Citrus Sinensis ID: 041256

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240----
Protein Sequence
MASIADREEETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFVRNNQNGASLSPYMALCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPGTLFIKFV
Secondary Structure (PSIPRED)
ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHccccccccHHHHHHHccccccccccccccHHHHHHHHHHcccccEEEEcccccEEcccccccccccccccccHHHHHHHcccccccccccccHHHHHcccccHHHccccccHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHccccccccEEEEcccccHHHHHHHHHHcccccEEEcccHHHHHcccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccHHHHHHHHHHHHcccHHHHHHHHHHHccHHHHHHcccccccEcHHHHHccccccccccccHHHHHHHHHHHHHHcccEEEEEccccEEEEccccHHccccccEccEccHHHHHHHccHHHHHHHccHHHHHHHcccHHHHHHcccHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccEEEEccccccHHHHHHcccccccEEEEEcHHHHcccccccccEEEEEc
Coil and Loop (DISEMBL)
masiadreeetNNFSYAMELASAIVLPAVMQAVVELDVFEIIskagpgaklSVAEIVAqiplkdnnpeaAAMTLDRVLRLLVSYNAlhcsfvdgqrlyslapvsayfvrnnqngaslspYMALCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMqiydylgvdsrfndvfnngmlSHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISkyphikginydlpyvikdapsypgtlfikfv
Flexible Loop (DISEMBL)
masiadreeetNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFVRNNQNGASLSPYMALCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDapsypgtlfikfv
Low Complexity Region (SEG)
MASIADREEETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFVRNNQNGASLSPYMALCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIVMEKVLESYKGFEHvkklvdvggglgITLNMIISKYPHIKGINYDLPYVIKDAPSYPGTLFIKFV
Disordered region (IsUnstruct)
*************FSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFVRNNQNGASLSPYMALCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPGTLFIKF*
Disordered Region (DISOPRED)
***********NNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFVRNNQNGASLSPYMALCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPGTLFIKFV
Disordered Region (DISEMBL)
**********TNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFVRNNQNGASLSPYMALCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPGTLFIKFV
Disordered Region (DISPRO)
*********ETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFVRNNQNGASLSPYMALCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPGTLFIKFV
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MASIADREEETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFVRNNQNGASLSPYMALCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPGTLFIKFV
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	244	2.2.26 [Sep-21-2011]
O81646	359	Caffeic acid 3-O-methyltr	N/A	no	0.938	0.637	0.529	3e-67
Q8W013	363	Caffeic acid 3-O-methyltr	N/A	no	0.926	0.622	0.538	4e-67
Q43046	365	Caffeic acid 3-O-methyltr	N/A	no	0.893	0.597	0.550	5e-67
Q00763	365	Caffeic acid 3-O-methyltr	N/A	no	0.893	0.597	0.550	1e-66
Q9XGV9	361	Caffeic acid 3-O-methyltr	N/A	no	0.954	0.645	0.532	1e-66
Q9FQY8	359	Caffeic acid 3-O-methyltr	N/A	no	0.926	0.629	0.523	5e-66
Q9SWC2	313	Caffeic acid 3-O-methyltr	N/A	no	0.893	0.696	0.528	6e-66
Q43609	365	Caffeic acid 3-O-methyltr	N/A	no	0.918	0.613	0.548	2e-65
Q9XGW0	361	Caffeic acid 3-O-methyltr	N/A	no	0.922	0.623	0.521	2e-65
Q8LL87	350	Caffeic acid 3-O-methyltr	N/A	no	0.918	0.64	0.536	4e-65

>sp|O81646|COMT1_CAPCH Caffeic acid 3-O-methyltransferase OS=Capsicum chinense GN=COMT PE=2 SV=1

 Score =  254 bits (650), Expect = 3e-67,   Method: Compositional matrix adjust.
 Identities = 127/240 (52%), Positives = 174/240 (72%), Gaps = 11/240 (4%)

Query: 3   SIADREEETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPL 62
           S+   E+E   F +AM+LASA VLP V++A VELD+ EI++K+GPGA +S +E+ AQ+P 
Sbjct: 7   SLTQTEDEA--FVFAMQLASASVLPMVLKATVELDLLEIMAKSGPGAFISPSELAAQLPT 64

Query: 63  KDNNPEAAAMTLDRVLRLLVSYNALHCSFV---DG--QRLYSLAPVSAYFVRNNQNGASL 117
           K  NPEA  M LDR+ RLL +Y+ L+C+     DG  +RLYSLAPV  +  +N  +G S+
Sbjct: 65  K--NPEAPVM-LDRMFRLLATYSVLNCTLRTLPDGRVERLYSLAPVCKFLTKNG-DGVSI 120

Query: 118 SPYMALCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHT 177
           +P + +  DKV ++ W+ L   +L+GG+ FNKA+GM  ++Y G D RFN VFN GM  HT
Sbjct: 121 APILLMNQDKVLMESWYHLTDAVLDGGVPFNKAYGMTTFEYHGTDPRFNKVFNCGMSDHT 180

Query: 178 SIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPG 237
           ++ M+K+LE Y GFE +  +VDVGGG G T+NMI+SKYP IKGIN+DLP+VI+DAPSYPG
Sbjct: 181 TLSMKKILEDYTGFEGLNSIVDVGGGTGATVNMIVSKYPSIKGINFDLPHVIRDAPSYPG 240

Catalyzes the conversion of caffeic acid to ferulic acid and of 5-hydroxyferulic acid to sinapic acid. The resulting products may subsequently be converted to the corresponding alcohols that are incorporated into lignins.
Capsicum chinense (taxid: 80379)
EC: 2EC: .EC: 1EC: .EC: 1EC: .EC: 6EC: 8

>sp|Q8W013|COMT1_CATRO Caffeic acid 3-O-methyltransferase OS=Catharanthus roseus GN=COMT1 PE=2 SV=1

 Score =  254 bits (649), Expect = 4e-67,   Method: Compositional matrix adjust.
 Identities = 127/236 (53%), Positives = 175/236 (74%), Gaps = 10/236 (4%)

Query: 7   REEETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNN 66
           +EEE    S AM LASA VLP V+++ +ELD+ E+I K+GPGA +S +E+ AQ+P +  N
Sbjct: 14  KEEEEACLS-AMRLASASVLPMVLKSAIELDLLELIKKSGPGAYVSPSELAAQLPTQ--N 70

Query: 67  PEAAAMTLDRVLRLLVSYNALHCSFVDG-----QRLYSLAPVSAYFVRNNQNGASLSPYM 121
           P+A  M LDR+LRLL SY+ L+C+  D      +RLYSLAPV  +  +N ++G S++  +
Sbjct: 71  PDAPVM-LDRILRLLASYSVLNCTLKDLPDGGIERLYSLAPVCKFLTKN-EDGVSMAALL 128

Query: 122 ALCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIVM 181
            +  DKV ++ W+ LK  +LEGGI FNKA+GM  ++Y G D RFN VFN GM +H++I+M
Sbjct: 129 LMNQDKVLMESWYHLKDAVLEGGIPFNKAYGMTAFEYHGKDPRFNKVFNQGMSNHSTIIM 188

Query: 182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPG 237
           +K+LE Y+GF+ +K +VDVGGG G TLNMI+SKYP IKGIN+DLP+VI+DAPSYPG
Sbjct: 189 KKILEIYQGFQGLKTVVDVGGGTGATLNMIVSKYPSIKGINFDLPHVIEDAPSYPG 244

Catalyzes the conversion of caffeic acid to ferulic acid and of 5-hydroxyferulic acid to sinapic acid. The resulting products may subsequently be converted to the corresponding alcohols that are incorporated into lignins.

