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Conserved domains on  [gi|325301271|ref|NP_001191684|]
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cytosolic Fe-S cluster assembly factor NARFL [Macaca mulatta]

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;
112-403 2.77e-108

Iron only hydrogenase large subunit, C-terminal domain;


:

Pssm-ID: 397172  Cd Length: 277  Bit Score: 322.26  E-value: 2.77e-108
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325301271  112 VVVSVSPQSRASLAARFQLNPTDTARKLTSFFKKIGVHFVFDTAFSRHFSLLESQREFVRRFRGqadcRQALPLLASACP 191
Cdd:pfam02906   3 VVAQIAPAVRGAFGEEFGLPPTVTTGKLVAALRKLGFDYVFDTAFGADLTIMEEATEFLERLEK----GKKLPMFTSCCP 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325301271  192 GWICYAEKTHGSFIlPYISTARSPQQVMGSLVKDFFAQQqrltpDKIYHVTVMPCYDKKLEASRPDFfnqeHQTRDVDCV 271
Cdd:pfam02906  79 GWVKYVEKYYPELL-PNLSTCKSPMQMFGALIKTYYAED-----LKIYVVSIMPCTAKKFEAARPEM----KGDRDVDAV 148

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325301271  272 LTTGEVFRLLEEEDVSLPDLEPAPLDSLCSGASAEeptSHRGGGSGGYLEHVFRHAARELFGIHVAEVTYKPLRN-KDFQ 350
Cdd:pfam02906 149 LTTRELAAMIKEAGIDFAKLEDEEFDNPLGESSGA---GRIFGVTGGVMEAALRTAYELLTGKELPAIEFKEVRGlEGIK 225

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 325301271  351 EVTLEKEGqVLLHFAMAYGFRNIQNLVQRLKRGRCPYHYVEVMACPSGCLNGG 403
Cdd:pfam02906 226 EATVEIGG-TTVKVAVVSGLKNARKLLEKIKAGELKYHFIEVMACPGGCIGGG 277
Fe_hyd_SSU smart00902
Iron hydrogenase small subunit; Many microorganisms, such as methanogenic, acetogenic, ...
 418-466 5.05e-12

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: 60.73  E-value: 5.05e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 325301271   418 QHVERLYGMVRA---EMPEDAPGVQELYTHWLQGTDSECAGRLLHTQYHAVE 466
Cdd:smart00902   1 QRAEALYNIDKSlplRKSHENPAVKKLYEEFLGGPLSHKAHELLHTHYHDRE 52
 
Name Accession Description Interval E-value
Fe_hyd_lg_C pfam02906
Iron only hydrogenase large subunit, C-terminal domain;
112-403 2.77e-108

Iron only hydrogenase large subunit, C-terminal domain;


Pssm-ID: 397172  Cd Length: 277  Bit Score: 322.26  E-value: 2.77e-108
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325301271  112 VVVSVSPQSRASLAARFQLNPTDTARKLTSFFKKIGVHFVFDTAFSRHFSLLESQREFVRRFRGqadcRQALPLLASACP 191
Cdd:pfam02906   3 VVAQIAPAVRGAFGEEFGLPPTVTTGKLVAALRKLGFDYVFDTAFGADLTIMEEATEFLERLEK----GKKLPMFTSCCP 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325301271  192 GWICYAEKTHGSFIlPYISTARSPQQVMGSLVKDFFAQQqrltpDKIYHVTVMPCYDKKLEASRPDFfnqeHQTRDVDCV 271
Cdd:pfam02906  79 GWVKYVEKYYPELL-PNLSTCKSPMQMFGALIKTYYAED-----LKIYVVSIMPCTAKKFEAARPEM----KGDRDVDAV 148

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325301271  272 LTTGEVFRLLEEEDVSLPDLEPAPLDSLCSGASAEeptSHRGGGSGGYLEHVFRHAARELFGIHVAEVTYKPLRN-KDFQ 350
Cdd:pfam02906 149 LTTRELAAMIKEAGIDFAKLEDEEFDNPLGESSGA---GRIFGVTGGVMEAALRTAYELLTGKELPAIEFKEVRGlEGIK 225

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 325301271  351 EVTLEKEGqVLLHFAMAYGFRNIQNLVQRLKRGRCPYHYVEVMACPSGCLNGG 403
Cdd:pfam02906 226 EATVEIGG-TTVKVAVVSGLKNARKLLEKIKAGELKYHFIEVMACPGGCIGGG 277
Nar1 COG4624
Iron only hydrogenase large subunit, C-terminal domain [Energy production and conversion];
63-462 2.54e-67

