Psyllid ID: psy6351

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------17
MKSELRCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGASTKEAQIRQDKQSIFYSLLGAELKNKQFLTTPVQIGLLSGRTSNGLNFINVNTYASEGGLKVAYEHDPSSSQNLVALAFGSNVAKHVLTVKQGLFTELLSYSLILVLQEDTAQWSIPYLRSPS
cHHHHHcccEEEEEEcccccccccccccccccccccEEEcccccccHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHcccccccccccEEEcccccccEEEEEEEcccccccEEEEEEccEEccEEEEEcccEEEEEccEEEEEEEcccccccccccccccc
cHHHHHcccEEEEEEEccccccccccccHHHHccccEEEcccccccHHHHHHHHHHHHHHHHHHcHHHcccccccHHHHHHHccccccccccccccccccccccEEEEEEccccccHHHHHHHHcccHHHEEEEccccHHHHHHHHHHHHHHHHcccccccccccccc
mkselrcghcggaaldvfceeppkseqtfelikhpkvivtphlgastkeAQIRQDKQSIFYSLLGAElknkqflttpvqigllsgrtsnglnfinvntyasegglkvayehdpsssqNLVALAFGSNVAKHVLTVKQGLFTELLSYSLILVLQEdtaqwsipylrsps
mkselrcghcggaALDVFCEEPPKSEQTFELIKHPKVIVTPHLGASTKEAQIRQDKQSIFYSLLGAELKNKQFLTTPVQIGLLSGRTSNGLNFINVNTYASEGGLKVAYEHDPSSSQNLVALAFGSNVAKHVLTVKQGLFTELLSYSLILVLqedtaqwsipylrsps
MKSELRCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGASTKEAQIRQDKQSIFYSLLGAELKNKQFLTTPVQIGLLSGRTSNGLNFINVNTYASEGGLKVAYEHDPSSSQNLVALAFGSNVAKHVLTVKQGLFTELLSYSLILVLQEDTAQWSIPYLRSPS
*****RCGHCGGAALDVFCE*******TFELIKHPKVIVTPHLGAST***QIRQDKQSIFYSLLGAELKNKQFLTTPVQIGLLSGRTSNGLNFINVNTYASEGGLKVAYEH*****QNLVALAFGSNVAKHVLTVKQGLFTELLSYSLILVLQEDTAQWSIPYL****
MKSELRCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGASTKEAQIRQDKQSIFYSLLGAELKNKQFLTTPVQIGLLSGRTSNGLNFINVNTYASEGGLKVAYEHDPSSSQNLVALAFGSNVAKHVLTVKQGLFTELLSYSLILVLQEDTAQWSIPYLRS**
********HCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGASTKEAQIRQDKQSIFYSLLGAELKNKQFLTTPVQIGLLSGRTSNGLNFINVNTYASEGGLKVAYEHDPSSSQNLVALAFGSNVAKHVLTVKQGLFTELLSYSLILVLQEDTAQWSIPYLRSPS
MKSELRCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGASTKEAQIRQDKQSIFYSLLGAELKNKQFLTTPVQIGLLSGRTSNGLNFINVNTYASEGGLKVAYEHDPSSSQNLVALAFGSNVAKHVLTVKQGLFTELLSYSLILVLQEDTAQWSIPYL****
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MKSELRCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGASTKEAQIRQDKQSIFYSLLGAELKNKQFLTTPVQIGLLSGRTSNGLNFINVNTYASEGGLKVAYEHDPSSSQNLVALAFGSNVAKHVLTVKQGLFTELLSYSLILVLQEDTAQWSIPYLRSPS
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query168 2.2.26 [Sep-21-2011]
A5GFY8 533 D-3-phosphoglycerate dehy yes N/A 0.273 0.086 0.612 1e-09
O43175 533 D-3-phosphoglycerate dehy yes N/A 0.273 0.086 0.612 2e-09
Q5R7M2 533 D-3-phosphoglycerate dehy yes N/A 0.273 0.086 0.612 2e-09
Q60HD7 533 D-3-phosphoglycerate dehy N/A N/A 0.273 0.086 0.612 2e-09
A5A6P1 533 D-3-phosphoglycerate dehy yes N/A 0.273 0.086 0.612 2e-09
O08651 533 D-3-phosphoglycerate dehy yes N/A 0.273 0.086 0.612 2e-09
Q61753 533 D-3-phosphoglycerate dehy yes N/A 0.273 0.086 0.612 3e-09
Q5EAD2 533 D-3-phosphoglycerate dehy yes N/A 0.273 0.086 0.612 3e-09
P35136 525 D-3-phosphoglycerate dehy yes N/A 0.267 0.085 0.625 4e-09
O04130 624 D-3-phosphoglycerate dehy yes N/A 0.267 0.072 0.638 8e-09
>sp|A5GFY8|SERA_PIG D-3-phosphoglycerate dehydrogenase OS=Sus scrofa GN=PHGDH PE=3 SV=1 Back     alignment and function desciption
 Score = 62.4 bits (150), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 30/49 (61%), Positives = 34/49 (69%), Gaps = 3/49 (6%)

Query: 5   LRCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGASTKEAQIR 53
           L+ G C GAALDVF EEPP+      L+ H KVI  PHLGAST+EAQ R
Sbjct: 249 LQSGQCAGAALDVFTEEPPRDR---ALVDHEKVISCPHLGASTREAQSR 294

Sus scrofa (taxid: 9823)
EC: 1EC: .EC: 1EC: .EC: 1EC: .EC: 9EC: 5
>sp|O43175|SERA_HUMAN D-3-phosphoglycerate dehydrogenase OS=Homo sapiens GN=PHGDH PE=1 SV=4 Back     alignment and function description
>sp|Q5R7M2|SERA_PONAB D-3-phosphoglycerate dehydrogenase OS=Pongo abelii GN=PHGDH PE=2 SV=3 Back     alignment and function description
>sp|Q60HD7|SERA_MACFA D-3-phosphoglycerate dehydrogenase OS=Macaca fascicularis GN=PHGDH PE=2 SV=4 Back     alignment and function description
>sp|A5A6P1|SERA_PANTR D-3-phosphoglycerate dehydrogenase OS=Pan troglodytes GN=PHGDH PE=2 SV=1 Back     alignment and function description
>sp|O08651|SERA_RAT D-3-phosphoglycerate dehydrogenase OS=Rattus norvegicus GN=Phgdh PE=1 SV=3 Back     alignment and function description
>sp|Q61753|SERA_MOUSE D-3-phosphoglycerate dehydrogenase OS=Mus musculus GN=Phgdh PE=1 SV=3 Back     alignment and function description
>sp|Q5EAD2|SERA_BOVIN D-3-phosphoglycerate dehydrogenase OS=Bos taurus GN=PHGDH PE=2 SV=3 Back     alignment and function description
>sp|P35136|SERA_BACSU D-3-phosphoglycerate dehydrogenase OS=Bacillus subtilis (strain 168) GN=serA PE=3 SV=3 Back     alignment and function description
>sp|O04130|SERA_ARATH D-3-phosphoglycerate dehydrogenase, chloroplastic OS=Arabidopsis thaliana GN=At1g17745 PE=1 SV=2 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query168
240991833 473 D-3-phosphoglycerate dehydrogenase, puta 0.761 0.270 0.345 2e-15
307177523 511 D-3-phosphoglycerate dehydrogenase [Camp 0.648 0.213 0.329 2e-15
332018401 511 D-3-phosphoglycerate dehydrogenase [Acro 0.297 0.097 0.745 3e-15
427789279 530 Putative glyoxylate/hydroxypyruvate redu 0.738 0.233 0.347 5e-15
56199498 331 phosphoglycerate dehydrogenase [Culicoid 0.291 0.148 0.795 9e-15
322801282 557 hypothetical protein SINV_07911 [Solenop 0.297 0.089 0.745 1e-14
312375947 1061 hypothetical protein AND_13366 [Anophele 0.470 0.074 0.518 2e-14
340727006 513 PREDICTED: d-3-phosphoglycerate dehydrog 0.291 0.095 0.755 5e-14
380017343 513 PREDICTED: d-3-phosphoglycerate dehydrog 0.291 0.095 0.755 6e-14
91083881 329 PREDICTED: similar to AGAP008849-PA isof 0.416 0.212 0.56 8e-14
>gi|240991833|ref|XP_002404432.1| D-3-phosphoglycerate dehydrogenase, putative [Ixodes scapularis] gi|215491559|gb|EEC01200.1| D-3-phosphoglycerate dehydrogenase, putative [Ixodes scapularis] Back     alignment and taxonomy information
 Score = 87.4 bits (215), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 64/185 (34%), Positives = 83/185 (44%), Gaps = 57/185 (30%)

Query: 3   SELRCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGASTKEAQIRQDKQ----- 57
           + L  GHCGGA LDVF EEPPK+ Q   LI HPKV+ TPHLGA+TKEAQ+R  ++     
Sbjct: 246 AALESGHCGGAGLDVFLEEPPKNTQ---LIAHPKVVCTPHLGANTKEAQLRVAQEIAEQF 302

Query: 58  ----------------------------------------------SIFYSLLGAELKNK 71
                                                         +   S+ G EL+ K
Sbjct: 303 VDLSQGKSVPGVVNAPSLSQTQVPENKPWADLCFLLPVGSTVNCSSTCALSVPGNELEKK 362