Catharanthus roseus (taxid: 4058)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 6

EC: 8

>sp|Q43046|COMT1_POPKI Caffeic acid 3-O-methyltransferase 1 OS=Populus kitakamiensis GN=HOMT1 PE=3 SV=1

 Score =  254 bits (648), Expect = 5e-67,   Method: Compositional matrix adjust.
 Identities = 125/227 (55%), Positives = 165/227 (72%), Gaps = 9/227 (3%)

Query: 16  YAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLD 75
           +AM+LASA VLP +++  +ELD+ EI++KAGPGA LS +EI + +P K  NP+A  M LD
Sbjct: 22  FAMQLASASVLPMILKTAIELDLLEIMAKAGPGAFLSTSEIASHLPTK--NPDAPVM-LD 78

Query: 76  RVLRLLVSYNALHCSFVD-----GQRLYSLAPVSAYFVRNNQNGASLSPYMALCLDKVCL 130
           R+LRLL SY+ L CS  D      +RLY LAPV  +  +N ++G S+SP   +  DKV +
Sbjct: 79  RILRLLASYSILTCSLKDLPDGKVERLYGLAPVCKFLTKN-EDGVSVSPLCLMNQDKVLM 137

Query: 131 DGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIVMEKVLESYKG 190
           + W+ LK  +LEGGI FNKA+GM  ++Y G D RFN VFN GM  H++I M+K+LE+YKG
Sbjct: 138 ESWYYLKDAILEGGIPFNKAYGMTAFEYHGTDPRFNKVFNKGMSDHSTITMKKILETYKG 197

Query: 191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPG 237
           FE +  LVDVGGG G  +N I+SKYP IKGIN+DLP+VI+DAPSYPG
Sbjct: 198 FEGLTSLVDVGGGTGAVVNTIVSKYPSIKGINFDLPHVIEDAPSYPG 244

Catalyzes the conversion of caffeic acid to ferulic acid and of 5-hydroxyferulic acid to sinapic acid. The resulting products may subsequently be converted to the corresponding alcohols that are incorporated into lignins.

Populus kitakamiensis (taxid: 34292)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 6

EC: 8

>sp|Q00763|COMT1_POPTM Caffeic acid 3-O-methyltransferase 1 OS=Populus tremuloides GN=OMT1 PE=1 SV=1

 Score =  253 bits (645), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 125/227 (55%), Positives = 165/227 (72%), Gaps = 9/227 (3%)

Query: 16  YAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLD 75
           +AM+LASA VLP +++  +ELD+ EI++KAGPGA LS +EI + +P K  NP+A  M LD
Sbjct: 22  FAMQLASASVLPMILKTAIELDLLEIMAKAGPGAFLSTSEIASHLPTK--NPDAPVM-LD 78

Query: 76  RVLRLLVSYNALHCSFVD-----GQRLYSLAPVSAYFVRNNQNGASLSPYMALCLDKVCL 130
           R+LRLL SY+ L CS  D      +RLY LAPV   F+  N++G S+SP   +  DKV +
Sbjct: 79  RILRLLASYSILTCSLKDLPDGKVERLYGLAPVCK-FLTKNEDGVSVSPLCLMNQDKVLM 137

Query: 131 DGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIVMEKVLESYKG 190
           + W+ LK  +L+GGI FNKA+GM  ++Y G D RFN VFN GM  H++I M+K+LE+YKG
Sbjct: 138 ESWYYLKDAILDGGIPFNKAYGMTAFEYHGTDPRFNKVFNKGMSDHSTITMKKILETYKG 197

Query: 191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPG 237
           FE +  LVDVGGG G  +N I+SKYP IKGIN+DLP+VI+DAPSYPG
Sbjct: 198 FEGLTSLVDVGGGTGAVVNTIVSKYPSIKGINFDLPHVIEDAPSYPG 244

Catalyzes the conversion of caffeic acid to ferulic acid and of 5-hydroxyferulic acid to sinapic acid. The resulting products may subsequently be converted to the corresponding alcohols that are incorporated into lignins.

Populus tremuloides (taxid: 3693)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 6

EC: 8

>sp|Q9XGV9|COMT2_OCIBA Caffeic acid 3-O-methyltransferase 2 OS=Ocimum basilicum GN=COMT2 PE=2 SV=1

 Score =  252 bits (644), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 131/246 (53%), Positives = 174/246 (70%), Gaps = 13/246 (5%)

Query: 1   MASIADR----EEETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEI 56
           M+S A+      +E  NF +AM+LASA VLP V+++ +ELD+ E+I KAG GA +S AE+
Sbjct: 1   MSSTANNPQINSDEEENFLFAMQLASASVLPMVLKSAIELDLLELIKKAGAGAFVSPAEL 60

Query: 57  VAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC---SFVDG--QRLYSLAPVSAYFVRNN 111
            AQ  L   N EA  M LDR+LRLL SY  L C   +  DG  QRLY LAPV  +  +N 
Sbjct: 61  AAQ--LLTTNAEAHVM-LDRILRLLTSYAILECRLKTLPDGGVQRLYGLAPVCKFLTKN- 116

Query: 112 QNGASLSPYMALCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNN 171
           ++G S++P   +  DKV ++ W+ LK  +L+GGI FNKA+GM  ++Y G D RFN VFN 
Sbjct: 117 EDGVSMAPLALMNQDKVLMESWYHLKDAVLDGGIPFNKAYGMTAFEYHGTDPRFNKVFNQ 176

Query: 172 GMLSHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKD 231
           GM +H++I M+K+LE+Y GF+ +K +VDVGGG G TLNMIISKYP IKGIN+DLP+V++D
Sbjct: 177 GMSNHSTITMKKILETYTGFDGLKTVVDVGGGTGATLNMIISKYPSIKGINFDLPHVVED 236

Query: 232 APSYPG 237
           APSYPG
Sbjct: 237 APSYPG 242

Catalyzes the conversion of caffeic acid to ferulic acid and of 5-hydroxyferulic acid to sinapic acid. The resulting products may subsequently be converted to the corresponding alcohols that are incorporated into lignins.

