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Conserved domains on  [gi|2025689086|gb|QTU91094|]
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hydroxymethylbilane synthase, partial [Lasiopodomys brandtii]

Protein Classification

type 2 periplasmic-binding domain-containing protein( domain architecture ID 229383)

type 2 periplasmic-binding protein (PBP2) is typically comprised of two globular subdomains connected by a flexible hinge; it binds its ligand in the cleft between these domains in a manner resembling a Venus flytrap; similar to the ligand-binding domains found in solute binding proteins that serve as initial receptors in the transport, signal transduction and channel gating

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Periplasmic_Binding_Protein_Type_2 super family cl21456
Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent ...
 1-168 1.29e-113

Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent the ligand-binding domains found in solute binding proteins that serve as initial receptors in the transport, signal transduction and channel gating. The PBP2 proteins share the same architecture as periplasmic binding proteins type 1 (PBP1), but have a different topology. They are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The origin of PBP module can be traced across the distant phyla, including eukaryotes, archebacteria, and prokaryotes. The majority of PBP2 proteins are involved in the uptake of a variety of soluble substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the family includes ionotropic glutamate receptors and unorthodox sensor proteins involved in signal transduction. The substrate binding domain of the LysR transcriptional regulators and the oligopeptide-like transport systems also contain the type 2 periplasmic binding fold and thus they are significantly homologous to that of the PBP2; however, these two families are grouped into a separate hierarchy of the PBP2 superfamily due to the large number of protein sequences.


The actual alignment was detected with superfamily member cd13645:

Pssm-ID: 473866 [Multi-domain]  Cd Length: 282  Bit Score: 323.80  E-value: 1.29e-113
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2025689086   1 LHPGMQFEIIAMSTTGDKILDTALSKIGEKSLFTKELEYALEKNEVDLVVHSLKDVPTILPPGFTIGAICKRENPCDAVV 80
Cdd:cd13645    26 LYPDLTFEIITMSTTGDKILDVALSKIGGKGLFTKELEAALLEGEVDLAVHSLKDLPTVLPPGFELGAILKREDPRDALV 105

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2025689086  81 FHPKFIGKTLETLPEKSAVGTSSLRRVAQLQRKFPHLEFRSIRGNLNTRLRKLDEQQ-EFSAIVLAVAGLQRMGWQNRVG 159
Cdd:cd13645   106 FHPGLNYKSLDDLPEGSVIGTSSLRRAAQLKRKYPHLRFKDIRGNLNTRLAKLDAPEsPYDAIILAAAGLERLGLEDRIS 185


                  ....*....
gi 2025689086 160 QILHPEECM 168
Cdd:cd13645   186 QDLSPETML 194
 
Name Accession Description Interval E-value
PBP2_HuPBGD_like cd13645
Human porphobilinogen deaminase possess type 2 periplasmic binding protein fold; ...
 1-168 1.29e-113

Human porphobilinogen deaminase possess type 2 periplasmic binding protein fold; Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophyll, and vitamin B12. HMBS catalyzes the conversion of porphobilinogen (PBG) into hydroxymethylbilane (HMB). This subfamily includes the three domains of human PBGD and its closely related proteins. Mutations in human PBGD cause AIP (acute intermittent porphyria), an inherited autosomal dominant disorder. The enzyme is believed to bind substrate through a hinge-bending motion of domains 1 and 2. The C-terminal domain 3 contains an invariant cysteine that forms the covalent attachment site for the DPM (dipyrromethane) cofactor. HMBS is found in all organisms except viruses. The domains 1 and 2 have the same overall topology as found in the type 2 periplasmic-binding proteins (PBP2), many of which are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor.


