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Conserved domains on  [gi|116666361|gb|ABK15388|]
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DNA-directed RNA polymerase, subunit D [Methanothrix thermoacetophila PT]

Protein Classification

RNA polymerase alpha/RpoL/Rpb11 family protein; DNA-directed RNA polymerase subunit alpha( domain architecture ID 10161705)

RNA polymerase alpha/RpoL/Rpb11 family protein such as DNA-directed RNA polymerase subunit L (RpoL) and DNA-directed RNA polymerase subunit alpha; DNA-directed RNA polymerase subunit alpha

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNAP_D cd07030
D subunit of Archaeal RNA polymerase; The D subunit of archaeal RNA polymerase (RNAP) is ...
 1-260 5.10e-131

D subunit of Archaeal RNA polymerase; The D subunit of archaeal RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The D subunit is equivalent to the RPB3 subunit of eukaryotic RNAP II. It contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization, and the other is an inserted beta sheet subdomain. The assembly of the two largest archaeal RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of the archaeal D/L heterodimer.


:

Pssm-ID: 132908 [Multi-domain]  Cd Length: 259  Bit Score: 370.83  E-value: 5.10e-131
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116666361   1 MNVELIELRDDRVRFLLTGVTPAFANAIRRSCIAEVPKLAIDEISIYENTSVLFDEQIALRLGLVPIRADDLSVYSTPdE 80
Cdd:cd07030    1 MEIEVLELDDDRARFVLEGVPPAFANAIRRAIISEVPTLAIDDVNIYENTSVLFDEMLAHRLGLIPLRTDLDLYKYRS-E 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116666361  81 CQCGGIGCPGCRIDFMLTAEGPATVHSRDIKFSDPSVRAAFDNIPLVVLGEGEKLVIEGFATLRTGKEHAKWQAGTLCGY 160
Cdd:cd07030   80 CSCGGAGCPLCTVTLTLSVEGPGTVYSGDLKSSDPDVKPVYDNIPIVKLGKGQKLVLEAYARLGRGKEHAKWQPTTACGY 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116666361 161 KNLPSIEISG-CNNCGRCVKVCPRGVLVLDENdSIKVRDITECSLCRLCVEECDQRAISVVPLEDAFIMSIESDGSINAK 239
Cdd:cd07030  160 KYYPVIEIDEdCDGCGKCVEECPRGVLELEEG-KVVVEDLEDCSLCKLCERACDAGAIRVGWDEDRFIFEVESDGSLPPK 238

                        250       260
                 ....*....|....*....|.
gi 116666361 240 DLVRMAAEELKKKALALQDTL 260
Cdd:cd07030  239 EILLEALRILKEKADELIEAL 259
 
Name Accession Description Interval E-value
RNAP_D cd07030
D subunit of Archaeal RNA polymerase; The D subunit of archaeal RNA polymerase (RNAP) is ...
 1-260 5.10e-131

D subunit of Archaeal RNA polymerase; The D subunit of archaeal RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The D subunit is equivalent to the RPB3 subunit of eukaryotic RNAP II. It contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization, and the other is an inserted beta sheet subdomain. The assembly of the two largest archaeal RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of the archaeal D/L heterodimer.


Pssm-ID: 132908 [Multi-domain]  Cd Length: 259  Bit Score: 370.83  E-value: 5.10e-131
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116666361   1 MNVELIELRDDRVRFLLTGVTPAFANAIRRSCIAEVPKLAIDEISIYENTSVLFDEQIALRLGLVPIRADDLSVYSTPdE 80
Cdd:cd07030    1 MEIEVLELDDDRARFVLEGVPPAFANAIRRAIISEVPTLAIDDVNIYENTSVLFDEMLAHRLGLIPLRTDLDLYKYRS-E 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116666361  81 CQCGGIGCPGCRIDFMLTAEGPATVHSRDIKFSDPSVRAAFDNIPLVVLGEGEKLVIEGFATLRTGKEHAKWQAGTLCGY 160
Cdd:cd07030   80 CSCGGAGCPLCTVTLTLSVEGPGTVYSGDLKSSDPDVKPVYDNIPIVKLGKGQKLVLEAYARLGRGKEHAKWQPTTACGY 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116666361 161 KNLPSIEISG-CNNCGRCVKVCPRGVLVLDENdSIKVRDITECSLCRLCVEECDQRAISVVPLEDAFIMSIESDGSINAK 239
Cdd:cd07030  160 KYYPVIEIDEdCDGCGKCVEECPRGVLELEEG-KVVVEDLEDCSLCKLCERACDAGAIRVGWDEDRFIFEVESDGSLPPK 238

                        250       260
                 ....*....|....*....|.
gi 116666361 240 DLVRMAAEELKKKALALQDTL 260
Cdd:cd07030  239 EILLEALRILKEKADELIEAL 259
PRK00783 PRK00783
DNA-directed RNA polymerase subunit D; Provisional
 1-264 3.02e-123

DNA-directed RNA polymerase subunit D; Provisional


Pssm-ID: 234837 [Multi-domain]  Cd Length: 263  Bit Score: 351.49  E-value: 3.02e-123
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116666361   1 MNVELIELRDDRVRFLLTGVTPAFANAIRRSCIAEVPKLAIDEISIYENTSVLFDEQIALRLGLVPIRADDLSvYSTPDE 80
Cdd:PRK00783   1 MEIEILELDDRSARFVVEGVTPAFANAIRRAMIADVPTMAIDDVRFYENTSVLFDEILAHRLGLIPLTTDLDK-YKPPEE 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116666361  81 CQCGGIGCPGCRIDFMLTAEGPATVHSRDIKFSDPSVRAAFDNIPLVVLGEGEKLVIEGFATLRTGKEHAKWQAGTLCGY 160
Cdd:PRK00783  80 CTCEGEGCPDCTVTLSLEVEGPKTVYSGDLKSSDPDVKPVDPNIPIVKLKEGQKLVLEAYARLGRGKEHAKWQPGSACGY 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116666361 161 KNLPSIEISG-CNNCGRCVKVCPRGVLVLDENdSIKVRDITECSLCRLCVEECDQRAISVVPLEDAFIMSIESDGSINAK 239
Cdd:PRK00783 160 KYYPRIEVSEdCDECEKCVEACPRGVLELKEG-KLVVTDLLNCSLCKLCERACPGKAIRVSDDENKFIFTVESDGSLPVE 238

                        250       260
                 ....*....|....*....|....*
gi 116666361 240 DLVRMAAEELKKKALALQDTLASIS 264
Cdd:PRK00783 239 EILLEALKILKRKADELIEALEELA 263
RPOLD smart00662
RNA polymerases D; DNA-directed RNA polymerase subunit D and bacterial alpha chain
 13-257 2.12e-61

RNA polymerases D; DNA-directed RNA polymerase subunit D and bacterial alpha chain


Pssm-ID: 214766 [Multi-domain]  Cd Length: 224  Bit Score: 192.83  E-value: 2.12e-61
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116666361    13 VRFLLTGVTPAFANAIRRSCIAEVPKLAIDEISIYENTSVLFDEQIALRLGLVPIRADdlSVYSTPDECQCGGIGCPGCR 92
Cdd:smart00662   1 AKFVLEPYGLTLANALRRVLLSSVPGMAVTSVYIEGNTSGVQDEVLAHRLGLKPLASD--PDGDEYQRDCECEEGCEKCS 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116666361    93 IDFMLTAEGPATVHSRDIKF-SDPSVRAAFDNIPLVVLGEGEKLVIEGFATLRTGKEHAKWQAGTLCGYKNLPSIEISGC 171
Cdd:smart00662  79 VTLTLDVKGPGEVTAGDLKSdSDPDVEIVNPDIPIAKLREGQELELEARAEKGRGYVHAKWSPVSTVEYRYIPRIPVDAS 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116666361   172 NNCGRCVK---VCPRGVLVLDEndsikvrditecslCRLCVEECDqraisvvplEDAFIMSIESDGSINAKDLVRMAAEE 248
Cdd:smart00662 159 FSPVDRVAyqvECPRVVQRTDC--------------CRECDEGEE---------YDKLIFDVETNGSLKPEEAVLEAAKI 215


                   ....*....
gi 116666361   249 LKKKALALQ 257
Cdd:smart00662 216 LKEKLEAFV 224
RNA_pol_L pfam01193
RNA polymerase Rpb3/Rpb11 dimerization domain; The two eukaryotic subunits Rpb3 and Rpb11 ...
 15-252 1.26e-32

RNA polymerase Rpb3/Rpb11 dimerization domain; The two eukaryotic subunits Rpb3 and Rpb11 dimerize to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerization domain of the alpha subunit/Rpb3 is interrupted by an insert domain (pfam01000). Some of the alpha subunits also contain iron-sulphur binding domains (pfam00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp.


