254781160

254781160

16S rRNA m3U1498 methyltransferase

GeneID in NCBI database:8210185Locus tag:CLIBASIA_05335
Protein GI in NCBI database:254781160Protein Accession:YP_003065573.1
Gene range:+(1156276, 1157013)Protein Length:245aa
Gene description:16S rRNA m3U1498 methyltransferase
COG prediction:[S] Uncharacterized protein conserved in bacteria
KEGG prediction:16S rRNA m3U1498 methyltransferase; K09761 ribosomal RNA small subunit methyltransferase E [EC:2.1.1.-]
SEED prediction:Ribosomal RNA small subunit methyltransferase E (EC 2.1.1.-)
Pathway involved in KEGG:not defined
Subsystem involved in SEED:Heat shock dnaK gene cluster extended
sequencesequence profile

Prediction of Local Sequence Properties

SourceSummaryResult
scaler
NCBI Databasesequence
PSIPREDsecondary structure
SSPROsecondary structure
DISEMBLcoil and loop
DISEMBLflexible loop
SEGlow complexity
DISOPREDdisordered
DISEMBLmissing residues
DISPROdisordered
TMHMMnone TM-Helix
TOPPRED2 TM-Helix
HMMTOPnone TM-Helix
MEMSATnone TM-Helix
MEMSAT_SVMnone TM-Helix
PHOBIUSnone TM-Helix
SignalP_HMMno
SignalP_NNno
COILScoiled coil
70% MSAconservation map
90% MSAconservation map
  
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-----
MKIHSHLKRLFVDFPLCIKTQGKASGDQYHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVGKSIRFKVEYQSRSQTKQSDVQYIFSPIKTNRLDYMIQKSVEMGMGAIRPVITRYTQNTHYNMDRVRTYTISAAEQCDILTLPFIYPPTTLEFLLKNWDHNCQIVFADETCGSENSLEKLHAIAHIPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRSDTAAVAAMALVQAICGDWY
ccccccccEEEcccccccccEEEEcHHHHHHHHHHcccccccEEEEEEccccEEEEEEEEccccEEEEEEEccccccccccEEEEEEccccHHHHHHHHHHHHccccEEEEEEEEcHHHHHHHHHHHHHHHHHHHHHccccccccccccccHHHHHHccccccEEEEccHHcccccccHHHccccccccEEEEEcccccccHHHHHHHHHccccEEEcccccccHHHHHHHHHHHHHHHHHcccc
ccccccccEEEEccccccccEEEccHHHHHHHHHHHEcccccEEEEEcccccEEEEEEEEccccEEEEEEEEccccccccEEEEEEccccccHHHHHHHHHHHHcHcEEccccHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHccccccEEEEccccHccccccHHHHcccccccEEEEEcccccccHHHHHHHHHcccEEEccccccEccHHHHHHHHHHHHHHHHcccc
mkihshlkrlfvdfplciktqgkasgdqYHYLAHVLRMKegdnillfngkdgewlSKISYVGKSIRFKVEyqsrsqtkqsdvqYIFSPIKTNRLDYMIQKSVemgmgairpvitrytqnthynmdRVRTYTISAaeqcdiltlpfiyppttLEFLLKNWDHNCQivfadetcgsensLEKLHAIAhipnvailigpeggyhseeketlhslpfvtplslgprilrsDTAAVAAMALVQAICGDWY
mkihshlkrLFVDFPLCIKTQGKASGDQYHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVGKSIRFKVEyqsrsqtkqsdvqyifspiktnrLDYMIQKSVEMGMGAIRPVITRytqnthynmDRVRTYTISAAEQCDILTLPFIYPPTTLEFLLKNWDHNCQIVFADETCGSENSLEKLHAIAHIPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRSDTAAVAAMALVQAICGDWY
MKIHSHLKRLFVDFPLCIKTQGKASGDQYHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVGKSIRFKVEYQSRSQTKQSDVQYIFSPIKTNRLDYMIQKSVEMGMGAIRPVITRYTQNTHYNMDRVRTYTISAAEQCDILTLPFIYPPTTLEFLLKNWDHNCQIVFADETCGSENSLEKLHAIAHIPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRSDTaavaamalvqaICGDWY
***HSHL*RLFVDFPLCIKTQGKASGDQYHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVGKSIRF**EY******KQSDVQYIFSPIKTNRLDYMIQKSVEMGMGAIRPVITRYTQNTHYNMDRVRTYTISAAEQCDILTLPFIYPPTTLEFLLKNWDHNCQIVFADETCG***********AHIPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRSDTAAVAAMALVQAICGDWY
MKIHSHLKRLFVDFPLCIKTQGKASGDQYHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVGKSIRFKVEY********SDVQYIFSPIKTNRLDYMIQKSVEMGMGAIRPVITRYTQNTHYNMDRVRTYTISAAEQCDILTLPFIYPPTTLEFLLKNWDHNCQIVFADETCGSENSLEKLHAIAHIPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRSDTAAVAAMALVQAICGDWY
****SHLKRLFVDFPLCIKTQGKASGDQYHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVGKSIRFKVEYQSRSQTKQSDVQYIFSPIKTNRLDYMIQKSVEMGMGAIRPVITRYTQNTHYNMDRVRTYTISAAEQCDILTLPFIYPPTTLEFLLKNWDHNCQIVFADETCGSENSLEKLHAIAHIPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRSDTAAVAAMALVQAICGDWY
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MKIHSHLKRLFVDFPLCIKTQGKASGDQYHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVGKSIRFKVEYQSRSQTKQSDVQYIFSPIKTNRLDYMIQKSVEMGMGAIRPVITRYTQNTHYNMDRVRTYTISAAEQCDILTLPFIYPPTTLEFLLKNWDHNCQIVFADETCGSENSLEKLHAIAHIPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRSDTAAVAAMALVQAICGDWY
MKIHSHLKRLFVDFPLCIKTQGKASGDQYHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVGKSIRFKVEYQSRSQTKQSDVQYIFSPIKTNRLDYMIQKSVEMGMGAIRPVITRYTQNTHYNMDRVRTYTISAAEQCDILTLPFIYPPTTLEFLLKNWDHNCQIVFADETCGSENSLEKLHAIAHIPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRSDTAAVAAMALVQAICGDWY
MKIHSHLKRLFVDFPLCIKTQGKASGDQYHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVGKSIRFKVEYQSRSQTKQSDVQYIFSPIKTNRLDYMIQKSVEMGMGAIRPVITRYTQNTHYNMDRVRTYTISAAEQCDILTLPFIYPPTTLEFLLKNWDHNCQIVFADETCGSENSLEKLHAIAHIPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRSDTAAVAAMALVQAICGDWY

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

No hits with e-value below 0.05

Close Homologs Detected BLAST or PSI-BLAST in the First 2 Iterations

IdentityAlignment graphLength Definition Round E-value
Target245 16S rRNA m3U1498 methyltransferase [Candidatus Liberiba
315122545254 16S rRNA m3U1498 methyltransferase [Candidatus Liberiba 1 2e-97
254720129248 16S ribosomal RNA methyltransferase RsmE [Brucella sp. 1 2e-60
319405184247 conserved hypothetical protein [Bartonella sp. AR 15-3] 1 4e-60
265985135242 conserved hypothetical protein [Brucella sp. 83/13] Len 1 9e-60
49473945244 hypothetical protein BQ02980 [Bartonella quintana str. 1 3e-56
325292039261 hypothetical protein AGROH133_04165 [Agrobacterium sp. 1 3e-55
148253212250 16S ribosomal RNA methyltransferase RsmE [Bradyrhizobiu 1 7e-55
121602013247 hypothetical protein BARBAKC583_0300 [Bartonella bacill 1 9e-55
319898419240 hypothetical protein BARCL_0241 [Bartonella clarridgeia 1 2e-54
256111326248 16S ribosomal RNA methyltransferase RsmE [Brucella meli 1 2e-54
>gi|315122545|ref|YP_004063034.1| 16S rRNA m3U1498 methyltransferase [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 254 Back     alignment and organism information
 Score =  359 bits (921), Expect = 2e-97,   Method: Compositional matrix adjust.
 Identities = 178/245 (72%), Positives = 211/245 (86%), Gaps = 2/245 (0%)

Query: 1   MKIHSHLKRLFVDFPLCIKTQGKASGDQYHYLAHVLRMKEGDNILLFNGKDGEWLSKISY 60
           MK+H  LKRLFV+F L  K QGKAS  QYHYLAHVLRMKE + +L+FNG+DGEW+S ISY
Sbjct: 1   MKMHPPLKRLFVNFSLQPKAQGKASDAQYHYLAHVLRMKEKEKVLIFNGEDGEWISTISY 60

Query: 61  VGKSIRFKVEYQSRSQTKQSDVQYIFSPIKTNRLDYMIQKSVEMGMGAIRPVITRYTQNT 120
           + KSI F VE+Q+R+QTK SD+ YIFSPIKTNRLDYMIQKSVEMG+ AIRPVITRYTQNT
Sbjct: 61  IKKSISFNVEHQTRTQTKPSDLHYIFSPIKTNRLDYMIQKSVEMGVSAIRPVITRYTQNT 120

Query: 121 HYNMDRVRTYTISAAEQCDILTLPFIYPPTTLEFLLKNWDHNCQIVFADETCGSENSLEK 180
           H N++R+RTY ISAAEQC+I++LP I+PP TL+ LL++WD N  IVFADETC  ENS  K
Sbjct: 121 HCNVNRMRTYAISAAEQCNIISLPSIHPPITLDTLLEDWDQNRHIVFADETCIHENS--K 178

Query: 181 LHAIAHIPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRSDTAAVAAMALVQAI 240
           + AIAHI ++A+LIGPEGG+H +EKE LHSLPFVTP+SLGPRILR+DTAAVAA+ALVQ+ 
Sbjct: 179 IQAIAHIVHMAVLIGPEGGFHPKEKEKLHSLPFVTPISLGPRILRADTAAVAAIALVQST 238

Query: 241 CGDWY 245
           CGDWY
Sbjct: 239 CGDWY 243


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|254720129|ref|ZP_05181940.1| 16S ribosomal RNA methyltransferase RsmE [Brucella sp. 83/13] Length = 248 Back     alignment and organism information
>gi|319405184|emb|CBI78789.1| conserved hypothetical protein [Bartonella sp. AR 15-3] Length = 247 Back     alignment and organism information
>gi|265985135|ref|ZP_06097870.1| conserved hypothetical protein [Brucella sp. 83/13] Length = 242 Back     alignment and organism information
>gi|49473945|ref|YP_031987.1| hypothetical protein BQ02980 [Bartonella quintana str. Toulouse] Length = 244 Back     alignment and organism information
>gi|325292039|ref|YP_004277903.1| hypothetical protein AGROH133_04165 [Agrobacterium sp. H13-3] Length = 261 Back     alignment and organism information
>gi|148253212|ref|YP_001237797.1| 16S ribosomal RNA methyltransferase RsmE [Bradyrhizobium sp. BTAi1] Length = 250 Back     alignment and organism information
>gi|121602013|ref|YP_988622.1| hypothetical protein BARBAKC583_0300 [Bartonella bacilliformis KC583] Length = 247 Back     alignment and organism information
>gi|319898419|ref|YP_004158512.1| hypothetical protein BARCL_0241 [Bartonella clarridgeiae 73] Length = 240 Back     alignment and organism information
>gi|256111326|ref|ZP_05452352.1| 16S ribosomal RNA methyltransferase RsmE [Brucella melitensis bv. 3 str. Ether] Length = 248 Back     alignment and organism information

Conserved Domains in CDD Database
Detected by RPS-BLAST and HHsearch

Conserved Domains in CDD Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target245 16S rRNA m3U1498 methyltransferase [Candidatus Liberiba
PRK11713234 PRK11713, PRK11713, 16S ribosomal RNA methyltransferase 2e-51
COG1385246 COG1385, COG1385, Uncharacterized protein conserved in 2e-47
TIGR00046240 TIGR00046, TIGR00046, RNA methyltransferase, RsmE famil 3e-25
pfam04452225 pfam04452, Methyltrans_RNA, RNA methyltransferase 1e-48
>gnl|CDD|183286 PRK11713, PRK11713, 16S ribosomal RNA methyltransferase RsmE; Provisional Back     alignment and domain information
>gnl|CDD|31575 COG1385, COG1385, Uncharacterized protein conserved in bacteria [Function unknown] Back     alignment and domain information
>gnl|CDD|129157 TIGR00046, TIGR00046, RNA methyltransferase, RsmE family Back     alignment and domain information
>gnl|CDD|146878 pfam04452, Methyltrans_RNA, RNA methyltransferase Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 245 16S rRNA m3U1498 methyltransferase [Candidatus Liberiba
PRK11713243 16S rRNA m3U1498 methyltransferase; Provisional 100.0
COG1385246 Uncharacterized protein conserved in bacteria [Function 100.0
pfam04452225 Methyltrans_RNA RNA methyltransferase. RNA methyltransf 100.0
TIGR00046258 TIGR00046 conserved hypothetical protein TIGR00046; Int 100.0
PRK02135199 hypothetical protein; Provisional 93.85
pfam04013199 DUF358 Protein of unknown function (DUF358). The protei 92.97
COG1901197 Uncharacterized conserved protein [Function unknown] 90.5
pfam00588142 SpoU_methylase SpoU rRNA Methylase family. This family 91.59
>PRK11713 16S rRNA m3U1498 methyltransferase; Provisional Back     alignment and domain information
>COG1385 Uncharacterized protein conserved in bacteria [Function unknown] Back     alignment and domain information
>pfam04452 Methyltrans_RNA RNA methyltransferase Back     alignment and domain information
>TIGR00046 TIGR00046 conserved hypothetical protein TIGR00046; InterPro: IPR006700 Methyltransferases (Mtases) are responsible for the transfer of methyl groups between two molecules Back     alignment and domain information
>PRK02135 hypothetical protein; Provisional Back     alignment and domain information
>pfam04013 DUF358 Protein of unknown function (DUF358) Back     alignment and domain information
>COG1901 Uncharacterized conserved protein [Function unknown] Back     alignment and domain information
>pfam00588 SpoU_methylase SpoU rRNA Methylase family Back     alignment and domain information

