|
Name |
Accession |
Description |
Interval |
E-value |
| TIGR01177 |
TIGR01177 |
putative methyltransferase, TIGR01177 family; This family of probable methyltransferases is ... |
17-332 |
1.25e-154 |
|
putative methyltransferase, TIGR01177 family; This family of probable methyltransferases is found exclusively in the Archaea. [Hypothetical proteins, Conserved]
Pssm-ID: 273486 [Multi-domain] Cd Length: 329 Bit Score: 436.87 E-value: 1.25e-154
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907989554 17 FLFYLSADNLEIARKEVLVLAERYGWVEDYQFEERLLLLDYAG-EKFFERLAYTNEVTKIYDICSVSELEQVFSEIPVYD 95
Cdd:TIGR01177 1 FYVELSGEHPELPLAELKALAEVYGRVGDVEGVDRGLAIISAPiIDILERLAFTHEVGRSYDTCAAKDLYDFVAGLEASD 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907989554 96 R---LCCVRVKGGKG----KTALERKLGALLWKRGAKVSVSNPEIVYKVYIQDDKCYVGLLEFERDTRQFFLRRPDRRPF 168
Cdd:TIGR01177 81 LdrkSFAVRVRDLRGysvdKARLERKIGAILKKKGFKVSLRRPDIVVRVVITEDIFYLGRVLEERDKEQFIERKPDRRPF 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907989554 169 LMPSAIKPKLARALVNLTGVLEGETLLDPMCGTGSFLIEAGLMGINPIGIDFIEKIVRGCRVNLEYYGIEG-SVLLGDAK 247
Cdd:TIGR01177 161 FKPGSMDPKLARAMVNLARVTEGDRVLDPFCGTGGFLIEAGLMGAKVIGCDIDWKMVAGARINLEHYGIEDfFVKRGDAT 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907989554 248 NLPLRDESVRGIATDYPYLRSTKAAGT-LDELYSKTSEEFERVLKKGGR--AAIVTNIDVESFFSN-FEIEMKTEERVHG 323
Cdd:TIGR01177 241 KLPLSSESVDAIATDPPYGRSTTAAGDgLESLYERSLEEFHEVLKSEGWivYAVPTRIDLESLAEDaFRVVKRFEVRVHR 320
|
....*....
gi 1907989554 324 SLTRRIYLL 332
Cdd:TIGR01177 321 SLTRHIYVA 329
|
|
| Trm11 |
COG1041 |
tRNA G10 N-methylase Trm11 [Translation, ribosomal structure and biogenesis]; tRNA G10 ... |
168-332 |
5.74e-69 |
|
tRNA G10 N-methylase Trm11 [Translation, ribosomal structure and biogenesis]; tRNA G10 N-methylase Trm11 is part of the Pathway/BioSystem: tRNA modification
Pssm-ID: 440663 [Multi-domain] Cd Length: 172 Bit Score: 213.27 E-value: 5.74e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907989554 168 FLMPSAIKPKLARALVNLTGVLEGETLLDPMCGTGSFLIEAGLMGINPIGIDFIEKIVRGCRVNLEYYGIEG-SVLLGDA 246
Cdd:COG1041 4 FFYPGSLDPRLARALVNLAGAKEGDTVLDPFCGTGTILIEAGLLGRRVIGSDIDPKMVEGARENLEHYGYEDaDVIRGDA 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907989554 247 KNLPLRDESVRGIATDYPYLRSTK-AAGTLDELYSKTSEEFERVLKKGGRAAIVTNIDVESFFSN--FEIEMKTEERVHG 323
Cdd:COG1041 84 RDLPLADESVDAIVTDPPYGRSSKiSGEELLELYEKALEEAARVLKPGGRVVIVTPRDIDELLEEagFKVLERHEQRVHK 163
|
....*....
gi 1907989554 324 SLTRRIYLL 332
Cdd:COG1041 164 SLTRYILVL 172
|
|
| UPF0020 |
pfam01170 |
Putative RNA methylase family UPF0020; This domain is probably a methylase. It is associated ... |
163-329 |
4.21e-65 |
|
Putative RNA methylase family UPF0020; This domain is probably a methylase. It is associated with the THUMP domain that also occurs with RNA modification domains.