Ocimum basilicum (taxid: 39350)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 6

EC: 8

>sp|Q9FQY8|COMT1_CAPAN Caffeic acid 3-O-methyltransferase OS=Capsicum annuum GN=COMT PE=2 SV=2

 Score =  251 bits (640), Expect = 5e-66,   Method: Compositional matrix adjust.
 Identities = 123/235 (52%), Positives = 171/235 (72%), Gaps = 9/235 (3%)

Query: 8   EEETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNP 67
           + E   F +AM+LASA VLP V+++ +ELD+ EI++KAGPGA +S +E+ AQ+P K  NP
Sbjct: 10  QTEDEAFLFAMQLASASVLPMVLKSALELDLLEIMAKAGPGAAISPSELAAQLPTK--NP 67

Query: 68  EAAAMTLDRVLRLLVSYNALHCSFV---DG--QRLYSLAPVSAYFVRNNQNGASLSPYMA 122
           EA  M LDR+LRLL +Y+ L+C+     DG  +RLYSLAPV     +N  +G S++P + 
Sbjct: 68  EAPVM-LDRMLRLLATYSVLNCTLRTLPDGRVERLYSLAPVCKLLTKN-ADGVSVAPLLL 125

Query: 123 LCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIVME 182
           +  DKV ++ W+ L   +L+GG+ FNKA+GM  ++Y G D RFN VFN GM  H+++ M+
Sbjct: 126 MNQDKVLMESWYHLTDAVLDGGVPFNKAYGMTAFEYHGTDPRFNKVFNRGMSDHSTMTMK 185

Query: 183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPG 237
           K+LE YKGFE +  +VDVGGG G T+NMI+SKYP IKGIN+DL +VI+DAP+YPG
Sbjct: 186 KILEDYKGFEGLNSIVDVGGGTGATVNMIVSKYPSIKGINFDLSHVIEDAPAYPG 240

Catalyzes the conversion of caffeic acid to ferulic acid and of 5-hydroxyferulic acid to sinapic acid. The resulting products may subsequently be converted to the corresponding alcohols that are incorporated into lignins.

Capsicum annuum (taxid: 4072)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 6

EC: 8

>sp|Q9SWC2|COMT1_EUCGL Caffeic acid 3-O-methyltransferase (Fragment) OS=Eucalyptus globulus GN=COMT1 PE=3 SV=1

 Score =  250 bits (639), Expect = 6e-66,   Method: Compositional matrix adjust.
 Identities = 120/227 (52%), Positives = 167/227 (73%), Gaps = 9/227 (3%)

Query: 16  YAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLD 75
           +AM+LA+A VLPAV+ A +ELD+ EI+++AGPGA L+  E+ +Q+P +  NP+A  M LD
Sbjct: 4   FAMQLATASVLPAVLTAAIELDLLEIMARAGPGAYLTPGEVASQLPTQ--NPDAPVM-LD 60

Query: 76  RVLRLLVSYNALHCSFVD-----GQRLYSLAPVSAYFVRNNQNGASLSPYMALCLDKVCL 130
           R+ RLL SY+ L C+  D      +RLY LAP+  + V+N ++G SL+P   +  D+V L
Sbjct: 61  RIFRLLASYSVLTCTLCDLPEGKVERLYGLAPLCKFLVKN-EDGVSLAPLRLIDQDRVFL 119

Query: 131 DGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIVMEKVLESYKG 190
           + W+ +K  +LEGGI F+KAHGM  +DY G D RFN +FN  M  H++I+M+K+LE+Y G
Sbjct: 120 ESWYYMKDAILEGGIPFHKAHGMTAFDYPGTDPRFNKIFNRAMSDHSTIMMKKILETYNG 179

Query: 191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPG 237
           FE +K +VDVGGG G  LNMI++KYP IKGIN+DLP+VI+DAPSYPG
Sbjct: 180 FEGLKTVVDVGGGTGAILNMIVAKYPSIKGINFDLPHVIEDAPSYPG 226

Catalyzes the conversion of caffeic acid to ferulic acid and of 5-hydroxyferulic acid to sinapic acid. The resulting products may subsequently be converted to the corresponding alcohols that are incorporated into lignins.

Eucalyptus globulus (taxid: 34317)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 6

EC: 8

>sp|Q43609|COMT1_PRUDU Caffeic acid 3-O-methyltransferase OS=Prunus dulcis GN=COMT1 PE=2 SV=1

 Score =  248 bits (634), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 129/235 (54%), Positives = 167/235 (71%), Gaps = 11/235 (4%)

Query: 8   EEETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNP 67
           +EE N F  AM+LASA VLP V++A +ELD+ EI++KAGPG  LS  +I +Q+P K  NP
Sbjct: 16  DEEANLF--AMQLASASVLPMVLKAAIELDLLEIMAKAGPGVFLSPTDIASQLPTK--NP 71

Query: 68  EAAAMTLDRVLRLLVSYNALHCSF---VDG--QRLYSLAPVSAYFVRNNQNGASLSPYMA 122
           +A  M LDR+LRLL SY+ L  S     DG  +RLY L PV  +  +N + G S++P   
Sbjct: 72  DAPVM-LDRMLRLLASYSILTYSLRTLADGKVERLYGLGPVCKFLTKNEE-GVSIAPLCL 129

Query: 123 LCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIVME 182
           +  DKV L+ W+ LK  +LEGGI FNKA+GM  ++Y G D RFN VFN GM  H++I M+
Sbjct: 130 MNQDKVLLESWYHLKDAVLEGGIPFNKAYGMTAFEYHGTDPRFNKVFNRGMADHSTITMK 189

Query: 183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPG 237
           K+LE+YKGFE +  +VDVGGG G  LNMI+SKYP IKGIN+DLP+VI+DAP YPG
Sbjct: 190 KILETYKGFEGLTSVVDVGGGTGAVLNMIVSKYPSIKGINFDLPHVIEDAPQYPG 244

Catalyzes the conversion of caffeic acid to ferulic acid and of 5-hydroxyferulic acid to sinapic acid. The resulting products may subsequently be converted to the corresponding alcohols that are incorporated into lignins.