Query: 72  -QFLTTPVQIGLLSGRTSNGLNFINVNTYASEGGLKVAYEHD--PSSSQNLVALAFGSNV 128
            QFL++   IG+L     +  NFIN    AS+ G+KV+++H   P      VAL   S  
Sbjct: 363 GQFLSSAACIGVLKHLGHSQANFINGTVLASDAGVKVSHKHSQGPRFGTTEVALTVKSGQ 422

Query: 129 AKHVL 133
           A H L
Sbjct: 423 ATHTL 427

Source: Ixodes scapularis

Species: Ixodes scapularis

Genus: Ixodes

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|307177523|gb|EFN66634.1| D-3-phosphoglycerate dehydrogenase [Camponotus floridanus] Back     alignment and taxonomy information
>gi|332018401|gb|EGI58995.1| D-3-phosphoglycerate dehydrogenase [Acromyrmex echinatior] Back     alignment and taxonomy information
>gi|427789279|gb|JAA60091.1| Putative glyoxylate/hydroxypyruvate reduct [Rhipicephalus pulchellus] Back     alignment and taxonomy information
>gi|56199498|gb|AAV84238.1| phosphoglycerate dehydrogenase [Culicoides sonorensis] Back     alignment and taxonomy information
>gi|322801282|gb|EFZ21969.1| hypothetical protein SINV_07911 [Solenopsis invicta] Back     alignment and taxonomy information
>gi|312375947|gb|EFR23183.1| hypothetical protein AND_13366 [Anopheles darlingi] Back     alignment and taxonomy information
>gi|340727006|ref|XP_003401842.1| PREDICTED: d-3-phosphoglycerate dehydrogenase-like [Bombus terrestris] Back     alignment and taxonomy information
>gi|380017343|ref|XP_003692617.1| PREDICTED: d-3-phosphoglycerate dehydrogenase-like [Apis florea] Back     alignment and taxonomy information
>gi|91083881|ref|XP_967558.1| PREDICTED: similar to AGAP008849-PA isoform 1 [Tribolium castaneum] gi|270006715|gb|EFA03163.1| hypothetical protein TcasGA2_TC013082 [Tribolium castaneum] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query168
ZFIN|ZDB-GENE-030131-647 528 phgdh "phosphoglycerate dehydr 0.291 0.092 0.615 2.9e-16
UNIPROTKB|J9P9I6 520 LOC607890 "Uncharacterized pro 0.273 0.088 0.632 8e-15
UNIPROTKB|J9P120 533 LOC607890 "Uncharacterized pro 0.273 0.086 0.632 8.7e-15
UNIPROTKB|L7N0I9 572 LOC607890 "Uncharacterized pro 0.273 0.080 0.632 1.1e-14
UNIPROTKB|Q5SZU1 499 PHGDH "D-3-phosphoglycerate de 0.273 0.092 0.612 1e-13
UNIPROTKB|O43175 533 PHGDH "D-3-phosphoglycerate de 0.273 0.086 0.612 1.3e-13
MGI|MGI:1355330 533 Phgdh "3-phosphoglycerate dehy 0.273 0.086 0.612 1.6e-13
RGD|61987 533 Phgdh "phosphoglycerate dehydr 0.273 0.086 0.612 2.1e-13
FB|FBgn0032350332 CG6287 [Drosophila melanogaste 0.291 0.147 0.653 1.7e-11
UNIPROTKB|E1C7Y3 525 PHGDH "Uncharacterized protein 0.297 0.095 0.622 2.8e-11
ZFIN|ZDB-GENE-030131-647 phgdh "phosphoglycerate dehydrogenase" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
 Score = 154 (59.3 bits), Expect = 2.9e-16, Sum P(2) = 2.9e-16
 Identities = 32/52 (61%), Positives = 34/52 (65%)

Query:     5 LRCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGASTKEAQIRQDK 56
             L  G CGGA LDVF EEPP+      L+ HP VI  PHLGASTKEAQ R  K
Sbjct:   249 LESGQCGGAGLDVFVEEPPRERA---LVNHPNVISCPHLGASTKEAQARCGK 297
GO:0016616 "oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor" evidence=IEA
GO:0051287 "NAD binding" evidence=IEA
GO:0055114 "oxidation-reduction process" evidence=IEA
GO:0008152 "metabolic process" evidence=IEA
GO:0000166 "nucleotide binding" evidence=IEA
GO:0004617 "phosphoglycerate dehydrogenase activity" evidence=IEA
GO:0048037 "cofactor binding" evidence=IEA
GO:0006564 "L-serine biosynthetic process" evidence=IEA
GO:0005575 "cellular_component" evidence=ND
UNIPROTKB|J9P9I6 LOC607890 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|J9P120 LOC607890 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|L7N0I9 LOC607890 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|Q5SZU1 PHGDH "D-3-phosphoglycerate dehydrogenase" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|O43175 PHGDH "D-3-phosphoglycerate dehydrogenase" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
MGI|MGI:1355330 Phgdh "3-phosphoglycerate dehydrogenase" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
RGD|61987 Phgdh "phosphoglycerate dehydrogenase" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
FB|FBgn0032350 CG6287 [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
UNIPROTKB|E1C7Y3 PHGDH "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query168
cd12173304 cd12173, PGDH_4, Phosphoglycerate dehydrogenases, 2e-20
PRK13581 526 PRK13581, PRK13581, D-3-phosphoglycerate dehydroge 2e-18
cd05303301 cd05303, PGDH_2, Phosphoglycerate dehydrogenase (P 5e-17
TIGR01327525 TIGR01327, PGDH, D-3-phosphoglycerate dehydrogenas 9e-16
COG0111324 COG0111, SerA, Phosphoglycerate dehydrogenase and 2e-14
cd12172306 cd12172, PGDH_like_2, Putative D-3-Phosphoglycerat 3e-14
PRK11790409 PRK11790, PRK11790, D-3-phosphoglycerate dehydroge 9e-13
cd12176304 cd12176, PGDH_3, Phosphoglycerate dehydrogenases, 6e-12
cd05198302 cd05198, formate_dh_like, Formate/glycerate and re 7e-12
pfam00389312 pfam00389, 2-Hacid_dh, D-isomer specific 2-hydroxy 9e-11
COG1052324 COG1052, LdhA, Lactate dehydrogenase and related d 1e-10
pfam02826175 pfam02826, 2-Hacid_dh_C, D-isomer specific 2-hydro 2e-10
cd12175311 cd12175, 2-Hacid_dh_11, Putative D-isomer specific 3e-10
cd05299312 cd05299, CtBP_dh, C-terminal binding protein (CtBP 1e-09
cd12171310 cd12171, 2-Hacid_dh_10, Putative D-isomer specific 4e-09
cd12177321 cd12177, 2-Hacid_dh_12, Putative D-isomer specific 5e-09
cd12168321 cd12168, Mand_dh_like, D-Mandelate Dehydrogenase-l 1e-08
cd05301309 cd05301, GDH, D-glycerate dehydrogenase/hydroxypyr 2e-08
PRK06487317 PRK06487, PRK06487, glycerate dehydrogenase; Provi 6e-08
cd12162307 cd12162, 2-Hacid_dh_4, Putative D-isomer specific 7e-08
cd12169308 cd12169, PGDH_like_1, Putative D-3-Phosphoglycerat 3e-07
cd12174305 cd12174, PGDH_like_3, Putative D-3-Phosphoglycerat 3e-07
cd12161315 cd12161, GDH_like_1, Putative glycerate dehydrogen 5e-07
cd12164306 cd12164, GDH_like_2, Putative glycerate dehydrogen 5e-07
cd12187329 cd12187, LDH_like_1, D-Lactate and related Dehydro 7e-07
cd05300313 cd05300, 2-Hacid_dh_1, Putative D-isomer specific 8e-07
cd12156301 cd12156, HPPR, Hydroxy(phenyl)pyruvate Reductase, 1e-06
PRK15469312 PRK15469, ghrA, bifunctional glyoxylate/hydroxypyr 4e-06
cd12178317 cd12178, 2-Hacid_dh_13, Putative D-isomer specific 8e-06
cd12155314 cd12155, PGDH_1, Phosphoglycerate Dehydrogenase, 2 1e-05
cd12163334 cd12163, 2-Hacid_dh_5, Putative D-isomer specific 2e-05
cd12167330 cd12167, 2-Hacid_dh_8, Putative D-isomer specific 2e-05
PRK13243333 PRK13243, PRK13243, glyoxylate reductase; Reviewed 3e-05
cd12186329 cd12186, LDH, D-Lactate dehydrogenase and D-2-Hydr 3e-05
cd12179306 cd12179, 2-Hacid_dh_14, Putative D-isomer specific 3e-04
PLN02928347 PLN02928, PLN02928, oxidoreductase family protein 3e-04
PRK08605332 PRK08605, PRK08605, D-lactate dehydrogenase; Valid 3e-04
cd12157318 cd12157, PTDH, Thermostable Phosphite Dehydrogenas 4e-04
cd12160310 cd12160, 2-Hacid_dh_3, Putative D-isomer specific 4e-04
cd12184330 cd12184, HGDH_like, (R)-2-Hydroxyglutarate Dehydro 4e-04
cd12183328 cd12183, LDH_like_2, D-Lactate and related Dehydro 0.001
cd12159303 cd12159, 2-Hacid_dh_2, Putative D-isomer specific 0.001
cd01619323 cd01619, LDH_like, D-Lactate and related Dehydroge 0.002
PRK06932314 PRK06932, PRK06932, glycerate dehydrogenase; Provi 0.002
cd12165314 cd12165, 2-Hacid_dh_6, Putative D-isomer specific 0.004
>gnl|CDD|240650 cd12173, PGDH_4, Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains Back     alignment and domain information 
 Score = 85.2 bits (212), Expect = 2e-20
 Identities = 28/49 (57%), Positives = 35/49 (71%), Gaps = 2/49 (4%)

