NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|768457934|gb|AJU15687|]
View 

intron-encoded reverse transcriptase aI2 (mitochondrion) [Saccharomyces cerevisiae YJM1190]

Protein Classification

RNA-dependent RNA polymerase family protein( domain architecture ID 10108786)

RNA-dependent RNA polymerase (RdRp) family protein similar to the RdRp catalytic domain of alpha-, beta-, gamma-, delta-coronaviruses, including three highly pathogenic human coronaviruses (CoVs) such as Middle East respiratory syndrome (MERS)-related CoV, Severe acute respiratory syndrome (SARS) CoV, and SARS-CoV-2

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
RT_G2_intron cd01651
RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA ...
 344-613 1.36e-80

RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).


:

Pssm-ID: 238828 [Multi-domain]  Cd Length: 226  Bit Score: 259.06  E-value: 1.36e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934 344 RRVEIPKTSGGFRPLSVGNPREKIVQESMRMMLEIIYNNSFSYYSHGFRPNLSCLTAIIQCKNYM-QYCNWFIKVDLNKC 422
Cdd:cd01651    1 RRVYIPKPNGKKRPLGIPTVRDRIVQEALKLVLEPIYEPRFSDCSYGFRPGRSAHDALKAIRRNVkGGYTWVIEGDIKGF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934 423 FDTIPHNMLINVLNERIKDKGFMDLLYKLLRAGYVdKNNNYHNTTLGIPQGSVVSPILCNIFLDKLDKYLENKFenefnt 502
Cdd:cd01651   81 FDNIDHDLLLKILKRRIGDKRVLRLIRKWLKAGVL-EDGKLVETEKGTPQGGVISPLLANIYLHELDKFVEEKL------ 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934 503 gnmsnrgrnpiynslsskiyrckllseklklirlrdhYQRNMGSDKSFKRAYFVRYADDIIIGVMGSHnDCKNILNDINN 582
Cdd:cd01651  154 -------------------------------------KEYYDTSDPKFRRLRYVRYADDFVIGVRGPK-EAEEIKELIRE 195

                        250       260       270
                 ....*....|....*....|....*....|..
gi 768457934 583 FLKEnLGMSINMDKSVIKH-SKEGVSFLGYDV 613
Cdd:cd01651  196 FLEE-LGLELNPEKTRITHfKSEGFDFLGFTF 226
Intron_maturas2 pfam01348
Type II intron maturase; Group II introns use intron-encoded reverse transcriptase, maturase ...
 638-781 4.16e-52

Type II intron maturase; Group II introns use intron-encoded reverse transcriptase, maturase and DNA endonuclease activities for site-specific insertion into DNA. Although this type of intron is self splicing in vitro they require a maturase protein for splicing in vivo. It has been shown that a specific region of the aI2 intron is needed for the maturase function. This region was found to be conserved in group II introns and called domain X.


:

Pssm-ID: 279664 [Multi-domain]  Cd Length: 140  Bit Score: 178.43  E-value: 4.16e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934  638 HTSLVVNAPIRSIVMKLNKHGYCSH-GILGKPRGVGRLIHEEMKTILMHYLAVGRGIMNYYRLATNFTTLRGRITYILFY 716
Cdd:pfam01348   1 TTRLVLNAPIRDIINKLAKAGFCKHyTEKGKPRSVGRWTDLDDRDILLRYNAIIRGILNYYSFADNKKRLYTRIYYILRL 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 768457934  717 SCCLTLARKFKLNTVKKVILKFGKVLVDPHSKVSFSIDDfKIRHKMNMTDsnytPDEILDRYKYM 781
Cdd:pfam01348  81 SCAKTLARKLKLGTVRKVIKKFGKKLSDFLIETFDSIDK-NFKLKTNLVD----PFTKTDWSLRT 140
Heme_Cu_Oxidase_I super family cl00275
Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in ...
 3-68 6.35e-23

Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily is diverse in terms of electron donors, subunit composition, and heme types. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. It has been proposed that Archaea acquired heme-copper oxidases through gene transfer from Gram-positive bacteria. Membership in the superfamily is defined by subunit I, which contains a heme-copper binuclear center (the active site where O2 is reduced to water) formed by a high-spin heme and a copper ion. It also contains a low-spin heme, believed to participate in the transfer of electrons to the binuclear center. Only subunit I is common to the entire superfamily. For every reduction of an O2 molecule, eight protons are taken from the inside aqueous compartment and four electrons are taken from the electron donor on the opposite side of the membrane. The four electrons and four of the protons are used in the reduction of O2; the four remaining protons are pumped across the membrane. This charge separation of four charges contributes to the electrochemical gradient used for ATP synthesis. Two proton channels, the D-pathway and K-pathway, leading to the binuclear center have been identified in subunit I of cytochrome c oxidase (CcO) and ubiquinol oxidase. A well-defined pathway for the transfer of pumped protons beyond the binuclear center has not been identified. Electron transfer occurs in two segments: from the electron donor to the low-spin heme, and from the low-spin heme to the binuclear center. The first segment can be a multi-step process and varies among the different families, while the second segment, a direct transfer, is consistent throughout the superfamily.


The actual alignment was detected with superfamily member MTH00153:

Pssm-ID: 469701  Cd Length: 511  Bit Score: 103.41  E-value: 6.35e-23
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 768457934   3 QRWLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSqyLHGNSQLFNVLVVGHAVLMIF 68
Cdd:MTH00153   2 NKWLFSTNHKDIGTLYFIFGAWSGMVGTSLSLLIRAELGQPGS--LIGDDQIYNVIVTAHAFIMIF 65
 
Name Accession Description Interval E-value
RT_G2_intron cd01651
RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA ...
 344-613 1.36e-80

RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).


