NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1213770854|emb|SBW09856|]
View 

hydroxymethylbilane synthase [uncultured Alphaproteobacteria bacterium]

Protein Classification

hydroxymethylbilane synthase( domain architecture ID 11415131)

hydroxymethylbilane synthase (porphobilinogen deaminase) is the third enzyme of the heme biosynthetic pathway and catalyzes the stepwise polymerization of four molecules of porphobilinogen (PBG) into the linear tetrapyrrole 1-hydroxymethylbilane

EC:  2.5.1.61
Gene Ontology:  GO:0006782|GO:0004418|GO:0033014
PubMed:  11741199|7592565
SCOP:  4000229

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

Name Accession Description Interval E-value
HemC COG0181
Porphobilinogen deaminase [Coenzyme transport and metabolism]; Porphobilinogen deaminase is ...
1-278 3.19e-123

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: 354.71  E-value: 3.19e-123
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854   1 MSHPLlTIGTRGSPLALAQTGMVAAALAAALPelaaDGAIATLVIKTSGDRILDRPLAEAGGKGLFTKEIDEAMLERRID 80
Cdd:COG0181     1 MTKTL-RIGTRGSPLALWQAEHVADRLEAAHP----GLEVELVPIKTKGDKILDRPLAKIGGKGLFTKELEEALLDGEID 75
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854  81 IAVHSMKDVPTWLPDGIDLPCMLPREDPRDAFLSPVAASLDALPAGATVGTASLRRGAFVLARRPDLKVVSFRGNVQSRL 160
Cdd:COG0181    76 IAVHSLKDVPTELPEGLVLAAVLEREDPRDALVSRDGASLDDLPEGAVVGTSSLRRQAQLLALRPDLEIVDLRGNVDTRL 155
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854 161 EKLGDGVVDATLLALAGLRRLGLADRAAGILSIEEMLPAVAQGAIGVTCRADDARAHDWLARIADARTFAEVACERAFLR 240
Cdd:COG0181   156 RKLDEGEYDAIILAAAGLKRLGLEDRITEVLDPEEMLPAPGQGALGIECRADDEELRELLAALNDPETRLAVTAERAFLA 235
                         250       260       270
                  ....*....|....*....|....*....|....*...
gi 1213770854 241 VLDGSCRTPIGGLARFgADGRLAFLGRLARADGSAIFE 278
Cdd:COG0181   236 ALEGGCQVPIGAYATL-EGDELTLRGLVASPDGSEVIR 272
 
Name Accession Description Interval E-value
HemC COG0181
Porphobilinogen deaminase [Coenzyme transport and metabolism]; Porphobilinogen deaminase is ...
1-278 3.19e-123

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: 354.71  E-value: 3.19e-123
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854   1 MSHPLlTIGTRGSPLALAQTGMVAAALAAALPelaaDGAIATLVIKTSGDRILDRPLAEAGGKGLFTKEIDEAMLERRID 80
Cdd:COG0181     1 MTKTL-RIGTRGSPLALWQAEHVADRLEAAHP----GLEVELVPIKTKGDKILDRPLAKIGGKGLFTKELEEALLDGEID 75
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854  81 IAVHSMKDVPTWLPDGIDLPCMLPREDPRDAFLSPVAASLDALPAGATVGTASLRRGAFVLARRPDLKVVSFRGNVQSRL 160
Cdd:COG0181    76 IAVHSLKDVPTELPEGLVLAAVLEREDPRDALVSRDGASLDDLPEGAVVGTSSLRRQAQLLALRPDLEIVDLRGNVDTRL 155
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854 161 EKLGDGVVDATLLALAGLRRLGLADRAAGILSIEEMLPAVAQGAIGVTCRADDARAHDWLARIADARTFAEVACERAFLR 240
Cdd:COG0181   156 RKLDEGEYDAIILAAAGLKRLGLEDRITEVLDPEEMLPAPGQGALGIECRADDEELRELLAALNDPETRLAVTAERAFLA 235
                         250       260       270
                  ....*....|....*....|....*....|....*...
gi 1213770854 241 VLDGSCRTPIGGLARFgADGRLAFLGRLARADGSAIFE 278
Cdd:COG0181   236 ALEGGCQVPIGAYATL-EGDELTLRGLVASPDGSEVIR 272
PLN02691 PLN02691
porphobilinogen deaminase
4-278 3.47e-121