Pssm-ID: 270363 [Multi-domain]  Cd Length: 282  Bit Score: 323.80  E-value: 1.29e-113
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2025689086   1 LHPGMQFEIIAMSTTGDKILDTALSKIGEKSLFTKELEYALEKNEVDLVVHSLKDVPTILPPGFTIGAICKRENPCDAVV 80
Cdd:cd13645    26 LYPDLTFEIITMSTTGDKILDVALSKIGGKGLFTKELEAALLEGEVDLAVHSLKDLPTVLPPGFELGAILKREDPRDALV 105

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2025689086  81 FHPKFIGKTLETLPEKSAVGTSSLRRVAQLQRKFPHLEFRSIRGNLNTRLRKLDEQQ-EFSAIVLAVAGLQRMGWQNRVG 159
Cdd:cd13645   106 FHPGLNYKSLDDLPEGSVIGTSSLRRAAQLKRKYPHLRFKDIRGNLNTRLAKLDAPEsPYDAIILAAAGLERLGLEDRIS 185


                  ....*....
gi 2025689086 160 QILHPEECM 168
Cdd:cd13645   186 QDLSPETML 194
HemC COG0181
Porphobilinogen deaminase [Coenzyme transport and metabolism]; Porphobilinogen deaminase is ...
 1-167 3.04e-92

Porphobilinogen deaminase [Coenzyme transport and metabolism]; Porphobilinogen deaminase is part of the Pathway/BioSystem: Heme biosynthesis


Pssm-ID: 439951 [Multi-domain]  Cd Length: 306  Bit Score: 270.35  E-value: 3.04e-92
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2025689086   1 LHPGMQFEIIAMSTTGDKILDTALSKIGEKSLFTKELEYALEKNEVDLVVHSLKDVPTILPPGFTIGAICKRENPCDAVV 80
Cdd:COG0181    29 AHPGLEVELVPIKTKGDKILDRPLAKIGGKGLFTKELEEALLDGEIDIAVHSLKDVPTELPEGLVLAAVLEREDPRDALV 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2025689086  81 FHPkfiGKTLETLPEKSAVGTSSLRRVAQLQRKFPHLEFRSIRGNLNTRLRKLDEqQEFSAIVLAVAGLQRMGWQNRVGQ 160
Cdd:COG0181   109 SRD---GASLDDLPEGAVVGTSSLRRQAQLLALRPDLEIVDLRGNVDTRLRKLDE-GEYDAIILAAAGLKRLGLEDRITE 184


                  ....*..
gi 2025689086 161 ILHPEEC 167
Cdd:COG0181   185 VLDPEEM 191
Porphobil_deam pfam01379
Porphobilinogen deaminase, dipyromethane cofactor binding domain;
5-168 4.11e-92

Porphobilinogen deaminase, dipyromethane cofactor binding domain;


Pssm-ID: 460180  Cd Length: 203  Bit Score: 266.16  E-value: 4.11e-92
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2025689086   5 MQFEIIAMSTTGDKILDTALSKIGEKSLFTKELEYALEKNEVDLVVHSLKDVPTILPPGFTIGAICKRENPCDAVVFHPK 84
Cdd:pfam01379  25 EEFEIVTIKTTGDKILDKPLAKIGGKGLFTKELEEALLDGEIDIAVHSLKDLPTELPEGLVLAAVLEREDPRDALVLSRD 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2025689086  85 fiGKTLETLPEKSAVGTSSLRRVAQLQRKFPHLEFRSIRGNLNTRLRKLDEqQEFSAIVLAVAGLQRMGWQNRVGQILHP 164
Cdd:pfam01379 105 --GSLLELLPEGAVVGTSSLRRRAQLLRLRPDLEVKDLRGNVDTRLRKLDE-GEYDAIILAAAGLKRLGLEDIITEYLDP 181


                  ....
gi 2025689086 165 EECM 168
Cdd:pfam01379 182 EEML 185
hemC TIGR00212
hydroxymethylbilane synthase; Alternate name hydroxymethylbilane synthase Biosynthesis of ...
 1-168 5.44e-73

hydroxymethylbilane synthase; Alternate name hydroxymethylbilane synthase Biosynthesis of cofactors, prosthetic groups, and carriers: Heme and porphyrin [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin]