Query: 5   LRCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGASTKEAQIR 53
           L+ G   GAALDVF +EPP ++    L+  P VI+TPHLGAST+EAQ R
Sbjct: 242 LKSGKIAGAALDVFEQEPPPAD--SPLLGLPNVILTPHLGASTEEAQER 288

Phosphoglycerate dehydrogenases (PGDHs) catalyze the initial step in the biosynthesis of L-serine from D-3-phosphoglycerate. PGDHs come in 3 distinct structural forms, with this first group being related to 2-hydroxy acid dehydrogenases, sharing structural similarity to formate and glycerate dehydrogenases. PGDH in E. coli and Mycobacterium tuberculosis form tetramers, with subunits containing a Rossmann-fold NAD binding domain. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. Length = 304
>gnl|CDD|237436 PRK13581, PRK13581, D-3-phosphoglycerate dehydrogenase; Provisional Back     alignment and domain information
>gnl|CDD|240628 cd05303, PGDH_2, Phosphoglycerate dehydrogenase (PGDH) NAD-binding and catalytic domains Back     alignment and domain information
>gnl|CDD|233358 TIGR01327, PGDH, D-3-phosphoglycerate dehydrogenase Back     alignment and domain information
>gnl|CDD|223189 COG0111, SerA, Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism] Back     alignment and domain information
>gnl|CDD|240649 cd12172, PGDH_like_2, Putative D-3-Phosphoglycerate Dehydrogenases, NAD-binding and catalytic domains Back     alignment and domain information
>gnl|CDD|236985 PRK11790, PRK11790, D-3-phosphoglycerate dehydrogenase; Provisional Back     alignment and domain information
>gnl|CDD|240653 cd12176, PGDH_3, Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains Back     alignment and domain information
>gnl|CDD|240622 cd05198, formate_dh_like, Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxy acid dehydrogenase family Back     alignment and domain information
>gnl|CDD|215893 pfam00389, 2-Hacid_dh, D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain Back     alignment and domain information
>gnl|CDD|223980 COG1052, LdhA, Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only] Back     alignment and domain information
>gnl|CDD|217244 pfam02826, 2-Hacid_dh_C, D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain Back     alignment and domain information
>gnl|CDD|240652 cd12175, 2-Hacid_dh_11, Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains Back     alignment and domain information
>gnl|CDD|240624 cd05299, CtBP_dh, C-terminal binding protein (CtBP), D-isomer-specific 2-hydroxyacid dehydrogenases related repressor Back     alignment and domain information
>gnl|CDD|240648 cd12171, 2-Hacid_dh_10, Putative D-isomer specific 2-hydroxyacid dehydrogenases Back     alignment and domain information
>gnl|CDD|240654 cd12177, 2-Hacid_dh_12, Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains Back     alignment and domain information
>gnl|CDD|240645 cd12168, Mand_dh_like, D-Mandelate Dehydrogenase-like dehydrogenases Back     alignment and domain information
>gnl|CDD|240626 cd05301, GDH, D-glycerate dehydrogenase/hydroxypyruvate reductase (GDH) Back     alignment and domain information
>gnl|CDD|180588 PRK06487, PRK06487, glycerate dehydrogenase; Provisional Back     alignment and domain information
>gnl|CDD|240639 cd12162, 2-Hacid_dh_4, Putative D-isomer specific 2-hydroxyacid dehydrogenases Back     alignment and domain information
>gnl|CDD|240646 cd12169, PGDH_like_1, Putative D-3-Phosphoglycerate Dehydrogenases Back     alignment and domain information
>gnl|CDD|240651 cd12174, PGDH_like_3, Putative D-3-Phosphoglycerate Dehydrogenases, NAD-binding and catalytic domains Back     alignment and domain information
>gnl|CDD|240638 cd12161, GDH_like_1, Putative glycerate dehydrogenase and related proteins of the D-specific 2-hydroxy dehydrogenase family Back     alignment and domain information
>gnl|CDD|240641 cd12164, GDH_like_2, Putative glycerate dehydrogenase and related proteins of the D-specific 2-hydroxy dehydrogenase family Back     alignment and domain information
>gnl|CDD|240663 cd12187, LDH_like_1, D-Lactate and related Dehydrogenase like proteins, NAD-binding and catalytic domains Back     alignment and domain information
>gnl|CDD|240625 cd05300, 2-Hacid_dh_1, Putative D-isomer specific 2-hydroxyacid dehydrogenase Back     alignment and domain information
>gnl|CDD|240633 cd12156, HPPR, Hydroxy(phenyl)pyruvate Reductase, D-isomer-specific 2-hydroxyacid-related dehydrogenase Back     alignment and domain information
>gnl|CDD|185366 PRK15469, ghrA, bifunctional glyoxylate/hydroxypyruvate reductase A; Provisional Back     alignment and domain information
>gnl|CDD|240655 cd12178, 2-Hacid_dh_13, Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains Back     alignment and domain information
>gnl|CDD|240632 cd12155, PGDH_1, Phosphoglycerate Dehydrogenase, 2-hydroxyacid dehydrogenase family Back     alignment and domain information
>gnl|CDD|240640 cd12163, 2-Hacid_dh_5, Putative D-isomer specific 2-hydroxyacid dehydrogenases Back     alignment and domain information
>gnl|CDD|240644 cd12167, 2-Hacid_dh_8, Putative D-isomer specific 2-hydroxyacid dehydrogenases Back     alignment and domain information
>gnl|CDD|183914 PRK13243, PRK13243, glyoxylate reductase; Reviewed Back     alignment and domain information
>gnl|CDD|240662 cd12186, LDH, D-Lactate dehydrogenase and D-2-Hydroxyisocaproic acid dehydrogenase (D-HicDH), NAD-binding and catalytic domains Back     alignment and domain information
>gnl|CDD|240656 cd12179, 2-Hacid_dh_14, Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains Back     alignment and domain information
>gnl|CDD|215501 PLN02928, PLN02928, oxidoreductase family protein Back     alignment and domain information
>gnl|CDD|181499 PRK08605, PRK08605, D-lactate dehydrogenase; Validated Back     alignment and domain information
>gnl|CDD|240634 cd12157, PTDH, Thermostable Phosphite Dehydrogenase Back     alignment and domain information
>gnl|CDD|240637 cd12160, 2-Hacid_dh_3, Putative D-isomer specific 2-hydroxyacid dehydrogenases Back     alignment and domain information
>gnl|CDD|240660 cd12184, HGDH_like, (R)-2-Hydroxyglutarate Dehydrogenase and related dehydrogenases, NAD-binding and catalytic domains Back     alignment and domain information
>gnl|CDD|240659 cd12183, LDH_like_2, D-Lactate and related Dehydrogenases, NAD-binding and catalytic domains Back     alignment and domain information
>gnl|CDD|240636 cd12159, 2-Hacid_dh_2, Putative D-isomer specific 2-hydroxyacid dehydrogenases Back     alignment and domain information
>gnl|CDD|240620 cd01619, LDH_like, D-Lactate and related Dehydrogenases, NAD-binding and catalytic domains Back     alignment and domain information
>gnl|CDD|235890 PRK06932, PRK06932, glycerate dehydrogenase; Provisional Back     alignment and domain information
>gnl|CDD|240642 cd12165, 2-Hacid_dh_6, Putative D-isomer specific 2-hydroxyacid dehydrogenases Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 168
TIGR01327525 PGDH D-3-phosphoglycerate dehydrogenase. This mode 100.0
PRK13581526 D-3-phosphoglycerate dehydrogenase; Provisional 99.98
COG0111324 SerA Phosphoglycerate dehydrogenase and related de 99.82
PRK11790409 D-3-phosphoglycerate dehydrogenase; Provisional 99.78
PRK13243333 glyoxylate reductase; Reviewed 99.77
PRK15409323 bifunctional glyoxylate/hydroxypyruvate reductase 99.77
KOG0068|consensus406 99.77
PRK06487317 glycerate dehydrogenase; Provisional 99.74
PLN02928347 oxidoreductase family protein 99.73
PLN03139386 formate dehydrogenase; Provisional 99.72
PLN02306386 hydroxypyruvate reductase 99.71
PRK12480330 D-lactate dehydrogenase; Provisional 99.7
PRK07574385 formate dehydrogenase; Provisional 99.69
TIGR00719208 sda_beta L-serine dehydratase, iron-sulfur-depende 99.69
PRK15469312 ghrA bifunctional glyoxylate/hydroxypyruvate reduc 99.68
PRK06932314 glycerate dehydrogenase; Provisional 99.67
COG1052324 LdhA Lactate dehydrogenase and related dehydrogena 99.66
PRK08605332 D-lactate dehydrogenase; Validated 99.65
PRK08410311 2-hydroxyacid dehydrogenase; Provisional 99.65
KOG0069|consensus336 99.55
PRK06436303 glycerate dehydrogenase; Provisional 99.55
PRK00257381 erythronate-4-phosphate dehydrogenase; Validated 99.49
PRK15438378 erythronate-4-phosphate dehydrogenase PdxB; Provis 99.45
KOG0067|consensus435 96.44
PF00389133 2-Hacid_dh: D-isomer specific 2-hydroxyacid dehydr 92.87
>TIGR01327 PGDH D-3-phosphoglycerate dehydrogenase Back     alignment and domain information 
Probab=100.00  E-value=5.2e-33  Score=252.19  Aligned_cols=157  Identities=30%  Similarity=0.369  Sum_probs=136.9