Pssm-ID: 460104 [Multi-domain]  Cd Length: 191  Bit Score: 117.89  E-value: 1.26e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116666361   15 FLLTGVTPAFANAIRRSCIAEVPKLAIDEISIYENTSVLFDEQIALRLGLVPIRADD-LSVYSTPDECQCGGIgcpgcri 93
Cdd:pfam01193   1 FLLRGEDHTLGNALRRILLSEVPGVAIDAVKIEGNTSEFSDEPGAHRLGLIPLLNLKeLFFKLSSDDDETLEL------- 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116666361   94 dfmlTAEGPATVHSRDIKFSDPSVRAAFDNIPLVVLGEGEKLVIEGFATLRTGKEHakwqagtlcgyknlpsieisgcnn 173
Cdd:pfam01193  74 ----DKEGPGEVTAGDINTDSDVEVIEIINPDLHIATLEEEAALEMELEVVKGRGY------------------------ 125

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 116666361  174 cgrcvkvcprgvlVLDENDSIKVRDITECSLCRLCVEECDQRAISVVPLEDAFIMSIESDGSINAKDLVRMAAEELKKK 252
Cdd:pfam01193 126 -------------VPAEKNKDVDDPIGDIPIDSIFSPVEKVNYVVENTDYDKLIFEVETDGSIPPEEALKEAAKILKEK 191
PreA COG1146
NAD-dependent dihydropyrimidine dehydrogenase, PreA subunit [Nucleotide transport and ...
 164-225 1.75e-10

NAD-dependent dihydropyrimidine dehydrogenase, PreA subunit [Nucleotide transport and metabolism];


Pssm-ID: 440761 [Multi-domain]  Cd Length: 67  Bit Score: 55.49  E-value: 1.75e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 116666361 164 PSIEISGCNNCGRCVKVCPRGVLVLDENDS-IKVRDITECSLCRLCVEECDQRAISVVPLEDA 225
Cdd:COG1146    3 PVIDTDKCIGCGACVEVCPVDVLELDEEGKkALVINPEECIGCGACELVCPVGAITVEDDEPE 65
napF TIGR00402
ferredoxin-type protein NapF; The gene codes for a ferredoxin-type cytosolic protein, NapF, of ...
 165-218 1.81e-06

ferredoxin-type protein NapF; The gene codes for a ferredoxin-type cytosolic protein, NapF, of the periplasmic nitrate reductase system, as in Escherichia coli. NapF interacts with the catalytic subunit, NapA, and may be an accessory protein for NapA maturation. [Energy metabolism, Electron transport]


Pssm-ID: 273060 [Multi-domain]  Cd Length: 101  Bit Score: 45.32  E-value: 1.81e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 116666361  165 SIEISGCNNCGRCVKVCPRGVLVLDENDSIKVR-DITECSLCRLCVEECDQRAIS 218
Cdd:TIGR00402  30 SLFSAVCTRCGECASACENNILQLGQQGQPTVEfDNAECDFCGKCAEACPTNAFH 84
 
Name Accession Description Interval E-value
RNAP_D cd07030
D subunit of Archaeal RNA polymerase; The D subunit of archaeal RNA polymerase (RNAP) is ...
 1-260 5.10e-131

D subunit of Archaeal RNA polymerase; The D subunit of archaeal RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The D subunit is equivalent to the RPB3 subunit of eukaryotic RNAP II. It contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization, and the other is an inserted beta sheet subdomain. The assembly of the two largest archaeal RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of the archaeal D/L heterodimer.


Pssm-ID: 132908 [Multi-domain]  Cd Length: 259  Bit Score: 370.83  E-value: 5.10e-131
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116666361   1 MNVELIELRDDRVRFLLTGVTPAFANAIRRSCIAEVPKLAIDEISIYENTSVLFDEQIALRLGLVPIRADDLSVYSTPdE 80
Cdd:cd07030    1 MEIEVLELDDDRARFVLEGVPPAFANAIRRAIISEVPTLAIDDVNIYENTSVLFDEMLAHRLGLIPLRTDLDLYKYRS-E 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116666361  81 CQCGGIGCPGCRIDFMLTAEGPATVHSRDIKFSDPSVRAAFDNIPLVVLGEGEKLVIEGFATLRTGKEHAKWQAGTLCGY 160
Cdd:cd07030   80 CSCGGAGCPLCTVTLTLSVEGPGTVYSGDLKSSDPDVKPVYDNIPIVKLGKGQKLVLEAYARLGRGKEHAKWQPTTACGY 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116666361 161 KNLPSIEISG-CNNCGRCVKVCPRGVLVLDENdSIKVRDITECSLCRLCVEECDQRAISVVPLEDAFIMSIESDGSINAK 239
Cdd:cd07030  160 KYYPVIEIDEdCDGCGKCVEECPRGVLELEEG-KVVVEDLEDCSLCKLCERACDAGAIRVGWDEDRFIFEVESDGSLPPK 238

                        250       260
                 ....*....|....*....|.
gi 116666361 240 DLVRMAAEELKKKALALQDTL 260
Cdd:cd07030  239 EILLEALRILKEKADELIEAL 259
PRK00783 PRK00783
DNA-directed RNA polymerase subunit D; Provisional
 1-264 3.02e-123

DNA-directed RNA polymerase subunit D; Provisional


Pssm-ID: 234837 [Multi-domain]  Cd Length: 263  Bit Score: 351.49  E-value: 3.02e-123
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116666361   1 MNVELIELRDDRVRFLLTGVTPAFANAIRRSCIAEVPKLAIDEISIYENTSVLFDEQIALRLGLVPIRADDLSvYSTPDE 80
Cdd:PRK00783   1 MEIEILELDDRSARFVVEGVTPAFANAIRRAMIADVPTMAIDDVRFYENTSVLFDEILAHRLGLIPLTTDLDK-YKPPEE 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116666361  81 CQCGGIGCPGCRIDFMLTAEGPATVHSRDIKFSDPSVRAAFDNIPLVVLGEGEKLVIEGFATLRTGKEHAKWQAGTLCGY 160
Cdd:PRK00783  80 CTCEGEGCPDCTVTLSLEVEGPKTVYSGDLKSSDPDVKPVDPNIPIVKLKEGQKLVLEAYARLGRGKEHAKWQPGSACGY 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116666361 161 KNLPSIEISG-CNNCGRCVKVCPRGVLVLDENdSIKVRDITECSLCRLCVEECDQRAISVVPLEDAFIMSIESDGSINAK 239
Cdd:PRK00783 160 KYYPRIEVSEdCDECEKCVEACPRGVLELKEG-KLVVTDLLNCSLCKLCERACPGKAIRVSDDENKFIFTVESDGSLPVE 238

                        250       260
                 ....*....|....*....|....*
gi 116666361 240 DLVRMAAEELKKKALALQDTLASIS 264
Cdd:PRK00783 239 EILLEALKILKRKADELIEALEELA 263
RPOLD smart00662
RNA polymerases D; DNA-directed RNA polymerase subunit D and bacterial alpha chain
 13-257 2.12e-61

RNA polymerases D; DNA-directed RNA polymerase subunit D and bacterial alpha chain