porphobilinogen deaminase


Pssm-ID: 215373 [Multi-domain]  Cd Length: 351  Bit Score: 351.38  E-value: 3.47e-121
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854   4 PLLTIGTRGSPLALAQTGMVAAALAAALPELAADGAIATLVIKTSGDRILDRPLAEAGGKGLFTKEIDEAMLERRIDIAV 83
Cdd:PLN02691   42 APIRIGTRGSPLALAQAYETRDLLKAAHPELAEEGALEIVIIKTTGDKILDQPLADIGGKGLFTKEIDDALLSGRIDIAV 121
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854  84 HSMKDVPTWLPDGIDLPCMLPREDPRDAFLSPVAASLDALPAGATVGTASLRRGAFVLARRPDLKVVSFRGNVQSRLEKL 163
Cdd:PLN02691  122 HSMKDVPTYLPEGTILPCNLPREDVRDAFISLKAKSLAELPAGSVVGTASLRRQSQILHKYPHLKVVNFRGNVQTRLRKL 201
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854 164 GDGVVDATLLALAGLRRLGLADRAAGILSIEEMLPAVAQGAIGVTCRADDARAHDWLARIADARTFAEVACERAFLRVLD 243
Cdd:PLN02691  202 QEGVVDATLLALAGLKRLDMTEHATSILSTDEMLPAVAQGAIGIACRTDDDKMLEYLASLNHEETRLAVACERAFLAALD 281
                         250       260       270
                  ....*....|....*....|....*....|....*
gi 1213770854 244 GSCRTPIGGLARFGADGRLAFLGRLARADGSAIFE 278
Cdd:PLN02691  282 GSCRTPIAGYARRDKDGNCDFRGLVASPDGKQVLE 316
PBP2_PBGD_1 cd13648
An uncharacterized subgroup of the PBGD family; the type 2 periplasmic binding protein fold; ...
5-278 8.81e-120

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: 345.17  E-value: 8.81e-120
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854   5 LLTIGTRGSPLALAQTGMVAAALAAALPELAADGAIATLVIKTSGDRILDRPLAEAGGKGLFTKEIDEAMLERRIDIAVH 84
Cdd:cd13648     1 PIRIGTRGSPLALAQAYETRDKLKEAHPELAEEGAIEIVIIKTTGDKILSQPLADIGGKGLFTKEIDDALLNGEIDIAVH 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854  85 SMKDVPTWLPDGIDLPCMLPREDPRDAFLSPVAASLDALPAGATVGTASLRRGAFVLARRPDLKVVSFRGNVQSRLEKLG 164
Cdd:cd13648    81 SMKDVPTYLPEGTILPCNLPREDVRDAFISPTAASLAELPAGSVVGTASLRRQAQILAKYPDLKCVNFRGNVQTRLRKLK 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854 165 DGVVDATLLALAGLRRLGLADRAAGILSIEEMLPAVAQGAIGVTCRADDARAHDWLARIADARTFAEVACERAFLRVLDG 244
Cdd:cd13648   161 EGVVDATLLALAGLKRLDMTEHVTSILSLDEMLPAVAQGAIGIACRSDDDKMAKYLAALNHEETRLAVSCERAFLATLDG 240
                         250       260       270
                  ....*....|....*....|....*....|....
gi 1213770854 245 SCRTPIGGLARFGaDGRLAFLGRLARADGSAIFE 278
Cdd:cd13648   241 SCRTPIAGYARRD-DGKLHFRGLIASPDGKKVLE 273
hemC TIGR00212
hydroxymethylbilane synthase; Alternate name hydroxymethylbilane synthase Biosynthesis of ...
6-278 1.78e-99

