjct: 41 EQVAERLQGAVAV-VSNKVMLDAATLAANPQLKLILVAATGTNNVDLAAARAQGITVCNC 99 Query: 105 PFSNTRSVAELVIGELLLLLRGVPEANAKAHRGVWNKLAAGSF------EARGKKLGIIG 158 T SVA+ + LL L + + N G W K + E GK LG++G Sbjct: 100 QGYGTPSVAQHTLALLLALATRLCDYNQAVADGQWAKASQFCLLDFPIVELEGKTLGLLG 159 Query: 159 YGHIGTQLGILAESLGMYVYFYDIENKLPLGNATQVQHLSDLLNMSDVVSLHVPENPSTK 218 +G +G + LAE+ GM V I + + L +LL D ++LH P N T+ Sbjct: 160 HGELGGAVARLAEAFGMRVLSGQIPGRPERADRLP---LDELLPQVDALTLHCPLNEHTR 216 Query: 219 NMMGAKEISLMKPGSLLINASRGTVVDIPALCDALASKHLAGAAIDVFPTEPATNSDPFT 278 +M+GA+E++L+KP +L++N +RG ++D AL DAL HL GAA DV EP N +P Sbjct: 217 HMLGARELALLKPNALVVNTARGGLIDEQALADALRGGHLGGAATDVLSVEPPVNGNPLL 276 Query: 279 SPLCEFDNVLLTPHIGGSTQEAQENI 304 P +++TPH E+++ I Sbjct: 277 EP--GIPRLIITPHSAWGAVESRQRI 300 Lambda K H 0.318 0.135 0.383 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: 243 Number of extensions: 11 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: 410 Length of database: 321 Length adjustment: 29 Effective length of query: 381 Effective length of database: 292 Effective search space: 111252 Effective search space used: 111252 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 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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