Pssm-ID: 214766 [Multi-domain]  Cd Length: 224  Bit Score: 192.83  E-value: 2.12e-61
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116666361    13 VRFLLTGVTPAFANAIRRSCIAEVPKLAIDEISIYENTSVLFDEQIALRLGLVPIRADdlSVYSTPDECQCGGIGCPGCR 92
Cdd:smart00662   1 AKFVLEPYGLTLANALRRVLLSSVPGMAVTSVYIEGNTSGVQDEVLAHRLGLKPLASD--PDGDEYQRDCECEEGCEKCS 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116666361    93 IDFMLTAEGPATVHSRDIKF-SDPSVRAAFDNIPLVVLGEGEKLVIEGFATLRTGKEHAKWQAGTLCGYKNLPSIEISGC 171
Cdd:smart00662  79 VTLTLDVKGPGEVTAGDLKSdSDPDVEIVNPDIPIAKLREGQELELEARAEKGRGYVHAKWSPVSTVEYRYIPRIPVDAS 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116666361   172 NNCGRCVK---VCPRGVLVLDEndsikvrditecslCRLCVEECDqraisvvplEDAFIMSIESDGSINAKDLVRMAAEE 248
Cdd:smart00662 159 FSPVDRVAyqvECPRVVQRTDC--------------CRECDEGEE---------YDKLIFDVETNGSLKPEEAVLEAAKI 215


                   ....*....
gi 116666361   249 LKKKALALQ 257
Cdd:smart00662 216 LKEKLEAFV 224
RNAP_II_RPB3 cd07031
RPB3 subunit of Eukaryotic RNA polymerase II; The eukaryotic RPB3 subunit of RNA polymerase ...
 2-257 4.33e-47

RPB3 subunit of Eukaryotic RNA polymerase II; The eukaryotic RPB3 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP II is responsible for the synthesis of mRNA precursor. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization, and the other is an inserted beta sheet subdomain. The RPB3 subunit heterodimerizes with the RPB11 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.


Pssm-ID: 132909 [Multi-domain]  Cd Length: 265  Bit Score: 157.77  E-value: 4.33e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116666361   2 NVELIELRDDRVRFLLTGVTPAFANAIRRSCIAEVPKLAIDEISIYENTSVLFDEQIALRLGLVPI---RADDLSVYStp 78
Cdd:cd07031    2 RVEITELTDDKVKFILENTDLSVANSLRRVMIAEVPTLAIDLVEIEENTSVLHDEFIAHRLGLIPLtsdDVDEFLYYS-- 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116666361  79 DECQCGGiGCPGCRIDFMLTA----EGPATVHSRDIKFS--------------DPSVRAAFDNIPLVVLGEGEKLVIEGF 140
Cdd:cd07031   80 RDCDCDE-FCDKCSVELTLDVkctgDQTREVTSRDLVSSgpkvndvvpvpirnDSEDNGEEDGILIVKLRKGQELKLRCI 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116666361 141 ATLRTGKEHAKWQAGTLCGYKNLPSIEIsgcnncgrcvkvcprgvlvlDENDSIKVRDITE--CSLCRLCVEEC--DQRA 216
Cdd:cd07031  159 AKKGIGKEHAKWSPTAAVTFEYDPDNAL--------------------RHTDYWYLEDEDKewPKSENACIEEPpeKDAL 218

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|.
gi 116666361 217 ISVVPLEDAFIMSIESDGSINAKDLVRMAAEELKKKALALQ 257
Cdd:cd07031  219 FDIDAKPDKFYFNVESTGALPPEQIVLSGLEILKKKLADLQ 259
RNAP_I_II_AC40 cd07032
AC40 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III; The eukaryotic AC40 subunit ...
 1-258 1.06e-46

AC40 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III; The eukaryotic AC40 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC40 subunit is the equivalent of the RPB3 subunit of RNAP II. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The RPB3 subunit heterodimerizes with the RPB11 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association. The homology of AC40 to RPB3 suggests a similar function. The AC40 subunit is likely to associate with the RPB11 counterpart, AC19, to form a heterodimer, which stabilizes the association of the two largest subunits of RNAP I and RNAP III.


Pssm-ID: 132910 [Multi-domain]  Cd Length: 291  Bit Score: 157.37  E-value: 1.06e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116666361   1 MNVELIELRDDRVRFLLTGVTPAFANAIRRSCIAEVPKLAIDEISIYENTSVLFDEQIALRLGLVPIRAD-DLSVYSTPD 79
Cdd:cd07032    1 FKIEIISLSDEELEFDLIGVDASIANAFRRILLAEVPTMAIEKVYIYNNTSVIQDEVLAHRLGLIPIKADpRLFEYREDS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116666361  80 ECQC---------GGIGCPGCRIDFML-----TAEGPATVHSRDIK----------FSDPSVRAAFDNIPLVVLGEGEKL 135
Cdd:cd07032   81 DDEPteentlvfeLKVKCTRNPNAPKDstdpdELYINHKVYSGDLKwvpigsqekrFADNPIRPVHPDILIAKLRPGQEI 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116666361 136 VIEGFATLRTGKEHAKWQAGTLCGYKNLPSIEISG---CNNCGRCVKVCPRGVLVLDEND---SIKVRDITECSLCR--L 207
Cdd:cd07032  161 DLELHCVKGIGKDHAKFSPVATASYRLLPEITLLKpitGEDAEKLQKCFPPGVIDIEEVKgkkKAVVANPRKDTLSRevL 240

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|.
gi 116666361 208 CVEEcDQRAISVVPLEDAFIMSIESDGSINAKDLVRMAAEELKKKALALQD 258
Cdd:cd07032  241 RHEE-FKDKVELGRVRDHFIFSIESTGALPPDVLFLEAIKILKEKCRKLLE 290
RNAP_RPB3_like cd07028
RPB3 subunit of RNA polymerase; The eukaryotic RPB3 subunit of RNA polymerase (RNAP), as well ...
 1-164 5.65e-34

RPB3 subunit of RNA polymerase; The eukaryotic RPB3 subunit of RNA polymerase (RNAP), as well as its archaeal (D subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar to the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the archaeal (D/L subunits) and bacterial (alpha subunit) counterparts.


Pssm-ID: 132906 [Multi-domain]  Cd Length: 212  Bit Score: 122.29  E-value: 5.65e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116666361   1 MNVELIELRDDRVRFLLTGVTPAFANAIRRSCIAEVPKLAIDEISIYENTSVLFDEQIALRLGLVPIRADD-LSVYSTPD 79
Cdd:cd07028    1 PQVKIREADKDNVDFILSGVDLAMANALRRVMIAEVPTMAVDSVEVETNTSVLADEILAHRLGLIPLQSMDiLQLYRSPE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116666361  80 ECQCGGIGCPGCRIDFMLTAEGPAT----VHSRDIKFSD-----PSVRAAFDNIPLVVLGEGEKLVIEGFATLRTGKEHA 150
Cdd:cd07028   81 EDCECEDHCDKCSVVLTLQAFAESEsttnVYSKDLVIVSnlmgrNIGHPIIQDILICKLRKGQEIKLTCVAKKGIGKEHA 160

                        170
                 ....*....|....
gi 116666361 151 KWQAGTLCGYKNLP 164
Cdd:cd07028  161 KFGPVAAIEFRYDP 174
RNA_pol_L pfam01193
RNA polymerase Rpb3/Rpb11 dimerization domain; The two eukaryotic subunits Rpb3 and Rpb11 ...
 15-252 1.26e-32

RNA polymerase Rpb3/Rpb11 dimerization domain; The two eukaryotic subunits Rpb3 and Rpb11 dimerize to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerization domain of the alpha subunit/Rpb3 is interrupted by an insert domain (pfam01000). Some of the alpha subunits also contain iron-sulphur binding domains (pfam00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp.