Pssm-ID: 238828 [Multi-domain]  Cd Length: 226  Bit Score: 259.06  E-value: 1.36e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934 344 RRVEIPKTSGGFRPLSVGNPREKIVQESMRMMLEIIYNNSFSYYSHGFRPNLSCLTAIIQCKNYM-QYCNWFIKVDLNKC 422
Cdd:cd01651    1 RRVYIPKPNGKKRPLGIPTVRDRIVQEALKLVLEPIYEPRFSDCSYGFRPGRSAHDALKAIRRNVkGGYTWVIEGDIKGF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934 423 FDTIPHNMLINVLNERIKDKGFMDLLYKLLRAGYVdKNNNYHNTTLGIPQGSVVSPILCNIFLDKLDKYLENKFenefnt 502
Cdd:cd01651   81 FDNIDHDLLLKILKRRIGDKRVLRLIRKWLKAGVL-EDGKLVETEKGTPQGGVISPLLANIYLHELDKFVEEKL------ 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934 503 gnmsnrgrnpiynslsskiyrckllseklklirlrdhYQRNMGSDKSFKRAYFVRYADDIIIGVMGSHnDCKNILNDINN 582
Cdd:cd01651  154 -------------------------------------KEYYDTSDPKFRRLRYVRYADDFVIGVRGPK-EAEEIKELIRE 195

                        250       260       270
                 ....*....|....*....|....*....|..
gi 768457934 583 FLKEnLGMSINMDKSVIKH-SKEGVSFLGYDV 613
Cdd:cd01651  196 FLEE-LGLELNPEKTRITHfKSEGFDFLGFTF 226
YkfC COG3344
Retron-type reverse transcriptase [Mobilome: prophages, transposons];
267-709 9.26e-73

Retron-type reverse transcriptase [Mobilome: prophages, transposons];


Pssm-ID: 442573 [Multi-domain]  Cd Length: 434  Bit Score: 245.37  E-value: 9.26e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934 267 LNKLMENNHNKTETINTRILKLMSDIRMLLIAYNKIKSKKGnmSKGSNNITLDGI--NIS-YLNKLSKDINTNMFKFSPV 343
Cdd:COG3344    3 LRRITEKAKPDPGARFTSLLEKILSRENLLEAYKRVKANKG--AAGIDGVTVEDFeeYLEeNLYDLRERLRSGSYRPQPV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934 344 RRVEIPKTSGGFRPLSVGNPREKIVQESMRMMLEIIYNNSFSYYSHGFRPNLSCLTAIIQCKNYMQY-CNWFIKVDLNKC 422
Cdd:COG3344   81 RRVEIPKPDGGVRPLGIPTVRDRVVQQAVKQVLEPIFEPDFSDSSYGFRPGRSAHDALKKAREYINEgYRWVVDADIKKF 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934 423 FDTIPHNMLINVLNERIKDKGFMDLLYKLLRAGYVDkNNNYHNTTLGIPQGSVVSPILCNIFLDKLDKYLEnkfenefnt 502
Cdd:COG3344  161 FDNVDHDLLMKRLRRRIKDKRVLRLIRRWLKAGVME-DGVVEEREEGTPQGGPLSPLLANIYLHELDKELE--------- 230

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934 503 gnmsNRGrnpiynslsskiyrckllseklklirlrdhyqrnmgsdksfkrAYFVRYADDIIIGVmGSHNDCKNILNDINN 582
Cdd:COG3344  231 ----RRG-------------------------------------------HRFVRYADDFVILC-RSKRAAERVLESLTE 262

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934 583 FLKEnLGMSINMDKSVIKHSKEGVSFLGYDVKVTPWEKRPYRMIKKGDNFIRVRHHTSLVVNAPIRSIVMKLNkhgycsh 662
Cdd:COG3344  263 RLEK-LGLELNPEKTRIVRPGDGFKFLGFSFRRGKGLGFKFRPRKSKRKKKRKRRRRTRRRSRKRRRRIRRLL------- 334

                        410       420       430       440
                 ....*....|....*....|....*....|....*....|....*..
gi 768457934 663 gilgKPRGVGRLIHEEMKTILMHYLAVGRGIMNYYRLATNFTTLRGR 709
Cdd:COG3344  335 ----RRLLLGWRRYLLLAELKRLLNALLRGRRRYYRRLWRKRRKKLR 377
group_II_RT_mat TIGR04416
group II intron reverse transcriptase/maturase; Members of this protein family are ...
 293-707 1.99e-65

group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]


Pssm-ID: 275209 [Multi-domain]  Cd Length: 354  Bit Score: 222.72  E-value: 1.99e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934  293 RMLLIAYNKIKSKKGnmSKGSNNITLDGIN---ISYLNKLSKDINTNMFKFSPVRRVEIPKTSGGFRPLSVGNPREKIVQ 369
Cdd:TIGR04416   2 ENLLLAYKRVKANKG--AAGVDGVTIEDFEeylEENLYKLWNRLKSGSYRPQPVRRVEIPKPNGKQRPLGIPTVRDRVVQ 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934  370 ESMRMMLEIIYNNSFSYYSHGFRPNLSCLTAIIQCKNYM-QYCNWFIKVDLNKCFDTIPHNMLINVLNERIKDKGFMDLL 448
Cdd:TIGR04416  80 QAVKQVLEPIFEPDFSENSYGFRPGRSAHDAIAKARKRLnRGYRWVVDADIKGFFDNINHDLLMKAVARRISDKRVLRLI 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934  449 YKLLRAGYVDkNNNYHNTTLGIPQGSVVSPILCNIFLDKLDKYLEnkfenefntgnmsNRGrnpiynslsskiyrcklls 528
Cdd:TIGR04416 160 RRWLKAGVME-DGEVQETEEGTPQGGVISPLLANIYLHYLDDEWE-------------KRG------------------- 206

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934  529 eklklirlrdhyqrnmgsdksfKRAYFVRYADDIIIGVmGSHNDCKNILNDINNFLKEnLGMSINMDKSVIKHSKE-GVS 607
Cdd:TIGR04416 207 ----------------------YKVRFVRYADDFVILC-RSKEAAERVLEALTKRLEE-LGLELNPEKTKIVHCKDgGFD 262

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934  608 FLGYDVkvtpwekRPYRMIKKGDNFIRVRHHTSlvvnapIRSIVMKLNKhgycshgILGKPRGVG--RLIhEEMKTILmh 685
Cdd:TIGR04416 263 FLGFTF-------RKRKSKNGKGKLLIKPSKKA------VKKFKEKIRE-------LTKRRRGLSleELI-KKLNPIL-- 319

                         410       420
                  ....*....|....*....|..
gi 768457934  686 ylavgRGIMNYYRLATNFTTLR 707
Cdd:TIGR04416 320 -----RGWANYFGIANSSRTFS 336
Intron_maturas2 pfam01348
Type II intron maturase; Group II introns use intron-encoded reverse transcriptase, maturase ...
 638-781 4.16e-52

Type II intron maturase; Group II introns use intron-encoded reverse transcriptase, maturase and DNA endonuclease activities for site-specific insertion into DNA. Although this type of intron is self splicing in vitro they require a maturase protein for splicing in vivo. It has been shown that a specific region of the aI2 intron is needed for the maturase function. This region was found to be conserved in group II introns and called domain X.


Pssm-ID: 279664 [Multi-domain]  Cd Length: 140  Bit Score: 178.43  E-value: 4.16e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934  638 HTSLVVNAPIRSIVMKLNKHGYCSH-GILGKPRGVGRLIHEEMKTILMHYLAVGRGIMNYYRLATNFTTLRGRITYILFY 716
Cdd:pfam01348   1 TTRLVLNAPIRDIINKLAKAGFCKHyTEKGKPRSVGRWTDLDDRDILLRYNAIIRGILNYYSFADNKKRLYTRIYYILRL 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 768457934  717 SCCLTLARKFKLNTVKKVILKFGKVLVDPHSKVSFSIDDfKIRHKMNMTDsnytPDEILDRYKYM 781
Cdd:pfam01348  81 SCAKTLARKLKLGTVRKVIKKFGKKLSDFLIETFDSIDK-NFKLKTNLVD----PFTKTDWSLRT 140
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 348-611 1.85e-28

Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.


Pssm-ID: 395031 [Multi-domain]  Cd Length: 189  Bit Score: 112.78  E-value: 1.85e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934  348 IPK-TSGGFRPLSVGNPREKIVQesMRMMLEIIYNNSFSYYSHGFRPNLSCLtaiiqcknymQYCNWFIKVDLNKCFDTI 426
Cdd:pfam00078   1 IPKkGKGKYRPISLLSIDYKALN--KIIVKRLKPENLDSPPQPGFRPGLAKL----------KKAKWFLKLDLKKAFDQV 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934  427 PHNMLINVLNERIKDKGFMDllykllragYVDKNNNYHNTTLGIPQGSVVSPILCNIFLDKLDKYLENKFENefntgnms 506
Cdd:pfam00078  69 PLDELDRKLTAFTTPPININ---------WNGELSGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKRAGL-------- 131

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934  507 nrgrnpiynslsskiyrckllseklklirlrdhyqrnmgsdksfkraYFVRYADDIIIGVmGSHNDCKNILNDINNFLKE 586
Cdd:pfam00078 132 -----------------------------------------------TLVRYADDILIFS-KSEEEHQEALEEVLEWLKE 163

                         250       260
                  ....*....|....*....|....*
gi 768457934  587 NlGMSINMDKSVIKHSKEGVSFLGY 611
Cdd:pfam00078 164 S-GLKINPEKTQFFLKSKEVKYLGV 187
COX1 MTH00153
cytochrome c oxidase subunit I; Provisional
 3-68 6.35e-23

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177210  Cd Length: 511  Bit Score: 103.41  E-value: 6.35e-23
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 768457934   3 QRWLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSqyLHGNSQLFNVLVVGHAVLMIF 68
Cdd:MTH00153   2 NKWLFSTNHKDIGTLYFIFGAWSGMVGTSLSLLIRAELGQPGS--LIGDDQIYNVIVTAHAFIMIF 65
Cyt_c_Oxidase_I cd01663
Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the ...
 9-68 3.08e-22

Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Only subunits I and II are essential for function, but subunit III, which is also conserved, may play a role in assembly or oxygen delivery to the active site. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Subunit I contains a heme-copper binuclear center (the active site where O2 is reduced to water) formed by a high-spin heme (heme a3) and a copper ion (CuB). It also contains a low-spin heme (heme a), believed to participate in the transfer of electrons to the binuclear center. For every reduction of an O2 molecule, eight protons are taken from the inside aqueous compartment and four electrons are taken from cytochrome c on the opposite side of the membrane. The four electrons and four of the protons are used in the reduction of O2; the four remaining protons are pumped across the membrane. This charge separation of four charges contributes to the electrochemical gradient used for ATP synthesis. Two proton channels, the D-pathway and K-pathway, leading to the binuclear center have been identified in subunit I. A well-defined pathway for the transfer of pumped protons beyond the binuclear center has not been identified. Electrons are transferred from cytochrome c (the electron donor) to heme a via the CuA binuclear site in subunit II, and directly from heme a to the binuclear center.


Pssm-ID: 238833  Cd Length: 488  Bit Score: 101.02  E-value: 3.08e-22
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934   9 TNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSQylHGNSQLFNVLVVGHAVLMIF 68
Cdd:cd01663    1 TNHKDIGTLYLIFGLWSGLVGTSLSLLIRLELSQPGSQ--LGNDQLYNVIVTAHALIMIF 58
CyoB COG0843
Heme/copper-type cytochrome/quinol oxidase, subunit 1 [Energy production and conversion];
2-68 4.61e-13

Heme/copper-type cytochrome/quinol oxidase, subunit 1 [Energy production and conversion];


Pssm-ID: 440605  Cd Length: 535  Bit Score: 72.47  E-value: 4.61e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 768457934   2 VQRWLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSQYLhgNSQLFNVLVVGHAVLMIF 68
Cdd:COG0843    6 WRRWLTTVDHKRIGIMYLVTAFVFLLIGGLLALLMRLQLAGPGLGLL--SPETYNQLFTMHGTIMIF 70
COX1 pfam00115
Cytochrome C and Quinol oxidase polypeptide I; Cytochrome c oxidase (E.C:7.1.1.9) is a key ...
 13-68 3.18e-09

Cytochrome C and Quinol oxidase polypeptide I; Cytochrome c oxidase (E.C:7.1.1.9) is a key enzyme in aerobic metabolism. Proton pumping haem-copper oxidases represent the terminal, energy-transfer enzymes of respiratory chains in prokaryotes and eukaryotes. The CuB-haem a3 (or haem o) binuclear centre, associated with the largest subunit I of cytochrome c and ubiquinol oxidases (E.C:1.10.3.11), is directly involved in the coupling between dioxygen reduction and proton pumping. Some terminal oxidases generate a transmembrane proton gradient across the plasma membrane (prokaryotes) or the mitochondrial inner membrane (eukaryotes). The enzyme complex consists of 3-4 subunits (prokaryotes) up to 13 polypeptides (mammals) of which only the catalytic subunit (equivalent to mammalian subunit I (COXI) is found in all haem-copper respiratory oxidases. The presence of a bimetallic centre (formed by a high-spin haem and copper B) as well as a low-spin haem, both ligated to six conserved histidine residues near the outer side of four transmembrane spans within CO I is common to all family members.


Pssm-ID: 459678  Cd Length: 432  Bit Score: 59.89  E-value: 3.18e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 768457934   13 DIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSQYLhgNSQLFNVLVVGHAVLMIF 68
Cdd:pfam00115   1 RIGLLYLVTALVWFLVGGLLGLLIRLQLAFPGLNFL--SPLTYNQLRTLHGNLMIF 54
 
Name Accession Description Interval E-value
RT_G2_intron cd01651
RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA ...
 344-613 1.36e-80

RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).


Pssm-ID: 238828 [Multi-domain]  Cd Length: 226  Bit Score: 259.06  E-value: 1.36e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934 344 RRVEIPKTSGGFRPLSVGNPREKIVQESMRMMLEIIYNNSFSYYSHGFRPNLSCLTAIIQCKNYM-QYCNWFIKVDLNKC 422
Cdd:cd01651    1 RRVYIPKPNGKKRPLGIPTVRDRIVQEALKLVLEPIYEPRFSDCSYGFRPGRSAHDALKAIRRNVkGGYTWVIEGDIKGF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934 423 FDTIPHNMLINVLNERIKDKGFMDLLYKLLRAGYVdKNNNYHNTTLGIPQGSVVSPILCNIFLDKLDKYLENKFenefnt 502
Cdd:cd01651   81 FDNIDHDLLLKILKRRIGDKRVLRLIRKWLKAGVL-EDGKLVETEKGTPQGGVISPLLANIYLHELDKFVEEKL------ 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934 503 gnmsnrgrnpiynslsskiyrckllseklklirlrdhYQRNMGSDKSFKRAYFVRYADDIIIGVMGSHnDCKNILNDINN 582
Cdd:cd01651  154 -------------------------------------KEYYDTSDPKFRRLRYVRYADDFVIGVRGPK-EAEEIKELIRE 195

                        250       260       270
                 ....*....|....*....|....*....|..
gi 768457934 583 FLKEnLGMSINMDKSVIKH-SKEGVSFLGYDV 613
Cdd:cd01651  196 FLEE-LGLELNPEKTRITHfKSEGFDFLGFTF 226
YkfC COG3344
Retron-type reverse transcriptase [Mobilome: prophages, transposons];
267-709 9.26e-73

Retron-type reverse transcriptase [Mobilome: prophages, transposons];


Pssm-ID: 442573 [Multi-domain]  Cd Length: 434  Bit Score: 245.37  E-value: 9.26e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934 267 LNKLMENNHNKTETINTRILKLMSDIRMLLIAYNKIKSKKGnmSKGSNNITLDGI--NIS-YLNKLSKDINTNMFKFSPV 343
Cdd:COG3344    3 LRRITEKAKPDPGARFTSLLEKILSRENLLEAYKRVKANKG--AAGIDGVTVEDFeeYLEeNLYDLRERLRSGSYRPQPV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934 344 RRVEIPKTSGGFRPLSVGNPREKIVQESMRMMLEIIYNNSFSYYSHGFRPNLSCLTAIIQCKNYMQY-CNWFIKVDLNKC 422
Cdd:COG3344   81 RRVEIPKPDGGVRPLGIPTVRDRVVQQAVKQVLEPIFEPDFSDSSYGFRPGRSAHDALKKAREYINEgYRWVVDADIKKF 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934 423 FDTIPHNMLINVLNERIKDKGFMDLLYKLLRAGYVDkNNNYHNTTLGIPQGSVVSPILCNIFLDKLDKYLEnkfenefnt 502
Cdd:COG3344  161 FDNVDHDLLMKRLRRRIKDKRVLRLIRRWLKAGVME-DGVVEEREEGTPQGGPLSPLLANIYLHELDKELE--------- 230

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934 503 gnmsNRGrnpiynslsskiyrckllseklklirlrdhyqrnmgsdksfkrAYFVRYADDIIIGVmGSHNDCKNILNDINN 582
Cdd:COG3344  231 ----RRG-------------------------------------------HRFVRYADDFVILC-RSKRAAERVLESLTE 262

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934 583 FLKEnLGMSINMDKSVIKHSKEGVSFLGYDVKVTPWEKRPYRMIKKGDNFIRVRHHTSLVVNAPIRSIVMKLNkhgycsh 662
Cdd:COG3344  263 RLEK-LGLELNPEKTRIVRPGDGFKFLGFSFRRGKGLGFKFRPRKSKRKKKRKRRRRTRRRSRKRRRRIRRLL------- 334