Pssm-ID: 395932 [Multi-domain] Cd Length: 184 Bit Score: 203.74 E-value: 4.21e-65
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907989554 163 PDRRPFLMPSAIKPKLARALVNLTGVLEGETLLDPMCGTGSFLIEAGLMGINPI-------------GIDFIEKIVRGCR 229
Cdd:pfam01170 1 RGYRPFNGPAPLKETLAAAMVNLAGWKPGDPLLDPMCGSGTILIEAALMGANIApgkfdarvraplyGSDIDRRMVQGAR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907989554 230 VNLEYYGIEGSVLL--GDAKNLPLRDESVRGIATDYPYLRSTKAAGTLDELYSKTSEEFERVLKKGGRAAIVT--NIDVE 305
Cdd:pfam01170 81 LNAENAGVGDLIEFvqADAADLPLLEGSVDVIVTNPPYGIRLGSKGALEALYPEFLREAKRVLRGGGWLVLLTaeNKDFE 160
|
170 180
....*....|....*....|....
gi 1907989554 306 SFFSNFEIEMKTEERVHGSLTRRI 329
Cdd:pfam01170 161 KAARERAWRKKKEFNVHIGGTRVI 184
|
|
| Trm14_Arch |
NF040721 |
tRNA (guanine(6)-N2)-methyltransferase; |
125-333 |
1.63e-20 |
|
tRNA (guanine(6)-N2)-methyltransferase;
Pssm-ID: 468685 [Multi-domain] Cd Length: 370 Bit Score: 90.89 E-value: 1.63e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907989554 125 KVSVSNPEIVYKVYIQDDKCYVGLleferDTR-QFFLRRPDRRPFLMPSAIKPKLARALVNLTGVLEGETLLDPMCGTGS 203
Cdd:NF040721 130 KVNLDEPDVIVRVELIFDELLVGI-----DTTgDEGLHKRGYRVYQHPAHLNPTIASSLIYLSGWKDEESLLDPMCGSGT 204
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907989554 204 FLIEAGLMGIN-P------------------------------IGIDFIEKIVRGCRVNLEYYGIEGSV--LLGDAKNLP 250
Cdd:NF040721 205 ILIEAALIKRNiPpgkfredfafkkifghellekikkdvelkiYGIEKFRKHLEGAKKNAENAGVDDTIkfIQGDATKLD 284
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907989554 251 LRDESVRGIATDYPY-LRSTKaAGTLDELYSKTSEEFERVLKKGGRAAIVTNID--VESFFSNFEIEMKTEERV-HGSLT 326
Cdd:NF040721 285 KYFDSVDVIVTNPPYgLRIGK-KRIIKKLYNNFLRSAKKILHKRSRIVVITAEKkiFEEAAAKNGFEIIEEFNVmYGGLL 363
|
....*..
gi 1907989554 327 RRIYLLR 333
Cdd:NF040721 364 TKVFVLK 370
|
|
| ubiE |
PRK00216 |
bifunctional demethylmenaquinone methyltransferase/2-methoxy-6-polyprenyl-1,4-benzoquinol ... |
180-298 |
3.54e-08 |
|
bifunctional demethylmenaquinone methyltransferase/2-methoxy-6-polyprenyl-1,4-benzoquinol methylase UbiE;
Pssm-ID: 234689 [Multi-domain] Cd Length: 239 Bit Score: 53.62 E-value: 3.54e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907989554 180 RALVNLTGVLEGETLLDPMCGTGSF---LIEAGLMGINPIGIDFIE---KIVRGcRVNLEYYGIEGSVLLGDAKNLPLRD 253
Cdd:PRK00216 41 RKTIKWLGVRPGDKVLDLACGTGDLaiaLAKAVGKTGEVVGLDFSEgmlAVGRE-KLRDLGLSGNVEFVQGDAEALPFPD 119
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|...
gi 1907989554 254 ESVRGIA--------TDYPylrstKAagtLDELYsktseefeRVLKKGGRAAI 298
Cdd:PRK00216 120 NSFDAVTiafglrnvPDID-----KA---LREMY--------RVLKPGGRLVI 156
|
|
| THUMP_ThiI |
cd11716 |
THUMP domain of thiamine biosynthesis protein ThiI; ThiI is an enzyme responsible for the ... |
99-146 |
6.35e-04 |
|
THUMP domain of thiamine biosynthesis protein ThiI; ThiI is an enzyme responsible for the formation of the modified base S(4)U (4-thiouridine) found at position 8 in some prokaryotic tRNAs. This modification acts as a signal for UV exposure, triggering a response that provides protection against its damaging effects. ThiI consists of an N-terminal THUMP domain, followed by an NFLD domain, and a C-terminal PP-loop pyrophosphatase domain. The N-terminal THUMP domain has been implicated in the recognition of the acceptor-stem region. The THUMP domain is named after thiouridine synthases, methylases and PSUSs. The domain consists of about 110 amino acid residues. It is predicted to be an RNA-binding domain and probably functions by delivering a variety of RNA modification enzymes to their targets.