Homologous Structures in PDB Database
Detected by PSI-BLAST, RPS-BLAST and HHsearch

Homologous Structures Detected by PSI-BLAST against Nonredundant Database

IdentityAlignment graphLength Definition E-value
Target245 16S rRNA m3U1498 methyltransferase [Candidatus Liberiba
1vhy_A257 Crystal Structure Of Haemophilus Influenzae Protein 5e-31
1nxz_A246 X-Ray Crystal Structure Of Protein Yggj_haein Of Ha 7e-31
1vhk_A268 Crystal Structure Of An Hypothetical Protein Length 6e-30
3kw2_A257 Crystal Structure Of Probable Rrna-Methyltransferas 7e-24
1z85_A234 Crystal Structure Of A Predicted Rna Methyltransfer 5e-19
1v6z_A228 Crystal Structure Of Tt1573 From Thermus Thermophil 2e-17
2egv_A229 Crystal Structure Of Rrna Methyltransferase With Sa 2e-14
>gi|40889966|pdb|1VHY|A Chain A, Crystal Structure Of Haemophilus Influenzae Protein Hi0303, Pfam Duf558 Length = 257 Back     alignment and structure
 Score =  138 bits (348), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 65/247 (26%), Positives = 111/247 (44%), Gaps = 15/247 (6%)

Query: 6   HLKRLFVDFPLCIKTQGKASGDQYHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVGKSI 65
            + R++    L  +TQ   S D  +++A VLR  EG+ + LF+G +  + +KI       
Sbjct: 4   RIPRIYHPISLENQTQCYLSEDAANHVARVLRXTEGEQLELFDGSNHIYPAKIIE-SNKK 62

Query: 66  RFKVE---YQSRSQTKQSDVQYIFSPIKTNRLDYMIQKSVEMGMGAIRPVITRYT----- 117
             KVE    +   +     +       +  R ++ IQKSVE+G+  I P+ +        
Sbjct: 63  SVKVEILGRELADKESHLKIHLGQVISRGERXEFTIQKSVELGVNVITPLWSERCGVKLD 122

Query: 118 -QNTHYNMDRVRTYTISAAEQCDILTLPFIYPPTTLEFLLKNWDHNCQIVFADETCGSEN 176
            +     + + +   I+A EQC    +P I P   L+      D   ++        S  
Sbjct: 123 AERXDKKIQQWQKIAIAACEQCGRNIVPEIRPLXKLQDWCAENDGALKLNLHPRAHYSIK 182

Query: 177 SLEKLHAIAHIPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRSDTAAVAAMAL 236
           +L  + A      V +LIG EGG  ++E        F T + LG R+LR++TA++AA++ 
Sbjct: 183 TLPTIPA----GGVRLLIGSEGGLSAQEIAQTEQQGF-TEILLGKRVLRTETASLAAISA 237

Query: 237 VQAICGD 243
           +Q   GD
Sbjct: 238 LQICFGD 244


>gi|29726851|pdb|1NXZ|A Chain A, X-Ray Crystal Structure Of Protein Yggj_haein Of Haemophilus Influenzae. Northeast Structural Genomics Consortium Target Ir73. Length = 246 Back     alignment and structure
>gi|40889937|pdb|1VHK|A Chain A, Crystal Structure Of An Hypothetical Protein Length = 268 Back     alignment and structure
>gi|284055742|pdb|3KW2|A Chain A, Crystal Structure Of Probable Rrna-Methyltransferase From Porphyromonas Gingivalis Length = 257 Back     alignment and structure
>gi|66361363|pdb|1Z85|A Chain A, Crystal Structure Of A Predicted Rna Methyltransferase (Tm1380) From Thermotoga Maritima Msb8 At 2.12 A Resolution Length = 234 Back     alignment and structure
>gi|58177000|pdb|1V6Z|A Chain A, Crystal Structure Of Tt1573 From Thermus Thermophilus Length = 228 Back     alignment and structure
gi|158428333|pdb|2EGV|A Chain A, Crystal Structure Of Rrna Methyltransferase With Sam Ligand Length = 229 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target245 16S rRNA m3U1498 methyltransferase [Candidatus Liberiba
3kw2_A257 Probable R-RNA methyltransferase; structural genomics, 3e-44
1vhy_A257 Hypothetical protein HI0303; PSI, protein structure ini 2e-41
1vhk_A268 Hypothetical protein YQEU; structural genomics, unknown 1e-39
1v6z_A228 Hypothetical protein TTHA0657; structural genomics, rik 2e-32
1z85_A234 Hypothetical protein TM1380; structural genomics, joint 9e-28
2egv_A229 UPF0088 protein AQ_165; RSME, methyltransferase, rRNA m 2e-27
>3kw2_A Probable R-RNA methyltransferase; structural genomics, unknown function, PSI-2, protein structure initiative; HET: MSE ADN; 2.00A {Porphyromonas gingivalis atcc 33277} Length = 257 Back     alignment and structure
 Score =  173 bits (440), Expect = 3e-44
 Identities = 48/235 (20%), Positives = 102/235 (43%), Gaps = 9/235 (3%)

Query: 18  IKTQGKASGDQYHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVGKSIRF--KVEYQSRS 75
           I+   +   D+  ++  VLRM+ GD + L +G+   + + I    +   +      +S  
Sbjct: 13  IEQSDRLPDDEAGHILRVLRMQAGDRLRLTDGRGSFFDAVIETADRKSCYVSVCGQESWQ 72

Query: 76  QTKQSDVQYIFSPIKTN-RLDYMIQKSVEMGMGAIRPVITRYTQNTHYNMDRVRTYTISA 134
           +  +  +    +P K + R+++M++K VE+G+  +  + + +++      +R+    ISA
Sbjct: 73  KPWRDRITIAIAPTKQSERMEWMLEKLVEIGVDEVVFIESEHSERRRIKAERLERIAISA 132