                        410       420       430       440
                 ....*....|....*....|....*....|....*....|....*..
gi 768457934 663 gilgKPRGVGRLIHEEMKTILMHYLAVGRGIMNYYRLATNFTTLRGR 709
Cdd:COG3344  335 ----RRLLLGWRRYLLLAELKRLLNALLRGRRRYYRRLWRKRRKKLR 377
group_II_RT_mat TIGR04416
group II intron reverse transcriptase/maturase; Members of this protein family are ...
 293-707 1.99e-65

group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]


Pssm-ID: 275209 [Multi-domain]  Cd Length: 354  Bit Score: 222.72  E-value: 1.99e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934  293 RMLLIAYNKIKSKKGnmSKGSNNITLDGIN---ISYLNKLSKDINTNMFKFSPVRRVEIPKTSGGFRPLSVGNPREKIVQ 369
Cdd:TIGR04416   2 ENLLLAYKRVKANKG--AAGVDGVTIEDFEeylEENLYKLWNRLKSGSYRPQPVRRVEIPKPNGKQRPLGIPTVRDRVVQ 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934  370 ESMRMMLEIIYNNSFSYYSHGFRPNLSCLTAIIQCKNYM-QYCNWFIKVDLNKCFDTIPHNMLINVLNERIKDKGFMDLL 448
Cdd:TIGR04416  80 QAVKQVLEPIFEPDFSENSYGFRPGRSAHDAIAKARKRLnRGYRWVVDADIKGFFDNINHDLLMKAVARRISDKRVLRLI 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934  449 YKLLRAGYVDkNNNYHNTTLGIPQGSVVSPILCNIFLDKLDKYLEnkfenefntgnmsNRGrnpiynslsskiyrcklls 528
Cdd:TIGR04416 160 RRWLKAGVME-DGEVQETEEGTPQGGVISPLLANIYLHYLDDEWE-------------KRG------------------- 206

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934  529 eklklirlrdhyqrnmgsdksfKRAYFVRYADDIIIGVmGSHNDCKNILNDINNFLKEnLGMSINMDKSVIKHSKE-GVS 607
Cdd:TIGR04416 207 ----------------------YKVRFVRYADDFVILC-RSKEAAERVLEALTKRLEE-LGLELNPEKTKIVHCKDgGFD 262

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934  608 FLGYDVkvtpwekRPYRMIKKGDNFIRVRHHTSlvvnapIRSIVMKLNKhgycshgILGKPRGVG--RLIhEEMKTILmh 685
Cdd:TIGR04416 263 FLGFTF-------RKRKSKNGKGKLLIKPSKKA------VKKFKEKIRE-------LTKRRRGLSleELI-KKLNPIL-- 319

                         410       420
                  ....*....|....*....|..
gi 768457934  686 ylavgRGIMNYYRLATNFTTLR 707
Cdd:TIGR04416 320 -----RGWANYFGIANSSRTFS 336
Intron_maturas2 pfam01348
Type II intron maturase; Group II introns use intron-encoded reverse transcriptase, maturase ...
 638-781 4.16e-52

Type II intron maturase; Group II introns use intron-encoded reverse transcriptase, maturase and DNA endonuclease activities for site-specific insertion into DNA. Although this type of intron is self splicing in vitro they require a maturase protein for splicing in vivo. It has been shown that a specific region of the aI2 intron is needed for the maturase function. This region was found to be conserved in group II introns and called domain X.


Pssm-ID: 279664 [Multi-domain]  Cd Length: 140  Bit Score: 178.43  E-value: 4.16e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934  638 HTSLVVNAPIRSIVMKLNKHGYCSH-GILGKPRGVGRLIHEEMKTILMHYLAVGRGIMNYYRLATNFTTLRGRITYILFY 716
Cdd:pfam01348   1 TTRLVLNAPIRDIINKLAKAGFCKHyTEKGKPRSVGRWTDLDDRDILLRYNAIIRGILNYYSFADNKKRLYTRIYYILRL 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 768457934  717 SCCLTLARKFKLNTVKKVILKFGKVLVDPHSKVSFSIDDfKIRHKMNMTDsnytPDEILDRYKYM 781
Cdd:pfam01348  81 SCAKTLARKLKLGTVRKVIKKFGKKLSDFLIETFDSIDK-NFKLKTNLVD----PFTKTDWSLRT 140
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 348-611 1.85e-28

Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.


Pssm-ID: 395031 [Multi-domain]  Cd Length: 189  Bit Score: 112.78  E-value: 1.85e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934  348 IPK-TSGGFRPLSVGNPREKIVQesMRMMLEIIYNNSFSYYSHGFRPNLSCLtaiiqcknymQYCNWFIKVDLNKCFDTI 426
Cdd:pfam00078   1 IPKkGKGKYRPISLLSIDYKALN--KIIVKRLKPENLDSPPQPGFRPGLAKL----------KKAKWFLKLDLKKAFDQV 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934  427 PHNMLINVLNERIKDKGFMDllykllragYVDKNNNYHNTTLGIPQGSVVSPILCNIFLDKLDKYLENKFENefntgnms 506
Cdd:pfam00078  69 PLDELDRKLTAFTTPPININ---------WNGELSGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKRAGL-------- 131

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934  507 nrgrnpiynslsskiyrckllseklklirlrdhyqrnmgsdksfkraYFVRYADDIIIGVmGSHNDCKNILNDINNFLKE 586
Cdd:pfam00078 132 -----------------------------------------------TLVRYADDILIFS-KSEEEHQEALEEVLEWLKE 163

                         250       260
                  ....*....|....*....|....*
gi 768457934  587 NlGMSINMDKSVIKHSKEGVSFLGY 611
Cdd:pfam00078 164 S-GLKINPEKTQFFLKSKEVKYLGV 187
COX1 MTH00153
cytochrome c oxidase subunit I; Provisional
 3-68 6.35e-23

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177210  Cd Length: 511  Bit Score: 103.41  E-value: 6.35e-23
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 768457934   3 QRWLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSqyLHGNSQLFNVLVVGHAVLMIF 68
Cdd:MTH00153   2 NKWLFSTNHKDIGTLYFIFGAWSGMVGTSLSLLIRAELGQPGS--LIGDDQIYNVIVTAHAFIMIF 65
Cyt_c_Oxidase_I cd01663
Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the ...
 9-68 3.08e-22

Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Only subunits I and II are essential for function, but subunit III, which is also conserved, may play a role in assembly or oxygen delivery to the active site. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Subunit I contains a heme-copper binuclear center (the active site where O2 is reduced to water) formed by a high-spin heme (heme a3) and a copper ion (CuB). It also contains a low-spin heme (heme a), believed to participate in the transfer of electrons to the binuclear center. For every reduction of an O2 molecule, eight protons are taken from the inside aqueous compartment and four electrons are taken from cytochrome c on the opposite side of the membrane. The four electrons and four of the protons are used in the reduction of O2; the four remaining protons are pumped across the membrane. This charge separation of four charges contributes to the electrochemical gradient used for ATP synthesis. Two proton channels, the D-pathway and K-pathway, leading to the binuclear center have been identified in subunit I. A well-defined pathway for the transfer of pumped protons beyond the binuclear center has not been identified. Electrons are transferred from cytochrome c (the electron donor) to heme a via the CuA binuclear site in subunit II, and directly from heme a to the binuclear center.


Pssm-ID: 238833  Cd Length: 488  Bit Score: 101.02  E-value: 3.08e-22
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934   9 TNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSQylHGNSQLFNVLVVGHAVLMIF 68
Cdd:cd01663    1 TNHKDIGTLYLIFGLWSGLVGTSLSLLIRLELSQPGSQ--LGNDQLYNVIVTAHALIMIF 58
COX1 MTH00167
cytochrome c oxidase subunit I; Provisional
 1-68 1.95e-21

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177222  Cd Length: 512  Bit Score: 98.98  E-value: 1.95e-21
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 768457934   1 MVQRWLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSqyLHGNSQLFNVLVVGHAVLMIF 68
Cdd:MTH00167   2 WINRWLFSTNHKDIGTLYFIFGAWAGMVGTALSLLIRAELSQPGS--LLGDDQIYNVIVTAHAFVMIF 67
COX1 MTH00116
cytochrome c oxidase subunit I; Provisional
 1-68 1.09e-19

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177177  Cd Length: 515  Bit Score: 93.62  E-value: 1.09e-19
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 768457934   1 MVQRWLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSqyLHGNSQLFNVLVVGHAVLMIF 68
Cdd:MTH00116   2 FITRWLFSTNHKDIGTLYLIFGAWAGMVGTALSLLIRAELGQPGT--LLGDDQIYNVIVTAHAFVMIF 67
COX1 MTH00142
cytochrome c oxidase subunit I; Provisional
 2-68 1.91e-19

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 214431  Cd Length: 511  Bit Score: 92.86  E-value: 1.91e-19
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 768457934   2 VQRWLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSqyLHGNSQLFNVLVVGHAVLMIF 68
Cdd:MTH00142   1 MMRWLFSTNHKDIGTLYFLFGAWAGMVGTGLSLLIRAELGQPGS--LLGDDQLYNVIVTAHAFVMIF 65
COX1 MTH00223
cytochrome c oxidase subunit I; Provisional
 4-68 1.64e-18

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177260  Cd Length: 512  Bit Score: 89.65  E-value: 1.64e-18
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 768457934   4 RWLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSqyLHGNSQLFNVLVVGHAVLMIF 68
Cdd:MTH00223   2 RWLFSTNHKDIGTLYLIFGMWSGLVGTSLSLLIRAELGQPGA--LLGDDQLYNVIVTAHAFVMIF 64
COX1 MTH00184
cytochrome c oxidase subunit I; Provisional
 4-68 7.81e-18

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177235  Cd Length: 519  Bit Score: 87.57  E-value: 7.81e-18
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 768457934   4 RWLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSqyLHGNSQLFNVLVVGHAVLMIF 68
Cdd:MTH00184   7 RWLFSTNHKDIGTLYLLFGAFAGMIGTAFSMLIRLELSAPGS--MLGDDHLYNVIVTAHAFVMIF 69
COX1 MTH00077
cytochrome c oxidase subunit I; Provisional
 1-68 9.36e-18

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 214419  Cd Length: 514  Bit Score: 87.30  E-value: 9.36e-18
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 768457934   1 MVQRWLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSqyLHGNSQLFNVLVVGHAVLMIF 68
Cdd:MTH00077   2 MITRWLFSTNHKDIGTLYLVFGAWAGMVGTALSLLIRAELSQPGT--LLGDDQIYNVIVTAHAFVMIF 67
COX1 MTH00103
cytochrome c oxidase subunit I; Validated
 1-68 5.17e-17

cytochrome c oxidase subunit I; Validated


Pssm-ID: 177165  Cd Length: 513  Bit Score: 84.93  E-value: 5.17e-17
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 768457934   1 MVQRWLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSqyLHGNSQLFNVLVVGHAVLMIF 68
Cdd:MTH00103   2 FINRWLFSTNHKDIGTLYLLFGAWAGMVGTALSLLIRAELGQPGT--LLGDDQIYNVIVTAHAFVMIF 67
COX1 MTH00182
cytochrome c oxidase subunit I; Provisional
 4-68 9.16e-17

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 214451  Cd Length: 525  Bit Score: 84.49  E-value: 9.16e-17
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 768457934   4 RWLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSqyLHGNSQLFNVLVVGHAVLMIF 68
Cdd:MTH00182   7 RWVFSTNHKDIGTLYLVFGAGAGMIGTAFSMLIRLELSAPGA--MLGDDHLYNVIVTAHAFIMIF 69
COX1 MTH00183
cytochrome c oxidase subunit I; Provisional
 1-68 1.18e-16