Pssm-ID: 212585 Cd Length: 166 Bit Score: 39.74 E-value: 6.35e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*
gi 1907989554 99 CVRVK-GGKG----KTALERKLGALLWKR--GAKVSVSNPEIVYKVYIQDDKCYV 146
Cdd:cd11716 103 KVRAKrADKSfpftSMEINREVGAALLENtpDLKVDLKNPDVTIRVEIREDGAYV 157
|
|
| THUMP |
smart00981 |
The THUMP domain is named after after thiouridine synthases, methylases and PSUSs; The THUMP ... |
99-148 |
3.41e-03 |
|
The THUMP domain is named after after thiouridine synthases, methylases and PSUSs; The THUMP domain consists of about 110 amino acid residues. The structure of ThiI reveals that the THUMP has a fold unlike that of previously characterised RNA-binding domains. It is predicted that this domain is an RNA-binding domain The THUMP domain probably functions by delivering a variety of RNA modification enzymes to their targets.
Pssm-ID: 214952 [Multi-domain] Cd Length: 83 Bit Score: 36.10 E-value: 3.41e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*..
gi 1907989554 99 CVRVKG-GK----GKTALERKLGALLWKR--GAKVSVSNPEIVYKVYIQDDKCYVGL 148
Cdd:smart00981 26 AVRAKRrGKnhefTSLEVKRAIGDKLLEKtgGRKVDLKNPDVVIRVELRKDKAYLSI 82
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| TIGR01177 |
TIGR01177 |
putative methyltransferase, TIGR01177 family; This family of probable methyltransferases is ... |
17-332 |
1.25e-154 |
|
putative methyltransferase, TIGR01177 family; This family of probable methyltransferases is found exclusively in the Archaea. [Hypothetical proteins, Conserved]
Pssm-ID: 273486 [Multi-domain] Cd Length: 329 Bit Score: 436.87 E-value: 1.25e-154
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907989554 17 FLFYLSADNLEIARKEVLVLAERYGWVEDYQFEERLLLLDYAG-EKFFERLAYTNEVTKIYDICSVSELEQVFSEIPVYD 95
Cdd:TIGR01177 1 FYVELSGEHPELPLAELKALAEVYGRVGDVEGVDRGLAIISAPiIDILERLAFTHEVGRSYDTCAAKDLYDFVAGLEASD 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907989554 96 R---LCCVRVKGGKG----KTALERKLGALLWKRGAKVSVSNPEIVYKVYIQDDKCYVGLLEFERDTRQFFLRRPDRRPF 168
Cdd:TIGR01177 81 LdrkSFAVRVRDLRGysvdKARLERKIGAILKKKGFKVSLRRPDIVVRVVITEDIFYLGRVLEERDKEQFIERKPDRRPF 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907989554 169 LMPSAIKPKLARALVNLTGVLEGETLLDPMCGTGSFLIEAGLMGINPIGIDFIEKIVRGCRVNLEYYGIEG-SVLLGDAK 247
Cdd:TIGR01177 161 FKPGSMDPKLARAMVNLARVTEGDRVLDPFCGTGGFLIEAGLMGAKVIGCDIDWKMVAGARINLEHYGIEDfFVKRGDAT 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907989554 248 NLPLRDESVRGIATDYPYLRSTKAAGT-LDELYSKTSEEFERVLKKGGR--AAIVTNIDVESFFSN-FEIEMKTEERVHG 323
Cdd:TIGR01177 241 KLPLSSESVDAIATDPPYGRSTTAAGDgLESLYERSLEEFHEVLKSEGWivYAVPTRIDLESLAEDaFRVVKRFEVRVHR 320
|
....*....
gi 1907989554 324 SLTRRIYLL 332
Cdd:TIGR01177 321 SLTRHIYVA 329
|
|
| Trm11 |
COG1041 |
tRNA G10 N-methylase Trm11 [Translation, ribosomal structure and biogenesis]; tRNA G10 ... |
168-332 |
5.74e-69 |
|
tRNA G10 N-methylase Trm11 [Translation, ribosomal structure and biogenesis]; tRNA G10 N-methylase Trm11 is part of the Pathway/BioSystem: tRNA modification
Pssm-ID: 440663 [Multi-domain] Cd Length: 172 Bit Score: 213.27 E-value: 5.74e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907989554 168 FLMPSAIKPKLARALVNLTGVLEGETLLDPMCGTGSFLIEAGLMGINPIGIDFIEKIVRGCRVNLEYYGIEG-SVLLGDA 246
Cdd:COG1041 4 FFYPGSLDPRLARALVNLAGAKEGDTVLDPFCGTGTILIEAGLLGRRVIGSDIDPKMVEGARENLEHYGYEDaDVIRGDA 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907989554 247 KNLPLRDESVRGIATDYPYLRSTK-AAGTLDELYSKTSEEFERVLKKGGRAAIVTNIDVESFFSN--FEIEMKTEERVHG 323
Cdd:COG1041 84 RDLPLADESVDAIVTDPPYGRSSKiSGEELLELYEKALEEAARVLKPGGRVVIVTPRDIDELLEEagFKVLERHEQRVHK 163
|
....*....
gi 1907989554 324 SLTRRIYLL 332
Cdd:COG1041 164 SLTRYILVL 172
|
|
| UPF0020 |
pfam01170 |
Putative RNA methylase family UPF0020; This domain is probably a methylase. It is associated ... |
163-329 |
4.21e-65 |
|
Putative RNA methylase family UPF0020; This domain is probably a methylase. It is associated with the THUMP domain that also occurs with RNA modification domains.
