Citrus Sinensis ID: 040494

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------
MIESYVVVHNIAKRHNVGTLARSATAFGVSEMILVGRRDFNAFGSHGSTSHVNFRHFHSLSDARVFLKSKDCDICGVEITDNAVDVTQHPFKKSTAFLLGNEGMGLSAKECEICDFFVYIPQYGGGTASLNVTVAASIVLHHFGVWAGFSERTRDGNKYVVAERSARQVRRSFCAEKPESIIEMRRSRRENASNGFFDGSGNDVSSSSLLDALFTDE
cccEEEEEcccccccHHHHHHHHHHHHcccEEEEccccccccccccccccEEEEEEEccHHHHHHHHHHccccEEEEEcccccEEcccccccccEEEEEccccccccHHHHHHcccEEEEcccccccccccHHHHHHHHHHHHHHcccccccccccccccHHHHHHHHHHHHHHHccHHHHHHHHHHHHHccccccccccccccccHHHHHHHHccc
cccEEEEEcccccccccHHHHHcHHHccccEEEEccccEEEEEEcccccccEcEEEcccHHHHHHHHHHcccEEEEEEcccccccccEccccccEEEEEEcccccccHHHHHHHccEEEEccccHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHcccEEccccHHHHHHHcccccHHHHHHHHHHHHHcccccccccccccccccHHHHHHHccc
MIESYVVVHNIAkrhnvgtlarsatAFGVSEMILVGRrdfnafgshgstshvnfrhfhSLSDARVFlkskdcdicgveitdnavdvtqhpfkkstafllgnegmglsakeceicdffvyipqygggtaSLNVTVAASIVLHHFgvwagfsertrdgnkyVVAERSARQVRRSFCAEKPESIIEMRRSrrenasngffdgsgndvsssslldalftde
MIESYVVVHniakrhnvgtlarsaTAFGVSEMILVGRRDFNAFGSHGSTSHVNFRHFHSLSDARVFLKSKDCDICGVEItdnavdvtqhpFKKSTAFLLGNEGMGLSAKECEICDFFVYIPQYGGGTASLNVTVAASIVLHHFGvwagfsertrdgnkyvvaersarqvrrsfcaekpesiiEMRRSRRENAsngffdgsgndvsssslldalftde
MIESYVVVHNIAKRHNVGTLARSATAFGVSEMILVGRRDFNAFGSHGSTSHVNFRHFHSLSDARVFLKSKDCDICGVEITDNAVDVTQHPFKKSTAFLLGNEGMGLSAKECEICDFFVYIPQYGGGTASLNVTVAASIVLHHFGVWAGFSERTRDGNKYVVAERSARQVRRSFCAEKPesiiemrrsrreNASNGFFDGSGNDVSSSSLLDALFTDE
***SYVVVHNIAKRHNVGTLARSATAFGVSEMILVGRRDFNAFGSHGSTSHVNFRHFHSLSDARVFLKSKDCDICGVEITDNAVDVTQHPFKKSTAFLLGNEGMGLSAKECEICDFFVYIPQYGGGTASLNVTVAASIVLHHFGVWAGFSERTRDGNKYVVA*******************************************************
MIESYVVVHNIAKRHNVGTLARSATAFGVSEMILVGRRDFNAFGSHGSTSHVNFRHFHSLSDARVFLKSKDCDICGVEITDNAVDVTQHPFKKSTAFLLGNEGMGLSAKECEICDFFVYIPQYGGGTASLNVTVAASIVLHHFGVWAG************************FCAEKPESIIE******************NDVSSSSLLDALFT**
MIESYVVVHNIAKRHNVGTLARSATAFGVSEMILVGRRDFNAFGSHGSTSHVNFRHFHSLSDARVFLKSKDCDICGVEITDNAVDVTQHPFKKSTAFLLGNEGMGLSAKECEICDFFVYIPQYGGGTASLNVTVAASIVLHHFGVWAGFSERTRDGNKYVVAERSARQVRRSFCAEKPESIIEMRRSRRENASNGFFDGSGNDVSSSSLLDALFTDE
MIESYVVVHNIAKRHNVGTLARSATAFGVSEMILVGRRDFNAFGSHGSTSHVNFRHFHSLSDARVFLKSKDCDICGVEITDNAVDVTQHPFKKSTAFLLGNEGMGLSAKECEICDFFVYIPQYGGGTASLNVTVAASIVLHHFGVWAGFSERTRDGNKYVVAERSARQVRRSFCAEKPESIIEMRRSRREN*S***************LLD******
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MIESYVVVHNIAKRHNVGTLARSATAFGVSEMILVGRRDFNAFGSHGSTSHVNFRHFHSLSDARVFLKSKDCDICGVEITDNAVDVTQHPFKKSTAFLLGNEGMGLSAKECEICDFFVYIPQYGGGTASLNVTVAASIVLHHFGVWAGFSERTRDGNKYVVAERSARQVRRSFCAEKPESIIEMRRSRRENASNGFFDGSGNDVSSSSLLDALFTDE
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query217 2.2.26 [Sep-21-2011]
P0AGJ4229 tRNA (guanosine(18)-2'-O) yes no 0.622 0.589 0.316 3e-12
P0AGJ2229 tRNA (guanosine(18)-2'-O) N/A no 0.622 0.589 0.316 3e-12
P0AGJ3229 tRNA (guanosine(18)-2'-O) N/A no 0.622 0.589 0.316 3e-12
Q4L3J1249 Putative TrmH family tRNA yes no 0.635 0.554 0.310 1e-10
Q49V41249 Putative TrmH family tRNA yes no 0.691 0.602 0.283 4e-10
Q7A1Q9248 Putative TrmH family tRNA yes no 0.635 0.556 0.303 4e-10
Q6GBV6248 Putative TrmH family tRNA yes no 0.635 0.556 0.303 4e-10
Q6GJD7248 Putative TrmH family tRNA yes no 0.635 0.556 0.303 4e-10
Q7A794248 Putative TrmH family tRNA yes no 0.635 0.556 0.303 4e-10
Q99W72248 Putative TrmH family tRNA yes no 0.635 0.556 0.303 4e-10
>sp|P0AGJ4|TRMH_SHIFL tRNA (guanosine(18)-2'-O)-methyltransferase OS=Shigella flexneri GN=trmH PE=3 SV=1 Back     alignment and function desciption
 Score = 72.0 bits (175), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 44/139 (31%), Positives = 71/139 (51%), Gaps = 4/139 (2%)

Query: 6   VVVHNIAKRHNVGTLARSATAFGVSEMILV---GRRDFNAFGSHGSTSHVNFRHFHSLSD 62
           V +  + K HNV  + R+A A GV E+  V    R    A  + GS S V  +   ++ D
Sbjct: 22  VCMEQVHKPHNVSAIIRTADAVGVHEVHAVWPGSRMRTMASAAAGSNSWVQVKTHRTIGD 81