Pssm-ID: 272963 [Multi-domain]  Cd Length: 292  Bit Score: 220.99  E-value: 5.44e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2025689086   1 LHPGMQFEIIAMSTTGDKILDTALSKIGEKSLFTKELEYALEKNEVDLVVHSLKDVPTILPPGFTIGAICKRENPCDAVV 80
Cdd:TIGR00212  25 VYPELDTEIVIIKTTGDKIQDKPLYDIGGKGLFTKELEQALLDGEIDLAVHSLKDVPTVLPEGLEIAAVLKREDPRDVLV 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2025689086  81 fHPKfiGKTLETLPEKSAVGTSSLRRVAQLQRKFPHLEFRSIRGNLNTRLRKLDEqQEFSAIVLAVAGLQRMGWQNRVGQ 160
Cdd:TIGR00212 105 -SRK--YLSLDSLPQGAKVGTSSLRRKAQLKAIRPDLKIEPLRGNIDTRLRKLDE-GEYDAIILAEAGLKRLGLEDVITE 180


                  ....*...
gi 2025689086 161 ILHPEECM 168
Cdd:TIGR00212 181 VLDPEVML 188
PLN02691 PLN02691
porphobilinogen deaminase
 6-166 2.11e-51

porphobilinogen deaminase


Pssm-ID: 215373 [Multi-domain]  Cd Length: 351  Bit Score: 167.64  E-value: 2.11e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2025689086   6 QFEIIAMSTTGDKILDTALSKIGEKSLFTKELEYALEKNEVDLVVHSLKDVPTILPPGFTIGAICKRENPCDAvvfhpkF 85
Cdd:PLN02691   77 ALEIVIIKTTGDKILDQPLADIGGKGLFTKEIDDALLSGRIDIAVHSMKDVPTYLPEGTILPCNLPREDVRDA------F 150

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2025689086  86 I---GKTLETLPEKSAVGTSSLRRVAQLQRKFPHLEFRSIRGNLNTRLRKLDEqQEFSAIVLAVAGLQRMGWQNRVGQIL 162
Cdd:PLN02691  151 IslkAKSLAELPAGSVVGTASLRRQSQILHKYPHLKVVNFRGNVQTRLRKLQE-GVVDATLLALAGLKRLDMTEHATSIL 229


                  ....
gi 2025689086 163 HPEE 166
Cdd:PLN02691  230 STDE 233
 
Name Accession Description Interval E-value
PBP2_HuPBGD_like cd13645
Human porphobilinogen deaminase possess type 2 periplasmic binding protein fold; ...
 1-168 1.29e-113

Human porphobilinogen deaminase possess type 2 periplasmic binding protein fold; Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophyll, and vitamin B12. HMBS catalyzes the conversion of porphobilinogen (PBG) into hydroxymethylbilane (HMB). This subfamily includes the three domains of human PBGD and its closely related proteins. Mutations in human PBGD cause AIP (acute intermittent porphyria), an inherited autosomal dominant disorder. The enzyme is believed to bind substrate through a hinge-bending motion of domains 1 and 2. The C-terminal domain 3 contains an invariant cysteine that forms the covalent attachment site for the DPM (dipyrromethane) cofactor. HMBS is found in all organisms except viruses. The domains 1 and 2 have the same overall topology as found in the type 2 periplasmic-binding proteins (PBP2), many of which are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor.


Pssm-ID: 270363 [Multi-domain]  Cd Length: 282  Bit Score: 323.80  E-value: 1.29e-113
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2025689086   1 LHPGMQFEIIAMSTTGDKILDTALSKIGEKSLFTKELEYALEKNEVDLVVHSLKDVPTILPPGFTIGAICKRENPCDAVV 80
Cdd:cd13645    26 LYPDLTFEIITMSTTGDKILDVALSKIGGKGLFTKELEAALLEGEVDLAVHSLKDLPTVLPPGFELGAILKREDPRDALV 105

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2025689086  81 FHPKFIGKTLETLPEKSAVGTSSLRRVAQLQRKFPHLEFRSIRGNLNTRLRKLDEQQ-EFSAIVLAVAGLQRMGWQNRVG 159
Cdd:cd13645   106 FHPGLNYKSLDDLPEGSVIGTSSLRRAAQLKRKYPHLRFKDIRGNLNTRLAKLDAPEsPYDAIILAAAGLERLGLEDRIS 185


