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Conserved domains on  [gi|84028170|sp|P03875|]
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RecName: Full=Putative COX1/OXI3 intron 1 protein

Protein Classification

HNH endonuclease( domain architecture ID 10108787)

HNH endonuclease signature motif containing protein catalyzes the hydrolysis of DNA

Graphical summary

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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 ...
 311-577 3.56e-89

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: 281.40  E-value: 3.56e-89
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170 311 RMVNIPKPKGGMRPLSVGNPRDKIVQEVMRMILDTIFDKKMSTHSHGFRKNMSCQTAIWEVRN-MFGGSNWFIEVDLKKC 389
Cdd:cd01651   1 RRVYIPKPNGKKRPLGIPTVRDRIVQEALKLVLEPIYEPRFSDCSYGFRPGRSAHDALKAIRRnVKGGYTWVIEGDIKGF 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170 390 FDTISHDLIIKELKRYISDKGFIDLVYKLLRAGYIdEKGTYHKPMLGLPQGSLISPILCNIVMTLVDNWLEDYINLYNkg 469
Cdd:cd01651  81 FDNIDHDLLLKILKRRIGDKRVLRLIRKWLKAGVL-EDGKLVETEKGTPQGGVISPLLANIYLHELDKFVEEKLKEYY-- 157

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170 470 kvkkqhptykklsrmiakakmfstrlklhkerakgptfIYNDPNFKRMKYVRYADDILIGVLGSKnDCKMIKRDLNNFLN 549
Cdd:cd01651 158 --------------------------------------DTSDPKFRRLRYVRYADDFVIGVRGPK-EAEEIKELIREFLE 198

                       250       260
                ....*....|....*....|....*...
gi 84028170 550 SLGLTMNEEKTLITCATETPARFLGYNI 577
Cdd:cd01651 199 ELGLELNPEKTRITHFKSEGFDFLGFTF 226
Intron_maturas2 pfam01348
Type II intron maturase; Group II introns use intron-encoded reverse transcriptase, maturase ...
 602-759 5.46e-54

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: 183.44  E-value: 5.46e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170   602 TTRPIINAPIRDIINKLATNGYCKHNKngRMGVPTRVGRWTYEEPRTIINNYKALGRGILNYYKLATNYKRLRERIYYVL 681
Cdd:pfam01348   1 TTRLVLNAPIRDIINKLAKAGFCKHYT--EKGKPRSVGRWTDLDDRDILLRYNAIIRGILNYYSFADNKKRLYTRIYYIL 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 84028170   682 YYSCVLTLASKYRLKTMSKTIKKFGynlniiendKLIANFPRNTFDNIKKIENHGmfmymseAKVTDPFEYIDSIKYM 759
Cdd:pfam01348  79 RLSCAKTLARKLKLGTVRKVIKKFG---------KKLSDFLIETFDSIDKNFKLK-------TNLVDPFTKTDWSLRT 140
Heme_Cu_Oxidase_I super family cl00275
Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in ...
 3-56 1.28e-16

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: 83.76  E-value: 1.28e-16
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 84028170    3 QRWLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSqyLHGNSQLFN 56
Cdd:MTH00153   2 NKWLFSTNHKDIGTLYFIFGAWSGMVGTSLSLLIRAELGQPGS--LIGDDQIYN 53
HNHc cd00085
HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic ...
 771-823 6.98e-04

HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and anaredoxins.


:

Pssm-ID: 238038 [Multi-domain]  Cd Length: 57  Bit Score: 38.22  E-value: 6.98e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 84028170 771 CSICN---STIDVEMHHVKQLHRGmlkatkdyitGRMITMNRkqIPLCKQCHIKTH 823
Cdd:cd00085  14 CPYCGkpgGTEGLEVDHIIPLSDG----------GNNDLDNL--VLLCRKCHRKKH 57
 
Name Accession Description Interval E-value
RT_G2_intron cd01651
RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA ...
 311-577 3.56e-89

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: 281.40  E-value: 3.56e-89
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170 311 RMVNIPKPKGGMRPLSVGNPRDKIVQEVMRMILDTIFDKKMSTHSHGFRKNMSCQTAIWEVRN-MFGGSNWFIEVDLKKC 389
Cdd:cd01651   1 RRVYIPKPNGKKRPLGIPTVRDRIVQEALKLVLEPIYEPRFSDCSYGFRPGRSAHDALKAIRRnVKGGYTWVIEGDIKGF 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170 390 FDTISHDLIIKELKRYISDKGFIDLVYKLLRAGYIdEKGTYHKPMLGLPQGSLISPILCNIVMTLVDNWLEDYINLYNkg 469
Cdd:cd01651  81 FDNIDHDLLLKILKRRIGDKRVLRLIRKWLKAGVL-EDGKLVETEKGTPQGGVISPLLANIYLHELDKFVEEKLKEYY-- 157

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170 470 kvkkqhptykklsrmiakakmfstrlklhkerakgptfIYNDPNFKRMKYVRYADDILIGVLGSKnDCKMIKRDLNNFLN 549
Cdd:cd01651 158 --------------------------------------DTSDPKFRRLRYVRYADDFVIGVRGPK-EAEEIKELIREFLE 198

                       250       260
                ....*....|....*....|....*...
gi 84028170 550 SLGLTMNEEKTLITCATETPARFLGYNI 577
Cdd:cd01651 199 ELGLELNPEKTRITHFKSEGFDFLGFTF 226
group_II_RT_mat TIGR04416
group II intron reverse transcriptase/maturase; Members of this protein family are ...
 260-675 3.68e-69

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: 232.73  E-value: 3.68e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170   260 DMLMLAYNRIKSKPGnmTPGT---TLETLDGMNMMYLNKLSNELGTGKFKFKPMRMVNIPKPKGGMRPLSVGNPRDKIVQ 336
Cdd:TIGR04416   2 ENLLLAYKRVKANKG--AAGVdgvTIEDFEEYLEENLYKLWNRLKSGSYRPQPVRRVEIPKPNGKQRPLGIPTVRDRVVQ 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170   337 EVMRMILDTIFDKKMSTHSHGFRKNMSCQTAIWEVR-NMFGGSNWFIEVDLKKCFDTISHDLIIKELKRYISDKGFIDLV 415
Cdd:TIGR04416  80 QAVKQVLEPIFEPDFSENSYGFRPGRSAHDAIAKARkRLNRGYRWVVDADIKGFFDNINHDLLMKAVARRISDKRVLRLI 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170   416 YKLLRAGYIdEKGTYHKPMLGLPQGSLISPILCNIVMtlvdNWLEDyinlynkgkvkkqhptykklsrmiakakmfstrl 495
Cdd:TIGR04416 160 RRWLKAGVM-EDGEVQETEEGTPQGGVISPLLANIYL----HYLDD---------------------------------- 200

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170   496 KLHKeraKGptfiyndpnfKRMKYVRYADDILIGVlGSKNDCKMIKRDLNNFLNSLGLTMNEEKTLITCATETPARFLGY 575
Cdd:TIGR04416 201 EWEK---RG----------YKVRFVRYADDFVILC-RSKEAAERVLEALTKRLEELGLELNPEKTKIVHCKDGGFDFLGF 266

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170   576 NISITPLK-RMPTVTKTIRGKTIRS-----RNTTRPIINAPIRDIINKLatngyckhnkngrmgvptrvgrwtyeepRTI 649
Cdd:TIGR04416 267 TFRKRKSKnGKGKLLIKPSKKAVKKfkekiRELTKRRRGLSLEELIKKL----------------------------NPI 318

                         410       420
                  ....*....|....*....|....*.
gi 84028170   650 InnykalgRGILNYYKLATNYKRLRE 675
Cdd:TIGR04416 319 L-------RGWANYFGIANSSRTFSK 337
YkfC COG3344
Retron-type reverse transcriptase [Mobilome: prophages, transposons];
258-711 3.49e-68

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


Pssm-ID: 442573 [Multi-domain]  Cd Length: 434  Bit Score: 232.66  E-value: 3.49e-68
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170 258 NVDMLMLAYNRIKSK---PGNmtPGTTLETLDGMNMMYLNKLSNELGTGKFKFKPMRMVNIPKPKGGMRPLSVGNPRDKI 334
Cdd:COG3344  27 SRENLLEAYKRVKANkgaAGI--DGVTVEDFEEYLEENLYDLRERLRSGSYRPQPVRRVEIPKPDGGVRPLGIPTVRDRV 104

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170 335 VQEVMRMILDTIFDKKMSTHSHGFRKNMSCQTAIWEVR-NMFGGSNWFIEVDLKKCFDTISHDLIIKELKRYISDKGFID 413
Cdd:COG3344 105 VQQAVKQVLEPIFEPDFSDSSYGFRPGRSAHDALKKAReYINEGYRWVVDADIKKFFDNVDHDLLMKRLRRRIKDKRVLR 184

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170 414 LVYKLLRAGyIDEKGTYHKPMLGLPQGSLISPILCNIVMTLVDNWLEDyinlynkgkvkkqhptykklsrmiakakmfst 493
Cdd:COG3344 185 LIRRWLKAG-VMEDGVVEEREEGTPQGGPLSPLLANIYLHELDKELER-------------------------------- 231

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170 494 rlklhkerakgptfiyndpnfKRMKYVRYADDILIGVlGSKNDCKMIKRDLNNFLNSLGLTMNEEKTLITCATETpARFL 573
Cdd:COG3344 232 ---------------------RGHRFVRYADDFVILC-RSKRAAERVLESLTERLEKLGLELNPEKTRIVRPGDG-FKFL 288

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170 574 GYNISITPLKRMPTVTKTIRGKTIRSRNTTRPIINAPIRDIINKLATNGyckhnkngrmgvptRVGRWTYEEPRTIINNY 653
Cdd:COG3344 289 GFSFRRGKGLGFKFRPRKSKRKKKRKRRRRTRRRSRKRRRRIRRLLRRL--------------LLGWRRYLLLAELKRLL 354

                       410       420       430       440       450
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 84028170 654 KALGRGILNYYKLATNYKRLRERIYYVLYYSCVltlASKYRLKTMSKTIKKFGYNLNI 711
Cdd:COG3344 355 NALLRGRRRYYRRLWRKRRKKLRRRLRLLLLRR---ARRRRAKRRARGRKRRWRIAAS 409
Intron_maturas2 pfam01348
Type II intron maturase; Group II introns use intron-encoded reverse transcriptase, maturase ...
 602-759 5.46e-54

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: 183.44  E-value: 5.46e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170   602 TTRPIINAPIRDIINKLATNGYCKHNKngRMGVPTRVGRWTYEEPRTIINNYKALGRGILNYYKLATNYKRLRERIYYVL 681
Cdd:pfam01348   1 TTRLVLNAPIRDIINKLAKAGFCKHYT--EKGKPRSVGRWTDLDDRDILLRYNAIIRGILNYYSFADNKKRLYTRIYYIL 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 84028170   682 YYSCVLTLASKYRLKTMSKTIKKFGynlniiendKLIANFPRNTFDNIKKIENHGmfmymseAKVTDPFEYIDSIKYM 759
Cdd:pfam01348  79 RLSCAKTLARKLKLGTVRKVIKKFG---------KKLSDFLIETFDSIDKNFKLK-------TNLVDPFTKTDWSLRT 140
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 315-577 1.43e-29

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: 116.25  E-value: 1.43e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170   315 IPKP-KGGMRPLSVGNPRDKIVQevmRMILDTIFDKK-MSTHSHGFRKNMSCQtaiwevrnmfGGSNWFIEVDLKKCFDT 392
Cdd:pfam00078   1 IPKKgKGKYRPISLLSIDYKALN---KIIVKRLKPENlDSPPQPGFRPGLAKL----------KKAKWFLKLDLKKAFDQ 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170   393 ISHDLIIKELKRYISDKGFIDlvykllragYIDEKGTYHKPMLGLPQGSLISPILCNIVMTLVDNWLEDYINLYnkgkvk 472
Cdd:pfam00078  68 VPLDELDRKLTAFTTPPININ---------WNGELSGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKRAGLT------ 132

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170   473 kqhptykklsrmiakakmfstrlklhkerakgptfiyndpnfkrmkYVRYADDILIGVlGSKNDCKMIKRDLNNFLNSLG 552
Cdd:pfam00078 133 ----------------------------------------------LVRYADDILIFS-KSEEEHQEALEEVLEWLKESG 165

                         250       260
                  ....*....|....*....|....*
gi 84028170   553 LTMNEEKTLITCATEtPARFLGYNI 577
Cdd:pfam00078 166 LKINPEKTQFFLKSK-EVKYLGVTL 189
COX1 MTH00153
cytochrome c oxidase subunit I; Provisional
 3-56 1.28e-16

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177210  Cd Length: 511  Bit Score: 83.76  E-value: 1.28e-16
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 84028170    3 QRWLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSqyLHGNSQLFN 56
Cdd:MTH00153   2 NKWLFSTNHKDIGTLYFIFGAWSGMVGTSLSLLIRAELGQPGS--LIGDDQIYN 53
Cyt_c_Oxidase_I cd01663
Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the ...
 9-56 5.27e-15

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: 78.68  E-value: 5.27e-15
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 84028170   9 TNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSQylHGNSQLFN 56
Cdd:cd01663   1 TNHKDIGTLYLIFGLWSGLVGTSLSLLIRLELSQPGSQ--LGNDQLYN 46
CyoB COG0843
Heme/copper-type cytochrome/quinol oxidase, subunit 1 [Energy production and conversion];
2-56 2.43e-08

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


Pssm-ID: 440605  Cd Length: 535  Bit Score: 57.44  E-value: 2.43e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 84028170   2 VQRWLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSQYLhgNSQLFN 56
Cdd:COG0843   6 WRRWLTTVDHKRIGIMYLVTAFVFLLIGGLLALLMRLQLAGPGLGLL--SPETYN 58
COX1 pfam00115
Cytochrome C and Quinol oxidase polypeptide I; Cytochrome c oxidase (E.C:7.1.1.9) is a key ...
 13-82 1.45e-04

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: 45.26  E-value: 1.45e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170    13 DIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSQYL-----------HGNSQLFngaptsAYISLMRTALVLWIINRYLK 81
Cdd:pfam00115   1 RIGLLYLVTALVWFLVGGLLGLLIRLQLAFPGLNFLspltynqlrtlHGNLMIF------WFATPFLFGFGNYLVPLMIG 74


                  .
gi 84028170    82 H 82
Cdd:pfam00115  75 A 75
HNHc cd00085
HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic ...
 771-823 6.98e-04

HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and anaredoxins.


Pssm-ID: 238038 [Multi-domain]  Cd Length: 57  Bit Score: 38.22  E-value: 6.98e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 84028170 771 CSICN---STIDVEMHHVKQLHRGmlkatkdyitGRMITMNRkqIPLCKQCHIKTH 823
Cdd:cd00085  14 CPYCGkpgGTEGLEVDHIIPLSDG----------GNNDLDNL--VLLCRKCHRKKH 57
HNHc smart00507
HNH nucleases;
770-820 9.97e-04

HNH nucleases;


Pssm-ID: 214702 [Multi-domain]  Cd Length: 52  Bit Score: 37.82  E-value: 9.97e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 84028170    770 PCSICNSTIDV--EMHHVKQLHRGMlkatkdyitgrmITMNRKQIPLCKQCHI 820
Cdd:smart00507  12 VCAYCGKPASEglEVDHIIPLSDGG------------NDDLDNLVLLCPKCHI 52
 
Name Accession Description Interval E-value
RT_G2_intron cd01651
RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA ...
 311-577 3.56e-89

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: 281.40  E-value: 3.56e-89
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170 311 RMVNIPKPKGGMRPLSVGNPRDKIVQEVMRMILDTIFDKKMSTHSHGFRKNMSCQTAIWEVRN-MFGGSNWFIEVDLKKC 389
Cdd:cd01651   1 RRVYIPKPNGKKRPLGIPTVRDRIVQEALKLVLEPIYEPRFSDCSYGFRPGRSAHDALKAIRRnVKGGYTWVIEGDIKGF 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170 390 FDTISHDLIIKELKRYISDKGFIDLVYKLLRAGYIdEKGTYHKPMLGLPQGSLISPILCNIVMTLVDNWLEDYINLYNkg 469
Cdd:cd01651  81 FDNIDHDLLLKILKRRIGDKRVLRLIRKWLKAGVL-EDGKLVETEKGTPQGGVISPLLANIYLHELDKFVEEKLKEYY-- 157

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170 470 kvkkqhptykklsrmiakakmfstrlklhkerakgptfIYNDPNFKRMKYVRYADDILIGVLGSKnDCKMIKRDLNNFLN 549
Cdd:cd01651 158 --------------------------------------DTSDPKFRRLRYVRYADDFVIGVRGPK-EAEEIKELIREFLE 198

                       250       260
                ....*....|....*....|....*...
gi 84028170 550 SLGLTMNEEKTLITCATETPARFLGYNI 577
Cdd:cd01651 199 ELGLELNPEKTRITHFKSEGFDFLGFTF 226
group_II_RT_mat TIGR04416
group II intron reverse transcriptase/maturase; Members of this protein family are ...
 260-675 3.68e-69

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: 232.73  E-value: 3.68e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170   260 DMLMLAYNRIKSKPGnmTPGT---TLETLDGMNMMYLNKLSNELGTGKFKFKPMRMVNIPKPKGGMRPLSVGNPRDKIVQ 336
Cdd:TIGR04416   2 ENLLLAYKRVKANKG--AAGVdgvTIEDFEEYLEENLYKLWNRLKSGSYRPQPVRRVEIPKPNGKQRPLGIPTVRDRVVQ 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170   337 EVMRMILDTIFDKKMSTHSHGFRKNMSCQTAIWEVR-NMFGGSNWFIEVDLKKCFDTISHDLIIKELKRYISDKGFIDLV 415
Cdd:TIGR04416  80 QAVKQVLEPIFEPDFSENSYGFRPGRSAHDAIAKARkRLNRGYRWVVDADIKGFFDNINHDLLMKAVARRISDKRVLRLI 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170   416 YKLLRAGYIdEKGTYHKPMLGLPQGSLISPILCNIVMtlvdNWLEDyinlynkgkvkkqhptykklsrmiakakmfstrl 495
Cdd:TIGR04416 160 RRWLKAGVM-EDGEVQETEEGTPQGGVISPLLANIYL----HYLDD---------------------------------- 200

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170   496 KLHKeraKGptfiyndpnfKRMKYVRYADDILIGVlGSKNDCKMIKRDLNNFLNSLGLTMNEEKTLITCATETPARFLGY 575
Cdd:TIGR04416 201 EWEK---RG----------YKVRFVRYADDFVILC-RSKEAAERVLEALTKRLEELGLELNPEKTKIVHCKDGGFDFLGF 266

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170   576 NISITPLK-RMPTVTKTIRGKTIRS-----RNTTRPIINAPIRDIINKLatngyckhnkngrmgvptrvgrwtyeepRTI 649
Cdd:TIGR04416 267 TFRKRKSKnGKGKLLIKPSKKAVKKfkekiRELTKRRRGLSLEELIKKL----------------------------NPI 318

                         410       420
                  ....*....|....*....|....*.
gi 84028170   650 InnykalgRGILNYYKLATNYKRLRE 675
Cdd:TIGR04416 319 L-------RGWANYFGIANSSRTFSK 337
YkfC COG3344
Retron-type reverse transcriptase [Mobilome: prophages, transposons];
258-711 3.49e-68

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


Pssm-ID: 442573 [Multi-domain]  Cd Length: 434  Bit Score: 232.66  E-value: 3.49e-68
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170 258 NVDMLMLAYNRIKSK---PGNmtPGTTLETLDGMNMMYLNKLSNELGTGKFKFKPMRMVNIPKPKGGMRPLSVGNPRDKI 334
Cdd:COG3344  27 SRENLLEAYKRVKANkgaAGI--DGVTVEDFEEYLEENLYDLRERLRSGSYRPQPVRRVEIPKPDGGVRPLGIPTVRDRV 104

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170 335 VQEVMRMILDTIFDKKMSTHSHGFRKNMSCQTAIWEVR-NMFGGSNWFIEVDLKKCFDTISHDLIIKELKRYISDKGFID 413
Cdd:COG3344 105 VQQAVKQVLEPIFEPDFSDSSYGFRPGRSAHDALKKAReYINEGYRWVVDADIKKFFDNVDHDLLMKRLRRRIKDKRVLR 184

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170 414 LVYKLLRAGyIDEKGTYHKPMLGLPQGSLISPILCNIVMTLVDNWLEDyinlynkgkvkkqhptykklsrmiakakmfst 493
Cdd:COG3344 185 LIRRWLKAG-VMEDGVVEEREEGTPQGGPLSPLLANIYLHELDKELER-------------------------------- 231

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170 494 rlklhkerakgptfiyndpnfKRMKYVRYADDILIGVlGSKNDCKMIKRDLNNFLNSLGLTMNEEKTLITCATETpARFL 573
Cdd:COG3344 232 ---------------------RGHRFVRYADDFVILC-RSKRAAERVLESLTERLEKLGLELNPEKTRIVRPGDG-FKFL 288

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170 574 GYNISITPLKRMPTVTKTIRGKTIRSRNTTRPIINAPIRDIINKLATNGyckhnkngrmgvptRVGRWTYEEPRTIINNY 653
Cdd:COG3344 289 GFSFRRGKGLGFKFRPRKSKRKKKRKRRRRTRRRSRKRRRRIRRLLRRL--------------LLGWRRYLLLAELKRLL 354

                       410       420       430       440       450
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 84028170 654 KALGRGILNYYKLATNYKRLRERIYYVLYYSCVltlASKYRLKTMSKTIKKFGYNLNI 711
Cdd:COG3344 355 NALLRGRRRYYRRLWRKRRKKLRRRLRLLLLRR---ARRRRAKRRARGRKRRWRIAAS 409
Intron_maturas2 pfam01348
Type II intron maturase; Group II introns use intron-encoded reverse transcriptase, maturase ...
 602-759 5.46e-54

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: 183.44  E-value: 5.46e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170   602 TTRPIINAPIRDIINKLATNGYCKHNKngRMGVPTRVGRWTYEEPRTIINNYKALGRGILNYYKLATNYKRLRERIYYVL 681
Cdd:pfam01348   1 TTRLVLNAPIRDIINKLAKAGFCKHYT--EKGKPRSVGRWTDLDDRDILLRYNAIIRGILNYYSFADNKKRLYTRIYYIL 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 84028170   682 YYSCVLTLASKYRLKTMSKTIKKFGynlniiendKLIANFPRNTFDNIKKIENHGmfmymseAKVTDPFEYIDSIKYM 759
Cdd:pfam01348  79 RLSCAKTLARKLKLGTVRKVIKKFG---------KKLSDFLIETFDSIDKNFKLK-------TNLVDPFTKTDWSLRT 140
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 315-577 1.43e-29

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: 116.25  E-value: 1.43e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170   315 IPKP-KGGMRPLSVGNPRDKIVQevmRMILDTIFDKK-MSTHSHGFRKNMSCQtaiwevrnmfGGSNWFIEVDLKKCFDT 392
Cdd:pfam00078   1 IPKKgKGKYRPISLLSIDYKALN---KIIVKRLKPENlDSPPQPGFRPGLAKL----------KKAKWFLKLDLKKAFDQ 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170   393 ISHDLIIKELKRYISDKGFIDlvykllragYIDEKGTYHKPMLGLPQGSLISPILCNIVMTLVDNWLEDYINLYnkgkvk 472
Cdd:pfam00078  68 VPLDELDRKLTAFTTPPININ---------WNGELSGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKRAGLT------ 132

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170   473 kqhptykklsrmiakakmfstrlklhkerakgptfiyndpnfkrmkYVRYADDILIGVlGSKNDCKMIKRDLNNFLNSLG 552
Cdd:pfam00078 133 ----------------------------------------------LVRYADDILIFS-KSEEEHQEALEEVLEWLKESG 165

                         250       260
                  ....*....|....*....|....*
gi 84028170   553 LTMNEEKTLITCATEtPARFLGYNI 577
Cdd:pfam00078 166 LKINPEKTQFFLKSK-EVKYLGVTL 189
RT_Bac_retron_I cd01646
RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The ...
 385-584 4.90e-17

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: 78.91  E-value: 4.90e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170 385 DLKKCFDTISHDLIIKELKRYISDK-------GFIDLVYKLLRAgyIDEKGTYhkpmlGLPQGSLISPILCNIVMTLVDN 457
Cdd:cd01646   2 DISNFYDSIYTHSLPWALHGKIKAKqllkllrLLGNLLDLLLLS--SQYGQTN-----GLPIGPLTSRFLANIYLNDVDH 74

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170 458 WLEDYINLYNkgkvkkqhptykklsrmiakakmfstrlklhkerakgptfiyndpnfkrmkYVRYADDILIGVLgSKNDC 537
Cdd:cd01646  75 ELKSKLKGVD---------------------------------------------------YVRYVDDIRIFAD-SKEEA 102

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*....
gi 84028170 538 KMIKRDLNNFLNSLGLTMNEEKTLITCATE--TPARFLGYNISITPLKR 584
Cdd:cd01646 103 EEILEELKEFLAELGLSLNLSKTEILPLPEgtASKDFLGYRFSPILLIK 151
COX1 MTH00153
cytochrome c oxidase subunit I; Provisional
 3-56 1.28e-16

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177210  Cd Length: 511  Bit Score: 83.76  E-value: 1.28e-16
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 84028170    3 QRWLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSqyLHGNSQLFN 56
Cdd:MTH00153   2 NKWLFSTNHKDIGTLYFIFGAWSGMVGTSLSLLIRAELGQPGS--LIGDDQIYN 53
COX1 MTH00167
cytochrome c oxidase subunit I; Provisional
 1-56 2.28e-15

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177222  Cd Length: 512  Bit Score: 79.72  E-value: 2.28e-15
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 84028170    1 MVQRWLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSqyLHGNSQLFN 56
Cdd:MTH00167   2 WINRWLFSTNHKDIGTLYFIFGAWAGMVGTALSLLIRAELSQPGS--LLGDDQIYN 55
Cyt_c_Oxidase_I cd01663
Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the ...
 9-56 5.27e-15

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: 78.68  E-value: 5.27e-15
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 84028170   9 TNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSQylHGNSQLFN 56
Cdd:cd01663   1 TNHKDIGTLYLIFGLWSGLVGTSLSLLIRLELSQPGSQ--LGNDQLYN 46
RT_nLTR_like cd01650
RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse ...
 311-589 1.22e-14

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: 73.86  E-value: 1.22e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170 311 RMVNIPKPKGGM-----RPLSVGNPRDKIVqevMRMILD---TIFDKKMSTHSHGFRKNMSCQTAIWEVRNMFGGSNWFI 382
Cdd:cd01650   3 RIILIPKKGKPSdpknyRPISLLSVLYKLL---EKILANrlrPVLEENILPNQFGFRPGRSTTDAILLLREVIEKAKEKK 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170 383 E------VDLKKCFDTISHDLIIKelkryisdkgfidlvykllragyidekgtyhkpMLGLPQGSLISPILCNIVMtlvd 456
Cdd:cd01650  80 KslvlvfLDFEKAFDSVDHEFLLK---------------------------------ALGVRQGDPLSPLLFNLAL---- 122

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170 457 NWLedyinlynkgkvkkqhptykklsrmiakakmfstrLKLHKERAKGPTfiyndpNFKRMKYVRYADDILIGVLGSKND 536
Cdd:cd01650 123 DDL-----------------------------------LRLLNKEEEIKL------GGPGITHLAYADDIVLFSEGKSRK 161

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|...
gi 84028170 537 CKMIKRDLNNFLNSLGLTMNEEKTLITCATETPARFLGYNISITPLKRMPTVT 589
Cdd:cd01650 162 LQELLQRLQEWSKESGLKINPSKSKVMLIGNKKKRLKDITLNGTPIEAVETFK 214
COX1 MTH00142
cytochrome c oxidase subunit I; Provisional
 2-56 1.27e-13

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 214431  Cd Length: 511  Bit Score: 74.37  E-value: 1.27e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 84028170    2 VQRWLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSqyLHGNSQLFN 56
Cdd:MTH00142   1 MMRWLFSTNHKDIGTLYFLFGAWAGMVGTGLSLLIRAELGQPGS--LLGDDQLYN 53
COX1 MTH00116
cytochrome c oxidase subunit I; Provisional
 1-56 1.59e-13

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177177  Cd Length: 515  Bit Score: 73.97  E-value: 1.59e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 84028170    1 MVQRWLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSqyLHGNSQLFN 56
Cdd:MTH00116   2 FITRWLFSTNHKDIGTLYLIFGAWAGMVGTALSLLIRAELGQPGT--LLGDDQIYN 55
COX1 MTH00223
cytochrome c oxidase subunit I; Provisional
 4-61 6.16e-13

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177260  Cd Length: 512  Bit Score: 71.93  E-value: 6.16e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 84028170    4 RWLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSqyLHGNSQLFNGAPTS 61
Cdd:MTH00223   2 RWLFSTNHKDIGTLYLIFGMWSGLVGTSLSLLIRAELGQPGA--LLGDDQLYNVIVTA 57
COX1 MTH00184
cytochrome c oxidase subunit I; Provisional
 4-56 8.03e-13

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177235  Cd Length: 519  Bit Score: 71.78  E-value: 8.03e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 84028170    4 RWLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSqyLHGNSQLFN 56
Cdd:MTH00184   7 RWLFSTNHKDIGTLYLLFGAFAGMIGTAFSMLIRLELSAPGS--MLGDDHLYN 57
COX1 MTH00077
cytochrome c oxidase subunit I; Provisional
 1-56 1.40e-12

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 214419  Cd Length: 514  Bit Score: 71.13  E-value: 1.40e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 84028170    1 MVQRWLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSqyLHGNSQLFN 56
Cdd:MTH00077   2 MITRWLFSTNHKDIGTLYLVFGAWAGMVGTALSLLIRAELSQPGT--LLGDDQIYN 55
COX1 MTH00103
cytochrome c oxidase subunit I; Validated
 1-56 1.44e-11

cytochrome c oxidase subunit I; Validated


Pssm-ID: 177165  Cd Length: 513  Bit Score: 67.60  E-value: 1.44e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 84028170    1 MVQRWLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSqyLHGNSQLFN 56
Cdd:MTH00103   2 FINRWLFSTNHKDIGTLYLLFGAWAGMVGTALSLLIRAELGQPGT--LLGDDQIYN 55
COX1 MTH00183
cytochrome c oxidase subunit I; Provisional
 1-56 1.72e-11

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177234  Cd Length: 516  Bit Score: 67.64  E-value: 1.72e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 84028170    1 MVQRWLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSqyLHGNSQLFN 56
Cdd:MTH00183   2 AITRWFFSTNHKDIGTLYLVFGAWAGMVGTALSLLIRAELSQPGA--LLGDDQIYN 55
COX1 MTH00182
cytochrome c oxidase subunit I; Provisional
 4-56 2.03e-11

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 214451  Cd Length: 525  Bit Score: 67.15  E-value: 2.03e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 84028170    4 RWLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSqyLHGNSQLFN 56
Cdd:MTH00182   7 RWVFSTNHKDIGTLYLVFGAGAGMIGTAFSMLIRLELSAPGA--MLGDDHLYN 57
COX1 MTH00079
cytochrome c oxidase subunit I; Provisional
 5-61 7.04e-11

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177148  Cd Length: 508  Bit Score: 65.47  E-value: 7.04e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 84028170    5 WLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGsqYLHGNSQLFNGAPTS 61
Cdd:MTH00079   7 WLESSNHKDIGTLYFLFGLWSGMVGTSLSLIIRLELSKPG--LLLGNGQLYNSVITA 61
RT_Bac_retron_II cd03487
RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The ...
 317-560 2.13e-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: 58.35  E-value: 2.13e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170 317 KPKGGMRPLSVGNPRDKIVQevmRMILDTIFDKkMSTH--SHGFRKNMSCQTAIwevrNMFGGSNWFIEVDLKKCFDTIS 394
Cdd:cd03487   1 KKNGGFRTIYAPKPELKAIQ---RKILSNLLSK-LPVHdaAHGFVKGRSIITNA----KPHCGAKYVLKLDIKDFFPSIT 72

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170 395 HDLIIKELKRY-ISDKGFIDLVYKLLragyidekgTYHKpmlGLPQGSLISPILCNIVMTLVDNwledyiNLYNkgkvkk 473
Cdd:cd03487  73 FERVRGVFRSLgYFSPDVATILAKLC---------TYNG---HLPQGAPTSPALSNLVFRKLDE------RLSK------ 128

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170 474 qhptykklsrmIAKAKMFstrlklhkerakgptfiyndpnfkrmKYVRYADDILIGvlGSKNDC---KMIKRDLNNFLNS 550
Cdd:cd03487 129 -----------LAKSNGL--------------------------TYTRYADDITFS--SNKKLKealDKLLEIIRSILSE 169

                       250
                ....*....|
gi 84028170 551 LGLTMNEEKT 560
Cdd:cd03487 170 EGFKINKSKT 179
Heme_Cu_Oxidase_I cd00919
Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in ...
 11-60 7.85e-09

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: 58.70  E-value: 7.85e-09
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 84028170  11 AKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSQYLhgNSQLFNGAPT 60
Cdd:cd00919   1 HKDIGLLYLIFAFVALLLGGLLALLIRLELATPGSLFL--DPQLYNQLVT 48
CyoB COG0843
Heme/copper-type cytochrome/quinol oxidase, subunit 1 [Energy production and conversion];
2-56 2.43e-08

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


Pssm-ID: 440605  Cd Length: 535  Bit Score: 57.44  E-value: 2.43e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 84028170   2 VQRWLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSQYLhgNSQLFN 56
Cdd:COG0843   6 WRRWLTTVDHKRIGIMYLVTAFVFLLIGGLLALLMRLQLAGPGLGLL--SPETYN 58
COX1 MTH00026
cytochrome c oxidase subunit I; Provisional
 4-56 9.51e-08

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 164599  Cd Length: 534  Bit Score: 55.40  E-value: 9.51e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 84028170    4 RWLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSqyLHGNSQLFN 56
Cdd:MTH00026   6 RWFFSCNHKDIGSLYLVFGALSGAIGTAFSMLIRLELSSPGS--MLGDDHLYN 56
RT_like cd00304
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
 437-577 9.45e-07

RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.


Pssm-ID: 238185 [Multi-domain]  Cd Length: 98  Bit Score: 47.73  E-value: 9.45e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170 437 LPQGSLISPILCNIVMTLVDNWledyinlynkgkvkkqhptykklsrmiakakmfstrlklHKERAKGPTFIyndpnfkr 516
Cdd:cd00304  12 LPQGSPLSPALANLYMEKLEAP---------------------------------------ILKQLLDITLI-------- 44

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 84028170 517 mkyvRYADDILigVLGSKNDCKMIKRDLNNFLNSLGLTMNEEKTLITCATEtPARFLGYNI 577
Cdd:cd00304  45 ----RYVDDLV--VIAKSEQQAVKKRELEEFLARLGLNLSDEKTQFTEKEK-KFKFLGILV 98
COX1 pfam00115
Cytochrome C and Quinol oxidase polypeptide I; Cytochrome c oxidase (E.C:7.1.1.9) is a key ...
 13-82 1.45e-04

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: 45.26  E-value: 1.45e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84028170    13 DIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSQYL-----------HGNSQLFngaptsAYISLMRTALVLWIINRYLK 81
Cdd:pfam00115   1 RIGLLYLVTALVWFLVGGLLGLLIRLQLAFPGLNFLspltynqlrtlHGNLMIF------WFATPFLFGFGNYLVPLMIG 74


                  .
gi 84028170    82 H 82
Cdd:pfam00115  75 A 75
HNHc cd00085
HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic ...
 771-823 6.98e-04

HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and anaredoxins.


Pssm-ID: 238038 [Multi-domain]  Cd Length: 57  Bit Score: 38.22  E-value: 6.98e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 84028170 771 CSICN---STIDVEMHHVKQLHRGmlkatkdyitGRMITMNRkqIPLCKQCHIKTH 823
Cdd:cd00085  14 CPYCGkpgGTEGLEVDHIIPLSDG----------GNNDLDNL--VLLCRKCHRKKH 57
HNHc smart00507
HNH nucleases;
770-820 9.97e-04

HNH nucleases;


Pssm-ID: 214702 [Multi-domain]  Cd Length: 52  Bit Score: 37.82  E-value: 9.97e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 84028170    770 PCSICNSTIDV--EMHHVKQLHRGMlkatkdyitgrmITMNRKQIPLCKQCHI 820
Cdd:smart00507  12 VCAYCGKPASEglEVDHIIPLSDGG------------NDDLDNLVLLCPKCHI 52
 
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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