Query: 135 AEQCDILTLPFIYPPTTLEFLLKNWDHNCQIVFADETCGSENSLEKLHAIAHI-----PN 189
            +Q    + P I     ++ ++ +       + A         + +             +
Sbjct: 133 MKQSLKASFPVIRVNIPIQTVIADTPKAAVRLIAYVDEAVRAEITQGRGYPSDFYHVGQD 192

Query: 190 VAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRSDTAAVAAMALVQAICGDW 244
           V ILIGPEG +   E E+     F  P+SLG   LR++TA + A   +  +   +
Sbjct: 193 VLILIGPEGDFSPSEVESALLAGF-APVSLGESRLRTETAGLVACQWIHTLQACY 246


>1vhy_A Hypothetical protein HI0303; PSI, protein structure initiative, NEW YORK SGX research center for structural genomics, nysgxrc; HET: MSE; 1.90A {Haemophilus influenzae} SCOP: b.122.1.2 c.116.1.5 PDB: 1nxz_A Length = 257 Back     alignment and structure
>1vhk_A Hypothetical protein YQEU; structural genomics, unknown function; 2.60A {Bacillus subtilis} SCOP: b.122.1.2 c.116.1.5 Length = 268 Back     alignment and structure
>1v6z_A Hypothetical protein TTHA0657; structural genomics, riken structural genomics/proteomics initiative, RSGI, transferase; 2.00A {Thermus thermophilus HB8} SCOP: b.122.1.2 c.116.1.5 PDB: 2cx8_A* 2z0y_A* Length = 228 Back     alignment and structure
>1z85_A Hypothetical protein TM1380; structural genomics, joint center for structural genomics, JCSG, protein structure initiative, PSI; 2.12A {Thermotoga maritima MSB8} Length = 234 Back     alignment and structure
>2egv_A UPF0088 protein AQ_165; RSME, methyltransferase, rRNA modification, PUA domain, M3U, SAM, structural genomics, NPPSFA; HET: SAM; 1.45A {Aquifex aeolicus} PDB: 2egw_A* Length = 229 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target245 16S rRNA m3U1498 methyltransferase [Candidatus Liberiba
1vhy_A257 Hypothetical protein HI0303; PSI, protein structure ini 100.0
1vhk_A268 Hypothetical protein YQEU; structural genomics, unknown 100.0
3kw2_A257 Probable R-RNA methyltransferase; structural genomics, 100.0
2egv_A229 UPF0088 protein AQ_165; RSME, methyltransferase, rRNA m 100.0
1v6z_A228 Hypothetical protein TTHA0657; structural genomics, rik 100.0
1z85_A234 Hypothetical protein TM1380; structural genomics, joint 100.0
2qwv_A208 UPF0217 protein VC_A1059; unknown function, structural 94.26
2qmm_A197 UPF0217 protein AF_1056; alpha/beta knot, SAM, structur 94.04
1to0_A167 Hypothetical UPF0247 protein YYDA; structural genomics, 90.49
1v2x_A194 TRNA (GM18) methyltransferase; DEEP trefoil knot, riken 92.91
2ha8_A184 TAR (HIV-1) RNA loop binding protein; methyltransferase 91.62
>1vhy_A Hypothetical protein HI0303; PSI, protein structure initiative, NEW YORK SGX research center for structural genomics, nysgxrc; HET: MSE; 1.90A {Haemophilus influenzae} SCOP: b.122.1.2 c.116.1.5 PDB: 1nxz_A Back     alignment and structure
Probab=100.00  E-value=0  Score=444.35  Aligned_cols=236  Identities=27%  Similarity=0.388  Sum_probs=204.7

Q ss_pred             CCCCCEEEECCCCCCCCEEEECHHHHHHHHHHCCCCCCCEEEEEECCCCEEEEEEECCCCC-CEEEEEEE-ECCCCCCCC
Q ss_conf             6778777408544788889987798759987035789888999977998798753023555-23899754-135555443
Q gi|254781160|r    4 HSHLKRLFVDFPLCIKTQGKASGDQYHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVGKS-IRFKVEYQ-SRSQTKQSD   81 (245)
Q Consensus         4 ~~~m~R~f~~~~l~~~~~i~L~~~~~hHl~kVlRlk~Gd~i~i~dg~g~~~~~~I~~~~k~-~~~~i~~~-~~~~~~~~~   81 (245)
                      -|||||||++.++..++++.|+++++|||.||||+++||.|.|+||+|+.|.|+|++++|+ +.+++... ...+.++++
T Consensus         2 ~Mr~pR~y~~~~l~~~~~i~L~~~~~hHl~kVLRlk~Gd~I~v~dg~G~~~~a~I~~~~k~~~~~~i~~~~~~~~~~~~~   81 (257)
T 1vhy_A            2 SLRIPRIYHPISLENQTQCYLSEDAANHVARVLRMTEGEQLELFDGSNHIYPAKIIESNKKSVKVEILGRELADKESHLK   81 (257)
T ss_dssp             ---CCEEECSSCCTTCSEEECCHHHHHHHHTTSCCCTTCEEEEECSSSEEEEEEEEEECSSCEEEEECCCEECCCCCSSC
T ss_pred             CCCCCEEEECCCCCCCCEEECCHHHHHHHHHHCCCCCCCEEEEEECCCCEEEEEEEECCCCEEEEEECCCHHHCCCCCEE
T ss_conf             87885798686568999898598998899983838999999999798999999999866863763100001211467404


Q ss_pred             CEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHH------HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC
Q ss_conf             135413445411567775444456656555542022011------22122335788999975123443433200000011
Q gi|254781160|r   82 VQYIFSPIKTNRLDYMIQKSVEMGMGAIRPVITRYTQNT------HYNMDRVRTYTISAAEQCDILTLPFIYPPTTLEFL  155 (245)
Q Consensus        82 i~l~~~~~k~~~~~~ilqk~tELGV~~I~p~~~~rs~~~------~~k~eR~~~ii~eA~eQsgr~~lP~i~~~~~l~~~  155 (245)
                      ++|+++++|+++|||+|||+|||||++|+|+.++||+.+      .+|++||++|+++|||||||+++|+|.++.+|+++
T Consensus        82 i~l~~~l~K~~~~~~il~k~tELGV~~I~p~~s~rs~~~~~~~~~~~k~~r~~~I~~eA~eQsgr~~lP~I~~~~~l~~~  161 (257)
T 1vhy_A           82 IHLGQVISRGERMEFTIQKSVELGVNVITPLWSERCGVKLDAERMDKKIQQWQKIAIAACEQCGRNIVPEIRPLMKLQDW  161 (257)
T ss_dssp             EEEEEEC----CCHHHHHHHHHTTCCEEEEEECTTSSSCCCHHHHHHHHHHHHHHHHHHHHHHCCSSCCEECCCEEHHHH
T ss_pred             EEEEEEECCHHHHHHHHHHHHHHCCCEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHH
T ss_conf             89998402338899999999974876899997102335465667887699999999999986599767865410038999