Pssm-ID: 395932 [Multi-domain] Cd Length: 184 Bit Score: 203.74 E-value: 4.21e-65
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907989554 163 PDRRPFLMPSAIKPKLARALVNLTGVLEGETLLDPMCGTGSFLIEAGLMGINPI-------------GIDFIEKIVRGCR 229
Cdd:pfam01170 1 RGYRPFNGPAPLKETLAAAMVNLAGWKPGDPLLDPMCGSGTILIEAALMGANIApgkfdarvraplyGSDIDRRMVQGAR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907989554 230 VNLEYYGIEGSVLL--GDAKNLPLRDESVRGIATDYPYLRSTKAAGTLDELYSKTSEEFERVLKKGGRAAIVT--NIDVE 305
Cdd:pfam01170 81 LNAENAGVGDLIEFvqADAADLPLLEGSVDVIVTNPPYGIRLGSKGALEALYPEFLREAKRVLRGGGWLVLLTaeNKDFE 160
|
170 180
....*....|....*....|....
gi 1907989554 306 SFFSNFEIEMKTEERVHGSLTRRI 329
Cdd:pfam01170 161 KAARERAWRKKKEFNVHIGGTRVI 184
|
|
| Trm14_Arch |
NF040721 |
tRNA (guanine(6)-N2)-methyltransferase; |
125-333 |
1.63e-20 |
|
tRNA (guanine(6)-N2)-methyltransferase;
Pssm-ID: 468685 [Multi-domain] Cd Length: 370 Bit Score: 90.89 E-value: 1.63e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907989554 125 KVSVSNPEIVYKVYIQDDKCYVGLleferDTR-QFFLRRPDRRPFLMPSAIKPKLARALVNLTGVLEGETLLDPMCGTGS 203
Cdd:NF040721 130 KVNLDEPDVIVRVELIFDELLVGI-----DTTgDEGLHKRGYRVYQHPAHLNPTIASSLIYLSGWKDEESLLDPMCGSGT 204
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907989554 204 FLIEAGLMGIN-P------------------------------IGIDFIEKIVRGCRVNLEYYGIEGSV--LLGDAKNLP 250
Cdd:NF040721 205 ILIEAALIKRNiPpgkfredfafkkifghellekikkdvelkiYGIEKFRKHLEGAKKNAENAGVDDTIkfIQGDATKLD 284
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907989554 251 LRDESVRGIATDYPY-LRSTKaAGTLDELYSKTSEEFERVLKKGGRAAIVTNID--VESFFSNFEIEMKTEERV-HGSLT 326
Cdd:NF040721 285 KYFDSVDVIVTNPPYgLRIGK-KRIIKKLYNNFLRSAKKILHKRSRIVVITAEKkiFEEAAAKNGFEIIEEFNVmYGGLL 363
|
....*..
gi 1907989554 327 RRIYLLR 333
Cdd:NF040721 364 TKVFVLK 370
|
|
| UbiE |
COG2226 |
Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; ... |
178-300 |
3.36e-13 |
|
Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG is part of the Pathway/BioSystem: Biotin biosynthesis
Pssm-ID: 441828 [Multi-domain] Cd Length: 143 Bit Score: 66.17 E-value: 3.36e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907989554 178 LARALVNLTGVLEGETLLDPMCGTGSFLIEAGLMGINPIGIDFIEKIVRGCRVNLEYYGIEGSVLLGDAKNLPLRDESV- 256
Cdd:COG2226 10 GREALLAALGLRPGARVLDLGCGTGRLALALAERGARVTGVDISPEMLELARERAAEAGLNVEFVVGDAEDLPFPDGSFd 89
|
90 100 110 120
....*....|....*....|....*....|....*....|....*
gi 1907989554 257 RGIATD-YPYLRSTKAAgtLDELYsktseefeRVLKKGGRAAIVT 300
Cdd:COG2226 90 LVISSFvLHHLPDPERA--LAEIA--------RVLKPGGRLVVVD 124
|
|
| RlmL |
COG0116 |
23S rRNA G2445 N2-methylase RlmL [Translation, ribosomal structure and biogenesis]; 23S rRNA ... |
126-214 |
8.65e-10 |
|
23S rRNA G2445 N2-methylase RlmL [Translation, ribosomal structure and biogenesis]; 23S rRNA G2445 N2-methylase RlmL is part of the Pathway/BioSystem: 23S rRNA modification
Pssm-ID: 439886 [Multi-domain] Cd Length: 369 Bit Score: 59.34 E-value: 8.65e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907989554 126 VSVSNPEIVYKVYIQDDKCYVGLleferDT-------RQFflrrpdrRPFLMPSAIKPKLARALVNLTGVLEGETLLDPM 198
Cdd:COG0116 129 VDEDGPDVRIHVHLLKDRATLSL-----DTsgeslhkRGY-------REAQGEAPLKETLAAALLLLSGWDGDRPLVDPM 196
|
90
....*....|....*.