Q ss_pred             CHHHHhcCCeeEEEeecCCCCCCCCCCChhhccCCceEEccCCCcchHHHHHHHHHHHHHHh------------------
Q psy6351           1 MKSELRCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGASTKEAQIRQDKQSIFYS------------------   62 (168)
Q Consensus         1 L~~AL~~G~i~gAaLDVf~~EP~~~~~~~pL~~~~nvilTPHig~~T~ea~~~~~~~~~~~~------------------   62 (168)
                      |++||++|+|+|||||||++||++++   |||++|||++|||+||+|.+++.+++..+++|+                  
T Consensus       239 L~~aL~~g~i~gAaLDVf~~EP~~~~---pL~~~~nvi~TPHia~~t~e~~~~~~~~~~~ni~~~~~g~~~~~~vn~~~~  315 (525)
T TIGR01327       239 LYEALEEGHVRAAALDVFEKEPPTDN---PLFDLDNVIATPHLGASTREAQENVATQVAEQVLDALKGLPVPNAVNAPGI  315 (525)
T ss_pred             HHHHHHcCCeeEEEEecCCCCCCCCC---hhhcCCCeEECCCccccHHHHHHHHHHHHHHHHHHHHcCCCCCceeeCCCC
Confidence            68999999999999999999997654   999999999999999999999999999999976                  


Q ss_pred             -----------------------------------hcccccc--ccccchHHHHHhhccCCCCCCccccChhhHHhhCCc
Q psy6351          63 -----------------------------------LLGAELK--NKQFLTTPVQIGLLSGRTSNGLNFINVNTYASEGGL  105 (168)
Q Consensus        63 -----------------------------------~~g~~~~--~~~~lt~a~l~~~L~~~~~~~vn~VNa~~la~~~GI  105 (168)
                                                         .|.|..+  ++..++.|.++|+|....++.+|++||..+||++||
T Consensus       316 ~~~~~~~~~~~~~la~riG~~a~ql~~~~~~~v~i~~~GsfA~~~~~~~~~a~l~GlL~~~~~~d~~~~nA~~iA~e~GI  395 (525)
T TIGR01327       316 DADVMEKLKPYLDLAEKLGKLAGQLLDGAVQSVEVTYRGELATENSEPLTRAALKGLLSPVLDDEVNMVNAPAVAKERGI  395 (525)
T ss_pred             CchhhhhhhhHHHHHHHHHHHHHHHcCCCceEEEEEEEcchhcccccHHHHHHHHHhCccccCCCccccCHHHHHHHcCC
Confidence                                               2333333  357899999999998766668999999999999999


Q ss_pred             eEEEEECCCCC--CceEEEEEeecC-------------cccEEEEcceEeeccccccEEEEeecCCCCCc
Q psy6351         106 KVAYEHDPSSS--QNLVALAFGSNV-------------AKHVLTVKQGLFTELLSYSLILVLQEDTAQWS  160 (168)
Q Consensus       106 ~v~e~~~~~~~--~n~itv~~~~~~-------------~~~l~~i~~~~~~~~~eG~~li~r~~D~pg~~  160 (168)
                      +|.+.+.+...  .|.++|++.++.             ..+|++||+|.+++.++|++|+++|.|+|||-
T Consensus       396 ~v~~~~~~~~~~hpNtv~i~l~~~~~~~~v~G~s~gGg~~~I~~ing~~v~~~~~~~~li~~~~D~pG~I  465 (525)
T TIGR01327       396 TVEESKSESSPDYKNYLSVTVTGDSGTVSVAGTVFGGFSPRIVEIDGFHVDLEPEGIMLIILHLDKPGVI  465 (525)
T ss_pred             EEEEEEccCCCCCCCEEEEEEEeCCcEEEEEEEEecCCcEEEEEECCEEEEEecCccEEEEEecCcCCcc
Confidence            99888876543  788888765432             46899999999999999999999999999983

This model represents a long form of D-3-phosphoglycerate dehydrogenase, the serA gene of one pathway of serine biosynthesis. Shorter forms, scoring between trusted and noise cutoff, include SerA from E. coli.
>PRK13581 D-3-phosphoglycerate dehydrogenase; Provisional Back     alignment and domain information
>COG0111 SerA Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism] Back     alignment and domain information
>PRK11790 D-3-phosphoglycerate dehydrogenase; Provisional Back     alignment and domain information
>PRK13243 glyoxylate reductase; Reviewed Back     alignment and domain information
>PRK15409 bifunctional glyoxylate/hydroxypyruvate reductase B; Provisional Back     alignment and domain information
>KOG0068|consensus Back     alignment and domain information
>PRK06487 glycerate dehydrogenase; Provisional Back     alignment and domain information
>PLN02928 oxidoreductase family protein Back     alignment and domain information
>PLN03139 formate dehydrogenase; Provisional Back     alignment and domain information
>PLN02306 hydroxypyruvate reductase Back     alignment and domain information
>PRK12480 D-lactate dehydrogenase; Provisional Back     alignment and domain information
>PRK07574 formate dehydrogenase; Provisional Back     alignment and domain information
>TIGR00719 sda_beta L-serine dehydratase, iron-sulfur-dependent, beta subunit Back     alignment and domain information
>PRK15469 ghrA bifunctional glyoxylate/hydroxypyruvate reductase A; Provisional Back     alignment and domain information
>PRK06932 glycerate dehydrogenase; Provisional Back     alignment and domain information
>COG1052 LdhA Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only] Back     alignment and domain information
>PRK08605 D-lactate dehydrogenase; Validated Back     alignment and domain information
>PRK08410 2-hydroxyacid dehydrogenase; Provisional Back     alignment and domain information
>KOG0069|consensus Back     alignment and domain information
>PRK06436 glycerate dehydrogenase; Provisional Back     alignment and domain information
>PRK00257 erythronate-4-phosphate dehydrogenase; Validated Back     alignment and domain information
>PRK15438 erythronate-4-phosphate dehydrogenase PdxB; Provisional Back     alignment and domain information
>KOG0067|consensus Back     alignment and domain information
>PF00389 2-Hacid_dh: D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain; InterPro: IPR006139 A number of NAD-dependent 2-hydroxyacid dehydrogenases which seem to be specific for the D-isomer of their substrate have been shown to be functionally and structurally related Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query168
2g76_A335 Crystal Structure Of Human 3-Phosphoglycerate Dehyd 2e-10
2ekl_A313 Structure Of St1218 Protein From Sulfolobus Tokodai 8e-10
1ygy_A 529 Crystal Structure Of D-3-Phosphoglycerate Dehydroge 9e-07
3ddn_A 528 Crystal Structure Of Hydroxypyruvic Acid Phosphate 1e-06
1wwk_A307 Crystal Structure Of Phosphoglycerate Dehydrogenase 8e-06
3k5p_A416 Crystal Structure Of Amino Acid-Binding Act: D-Isom 8e-06
2p9c_A410 Crystal Structure Of Serine Bound G336v Mutant Of E 2e-05
2p9g_A410 Crystal Structure Of Serine Bound G336v,G337v Doubl 4e-05
1sc6_A404 Crystal Structure Of W139g D-3-Phosphoglycerate Deh 4e-05
1psd_A409 The Allosteric Ligand Site In The Vmax-Type Coopera 9e-05
3kbo_A315 2.14 Angstrom Crystal Structure Of Putative Oxidore 9e-05
1yba_A410 The Active Form Of Phosphoglycerate Dehydrogenase L 1e-04
2dbr_A334 Crystal Structure Of Glyoxylate Reductase (Ph0597) 4e-04
2dbq_A334 Crystal Structure Of Glyoxylate Reductase (Ph0597) 4e-04
>pdb|2G76|A Chain A, Crystal Structure Of Human 3-Phosphoglycerate Dehydrogenase Length = 335 Back     alignment and structure 
Iteration: 1