Q ss_pred             CCCCCCCCCCCCCCCHHCCCCCHHHHHCCCCCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHH
Q ss_conf             23332233321263000121102221003678835999888888888999999957995586368874004489999999
Q gi|254781160|r  156 LKNWDHNCQIVFADETCGSENSLEKLHAIAHIPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRSDTAAVAAMA  235 (245)
Q Consensus       156 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~IGPEGGfs~~E~~~l~~~~~~~~vsLG~~ILR~ETA~i~als  235 (245)
                      +...+......+.+.   .......+ .....++++++||||||||++|+++|+++|| ++++||++|||||||+|+|+|
T Consensus       162 ~~~~~~~~~~~~~~~---~~~~~~~~-~~~~~~~i~i~IGPEGGfs~~E~~~l~~~~~-~~vsLG~~ILR~ETA~i~als  236 (257)
T 1vhy_A          162 CAENDGALKLNLHPR---AHYSIKTL-PTIPAGGVRLLIGSEGGLSAQEIAQTEQQGF-TEILLGKRVLRTETASLAAIS  236 (257)
T ss_dssp             HTCCSSCEEEEECTT---CCCBGGGC-CCCCTTCEEEEECCTTCCCHHHHHHHHHTTC-EEEBCCSSCCCHHHHHHHHHH
T ss_pred             HHHCCCCCCHHHHHH---HHHHHHHH-HHHCCCCEEEEECCCCCCCHHHHHHHHHCCC-EEEECCCCCCHHHHHHHHHHH
T ss_conf             861544421011024---44456666-5303686589985777889899999998798-783268981668879999999


Q ss_pred             HHHHHHCCC
Q ss_conf             999984786
Q gi|254781160|r  236 LVQAICGDW  244 (245)
Q Consensus       236 ~~~~~~g~~  244 (245)
                      ++++++|||
T Consensus       237 ~~~~~~g~~  245 (257)
T 1vhy_A          237 ALQICFGDL  245 (257)
T ss_dssp             HHHHHHSGG
T ss_pred             HHHHHHCCC
T ss_conf             999984865



>1vhk_A Hypothetical protein YQEU; structural genomics, unknown function; 2.60A {Bacillus subtilis} SCOP: b.122.1.2 c.116.1.5 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
>2egv_A UPF0088 protein AQ_165; RSME, methyltransferase, rRNA modification, PUA domain, M3U, SAM, structural genomics, NPPSFA; HET: SAM; 1.45A {Aquifex aeolicus} PDB: 2egw_A* Back     alignment and structure
>1v6z_A Hypothetical protein TTHA0657; structural genomics, riken structural genomics/proteomics initiative, RSGI, transferase; 2.00A {Thermus thermophilus HB8} SCOP: b.122.1.2 c.116.1.5 PDB: 2cx8_A* 2z0y_A* Back     alignment and structure
>1z85_A Hypothetical protein TM1380; structural genomics, joint center for structural genomics, JCSG, protein structure initiative, PSI; 2.12A {Thermotoga maritima MSB8} 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
>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
>1to0_A Hypothetical UPF0247 protein YYDA; structural genomics, unknown function, PSI, protein structure initiative; 2.50A {Bacillus subtilis} SCOP: c.116.1.3 Back     alignment and structure
>1v2x_A TRNA (GM18) methyltransferase; DEEP trefoil knot, riken structural genomics/proteomics initiative, RSGI, structural genomics; HET: SAM; 1.50A {Thermus thermophilus} SCOP: c.116.1.1 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

Homologous Domains in SCOP and MMDB Database
Detected by RPS-BLAST and HHsearch

Homologous Domains in SCOP70 (Version1.75) Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 245 16S rRNA m3U1498 methyltransferase [Candidatus Liberiba
d1vhka2180 c.116.1.5 (A:74-253) Hypothetical protein YqeU {Bacillu 3e-30
d1nxza2174 c.116.1.5 (A:74-247) Hypothetical protein HI0303 {Haemo 7e-30
d1v6za2162 c.116.1.5 (A:67-228) Hypothetical protein TTHA0657 (TT1 1e-28
d1nxza172 b.122.1.2 (A:2-73) Hypothetical protein HI0303 {Haemoph 8e-13
d1vhka172 b.122.1.2 (A:2-73) Hypothetical protein YqeU {Bacillus 8e-12
>d1vhka2 c.116.1.5 (A:74-253) Hypothetical protein YqeU {Bacillus subtilis [TaxId: 1423]} Length = 180 Back     information, alignment and structure

class: Alpha and beta proteins (a/b)
fold: alpha/beta knot
superfamily: alpha/beta knot
family: YggJ C-terminal domain-like
domain: Hypothetical protein YqeU
species: Bacillus subtilis [TaxId: 1423]
 Score =  125 bits (316), Expect = 3e-30
 Identities = 43/170 (25%), Positives = 69/170 (40%), Gaps = 11/170 (6%)

Query: 81  DVQYIFSPIKTNRLDYMIQKSVEMGMGAIRPVITRYT------QNTHYNMDRVRTYTISA 134
            V       K ++L+++IQK  E+G  A  P     +      +      +R       A
Sbjct: 7   KVYIASGLPKGDKLEWIIQKGTELGAHAFIPFQAARSVVKLDDKKAKKKRERWTKIAKEA 66

Query: 135 AEQCDILTLPFIYPPTTLEFLLKNWDHNCQIVFADETCGSENSLEKLHAIA----HIPNV 190
           AEQ     +P +    + + LL+      + V A E    +  +    AI        ++
Sbjct: 67  AEQSYRNEVPRVMDVHSFQQLLQRMQDFDKCVVAYEESSKQGEISAFSAIVSSLPKGSSL 126

Query: 191 AILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRSDTAAVAAMALVQAI 240
            I+ GPEGG    E E L     V    LGPRILR++TA + A++ +   
Sbjct: 127 LIVFGPEGGLTEAEVERLTEQDGV-TCGLGPRILRTETAPLYALSAISYQ 175