Prunus dulcis (taxid: 3755)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 6

EC: 8

>sp|Q9XGW0|COMT1_OCIBA Caffeic acid 3-O-methyltransferase 1 OS=Ocimum basilicum GN=COMT1 PE=2 SV=1

 Score =  248 bits (634), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 122/234 (52%), Positives = 169/234 (72%), Gaps = 9/234 (3%)

Query: 9   EETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPE 68
           +E  NF +AM+LASA VLP V+++ +ELD+ E+I K+G GA +S  ++ AQ+P    NP+
Sbjct: 13  DEEENFLFAMQLASASVLPMVLKSAIELDLLELIKKSGAGAFVSPVDLAAQLPT--TNPD 70

Query: 69  AAAMTLDRVLRLLVSYNALHC---SFVDG--QRLYSLAPVSAYFVRNNQNGASLSPYMAL 123
           A  M LDR+LRLL SY  L C   +  DG  +RLY LAPV  +  +N ++G S++P   +
Sbjct: 71  AHVM-LDRILRLLTSYAILECRLKTLPDGGVERLYGLAPVCKFLTKN-EDGVSMAPLTLM 128

Query: 124 CLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIVMEK 183
             DKV ++ W+ L   +++GGI FNKA+GM  ++Y G D RFN VFN GM +H++I M+K
Sbjct: 129 NQDKVLMESWYHLSDAVVDGGIPFNKAYGMTAFEYHGTDPRFNKVFNQGMSNHSTITMKK 188

Query: 184 VLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPG 237
           +LE+Y GF+ +K +VDVGGG G TLNMI+SKYP IKGIN+DLP+VI+DAPSYPG
Sbjct: 189 ILETYTGFDGLKTVVDVGGGTGATLNMIVSKYPSIKGINFDLPHVIEDAPSYPG 242

Catalyzes the conversion of caffeic acid to ferulic acid and of 5-hydroxyferulic acid to sinapic acid. The resulting products may subsequently be converted to the corresponding alcohols that are incorporated into lignins.

Ocimum basilicum (taxid: 39350)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 6

EC: 8

>sp|Q8LL87|COMT1_COFCA Caffeic acid 3-O-methyltransferase OS=Coffea canephora PE=2 SV=1

 Score =  247 bits (631), Expect = 4e-65,   Method: Compositional matrix adjust.
 Identities = 126/235 (53%), Positives = 172/235 (73%), Gaps = 11/235 (4%)

Query: 8   EEETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNP 67
           EEE   F  AM LASA VLP V+++ +ELD+ E+I+KAGPGA +S +E+ AQ+P   +NP
Sbjct: 3   EEEACLF--AMSLASASVLPMVLKSAIELDLLELIAKAGPGAYVSPSELAAQLP--THNP 58

Query: 68  EAAAMTLDRVLRLLVSYNALHC---SFVDG--QRLYSLAPVSAYFVRNNQNGASLSPYMA 122
           EA  M LDR+LRLL +Y+ L C   +  DG  +RLY LAPV  +  +N  +G S++P + 
Sbjct: 59  EAPIM-LDRILRLLATYSVLDCKLNNLADGGVERLYGLAPVCKFLTKN-ADGVSMAPLLL 116

Query: 123 LCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIVME 182
           +  DKV ++ W+ LK  +L+GGI FNKA+GM  ++Y G D RFN VFN GM +H++I M+
Sbjct: 117 MNQDKVLMESWYHLKDAVLDGGIPFNKAYGMTAFEYHGTDPRFNKVFNQGMSNHSTITMK 176

Query: 183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPG 237
           K+LE Y+GFE +K +VDVGGG G TLNMIISKYP IKGIN++LP+V++DAPS+ G
Sbjct: 177 KILEVYRGFEGLKTVVDVGGGTGATLNMIISKYPTIKGINFELPHVVEDAPSHSG 231

Catalyzes the conversion of caffeic acid to ferulic acid and of 5-hydroxyferulic acid to sinapic acid. The resulting products may subsequently be converted to the corresponding alcohols that are incorporated into lignins.

Coffea canephora (taxid: 49390)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 6

EC: 8

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	244
255548061	359	o-methyltransferase, putative [Ricinus c	0.930	0.632	0.6	1e-70
97974184	364	Caffeic acid 3-O-methyltransferase [Ipom	0.946	0.634	0.553	1e-68
97974173	364	Caffeic acid 3-O-methyltransferase [Ipom	0.946	0.634	0.549	2e-68
359490765	360	PREDICTED: caffeic acid 3-O-methyltransf	0.942	0.638	0.560	4e-68
359490763	364	PREDICTED: caffeic acid 3-O-methyltransf	0.942	0.631	0.560	5e-68
71482940	362	S-methyltransferase [Catharanthus roseus	0.954	0.643	0.508	9e-67
224128073	358	catechol o-methyltransferase related [Po	0.926	0.631	0.539	4e-66
388504612	365	unknown [Lotus japonicus]	0.918	0.613	0.565	7e-66
154091348	365	caffeic acid O-methyl transferase [Leuca	0.918	0.613	0.557	1e-65
307090030	363	caffeic acid O-methyltransferase [Camell	0.938	0.630	0.537	1e-65

>gi|255548061|ref|XP_002515087.1| o-methyltransferase, putative [Ricinus communis] gi|223545567|gb|EEF47071.1| o-methyltransferase, putative [Ricinus communis]

 Score =  271 bits (694), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 138/230 (60%), Positives = 168/230 (73%), Gaps = 3/230 (1%)

Query: 8   EEETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNP 67
           EE   NF YAM+LA    LP  + A +EL VFEII+KAGP +KLS +EI A+IP    NP
Sbjct: 14  EEHDENFGYAMQLALGSALPMSLHAAIELGVFEIIAKAGPESKLSASEITAEIP-DVQNP 72

Query: 68  EAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFVRNNQNGASLSPYMALCLDK 127
           +AA +TLDRVLRLL S+N L CS    +RLYSL PVS YFV N Q+G SL P+MAL  DK
Sbjct: 73  DAA-ITLDRVLRLLASHNVLGCSLNGLERLYSLNPVSKYFVPN-QDGISLGPFMALIQDK 130

Query: 128 VCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIVMEKVLES 187
           V LD W  LK  +LEGG  FNK HG   + Y G+DSRFN VFN  M  HT++V+ K+LE+
Sbjct: 131 VFLDSWTKLKDAVLEGGSPFNKFHGTHCFGYSGLDSRFNHVFNTAMFHHTNLVITKILET 190

Query: 188 YKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPG 237
           YKGF+ +K+L+DVGGGLG TL  IISKYPH+KGIN+DLP+V+K AP+ PG
Sbjct: 191 YKGFKQLKQLIDVGGGLGHTLKAIISKYPHLKGINFDLPHVVKYAPAIPG 240

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|97974184|dbj|BAE94403.1| Caffeic acid 3-O-methyltransferase [Ipomoea nil]

 Score =  265 bits (678), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 134/242 (55%), Positives = 179/242 (73%), Gaps = 11/242 (4%)

Query: 1   MASIADREEETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQI 60
           M +  D +EE + F  AM+LASA VLP V+++ +ELD+ E+I+KAGPGA +S +E+ AQ+
Sbjct: 10  MTNRVDSDEEASLF--AMQLASASVLPMVLKSAIELDLLELIAKAGPGAAVSPSELAAQL 67