Pssm-ID: 460104 [Multi-domain]  Cd Length: 191  Bit Score: 117.89  E-value: 1.26e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116666361   15 FLLTGVTPAFANAIRRSCIAEVPKLAIDEISIYENTSVLFDEQIALRLGLVPIRADD-LSVYSTPDECQCGGIgcpgcri 93
Cdd:pfam01193   1 FLLRGEDHTLGNALRRILLSEVPGVAIDAVKIEGNTSEFSDEPGAHRLGLIPLLNLKeLFFKLSSDDDETLEL------- 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116666361   94 dfmlTAEGPATVHSRDIKFSDPSVRAAFDNIPLVVLGEGEKLVIEGFATLRTGKEHakwqagtlcgyknlpsieisgcnn 173
Cdd:pfam01193  74 ----DKEGPGEVTAGDINTDSDVEVIEIINPDLHIATLEEEAALEMELEVVKGRGY------------------------ 125

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 116666361  174 cgrcvkvcprgvlVLDENDSIKVRDITECSLCRLCVEECDQRAISVVPLEDAFIMSIESDGSINAKDLVRMAAEELKKK 252
Cdd:pfam01193 126 -------------VPAEKNKDVDDPIGDIPIDSIFSPVEKVNYVVENTDYDKLIFEVETDGSIPPEEALKEAAKILKEK 191
PRK14979 PRK14979
DNA-directed RNA polymerase subunit D; Provisional
 23-153 3.14e-32

DNA-directed RNA polymerase subunit D; Provisional


Pssm-ID: 237878 [Multi-domain]  Cd Length: 195  Bit Score: 117.25  E-value: 3.14e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116666361  23 AFANAIRRSCIAEVPKLAIDEISIYENTSVLFDEQIALRLGLVPIRADDLSvystPDECqcggigcpgcrIDFMLTAEGP 102
Cdd:PRK14979  25 SFSSALRRIMISEVPTYAIENVYFYENSSSMYDEILAHRLGLIPIKGKPVS----GDEV-----------ITFTLSKEGP 89

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 116666361 103 ATVHSRDIKFSDPSVraAFDNIPLVVLGEGEKLVIEGFATLRTGKEHAKWQ 153
Cdd:PRK14979  90 CTVYSSDLKSENGEV--AFKNIPIVKLAEGQKLEIECEALVGTGKIHAKWQ 138
RNA_pol_A_bac pfam01000
RNA polymerase Rpb3/RpoA insert domain; Members of this family include: alpha subunit from ...
 58-151 4.94e-13

RNA polymerase Rpb3/RpoA insert domain; Members of this family include: alpha subunit from eubacteria alpha subunits from chloroplasts Rpb3 subunits from eukaryotes RpoD subunits from archaeal


Pssm-ID: 425983  Cd Length: 117  Bit Score: 63.81  E-value: 4.94e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116666361   58 IALRLGLVPI-RADDLSVYSTPDECQCGGIGCPGCRIDFMLTAEGPATVHSRDIKfSDPSVRAAFDNIPLVVLGEGEKLV 136
Cdd:pfam01000   6 VAHEFGLIPGvSEDVLEIILNLKELVCKEEGCEECSVTLTLDVKGPGEVTAGDLE-SDPDVEIVNPDILIATLRKGQELE 84

                          90
                  ....*....|....*
gi 116666361  137 IEGFATLRTGKEHAK 151
Cdd:pfam01000  85 LEAYAKKGRGYVHAK 99
PreA COG1146
NAD-dependent dihydropyrimidine dehydrogenase, PreA subunit [Nucleotide transport and ...
 164-225 1.75e-10

NAD-dependent dihydropyrimidine dehydrogenase, PreA subunit [Nucleotide transport and metabolism];


Pssm-ID: 440761 [Multi-domain]  Cd Length: 67  Bit Score: 55.49  E-value: 1.75e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 116666361 164 PSIEISGCNNCGRCVKVCPRGVLVLDENDS-IKVRDITECSLCRLCVEECDQRAISVVPLEDA 225
Cdd:COG1146    3 PVIDTDKCIGCGACVEVCPVDVLELDEEGKkALVINPEECIGCGACELVCPVGAITVEDDEPE 65
COG1149 COG1149
MinD superfamily P-loop ATPase, contains an inserted ferredoxin domain [General function ...
 164-221 2.42e-10

MinD superfamily P-loop ATPase, contains an inserted ferredoxin domain [General function prediction only];


Pssm-ID: 440763 [Multi-domain]  Cd Length: 68  Bit Score: 55.12  E-value: 2.42e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 116666361 164 PSIEISGCNNCGRCVKVCPRGVLVLDENDSIKVRDiTECSLCRLCVEECDQRAISVVP 221
Cdd:COG1149    6 PVIDEEKCIGCGLCVEVCPEGAIKLDDGGAPVVDP-DLCTGCGACVGVCPTGAITLEE 62
NapF COG1145
Ferredoxin [Energy production and conversion];
1-223 1.00e-08

Ferredoxin [Energy production and conversion];


Pssm-ID: 440760 [Multi-domain]  Cd Length: 238  Bit Score: 54.34  E-value: 1.00e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116666361   1 MNVELIELRDDRVRFLLTGVTPAFANAIRRSCIAEVPKLAIDEISIYENTSVLFDEQIALRLGLVPIRADDLSVYSTPDE 80
Cdd:COG1145   19 YAVVTGILGKIILNVIAGALLKAVALGGLLPIIGILAKEAFDALKDVLGILGAIVIGIGAGEIVRVGIAAADLNLKAVAL 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116666361  81 CQCGGIGCPGCRIDFMLTAEGPATVHSRDIKFSDPSVRAAFDNIPLVVLGEGEKLVIEGFATLRTGKEHAKWQAgtlcgY 160
Cdd:COG1145   99 VLLLALAVAGAAKRLIISAVKLVAGLVVAAGEVLLVIAAALAEAGLAILGAAAPVDALAISGGKKIEEELKIAI-----K 173

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 116666361 161 KNLPSIEISGCNNCGRCVKVCPRGVLVLDENDSIKVRDITECSLCRLCVEECDQRAISVVPLE 223
Cdd:COG1145  174 KAKAVIDAEKCIGCGLCVKVCPTGAIRLKDGKPQIVVDPDKCIGCGACVKVCPVGAISLEPKE 236
COG2768 COG2768
Uncharacterized Fe-S cluster protein [Function unknown];
164-228 3.79e-08

Uncharacterized Fe-S cluster protein [Function unknown];


Pssm-ID: 442050 [Multi-domain]  Cd Length: 74  Bit Score: 49.34  E-value: 3.79e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 116666361 164 PSIEISGCNNCGRCVKVCPRGVLVLDENdsIKVRDITECSLCRLCVEECDQRAISVVPLEDAFIM 228
Cdd:COG2768    6 PYVDEEKCIGCGACVKVCPVGAISIEDG--KAVIDPEKCIGCGACIEVCPVGAIKIEWEEDEEFQ 68
PorD COG1144
Pyruvate:ferredoxin oxidoreductase or related 2-oxoacid:ferredoxin oxidoreductase, delta ...
 164-224 1.17e-07

Pyruvate:ferredoxin oxidoreductase or related 2-oxoacid:ferredoxin oxidoreductase, delta subunit [Energy production and conversion]; Pyruvate:ferredoxin oxidoreductase or related 2-oxoacid:ferredoxin oxidoreductase, delta subunit is part of the Pathway/BioSystem: Pyruvate oxidation


Pssm-ID: 440759 [Multi-domain]  Cd Length: 84  Bit Score: 48.12  E-value: 1.17e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 116666361 164 PSIEISGCNNCGRCVKVCPRGVLVLDENDSIKVrDITECSLCRLCVEECDQRAISVVPLED 224
Cdd:COG1144   25 PVVDEDKCIGCGLCWIVCPDGAIRVDDGKYYGI-DYDYCKGCGICAEVCPVKAIEMVPEEK 84
DsrA COG2221
Dissimilatory sulfite reductase (desulfoviridin), alpha and beta subunits [Inorganic ion ...
 164-219 1.40e-07

Dissimilatory sulfite reductase (desulfoviridin), alpha and beta subunits [Inorganic ion transport and metabolism];


Pssm-ID: 441823 [Multi-domain]  Cd Length: 69  Bit Score: 47.74  E-value: 1.40e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 116666361 164 PSIEISGCNNCGRCVKVCPRGVLVLDeNDSIKVrDITECSLCRLCVEECDQRAISV 219
Cdd:COG2221   10 PKIDEEKCIGCGLCVAVCPTGAISLD-DGKLVI-DEEKCIGCGACIRVCPTGAIKG 63
NuoI COG1143
Formate hydrogenlyase subunit 6/NADH:ubiquinone oxidoreductase 23 kD subunit (chain I) [Energy ...
 171-225 2.48e-07

Formate hydrogenlyase subunit 6/NADH:ubiquinone oxidoreductase 23 kD subunit (chain I) [Energy production and conversion]; Formate hydrogenlyase subunit 6/NADH:ubiquinone oxidoreductase 23 kD subunit (chain I) is part of the Pathway/BioSystem: NADH dehydrogenase


Pssm-ID: 440758 [Multi-domain]  Cd Length: 66  Bit Score: 47.05  E-value: 2.48e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 116666361 171 CNNCGRCVKVCPRGVLVLDENDSIKVRDITE--CSLCRLCVEECDQRAISVVPLEDA 225
Cdd:COG1143    4 CIGCGLCVRVCPVDAITIEDGEPGKVYVIDPdkCIGCGLCVEVCPTGAISMTPFELA 60
MtMvhB_like cd10549
Uncharacterized polyferredoxin-like protein; This family contains uncharacterized ...
 166-220 5.64e-07

Uncharacterized polyferredoxin-like protein; This family contains uncharacterized polyferredoxin protein similar to Methanobacterium thermoautotrophicum MvhB. The mvhB is a gene of the methylviologen-reducing hydrogenase operon. It is predicted to contain 12 [4Fe-4S] clusters, and was therefore suggested to be a polyferredoxin. As a subfamily of the beta subunit of the DMSO Reductase (DMSOR) family, it is predicted to function as electron carrier in the reducing reaction.