Query: 63  ARVFLKSKDCDICGVEITDNAVDVTQHPFKKSTAFLLGNEGMGLSAKECEICDFFVYIPQ 122
           A   LK +   I    ++DNAVD  +  + + T  L+G E  G++ +   + D  + IP 
Sbjct: 82  AVAHLKGQGMQILATHLSDNAVDFREIDYTRPTCILMGQEKTGITQEALALADQDIIIPM 141

Query: 123 YGGGTASLNVTVAASIVLH 141
             G   SLNV+VA++++L+
Sbjct: 142 I-GMVQSLNVSVASALILY 159
Specifically methylates guanosine-18 in various tRNAs.
Shigella flexneri (taxid: 623)
EC: 2EC: .EC: 1EC: .EC: 1EC: .EC: 3EC: 4
>sp|P0AGJ2|TRMH_ECOLI tRNA (guanosine(18)-2'-O)-methyltransferase OS=Escherichia coli (strain K12) GN=trmH PE=1 SV=1 Back     alignment and function description
>sp|P0AGJ3|TRMH_ECO57 tRNA (guanosine(18)-2'-O)-methyltransferase OS=Escherichia coli O157:H7 GN=trmH PE=3 SV=1 Back     alignment and function description
>sp|Q4L3J1|TRMHL_STAHJ Putative TrmH family tRNA/rRNA methyltransferase OS=Staphylococcus haemolyticus (strain JCSC1435) GN=SH2477 PE=3 SV=1 Back     alignment and function description
>sp|Q49V41|TRMHL_STAS1 Putative TrmH family tRNA/rRNA methyltransferase OS=Staphylococcus saprophyticus subsp. saprophyticus (strain ATCC 15305 / DSM 20229) GN=SSP2224 PE=3 SV=1 Back     alignment and function description
>sp|Q7A1Q9|TRMHL_STAAW Putative TrmH family tRNA/rRNA methyltransferase OS=Staphylococcus aureus (strain MW2) GN=MW0487 PE=3 SV=1 Back     alignment and function description
>sp|Q6GBV6|TRMHL_STAAS Putative TrmH family tRNA/rRNA methyltransferase OS=Staphylococcus aureus (strain MSSA476) GN=SAS0489 PE=3 SV=1 Back     alignment and function description
>sp|Q6GJD7|TRMHL_STAAR Putative TrmH family tRNA/rRNA methyltransferase OS=Staphylococcus aureus (strain MRSA252) GN=SAR0535 PE=3 SV=1 Back     alignment and function description
>sp|Q7A794|TRMHL_STAAN Putative TrmH family tRNA/rRNA methyltransferase OS=Staphylococcus aureus (strain N315) GN=SA0490 PE=1 SV=1 Back     alignment and function description
>sp|Q99W72|TRMHL_STAAM Putative TrmH family tRNA/rRNA methyltransferase OS=Staphylococcus aureus (strain Mu50 / ATCC 700699) GN=SAV0531 PE=1 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query217
225432460217 PREDICTED: uncharacterized protein LOC10 0.995 0.995 0.828 1e-101
449432771218 PREDICTED: putative TrmH family tRNA/rRN 0.995 0.990 0.810 5e-99
385276436221 NEP-TC [Solanum betaceum] 0.990 0.972 0.767 3e-96
224102553216 predicted protein [Populus trichocarpa] 0.981 0.986 0.8 7e-96
351725083218 uncharacterized protein LOC100305780 [Gl 0.986 0.981 0.780 1e-92
297804698222 tRNA/rRNA methyltransferase family prote 0.990 0.968 0.775 2e-91
5281018278 OBP33pep like protein [Arabidopsis thali 0.990 0.773 0.766 5e-91
357478515218 tRNA guanosine-2'-O-methyltransferase [M 0.995 0.990 0.768 5e-91
15234624222 tRNA/rRNA methyltransferase (SpoU) famil 0.990 0.968 0.766 2e-90
388495754218 unknown [Medicago truncatula] 0.995 0.990 0.759 1e-89
>gi|225432460|ref|XP_002278797.1| PREDICTED: uncharacterized protein LOC100252797 [Vitis vinifera] gi|147777374|emb|CAN73835.1| hypothetical protein VITISV_043470 [Vitis vinifera] gi|297736948|emb|CBI26149.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
 Score =  372 bits (955), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 179/216 (82%), Positives = 195/216 (90%)

Query: 1   MIESYVVVHNIAKRHNVGTLARSATAFGVSEMILVGRRDFNAFGSHGSTSHVNFRHFHSL 60
           ++ESYVVVHNIAKRHNVGTLARSA+A GVSE+ILVGRRDFN+FGSHGSTSH+ FRHFHSL
Sbjct: 2   VVESYVVVHNIAKRHNVGTLARSASALGVSELILVGRRDFNSFGSHGSTSHLRFRHFHSL 61

Query: 61  SDARVFLKSKDCDICGVEITDNAVDVTQHPFKKSTAFLLGNEGMGLSAKECEICDFFVYI 120
            DAR FLK KDCDICGVEITDNAV V QHPFK+STAFLLGNEG GLS KECEICDFFVYI
Sbjct: 62  LDARHFLKEKDCDICGVEITDNAVAVNQHPFKRSTAFLLGNEGTGLSVKECEICDFFVYI 121

Query: 121 PQYGGGTASLNVTVAASIVLHHFGVWAGFSERTRDGNKYVVAERSARQVRRSFCAEKPES 180
           PQYGGGTASLNVTVAASIVLHHFGVWAGFSER RDGNK+VVAER A+QVRR++C E  +S
Sbjct: 122 PQYGGGTASLNVTVAASIVLHHFGVWAGFSERIRDGNKFVVAERPAQQVRRNYCTETADS 181

Query: 181 IIEMRRSRRENASNGFFDGSGNDVSSSSLLDALFTD 216
           IIE R+ RR+NASNGFFD SG+  S S+LLDALF D
Sbjct: 182 IIEERKIRRQNASNGFFDESGSGESPSNLLDALFGD 217