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: 294.18  E-value: 1.78e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854   6 LTIGTRGSPLALAQTGMVAAALAAALPELaadgAIATLVIKTSGDRILDRPLAEAGGKGLFTKEIDEAMLERRIDIAVHS 85
Cdd:TIGR00212   1 LRIGTRGSKLALAQANLVREQLKAVYPEL----DTEIVIIKTTGDKIQDKPLYDIGGKGLFTKELEQALLDGEIDLAVHS 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854  86 MKDVPTWLPDGIDLPCMLPREDPRDAFLSPVAASLDALPAGATVGTASLRRGAFVLARRPDLKVVSFRGNVQSRLEKLGD 165
Cdd:TIGR00212  77 LKDVPTVLPEGLEIAAVLKREDPRDVLVSRKYLSLDSLPQGAKVGTSSLRRKAQLKAIRPDLKIEPLRGNIDTRLRKLDE 156
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854 166 GVVDATLLALAGLRRLGLADRAAGILSIEEMLPAVAQGAIGVTCRADDARAHDWLARIADARTFAEVACERAFLRVLDGS 245
Cdd:TIGR00212 157 GEYDAIILAEAGLKRLGLEDVITEVLDPEVMLPAPGQGAIAVECRKDDTEIKEILKEINHPPTRVEATAERAFLKELGGG 236
                         250       260       270
                  ....*....|....*....|....*....|...
gi 1213770854 246 CRTPIGGLARFGADgRLAFLGRLARADGSAIFE 278
Cdd:TIGR00212 237 CQTPIGAYAEYNGN-KLTLIAMVADLDGKEVIR 268
Porphobil_deam pfam01379
Porphobilinogen deaminase, dipyromethane cofactor binding domain;
6-215 4.22e-87

Porphobilinogen deaminase, dipyromethane cofactor binding domain;


Pssm-ID: 460180  Cd Length: 203  Bit Score: 259.23  E-value: 4.22e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854   6 LTIGTRGSPLALAQTGMVAAALAAALpelaadgaIATLVIKTSGDRILDRPLAEAGGKGLFTKEIDEAMLERRIDIAVHS 85
Cdd:pfam01379   1 IRIGTRGSKLALAQAEHVADRLEAEE--------FEIVTIKTTGDKILDKPLAKIGGKGLFTKELEEALLDGEIDIAVHS 72
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854  86 MKDVPTWLPDGIDLPCMLPREDPRDAFL-SPVAASLDALPAGATVGTASLRRGAFVLARRPDLKVVSFRGNVQSRLEKLG 164
Cdd:pfam01379  73 LKDLPTELPEGLVLAAVLEREDPRDALVlSRDGSLLELLPEGAVVGTSSLRRRAQLLRLRPDLEVKDLRGNVDTRLRKLD 152
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1213770854 165 DGVVDATLLALAGLRRLGLADRAAGILSIEEMLPAVAQGAIGVTCRADDAR 215
Cdd:pfam01379 153 EGEYDAIILAAAGLKRLGLEDIITEYLDPEEMLPAVGQGALAIECRADDEE 203
 
Name Accession Description Interval E-value
HemC COG0181
Porphobilinogen deaminase [Coenzyme transport and metabolism]; Porphobilinogen deaminase is ...
1-278 3.19e-123

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: 354.71  E-value: 3.19e-123
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854   1 MSHPLlTIGTRGSPLALAQTGMVAAALAAALPelaaDGAIATLVIKTSGDRILDRPLAEAGGKGLFTKEIDEAMLERRID 80
Cdd:COG0181     1 MTKTL-RIGTRGSPLALWQAEHVADRLEAAHP----GLEVELVPIKTKGDKILDRPLAKIGGKGLFTKELEEALLDGEID 75
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854  81 IAVHSMKDVPTWLPDGIDLPCMLPREDPRDAFLSPVAASLDALPAGATVGTASLRRGAFVLARRPDLKVVSFRGNVQSRL 160
Cdd:COG0181    76 IAVHSLKDVPTELPEGLVLAAVLEREDPRDALVSRDGASLDDLPEGAVVGTSSLRRQAQLLALRPDLEIVDLRGNVDTRL 155
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854 161 EKLGDGVVDATLLALAGLRRLGLADRAAGILSIEEMLPAVAQGAIGVTCRADDARAHDWLARIADARTFAEVACERAFLR 240
Cdd:COG0181   156 RKLDEGEYDAIILAAAGLKRLGLEDRITEVLDPEEMLPAPGQGALGIECRADDEELRELLAALNDPETRLAVTAERAFLA 235
                         250       260       270
                  ....*....|....*....|....*....|....*...
gi 1213770854 241 VLDGSCRTPIGGLARFgADGRLAFLGRLARADGSAIFE 278
Cdd:COG0181   236 ALEGGCQVPIGAYATL-EGDELTLRGLVASPDGSEVIR 272
PLN02691 PLN02691
porphobilinogen deaminase
4-278 3.47e-121