Pssm-ID: 319871 [Multi-domain]  Cd Length: 128  Bit Score: 47.39  E-value: 5.64e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 116666361 166 IEISGCNNCGRCVKVCPRGVLVLDENDSIKVrDITECSLCRLCVEECDQRAISVV 220
Cdd:cd10549   75 IDEEKCIGCGLCVKVCPVDAITLEDELEIVI-DKEKCIGCGICAEVCPVNAIKLV 128
NapH COG0348
Polyferredoxin NapH [Energy production and conversion];
171-218 1.19e-06

Polyferredoxin NapH [Energy production and conversion];


Pssm-ID: 440117 [Multi-domain]  Cd Length: 263  Bit Score: 48.52  E-value: 1.19e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 116666361 171 CNNCGRCVKVCPRGvlvldendsIKVRDIT----ECSLCRLCVEECDQRAIS 218
Cdd:COG0348  212 CIDCGLCVKVCPMG---------IDIRKGEinqsECINCGRCIDACPKDAIR 254
HdrA COG1148
Heterodisulfide reductase, subunit A (polyferredoxin) [Energy production and conversion];
164-229 1.22e-06

Heterodisulfide reductase, subunit A (polyferredoxin) [Energy production and conversion];


Pssm-ID: 440762 [Multi-domain]  Cd Length: 563  Bit Score: 49.09  E-value: 1.22e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 116666361 164 PSIEISGCNNCGRCVKVCPRGVLVLDENDSIKVrDITECSLCRLCVEECDQRAISVVPLEDAFIMS 229
Cdd:COG1148  491 AEVDPEKCTGCGRCVEVCPYGAISIDEKGVAEV-NPALCKGCGTCAAACPSGAISLKGFTDDQILA 555
IorA COG4231
TPP-dependent indolepyruvate ferredoxin oxidoreductase, alpha subunit [Energy production and ...
 171-220 1.23e-06

TPP-dependent indolepyruvate ferredoxin oxidoreductase, alpha subunit [Energy production and conversion];


Pssm-ID: 443375 [Multi-domain]  Cd Length: 76  Bit Score: 45.03  E-value: 1.23e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 116666361 171 CNNCGRCVKVCPRGVLVLDENdsiKVR-DITECSLCRLCVEECDQRAISVV 220
Cdd:COG4231   24 CTGCGACVKVCPADAIEEGDG---KAViDPDLCIGCGSCVQVCPVDAIKLE 71
napF TIGR00402
ferredoxin-type protein NapF; The gene codes for a ferredoxin-type cytosolic protein, NapF, of ...
 165-218 1.81e-06

ferredoxin-type protein NapF; The gene codes for a ferredoxin-type cytosolic protein, NapF, of the periplasmic nitrate reductase system, as in Escherichia coli. NapF interacts with the catalytic subunit, NapA, and may be an accessory protein for NapA maturation. [Energy metabolism, Electron transport]


Pssm-ID: 273060 [Multi-domain]  Cd Length: 101  Bit Score: 45.32  E-value: 1.81e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 116666361  165 SIEISGCNNCGRCVKVCPRGVLVLDENDSIKVR-DITECSLCRLCVEECDQRAIS 218
Cdd:TIGR00402  30 SLFSAVCTRCGECASACENNILQLGQQGQPTVEfDNAECDFCGKCAEACPTNAFH 84
Fer4_7 pfam12838
4Fe-4S dicluster domain; Superfamily includes proteins containing domains which bind to ...
 171-212 2.89e-06

4Fe-4S dicluster domain; Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contains two 4Fe4S clusters.


Pssm-ID: 463724 [Multi-domain]  Cd Length: 51  Bit Score: 43.67  E-value: 2.89e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 116666361  171 CNNCGRCVKVCPRGVLVLDENDSIKVRDITE-----CSLCRLCVEEC 212
Cdd:pfam12838   1 CIGCGACVAACPVGAITLDEVGEKKGTKTVVidperCVGCGACVAVC 47
MtMvhB_like cd10549
Uncharacterized polyferredoxin-like protein; This family contains uncharacterized ...
 164-220 4.56e-06

Uncharacterized polyferredoxin-like protein; This family contains uncharacterized polyferredoxin protein similar to Methanobacterium thermoautotrophicum MvhB. The mvhB is a gene of the methylviologen-reducing hydrogenase operon. It is predicted to contain 12 [4Fe-4S] clusters, and was therefore suggested to be a polyferredoxin. As a subfamily of the beta subunit of the DMSO Reductase (DMSOR) family, it is predicted to function as electron carrier in the reducing reaction.


Pssm-ID: 319871 [Multi-domain]  Cd Length: 128  Bit Score: 45.08  E-value: 4.56e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 116666361 164 PSIEISGCNNCGRCVKVCPRGVLVLDENDSIKVRDITE-------CSLCRLCVEECDQRAISVV 220
Cdd:cd10549   35 PEIDEDKCVFCGACVEVCPTGAIELTPEGKEYVPKEKEaeideekCIGCGLCVKVCPVDAITLE 98
DMSOR_beta_like cd10550
uncharacterized subfamily of DMSO Reductase beta subunit family; This family consists of the ...
 166-221 9.40e-06

uncharacterized subfamily of DMSO Reductase beta subunit family; This family consists of the small beta iron-sulfur (FeS) subunit of the DMSO Reductase (DMSOR) family. Members of this family also contain a large, periplasmic molybdenum-containing alpha subunit and may have a small gamma subunit as well. Examples of heterodimeric members with alpha and beta subunits include arsenite oxidase, and tungsten-containing formate dehydrogenase (FDH-T) while heterotrimeric members containing alpha, beta, and gamma subunits include formate dehydrogenase-N (FDH-N), and nitrate reductase (NarGHI). The beta subunit contains four Fe4/S4 and/or Fe3/S4 clusters which transfer the electrons from the alpha subunit to a hydrophobic integral membrane protein, presumably a cytochrome containing two b-type heme groups. The reducing equivalents are then transferred to menaquinone, which finally reduces the electron-accepting enzyme system.


Pssm-ID: 319872 [Multi-domain]  Cd Length: 130  Bit Score: 44.10  E-value: 9.40e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 116666361 166 IEISGCNNCGR--CVKVCPRGVLVLDENDSIKVRDITECSLCRLCVEECDQRAISVVP 221
Cdd:cd10550   44 DVPVVCRQCEDapCVEACPVGAISRDEETGAVVVDEDKCIGCGMCVEACPFGAIRVDP 101
PRK07118 PRK07118
Fe-S cluster domain-containing protein;
170-217 1.24e-05

Fe-S cluster domain-containing protein;


Pssm-ID: 235941 [Multi-domain]  Cd Length: 280  Bit Score: 45.31  E-value: 1.24e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 116666361 170 GCNNCGRCVKVCPRGVLVLDENdsIKVRDITECSLCRLCVEECDQRAI 217
Cdd:PRK07118 214 GCIGCGKCVKACPAGAITMENN--LAVIDQEKCTSCGKCVEKCPTKAI 259
MtMvhB_like cd10549
Uncharacterized polyferredoxin-like protein; This family contains uncharacterized ...
 170-221 1.28e-05

Uncharacterized polyferredoxin-like protein; This family contains uncharacterized polyferredoxin protein similar to Methanobacterium thermoautotrophicum MvhB. The mvhB is a gene of the methylviologen-reducing hydrogenase operon. It is predicted to contain 12 [4Fe-4S] clusters, and was therefore suggested to be a polyferredoxin. As a subfamily of the beta subunit of the DMSO Reductase (DMSOR) family, it is predicted to function as electron carrier in the reducing reaction.


Pssm-ID: 319871 [Multi-domain]  Cd Length: 128  Bit Score: 43.54  E-value: 1.28e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 116666361 170 GCNNCGRCVKVCPRGVLVLDENDSIKVR---DITECSLCRLCVEECDQRAISVVP 221
Cdd:cd10549    7 KCIGCGICVKACPTDAIELGPNGAIARGpeiDEDKCVFCGACVEVCPTGAIELTP 61
NapF_like cd10564
NapF, iron-sulfur subunit of periplasmic nitrate reductase; This family contains NapF protein, ...
 163-221 2.02e-05

NapF, iron-sulfur subunit of periplasmic nitrate reductase; This family contains NapF protein, the iron-sulfur subunit of periplasmic nitrate reductase. The periplasmic nitrate reductase NapABC of Escherichia coli likely functions during anaerobic growth in low-nitrate environments; napF operon expression is activated by cyclic AMP receptor protein (Crp). NapF is a subfamily of the beta subunit of DMSO reductase (DMSOR) family. DMSOR family members have a large, periplasmic molybdenum-containing alpha subunit as well as a small beta FeS subunit, and may also have a small gamma subunit. The beta subunit contains four Fe4/S4 and/or Fe3/S4 clusters which transfer the electrons from the alpha subunit to a hydrophobic integral membrane protein, presumably a cytochrome containing two b-type heme groups. The reducing equivalents are then transferred to menaquinone, which finally reduces the electron-accepting enzyme system.


Pssm-ID: 319886 [Multi-domain]  Cd Length: 139  Bit Score: 43.39  E-value: 2.02e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 116666361 163 LPSIEIS--GCNNCGRCVKVCPRGVLVLDENDSIKVR-DITE-C-----SLCRLCVEECDQRAISVVP 221
Cdd:cd10564   37 FPELDFSrgECTFCGACAEACPEGALDPAREAPWPLRaEIGDsClalqgVECRSCQDACPTQAIRFRP 104
NapF_like cd10564
NapF, iron-sulfur subunit of periplasmic nitrate reductase; This family contains NapF protein, ...
 168-218 2.31e-05

NapF, iron-sulfur subunit of periplasmic nitrate reductase; This family contains NapF protein, the iron-sulfur subunit of periplasmic nitrate reductase. The periplasmic nitrate reductase NapABC of Escherichia coli likely functions during anaerobic growth in low-nitrate environments; napF operon expression is activated by cyclic AMP receptor protein (Crp). NapF is a subfamily of the beta subunit of DMSO reductase (DMSOR) family. DMSOR family members have a large, periplasmic molybdenum-containing alpha subunit as well as a small beta FeS subunit, and may also have a small gamma subunit. The beta subunit contains four Fe4/S4 and/or Fe3/S4 clusters which transfer the electrons from the alpha subunit to a hydrophobic integral membrane protein, presumably a cytochrome containing two b-type heme groups. The reducing equivalents are then transferred to menaquinone, which finally reduces the electron-accepting enzyme system.


Pssm-ID: 319886 [Multi-domain]  Cd Length: 139  Bit Score: 43.00  E-value: 2.31e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 116666361 168 ISGCNNCGRCVKVCPRGVLVLDENDSIKVR-DITECSLCRLCVEECDQRAIS 218
Cdd:cd10564   12 LDLCTRCGDCVEACPEGIIVRGDGGFPELDfSRGECTFCGACAEACPEGALD 63
PRK07118 PRK07118
Fe-S cluster domain-containing protein;
163-220 4.04e-05

Fe-S cluster domain-containing protein;


Pssm-ID: 235941 [Multi-domain]  Cd Length: 280  Bit Score: 43.77  E-value: 4.04e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 116666361 163 LPSIEISGCNNCGRCVKVCPRGVLVLDENDSI------------KVRDITE--CSLCRLCVEECDQRAISVV 220
Cdd:PRK07118 162 LPVVDEDKCTGCGACVKACPRNVIELIPKSARvfvacnskdkgkAVKKVCEvgCIGCGKCVKACPAGAITME 233
Fer4_9 pfam13187
4Fe-4S dicluster domain;
171-217 4.83e-05

4Fe-4S dicluster domain;


Pssm-ID: 463801 [Multi-domain]  Cd Length: 50  Bit Score: 39.84  E-value: 4.83e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 116666361  171 CNNCGRCVKVCPRGVLVLDENDSIKVRDITE--CSLCRLCVEECDQRAI 217
Cdd:pfam13187   2 CTGCGACVAACPAGAIVPDLVGQTIRGDIAGlaCIGCGACVDACPRGAI 50
Nar1 COG4624
Iron only hydrogenase large subunit, C-terminal domain [Energy production and conversion];
171-220 7.38e-05

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


Pssm-ID: 443663 [Multi-domain]  Cd Length: 450  Bit Score: 43.48  E-value: 7.38e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 116666361 171 CNNCGRCVKVCPrgVLVLDENDSIKVRDITECSLCRLCVEECDQRAISVV 220
Cdd:COG4624   93 CKNCYPCVRACP--VKAIKVDDGKAEIDEEKCISCGQCVAVCPFGAITEK 140
NarH_like cd16365
beta FeS subunits DMSOR NarH-like family; This subfamily contains beta FeS subunits of several ...
 142-217 1.09e-04

beta FeS subunits DMSOR NarH-like family; This subfamily contains beta FeS subunits of several DMSO reductase superfamily, including nitrate reductase A, ethylbenzene dehydrogenase and selenate reductase. DMSO Reductase (DMSOR) family members have a large, periplasmic molybdenum-containing alpha subunit as well as a small beta FeS subunit, and may also have a small gamma subunit. . The beta subunits of DMSOR contains four Fe4/S4 and/or Fe3/S4 clusters which transfer the electrons from the alpha subunit to a hydrophobic integral membrane protein, presumably a cytochrome containing two b-type heme groups. The reducing equivalents are then transferred to menaquinone, which finally reduces the electron-accepting enzyme system. Nitrate reductase A contains three subunits (the catalytic subunit NarG, the catalytic subunit NarH with four [Fe-S] clusters, and integral membrane subunit NarI) and often forms a respiratory chain with the formate dehydrogenase via the lipid soluble quinol pool. Ethylbenzene dehydrogenase oxidizes the hydrocarbon ethylbenzene to (S)-1-phenylethanol. Selenate reductase catalyzes reduction of selenate to selenite in bacterial species that can obtain energy by respiring anaerobically with selenate as the terminal electron acceptor.


Pssm-ID: 319887 [Multi-domain]  Cd Length: 201  Bit Score: 42.18  E-value: 1.09e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116666361 142 TLRTGKEHAKWQAGTLCGYKNLPS----IEISG-------------CNNCGR--CVKVCPRGVLVLDENDSIKVRDITEC 202
Cdd:cd16365   27 TYRKGQEYMWWNNVETKPGGGYPQdwevKTIDNggntrfffylqrlCNHCTNpaCLAACPRGAIYKREEDGIVLIDQKRC 106

                         90
                 ....*....|....*
gi 116666361 203 SLCRLCVEECDQRAI 217
Cdd:cd16365  107 RGYRKCVEQCPYKKI 121
Fer4_10 pfam13237
4Fe-4S dicluster domain; This family includes proteins containing domains which bind to ...
 163-212 1.19e-04

4Fe-4S dicluster domain; This family includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. The structure of the domain is an alpha-antiparallel beta sandwich.