Query: 61  PLKDNNPEAAAMTLDRVLRLLVSYNALHCSFV---DG--QRLYSLAPVSAYFVRNNQNGA 115
           P    NP+AA M LDR+LRLL +Y+ L+CS     DG  +RLYSLAPV  Y  +N  +G 
Sbjct: 68  PT--TNPDAAVM-LDRILRLLCTYSVLNCSLRTLPDGRVERLYSLAPVCKYLTKNG-DGV 123

Query: 116 SLSPYMALCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLS 175
           S++P + +  DKV ++ W+ LK  +LEGGI FNKA+GM  ++Y G D RFN VFN GM  
Sbjct: 124 SMAPLLLMNQDKVLMESWYHLKDAVLEGGIPFNKAYGMTAFEYHGTDPRFNKVFNRGMSD 183

Query: 176 HTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSY 235
           H++I M+K+L+ YKGFE +K LVDVGGG G TLNMI+SKYP+IKGIN+DLP+VI+DAP Y
Sbjct: 184 HSTITMKKILDDYKGFEGLKSLVDVGGGTGATLNMILSKYPNIKGINFDLPHVIEDAPKY 243

Query: 236 PG 237
           PG
Sbjct: 244 PG 245

Source: Ipomoea nil

Species: Ipomoea nil

Genus: Ipomoea

Family: Convolvulaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|97974173|dbj|BAE94400.1| Caffeic acid 3-O-methyltransferase [Ipomoea nil] gi|97974195|dbj|BAE94406.1| Caffeic acid 3-O-methyltransferase [Ipomoea nil]

 Score =  264 bits (675), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 133/242 (54%), Positives = 179/242 (73%), Gaps = 11/242 (4%)

Query: 1   MASIADREEETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQI 60
           M +  D +EE + F  AM+LASA VLP V+++ +ELD+ E+I+KAGPGA +S +E+ AQ+
Sbjct: 10  MTNRVDSDEEASLF--AMQLASASVLPMVLKSAIELDLLELIAKAGPGAAVSPSELAAQL 67

Query: 61  PLKDNNPEAAAMTLDRVLRLLVSYNALHCSFV---DG--QRLYSLAPVSAYFVRNNQNGA 115
           P    NP+AA M LDR+LRLL +Y+ L+CS     DG  +RLYSLAPV  Y  +N  +G 
Sbjct: 68  PT--TNPDAAVM-LDRILRLLCTYSVLNCSLRTLPDGRVERLYSLAPVCKYLTKNG-DGV 123

Query: 116 SLSPYMALCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLS 175
           S++P + +  DKV ++ W+ LK  +LEGGI FNKA+GM  ++Y G D RFN VFN GM  
Sbjct: 124 SMAPLLLMNQDKVLMESWYHLKDAVLEGGIPFNKAYGMTAFEYHGTDPRFNKVFNRGMSD 183

Query: 176 HTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSY 235
           H++I M+K+L+ YKGFE +K LVDVGGG G TLNMI+SKYP+IKGIN+DLP+VI+D+P Y
Sbjct: 184 HSTITMKKILDDYKGFEGLKSLVDVGGGTGATLNMILSKYPNIKGINFDLPHVIEDSPKY 243

Query: 236 PG 237
           PG
Sbjct: 244 PG 245

Source: Ipomoea nil

Species: Ipomoea nil

Genus: Ipomoea

Family: Convolvulaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359490765|ref|XP_003634162.1| PREDICTED: caffeic acid 3-O-methyltransferase 1-like isoform 2 [Vitis vinifera]

 Score =  263 bits (673), Expect = 4e-68,   Method: Compositional matrix adjust.
 Identities = 135/241 (56%), Positives = 176/241 (73%), Gaps = 11/241 (4%)

Query: 2   ASIADREEETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIP 61
            +I + +EE + FS  M+L SA VLP V+++ +ELD+ EII+KAGPGA +S +EI AQIP
Sbjct: 9   TTILESDEEASLFS--MQLVSASVLPMVLKSALELDLLEIIAKAGPGAFVSTSEIAAQIP 66

Query: 62  LKDNNPEAAAMTLDRVLRLLVSYNALHCSF---VDG--QRLYSLAPVSAYFVRNNQNGAS 116
              +NPEA  M LDR+LRLL +Y  + CS     DG  +RLY LAPV  Y  RN ++G S
Sbjct: 67  --THNPEAPVM-LDRILRLLATYAVVKCSLRNLPDGGVERLYGLAPVCKYLTRN-EDGVS 122

Query: 117 LSPYMALCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSH 176
           ++P + +  DKV ++ W+ LK  +L+GGI FNKA+GM  ++Y G D RFN VFNNGM  H
Sbjct: 123 VAPLLLMNQDKVLMESWYYLKDAVLDGGIPFNKAYGMTAFEYHGTDPRFNKVFNNGMSGH 182

Query: 177 TSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYP 236
           ++I M+K+LE+YKGFE +  +VDVGGG G TLNMIISKYP IKGIN+DLP+VI DAPSYP
Sbjct: 183 STITMKKILEAYKGFEGLTSIVDVGGGTGATLNMIISKYPTIKGINFDLPHVIDDAPSYP 242

Query: 237 G 237
           G
Sbjct: 243 G 243

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359490763|ref|XP_003634161.1| PREDICTED: caffeic acid 3-O-methyltransferase 1-like isoform 1 [Vitis vinifera]

 Score =  263 bits (672), Expect = 5e-68,   Method: Compositional matrix adjust.
 Identities = 135/241 (56%), Positives = 176/241 (73%), Gaps = 11/241 (4%)

Query: 2   ASIADREEETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIP 61
            +I + +EE + FS  M+L SA VLP V+++ +ELD+ EII+KAGPGA +S +EI AQIP
Sbjct: 9   TTILESDEEASLFS--MQLVSASVLPMVLKSALELDLLEIIAKAGPGAFVSTSEIAAQIP 66

Query: 62  LKDNNPEAAAMTLDRVLRLLVSYNALHCSF---VDG--QRLYSLAPVSAYFVRNNQNGAS 116
              +NPEA  M LDR+LRLL +Y  + CS     DG  +RLY LAPV  Y  RN ++G S
Sbjct: 67  --THNPEAPVM-LDRILRLLATYAVVKCSLRNLPDGGVERLYGLAPVCKYLTRN-EDGVS 122

Query: 117 LSPYMALCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSH 176
           ++P + +  DKV ++ W+ LK  +L+GGI FNKA+GM  ++Y G D RFN VFNNGM  H
Sbjct: 123 VAPLLLMNQDKVLMESWYYLKDAVLDGGIPFNKAYGMTAFEYHGTDPRFNKVFNNGMSGH 182

