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Conserved domains on  [gi|14165461|ref|NP_114174|]
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nuclear prelamin A recognition factor isoform b [Homo sapiens]

Protein Classification

nuclear prelamin A recognition factor family protein( domain architecture ID 10502698)

nuclear prelamin A recognition factor (NARF) family protein similar to NARF that evolved from an ancestral Fe-hydrogenase but does not produce hydrogen

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Fe_hyd_lg_C pfam02906
Iron only hydrogenase large subunit, C-terminal domain;
92-427 3.03e-72

Iron only hydrogenase large subunit, C-terminal domain;


:

Pssm-ID: 397172  Cd Length: 277  Bit Score: 230.58  E-value: 3.03e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14165461    92 KVLVVSVCPQSLPYFAAKFNLSVTDASRRLCGFLKSLGVHYVFDTTIAADFSILESQKEFVRRYrqhsEEERTLPMLTSA 171
Cdd:pfam02906   1 KKVVAQIAPAVRGAFGEEFGLPPTVTTGKLVAALRKLGFDYVFDTAFGADLTIMEEATEFLERL----EKGKKLPMFTSC 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14165461   172 CPGWVRYAERVLGRpITAHLCTAKSPQQVMGSLVKDYFARQqnlspEKIFHVIVAPCYDKKLEALQESlppaLHGSRGAD 251
Cdd:pfam02906  77 CPGWVKYVEKYYPE-LLPNLSTCKSPMQMFGALIKTYYAED-----LKIYVVSIMPCTAKKFEAARPE----MKGDRDVD 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14165461   252 CVLTseisqawwctpvitaTREAAA--------RESLEPGrqrlqrdkiaPLDSSLGGGGEIAQImeqgdlsvrdaavdt 323
Cdd:pfam02906 147 AVLT---------------TRELAAmikeagidFAKLEDE----------EFDNPLGESSGAGRI--------------- 186

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14165461   324 lFGdlkedkvtrhdgaSSDGHLAHIFRHAAKELFNEDVEEVTYRALRN-KDFQEVTLEKNGeVVLRFAAAYGFRNIQNMI 402
Cdd:pfam02906 187 -FG-------------VTGGVMEAALRTAYELLTGKELPAIEFKEVRGlEGIKEATVEIGG-TTVKVAVVSGLKNARKLL 251

                         330       340
                  ....*....|....*....|....*
gi 14165461   403 LKLKKGKFPFHFVEVLACAGGCLNG 427
Cdd:pfam02906 252 EKIKAGELKYHFIEVMACPGGCIGG 276
Fe_hyd_SSU smart00902
Iron hydrogenase small subunit; Many microorganisms, such as methanogenic, acetogenic, ...
 444-492 1.17e-15

Iron hydrogenase small subunit; Many microorganisms, such as methanogenic, acetogenic, nitrogen-fixing, photosynthetic, or sulphate-reducing bacteria, metabolise hydrogen. Hydrogen activation is mediated by a family of enzymes, termed hydrogenases, which either provide these organisms with reducing power from hydrogen oxidation, or act as electron sinks. There are two hydrogenases families that differ functionally from each other: NiFe hydrogenases tend to be more involved in hydrogen oxidation, while Iron-only FeFe (Fe only) hydrogenases in hydrogen production. Fe only hydrogenases show a common core structure, which contains a moiety, deeply buried inside the protein, with an Fe-Fe dinuclear centre, nonproteic bridging, terminal CO and CN- ligands attached to each of the iron atoms, and a dithio moiety, which also bridges the two iron atoms and has been tentatively assigned as a di(thiomethyl)amine. This common core also harbours three [4Fe-4S] iron-sulphur clusters. In FeFe hydrogenases, as in NiFe hydrogenases, the set of iron-sulphur clusters is dispersed regularly between the dinuclear Fe-Fe centre and the molecular surface. These clusters are distant by about 1.2 nm from each other but the [4Fe-4S] cluster closest to the dinuclear centre is covalently bound to one of the iron atoms though a thiolate bridging ligand. The moiety including the dinuclear centre, the thiolate bridging ligand, and the proximal [4Fe-4S] cluster is known as the H-cluster. A channel, lined with hydrophobic amino acid side chains, nearly connects the dinuclear centre and the molecular surface. Furthermore hydrogen-bonded water molecule sites have been identified at the interior and at the surface of the protein. The small subunit is comprised of alternating random coil and alpha helical structures that encompass the large subunit in a novel protein fold.


:

Pssm-ID: 214899 [Multi-domain]  Cd Length: 52  Bit Score: 70.74  E-value: 1.17e-15
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 14165461    444 RQMEGIYADI---PVRRPESSAHVQELYQEWLEGINSPKAREVLHTTYQSQE 492
Cdd:smart00902   1 QRAEALYNIDkslPLRKSHENPAVKKLYEEFLGGPLSHKAHELLHTHYHDRE 52
 
Name Accession Description Interval E-value
Fe_hyd_lg_C pfam02906
Iron only hydrogenase large subunit, C-terminal domain;
92-427 3.03e-72

Iron only hydrogenase large subunit, C-terminal domain;


Pssm-ID: 397172  Cd Length: 277  Bit Score: 230.58  E-value: 3.03e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14165461    92 KVLVVSVCPQSLPYFAAKFNLSVTDASRRLCGFLKSLGVHYVFDTTIAADFSILESQKEFVRRYrqhsEEERTLPMLTSA 171
Cdd:pfam02906   1 KKVVAQIAPAVRGAFGEEFGLPPTVTTGKLVAALRKLGFDYVFDTAFGADLTIMEEATEFLERL----EKGKKLPMFTSC 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14165461   172 CPGWVRYAERVLGRpITAHLCTAKSPQQVMGSLVKDYFARQqnlspEKIFHVIVAPCYDKKLEALQESlppaLHGSRGAD 251
Cdd:pfam02906  77 CPGWVKYVEKYYPE-LLPNLSTCKSPMQMFGALIKTYYAED-----LKIYVVSIMPCTAKKFEAARPE----MKGDRDVD 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14165461   252 CVLTseisqawwctpvitaTREAAA--------RESLEPGrqrlqrdkiaPLDSSLGGGGEIAQImeqgdlsvrdaavdt 323
Cdd:pfam02906 147 AVLT---------------TRELAAmikeagidFAKLEDE----------EFDNPLGESSGAGRI--------------- 186

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14165461   324 lFGdlkedkvtrhdgaSSDGHLAHIFRHAAKELFNEDVEEVTYRALRN-KDFQEVTLEKNGeVVLRFAAAYGFRNIQNMI 402
Cdd:pfam02906 187 -FG-------------VTGGVMEAALRTAYELLTGKELPAIEFKEVRGlEGIKEATVEIGG-TTVKVAVVSGLKNARKLL 251

                         330       340
                  ....*....|....*....|....*
gi 14165461   403 LKLKKGKFPFHFVEVLACAGGCLNG 427
Cdd:pfam02906 252 EKIKAGELKYHFIEVMACPGGCIGG 276
Nar1 COG4624
Iron only hydrogenase large subunit, C-terminal domain [Energy production and conversion];
46-489 9.17e-53

Iron only hydrogenase large subunit, C-terminal domain [Energy production and conversion];


Pssm-ID: 443663 [Multi-domain]  Cd Length: 450  Bit Score: 184.84  E-value: 9.17e-53
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14165461  46 AKIFLSDCLACDSCMTAEEgvqlsqQNAK----DFFRVLNLNKkcdtSKHKVlVVSVCPqSlpyFAAKFNLSVTdaSRRL 121
Cdd:COG4624 115 AEIDEEKCISCGQCVAVCP------FGAIteksDIEKVKKALK----DPEKV-VAQVAP-A---VRGQFGGTVT--PGKL 177

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14165461 122 CGFLKSLGVHYVFDTTIAADFSILESQKEFVRRYrqhseEERTLPMLTSACPGWVRYAERVlgRP-ITAHLCTAKSPQQV 200
Cdd:COG4624 178 VAALKKLGFDDVFETAFGADLTIMEEAKELLERL-----KKGKLPMITSCCPAWVKLIEKY--YPeLLPNLSPCKSPMQA 250