Pssm-ID: 404174 [Multi-domain]  Cd Length: 56  Bit Score: 39.16  E-value: 1.19e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 116666361  163 LPSIEISGCNNCGRCVKVCP-----RGVLVLDENDSIKVRDITECSLCRLCVEEC 212
Cdd:pfam13237   1 KVVIDPDKCIGCGRCTAACPagltrVGAIVERLEGEAVRIGVWKCIGCGACVEAC 55
HycB COG1142
Fe-S-cluster-containing hydrogenase component 2 [Energy production and conversion];
171-220 1.56e-04

Fe-S-cluster-containing hydrogenase component 2 [Energy production and conversion];


Pssm-ID: 440757 [Multi-domain]  Cd Length: 138  Bit Score: 40.80  E-value: 1.56e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 116666361 171 CNNCGRCVKVCPRGVLVLDENDSIKVrdITECSLCR------LCVEECDQRAISVV 220
Cdd:COG1142   83 CIGCGLCVLACPFGAITMVGEKSRAV--AVKCDLCGgreggpACVEACPTGALRLV 136
PRK13795 PRK13795
hypothetical protein; Provisional
 122-212 2.16e-04

hypothetical protein; Provisional


Pssm-ID: 237510 [Multi-domain]  Cd Length: 636  Bit Score: 42.29  E-value: 2.16e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116666361 122 DNIPLVVLGEGEKLVIEGFATLRTGKEHAKWQAGTLCGYKNLpsIEISGCNNCGRCVKVCPRGVLVLDENDSIKVRDITE 201
Cdd:PRK13795 536 EELGMVLTKKGTVKVFASGNIWARSEDKEAAASLFKDAARLL--RRAAECVGCGVCVGACPTGAIRIEEGKRKISVDEEK 613

                         90
                 ....*....|.
gi 116666361 202 CSLCRLCVEEC 212
Cdd:PRK13795 614 CIHCGKCTEVC 624
RnfB COG2878
Na+-translocating ferredoxin:NAD+ oxidoreductase RNF, RnfB subunit [Energy production and ...
 170-223 2.80e-04

Na+-translocating ferredoxin:NAD+ oxidoreductase RNF, RnfB subunit [Energy production and conversion]; Na+-translocating ferredoxin:NAD+ oxidoreductase RNF, RnfB subunit is part of the Pathway/BioSystem: Na+-translocating Fd:NADH oxidoreductase


Pssm-ID: 442125 [Multi-domain]  Cd Length: 254  Bit Score: 41.13  E-value: 2.80e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 116666361 170 GCNNCGRCVKVCPRGVLVLDENDSIKVrDITECSLCRLCVEECDQRAISVVPLE 223
Cdd:COG2878  138 GCIGCGDCIKACPFDAIVGAAKGMHTV-DEDKCTGCGLCVEACPVDCIEMVPVS 190
PRK08348 PRK08348
NADH-plastoquinone oxidoreductase subunit; Provisional
 171-221 8.08e-04

NADH-plastoquinone oxidoreductase subunit; Provisional


Pssm-ID: 181399 [Multi-domain]  Cd Length: 120  Bit Score: 38.28  E-value: 8.08e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 116666361 171 CNNCGRCVKVCPRGVLV-LDENDSIKVRdITECSLCRLCVEECDQRAISVVP 221
Cdd:PRK08348  44 CVGCRMCVTVCPAGVFVyLPEIRKVALW-TGRCVFCGQCVDVCPTGALQMSD 94
porD PRK09624
pyruvate ferredoxin oxidoreductase subunit delta; Reviewed
 163-220 8.40e-04

pyruvate ferredoxin oxidoreductase subunit delta; Reviewed


Pssm-ID: 170017 [Multi-domain]  Cd Length: 105  Bit Score: 38.09  E-value: 8.40e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 116666361 163 LPSIEISGCNNCGRCVKVCPRGVLVLDEnDSIKVRDITECSLCRLCVEECDQRAISVV 220
Cdd:PRK09624  45 MPEFNRDKCVRCYLCYIYCPEPAIYLDE-EGYPVFDYDYCKGCGICANECPTKAIEMV 101
GlpC COG0247
Fe-S cluster-containing oxidoreductase, includes glycolate oxidase subunit GlcF [Energy ...
 171-212 1.25e-03

Fe-S cluster-containing oxidoreductase, includes glycolate oxidase subunit GlcF [Energy production and conversion];


Pssm-ID: 440017 [Multi-domain]  Cd Length: 420  Bit Score: 39.68  E-value: 1.25e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 116666361 171 CNNCGRCVKVCPRGVLVLDENDSIKVR--------------DITE--------CSLCRLCVEEC 212
Cdd:COG0247   80 CVGCGFCRAMCPSYKATGDEKDSPRGRinllrevlegelplDLSEevyevldlCLTCKACETAC 143
Fer4_18 pfam13746
4Fe-4S dicluster domain; This family includes proteins containing domains which bind to ...
 171-214 2.12e-03

4Fe-4S dicluster domain; This family includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. The structure of the domain is an alpha-antiparallel beta sandwich.


Pssm-ID: 404610 [Multi-domain]  Cd Length: 114  Bit Score: 36.99  E-value: 2.12e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 116666361  171 CNNCGRCVKVCPRGVlvlDENDSIKVrditECSLCRLCVEECDQ 214
Cdd:pfam13746  61 CIDCESCVQVCPTGI---DIRKGLQL----ECINCGLCIDACNT 97
PRK08318 PRK08318
NAD-dependent dihydropyrimidine dehydrogenase subunit PreA;
160-223 2.86e-03

NAD-dependent dihydropyrimidine dehydrogenase subunit PreA;


Pssm-ID: 236237 [Multi-domain]  Cd Length: 420  Bit Score: 38.77  E-value: 2.86e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116666361 160 YKNLPSIEISGCNNCGRCVKVCPRG-----VLVLDENDSIKVRDiTECSLCRLCVEECD-QRAISVVPLE 223
Cdd:PRK08318 333 YIVYARIDQDKCIGCGRCYIACEDTshqaiEWDEDGTRTPEVIE-EECVGCNLCAHVCPvEGCITMGEVK 401
PRK13984 PRK13984
putative oxidoreductase; Provisional
 171-244 3.83e-03

putative oxidoreductase; Provisional


Pssm-ID: 172486 [Multi-domain]  Cd Length: 604  Bit Score: 38.21  E-value: 3.83e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116666361 171 CNNCGRCVKVCPRGVLVLDENDSIK----------VRDITECSLCRLCVEEC-------DQRAISVVPLEDAFIMSIESD 233
Cdd:PRK13984  47 CIGCGTCSKICPTDAITMVEVPDLPqeygkkpqrpVIDYGRCSFCALCVDICttgslkmTREYIHISPDPEDFIFMPTEK 126

                         90
                 ....*....|.
gi 116666361 234 GsINAKDLVRM 244
Cdd:PRK13984 127 G-INAKEPDNA 136
Fer4_17 pfam13534
4Fe-4S dicluster domain; This family includes proteins containing domains which bind to ...
 171-212 4.00e-03

4Fe-4S dicluster domain; This family includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. The structure of the domain is an alpha-antiparallel beta sandwich.


Pssm-ID: 433287 [Multi-domain]  Cd Length: 61  Bit Score: 34.74  E-value: 4.00e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 116666361  171 CNNCGRCVKVCPRGVLVLDENDSI-------------KVRDITECSLCRLCVEEC 212
Cdd:pfam13534   2 CIQCGCCVDECPRYLLNGDEPKKLmraaylgdleelqANKVANLCSECGLCEYAC 56
DMSOR_beta_like cd16371
uncharacterized subfamily of DMSO Reductase beta subunit family; This family consists of the ...
 171-219 4.48e-03

uncharacterized subfamily of DMSO Reductase beta subunit family; This family consists of the small beta iron-sulfur (FeS) subunit of the DMSO Reductase (DMSOR) family. Members of this family also contain a large, periplasmic molybdenum-containing alpha subunit and may have a small gamma subunit as well. Examples of heterodimeric members with alpha and beta subunits include arsenite oxidase, and tungsten-containing formate dehydrogenase (FDH-T) while heterotrimeric members containing alpha, beta, and gamma subunits include formate dehydrogenase-N (FDH-N), and nitrate reductase (NarGHI). The beta subunit contains four Fe4/S4 and/or Fe3/S4 clusters which transfer the electrons from the alpha subunit to a hydrophobic integral membrane protein, presumably a cytochrome containing two b-type heme groups. The reducing equivalents are then transferred to menaquinone, which finally reduces the electron-accepting enzyme system.