porphobilinogen deaminase


Pssm-ID: 215373 [Multi-domain]  Cd Length: 351  Bit Score: 351.38  E-value: 3.47e-121
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854   4 PLLTIGTRGSPLALAQTGMVAAALAAALPELAADGAIATLVIKTSGDRILDRPLAEAGGKGLFTKEIDEAMLERRIDIAV 83
Cdd:PLN02691   42 APIRIGTRGSPLALAQAYETRDLLKAAHPELAEEGALEIVIIKTTGDKILDQPLADIGGKGLFTKEIDDALLSGRIDIAV 121
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854  84 HSMKDVPTWLPDGIDLPCMLPREDPRDAFLSPVAASLDALPAGATVGTASLRRGAFVLARRPDLKVVSFRGNVQSRLEKL 163
Cdd:PLN02691  122 HSMKDVPTYLPEGTILPCNLPREDVRDAFISLKAKSLAELPAGSVVGTASLRRQSQILHKYPHLKVVNFRGNVQTRLRKL 201
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854 164 GDGVVDATLLALAGLRRLGLADRAAGILSIEEMLPAVAQGAIGVTCRADDARAHDWLARIADARTFAEVACERAFLRVLD 243
Cdd:PLN02691  202 QEGVVDATLLALAGLKRLDMTEHATSILSTDEMLPAVAQGAIGIACRTDDDKMLEYLASLNHEETRLAVACERAFLAALD 281
                         250       260       270
                  ....*....|....*....|....*....|....*
gi 1213770854 244 GSCRTPIGGLARFGADGRLAFLGRLARADGSAIFE 278
Cdd:PLN02691  282 GSCRTPIAGYARRDKDGNCDFRGLVASPDGKQVLE 316
PBP2_PBGD_1 cd13648
An uncharacterized subgroup of the PBGD family; the type 2 periplasmic binding protein fold; ...
5-278 8.81e-120

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: 345.17  E-value: 8.81e-120
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854   5 LLTIGTRGSPLALAQTGMVAAALAAALPELAADGAIATLVIKTSGDRILDRPLAEAGGKGLFTKEIDEAMLERRIDIAVH 84
Cdd:cd13648     1 PIRIGTRGSPLALAQAYETRDKLKEAHPELAEEGAIEIVIIKTTGDKILSQPLADIGGKGLFTKEIDDALLNGEIDIAVH 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854  85 SMKDVPTWLPDGIDLPCMLPREDPRDAFLSPVAASLDALPAGATVGTASLRRGAFVLARRPDLKVVSFRGNVQSRLEKLG 164
Cdd:cd13648    81 SMKDVPTYLPEGTILPCNLPREDVRDAFISPTAASLAELPAGSVVGTASLRRQAQILAKYPDLKCVNFRGNVQTRLRKLK 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854 165 DGVVDATLLALAGLRRLGLADRAAGILSIEEMLPAVAQGAIGVTCRADDARAHDWLARIADARTFAEVACERAFLRVLDG 244
Cdd:cd13648   161 EGVVDATLLALAGLKRLDMTEHVTSILSLDEMLPAVAQGAIGIACRSDDDKMAKYLAALNHEETRLAVSCERAFLATLDG 240
                         250       260       270
                  ....*....|....*....|....*....|....
gi 1213770854 245 SCRTPIGGLARFGaDGRLAFLGRLARADGSAIFE 278
Cdd:cd13648   241 SCRTPIAGYARRD-DGKLHFRGLIASPDGKKVLE 273
hemC TIGR00212
hydroxymethylbilane synthase; Alternate name hydroxymethylbilane synthase Biosynthesis of ...
6-278 1.78e-99