gi 1907989554 199 CGTGSFLIEAGLMGIN 214
Cdd:COG0116 197 CGSGTILIEAALIAAN 212
|
|
| HsdM |
COG0286 |
Type I restriction-modification system, DNA methylase subunit [Defense mechanisms]; |
178-301 |
1.07e-09 |
|
Type I restriction-modification system, DNA methylase subunit [Defense mechanisms];
Pssm-ID: 440055 [Multi-domain] Cd Length: 243 Bit Score: 57.89 E-value: 1.07e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907989554 178 LARALVNLTGVLEGETLLDPMCGTGSFLIEAG----------LMGINPIGIDFIEKIVRGCRVNLEYYGI-EGSVLLGDA 246
Cdd:COG0286 31 VVRLMVELLDPKPGETVYDPACGSGGFLVEAAeylkehggdeRKKLSLYGQEINPTTYRLAKMNLLLHGIgDPNIELGDT 110
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907989554 247 knlpLRDESVRGIATDY-----PYLRSTKAAGTLDELYSKTSEEFERV--------------LKKGGRAAIVTN 301
Cdd:COG0286 111 ----LSNDGDELEKFDVvlanpPFGGKWKKEELKDDLLGRFGYGLPPKsnadllflqhilslLKPGGRAAVVLP 180
|
|
| THUMP |
pfam02926 |
THUMP domain; The THUMP domain is named after after thiouridine synthases, methylases and ... |
31-149 |
4.50e-09 |
|
THUMP domain; The THUMP domain is named after after thiouridine synthases, methylases and PSUSs. The THUMP domain consists of about 110 amino acid residues. The structure of ThiI reveals that the THUMP has a fold unlike that of previously characterized RNA-binding domains. It is predicted that this domain is an RNA-binding domain The THUMP domain probably functions by delivering a variety of RNA modification enzymes to their targets.
Pssm-ID: 460749 Cd Length: 143 Bit Score: 54.37 E-value: 4.50e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907989554 31 KEVLVLAERYGW-VEDYQFEERLLLLDYAGEKFFERLAYTNEVTKIYD--------ICSVSELEQVFSEIPVYDRL---- 97
Cdd:pfam02926 1 KEIEELLKKGGInVEVVRSGRGRILVVLKGENPEEDRELLKEALEKAPgierfpvaETCEADLEDILELAKEIIKDkfkk 80
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907989554 98 ----CCVRVKG-----GKGKTALERKLGALLWKR-GAKVSVSNPEIVYKVYIQDDKCYVGLL 149
Cdd:pfam02926 81 egetFAVRVKRrgknhEFTSLEINREVGKAIVEKtGLKVDLENPDIVVHVEIIKDKAYISID 142
|
|
| Methyltransf_25 |
pfam13649 |
Methyltransferase domain; This family appears to be a methyltransferase domain. |
195-294 |
2.96e-08 |
|
Methyltransferase domain; This family appears to be a methyltransferase domain.
Pssm-ID: 463945 [Multi-domain] Cd Length: 96 Bit Score: 50.64 E-value: 2.96e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907989554 195 LDPMCGTGSFLIE-AGLMGINPIGIDFIEKIVRGCRVNLEYYGIEGSVLLGDAKNLPLRDESVRGI--ATDYPYLRSTKA 271
Cdd:pfam13649 2 LDLGCGTGRLTLAlARRGGARVTGVDLSPEMLERARERAAEAGLNVEFVQGDAEDLPFPDGSFDLVvsSGVLHHLPDPDL 81
|
90 100
....*....|....*....|...
