Citrus Sinensis ID: 025787

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------25
Protein Sequence
MSTCRAIIRTSFSFVESKFYFLPSKSFLSLSLRSQKPGPISPYSVRTRQYGSVQAAISLENGNNLIDDENDTPSKDNVEKLLTNPDDVTQFMKMERSCMVNDGVGSMESLSNKRWFPYLDRYKCGDVYLSSSEVVEALSPYLMEERKERFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIELWDAPRECFNVLRSRGYRIATTHVGMDACCA
Secondary Structure (PSIPRED)
ccccccHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHccccHHHHHHHHccccccccccccccccccccccccccccccccccccHHHHHHHHcccccHHHHHHHHHHHHHccccEEEEEccccccccHHHHHHHHHHHcccEEEEEcccccccccccccccccccccEEEEEEccHHHHHHHHHHcccEEEEEEcccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccEEEEEEcHHcccccccccccccccHHHHHHcccccHHHHHHHccccccccccccccccccccccccccccEccccEEcHHHHHHHHHHHccHHHHHHHHHHHHHccccEEEEEEccccccccEEEEEcHHHcccEEEEEEEccccccccccccHHcccccEEEccccccHHHHHHHHHHcccEEEEEccccccccc
Coil and Loop (DISEMBL)
MSTCRAIIRTSFSFVeskfyflpsksflslslrsqkpgpispysvrtrqYGSVQAAISlengnnliddendtpskdnveklltnpdDVTQFMKMERScmvndgvgsmeslsnkrwfpyldrykcgdvylsSSEVVEALSPYLMEERKERFVNVVKNRSYSVCLVVEGlsdfgnvsatfrsadalgvQSVHVVscdsskryrenrhvsmgaekWLDIELWDAPRECFNVLRSRgyriatthvgmdacca
Flexible Loop (DISEMBL)
mstcraiirtsfsfveskfyFLPSKSFLSLSLRSQKPGPISPYSVRTRQYGSVQAAISlengnnliddendtpskdnveKLLTNPDDVTQFMKMERSCMVNDGVGSMESLSNKRWFPYLDRYKCGDVYLSSSEVVEALSPYLMEERKERFVNVVKNRSYSVCLVVEGLSDFGNVSATFrsadalgvqSVHVvscdsskryrenrhvsmgaekwldieLWDAPRECFNVLRSRGYriatthvgmdacCA
Low Complexity Region (SEG)
MSTCRAIIRTSFSFVEskfyflpsksflslslrsqkPGPISPYSVRTRQYGSVQAAISLENGNNLIDDENDTPSKDNVEKLLTNPDDVTQFMKMERSCMVNDGVGSMESLSNKRWFPYLDRYKCGDVYLSSSEVVEALSPYLMEERKERFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIELWDAPRECFNVLRSRGYRIATTHVGMDACCA
Disordered region (IsUnstruct)
***CRAIIRTSFSFVESKFYFLPSKSFLSL*******************************************************************CMVNDGVGSMESLSNKRWFPYLDRYKCGDVYLSSSEVVEALSPYLMEERKERFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIELWDAPRECFNVLRSRGYRIATTHVGMDAC**
Disordered Region (DISOPRED)
*******************************************************************************KLLTNPDDVTQ********************SNKRWFPYLDRYKCGDVYLSSSEVVEALSPYLMEERKERFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIELWDAPRECFNVLRSRGYRIATTHVGMDACC*
Disordered Region (DISEMBL)
MSTCRAIIRTSFSFVESKFYFLPSKSFLSLSLRSQKPGPISPYSVRTRQYGSVQAAISLENGNNLIDDENDTPSKDNVEKLLTNPDDVTQFMKMERSCMVNDGVGSMESLSNKRWFPYLDRYKCGDVYLSSSEVVEALSPYLMEERKERFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIELWDAPRECFNVLRSRGYRIATTHVGMDACCA
Disordered Region (DISPRO)
***CRAIIRTSFSFVESKFYFLPSKSFLSLSLRSQKPGPISPYSVRTRQYGSVQAAISLENGNNLI*******SKDNVEKLLTNPDDVTQFMKMERSC******GSM**LSNKRWFPYLDRYKCGDVYLSSSEVVEALSPYLMEERKERFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIELWDAPRECFNVLRSRGYRIATTHVGMDACCA
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSTCRAIIRTSFSFVESKFYFLPSKSFLSLSLRSQKPGPISPYSVRTRQYGSVQAAISLENGNNLIDDENDTPSKDNVEKLLTNPDDVTQFMKMERSCMVNDGVGSMESLSNKRWFPYLDRYKCGDVYLSSSEVVEALSPYLMEERKERFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIELWDAPRECFNVLRSRGYRIATTHVGMDACCA
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	248	2.2.26 [Sep-21-2011]
O51081	218	Putative tRNA/rRNA methyl	yes	no	0.415	0.472	0.276	3e-08
O67577	211	tRNA (guanosine(18)-2'-O)	yes	no	0.419	0.492	0.247	4e-05
P0AGJ4	229	tRNA (guanosine(18)-2'-O)	yes	no	0.399	0.432	0.277	0.0006
P0AGJ2	229	tRNA (guanosine(18)-2'-O)	N/A	no	0.399	0.432	0.277	0.0006
P0AGJ3	229	tRNA (guanosine(18)-2'-O)	N/A	no	0.399	0.432	0.277	0.0006

>sp|O51081|Y052_BORBU Putative tRNA/rRNA methyltransferase BB_0052 OS=Borrelia burgdorferi (strain ATCC 35210 / B31 / CIP 102532 / DSM 4680) GN=BB_0052 PE=3 SV=1

 Score = 58.9 bits (141), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 29/105 (27%), Positives = 57/105 (54%), Gaps = 2/105 (1%)

Query: 135 VEALSPYLMEERKERFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSC 194
           +  LS ++ +E+K R   V+  R+  +  V+E +    N SAT R+ + LG+  VHV+  
Sbjct: 9   IGVLSKFITDEKKARIEKVLNLRTNYLTFVLEDIFQSQNASATIRTGEILGLSDVHVI-- 66

Query: 195 DSSKRYRENRHVSMGAEKWLDIELWDAPRECFNVLRSRGYRIATT 239
           +   ++  N  V++G+ +W+++  +   +   + L+S GY I  T
Sbjct: 67  EKKNKHTLNPDVTLGSSQWINLNKYKNAKFAIDRLKSDGYSIVAT 111

Borrelia burgdorferi (strain ATCC 35210 / B31 / CIP 102532 / DSM 4680) (taxid: 224326)
EC: 2EC: .EC: 1EC: .EC: 1EC: .EC: -

>sp|O67577|TRMH_AQUAE tRNA (guanosine(18)-2'-O)-methyltransferase OS=Aquifex aeolicus (strain VF5) GN=trmH PE=1 SV=1

 Score = 48.9 bits (115), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 26/105 (24%), Positives = 56/105 (53%), Gaps = 1/105 (0%)

Query: 142 LMEERKERFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYR 201
           ++E+R +R   V++ R   + +  + + +  N SA  R+ DA+GV  ++    +  K+ +
Sbjct: 7   VLEKRLKRLREVLEKRQKDLIVFADNVKNEHNFSAIVRTCDAVGVLYLYYYHAEG-KKAK 65

Query: 202 ENRHVSMGAEKWLDIELWDAPRECFNVLRSRGYRIATTHVGMDAC 246
            N  ++ G+ KW+ IE  D P +     ++RG++I  T +  ++ 
Sbjct: 66  INEGITQGSHKWVFIEKVDNPVQKLLEFKNRGFQIVATWLSKESV 110

Specifically methylates guanosine-18 in various tRNAs.

Aquifex aeolicus (strain VF5) (taxid: 224324)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 3

EC: 4

>sp|P0AGJ4|TRMH_SHIFL tRNA (guanosine(18)-2'-O)-methyltransferase OS=Shigella flexneri GN=trmH PE=3 SV=1

 Score = 44.7 bits (104), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 28/101 (27%), Positives = 47/101 (46%), Gaps = 2/101 (1%)

Query: 146 RKERFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRH 205
           R  R   ++  R   + + +E +    NVSA  R+ADA+GV  VH V   S  R R    
Sbjct: 5   RYARICEMLARRQPDLTVCMEQVHKPHNVSAIIRTADAVGVHEVHAVWPGS--RMRTMAS 62

Query: 206 VSMGAEKWLDIELWDAPRECFNVLRSRGYRIATTHVGMDAC 246
            + G+  W+ ++      +    L+ +G +I  TH+  +A 
Sbjct: 63  AAAGSNSWVQVKTHRTIGDAVAHLKGQGMQILATHLSDNAV 103

Specifically methylates guanosine-18 in various tRNAs.

Shigella flexneri (taxid: 623)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 3

EC: 4

>sp|P0AGJ2|TRMH_ECOLI tRNA (guanosine(18)-2'-O)-methyltransferase OS=Escherichia coli (strain K12) GN=trmH PE=1 SV=1

 Score = 44.7 bits (104), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 28/101 (27%), Positives = 47/101 (46%), Gaps = 2/101 (1%)

Query: 146 RKERFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRH 205
           R  R   ++  R   + + +E +    NVSA  R+ADA+GV  VH V   S  R R    
Sbjct: 5   RYARICEMLARRQPDLTVCMEQVHKPHNVSAIIRTADAVGVHEVHAVWPGS--RMRTMAS 62

Query: 206 VSMGAEKWLDIELWDAPRECFNVLRSRGYRIATTHVGMDAC 246
            + G+  W+ ++      +    L+ +G +I  TH+  +A 
Sbjct: 63  AAAGSNSWVQVKTHRTIGDAVAHLKGQGMQILATHLSDNAV 103

Specifically methylates guanosine-18 in various tRNAs.

Escherichia coli (strain K12) (taxid: 83333)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 3

EC: 4

>sp|P0AGJ3|TRMH_ECO57 tRNA (guanosine(18)-2'-O)-methyltransferase OS=Escherichia coli O157:H7 GN=trmH PE=3 SV=1

 Score = 44.7 bits (104), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 28/101 (27%), Positives = 47/101 (46%), Gaps = 2/101 (1%)

Query: 146 RKERFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRH 205
           R  R   ++  R   + + +E +    NVSA  R+ADA+GV  VH V   S  R R    
Sbjct: 5   RYARICEMLARRQPDLTVCMEQVHKPHNVSAIIRTADAVGVHEVHAVWPGS--RMRTMAS 62

Query: 206 VSMGAEKWLDIELWDAPRECFNVLRSRGYRIATTHVGMDAC 246
            + G+  W+ ++      +    L+ +G +I  TH+  +A 
Sbjct: 63  AAAGSNSWVQVKTHRTIGDAVAHLKGQGMQILATHLSDNAV 103

Specifically methylates guanosine-18 in various tRNAs.

Escherichia coli O157:H7 (taxid: 83334)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 3

EC: 4

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	248
225452930	372	PREDICTED: tRNA (guanosine(18)-2'-O)-met	0.955	0.637	0.577	3e-74
296082972	369	unnamed protein product [Vitis vinifera]	0.955	0.642	0.577	3e-74
255584325	334	rRNA methylase, putative [Ricinus commun	0.870	0.646	0.621	8e-74
297807561	350	tRNA/rRNA methyltransferase family prote	0.923	0.654	0.559	1e-67
449438036	370	PREDICTED: tRNA (guanosine(18)-2'-O)-met	0.975	0.654	0.527	3e-67
15242287	350	tRNA/rRNA methyltransferase (SpoU) famil	0.947	0.671	0.562	4e-67
356523592	322	PREDICTED: tRNA (guanosine(18)-2'-O)-met	0.685	0.527	0.646	4e-61
224080139	269	predicted protein [Populus trichocarpa]	0.629	0.579	0.706	4e-61
40715982	368	rRNA methylase-like protein [Viscum albu	0.830	0.559	0.557	1e-59
357502123	322	tRNA guanosine-2'-O-methyltransferase [M	0.854	0.658	0.516	4e-56

>gi|225452930|ref|XP_002278944.1| PREDICTED: tRNA (guanosine(18)-2'-O)-methyltransferase-like [Vitis vinifera]

 Score =  284 bits (726), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 153/265 (57%), Positives = 185/265 (69%), Gaps = 28/265 (10%)

Query: 1   MSTCRAIIRTSFSFVE-------SKFYFLP-----SKSFLSLSLR--------SQKPGPI 40
           MS C+ ++R S S +E         F F+P     S S +S SLR        S     +
Sbjct: 4   MSACKTLVRISISSLEFSLVCNQRNFSFIPLPNHPSFSPISSSLRFASLLSPASSISLGL 63

Query: 41  SPYSVRTRQYGSVQAAISLENGNNLIDDENDTPSKDNVEKLLTNPDDVTQFMKMERSCMV 100
           + + + +R Y  V  ++ +E   +L DD N    KD VE LLTN DDV + MKMER  M 
Sbjct: 64  TRHKLHSRPYVHVAESVGVET-TDLEDDSN----KDIVEHLLTNTDDVGRLMKMERRSMT 118

Query: 101 NDGVGSMESLSNKRWFPYLDRYKCGDVYLSSSEVVEALSPYLMEERKERFVNVVKNRSYS 160
            DG    E + +KRWFPYLD++K G  +LSSSE++EA+ PY+ME RKERF NVVK+RSYS
Sbjct: 119 GDG---GELIQSKRWFPYLDKFKTGTTFLSSSEILEAMDPYIMEVRKERFRNVVKSRSYS 175

Query: 161 VCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIELWD 220
           VCLVVEGL DFGNVSA FRSADALG QSVHVVSCDSSKRY++NRHVSMGAEKWLDIELW+
Sbjct: 176 VCLVVEGLCDFGNVSAAFRSADALGFQSVHVVSCDSSKRYKDNRHVSMGAEKWLDIELWN 235

Query: 221 APRECFNVLRSRGYRIATTHVGMDA 245
           + +ECF VL+SRGYRIATTHVGMDA
Sbjct: 236 STQECFEVLKSRGYRIATTHVGMDA 260

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296082972|emb|CBI22273.3| unnamed protein product [Vitis vinifera]

 Score =  284 bits (726), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 153/265 (57%), Positives = 185/265 (69%), Gaps = 28/265 (10%)

Query: 1   MSTCRAIIRTSFSFVE-------SKFYFLP-----SKSFLSLSLR--------SQKPGPI 40
           MS C+ ++R S S +E         F F+P     S S +S SLR        S     +
Sbjct: 1   MSACKTLVRISISSLEFSLVCNQRNFSFIPLPNHPSFSPISSSLRFASLLSPASSISLGL 60

Query: 41  SPYSVRTRQYGSVQAAISLENGNNLIDDENDTPSKDNVEKLLTNPDDVTQFMKMERSCMV 100
           + + + +R Y  V  ++ +E   +L DD N    KD VE LLTN DDV + MKMER  M 
Sbjct: 61  TRHKLHSRPYVHVAESVGVET-TDLEDDSN----KDIVEHLLTNTDDVGRLMKMERRSMT 115

Query: 101 NDGVGSMESLSNKRWFPYLDRYKCGDVYLSSSEVVEALSPYLMEERKERFVNVVKNRSYS 160
            DG    E + +KRWFPYLD++K G  +LSSSE++EA+ PY+ME RKERF NVVK+RSYS
Sbjct: 116 GDG---GELIQSKRWFPYLDKFKTGTTFLSSSEILEAMDPYIMEVRKERFRNVVKSRSYS 172

Query: 161 VCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIELWD 220
           VCLVVEGL DFGNVSA FRSADALG QSVHVVSCDSSKRY++NRHVSMGAEKWLDIELW+
Sbjct: 173 VCLVVEGLCDFGNVSAAFRSADALGFQSVHVVSCDSSKRYKDNRHVSMGAEKWLDIELWN 232

Query: 221 APRECFNVLRSRGYRIATTHVGMDA 245
           + +ECF VL+SRGYRIATTHVGMDA
Sbjct: 233 STQECFEVLKSRGYRIATTHVGMDA 257

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255584325|ref|XP_002532898.1| rRNA methylase, putative [Ricinus communis] gi|223527332|gb|EEF29478.1| rRNA methylase, putative [Ricinus communis]

 Score =  282 bits (722), Expect = 8e-74,   Method: Compositional matrix adjust.
 Identities = 156/251 (62%), Positives = 174/251 (69%), Gaps = 35/251 (13%)

Query: 1   MSTCRAI----IRTSF-SFVESKFYFLPSKSFLSLSLRSQKPGPISPYSVRTRQYGSVQA 55
           MSTCR +    IR S  S  +SK  FL              P    PY    R Y S+QA
Sbjct: 1   MSTCRTLNLTQIRISICSLKKSKPCFL-------------NPRTAGPYRPSARSYSSIQA 47

Query: 56  A-ISLENGNNLIDDENDTPSKDNVEKLLTNPDDVTQFMKMERSCMVNDGVGSMESLSNKR 114
           A +SLE+ +   D +N+T     VE LL+N DDV + MKMER              S  R
Sbjct: 48  AAVSLESAD---DSKNET-----VEHLLSNRDDVLRLMKMERRPDAEK--------SGSR 91

Query: 115 WFPYLDRYKCGDVYLSSSEVVEALSPYLMEERKERFVNVVKNRSYSVCLVVEGLSDFGNV 174
           WFPYLDRYKCG   LS SEV+EA+ PY+ME+RKERF NVVKNRSYSVCLVVEGLSDFGNV
Sbjct: 92  WFPYLDRYKCGSGELSGSEVLEAVGPYIMEDRKERFANVVKNRSYSVCLVVEGLSDFGNV 151

Query: 175 SATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIELWDAPRECFNVLRSRGY 234
           SA FRSADALG QSVHVVSCDSSKRYR+NRHVSMGAEKWLDIELWD+ +ECF VL+SRGY
Sbjct: 152 SAAFRSADALGFQSVHVVSCDSSKRYRDNRHVSMGAEKWLDIELWDSTQECFEVLKSRGY 211