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: 294.18  E-value: 1.78e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854   6 LTIGTRGSPLALAQTGMVAAALAAALPELaadgAIATLVIKTSGDRILDRPLAEAGGKGLFTKEIDEAMLERRIDIAVHS 85
Cdd:TIGR00212   1 LRIGTRGSKLALAQANLVREQLKAVYPEL----DTEIVIIKTTGDKIQDKPLYDIGGKGLFTKELEQALLDGEIDLAVHS 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854  86 MKDVPTWLPDGIDLPCMLPREDPRDAFLSPVAASLDALPAGATVGTASLRRGAFVLARRPDLKVVSFRGNVQSRLEKLGD 165
Cdd:TIGR00212  77 LKDVPTVLPEGLEIAAVLKREDPRDVLVSRKYLSLDSLPQGAKVGTSSLRRKAQLKAIRPDLKIEPLRGNIDTRLRKLDE 156
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854 166 GVVDATLLALAGLRRLGLADRAAGILSIEEMLPAVAQGAIGVTCRADDARAHDWLARIADARTFAEVACERAFLRVLDGS 245
Cdd:TIGR00212 157 GEYDAIILAEAGLKRLGLEDVITEVLDPEVMLPAPGQGAIAVECRKDDTEIKEILKEINHPPTRVEATAERAFLKELGGG 236
                         250       260       270
                  ....*....|....*....|....*....|...
gi 1213770854 246 CRTPIGGLARFGADgRLAFLGRLARADGSAIFE 278
Cdd:TIGR00212 237 CQTPIGAYAEYNGN-KLTLIAMVADLDGKEVIR 268
PBP2_EcHMBS_like cd13646
cd00494; Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), ...
6-278 7.28e-97

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: 286.83  E-value: 7.28e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854   6 LTIGTRGSPLALAQTGMVAAALAAALPELaadgAIATLVIKTSGDRILDRPLAEAGGKGLFTKEIDEAMLERRIDIAVHS 85
Cdd:cd13646     2 LRIGTRGSKLALWQANHVKDRLKAEHPGL----EVELVEITTKGDKILDVPLSKIGGKGLFVKEIEEALLAGRIDLAVHS 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854  86 MKDVPTWLPDGIDLPCMLPREDPRDAFLSPVAASLDALPAGATVGTASLRRGAFVLARRPDLKVVSFRGNVQSRLEKLGD 165
Cdd:cd13646    78 LKDVPTVLPEGLTLAAIPKREDPRDALVSRKGKTLEELPEGARVGTSSLRRQAQLLALRPDLEIKDLRGNVDTRLRKLEE 157
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854 166 GVVDATLLALAGLRRLGLADRAAGILSIEEMLPAVAQGAIGVTCRADDARAHDWLARIADARTFAEVACERAFLRVLDGS 245
Cdd:cd13646   158 GEYDAIILAAAGLKRLGLESRIREELSPDEMLPAVGQGALGIECRADDEELLELLAPLNDEETALCVTAERAFLARLEGG 237
                         250       260       270
                  ....*....|....*....|....*....|...
gi 1213770854 246 CRTPIGGLARFgADGRLAFLGRLARADGSAIFE 278
Cdd:cd13646   238 CQVPIGAYAVL-EGGELKLRALVGSPDGSRVIR 269
PBP2_HMBS cd00494
Hydroxymethylbilane synthase possesses the type 2 periplasmic binding protein fold; ...
6-278 2.93e-93

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: 277.63  E-value: 2.93e-93
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854   6 LTIGTRGSPLALAQTGMVAAALAAALPelaaDGAIATLVIKTSGDRILDRPLAEAGGKGLFTKEIDEAMLERRIDIAVHS 85
Cdd:cd00494     2 LRIGTRGSPLALAQAEEVRATLRAAHP----GLELEIVPIKTTGDKILDTPLAKVGGKGLFTKELDEALLEGEADIAVHS 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854  86 MKDVPTWLPDGIDLPCMLPREDPRDAFLSPVAASLDALPAGATVGTASLRRGAFVLARRPDLKVVSFRGNVQSRLEKLGD 165
Cdd:cd00494    78 LKDLPTELPPGLVLAAILPREDPRDALVSPDNLTLDELPAGARVGTSSLRRRAQLLHLRPDLEVVPIRGNVETRLAKLDN 157
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854 166 GVVDATLLALAGLRRLGLADRAAGILSIEEMLPAVAQGAIGVTCRADDARAHDWLARIADARTFAEVACERAFLRVLDGS 245
Cdd:cd00494   158 GEIDAIVLAAAGLKRLGLEDRIARILSPDEMLPAPGQGALAIEVREDDDKTVDLLAALDDPESRLEVTAERAFLATLEGG 237
                         250       260       270
                  ....*....|....*....|....*....|...
gi 1213770854 246 CRTPIGGLARFgADGRLAFLGRLARADGSAIFE 278
Cdd:cd00494   238 CRVPIAAYATL-DGDELTLRALVLSLDGSEFIR 269
Porphobil_deam pfam01379
Porphobilinogen deaminase, dipyromethane cofactor binding domain;
6-215 4.22e-87

Porphobilinogen deaminase, dipyromethane cofactor binding domain;


Pssm-ID: 460180  Cd Length: 203  Bit Score: 259.23  E-value: 4.22e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854   6 LTIGTRGSPLALAQTGMVAAALAAALpelaadgaIATLVIKTSGDRILDRPLAEAGGKGLFTKEIDEAMLERRIDIAVHS 85
Cdd:pfam01379   1 IRIGTRGSKLALAQAEHVADRLEAEE--------FEIVTIKTTGDKILDKPLAKIGGKGLFTKELEEALLDGEIDIAVHS 72
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854  86 MKDVPTWLPDGIDLPCMLPREDPRDAFL-SPVAASLDALPAGATVGTASLRRGAFVLARRPDLKVVSFRGNVQSRLEKLG 164
Cdd:pfam01379  73 LKDLPTELPEGLVLAAVLEREDPRDALVlSRDGSLLELLPEGAVVGTSSLRRRAQLLRLRPDLEVKDLRGNVDTRLRKLD 152
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1213770854 165 DGVVDATLLALAGLRRLGLADRAAGILSIEEMLPAVAQGAIGVTCRADDAR 215
Cdd:pfam01379 153 EGEYDAIILAAAGLKRLGLEDIITEYLDPEEMLPAVGQGALAIECRADDEE 203
PBP2_PBGD_2 cd13647
An uncharacterized subgroup of the PBGD family; the type 2 periplasmic binding protein fold; ...
6-255 5.46e-84

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: 254.14  E-value: 5.46e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854   6 LTIGTRGSPLALAQTGMVAAALAAALPELAADgaiaTLVIKTSGDRILDRPLAEAGGKGLFTKEIDEAMLERRIDIAVHS 85
Cdd:cd13647     2 IRIGTRKSKLALIQANKVIEALKKKFPEIEVE----IKPIKTTGDKILDKPLWKIGGKGLFTKELEKALLNGEIDIAVHS 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854  86 MKDVPTWLPDGIDLPCMLPREDPRDAFLSPVAASLDALPAGATVGTASLRRGAFVLARRPDLKVVSFRGNVQSRLEKLGD 165
Cdd:cd13647    78 LKDVPAELPDGLEIVAVLKREDPRDVLVSKKNKSIFNLPSGAKIGTSSLRRKAQLKKFRPDLKIKPIRGNVDTRLRKLKE 157
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854 166 GVVDATLLALAGLRRLGLADRAAGILSIEE-MLPAVAQGAIGVTCRADDARAHDWLARIADARTFAEVACERAFLRVLDG 244
Cdd:cd13647   158 GEYDGIILAAAGLKRLGLEDDEINYQILDLvMLPAPGQGAIAVECRKKDQELFSLLKQINHEETFNAVEAEREFLKELDG 237
                         250
                  ....*....|.
gi 1213770854 245 SCRTPIGGLAR 255
Cdd:cd13647   238 GCHTPIGAYAE 248
PBP2_HuPBGD_like cd13645
Human porphobilinogen deaminase possess type 2 periplasmic binding protein fold; ...
6-274 4.78e-76