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|449432771|ref|XP_004134172.1| PREDICTED: putative TrmH family tRNA/rRNA methyltransferase-like [Cucumis sativus] gi|449495429|ref|XP_004159839.1| PREDICTED: putative TrmH family tRNA/rRNA methyltransferase-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|385276436|gb|AFI57511.1| NEP-TC [Solanum betaceum] Back     alignment and taxonomy information
>gi|224102553|ref|XP_002312722.1| predicted protein [Populus trichocarpa] gi|118483281|gb|ABK93543.1| unknown [Populus trichocarpa] gi|222852542|gb|EEE90089.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|351725083|ref|NP_001236568.1| uncharacterized protein LOC100305780 [Glycine max] gi|255626589|gb|ACU13639.1| unknown [Glycine max] Back     alignment and taxonomy information
>gi|297804698|ref|XP_002870233.1| tRNA/rRNA methyltransferase family protein [Arabidopsis lyrata subsp. lyrata] gi|297316069|gb|EFH46492.1| tRNA/rRNA methyltransferase family protein [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|5281018|emb|CAB45991.1| OBP33pep like protein [Arabidopsis thaliana] gi|7268299|emb|CAB78594.1| OBP33pep like protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|357478515|ref|XP_003609543.1| tRNA guanosine-2'-O-methyltransferase [Medicago truncatula] gi|355510598|gb|AES91740.1| tRNA guanosine-2'-O-methyltransferase [Medicago truncatula] Back     alignment and taxonomy information
>gi|15234624|ref|NP_193287.1| tRNA/rRNA methyltransferase (SpoU) family protein [Arabidopsis thaliana] gi|26449903|dbj|BAC42073.1| OBP33pep like protein [Arabidopsis thaliana] gi|28827336|gb|AAO50512.1| putative OBP33pep protein [Arabidopsis thaliana] gi|332658215|gb|AEE83615.1| tRNA/rRNA methyltransferase (SpoU) family protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|388495754|gb|AFK35943.1| unknown [Medicago truncatula] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query217
TAIR|locus:2130310222 AT4G15520 [Arabidopsis thalian 0.990 0.968 0.733 2.5e-81
GENEDB_PFALCIPARUM|PF10_0300257 PF10_0300 "RNA methyltransfera 0.764 0.645 0.390 1.1e-32
UNIPROTKB|Q8IJ98257 PF10_0300 "RNA methyltransfera 0.764 0.645 0.390 1.1e-32
TIGR_CMR|CPS_4975235 CPS_4975 "tRNA (guanosine-2'-O 0.622 0.574 0.302 3e-14
UNIPROTKB|P0AGJ2229 trmH [Escherichia coli K-12 (t 0.622 0.589 0.316 2.7e-13
ZFIN|ZDB-GENE-090313-347191 si:dkey-85a20.4 "si:dkey-85a20 0.631 0.717 0.319 2.5e-10
UNIPROTKB|Q3A9P4237 CHY_2335 "RNA methyltransferas 0.612 0.561 0.3 7.4e-09
TIGR_CMR|CHY_2335237 CHY_2335 "RNA methyltransferas 0.612 0.561 0.3 7.4e-09
TIGR_CMR|CPS_0784180 CPS_0784 "RNA methyltransferas 0.617 0.744 0.280 7.6e-09
TAIR|locus:2151001350 AT5G15390 [Arabidopsis thalian 0.760 0.471 0.274 3.7e-08
TAIR|locus:2130310 AT4G15520 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 816 (292.3 bits), Expect = 2.5e-81, P = 2.5e-81
 Identities = 160/218 (73%), Positives = 177/218 (81%)

Query:     3 ESYVVVHNIAKRHNVGTLARSATAFGVSEMILVGRRDFNAFGSHGSTSHVNFRHFHSLSD 62
             ESYVVVHNIAKRHNVGTLARSATAFGV+E+ILVGRRDFNAFGSHGS SH+ FRHFHSL +
Sbjct:     5 ESYVVVHNIAKRHNVGTLARSATAFGVTELILVGRRDFNAFGSHGSASHIRFRHFHSLIE 64

Query:    63 ARVFLKS-KDCDICGVEITDNAVDVTQHPFKKSTAFLLGNEGMGLSAKECEICDFFVYIP 121
             AR +LK  KDCDICGVEI D A  V +HPFK++TAFLLGNEG GLSAKE EICDFFVYIP
Sbjct:    65 ARNYLKEEKDCDICGVEIADGASAVNEHPFKRNTAFLLGNEGSGLSAKEYEICDFFVYIP 124

Query:   122 QYGGGTASLNVTVAASIVLHHFGVWAGFSERTRDGNKYVVAERSARQVRRSFCAEKPXXX 181
             QYG GTASLNVTVAASIVLHHFGVWAGFSER RDG+K++VA+R  RQ RR+FCA      
Sbjct:   125 QYGCGTASLNVTVAASIVLHHFGVWAGFSERVRDGSKFIVADRPVRQGRRNFCAGTEESV 184

Query:   182 XXXXXXXXXNASNGFFDGSGND--VSSSSLLDALFTDE 217
                      +A NGFFD +GN+   SSS LLD LF +E
Sbjct:   185 IEERKLRKESAENGFFDDNGNENGSSSSDLLDGLFLNE 222
GO:0003723 "RNA binding" evidence=IEA;ISS
GO:0005737 "cytoplasm" evidence=ISM
GO:0006396 "RNA processing" evidence=IEA;ISS
GO:0008173 "RNA methyltransferase activity" evidence=IEA;ISS
GO:0006635 "fatty acid beta-oxidation" evidence=RCA
GO:0016558 "protein import into peroxisome matrix" evidence=RCA
GENEDB_PFALCIPARUM|PF10_0300 PF10_0300 "RNA methyltransferase, putative" [Plasmodium falciparum (taxid:5833)] Back     alignment and assigned GO terms
UNIPROTKB|Q8IJ98 PF10_0300 "RNA methyltransferase, putative" [Plasmodium falciparum 3D7 (taxid:36329)] Back     alignment and assigned GO terms
TIGR_CMR|CPS_4975 CPS_4975 "tRNA (guanosine-2'-O-)-methyltransferase" [Colwellia psychrerythraea 34H (taxid:167879)] Back     alignment and assigned GO terms
UNIPROTKB|P0AGJ2 trmH [Escherichia coli K-12 (taxid:83333)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-090313-347 si:dkey-85a20.4 "si:dkey-85a20.4" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
UNIPROTKB|Q3A9P4 CHY_2335 "RNA methyltransferase, TrmH family, group 3" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)] Back     alignment and assigned GO terms
TIGR_CMR|CHY_2335 CHY_2335 "RNA methyltransferase, TrmH family, group 3" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)] Back     alignment and assigned GO terms
TIGR_CMR|CPS_0784 CPS_0784 "RNA methyltransferase, TrmH family" [Colwellia psychrerythraea 34H (taxid:167879)] Back     alignment and assigned GO terms
TAIR|locus:2151001 AT5G15390 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms

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 LevelEC numberConfidence of Prediction
3rd Layer2.1.1.34LOW CONFIDENCE prediction!
3rd Layer2.1.10.691

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
GSVIVG00019864001
SubName- Full=Putative uncharacterized protein (Chromosome chr5 scaffold_2, whole genome shotgun sequence); (217 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 ?Alignment Graph ?Length ? Definition ? E-value ?
Query217
pfam00588142 pfam00588, SpoU_methylase, SpoU rRNA Methylase fam 4e-36
COG0566260 COG0566, SpoU, rRNA methylases [Translation, ribos 1e-24
TIGR00186237 TIGR00186, rRNA_methyl_3, rRNA methylase, putative 7e-13
PRK11081229 PRK11081, PRK11081, tRNA guanosine-2'-O-methyltran 1e-12
COG0565242 COG0565, LasT, rRNA methylase [Translation, riboso 4e-09
TIGR00050233 TIGR00050, rRNA_methyl_1, RNA methyltransferase, T 3e-05
PRK10433228 PRK10433, PRK10433, putative RNA methyltransferase 0.003
>gnl|CDD|216010 pfam00588, SpoU_methylase, SpoU rRNA Methylase family Back     alignment and domain information 
 Score =  123 bits (312), Expect = 4e-36
 Identities = 48/143 (33%), Positives = 68/143 (47%), Gaps = 9/143 (6%)