 Score = 61.6 bits (148), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 30/49 (61%), Positives = 33/49 (67%), Gaps = 3/49 (6%)
Query: 5   LRCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGASTKEAQIR 53
           L+ G C GAALDVF EEPP+      L+ H  VI  PHLGASTKEAQ R
Sbjct: 269 LQSGQCAGAALDVFTEEPPRDRA---LVDHENVISCPHLGASTKEAQSR 314
>pdb|2EKL|A Chain A, Structure Of St1218 Protein From Sulfolobus Tokodaii Length = 313 Back     alignment and structure
>pdb|1YGY|A Chain A, Crystal Structure Of D-3-Phosphoglycerate Dehydrogenase From Mycobacterium Tuberculosis Length = 529 Back     alignment and structure
>pdb|3DDN|A Chain A, Crystal Structure Of Hydroxypyruvic Acid Phosphate Bound D-3- Phosphoglycerate Dehydrogenase In Mycobacterium Tuberculosis Length = 528 Back     alignment and structure
>pdb|1WWK|A Chain A, Crystal Structure Of Phosphoglycerate Dehydrogenase From Pyrococcus Horikoshii Ot3 Length = 307 Back     alignment and structure
>pdb|3K5P|A Chain A, Crystal Structure Of Amino Acid-Binding Act: D-Isomer Specific 2- Hydroxyacid Dehydrogenase Catalytic Domain From Brucella Melitensis Length = 416 Back     alignment and structure
>pdb|2P9C|A Chain A, Crystal Structure Of Serine Bound G336v Mutant Of E.Coli Phosphoglycerate Dehydrogenase Length = 410 Back     alignment and structure
>pdb|2P9G|A Chain A, Crystal Structure Of Serine Bound G336v,G337v Double Mutant Of E.Coli Phosphoglycerate Dehydrogenase Length = 410 Back     alignment and structure
>pdb|1SC6|A Chain A, Crystal Structure Of W139g D-3-Phosphoglycerate Dehydrogenase Complexed With Nad+ Length = 404 Back     alignment and structure
>pdb|1PSD|A Chain A, The Allosteric Ligand Site In The Vmax-Type Cooperative Enzyme Phosphoglycerate Dehydrogenase Length = 409 Back     alignment and structure
>pdb|3KBO|A Chain A, 2.14 Angstrom Crystal Structure Of Putative Oxidoreductase (ycdw) From Salmonella Typhimurium In Complex With Nadp Length = 315 Back     alignment and structure
>pdb|1YBA|A Chain A, The Active Form Of Phosphoglycerate Dehydrogenase Length = 410 Back     alignment and structure
>pdb|2DBR|A Chain A, Crystal Structure Of Glyoxylate Reductase (Ph0597) From Pyrococcus Horikoshii Ot3, Complexed With Nadp (P1) Length = 334 Back     alignment and structure
>pdb|2DBQ|A Chain A, Crystal Structure Of Glyoxylate Reductase (Ph0597) From Pyrococcus Horikoshii Ot3, Complexed With Nadp (I41) Length = 334 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query168
2ekl_A313 D-3-phosphoglycerate dehydrogenase; structural gen 8e-24
2g76_A335 3-PGDH, D-3-phosphoglycerate dehydrogenase; oxidor 8e-22
1wwk_A307 Phosphoglycerate dehydrogenase; riken structural g 4e-21
3k5p_A416 D-3-phosphoglycerate dehydrogenase; niaid, ssgcid, 2e-20
1sc6_A404 PGDH, D-3-phosphoglycerate dehydrogenase; alloster 4e-20
1ygy_A 529 PGDH, D-3-phosphoglycerate dehydrogenase; oxidored 6e-20
1mx3_A347 CTBP1, C-terminal binding protein 1; nuclear prote 3e-19
3jtm_A351 Formate dehydrogenase, mitochondrial; mitochondrio 3e-18
2nac_A393 NAD-dependent formate dehydrogenase; oxidoreductas 1e-17
2o4c_A380 Erythronate-4-phosphate dehydrogenase; erythronate 2e-16
3gvx_A290 Glycerate dehydrogenase related protein; NYSGXRC, 2e-16
3gg9_A352 D-3-phosphoglycerate dehydrogenase oxidoreductase; 2e-16
2j6i_A364 Formate dehydrogenase; oxidoreductase, D-specific- 6e-16
2d0i_A333 Dehydrogenase; structural genomics, NPPSFA, nation 7e-16
3oet_A381 Erythronate-4-phosphate dehydrogenase; structural 2e-15
2pi1_A334 D-lactate dehydrogenase; oxidoreductase, D-LDH, NA 6e-13
1dxy_A333 D-2-hydroxyisocaproate dehydrogenase; D-2-hydroxyc 1e-12
4e5n_A330 Thermostable phosphite dehydrogenase; D-2-hydroxya 3e-12
2w2k_A348 D-mandelate dehydrogenase; 2-hydroxyacid dehydroge 4e-12
1qp8_A303 Formate dehydrogenase; oxidoreductase; HET: NDP; 2 4e-12
1j4a_A333 D-LDH, D-lactate dehydrogenase; NAD-dependent dehy 6e-12
2dbq_A334 Glyoxylate reductase; D-3-phosphoglycerate dehydro 7e-12
1gdh_A320 D-glycerate dehydrogenase; oxidoreductase(CHOH (D) 1e-11
1xdw_A331 NAD+-dependent (R)-2-hydroxyglutarate dehydrogenas 1e-11
3evt_A324 Phosphoglycerate dehydrogenase; structural genomic 6e-11
2cuk_A311 Glycerate dehydrogenase/glyoxylate reductase; stru 5e-10
4g2n_A345 D-isomer specific 2-hydroxyacid dehydrogenase, Na; 6e-10
2gcg_A330 Glyoxylate reductase/hydroxypyruvate reductase; NA 8e-10
3pp8_A315 Glyoxylate/hydroxypyruvate reductase A; structural 4e-09
3ba1_A333 HPPR, hydroxyphenylpyruvate reductase; two domain 7e-09
4dgs_A340 Dehydrogenase; structural genomics, PSI-biology, N 8e-09
3hg7_A324 D-isomer specific 2-hydroxyacid dehydrogenase FAM 2e-08
>2ekl_A D-3-phosphoglycerate dehydrogenase; structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: NAD; 1.77A {Sulfolobus tokodaii} Length = 313 Back     alignment and structure
 Score = 93.8 bits (234), Expect = 8e-24
 Identities = 27/49 (55%), Positives = 32/49 (65%)