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: 234.05  E-value: 4.78e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854   6 LTIGTRGSPLALAQTGMVAAALAAALPELAADgaiaTLVIKTSGDRILDRPLAEAGGKGLFTKEIDEAMLERRIDIAVHS 85
Cdd:cd13645     2 IRIGTRKSQLALIQTEYVREELKKLYPDLTFE----IITMSTTGDKILDVALSKIGGKGLFTKELEAALLEGEVDLAVHS 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854  86 MKDVPTWLPDGIDLPCMLPREDPRDAFLSP---VAASLDALPAGATVGTASLRRGAFVLARRPDLKVVSFRGNVQSRLEK 162
Cdd:cd13645    78 LKDLPTVLPPGFELGAILKREDPRDALVFHpglNYKSLDDLPEGSVIGTSSLRRAAQLKRKYPHLRFKDIRGNLNTRLAK 157
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854 163 L--GDGVVDATLLALAGLRRLGLADRAAGILSIEEMLPAVAQGAIGVTCRADDARAHDWLARIADARTFAEVACERAFLR 240
Cdd:cd13645   158 LdaPESPYDAIILAAAGLERLGLEDRISQDLSPETMLYAVGQGALAVECRAGDQKILELLKVLDDPETTLRCLAERAFLR 237
                         250       260       270
                  ....*....|....*....|....*....|....
gi 1213770854 241 VLDGSCRTPIGGLARFGADGRLAFLGRLARADGS 274
Cdd:cd13645   238 HLEGGCSVPIAVHSALKEGGELYLTGIVLSLDGS 271
PBP2_HemC_archaea cd13644
Archaeal HemC of hydroxymethylbilane synthase family; the type 2 periplasmic binding protein ...
6-274 7.28e-73

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: 225.65  E-value: 7.28e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854   6 LTIGTRGSPLALAQTGMVAAALAAALPELaadgaIATLVIKTSGDRILDRPLAEAGGKGLFTKEIDEAMLERRIDIAVHS 85
Cdd:cd13644     2 IRVATRGSRLALAQTEEVIEELKERGPVE-----VEIKIIKTKGDRDSDRPLYSIGGKGVFVKELDRAVLEGEADIAVHS 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854  86 MKDVPTWLPDGIDLPCMLPREDPRDAFLSPVAASLDALPAGATVGTASLRRGAFVLARRPDLKVVSFRGNVQSRLEKLGD 165
Cdd:cd13644    77 LKDVPSEIDPGLVIAAVPKRESPNDVLVSRDGSTLEELPPGAVVGTSSLRRRAQILRLRPDLRVEPLRGNVDTRIRKLRE 156
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854 166 GVVDATLLAlaglrrlgladrAAGI-----------LSIEEMLPAVAQGAIGVTCRADDARAHDWLARIADARTFAEVAC 234
Cdd:cd13644   157 GEYDAIVLA------------EAGLkrlgldvkyspLSPEDFVPAPGQGILAVVARADDEKVIALLKKIEDPDSRVEAEA 224
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|
gi 1213770854 235 ERAFLRVLDGSCRTPIGGLARfGADGRLAFLGRLARADGS 274
Cdd:cd13644   225 ERALLEELGGGCRTPVGVYAR-ATGGMVRLTAEAFSVDGS 263
PRK01066 PRK01066
porphobilinogen deaminase; Provisional
6-170 3.41e-17

porphobilinogen deaminase; Provisional


Pssm-ID: 167150  Cd Length: 231  Bit Score: 79.03  E-value: 3.41e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854   6 LTIGTRGSPLALAQTGMVAAALAAALPELAadGAIATlvIKTSGDRILDRPLAEAGGKGLFTKEIDEAMLERRIDIAVHS 85
Cdd:PRK01066   18 LRIASRQSSLAVAQVHECLRLLRSFFPKLW--FQIST--TTTQGDLDQKTPLHLVENTGFFTDDVDFLVLSGQCDLAIHS 93
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213770854  86 MKDVPTwlPDGIDLPCMLPREDPRDAFLSPVAASLDALPAGATVGTASLRRGAFVLARRPDLKVVSFRGNVQSRLEKLGD 165
Cdd:PRK01066   94 AKDLPE--PPKLTVVAITAGLDPRDLLVYAEKYLSQPLPRRPRIGSSSLRREELLKLLFPSGIILDIRGTIEERLKLLEE 171

                  ....*
gi 1213770854 166 GVVDA 170
Cdd:PRK01066  172 KKYDA 176
Porphobil_deamC pfam03900
Porphobilinogen deaminase, C-terminal domain;
229-278 8.76e-08

Porphobilinogen deaminase, C-terminal domain;


Pssm-ID: 461087 [Multi-domain]  Cd Length: 72  Bit Score: 48.46  E-value: 8.76e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1213770854 229 FAEVACERAFLRVLDGSCRTPIGGLARFgADGRLAFLGRLARADGSAIFE 278
Cdd:pfam03900   1 ALCVLAERAFLKELEGGCQVPIGVYAVY-KDGELKLKGLVGSPDGSIVIE 49
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH