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Conserved domains on  [gi|489643399|ref|WP_003547839|]
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GIY-YIG nuclease family protein [Lactobacillus acidophilus]

Protein Classification

GIY-YIG nuclease family protein( domain architecture ID 11467889)

uncharacterized GIY-YIG nuclease family protein; uncharacterized protein of the GIY-YIG nuclease superfamily

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TrmN6 COG4123
tRNA1(Val) A37 N6-methylase TrmN6 [Translation, ribosomal structure and biogenesis]; tRNA1(Val) ...
 8-247 2.50e-80

tRNA1(Val) A37 N6-methylase TrmN6 [Translation, ribosomal structure and biogenesis]; tRNA1(Val) A37 N6-methylase TrmN6 is part of the Pathway/BioSystem: tRNA modification


:

Pssm-ID: 443299 [Multi-domain]  Cd Length: 238  Bit Score: 244.67  E-value: 2.50e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489643399   8 ERIDYMYSDDLRIIQDKTAFSFSMDTLLLAYWAKdvIRDRDKVADLCAGNCAATIYMAY-FNRAHYDAIEIQDEIYSQAK 86
Cdd:COG4123    1 ERLDGFLFKQFRIIQPRCGYRFGTDAVLLAAFAP--VKKGGRVLDLGTGTGVIALMLAQrSPGARITGVEIQPEAAELAR 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489643399  87 RSVELNDMENRISVYKDNVLNASKHLRKDSYDVVTVNPPYFKAPEGHeVNPDPKKAIARHELLINLEQIIEVASGLLKMK 166
Cdd:COG4123   79 RNVALNGLEDRITVIHGDLKEFAAELPPGSFDLVVSNPPYFKAGSGR-KSPDEARAIARHEDALTLEDLIRAAARLLKPG 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489643399 167 GKMFMVHRPERLAEICYYCMRHDLSIKLVQPFVSHRDEDANLIIVEAVKHtGTDGTELKDAIEVHDQSGEFRPLIQRIVR 246
Cdd:COG4123  158 GRFALIHPAERLAEILAALRKYGLGPKRLRPVHPRPGKPAKRVLLEARKG-GRAGLRILPPLVIHDEDGEYTPEVKALLR 236


                 .
gi 489643399 247 E 247
Cdd:COG4123  237 D 237
GIY-YIG_UPF0213 cd10456
The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific ...
 261-326 3.94e-33

The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific endonuclease SLX1; This family contains a group of uncharacterized proteins found mainly in bacteria and several in dsDNA viruses. Although their function roles have not been recognized, these proteins show significant sequence similarities with the N-terminal GIY-YIG endonuclease domain of structure-specific endonuclease subunit SLX1, which binds another structure-specific endonuclease subunit SLX4 to form an active heterodimeric SLX1-SLX4 complex. This complex functions as a 5' flap endonuclease in yeast, and has also been identified as a Holliday junction resolvase in human.


:

Pssm-ID: 198403  Cd Length: 68  Bit Score: 117.13  E-value: 3.94e-33
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489643399 261 YYFYVLLCNDGSFYGGFTNDLEHRLKMHNDGKGAKYTKSRRPVKMIYHEKFDDKRLALKREYWFKH 326
Cdd:cd10456    1 WYVYILRCADGSLYTGITTDLERRLAEHNSGKGAKYTRGRRPVKLVYSEEFDDRSEALKREYRIKK 66
 
Name Accession Description Interval E-value
TrmN6 COG4123
tRNA1(Val) A37 N6-methylase TrmN6 [Translation, ribosomal structure and biogenesis]; tRNA1(Val) ...
 8-247 2.50e-80

tRNA1(Val) A37 N6-methylase TrmN6 [Translation, ribosomal structure and biogenesis]; tRNA1(Val) A37 N6-methylase TrmN6 is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 443299 [Multi-domain]  Cd Length: 238  Bit Score: 244.67  E-value: 2.50e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489643399   8 ERIDYMYSDDLRIIQDKTAFSFSMDTLLLAYWAKdvIRDRDKVADLCAGNCAATIYMAY-FNRAHYDAIEIQDEIYSQAK 86
Cdd:COG4123    1 ERLDGFLFKQFRIIQPRCGYRFGTDAVLLAAFAP--VKKGGRVLDLGTGTGVIALMLAQrSPGARITGVEIQPEAAELAR 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489643399  87 RSVELNDMENRISVYKDNVLNASKHLRKDSYDVVTVNPPYFKAPEGHeVNPDPKKAIARHELLINLEQIIEVASGLLKMK 166
Cdd:COG4123   79 RNVALNGLEDRITVIHGDLKEFAAELPPGSFDLVVSNPPYFKAGSGR-KSPDEARAIARHEDALTLEDLIRAAARLLKPG 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489643399 167 GKMFMVHRPERLAEICYYCMRHDLSIKLVQPFVSHRDEDANLIIVEAVKHtGTDGTELKDAIEVHDQSGEFRPLIQRIVR 246
Cdd:COG4123  158 GRFALIHPAERLAEILAALRKYGLGPKRLRPVHPRPGKPAKRVLLEARKG-GRAGLRILPPLVIHDEDGEYTPEVKALLR 236


                 .
gi 489643399 247 E 247
Cdd:COG4123  237 D 237
GIY-YIG_UPF0213 cd10456
The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific ...
 261-326 3.94e-33

The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific endonuclease SLX1; This family contains a group of uncharacterized proteins found mainly in bacteria and several in dsDNA viruses. Although their function roles have not been recognized, these proteins show significant sequence similarities with the N-terminal GIY-YIG endonuclease domain of structure-specific endonuclease subunit SLX1, which binds another structure-specific endonuclease subunit SLX4 to form an active heterodimeric SLX1-SLX4 complex. This complex functions as a 5' flap endonuclease in yeast, and has also been identified as a Holliday junction resolvase in human.


Pssm-ID: 198403  Cd Length: 68  Bit Score: 117.13  E-value: 3.94e-33
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489643399 261 YYFYVLLCNDGSFYGGFTNDLEHRLKMHNDGKGAKYTKSRRPVKMIYHEKFDDKRLALKREYWFKH 326
Cdd:cd10456    1 WYVYILRCADGSLYTGITTDLERRLAEHNSGKGAKYTRGRRPVKLVYSEEFDDRSEALKREYRIKK 66
YhbQ COG2827
Predicted endonuclease, GIY-YIG superfamily [Replication, recombination and repair];
261-339 6.61e-33

Predicted endonuclease, GIY-YIG superfamily [Replication, recombination and repair];


Pssm-ID: 442075 [Multi-domain]  Cd Length: 82  Bit Score: 117.15  E-value: 6.61e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489643399 261 YYFYVLLC-NDGSFYGGFTNDLEHRLKMHNDGKGAKYTKSRRPVKMIYHEKFDDKRLALKREYWFKHHSRAWKEKFLREH 339
Cdd:COG2827    3 YYVYILRCaDNGTLYTGVTNDLERRLAEHNSGKGAKFTRKRRPVKLVYYEEFEDRSEALKREKQIKKWSRAKKEALIEGD 82
PRK00329 PRK00329
GIY-YIG nuclease superfamily protein; Validated
 261-336 4.93e-31

GIY-YIG nuclease superfamily protein; Validated


Pssm-ID: 178979  Cd Length: 86  Bit Score: 112.32  E-value: 4.93e-31
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489643399 261 YYFYVLLCNDGSFYGGFTNDLEHRLKMHNDGKGAKYTKSRRPVKMIYHEKFDDKRLALKREYWFKHHSRAWKEKFL 336
Cdd:PRK00329   7 WFLYLLRCADGSLYTGITTDVERRFAQHQSGKGAKYTRGRPPLTLVFVEPVGDRSEALRAEYRFKQLTKKQKERLV 82
GIY-YIG pfam01541
GIY-YIG catalytic domain; This domain called GIY-YIG is found in the amino terminal region of ...
 261-334 1.35e-12

GIY-YIG catalytic domain; This domain called GIY-YIG is found in the amino terminal region of excinuclease abc subunit c (uvrC), bacteriophage T4 endonucleases segA, segB, segC, segD and segE; it is also found in putative endonucleases encoded by group I introns of fungi and phage. The structure of I-TevI a GIY-YIG endonuclease, reveals a novel alpha/beta-fold with a central three-stranded antiparallel beta-sheet flanked by three helices. The most conserved and putative catalytic residues are located on a shallow, concave surface and include a metal coordination site.


Pssm-ID: 426314 [Multi-domain]  Cd Length: 78  Bit Score: 62.36  E-value: 1.35e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489643399  261 YYFYVLLCNDGSF-YGGFTNDLEHRLKMHNDGKGAKYTKSR--RPVKMIYHEKFDDKRLALKREYWFKHHSRAWKEK 334
Cdd:pfam01541   2 GGIYIIRNKDNKLlYVGSTKNLERRLNQHNAGKGAKYTRGKgvEPFKLIYLEEFPTKSEALELEKYLIKLYRPNKYN 78
MTS pfam05175
Methyltransferase small domain; This domain is found in ribosomal RNA small subunit ...
 49-172 4.24e-07

Methyltransferase small domain; This domain is found in ribosomal RNA small subunit methyltransferase C as well as other methyltransferases.


Pssm-ID: 428349 [Multi-domain]  Cd Length: 170  Bit Score: 49.13  E-value: 4.24e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489643399   49 KVADLCAGNCAATIYMAYFN-RAHYDAIEIQDEIYSQAKRSVELNDMENrISVYKDNVLNASKhlrKDSYDVVTVNPPyF 127
Cdd:pfam05175  34 KVLDLGCGAGVLGAALAKESpDAELTMVDINARALESARENLAANGLEN-GEVVASDVYSGVE---DGKFDLIISNPP-F 108

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 489643399  128 KApeGHEVNPDpkkaIArhellinlEQIIEVASGLLKMKGKMFMV 172
Cdd:pfam05175 109 HA--GLATTYN----VA--------QRFIADAKRHLRPGGELWIV 139
PRK14967 PRK14967
putative methyltransferase; Provisional
 32-173 1.47e-06

putative methyltransferase; Provisional


Pssm-ID: 184931 [Multi-domain]  Cd Length: 223  Bit Score: 48.51  E-value: 1.47e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489643399  32 DTLLLAywakDVIRDRD-----KVADLCAGNCAATIYMAYFNRAHYDAIEIQdeiySQAKRSVELNDMENRISVykdNVL 106
Cdd:PRK14967  21 DTQLLA----DALAAEGlgpgrRVLDLCTGSGALAVAAAAAGAGSVTAVDIS----RRAVRSARLNALLAGVDV---DVR 89

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489643399 107 NAS--KHLRKDSYDVVTVNPPYFKAPEGHEVNPDPKKAI-ARHELLINLEQIIEVASGLLKMKGKMFMVH 173
Cdd:PRK14967  90 RGDwaRAVEFRPFDVVVSNPPYVPAPPDAPPSRGPARAWdAGPDGRAVLDRLCDAAPALLAPGGSLLLVQ 159
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 49-134 3.04e-04

S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).


Pssm-ID: 100107 [Multi-domain]  Cd Length: 107  Bit Score: 39.72  E-value: 3.04e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489643399  49 KVADLCAGNCAATIYMAYFNRAHYDAIEIQDEIYSQAKRsVELNDMENRISVYKDNVLNASKhLRKDSYDVVTVNPPYFK 128
Cdd:cd02440    1 RVLDLGCGTGALALALASGPGARVTGVDISPVALELARK-AAAALLADNVEVLKGDAEELPP-EADESFDVIISDPPLHH 78


                 ....*.
gi 489643399 129 APEGHE 134
Cdd:cd02440   79 LVEDLA 84
 
Name Accession Description Interval E-value
TrmN6 COG4123
tRNA1(Val) A37 N6-methylase TrmN6 [Translation, ribosomal structure and biogenesis]; tRNA1(Val) ...
 8-247 2.50e-80

tRNA1(Val) A37 N6-methylase TrmN6 [Translation, ribosomal structure and biogenesis]; tRNA1(Val) A37 N6-methylase TrmN6 is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 443299 [Multi-domain]  Cd Length: 238  Bit Score: 244.67  E-value: 2.50e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489643399   8 ERIDYMYSDDLRIIQDKTAFSFSMDTLLLAYWAKdvIRDRDKVADLCAGNCAATIYMAY-FNRAHYDAIEIQDEIYSQAK 86
Cdd:COG4123    1 ERLDGFLFKQFRIIQPRCGYRFGTDAVLLAAFAP--VKKGGRVLDLGTGTGVIALMLAQrSPGARITGVEIQPEAAELAR 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489643399  87 RSVELNDMENRISVYKDNVLNASKHLRKDSYDVVTVNPPYFKAPEGHeVNPDPKKAIARHELLINLEQIIEVASGLLKMK 166
Cdd:COG4123   79 RNVALNGLEDRITVIHGDLKEFAAELPPGSFDLVVSNPPYFKAGSGR-KSPDEARAIARHEDALTLEDLIRAAARLLKPG 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489643399 167 GKMFMVHRPERLAEICYYCMRHDLSIKLVQPFVSHRDEDANLIIVEAVKHtGTDGTELKDAIEVHDQSGEFRPLIQRIVR 246
Cdd:COG4123  158 GRFALIHPAERLAEILAALRKYGLGPKRLRPVHPRPGKPAKRVLLEARKG-GRAGLRILPPLVIHDEDGEYTPEVKALLR 236


                 .
gi 489643399 247 E 247
Cdd:COG4123  237 D 237
GIY-YIG_UPF0213 cd10456
The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific ...
 261-326 3.94e-33

The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific endonuclease SLX1; This family contains a group of uncharacterized proteins found mainly in bacteria and several in dsDNA viruses. Although their function roles have not been recognized, these proteins show significant sequence similarities with the N-terminal GIY-YIG endonuclease domain of structure-specific endonuclease subunit SLX1, which binds another structure-specific endonuclease subunit SLX4 to form an active heterodimeric SLX1-SLX4 complex. This complex functions as a 5' flap endonuclease in yeast, and has also been identified as a Holliday junction resolvase in human.


Pssm-ID: 198403  Cd Length: 68  Bit Score: 117.13  E-value: 3.94e-33
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489643399 261 YYFYVLLCNDGSFYGGFTNDLEHRLKMHNDGKGAKYTKSRRPVKMIYHEKFDDKRLALKREYWFKH 326
Cdd:cd10456    1 WYVYILRCADGSLYTGITTDLERRLAEHNSGKGAKYTRGRRPVKLVYSEEFDDRSEALKREYRIKK 66
YhbQ COG2827
Predicted endonuclease, GIY-YIG superfamily [Replication, recombination and repair];
261-339 6.61e-33

Predicted endonuclease, GIY-YIG superfamily [Replication, recombination and repair];


Pssm-ID: 442075 [Multi-domain]  Cd Length: 82  Bit Score: 117.15  E-value: 6.61e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489643399 261 YYFYVLLC-NDGSFYGGFTNDLEHRLKMHNDGKGAKYTKSRRPVKMIYHEKFDDKRLALKREYWFKHHSRAWKEKFLREH 339
Cdd:COG2827    3 YYVYILRCaDNGTLYTGVTNDLERRLAEHNSGKGAKFTRKRRPVKLVYYEEFEDRSEALKREKQIKKWSRAKKEALIEGD 82
PRK00329 PRK00329
GIY-YIG nuclease superfamily protein; Validated
 261-336 4.93e-31

GIY-YIG nuclease superfamily protein; Validated


Pssm-ID: 178979  Cd Length: 86  Bit Score: 112.32  E-value: 4.93e-31
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489643399 261 YYFYVLLCNDGSFYGGFTNDLEHRLKMHNDGKGAKYTKSRRPVKMIYHEKFDDKRLALKREYWFKHHSRAWKEKFL 336
Cdd:PRK00329   7 WFLYLLRCADGSLYTGITTDVERRFAQHQSGKGAKYTRGRPPLTLVFVEPVGDRSEALRAEYRFKQLTKKQKERLV 82
GIY-YIG_SLX1_like cd10449
Catalytic GIY-YIG domain of yeast structure-specific endonuclease subunit SLX1 and its ...
 262-328 2.46e-17

Catalytic GIY-YIG domain of yeast structure-specific endonuclease subunit SLX1 and its homologs; Structure-specific endonuclease subunit SLX1 is a highly conserved protein from yeast to human, with an N-terminal GIY-YIG endonuclease domain and a C-terminal PHD-type zinc finger postulated to mediate protein-protein or protein-DNA interaction. SLX1 forms active heterodimeric complexes with its SLX4 partner, which has additional roles in the DNA damage response that are distinct from the function of the heterodimeric SLX1-SLX4 nuclease. In yeast, the SLX1-SLX4 complex functions as a 5' flap endonuclease that maintains ribosomal DNA copy number, where SLX1 and SLX4 are shown to be catalytic and regulatory subunits, respectively. This endonuclease introduces single-strand cuts in duplex DNA on the 3' side of junctions with single-strand DNA. In addition to 5' flap endonuclease activity, human SLX1-SLX4 complex has been identified as a Holliday junction resolvase that promotes symmetrical cleavage of static and migrating Holliday junctions. SLX1 also associates with MUS81, EME1, C20orf94, PLK1, and ERCC1. Some eukaryotic SLX1 homologs lack the zinc finger domain, but possess intrinsically unstructured extensions of unknown function. These unstructured segments might be involved in interactions with other proteins.


Pssm-ID: 198396  Cd Length: 67  Bit Score: 75.32  E-value: 2.46e-17
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489643399 262 YFYVLLC-NDGSFYGGFTNDLEHRLKMHNDGKGAKYTKsRRPVKMIYHEKFDDKRLALKREYWFKHHS 328
Cdd:cd10449    1 YVYILYSeKLDRYYIGYTSDLERRLEQHNSGKSKFTSK-YRPWELVYSEAFESKSEALKREKYLKSGK 67
GIY-YIG pfam01541
GIY-YIG catalytic domain; This domain called GIY-YIG is found in the amino terminal region of ...
 261-334 1.35e-12

GIY-YIG catalytic domain; This domain called GIY-YIG is found in the amino terminal region of excinuclease abc subunit c (uvrC), bacteriophage T4 endonucleases segA, segB, segC, segD and segE; it is also found in putative endonucleases encoded by group I introns of fungi and phage. The structure of I-TevI a GIY-YIG endonuclease, reveals a novel alpha/beta-fold with a central three-stranded antiparallel beta-sheet flanked by three helices. The most conserved and putative catalytic residues are located on a shallow, concave surface and include a metal coordination site.


Pssm-ID: 426314 [Multi-domain]  Cd Length: 78  Bit Score: 62.36  E-value: 1.35e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489643399  261 YYFYVLLCNDGSF-YGGFTNDLEHRLKMHNDGKGAKYTKSR--RPVKMIYHEKFDDKRLALKREYWFKHHSRAWKEK 334
Cdd:pfam01541   2 GGIYIIRNKDNKLlYVGSTKNLERRLNQHNAGKGAKYTRGKgvEPFKLIYLEEFPTKSEALELEKYLIKLYRPNKYN 78
GIY-YIG_unchar_3 cd10448
GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; The family includes ...
 261-340 1.45e-12

GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; The family includes a group of uncharacterized bacterial proteins with a GIY-YIG domain that shows statistically significant similarity to the N-terminal catalytic domains of GIY-YIG family of intron-encoded homing endonuclease I-TevI and catalytic GIY-YIG domain of nucleotide excision repair endonuclease UvrC.


Pssm-ID: 198395  Cd Length: 87  Bit Score: 62.51  E-value: 1.45e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489643399 261 YYFYVLL-CNDGSFYGGFTNDLEHRLKMHNDGKGAKYTKSRRPVKMIYHEKFDDKRLALKREYWFKHHSRAWKEKFLREH 339
Cdd:cd10448    1 YYVYILAnKRNGTLYIGVTSDLIRRIYEHKEGLGSGFTSKYNVTRLVYYEEFEDIEEAIAREKQLKKWRRAWKINLIEKM 80


                 .
gi 489643399 340 N 340
Cdd:cd10448   81 N 81
HemK COG2890
Methylase of polypeptide chain release factors [Translation, ribosomal structure and ...
 32-171 1.41e-09

Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis];


Pssm-ID: 442135 [Multi-domain]  Cd Length: 282  Bit Score: 58.24  E-value: 1.41e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489643399  32 DTLLLAYWAKDVIRDRD--KVADLCAGN-C-AATIyMAYFNRAHYDAIEIQDEIYSQAKRSVELNDMENRISVYKDNVLN 107
Cdd:COG2890   96 ETEELVELALALLPAGAppRVLDLGTGSgAiALAL-AKERPDARVTAVDISPDALAVARRNAERLGLEDRVRFLQGDLFE 174

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489643399 108 ASKHLRKdsYDVVTVNPPYFKAPEGHEVNPDpkkaIARHE-----------LLInLEQIIEVASGLLKMKGKMFM 171
Cdd:COG2890  175 PLPGDGR--FDLIVSNPPYIPEDEIALLPPE----VRDHEprlaldggedgLDF-YRRIIAQAPRLLKPGGWLLL 242
GIY-YIG_SLX1 cd10455
Catalytic GIY-YIG domain of yeast structure-specific endonuclease subunit SLX1 and its ...
 260-326 3.13e-08

Catalytic GIY-YIG domain of yeast structure-specific endonuclease subunit SLX1 and its eukaryotic homologs; Structure-specific endonuclease subunit SLX1 is a highly conserved protein from yeast to human, with an N-terminal GIY-YIG endonuclease domain and a C-terminal PHD-type zinc finger postulated to mediate protein-protein or protein-DNA interaction. SLX1 forms active heterodimeric complexes with its SLX4 partner, which has additional roles in the DNA damage response that are distinct from the function of the heterodimeric SLX1-SLX4 nuclease. In yeast, the SLX1-SLX4 complex functions as a 5' flap endonuclease that maintains ribosomal DNA copy number, where SLX1 and SLX4 are shown to be catalytic and regulatory subunits, respectively. This endonuclease introduces single-strand cuts in duplex DNA on the 3' side of junctions with single-strand DNA. In addition to 5' flap endonuclease activity, human SLX1-SLX4 complex has been identified as a Holliday junction resolvase that promotes symmetrical cleavage of static and migrating Holliday junctions. SLX1 also associates with MUS81, EME1, C20orf94, PLK1, and ERCC1. Some eukaryotic SLX1 homologs lack the zinc finger domain, but possess intrinsically unstructured extensions of unknown function. These unstructured segments might be involved in interactions with other proteins.


Pssm-ID: 198402  Cd Length: 76  Bit Score: 49.92  E-value: 3.13e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489643399 260 LYYFYVLLCND----GSFYGGFTNDLEHRLKMHNDG--KGAKYTKSRRPVKM--IYHeKFDDKRLALKREYWFKH 326
Cdd:cd10455    1 FYGVYLLRSLNpkykGRTYIGFTVNPPRRLRQHNGElkGGAKKTSRKRPWEMvlIVH-GFPSKVAALQFEWAWQH 74
MTS pfam05175
Methyltransferase small domain; This domain is found in ribosomal RNA small subunit ...
 49-172 4.24e-07

Methyltransferase small domain; This domain is found in ribosomal RNA small subunit methyltransferase C as well as other methyltransferases.


Pssm-ID: 428349 [Multi-domain]  Cd Length: 170  Bit Score: 49.13  E-value: 4.24e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489643399   49 KVADLCAGNCAATIYMAYFN-RAHYDAIEIQDEIYSQAKRSVELNDMENrISVYKDNVLNASKhlrKDSYDVVTVNPPyF 127
Cdd:pfam05175  34 KVLDLGCGAGVLGAALAKESpDAELTMVDINARALESARENLAANGLEN-GEVVASDVYSGVE---DGKFDLIISNPP-F 108

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 489643399  128 KApeGHEVNPDpkkaIArhellinlEQIIEVASGLLKMKGKMFMV 172
Cdd:pfam05175 109 HA--GLATTYN----VA--------QRFIADAKRHLRPGGELWIV 139
PRK14967 PRK14967
putative methyltransferase; Provisional
 32-173 1.47e-06

putative methyltransferase; Provisional


Pssm-ID: 184931 [Multi-domain]  Cd Length: 223  Bit Score: 48.51  E-value: 1.47e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489643399  32 DTLLLAywakDVIRDRD-----KVADLCAGNCAATIYMAYFNRAHYDAIEIQdeiySQAKRSVELNDMENRISVykdNVL 106
Cdd:PRK14967  21 DTQLLA----DALAAEGlgpgrRVLDLCTGSGALAVAAAAAGAGSVTAVDIS----RRAVRSARLNALLAGVDV---DVR 89

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489643399 107 NAS--KHLRKDSYDVVTVNPPYFKAPEGHEVNPDPKKAI-ARHELLINLEQIIEVASGLLKMKGKMFMVH 173
Cdd:PRK14967  90 RGDwaRAVEFRPFDVVVSNPPYVPAPPDAPPSRGPARAWdAGPDGRAVLDRLCDAAPALLAPGGSLLLVQ 159
RsmC COG2813
16S rRNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]; 16S rRNA ...
 48-172 3.12e-06

16S rRNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]; 16S rRNA G1207 methylase RsmC is part of the Pathway/BioSystem: 16S rRNA modification


Pssm-ID: 442062 [Multi-domain]  Cd Length: 191  Bit Score: 47.11  E-value: 3.12e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489643399  48 DKVADLCAGNCAATIYMAYFN-RAHYDAIEIqDE--IYSqAKRSVELNDMENrISVYKDNVLNaskHLRKDSYDVVTVNP 124
Cdd:COG2813   51 GRVLDLGCGYGVIGLALAKRNpEARVTLVDV-NAraVEL-ARANAAANGLEN-VEVLWSDGLS---GVPDGSFDLILSNP 124

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 489643399 125 PyFKApeGHEVNPDPkkaiarhellinLEQIIEVASGLLKMKGKMFMV 172
Cdd:COG2813  125 P-FHA--GRAVDKEV------------AHALIADAARHLRPGGELWLV 157
GIY-YIG_SF cd00719
GIY-YIG nuclease domain superfamily; The GIY-YIG nuclease domain superfamily includes a large ...
 259-327 2.94e-05

GIY-YIG nuclease domain superfamily; The GIY-YIG nuclease domain superfamily includes a large and diverse group of proteins involved in many cellular processes, such as class I homing GIY-YIG family endonucleases, prokaryotic nucleotide excision repair proteins UvrC and Cho, type II restriction enzymes, the endonuclease/reverse transcriptase of eukaryotic retrotransposable elements, and a family of eukaryotic enzymes that repair stalled replication forks. All of these members contain a conserved GIY-YIG nuclease domain that may serve as a scaffold for the coordination of a divalent metal ion required for catalysis of the phosphodiester bond cleavage. By combining with different specificity, targeting, or other domains, the GIY-YIG nucleases may perform different functions.


Pssm-ID: 198380 [Multi-domain]  Cd Length: 69  Bit Score: 41.58  E-value: 2.94e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489643399 259 GLYYFYvlLCNDGSFYGGFTNDLEHRLKMHNDGKGAKYTKSRRPVKMIYHEKFD-DKRLALKREYWFKHH 327
Cdd:cd00719    1 GVYVLY--DEDNGLIYVGQTKNLRNRIKEHLRKQRSDWTKGLKPFEILYLEVAPeAESELLDLEAALIKK 68
PRK14968 PRK14968
putative methyltransferase; Provisional
 32-136 7.32e-05

putative methyltransferase; Provisional


Pssm-ID: 237872 [Multi-domain]  Cd Length: 188  Bit Score: 42.96  E-value: 7.32e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489643399  32 DTLLLAYWAkdVIRDRDKVADLCAGNCAATIYMAyfNRAHY-DAIEIQDEIYSQAKRSVELNDMENR-ISVYKDNVLNAs 109
Cdd:PRK14968  11 DSFLLAENA--VDKKGDRVLEVGTGSGIVAIVAA--KNGKKvVGVDINPYAVECAKCNAKLNNIRNNgVEVIRSDLFEP- 85

                         90       100
                 ....*....|....*....|....*..
gi 489643399 110 khLRKDSYDVVTVNPPYFKAPEGHEVN 136
Cdd:PRK14968  86 --FRGDKFDVILFNPPYLPTEEEEEWD 110
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 49-134 3.04e-04

S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).


Pssm-ID: 100107 [Multi-domain]  Cd Length: 107  Bit Score: 39.72  E-value: 3.04e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489643399  49 KVADLCAGNCAATIYMAYFNRAHYDAIEIQDEIYSQAKRsVELNDMENRISVYKDNVLNASKhLRKDSYDVVTVNPPYFK 128
Cdd:cd02440    1 RVLDLGCGTGALALALASGPGARVTGVDISPVALELARK-AAAALLADNVEVLKGDAEELPP-EADESFDVIISDPPLHH 78


                 ....*.
gi 489643399 129 APEGHE 134
Cdd:cd02440   79 LVEDLA 84
 
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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