gi 1907989554 272 AGTLDELYsktseefeRVLKKGG 294
Cdd:pfam13649 82 EAALREIA--------RVLKPGG 96
|
|
| ubiE |
PRK00216 |
bifunctional demethylmenaquinone methyltransferase/2-methoxy-6-polyprenyl-1,4-benzoquinol ... |
180-298 |
3.54e-08 |
|
bifunctional demethylmenaquinone methyltransferase/2-methoxy-6-polyprenyl-1,4-benzoquinol methylase UbiE;
Pssm-ID: 234689 [Multi-domain] Cd Length: 239 Bit Score: 53.62 E-value: 3.54e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907989554 180 RALVNLTGVLEGETLLDPMCGTGSF---LIEAGLMGINPIGIDFIE---KIVRGcRVNLEYYGIEGSVLLGDAKNLPLRD 253
Cdd:PRK00216 41 RKTIKWLGVRPGDKVLDLACGTGDLaiaLAKAVGKTGEVVGLDFSEgmlAVGRE-KLRDLGLSGNVEFVQGDAEALPFPD 119
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|...
gi 1907989554 254 ESVRGIA--------TDYPylrstKAagtLDELYsktseefeRVLKKGGRAAI 298
Cdd:PRK00216 120 NSFDAVTiafglrnvPDID-----KA---LREMY--------RVLKPGGRLVI 156
|
|
| UbiG |
COG2227 |
2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase [Coenzyme transport and ... |
188-300 |
4.03e-07 |
|
2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase [Coenzyme transport and metabolism]; 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase is part of the Pathway/BioSystem: Ubiquinone biosynthesis
Pssm-ID: 441829 [Multi-domain] Cd Length: 126 Bit Score: 48.48 E-value: 4.03e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907989554 188 VLEGETLLDPMCGTGSFLIEAGLMGINPIGIDFIEKIVRGCRVNLEYYGIEgsVLLGDAKNLPLRDESVRGIATDY--PY 265
Cdd:COG2227 22 LPAGGRVLDVGCGTGRLALALARRGADVTGVDISPEALEIARERAAELNVD--FVQGDLEDLPLEDGSFDLVICSEvlEH 99
|
90 100 110
....*....|....*....|....*....|....*
gi 1907989554 266 LRSTKAAgtLDELYsktseefeRVLKKGGRAAIVT 300
Cdd:COG2227 100 LPDPAAL--LRELA--------RLLKPGGLLLLST 124
|
|
| Methyltransf_11 |
pfam08241 |
Methyltransferase domain; Members of this family are SAM dependent methyltransferases. |
195-298 |
4.70e-07 |
|
Methyltransferase domain; Members of this family are SAM dependent methyltransferases.
Pssm-ID: 462406 [Multi-domain] Cd Length: 94 Bit Score: 47.27 E-value: 4.70e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907989554 195 LDPMCGTGSFLIEAGLMGINPIGIDFIEKIVRGCRVNLEYYGIEgsVLLGDAKNLPLRDESVRGIAtdypylrSTKAAGT 274
Cdd:pfam08241 1 LDVGCGTGLLTELLARLGARVTGVDISPEMLELAREKAPREGLT--FVVGDAEDLPFPDNSFDLVL-------SSEVLHH 71
|
90 100
....*....|....*....|....
gi 1907989554 275 LDELySKTSEEFERVLKKGGRAAI 298
Cdd:pfam08241 72 VEDP-ERALREIARVLKPGGILII 94
|
|
| PRK08317 |
PRK08317 |
hypothetical protein; Provisional |
190-307 |
9.28e-07 |
|
hypothetical protein; Provisional
Pssm-ID: 181382 [Multi-domain] Cd Length: 241 Bit Score: 49.16 E-value: 9.28e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907989554 190 EGETLLDPMCGTGSFLIE-AGLMGinP----IGIDFIEKIVRGCRVNLEYYGIEGSVLLGDAKNLPLRDESVRGIATD-- 262
Cdd:PRK08317 19 PGDRVLDVGCGPGNDARElARRVG--PegrvVGIDRSEAMLALAKERAAGLGPNVEFVRGDADGLPFPDGSFDAVRSDrv 96
|
90 100 110 120
....*....|....*....|....*....|....*....|....*
gi 1907989554 263 YPYLRSTKAAgtLDELYsktseefeRVLKKGGRAAIVTNiDVESF 307
Cdd:PRK08317 97 LQHLEDPARA--LAEIA--------RVLRPGGRVVVLDT-DWDTL 130
|
|
| rlmL |
PRK11783 |
bifunctional 23S rRNA (guanine(2069)-N(7))-methyltransferase RlmK/23S rRNA (guanine(2445)-N(2)) ... |
174-211 |
2.59e-06 |
|
bifunctional 23S rRNA (guanine(2069)-N(7))-methyltransferase RlmK/23S rRNA (guanine(2445)-N(2))-methyltransferase RlmL;
Pssm-ID: 236981 [Multi-domain] Cd Length: 702 Bit Score: 49.03 E-value: 2.59e-06
10 20 30
....*....|....*....|....*....|....*....
gi 1907989554 174 IKPKLARALVNLTGVLE-GETLLDPMCGTGSFLIEAGLM 211
Cdd:PRK11783 173 LKENLAAAILLRSGWPQeGTPLLDPMCGSGTLLIEAAMM 211
|
|
| N6_Mtase |
pfam02384 |
N-6 DNA Methylase; Restriction-modification (R-M) systems protect a bacterial cell against ... |
178-299 |
1.10e-04 |
|
N-6 DNA Methylase; Restriction-modification (R-M) systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The R-M system is a complex containing three polypeptides: M (this family), S (pfam01420), and R. This family consists of N-6 adenine-specific DNA methylase EC:2.1.1.72 from Type I and Type IC restriction systems. These methylases have the same sequence specificity as their corresponding restriction enzymes.