>d1nxza2 c.116.1.5 (A:74-247) Hypothetical protein HI0303 {Haemophilus influenzae [TaxId: 727]} Length = 174 Back     information, alignment and structure
>d1v6za2 c.116.1.5 (A:67-228) Hypothetical protein TTHA0657 (TT1575) {Thermus thermophilus [TaxId: 274]} Length = 162 Back     information, alignment and structure
>d1nxza1 b.122.1.2 (A:2-73) Hypothetical protein HI0303 {Haemophilus influenzae [TaxId: 727]} Length = 72 Back     information, alignment and structure
>d1vhka1 b.122.1.2 (A:2-73) Hypothetical protein YqeU {Bacillus subtilis [TaxId: 1423]} Length = 72 Back     information, alignment and structure

Homologous Domains in SCOP70 (Version 1.75) Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target245 16S rRNA m3U1498 methyltransferase [Candidatus Liberiba
d1nxza2174 Hypothetical protein HI0303 {Haemophilus influenzae [Ta 100.0
d1vhka2180 Hypothetical protein YqeU {Bacillus subtilis [TaxId: 14 100.0
d1v6za2162 Hypothetical protein TTHA0657 (TT1575) {Thermus thermop 100.0
d1nxza172 Hypothetical protein HI0303 {Haemophilus influenzae [Ta 99.58
d1vhka172 Hypothetical protein YqeU {Bacillus subtilis [TaxId: 14 99.4
d1v6za163 Hypothetical protein TTHA0657 (TT1575) {Thermus thermop 96.55
d2qwva1201 Uncharacterized protein VCA1059 {Vibrio cholerae [TaxId 94.77
d2qmma1194 Uncharacterized protein AF1056 {Archaeoglobus fulgidus 94.38
>d1nxza2 c.116.1.5 (A:74-247) Hypothetical protein HI0303 {Haemophilus influenzae [TaxId: 727]} Back     information, alignment and structure
class: Alpha and beta proteins (a/b)
fold: alpha/beta knot
superfamily: alpha/beta knot
family: YggJ C-terminal domain-like
domain: Hypothetical protein HI0303
species: Haemophilus influenzae [TaxId: 727]
Probab=100.00  E-value=0  Score=325.43  Aligned_cols=163  Identities=27%  Similarity=0.394  Sum_probs=141.1

Q ss_pred             CCCCCCEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHH------HHHHHHHHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf             55443135413445411567775444456656555542022011------221223357889999751234434332000
Q gi|254781160|r   77 TKQSDVQYIFSPIKTNRLDYMIQKSVEMGMGAIRPVITRYTQNT------HYNMDRVRTYTISAAEQCDILTLPFIYPPT  150 (245)
Q Consensus        77 ~~~~~i~l~~~~~k~~~~~~ilqk~tELGV~~I~p~~~~rs~~~------~~k~eR~~~ii~eA~eQsgr~~lP~i~~~~  150 (245)
                      +++.+|+|+|+++|+++|||+|||+|||||++|+|++++||+.+      .++++||++|+++|||||||+++|+|.++.
T Consensus         2 e~~~~i~l~~al~k~~~~~~ilqk~tELGV~~i~p~~s~rs~~~~~~~~~~~k~~r~~~i~~~A~eQsgr~~lP~i~~~~   81 (174)
T d1nxza2           2 ESHLKIHLGQVISRGERMEFTIQKSVELGVNVITPLWSERCGVKLDAERMDKKIQQWQKIAIAACEQCGRNIVPEIRPLM   81 (174)
T ss_dssp             CCSSCEEEEEECCSSSCHHHHHHHHHHTTCCEEEEEECTTSCCCCCHHHHHHHHHHHHHHHHHHHHHHCCSSCCEECCCE
T ss_pred             CCCCEEEEEEEECCCCHHHHHHHHHHHHCCCEEEECHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHH
T ss_conf             99963899995127625999999998008035896157645323106678860899999999998732733255314102


Q ss_pred             CCCCCCCCCCCCCCCCCCCCHHCCCCCHHHHHCCCCCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEECCCCCCCHHHHH
Q ss_conf             00011233322333212630001211022210036788359998888888889999999579955863688740044899
Q gi|254781160|r  151 TLEFLLKNWDHNCQIVFADETCGSENSLEKLHAIAHIPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRSDTAA  230 (245)
Q Consensus       151 ~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~IGPEGGfs~~E~~~l~~~~~~~~vsLG~~ILR~ETA~  230 (245)
                      +|+++++..+....+.+++...   .....+ .....++++++||||||||++|+++|+++|| .+++||+||||+|||+
T Consensus        82 ~l~~~l~~~~~~~~~~~~~~~~---~~~~~~-~~~~~~~i~iiIGPEGGfs~~E~~~~~~~g~-~~v~LG~~ILR~ETA~  156 (174)
T d1nxza2          82 KLQDWCAENDGALKLNLHPRAH---YSIKTL-PTIPAGGVRLLIGSEGGLSAQEIAQTEQQGF-TEILLGKRVLRTETAS  156 (174)
T ss_dssp             EHHHHHHCCSSCEEEEECTTCS---CBGGGC-CCCCTTCEEEEECCTTCCCHHHHHHHHHTTC-EEEBCCSSCCCHHHHH
T ss_pred             HHHHHHHHHCCHHHHHHHHHHH---HHHHHH-CCCCCCCEEEEECCCCCCCHHHHHHHHHCCC-EEEECCCCCCHHHHHH
T ss_conf             3778876401014443201234---455432-0278874799974776869899999997798-6866899812687699


Q ss_pred             HHHHHHHHHHHCCC
Q ss_conf             99999999984786
Q gi|254781160|r  231 VAAMALVQAICGDW  244 (245)
Q Consensus       231 i~als~~~~~~g~~  244 (245)
                      ++|+|++++++|||
T Consensus       157 i~als~l~~~~gdl  170 (174)
T d1nxza2         157 LAAISALQICFGDL  170 (174)
T ss_dssp             HHHHHHHHHHHSST
T ss_pred             HHHHHHHHHHHCCC
T ss_conf             99999999994653



>d1vhka2 c.116.1.5 (A:74-253) Hypothetical protein YqeU {Bacillus subtilis [TaxId: 1423]} Back     information, alignment and structure
>d1v6za2 c.116.1.5 (A:67-228) Hypothetical protein TTHA0657 (TT1575) {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1nxza1 b.122.1.2 (A:2-73) Hypothetical protein HI0303 {Haemophilus influenzae [TaxId: 727]} Back     information, alignment and structure
>d1vhka1 b.122.1.2 (A:2-73) Hypothetical protein YqeU {Bacillus subtilis [TaxId: 1423]} Back     information, alignment and structure
>d1v6za1 b.122.1.2 (A:4-66) Hypothetical protein TTHA0657 (TT1575) {Thermus thermophilus [TaxId: 274]} 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