Query: 5   YVVVHNIAKRHNVGTLARSATAFGVSEMILVGRRDFNAFG------SHGSTSHVNFRHFH 58
            VV+       N+G +AR+A AFG   +ILV  R  + +       S G+  H+      
Sbjct: 3   IVVLDEPQDPGNLGAIARTAAAFGADGLILVEPRCADPYNPKAIRASAGALFHLPLVIVD 62

Query: 59  SLSDARVFLKSKDCDICGVEITDNAVDVTQHPFKKSTAFLLGNEGMGLSAKECEICDFFV 118
           +L +A   LK     I     +     + +  F K  A + GNEG GLS +  E+CD  V
Sbjct: 63  NLEEALKDLKEAGFWIIAT--SLKGKPLYEIDFPKKVALVFGNEGTGLSNEVLELCDRLV 120

Query: 119 YIPQYGGGTASLNVTVAASIVLH 141
            IP   G   SLNV VAA+I+L+
Sbjct: 121 RIPMS-GEVESLNVAVAAAIILY 142

This family of proteins probably use S-AdoMet. Length = 142
>gnl|CDD|223640 COG0566, SpoU, rRNA methylases [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|129290 TIGR00186, rRNA_methyl_3, rRNA methylase, putative, group 3 Back     alignment and domain information
>gnl|CDD|236837 PRK11081, PRK11081, tRNA guanosine-2'-O-methyltransferase; Provisional Back     alignment and domain information
>gnl|CDD|223639 COG0565, LasT, rRNA methylase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|232800 TIGR00050, rRNA_methyl_1, RNA methyltransferase, TrmH family, group 1 Back     alignment and domain information
>gnl|CDD|236693 PRK10433, PRK10433, putative RNA methyltransferase; Provisional Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 217
PRK11081229 tRNA guanosine-2'-O-methyltransferase; Provisional 100.0
COG0566260 SpoU rRNA methylases [Translation, ribosomal struc 100.0
PF00588142 SpoU_methylase: SpoU rRNA Methylase family; InterP 100.0
PRK11181244 23S rRNA (guanosine-2'-O-)-methyltransferase; Prov 100.0
TIGR00186237 rRNA_methyl_3 rRNA methylase, putative, group 3. t 100.0
PRK10864346 putative methyltransferase; Provisional 100.0
TIGR00185153 rRNA_methyl_2 rRNA methylase, putative, group 2. t 100.0
PRK10358157 putative rRNA methylase; Provisional 100.0
TIGR00050233 rRNA_methyl_1 RNA methyltransferase, TrmH family, 99.98
PRK15114245 tRNA (cytidine/uridine-2'-O-)-methyltransferase Tr 99.97
PRK10433228 putative RNA methyltransferase; Provisional 99.97
COG0219155 CspR Predicted rRNA methylase (SpoU class) [Transl 99.95
COG0565242 LasT rRNA methylase [Translation, ribosomal struct 99.94
KOG2506371 consensus SpoU rRNA Methylase family protein [Tran 99.92
KOG0838271 consensus RNA Methylase, SpoU family [RNA processi 99.92
KOG08391477 consensus RNA Methylase, SpoU family [RNA processi 99.86
PF09936185 Methyltrn_RNA_4: SAM-dependent RNA methyltransfera 98.89
KOG0838271 consensus RNA Methylase, SpoU family [RNA processi 98.72
PRK03958176 tRNA 2'-O-methylase; Reviewed 98.72
COG4080147 SpoU rRNA Methylase family enzyme [General functio 98.32
COG4752190 Uncharacterized protein conserved in bacteria [Fun 98.0
PF09895106 DUF2122: RecB-family nuclease (DUF2122); InterPro: 96.56
COG1303179 Uncharacterized protein conserved in archaea [Func 96.38
PRK12703 339 tRNA 2'-O-methylase; Reviewed 95.95
PRK02135201 hypothetical protein; Provisional 92.7
PF14419173 SPOUT_MTase_2: AF2226-like SPOUT RNA Methylase fus 92.61
PF01994120 Trm56: tRNA ribose 2'-O-methyltransferase, aTrm56; 92.53
PF04013199 Methyltrn_RNA_2: Putative SAM-dependent RNA methyl 92.47
PF04407173 DUF531: Protein of unknown function (DUF531); Inte 83.13
COG1385246 Uncharacterized protein conserved in bacteria [Fun 80.74
>PRK11081 tRNA guanosine-2'-O-methyltransferase; Provisional Back     alignment and domain information 
Probab=100.00  E-value=3.3e-40  Score=282.59  Aligned_cols=144  Identities=29%  Similarity=0.412  Sum_probs=134.3

Q ss_pred             CceEEEEeCCCCcccHHHHHHHhHHHCCCcEEEeCCCC-C--CccccCCCccceeeEEeCCHHHHHHHhhhCCCcEEEEE
Q 040494            2 IESYVVVHNIAKRHNVGTLARSATAFGVSEMILVGRRD-F--NAFGSHGSTSHVNFRHFHSLSDARVFLKSKDCDICGVE   78 (217)
Q Consensus         2 ~~~~vvLd~v~~p~NlG~I~Rsa~afGv~~v~lv~~~~-~--~~~~s~Ga~~~~~i~~~~s~~~~l~~l~~~g~~v~~~~   78 (217)
                      ++++||||+|+||+|+|+|+|||+|||++.|+++.+.. +  ..++|+|+.+|+++.++.++.++++.|++.|+.|++++
T Consensus        18 ~~l~vvLd~V~~p~NlGAIiRta~AfGv~~V~~v~~~~~~~~~~~~s~Ga~~wv~i~~~~~~~~~i~~lk~~g~~i~at~   97 (229)
T PRK11081         18 PDLTVCMEQVHKPHNVSAIIRTADAVGVHEVHAVWPGSRMRTMGSTAAGSNSWVQVKTHRTIGDAVAHLKGQGMQILATH   97 (229)
T ss_pred             CCeEEEEeCCCCcchHHHHHHHHHHhCCCeEEEecCCCccchhhhhcCCchheEEEEEeCCHHHHHHHHHhCCCEEEEEe
Confidence            67999999999999999999999999999999986542 2  23689999999999999999999999999999999999


Q ss_pred             ecCCcccccccCCCCCEEEEEcCCCCCCCHHHHhhCCcEEEEcCCCCCCCcccHHHHHHHHHHHHHhc
Q 040494           79 ITDNAVDVTQHPFKKSTAFLLGNEGMGLSAKECEICDFFVYIPQYGGGTASLNVTVAASIVLHHFGVW  146 (217)
Q Consensus        79 ~~~~~~~l~~~~~~~~~alV~GnE~~GLs~~~l~~cD~~v~IP~~g~~~~SLNVsvAaaIvL~e~~~~  146 (217)
                      ..+++.++.++++++|++||||||+.|||+++++.||..|+|||.|+ ++|||||||+||+|||+.++
T Consensus        98 ~~~~a~~l~~~d~~~p~alV~GnE~~GlS~e~l~~~D~~v~IPM~G~-v~SLNVSvAaaIiLyE~~Rq  164 (229)
T PRK11081         98 LSDTAVDFREIDYTRPTCILMGQEKTGISQEALALADQDIIIPMIGM-VQSLNVSVASALILYEAQRQ  164 (229)
T ss_pred             CCCCCccHhHhcccCCeEEEECCCCCCCCHHHHhcCCCEEEEeCCCC-CCceeHHHHHHHHHHHHHHh
Confidence            87888999999999999999999999999999999999999999996 99999999999999999554