Pssm-ID: 426749 [Multi-domain] Cd Length: 310 Bit Score: 43.46 E-value: 1.10e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907989554 178 LARALVNLTGVLEGETLLDPMCGTGSFLIEA----GLMGINPI-----GIDFIEKIVRGCRVNLEYYGIEGS---VLLGD 245
Cdd:pfam02384 33 VSKLIVELLDPKPGESIYDPACGSGGFLIQAekfvKEHDGDTNdlsiyGQEKNPTTYRLARMNMILHGIEYDdfhIRHGD 112
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907989554 246 AKNLPL--RDESVRGIATDYPYLRSTKAAGTL--DELYS-------KTSEEFE------RVLKKGGRAAIV 299
Cdd:pfam02384 113 TLTSPKfeDDKKFDVVVANPPFSDKWDANDTLenDPRFRpaygvapKSNADLAflqhiiYYLAPGGRAAVV 183
|
|
| Methyltransf_31 |
pfam13847 |
Methyltransferase domain; This family appears to have methyltransferase activity. |
190-300 |
2.81e-04 |
|
Methyltransferase domain; This family appears to have methyltransferase activity.
Pssm-ID: 463998 [Multi-domain] Cd Length: 150 Bit Score: 40.86 E-value: 2.81e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907989554 190 EGETLLDPMCGTGSFLIE-AGLMGINP--IGIDFIEKIVRGCRVNLEYYGIEG-SVLLGDAKNLP--LRDESVrgiatDY 263
Cdd:pfam13847 3 KGMRVLDLGCGTGHLSFElAEELGPNAevVGIDISEEAIEKARENAQKLGFDNvEFEQGDIEELPelLEDDKF-----DV 77
|
90 100 110
....*....|....*....|....*....|....*..
gi 1907989554 264 PYLRSTKAAGTLDElysKTSEEFERVLKKGGRAAIVT 300
Cdd:pfam13847 78 VISNCVLNHIPDPD---KVLQEILRVLKPGGRLIISD 111
|
|
| COG2263 |
COG2263 |
Predicted RNA methylase [General function prediction only]; |
176-307 |
3.09e-04 |
|
Predicted RNA methylase [General function prediction only];
Pssm-ID: 441864 [Multi-domain] Cd Length: 199 Bit Score: 41.43 E-value: 3.09e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907989554 176 PKLARALVN---LTGVLEGETLLDPMCGTGSFLIEAGLMGINP-IGIDFIEKIVRGCRVNLEYYGIEGSVLLGDAKNLPL 251
Cdd:COG2263 28 AELAAELLHlayLRGDIEGKTVLDLGCGTGMLAIGAALLGAKKvVGVDIDPEALEIARENAERLGVRVDFIRADVTRIPL 107
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907989554 252 RDE-----------SVRGIAtDYPYLRstKAAGTLDELYSKTSEEFERVLKK--GGRAAIVTNIDVESF 307
Cdd:COG2263 108 GGSvdtvvmnppfgAQRRHA-DRPFLE--KALEIAAVIYSIHNAGSLDFVERfaADRGGEITHVFRAEF 173
|
|
| THUMP_ThiI |
cd11716 |
THUMP domain of thiamine biosynthesis protein ThiI; ThiI is an enzyme responsible for the ... |
99-146 |
6.35e-04 |
|
THUMP domain of thiamine biosynthesis protein ThiI; ThiI is an enzyme responsible for the formation of the modified base S(4)U (4-thiouridine) found at position 8 in some prokaryotic tRNAs. This modification acts as a signal for UV exposure, triggering a response that provides protection against its damaging effects. ThiI consists of an N-terminal THUMP domain, followed by an NFLD domain, and a C-terminal PP-loop pyrophosphatase domain. The N-terminal THUMP domain has been implicated in the recognition of the acceptor-stem region. The THUMP domain is named after thiouridine synthases, methylases and PSUSs. The domain consists of about 110 amino acid residues. It is predicted to be an RNA-binding domain and probably functions by delivering a variety of RNA modification enzymes to their targets.