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14165461 201 MGSLVKDYFArqqnlspEKIFHVIVAPCYDKKLEALQESLPPALhgsrgaDCVLTseisqawwctpvitaTReaaaresl 280
Cdd:COG4624 251 FGALIKTYYA-------PDIKVVFIGPCIAKKFEAKRPEMKGDV------DYVLT---------------FR-------- 294

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14165461 281 epgrqrlqrdkiapldsslggggEIAQIMEQGDLSvrdaavdtlFGDLKEDKVtrhDGASSdgHLAHIF----------R 350
Cdd:COG4624 295 -----------------------ELARMIKEAGID---------LANLEEEEF---DNESS--GAGRIFgvtggvmeaaL 337

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14165461 351 HAAKELFNEDVEevtyralrnkdfqevtlekngevvLRFAAAYGFRNIQNMILKLKKGKFPFHFVEVLACAGGCLNGRGQ 430
Cdd:COG4624 338 RTAYELLPDGLE------------------------LKVAVVSGLKNCRKLLEEIKAGKIDYHFIEVMACPGGCIGGPGQ 393

                       410       420       430       440       450       460
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 14165461 431 aqtPDGHADKALLRQMEGIYADI-PVRRPESSAHVQELYQEWLEGINSPKAREVLHTTYQ 489
Cdd:COG4624 394 ---PIPPGSLEKRRKRVALYAKEaPIRKSHENPEILDLYREFLGKPLSEKAHELLHTHYR 450
Fe_hyd_SSU smart00902
Iron hydrogenase small subunit; Many microorganisms, such as methanogenic, acetogenic, ...
 444-492 1.17e-15

Iron hydrogenase small subunit; Many microorganisms, such as methanogenic, acetogenic, nitrogen-fixing, photosynthetic, or sulphate-reducing bacteria, metabolise hydrogen. Hydrogen activation is mediated by a family of enzymes, termed hydrogenases, which either provide these organisms with reducing power from hydrogen oxidation, or act as electron sinks. There are two hydrogenases families that differ functionally from each other: NiFe hydrogenases tend to be more involved in hydrogen oxidation, while Iron-only FeFe (Fe only) hydrogenases in hydrogen production. Fe only hydrogenases show a common core structure, which contains a moiety, deeply buried inside the protein, with an Fe-Fe dinuclear centre, nonproteic bridging, terminal CO and CN- ligands attached to each of the iron atoms, and a dithio moiety, which also bridges the two iron atoms and has been tentatively assigned as a di(thiomethyl)amine. This common core also harbours three [4Fe-4S] iron-sulphur clusters. In FeFe hydrogenases, as in NiFe hydrogenases, the set of iron-sulphur clusters is dispersed regularly between the dinuclear Fe-Fe centre and the molecular surface. These clusters are distant by about 1.2 nm from each other but the [4Fe-4S] cluster closest to the dinuclear centre is covalently bound to one of the iron atoms though a thiolate bridging ligand. The moiety including the dinuclear centre, the thiolate bridging ligand, and the proximal [4Fe-4S] cluster is known as the H-cluster. A channel, lined with hydrophobic amino acid side chains, nearly connects the dinuclear centre and the molecular surface. Furthermore hydrogen-bonded water molecule sites have been identified at the interior and at the surface of the protein. The small subunit is comprised of alternating random coil and alpha helical structures that encompass the large subunit in a novel protein fold.


Pssm-ID: 214899 [Multi-domain]  Cd Length: 52  Bit Score: 70.74  E-value: 1.17e-15
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 14165461    444 RQMEGIYADI---PVRRPESSAHVQELYQEWLEGINSPKAREVLHTTYQSQE 492
Cdd:smart00902   1 QRAEALYNIDkslPLRKSHENPAVKKLYEEFLGGPLSHKAHELLHTHYHDRE 52
Fe_hyd_SSU pfam02256
Iron hydrogenase small subunit; This family represents the small subunit of the Fe-only ...
 439-490 8.94e-12

Iron hydrogenase small subunit; This family represents the small subunit of the Fe-only hydrogenases EC:1.18.99.1. The subunit is comprised of alternating random coil and alpha helical structures that encompasses the large subunit in a novel protein fold.


Pssm-ID: 460511 [Multi-domain]  Cd Length: 56  Bit Score: 59.82  E-value: 8.94e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 14165461   439 DKALLRQMEGIYAD---IPVRRPESSAHVQELYQEWLEGINSPKAREVLHTTYQS 490
Cdd:pfam02256   1 DDIRKKRAEALYKIdknKPLRKSHENPAVKKLYEEFLGEPLSHKAHELLHTHYTP 55
 
Name Accession Description Interval E-value
Fe_hyd_lg_C pfam02906
Iron only hydrogenase large subunit, C-terminal domain;
92-427 3.03e-72

Iron only hydrogenase large subunit, C-terminal domain;


Pssm-ID: 397172  Cd Length: 277  Bit Score: 230.58  E-value: 3.03e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14165461    92 KVLVVSVCPQSLPYFAAKFNLSVTDASRRLCGFLKSLGVHYVFDTTIAADFSILESQKEFVRRYrqhsEEERTLPMLTSA 171
Cdd:pfam02906   1 KKVVAQIAPAVRGAFGEEFGLPPTVTTGKLVAALRKLGFDYVFDTAFGADLTIMEEATEFLERL----EKGKKLPMFTSC 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14165461   172 CPGWVRYAERVLGRpITAHLCTAKSPQQVMGSLVKDYFARQqnlspEKIFHVIVAPCYDKKLEALQESlppaLHGSRGAD 251
Cdd:pfam02906  77 CPGWVKYVEKYYPE-LLPNLSTCKSPMQMFGALIKTYYAED-----LKIYVVSIMPCTAKKFEAARPE----MKGDRDVD 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14165461   252 CVLTseisqawwctpvitaTREAAA--------RESLEPGrqrlqrdkiaPLDSSLGGGGEIAQImeqgdlsvrdaavdt 323
Cdd:pfam02906 147 AVLT---------------TRELAAmikeagidFAKLEDE----------EFDNPLGESSGAGRI--------------- 186

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14165461   324 lFGdlkedkvtrhdgaSSDGHLAHIFRHAAKELFNEDVEEVTYRALRN-KDFQEVTLEKNGeVVLRFAAAYGFRNIQNMI 402
Cdd:pfam02906 187 -FG-------------VTGGVMEAALRTAYELLTGKELPAIEFKEVRGlEGIKEATVEIGG-TTVKVAVVSGLKNARKLL 251

                         330       340
                  ....*....|....*....|....*
gi 14165461   403 LKLKKGKFPFHFVEVLACAGGCLNG 427
Cdd:pfam02906 252 EKIKAGELKYHFIEVMACPGGCIGG 276
Nar1 COG4624
Iron only hydrogenase large subunit, C-terminal domain [Energy production and conversion];
46-489 9.17e-53

Iron only hydrogenase large subunit, C-terminal domain [Energy production and conversion];


Pssm-ID: 443663 [Multi-domain]  Cd Length: 450  Bit Score: 184.84  E-value: 9.17e-53
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14165461  46 AKIFLSDCLACDSCMTAEEgvqlsqQNAK----DFFRVLNLNKkcdtSKHKVlVVSVCPqSlpyFAAKFNLSVTdaSRRL 121
Cdd:COG4624 115 AEIDEEKCISCGQCVAVCP------FGAIteksDIEKVKKALK----DPEKV-VAQVAP-A---VRGQFGGTVT--PGKL 177

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14165461 122 CGFLKSLGVHYVFDTTIAADFSILESQKEFVRRYrqhseEERTLPMLTSACPGWVRYAERVlgRP-ITAHLCTAKSPQQV 200
Cdd:COG4624 178 VAALKKLGFDDVFETAFGADLTIMEEAKELLERL-----KKGKLPMITSCCPAWVKLIEKY--YPeLLPNLSPCKSPMQA 250

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14165461 201 MGSLVKDYFArqqnlspEKIFHVIVAPCYDKKLEALQESLPPALhgsrgaDCVLTseisqawwctpvitaTReaaaresl 280
Cdd:COG4624 251 FGALIKTYYA-------PDIKVVFIGPCIAKKFEAKRPEMKGDV------DYVLT---------------FR-------- 294

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14165461 281 epgrqrlqrdkiapldsslggggEIAQIMEQGDLSvrdaavdtlFGDLKEDKVtrhDGASSdgHLAHIF----------R 350
Cdd:COG4624 295 -----------------------ELARMIKEAGID---------LANLEEEEF---DNESS--GAGRIFgvtggvmeaaL 337

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14165461 351 HAAKELFNEDVEevtyralrnkdfqevtlekngevvLRFAAAYGFRNIQNMILKLKKGKFPFHFVEVLACAGGCLNGRGQ 430
Cdd:COG4624 338 RTAYELLPDGLE------------------------LKVAVVSGLKNCRKLLEEIKAGKIDYHFIEVMACPGGCIGGPGQ 393

                       410       420       430       440       450       460
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 14165461 431 aqtPDGHADKALLRQMEGIYADI-PVRRPESSAHVQELYQEWLEGINSPKAREVLHTTYQ 489
Cdd:COG4624 394 ---PIPPGSLEKRRKRVALYAKEaPIRKSHENPEILDLYREFLGKPLSEKAHELLHTHYR 450
Fe_hyd_SSU smart00902
Iron hydrogenase small subunit; Many microorganisms, such as methanogenic, acetogenic, ...
 444-492 1.17e-15

Iron hydrogenase small subunit; Many microorganisms, such as methanogenic, acetogenic, nitrogen-fixing, photosynthetic, or sulphate-reducing bacteria, metabolise hydrogen. Hydrogen activation is mediated by a family of enzymes, termed hydrogenases, which either provide these organisms with reducing power from hydrogen oxidation, or act as electron sinks. There are two hydrogenases families that differ functionally from each other: NiFe hydrogenases tend to be more involved in hydrogen oxidation, while Iron-only FeFe (Fe only) hydrogenases in hydrogen production. Fe only hydrogenases show a common core structure, which contains a moiety, deeply buried inside the protein, with an Fe-Fe dinuclear centre, nonproteic bridging, terminal CO and CN- ligands attached to each of the iron atoms, and a dithio moiety, which also bridges the two iron atoms and has been tentatively assigned as a di(thiomethyl)amine. This common core also harbours three [4Fe-4S] iron-sulphur clusters. In FeFe hydrogenases, as in NiFe hydrogenases, the set of iron-sulphur clusters is dispersed regularly between the dinuclear Fe-Fe centre and the molecular surface. These clusters are distant by about 1.2 nm from each other but the [4Fe-4S] cluster closest to the dinuclear centre is covalently bound to one of the iron atoms though a thiolate bridging ligand. The moiety including the dinuclear centre, the thiolate bridging ligand, and the proximal [4Fe-4S] cluster is known as the H-cluster. A channel, lined with hydrophobic amino acid side chains, nearly connects the dinuclear centre and the molecular surface. Furthermore hydrogen-bonded water molecule sites have been identified at the interior and at the surface of the protein. The small subunit is comprised of alternating random coil and alpha helical structures that encompass the large subunit in a novel protein fold.


Pssm-ID: 214899 [Multi-domain]  Cd Length: 52  Bit Score: 70.74  E-value: 1.17e-15
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 14165461    444 RQMEGIYADI---PVRRPESSAHVQELYQEWLEGINSPKAREVLHTTYQSQE 492
Cdd:smart00902   1 QRAEALYNIDkslPLRKSHENPAVKKLYEEFLGGPLSHKAHELLHTHYHDRE 52
Fe_hyd_SSU pfam02256
Iron hydrogenase small subunit; This family represents the small subunit of the Fe-only ...
 439-490 8.94e-12

Iron hydrogenase small subunit; This family represents the small subunit of the Fe-only hydrogenases EC:1.18.99.1. The subunit is comprised of alternating random coil and alpha helical structures that encompasses the large subunit in a novel protein fold.


Pssm-ID: 460511 [Multi-domain]  Cd Length: 56  Bit Score: 59.82  E-value: 8.94e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 14165461   439 DKALLRQMEGIYAD---IPVRRPESSAHVQELYQEWLEGINSPKAREVLHTTYQS 490
Cdd:pfam02256   1 DDIRKKRAEALYKIdknKPLRKSHENPAVKKLYEEFLGEPLSHKAHELLHTHYTP 55
 
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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