Query: 235 RIATTHVGMDA 245
           RIATTHVGMDA
Sbjct: 212 RIATTHVGMDA 222

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297807561|ref|XP_002871664.1| tRNA/rRNA methyltransferase family protein [Arabidopsis lyrata subsp. lyrata] gi|297317501|gb|EFH47923.1| tRNA/rRNA methyltransferase family protein [Arabidopsis lyrata subsp. lyrata]

 Score =  261 bits (668), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 142/254 (55%), Positives = 176/254 (69%), Gaps = 25/254 (9%)

Query: 1   MSTCRAIIR---TSFSFV------ESKFYFLPSKSFLSLSLRSQKPGPISPYSVRTRQYG 51
           M++C++IIR   +SF FV       S  + LP ++F  LS+    P  I       R + 
Sbjct: 1   MNSCKSIIRASISSFPFVPLPNPNSSITFILPVRAFPPLSVLHPNPSCIG---TARRTFH 57

Query: 52  SVQAAISLENGNNLIDDENDTPSKDNVEKLLT-NPDDVTQFMKMERSCMVNDGVGSMESL 110
            V AA+S E+         D+P KD V+ LLT N  D +  MKMER C ++DG G     
Sbjct: 58  GV-AALSPESLTE------DSP-KDTVKDLLTTNRGDASSMMKMERRCSLSDGEGDCRG- 108

Query: 111 SNKRWFPYLDRYKCGDVYLSSSEVVEALSPYLMEERKERFVNVVKNRSYSVCLVVEGLSD 170
               WFPY DR++C +V+LSS EV+EA++P++MEER +RF  VV+NRS+SVCLVVEGLSD
Sbjct: 109 ---SWFPYEDRFRCAEVHLSSREVLEAVTPHMMEERTDRFRRVVENRSFSVCLVVEGLSD 165

Query: 171 FGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIELWDAPRECFNVLR 230
           FGN+SA FRSADALG+QSVHVVSC SSKRY  NRHVSMGAEKWLDIE WD P+ECF VL+
Sbjct: 166 FGNISAAFRSADALGIQSVHVVSCGSSKRYNGNRHVSMGAEKWLDIEFWDTPKECFKVLK 225

Query: 231 SRGYRIATTHVGMD 244
           SRGYRIATTH+GMD
Sbjct: 226 SRGYRIATTHLGMD 239

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449438036|ref|XP_004136796.1| PREDICTED: tRNA (guanosine(18)-2'-O)-methyltransferase-like [Cucumis sativus]

 Score =  260 bits (665), Expect = 3e-67,   Method: Compositional matrix adjust.
 Identities = 136/258 (52%), Positives = 176/258 (68%), Gaps = 16/258 (6%)

Query: 1   MSTCRAIIRTSFSFVES----------KFYFLPSKSFLSLSLR-SQKPGPISPYSVRTRQ 49
           M++CR + R+S   ++S             FLPS    S SL  + +    +P +V TR 
Sbjct: 1   MASCRIVSRSSLFLLQSCSPRRTQRIFSSVFLPSLHLPSFSLFFTNRFSRSNPNAVSTRC 60

Query: 50  YGSVQAAISLENGNNLIDDEN--DTPSKDNVEKLLTNPDDVTQFMKMERSCMVNDGVGSM 107
           + S+ AA S     +++ D    +  ++D VE LLT+ +DV + MKMER  +  DG    
Sbjct: 61  FASISAATSPLEVEDIVADVEPPEVRTQDTVEHLLTHSNDVARLMKMERRSVELDGA--- 117

Query: 108 ESLSNKRWFPYLDRYKCGDVYLSSSEVVEALSPYLMEERKERFVNVVKNRSYSVCLVVEG 167
           E     RWFPYLD+Y CG  +L+S E++EAL   +++ RKERF NVV+NRSYSVCLVVEG
Sbjct: 118 EYPHKGRWFPYLDKYSCGSSWLNSGEILEALDSLILDSRKERFKNVVRNRSYSVCLVVEG 177

Query: 168 LSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIELWDAPRECFN 227
           L+DFGNVSA FRSADALG QSVHVVSCD+SKRYRENRHVSMGAEKWLDIELW++  ECF 
Sbjct: 178 LTDFGNVSAAFRSADALGFQSVHVVSCDASKRYRENRHVSMGAEKWLDIELWNSTPECFK 237

Query: 228 VLRSRGYRIATTHVGMDA 245
           +L+SRGYRI +TH+G +A
Sbjct: 238 ILKSRGYRIVSTHLGANA 255

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15242287|ref|NP_197043.1| tRNA/rRNA methyltransferase (SpoU) family protein [Arabidopsis thaliana] gi|7671508|emb|CAB89349.1| rRNA methylase-like protein [Arabidopsis thaliana] gi|110737570|dbj|BAF00727.1| rRNA methylase - like protein [Arabidopsis thaliana] gi|332004772|gb|AED92155.1| tRNA/rRNA methyltransferase (SpoU) family protein [Arabidopsis thaliana]

 Score =  260 bits (665), Expect = 4e-67,   Method: Compositional matrix adjust.
 Identities = 139/247 (56%), Positives = 174/247 (70%), Gaps = 12/247 (4%)

Query: 1   MSTCRAIIRTSFSFVESKFYFLPSKSFLSLSLRSQKPGPISPYSVRTRQYGSVQAAISLE 60
           M++C+++IR S S     F  LP+ +F S++  S +    SP SV       +  A    
Sbjct: 1   MNSCKSLIRASISSF--PFVPLPNPNF-SITFISVRA--FSPLSVLHPNSSCIVTARRTF 55

Query: 61  NGNNLIDDENDTPS--KDNVEKLLT-NPDDVTQFMKMERSCMVNDGVGSMESLSNKRWFP 117
           +G   +  E+ T    KD V+ LLT N  + +  MKMER C +++G G         WFP
Sbjct: 56  HGAVALSPESLTEESPKDTVKGLLTTNRGEASSLMKMERRCSLSNGEGDCRG----SWFP 111

Query: 118 YLDRYKCGDVYLSSSEVVEALSPYLMEERKERFVNVVKNRSYSVCLVVEGLSDFGNVSAT 177
           Y DR++CG+V+LSS EV+EA+SP++MEER +RF  VV+NRSYSVCLVVEGLSDFGN+SA 
Sbjct: 112 YEDRFRCGEVHLSSREVLEAVSPHMMEERTDRFRRVVENRSYSVCLVVEGLSDFGNISAA 171

Query: 178 FRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIELWDAPRECFNVLRSRGYRIA 237
           FRSADALG+QSVHVVSCDSSKRY  NRHVSMGAEKWLDIE WD P+ECF VL+SRGYRIA
Sbjct: 172 FRSADALGIQSVHVVSCDSSKRYNGNRHVSMGAEKWLDIEFWDTPKECFKVLKSRGYRIA 231

Query: 238 TTHVGMD 244
           TTH+GMD
Sbjct: 232 TTHLGMD 238

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356523592|ref|XP_003530421.1| PREDICTED: tRNA (guanosine(18)-2'-O)-methyltransferase-like [Glycine max]

 Score =  240 bits (612), Expect = 4e-61,   Method: Compositional matrix adjust.
 Identities = 115/178 (64%), Positives = 143/178 (80%), Gaps = 8/178 (4%)

Query: 69  ENDTPSKDNVEKLLTNPDDVTQFMKMERSCMVNDGVGSMESLSNKRWFPYLDRYKCGD-V 127
           E   P   +V+ LLT+PD V+  MKM+R  +       +    + RWFPYLD Y+C +  
Sbjct: 43  EEPEPQSPSVQHLLTSPDGVSTLMKMDRKPL-------LPHEPHVRWFPYLDAYRCRNGC 95

Query: 128 YLSSSEVVEALSPYLMEERKERFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQ 187
            LSS+EVV+AL+P + ++R++RF +VV+NRSYSVCLVVEGL DFGNVSATFRSADALGVQ
Sbjct: 96  VLSSAEVVQALAPCISDDRRQRFGSVVRNRSYSVCLVVEGLCDFGNVSATFRSADALGVQ 155

Query: 188 SVHVVSCDSSKRYRENRHVSMGAEKWLDIELWDAPRECFNVLRSRGYRIATTHVGMDA 245
           SVHVVSCD++KRY++NRHVSMGAEKWLDIELWD+ +ECF +L+SRGYRIATTHVGMDA
Sbjct: 156 SVHVVSCDANKRYKDNRHVSMGAEKWLDIELWDSTKECFKMLKSRGYRIATTHVGMDA 213

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224080139|ref|XP_002306029.1| predicted protein [Populus trichocarpa] gi|222848993|gb|EEE86540.1| predicted protein [Populus trichocarpa]

 Score =  240 bits (612), Expect = 4e-61,   Method: Compositional matrix adjust.
 Identities = 113/160 (70%), Positives = 131/160 (81%), Gaps = 4/160 (2%)

Query: 86  DDVTQFMKMERSCMVNDGVGSMESLSNKRWFPYLDRYKCGDVYLSSSEVVEALSPYLMEE 145
           DDV + MKMER           +++    WFPY DR+KC  V LSSSEV+EA+ PY+MEE
Sbjct: 2   DDVLRLMKMERRITKTHD----DTVLGSHWFPYFDRFKCEGVDLSSSEVLEAVGPYMMEE 57

Query: 146 RKERFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRH 205
           RKER  N VK+RSYS+CLVVEGL+DFGNVSA FRSADALG QSVHV+SCDSSKRY+ENRH
Sbjct: 58  RKERIRNTVKSRSYSLCLVVEGLTDFGNVSAVFRSADALGFQSVHVISCDSSKRYKENRH 117

Query: 206 VSMGAEKWLDIELWDAPRECFNVLRSRGYRIATTHVGMDA 245
           VSMGAEKWLDIELWD+ ++CF VL+SRGYRIATTHVG+DA
Sbjct: 118 VSMGAEKWLDIELWDSAKDCFQVLKSRGYRIATTHVGIDA 157

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|40715982|gb|AAR88654.1| rRNA methylase-like protein [Viscum album]

 Score =  235 bits (600), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 122/219 (55%), Positives = 159/219 (72%), Gaps = 13/219 (5%)

Query: 30  LSLRSQKPGPISPYSVR--TRQYGSVQAAISLE-NGNNLIDDENDTPSKDNVEKLLTNPD 86
           ++LRS   G +S Y+ R  +R       A++LE +G+ +  +  +  SK+ VEKLL++  
Sbjct: 48  VTLRSPNLG-LSIYTPRAPSRFCSFSHGALALEISGDGVTSETLEGSSKETVEKLLSDRT 106

Query: 87  DVTQFMKMERSCMVNDGVGSMESLSNKRWFPYLDRYKCGDVYLSSSEVVEALSPYLMEER 146
           +V + MKMER          +E+  + RWFPYLD +K G++ LSSSE++EAL P+++  R
Sbjct: 107 NVDRMMKMERK---------LEATEHTRWFPYLDMFKAGNIDLSSSEILEALDPFILGSR 157

Query: 147 KERFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHV 206
           KER  +VVKNRSYSV LVVEG +DFGN+SA FRSADALG+QSVHV+SC SSKRYRENRHV
Sbjct: 158 KERIKDVVKNRSYSVWLVVEGATDFGNISAVFRSADALGLQSVHVISCGSSKRYRENRHV 217

Query: 207 SMGAEKWLDIELWDAPRECFNVLRSRGYRIATTHVGMDA 245
           SMGAEKWLDIELWD+ +ECF  L+SRGYRI T H+  DA
Sbjct: 218 SMGAEKWLDIELWDSTQECFRNLKSRGYRIVTAHLESDA 256

Source: Viscum album

Species: Viscum album

Genus: Viscum

Family: Viscaceae

Order: Santalales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357502123|ref|XP_003621350.1| tRNA guanosine-2'-O-methyltransferase [Medicago truncatula] gi|355496365|gb|AES77568.1| tRNA guanosine-2'-O-methyltransferase [Medicago truncatula]

 Score =  224 bits (570), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 127/246 (51%), Positives = 159/246 (64%), Gaps = 34/246 (13%)

Query: 1   MSTCRAIIRTSFSFVESKFYFLPSKSFLSLSLRSQKPGPISPYSVRTRQYGSVQAAISLE 60
           MS+C+ ++ +S S   S F F PS   LS SLR  K      Y+  T Q           
Sbjct: 1   MSSCKTMLCSSLS---STFKFKPS---LSSSLRRHKSTSRCCYT--TPQ----------- 41

Query: 61  NGNNLIDDENDTPSKDNVEKLLTNPDDVTQFMKMERSCMVNDGVGSMESLSNKRWFPYLD 120
                I   NDT     +  +L + + VT  MKM+R  + +         +  RWFPYLD
Sbjct: 42  --TTAIPQPNDT-----IHNILNSNEGVTTLMKMQRKPLHHQP-------TQPRWFPYLD 87

Query: 121 RYKCGD-VYLSSSEVVEALSPYLMEERKERFVNVVKNRSYSVCLVVEGLSDFGNVSATFR 179
            ++C +   ++SSEV+EA+ P + E RKERF   V NRSY+VCLVVEGL DFGNVSA FR
Sbjct: 88  SFRCENGCEVTSSEVIEAVGPCISETRKERFGKAVLNRSYNVCLVVEGLCDFGNVSAAFR 147

Query: 180 SADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIELWDAPRECFNVLRSRGYRIATT 239
           SADALGVQSVHVVS D++KRY++NRHVSMGAEKWLDIELWD+ +ECF +L+SRGYRIATT
Sbjct: 148 SADALGVQSVHVVSSDANKRYKDNRHVSMGAEKWLDIELWDSTKECFEMLKSRGYRIATT 207

Query: 240 HVGMDA 245
           HVG+DA
Sbjct: 208 HVGIDA 213

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	248
TAIR|locus:2151001	350	AT5G15390 [Arabidopsis thalian	0.931	0.66	0.541	4.8e-62
DICTYBASE|DDB_G0271370	310	DDB_G0271370 "tRNA guanosine-2	0.423	0.338	0.280	1.4e-09
TIGR_CMR|CPS_4975	235	CPS_4975 "tRNA (guanosine-2'-O	0.383	0.404	0.237	0.00057

TAIR|locus:2151001 AT5G15390 [Arabidopsis thaliana (taxid:3702)]

 Score = 634 (228.2 bits), Expect = 4.8e-62, P = 4.8e-62
 Identities = 136/251 (54%), Positives = 171/251 (68%)

Query:     1 MSTCRAIIR---TSFSFVEX---XXXXXXXXXXXXXXXXXXXPGPISPYSVRTRQYGSVQ 54
             M++C+++IR   +SF FV                        P      + R   +G+V 
Sbjct:     1 MNSCKSLIRASISSFPFVPLPNPNFSITFISVRAFSPLSVLHPNSSCIVTARRTFHGAV- 59

Query:    55 AAISLENGNNLIDDENDTPSKDNVEKLLT-NPDDVTQFMKMERSCMVNDGVGSMESLSNK 113
              A+S E+    + +E+  P KD V+ LLT N  + +  MKMER C +++G G        
Sbjct:    60 -ALSPES----LTEES--P-KDTVKGLLTTNRGEASSLMKMERRCSLSNGEGDCRG---- 107

Query:   114 RWFPYLDRYKCGDVYLSSSEVVEALSPYLMEERKERFVNVVKNRSYSVCLVVEGLSDFGN 173
              WFPY DR++CG+V+LSS EV+EA+SP++MEER +RF  VV+NRSYSVCLVVEGLSDFGN
Sbjct:   108 SWFPYEDRFRCGEVHLSSREVLEAVSPHMMEERTDRFRRVVENRSYSVCLVVEGLSDFGN 167

Query:   174 VSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIELWDAPRECFNVLRSRG 233
             +SA FRSADALG+QSVHVVSCDSSKRY  NRHVSMGAEKWLDIE WD P+ECF VL+SRG
Sbjct:   168 ISAAFRSADALGIQSVHVVSCDSSKRYNGNRHVSMGAEKWLDIEFWDTPKECFKVLKSRG 227

Query:   234 YRIATTHVGMD 244
             YRIATTH+GMD
Sbjct:   228 YRIATTHLGMD 238

GO:0003723 "RNA binding" evidence=IEA;ISS

GO:0006396 "RNA processing" evidence=IEA;ISS

GO:0008173 "RNA methyltransferase activity" evidence=IEA;ISS

GO:0009507 "chloroplast" evidence=ISM

DICTYBASE|DDB_G0271370 DDB_G0271370 "tRNA guanosine-2'-O-methyltransferase" [Dictyostelium discoideum (taxid:44689)]

 Score = 155 (59.6 bits), Expect = 1.4e-09, P = 1.4e-09
 Identities = 30/107 (28%), Positives = 62/107 (57%)

Query:   132 SEVVEALSPYLMEERKERFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHV 191
             + V   + P++ ++R +RF + + NR+    +V E L + GN +A  RSADA+G+Q++ +
Sbjct:    26 NNVSNKIKPFISDKRLKRFEDSINNRNKRFIIVCENLDNPGNFAAVVRSADAIGIQNLCL 85

Query:   192 VSCDSS--KRYRENRHVSMGAEKWLDIELWDAPRECFNVLRSRGYRI 236
             ++   +    + +   VS+G+ KW+ +  + +  +C   L+ +GY I
Sbjct:    86 INEGGNLDSNFEKYDRVSLGSGKWVTVNKYYSTTKCIEKLKEQGYSI 132

GO:0008173 "RNA methyltransferase activity" evidence=IEA

GO:0006396 "RNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0001510 "RNA methylation" evidence=IEA

TIGR_CMR|CPS_4975 CPS_4975 "tRNA (guanosine-2'-O-)-methyltransferase" [Colwellia psychrerythraea 34H (taxid:167879)]