Query: 177 TSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYP 236
           ++I M+K+LE+YKGFE +  +VDVGGG G TLNMIISKYP IKGIN+DLP+VI DAPSYP
Sbjct: 183 STITMKKILEAYKGFEGLTSIVDVGGGTGATLNMIISKYPTIKGINFDLPHVIDDAPSYP 242

Query: 237 G 237
           G
Sbjct: 243 G 243

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|71482940|gb|AAZ32409.1| S-methyltransferase [Catharanthus roseus]

 Score =  259 bits (661), Expect = 9e-67,   Method: Compositional matrix adjust.
 Identities = 123/242 (50%), Positives = 181/242 (74%), Gaps = 9/242 (3%)

Query: 5   ADREEETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKD 64
           +  +E+ ++ SYA++L  +  LP V+ AV++L+VFEII+KAGPGAKLS ++IV+Q+P K 
Sbjct: 9   SSNKEDDDHSSYALQLVFSGALPMVLNAVIKLNVFEIIAKAGPGAKLSPSQIVSQMPTK- 67

Query: 65  NNPEAAAMTLDRVLRLLVSYNALHCSFVD-----GQRLYSLAPVSAYFVRNNQNGASLSP 119
            NPEA  + LDR+LR+L SY+ L CS VD     GQR+Y L+PVS YFV+N +NG    P
Sbjct: 68  -NPEAP-VVLDRMLRMLASYSVLTCSVVDFSHGSGQRVYGLSPVSKYFVKN-ENGGCFGP 124

Query: 120 YMALCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSI 179
            + L  DKV  D W+ L   +LEGG AFN+A+ M I+ Y G++ +FN+ FN   ++H  +
Sbjct: 125 LLDLLQDKVLTDIWYELAPAVLEGGTAFNRAYNMHIFKYTGINQKFNETFNTATINHAKV 184

Query: 180 VMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPGTL 239
           +++++L++YKGFE++K LVDVGGGLG+TL++I SKYP++KGINYDLP+V ++AP+YPG +
Sbjct: 185 IVQEILKNYKGFENLKTLVDVGGGLGVTLDLITSKYPNLKGINYDLPHVTQNAPTYPGVV 244

Query: 240 FI 241
            +
Sbjct: 245 HV 246

Source: Catharanthus roseus

Species: Catharanthus roseus

Genus: Catharanthus

Family: Apocynaceae

Order: Gentianales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224128073|ref|XP_002320237.1| catechol o-methyltransferase related [Populus trichocarpa] gi|118481911|gb|ABK92890.1| unknown [Populus trichocarpa] gi|222861010|gb|EEE98552.1| catechol o-methyltransferase related [Populus trichocarpa]

 Score =  256 bits (655), Expect = 4e-66,   Method: Compositional matrix adjust.
 Identities = 124/230 (53%), Positives = 170/230 (73%), Gaps = 4/230 (1%)

Query: 8   EEETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNP 67
           E +  NF YAM+LA + VLP  M + ++L +FEII+KAGP AKLS +++ AQ+P K  NP
Sbjct: 14  EAKDENFGYAMQLALSSVLPMTMYSAIQLGIFEIIAKAGPDAKLSASDVAAQLPTK--NP 71

Query: 68  EAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFVRNNQNGASLSPYMALCLDK 127
           +A  M LDR+LRLL S++ L CS    +RLYSLAPVS ++VRN ++G SL P+MAL  D 
Sbjct: 72  DAP-MMLDRILRLLASHDVLGCSVDGSERLYSLAPVSKHYVRN-KDGVSLGPFMALIQDN 129

Query: 128 VCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIVMEKVLES 187
           V L  W  LK  +LEGG+AF++ HG   ++Y G+D RFN VFN  M + T++V+E +LE+
Sbjct: 130 VFLQSWSQLKDAVLEGGVAFDRVHGAHAFEYPGLDPRFNQVFNTAMYNQTTVVLENMLEA 189

Query: 188 YKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPG 237
           Y GF+++K+LV++GGG+G T+  IISKYP IKGIN+DLP+VI+ APS PG
Sbjct: 190 YTGFKNLKQLVEIGGGMGHTIKAIISKYPQIKGINFDLPHVIEHAPSCPG 239

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388504612|gb|AFK40372.1| unknown [Lotus japonicus]

 Score =  256 bits (653), Expect = 7e-66,   Method: Compositional matrix adjust.
 Identities = 133/235 (56%), Positives = 171/235 (72%), Gaps = 11/235 (4%)

Query: 8   EEETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNP 67
           +EE N F  AM+LASA VLP V+++ +ELD+ E I+KAG GA+LS AEI +Q+P    NP
Sbjct: 16  DEEANLF--AMQLASASVLPMVLKSAIELDLLEFIAKAGTGAQLSPAEIASQLPT--TNP 71

Query: 68  EAAAMTLDRVLRLLVSYNALHCSF---VDG--QRLYSLAPVSAYFVRNNQNGASLSPYMA 122
           +A  + LDR+LRLL  YN L CS     DG  QRLY LAPV+ Y V+N ++G S+S    
Sbjct: 72  DAPTV-LDRMLRLLACYNILTCSVRTEQDGKVQRLYGLAPVAKYLVKN-EDGVSISALNL 129

Query: 123 LCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIVME 182
           +  DKV ++ W+ LK  +LEGGI FNKA+GM  ++Y G D RFN VFN GM  H++I M+
Sbjct: 130 MNQDKVLMESWYHLKDAVLEGGIPFNKAYGMTAFEYHGTDPRFNKVFNKGMSDHSTITMK 189

Query: 183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPG 237
           K+LE+Y GFE +K LVDVGGG G  +NMI+SKYP IKGIN+DLP+VI+DAPSYPG
Sbjct: 190 KILETYTGFEGLKSLVDVGGGTGAVINMIVSKYPTIKGINFDLPHVIEDAPSYPG 244

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|154091348|gb|ABS57468.1| caffeic acid O-methyl transferase [Leucaena leucocephala] gi|155966780|gb|ABU41320.1| caffeic acid o-methyl transferase [Leucaena leucocephala]

 Score =  255 bits (652), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 131/235 (55%), Positives = 172/235 (73%), Gaps = 11/235 (4%)

Query: 8   EEETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNP 67
           +EE N F  AM+LASA VLP ++++ +ELD+ EII+KAGP A+LS + I AQ+P K  NP
Sbjct: 16  DEEANLF--AMQLASASVLPMILKSALELDLLEIIAKAGPNAQLSPSNIAAQLPTK--NP 71

Query: 68  EAAAMTLDRVLRLLVSYNALHCS---FVDG--QRLYSLAPVSAYFVRNNQNGASLSPYMA 122
           +AA M LDR++RLL  YN L CS     DG  +RLY LAPV+ Y V+N ++G S++P   
Sbjct: 72  DAAVM-LDRMMRLLACYNVLSCSVRTLPDGKIERLYGLAPVAKYLVKN-EDGVSIAPLNL 129