Pssm-ID: 212585 Cd Length: 166 Bit Score: 39.74 E-value: 6.35e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*
gi 1907989554 99 CVRVK-GGKG----KTALERKLGALLWKR--GAKVSVSNPEIVYKVYIQDDKCYV 146
Cdd:cd11716 103 KVRAKrADKSfpftSMEINREVGAALLENtpDLKVDLKNPDVTIRVEIREDGAYV 157
|
|
| ThiI |
COG0301 |
Adenylyl- and sulfurtransferase ThiI (thiamine and tRNA 4-thiouridine biosynthesis) [Coenzyme ... |
99-146 |
7.78e-04 |
|
Adenylyl- and sulfurtransferase ThiI (thiamine and tRNA 4-thiouridine biosynthesis) [Coenzyme transport and metabolism, Translation, ribosomal structure and biogenesis]; Adenylyl- and sulfurtransferase ThiI (thiamine and tRNA 4-thiouridine biosynthesis) is part of the Pathway/BioSystem: Thiamine biosynthesis
Pssm-ID: 440070 [Multi-domain] Cd Length: 382 Bit Score: 40.84 E-value: 7.78e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*.
gi 1907989554 99 CVRVKGgKGKTA------LERKLGALLWKR--GAKVSVSNPEIVYKVYIQDDKCYV 146
Cdd:COG0301 104 KVRAKR-AGKHFpftspeLEREVGGALLENtpGLKVDLKNPDVTIRVEVRDDKAYV 158
|
|
| AdoMet_MTases |
cd02440 |
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ... |
193-299 |
1.24e-03 |
|
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: 37.79 E-value: 1.24e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907989554 193 TLLDPMCGTGSFLIE-AGLMGINPIGIDFIEKIVRGCRVNLEYYGIEG-SVLLGDA-KNLPLRDESVRGIATDYPYlrst 269
Cdd:cd02440 1 RVLDLGCGTGALALAlASGPGARVTGVDISPVALELARKAAAALLADNvEVLKGDAeELPPEADESFDVIISDPPL---- 76
|
90 100 110
....*....|....*....|....*....|
gi 1907989554 270 kaaGTLDELYSKTSEEFERVLKKGGRAAIV 299
Cdd:cd02440 77 ---HHLVEDLARFLEEARRLLKPGGVLVLT 103
|
|
| THUMP |
smart00981 |
The THUMP domain is named after after thiouridine synthases, methylases and PSUSs; The THUMP ... |
99-148 |
3.41e-03 |
|
The THUMP domain is named after after thiouridine synthases, methylases and PSUSs; The THUMP domain consists of about 110 amino acid residues. The structure of ThiI reveals that the THUMP has a fold unlike that of previously characterised RNA-binding domains. It is predicted that this domain is an RNA-binding domain The THUMP domain probably functions by delivering a variety of RNA modification enzymes to their targets.
Pssm-ID: 214952 [Multi-domain] Cd Length: 83 Bit Score: 36.10 E-value: 3.41e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*..
gi 1907989554 99 CVRVKG-GK----GKTALERKLGALLWKR--GAKVSVSNPEIVYKVYIQDDKCYVGL 148
Cdd:smart00981 26 AVRAKRrGKnhefTSLEVKRAIGDKLLEKtgGRKVDLKNPDVVIRVELRKDKAYLSI 82
|
|
| N6_N4_Mtase |
pfam01555 |
DNA methylase; Members of this family are DNA methylases. The family contains both N-4 ... |
173-226 |
4.03e-03 |
|
DNA methylase; Members of this family are DNA methylases. The family contains both N-4 cytosine-specific DNA methylases and N-6 Adenine-specific DNA methylases.
Pssm-ID: 396230 [Multi-domain] Cd Length: 221 Bit Score: 38.15 E-value: 4.03e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*
gi 1907989554 173 AIKP-KLARALVNLTgVLEGETLLDPMCGTGSFLIEAGLMGINPIGIDFIEKIVR 226
Cdd:pfam01555 164 TQKPeALLERLILAS-TNPGDIVLDPFAGSGTTGAAAKELGRNFIGIEIEEEYVE 217
|
|
| YhdJ |
COG0863 |
DNA modification methylase [Replication, recombination and repair]; |
173-226 |
7.52e-03 |
|
DNA modification methylase [Replication, recombination and repair];
Pssm-ID: 440623 Cd Length: 236 Bit Score: 37.21 E-value: 7.52e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*....
gi 1907989554 173 AIKP-KLARALVNLTGVlEGETLLDPMCGTGSFLIEAGLMGINPIGID----FIEKIVR 226
Cdd:COG0863 165 TQKPvELLERLILASSN-PGDIVLDPFAGSGTTLVAAERLGRRFIGIEidpeYVEVARR 222
|
|
| |