 Score = 108 (43.1 bits), Expect = 0.00057, P = 0.00057
 Identities = 23/97 (23%), Positives = 47/97 (48%)

Query:   145 ERKERFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENR 204
             ER  R   ++  R   + + +EGL    N++A  R+ DA+G+  VH V        R   
Sbjct:     4 ERLARINTMLDKRQPDLTVCMEGLHKSHNLAAVVRTCDAIGISDVHAVWKSEEAEVRGGS 63

Query:   205 HVSMGAEKWLDIELWDAPRECFNVLRSRGYRIATTHV 241
               + G++ W+D+  +    +    L+++G ++  T++
Sbjct:    64 --AAGSQNWIDVHNYHKTADAIAALKAQGMQVLVTNL 98


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.318   0.132   0.394    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      248       228   0.00081  113 3  11 22  0.40    33
                                                     32  0.41    36


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  3
  No. of states in DFA:  607 (65 KB)
  Total size of DFA:  191 KB (2109 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  21.68u 0.10s 21.78t   Elapsed:  00:00:01
  Total cpu time:  21.68u 0.10s 21.78t   Elapsed:  00:00:01
  Start:  Sat May 11 02:31:29 2013   End:  Sat May 11 02:31:30 2013

GO:0006396 "RNA processing" evidence=ISS

GO:0009020 "tRNA (guanosine-2'-O-)-methyltransferase activity" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	2.1.1	LOW CONFIDENCE prediction!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00021031001 SubName- Full=Chromosome chr14 scaffold_21, whole genome shotgun sequence; (369 aa) (Vitis vinifera)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	248
pfam00588	142	pfam00588, SpoU_methylase, SpoU rRNA Methylase fam	1e-14
COG0566	260	COG0566, SpoU, rRNA methylases [Translation, ribos	6e-11
PRK11081	229	PRK11081, PRK11081, tRNA guanosine-2'-O-methyltran	9e-10
TIGR00186	237	TIGR00186, rRNA_methyl_3, rRNA methylase, putative	2e-04

>gnl|CDD|216010 pfam00588, SpoU_methylase, SpoU rRNA Methylase family

 Score = 68.3 bits (168), Expect = 1e-14
 Identities = 21/84 (25%), Positives = 36/84 (42%), Gaps = 1/84 (1%)

Query: 160 SVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRY-RENRHVSMGAEKWLDIEL 218
            + +V++   D GN+ A  R+A A G   + +V    +  Y  +    S GA   L + +
Sbjct: 1   PLIVVLDEPQDPGNLGAIARTAAAFGADGLILVEPRCADPYNPKAIRASAGALFHLPLVI 60

Query: 219 WDAPRECFNVLRSRGYRIATTHVG 242
            D   E    L+  G+ I  T + 
Sbjct: 61  VDNLEEALKDLKEAGFWIIATSLK 84

This family of proteins probably use S-AdoMet. Length = 142

>gnl|CDD|223640 COG0566, SpoU, rRNA methylases [Translation, ribosomal structure and biogenesis]

 Score = 60.4 bits (147), Expect = 6e-11
 Identities = 32/130 (24%), Positives = 54/130 (41%), Gaps = 20/130 (15%)

Query: 126 DVYLSSSEVVEALSPYLMEERKERFVNVVKNRSY------------SVCLVVEGLSDFGN 173
            VY+ S  +++ LS     E  +  V VVK R Y             + LV++G++D  N
Sbjct: 66  PVYVVSEAILDKLSGT---ENHQGIVAVVKKRRYPLLDDLLDAEAQPLLLVLDGVTDPHN 122

Query: 174 VSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIELW---DAPRECFNVLR 230
           + A  R+ADA GV  V +    +     +    S GA     + +    +  R    +L+
Sbjct: 123 LGAIIRTADAFGVDGVILPKRRADPLNPKVIRASAGA--AFHVPVIRVTNLARTLLELLK 180

Query: 231 SRGYRIATTH 240
             G+ +  T 
Sbjct: 181 EAGFWVVATS 190

Length = 260

>gnl|CDD|236837 PRK11081, PRK11081, tRNA guanosine-2'-O-methyltransferase; Provisional

 Score = 56.9 bits (138), Expect = 9e-10
 Identities = 30/103 (29%), Positives = 47/103 (45%), Gaps = 6/103 (5%)

Query: 145 ERKERFVNVVKNR--SYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRE 202
           ER  R   ++  R    +VC+  E +    NVSA  R+ADA+GV  VH V   S  R   
Sbjct: 4   ERYARICEMLARRQPDLTVCM--EQVHKPHNVSAIIRTADAVGVHEVHAVWPGSRMRTM- 60

Query: 203 NRHVSMGAEKWLDIELWDAPRECFNVLRSRGYRIATTHVGMDA 245
               + G+  W+ ++      +    L+ +G +I  TH+   A
Sbjct: 61  -GSTAAGSNSWVQVKTHRTIGDAVAHLKGQGMQILATHLSDTA 102

Length = 229

>gnl|CDD|129290 TIGR00186, rRNA_methyl_3, rRNA methylase, putative, group 3

 Score = 41.2 bits (97), Expect = 2e-04
 Identities = 20/108 (18%), Positives = 43/108 (39%), Gaps = 3/108 (2%)

Query: 133 EVVEALSPYLMEERKERFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVV 192
            +   + P L ++  +      K++     L+++ ++D  N+ A  R+A+A GV  V ++
Sbjct: 64  GIAAKVKPILYKDLND-LYKTAKSKKQPFLLILDEITDPHNLGAILRTAEAFGVDGV-IL 121

Query: 193 SCDSSKRYREN-RHVSMGAEKWLDIELWDAPRECFNVLRSRGYRIATT 239
               S          S GA +++ +            L+  G+    T
Sbjct: 122 PKRRSAPLNSTVVKTSSGAVEYVPLARVTNLSRTITKLKESGFWTVGT 169

this is part of the trmH (spoU) family of rRNA methylases [Protein synthesis, tRNA and rRNA base modification]. Length = 237

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	248
COG0566	260	SpoU rRNA methylases [Translation, ribosomal struc	99.94
PRK11181	244	23S rRNA (guanosine-2'-O-)-methyltransferase; Prov	99.92
TIGR00186	237	rRNA_methyl_3 rRNA methylase, putative, group 3. t	99.91
PRK11081	229	tRNA guanosine-2'-O-methyltransferase; Provisional	99.89
PRK10864	346	putative methyltransferase; Provisional	99.88
PF00588	142	SpoU_methylase: SpoU rRNA Methylase family; InterP	99.81
TIGR00185	153	rRNA_methyl_2 rRNA methylase, putative, group 2. t	99.72
KOG2506	371	consensus SpoU rRNA Methylase family protein [Tran	99.69
PRK10358	157	putative rRNA methylase; Provisional	99.65
KOG0838	271	consensus RNA Methylase, SpoU family [RNA processi	99.58
TIGR00050	233	rRNA_methyl_1 RNA methyltransferase, TrmH family,	99.33
PRK15114	245	tRNA (cytidine/uridine-2'-O-)-methyltransferase Tr	99.27
PRK10433	228	putative RNA methyltransferase; Provisional	98.9
KOG0839	1477	consensus RNA Methylase, SpoU family [RNA processi	98.43
COG0219	155	CspR Predicted rRNA methylase (SpoU class) [Transl	98.4
COG0565	242	LasT rRNA methylase [Translation, ribosomal struct	96.48

>COG0566 SpoU rRNA methylases [Translation, ribosomal structure and biogenesis]

Probab=99.94  E-value=2.3e-26  Score=207.90  Aligned_cols=135  Identities=21%  Similarity=0.275  Sum_probs=109.8

Q ss_pred             EeeccCcCCc-CCCCc----cC-cEEEccHHHHHHcCCCccchhhh---------hHHHHhhcCCCceEEEEeCCCCCCc
Q 025787          109 SLSNKRWFPY-LDRYK----CG-DVYLSSSEVVEALSPYLMEERKE---------RFVNVVKNRSYSVCLVVEGLSDFGN  173 (248)
Q Consensus       109 ~l~~~~~~~~-~~~~~----~~-~v~~vs~~vl~~ls~~~~~~R~~---------~l~evl~~r~~~lilVLD~I~DP~N  173 (248)
                      +|+++.+.+. .+.+.    .. +++.++++++++++++.+|++..         ..++++.....+++|+||+|+||||
T Consensus        43 i~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~l~~~~~~~~hqGi~a~~~~~~~~~~~~~~~~~~~~l~lvLd~V~DP~N  122 (260)
T COG0566          43 ILVTEGRLPRFEELLALAAAKGIPVYVVSEAILDKLSGTENHQGIVAVVKKRRYPLLDDLLDAEAQPLLLVLDGVTDPHN  122 (260)
T ss_pred             EEEecccchhHHHHHHHHHhcCCeEEEECHHHHHHHhCCCCCCeEEEEEecccccchhhhhhcccCCEEEEEecCcCCcc
Confidence            6677666533 22222    12 79999999999999999887754         2222221113579999999999999


Q ss_pred             HHHHHHHHHHHCCCeEEEcCCCCCCCCcccccccCCCccceEEEEeC-CHHHHHHHHHHCCceEEEEeeCC
Q 025787          174 VSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIELWD-APRECFNVLRSRGYRIATTHVGM  243 (248)
Q Consensus       174 lGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R~SmGA~~~v~i~~~~-~l~~~L~~Lk~~G~~ivAt~l~~  243 (248)
                      +|||+|||+|||+++||+..+++|+++++++|+|||+++++|+.+.. +..+.++.++++||+|+|+++++
T Consensus       123 lGaIiRtA~a~Gv~~Vi~~~~~~~~~~~~v~r~s~Ga~~~vp~~~~~n~~~~~~~~~~~~G~~v~~t~~~~  193 (260)
T COG0566         123 LGAIIRTADAFGVDGVILPKRRADPLNPKVIRASAGAAFHVPVIRVTNLARTLLELLKEAGFWVVATSLDG  193 (260)
T ss_pred             hhhHHhhHHHhCCCEEEECCCccCCccceeEEecCChheeceeEEEeccHHHHHHHHHHcCeEEEEECCCC
Confidence            99999999999999999999999999999999999999999988877 46667777777999999999987

>PRK11181 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional

Probab=99.92  E-value=1e-24  Score=195.18  Aligned_cols=118  Identities=19%  Similarity=0.222  Sum_probs=105.3

Q ss_pred             cEEEccHHHHHHcCCCccchhhh------------hHHHHhhcCCCceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcC
Q 025787          126 DVYLSSSEVVEALSPYLMEERKE------------RFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVS  193 (248)
Q Consensus       126 ~v~~vs~~vl~~ls~~~~~~R~~------------~l~evl~~r~~~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~  193 (248)
                      +++.+++++|++++++.+|++..            .++++++.+..++++|||+|+||+|+|||+|||+|||+++|++.+
T Consensus        49 ~~~~v~~~~l~~ls~~~~~qGv~a~~~~~~~~~~~~~~~~~~~~~~~~~lvLd~v~dp~NlGai~Rta~a~G~~~vi~~~  128 (244)
T PRK11181         49 VIQLANRQTLDEKAEGAVHQGIIARVKPGRQLQENDLPDLLASLEQPFLLILDGVTDPHNLGACLRSADAAGVHAVIVPK  128 (244)
T ss_pred             cEEEeCHHHHhhhhcCCCCceEEEEEecccccchhhHHHHHhcCCCCEEEEEcCCCCcchHHHHHHHHHHcCCCEEEECC
Confidence            58899999999999988775432            344555444457999999999999999999999999999999999


Q ss_pred             CCCCCCCcccccccCCCccceEEEEeCCHHHHHHHHHHCCceEEEEeeCC
Q 025787          194 CDSSKRYRENRHVSMGAEKWLDIELWDAPRECFNVLRSRGYRIATTHVGM  243 (248)
Q Consensus       194 ~~~dp~~~k~~R~SmGA~~~v~i~~~~~l~~~L~~Lk~~G~~ivAt~l~~  243 (248)
                      +++++++++++|+|||+.+|+++.++.++.++++.||++||+++|++.++
T Consensus       129 ~~~~~~~~~~~r~s~Ga~~~l~~~~~~~~~~~l~~l~~~g~~i~~t~~~~  178 (244)
T PRK11181        129 DRSAQLNATAKKVACGAAETVPLIRVTNLARTMRMLQEKNIWIVGTAGEA  178 (244)
T ss_pred             CCCCCCCCceEEecCCHHHcCeEEEcCCHHHHHHHHHHCCCEEEEEeCCC
Confidence            99999999999999999999999999999999999999999999998764

>TIGR00186 rRNA_methyl_3 rRNA methylase, putative, group 3

Probab=99.91  E-value=4.4e-24  Score=190.18  Aligned_cols=120  Identities=17%  Similarity=0.240  Sum_probs=106.2

Q ss_pred             cEEEccHHHHHHcCCCccchhhh---------hHHHHhh---cCCCceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcC
Q 025787          126 DVYLSSSEVVEALSPYLMEERKE---------RFVNVVK---NRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVS  193 (248)
Q Consensus       126 ~v~~vs~~vl~~ls~~~~~~R~~---------~l~evl~---~r~~~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~  193 (248)
                      +++.+++++|++++++.+|++..         .++++++   +...+++++||+|+||+|+|+|+|||+|||+++|++++
T Consensus        44 ~~~~v~~~~l~~l~~~~~~qGv~a~~~~~~~~~~~~~~~~~~~~~~~~~lvLd~v~dp~NlGaI~Rta~afG~~~vil~~  123 (237)
T TIGR00186        44 NIQLVDRQKLDQLTKGGNHQGIAAKVKPILYKDLNDLYKTAKSKKQPFLLILDEITDPHNLGAILRTAEAFGVDGVILPK  123 (237)
T ss_pred             cEEEeCHHHHHHHhCCCCCCeEEEEEecCCCCCHHHHHHhhhccCCCEEEEEcCCCCCccHHHHHHHHHHcCCCEEEECC
Confidence            58899999999999988775431         4555542   22347899999999999999999999999999999999


Q ss_pred             CCCCCCCcccccccCCCccceEEEEeCCHHHHHHHHHHCCceEEEEeeCCCc
Q 025787          194 CDSSKRYRENRHVSMGAEKWLDIELWDAPRECFNVLRSRGYRIATTHVGMDA  245 (248)
Q Consensus       194 ~~~dp~~~k~~R~SmGA~~~v~i~~~~~l~~~L~~Lk~~G~~ivAt~l~~~A  245 (248)
                      .+++|++++++|+|||+.+|+++.++.++.++++.|+++||+++|++..+++
T Consensus       124 ~~~~~~~~~~~r~s~Ga~~~l~~~~~~~~~~~l~~l~~~g~~i~~~~~~~~~  175 (237)
T TIGR00186       124 RRSAPLNSTVVKTSSGAVEYVPLARVTNLSRTITKLKESGFWTVGTDLDAQD  175 (237)
T ss_pred             CCcCCCCCceeeeeccccceeEEEEeCCHHHHHHHHHHCCCEEEEEecCCCc
Confidence            9999999999999999999999999999999999999999999999987654

this is part of the trmH (spoU) family of rRNA methylases

>PRK11081 tRNA guanosine-2'-O-methyltransferase; Provisional

Probab=99.89  E-value=1.2e-22  Score=180.97  Aligned_cols=103  Identities=28%  Similarity=0.416  Sum_probs=93.7

Q ss_pred             cchhhhhHHHHhhcCCCceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCCCCCcccccccCCCccceEEEEeCCH
Q 025787          143 MEERKERFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIELWDAP  222 (248)
Q Consensus       143 ~~~R~~~l~evl~~r~~~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R~SmGA~~~v~i~~~~~l  222 (248)
                      +++|..+|+++|++++++++||||+|+||+|+|||+|||+|||+++|+++....  ..+...|+|||+.+|+++..+.++
T Consensus         2 ~~~r~~ri~~~l~~r~~~l~vvLd~V~~p~NlGAIiRta~AfGv~~V~~v~~~~--~~~~~~~~s~Ga~~wv~i~~~~~~   79 (229)
T PRK11081          2 NPERYARICEMLARRQPDLTVCMEQVHKPHNVSAIIRTADAVGVHEVHAVWPGS--RMRTMGSTAAGSNSWVQVKTHRTI   79 (229)
T ss_pred             CchhHHhHHHHHhcCCCCeEEEEeCCCCcchHHHHHHHHHHhCCCeEEEecCCC--ccchhhhhcCCchheEEEEEeCCH
Confidence            578889999999998889999999999999999999999999999999986543  246788999999999999999999


Q ss_pred             HHHHHHHHHCCceEEEEeeCCCccc
Q 025787          223 RECFNVLRSRGYRIATTHVGMDACC  247 (248)
Q Consensus       223 ~~~L~~Lk~~G~~ivAt~l~~~Av~  247 (248)
                      .++++.||++||+|+|+++++++++
T Consensus        80 ~~~i~~lk~~g~~i~at~~~~~a~~  104 (229)
T PRK11081         80 GDAVAHLKGQGMQILATHLSDTAVD  104 (229)
T ss_pred             HHHHHHHHhCCCEEEEEeCCCCCcc
Confidence            9999999999999999999877653

>PRK10864 putative methyltransferase; Provisional

Probab=99.88  E-value=2.4e-22  Score=188.36  Aligned_cols=117  Identities=15%  Similarity=0.126  Sum_probs=103.2

Q ss_pred             cEEEccHHHHHHcCCCccchhhh---------hHHHHhhc-CCCceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCC
Q 025787          126 DVYLSSSEVVEALSPYLMEERKE---------RFVNVVKN-RSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCD  195 (248)
Q Consensus       126 ~v~~vs~~vl~~ls~~~~~~R~~---------~l~evl~~-r~~~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~  195 (248)
                      +++++++++|++++++.+|+++.         .++++++. ...+++||||+|+||+|+|+|+|||+|||+++||+.+. 
T Consensus       154 ~v~~V~~~~l~kls~~~~hqGV~A~v~~~~~~~l~~~l~~~~~~~~vlvLd~I~DP~NlGaIiRTA~afGv~~Vil~~~-  232 (346)
T PRK10864        154 AYHVVDEAELTKASGTEHHGGVCFLIKKRNGTDVQQWLAQAGAQDCVLALEDVGNPHNLGGIMRSCAHFGVKGVVVQDA-  232 (346)
T ss_pred             cEEEeCHHHHHHHhCCCCCCeEEEEEeCCCCCCHHHHhhccccCCeEEEEeCCCCCCcHHHHHHHHHHhCCCEEEECCC-
Confidence            68999999999999998886542         45666552 12458999999999999999999999999999999875 


Q ss_pred             CCCCCcccccccCCCccceEEEEeCCHHHHHHHHHHCCceEEEEeeCC
Q 025787          196 SSKRYRENRHVSMGAEKWLDIELWDAPRECFNVLRSRGYRIATTHVGM  243 (248)
Q Consensus       196 ~dp~~~k~~R~SmGA~~~v~i~~~~~l~~~L~~Lk~~G~~ivAt~l~~  243 (248)
                      .++++++++|+|||+.+|+++..+.++.++|+.||++||+|++++..+
T Consensus       233 ~~~~~~kvvRaS~Ga~~~v~i~~~~nl~~~L~~lk~~G~~Iv~t~~~~  280 (346)
T PRK10864        233 ALLESGAAIRTAEGGAEHVQPITGDSFVDVLDDFRQAGYTIVTTSSHK  280 (346)
T ss_pred             CCCCchhHHHHhcChhhcceEEEeCCHHHHHHHHHHCCCEEEEEeCCC
Confidence            477899999999999999999999999999999999999999998754

>PF00588 SpoU_methylase: SpoU rRNA Methylase family; InterPro: IPR001537 The spoU gene of Escherichia coli codes for a protein that shows strong similarities to previously characterised 2'-O-methyltransferases [, ]

Probab=99.81  E-value=3.8e-20  Score=151.45  Aligned_cols=85  Identities=29%  Similarity=0.396  Sum_probs=79.0

Q ss_pred             ceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcC-CCCCCCCcccccccCCCccceEEEEeCCHHHHHHHHHHCCceEEE
Q 025787          160 SVCLVVEGLSDFGNVSATFRSADALGVQSVHVVS-CDSSKRYRENRHVSMGAEKWLDIELWDAPRECFNVLRSRGYRIAT  238 (248)
Q Consensus       160 ~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~-~~~dp~~~k~~R~SmGA~~~v~i~~~~~l~~~L~~Lk~~G~~ivA  238 (248)
                      ++++|||+++||+|+|+|+|||++||+++|++++ ++.|++++++.|+|+|+.+|+++..+.++.++++.+++.||++++
T Consensus         1 ~l~vvl~~~~~p~NlG~i~Rta~afG~~~v~l~~~~~~~~~~~~~~r~s~g~~~~~~~~~~~~~~~~l~~~~~~g~~i~~   80 (142)
T PF00588_consen    1 MLIVVLDNVQDPGNLGAIIRTAAAFGVDGVILVGPRCADPYNPKVLRASAGAHEHLPIRRVDDLEEALKDLKENGYTIVA   80 (142)
T ss_dssp             SEEEEEES-SSHHHHHHHHHHHHHTTESEEEEESSSSSTTTSHHHHHHTTTGHHCSHEEEESSHHHHHHHHHHTTEEEEE
T ss_pred             CEEEEEeCCCCcCcHHHHHHHHHHhCCchhheeccccccccccccccccCChhhhhheeeeehhhhhcccccccccccce
Confidence            4789999999999999999999999999999987 777899999999999999999999999999999999999999999


Q ss_pred             EeeCCC
Q 025787          239 THVGMD  244 (248)
Q Consensus       239 t~l~~~  244 (248)
                      ++.+++
T Consensus        81 ~~~~~~   86 (142)
T PF00588_consen   81 TSPGAT   86 (142)
T ss_dssp             ESTTSC
T ss_pred             eeeccc
Confidence            998544

The Pet56 protein of Saccharomyces cerevisiae has been shown to be required for ribose methylation at a universally conserved nucleotide in the peptidyl transferase centre of the mitochondrial large ribosomal RNA (21S rRNA). Cells reduced in this activity were deficient in formation of functional large subunits of the mitochondrial ribosome. The Pet56 protein catalyzes the site-specific formation of 2'-O-methylguanosine on in vitro transcripts of both mitochondrial 21S rRNA and E. coli 23S rRNA providing evidence for an essential modified nucleotide in rRNA [].; GO: 0003723 RNA binding, 0008173 RNA methyltransferase activity, 0006396 RNA processing; PDB: 3N4J_A 3N4K_A 1IPA_A 3ONP_A 3NK6_A 3NK7_A 3IC6_A 1GZ0_D 1MXI_A 1J85_A ....

>TIGR00185 rRNA_methyl_2 rRNA methylase, putative, group 2

Probab=99.72  E-value=1.2e-17  Score=139.87  Aligned_cols=80  Identities=8%  Similarity=-0.000  Sum_probs=71.1

Q ss_pred             eEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCCCCCcccccccCCCccceEEEEeCCHHHHHHHHHHCCceEEEEe
Q 025787          161 VCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIELWDAPRECFNVLRSRGYRIATTH  240 (248)
Q Consensus       161 lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R~SmGA~~~v~i~~~~~l~~~L~~Lk~~G~~ivAt~  240 (248)
                      +-+|||++|||+|+|+|+|||+|||++++++.+++.++..++..|++||+.+++++.++.++.+++++||+.|  +++++
T Consensus         2 ~~vvL~~v~dP~NlG~iiRta~afGv~~vi~~~~~~~~~~~~~~ra~~~~~~~~~~~~~~~~~~~l~~l~~~g--v~~~~   79 (153)
T TIGR00185         2 LNIVLYEPEIPPNTGNIARTCAATGTRLHLIEPLGFFLDDKRLKRAGLDYWEFVQLFYHKSWEEFLEAEKPQK--LFALT   79 (153)
T ss_pred             eEEEEcCCCCCChHHHHHHHHHHhCCEEEEECCCCCCCccHHHHhhccchHhcCCeEEeCCHHHHHHhCcCCC--EEEEe
Confidence            4589999999999999999999999998988777666666777899999999999999999999999999999  66766


Q ss_pred             eC
Q 025787          241 VG  242 (248)
Q Consensus       241 l~  242 (248)
                      ..
T Consensus        80 ~~   81 (153)
T TIGR00185        80 KK   81 (153)
T ss_pred             CC
Confidence            54

this is part of the trmH (spoU) family of rRNA methylases

>KOG2506 consensus SpoU rRNA Methylase family protein [Translation, ribosomal structure and biogenesis]

Probab=99.69  E-value=1.4e-17  Score=153.52  Aligned_cols=92  Identities=20%  Similarity=0.128  Sum_probs=79.4

Q ss_pred             cEEEccHHHHHHcCCCccchhhhhHH-----HH----------hhcCCCceEEEEeCCCCCCcHHHHHHHHHHHCCCeEE
Q 025787          126 DVYLSSSEVVEALSPYLMEERKERFV-----NV----------VKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVH  190 (248)
Q Consensus       126 ~v~~vs~~vl~~ls~~~~~~R~~~l~-----ev----------l~~r~~~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vi  190 (248)
                      .++-++..++++.++.++|+...++.     +-          ......+++||+|+|+||||+|+|+|||+|||+++|+
T Consensus       168 ~i~kVks~d~K~wSsLvSP~svmaIf~~P~d~hl~k~~a~~q~~~s~~lp~~lvcdnirdpgnlgti~rsaaa~~cs~v~  247 (371)
T KOG2506|consen  168 RIVKVKSLDMKKWSSLVSPESVMAIFLMPIDLHLDKDIATDQNKWSPSLPRVLVCDNIRDPGNLGTIVRSAAAFNCSGVF  247 (371)
T ss_pred             eEEeccHHHHHHHhcccCCcchhhhccCcchhchhhhHHHHHhccCCCCCeEEEeccCCCCcchHHHHHHHhhCCCccee
Confidence            46788999999999999986654322     11          1123467999999999999999999999999999999


Q ss_pred             EcCCCCCCCCcccccccCCCccceEEE
Q 025787          191 VVSCDSSKRYRENRHVSMGAEKWLDIE  217 (248)
Q Consensus       191 l~~~~~dp~~~k~~R~SmGA~~~v~i~  217 (248)
                      ++++|+|||.+|+.|++||+.|.+||.
T Consensus       248 lt~gccdpwe~kalrag~ga~fr~pi~  274 (371)
T KOG2506|consen  248 LTPGCCDPWEDKALRAGRGASFRLPIV  274 (371)
T ss_pred             ecCCcCCccchhhhhccCCcceeccee
Confidence            999999999999999999999999997

>PRK10358 putative rRNA methylase; Provisional

Probab=99.65  E-value=4.2e-16  Score=131.54  Aligned_cols=80  Identities=6%  Similarity=-0.055  Sum_probs=64.8

Q ss_pred             eEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCCCCCccccccc-CCCccceEEEEeCCHHHHHHHHHHCCceEEEE
Q 025787          161 VCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVS-MGAEKWLDIELWDAPRECFNVLRSRGYRIATT  239 (248)
Q Consensus       161 lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R~S-mGA~~~v~i~~~~~l~~~L~~Lk~~G~~ivAt  239 (248)
                      +.+||++++||||+|||+|||+|||++.|++.+ ++|++++|++|++ +|...|+++..+.++.++++++  .+++++++
T Consensus         2 ~~ivL~~~~dPgNlGti~Rta~a~G~~~viv~~-~~d~~~~k~~raag~~~~~~~~~~~~~~l~~~l~~~--~~~~v~~~   78 (157)
T PRK10358          2 LNIVLFEPEIPPNTGNIIRLCANTGFRLHIIEP-MGFAWDDKRLRRAGLDYHEFTAVTRHHDYAAFLEAE--NPQRLFAL   78 (157)
T ss_pred             eEEEEeCCCCcChHHHHHHHHHHhCCEEEEECC-CCCCCChHHHHhcccccccceeeEEcCCHHHHHHhC--CCceEEEE
Confidence            468999999999999999999999998888755 5699999998874 4444555667778888887743  46899999


Q ss_pred             eeCC
Q 025787          240 HVGM  243 (248)
Q Consensus       240 ~l~~  243 (248)
                      +..+
T Consensus        79 ~~~~   82 (157)
T PRK10358         79 TTKG   82 (157)
T ss_pred             eCCC
Confidence            8864

>KOG0838 consensus RNA Methylase, SpoU family [RNA processing and modification]

Probab=99.58  E-value=3.5e-15  Score=134.44  Aligned_cols=127  Identities=25%  Similarity=0.254  Sum_probs=98.3

Q ss_pred             cCCcCCCCccCcEEEccHHHHHHcCCCccchhhh-hHH--HHhhcCCCceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEE
Q 025787          115 WFPYLDRYKCGDVYLSSSEVVEALSPYLMEERKE-RFV--NVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHV  191 (248)
Q Consensus       115 ~~~~~~~~~~~~v~~vs~~vl~~ls~~~~~~R~~-~l~--evl~~r~~~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil  191 (248)
                      |+.+...+....++++.+++++.++......... +..  .++   ...+.++||++.||+|+|||+|+|++||++++++
T Consensus        66 ~~~~~~~~~~~e~~~v~~~~~~~~s~h~L~~~t~~r~h~g~~l---easl~vylde~tDp~n~gaI~rsA~~lg~~~v~l  142 (271)
T KOG0838|consen   66 LLQSATDFRSTEFELVLRRDIEAVSKHDLNSLTDFRPHNGILL---EASLCVYLDEVTDPQNIGAIIRSAYFLGADGVLL  142 (271)
T ss_pred             eeccccccCcceeeehhhhhhhccChhhHHHHHhhccccceEE---eeEEEeeccCccCCcchHHHHHhHHHhcCCceEE
Confidence            4444333433356666667776666532221111 000  011   2358899999999999999999999999999999


Q ss_pred             cCCCCCCCCcccccccCCCccceEEEEeCCHHHHHHHHHHCCceEEEEeeCCC
Q 025787          192 VSCDSSKRYRENRHVSMGAEKWLDIELWDAPRECFNVLRSRGYRIATTHVGMD  244 (248)
Q Consensus       192 ~~~~~dp~~~k~~R~SmGA~~~v~i~~~~~l~~~L~~Lk~~G~~ivAt~l~~~  244 (248)
                      +.+...+.++.+.++|+|+.+|++|.+|++..++++..+++||+++++....+
T Consensus       143 v~~n~s~lS~~vskss~gale~l~I~q~~~~~efl~vsvaaG~~l~~t~~~~~  195 (271)
T KOG0838|consen  143 VKGNSSPLSPVVSKSSAGALEVLPIRQVDNPLEFLNVSVAAGIRLHGTCSWAP  195 (271)
T ss_pred             EeccCCCCchhHHHhhhchhheeeHHHcCCHHHHHHHHHhCceEEEEeecCcC
Confidence            99988999999999999999999999999999999999999999999887655

>TIGR00050 rRNA_methyl_1 RNA methyltransferase, TrmH family, group 1

Probab=99.33  E-value=2e-12  Score=115.47  Aligned_cols=77  Identities=21%  Similarity=0.246  Sum_probs=66.4

Q ss_pred             eEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCCCCCcccccccCCCccceEEE-EeCCHHHHHHHHHHCCceEEEE
Q 025787          161 VCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIE-LWDAPRECFNVLRSRGYRIATT  239 (248)
Q Consensus       161 lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R~SmGA~~~v~i~-~~~~l~~~L~~Lk~~G~~ivAt  239 (248)
                      +.+||++++||+|+|+|+|+|++||+++++++..+++ +++++.|+|+||.+|++.. .+++++++++.   .+ .++|+
T Consensus         4 i~vvL~~~~~p~NiGaiaR~~~~fG~~~l~lv~p~~~-~~~~a~~~a~ga~~~l~~~~v~~~l~eal~~---~~-~vv~t   78 (233)
T TIGR00050         4 IRIVLVEPSHSGNIGSIARAMKNMGLTELCLVNPKSH-LEEEAYALAAGARDILDNAKVVDDLDEALDD---CD-LVVGT   78 (233)
T ss_pred             eEEEEECCCCCCCHHHHHHHHHhCCCCEEEEeCCCcC-CCHHHHHHhCChHHhhccCEEECCHHHHHhc---CC-EEEEE
Confidence            7899999999999999999999999999999998877 6889999999999999864 46888887764   34 47777


Q ss_pred             eeC
Q 025787          240 HVG  242 (248)
Q Consensus       240 ~l~  242 (248)
                      +..
T Consensus        79 t~~   81 (233)
T TIGR00050        79 SAR   81 (233)
T ss_pred             CCC
Confidence            643

This is part of the trmH (spoU) family of S-adenosyl-L-methionine (AdoMet)-dependent methyltransferases, and is now characterized, in E. coli, as a tRNA:Cm32/Um32 methyltransferase. It may be named TrMet(Xm32), or TrmJ, according to the nomenclature style chosen

>PRK15114 tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ; Provisional

Probab=99.27  E-value=9.2e-12  Score=112.10  Aligned_cols=79  Identities=15%  Similarity=0.174  Sum_probs=63.1

Q ss_pred             ceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCCCCCcccccccCCCccceEEE-EeCCHHHHHHHHHHCCceEEE
Q 025787          160 SVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIE-LWDAPRECFNVLRSRGYRIAT  238 (248)
Q Consensus       160 ~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R~SmGA~~~v~i~-~~~~l~~~L~~Lk~~G~~ivA  238 (248)
                      .+.+||++++||||||+|+|+|++||+++++++..++|++++ ++|+|+||.+.+... .+++++++++.    ...++|
T Consensus         4 ~i~vVLv~~~~pgNiGaiaRa~~~fG~~~l~lv~p~~~~~~~-a~~~a~GA~~~l~~a~i~~~l~eal~~----~~~vva   78 (245)
T PRK15114          4 NIRIVLVETSHTGNMGSVARAMKTMGLTNLWLVNPLVKPDSQ-AIALAAGASDVIGNATIVDTLDEALAG----CSLVVG   78 (245)
T ss_pred             CeEEEEeCCCCCCcHHHHHHHHHhcCCCEEEEeCCCCCCcCH-HHHHcCCchhhcccCeEecCHHHHHhc----CCEEEE
Confidence            378999999999999999999999999999999999888654 899999999533221 24666665543    346999


Q ss_pred             EeeCC
Q 025787          239 THVGM  243 (248)
Q Consensus       239 t~l~~  243 (248)
                      |+...
T Consensus        79 tt~r~   83 (245)
T PRK15114         79 TSARS   83 (245)
T ss_pred             EcCCc
Confidence            98654

>PRK10433 putative RNA methyltransferase; Provisional

Probab=98.90  E-value=3.4e-09  Score=94.81  Aligned_cols=76  Identities=21%  Similarity=0.341  Sum_probs=63.2

Q ss_pred             eEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCCCCCcccccccCCCccceEE-EEeCCHHHHHHHHHHCCceEEEE
Q 025787          161 VCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDI-ELWDAPRECFNVLRSRGYRIATT  239 (248)
Q Consensus       161 lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R~SmGA~~~v~i-~~~~~l~~~L~~Lk~~G~~ivAt  239 (248)
                      +.+||.++++|+|||+|.|++.+||++.++++..+..+ ...+.+.++||..|++- ..+++++++++.   .+|.+.++
T Consensus         3 i~vVLv~p~~p~NiGaiaRam~nfG~~~L~lV~p~~~~-~~~a~~~A~gA~d~L~~a~v~~tL~eAl~d---~~~vigtt   78 (228)
T PRK10433          3 LTIILVAPARAENVGAAARAMKTMGFSELRIVDSQAHL-EPAARWVAHGSGDILDNAKVFDTLAEALHD---VDFTVATT   78 (228)
T ss_pred             eEEEEEcCCCCccHHHHHHHHHHCCCCEEEEeCCCCCC-cHHHHHHhccHHHHhcCceEECCHHHHHHh---CCeEEEEc
Confidence            67999999999999999999999999999999876543 56678999999999984 346898888877   46655544


Q ss_pred             e
Q 025787          240 H  240 (248)
Q Consensus       240 ~  240 (248)
                      .
T Consensus        79 a   79 (228)
T PRK10433         79 A   79 (228)
T ss_pred             c
Confidence            4

>KOG0839 consensus RNA Methylase, SpoU family [RNA processing and modification]

Probab=98.43  E-value=2.2e-07  Score=97.15  Aligned_cols=89  Identities=19%  Similarity=0.273  Sum_probs=75.3

Q ss_pred             CCceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCCCCCcccccccCCCccceEEEEe--CCHHHHHHHHHHCCce
Q 025787          158 SYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIELW--DAPRECFNVLRSRGYR  235 (248)
Q Consensus       158 ~~~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R~SmGA~~~v~i~~~--~~l~~~L~~Lk~~G~~  235 (248)
                      ...+|||.-=|..|.|+|.|.|||+.||++-+.+.+-.+ ...+...-.||-|..|+|++.+  +++...|++.|.+||+
T Consensus      1324 rssLIVVASLVDKppNLgGicRTcEVFgvs~LvVad~~v-i~DkQFk~lSVtAE~W~pieeVk~~~L~~fLq~kK~EGyT 1402 (1477)
T KOG0839|consen 1324 RSSLIVVASLVDKPPNLGGICRTCEVFGVSLLVVADIKV-INDKQFKNLSVTAERWMPIEEVKLDELASFLQEKKKEGYT 1402 (1477)
T ss_pred             ceeEEEEeecccCCCccchhhhhhhhhCcceEEEeeeee-ecchhhhheeeeHHhccchhccChHHHHHHHHHhhhcCcE
Confidence            357999999999999999999999999999877755432 1234456789999999999854  6899999999999999


Q ss_pred             EEEEeeCCCccc
Q 025787          236 IATTHVGMDACC  247 (248)
Q Consensus       236 ivAt~l~~~Av~  247 (248)
                      |+|++.+++||.
T Consensus      1403 iIglEQTakSV~ 1414 (1477)
T KOG0839|consen 1403 IIGLEQTAKSVK 1414 (1477)
T ss_pred             EEeehhcccccc
Confidence            999999999874

>COG0219 CspR Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]

Probab=98.40  E-value=1.1e-06  Score=74.32  Aligned_cols=83  Identities=10%  Similarity=0.018  Sum_probs=69.9

Q ss_pred             eEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCCCCCcccccccCCCccceEEEEeCCHHHHHHHHHHCCceEEEEe
Q 025787          161 VCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIELWDAPRECFNVLRSRGYRIATTH  240 (248)
Q Consensus       161 lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R~SmGA~~~v~i~~~~~l~~~L~~Lk~~G~~ivAt~  240 (248)
                      +-+||-+-+-|.|.|+|+|+|+++|..=.++=+-.-+.-.++..|+.+-.+..+.+..|+++++++++.+. |-++++.+
T Consensus         3 ~~IvL~~PeIP~NTGNI~R~ca~tga~LhlI~PlGF~l~dk~lkRAGlDY~~~~~l~~h~s~e~fl~~~~~-~~rl~~~t   81 (155)
T COG0219           3 LNIVLYQPEIPPNTGNIIRTCAATGAELHLIEPLGFDLDDKRLKRAGLDYHEKASLTEHDSLEAFLEAEPI-GGRLFALT   81 (155)
T ss_pred             cEEEEECCCCCCchhHHHHHHHhcCCeEEEEccCCCccchhhhhhcccchHhhcceEEeCCHHHHHhhccC-CceEEEEE
Confidence            56899999999999999999999999754444444454457789999999999999999999999999988 88888887


Q ss_pred             eCCC
Q 025787          241 VGMD  244 (248)
Q Consensus       241 l~~~  244 (248)
                      ..+.
T Consensus        82 t~~~   85 (155)
T COG0219          82 TKGT   85 (155)
T ss_pred             eccc
Confidence            6543

>COG0565 LasT rRNA methylase [Translation, ribosomal structure and biogenesis]

Probab=96.48  E-value=0.0069  Score=54.96  Aligned_cols=69  Identities=20%  Similarity=0.301  Sum_probs=56.8

Q ss_pred             ceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCCCCCcccccccCCCccceEE-EEeCCHHHHHHHH
Q 025787          160 SVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDI-ELWDAPRECFNVL  229 (248)
Q Consensus       160 ~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R~SmGA~~~v~i-~~~~~l~~~L~~L  229 (248)
                      .+.+||=+-+-|+|||++.|...-||++.++++..++. ....+.+.|+||..-+.= ..+++++++|..+
T Consensus         4 ~i~iVLVep~~~gNIG~vARaMKNfGl~eL~LV~Pr~~-~~eeA~a~A~gA~dile~A~i~~tL~eAl~d~   73 (242)
T COG0565           4 NIRIVLVEPSHPGNIGSVARAMKNFGLSELRLVNPRAG-LDEEARALAAGARDILENAKIVDTLEEALADC   73 (242)
T ss_pred             ccEEEEEcCCCCccHHHHHHHHHhCCcceEEEECCCCC-CCHHHHHHhccchhhhccCeeecCHHHHhcCC
Confidence            36788889999999999999999999999999998866 467899999999855542 2357888887744

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	248
1zjr_A	211	Crystal Structure Of A. Aeolicus TrmhSPOU TRNA MODI		2e-06
1v2x_A	194	Trmh Length = 194		3e-04

>pdb|1ZJR|A Chain A, Crystal Structure Of A. Aeolicus TrmhSPOU TRNA MODIFYING ENZYME Length = 211

Iteration: 1
 Score = 48.9 bits (115), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 26/105 (24%), Positives = 56/105 (53%), Gaps = 1/105 (0%)
Query: 142 LMEERKERFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYR 201
           ++E+R +R   V++ R   + +  + + +  N SA  R+ DA+GV  ++    +  K+ +
Sbjct: 7   VLEKRLKRLREVLEKRQKDLIVFADNVKNEHNFSAIVRTCDAVGVLYLYYYHAEG-KKAK 65
Query: 202 ENRHVSMGAEKWLDIELWDAPRECFNVLRSRGYRIATTHVGMDAC 246
            N  ++ G+ KW+ IE  D P +     ++RG++I  T +  ++ 
Sbjct: 66  INEGITQGSHKWVFIEKVDNPVQKLLEFKNRGFQIVATWLSKESV 110

>pdb|1V2X|A Chain A, Trmh Length = 194

Iteration: 1
 Score = 42.0 bits (97), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 26/94 (27%), Positives = 46/94 (48%), Gaps = 4/94 (4%)
Query: 153 VVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVS-CDSSKRYRENRHVSMGAE 211
           V++ R   + +++E +    N+SA  R+ DA+GV   H V+       + E    S G+ 
Sbjct: 15  VLRRRQPDLTVLLENVHKPHNLSAILRTCDAVGVLEAHAVNPTGGVPTFNET---SGGSH 71
Query: 212 KWLDIELWDAPRECFNVLRSRGYRIATTHVGMDA 245
           KW+ + +     E F  L+ RG+ +  T +  DA
Sbjct: 72  KWVYLRVHPDLHEAFRFLKERGFTVYATALREDA 105

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	248
1zjr_A	211	TRNA (guanosine-2'-O-)-methyltransferase; methylas	3e-28
1v2x_A	194	TRNA (GM18) methyltransferase; DEEP trefoil knot,	2e-25
2ha8_A	184	TAR (HIV-1) RNA loop binding protein; methyltransf	4e-14
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-04

>1zjr_A TRNA (guanosine-2'-O-)-methyltransferase; methylase, RNA modifying enzyme, topological knot; 1.85A {Aquifex aeolicus} Length = 211

 Score =  105 bits (265), Expect = 3e-28
 Identities = 26/108 (24%), Positives = 57/108 (52%), Gaps = 1/108 (0%)

Query: 138 LSPYLMEERKERFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSS 197
           +   ++E+R +R   V++ R   + +  + + +  N SA  R+ DA+GV  ++    +  
Sbjct: 3   MEYLVLEKRLKRLREVLEKRQKDLIVFADNVKNEHNFSAIVRTCDAVGVLYLYYYHAE-G 61

Query: 198 KRYRENRHVSMGAEKWLDIELWDAPRECFNVLRSRGYRIATTHVGMDA 245
           K+ + N  ++ G+ KW+ IE  D P +     ++RG++I  T +  ++
Sbjct: 62  KKAKINEGITQGSHKWVFIEKVDNPVQKLLEFKNRGFQIVATWLSKES 109

>1v2x_A TRNA (GM18) methyltransferase; DEEP trefoil knot, riken structural genomics/proteomics INIT RSGI, structural genomics; HET: SAM; 1.50A {Thermus thermophilus} SCOP: c.116.1.1 Length = 194

 Score = 97.6 bits (244), Expect = 2e-25
 Identities = 28/103 (27%), Positives = 49/103 (47%), Gaps = 2/103 (1%)

Query: 144 EERKERFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYREN 203
           E R+ R   V++ R   + +++E +    N+SA  R+ DA+GV   H V  + +      
Sbjct: 6   EARRRRIEEVLRRRQPDLTVLLENVHKPHNLSAILRTCDAVGVLEAHAV--NPTGGVPTF 63

Query: 204 RHVSMGAEKWLDIELWDAPRECFNVLRSRGYRIATTHVGMDAC 246
              S G+ KW+ + +     E F  L+ RG+ +  T +  DA 
Sbjct: 64  NETSGGSHKWVYLRVHPDLHEAFRFLKERGFTVYATALREDAR 106

>2ha8_A TAR (HIV-1) RNA loop binding protein; methyltransferase, structural genomics, structural genomics consortium, SGC, RNA binding protein; HET: SAH; 1.60A {Homo sapiens} Length = 184

 Score = 67.3 bits (165), Expect = 4e-14
 Identities = 18/110 (16%), Positives = 40/110 (36%), Gaps = 3/110 (2%)

Query: 138 LSPYLMEERKERFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSS 197
           +S   +E   +     +      + +V   +    N+    R+ +  G   + V S    
Sbjct: 4   VSDLDLELLFQDRAARLGKSISRLIVVASLIDKPTNLGGLCRTCEVFGASVLVVGS-LQC 62

Query: 198 KRYRENRHVSMGAEKWLDIELWDAP--RECFNVLRSRGYRIATTHVGMDA 245
              ++ +H+S+ AE+WL +     P   +     ++ GY I        +
Sbjct: 63  ISDKQFQHLSVSAEQWLPLVEVKPPQLIDYLQQKKTEGYTIIGVEQTAKS 112

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 56.8 bits (136), Expect = 2e-09
 Identities = 49/260 (18%), Positives = 82/260 (31%), Gaps = 69/260 (26%)

Query: 14  FVESKFYFLPSKSFLSLSLRSQKPGPISPYSVRTRQYGSVQAAISLENGNNLIDDENDTP 73
           FVE       +  FL   +++++  P    S+ TR Y  ++    L N N +    N   
Sbjct: 82  FVEEVLR--INYKFLMSPIKTEQRQP----SMMTRMY--IEQRDRLYNDNQVFAKYN-VS 132

Query: 74  SKDNVEKL------LTNPDDVTQF-MK-MERSCMVNDGVGSMESLSNKRWFP----YLDR 121
                 KL      L    +V    +    ++ +  D   S +             +L+ 
Sbjct: 133 RLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCK---MDFKIFWLNL 189

Query: 122 YKCGDVYLSSSEVVEALS--------------------PYLMEERKERFVNVVKNRSYSV 161
             C     S   V+E L                        +   +     ++K++ Y  
Sbjct: 190 KNCN----SPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYEN 245

Query: 162 CLVVEGLSD---------FGNVSA----TFRS---ADALGVQSV-HVVSCDSSKRYRENR 204
           CL+V  L +         F N+S     T R     D L   +  H+     S     + 
Sbjct: 246 CLLV--LLNVQNAKAWNAF-NLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDE 302

Query: 205 HVSMGAEKWLDIELWDAPRE 224
             S+   K+LD    D PRE
Sbjct: 303 VKSLLL-KYLDCRPQDLPRE 321

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 39.8 bits (92), Expect = 7e-04
 Identities = 23/119 (19%), Positives = 45/119 (37%), Gaps = 21/119 (17%)

Query: 45  VRTRQYGSVQAAISLENGNNL-IDDENDTPSKDNVEKLL-----TNPDDVTQFMKMERSC 98
           + TR +  V   +S     ++ +D  + T + D V+ LL       P D+          
Sbjct: 270 LTTR-FKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLP-----REVL 323

Query: 99  MVNDGVGSM--ESLSN--KRW--FPYLDRYKCGDVYLSSSEVVEALSPYLMEERKERFV 151
             N    S+  ES+ +    W  + +++  K   + + SS  +  L P    +  +R  
Sbjct: 324 TTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTI-IESS--LNVLEPAEYRKMFDRLS 379

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	248
3nk6_A	277	23S rRNA methyltransferase; nosiheptide, nosihepti	99.94
1x7o_A	287	Avirb, rRNA methyltransferase; SPOU, C-terminal kn	99.92
1ipa_A	274	RRMH, RNA 2'-O-ribose methyltransferase; DEEP tref	99.92
2i6d_A	257	RNA methyltransferase, TRMH family; stuctural geno	99.91
1gz0_A	253	Hypothetical tRNA/RRNA methyltransferase YJFH; 2'O	99.9
1v2x_A	194	TRNA (GM18) methyltransferase; DEEP trefoil knot,	99.87
1zjr_A	211	TRNA (guanosine-2'-O-)-methyltransferase; methylas	99.86
3e5y_A	160	TRMH family RNA methyltransferase; ssgcid, protein	99.82
3n4j_A	165	RNA methyltransferase; center for structural genom	99.8
2ha8_A	184	TAR (HIV-1) RNA loop binding protein; methyltransf	99.79
3l8u_A	182	SMU.1707C, putative rRNA methylase; methyltransfer	99.79
3kty_A	173	Probable methyltransferase; alpha-beta-alpha sandw	99.67
3ilk_A	244	Uncharacterized tRNA/RRNA methyltransferase HI038;	99.49
3ic6_A	223	Putative methylase family protein; putative methyl	99.46
3onp_A	249	TRNA/RRNA methyltransferase (SPOU); structural gen	99.45
3dcm_X	192	AdoMet, uncharacterized protein TM_1570; trefoil k	85.64

>3nk6_A 23S rRNA methyltransferase; nosiheptide, nosiheptide-resistance methyltransferase, 23S R methyltransferase; 2.00A {Streptomyces actuosus} PDB: 3nk7_A* 3gyq_A*

Probab=99.94  E-value=2.3e-27  Score=214.59  Aligned_cols=162  Identities=15%  Similarity=0.099  Sum_probs=124.1

Q ss_pred             ccccCCCCCchHHHHhhhcCcHHHHhHHHhhhhcCCCCCCCeE--E-----------------EeeccCcCCcCCCCc--
Q 025787           65 LIDDENDTPSKDNVEKLLTNPDDVTQFMKMERSCMVNDGVGSM--E-----------------SLSNKRWFPYLDRYK--  123 (248)
Q Consensus        65 ~~~~~~~~~p~~~~~~ll~t~~~~~~L~~~~~r~~~~~~~glf--E-----------------~l~~~~~~~~~~~~~--  123 (248)
                      +..|+++.+|+         ...|++|.    + +.+.+.|+|  |                 +|+++.+....+.+.  
T Consensus         7 ~~~I~S~~n~~---------iK~~~~L~----~-k~R~~~g~flveG~~~V~eaL~~~~~i~~l~~~~~~~~~~~l~~~~   72 (277)
T 3nk6_A            7 PAIITNASDPA---------VQRIIDVT----K-HSRASIKTTLIEDTEPLMECIRAGVQFIEVYGSSGTPLDPALLDLC   72 (277)
T ss_dssp             CCTTSBCSSCS---------HHHHHHHH----H-TC----CEEEEESHHHHHHHHHTTCCEEEEEEETTSCCCHHHHHHH
T ss_pred             ceeecCCCChH---------HHHHHHHh----h-hhHhhcCCEEEEeHHHHHHHHhCCCCeEEEEEeCCccCcHHHHHHH
Confidence            45678888888         55566554    2 445677888  6                 566665544311111  


Q ss_pred             --cC-cEEEccHHHHHHcCCCccchhhh---------hHHHHhhcCCCceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEE
Q 025787          124 --CG-DVYLSSSEVVEALSPYLMEERKE---------RFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHV  191 (248)
Q Consensus       124 --~~-~v~~vs~~vl~~ls~~~~~~R~~---------~l~evl~~r~~~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil  191 (248)
                        .. +++.+++++|++++++.+|++..         .+++++... .+ +||||+|+||||+|+|+|||+|||+++|++
T Consensus        73 ~~~~~~v~~v~~~~l~~ls~~~~~qGv~a~~~~~~~~~l~~~~~~~-~~-~lvLd~v~dP~NlGaI~Rta~a~G~~~vil  150 (277)
T 3nk6_A           73 RQREIPVRLIDVSIVNQLFKAERKAKVFGIARVPRPARLADIAERG-GD-VVVLDGVKIVGNIGAIVRTSLALGAAGIVL  150 (277)
T ss_dssp             HHTTCCEEEECHHHHTTCC-----CCEEEEEECCCCCCHHHHHHHC-SC-EEEEESCCCHHHHHHHHHHHHHTTCSEEEE
T ss_pred             HhcCCcEEEECHHHHHHhhCCCCCCeEEEEEecCCCCCHHHHhccC-CC-EEEEEcCCCcchHHHHHHHHHHcCCCEEEE
Confidence              12 79999999999999998886542         566766432 35 999999999999999999999999999999


Q ss_pred             cC-CCCCCCCcccccccCCCccceEEEEeCCHHHHHHHHHHCCceEEEEeeCC
Q 025787          192 VS-CDSSKRYRENRHVSMGAEKWLDIELWDAPRECFNVLRSRGYRIATTHVGM  243 (248)
Q Consensus       192 ~~-~~~dp~~~k~~R~SmGA~~~v~i~~~~~l~~~L~~Lk~~G~~ivAt~l~~  243 (248)
                      .+ +++|+++++++|+|||+.+|+++.++ |+.++++.||++||++||++..+
T Consensus       151 ~~~~~~~~~~~~v~ras~Ga~~~l~i~~~-~l~~~l~~lk~~g~~v~~~~~~~  202 (277)
T 3nk6_A          151 VDSDLATIADRRLLRASRGYVFSLPVVLA-DREEAVSFLRDNDIALMVLDTDG  202 (277)
T ss_dssp             ESCCCSCTTCHHHHHHTTTCTTTSCEEEC-CHHHHHHHHHHTTCCEEEECTTC
T ss_pred             cCCCCcCCCCHHHHHHhCChhhcCeEEEE-CHHHHHHHHHhcCCeEEEEecCC
Confidence            99 88999999999999999999999998 99999999999999999999865

>1x7o_A Avirb, rRNA methyltransferase; SPOU, C-terminal knot, seMet; 2.37A {Streptomyces viridochromogenes} PDB: 1x7p_A*

Probab=99.92  E-value=6.8e-26  Score=205.82  Aligned_cols=117  Identities=17%  Similarity=0.153  Sum_probs=104.4

Q ss_pred             cEEEccHHHHHHcCCCc-cchhhh--------hHHHHhhcCCCceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCC
Q 025787          126 DVYLSSSEVVEALSPYL-MEERKE--------RFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDS  196 (248)
Q Consensus       126 ~v~~vs~~vl~~ls~~~-~~~R~~--------~l~evl~~r~~~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~  196 (248)
                      +++.+++++|++++++. +|++..        .+++++. ...+++||||+|+||||+|+|+|||+|||+++|++++.++
T Consensus        84 ~v~~v~~~~l~~ls~~~~~~qGv~a~~~~~~~~l~~~~~-~~~~l~lvLd~i~dP~NlGaIiRta~a~G~~~vil~~~~~  162 (287)
T 1x7o_A           84 EQIAMAPDLLMELGEKNEAPPEVVAVVEMPADDLDRIPV-REDFLGVLFDRPTSPGNIGSIIRSADALGAHGLIVAGHAA  162 (287)
T ss_dssp             EEEEECHHHHTTSSCSSSCCCSEEEEEECCCCCGGGSCC-CTTCEEEEEESCSCHHHHHHHHHHHHHTTCCEEEEESSSS
T ss_pred             cEEEeCHHHHHHHhCCCCCCCcEEEEEecCCCCHHHHhc-ccCCEEEEEeCCCCcchHHHHHHHhHhcccCEEEEECCCc
Confidence            68999999999999998 887653        2333332 1246899999999999999999999999999999999999


Q ss_pred             CCCCcccccccCCCccceEEEEeCCHHHHHHHH---HHCCce--EEEEeeCC
Q 025787          197 SKRYRENRHVSMGAEKWLDIELWDAPRECFNVL---RSRGYR--IATTHVGM  243 (248)
Q Consensus       197 dp~~~k~~R~SmGA~~~v~i~~~~~l~~~L~~L---k~~G~~--ivAt~l~~  243 (248)
                      |+++++++|+|||+.+|+++.++.++.++++.|   +++||+  ++|++..+
T Consensus       163 d~~~~kv~ras~Ga~~~l~i~~~~~l~~~l~~l~~~~~~g~~~~i~~~~~~~  214 (287)
T 1x7o_A          163 DVYDPKSVRSSTGSLFSLPAVRVPSPGEVMDWVEARRAAGTPIVLVGTDEHG  214 (287)
T ss_dssp             CTTSHHHHHHTTTGGGTSCEEEESSHHHHHHHHHHHHHHTCCCEEEEECTTC
T ss_pred             CccCHHHHhhhcCcceeeeEEEeCCHHHHHHHHHHHHhcCCceEEEEEECCC
Confidence            999999999999999999999999999999999   999999  99999863

>1ipa_A RRMH, RNA 2'-O-ribose methyltransferase; DEEP trefoil knot, rossmann fold, EL30-like fold, riken structural genomics/proteomics initiative; 2.40A {Thermus thermophilus} SCOP: c.116.1.1 d.79.3.3

Probab=99.92  E-value=8.3e-26  Score=204.03  Aligned_cols=115  Identities=21%  Similarity=0.149  Sum_probs=101.7

Q ss_pred             cEEEccHHHHHHcCCCccchhhh--------hHHHHhhcCCCceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCC
Q 025787          126 DVYLSSSEVVEALSPYLMEERKE--------RFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSS  197 (248)
Q Consensus       126 ~v~~vs~~vl~~ls~~~~~~R~~--------~l~evl~~r~~~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~d  197 (248)
                      +++.+++++|++++++.+|++..        .+++++. ...+++||||+|+||+|+|+|+|||+|||+++|++.+. +|
T Consensus        75 ~v~~v~~~~l~~ls~~~~~qGv~a~~~~~~~~l~~~~~-~~~~~~lvLd~i~dp~NlGaI~Rta~a~G~~~vil~~~-~~  152 (274)
T 1ipa_A           75 ALLEVSEAVLKKLSVRDNPAGLIALARMPERTLEEYRP-SPDALILVAVGLEKPGNLGAVLRSADAAGAEAVLVAGG-VD  152 (274)
T ss_dssp             EEEEECHHHHHHHCCSSSCCSEEEEEECCCCCCCCCCC-CTTCEEEEEESCCCHHHHHHHHHHHHHHTCSEEEEESC-CC
T ss_pred             cEEEeCHHHHHHHhCCCCCCeEEEEEeCCCCCHHHHhc-cCCCeEEEEeCCCCcchHHHHHHHHHhhccCEEEEeCC-cC
Confidence            58999999999999999887754        1222211 12458999999999999999999999999999999999 99


Q ss_pred             CCCcccccccCCCccceEEEEeCCHHHHHHHHHHCCceEEEEeeCC
Q 025787          198 KRYRENRHVSMGAEKWLDIELWDAPRECFNVLRSRGYRIATTHVGM  243 (248)
Q Consensus       198 p~~~k~~R~SmGA~~~v~i~~~~~l~~~L~~Lk~~G~~ivAt~l~~  243 (248)
                      +++++++|+|||+.+|+++.+ .++.++++.|+++||++||++..+
T Consensus       153 ~~~~~v~ras~Ga~~~l~~~~-~~l~~~l~~l~~~g~~i~~~~~~~  197 (274)
T 1ipa_A          153 LYSPQVIRNSTGVVFSLRTLA-ASESEVLDWIKQHNLPLVATTPHA  197 (274)
T ss_dssp             TTCHHHHHHTTTGGGTSCEEE-ECHHHHHHHHHHTTCCEEEECTTC
T ss_pred             cCCHHHHHHcCChhhcceeEe-CCHHHHHHHHHHcCCEEEEEeCCC
Confidence            999999999999999999988 899999999999999999999875

>2i6d_A RNA methyltransferase, TRMH family; stuctural genomics, PORP gingivalis, knot, structural genomics, PSI-2, protein struc initiative; HET: MSE; 1.85A {Porphyromonas gingivalis}

Probab=99.91  E-value=1e-25  Score=201.51  Aligned_cols=117  Identities=16%  Similarity=0.175  Sum_probs=102.1

Q ss_pred             cEEEccH-HHHHHcCCCccchhhhhHHHH----hhcCCCceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCCCCC
Q 025787          126 DVYLSSS-EVVEALSPYLMEERKERFVNV----VKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRY  200 (248)
Q Consensus       126 ~v~~vs~-~vl~~ls~~~~~~R~~~l~ev----l~~r~~~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~  200 (248)
                      +++.+++ ++|++++++.+|++...+-+.    ++.- .+++||||+|+||+|+|+|+|||+|||+++|++++.++|+++
T Consensus        65 ~v~~v~~~~~l~~ls~~~~~qGv~a~~~~~~~~l~~~-~~~~lvLd~v~dp~NlGaI~Rta~a~G~~~vil~~~~~~~~~  143 (257)
T 2i6d_A           65 EVVELPESFDFKRISTQTTPQPLMAVFDLPAEPEPVV-EGLTLLLDGVQDPGNVGTILRTADWFGIRHVWLGTGSADVFS  143 (257)
T ss_dssp             EEEEECTTCCGGGTCCSSSCCSEEEEEECCCCCCCCC-CSEEEEEESCCCHHHHHHHHHHHHHHTCCEEEECTTCCCTTS
T ss_pred             CEEEeChHHHHHHHhcCCCCCeEEEEEECCCCChHHh-CCeEEEEECCCCcchHHHHHHHHHHhCCCEEEEcCCCCCcCC
Confidence            6899999 999999999988776421110    1110 258999999999999999999999999999999999999999


Q ss_pred             cccccccCCCccceEEEEeCCHHHHHHHHHHCCceEEEEeeCC
Q 025787          201 RENRHVSMGAEKWLDIELWDAPRECFNVLRSRGYRIATTHVGM  243 (248)
Q Consensus       201 ~k~~R~SmGA~~~v~i~~~~~l~~~L~~Lk~~G~~ivAt~l~~  243 (248)
                      ++++|+|||+.+|+++..+.++.++++.|+++||+++|++..+
T Consensus       144 ~~v~ras~Ga~~~l~~~~~~~l~~~l~~l~~~g~~i~~~~~~~  186 (257)
T 2i6d_A          144 PKVVQASMGALARVQPTPLKNTVDTLAYFRRQGIPVYGAFLDG  186 (257)
T ss_dssp             HHHHHTSTTGGGTCEEEECSCHHHHHHHHHHTTCCEEEEEEEE
T ss_pred             HHHheecCCcceeeeEEEeCCHHHHHHHHHHCCCEEEEEECCC
Confidence            9999999999999999855899999999999999999999864

>1gz0_A Hypothetical tRNA/RRNA methyltransferase YJFH; 2'O-methyltransferase, knot, montreal- kingston bacterial structural genomics initiative, BSGI; 2.5A {Escherichia coli} SCOP: c.116.1.1 d.79.3.3

Probab=99.90  E-value=2.9e-24  Score=191.73  Aligned_cols=118  Identities=19%  Similarity=0.220  Sum_probs=105.5

Q ss_pred             cEEEccHHHHHHcCCCccchhhh------------hHHHHhhcCCCceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcC
Q 025787          126 DVYLSSSEVVEALSPYLMEERKE------------RFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVS  193 (248)
Q Consensus       126 ~v~~vs~~vl~~ls~~~~~~R~~------------~l~evl~~r~~~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~  193 (248)
                      +++.+++++|++++++.+|++..            .+.++++.+..++++|||+++||+|+|||+|||+|||+++|++..
T Consensus        59 ~v~~v~~~~l~~ls~~~~~qGv~a~~~~~~~~~~~~l~~~~~~~~~~~~lvLd~v~dp~NlGaI~Rta~a~G~~~vil~~  138 (253)
T 1gz0_A           59 VIQLANRQYLDEKSDGAVHQGIIARVKPGRQYQENDLPDLIASLDQPFLLILDGVTDPHNLGACLRSADAAGVHAVIVPK  138 (253)
T ss_dssp             EEEEECSHHHHHTTTSCCCTTEEEEECCCCCCCGGGHHHHHHTCSSCEEEEEESCCCHHHHHHHHHHHHHHTCSEEEEES
T ss_pred             cEEEeCHHHHHHHhCCCCCcEEEEEEeccccCcHHHHHHHHhccCCCEEEEEeCCCCcCcHHHHHHHHHHhCCCEEEEeC
Confidence            68999999999999998876542            455555433457999999999999999999999999999999999


Q ss_pred             CCCCCCCcccccccCCCccceEEEEeCCHHHHHHHHHHCCceEEEEeeCC
Q 025787          194 CDSSKRYRENRHVSMGAEKWLDIELWDAPRECFNVLRSRGYRIATTHVGM  243 (248)
Q Consensus       194 ~~~dp~~~k~~R~SmGA~~~v~i~~~~~l~~~L~~Lk~~G~~ivAt~l~~  243 (248)
                      +++|+++++++|+|||+.+|+++.++.++.++++.|+++||+++|++..+
T Consensus       139 ~~~~~~~~~~~ras~Ga~~~l~~~~~~~~~~~l~~l~~~g~~i~~~~~~~  188 (253)
T 1gz0_A          139 DRSAQLNATAKKVACGAAESVPLIRVTNLARTMRMLQEENIWIVGTAGEA  188 (253)
T ss_dssp             SSSCCCCHHHHHHHTTHHHHSCEEEESCHHHHHHHHHHTTCEEEEECTTC
T ss_pred             CCCCCCCHHHHhhhcchheEEEEEEeCCHHHHHHHHHHCCCEEEEEECCC
Confidence            99999999999999999999999999999999999999999999998653

>1v2x_A TRNA (GM18) methyltransferase; DEEP trefoil knot, riken structural genomics/proteomics INIT RSGI, structural genomics; HET: SAM; 1.50A {Thermus thermophilus} SCOP: c.116.1.1

Probab=99.87  E-value=3e-22  Score=172.09  Aligned_cols=103  Identities=27%  Similarity=0.443  Sum_probs=92.5

Q ss_pred             ccchhhhhHHHHhhcCCCceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCCCCCcccccccCCCccceEEEEeCC
Q 025787          142 LMEERKERFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIELWDA  221 (248)
Q Consensus       142 ~~~~R~~~l~evl~~r~~~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R~SmGA~~~v~i~~~~~  221 (248)
                      .++.|+.+++++++++..+++||||+++||+|+|+|+|||+|||+++|+++..+.++  +++.|+|||+.+|+++..+.+
T Consensus         4 ~~~~~~~~~~~~l~~~~~~~~vvLd~~~dp~NlGaI~Rta~a~G~~~v~l~~~~~~~--~~~~r~s~Ga~~~l~~~~~~~   81 (194)
T 1v2x_A            4 RTEARRRRIEEVLRRRQPDLTVLLENVHKPHNLSAILRTCDAVGVLEAHAVNPTGGV--PTFNETSGGSHKWVYLRVHPD   81 (194)
T ss_dssp             CCCCHHHHHHHHHTTCBTTEEEEEESCCCHHHHHHHHHHHHHHTBSEEEEESGGGGS--CCCCSSCSSGGGTSEEEEESS
T ss_pred             cchhhHhhHHHHHhcCCCCEEEEEeCCCCcChHHHHHHHHHHhCCCEEEEeCCCCCc--hhhHHHCCCChheeeeEecCC
Confidence            345678899999987667899999999999999999999999999999999876664  789999999999999999999


Q ss_pred             HHHHHHHHHHCCceEEEEeeCCCcc
Q 025787          222 PRECFNVLRSRGYRIATTHVGMDAC  246 (248)
Q Consensus       222 l~~~L~~Lk~~G~~ivAt~l~~~Av  246 (248)
                      +.++++.++++||+++|++...+++
T Consensus        82 l~~~l~~l~~~g~~i~~~~~~~~~~  106 (194)
T 1v2x_A           82 LHEAFRFLKERGFTVYATALREDAR  106 (194)
T ss_dssp             HHHHHHHHHHTTCEEEEECCCTTSE
T ss_pred             HHHHHHHHHHCCCEEEEEecCCCCc
Confidence            9999999999999999999765543

>1zjr_A TRNA (guanosine-2'-O-)-methyltransferase; methylase, RNA modifying enzyme, topological knot; 1.85A {Aquifex aeolicus}

Probab=99.86  E-value=4.5e-22  Score=173.25  Aligned_cols=106  Identities=25%  Similarity=0.427  Sum_probs=93.1

Q ss_pred             CCccchhhhhHHHHhhcCCCceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCCCCCcccccccCCCccceEEEEe
Q 025787          140 PYLMEERKERFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIELW  219 (248)
Q Consensus       140 ~~~~~~R~~~l~evl~~r~~~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R~SmGA~~~v~i~~~  219 (248)
                      .+.++.|+.++++++++++.+++||||+++||+|+|+|+|||+|||+++|+++..+.++ ...+.|+|||+.+|+++..+
T Consensus         5 ~~~~~~~~~~~~~~l~~~~~~l~vvLd~i~dp~NlGaI~Rta~a~G~~~v~lv~~~~~~-~~~~~r~s~Ga~~~l~~~~~   83 (211)
T 1zjr_A            5 YLVLEKRLKRLREVLEKRQKDLIVFADNVKNEHNFSAIVRTCDAVGVLYLYYYHAEGKK-AKINEGITQGSHKWVFIEKV   83 (211)
T ss_dssp             -CHHHHHHHHHHHHHTTCEEEEEEEEESCCCHHHHHHHHHHHHHHTEEEEEEECSSTTC-CCCCHHHHTTGGGSSEEEEC
T ss_pred             cccChhhHhhHHHHHhccCCCeEEEEECCCCcCcHHHHHHHHHHhCCCEEEEeCCCcCc-hHHHHHHcCCCcccceeEec
Confidence            45678888899999986666799999999999999999999999999999999887664 22456999999999999999


Q ss_pred             CCHHHHHHHHHHCCceEEEEeeCCCcc
Q 025787          220 DAPRECFNVLRSRGYRIATTHVGMDAC  246 (248)
Q Consensus       220 ~~l~~~L~~Lk~~G~~ivAt~l~~~Av  246 (248)
                      .++.++++.++++||+++|++...+++
T Consensus        84 ~~l~~~l~~l~~~g~~i~~~~~~~~~~  110 (211)
T 1zjr_A           84 DNPVQKLLEFKNRGFQIVATWLSKESV  110 (211)
T ss_dssp             SCHHHHHHHHHHTTCEEEEEBCSTTSE
T ss_pred             CCHHHHHHHHHHCCCEEEEEecCCCCc
Confidence            999999999999999999999875553

>3e5y_A TRMH family RNA methyltransferase; ssgcid, protein knot, decode, structural genomics; 2.40A {Burkholderia pseudomallei 305} SCOP: c.116.1.0

Probab=99.82  E-value=3.4e-21  Score=160.87  Aligned_cols=85  Identities=7%  Similarity=-0.045  Sum_probs=79.6

Q ss_pred             CceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCCCCCcccccccCCCccceEEEEeCCHHHHHHHHHHCCceEEE
Q 025787          159 YSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIELWDAPRECFNVLRSRGYRIAT  238 (248)
Q Consensus       159 ~~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R~SmGA~~~v~i~~~~~l~~~L~~Lk~~G~~ivA  238 (248)
                      +.++||||+++||+|+|+|+|||+|||++.|++.+.+.|++++++.|+|||+.+|+++.++.++.++++.||++||+++|
T Consensus         4 ~~l~vvLd~i~dp~NlGaI~Rta~a~G~~~viv~~~~~~~~~~~~~ras~g~~~~~~~~~~~~l~~~l~~l~~~g~~i~~   83 (160)
T 3e5y_A            4 SMFNVVLVEPEIPPNTGNVIRLCANTGARLHLIEPLGFPLDDAKMRRAGLDYHEYAQMRVHRDWDAFVAAEAPDPARMFA   83 (160)
T ss_dssp             -CCEEEEESCCCHHHHHHHHHHHHHHTCEEEEESSCSSCCCHHHHHHTTCCHHHHHTCEEESSHHHHHHHHCCCGGGEEE
T ss_pred             CcEEEEEeCCCCCCcHHHHHHHHHHcCCcEEEECCCCCCCccHHHHHHcCCchhhcceEEeCCHHHHHHHHHhCCCEEEE
Confidence            45899999999999999999999999999999888888888889999999999999999999999999999999999999


Q ss_pred             EeeCC
Q 025787          239 THVGM  243 (248)
Q Consensus       239 t~l~~  243 (248)
                      ++..+
T Consensus        84 ~~~~~   88 (160)
T 3e5y_A           84 FTTRG   88 (160)
T ss_dssp             ECSTT
T ss_pred             EecCC
Confidence            99764

>3n4j_A RNA methyltransferase; center for structural genomics of INF diseases, csgid; 1.47A {Yersinia pestis} SCOP: c.116.1.1 PDB: 3n4k_A* 1mxi_A* 1j85_A*

Probab=99.80  E-value=1.4e-20  Score=158.08  Aligned_cols=84  Identities=11%  Similarity=0.025  Sum_probs=78.9

Q ss_pred             ceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCCCCCcccccccCCCccceEEEEeCCHHHHHHHHHH---CCceE
Q 025787          160 SVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIELWDAPRECFNVLRS---RGYRI  236 (248)
Q Consensus       160 ~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R~SmGA~~~v~i~~~~~l~~~L~~Lk~---~G~~i  236 (248)
                      .++||||+++||+|+|+|+|||+|||++.|++.+.+.|++.+++.|++||+.+|+++..+.+++++++.||+   +||++
T Consensus         4 ~~~vvL~~~~dp~NlGaI~Rta~a~G~~~viv~~~~~~~~~~~~~ras~g~~~~~~~~~~~~l~~~l~~lk~~~~~g~~i   83 (165)
T 3n4j_A            4 MLNIVLFEPEIPPNTGNIIRLCANTGCQLHLIKPLGFTWDDKRLRRAGLDYHEFADIKHHHDYQAFLDSEKLDSTQPARL   83 (165)
T ss_dssp             CEEEEEESCCCHHHHHHHHHHHHHHTCEEEEESCCSSCCCHHHHHHTTCCHHHHTTCEEESSHHHHHHHTTCCSSSCTTE
T ss_pred             cEEEEEeCCCCCCcHHHHHHHHHHcCCeEEEECCCCCCCccHHHHHhccCceeecCeEEeCCHHHHHHHHHhhccCCCEE
Confidence            589999999999999999999999999999988888888888899999999999999999999999999999   99999


Q ss_pred             EEEeeCC
Q 025787          237 ATTHVGM  243 (248)
Q Consensus       237 vAt~l~~  243 (248)
                      +|++..+
T Consensus        84 ~~~~~~~   90 (165)
T 3n4j_A           84 FALTTKG   90 (165)
T ss_dssp             EEECTTC
T ss_pred             EEEEcCC
Confidence            9999753

>2ha8_A TAR (HIV-1) RNA loop binding protein; methyltransferase, structural genomics, structural genomics consortium, SGC, RNA binding protein; HET: SAH; 1.60A {Homo sapiens}

Probab=99.79  E-value=4.6e-20  Score=157.24  Aligned_cols=89  Identities=17%  Similarity=0.215  Sum_probs=78.4

Q ss_pred             cCCCceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCCCCCcccc-cccCCCccceEEEEe--CCHHHHHHHHHHC
Q 025787          156 NRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENR-HVSMGAEKWLDIELW--DAPRECFNVLRSR  232 (248)
Q Consensus       156 ~r~~~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~-R~SmGA~~~v~i~~~--~~l~~~L~~Lk~~  232 (248)
                      +++.+++||||+|+||+|+|+|+|||+|||+++|++.+  .++++++.+ |+|||+.+|+++..+  .++.++++.+|++
T Consensus        22 ~~~~~~~vvLd~i~dp~NlGaI~Rta~a~G~~~vil~~--~~~~~~k~~~r~s~ga~~~l~~~~~~~~~~~~~l~~lk~~   99 (184)
T 2ha8_A           22 KSISRLIVVASLIDKPTNLGGLCRTCEVFGASVLVVGS--LQCISDKQFQHLSVSAEQWLPLVEVKPPQLIDYLQQKKTE   99 (184)
T ss_dssp             CCCCCCEEECTTCCCHHHHHHHHHHHHHTTCSEEEESC--GGGGGSHHHHHHHTTGGGTSCEEECCGGGHHHHHHHHHHT
T ss_pred             CCCCCEEEEEcCCCCCCcHHHHHHHHHHhCCCEEEECC--CCCCCcccceeecCCccceEEEEEEcCCCHHHHHHHHHHC
Confidence            45567899999999999999999999999999999976  455677776 889999999999875  7999999999999


Q ss_pred             CceEEEEeeCCCcc
Q 025787          233 GYRIATTHVGMDAC  246 (248)
Q Consensus       233 G~~ivAt~l~~~Av  246 (248)
                      ||+++|++..+++.
T Consensus       100 g~~i~~~~~~~~~~  113 (184)
T 2ha8_A          100 GYTIIGVEQTAKSL  113 (184)
T ss_dssp             TCEEEEECCCTTCE
T ss_pred             CCEEEEEECCCCCc
Confidence            99999999875543

>3l8u_A SMU.1707C, putative rRNA methylase; methyltransferase, knotted protein; 2.00A {Streptococcus mutans} SCOP: c.116.1.0

Probab=99.79  E-value=1.4e-19  Score=154.48  Aligned_cols=87  Identities=9%  Similarity=-0.023  Sum_probs=70.9

Q ss_pred             hhcCCCceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCCCCCcccccccCCCccceEEEEeCCHHHHHHHHHHCC
Q 025787          154 VKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIELWDAPRECFNVLRSRG  233 (248)
Q Consensus       154 l~~r~~~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R~SmGA~~~v~i~~~~~l~~~L~~Lk~~G  233 (248)
                      .+++..+++||||+++||+|+|+|+|||+|||++.|++.+.+.|++++++.|+|||+.+++++..+.++.++++.+   |
T Consensus        11 ~~~~~~~l~vvLd~v~dP~NlGaI~Rta~afG~~~viv~~~~~~~~~~~~~ras~g~~~~v~i~~~~~l~~~l~~l---g   87 (182)
T 3l8u_A           11 KLLTLGRNHVVLFQPQIPANTGNIARTCAATNTSLHIIRPMGFPIDDKKMKRAGLDYWDKLDVHFYDSLNDFMNIC---S   87 (182)
T ss_dssp             ----CCCEEEEEESCCCHHHHHHHHHHHHHHTCEEEEESCCSSCCCTTTC------CCC-CCEEEESSHHHHHHHC---C
T ss_pred             hhcCCCCEEEEEeCCCCcCcHHHHHHHHHHcCCcEEEECCCCCCCCcHHHHHhCcChhhhCCeEEcCCHHHHHHHC---C
Confidence            3455678999999999999999999999999999999998888888899999999999999999999999999988   9


Q ss_pred             ceEEEEeeCC
Q 025787          234 YRIATTHVGM  243 (248)
Q Consensus       234 ~~ivAt~l~~  243 (248)
                      |++++++..+
T Consensus        88 ~~i~~~~~~~   97 (182)
T 3l8u_A           88 GKLHLITKFA   97 (182)
T ss_dssp             SEEEEECSSC
T ss_pred             CEEEEEEcCC
Confidence            9999998753

>3kty_A Probable methyltransferase; alpha-beta-alpha sandwich, structural genomics, PSI-2, prote structure initiative; 2.30A {Bordetella pertussis}

Probab=99.67  E-value=2.6e-17  Score=138.53  Aligned_cols=80  Identities=18%  Similarity=0.174  Sum_probs=68.8

Q ss_pred             ceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCC-CCCCC-CcccccccCCCccceEE-EEeCCHHHHHHHHHHCCceE
Q 025787          160 SVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSC-DSSKR-YRENRHVSMGAEKWLDI-ELWDAPRECFNVLRSRGYRI  236 (248)
Q Consensus       160 ~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~-~~dp~-~~k~~R~SmGA~~~v~i-~~~~~l~~~L~~Lk~~G~~i  236 (248)
                      ++++|||+++||+|+|+|+|||++||+++|+++.. +.|++ +++++|+|||+.+|+++ ..+++++++++.++    ++
T Consensus        10 ~~~vvL~~~~dp~N~Gai~Rta~a~G~~~l~lv~~~~~d~~~~~~~~r~a~Ga~~~l~~~~~~~~l~~~l~~~~----~v   85 (173)
T 3kty_A           10 RVRFIMTQPSHPGNVGSAARAIKTMGFGELVLVAPRFPDMTAQPEAVALASGALDVLERAAVHDTLEEALAPVT----LA   85 (173)
T ss_dssp             TEEEEEESCCCHHHHHHHHHHHHHTTCCCEEEESCSSTTGGGSHHHHHHHTTCHHHHHTCEEESCHHHHHTTCS----EE
T ss_pred             CeEEEEeCCCCCCcHHHHHHHHHHcCCCEEEEeCCCccccCCCHHHHHHcCCHHHhhchheecCCHHHHHHhCC----eE
Confidence            68999999999999999999999999999998765 44654 89999999999999995 45689999888775    68


Q ss_pred             EEEeeCC
Q 025787          237 ATTHVGM  243 (248)
Q Consensus       237 vAt~l~~  243 (248)
                      +|++...
T Consensus        86 ~~t~~~~   92 (173)
T 3kty_A           86 FALTTRV   92 (173)
T ss_dssp             EEEECC-
T ss_pred             EEEcccc
Confidence            8888754

>3ilk_A Uncharacterized tRNA/RRNA methyltransferase HI038; APC63004, methylase family protein, haemophilus influenzae R structural genomics; 2.01A {Haemophilus influenzae}

Probab=99.49  E-value=7.9e-15  Score=130.53  Aligned_cols=79  Identities=19%  Similarity=0.254  Sum_probs=68.2

Q ss_pred             ceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCCCCCcccccccCCCccceE-EEEeCCHHHHHHHHHHCCceEEE
Q 025787          160 SVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLD-IELWDAPRECFNVLRSRGYRIAT  238 (248)
Q Consensus       160 ~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R~SmGA~~~v~-i~~~~~l~~~L~~Lk~~G~~ivA  238 (248)
                      .+.||||+++||+|+|+|+|||++||+++|+++..+  +++++++|+|+||.++++ +..+++++++++.+   + .++|
T Consensus         7 ~l~vVL~~~~dP~NiGai~Rta~a~G~~~l~lv~p~--~~~~~a~r~A~GA~~~l~~~~~~~~l~eal~~~---~-~vva   80 (244)
T 3ilk_A            7 NIRIVLIETSHSGNIGSAARAMKTMGLTQLCLVSPK--SVDEQSYALSAGAENIVKNARVVDSFDEAVDDC---S-LVIG   80 (244)
T ss_dssp             TEEEEEESCCSHHHHHHHHHHHHHHTCCEEEEESCS--CCSHHHHHTTTTCHHHHHHCEEESSHHHHTTTC---S-EEEE
T ss_pred             CcEEEEECCCCcChHHHHHHHHHHhCCCEEEEECCC--CCCHHHHHHcCChhheeceeEEeCCHHHHHHhC---C-eEEE
Confidence            589999999999999999999999999999999887  778999999999997776 34578988888765   3 7888


Q ss_pred             EeeCCC
Q 025787          239 THVGMD  244 (248)
Q Consensus       239 t~l~~~  244 (248)
                      ++....
T Consensus        81 tt~~~~   86 (244)
T 3ilk_A           81 TSARLR   86 (244)
T ss_dssp             ECCCCG
T ss_pred             EccCCC
Confidence            887644

>3ic6_A Putative methylase family protein; putative methylase family Pro structural genomics, PSI-2, protein structure initiative; 2.59A {Neisseria gonorrhoeae fa 1090}

Probab=99.46  E-value=2e-14  Score=126.64  Aligned_cols=82  Identities=13%  Similarity=0.148  Sum_probs=68.0

Q ss_pred             ceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCCCC-------------------CcccccccCCCccceEE-EEe
Q 025787          160 SVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKR-------------------YRENRHVSMGAEKWLDI-ELW  219 (248)
Q Consensus       160 ~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~-------------------~~k~~R~SmGA~~~v~i-~~~  219 (248)
                      .++||||+++||+|+|+|+|||++||+++|+++..+++++                   ++++.|+|+|+.++++. ..+
T Consensus        17 ~l~vVLd~~~dP~NiGaI~Rta~afG~~~l~Lv~p~~~~~~~~~~~~~~~p~~~~~~~~~~~a~~~aaGA~~~l~~~~v~   96 (223)
T 3ic6_A           17 NIRIILTRTSHPANIGSAARAMKTMGLHRLTIVTPNLMATPMTENPPVFNPDDVQSFALPEESFILASGAADVLHNAEIV   96 (223)
T ss_dssp             GEEEEEESCCCHHHHHHHHHHHHHTTCCCEEEESCCCCCBTTBSSCCCCCTTCGGGCCCCHHHHHHHGGGHHHHHTCEEE
T ss_pred             CEEEEEeCCCCCChHHHHHHHHHHcCCCEEEEeCCCccccccccccccccccccccccCCHHHHHHhCCccccCceEEEe
Confidence            5899999999999999999999999999999988776653                   35899999999988764 446


Q ss_pred             CCHHHHHHHHHHCCceEEEEeeCCCc
Q 025787          220 DAPRECFNVLRSRGYRIATTHVGMDA  245 (248)
Q Consensus       220 ~~l~~~L~~Lk~~G~~ivAt~l~~~A  245 (248)
                      ++++++++.+    ++++|++...+.
T Consensus        97 ~~l~eal~~~----~~vvatt~~~~~  118 (223)
T 3ic6_A           97 ATLDEALADT----TIACALTSRRRE  118 (223)
T ss_dssp             SCHHHHHTTE----EEEEEECCSCC-
T ss_pred             CCHHHHHHhC----CeEEEEeccCCc
Confidence            8888877654    578999876543

>3onp_A TRNA/RRNA methyltransferase (SPOU); structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 1.90A {Rhodobacter sphaeroides}

Probab=99.45  E-value=2.6e-14  Score=127.39  Aligned_cols=81  Identities=15%  Similarity=0.112  Sum_probs=68.7

Q ss_pred             ceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCCCCCcccccccCCCccceE-EEEeCCHHHHHHHHHHCCceEEE
Q 025787          160 SVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLD-IELWDAPRECFNVLRSRGYRIAT  238 (248)
Q Consensus       160 ~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R~SmGA~~~v~-i~~~~~l~~~L~~Lk~~G~~ivA  238 (248)
                      ++.||||+++||+|+|+|+|+|++||+++++++..++++++++++|.|+|+.+.++ +..+++++++++.+    ..++|
T Consensus         4 ~~~vVL~~~~dP~NiGai~Rta~a~G~~~l~Lv~p~~~~~~~~a~~~a~GA~~~l~~~~~~~~l~eal~~~----~~v~a   79 (249)
T 3onp_A            4 EPVFILVRPQMGENIGAAARAMLNFGLGRLRIVDPRDGWPNPKAVAMASGAGRLLDHAGLFPTVAEAIRDC----DYVFA   79 (249)
T ss_dssp             CCEEEEESCCCHHHHHHHHHHHHHTTCCCEEEESCTTCSSCHHHHHHHGGGHHHHHTCEEESSHHHHHTTC----SEEEE
T ss_pred             ceEEEEeCCCCCChHHHHHHHHHHcCCCEEEEeCCCcCCCcHHHHHHcCCccccCceEEEeCCHHHHHHhC----CeEEE
Confidence            57999999999999999999999999999999998877778999999999996444 44478998888755    36888


Q ss_pred             EeeCCC
Q 025787          239 THVGMD  244 (248)
Q Consensus       239 t~l~~~  244 (248)
                      ++....
T Consensus        80 tt~~~~   85 (249)
T 3onp_A           80 TTARGR   85 (249)
T ss_dssp             EESSCC
T ss_pred             EcCCCC
Confidence            877544

>3dcm_X AdoMet, uncharacterized protein TM_1570; trefoil knot, spout mtase, adoMet binding, transferase; HET: SAM; 2.00A {Thermotoga maritima}

Probab=85.64  E-value=0.68  Score=39.49  Aligned_cols=67  Identities=13%  Similarity=0.129  Sum_probs=48.6

Q ss_pred             cHHHHHHHHHHHCCCeEEEcCCCCCCCCccccc------ccCCCc---------cceEEEEeCCHHHHHHHHHH---CCc
Q 025787          173 NVSATFRSADALGVQSVHVVSCDSSKRYRENRH------VSMGAE---------KWLDIELWDAPRECFNVLRS---RGY  234 (248)
Q Consensus       173 NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R------~SmGA~---------~~v~i~~~~~l~~~L~~Lk~---~G~  234 (248)
                      |||.|.|++.-||++..+++....++. ..+.+      .+.|+.         ..+.+  +++++++++.+.+   +++
T Consensus        30 dihdiARamkt~Gl~~l~LV~P~~~~~-~~a~~~~~~w~~~~Ga~~np~r~d~L~~a~v--v~sL~eAl~~~~~~~g~~p  106 (192)
T 3dcm_X           30 DVHDIARTARTYNLKGYYIVTNLRAQQ-DMVSKMLKFWREGFGSRYNPSRAESLKLVKL--KSYLEDVLEDIESVEGERP  106 (192)
T ss_dssp             HHHHHHHHHHHTTCSEEEEECCCHHHH-HHHHHHHHHHHTSGGGGTCSSSHHHHTTEEE--ESSHHHHHHHHHHHHSSCC
T ss_pred             cHHHHHHHHHhcCCceEEEECCccccH-HHHHHHHHhhhcccCcccCcCHHHHhccCeE--ECCHHHHHHHHHhhcCCcc
Confidence            599999999999999999998764321 11222      245552         44444  5899999999974   678


Q ss_pred             eEEEEeeC
Q 025787          235 RIATTHVG  242 (248)
Q Consensus       235 ~ivAt~l~  242 (248)
                      .++||+..
T Consensus       107 ~vvaTsAr  114 (192)
T 3dcm_X          107 LIFFTSAK  114 (192)
T ss_dssp             EEEECCSS
T ss_pred             EEEEeCCC
Confidence            89998754

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	248
d1v2xa_	191	c.116.1.1 (A:) tRNA (Gm18) methyltransferase TrmH	1e-08
d1gz0a1	166	c.116.1.1 (A:78-243) RlmB, C-terminal domain {Esch	2e-05
d1mxia_	156	c.116.1.1 (A:) Hypothetical tRNA/rRNA methyltransf	3e-04

>d1v2xa_ c.116.1.1 (A:) tRNA (Gm18) methyltransferase TrmH {Thermus thermophilus [TaxId: 274]} Length = 191

class: Alpha and beta proteins (a/b)
fold: alpha/beta knot
superfamily: alpha/beta knot
family: SpoU-like RNA 2'-O ribose methyltransferase
domain: tRNA (Gm18) methyltransferase TrmH
species: Thermus thermophilus [TaxId: 274]

 Score = 51.5 bits (122), Expect = 1e-08
 Identities = 27/104 (25%), Positives = 48/104 (46%), Gaps = 2/104 (1%)

Query: 144 EERKERFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYREN 203
           E R+ R   V++ R   + +++E +    N+SA  R+ DA+GV   H    + +      
Sbjct: 6   EARRRRIEEVLRRRQPDLTVLLENVHKPHNLSAILRTCDAVGVLEAHA--VNPTGGVPTF 63

Query: 204 RHVSMGAEKWLDIELWDAPRECFNVLRSRGYRIATTHVGMDACC 247
              S G+ KW+ + +     E F  L+ RG+ +  T +  DA  
Sbjct: 64  NETSGGSHKWVYLRVHPDLHEAFRFLKERGFTVYATALREDARD 107

>d1gz0a1 c.116.1.1 (A:78-243) RlmB, C-terminal domain {Escherichia coli [TaxId: 562]} Length = 166

class: Alpha and beta proteins (a/b)
fold: alpha/beta knot
superfamily: alpha/beta knot
family: SpoU-like RNA 2'-O ribose methyltransferase
domain: RlmB, C-terminal domain
species: Escherichia coli [TaxId: 562]

 Score = 41.4 bits (96), Expect = 2e-05
 Identities = 18/82 (21%), Positives = 38/82 (46%)

Query: 146 RKERFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRH 205
           ++    +++ +      L+++G++D  N+ A  RSADA GV +V V    S++     + 
Sbjct: 4   QENDLPDLIASLDQPFLLILDGVTDPHNLGACLRSADAAGVHAVIVPKDRSAQLNATAKK 63

Query: 206 VSMGAEKWLDIELWDAPRECFN 227
           V+ GA + + +           
Sbjct: 64  VACGAAESVPLIRVTNLARTMR 85

>d1mxia_ c.116.1.1 (A:) Hypothetical tRNA/rRNA methyltransfease HI0766 (YibK homologue) {Haemophilus influenzae [TaxId: 727]} Length = 156

class: Alpha and beta proteins (a/b)
fold: alpha/beta knot
superfamily: alpha/beta knot
family: SpoU-like RNA 2'-O ribose methyltransferase
domain: Hypothetical tRNA/rRNA methyltransfease HI0766 (YibK homologue)
species: Haemophilus influenzae [TaxId: 727]

 Score = 38.3 bits (88), Expect = 3e-04
 Identities = 7/76 (9%), Positives = 18/76 (23%)

Query: 172 GNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIELWDAPRECFNVLRS 231
            N     R     G +   +     +   +  R   +   ++ +I+            + 
Sbjct: 13  QNTGNIIRLCANTGFRLHLIEPLGFTWDDKRLRRSGLDYHEFAEIKRHKTFEAFLESEKP 72

Query: 232 RGYRIATTHVGMDACC 247
           +     TT        
Sbjct: 73  KRLFALTTKGCPAHSQ 88

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	248
d1gz0a1	166	RlmB, C-terminal domain {Escherichia coli [TaxId:	99.85
d1v2xa_	191	tRNA (Gm18) methyltransferase TrmH {Thermus thermo	99.78
d1ipaa1	158	RrmA (RrmH), C-terminal domain {Thermus thermophil	99.76
d1mxia_	156	Hypothetical tRNA/rRNA methyltransfease HI0766 (Yi	99.27
d1ipaa2	105	RrmA (RrmH), N-terminal domain {Thermus thermophil	94.48

>d1gz0a1 c.116.1.1 (A:78-243) RlmB, C-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: alpha/beta knot
superfamily: alpha/beta knot
family: SpoU-like RNA 2'-O ribose methyltransferase
domain: RlmB, C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=99.85  E-value=8.8e-22  Score=162.23  Aligned_cols=96  Identities=22%  Similarity=0.267  Sum_probs=90.2

Q ss_pred             hhHHHHhhcCCCceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCCCCCcccccccCCCccceEEEEeCCHHHHHH
Q 025787          148 ERFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIELWDAPRECFN  227 (248)
Q Consensus       148 ~~l~evl~~r~~~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R~SmGA~~~v~i~~~~~l~~~L~  227 (248)
                      ..+++++.+.+.+++||||+|+||+|+|+|+|||+|||+++|+++..+++++++++.|+|+|+.+|+++..+.++.++++
T Consensus         6 ~~l~~~~~~~~~~~~vvLd~i~~p~N~GaiiRta~afG~~~v~~~~~~~~~~~~~~~r~s~g~~~~v~~~~~~~~~~~l~   85 (166)
T d1gz0a1           6 NDLPDLIASLDQPFLLILDGVTDPHNLGACLRSADAAGVHAVIVPKDRSAQLNATAKKVACGAAESVPLIRVTNLARTMR   85 (166)
T ss_dssp             GGHHHHHHTCSSCEEEEEESCCCHHHHHHHHHHHHHHTCSEEEEESSSSCCCCHHHHHHHTTHHHHSCEEEESCHHHHHH
T ss_pred             ccHHHHHhccCCCEEEEEeCCCCcchHHHHHHHHHhcCCceeeeecccccccchhhheeccCcceEeceeecCCHHHHHH
Confidence            36888888777789999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHCCceEEEEeeCC
Q 025787          228 VLRSRGYRIATTHVGM  243 (248)
Q Consensus       228 ~Lk~~G~~ivAt~l~~  243 (248)
                      .+++.||++++++...
T Consensus        86 ~~~~~~~~~~~~~~~~  101 (166)
T d1gz0a1          86 MLQEENIWIVGTAGEA  101 (166)
T ss_dssp             HHHHTTCEEEEECTTC
T ss_pred             Hhcccccccccccccc
Confidence            9999999999988654

>d1v2xa_ c.116.1.1 (A:) tRNA (Gm18) methyltransferase TrmH {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: alpha/beta knot
superfamily: alpha/beta knot
family: SpoU-like RNA 2'-O ribose methyltransferase
domain: tRNA (Gm18) methyltransferase TrmH
species: Thermus thermophilus [TaxId: 274]

Probab=99.78  E-value=3.3e-19  Score=150.44  Aligned_cols=102  Identities=27%  Similarity=0.446  Sum_probs=91.4

Q ss_pred             chhhhhHHHHhhcCCCceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCCCCCcccccccCCCccceEEEEeCCHH
Q 025787          144 EERKERFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIELWDAPR  223 (248)
Q Consensus       144 ~~R~~~l~evl~~r~~~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R~SmGA~~~v~i~~~~~l~  223 (248)
                      ..|..++++++++++++++||||+|+||+|+|+|+|||+|||++.|+++..++++  +...++++|+..|+++..+.+..
T Consensus         6 ~~r~~~~~~~l~~~~~~~~vvLd~i~~p~NiG~IiRta~afG~~~v~l~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~   83 (191)
T d1v2xa_           6 EARRRRIEEVLRRRQPDLTVLLENVHKPHNLSAILRTCDAVGVLEAHAVNPTGGV--PTFNETSGGSHKWVYLRVHPDLH   83 (191)
T ss_dssp             CCHHHHHHHHHTTCBTTEEEEEESCCCHHHHHHHHHHHHHHTBSEEEEESGGGGS--CCCCSSCSSGGGTSEEEEESSHH
T ss_pred             HHHHHHHHHHHhcCCCCEEEEEeCCCCCchHHHHHHHHHhhccccccccCCcccc--ceeeecchhhheeecccccchhh
Confidence            4456689999998888999999999999999999999999999999999877665  34678999999999999999999


Q ss_pred             HHHHHHHHCCceEEEEeeCCCccc
Q 025787          224 ECFNVLRSRGYRIATTHVGMDACC  247 (248)
Q Consensus       224 ~~L~~Lk~~G~~ivAt~l~~~Av~  247 (248)
                      ++++.+++.||.+++++...++.+
T Consensus        84 ~~l~~l~~~~~~i~~~~~~~~~~~  107 (191)
T d1v2xa_          84 EAFRFLKERGFTVYATALREDARD  107 (191)
T ss_dssp             HHHHHHHHTTCEEEEECCCTTSEE
T ss_pred             hHHHHHhhcCCccccccccccccc
Confidence            999999999999999999877653

>d1ipaa1 c.116.1.1 (A:106-263) RrmA (RrmH), C-terminal domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: alpha/beta knot
superfamily: alpha/beta knot
family: SpoU-like RNA 2'-O ribose methyltransferase
domain: RrmA (RrmH), C-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=99.76  E-value=6.1e-19  Score=143.73  Aligned_cols=85  Identities=25%  Similarity=0.246  Sum_probs=77.0

Q ss_pred             CceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCCCCCcccccccCCCccceEEEEeCCHHHHHHHHHHCCceEEE
Q 025787          159 YSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIELWDAPRECFNVLRSRGYRIAT  238 (248)
Q Consensus       159 ~~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R~SmGA~~~v~i~~~~~l~~~L~~Lk~~G~~ivA  238 (248)
                      .+++||||+|+||+|+|+|+|||++||++.|++.+. .++++++++|+|+|+.+|+++.. .+..++++.+++.||++++
T Consensus        10 ~~~~lvld~i~dP~NlGai~Rta~~fG~~~v~~~~~-~~~~~~~~~r~s~g~~~~~~~~~-~~~~~~~~~~~~~~~~i~~   87 (158)
T d1ipaa1          10 DALILVAVGLEKPGNLGAVLRSADAAGAEAVLVAGG-VDLYSPQVIRNSTGVVFSLRTLA-ASESEVLDWIKQHNLPLVA   87 (158)
T ss_dssp             TCEEEEEESCCCHHHHHHHHHHHHHHTCSEEEEESC-CCTTCHHHHHHTTTGGGTSCEEE-ECHHHHHHHHHHTTCCEEE
T ss_pred             CCEEEEEeCCCCCchHHHHHHHHHhhccchhhhccc-ccccchhhheecccceeeecccc-cchHHHHHHHHhhcccccc
Confidence            469999999999999999999999999999988764 68999999999999999999876 4567899999999999999


Q ss_pred             EeeCCCc
Q 025787          239 THVGMDA  245 (248)
Q Consensus       239 t~l~~~A  245 (248)
                      ++.+.++
T Consensus        88 ~~~~~~~   94 (158)
T d1ipaa1          88 TTPHAEA   94 (158)
T ss_dssp             ECTTCSS
T ss_pred             ccccccc
Confidence            9987654

>d1mxia_ c.116.1.1 (A:) Hypothetical tRNA/rRNA methyltransfease HI0766 (YibK homologue) {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: alpha/beta knot
superfamily: alpha/beta knot
family: SpoU-like RNA 2'-O ribose methyltransferase
domain: Hypothetical tRNA/rRNA methyltransfease HI0766 (YibK homologue)
species: Haemophilus influenzae [TaxId: 727]

Probab=99.27  E-value=2.4e-12  Score=103.25  Aligned_cols=69  Identities=9%  Similarity=0.016  Sum_probs=58.2

Q ss_pred             eEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCCCCCcccccccCCCccceEEEEeCCHHHHHHHH
Q 025787          161 VCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIELWDAPRECFNVL  229 (248)
Q Consensus       161 lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R~SmGA~~~v~i~~~~~l~~~L~~L  229 (248)
                      +-+||++.+||+|+|+|+|||+|||++.|++.+++.++...+..++++|+.++.+.....+....+...
T Consensus         2 ~~ivL~~p~~P~NlGai~Rta~afGv~~v~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   70 (156)
T d1mxia_           2 LDIVLYEPEIPQNTGNIIRLCANTGFRLHLIEPLGFTWDDKRLRRSGLDYHEFAEIKRHKTFEAFLESE   70 (156)
T ss_dssp             CEEEEESCCCHHHHHHHHHHHHHHTCEEEEESSCSSCTTCHHHHTTSCCGGGSSSCEEESSHHHHHHHH
T ss_pred             eEEEEeCCCCCCcHHHHHHHHHHcCCcEEEEecCCCcccchhhhhcccccceeeeeeeechhhhhhhhh
Confidence            468999999999999999999999999999998887777777888888888888888777655554444

>d1ipaa2 d.79.3.3 (A:1-105) RrmA (RrmH), N-terminal domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Bacillus chorismate mutase-like
superfamily: L30e-like
family: RNA 2'-O ribose methyltransferase substrate binding domain
domain: RrmA (RrmH), N-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=94.48  E-value=0.0051  Score=44.61  Aligned_cols=68  Identities=10%  Similarity=-0.006  Sum_probs=42.3

Q ss_pred             ccCCCCCchHHHHhhhcCcHHHHhHHHhhhhcCCCCCCCeE--E-----------------EeeccCcCCc-C-C----C
Q 025787           67 DDENDTPSKDNVEKLLTNPDDVTQFMKMERSCMVNDGVGSM--E-----------------SLSNKRWFPY-L-D----R  121 (248)
Q Consensus        67 ~~~~~~~p~~~~~~ll~t~~~~~~L~~~~~r~~~~~~~glf--E-----------------~l~~~~~~~~-~-~----~  121 (248)
                      .|++..+|+            ++++.++..+ +.+.+.|.|  |                 +++++.++.. . .    .
T Consensus         2 ~ItS~~N~~------------iK~~~~L~~~-k~R~~~g~flvEG~r~v~eal~~g~~i~~i~~~~~~~~~~~~~~~~~~   68 (105)
T d1ipaa2           2 RITSTANPR------------IKELARLLER-KHRDSQRRFLIEGAREIERALQAGIELEQALVWEGGLNPEEQQVYAAL   68 (105)
T ss_dssp             EECCTTSHH------------HHHHHGGGSH-HHHHHHTEEEEESHHHHHHHHHTTCCEEEEEEETTCCCHHHHHHHHCC
T ss_pred             cccCCCCHH------------HHHHHHHhcc-cchhhhCeEEEEcHHHHHHHHHcCCCceEEEEehhhhccchHHHHHHH
Confidence            466677777            4444443222 345667888  6                 5777766554 1 1    1


Q ss_pred             Cc-cC-cEEEccHHHHHHcCCCccchhh
Q 025787          122 YK-CG-DVYLSSSEVVEALSPYLMEERK  147 (248)
Q Consensus       122 ~~-~~-~v~~vs~~vl~~ls~~~~~~R~  147 (248)
                      .. .. +++.+++++|++++++.+|++.
T Consensus        69 ~~~~~~~~~~vs~~~~~~ls~~~tpqGi   96 (105)
T d1ipaa2          69 GRVGRLALLEVSEAVLKKLSVRDNPAGL   96 (105)
T ss_dssp             -----CEEEEECHHHHHHHCCSSSCCSE
T ss_pred             hhcCCCeEEEECHHHHHHHhCCCCCCcE
Confidence            11 12 6899999999999999888654