Query: 123 LCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIVME 182
           +  DKV ++ W+ LK  +LEGGI FNKAHGM  ++Y G D RFN VFN GM  H++I M+
Sbjct: 130 MNQDKVLMESWYYLKDAVLEGGIPFNKAHGMTSFEYHGKDLRFNKVFNKGMADHSTITMK 189

Query: 183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPG 237
           K+LE+Y GFE +  LVDVGGG G  ++MI+SKYP I GIN+DLP+VI+DAPSYPG
Sbjct: 190 KILETYTGFEGLTSLVDVGGGTGAVISMIVSKYPSINGINFDLPHVIEDAPSYPG 244

Source: Leucaena leucocephala

Species: Leucaena leucocephala

Genus: Leucaena

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|307090030|gb|ADN27527.1| caffeic acid O-methyltransferase [Camellia sinensis]

 Score =  255 bits (651), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 129/240 (53%), Positives = 175/240 (72%), Gaps = 11/240 (4%)

Query: 3   SIADREEETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPL 62
           +I   EEE   F  AM+LASA VLP V+++ +ELD+ EI++KAGPGA +S +E+ AQ+P 
Sbjct: 9   TIHTDEEEACLF--AMQLASASVLPMVLKSAIELDLLEIMAKAGPGAYVSPSEVAAQLPT 66

Query: 63  KDNNPEAAAMTLDRVLRLLVSYNALHCSFVD-----GQRLYSLAPVSAYFVRNNQNGASL 117
           K  NP+AA M LDR+LRLL SY+ L+C+  D      +RLY LAPV  +  RN  +G S+
Sbjct: 67  K--NPDAAVM-LDRILRLLTSYSVLNCTLRDLPNGGVERLYGLAPVCKFLTRN-ADGVSM 122

Query: 118 SPYMALCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHT 177
           +P + +  DKV ++ W+ LK  +LEGGI FNKA+GM  ++Y G D RFN VFN GM +H+
Sbjct: 123 APLLLMNQDKVLMESWYYLKDTVLEGGIPFNKAYGMTAFEYHGTDPRFNKVFNQGMSNHS 182

Query: 178 SIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPG 237
           +I M+K+L+ Y GF+ +  +VDVGGG G TLNMI+SK+P IKGIN+DLP+VI+DAPSYPG
Sbjct: 183 TITMKKILDIYGGFDGLTTVVDVGGGTGATLNMIVSKHPTIKGINFDLPHVIEDAPSYPG 242

Source: Camellia sinensis

Species: Camellia sinensis

Genus: Camellia

Family: Theaceae

Order: Ericales

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	244
TAIR|locus:2153423	363	OMT1 "AT5G54160" [Arabidopsis	0.872	0.586	0.5	8e-53
UNIPROTKB|Q6ZD89	368	ROMT-9 "Flavone 3'-O-methyltra	0.942	0.625	0.403	1e-43
UNIPROTKB|Q84N28	360	OMT1 "Flavone O-methyltransfer	0.954	0.647	0.410	2.2e-43
TAIR|locus:2204695	381	AT1G77530 [Arabidopsis thalian	0.901	0.577	0.395	2.6e-40
TAIR|locus:2204680	381	AT1G77520 [Arabidopsis thalian	0.901	0.577	0.386	3.7e-39
TAIR|locus:2199582	373	IGMT4 "indole glucosinolate O-	0.893	0.584	0.403	5.5e-38
TAIR|locus:2030081	367	IGMT5 "indole glucosinolate O-	0.926	0.615	0.378	5.5e-38
TAIR|locus:2199587	373	IGMT2 "indole glucosinolate O-	0.893	0.584	0.403	1.9e-37
TAIR|locus:2199607	373	IGMT1 "indole glucosinolate O-	0.893	0.584	0.399	3e-37
TAIR|locus:2038026	352	AT1G33030 [Arabidopsis thalian	0.922	0.639	0.371	3.9e-37

TAIR|locus:2153423 OMT1 "AT5G54160" [Arabidopsis thaliana (taxid:3702)]

 Score = 547 (197.6 bits), Expect = 8.0e-53, P = 8.0e-53
 Identities = 115/230 (50%), Positives = 159/230 (69%)

Query:    16 YAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLD 75
             +AM+LASA VLP  +++ +ELD+ EI++K G  + +S  EI +++P K  NPEA  M LD
Sbjct:    22 FAMQLASASVLPMALKSALELDLLEIMAKNG--SPMSPTEIASKLPTK--NPEAPVM-LD 76

Query:    76 RVLRLLVSYNALHCS----FVDG-QRLYSLAPVSAYFVRNNQNGASLSPYMALCL---DK 127
             R+LRLL SY+ L CS      DG +R+Y L PV  Y  +N ++G S++   ALCL   DK
Sbjct:    77 RILRLLTSYSVLTCSNRKLSGDGVERIYGLGPVCKYLTKN-EDGVSIA---ALCLMNQDK 132

Query:   128 VCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIVMEKVLES 187
             V ++ W+ LK  +L+GGI FNKA+GM  ++Y G D RFN VFNNGM +H++I M+K+LE+
Sbjct:   133 VLMESWYHLKDAILDGGIPFNKAYGMSAFEYHGTDPRFNKVFNNGMSNHSTITMKKILET 192

Query:   188 YKGFEHXXXXXXXXXXXXITLNMIISKYPHIKGINYDLPYVIKDAPSYPG 237
             YKGFE              TL MI+SKYP++KGIN+DLP+VI+DAPS+PG
Sbjct:   193 YKGFEGLTSLVDVGGGIGATLKMIVSKYPNLKGINFDLPHVIEDAPSHPG 242

GO:0030744 "luteolin O-methyltransferase activity" evidence=IDA

GO:0030755 "quercetin 3-O-methyltransferase activity" evidence=IDA

GO:0033799 "myricetin 3'-O-methyltransferase activity" evidence=IDA

GO:0047763 "caffeate O-methyltransferase activity" evidence=ISS;IMP

GO:0051555 "flavonol biosynthetic process" evidence=IDA

GO:0009809 "lignin biosynthetic process" evidence=IMP

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

GO:0009506 "plasmodesma" evidence=IDA

GO:0006598 "polyamine catabolic process" evidence=RCA

GO:0009611 "response to wounding" evidence=RCA

GO:0009698 "phenylpropanoid metabolic process" evidence=RCA

GO:0009805 "coumarin biosynthetic process" evidence=RCA

GO:0009963 "positive regulation of flavonoid biosynthetic process" evidence=RCA

GO:0016126 "sterol biosynthetic process" evidence=RCA

GO:0042398 "cellular modified amino acid biosynthetic process" evidence=RCA

GO:0005829 "cytosol" evidence=TAS

UNIPROTKB|Q6ZD89 ROMT-9 "Flavone 3'-O-methyltransferase 1" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 461 (167.3 bits), Expect = 1.0e-43, P = 1.0e-43
 Identities = 100/248 (40%), Positives = 150/248 (60%)