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177234  Cd Length: 516  Bit Score: 83.82  E-value: 1.18e-16
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 768457934   1 MVQRWLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSqyLHGNSQLFNVLVVGHAVLMIF 68
Cdd:MTH00183   2 AITRWFFSTNHKDIGTLYLVFGAWAGMVGTALSLLIRAELSQPGA--LLGDDQIYNVIVTAHAFVMIF 67
COX1 MTH00079
cytochrome c oxidase subunit I; Provisional
 5-68 1.53e-15

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177148  Cd Length: 508  Bit Score: 80.49  E-value: 1.53e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 768457934   5 WLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGsqYLHGNSQLFNVLVVGHAVLMIF 68
Cdd:MTH00079   7 WLESSNHKDIGTLYFLFGLWSGMVGTSLSLIIRLELSKPG--LLLGNGQLYNSVITAHAILMIF 68
RT_Bac_retron_I cd01646
RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The ...
 418-622 6.63e-15

RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.


Pssm-ID: 238824 [Multi-domain]  Cd Length: 158  Bit Score: 73.13  E-value: 6.63e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934 418 DLNKCFDTIPHNMLINVLNERIKDK-------GFMDLLYKLLRAGyvdknnNYHNTTlGIPQGSVVSPILCNIFLDKLDK 490
Cdd:cd01646    2 DISNFYDSIYTHSLPWALHGKIKAKqllkllrLLGNLLDLLLLSS------QYGQTN-GLPIGPLTSRFLANIYLNDVDH 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934 491 YLENKFenefntgnmsnrgrnpiynslsskiyrckllseklklirlrdhyqrnmgsdksfKRAYFVRYADDIIIGVmGSH 570
Cdd:cd01646   75 ELKSKL------------------------------------------------------KGVDYVRYVDDIRIFA-DSK 99

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 768457934 571 NDCKNILNDINNFLKEnLGMSINMDKSVIKHSKEG---VSFLGYDVKVTPWEKRP 622
Cdd:cd01646  100 EEAEEILEELKEFLAE-LGLSLNLSKTEILPLPEGtasKDFLGYRFSPILLIKSS 153
Heme_Cu_Oxidase_I cd00919
Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in ...
 11-68 4.15e-14

Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily is diverse in terms of electron donors, subunit composition, and heme types. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. It has been proposed that Archaea acquired heme-copper oxidases through gene transfer from Gram-positive bacteria. Membership in the superfamily is defined by subunit I, which contains a heme-copper binuclear center (the active site where O2 is reduced to water) formed by a high-spin heme and a copper ion. It also contains a low-spin heme, believed to participate in the transfer of electrons to the binuclear center. Only subunit I is common to the entire superfamily. For every reduction of an O2 molecule, eight protons are taken from the inside aqueous compartment and four electrons are taken from the electron donor on the opposite side of the membrane. The four electrons and four of the protons are used in the reduction of O2; the four remaining protons are pumped across the membrane. This charge separation of four charges contributes to the electrochemical gradient used for ATP synthesis. Two proton channels, the D-pathway and K-pathway, leading to the binuclear center have been identified in subunit I of cytochrome c oxidase (CcO) and ubiquinol oxidase. A well-defined pathway for the transfer of pumped protons beyond the binuclear center has not been identified. Electron transfer occurs in two segments: from the electron donor to the low-spin heme, and from the low-spin heme to the binuclear center. The first segment can be a multi-step process and varies among the different families, while the second segment, a direct transfer, is consistent throughout the superfamily.


Pssm-ID: 238461  Cd Length: 463  Bit Score: 75.64  E-value: 4.15e-14
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 768457934  11 AKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSQYLhgNSQLFNVLVVGHAVLMIF 68
Cdd:cd00919    1 HKDIGLLYLIFAFVALLLGGLLALLIRLELATPGSLFL--DPQLYNQLVTAHGVIMIF 56
CyoB COG0843
Heme/copper-type cytochrome/quinol oxidase, subunit 1 [Energy production and conversion];
2-68 4.61e-13

Heme/copper-type cytochrome/quinol oxidase, subunit 1 [Energy production and conversion];


Pssm-ID: 440605  Cd Length: 535  Bit Score: 72.47  E-value: 4.61e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 768457934   2 VQRWLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSQYLhgNSQLFNVLVVGHAVLMIF 68
Cdd:COG0843    6 WRRWLTTVDHKRIGIMYLVTAFVFLLIGGLLALLMRLQLAGPGLGLL--SPETYNQLFTMHGTIMIF 70
COX1 MTH00026
cytochrome c oxidase subunit I; Provisional
 4-68 2.69e-12

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 164599  Cd Length: 534  Bit Score: 70.04  E-value: 2.69e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 768457934   4 RWLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSqyLHGNSQLFNVLVVGHAVLMIF 68
Cdd:MTH00026   6 RWFFSCNHKDIGSLYLVFGALSGAIGTAFSMLIRLELSSPGS--MLGDDHLYNVIVTAHAFVMIF 68
RT_nLTR_like cd01650
RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse ...
 348-599 4.95e-12

RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.


Pssm-ID: 238827 [Multi-domain]  Cd Length: 220  Bit Score: 66.16  E-value: 4.95e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934 348 IPKTS-----GGFRPLSVGNPR----EKIVQESMR-MMLEIIYNNSfsyysHGFRPNLSCLTAII-------QCKNYMQY 410
Cdd:cd01650    7 IPKKGkpsdpKNYRPISLLSVLykllEKILANRLRpVLEENILPNQ-----FGFRPGRSTTDAILllrevieKAKEKKKS 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934 411 CNwFIKVDLNKCFDTIPHNMLINVlnerikdkgfmdllykllragyvdknnnyhnttLGIPQGSVVSPILCNIFLDKLDK 490
Cdd:cd01650   82 LV-LVFLDFEKAFDSVDHEFLLKA---------------------------------LGVRQGDPLSPLLFNLALDDLLR 127

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934 491 YLENKFENEFNTGNMSnrgrnpiynslsskiyrckllseklklirlrdhyqrnmgsdksfkrayFVRYADDIIIGVMGSH 570
Cdd:cd01650  128 LLNKEEEIKLGGPGIT------------------------------------------------HLAYADDIVLFSEGKS 159

                        250       260
                 ....*....|....*....|....*....
gi 768457934 571 NDCKNILNDINNFLKENlGMSINMDKSVI 599
Cdd:cd01650  160 RKLQELLQRLQEWSKES-GLKINPSKSKV 187
RT_Bac_retron_II cd03487
RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The ...
 350-628 1.41e-09

RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.