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 245 16S rRNA m3U1498 methyltransferase [Candidatus Lib
1vhk_A_78-268191 (A:78-268) Hypothetical protein YQEU; structural g 1e-35
3kw2_A_75-257183 (A:75-257) Probable R-RNA methyltransferase; struc 1e-35
1vhy_A_78-257180 (A:78-257) Hypothetical protein HI0303; PSI, prote 7e-35
2egv_A_68-229162 (A:68-229) UPF0088 protein AQ_165; RSME, methyltra 2e-33
1v6z_A_68-228161 (A:68-228) Hypothetical protein TTHA0657; structur 1e-32
1z85_A_83-234152 (A:83-234) Hypothetical protein TM1380; structural 5e-31
1vhy_A_1-7777 (A:1-77) Hypothetical protein HI0303; PSI, protein 1e-12
3kw2_A_1-7474 (A:1-74) Probable R-RNA methyltransferase; structu 1e-10
1vhk_A_1-7777 (A:1-77) Hypothetical protein YQEU; structural gen 3e-10
1z85_A_1-8282 (A:1-82) Hypothetical protein TM1380; structural g 6e-10
>1vhk_A (A:78-268) Hypothetical protein YQEU; structural genomics, unknown function; 2.60A {Bacillus subtilis}Length = 191 Back     alignment and structure
 Score =  144 bits (364), Expect = 1e-35
 Identities = 42/174 (24%), Positives = 67/174 (38%), Gaps = 11/174 (6%)

Query: 81  DVQYIFSPIKTNRLDYMIQKSVEMGMGAIRPVITRYTQ------NTHYNMDRVRTYTISA 134
            V       K ++L+++IQK  E+G  A  P     +             +R       A
Sbjct: 5   KVYIASGLPKGDKLEWIIQKGTELGAHAFIPFQAARSVVKLDDKKAKKKRERWTKIAKEA 64

Query: 135 AEQCDILTLPFIYPPTTLEFLLKNWDHNCQIVFADETCGSENSLEKLHAIAHIP----NV 190
           AEQ     +P +    + + LL+      + V A E    +  +    AI        ++
Sbjct: 65  AEQSYRNEVPRVXDVHSFQQLLQRXQDFDKCVVAYEESSKQGEISAFSAIVSSLPKGSSL 124

Query: 191 AILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRSDTAAVAAMALVQAICGDW 244
            I+ GPEGG    E E L          LGPRILR++TA + A++ +       
Sbjct: 125 LIVFGPEGGLTEAEVERLTEQDG-VTCGLGPRILRTETAPLYALSAISYQTELL 177


>3kw2_A (A:75-257) Probable R-RNA methyltransferase; structural genomics, unknown function, PSI-2, protein structure initiative; HET: MSE ADN; 2.00A {Porphyromonas gingivalis atcc 33277}Length = 183 Back     alignment and structure
>1vhy_A (A:78-257) Hypothetical protein HI0303; PSI, protein structure initiative, NEW YORK SGX research center for structural genomics, nysgxrc; HET: MSE; 1.90A {Haemophilus influenzae}Length = 180 Back     alignment and structure
>2egv_A (A:68-229) UPF0088 protein AQ_165; RSME, methyltransferase, rRNA modification, PUA domain, M3U, SAM, structural genomics, NPPSFA; HET: SAM; 1.45A {Aquifex aeolicus} PDB: 2egw_A*Length = 162 Back     alignment and structure
>1v6z_A (A:68-228) Hypothetical protein TTHA0657; structural genomics, riken structural genomics/proteomics initiative, RSGI, transferase; 2.00A {Thermus thermophilus HB8}Length = 161 Back     alignment and structure
>1z85_A (A:83-234) Hypothetical protein TM1380; structural genomics, joint center for structural genomics, JCSG, protein structure initiative, PSI; 2.12A {Thermotoga maritima MSB8}Length = 152 Back     alignment and structure
>1vhy_A (A:1-77) Hypothetical protein HI0303; PSI, protein structure initiative, NEW YORK SGX research center for structural genomics, nysgxrc; HET: MSE; 1.90A {Haemophilus influenzae}Length = 77 Back     alignment and structure
>3kw2_A (A:1-74) Probable R-RNA methyltransferase; structural genomics, unknown function, PSI-2, protein structure initiative; HET: MSE ADN; 2.00A {Porphyromonas gingivalis atcc 33277}Length = 74 Back     alignment and structure
>1vhk_A (A:1-77) Hypothetical protein YQEU; structural genomics, unknown function; 2.60A {Bacillus subtilis}Length = 77 Back     alignment and structure
>1z85_A (A:1-82) Hypothetical protein TM1380; structural genomics, joint center for structural genomics, JCSG, protein structure initiative, PSI; 2.12A {Thermotoga maritima MSB8}Length = 82 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target245 16S rRNA m3U1498 methyltransferase [Candidatus Liberiba
1vhk_A_78-268191 Hypothetical protein YQEU; structural genomics, un 100.0
1vhy_A_78-257180 Hypothetical protein HI0303; PSI, protein structur 100.0
3kw2_A_75-257183 Probable R-RNA methyltransferase; structural genom 100.0
1v6z_A_68-228161 Hypothetical protein TTHA0657; structural genomics 100.0
2egv_A_68-229162 UPF0088 protein AQ_165; RSME, methyltransferase, r 100.0
1z85_A_83-234152 Hypothetical protein TM1380; structural genomics, 100.0
1ipa_A_109-274166 RRMH, RNA 2'-O-ribose methyltransferase; DEEP tref 91.94
1v2x_A_21-176156 TRNA (GM18) methyltransferase; DEEP trefoil knot, 90.98
1vhy_A_1-7777 Hypothetical protein HI0303; PSI, protein structur 99.62
3kw2_A_1-7474 Probable R-RNA methyltransferase; structural genom 99.58
1vhk_A_1-7777 Hypothetical protein YQEU; structural genomics, un 99.51
1z85_A_1-8282 Hypothetical protein TM1380; structural genomics, 99.51
2egv_A_1-6767 UPF0088 protein AQ_165; RSME, methyltransferase, r 97.78
1v6z_A_1-6767 Hypothetical protein TTHA0657; structural genomics 97.09
2qwv_A_208 UPF0217 protein VC_A1059; unknown function, struct 94.39
2qmm_A_197 UPF0217 protein AF_1056; alpha/beta knot, SAM, str 94.19
>1vhk_A (A:78-268) Hypothetical protein YQEU; structural genomics, unknown function; 2.60A {Bacillus subtilis} Back     alignment and structure
Probab=100.00  E-value=0  Score=321.22  Aligned_cols=168  Identities=24%  Similarity=0.288  Sum_probs=148.9