>COG0566 SpoU rRNA methylases [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>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 [, ] Back     alignment and domain information
>PRK11181 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional Back     alignment and domain information
>TIGR00186 rRNA_methyl_3 rRNA methylase, putative, group 3 Back     alignment and domain information
>PRK10864 putative methyltransferase; Provisional Back     alignment and domain information
>TIGR00185 rRNA_methyl_2 rRNA methylase, putative, group 2 Back     alignment and domain information
>PRK10358 putative rRNA methylase; Provisional Back     alignment and domain information
>TIGR00050 rRNA_methyl_1 RNA methyltransferase, TrmH family, group 1 Back     alignment and domain information
>PRK15114 tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ; Provisional Back     alignment and domain information
>PRK10433 putative RNA methyltransferase; Provisional Back     alignment and domain information
>COG0219 CspR Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>COG0565 LasT rRNA methylase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>KOG2506 consensus SpoU rRNA Methylase family protein [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>KOG0838 consensus RNA Methylase, SpoU family [RNA processing and modification] Back     alignment and domain information
>KOG0839 consensus RNA Methylase, SpoU family [RNA processing and modification] Back     alignment and domain information
>PF09936 Methyltrn_RNA_4: SAM-dependent RNA methyltransferase; InterPro: IPR019230 This entry contains proteins that have no known function Back     alignment and domain information
>KOG0838 consensus RNA Methylase, SpoU family [RNA processing and modification] Back     alignment and domain information
>PRK03958 tRNA 2'-O-methylase; Reviewed Back     alignment and domain information
>COG4080 SpoU rRNA Methylase family enzyme [General function prediction only] Back     alignment and domain information
>COG4752 Uncharacterized protein conserved in bacteria [Function unknown] Back     alignment and domain information
>PF09895 DUF2122: RecB-family nuclease (DUF2122); InterPro: IPR018665 This family of archaeal proteins include RecB nuclease-like proteins as well as proteins of no known function Back     alignment and domain information
>COG1303 Uncharacterized protein conserved in archaea [Function unknown] Back     alignment and domain information
>PRK12703 tRNA 2'-O-methylase; Reviewed Back     alignment and domain information
>PRK02135 hypothetical protein; Provisional Back     alignment and domain information
>PF14419 SPOUT_MTase_2: AF2226-like SPOUT RNA Methylase fused to THUMP Back     alignment and domain information
>PF01994 Trm56: tRNA ribose 2'-O-methyltransferase, aTrm56; InterPro: IPR002845 This entry represents tRNA ribose 2'-O-methyltransferase aTrm56, which specifically catalyzes the AdoMet-dependent 2'-O-ribose methylation of cytidine at position 56 in tRNAs Back     alignment and domain information
>PF04013 Methyltrn_RNA_2: Putative SAM-dependent RNA methyltransferase; InterPro: IPR007158 The proteins in this family are around 200 amino acids long with the exception of O29206 from SWISSPROT that has an additional 100 amino acids at its N terminus Back     alignment and domain information
>PF04407 DUF531: Protein of unknown function (DUF531); InterPro: IPR007501 This is a family of hypothetical archaeal proteins Back     alignment and domain information
>COG1385 Uncharacterized protein conserved in bacteria [Function unknown] Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query217
1v2x_A194 Trmh Length = 194 3e-10
2ha8_A184 Methyltransferase Domain Of Human Tar (Hiv-1) Rna B 3e-09
1zjr_A211 Crystal Structure Of A. Aeolicus TrmhSPOU TRNA MODI 2e-07
1gz0_A253 23s Ribosomal Rna G2251 2'o-Methyltransferase Rlmb 1e-04
2i6d_A257 The Structure Of A Putative Rna Methyltransferase O 2e-04
>pdb|1V2X|A Chain A, Trmh Length = 194 Back     alignment and structure 
Iteration: 1

 Score = 61.6 bits (148), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 50/156 (32%), Positives = 74/156 (47%), Gaps = 9/156 (5%)
Query: 6   VVVHNIAKRHNVGTLARSATAFGVSEMILV----GRRDFNAFGSHGSTSHVNFRHFHSLS 61
           V++ N+ K HN+  + R+  A GV E   V    G   FN   S GS   V  R    L 
Sbjct: 25  VLLENVHKPHNLSAILRTCDAVGVLEAHAVNPTGGVPTFNE-TSGGSHKWVYLRVHPDLH 83
Query: 62  DARVFLKSKDCDICGVEITDNAVDVTQHPFKKSTAFLLGNEGMGLSAKECEICDFFVYIP 121
           +A  FLK +   +    + ++A D  +  + K TA L G E  G+S +   + D  + IP
Sbjct: 84  EAFRFLKERGFTVYATALREDARDFREVDYTKPTAVLFGAEKWGVSEEALALADGAIKIP 143
Query: 122 QYGGGTASLNVTVAASIVL---HHFGVWAGFSERTR 154
              G   SLNV+VAA+++L       + AG  +R R
Sbjct: 144 ML-GMVQSLNVSVAAAVILFEAQRQRLKAGLYDRPR 178
>pdb|2HA8|A Chain A, Methyltransferase Domain Of Human Tar (Hiv-1) Rna Binding Protein 1 Length = 184 Back     alignment and structure
>pdb|1ZJR|A Chain A, Crystal Structure Of A. Aeolicus TrmhSPOU TRNA MODIFYING ENZYME Length = 211 Back     alignment and structure
>pdb|1GZ0|A Chain A, 23s Ribosomal Rna G2251 2'o-Methyltransferase Rlmb Length = 253 Back     alignment and structure
>pdb|2I6D|A Chain A, The Structure Of A Putative Rna Methyltransferase Of The Trmh Family From Porphyromonas Gingivalis Length = 257 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query217
2ha8_A184 TAR (HIV-1) RNA loop binding protein; methyltransf 3e-30
1zjr_A211 TRNA (guanosine-2'-O-)-methyltransferase; methylas 4e-29
1v2x_A194 TRNA (GM18) methyltransferase; DEEP trefoil knot, 2e-28
1x7o_A287 Avirb, rRNA methyltransferase; SPOU, C-terminal kn 1e-26
1ipa_A274 RRMH, RNA 2'-O-ribose methyltransferase; DEEP tref 9e-25
2i6d_A257 RNA methyltransferase, TRMH family; stuctural geno 4e-22
3nk6_A277 23S rRNA methyltransferase; nosiheptide, nosihepti 7e-22
1gz0_A253 Hypothetical tRNA/RRNA methyltransferase YJFH; 2'O 2e-16
3ilk_A244 Uncharacterized tRNA/RRNA methyltransferase HI038; 5e-08
3kty_A173 Probable methyltransferase; alpha-beta-alpha sandw 5e-07
3ic6_A223 Putative methylase family protein; putative methyl 2e-06
3onp_A249 TRNA/RRNA methyltransferase (SPOU); structural gen 3e-06
>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 Back     alignment and structure
 Score =  109 bits (274), Expect = 3e-30
 Identities = 43/144 (29%), Positives = 68/144 (47%), Gaps = 7/144 (4%)

