Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate PfGW456L13_4945 Glyoxylate reductase (EC 1.1.1.79) / Glyoxylate reductase (EC 1.1.1.26) / Hydroxypyruvate reductase (EC 1.1.1.81); 2-ketoaldonate reductase, broad specificity (EC 1.1.1.215) (EC 1.1.1.-)
Query= BRENDA::Q9Z564 (529 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4945 Length = 324 Score = 177 bits (449), Expect = 5e-49 Identities = 108/320 (33%), Positives = 172/320 (53%), Gaps = 8/320 (2%) Query: 4 KPVVLIAEELSPATVDALGPDFEI---RHCNGADRAELLPAIADVDAILVRSATKVDAEA 60 K VL ++P ++ L DF++ NG A+ A+ L+ K+ Sbjct: 2 KKTVLAFSRVTPPMIERLQQDFDVIVPNPKNGDINAQFNEALPHAHG-LIGVGRKLGRAQ 60 Query: 61 VAAAKKLKVVARAGVGLDNVDVSAATKAGVMVVNAPTSNIVTAAELACGLIVATARNIPQ 120 + A L+VV+ VG DN D++ + G+M+ N P + A+LA L++++AR + + Sbjct: 61 LENATTLEVVSSVSVGYDNYDLAYFNERGIMLTNTPDVLTESTADLAFALLMSSARRVAE 120 Query: 121 ANAALKNGEWKRS---KYTGVELAEKTLGVVGLGRIGALVAQR-MSAFGMKVVAYDPYVQ 176 +A K G+W+ + + G ++ KTLG+VG+G IG +A+R F M V+ + Sbjct: 121 LDAWTKAGQWQATVGAQLFGCDVHGKTLGIVGMGNIGTAIARRGRLGFNMPVIYSGNSRK 180 Query: 177 PARAAQMGVKVLSLDELLEVSDFITVHLPKTPETLGLIGDEALRKVKPSVRIVNAARGGI 236 ++G + SLD+LL +DF+ + +P + +T LI L +KPS +VN +RG + Sbjct: 181 TELEQELGAQFRSLDQLLAEADFVCLVVPLSEKTKHLISHRELALMKPSAILVNISRGPV 240 Query: 237 VDEEALYSALKEGRVAGAGLDVYAKEPCTDSPLFEFDQVVATPHLGASTDEAQEKAGIAV 296 VDE AL AL+ R+ GAGLDVY KEP +SPLF+ V PH+G++T E ++ Sbjct: 241 VDEPALIEALQNNRIRGAGLDVYEKEPLAESPLFQLKNAVTLPHIGSATHETRDAMANRA 300 Query: 297 AKSVRLALAGELVPDAVNVQ 316 ++R AL GE D VN Q Sbjct: 301 LANLRSALLGERPQDLVNPQ 320 Lambda K H 0.315 0.133 0.362 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: 363 Number of extensions: 20 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: 529 Length of database: 324 Length adjustment: 31 Effective length of query: 498 Effective length of database: 293 Effective search space: 145914 Effective search space used: 145914 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 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