                  ....*....
gi 2025689086 160 QILHPEECM 168
Cdd:cd13645   186 QDLSPETML 194
HemC COG0181
Porphobilinogen deaminase [Coenzyme transport and metabolism]; Porphobilinogen deaminase is ...
 1-167 3.04e-92

Porphobilinogen deaminase [Coenzyme transport and metabolism]; Porphobilinogen deaminase is part of the Pathway/BioSystem: Heme biosynthesis


Pssm-ID: 439951 [Multi-domain]  Cd Length: 306  Bit Score: 270.35  E-value: 3.04e-92
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2025689086   1 LHPGMQFEIIAMSTTGDKILDTALSKIGEKSLFTKELEYALEKNEVDLVVHSLKDVPTILPPGFTIGAICKRENPCDAVV 80
Cdd:COG0181    29 AHPGLEVELVPIKTKGDKILDRPLAKIGGKGLFTKELEEALLDGEIDIAVHSLKDVPTELPEGLVLAAVLEREDPRDALV 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2025689086  81 FHPkfiGKTLETLPEKSAVGTSSLRRVAQLQRKFPHLEFRSIRGNLNTRLRKLDEqQEFSAIVLAVAGLQRMGWQNRVGQ 160
Cdd:COG0181   109 SRD---GASLDDLPEGAVVGTSSLRRQAQLLALRPDLEIVDLRGNVDTRLRKLDE-GEYDAIILAAAGLKRLGLEDRITE 184


                  ....*..
gi 2025689086 161 ILHPEEC 167
Cdd:COG0181   185 VLDPEEM 191
Porphobil_deam pfam01379
Porphobilinogen deaminase, dipyromethane cofactor binding domain;
5-168 4.11e-92

Porphobilinogen deaminase, dipyromethane cofactor binding domain;


Pssm-ID: 460180  Cd Length: 203  Bit Score: 266.16  E-value: 4.11e-92
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2025689086   5 MQFEIIAMSTTGDKILDTALSKIGEKSLFTKELEYALEKNEVDLVVHSLKDVPTILPPGFTIGAICKRENPCDAVVFHPK 84
Cdd:pfam01379  25 EEFEIVTIKTTGDKILDKPLAKIGGKGLFTKELEEALLDGEIDIAVHSLKDLPTELPEGLVLAAVLEREDPRDALVLSRD 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2025689086  85 fiGKTLETLPEKSAVGTSSLRRVAQLQRKFPHLEFRSIRGNLNTRLRKLDEqQEFSAIVLAVAGLQRMGWQNRVGQILHP 164
Cdd:pfam01379 105 --GSLLELLPEGAVVGTSSLRRRAQLLRLRPDLEVKDLRGNVDTRLRKLDE-GEYDAIILAAAGLKRLGLEDIITEYLDP 181


                  ....
gi 2025689086 165 EECM 168
Cdd:pfam01379 182 EEML 185
PBP2_HMBS cd00494
Hydroxymethylbilane synthase possesses the type 2 periplasmic binding protein fold; ...
 2-168 9.08e-85

Hydroxymethylbilane synthase possesses the type 2 periplasmic binding protein fold; Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophyll, vitamin B12 and related macrocycles. HMBS catalyzes the conversion of porphobilinogen (PBG) into hydroxymethylbilane (HMB). This family includes the three domains of HMBS. The enzyme is believed to bind substrate through a hinge-bending motion of domains 1 and 2. The C-terminal domain 3 contains an invariant cysteine that forms the covalent attachment site for the DPM (dipyrromethane) cofactor. HMBS is found in all organisms except viruses. The domains 1 and 2 have the same overall topology as found in the type 2 periplasmic-binding proteins (PBP2), many of which are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor.