Query: 5   LRCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGASTKEAQIR 53
           ++ G     A DVF  EPPK E   EL+KH +VIVT H+GA TKEAQ R
Sbjct: 246 IKKGKVYAYATDVFWNEPPKEEWELELLKHERVIVTTHIGAQTKEAQKR 294
>2g76_A 3-PGDH, D-3-phosphoglycerate dehydrogenase; oxidoreductase, phosphoglycerate dehydrogenase deficiency, S metabolism, 2-hydroxyacid dehydrogenases; HET: NAD; 1.70A {Homo sapiens} Length = 335 Back     alignment and structure
>1wwk_A Phosphoglycerate dehydrogenase; riken structural genomics/proteomics initiative, RSGI, structural genomics, oxidoreductase; HET: NAD; 1.90A {Pyrococcus horikoshii} Length = 307 Back     alignment and structure
>3k5p_A D-3-phosphoglycerate dehydrogenase; niaid, ssgcid, seattle structural genomics center for infect disease, brucellosis; 2.15A {Brucella melitensis biovar abortus} Length = 416 Back     alignment and structure
>1sc6_A PGDH, D-3-phosphoglycerate dehydrogenase; allosteric regulation phosphoglycerate dehydrogenase PGDH, oxidoreductase; HET: NAD; 2.09A {Escherichia coli} SCOP: c.2.1.4 c.23.12.1 d.58.18.1 PDB: 1psd_A* 1yba_A* 2p9c_A* 2p9e_A* 2pa3_A* 2p9g_A* Length = 404 Back     alignment and structure
>1ygy_A PGDH, D-3-phosphoglycerate dehydrogenase; oxidoreductase, serine biosy structural genomics, PSI, protein structure initiative; HET: TAR; 2.30A {Mycobacterium tuberculosis} SCOP: c.2.1.4 c.23.12.1 d.58.18.1 d.81.2.2 PDB: 3dc2_A* 3ddn_A* Length = 529 Back     alignment and structure
>1mx3_A CTBP1, C-terminal binding protein 1; nuclear protein, phosphorylation, transcriptional corepresso transcription repressor; HET: NAD; 1.95A {Homo sapiens} SCOP: c.2.1.4 c.23.12.1 PDB: 1hku_A* 1hl3_A* 2hu2_A* 3ga0_A 2ome_A* Length = 347 Back     alignment and structure
>3jtm_A Formate dehydrogenase, mitochondrial; mitochondrion, NAD, oxidoreductase, T peptide; 1.30A {Arabidopsis thaliana} PDB: 3n7u_A* 3naq_A Length = 351 Back     alignment and structure
>2nac_A NAD-dependent formate dehydrogenase; oxidoreductase(aldehyde(D),NAD+(A)); 1.80A {Pseudomonas SP} SCOP: c.2.1.4 c.23.12.1 PDB: 2nad_A* 2go1_A 2gug_A* 2gsd_A* 3fn4_A Length = 393 Back     alignment and structure
>2o4c_A Erythronate-4-phosphate dehydrogenase; erythronate-4-phsphate, NAD, tartrate, phosph oxidoreductase; HET: NAD TLA; 2.30A {Pseudomonas aeruginosa} Length = 380 Back     alignment and structure
>3gvx_A Glycerate dehydrogenase related protein; NYSGXRC, PSI-II, 11143J, structural genomics, protein structure initiative; 2.20A {Thermoplasma acidophilum} Length = 290 Back     alignment and structure
>3gg9_A D-3-phosphoglycerate dehydrogenase oxidoreductase; structural genomics, PSI-2, P structure initiative; 1.90A {Ralstonia solanacearum} Length = 352 Back     alignment and structure
>2j6i_A Formate dehydrogenase; oxidoreductase, D-specific-2- hydroxy acid dehydrogenase, cofactor regenerator, yeast, CBFDH; HET: PG4; 1.55A {Candida boidinii} PDB: 2fss_A Length = 364 Back     alignment and structure
>2d0i_A Dehydrogenase; structural genomics, NPPSFA, national project protein structural and functional analyses; 1.95A {Pyrococcus horikoshii} Length = 333 Back     alignment and structure
>3oet_A Erythronate-4-phosphate dehydrogenase; structural genomics, center for structural genomics of infec diseases, csgid; HET: NAD; 2.36A {Salmonella enterica subsp} Length = 381 Back     alignment and structure
>1dxy_A D-2-hydroxyisocaproate dehydrogenase; D-2-hydroxycarboxylate dehydrogenase, D-lactate dehydrogenas oxidoreductase; HET: NAD; 1.86A {Lactobacillus casei} SCOP: c.2.1.4 c.23.12.1 Length = 333 Back     alignment and structure
>4e5n_A Thermostable phosphite dehydrogenase; D-2-hydroxyacid dehydrogenase, oxidoreductase; HET: NAD; 1.70A {Pseudomonas stutzeri} PDB: 4e5k_A* 4ebf_A* 4e5p_A* 4e5m_A* Length = 330 Back     alignment and structure
>2w2k_A D-mandelate dehydrogenase; 2-hydroxyacid dehydrogenase, oxidoreductase; 1.85A {Rhodotorula graminis} PDB: 2w2l_A* 2w2l_D* 2w2k_B Length = 348 Back     alignment and structure
>1qp8_A Formate dehydrogenase; oxidoreductase; HET: NDP; 2.80A {Pyrobaculum aerophilum} SCOP: c.2.1.4 c.23.12.1 Length = 303 Back     alignment and structure
>1j4a_A D-LDH, D-lactate dehydrogenase; NAD-dependent dehydrogenase, reversible interconversion of pyruvate INTO D-lactate; 1.90A {Lactobacillus delbrueckii subsp} SCOP: c.2.1.4 c.23.12.1 PDB: 1j49_A* 2dld_A* Length = 333 Back     alignment and structure
>2dbq_A Glyoxylate reductase; D-3-phosphoglycerate dehydrogenase, ST genomics, NPPSFA; HET: NAP; 1.70A {Pyrococcus horikoshii} PDB: 2dbr_A* 2dbz_A* Length = 334 Back     alignment and structure
>1gdh_A D-glycerate dehydrogenase; oxidoreductase(CHOH (D)-NAD(P)+ (A)); 2.40A {Hyphomicrobium methylovorum} SCOP: c.2.1.4 c.23.12.1 Length = 320 Back     alignment and structure
>1xdw_A NAD+-dependent (R)-2-hydroxyglutarate dehydrogenase; structural variant of the BAB rossmann fold, oxidoreductase; 1.98A {Acidaminococcus fermentans} Length = 331 Back     alignment and structure
>3evt_A Phosphoglycerate dehydrogenase; structural genomics, PSI-2, protein structure initiative; 2.20A {Lactobacillus plantarum} Length = 324 Back     alignment and structure
>2cuk_A Glycerate dehydrogenase/glyoxylate reductase; structural genomics, riken structur genomics/proteomics initiative, RSGI, NPPSFA; HET: NHE; 2.00A {Thermus thermophilus} Length = 311 Back     alignment and structure
>4g2n_A D-isomer specific 2-hydroxyacid dehydrogenase, Na; structural genomics, protein structure initiative, nysgrc, P biology; 1.70A {Polaromonas SP} Length = 345 Back     alignment and structure
>2gcg_A Glyoxylate reductase/hydroxypyruvate reductase; NAD(P) rossmann fold, formate/glycerate dehydrogenase substr binding domain, oxidoreductase; HET: NDP; 2.20A {Homo sapiens} PDB: 2wwr_A 2h1s_A 2q50_A Length = 330 Back     alignment and structure
>3pp8_A Glyoxylate/hydroxypyruvate reductase A; structural genomics, center for structural genomics of infec diseases, csgid; 2.10A {Salmonella enterica subsp} PDB: 3kbo_A Length = 315 Back     alignment and structure
>3ba1_A HPPR, hydroxyphenylpyruvate reductase; two domain protein, substrate binding domain, cofactor bindi domain, oxidoreductase; 1.47A {Solenostemon scutellarioides} PDB: 3baz_A* Length = 333 Back     alignment and structure
>4dgs_A Dehydrogenase; structural genomics, PSI-biology, NEW YORK structural genomi research consortium, nysgrc, oxidoreductase; 2.50A {Sinorhizobium meliloti} Length = 340 Back     alignment and structure
>3hg7_A D-isomer specific 2-hydroxyacid dehydrogenase FAM protein; structural genomics; 1.80A {Aeromonas salmonicida subsp} Length = 324 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query168
1ygy_A529 PGDH, D-3-phosphoglycerate dehydrogenase; oxidored 99.94
1sc6_A404 PGDH, D-3-phosphoglycerate dehydrogenase; alloster 99.8
4dgs_A340 Dehydrogenase; structural genomics, PSI-biology, N 99.76
4g2n_A345 D-isomer specific 2-hydroxyacid dehydrogenase, Na; 99.75
3k5p_A416 D-3-phosphoglycerate dehydrogenase; niaid, ssgcid, 99.75
3gg9_A352 D-3-phosphoglycerate dehydrogenase oxidoreductase; 99.75
3evt_A324 Phosphoglycerate dehydrogenase; structural genomic 99.73
4e5n_A330 Thermostable phosphite dehydrogenase; D-2-hydroxya 99.73
3hg7_A324 D-isomer specific 2-hydroxyacid dehydrogenase FAM 99.72
3pp8_A315 Glyoxylate/hydroxypyruvate reductase A; structural 99.72
3jtm_A351 Formate dehydrogenase, mitochondrial; mitochondrio 99.72
2j6i_A364 Formate dehydrogenase; oxidoreductase, D-specific- 99.71
1j4a_A333 D-LDH, D-lactate dehydrogenase; NAD-dependent dehy 99.71
3kb6_A334 D-lactate dehydrogenase; oxidoreductase, D-LDH, NA 99.71
4hy3_A365 Phosphoglycerate oxidoreductase; PSI-biology, stru 99.71
1dxy_A333 D-2-hydroxyisocaproate dehydrogenase; D-2-hydroxyc 99.7
2yq5_A343 D-isomer specific 2-hydroxyacid dehydrogenase; oxi 99.7
2pi1_A334 D-lactate dehydrogenase; oxidoreductase, D-LDH, NA 99.7
1xdw_A331 NAD+-dependent (R)-2-hydroxyglutarate dehydrogenas 99.69
2nac_A393 NAD-dependent formate dehydrogenase; oxidoreductas 99.64
1qp8_A303 Formate dehydrogenase; oxidoreductase; HET: NDP; 2 99.64
2d0i_A333 Dehydrogenase; structural genomics, NPPSFA, nation 99.61
3ba1_A333 HPPR, hydroxyphenylpyruvate reductase; two domain 99.6
2g76_A335 3-PGDH, D-3-phosphoglycerate dehydrogenase; oxidor 99.6
2w2k_A348 D-mandelate dehydrogenase; 2-hydroxyacid dehydroge 99.59
2cuk_A311 Glycerate dehydrogenase/glyoxylate reductase; stru 99.58
1wwk_A307 Phosphoglycerate dehydrogenase; riken structural g 99.58
2dbq_A334 Glyoxylate reductase; D-3-phosphoglycerate dehydro 99.58
1mx3_A347 CTBP1, C-terminal binding protein 1; nuclear prote 99.56
1gdh_A320 D-glycerate dehydrogenase; oxidoreductase(CHOH (D) 99.54
2ekl_A313 D-3-phosphoglycerate dehydrogenase; structural gen 99.54
2gcg_A330 Glyoxylate reductase/hydroxypyruvate reductase; NA 99.52
3gvx_A290 Glycerate dehydrogenase related protein; NYSGXRC, 99.51
2o4c_A380 Erythronate-4-phosphate dehydrogenase; erythronate 99.49
3oet_A381 Erythronate-4-phosphate dehydrogenase; structural 99.49
3d64_A494 Adenosylhomocysteinase; structural genomics, ssgci 97.78
1v8b_A479 Adenosylhomocysteinase; hydrolase; HET: NAD ADN; 2 97.71
1gtm_A419 Glutamate dehydrogenase; oxidoreductase, NAD, NADP 97.04
3ce6_A494 Adenosylhomocysteinase; protein-substrate complex, 88.72
2vhw_A377 Alanine dehydrogenase; NAD, secreted, oxidoreducta 87.86
>1ygy_A PGDH, D-3-phosphoglycerate dehydrogenase; oxidoreductase, serine biosy structural genomics, PSI, protein structure initiative; HET: TAR; 2.30A {Mycobacterium tuberculosis} SCOP: c.2.1.4 c.23.12.1 d.58.18.1 d.81.2.2 PDB: 3dc2_A* 3ddn_A* Back     alignment and structure
Probab=99.94  E-value=1.7e-26  Score=208.07  Aligned_cols=156  Identities=25%  Similarity=0.346  Sum_probs=134.6

Q ss_pred             CHHHHhcCCeeEEEeecCCCCCCCCCCChhhccCCceEEccCCCcchHHHHHHHHHHHHHHh------------------
Q psy6351           1 MKSELRCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGASTKEAQIRQDKQSIFYS------------------   62 (168)
Q Consensus         1 L~~AL~~G~i~gAaLDVf~~EP~~~~~~~pL~~~~nvilTPHig~~T~ea~~~~~~~~~~~~------------------   62 (168)
                      |++||++|+|+||++|||+.||..++   |||+++|+++|||++|+|.+++.+++..+++++                  
T Consensus       242 L~~al~~g~i~ga~lDv~~~eP~~~~---~L~~~~~vilTPh~~~~t~ea~~~~~~~~~~~l~~~l~~~~~~~~v~~~~~  318 (529)
T 1ygy_A          242 LADAITGGHVRAAGLDVFATEPCTDS---PLFELAQVVVTPHLGASTAEAQDRAGTDVAESVRLALAGEFVPDAVNVGGG  318 (529)
T ss_dssp             HHHHHHTSSEEEEEESSCSSSSCSCC---GGGGCTTEEECSSCSSCBHHHHHHHHHHHHHHHHHHHTTCCCTTBCSCCST
T ss_pred             HHHHHHcCCccEEEEeeccCCCCCCc---hHHhCCCEEEccccCCCCHHHHHHHHHHHHHHHHHHHcCCCCCcccCCccc
Confidence            46899999999999999999998654   999999999999999999999999999888865                  