Q ss_pred             CCCCCCEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHH------HHHHHHHHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf             55443135413445411567775444456656555542022011------221223357889999751234434332000
Q gi|254781160|r   77 TKQSDVQYIFSPIKTNRLDYMIQKSVEMGMGAIRPVITRYTQNT------HYNMDRVRTYTISAAEQCDILTLPFIYPPT  150 (245)
Q Consensus        77 ~~~~~i~l~~~~~k~~~~~~ilqk~tELGV~~I~p~~~~rs~~~------~~k~eR~~~ii~eA~eQsgr~~lP~i~~~~  150 (245)
                      +++++|+|+++++|+++|||+|||+|||||++|+|+.|+||+.+      .+|.+||++|+++|||||||+++|+|..+.
T Consensus         1 Ep~~~i~L~~a~~K~~~~d~il~katELGV~~i~p~~serS~~~~~~~~~~~k~er~~~i~~eA~kQs~r~~lP~I~~~~   80 (191)
T 1vhk_A            1 ELPIKVYIASGLPKGDKLEWIIQKGTELGAHAFIPFQAARSVVKLDDKKAKKKRERWTKIAKEAAEQSYRNEVPRVXDVH   80 (191)
T ss_dssp             CCSSEEEEEEECCSTTHHHHHHHHHHHTTCCEEEEECCTTCCCC---------HHHHHHHHHHHHHHTTCSSCCEECCCB
T ss_pred             CCCEEEEEEEECCCCCHHHHHHHHHHEEEEEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCC
T ss_conf             44402688750133311789997421055458998631455220133116778999999999999851887313321357


Q ss_pred             CCCCCCCCCCCCCCCCCCCCHHCCCCCH----HHHHCCCCCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEECCCCCCCH
Q ss_conf             0001123332233321263000121102----221003678835999888888888999999957995586368874004
Q gi|254781160|r  151 TLEFLLKNWDHNCQIVFADETCGSENSL----EKLHAIAHIPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRS  226 (245)
Q Consensus       151 ~l~~~l~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~i~i~IGPEGGfs~~E~~~l~~~~~~~~vsLG~~ILR~  226 (245)
                      +|+++++...+.+.++++++........    .........+++.++||||||||++|+++|.++|| .+++||++|||+
T Consensus        81 ~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~i~IGPEGGfs~~E~~~l~~~gf-~~vsLG~rILR~  159 (191)
T 1vhk_A           81 SFQQLLQRXQDFDKCVVAYEESSKQGEISAFSAIVSSLPKGSSLLIVFGPEGGLTEAEVERLTEQDG-VTCGLGPRILRT  159 (191)
T ss_dssp             CHHHHHHHGGGSSEEEEECC--------CHHHHHHHTCCTTCEEEEEECCTTCCCHHHHHHHHHTTC-EEECCCSSCCCT
T ss_pred             CHHHHHHHCCCCCEEEEEECCCCCCCCHHHHHHHHHHHCCCCEEEEEECCCCCCCHHHHHHHHHCCC-EEEECCCCCCHH
T ss_conf             8999987432443399960222233314678887764247981899983898899999999998899-997789982467


Q ss_pred             HHHHHHHHHHHHHHHCCCC
Q ss_conf             4899999999999847869
Q gi|254781160|r  227 DTAAVAAMALVQAICGDWY  245 (245)
Q Consensus       227 ETA~i~als~~~~~~g~~~  245 (245)
                      |||+|+|+|++++++|||-
T Consensus       160 ETA~i~als~i~~~~~~~~  178 (191)
T 1vhk_A          160 ETAPLYALSAISYQTELLR  178 (191)
T ss_dssp             TTHHHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHHHHHHHHHHC
T ss_conf             7599999999999888756



>1vhy_A (A:78-257) Hypothetical protein HI0303; PSI, protein structure initiative, NEW YORK SGX research center for structural genomics, nysgxrc; HET: MSE; 1.90A {Haemophilus influenzae} Back     alignment and structure
>3kw2_A (A:75-257) 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
>1v6z_A (A:68-228) Hypothetical protein TTHA0657; structural genomics, riken structural genomics/proteomics initiative, RSGI, transferase; 2.00A {Thermus thermophilus HB8} Back     alignment and structure
>2egv_A (A:68-229) UPF0088 protein AQ_165; RSME, methyltransferase, rRNA modification, PUA domain, M3U, SAM, structural genomics, NPPSFA; HET: SAM; 1.45A {Aquifex aeolicus} PDB: 2egw_A* Back     alignment and structure
>1z85_A (A:83-234) Hypothetical protein TM1380; structural genomics, joint center for structural genomics, JCSG, protein structure initiative, PSI; 2.12A {Thermotoga maritima MSB8} Back     alignment and structure
>1ipa_A (A:109-274) RRMH, RNA 2'-O-ribose methyltransferase; DEEP trefoil knot, rossmann fold, EL30-like fold, riken structural genomics/proteomics initiative; 2.40A {Thermus thermophilus} Back     alignment and structure
>1v2x_A (A:21-176) TRNA (GM18) methyltransferase; DEEP trefoil knot, riken structural genomics/proteomics initiative, RSGI, structural genomics; HET: SAM; 1.50A {Thermus thermophilus} Back     alignment and structure
>1vhy_A (A:1-77) Hypothetical protein HI0303; PSI, protein structure initiative, NEW YORK SGX research center for structural genomics, nysgxrc; HET: MSE; 1.90A {Haemophilus influenzae} Back     alignment and structure
>3kw2_A (A:1-74) 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
>1vhk_A (A:1-77) Hypothetical protein YQEU; structural genomics, unknown function; 2.60A {Bacillus subtilis} Back     alignment and structure
>1z85_A (A:1-82) Hypothetical protein TM1380; structural genomics, joint center for structural genomics, JCSG, protein structure initiative, PSI; 2.12A {Thermotoga maritima MSB8} Back     alignment and structure
>2egv_A (A:1-67) UPF0088 protein AQ_165; RSME, methyltransferase, rRNA modification, PUA domain, M3U, SAM, structural genomics, NPPSFA; HET: SAM; 1.45A {Aquifex aeolicus} PDB: 2egw_A* Back     alignment and structure
>1v6z_A (A:1-67) Hypothetical protein TTHA0657; structural genomics, riken structural genomics/proteomics initiative, RSGI, transferase; 2.00A {Thermus thermophilus HB8} Back     alignment and structure
>2qwv_A (A:) UPF0217 protein VC_A1059; unknown function, structural genomics, PSI- 2, protein structure initiative; 2.60A {Vibrio cholerae o1 biovar eltor str} Back     alignment and structure
>2qmm_A (A:) UPF0217 protein AF_1056; alpha/beta knot, SAM, structural genomics, PSI-2, protein structure initiative; HET: SAM; 1.85A {Archaeoglobus fulgidus dsm 4304} Back     alignment and structure