Pssm-ID: 270213 [Multi-domain]  Cd Length: 274  Bit Score: 250.28  E-value: 9.08e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2025689086   2 HPGMQFEIIAMSTTGDKILDTALSKIGEKSLFTKELEYALEKNEVDLVVHSLKDVPTILPPGFTIGAICKRENPCDAVVF 81
Cdd:cd00494    27 HPGLELEIVPIKTTGDKILDTPLAKVGGKGLFTKELDEALLEGEADIAVHSLKDLPTELPPGLVLAAILPREDPRDALVS 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2025689086  82 HPkfiGKTLETLPEKSAVGTSSLRRVAQLQRKFPHLEFRSIRGNLNTRLRKLDEqQEFSAIVLAVAGLQRMGWQNRVGQI 161
Cdd:cd00494   107 PD---NLTLDELPAGARVGTSSLRRRAQLLHLRPDLEVVPIRGNVETRLAKLDN-GEIDAIVLAAAGLKRLGLEDRIARI 182


                  ....*..
gi 2025689086 162 LHPEECM 168
Cdd:cd00494   183 LSPDEML 189
PBP2_EcHMBS_like cd13646
cd00494; Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), ...
 1-167 1.92e-83

cd00494; Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophyll, and vitamin B12. HMBS catalyzes the conversion of porphobilinogen (PBG) into hydroxymethylbilane (HMB). This subfamily includes the three domains of Escherichia coli HMBS and its closely related proteins. The enzyme is believed to bind substrate through a hinge-bending motion of domains 1 and 2. The C-terminal domain 3 contains an invariant cysteine that forms the covalent attachment site for the DPM (dipyrromethane) cofactor. HMBS is found in all organisms except viruses. The domains 1 and 2 have the same overall topology as found in the type 2 periplasmic-binding proteins (PBP2), many of which are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor.


Pssm-ID: 270364 [Multi-domain]  Cd Length: 274  Bit Score: 246.77  E-value: 1.92e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2025689086   1 LHPGMQFEIIAMSTTGDKILDTALSKIGEKSLFTKELEYALEKNEVDLVVHSLKDVPTILPPGFTIGAICKRENPCDAVV 80
Cdd:cd13646    26 EHPGLEVELVEITTKGDKILDVPLSKIGGKGLFVKEIEEALLAGRIDLAVHSLKDVPTVLPEGLTLAAIPKREDPRDALV 105

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2025689086  81 FHPkfiGKTLETLPEKSAVGTSSLRRVAQLQRKFPHLEFRSIRGNLNTRLRKLDEqQEFSAIVLAVAGLQRMGWQNRVGQ 160
Cdd:cd13646   106 SRK---GKTLEELPEGARVGTSSLRRQAQLLALRPDLEIKDLRGNVDTRLRKLEE-GEYDAIILAAAGLKRLGLESRIRE 181


                  ....*..
gi 2025689086 161 ILHPEEC 167
Cdd:cd13646   182 ELSPDEM 188
hemC TIGR00212
hydroxymethylbilane synthase; Alternate name hydroxymethylbilane synthase Biosynthesis of ...
 1-168 5.44e-73

hydroxymethylbilane synthase; Alternate name hydroxymethylbilane synthase Biosynthesis of cofactors, prosthetic groups, and carriers: Heme and porphyrin [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin]


Pssm-ID: 272963 [Multi-domain]  Cd Length: 292  Bit Score: 220.99  E-value: 5.44e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2025689086   1 LHPGMQFEIIAMSTTGDKILDTALSKIGEKSLFTKELEYALEKNEVDLVVHSLKDVPTILPPGFTIGAICKRENPCDAVV 80
Cdd:TIGR00212  25 VYPELDTEIVIIKTTGDKIQDKPLYDIGGKGLFTKELEQALLDGEIDLAVHSLKDVPTVLPEGLEIAAVLKREDPRDVLV 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2025689086  81 fHPKfiGKTLETLPEKSAVGTSSLRRVAQLQRKFPHLEFRSIRGNLNTRLRKLDEqQEFSAIVLAVAGLQRMGWQNRVGQ 160
Cdd:TIGR00212 105 -SRK--YLSLDSLPQGAKVGTSSLRRKAQLKAIRPDLKIEPLRGNIDTRLRKLDE-GEYDAIILAEAGLKRLGLEDVITE 180


                  ....*...
gi 2025689086 161 ILHPEECM 168
Cdd:TIGR00212 181 VLDPEVML 188
PBP2_PBGD_2 cd13647
An uncharacterized subgroup of the PBGD family; the type 2 periplasmic binding protein fold; ...
 1-168 2.69e-58

An uncharacterized subgroup of the PBGD family; the type 2 periplasmic binding protein fold; Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophyll, and vitamin B12. HMBS catalyzes the conversion of porphobilinogen (PBG) into hydroxymethylbilane (HMB). This subfamily includes the three domains of HMBS. The enzyme is believed to bind substrate through a hinge-bending motion of domains 1 and 2. The C-terminal domain 3 contains an invariant cysteine that forms the covalent attachment site for the DPM (dipyrromethane) cofactor. HMBS is found in all organisms except viruses. The domains 1 and 2 have the same overall topology as found in the type 2 periplasmic-binding proteins (PBP2), many of which are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor.


Pssm-ID: 270365 [Multi-domain]  Cd Length: 282  Bit Score: 183.26  E-value: 2.69e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2025689086   1 LHPGMQFEIIAMSTTGDKILDTALSKIGEKSLFTKELEYALEKNEVDLVVHSLKDVPTILPPGFTIGAICKRENPCDAVV 80
Cdd:cd13647    26 KFPEIEVEIKPIKTTGDKILDKPLWKIGGKGLFTKELEKALLNGEIDIAVHSLKDVPAELPDGLEIVAVLKREDPRDVLV 105

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2025689086  81 FhpkFIGKTLETLPEKSAVGTSSLRRVAQLQRKFPHLEFRSIRGNLNTRLRKLDEqQEFSAIVLAVAGLQRMGWQNRVGQ 160
Cdd:cd13647   106 S---KKNKSIFNLPSGAKIGTSSLRRKAQLKKFRPDLKIKPIRGNVDTRLRKLKE-GEYDGIILAAAGLKRLGLEDDEIN 181


                  ....*...
gi 2025689086 161 ILHPEECM 168
Cdd:cd13647   182 YQILDLVM 189
PLN02691 PLN02691
porphobilinogen deaminase
 6-166 2.11e-51

porphobilinogen deaminase


Pssm-ID: 215373 [Multi-domain]  Cd Length: 351  Bit Score: 167.64  E-value: 2.11e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2025689086   6 QFEIIAMSTTGDKILDTALSKIGEKSLFTKELEYALEKNEVDLVVHSLKDVPTILPPGFTIGAICKRENPCDAvvfhpkF 85
Cdd:PLN02691   77 ALEIVIIKTTGDKILDQPLADIGGKGLFTKEIDDALLSGRIDIAVHSMKDVPTYLPEGTILPCNLPREDVRDA------F 150

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2025689086  86 I---GKTLETLPEKSAVGTSSLRRVAQLQRKFPHLEFRSIRGNLNTRLRKLDEqQEFSAIVLAVAGLQRMGWQNRVGQIL 162
Cdd:PLN02691  151 IslkAKSLAELPAGSVVGTASLRRQSQILHKYPHLKVVNFRGNVQTRLRKLQE-GVVDATLLALAGLKRLDMTEHATSIL 229


                  ....
gi 2025689086 163 HPEE 166
Cdd:PLN02691  230 STDE 233
PBP2_PBGD_1 cd13648
An uncharacterized subgroup of the PBGD family; the type 2 periplasmic binding protein fold; ...
 1-166 2.43e-51

An uncharacterized subgroup of the PBGD family; the type 2 periplasmic binding protein fold; Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophyll, and vitamin B12. HMBS catalyzes the conversion of porphobilinogen (PBG) into hydroxymethylbilane (HMB). This subfamily includes the three domains of HMBS. The enzyme is believed to bind substrate through a hinge-bending motion of domains 1 and 2. The C-terminal domain 3 contains an invariant cysteine that forms the covalent attachment site for the DPM (dipyrromethane) cofactor. HMBS is found in all organisms except viruses. The domains 1 and 2 have the same overall topology as found in the type 2 periplasmic-binding proteins (PBP2), many of which are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor.


