Citrus Sinensis ID: 038639

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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-------23
Protein Sequence
MLAPNKPLYSTDPTSIELLNTQVALYPKCSHNSNRLWPFLFVSSPTITKTQTRTRTHDAKPQFETFDSNNNDYFKPIRGQELELVCESLAYKGKGVCKVADTGFVVLCDRVLPGEKFIGRVTRKKGSYAEMEFSFGPKRWFPKESLPKRGDHIENYALGLHAPGFFDKVLNIDKCLLQSEPANLVLAAVQDYWRDPQLGLSPYDVHSHSGFLKHLMLRTGSFMICAPVM
Secondary Structure (PSIPRED)
ccccccccccccccEEEEEccEEEccccccccccccEEEEEcccccEEEEcccEEcccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHcccEEEcccccccccEEcccccccccccEEEEEEcccccccccccccccccccccEEEEEcccccccEEEccccccccHHHHHHHHHHHHHHHccccccccccccccEEEEEEEEEEEccEEEEEEEc
Secondary Structure Prediction (SSPRO)
ccccccccccccccHHHHHccEEEEcccccccccccccHHHEccccccccccccccccccccccccccccccccccccccEEEEEEEEEcccccEEEEEccccEEEEEcccccccEEEEEEEcccccccEEEEEccccccccHHHHccccccccccccEEcccccccEEEEccccccccccHHHHHHHHHHHHHHcccccccccccccccHHHEEEEEccEEEEEEEcc
Coil and Loop (DISEMBL)
mlapnkplystdptsiELLNTQValypkcshnsnrlwpflfvssptitktqtrtrthdakpqfetfdsnnndyfkpirgQELELVCESLAYkgkgvckvadtGFVVLcdrvlpgekfigrvtrkkgsyaemefsfgpkrwfpkeslpkrgdhienyalglhapgffdkVLNIDkcllqsepANLVLAAVQDywrdpqlglspydvhshsgFLKHLMLRTGSfmicapvm
Flexible Loop (DISEMBL)
mlapnkplystdptSIELLNTQVALYPKCSHNSNRLWPFLfvssptitktqtrtrthdakpqfetfdsnnndyFKPIRGQELELVCESLAYKGKGVCKVADTGFVVLcdrvlpgekfigrvtrkkgsyaemefsfgpkrwfpkeSLPKRGDHIENYALGLHAPGFFDKVLNIDKCLLQSEPANLVLAAVQDYWRDPQLGLSPYDVHSHSGFLKHLMLRTGSFMICAPVM
Low Complexity Region (SEG)
MLAPNKPLYSTDPTSIELLNTQVALYPKCSHNSNRLWPFLFVSSPtitktqtrtrtHDAKPQFETFDSNNNDYFKPIRGQELELVCESLAYKGKGVCKVADTGFVVLCDRVLPGEKFIGRVTRKKGSYAEMEFSFGPKRWFPKESLPKRGDHIENYALGLHAPGFFDKVLNIDKCLLQSEPANLVLAAVQDYWRDPQLGLSPYDVHSHSGFLKHLMLRTGSFMICAPVM
Disordered region (IsUnstruct)
***************IELLNTQVALYPKCSHNSNRLWPFLFVSSPTI***********************NDYFKPIRGQELELVCESLAYKGKGVCKVADTGFVVLCDRVLPGEKFIGRVTRKKGSYAEMEFSFGPKRWFPKESLPKRGDHIENYALGLHAPGFFDKVLNIDKCLLQSEPANLVLAAVQDYWRDPQLGLSPYDVHSHSGFLKHLMLRTGSFMICA***
Disordered Region (DISOPRED)
******P***TDPTSIELLNTQVALYPKCSHNSNRLWPFLFVSSP*************************NDYFKPIRGQELELVCESLAYKGKGVCKVADTGFVVLCDRVLPGEKFIGRVTRKKGSYAEMEFSFGPKRWFPKESL*****HIENYALGLHAPGFFDKVLNIDKCLLQSEPANLVLAAVQDYWRDPQLGLSPYDVHSHSGFLKHLMLRTGSFMICAPVM
Disordered Region (DISEMBL)
MLAPNKPLYSTDPTSIELLNTQVALYPKCSHNSNRLWPFLFVSSPTIT*********DAKPQFETFDSNNNDYFKPIRGQELELVCESLAYKGKGVCKVADTGFVVLCDRVLPGEKFIGRVTRKKGSYAEMEFSFGPKRWFPKESLPKRGDHIENYALGLHAPGFFDKVLNIDKCLLQSEPANLVLAAVQDYWRDPQLGLSPYDVHSHSGFLKHLMLRTGSFMICAPVM
Disordered Region (DISPRO)
*L**NKPLYSTDPTSIELLNTQVALYPKCSHNSNRLWPFLFVSSPTI************************DYFKPIRGQELELVCESLAYKGKGVCKVADTGFVVLCDRVLPGEKFIGRVTRKKGSYAEMEFSFGPKRWFPKESLPKRGDHIENYALGLHAPGFFDKVLNIDKCLLQSEPANLVLAAVQDYWRDPQLGLSPYDVHSHSGFLKHLMLRTGSFMICAPVM
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLAPNKPLYSTDPTSIELLNTQVALYPKCSHNSNRLWPFLFVSSPTITKTQTRTRTHDAKPQFETFDSNNNDYFKPIRGQELELVCESLAYKGKGVCKVADTGFVVLCDRVLPGEKFIGRVTRKKGSYAEMEFSFGPKRWFPKESLPKRGDHIENYALGLHAPGFFDKVLNIDKCLLQSEPANLVLAAVQDYWRDPQLGLSPYDVHSHSGFLKHLMLRTGSFMICAPVM
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	229	2.2.26 [Sep-21-2011]
Q8AA22	454	Uncharacterized RNA methy	yes	no	0.393	0.198	0.358	9e-11
Q8KGF9	483	Uncharacterized RNA methy	yes	no	0.371	0.175	0.380	5e-10
Q7MVG9	465	Uncharacterized RNA methy	yes	no	0.397	0.195	0.354	2e-08
Q97J51	456	Uncharacterized RNA methy	yes	no	0.358	0.179	0.3	0.0002
Q8R933	450	Uncharacterized RNA methy	yes	no	0.388	0.197	0.307	0.0007
Q892Z2	456	Uncharacterized RNA methy	yes	no	0.353	0.177	0.292	0.0007
Q891A0	460	Uncharacterized RNA methy	no	no	0.432	0.215	0.281	0.0008

>sp|Q8AA22|Y643_BACTN Uncharacterized RNA methyltransferase BT_0643 OS=Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) GN=BT_0643 PE=3 SV=1

 Score = 67.4 bits (163), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 33/92 (35%), Positives = 55/92 (59%), Gaps = 2/92 (2%)

Query: 130 EMEFSFGPKRWFPKESLPKRGDHIENYALGLHAPGFFDKVLNIDKCLLQSEPANLVLAAV 189
           ++EF+F  KRW   + + +   + +  A+G H PG FDKVL I+KC LQ + +N +  AV
Sbjct: 115 KLEFTFSNKRWLTNDEVRQDVKYDQMNAVGFHIPGAFDKVLAIEKCWLQDDISNRIRNAV 174

Query: 190 QDYWRDPQLGLSPYDVHSHSGFLKHLMLRTGS 221
           +DY  +     S  ++ +  G L++L++RT S
Sbjct: 175 RDYAYEHD--YSFINLRTQEGMLRNLIIRTSS 204

Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (taxid: 226186)
EC: 2EC: .EC: 1EC: .EC: 1EC: .EC: -

>sp|Q8KGF9|Y009_CHLTE Uncharacterized RNA methyltransferase CT0009 OS=Chlorobium tepidum (strain ATCC 49652 / DSM 12025 / TLS) GN=CT0009 PE=3 SV=1

 Score = 64.7 bits (156), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 35/92 (38%), Positives = 54/92 (58%), Gaps = 7/92 (7%)

Query: 130 EMEFSFGPKRWFPKESLPKRGDHI---ENYALGLHAPGFFDKVLNIDKCLLQSEPANLVL 186
           ++EFS    R+  +  +    D +   + +ALG HAPG F+KVL++D C L  E  N VL
Sbjct: 141 KVEFSCSNMRYLLQSEID--SDQLAKPKTFALGFHAPGNFEKVLDLDTCYLAKECMNRVL 198

Query: 187 AAVQDYWRDPQLGLSPYDVHSHSGFLKHLMLR 218
             ++D+    + GL PY   +H G+L++LMLR
Sbjct: 199 NVLRDFA--IERGLEPYAAKAHEGYLRNLMLR 228

Chlorobium tepidum (strain ATCC 49652 / DSM 12025 / TLS) (taxid: 194439)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: -

>sp|Q7MVG9|Y1095_PORGI Uncharacterized RNA methyltransferase PG_1095 OS=Porphyromonas gingivalis (strain ATCC BAA-308 / W83) GN=PG_1095 PE=3 SV=1

 Score = 59.7 bits (143), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 34/96 (35%), Positives = 56/96 (58%), Gaps = 5/96 (5%)

Query: 130 EMEFSFGPKRWF-PKESLPKRGDHIEN--YALGLHAPGFFDKVLNIDKCLLQSEPANLVL 186
           ++EF+F  KRW  P+E     GD      Y LG H PG FDKVL+I +C L ++ ++ + 
Sbjct: 120 KLEFTFSNKRWLLPEEVQEVDGDFSPEVRYGLGFHIPGMFDKVLDIRECHLGAKVSDEIR 179

Query: 187 AAVQDY-WRDPQLGLSPYDVHSHSGFLKHLMLRTGS 221
             +++Y  +DP+     +D+ +  G ++ LM+RT S
Sbjct: 180 LFIREYCMQDPER-YPFFDLRNQEGLMRTLMIRTTS 214

Porphyromonas gingivalis (strain ATCC BAA-308 / W83) (taxid: 242619)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: -

>sp|Q97J51|Y1435_CLOAB Uncharacterized RNA methyltransferase CA_C1435 OS=Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787) GN=CA_C1435 PE=3 SV=1

 Score = 45.8 bits (107), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 30/100 (30%), Positives = 49/100 (49%), Gaps = 18/100 (18%)

Query: 130 EMEFSFGPKRWFPKESLPKRGDHIENYALGLHAPGFFDKVLNIDKCLLQSEPANLVLAAV 189
           +ME++FG           K G+      LG+HA      ++N DKC +  E   ++L  V
Sbjct: 130 KMEYTFG--------DFVKGGE----LTLGMHAKNSGFSIVNTDKCNIVDEDFRIILKTV 177

Query: 190 QDYWRDPQLGLSPYDVHSHSGFLKHLMLR----TGSFMIC 225
            +Y+R   L +  Y V  H G+L++L++R    TG  +I 
Sbjct: 178 VEYFRKKDLPI--YKVMQHVGYLRNLVVRKAKNTGEILIA 215

Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787) (taxid: 272562)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: -

>sp|Q8R933|Y1797_THETN Uncharacterized RNA methyltransferase TTE1797 OS=Thermoanaerobacter tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4) GN=TTE1797 PE=3 SV=1

 Score = 44.3 bits (103), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 32/104 (30%), Positives = 47/104 (45%), Gaps = 15/104 (14%)

Query: 118 IGRVTRKKGSYAEMEFSFGPKRWFPKESLPKRGDHIENYALGLHAPGFFDKVLNIDKCLL 177
           I R  +  G   +ME++FG  R   K             ALGLH  G F  V+  DKC +
Sbjct: 115 IERSPKVYGYRNKMEYTFGTDREGKK-------------ALGLHRKGKFYDVVMTDKCNI 161

Query: 178 QSEPANLVLAAVQDYWRDPQLGLSPYDVHSHSGFLKHLMLRTGS 221
             E     L+   +Y  +  L    YD  +H G+L++L++R  S
Sbjct: 162 VDEDFTKALSLTFNYALEKNLPF--YDKKTHEGYLRYLVVRKAS 203

Thermoanaerobacter tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4) (taxid: 273068)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: -

>sp|Q892Z2|Y1941_CLOTE Uncharacterized RNA methyltransferase CTC_01941 OS=Clostridium tetani (strain Massachusetts / E88) GN=CTC_01941 PE=3 SV=1

 Score = 44.3 bits (103), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 29/99 (29%), Positives = 51/99 (51%), Gaps = 18/99 (18%)

Query: 130 EMEFSFGPKRWFPKESLPKRGDHIENYALGLHAPGFFDKVLNIDKCLLQSEPANLVLAAV 189
           +MEF+FG         L K G+      LG+HA G    +++ D+C +  E    +L A 
Sbjct: 129 KMEFTFG--------DLKKGGE----LNLGMHAKGMSFGIISADECKIVDEDYRNILNAT 176

Query: 190 QDYWRDPQLGLSPYDVHSHSGFLKHLMLR----TGSFMI 224
            +Y+R+ Q  L  Y + +  G+L++L++R    TG  ++
Sbjct: 177 LNYFREKQ--LPHYRIMAREGYLRNLVIRKAENTGEVLV 213

Clostridium tetani (strain Massachusetts / E88) (taxid: 212717)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: -

>sp|Q891A0|Y2481_CLOTE Uncharacterized RNA methyltransferase CTC_02481 OS=Clostridium tetani (strain Massachusetts / E88) GN=CTC_02481 PE=3 SV=1

 Score = 44.3 bits (103), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 31/110 (28%), Positives = 53/110 (48%), Gaps = 11/110 (10%)

Query: 123 RKKGSYAEMEFSFG---PKRWFPKESLPKRGDHIENYALGLHAPGFFDKVLNIDKCLLQS 179
           R  G   E+E   G   P R+  K  LP  G       +G +AP   + ++++  C +Q 
Sbjct: 110 RLGGIDVEVEEVLGMENPYRYRNKVQLP-IGKEKGKVNIGFYAPRSHN-IIDLKSCFIQD 167

Query: 180 EPANLVLAAVQDYWRDPQLGLSPYDVHSHSGFLKHLML----RTGSFMIC 225
           E A+ ++  ++++    +  +S YD   H G L+H+M+    RTG  MI 
Sbjct: 168 EKADKIIKILKEWIE--KFNVSIYDEKEHKGNLRHIMVRTAFRTGQIMIV 215

Clostridium tetani (strain Massachusetts / E88) (taxid: 212717)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: -

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	229
356547359	533	PREDICTED: uncharacterized RNA methyltra	0.397	0.170	0.776	4e-36
19310570	564	unknown protein [Arabidopsis thaliana]	0.366	0.148	0.780	1e-35
42565079	554	RNA methyltransferase family protein [Ar	0.366	0.151	0.780	1e-35
356557321	535	PREDICTED: LOW QUALITY PROTEIN: uncharac	0.397	0.170	0.760	7e-35
255549690	577	RNA m5u methyltransferase, putative [Ric	0.397	0.157	0.758	1e-34
297835104	559	RNA methyltransferase family protein [Ar	0.397	0.162	0.758	3e-34
147797617	1255	hypothetical protein VITISV_023490 [Viti	0.388	0.070	0.714	7e-34
449447830	562	PREDICTED: uncharacterized RNA methyltra	0.358	0.145	0.758	1e-33
225442369	570	PREDICTED: uncharacterized RNA methyltra	0.388	0.156	0.714	3e-33
357454725	560	23S rRNA (uracil-5-)-methyltransferase r	0.397	0.162	0.698	3e-33

>gi|356547359|ref|XP_003542081.1| PREDICTED: uncharacterized RNA methyltransferase CT0009-like [Glycine max]

 Score =  157 bits (397), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 73/94 (77%), Positives = 79/94 (84%), Gaps = 3/94 (3%)

Query: 130 EMEFSFGPKRWFPKESLPKR---GDHIENYALGLHAPGFFDKVLNIDKCLLQSEPANLVL 186
           +MEFSFGP+RW PKESL  R    D  ENYALGLHAPGFFDK+LN+D CLLQS PAN VL
Sbjct: 178 KMEFSFGPQRWLPKESLQDRIVDDDTNENYALGLHAPGFFDKILNVDNCLLQSHPANKVL 237

Query: 187 AAVQDYWRDPQLGLSPYDVHSHSGFLKHLMLRTG 220
           AAVQ+ WRDPQLG SPY+VHSH GFLKHLMLRTG
Sbjct: 238 AAVQECWRDPQLGFSPYNVHSHKGFLKHLMLRTG 271

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|19310570|gb|AAL85018.1| unknown protein [Arabidopsis thaliana]

 Score =  155 bits (392), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 71/91 (78%), Positives = 78/91 (85%)

Query: 130 EMEFSFGPKRWFPKESLPKRGDHIENYALGLHAPGFFDKVLNIDKCLLQSEPANLVLAAV 189
           +MEFSFGP+RW P E L +R D  +N+ALGLHAPGFFDKVLN+DKCLLQSEP NLVLAAV
Sbjct: 212 KMEFSFGPQRWLPIEMLNERQDGPKNFALGLHAPGFFDKVLNVDKCLLQSEPGNLVLAAV 271

Query: 190 QDYWRDPQLGLSPYDVHSHSGFLKHLMLRTG 220
           QD WRDP+L LSPYD  SH GFLKHLMLRTG
Sbjct: 272 QDCWRDPELSLSPYDCRSHVGFLKHLMLRTG 302

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|42565079|ref|NP_188767.2| RNA methyltransferase family protein [Arabidopsis thaliana] gi|9280234|dbj|BAB01724.1| RNA methyltransferase-like protein [Arabidopsis thaliana] gi|332642969|gb|AEE76490.1| RNA methyltransferase family protein [Arabidopsis thaliana]

 Score =  155 bits (392), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 71/91 (78%), Positives = 78/91 (85%)

Query: 130 EMEFSFGPKRWFPKESLPKRGDHIENYALGLHAPGFFDKVLNIDKCLLQSEPANLVLAAV 189
           +MEFSFGP+RW P E L +R D  +N+ALGLHAPGFFDKVLN+DKCLLQSEP NLVLAAV
Sbjct: 202 KMEFSFGPQRWLPIEMLNERQDGPKNFALGLHAPGFFDKVLNVDKCLLQSEPGNLVLAAV 261

Query: 190 QDYWRDPQLGLSPYDVHSHSGFLKHLMLRTG 220
           QD WRDP+L LSPYD  SH GFLKHLMLRTG
Sbjct: 262 QDCWRDPELSLSPYDCRSHVGFLKHLMLRTG 292

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356557321|ref|XP_003546965.1| PREDICTED: LOW QUALITY PROTEIN: uncharacterized RNA methyltransferase CT0009-like [Glycine max]

 Score =  153 bits (386), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 73/96 (76%), Positives = 78/96 (81%), Gaps = 5/96 (5%)

Query: 130 EMEFSFGPKRWFPKESLPKR--GDHI---ENYALGLHAPGFFDKVLNIDKCLLQSEPANL 184
           EMEFSFGP+RW PKE L  R   D +   ENYALGLHAPGFFDK+LN+D CLLQS PAN 
Sbjct: 183 EMEFSFGPRRWLPKELLQDRRADDDVGNNENYALGLHAPGFFDKILNVDNCLLQSHPANK 242

Query: 185 VLAAVQDYWRDPQLGLSPYDVHSHSGFLKHLMLRTG 220
           VLAAVQ+ WRDPQLG SPY VHSH GFLKHLMLRTG
Sbjct: 243 VLAAVQECWRDPQLGFSPYSVHSHKGFLKHLMLRTG 278

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255549690|ref|XP_002515896.1| RNA m5u methyltransferase, putative [Ricinus communis] gi|223544801|gb|EEF46316.1| RNA m5u methyltransferase, putative [Ricinus communis]

 Score =  152 bits (384), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 69/91 (75%), Positives = 76/91 (83%)

Query: 130 EMEFSFGPKRWFPKESLPKRGDHIENYALGLHAPGFFDKVLNIDKCLLQSEPANLVLAAV 189
           +MEFSFG K+W P+E L ++ D   NYALGLHAPG FDKVLN+DKCLLQSEPAN VLA V
Sbjct: 225 KMEFSFGSKKWLPRELLGEKQDGSVNYALGLHAPGCFDKVLNVDKCLLQSEPANTVLATV 284

Query: 190 QDYWRDPQLGLSPYDVHSHSGFLKHLMLRTG 220
           QD WRD Q GL+PYDVHSH GFLKHLMLRTG
Sbjct: 285 QDCWRDSQFGLTPYDVHSHDGFLKHLMLRTG 315

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297835104|ref|XP_002885434.1| RNA methyltransferase family protein [Arabidopsis lyrata subsp. lyrata] gi|297331274|gb|EFH61693.1| RNA methyltransferase family protein [Arabidopsis lyrata subsp. lyrata]

 Score =  150 bits (380), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 69/91 (75%), Positives = 77/91 (84%)

Query: 130 EMEFSFGPKRWFPKESLPKRGDHIENYALGLHAPGFFDKVLNIDKCLLQSEPANLVLAAV 189
           +MEFSFGP+RW P E L ++ D  +N+ALGLHAPGFFDKVLN+DKCLLQSEP NLVLAAV
Sbjct: 200 KMEFSFGPQRWLPIEMLHEKEDGPKNFALGLHAPGFFDKVLNVDKCLLQSEPGNLVLAAV 259

Query: 190 QDYWRDPQLGLSPYDVHSHSGFLKHLMLRTG 220
           QD WRDP L LSPY+  SH GFLKHLMLRTG
Sbjct: 260 QDCWRDPALSLSPYNCRSHVGFLKHLMLRTG 290

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147797617|emb|CAN65004.1| hypothetical protein VITISV_023490 [Vitis vinifera]

 Score =  149 bits (377), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 65/91 (71%), Positives = 78/91 (85%)

Query: 130 EMEFSFGPKRWFPKESLPKRGDHIENYALGLHAPGFFDKVLNIDKCLLQSEPANLVLAAV 189
           +MEFSF  ++W P+E L ++ D    YALGLHAPGFFDKVLN++KCLLQSEPAN+VLAA+
Sbjct: 190 KMEFSFATQKWLPRELLHEKEDGASGYALGLHAPGFFDKVLNVNKCLLQSEPANMVLAAI 249

Query: 190 QDYWRDPQLGLSPYDVHSHSGFLKHLMLRTG 220
           Q+ WRDPQ GLSPY+VHSH GFLKHL+LRTG
Sbjct: 250 QECWRDPQFGLSPYNVHSHDGFLKHLVLRTG 280

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449447830|ref|XP_004141670.1| PREDICTED: uncharacterized RNA methyltransferase BT_0643-like [Cucumis sativus] gi|449480609|ref|XP_004155944.1| PREDICTED: uncharacterized RNA methyltransferase BT_0643-like [Cucumis sativus]

 Score =  149 bits (375), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 69/91 (75%), Positives = 78/91 (85%)

Query: 130 EMEFSFGPKRWFPKESLPKRGDHIENYALGLHAPGFFDKVLNIDKCLLQSEPANLVLAAV 189
           +MEFSFG KRW PK++L ++ +  E  ALGLHAPGFFDKVLN+DKCLLQS PAN VLA+V
Sbjct: 203 KMEFSFGSKRWVPKDALKEKQEGDEINALGLHAPGFFDKVLNVDKCLLQSGPANQVLASV 262

Query: 190 QDYWRDPQLGLSPYDVHSHSGFLKHLMLRTG 220
           Q+ WRDP LGLSPYDVHSH GFLKHLMLRTG
Sbjct: 263 QECWRDPLLGLSPYDVHSHKGFLKHLMLRTG 293

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225442369|ref|XP_002276511.1| PREDICTED: uncharacterized RNA methyltransferase CT0009 [Vitis vinifera] gi|297743126|emb|CBI35993.3| unnamed protein product [Vitis vinifera]

 Score =  147 bits (371), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 65/91 (71%), Positives = 77/91 (84%)

Query: 130 EMEFSFGPKRWFPKESLPKRGDHIENYALGLHAPGFFDKVLNIDKCLLQSEPANLVLAAV 189
           +MEFSF  ++W P+E L ++ D    YALGLHAPGFFDKVLN++KCLLQSEPAN VLAA+
Sbjct: 218 KMEFSFATQKWLPRELLHEKEDGASGYALGLHAPGFFDKVLNVNKCLLQSEPANTVLAAI 277

Query: 190 QDYWRDPQLGLSPYDVHSHSGFLKHLMLRTG 220
           Q+ WRDPQ GLSPY+VHSH GFLKHL+LRTG
Sbjct: 278 QECWRDPQFGLSPYNVHSHDGFLKHLVLRTG 308

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357454725|ref|XP_003597643.1| 23S rRNA (uracil-5-)-methyltransferase rumA [Medicago truncatula] gi|355486691|gb|AES67894.1| 23S rRNA (uracil-5-)-methyltransferase rumA [Medicago truncatula]

 Score =  147 bits (371), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 65/93 (69%), Positives = 79/93 (84%), Gaps = 2/93 (2%)

Query: 130 EMEFSFGPKRWFPKESLPKRGDHI--ENYALGLHAPGFFDKVLNIDKCLLQSEPANLVLA 187
           +MEFSFGP +W PKESL +R      ENY+LGLH PGFFDK++N++KCLLQ++PAN VLA
Sbjct: 206 KMEFSFGPYKWLPKESLHERNVDAGSENYSLGLHVPGFFDKIINVEKCLLQTDPANKVLA 265

Query: 188 AVQDYWRDPQLGLSPYDVHSHSGFLKHLMLRTG 220
           A+Q+ WRDPQLG SPY+VHSH GFLKHLMLR+G
Sbjct: 266 AIQECWRDPQLGFSPYNVHSHKGFLKHLMLRSG 298

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	229
TAIR|locus:2094776	554	AT3G21300 [Arabidopsis thalian	0.397	0.164	0.780	5e-58
UNIPROTKB|O31503	459	rlmCD "23S rRNA (uracil-C(5))-	0.275	0.137	0.310	0.00016

TAIR|locus:2094776 AT3G21300 [Arabidopsis thaliana (taxid:3702)]

 Score = 383 (139.9 bits), Expect = 5.0e-58, Sum P(2) = 5.0e-58
 Identities = 71/91 (78%), Positives = 78/91 (85%)

Query:   130 EMEFSFGPKRWFPKESLPKRGDHIENYALGLHAPGFFDKVLNIDKCLLQSEPANLVLAAV 189
             +MEFSFGP+RW P E L +R D  +N+ALGLHAPGFFDKVLN+DKCLLQSEP NLVLAAV
Sbjct:   202 KMEFSFGPQRWLPIEMLNERQDGPKNFALGLHAPGFFDKVLNVDKCLLQSEPGNLVLAAV 261

Query:   190 QDYWRDPQLGLSPYDVHSHSGFLKHLMLRTG 220
             QD WRDP+L LSPYD  SH GFLKHLMLRTG
Sbjct:   262 QDCWRDPELSLSPYDCRSHVGFLKHLMLRTG 292

GO:0003723 "RNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0006396 "RNA processing" evidence=IEA

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

UNIPROTKB|O31503 rlmCD "23S rRNA (uracil-C(5))-methyltransferase RlmCD" [Bacillus subtilis subsp. subtilis str. 168 (taxid:224308)]

 Score = 82 (33.9 bits), Expect = 0.00016, Sum P(2) = 0.00016
 Identities = 23/74 (31%), Positives = 40/74 (54%)

Query:   159 GLHAPGFFDK----VLNIDKCLLQSEPANLVLAAVQDYWRDPQLGLSPYDVHSHSGFLKH 214
             GL A GF+ +    ++++  CL+Q    +  + AV+D   +   G+  Y+   H G+L+H
Sbjct:   147 GLVA-GFYQQRSHDIIDMSACLIQQSKNDEAVQAVKDICAN--YGVKAYNEERHKGWLRH 203

Query:   215 LMLR----TGSFMI 224
             +M+R    TG  MI
Sbjct:   204 IMVRYGVVTGEMMI 217

GO:0031167 "rRNA methylation" evidence=IDA

GO:0070041 "rRNA (uridine-C5-)-methyltransferase activity" evidence=IDA

---

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

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

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	229
COG2265	432	COG2265, TrmA, SAM-dependent methyltransferases re	1e-07
PRK13168	443	PRK13168, rumA, 23S rRNA m(5)U1939 methyltransfera	0.002

>gnl|CDD|225174 COG2265, TrmA, SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]

 Score = 50.8 bits (122), Expect = 1e-07
 Identities = 18/65 (27%), Positives = 36/65 (55%), Gaps = 6/65 (9%)

Query: 164 GFFDK----VLNIDKCLLQSEPANLVLAAVQDYWRDPQLGLSPYDVHSHSGFLKHLMLRT 219
           GFF +    +++ID+C +    +N +L  +++     +LGL PY+     G L+ ++LR 
Sbjct: 141 GFFRQGSHEIVDIDECPVFPPRSNEILPLLRELLA--KLGLPPYNEKKKKGILRLIVLRE 198

Query: 220 GSFMI 224
           G  ++
Sbjct: 199 GQEVM 203

Length = 432

>gnl|CDD|237291 PRK13168, rumA, 23S rRNA m(5)U1939 methyltransferase; Reviewed

 Score = 38.6 bits (91), Expect = 0.002
 Identities = 20/61 (32%), Positives = 29/61 (47%), Gaps = 6/61 (9%)

Query: 74  FKPIRG----QELELVCESLAYKGKGVCKVADTGFVVLCDRVLPGEKFIGRVTRKKGSYA 129
           + P R     Q + +  ESL + G+GV +    G  V  +  LPGE+   +VT  K  YA
Sbjct: 4   YSPKRRVTTRQIITVTIESLDHDGRGVARHN--GKTVFIEGALPGERVEVQVTEDKKQYA 61

Query: 130 E 130
            
Sbjct: 62  R 62

Length = 443

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	229
COG2265	432	TrmA SAM-dependent methyltransferases related to t	99.92
PRK13168	443	rumA 23S rRNA m(5)U1939 methyltransferase; Reviewe	99.91
TIGR00479	431	rumA 23S rRNA (uracil-5-)-methyltransferase RumA.	99.9
TIGR02085	374	meth_trns_rumB 23S rRNA (uracil-5-)-methyltransfer	99.18
COG3269	73	Predicted RNA-binding protein, contains TRAM domai	99.13
PRK12336	201	translation initiation factor IF-2 subunit beta; P	98.81
PRK03522	315	rumB 23S rRNA methyluridine methyltransferase; Rev	98.73
PF01938	61	TRAM: TRAM domain; InterPro: IPR002792 The TRAM (a	98.68
PRK05031	362	tRNA (uracil-5-)-methyltransferase; Validated	98.6
TIGR02143	353	trmA_only tRNA (uracil-5-)-methyltransferase. This	98.23
PF05958	352	tRNA_U5-meth_tr: tRNA (Uracil-5-)-methyltransferas	98.12
KOG2187	534	consensus tRNA uracil-5-methyltransferase and rela	97.59
PF08206	58	OB_RNB: Ribonuclease B OB domain; InterPro: IPR013	94.3

>COG2265 TrmA SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]

Probab=99.92  E-value=3.4e-25  Score=209.62  Aligned_cols=137  Identities=31%  Similarity=0.542  Sum_probs=124.4

Q ss_pred             cEEEEEEeeeCCCCcEEEEEcCCCcEEEecCCCCCcEEEEEEEeecCCeee-----------------------------
Q 038639           80 QELELVCESLAYKGKGVCKVADTGFVVLCDRVLPGEKFIGRVTRKKGSYAE-----------------------------  130 (229)
Q Consensus        80 ~~i~l~I~~l~~~G~GVar~~~~G~vVFVpgaLPGE~V~vrI~k~kk~y~~-----------------------------  130 (229)
                      +.++++|++|+++|.|||+++  |++|||||+||||+|++++++.+++|++                             
T Consensus         3 ~~~~~~I~~l~~~G~Gva~~~--~~~vfVp~alPge~v~~~~~~~~~~~~~a~~~~i~~~Sp~R~~~~c~~~g~cggC~l   80 (432)
T COG2265           3 QIIEVTIEDLGHNGEGVARHD--GKVVFVPGALPGEEVEVRVTKVKKKYAEAKLVKVLEASPDRVDPPCPHFGRCGGCQL   80 (432)
T ss_pred             ceEEEEEEEcCCCCeeEEEec--CceEEeCCCCCCcEEEEEEEeccccceeeEeeeeccCChhhcCCCCccccccccccc
Confidence            678999999999999999997  8899999999999999999999999998                             


Q ss_pred             eeecccccccchhhccCcc----C----------------------------CCCCceeEEEeccCCCCceEeCCCCcCC
Q 038639          131 MEFSFGPKRWFPKESLPKR----G----------------------------DHIENYALGLHAPGFFDKVLNIDKCLLQ  178 (229)
Q Consensus       131 qhlsY~~QL~~K~~~l~~~----~----------------------------~~~g~~~lGf~~rgS~~~IVdie~CpL~  178 (229)
                      ||++|+.||++|++.|.+.    +                            ..++.+.+||++++|| +||++++|+++
T Consensus        81 qhl~y~~QL~~K~~~l~~~l~~~~~~~~~~~~~~~~~~~~~yR~ka~~~v~~~~~~~l~~Gf~~~~s~-~iv~i~~C~v~  159 (432)
T COG2265          81 QHLSYEAQLEFKREQLKELLKRIGGSEVEIDPTVGMSPPWGYRNRARFSVRGSGKGQLLAGFFRQGSH-EIVDIDECPVF  159 (432)
T ss_pred             cCCCHHHHHHHHHHHHHHHHHHhcCCCcccccccCCCCCcCceeEEEEEEEEcCCCcEEEEeeccCCC-ceecccccCcc
Confidence            8999999999998665431    0                            0123577899999997 89999999999


Q ss_pred             ChhHHHHHHHHHHHHhcCCCCCCCCcCCCCccceeEEEEEeec
Q 038639          179 SEPANLVLAAVQDYWRDPQLGLSPYDVHSHSGFLKHLMLRTGS  221 (229)
Q Consensus       179 ~~~in~il~~lr~~l~~~~~~l~~Yd~~~~~G~LRhLvVR~s~  221 (229)
                      ++.++.++..++++++.  ..+++||+..+.|.|+++++|.|.
T Consensus       160 ~~~~~~il~~l~~~l~~--~~~~~y~~~~~~g~l~~~~~~~g~  200 (432)
T COG2265         160 PPRSNEILPLLRELLAK--LGLPPYNEKKKKGILRLIVLREGQ  200 (432)
T ss_pred             CHhHHHHHHHHHHHHHH--cCCCccchhhccceEEEEEeccCc
Confidence            99999999999999997  899999999999999999999986

>PRK13168 rumA 23S rRNA m(5)U1939 methyltransferase; Reviewed

Probab=99.91  E-value=4.9e-24  Score=201.54  Aligned_cols=125  Identities=22%  Similarity=0.340  Sum_probs=109.4

Q ss_pred             ccccCCCCCCCCCCCcEEEEEEeeeCCCCcEEEEEcCCCcEEEecCCCCCcEEEEEEEeecCCeee--------------
Q 038639           65 TFDSNNNDYFKPIRGQELELVCESLAYKGKGVCKVADTGFVVLCDRVLPGEKFIGRVTRKKGSYAE--------------  130 (229)
Q Consensus        65 ~~~~~~~~~~~~k~~~~i~l~I~~l~~~G~GVar~~~~G~vVFVpgaLPGE~V~vrI~k~kk~y~~--------------  130 (229)
                      +|+||+++.   ..-++++++|++++++|+|||+.+  |++|||||++|||+|+++|++.+++|++              
T Consensus         2 ~~~~~~~~~---~~~~~~~l~i~~l~~~G~Gv~~~~--~~~vfV~~~lPGe~v~v~i~~~~~~~~~~~~~~vl~~sp~Rv   76 (443)
T PRK13168          2 QFYSPKRRV---TTRQIITVTIESLDHDGRGVARHN--GKTVFIEGALPGERVEVQVTEDKKQYARAKVVRILKPSPERV   76 (443)
T ss_pred             CccCCCCCC---CCCcEEEEEEEEcCCCCceEEEEC--CEEEEeCCCCCCCEEEEEEEEecCcEEEEEEEEEecCCcccC
Confidence            789999887   466788999999999999999996  8999999999999999999999998887              


Q ss_pred             ---------------eeecccccccchhhccCcc----C---------------------------C--CCCceeEEEec
Q 038639          131 ---------------MEFSFGPKRWFPKESLPKR----G---------------------------D--HIENYALGLHA  162 (229)
Q Consensus       131 ---------------qhlsY~~QL~~K~~~l~~~----~---------------------------~--~~g~~~lGf~~  162 (229)
                                     ||++|+.||++|++.+++.    +                           .  .++...+|||+
T Consensus        77 ~p~C~~~~~CGGC~~qh~~y~~Ql~~K~~~v~~~l~r~~~~~~~~~~~~i~~~~~~YRnk~~~~~~~~~~~g~~~~G~~~  156 (443)
T PRK13168         77 TPRCPHFGVCGGCQLQHLSIDAQIASKQRALEDLLKHLAGVEPEEVLPPIAGPPWGYRRRARLSVRYVPKKGQLLVGFRE  156 (443)
T ss_pred             CCCCCcCCcCcCchhcCCCHHHHHHHHHHHHHHHHHHhcCCCcccccCCCcCCCCCCCceEEEEeeeecCCCCEEEEEec
Confidence                           9999999999998775431    0                           0  02335699999


Q ss_pred             cCCCCceEeCCCCcCCChhHHHHHHHHHHHHhc
Q 038639          163 PGFFDKVLNIDKCLLQSEPANLVLAAVQDYWRD  195 (229)
Q Consensus       163 rgS~~~IVdie~CpL~~~~in~il~~lr~~l~~  195 (229)
                      ++|| ++|++++|+|++|.+++++..+++++..
T Consensus       157 ~~s~-~vv~i~~C~l~~~~~~~~~~~~~~~~~~  188 (443)
T PRK13168        157 KNSS-DIVDIDQCPVLVPPLSALLPPLRALLSS  188 (443)
T ss_pred             CCCc-eeEECCCCccCCHhHHHHHHHHHHHHHH
Confidence            9997 8999999999999999999999999874

>TIGR00479 rumA 23S rRNA (uracil-5-)-methyltransferase RumA

Probab=99.90  E-value=6.8e-24  Score=199.36  Aligned_cols=128  Identities=30%  Similarity=0.433  Sum_probs=112.7

Q ss_pred             eCCCCcEEEEEcCCCcEEEecCCCCCcEEEEEEEeecCCeee-----------------------------eeecccccc
Q 038639           89 LAYKGKGVCKVADTGFVVLCDRVLPGEKFIGRVTRKKGSYAE-----------------------------MEFSFGPKR  139 (229)
Q Consensus        89 l~~~G~GVar~~~~G~vVFVpgaLPGE~V~vrI~k~kk~y~~-----------------------------qhlsY~~QL  139 (229)
                      ++++|+|||+.+  |+++||||+||||+|+++|++.+++|++                             ||++|++|+
T Consensus         1 l~~~G~Gv~~~~--~~~vfV~~~lpGe~v~~~i~~~~~~~~~~~~~~i~~~S~~Rv~p~C~~~~~CGGC~~qh~~y~~Ql   78 (431)
T TIGR00479         1 LDHQGEGVARFN--GKVVFVPNALPGEKVEVRVTKVKRQYALARVKKIREPSPERTRPPCPVFDQCGGCQLQHLDYEFQL   78 (431)
T ss_pred             CCCCCcEEEEEC--CEEEEeCCCCCCCEEEEEEEEecCceeEEEeeeecCCCcCcCCCCCCCCCCCCCCcccCCCHHHHH
Confidence            578999999986  8999999999999999999999998877                             999999999


Q ss_pred             cchhhccCcc----C---------------C-----------C----CCceeEEEeccCCCCceEeCCCCcCCChhHHHH
Q 038639          140 WFPKESLPKR----G---------------D-----------H----IENYALGLHAPGFFDKVLNIDKCLLQSEPANLV  185 (229)
Q Consensus       140 ~~K~~~l~~~----~---------------~-----------~----~g~~~lGf~~rgS~~~IVdie~CpL~~~~in~i  185 (229)
                      ++|+++|.++    +               .           .    +++..+||++++|| ++|++++|+|++|.++++
T Consensus        79 ~~K~~~v~~~l~r~~~~~~~~~~~~~~~~~~~~~YRnr~~~~v~~~~~g~~~~G~~~~~s~-~vv~i~~C~i~~~~i~~~  157 (431)
T TIGR00479        79 RSKQQQVIALLERIGKFTSEPIEPLPTIGGDPWGYRNKARLSLGRSPSGQIQAGFYQKGSH-DIVPIKQCPVQDPALNLL  157 (431)
T ss_pred             HHHHHHHHHHHHHhcCCCcCCceecCCcCCCCCcccceeEEEeeecCCCCEEEeeecCCCc-ceEcCCCCCCCCHHHHHH
Confidence            9997664331    0               0           0    23356899999998 899999999999999999


Q ss_pred             HHHHHHHHhcCCCCCCCCcCCCCccceeEEEEEeec
Q 038639          186 LAAVQDYWRDPQLGLSPYDVHSHSGFLKHLMLRTGS  221 (229)
Q Consensus       186 l~~lr~~l~~~~~~l~~Yd~~~~~G~LRhLvVR~s~  221 (229)
                      +..+++++.+  .++++|+..+++|+||+++||.+.
T Consensus       158 ~~~~~~~~~~--~~~~~~~~~~~~g~lr~i~ir~~~  191 (431)
T TIGR00479       158 LPKVKAILEN--FGASIYLEHKELGKARHGVLRIGR  191 (431)
T ss_pred             HHHHHHHHHH--cCCCccccccCcccceEEEEEEec
Confidence            9999999996  899999999999999999999863

This protein family was first proposed to be RNA methyltransferases by homology to the TrmA family. The member from E. coli has now been shown to act as the 23S RNA methyltransferase for the conserved U1939. The gene is now designated rumA and was previously designated ygcA.

>TIGR02085 meth_trns_rumB 23S rRNA (uracil-5-)-methyltransferase RumB

Probab=99.18  E-value=2.7e-11  Score=112.82  Aligned_cols=86  Identities=21%  Similarity=0.352  Sum_probs=72.5

Q ss_pred             eeecccccccchhhccCcc---C------------C--------------CCCceeEEEeccCCCCceEeCCCCcCCChh
Q 038639          131 MEFSFGPKRWFPKESLPKR---G------------D--------------HIENYALGLHAPGFFDKVLNIDKCLLQSEP  181 (229)
Q Consensus       131 qhlsY~~QL~~K~~~l~~~---~------------~--------------~~g~~~lGf~~rgS~~~IVdie~CpL~~~~  181 (229)
                      ||++|++|+++|+++|++.   +            .              .+++..+||+.++ + .+|++++|+|++|.
T Consensus        16 qhl~y~~Ql~~K~~~v~~~l~r~~~~~~~~~~i~~~~~~YRnr~~l~v~~~~~~~~~G~~~~~-~-~~v~i~~C~i~~~~   93 (374)
T TIGR02085        16 LAQPYSEQLTNKQQHLKELLAPNATVVQWLAPVTSAEQAFRNKAKMVVSGSVERPILGILHRD-G-TPLDLCDCPLYPQS   93 (374)
T ss_pred             cCCCHHHHHHHHHHHHHHHHhhcCCCccccCCcCCCCccccceEEEEEEEcCCcEEEeEecCC-C-cEEcCccCCCCCHh
Confidence            9999999999997764331   0            0              0233568987766 5 69999999999999


Q ss_pred             HHHHHHHHHHHHhcCCCCCCCCcCCCCccceeEEEEEee
Q 038639          182 ANLVLAAVQDYWRDPQLGLSPYDVHSHSGFLKHLMLRTG  220 (229)
Q Consensus       182 in~il~~lr~~l~~~~~~l~~Yd~~~~~G~LRhLvVR~s  220 (229)
                      ++.++..+++++..  .+++.||+.+++|+|||++||.+
T Consensus        94 ~~~~~~~~~~~~~~--~~~~~~~~~~~~g~lr~i~ir~~  130 (374)
T TIGR02085        94 FQPVFAYLKNFIAR--AGLTPYNVAKKKGELKFILLTES  130 (374)
T ss_pred             HHHHHHHHHHHHHH--cCCCCccccCCCccceEEEEEEe
Confidence            99999999999986  89999999999999999999976

This family consists of RNA methyltransferases designated RumB, formerly YbjF. Members act on 23S rRNA U747 and the equivalent position in other proteobacterial species. This family is homologous to the other 23S rRNA methyltransferase RumA and to the tRNA methyltransferase TrmA.

>COG3269 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]

Probab=99.13  E-value=3e-10  Score=82.99  Aligned_cols=57  Identities=25%  Similarity=0.383  Sum_probs=53.3

Q ss_pred             CCCCCCCCcEEEEEEeeeCCCCcEEEEEcCCCcEEEecCCCCCcEEEEEEEeecCCeee
Q 038639           72 DYFKPIRGQELELVCESLAYKGKGVCKVADTGFVVLCDRVLPGEKFIGRVTRKKGSYAE  130 (229)
Q Consensus        72 ~~~~~k~~~~i~l~I~~l~~~G~GVar~~~~G~vVFVpgaLPGE~V~vrI~k~kk~y~~  130 (229)
                      ....+..|+..+++|++++..|.|+|+.+  |.+||||++-+||+|.++|.+.+.+|++
T Consensus         9 ~~~PVeeGe~y~V~I~d~g~~GDGiarve--GfvVFVp~a~~Gd~V~vkI~~v~~~~af   65 (73)
T COG3269           9 RTPPVEEGETYEVEIEDVGDQGDGIARVE--GFVVFVPGAEVGDEVKVKITKVKPNFAF   65 (73)
T ss_pred             CCCCcccCCEEEEEEEEeccCCCceEEEE--EEEEEeCCCCCCCeeeEEEEEeecccee
Confidence            44566889999999999999999999998  9999999999999999999999999986

>PRK12336 translation initiation factor IF-2 subunit beta; Provisional

Probab=98.81  E-value=2e-08  Score=86.69  Aligned_cols=55  Identities=20%  Similarity=0.258  Sum_probs=49.4

Q ss_pred             CCCCCCcEEEEEEeeeCCCCcEEEEEcCCCcEEEecCCCCCcEEEEEEEeecCCeee
Q 038639           74 FKPIRGQELELVCESLAYKGKGVCKVADTGFVVLCDRVLPGEKFIGRVTRKKGSYAE  130 (229)
Q Consensus        74 ~~~k~~~~i~l~I~~l~~~G~GVar~~~~G~vVFVpgaLPGE~V~vrI~k~kk~y~~  130 (229)
                      ..++.++.++++|++++++|.|+++.+  |+++||+|++|||+|++++++.+++|++
T Consensus       143 ~~~~~~e~~~v~Ie~l~~~G~GVak~~--g~~vfV~galpGE~V~vri~k~kk~~~~  197 (201)
T PRK12336        143 EAIEEGKTYEVEITGTGRKGDGVAKKG--KYTIFVPGAKKGEVVKVKIKKISGNLAF  197 (201)
T ss_pred             CCCccCCEEEEEEEEccCCCceEEEEC--CEEEEeCCCCCCCEEEEEEEEecCCcee
Confidence            345778889999999999999999996  8999999999999999999999888653

>PRK03522 rumB 23S rRNA methyluridine methyltransferase; Reviewed

Probab=98.73  E-value=3.1e-08  Score=90.09  Aligned_cols=63  Identities=27%  Similarity=0.402  Sum_probs=57.4

Q ss_pred             CceeEEEeccCCCCceEeCCCCcCCChhHHHHHHHHHHHHhcCCCCCCCCcCCCCccceeEEEEEee
Q 038639          154 ENYALGLHAPGFFDKVLNIDKCLLQSEPANLVLAAVQDYWRDPQLGLSPYDVHSHSGFLKHLMLRTG  220 (229)
Q Consensus       154 g~~~lGf~~rgS~~~IVdie~CpL~~~~in~il~~lr~~l~~~~~~l~~Yd~~~~~G~LRhLvVR~s  220 (229)
                      ++..+|||++++.  +|++++|||++|.+++++..+++++++  .++++|++..++|+|||++||.+
T Consensus         8 ~~~~~G~~~~~~~--~v~i~~C~i~~~~~~~~~~~l~~~~~~--~~~~~~~~~~~~g~lr~~~ir~~   70 (315)
T PRK03522          8 ERPLLGILHRDGT--PVDLCDCPLYPASFAPVFAALKPFIAR--AGLTPYNVARKRGELKYILLTES   70 (315)
T ss_pred             CccEEeEEcCCCc--EEcCCCCcCCCHHHHHHHHHHHHHHHH--cCCCCCcCCCCCceeeEEEEEee
Confidence            4567899998763  699999999999999999999999986  89999999999999999999976

>PF01938 TRAM: TRAM domain; InterPro: IPR002792 The TRAM (after TRM2 and miaB) domain is a 60-70-residue-long module that is found in: Two distinct classes of tRNA-modifying enzymes, namely uridine methylases of the TRM2 family and enzymes of the miaB family that are involved in 2- methylthioadenine formation In several other proteins associated with the translation machinery In a family of small uncharacterised archaeal proteins that are predicted to have a role in the regulation of tRNA modification and/or translation The TRAM domain can be found alone or in association with other domains, such as the catalytic biotin/lipoate synthetase-like domain, the RNA methylase domain, the ribosomal S2 domain and the eIF2-beta domain

Probab=98.68  E-value=1.2e-07  Score=66.33  Aligned_cols=53  Identities=34%  Similarity=0.507  Sum_probs=44.2

Q ss_pred             CCCcEEEEEEeeeCCCCcEEEEEcCCCcEEEecCCCC--CcEEEEEEEeecCCeee
Q 038639           77 IRGQELELVCESLAYKGKGVCKVADTGFVVLCDRVLP--GEKFIGRVTRKKGSYAE  130 (229)
Q Consensus        77 k~~~~i~l~I~~l~~~G~GVar~~~~G~vVFVpgaLP--GE~V~vrI~k~kk~y~~  130 (229)
                      ..|+.+++.|++++++|.++||.+ +++.|||+++.|  ||.|.++|++.++.|++
T Consensus         3 ~~G~~~~VlVe~~~~~g~~~gr~~-~~~~V~v~~~~~~iG~~v~v~I~~~~~~~l~   57 (61)
T PF01938_consen    3 YVGKTLEVLVEELGDEGQGIGRTD-NGKVVFVPGGLPLIGEFVKVRITKAKKNYLF   57 (61)
T ss_dssp             -TTEEEEEEEEEE-TTSEEEEEET--TEEEEETT--T--TEEEEEEEEEE-SSEEE
T ss_pred             cCCcEEEEEEEEecCCCEEEEEeC-CCeEEEECCCCCCCCCEEEEEEEEeeCCcEE
Confidence            368999999999999999999997 589999999999  99999999999998864

The TRAM domain is predicted to bind tRNA and deliver the RNA-modifying enzymatic domain to their targets []. Secondary structure prediction indicates that the TRAM domain adopts a simple beta-barrel fold. The conservation pattern of the TRAM domain consists primarily of small and hydrophobic residues that correspond to five beta-strands in the predicted secondary structure [].; PDB: 1YEZ_A 2BH2_A 1UWV_A 1YVC_A.

>PRK05031 tRNA (uracil-5-)-methyltransferase; Validated

Probab=98.60  E-value=3.4e-08  Score=91.81  Aligned_cols=64  Identities=14%  Similarity=0.095  Sum_probs=53.9

Q ss_pred             eeecccccccchhhccCcc----C---------C-------------CC-CceeEEEeccCCCCceEeCCCCcCCChhHH
Q 038639          131 MEFSFGPKRWFPKESLPKR----G---------D-------------HI-ENYALGLHAPGFFDKVLNIDKCLLQSEPAN  183 (229)
Q Consensus       131 qhlsY~~QL~~K~~~l~~~----~---------~-------------~~-g~~~lGf~~rgS~~~IVdie~CpL~~~~in  183 (229)
                      ||++|+.|+++|+++|++.    +         .             .. ++..+|||+++|| ++|++++|+|++|.++
T Consensus         7 qhl~y~~Ql~~K~~~v~~~l~r~~~~~~~i~~s~~~~YRnr~~~~v~~~~g~~~~G~~~~~s~-~vv~i~~C~i~~~~~~   85 (362)
T PRK05031          7 PPEQYEAQLAEKVARLKELFAPFSAPEPEVFRSPPSHYRMRAEFRIWHEGDDLYYAMFDQQTK-QRIRIDQFPIASELIN   85 (362)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHhcCCCCCCcccCCcccccceEEEEEEEeCCCEEEEEEeCCCC-CeEECccCcCCCHHHH
Confidence            8999999999998886552    1         0             01 4456999999997 8999999999999999


Q ss_pred             HHHHHHHHHHhc
Q 038639          184 LVLAAVQDYWRD  195 (229)
Q Consensus       184 ~il~~lr~~l~~  195 (229)
                      +++..++++++.
T Consensus        86 ~~~~~~~~~~~~   97 (362)
T PRK05031         86 ALMPALLAALRA   97 (362)
T ss_pred             HHHHHHHHHHHh
Confidence            999999999874

>TIGR02143 trmA_only tRNA (uracil-5-)-methyltransferase

Probab=98.23  E-value=1.3e-06  Score=81.16  Aligned_cols=61  Identities=13%  Similarity=0.064  Sum_probs=49.9

Q ss_pred             cccccccchhhccCcc----C----------------------CC-CCceeEEEeccCCCCceEeCCCCcCCChhHHHHH
Q 038639          134 SFGPKRWFPKESLPKR----G----------------------DH-IENYALGLHAPGFFDKVLNIDKCLLQSEPANLVL  186 (229)
Q Consensus       134 sY~~QL~~K~~~l~~~----~----------------------~~-~g~~~lGf~~rgS~~~IVdie~CpL~~~~in~il  186 (229)
                      +|+.|+++|++.|++.    +                      .. +|++.+||++++|| ++|++++|+|++|.++.++
T Consensus         1 ~y~~Ql~~K~~~v~~~l~r~~~~~~~v~~s~~~~YRnr~~~~~~~~~g~~~~G~~~~~s~-~iv~i~~C~i~~~~i~~~~   79 (353)
T TIGR02143         1 QYTAQLAEKVSRLKDLFAPFDAPEPEVFESPDKHYRMRAEFRIWHEGDDLYYAMFDQQTK-SKIRVDQFPAASELINRLM   79 (353)
T ss_pred             ChHHHHHHHHHHHHHHHHhcCCCcCCCcCCccccccceEEEEEEecCCcEEEEEEeCCCC-CeEECCCCcCCCHHHHHHH
Confidence            5899999998776542    1                      01 24456899999998 8999999999999999999


Q ss_pred             HHHHHHHhc
Q 038639          187 AAVQDYWRD  195 (229)
Q Consensus       187 ~~lr~~l~~  195 (229)
                      ..+++++..
T Consensus        80 ~~~~~~l~~   88 (353)
T TIGR02143        80 PALIAALRQ   88 (353)
T ss_pred             HHHHHHHHh
Confidence            999999874

This family consists exclusively of proteins believed to act as tRNA (uracil-5-)-methyltransferase. All members of far are proteobacterial. The seed alignment was taken directly from pfam05958 in Pfam 12.0, but higher cutoffs are used to select only functionally equivalent proteins. Homologous proteins excluded by the higher cutoff scores of this model include other uracil methyltransferases, such as RumA, active on rRNA.

>PF05958 tRNA_U5-meth_tr: tRNA (Uracil-5-)-methyltransferase; InterPro: IPR010280 This family consists of (uracil-5-)-methyltransferases 2

Probab=98.12  E-value=1.2e-06  Score=81.21  Aligned_cols=61  Identities=18%  Similarity=0.404  Sum_probs=46.7

Q ss_pred             cccccccchhhccCcc----C-----------------------CCCCceeEEEeccCCCCceEeCCCCcCCChhHHHHH
Q 038639          134 SFGPKRWFPKESLPKR----G-----------------------DHIENYALGLHAPGFFDKVLNIDKCLLQSEPANLVL  186 (229)
Q Consensus       134 sY~~QL~~K~~~l~~~----~-----------------------~~~g~~~lGf~~rgS~~~IVdie~CpL~~~~in~il  186 (229)
                      +|+.||++|+++|.++    +                       ..+++..+|||+++|| ++|++++|||++|.+++++
T Consensus         1 ~Y~~QL~~K~~~l~~~l~~~~~~~~~i~~s~~~~YRnKa~~~v~~~~~~~~~g~~~~~s~-~iv~i~~C~i~~~~In~~l   79 (352)
T PF05958_consen    1 KYEKQLEFKQQILKELLRRIGKLEIEIIASPPWGYRNKARFPVRKDKGKLILGFFRRGSH-EIVDIEECPIADPEINKLL   79 (352)
T ss_dssp             GHHHHHHHHHHHHHHHHTTT-----EEE---SSS-BSEEEEEEEECTTCEEEEEEECTTS--EEE-S--TTB-HHHHHHH
T ss_pred             ChHHHHHHHHHHHHHHHHhcCCCCCceecCCChhcccEEEEEEEEcCCcEEEEEEecCCC-ceEECCCCccccHHHHHHH
Confidence            5999999999887653    1                       0145677899999998 8999999999999999999


Q ss_pred             HHHHHHHhc
Q 038639          187 AAVQDYWRD  195 (229)
Q Consensus       187 ~~lr~~l~~  195 (229)
                      ..++++++.
T Consensus        80 ~~l~~~l~~   88 (352)
T PF05958_consen   80 PALRELLKK   88 (352)
T ss_dssp             HHHHHHHTT
T ss_pred             HHHHHHHhh
Confidence            999999963

1.1.35 from EC from bacteria, archaea and eukaryotes. A 5-methyluridine (m(5)U) residue at position 54 is a conserved feature of bacterial and eukaryotic tRNAs. The methylation of U54 is catalysed by the tRNA(m5U54)methyltransferase, which in Saccharomyces cerevisiae is encoded by the nonessential TRM2 gene. It is thought that tRNA modification enzymes might have a role in tRNA maturation not necessarily linked to their known catalytic activity []. This protein family also contains the 23SrRNA methyltransferases, first proposed to be RNA methyltransferases by homology to the TrmA family. The member from Escherichia coli has now been shown to act as the 23S RNA methyltransferase for the conserved U1939. The gene is now designated rumA and was previously designated ygcA [].; GO: 0008173 RNA methyltransferase activity, 0006396 RNA processing; PDB: 2VS1_A 2JJQ_A 2BH2_A 1UWV_A 3BT7_B.

>KOG2187 consensus tRNA uracil-5-methyltransferase and related tRNA-modifying enzymes [Translation, ribosomal structure and biogenesis]

Probab=97.59  E-value=0.00011  Score=71.21  Aligned_cols=139  Identities=29%  Similarity=0.362  Sum_probs=100.6

Q ss_pred             CCcEEEEEEeeeCCCCcEEEEEcCCCcEEEecCCCCCcEEEEEEEeecCCeee------------------eeecccccc
Q 038639           78 RGQELELVCESLAYKGKGVCKVADTGFVVLCDRVLPGEKFIGRVTRKKGSYAE------------------MEFSFGPKR  139 (229)
Q Consensus        78 ~~~~i~l~I~~l~~~G~GVar~~~~G~vVFVpgaLPGE~V~vrI~k~kk~y~~------------------qhlsY~~QL  139 (229)
                      ......++.+.....|.++-..++..+..+..-+.+|..........+  +..                  -.++|.+||
T Consensus        62 ~~~~~~~~~et~~~~~ka~~~v~g~~~k~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~r~~~~~Vtpl~~~Sy~~qL  139 (534)
T KOG2187|consen   62 MPKYAYVTFETPSDAGKAINLVDGLLYKGFILRVQLGATEVGSLRRRK--SQPGPTEPPQQRTARDVVTPLEYLSYGEQL  139 (534)
T ss_pred             CCCceEEEEeccchhhhHHHHHhhhhhhcchhhhhhcccccccccccc--cCCCcCccccchhhhhhcceeeeeccccch
Confidence            344567888888888877766653345566777778877766555544  111                  467999999


Q ss_pred             cchhhc----cCcc---------------C------C------------------------------C-CCceeEEEecc
Q 038639          140 WFPKES----LPKR---------------G------D------------------------------H-IENYALGLHAP  163 (229)
Q Consensus       140 ~~K~~~----l~~~---------------~------~------------------------------~-~g~~~lGf~~r  163 (229)
                      ++|..-    |+..               +      +                              . .....+|-+..
T Consensus       140 ~lk~~~~~~vl~kl~~~~~~li~~kv~~~~~~~~~~d~~Le~I~pSp~~~~yrnKceFsvg~~~~g~~~~vgf~lg~~~~  219 (534)
T KOG2187|consen  140 ELKQLSQEAVLQKLERLIGDLIRAKVAFLGPQYHLHDRVLEVIIPSPIQNGYRNKCEFSVGQLLDGEDDTVGFVLGRFSK  219 (534)
T ss_pred             hhhhccHHHHHHHHHHHHHHHHhheeecccccchhhcccccccccCccccCchhcceeeccccccCCcCceeeeeeeeec
Confidence            999422    1110               0      0                              0 12345677888


Q ss_pred             CCCCceEeCCCCcCCChhHHHHHHHHHHHHhcCCCCCCCCcCCCCccceeEEEEEeec
Q 038639          164 GFFDKVLNIDKCLLQSEPANLVLAAVQDYWRDPQLGLSPYDVHSHSGFLKHLMLRTGS  221 (229)
Q Consensus       164 gS~~~IVdie~CpL~~~~in~il~~lr~~l~~~~~~l~~Yd~~~~~G~LRhLvVR~s~  221 (229)
                      |.+ .++.=-+|.+.++..+.++..+++++++  ..+.+||+..+.|++|+|+||...
T Consensus       220 g~~-~~~~pvd~~llp~~~~~V~s~~Q~f~R~--t~l~P~~~~~~~G~wk~LtVRt~~  274 (534)
T KOG2187|consen  220 GAF-AVVAPVDVKLLPEIMSQVASAVQEFYRE--TKLSPYDDFPKGGFWKQLTVRTEF  274 (534)
T ss_pred             Cce-EEeccccccccChHHHHHHHHHHHHHhc--CCCccccccCCCCceeeeEEEecc
Confidence            887 6777678888889999999999999996  899999999999999999999443

>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies

Probab=94.30  E-value=0.19  Score=34.76  Aligned_cols=37  Identities=24%  Similarity=0.313  Sum_probs=26.9

Q ss_pred             eeeCCCCcEEEEEcCCCcEEEec-----CCCCCcEEEEEEEe
Q 038639           87 ESLAYKGKGVCKVADTGFVVLCD-----RVLPGEKFIGRVTR  123 (229)
Q Consensus        87 ~~l~~~G~GVar~~~~G~vVFVp-----gaLPGE~V~vrI~k  123 (229)
                      .++..+|+|.+..++.+.-+|||     +|+.||+|.|++++
T Consensus         3 ~~~~~~GfGFv~~~~~~~DifIp~~~l~~A~~gD~V~v~i~~   44 (58)
T PF08206_consen    3 LKIHPKGFGFVIPDDGGEDIFIPPRNLNGAMDGDKVLVRITP   44 (58)
T ss_dssp             EEE-SSS-EEEEECT-TEEEEE-HHHHTTS-TT-EEEEEEEE
T ss_pred             EEEEcCCCEEEEECCCCCCEEECHHHHCCCCCCCEEEEEEec
Confidence            45678999999987436789998     99999999999998

; PDB: 2ID0_D 2IX1_A 2IX0_A.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	229
2jjq_A	425	Uncharacterized RNA methyltransferase pyrab10780;	4e-30
1yvc_A	70	MRR5; structure, autostructure, autoassign, northe	1e-10
1yez_A	68	MM1357; MAR30, autostructure, northeast structural	2e-10
1uwv_A	433	23S rRNA (uracil-5-)-methyltransferase RUMA; RNA m	2e-08
1uwv_A	433	23S rRNA (uracil-5-)-methyltransferase RUMA; RNA m	5e-08

>2jjq_A Uncharacterized RNA methyltransferase pyrab10780; metal-binding, tRNA methyltransferase, S-adenosyl-L-methionine, iron, 4Fe-4S, iron-sulfur; HET: SAH; 1.8A {Pyrococcus abyssi} PDB: 2vs1_A* Length = 425

 Score =  114 bits (288), Expect = 4e-30
 Identities = 32/203 (15%), Positives = 64/203 (31%), Gaps = 65/203 (32%)

Query: 78  RGQELELVCESLAYKGKGVCKVADTGFVVLCDRVLPGEKFIGRVTRKKGSYAE------M 131
           RG  +  V   L   G GV K       +L     PG++ I     +            +
Sbjct: 17  RGSHMRGVIRKLNDDGFGVLK------GILVPFSAPGDEIIVERVERVKKRRVASQWKLV 70

Query: 132 EFSFGPKRWFP---------------------------------KESLPKRG-DHIENY- 156
             S  P R  P                                    +       I  + 
Sbjct: 71  RSS--PLRVGPRCKAFGKCGGCTLQHLNYDYQLEFKRKKLKRILGFEVEVVPSPKIFGHR 128

Query: 157 ----------ALGLHAPGFFDKVLNIDKCLLQSEPANLVLAAVQDYWRDPQLGLSPYDVH 206
                      +G    G + K+++ID+C +  + +   +  ++++  +    +S +++ 
Sbjct: 129 NRIDLAITKDGIGFRERGKWWKIVDIDECPVFGKTSREAIERLKEFIEE--EKISVWNIK 186

Query: 207 SHSGFLKHLMLRTGSF----MIC 225
              GFL++++LR G F    M+ 
Sbjct: 187 KDEGFLRYMVLREGKFTEEVMVN 209

>1yvc_A MRR5; structure, autostructure, autoassign, northeast structural genomics, autoqf, PSI, protein structure initiative; NMR {Methanococcus maripaludis} SCOP: b.40.4.12 Length = 70

 Score = 54.6 bits (132), Expect = 1e-10
 Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 3/58 (5%)

Query: 76  PIR-GQELELVCESLAYKGKGVCKVADTGFVVLCDRVLPGEKFIGRVTRKKGSYAEME 132
           P+  G+E E+  E +   G G+ ++   GFVV       G     +VT  K  +A  E
Sbjct: 12  PVEAGKEYEVTIEDMGKGGDGIARID--GFVVFVPNAEKGSVINVKVTAVKEKFAFAE 67

>1yez_A MM1357; MAR30, autostructure, northeast structural genomics, PSI, PR structure initiative, northeast structural genomics consort NESG; NMR {Methanosarcina mazei} SCOP: b.40.4.12 Length = 68

 Score = 54.2 bits (131), Expect = 2e-10
 Identities = 12/57 (21%), Positives = 27/57 (47%), Gaps = 3/57 (5%)

Query: 75  KPIR-GQELELVCESLAYKGKGVCKVADTGFVVLCDRVLPGEKFIGRVTRKKGSYAE 130
            P+  G+  ++  + +A +G G+ ++   GFV+       G++   +V R    +A 
Sbjct: 9   VPVEEGEVYDVTIQDIARQGDGIARIE--GFVIFVPGTKVGDEVRIKVERVLPKFAF 63

>1uwv_A 23S rRNA (uracil-5-)-methyltransferase RUMA; RNA modification, iron-sulfur cluster, RNA processing; 1.95A {Escherichia coli} SCOP: b.40.4.12 c.66.1.40 PDB: 2bh2_A* Length = 433

 Score = 52.5 bits (127), Expect = 2e-08
 Identities = 12/69 (17%), Positives = 27/69 (39%), Gaps = 8/69 (11%)

Query: 157 ALGLHAPGFFDKVLNIDKCLLQSEPANLVLAAVQDYWRDPQLGLSPYDVHSHSGFLKHLM 216
            +G    G  D ++++ +C + +     +L  V+         L       H G ++ + 
Sbjct: 145 QMGFRKAGSSD-IVDVKQCPILAPQLEALLPKVRAC-------LGSLQAMRHLGHVELVQ 196

Query: 217 LRTGSFMIC 225
             +G+ MI 
Sbjct: 197 ATSGTLMIL 205

>1uwv_A 23S rRNA (uracil-5-)-methyltransferase RUMA; RNA modification, iron-sulfur cluster, RNA processing; 1.95A {Escherichia coli} SCOP: b.40.4.12 c.66.1.40 PDB: 2bh2_A* Length = 433

 Score = 51.4 bits (124), Expect = 5e-08
 Identities = 14/56 (25%), Positives = 21/56 (37%), Gaps = 2/56 (3%)

Query: 75  KPIRGQELELVCESLAYKGKGVCKVADTGFVVLCDRVLPGEKFIGRVTRKKGSYAE 130
           +    Q + +    L   G+GV +    G  +    +LP E     VT  K  YA 
Sbjct: 10  RTTTRQIITVSVNDLDSFGQGVARHN--GKTLFIPGLLPQENAEVTVTEDKKQYAR 63

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	229
1uwv_A	433	23S rRNA (uracil-5-)-methyltransferase RUMA; RNA m	99.93
2jjq_A	425	Uncharacterized RNA methyltransferase pyrab10780;	99.93
1yvc_A	70	MRR5; structure, autostructure, autoassign, northe	99.5
1yez_A	68	MM1357; MAR30, autostructure, northeast structural	99.49
3bt7_A	369	TRNA (uracil-5-)-methyltransferase; methyluridine,	98.25
2as0_A	396	Hypothetical protein PH1915; RNA methyltransferase	96.97
3c0k_A	396	UPF0064 protein YCCW; PUA domain, adoMet dependent	96.89
2b78_A	385	Hypothetical protein SMU.776; structure genomics,	96.04
1wxx_A	382	TT1595, hypothetical protein TTHA1280; thermus the	95.48

>1uwv_A 23S rRNA (uracil-5-)-methyltransferase RUMA; RNA modification, iron-sulfur cluster, RNA processing; 1.95A {Escherichia coli} SCOP: b.40.4.12 c.66.1.40 PDB: 2bh2_A*

Probab=99.93  E-value=9.9e-26  Score=210.23  Aligned_cols=142  Identities=19%  Similarity=0.268  Sum_probs=114.1

Q ss_pred             cccCCCCCCCCCCCcEEEEEEeeeCCCCcEEEEEcCCCcEEEecCCCCCcEEEEEEEeecCCeee---------------
Q 038639           66 FDSNNNDYFKPIRGQELELVCESLAYKGKGVCKVADTGFVVLCDRVLPGEKFIGRVTRKKGSYAE---------------  130 (229)
Q Consensus        66 ~~~~~~~~~~~k~~~~i~l~I~~l~~~G~GVar~~~~G~vVFVpgaLPGE~V~vrI~k~kk~y~~---------------  130 (229)
                      |++++++.  + +++.++++|++++++|+|||+++  |++|||||+||||+|+++|++.+++|++               
T Consensus         4 ~~~~~~~~--~-~~~~~~~~i~~l~~~G~Gv~~~~--g~~vfV~~alpGe~v~~~i~~~~~~~~~~~~~~i~~~S~~Rv~   78 (433)
T 1uwv_A            4 FYSAKRRT--T-TRQIITVSVNDLDSFGQGVARHN--GKTLFIPGLLPQENAEVTVTEDKKQYARAKVVRRLSDSPERET   78 (433)
T ss_dssp             --------------CCEEEEEEEECTTSEEEEEET--TEEEEEETCCTTCEEEEEEEEECSSEEEEEEEEECCCCTTBCC
T ss_pred             ccCCCCcC--C-CCCEEEEEEEEecCCCceEEEeC--CEEEEcCCCCCCCEEEEEEEeecCCceeEEeccccCCCCCcCC
Confidence            44554333  2 34678999999999999999996  9999999999999999999999999987               


Q ss_pred             --------------eeecccccccchhhccCcc----------C-------------C---CCCceeEEEeccCCCCceE
Q 038639          131 --------------MEFSFGPKRWFPKESLPKR----------G-------------D---HIENYALGLHAPGFFDKVL  170 (229)
Q Consensus       131 --------------qhlsY~~QL~~K~~~l~~~----------~-------------~---~~g~~~lGf~~rgS~~~IV  170 (229)
                                    ||++|+.|++||++.|.+.          +             .   .+++..+|||+++|| ++|
T Consensus        79 p~C~~~~~CGGC~~qh~~y~~Ql~~K~~~v~~~l~~~~~~~~~~~~~~YRnr~~~~~~~~~~~~~~~~Gf~~~~s~-~iv  157 (433)
T 1uwv_A           79 PRCPHFGVCGGCQQQHASVDLQQRSKSAALARLMKHDVSEVIADVPWGYRRRARLSLNYLPKTQQLQMGFRKAGSS-DIV  157 (433)
T ss_dssp             CSCTTTTTBTTCSCTTBCHHHHHHHHHHHHHHHHTSCCCEEECCCSSSCBSEEEEEEEEETTTTEEEEEEEBTTSS-CEE
T ss_pred             CCCCCCCCCCCccccCCCHHHHHHHHHHHHHHHHHHhhcccccCCccccCceEEEeeeEccCCCcEEEEEEcCCCC-cEE
Confidence                          8999999999998775431          0             0   134567899999997 899


Q ss_pred             eCCCCcCCChhHHHHHHHHHHHHhcCCCCCCCCcCCCCccceeEEEEEeecCc
Q 038639          171 NIDKCLLQSEPANLVLAAVQDYWRDPQLGLSPYDVHSHSGFLKHLMLRTGSFM  223 (229)
Q Consensus       171 die~CpL~~~~in~il~~lr~~l~~~~~~l~~Yd~~~~~G~LRhLvVR~s~~~  223 (229)
                      ++++|||++|.+++++..++++++.  .++        .|.++|++||.+..+
T Consensus       158 ~i~~C~i~~~~~~~~~~~l~~~~~~--~~~--------~~~~~~i~~~~~~~~  200 (433)
T 1uwv_A          158 DVKQCPILAPQLEALLPKVRACLGS--LQA--------MRHLGHVELVQATSG  200 (433)
T ss_dssp             ECSCCTTBCHHHHHHHHHHHHHHTT--CGG--------GGGEEEEEEEEETTE
T ss_pred             ECccCcCCCHHHHHHHHHHHHHHHh--cCC--------CCCccEEEEEEeCCC
Confidence            9999999999999999999999985  332        367999999987543

>2jjq_A Uncharacterized RNA methyltransferase pyrab10780; metal-binding, tRNA methyltransferase, S-adenosyl-L-methionine, iron, 4Fe-4S, iron-sulfur; HET: SAH; 1.8A {Pyrococcus abyssi} PDB: 2vs1_A*

Probab=99.93  E-value=4e-26  Score=213.52  Aligned_cols=137  Identities=20%  Similarity=0.386  Sum_probs=114.8

Q ss_pred             CCCCCcEEEEEEeeeCCCCcEEEEEcCCCcEEEecCCCCCcEEEEEEEeecCCeee------------------------
Q 038639           75 KPIRGQELELVCESLAYKGKGVCKVADTGFVVLCDRVLPGEKFIGRVTRKKGSYAE------------------------  130 (229)
Q Consensus        75 ~~k~~~~i~l~I~~l~~~G~GVar~~~~G~vVFVpgaLPGE~V~vrI~k~kk~y~~------------------------  130 (229)
                      .+..|+.++++|++++++|+|||+      +|||||+||||+|+++|++.|++|++                        
T Consensus        14 ~~~~~~~~~~~I~~l~~~G~Gv~~------~vfV~~alPGe~v~~~i~~~k~~~~~a~~~~v~~~S~~Rv~p~C~~~~~C   87 (425)
T 2jjq_A           14 LVPRGSHMRGVIRKLNDDGFGVLK------GILVPFSAPGDEIIVERVERVKKRRVASQWKLVRSSPLRVGPRCKAFGKC   87 (425)
T ss_dssp             -------CEEECCEECTTSCEEET------TEEETTCCTTCEEEEEEEEESSSSEEEEEEEEEECCTTBCC---------
T ss_pred             ccCCCCEEEEEEEEeccCCeEEEE------EEEeCCCCCCCEEEEEEEEecCCceEEEEcccCCCCccccCCCCCCcCCC
Confidence            345678889999999999999996      79999999999999999999999987                        


Q ss_pred             -----eeecccccccchhhccCccC-------------CC--------CCceeEEEeccCC-CCceEeCCCCcCCChhHH
Q 038639          131 -----MEFSFGPKRWFPKESLPKRG-------------DH--------IENYALGLHAPGF-FDKVLNIDKCLLQSEPAN  183 (229)
Q Consensus       131 -----qhlsY~~QL~~K~~~l~~~~-------------~~--------~g~~~lGf~~rgS-~~~IVdie~CpL~~~~in  183 (229)
                           ||++|+.|++||++.+++.+             .+        .. ..+|||+++| | ++|++++|||++|.++
T Consensus        88 GGC~lqh~~y~~Ql~~K~~~l~r~~~~~~~~~~s~~~~~YRnk~~~~v~~-g~~Gf~~~~s~~-~iv~i~~C~i~~~~~~  165 (425)
T 2jjq_A           88 GGCTLQHLNYDYQLEFKRKKLKRILGFEVEVVPSPKIFGHRNRIDLAITK-DGIGFRERGKWW-KIVDIDECPVFGKTSR  165 (425)
T ss_dssp             --CTTTTBCHHHHHHHHHHHHHHHHSSCCEEECCSCSSSCBCEEEEEEET-TEEEEEC--CTT-SEEECSCBTTTBHHHH
T ss_pred             CCccCcCCCHHHHHHHHHHHHHHccCCCCceecCCCcCCccceEEEEecC-CCeEEeeCCCCC-cEEECcCCccCCHHHH
Confidence                 89999999999987654320             01        11 1289999999 7 8999999999999999


Q ss_pred             HHHHHHHHHHhcCCCCCCCCcCCCCccceeEEEEEeec
Q 038639          184 LVLAAVQDYWRDPQLGLSPYDVHSHSGFLKHLMLRTGS  221 (229)
Q Consensus       184 ~il~~lr~~l~~~~~~l~~Yd~~~~~G~LRhLvVR~s~  221 (229)
                      +++..++++++.  .++++||..++.|+|||++||.+.
T Consensus       166 ~~~~~l~~~~~~--~~~~~y~~~~~~g~lr~~~vr~~~  201 (425)
T 2jjq_A          166 EAIERLKEFIEE--EKISVWNIKKDEGFLRYMVLREGK  201 (425)
T ss_dssp             HHHHHHHHHHHH--HTCCBBBTTTTBCSEEEEEEEECT
T ss_pred             HHHHHHHHHHHH--cCCCccccccCCCcceEEEEEEcc
Confidence            999999999996  899999999999999999999886

>1yvc_A MRR5; structure, autostructure, autoassign, northeast structural genomics, autoqf, PSI, protein structure initiative; NMR {Methanococcus maripaludis} SCOP: b.40.4.12

Probab=99.50  E-value=7.9e-14  Score=100.05  Aligned_cols=54  Identities=28%  Similarity=0.423  Sum_probs=50.5

Q ss_pred             CCCCCcEEEEEEeeeCCCCcEEEEEcCCCcEEEecCCCCCcEEEEEEEeecCCeee
Q 038639           75 KPIRGQELELVCESLAYKGKGVCKVADTGFVVLCDRVLPGEKFIGRVTRKKGSYAE  130 (229)
Q Consensus        75 ~~k~~~~i~l~I~~l~~~G~GVar~~~~G~vVFVpgaLPGE~V~vrI~k~kk~y~~  130 (229)
                      .+++++.++++|++++++|.|||+.+  |+++|||++||||+|+++|++.+++|++
T Consensus        12 ~~~~~~~~~v~I~~l~~~G~Gva~~~--g~~vfV~~alPGE~V~v~i~k~kk~~~~   65 (70)
T 1yvc_A           12 PVEAGKEYEVTIEDMGKGGDGIARID--GFVVFVPNAEKGSVINVKVTAVKEKFAF   65 (70)
T ss_dssp             SSCTTCEEEEECCEECTTSCEEEEET--TEEEEETTCCTTCEEEEEEEEECSSCEE
T ss_pred             cccCCCEEEEEEEEcCCCccEEEEEC--CEEEEccCCCCCCEEEEEEEEeeCCeEE
Confidence            45789999999999999999999996  8999999999999999999999999875

>1yez_A MM1357; MAR30, autostructure, northeast structural genomics, PSI, PR structure initiative, northeast structural genomics consort NESG; NMR {Methanosarcina mazei} SCOP: b.40.4.12

Probab=99.49  E-value=7.8e-14  Score=99.33  Aligned_cols=55  Identities=20%  Similarity=0.393  Sum_probs=51.0

Q ss_pred             CCCCCCcEEEEEEeeeCCCCcEEEEEcCCCcEEEecCCCCCcEEEEEEEeecCCeee
Q 038639           74 FKPIRGQELELVCESLAYKGKGVCKVADTGFVVLCDRVLPGEKFIGRVTRKKGSYAE  130 (229)
Q Consensus        74 ~~~k~~~~i~l~I~~l~~~G~GVar~~~~G~vVFVpgaLPGE~V~vrI~k~kk~y~~  130 (229)
                      ..+++++.++++|++++++|.|||+++  |++|||||+||||+|+++|++.+++|++
T Consensus         9 ~~~~~~~~~~~~I~~l~~~G~Gva~~~--g~~vfV~~alPGE~V~v~i~k~kk~~~~   63 (68)
T 1yez_A            9 VPVEEGEVYDVTIQDIARQGDGIARIE--GFVIFVPGTKVGDEVRIKVERVLPKFAF   63 (68)
T ss_dssp             CSCCTTEEEEEECCEEETTTEEEEEET--TEEEEEESCCTTCEEEEEEEEECSSCEE
T ss_pred             CccCCCCEEEEEEEEcCCCccEEEEEC--CEEEECcCCCCCCEEEEEEEEecCCEEE
Confidence            346789999999999999999999996  8999999999999999999999999875

>3bt7_A TRNA (uracil-5-)-methyltransferase; methyluridine, methyltransferase, TRMA, RUMT; HET: 5MU; 2.43A {Escherichia coli}

Probab=98.25  E-value=3.4e-07  Score=83.10  Aligned_cols=64  Identities=11%  Similarity=-0.031  Sum_probs=53.6

Q ss_pred             eeecccccccchhhccCcc----C------------C-----------CCCceeEEEeccCCCCceEeCCCCcCCChhHH
Q 038639          131 MEFSFGPKRWFPKESLPKR----G------------D-----------HIENYALGLHAPGFFDKVLNIDKCLLQSEPAN  183 (229)
Q Consensus       131 qhlsY~~QL~~K~~~l~~~----~------------~-----------~~g~~~lGf~~rgS~~~IVdie~CpL~~~~in  183 (229)
                      ||++|+.|++||++.|.+.    +            .           .++.+.+|||+++|| .+|++++|++++|.++
T Consensus        10 ~~~~y~~Ql~~K~~~v~~~l~r~~~~~~~~~~~~~~~yRnr~~~~v~~~~~~~~~G~~~~~s~-~iv~i~~C~i~~~~i~   88 (369)
T 3bt7_A           10 PTEQYEAQLAEKVVRLQSMMAPFSDLVPEVFRSPVSHYRMRAEFRIWHDGDDLYHIIFDQQTK-SRIRVDSFPAASELIN   88 (369)
T ss_dssp             CGGGHHHHHHHHHHHHHHHHTTTCCCCCEEECCCSSSCBSEEEEEEEEETTEEEEEEECTTTC-CEEECSCCTTBCHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHHhcCCCCCCccCCCccccceEEEEEEEEcCCcEEEEEEECCCC-CEEeCcCCccCCHHHH
Confidence            7999999999998876542    1            0           134567899999998 8999999999999999


Q ss_pred             HHHHHHHHHHhc
Q 038639          184 LVLAAVQDYWRD  195 (229)
Q Consensus       184 ~il~~lr~~l~~  195 (229)
                      +++..++++++.
T Consensus        89 ~~l~~l~~~~~~  100 (369)
T 3bt7_A           89 QLMTAMIAGVRN  100 (369)
T ss_dssp             HHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHh
Confidence            999999998863

>2as0_A Hypothetical protein PH1915; RNA methyltransferase, structural genomics, PSI, protein structure initiative; 1.80A {Pyrococcus horikoshii} SCOP: b.122.1.9 c.66.1.51

Probab=96.97  E-value=0.00041  Score=63.07  Aligned_cols=61  Identities=11%  Similarity=0.263  Sum_probs=55.4

Q ss_pred             eeEEEeccCC---CCceEeCC-CCcCCChhHHHHHHHHHHHHhcCCC--CCCCCcCCCCcc-ceeEEEEEe
Q 038639          156 YALGLHAPGF---FDKVLNID-KCLLQSEPANLVLAAVQDYWRDPQL--GLSPYDVHSHSG-FLKHLMLRT  219 (229)
Q Consensus       156 ~~lGf~~rgS---~~~IVdie-~CpL~~~~in~il~~lr~~l~~~~~--~l~~Yd~~~~~G-~LRhLvVR~  219 (229)
                      +.+|||.++|   + +||+++ +|+|.++.+++.+..++++.+.  .  +...|+...+.| +|++|+|+.
T Consensus        49 l~~G~~~~~s~~~~-ri~~~~~~~~i~~~~~~~~l~~~~~~~~~--~~~~~~~yrl~~~~gd~l~gl~vd~  116 (396)
T 2as0_A           49 LGKGFANPNSNIMV-RIVTKDKDVEINKDLFKRRIKKANEYRKK--VLKYTNVYRMVYGEADYLPGLIVDR  116 (396)
T ss_dssp             EEEEEECTTSSEEE-EEEESCTTCCCSHHHHHHHHHHHHHHHHH--TSCCCSEEEEEEGGGGTCTTEEEEE
T ss_pred             EEEEEECCCChHHe-ehhccCCCCCCCHHHHHHHHHHHHHHHHH--HhcCCCeEEEEecCCCCCCcEEEEE
Confidence            6789999999   6 799999 9999999999999999999986  5  788999999988 899999985

>3c0k_A UPF0064 protein YCCW; PUA domain, adoMet dependent methyltransferase fold; 2.00A {Escherichia coli K12}

Probab=96.89  E-value=0.0004  Score=63.18  Aligned_cols=64  Identities=19%  Similarity=0.173  Sum_probs=56.1

Q ss_pred             CCc-eeEEEeccCC---CCceEeCC-CCcCCChhHHHHHHHHHHHHhcCCC----CCCCCcCCCCcc-ceeEEEEEe
Q 038639          153 IEN-YALGLHAPGF---FDKVLNID-KCLLQSEPANLVLAAVQDYWRDPQL----GLSPYDVHSHSG-FLKHLMLRT  219 (229)
Q Consensus       153 ~g~-~~lGf~~rgS---~~~IVdie-~CpL~~~~in~il~~lr~~l~~~~~----~l~~Yd~~~~~G-~LRhLvVR~  219 (229)
                      +++ +.+|||.++|   + ++|+++ +|+|.++.+++.+..++++.+.  .    ++..|+...+.| +|++|+|+.
T Consensus        46 ~g~~l~~G~~~~~s~~~~-ri~~~~~~~~i~~~~~~~~l~~a~~~~~~--~~~~~~~~~yrl~~~egd~l~gl~vd~  119 (396)
T 3c0k_A           46 QGKWLARGAYSPASQIRA-RVWTFDPSESIDIAFFSRRLQQAQKWRDW--LAQKDGLDSYRLIAGESDGLPGITIDR  119 (396)
T ss_dssp             TCCEEEEEEECTTSSEEE-EEEESCTTCCCSHHHHHHHHHHHHHHHHH--HHHHHTCSEEEEEEGGGGTCTTEEEEE
T ss_pred             CCCEEEEEEECCCCCEEE-EEEECCCCCCCCHHHHHHHHHHHHHHHHH--HHhcCCCceEEEEecCCCCCCceEEEE
Confidence            344 6789999999   6 799999 9999999999999998888875  4    788999999999 899999985

>2b78_A Hypothetical protein SMU.776; structure genomics, methyltransferase, caries, structural genomics, unknown function; 2.00A {Streptococcus mutans} SCOP: b.122.1.9 c.66.1.51 PDB: 3ldf_A*

Probab=96.04  E-value=0.0031  Score=57.41  Aligned_cols=62  Identities=6%  Similarity=0.019  Sum_probs=50.4

Q ss_pred             eeEEEeccCCC--CceEeCCCCcCCChhH----HHHHHHHHHHHhcCCCCCCCCcCCCCcc-ceeEEEEEe
Q 038639          156 YALGLHAPGFF--DKVLNIDKCLLQSEPA----NLVLAAVQDYWRDPQLGLSPYDVHSHSG-FLKHLMLRT  219 (229)
Q Consensus       156 ~~lGf~~rgS~--~~IVdie~CpL~~~~i----n~il~~lr~~l~~~~~~l~~Yd~~~~~G-~LRhLvVR~  219 (229)
                      +.+|||.++|+  ++|++.++|+|.++.+    .+++...++++.+  .+++.|+...+.| +|++|+||.
T Consensus        46 l~~g~~~~~s~i~~ri~~~~~~~i~~~~~~~~~~~a~~~r~~~~~~--~~~~~yr~~~~egd~l~gl~vd~  114 (385)
T 2b78_A           46 LGTAYLSKQNKGVGWLISPKKVSLNVTYFIKLFQWSKDKRKNFAHS--KLTTAYRLFNQDGDSFGGVTIDC  114 (385)
T ss_dssp             EEEEEEEEETTEEEEEEESSCCCCCHHHHHHHHHHHHHTTHHHHHC--SSCCEEEEEEGGGGTCTTEEEEE
T ss_pred             EEEEEECCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHhcC--CCCceEEEEeCCCCCCCceEEEE
Confidence            67899999994  3799999999999864    4444444888874  5789999999997 699999996

>1wxx_A TT1595, hypothetical protein TTHA1280; thermus thermophillus, methyltransferase, adoMet, structural genomics; 1.80A {Thermus thermophilus} SCOP: b.122.1.9 c.66.1.51 PDB: 1wxw_A 2cww_A*

Probab=95.48  E-value=0.0037  Score=56.51  Aligned_cols=62  Identities=18%  Similarity=0.065  Sum_probs=46.4

Q ss_pred             eeEEEeccCC---CCceEeCC-CCcCCChhHHHHHHHHHHHHhcC--CCCCCCCcCCCCcc-ceeEEEEEe
Q 038639          156 YALGLHAPGF---FDKVLNID-KCLLQSEPANLVLAAVQDYWRDP--QLGLSPYDVHSHSG-FLKHLMLRT  219 (229)
Q Consensus       156 ~~lGf~~rgS---~~~IVdie-~CpL~~~~in~il~~lr~~l~~~--~~~l~~Yd~~~~~G-~LRhLvVR~  219 (229)
                      +.+|||.++|   + +|++++ +|+|.++ +.+.+....++.++-  +.+++.|+...+.| +|++|+||.
T Consensus        44 l~~g~~~~~s~~~~-ri~~~~~~~~i~~~-~~~~l~~~~~~r~~~~~~~~~~~yr~~~~~~d~l~~l~vd~  112 (382)
T 1wxx_A           44 LALALYNPHTDLAV-RAYRFAPAEDPVAA-LLENLAQALARREAVLRQDPEGGYRLVHAEGDLLPGLVVDY  112 (382)
T ss_dssp             EEEEEECTTSSSCE-EEEESSCCSCHHHH-HHHHHHHHHHHHHHHHHHCTTSEEEEEEGGGGTCTTEEEEE
T ss_pred             EEEEEECCCCCEEE-EEEECCCCCCcCHH-HHHHHHHHHHHHHHHHhcCCCCeEEEEeCCCCCCCcEEEEE
Confidence            6789999999   6 899999 9999888 655554443322210  02788999999887 899999996

---

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	229
d1yeza1	68	b.40.4.12 (A:1-68) Hypothetical protein MM1357 {Me	1e-13
d1yvca1	69	b.40.4.12 (A:1-69) Hypothetical protein MMP0076 {M	3e-13
d1uwva1	60	b.40.4.12 (A:15-74) rRNA (Uracil-5-)-methyltransfe	1e-12

>d1yeza1 b.40.4.12 (A:1-68) Hypothetical protein MM1357 {Methanosarcina mazei [TaxId: 2209]} Length = 68

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: TRAM domain
domain: Hypothetical protein MM1357
species: Methanosarcina mazei [TaxId: 2209]

 Score = 61.6 bits (150), Expect = 1e-13
 Identities = 12/56 (21%), Positives = 27/56 (48%), Gaps = 3/56 (5%)

Query: 76  PIR-GQELELVCESLAYKGKGVCKVADTGFVVLCDRVLPGEKFIGRVTRKKGSYAE 130
           P+  G+  ++  + +A +G G+ ++   GFV+       G++   +V R    +A 
Sbjct: 10  PVEEGEVYDVTIQDIARQGDGIARIE--GFVIFVPGTKVGDEVRIKVERVLPKFAF 63

>d1yvca1 b.40.4.12 (A:1-69) Hypothetical protein MMP0076 {Methanococcus maripaludis [TaxId: 39152]} Length = 69

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: TRAM domain
domain: Hypothetical protein MMP0076
species: Methanococcus maripaludis [TaxId: 39152]

 Score = 60.5 bits (147), Expect = 3e-13
 Identities = 16/57 (28%), Positives = 25/57 (43%), Gaps = 3/57 (5%)

Query: 75  KPIR-GQELELVCESLAYKGKGVCKVADTGFVVLCDRVLPGEKFIGRVTRKKGSYAE 130
            P+  G+E E+  E +   G G+ ++   GFVV       G     +VT  K  +A 
Sbjct: 11  VPVEAGKEYEVTIEDMGKGGDGIARID--GFVVFVPNAEKGSVINVKVTAVKEKFAF 65

>d1uwva1 b.40.4.12 (A:15-74) rRNA (Uracil-5-)-methyltransferase RumA, N-terminal domain {Escherichia coli [TaxId: 562]} Length = 60

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: TRAM domain
domain: rRNA (Uracil-5-)-methyltransferase RumA, N-terminal domain
species: Escherichia coli [TaxId: 562]

 Score = 58.5 bits (142), Expect = 1e-12
 Identities = 14/51 (27%), Positives = 20/51 (39%), Gaps = 2/51 (3%)

Query: 80  QELELVCESLAYKGKGVCKVADTGFVVLCDRVLPGEKFIGRVTRKKGSYAE 130
           Q + +    L   G+GV +    G  +    +LP E     VT  K  YA 
Sbjct: 1   QIITVSVNDLDSFGQGVARHN--GKTLFIPGLLPQENAEVTVTEDKKQYAR 49

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	229
d1yvca1	69	Hypothetical protein MMP0076 {Methanococcus maripa	99.68
d1yeza1	68	Hypothetical protein MM1357 {Methanosarcina mazei	99.62
d1uwva1	60	rRNA (Uracil-5-)-methyltransferase RumA, N-termina	99.55
d1uwva2	358	rRNA (Uracil-5-)-methyltransferase RumA, catalytic	98.9
d2ix0a2	79	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	95.47

>d1yvca1 b.40.4.12 (A:1-69) Hypothetical protein MMP0076 {Methanococcus maripaludis [TaxId: 39152]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: TRAM domain
domain: Hypothetical protein MMP0076
species: Methanococcus maripaludis [TaxId: 39152]

Probab=99.68  E-value=8.1e-17  Score=114.12  Aligned_cols=63  Identities=25%  Similarity=0.379  Sum_probs=58.3

Q ss_pred             cccCCCCCCCCCCCcEEEEEEeeeCCCCcEEEEEcCCCcEEEecCCCCCcEEEEEEEeecCCeee
Q 038639           66 FDSNNNDYFKPIRGQELELVCESLAYKGKGVCKVADTGFVVLCDRVLPGEKFIGRVTRKKGSYAE  130 (229)
Q Consensus        66 ~~~~~~~~~~~k~~~~i~l~I~~l~~~G~GVar~~~~G~vVFVpgaLPGE~V~vrI~k~kk~y~~  130 (229)
                      |+.|+.+...+++|+.++++|++++++|.|||+++  |+++||+|+||||+|+++|++.+++|++
T Consensus         3 ~~k~~~~~~pvk~g~~~~v~I~~l~~~G~Giar~~--g~vvfV~~alPGe~V~v~I~k~kk~~~~   65 (69)
T d1yvca1           3 FGKPAMKNVPVEAGKEYEVTIEDMGKGGDGIARID--GFVVFVPNAEKGSVINVKVTAVKEKFAF   65 (69)
T ss_dssp             SSSSTTSCCSSCTTCEEEEECCEECTTSCEEEEET--TEEEEETTCCTTCEEEEEEEEECSSCEE
T ss_pred             cccchhccCCCCCCCEEEEEEEECCCCCcEEEEEC--CEEEEeCCCCCCCEEEEEEEEecCCcEE
Confidence            55677777788999999999999999999999996  9999999999999999999999999985

>d1yeza1 b.40.4.12 (A:1-68) Hypothetical protein MM1357 {Methanosarcina mazei [TaxId: 2209]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: TRAM domain
domain: Hypothetical protein MM1357
species: Methanosarcina mazei [TaxId: 2209]

Probab=99.62  E-value=5.2e-16  Score=109.54  Aligned_cols=59  Identities=19%  Similarity=0.364  Sum_probs=54.5

Q ss_pred             CCCCCCCCCCcEEEEEEeeeCCCCcEEEEEcCCCcEEEecCCCCCcEEEEEEEeecCCeee
Q 038639           70 NNDYFKPIRGQELELVCESLAYKGKGVCKVADTGFVVLCDRVLPGEKFIGRVTRKKGSYAE  130 (229)
Q Consensus        70 ~~~~~~~k~~~~i~l~I~~l~~~G~GVar~~~~G~vVFVpgaLPGE~V~vrI~k~kk~y~~  130 (229)
                      +.+...+++|+.++++|++++++|+|||+++  |+++||||+||||+|+++|++.+++|++
T Consensus         5 ~~~~~pv~~g~~~~l~I~~l~~~G~Gi~~~~--g~vvfV~galpGe~v~v~i~k~kk~~~~   63 (68)
T d1yeza1           5 ESRSVPVEEGEVYDVTIQDIARQGDGIARIE--GFVIFVPGTKVGDEVRIKVERVLPKFAF   63 (68)
T ss_dssp             CCCCCSCCTTEEEEEECCEEETTTEEEEEET--TEEEEEESCCTTCEEEEEEEEECSSCEE
T ss_pred             cCCCCCcCCCCEEEEEEEECCCCCcEEEEEC--CEEEEeCCCCCCCEEEEEEEEEeCCeEE
Confidence            3456677899999999999999999999996  9999999999999999999999999985

>d1uwva1 b.40.4.12 (A:15-74) rRNA (Uracil-5-)-methyltransferase RumA, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: TRAM domain
domain: rRNA (Uracil-5-)-methyltransferase RumA, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=99.55  E-value=4.9e-15  Score=101.86  Aligned_cols=49  Identities=29%  Similarity=0.373  Sum_probs=46.6

Q ss_pred             cEEEEEEeeeCCCCcEEEEEcCCCcEEEecCCCCCcEEEEEEEeecCCeee
Q 038639           80 QELELVCESLAYKGKGVCKVADTGFVVLCDRVLPGEKFIGRVTRKKGSYAE  130 (229)
Q Consensus        80 ~~i~l~I~~l~~~G~GVar~~~~G~vVFVpgaLPGE~V~vrI~k~kk~y~~  130 (229)
                      |+++++|++|+++|+|||+++  |+++||||+||||+|+++|++.+++|++
T Consensus         1 q~i~v~I~~l~~~G~Gv~r~~--g~vvfV~~alPGE~V~v~i~~~~~~~~~   49 (60)
T d1uwva1           1 QIITVSVNDLDSFGQGVARHN--GKTLFIPGLLPQENAEVTVTEDKKQYAR   49 (60)
T ss_dssp             CCEEEEEEEECTTSEEEEEET--TEEEEEETCCTTCEEEEEEEEECSSEEE
T ss_pred             CEEEEEEEECCCCCcEEEEEC--CEEEEECCCCCCCEEEEEEEEecCCeEE
Confidence            468999999999999999996  9999999999999999999999999987

>d1uwva2 c.66.1.40 (A:75-432) rRNA (Uracil-5-)-methyltransferase RumA, catalytic domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: (Uracil-5-)-methyltransferase
domain: rRNA (Uracil-5-)-methyltransferase RumA, catalytic domain
species: Escherichia coli [TaxId: 562]

Probab=98.90  E-value=2.4e-10  Score=100.66  Aligned_cols=79  Identities=11%  Similarity=0.235  Sum_probs=63.5

Q ss_pred             eeecccccccchhhccCcc------------C--------------CCCCceeEEEeccCCCCceEeCCCCcCCChhHHH
Q 038639          131 MEFSFGPKRWFPKESLPKR------------G--------------DHIENYALGLHAPGFFDKVLNIDKCLLQSEPANL  184 (229)
Q Consensus       131 qhlsY~~QL~~K~~~l~~~------------~--------------~~~g~~~lGf~~rgS~~~IVdie~CpL~~~~in~  184 (229)
                      ||++|+.|+++|++.|++.            +              ..+++..+||++++|| .+|++++|+|++|.+++
T Consensus        19 qh~~y~~Ql~~K~~~l~~~~~~~~~~v~~~~p~~YR~r~~~~v~~~~~~~~~~~Gf~~~~s~-~iV~i~~C~i~~~~i~~   97 (358)
T d1uwva2          19 QHASVDLQQRSKSAALARLMKHDVSEVIADVPWGYRRRARLSLNYLPKTQQLQMGFRKAGSS-DIVDVKQCPILAPQLEA   97 (358)
T ss_dssp             TTBCHHHHHHHHHHHHHHHHTSCCCEEECCCSSSCBSEEEEEEEEETTTTEEEEEEEBTTSS-CEEECSCCTTBCHHHHH
T ss_pred             cCCCHHHHHHHHHHHHHHhcCcccCcccCCCCCCCcceEEEEeeEecCCCceEEEEEecCCc-eeeeccccccccHHHHH
Confidence            9999999999999887663            0              0135678999999998 89999999999999999


Q ss_pred             HHHHHHHHHhcCCCCCCCCcCCCCccceeEEEE
Q 038639          185 VLAAVQDYWRDPQLGLSPYDVHSHSGFLKHLML  217 (229)
Q Consensus       185 il~~lr~~l~~~~~~l~~Yd~~~~~G~LRhLvV  217 (229)
                      ++..+++++..       |+...+.|.++.+..
T Consensus        98 ~l~~lr~~l~~-------~~~~~~~~~~~~~~~  123 (358)
T d1uwva2          98 LLPKVRACLGS-------LQAMRHLGHVELVQA  123 (358)
T ss_dssp             HHHHHHHHHTT-------CGGGGGEEEEEEEEE
T ss_pred             HHHHHHHhhhc-------ccccccceEEEEEEe
Confidence            99999999873       555555665544433

>d2ix0a2 b.40.4.5 (A:4-82) Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Exoribonuclease 2, RNB
species: Escherichia coli [TaxId: 562]

Probab=95.47  E-value=0.013  Score=40.71  Aligned_cols=41  Identities=20%  Similarity=0.258  Sum_probs=31.5

Q ss_pred             EEeeeCCCCcEEEEEcCCCcEEEec-----CCCCCcEEEEEEEeecC
Q 038639           85 VCESLAYKGKGVCKVADTGFVVLCD-----RVLPGEKFIGRVTRKKG  126 (229)
Q Consensus        85 ~I~~l~~~G~GVar~~~~G~vVFVp-----gaLPGE~V~vrI~k~kk  126 (229)
                      =+.+++.+|+|....+ ++.-+|||     +|+.||+|+|+|++.++
T Consensus        21 G~i~~~~~G~GFv~~d-~~~DifI~~~~~~~A~~GD~V~v~i~~~~~   66 (79)
T d2ix0a2          21 GVVKATEKGFGFLEVD-AQKSYFIPPPQMKKVMHGDRIIAVIHSEKE   66 (79)
T ss_dssp             EEEECCC--CEEEEEE-TTEEEEECHHHHTTCCTTCEEEEEEECC--
T ss_pred             EEEEEeCCCcEEEEEC-CCCcEEECHHHHcCCCCCCEEEEEEEeCCC
Confidence            3457889999999887 57789998     89999999999986544