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


Pssm-ID: 443663 [Multi-domain]  Cd Length: 450  Bit Score: 222.59  E-value: 2.54e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325301271  63 KAKVSLNDCLACSGCITSAETVLITQQSheELKKVLDAnkMAAPSQqrlVVVSVSPqsraslAARFQLNPTDTARKLTSF 142
Cdd:COG4624  114 KAEIDEEKCISCGQCVAVCPFGAITEKS--DIEKVKKA--LKDPEK---VVAQVAP------AVRGQFGGTVTPGKLVAA 180

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325301271 143 FKKIGVHFVFDTAFSRHFSLLESQREFVRRFRgqadcRQALPLLASACPGWICYAEKTHGSFIlPYISTARSPQQVMGSL 222
Cdd:COG4624  181 LKKLGFDDVFETAFGADLTIMEEAKELLERLK-----KGKLPMITSCCPAWVKLIEKYYPELL-PNLSPCKSPMQAFGAL 254

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325301271 223 VKDFFAqqqrltpDKIYHVTVMPCYDKKLEASRPDFfnqehqTRDVDCVLTTGEVFRLLEEEDVSLPDLEPAPLDSLCSG 302
Cdd:COG4624  255 IKTYYA-------PDIKVVFIGPCIAKKFEAKRPEM------KGDVDYVLTFRELARMIKEAGIDLANLEEEEFDNESSG 321

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325301271 303 ASaeeptshRG-GGSGGYLEHVFRHAARELfgihvaevtykplrnkdfqevtlekEGQVLLHFAMAYGFRNIQNLVQRLK 381
Cdd:COG4624  322 AG-------RIfGVTGGVMEAALRTAYELL-------------------------PDGLELKVAVVSGLKNCRKLLEEIK 369

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325301271 382 RGRCPYHYVEVMACPSGCLNGGGQLQAPDrPSRELLQHVERLYGMVRAEMPEDAPGVQELYTHWLQGTDSECAGRLLHTQ 461
Cdd:COG4624  370 AGKIDYHFIEVMACPGGCIGGPGQPIPPG-SLEKRRKRVALYAKEAPIRKSHENPEILDLYREFLGKPLSEKAHELLHTH 448


                 .
gi 325301271 462 Y 462
Cdd:COG4624  449 Y 449
Fe_hyd_SSU smart00902
Iron hydrogenase small subunit; Many microorganisms, such as methanogenic, acetogenic, ...
 418-466 5.05e-12

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: 60.73  E-value: 5.05e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 325301271   418 QHVERLYGMVRA---EMPEDAPGVQELYTHWLQGTDSECAGRLLHTQYHAVE 466
Cdd:smart00902   1 QRAEALYNIDKSlplRKSHENPAVKKLYEEFLGGPLSHKAHELLHTHYHDRE 52
Fe_hyd_SSU pfam02256
Iron hydrogenase small subunit; This family represents the small subunit of the Fe-only ...
 415-465 1.26e-04

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: 39.79  E-value: 1.26e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 325301271  415 ELLQHVERLYGM-----VRAemPEDAPGVQELYTHWLQGTDSECAGRLLHTQYHAV 465
Cdd:pfam02256   3 IRKKRAEALYKIdknkpLRK--SHENPAVKKLYEEFLGEPLSHKAHELLHTHYTPR 56
 
Name Accession Description Interval E-value
Fe_hyd_lg_C pfam02906
Iron only hydrogenase large subunit, C-terminal domain;
112-403 2.77e-108

Iron only hydrogenase large subunit, C-terminal domain;


Pssm-ID: 397172  Cd Length: 277  Bit Score: 322.26  E-value: 2.77e-108
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325301271  112 VVVSVSPQSRASLAARFQLNPTDTARKLTSFFKKIGVHFVFDTAFSRHFSLLESQREFVRRFRGqadcRQALPLLASACP 191
Cdd:pfam02906   3 VVAQIAPAVRGAFGEEFGLPPTVTTGKLVAALRKLGFDYVFDTAFGADLTIMEEATEFLERLEK----GKKLPMFTSCCP 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325301271  192 GWICYAEKTHGSFIlPYISTARSPQQVMGSLVKDFFAQQqrltpDKIYHVTVMPCYDKKLEASRPDFfnqeHQTRDVDCV 271
Cdd:pfam02906  79 GWVKYVEKYYPELL-PNLSTCKSPMQMFGALIKTYYAED-----LKIYVVSIMPCTAKKFEAARPEM----KGDRDVDAV 148

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325301271  272 LTTGEVFRLLEEEDVSLPDLEPAPLDSLCSGASAEeptSHRGGGSGGYLEHVFRHAARELFGIHVAEVTYKPLRN-KDFQ 350
Cdd:pfam02906 149 LTTRELAAMIKEAGIDFAKLEDEEFDNPLGESSGA---GRIFGVTGGVMEAALRTAYELLTGKELPAIEFKEVRGlEGIK 225

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 325301271  351 EVTLEKEGqVLLHFAMAYGFRNIQNLVQRLKRGRCPYHYVEVMACPSGCLNGG 403
Cdd:pfam02906 226 EATVEIGG-TTVKVAVVSGLKNARKLLEKIKAGELKYHFIEVMACPGGCIGGG 277
Nar1 COG4624
Iron only hydrogenase large subunit, C-terminal domain [Energy production and conversion];
63-462 2.54e-67

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


Pssm-ID: 443663 [Multi-domain]  Cd Length: 450  Bit Score: 222.59  E-value: 2.54e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325301271  63 KAKVSLNDCLACSGCITSAETVLITQQSheELKKVLDAnkMAAPSQqrlVVVSVSPqsraslAARFQLNPTDTARKLTSF 142
Cdd:COG4624  114 KAEIDEEKCISCGQCVAVCPFGAITEKS--DIEKVKKA--LKDPEK---VVAQVAP------AVRGQFGGTVTPGKLVAA 180

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325301271 143 FKKIGVHFVFDTAFSRHFSLLESQREFVRRFRgqadcRQALPLLASACPGWICYAEKTHGSFIlPYISTARSPQQVMGSL 222
Cdd:COG4624  181 LKKLGFDDVFETAFGADLTIMEEAKELLERLK-----KGKLPMITSCCPAWVKLIEKYYPELL-PNLSPCKSPMQAFGAL 254

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325301271 223 VKDFFAqqqrltpDKIYHVTVMPCYDKKLEASRPDFfnqehqTRDVDCVLTTGEVFRLLEEEDVSLPDLEPAPLDSLCSG 302
Cdd:COG4624  255 IKTYYA-------PDIKVVFIGPCIAKKFEAKRPEM------KGDVDYVLTFRELARMIKEAGIDLANLEEEEFDNESSG 321

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325301271 303 ASaeeptshRG-GGSGGYLEHVFRHAARELfgihvaevtykplrnkdfqevtlekEGQVLLHFAMAYGFRNIQNLVQRLK 381
Cdd:COG4624  322 AG-------RIfGVTGGVMEAALRTAYELL-------------------------PDGLELKVAVVSGLKNCRKLLEEIK 369

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325301271 382 RGRCPYHYVEVMACPSGCLNGGGQLQAPDrPSRELLQHVERLYGMVRAEMPEDAPGVQELYTHWLQGTDSECAGRLLHTQ 461
Cdd:COG4624  370 AGKIDYHFIEVMACPGGCIGGPGQPIPPG-SLEKRRKRVALYAKEAPIRKSHENPEILDLYREFLGKPLSEKAHELLHTH 448


                 .
gi 325301271 462 Y 462
Cdd:COG4624  449 Y 449
Fe_hyd_SSU smart00902
Iron hydrogenase small subunit; Many microorganisms, such as methanogenic, acetogenic, ...
 418-466 5.05e-12

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: 60.73  E-value: 5.05e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 325301271   418 QHVERLYGMVRA---EMPEDAPGVQELYTHWLQGTDSECAGRLLHTQYHAVE 466
Cdd:smart00902   1 QRAEALYNIDKSlplRKSHENPAVKKLYEEFLGGPLSHKAHELLHTHYHDRE 52
Fe_hyd_SSU pfam02256
Iron hydrogenase small subunit; This family represents the small subunit of the Fe-only ...
 415-465 1.26e-04

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: 39.79  E-value: 1.26e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 325301271  415 ELLQHVERLYGM-----VRAemPEDAPGVQELYTHWLQGTDSECAGRLLHTQYHAV 465
Cdd:pfam02256   3 IRKKRAEALYKIdknkpLRK--SHENPAVKKLYEEFLGEPLSHKAHELLHTHYTPR 56
 
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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