Pssm-ID: 270366 [Multi-domain]  Cd Length: 278  Bit Score: 165.28  E-value: 2.43e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2025689086   1 LHPGMQFEIIAMSTTGDKILDTALSKIGEKSLFTKELEYALEKNEVDLVVHSLKDVPTILPPGFTIGAICKRENPCDAVV 80
Cdd:cd13648    30 LAEEGAIEIVIIKTTGDKILSQPLADIGGKGLFTKEIDDALLNGEIDIAVHSMKDVPTYLPEGTILPCNLPREDVRDAFI 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2025689086  81 FHpkfIGKTLETLPEKSAVGTSSLRRVAQLQRKFPHLEFRSIRGNLNTRLRKLDEQQeFSAIVLAVAGLQRMGWQNRVGQ 160
Cdd:cd13648   110 SP---TAASLAELPAGSVVGTASLRRQAQILAKYPDLKCVNFRGNVQTRLRKLKEGV-VDATLLALAGLKRLDMTEHVTS 185


                  ....*.
gi 2025689086 161 ILHPEE 166
Cdd:cd13648   186 ILSLDE 191
PBP2_HemC_archaea cd13644
Archaeal HemC of hydroxymethylbilane synthase family; the type 2 periplasmic binding protein ...
 4-166 1.92e-50

Archaeal HemC of hydroxymethylbilane synthase family; the type 2 periplasmic binding protein fold; Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophyll, and vitamin B12. HMBS catalyzes the conversion of porphobilinogen (PBG) into hydroxymethylbilane (HMB). This subfamily includes the three domains of HMBS. The enzyme is believed to bind substrate through a hinge-bending motion of domains 1 and 2. The C-terminal domain 3 contains an invariant cysteine that forms the covalent attachment site for the DPM (dipyrromethane) cofactor. HMBS is found in all organisms except viruses. The domains 1 and 2 have the same overall topology as found in the type 2 periplasmic-binding proteins (PBP2), many of which are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor.


Pssm-ID: 270362 [Multi-domain]  Cd Length: 273  Bit Score: 162.86  E-value: 1.92e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2025689086   4 GMQFEIIAMSTTGDKILDTALSKIGEKSLFTKELEYALEKNEVDLVVHSLKDVPTILPPGFTIGAICKRENPCDAVVfhp 83
Cdd:cd13644    28 PVEVEIKIIKTKGDRDSDRPLYSIGGKGVFVKELDRAVLEGEADIAVHSLKDVPSEIDPGLVIAAVPKRESPNDVLV--- 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2025689086  84 KFIGKTLETLPEKSAVGTSSLRRVAQLQRKFPHLEFRSIRGNLNTRLRKLDEqQEFSAIVLAVAGLQRMGWQNRVgQILH 163
Cdd:cd13644   105 SRDGSTLEELPPGAVVGTSSLRRRAQILRLRPDLRVEPLRGNVDTRIRKLRE-GEYDAIVLAEAGLKRLGLDVKY-SPLS 182


                  ...
gi 2025689086 164 PEE 166
Cdd:cd13644   183 PED 185
PRK01066 PRK01066
porphobilinogen deaminase; Provisional
 3-164 4.27e-29

porphobilinogen deaminase; Provisional


Pssm-ID: 167150  Cd Length: 231  Bit Score: 106.76  E-value: 4.27e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2025689086   3 PGMQFEIIAMSTTGDKILDTALSKIGEKSLFTKELEYALEKNEVDLVVHSLKDVPTilPPGFTIGAICKRENPCDAVVFH 82
Cdd:PRK01066   44 PKLWFQISTTTTQGDLDQKTPLHLVENTGFFTDDVDFLVLSGQCDLAIHSAKDLPE--PPKLTVVAITAGLDPRDLLVYA 121

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2025689086  83 PKFigkTLETLPEKSAVGTSSLRRVAQLQRKFPHLEFRSIRGNLNTRLRKLDEQQeFSAIVLAVAGLQRMGWQNRVGQIL 162
Cdd:PRK01066  122 EKY---LSQPLPRRPRIGSSSLRREELLKLLFPSGIILDIRGTIEERLKLLEEKK-YDAIVVAKAAVLRLGLRLPYTKEL 197


                  ..
gi 2025689086 163 HP 164
Cdd:PRK01066  198 PP 199
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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