Pssm-ID: 239569 [Multi-domain]  Cd Length: 214  Bit Score: 58.74  E-value: 1.41e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934 350 KTSGGFRPLSVGNPREKIVQESmrmmleiIYNNSFSY-----YSHGFRPNLSCLT-AIIQCKNymqycNWFIKVDLNKCF 423
Cdd:cd03487    1 KKNGGFRTIYAPKPELKAIQRK-------ILSNLLSKlpvhdAAHGFVKGRSIITnAKPHCGA-----KYVLKLDIKDFF 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934 424 DTIPHNMLINVLNER-IKDKGFMDLLYKLLragyvdknnnYHNTTLgiPQGSVVSPILCNIFLDKLDKYLENkfenefnt 502
Cdd:cd03487   69 PSITFERVRGVFRSLgYFSPDVATILAKLC----------TYNGHL--PQGAPTSPALSNLVFRKLDERLSK-------- 128

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934 503 gnmsnrgrnpiynslsskiyrcklLSEKLKLIrlrdhyqrnmgsdksfkrayFVRYADDIIIgvmGSHNDCKNILNDINN 582
Cdd:cd03487  129 ------------------------LAKSNGLT--------------------YTRYADDITF---SSNKKLKEALDKLLE 161

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*....
gi 768457934 583 FLKENL---GMSINMDKSVIKHSKEGVSFLGydVKVTPWEKRPYRMIKK 628
Cdd:cd03487  162 IIRSILseeGFKINKSKTRISSKGSRQIVTG--LVVNNGKPSLPRKEKR 208
COX1 pfam00115
Cytochrome C and Quinol oxidase polypeptide I; Cytochrome c oxidase (E.C:7.1.1.9) is a key ...
 13-68 3.18e-09

Cytochrome C and Quinol oxidase polypeptide I; Cytochrome c oxidase (E.C:7.1.1.9) is a key enzyme in aerobic metabolism. Proton pumping haem-copper oxidases represent the terminal, energy-transfer enzymes of respiratory chains in prokaryotes and eukaryotes. The CuB-haem a3 (or haem o) binuclear centre, associated with the largest subunit I of cytochrome c and ubiquinol oxidases (E.C:1.10.3.11), is directly involved in the coupling between dioxygen reduction and proton pumping. Some terminal oxidases generate a transmembrane proton gradient across the plasma membrane (prokaryotes) or the mitochondrial inner membrane (eukaryotes). The enzyme complex consists of 3-4 subunits (prokaryotes) up to 13 polypeptides (mammals) of which only the catalytic subunit (equivalent to mammalian subunit I (COXI) is found in all haem-copper respiratory oxidases. The presence of a bimetallic centre (formed by a high-spin haem and copper B) as well as a low-spin haem, both ligated to six conserved histidine residues near the outer side of four transmembrane spans within CO I is common to all family members.


Pssm-ID: 459678  Cd Length: 432  Bit Score: 59.89  E-value: 3.18e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 768457934   13 DIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSQYLhgNSQLFNVLVVGHAVLMIF 68
Cdd:pfam00115   1 RIGLLYLVTALVWFLVGGLLGLLIRLQLAFPGLNFL--SPLTYNQLRTLHGNLMIF 54
TERT cd01648
TERT: Telomerase reverse transcriptase (TERT). Telomerase is a ribonucleoprotein (RNP) that ...
 417-498 4.81e-06

TERT: Telomerase reverse transcriptase (TERT). Telomerase is a ribonucleoprotein (RNP) that synthesizes telomeric DNA repeats. The telomerase RNA subunit provides the template for synthesis of these repeats. The catalytic subunit of RNP is known as telomerase reverse transcriptase (TERT). The reverse transcriptase (RT) domain is located in the C-terminal region of the TERT polypeptide. Single amino acid substitutions in this region lead to telomere shortening and senescence. Telomerase is an enzyme that, in certain cells, maintains the physical ends of chromosomes (telomeres) during replication. In somatic cells, replication of the lagging strand requires the continual presence of an RNA primer approximately 200 nucleotides upstream, which is complementary to the template strand. Since there is a region of DNA less than 200 base pairs from the end of the chromosome where this is not possible, the chromosome is continually shortened. However, a surplus of repetitive DNA at the chromosome ends protects against the erosion of gene-encoding DNA. Telomerase is not normally expressed in somatic cells. It has been suggested that exogenous TERT may extend the lifespan of, or even immortalize, the cell. However, recent studies have shown that telomerase activity can be induced by a number of oncogenes. Conversely, the oncogene c-myc can be activated in human TERT immortalized cells. Sequence comparisons place the telomerase proteins in the RT family but reveal hallmarks that distinguish them from retroviral and retrotransposon relatives.


Pssm-ID: 238826  Cd Length: 119  Bit Score: 46.49  E-value: 4.81e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768457934 417 VDLNKCFDTIPHnmlinvlnerikdkgfmdllykllragyvdknnnYHNTTLGIPQGSVVSPILCNIFLDKLD-KYLENK 495
Cdd:cd01648    1 TDIKKCYDSIPQ----------------------------------YYRQKVGIPQGSPLSSLLCSLYYADLEnKYLSFL 46


                 ...
gi 768457934 496 FEN 498
Cdd:cd01648   47 DVI 49
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH