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Conserved domains on  [gi|6912524|ref|NP_036468|]
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nuclear prelamin A recognition factor isoform a [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;
92-381 1.55e-80

Iron only hydrogenase large subunit, C-terminal domain;


:

Pssm-ID: 397172  Cd Length: 277  Bit Score: 250.61  E-value: 1.55e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6912524     92 KVLVVSVCPQSLPYFAAKFNLSVTDASRRLCGFLKSLGVHYVFDTTIAADFSILESQKEFVRRYrqhsEEERTLPMLTSA 171
Cdd:pfam02906   1 KKVVAQIAPAVRGAFGEEFGLPPTVTTGKLVAALRKLGFDYVFDTAFGADLTIMEEATEFLERL----EKGKKLPMFTSC 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6912524    172 CPGWVRYAERVLGRpITAHLCTAKSPQQVMGSLVKDYFARQqnlspEKIFHVIVAPCYDKKLEALQESLppalHGSRGAD 251
Cdd:pfam02906  77 CPGWVKYVEKYYPE-LLPNLSTCKSPMQMFGALIKTYYAED-----LKIYVVSIMPCTAKKFEAARPEM----KGDRDVD 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6912524    252 CVLTSGEIAQIMEQGDL---SVRDAAVDTLFGDlkedkvTRHDG---ASSDGHLAHIFRHAAKELFNEDVEEVTYRALRN 325
Cdd:pfam02906 147 AVLTTRELAAMIKEAGIdfaKLEDEEFDNPLGE------SSGAGrifGVTGGVMEAALRTAYELLTGKELPAIEFKEVRG 220

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 6912524    326 -KDFQEVTLEKNGeVVLRFAAAYGFRNIQNMILKLKKGKFPFHFVEVLACAGGCLNG 381
Cdd:pfam02906 221 lEGIKEATVEIGG-TTVKVAVVSGLKNARKLLEKIKAGELKYHFIEVMACPGGCIGG 276
Fe_hyd_SSU smart00902
Iron hydrogenase small subunit; Many microorganisms, such as methanogenic, acetogenic, ...
 398-446 1.93e-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: 70.36  E-value: 1.93e-15
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 6912524     398 RQMEGIYADI---PVRRPESSAHVQELYQEWLEGINSPKAREVLHTTYQSQE 446
Cdd:smart00902   1 QRAEALYNIDkslPLRKSHENPAVKKLYEEFLGGPLSHKAHELLHTHYHDRE 52
 
Name Accession Description Interval E-value
Fe_hyd_lg_C pfam02906
Iron only hydrogenase large subunit, C-terminal domain;
92-381 1.55e-80

Iron only hydrogenase large subunit, C-terminal domain;


Pssm-ID: 397172  Cd Length: 277  Bit Score: 250.61  E-value: 1.55e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6912524     92 KVLVVSVCPQSLPYFAAKFNLSVTDASRRLCGFLKSLGVHYVFDTTIAADFSILESQKEFVRRYrqhsEEERTLPMLTSA 171
Cdd:pfam02906   1 KKVVAQIAPAVRGAFGEEFGLPPTVTTGKLVAALRKLGFDYVFDTAFGADLTIMEEATEFLERL----EKGKKLPMFTSC 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6912524    172 CPGWVRYAERVLGRpITAHLCTAKSPQQVMGSLVKDYFARQqnlspEKIFHVIVAPCYDKKLEALQESLppalHGSRGAD 251
Cdd:pfam02906  77 CPGWVKYVEKYYPE-LLPNLSTCKSPMQMFGALIKTYYAED-----LKIYVVSIMPCTAKKFEAARPEM----KGDRDVD 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6912524    252 CVLTSGEIAQIMEQGDL---SVRDAAVDTLFGDlkedkvTRHDG---ASSDGHLAHIFRHAAKELFNEDVEEVTYRALRN 325
Cdd:pfam02906 147 AVLTTRELAAMIKEAGIdfaKLEDEEFDNPLGE------SSGAGrifGVTGGVMEAALRTAYELLTGKELPAIEFKEVRG 220

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 6912524    326 -KDFQEVTLEKNGeVVLRFAAAYGFRNIQNMILKLKKGKFPFHFVEVLACAGGCLNG 381
Cdd:pfam02906 221 lEGIKEATVEIGG-TTVKVAVVSGLKNARKLLEKIKAGELKYHFIEVMACPGGCIGG 276
Nar1 COG4624
Iron only hydrogenase large subunit, C-terminal domain [Energy production and conversion];
46-443 1.52e-59