Pssm-ID: 319893 [Multi-domain]  Cd Length: 140  Bit Score: 36.39  E-value: 4.48e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 116666361 171 CNNCGRCVKVCPRGVLVLDENDSIkvrdITECSLC--RL-------CVEECDQRAISV 219
Cdd:cd16371   86 CIGCGYCVWACPYGAPQYNPETGK----MDKCDMCvdRLdegekpaCVAACPTRALDF 139
oorD PRK09626
2-oxoglutarate-acceptor oxidoreductase subunit OorD; Reviewed
 169-219 5.30e-03

2-oxoglutarate-acceptor oxidoreductase subunit OorD; Reviewed


Pssm-ID: 236597 [Multi-domain]  Cd Length: 103  Bit Score: 35.47  E-value: 5.30e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 116666361 169 SGCNNCGRCVKVCPRGVL--VLDENDS----IKVRDITECSLCRLCVEECDQRAISV 219
Cdd:PRK09626  16 SRCKACDICVSVCPAGVLamRIDPHAVlgkmIKVVHPESCIGCRECELHCPDFAIYV 72
Fer4_8 pfam13183
4Fe-4S dicluster domain; Superfamily includes proteins containing domains which bind to ...
 171-212 5.79e-03

4Fe-4S dicluster domain; Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contains two 4Fe4S clusters.


Pssm-ID: 433017 [Multi-domain]  Cd Length: 64  Bit Score: 34.59  E-value: 5.79e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 116666361  171 CNNCGRCVKVCPRgVLVLDENDSIKVRD------------------ITECSLCRLCVEEC 212
Cdd:pfam13183   2 CIRCGACLAACPV-YLVTGGRFPGDPRGgaaallgrlealeglaegLWLCTLCGACTEVC 60
SIMIBI_bact_arch cd03110
bacterial and archaeal subfamily of SIMIBI; Uncharacterized bacterial and archaeal subfamily ...
 163-258 5.83e-03

bacterial and archaeal subfamily of SIMIBI; Uncharacterized bacterial and archaeal subfamily of SIMIBI superfamily. Proteins in this superfamily contain an ATP-binding domain and use energy from hydrolysis of ATP to transfer electron or ion. The specific function of this family is unknown.


Pssm-ID: 349764 [Multi-domain]  Cd Length: 246  Bit Score: 37.36  E-value: 5.83e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116666361 163 LPSIEISGCNNCGRCVKVCPRGVLVLDENDSIKVRDIteCSLCRLCVEECDQRAISVVPLEDAFIMSIESD--------- 233
Cdd:cd03110   58 KAFIDQEKCIRCGNCERVCKFGAILEFFQKLIVDESL--CEGCGACVIICPRGAIYLKDRDTGKIFISSSDggplvhgrl 135

                         90       100
                 ....*....|....*....|....*..
gi 116666361 234 --GSINAKDLVRmaaeELKKKALALQD 258
Cdd:cd03110  136 niGEENSGKLVT----ELRKKALERSK 158
DMSOR_beta_like cd16372
uncharacterized subfamily of DMSO Reductase beta subunit family; This family consists of the ...
 166-220 6.68e-03

uncharacterized subfamily of DMSO Reductase beta subunit family; This family consists of the small beta iron-sulfur (FeS) subunit of the DMSO Reductase (DMSOR) family. Members of this family also contain a large, periplasmic molybdenum-containing alpha subunit and may have a small gamma subunit as well. Examples of heterodimeric members with alpha and beta subunits include arsenite oxidase, and tungsten-containing formate dehydrogenase (FDH-T) while heterotrimeric members containing alpha, beta, and gamma subunits include formate dehydrogenase-N (FDH-N), and nitrate reductase (NarGHI). The beta subunit contains four Fe4/S4 and/or Fe3/S4 clusters which transfer the electrons from the alpha subunit to a hydrophobic integral membrane protein, presumably a cytochrome containing two b-type heme groups. The reducing equivalents are then transferred to menaquinone, which finally reduces the electron-accepting enzyme system.


Pssm-ID: 319894 [Multi-domain]  Cd Length: 125  Bit Score: 35.77  E-value: 6.68e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116666361 166 IEISGCNNCGRCVKVCP--------RGVLVLDENDSI---------------KVRDITE---CSLCRLCVEECDQRAISV 219
Cdd:cd16372   44 YAINVCNQCGECIDVCPtgaitrdaNGVVMINKKLCVgclmcvgfcpegamfKHEDYPEpfkCIACGICVKACPTGALEL 123


                 .
gi 116666361 220 V 220
Cdd:cd16372  124 V 124
EBDH_beta cd10555
beta subunit of ethylbenzene-dehydrogenase (EBDH); This subfamily includes ethylbenzene ...
 160-212 7.14e-03

beta subunit of ethylbenzene-dehydrogenase (EBDH); This subfamily includes ethylbenzene dehydrogenase (EBDH, EC 1.17.99.2), a member of the DMSO reductase family. EBDH oxidizes the hydrocarbon ethylbenzene to (S)-1-phenylethanol. It is a heterotrimer, with the alpha subunit containing the catalytic center with a molybdenum held by two molybdopterin-guanine dinucleotides, the beta subunit containing four iron-sulfur clusters (the electron transfer subunit) and the gamma subunit containing a methionine and a lysine as axial heme ligands. During catalysis, electrons produced by substrate oxidation are transferred to a heme in the gamma subunit and then presumably to a separate cytochrome involved in nitrate respiration.


Pssm-ID: 319877 [Multi-domain]  Cd Length: 316  Bit Score: 37.28  E-value: 7.14e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 116666361 160 YKNLPSIeisgCNNCGR--CVKVCPRGVLVLDENDSIKVRDITECSLCRLCVEEC 212
Cdd:cd10555  126 YFYLPRI----CNHCTNpaCLAACPRKAIYKREEDGIVLVDQDRCRGYRYCVEAC 176
Fer4_16 pfam13484
4Fe-4S double cluster binding domain;
171-212 7.25e-03

4Fe-4S double cluster binding domain;


Pssm-ID: 463893 [Multi-domain]  Cd Length: 65  Bit Score: 34.39  E-value: 7.25e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 116666361  171 CNNCGRCVKVCPRGVLVLDE--------------------NDSIKVRDITECSLCRLCVEEC 212
Cdd:pfam13484   1 CGSCGKCIDACPTGAIVGPEgvldarrcisyltiekkgliPDELRCLLGNRCYGCDICQDVC 62
RNAP_RPB11_RPB3 cd00460
RPB11 and RPB3 subunits of RNA polymerase; The eukaryotic RPB11 and RPB3 subunits of RNA ...
 223-252 7.32e-03

RPB11 and RPB3 subunits of RNA polymerase; The eukaryotic RPB11 and RPB3 subunits of RNA polymerase (RNAP), as well as their archaeal (L and D subunits) and bacterial (alpha subunit) counterparts, are involved in the assembly of RNAP, a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the archaeal (D/L subunits) and bacterial (alpha subunit) counterparts.


Pssm-ID: 132901  Cd Length: 86  Bit Score: 34.70  E-value: 7.32e-03
                         10        20        30
                 ....*....|....*....|....*....|
gi 116666361 223 EDAFIMSIESDGSINAKDLVRMAAEELKKK 252
Cdd:cd00460   53 EDKFILRIETVGSIPPEEALRRAVEILRKK 82
napH PRK09477
quinol dehydrogenase membrane component; Provisional
 171-218 9.12e-03

quinol dehydrogenase membrane component; Provisional


Pssm-ID: 236535 [Multi-domain]  Cd Length: 271  Bit Score: 36.80  E-value: 9.12e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 116666361 171 CNNCGRCVKVCP-RGVL---VLDENDSIKVRDiTECSLCRLCVEECDQRAIS 218
Cdd:PRK09477 210 CTRCMDCFHVCPePQVLrppLKGKQSPSQVTS-GDCITCGRCIDVCSEDVFN 260
 
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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