Q ss_pred             ---------------------------------hcccccc--ccccchHHHHHhhccCCCCCCccccChhhHHhhCCceE
Q psy6351          63 ---------------------------------LLGAELK--NKQFLTTPVQIGLLSGRTSNGLNFINVNTYASEGGLKV  107 (168)
Q Consensus        63 ---------------------------------~~g~~~~--~~~~lt~a~l~~~L~~~~~~~vn~VNa~~la~~~GI~v  107 (168)
                                                       .|+|+..  +...++++.|+++|+...++.+|++|+..+|+++||++
T Consensus       319 ~~hd~i~P~l~La~~lg~~~~qla~g~~~ditria~G~~~~~~i~~~n~a~l~g~L~~~~~~~~~~vnA~~iA~e~Gi~i  398 (529)
T 1ygy_A          319 VVNEEVAPWLDLVRKLGVLAGVLSDELPVSLSVQVRGELAAEEVEVLRLSALRGLFSAVIEDAVTFVNAPALAAERGVTA  398 (529)
T ss_dssp             TSCTTTTTHHHHHHHHHHHHHHTSSSCCSEEEEEEEEGGGGSCCHHHHHHHHHHHTGGGSCTTCCCCCHHHHHHHHSCEE
T ss_pred             ccchhhhhHHHHHHHHHHHHHHHhCCCceEEEEEEEeeccccCCcHHHHHHHHHhcCCCCCCCccccCHHHHHHHcCCEE
Confidence                                             1112221  23567899999999987777799999999999999999


Q ss_pred             EEEECCCC--CCceEEEEEee-c--------------CcccEEEEcceEeeccccccEEEEeecCCCCC
Q psy6351         108 AYEHDPSS--SQNLVALAFGS-N--------------VAKHVLTVKQGLFTELLSYSLILVLQEDTAQW  159 (168)
Q Consensus       108 ~e~~~~~~--~~n~itv~~~~-~--------------~~~~l~~i~~~~~~~~~eG~~li~r~~D~pg~  159 (168)
                      .+.+.+.+  +.|.+++++.+ +              +.+++++||+|.+++.++|++|+++|.|+||+
T Consensus       399 ~~~~~~~~~~~~n~v~v~~~~~~~~~~~v~Gt~~gg~g~~~i~~i~g~~v~~~~~~~~l~v~~~D~PG~  467 (529)
T 1ygy_A          399 EICKASESPNHRSVVDVRAVGADGSVVTVSGTLYGPQLSQKIVQINGRHFDLRAQGINLIIHYVDRPGA  467 (529)
T ss_dssp             EEEEESCCSSSSEEEEEEEECTTSCEEEEEEEEETTTTEEEEEEETTEEEEEESCSEEEEEEESCCTTH
T ss_pred             EEEEccCCCCCCCEEEEEEEECCCCEEEEEEEEeCCCCcEEEEEECCEEEEecCCccEEEEEcCCCCch
Confidence            99886543  48999998875 2              46799999999999999999999999999997
>1sc6_A PGDH, D-3-phosphoglycerate dehydrogenase; allosteric regulation phosphoglycerate dehydrogenase PGDH, oxidoreductase; HET: NAD; 2.09A {Escherichia coli} SCOP: c.2.1.4 c.23.12.1 d.58.18.1 PDB: 1psd_A* 1yba_A* 2p9c_A* 2p9e_A* 2pa3_A* 2p9g_A* Back     alignment and structure
>4dgs_A Dehydrogenase; structural genomics, PSI-biology, NEW YORK structural genomi research consortium, nysgrc, oxidoreductase; 2.50A {Sinorhizobium meliloti} Back     alignment and structure
>4g2n_A D-isomer specific 2-hydroxyacid dehydrogenase, Na; structural genomics, protein structure initiative, nysgrc, P biology; 1.70A {Polaromonas SP} Back     alignment and structure
>3k5p_A D-3-phosphoglycerate dehydrogenase; niaid, ssgcid, seattle structural genomics center for infect disease, brucellosis; 2.15A {Brucella melitensis biovar abortus} Back     alignment and structure
>3gg9_A D-3-phosphoglycerate dehydrogenase oxidoreductase; structural genomics, PSI-2, P structure initiative; 1.90A {Ralstonia solanacearum} Back     alignment and structure
>3evt_A Phosphoglycerate dehydrogenase; structural genomics, PSI-2, protein structure initiative; 2.20A {Lactobacillus plantarum} Back     alignment and structure
>4e5n_A Thermostable phosphite dehydrogenase; D-2-hydroxyacid dehydrogenase, oxidoreductase; HET: NAD; 1.70A {Pseudomonas stutzeri} PDB: 4e5k_A* 4ebf_A* 4e5p_A* 4e5m_A* Back     alignment and structure
>3hg7_A D-isomer specific 2-hydroxyacid dehydrogenase FAM protein; structural genomics; 1.80A {Aeromonas salmonicida subsp} Back     alignment and structure
>3pp8_A Glyoxylate/hydroxypyruvate reductase A; structural genomics, center for structural genomics of infec diseases, csgid; 2.10A {Salmonella enterica subsp} PDB: 3kbo_A Back     alignment and structure
>3jtm_A Formate dehydrogenase, mitochondrial; mitochondrion, NAD, oxidoreductase, T peptide; 1.30A {Arabidopsis thaliana} PDB: 3n7u_A* 3naq_A Back     alignment and structure
>2j6i_A Formate dehydrogenase; oxidoreductase, D-specific-2- hydroxy acid dehydrogenase, cofactor regenerator, yeast, CBFDH; HET: PG4; 1.55A {Candida boidinii} PDB: 2fss_A Back     alignment and structure
>1j4a_A D-LDH, D-lactate dehydrogenase; NAD-dependent dehydrogenase, reversible interconversion of pyruvate INTO D-lactate; 1.90A {Lactobacillus delbrueckii subsp} SCOP: c.2.1.4 c.23.12.1 PDB: 1j49_A* 2dld_A* Back     alignment and structure
>3kb6_A D-lactate dehydrogenase; oxidoreductase, D-LDH, NAD, structural genomics, NPPSFA, NAT project on protein structural and functional analyses; HET: MSE NAD 1PE; 2.12A {Aquifex aeolicus} Back     alignment and structure
>4hy3_A Phosphoglycerate oxidoreductase; PSI-biology, structural genomics, protein structure initiati acid transport and metabolism, NAD binding domain.; 2.80A {Rhizobium etli} Back     alignment and structure
>1dxy_A D-2-hydroxyisocaproate dehydrogenase; D-2-hydroxycarboxylate dehydrogenase, D-lactate dehydrogenas oxidoreductase; HET: NAD; 1.86A {Lactobacillus casei} SCOP: c.2.1.4 c.23.12.1 Back     alignment and structure
>2yq5_A D-isomer specific 2-hydroxyacid dehydrogenase; oxidoreductase; HET: NAD; 2.75A {Lactobacillus delbrueckii subsp} PDB: 2yq4_A* Back     alignment and structure
>1xdw_A NAD+-dependent (R)-2-hydroxyglutarate dehydrogenase; structural variant of the BAB rossmann fold, oxidoreductase; 1.98A {Acidaminococcus fermentans} Back     alignment and structure
>2nac_A NAD-dependent formate dehydrogenase; oxidoreductase(aldehyde(D),NAD+(A)); 1.80A {Pseudomonas SP} SCOP: c.2.1.4 c.23.12.1 PDB: 2nad_A* 2go1_A 2gug_A* 2gsd_A* 3fn4_A Back     alignment and structure
>1qp8_A Formate dehydrogenase; oxidoreductase; HET: NDP; 2.80A {Pyrobaculum aerophilum} SCOP: c.2.1.4 c.23.12.1 Back     alignment and structure
>2d0i_A Dehydrogenase; structural genomics, NPPSFA, national project protein structural and functional analyses; 1.95A {Pyrococcus horikoshii} Back     alignment and structure
>3ba1_A HPPR, hydroxyphenylpyruvate reductase; two domain protein, substrate binding domain, cofactor bindi domain, oxidoreductase; 1.47A {Solenostemon scutellarioides} PDB: 3baz_A* Back     alignment and structure
>2g76_A 3-PGDH, D-3-phosphoglycerate dehydrogenase; oxidoreductase, phosphoglycerate dehydrogenase deficiency, S metabolism, 2-hydroxyacid dehydrogenases; HET: NAD; 1.70A {Homo sapiens} Back     alignment and structure
>2w2k_A D-mandelate dehydrogenase; 2-hydroxyacid dehydrogenase, oxidoreductase; 1.85A {Rhodotorula graminis} PDB: 2w2l_A* 2w2l_D* 2w2k_B Back     alignment and structure
>2cuk_A Glycerate dehydrogenase/glyoxylate reductase; structural genomics, riken structur genomics/proteomics initiative, RSGI, NPPSFA; HET: NHE; 2.00A {Thermus thermophilus} Back     alignment and structure
>1wwk_A Phosphoglycerate dehydrogenase; riken structural genomics/proteomics initiative, RSGI, structural genomics, oxidoreductase; HET: NAD; 1.90A {Pyrococcus horikoshii} Back     alignment and structure
>2dbq_A Glyoxylate reductase; D-3-phosphoglycerate dehydrogenase, ST genomics, NPPSFA; HET: NAP; 1.70A {Pyrococcus horikoshii} PDB: 2dbr_A* 2dbz_A* Back     alignment and structure
>1mx3_A CTBP1, C-terminal binding protein 1; nuclear protein, phosphorylation, transcriptional corepresso transcription repressor; HET: NAD; 1.95A {Homo sapiens} SCOP: c.2.1.4 c.23.12.1 PDB: 1hku_A* 1hl3_A* 2hu2_A* 3ga0_A 2ome_A* Back     alignment and structure
>1gdh_A D-glycerate dehydrogenase; oxidoreductase(CHOH (D)-NAD(P)+ (A)); 2.40A {Hyphomicrobium methylovorum} SCOP: c.2.1.4 c.23.12.1 Back     alignment and structure
>2ekl_A D-3-phosphoglycerate dehydrogenase; structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: NAD; 1.77A {Sulfolobus tokodaii} Back     alignment and structure
>2gcg_A Glyoxylate reductase/hydroxypyruvate reductase; NAD(P) rossmann fold, formate/glycerate dehydrogenase substr binding domain, oxidoreductase; HET: NDP; 2.20A {Homo sapiens} PDB: 2wwr_A 2h1s_A 2q50_A Back     alignment and structure
>3gvx_A Glycerate dehydrogenase related protein; NYSGXRC, PSI-II, 11143J, structural genomics, protein structure initiative; 2.20A {Thermoplasma acidophilum} Back     alignment and structure
>2o4c_A Erythronate-4-phosphate dehydrogenase; erythronate-4-phsphate, NAD, tartrate, phosph oxidoreductase; HET: NAD TLA; 2.30A {Pseudomonas aeruginosa} Back     alignment and structure
>3oet_A Erythronate-4-phosphate dehydrogenase; structural genomics, center for structural genomics of infec diseases, csgid; HET: NAD; 2.36A {Salmonella enterica subsp} Back     alignment and structure
>3d64_A Adenosylhomocysteinase; structural genomics, ssgcid, S-adenosyl-L-homocysteine hydro NAD, one-carbon metabolism; HET: NAD; 2.30A {Burkholderia pseudomallei} PDB: 3glq_A* Back     alignment and structure
>1v8b_A Adenosylhomocysteinase; hydrolase; HET: NAD ADN; 2.40A {Plasmodium falciparum} SCOP: c.2.1.4 c.23.12.3 Back     alignment and structure
>1gtm_A Glutamate dehydrogenase; oxidoreductase, NAD, NADP; 2.20A {Pyrococcus furiosus} SCOP: c.2.1.7 c.58.1.1 PDB: 1bvu_A 1euz_A Back     alignment and structure
>3ce6_A Adenosylhomocysteinase; protein-substrate complex, dimer of dimers, NAD binding DOMA amino acid insertional region, hydrolase; HET: ADN NAD; 1.60A {Mycobacterium tuberculosis} PDB: 3dhy_A* 2zj0_A* 2ziz_A* 2zj1_A* Back     alignment and structure
>2vhw_A Alanine dehydrogenase; NAD, secreted, oxidoreductase; HET: NAI; 2.0A {Mycobacterium tuberculosis} PDB: 2vhx_A* 2vhy_A 2vhz_A* 2vhv_A* 2voe_A 2voj_A* Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 168
d1gdha1191 c.2.1.4 (A:101-291) D-glycerate dehydrogenase {Hyp 6e-13
d1sc6a1188 c.2.1.4 (A:108-295) Phosphoglycerate dehydrogenase 6e-11
d1ygya1184 c.2.1.4 (A:99-282) Phosphoglycerate dehydrogenase 1e-10
d2naca1188 c.2.1.4 (A:148-335) Formate dehydrogenase {Pseudom 1e-10
d1mx3a1193 c.2.1.4 (A:126-318) Transcription corepressor CtbP 8e-10
d1qp8a1181 c.2.1.4 (A:83-263) Putative formate dehydrogenase 9e-10
d1dxya1199 c.2.1.4 (A:101-299) D-2-hydroxyisocaproate dehydro 4e-06
d1j4aa1197 c.2.1.4 (A:104-300) D-lactate dehydrogenase {Lacto 2e-05
>d1gdha1 c.2.1.4 (A:101-291) D-glycerate dehydrogenase {Hyphomicrobium methylovorum [TaxId: 84]} Length = 191 Back     information, alignment and structure

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Formate/glycerate dehydrogenases, NAD-domain
domain: D-glycerate dehydrogenase
species: Hyphomicrobium methylovorum [TaxId: 84]

 Score = 61.5 bits (148), Expect = 6e-13
 Identities = 13/46 (28%), Positives = 20/46 (43%), Gaps = 3/46 (6%)

Query: 1   MKSELRCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGAS 46
           + + L  G    A  DVF  EP  +E        P   + PH+G++
Sbjct: 149 VVAALEAGRLAYAGFDVFAGEPNINE---GYYDLPNTFLFPHIGSA 191
>d1sc6a1 c.2.1.4 (A:108-295) Phosphoglycerate dehydrogenase {Escherichia coli [TaxId: 562]} Length = 188 Back     information, alignment and structure
>d1ygya1 c.2.1.4 (A:99-282) Phosphoglycerate dehydrogenase {Mycobacterium tuberculosis [TaxId: 1773]} Length = 184 Back     information, alignment and structure
>d2naca1 c.2.1.4 (A:148-335) Formate dehydrogenase {Pseudomonas sp., strain 101 [TaxId: 306]} Length = 188 Back     information, alignment and structure
>d1mx3a1 c.2.1.4 (A:126-318) Transcription corepressor CtbP {Human (Homo sapiens), Ctbp1 [TaxId: 9606]} Length = 193 Back     information, alignment and structure
>d1qp8a1 c.2.1.4 (A:83-263) Putative formate dehydrogenase {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Length = 181 Back     information, alignment and structure
>d1dxya1 c.2.1.4 (A:101-299) D-2-hydroxyisocaproate dehydrogenase {Lactobacillus casei [TaxId: 1582]} Length = 199 Back     information, alignment and structure
>d1j4aa1 c.2.1.4 (A:104-300) D-lactate dehydrogenase {Lactobacillus helveticus [TaxId: 1587]} Length = 197 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

Original result of HHsearch against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query168
d1ygya4135 D-3-phosphoglycerate dehydrogenase SerA {Mycobacte 99.45
d1j4aa1197 D-lactate dehydrogenase {Lactobacillus helveticus 97.39
d1dxya1199 D-2-hydroxyisocaproate dehydrogenase {Lactobacillu 97.39
>d1ygya4 d.81.2.2 (A:317-451) D-3-phosphoglycerate dehydrogenase SerA {Mycobacterium tuberculosis [TaxId: 1773]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: FwdE/GAPDH domain-like
superfamily: Serine metabolism enzymes domain
family: SerA intervening domain-like
domain: D-3-phosphoglycerate dehydrogenase SerA
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=99.45  E-value=9.9e-14  Score=103.13  Aligned_cols=81  Identities=17%  Similarity=0.270  Sum_probs=66.0

Q ss_pred             hcccccc--ccccchHHHHHhhccCCCCCCccccChhhHHhhCCceEEEEECCCCC--CceEEEEEee-cC---------
Q psy6351          63 LLGAELK--NKQFLTTPVQIGLLSGRTSNGLNFINVNTYASEGGLKVAYEHDPSSS--QNLVALAFGS-NV---------  128 (168)
Q Consensus        63 ~~g~~~~--~~~~lt~a~l~~~L~~~~~~~vn~VNa~~la~~~GI~v~e~~~~~~~--~n~itv~~~~-~~---------  128 (168)
                      .|.|+++  +++++|.+.|+|+|.+...+.+|+|||+.+||+|||+|.+.+.+.+.  .|+|+|++.+ ++         
T Consensus        36 ~~~G~~a~~~~~~lt~a~l~G~L~~~~~~~VN~VNA~~iAkerGI~v~~~~~~~~~~~~n~i~v~~~~~~~~~~~v~Gtv  115 (135)
T d1ygya4          36 QVRGELAAEEVEVLRLSALRGLFSAVIEDAVTFVNAPALAAERGVTAEICKASESPNHRSVVDVRAVGADGSVVTVSGTL  115 (135)
T ss_dssp             EEEEGGGGSCCHHHHHHHHHHHTGGGSCTTCCCCCHHHHHHHHSCEEEEEEESCCSSSSEEEEEEEECTTSCEEEEEEEE
T ss_pred             EEEeecccccccHHHHHHHHHHHhcccccccchhhHHHHHHHcCCEEEEEECCCCCCCcccEEEEEEeCCCcEEEEEEEE
Confidence            4556653  57999999999999998788999999999999999999998876654  8888887532 21         


Q ss_pred             -----cccEEEEcceEeecc
Q psy6351         129 -----AKHVLTVKQGLFTEL  143 (168)
Q Consensus       129 -----~~~l~~i~~~~~~~~  143 (168)
                           .+||++||+|.+|++
T Consensus       116 ~g~~~~~RIv~Idg~~vdvk  135 (135)
T d1ygya4         116 YGPQLSQKIVQINGRHFDLR  135 (135)
T ss_dssp             ETTTTEEEEEEETTEEEEEE
T ss_pred             ECCCCcEEEEEECCEEEeeC
Confidence                 368899999988763
>d1j4aa1 c.2.1.4 (A:104-300) D-lactate dehydrogenase {Lactobacillus helveticus [TaxId: 1587]} Back     information, alignment and structure
>d1dxya1 c.2.1.4 (A:101-299) D-2-hydroxyisocaproate dehydrogenase {Lactobacillus casei [TaxId: 1582]} Back     information, alignment and structure