Query: 6   VVVHNIAKRHNVGTLARSATAFGVSEMILVGRRDFN--AFG--SHGSTSHVNFRHF--HS 59
           VV   I K  N+G L R+   FG S +++   +  +   F   S  +   +         
Sbjct: 29  VVASLIDKPTNLGGLCRTCEVFGASVLVVGSLQCISDKQFQHLSVSAEQWLPLVEVKPPQ 88

Query: 60  LSDARVFLKSKDCDICGVEITDNAVDVTQHPFKKSTAFLLGNEGMGLSAKECEICDFFVY 119
           L D     K++   I GVE T  ++D+TQ+ F + +  LLGNE  G+ A   +  D  V 
Sbjct: 89  LIDYLQQKKTEGYTIIGVEQTAKSLDLTQYCFPEKSLLLLGNEREGIPANLIQQLDVCVE 148

Query: 120 IPQYGGGTASLNVTVAASIVLHHF 143
           IPQ  G   SLNV V+ ++++  +
Sbjct: 149 IPQQ-GIIRSLNVHVSGALLIWEY 171
>1zjr_A TRNA (guanosine-2'-O-)-methyltransferase; methylase, RNA modifying enzyme, topological knot; 1.85A {Aquifex aeolicus} Length = 211 Back     alignment and structure
>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 Back     alignment and structure
>1x7o_A Avirb, rRNA methyltransferase; SPOU, C-terminal knot, seMet; 2.37A {Streptomyces viridochromogenes} PDB: 1x7p_A* Length = 287 Back     alignment and structure
>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 Length = 274 Back     alignment and structure
>2i6d_A RNA methyltransferase, TRMH family; stuctural genomics, PORP gingivalis, knot, structural genomics, PSI-2, protein struc initiative; HET: MSE; 1.85A {Porphyromonas gingivalis} Length = 257 Back     alignment and structure
>3nk6_A 23S rRNA methyltransferase; nosiheptide, nosiheptide-resistance methyltransferase, 23S R methyltransferase; 2.00A {Streptomyces actuosus} PDB: 3nk7_A* 3gyq_A* Length = 277 Back     alignment and structure
>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 Length = 253 Back     alignment and structure
>3ilk_A Uncharacterized tRNA/RRNA methyltransferase HI038; APC63004, methylase family protein, haemophilus influenzae R structural genomics; 2.01A {Haemophilus influenzae} Length = 244 Back     alignment and structure
>3kty_A Probable methyltransferase; alpha-beta-alpha sandwich, structural genomics, PSI-2, prote structure initiative; 2.30A {Bordetella pertussis} Length = 173 Back     alignment and structure
>3ic6_A Putative methylase family protein; putative methylase family Pro structural genomics, PSI-2, protein structure initiative; 2.59A {Neisseria gonorrhoeae fa 1090} Length = 223 Back     alignment and structure
>3onp_A TRNA/RRNA methyltransferase (SPOU); structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 1.90A {Rhodobacter sphaeroides} Length = 249 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query217
3e5y_A160 TRMH family RNA methyltransferase; ssgcid, protein 100.0
1v2x_A194 TRNA (GM18) methyltransferase; DEEP trefoil knot, 100.0
3n4j_A165 RNA methyltransferase; center for structural genom 100.0
2ha8_A184 TAR (HIV-1) RNA loop binding protein; methyltransf 100.0
1zjr_A211 TRNA (guanosine-2'-O-)-methyltransferase; methylas 100.0
3l8u_A182 SMU.1707C, putative rRNA methylase; methyltransfer 100.0
1gz0_A253 Hypothetical tRNA/RRNA methyltransferase YJFH; 2'O 100.0
1ipa_A274 RRMH, RNA 2'-O-ribose methyltransferase; DEEP tref 100.0
3nk6_A277 23S rRNA methyltransferase; nosiheptide, nosihepti 100.0
2i6d_A257 RNA methyltransferase, TRMH family; stuctural geno 100.0
1x7o_A287 Avirb, rRNA methyltransferase; SPOU, C-terminal kn 100.0
3kty_A173 Probable methyltransferase; alpha-beta-alpha sandw 100.0
3ilk_A244 Uncharacterized tRNA/RRNA methyltransferase HI038; 100.0
3onp_A249 TRNA/RRNA methyltransferase (SPOU); structural gen 100.0
3ic6_A223 Putative methylase family protein; putative methyl 99.98
3dcm_X192 AdoMet, uncharacterized protein TM_1570; trefoil k 99.84
2o3a_A178 UPF0106 protein AF_0751; structural genomics, unkn 96.47
2yy8_A201 ATRM56, UPF0106 protein PH0461; DEEP trefoil knot, 95.55
2qmm_A197 UPF0217 protein AF_1056; alpha/beta knot, SAM, str 93.92
2qwv_A208 UPF0217 protein VC_A1059; unknown function, struct 92.73
3aia_A211 UPF0217 protein MJ1640; DUF358, rRNA methyltransfe 92.57
3kw2_A257 Probable R-RNA methyltransferase; structural genom 86.17
1ns5_A155 Hypothetical protein YBEA; structural genomics, PS 80.1
>3e5y_A TRMH family RNA methyltransferase; ssgcid, protein knot, decode, structural genomics; 2.40A {Burkholderia pseudomallei 305} SCOP: c.116.1.0 Back     alignment and structure
Probab=100.00  E-value=5.9e-41  Score=271.70  Aligned_cols=146  Identities=17%  Similarity=0.175  Sum_probs=131.6

Q ss_pred             CceEEEEeCCCCcccHHHHHHHhHHHCCCcEEEeCCCCCCc------cccCCCccceeeEEeCCHHHHHHHhhhCCCcEE
Q 040494            2 IESYVVVHNIAKRHNVGTLARSATAFGVSEMILVGRRDFNA------FGSHGSTSHVNFRHFHSLSDARVFLKSKDCDIC   75 (217)
Q Consensus         2 ~~~~vvLd~v~~p~NlG~I~Rsa~afGv~~v~lv~~~~~~~------~~s~Ga~~~~~i~~~~s~~~~l~~l~~~g~~v~   75 (217)
                      |.++||||+|+||+|+|+|+|||++||++ .+++.+.++++      ++++|+.+++|+.++.+++++++.++++|++++
T Consensus         4 ~~l~vvLd~i~dp~NlGaI~Rta~a~G~~-~viv~~~~~~~~~~~~~ras~g~~~~~~~~~~~~l~~~l~~l~~~g~~i~   82 (160)
T 3e5y_A            4 SMFNVVLVEPEIPPNTGNVIRLCANTGAR-LHLIEPLGFPLDDAKMRRAGLDYHEYAQMRVHRDWDAFVAAEAPDPARMF   82 (160)
T ss_dssp             -CCEEEEESCCCHHHHHHHHHHHHHHTCE-EEEESSCSSCCCHHHHHHTTCCHHHHHTCEEESSHHHHHHHHCCCGGGEE
T ss_pred             CcEEEEEeCCCCCCcHHHHHHHHHHcCCc-EEEECCCCCCCccHHHHHHcCCchhhcceEEeCCHHHHHHHHHhCCCEEE
Confidence            45899999999999999999999999995 55566555443      578999999999999999999999999999999


Q ss_pred             EEEecCCcccccccCCCCCEEEEEcCCCCCCCHHHHhh--CCcEEEEcCCCCCCCcccHHHHHHHHHHHHHhccCch
Q 040494           76 GVEITDNAVDVTQHPFKKSTAFLLGNEGMGLSAKECEI--CDFFVYIPQYGGGTASLNVTVAASIVLHHFGVWAGFS  150 (217)
Q Consensus        76 ~~~~~~~~~~l~~~~~~~~~alV~GnE~~GLs~~~l~~--cD~~v~IP~~g~~~~SLNVsvAaaIvL~e~~~~~~~~  150 (217)
                      +++. .++++++++++++|++||||||+.|||+++++.  ||..|+|||.|. ++|||||+|++|+|||+.++..++
T Consensus        83 ~~~~-~~~~~~~~~~~~~~~alv~G~E~~Gls~~~l~~~~~d~~v~IPm~g~-~~SLNvsvAaaI~lye~~rq~~~~  157 (160)
T 3e5y_A           83 AFTT-RGSGRFHDRAFEPGDWFVFGAETRGLAPALVDRFAPEQRVRLPMRPG-NRSLNLSNTVAVVVFEAWRQAGFE  157 (160)
T ss_dssp             EECS-TTCEEGGGSCCCTTCEEEEEBTTTBSCHHHHTTSCGGGEEECCCCSS-SCCCCHHHHHHHHHHHHHHHTTTT
T ss_pred             EEec-CCCccccccCCCCCEEEEECCCcCCCCHHHHhhccCCeEEEEcCCCC-CCeehHHHHHHHHHHHHHHhccCC
Confidence            9996 577899999999999999999999999999999  999999999995 999999999999999997765543
>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 Back     alignment and structure
>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* Back     alignment and structure
>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} Back     alignment and structure
>1zjr_A TRNA (guanosine-2'-O-)-methyltransferase; methylase, RNA modifying enzyme, topological knot; 1.85A {Aquifex aeolicus} Back     alignment and structure
>3l8u_A SMU.1707C, putative rRNA methylase; methyltransferase, knotted protein; 2.00A {Streptococcus mutans} SCOP: c.116.1.0 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>3nk6_A 23S rRNA methyltransferase; nosiheptide, nosiheptide-resistance methyltransferase, 23S R methyltransferase; 2.00A {Streptomyces actuosus} PDB: 3nk7_A* 3gyq_A* Back     alignment and structure
>2i6d_A RNA methyltransferase, TRMH family; stuctural genomics, PORP gingivalis, knot, structural genomics, PSI-2, protein struc initiative; HET: MSE; 1.85A {Porphyromonas gingivalis} Back     alignment and structure
>1x7o_A Avirb, rRNA methyltransferase; SPOU, C-terminal knot, seMet; 2.37A {Streptomyces viridochromogenes} PDB: 1x7p_A* Back     alignment and structure
>3kty_A Probable methyltransferase; alpha-beta-alpha sandwich, structural genomics, PSI-2, prote structure initiative; 2.30A {Bordetella pertussis} Back     alignment and structure
>3ilk_A Uncharacterized tRNA/RRNA methyltransferase HI038; APC63004, methylase family protein, haemophilus influenzae R structural genomics; 2.01A {Haemophilus influenzae} Back     alignment and structure
>3onp_A TRNA/RRNA methyltransferase (SPOU); structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 1.90A {Rhodobacter sphaeroides} Back     alignment and structure
>3ic6_A Putative methylase family protein; putative methylase family Pro structural genomics, PSI-2, protein structure initiative; 2.59A {Neisseria gonorrhoeae fa 1090} Back     alignment and structure
>3dcm_X AdoMet, uncharacterized protein TM_1570; trefoil knot, spout mtase, adoMet binding, transferase; HET: SAM; 2.00A {Thermotoga maritima} Back     alignment and structure
>2o3a_A UPF0106 protein AF_0751; structural genomics, unknown function, PSI-2, protein structure initiative; 2.20A {Archaeoglobus fulgidus} SCOP: c.116.1.8 Back     alignment and structure
>2yy8_A ATRM56, UPF0106 protein PH0461; DEEP trefoil knot, structural genomics, NPPSFA; HET: SAM MTA; 2.48A {Pyrococcus horikoshii} Back     alignment and structure
>2qmm_A UPF0217 protein AF_1056; alpha/beta knot, SAM, structural genomics, PSI-2, protein structure initiative; HET: SAM; 1.85A {Archaeoglobus fulgidus dsm 4304} SCOP: c.116.1.7 Back     alignment and structure
>2qwv_A UPF0217 protein VC_A1059; unknown function, structural genomics, PSI- 2, protein structure initiative; 2.60A {Vibrio cholerae o1 biovar eltor str} SCOP: c.116.1.7 Back     alignment and structure
>3kw2_A Probable R-RNA methyltransferase; structural genomics, unknown function, PSI-2, protein structure initiative; HET: MSE ADN; 2.00A {Porphyromonas gingivalis atcc 33277} Back     alignment and structure
>1ns5_A Hypothetical protein YBEA; structural genomics, PSI, protein structure initiative, northeast structural genomics consortium, NESG; 1.68A {Escherichia coli} SCOP: c.116.1.3 Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

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

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 217
d1gz0a1166 c.116.1.1 (A:78-243) RlmB, C-terminal domain {Esch 1e-21
d1mxia_156 c.116.1.1 (A:) Hypothetical tRNA/rRNA methyltransf 3e-17
d1ipaa1158 c.116.1.1 (A:106-263) RrmA (RrmH), C-terminal doma 8e-17
d1v2xa_191 c.116.1.1 (A:) tRNA (Gm18) methyltransferase TrmH 7e-16
>d1gz0a1 c.116.1.1 (A:78-243) RlmB, C-terminal domain {Escherichia coli [TaxId: 562]} Length = 166 Back     information, alignment and structure

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 = 85.7 bits (211), Expect = 1e-21
 Identities = 36/144 (25%), Positives = 58/144 (40%), Gaps = 7/144 (4%)

Query: 5   YVVVHNIAKRHNVGTLARSATAFGVSEMILVGRRDFNAFGSH-----GSTSHVNFRHFHS 59
            +++  +   HN+G   RSA A GV  +I+   R      +      G+   V      +
Sbjct: 20  LLILDGVTDPHNLGACLRSADAAGVHAVIVPKDRSAQLNATAKKVACGAAESVPLIRVTN 79

Query: 60  LSDARVFLKSKDCDICGVEITDNAVDVTQHPFKKSTAFLLGNEGMGLSAKECEICDFFVY 119
           L+     L+ ++  I      +    + Q       A ++G EG G+     E CD  + 
Sbjct: 80  LARTMRMLQEENIWIV-GTAGEADHTLYQSKMTGRLALVMGAEGEGMRRLTREHCDELIS 138

Query: 120 IPQYGGGTASLNVTVAASIVLHHF 143
           IP   G  +SLNV+VA  I L   
Sbjct: 139 IPMA-GSVSSLNVSVATGICLFEA 161
>d1mxia_ c.116.1.1 (A:) Hypothetical tRNA/rRNA methyltransfease HI0766 (YibK homologue) {Haemophilus influenzae [TaxId: 727]} Length = 156 Back     information, alignment and structure
>d1ipaa1 c.116.1.1 (A:106-263) RrmA (RrmH), C-terminal domain {Thermus thermophilus [TaxId: 274]} Length = 158 Back     information, alignment and structure
>d1v2xa_ c.116.1.1 (A:) tRNA (Gm18) methyltransferase TrmH {Thermus thermophilus [TaxId: 274]} Length = 191 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query217
d1gz0a1166 RlmB, C-terminal domain {Escherichia coli [TaxId: 100.0
d1v2xa_191 tRNA (Gm18) methyltransferase TrmH {Thermus thermo 100.0
d1ipaa1158 RrmA (RrmH), C-terminal domain {Thermus thermophil 100.0
d1mxia_156 Hypothetical tRNA/rRNA methyltransfease HI0766 (Yi 100.0
d2o3aa1167 Uncharacterized protein AF0751 {Archaeoglobus fulg 95.36
d2qwva1201 Uncharacterized protein VCA1059 {Vibrio cholerae [ 94.56
d2qmma1194 Uncharacterized protein AF1056 {Archaeoglobus fulg 89.12
d1vhka2180 Hypothetical protein YqeU {Bacillus subtilis [TaxI 87.38
d1k3ra2191 Hypothetical protein MTH1 (MT0001), dimerisation d 84.07
>d1gz0a1 c.116.1.1 (A:78-243) RlmB, C-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
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=100.00  E-value=1.2e-39  Score=262.65  Aligned_cols=143  Identities=27%  Similarity=0.368  Sum_probs=132.0

Q ss_pred             CceEEEEeCCCCcccHHHHHHHhHHHCCCcEEEeCCCC--CCc---cccCCCccceeeEEeCCHHHHHHHhhhCCCcEEE
Q 040494            2 IESYVVVHNIAKRHNVGTLARSATAFGVSEMILVGRRD--FNA---FGSHGSTSHVNFRHFHSLSDARVFLKSKDCDICG   76 (217)
Q Consensus         2 ~~~~vvLd~v~~p~NlG~I~Rsa~afGv~~v~lv~~~~--~~~---~~s~Ga~~~~~i~~~~s~~~~l~~l~~~g~~v~~   76 (217)
                      .+++||||+|+||+|+|+|+|+|++||++.|+++++.+  +++   ++++|+.+++|+..+.++.++++.+++.++.+++
T Consensus        17 ~~~~vvLd~i~~p~N~GaiiRta~afG~~~v~~~~~~~~~~~~~~~r~s~g~~~~v~~~~~~~~~~~l~~~~~~~~~~~~   96 (166)
T d1gz0a1          17 QPFLLILDGVTDPHNLGACLRSADAAGVHAVIVPKDRSAQLNATAKKVACGAAESVPLIRVTNLARTMRMLQEENIWIVG   96 (166)
T ss_dssp             SCEEEEEESCCCHHHHHHHHHHHHHHTCSEEEEESSSSCCCCHHHHHHHTTHHHHSCEEEESCHHHHHHHHHHTTCEEEE
T ss_pred             CCEEEEEeCCCCcchHHHHHHHHHhcCCceeeeecccccccchhhheeccCcceEeceeecCCHHHHHHHhccccccccc
Confidence            35899999999999999999999999999999987542  344   6899999999999999999999999999999999


Q ss_pred             EEecCCcccccccCCCCCEEEEEcCCCCCCCHHHHhhCCcEEEEcCCCCCCCcccHHHHHHHHHHHHHhc
Q 040494           77 VEITDNAVDVTQHPFKKSTAFLLGNEGMGLSAKECEICDFFVYIPQYGGGTASLNVTVAASIVLHHFGVW  146 (217)
Q Consensus        77 ~~~~~~~~~l~~~~~~~~~alV~GnE~~GLs~~~l~~cD~~v~IP~~g~~~~SLNVsvAaaIvL~e~~~~  146 (217)
                      ++. ....++.++++++|++||||+|+.|||+++++.||..|+|||.|. ++|||||+|++|+|||+.|+
T Consensus        97 ~~~-~~~~~~~~~~~~~~~~lv~G~E~~Gls~~~l~~~d~~v~IPm~~~-~~SLNvs~A~~I~lye~~rq  164 (166)
T d1gz0a1          97 TAG-EADHTLYQSKMTGRLALVMGAEGEGMRRLTREHCDELISIPMAGS-VSSLNVSVATGICLFEAVRQ  164 (166)
T ss_dssp             ECT-TCSEEGGGSCCCSSEEEEEEBTTTBSCHHHHHTCSEEEECCCSSS-SCCCCHHHHHHHHHHHHHHH
T ss_pred             ccc-cccccHHHhhccCCeEEEeccCcCCCCHHHHHhCCEEEEEcCcCC-CCceeHHHHHHHHHHHHHHc
Confidence            884 567789999999999999999999999999999999999999996 99999999999999999664
>d1v2xa_ c.116.1.1 (A:) tRNA (Gm18) methyltransferase TrmH {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1ipaa1 c.116.1.1 (A:106-263) RrmA (RrmH), C-terminal domain {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1mxia_ c.116.1.1 (A:) Hypothetical tRNA/rRNA methyltransfease HI0766 (YibK homologue) {Haemophilus influenzae [TaxId: 727]} Back     information, alignment and structure
>d2o3aa1 c.116.1.8 (A:1-167) Uncharacterized protein AF0751 {Archaeoglobus fulgidus [TaxId: 2234]} Back     information, alignment and structure
>d2qwva1 c.116.1.7 (A:5-205) Uncharacterized protein VCA1059 {Vibrio cholerae [TaxId: 666]} Back     information, alignment and structure
>d2qmma1 c.116.1.7 (A:95-288) Uncharacterized protein AF1056 {Archaeoglobus fulgidus [TaxId: 2234]} Back     information, alignment and structure
>d1vhka2 c.116.1.5 (A:74-253) Hypothetical protein YqeU {Bacillus subtilis [TaxId: 1423]} Back     information, alignment and structure
>d1k3ra2 c.116.1.2 (A:1-92,A:164-262) Hypothetical protein MTH1 (MT0001), dimerisation domain {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} Back     information, alignment and structure