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


Pssm-ID: 443663 [Multi-domain]  Cd Length: 450  Bit Score: 201.41  E-value: 1.52e-59
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6912524   46 AKIFLSDCLACDSCMTAEEgvqlsqQNAK----DFFRVLNLNKkcdtSKHKVlVVSVCPqSlpyFAAKFNLSVTdaSRRL 121
Cdd:COG4624 115 AEIDEEKCISCGQCVAVCP------FGAIteksDIEKVKKALK----DPEKV-VAQVAP-A---VRGQFGGTVT--PGKL 177

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6912524  122 CGFLKSLGVHYVFDTTIAADFSILESQKEFVRRYrqhseEERTLPMLTSACPGWVRYAERVlgRP-ITAHLCTAKSPQQV 200
Cdd:COG4624 178 VAALKKLGFDDVFETAFGADLTIMEEAKELLERL-----KKGKLPMITSCCPAWVKLIEKY--YPeLLPNLSPCKSPMQA 250

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6912524  201 MGSLVKDYFArqqnlspEKIFHVIVAPCYDKKLEALQESLPPALhgsrgaDCVLTSGEIAQIMEQGDLSvrdaavdtlFG 280
Cdd:COG4624 251 FGALIKTYYA-------PDIKVVFIGPCIAKKFEAKRPEMKGDV------DYVLTFRELARMIKEAGID---------LA 308

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6912524  281 DLKEDKVtrhDGASSdgHLAHIF----------RHAAKELFNEDVEevtyralrnkdfqevtlekngevvLRFAAAYGFR 350
Cdd:COG4624 309 NLEEEEF---DNESS--GAGRIFgvtggvmeaaLRTAYELLPDGLE------------------------LKVAVVSGLK 359

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6912524  351 NIQNMILKLKKGKFPFHFVEVLACAGGCLNGRGQaqtPDGHADKALLRQMEGIYADI-PVRRPESSAHVQELYQEWLEGI 429
Cdd:COG4624 360 NCRKLLEEIKAGKIDYHFIEVMACPGGCIGGPGQ---PIPPGSLEKRRKRVALYAKEaPIRKSHENPEILDLYREFLGKP 436

                       410
                ....*....|....
gi 6912524  430 NSPKAREVLHTTYQ 443
Cdd:COG4624 437 LSEKAHELLHTHYR 450
Fe_hyd_SSU smart00902
Iron hydrogenase small subunit; Many microorganisms, such as methanogenic, acetogenic, ...
 398-446 1.93e-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: 70.36  E-value: 1.93e-15
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 6912524     398 RQMEGIYADI---PVRRPESSAHVQELYQEWLEGINSPKAREVLHTTYQSQE 446
Cdd:smart00902   1 QRAEALYNIDkslPLRKSHENPAVKKLYEEFLGGPLSHKAHELLHTHYHDRE 52
Fe_hyd_SSU pfam02256
Iron hydrogenase small subunit; This family represents the small subunit of the Fe-only ...
 393-444 1.31e-11

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: 59.44  E-value: 1.31e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 6912524    393 DKALLRQMEGIYAD---IPVRRPESSAHVQELYQEWLEGINSPKAREVLHTTYQS 444
Cdd:pfam02256   1 DDIRKKRAEALYKIdknKPLRKSHENPAVKKLYEEFLGEPLSHKAHELLHTHYTP 55
 
Name Accession Description Interval E-value
Fe_hyd_lg_C pfam02906
Iron only hydrogenase large subunit, C-terminal domain;
92-381 1.55e-80

Iron only hydrogenase large subunit, C-terminal domain;


Pssm-ID: 397172  Cd Length: 277  Bit Score: 250.61  E-value: 1.55e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6912524     92 KVLVVSVCPQSLPYFAAKFNLSVTDASRRLCGFLKSLGVHYVFDTTIAADFSILESQKEFVRRYrqhsEEERTLPMLTSA 171
Cdd:pfam02906   1 KKVVAQIAPAVRGAFGEEFGLPPTVTTGKLVAALRKLGFDYVFDTAFGADLTIMEEATEFLERL----EKGKKLPMFTSC 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6912524    172 CPGWVRYAERVLGRpITAHLCTAKSPQQVMGSLVKDYFARQqnlspEKIFHVIVAPCYDKKLEALQESLppalHGSRGAD 251
Cdd:pfam02906  77 CPGWVKYVEKYYPE-LLPNLSTCKSPMQMFGALIKTYYAED-----LKIYVVSIMPCTAKKFEAARPEM----KGDRDVD 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6912524    252 CVLTSGEIAQIMEQGDL---SVRDAAVDTLFGDlkedkvTRHDG---ASSDGHLAHIFRHAAKELFNEDVEEVTYRALRN 325
Cdd:pfam02906 147 AVLTTRELAAMIKEAGIdfaKLEDEEFDNPLGE------SSGAGrifGVTGGVMEAALRTAYELLTGKELPAIEFKEVRG 220

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 6912524    326 -KDFQEVTLEKNGeVVLRFAAAYGFRNIQNMILKLKKGKFPFHFVEVLACAGGCLNG 381
Cdd:pfam02906 221 lEGIKEATVEIGG-TTVKVAVVSGLKNARKLLEKIKAGELKYHFIEVMACPGGCIGG 276
Nar1 COG4624
Iron only hydrogenase large subunit, C-terminal domain [Energy production and conversion];
46-443 1.52e-59

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


Pssm-ID: 443663 [Multi-domain]  Cd Length: 450  Bit Score: 201.41  E-value: 1.52e-59
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6912524   46 AKIFLSDCLACDSCMTAEEgvqlsqQNAK----DFFRVLNLNKkcdtSKHKVlVVSVCPqSlpyFAAKFNLSVTdaSRRL 121
Cdd:COG4624 115 AEIDEEKCISCGQCVAVCP------FGAIteksDIEKVKKALK----DPEKV-VAQVAP-A---VRGQFGGTVT--PGKL 177

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6912524  122 CGFLKSLGVHYVFDTTIAADFSILESQKEFVRRYrqhseEERTLPMLTSACPGWVRYAERVlgRP-ITAHLCTAKSPQQV 200
Cdd:COG4624 178 VAALKKLGFDDVFETAFGADLTIMEEAKELLERL-----KKGKLPMITSCCPAWVKLIEKY--YPeLLPNLSPCKSPMQA 250

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6912524  201 MGSLVKDYFArqqnlspEKIFHVIVAPCYDKKLEALQESLPPALhgsrgaDCVLTSGEIAQIMEQGDLSvrdaavdtlFG 280
Cdd:COG4624 251 FGALIKTYYA-------PDIKVVFIGPCIAKKFEAKRPEMKGDV------DYVLTFRELARMIKEAGID---------LA 308

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6912524  281 DLKEDKVtrhDGASSdgHLAHIF----------RHAAKELFNEDVEevtyralrnkdfqevtlekngevvLRFAAAYGFR 350
Cdd:COG4624 309 NLEEEEF---DNESS--GAGRIFgvtggvmeaaLRTAYELLPDGLE------------------------LKVAVVSGLK 359

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6912524  351 NIQNMILKLKKGKFPFHFVEVLACAGGCLNGRGQaqtPDGHADKALLRQMEGIYADI-PVRRPESSAHVQELYQEWLEGI 429
Cdd:COG4624 360 NCRKLLEEIKAGKIDYHFIEVMACPGGCIGGPGQ---PIPPGSLEKRRKRVALYAKEaPIRKSHENPEILDLYREFLGKP 436

                       410
                ....*....|....
gi 6912524  430 NSPKAREVLHTTYQ 443
Cdd:COG4624 437 LSEKAHELLHTHYR 450
Fe_hyd_SSU smart00902
Iron hydrogenase small subunit; Many microorganisms, such as methanogenic, acetogenic, ...
 398-446 1.93e-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: 70.36  E-value: 1.93e-15
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 6912524     398 RQMEGIYADI---PVRRPESSAHVQELYQEWLEGINSPKAREVLHTTYQSQE 446
Cdd:smart00902   1 QRAEALYNIDkslPLRKSHENPAVKKLYEEFLGGPLSHKAHELLHTHYHDRE 52
Fe_hyd_SSU pfam02256
Iron hydrogenase small subunit; This family represents the small subunit of the Fe-only ...
 393-444 1.31e-11

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: 59.44  E-value: 1.31e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 6912524    393 DKALLRQMEGIYAD---IPVRRPESSAHVQELYQEWLEGINSPKAREVLHTTYQS 444
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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