Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95; 2-oxoglutarate reductase; EC 1.1.1.399 (uncharacterized)
to candidate WP_057687229.1 ABB28_RS15235 D-glycerate dehydrogenase
Query= curated2:O33116 (528 letters) >NCBI__GCF_001431535.1:WP_057687229.1 Length = 345 Score = 187 bits (476), Expect = 4e-52 Identities = 124/328 (37%), Positives = 185/328 (56%), Gaps = 14/328 (4%) Query: 4 PVVLIADKLAQSTVAALGDQVEVRWVDGPD---RTKLLAAVPEADALLVRSATTVDAEVL 60 PVV ++ L + + L QVE+ D + +L + D ++ + A L Sbjct: 6 PVVWVSQPLIDAVIEPLRAQVELITTDAVTAWTQEQLAERLRGVDGAIITLNERIGAAQL 65 Query: 61 AAAPKLKIVARAGVGLDNVDVDAATARGVLVVNAPTSNIHSAAEHALALLLAASRQIAEA 120 A A +L+++A GVG +N+DVDA +A GVL N P + A+ ALL+AA+R+I E+ Sbjct: 66 AGADRLQVIANVGVGYNNLDVDALSAAGVLASNTPDVLTETTADLGFALLMAAARRITES 125 Query: 121 DASLRAHIWKRSSFS---GTEIFGKTVGVVGLGRIGQLVAARIA-AFGAHVIAYDPYVAP 176 + LR W + SF G +I G T+G++G+GRIGQ +A R A FG V+ ++ P Sbjct: 126 ERWLRDGQWGQWSFQTMLGADIHGSTLGILGMGRIGQGIARRGAHGFGMRVLYHNRSRLP 185 Query: 177 ARA-AQLGIELMSFDDLLARADFISVHLPKTPETAGLIDKEALAKTKPGVIIVNAARGGL 235 A A++G + D LLA++D + + LP T + LI+ ALAK KP +VN ARGG+ Sbjct: 186 AATEAEVGAQYAELDALLAQSDHLVLVLPYTAASHHLINASALAKMKPTATLVNIARGGI 245 Query: 236 VDEVALADAVRSGHVRAAGLDVFATEPCTDSPLFELSQVVVTPHLGAS---TAEAQDRAG 292 VDE+ALADA+ G + AAGLDV+ EP L L VV+TPH+G++ T +A + Sbjct: 246 VDELALADALAHGRLAAAGLDVYEGEPQVRPELLALRNVVLTPHIGSASLGTRKAMVQLA 305 Query: 293 TDVAESVRLALAGEF--VPDAVNVDGGV 318 D + L +AGE +P A+N D + Sbjct: 306 VDNLLAA-LGVAGEAPRMPSAINADAAL 332 Lambda K H 0.317 0.132 0.364 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: 423 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: 528 Length of database: 345 Length adjustment: 32 Effective length of query: 496 Effective length of database: 313 Effective search space: 155248 Effective search space used: 155248 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: 51 (24.3 bits)
This GapMind analysis is from Apr 10 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