Query:     1 MASIADREEETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKA---GPGAK---LSVA 54
             MA+ AD E       YA++LAS+ +LP  ++  +EL + E +  A   G G K   L+ A
Sbjct:     8 MAAAADEEA----CMYALQLASSSILPMTLKNAIELGLLETLQSAAVAGGGGKAALLTPA 63

Query:    55 EIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDG-----QRLYSLAPVSAYFVR 109
             E+  ++P K N P AA M +DR+LRLL SYN + C   +G      R Y+ APV  +   
Sbjct:    64 EVADKLPSKAN-PAAADM-VDRMLRLLASYNVVRCEMEEGADGKLSRRYAAAPVCKWLTP 121

Query:   110 NNQNGASLSPYMALCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVF 169
             N ++G S++    +  DKV ++ W+ LK  +L+GGI FNKA+GM  ++Y G D+RFN VF
Sbjct:   122 N-EDGVSMAALALMNQDKVLMESWYYLKDAVLDGGIPFNKAYGMTAFEYHGTDARFNRVF 180

Query:   170 NNGMLSHTSIVMEKVLESYKGFEHXXXXXXXXXXXXITLNMIISKYPHIKGINYDLPYVI 229
             N GM +H+ I+ +K+L+ Y GF+              T+  ++S++PHI+GINYDLP+VI
Sbjct:   181 NEGMKNHSVIITKKLLDLYTGFDAASTVVDVGGGVGATVAAVVSRHPHIRGINYDLPHVI 240

Query:   230 KDAPSYPG 237
              +AP +PG
Sbjct:   241 SEAPPFPG 248

GO:0030744 "luteolin O-methyltransferase activity" evidence=IDA

GO:0032259 "methylation" evidence=IDA

UNIPROTKB|Q84N28 OMT1 "Flavone O-methyltransferase 1" [Triticum aestivum (taxid:4565)]

 Score = 458 (166.3 bits), Expect = 2.2e-43, P = 2.2e-43
 Identities = 101/246 (41%), Positives = 147/246 (59%)

Query:     1 MASIADREEETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQI 60
             MA+ AD E       YA++L S+ +LP  ++  +EL + E +  AG G  L+ AE+ A++
Sbjct:     8 MAASADEEA----CMYALQLVSSSILPMTLKNAIELGLLETLVAAG-GKLLTPAEVAAKL 62

Query:    61 PLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQ-----RLYSLAPVSAYFVRNNQNGA 115
             P    NP AA M +DR+LRLL SYN + C+  +G+     R Y  APV   F+  N++G 
Sbjct:    63 P-STANPAAADM-VDRMLRLLASYNVVSCTMEEGKDGRLSRRYRAAPVCK-FLTPNEDGV 119

Query:   116 SLSPYMALCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLS 175
             S++    +  DKV ++ W+ LK  +L+GGI FNKA+GM  ++Y G D RFN VFN GM +
Sbjct:   120 SMAALALMNQDKVLMESWYYLKDAVLDGGIPFNKAYGMSAFEYHGTDPRFNRVFNEGMKN 179

Query:   176 HTSIVMEKVLESYKGFEHXXXXXXXXXXXXITLNMIISKYPHIKGINYDLPYVIKDAPSY 235
             H+ I+ +K+LE YKGFE              T+  I + YP IKGIN+DLP+VI +A  +
Sbjct:   180 HSIIITKKLLEVYKGFEGLGTIVDVGGGVGATVGAITAAYPAIKGINFDLPHVISEAQPF 239

Query:   236 PGTLFI 241
             PG   +
Sbjct:   240 PGVTHV 245

GO:0009611 "response to wounding" evidence=IDA

GO:0009723 "response to ethylene stimulus" evidence=IDA

GO:0009751 "response to salicylic acid stimulus" evidence=IDA

GO:0042542 "response to hydrogen peroxide" evidence=IDA

TAIR|locus:2204695 AT1G77530 [Arabidopsis thaliana (taxid:3702)]

 Score = 429 (156.1 bits), Expect = 2.6e-40, P = 2.6e-40
 Identities = 91/230 (39%), Positives = 135/230 (58%)

Query:    17 AMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDR 76
             A  + +A+  P V++A +EL V + I+ A  G  LS +EI   +P K  NPEA  + LDR
Sbjct:    33 AESIVNAVAFPMVLKAALELGVIDTIAAASNGTWLSPSEIAVSLPNKPTNPEAPVL-LDR 91

Query:    77 VLRLLVSYNALHCSFVD----GQ-----RLYSLAPVSAYFVRNNQNGASLSPYMALCLDK 127
             +LRLLVS++ L C  V+    GQ     R+Y+  P+  YF++++    SLS  + L   +
Sbjct:    92 MLRLLVSHSILKCCMVESRENGQTGKIERVYAAEPICKYFLKDSDGSGSLSSLLLLLHSQ 151

Query:   128 VCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIVMEKVLES 187
             V L  W  LK  +LEG  AF+ AH M++++Y+  D +F+ +F+  M   +++VM+KVLE 
Sbjct:   152 VILKTWTNLKDVILEGKDAFSSAHDMRLFEYISSDDQFSKLFHRAMSESSTMVMKKVLEE 211

Query:   188 YKGFEHXXXXXXXXXXXXITLNMIISKYPHIKGINYDLPYVIKDAPSYPG 237
             Y+GFE               L +I SKYPHIKG+N+DL  V+  AP YPG
Sbjct:   212 YRGFEDVNTLVDVGGGIGTILGLITSKYPHIKGVNFDLAQVLTQAPFYPG 261

GO:0005634 "nucleus" evidence=ISM

GO:0008168 "methyltransferase activity" evidence=IEA

GO:0008171 "O-methyltransferase activity" evidence=IEA;ISS

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0009809 "lignin biosynthetic process" evidence=ISS

GO:0005829 "cytosol" evidence=TAS

TAIR|locus:2204680 AT1G77520 [Arabidopsis thaliana (taxid:3702)]

 Score = 418 (152.2 bits), Expect = 3.7e-39, P = 3.7e-39
 Identities = 89/230 (38%), Positives = 129/230 (56%)

Query:    17 AMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDR 76
             A  + + +  P V++A  EL V + I+ AG    LS  EI   +P K  NPEA  + LDR
Sbjct:    33 AESIVNTVAFPMVLKAAFELGVIDTIAAAGNDTWLSPCEIACSLPTKPTNPEAPVL-LDR 91

Query:    77 VLRLLVSYNALHCSFVD-GQ--------RLYSLAPVSAYFVRNNQNGASLSPYMALCLDK 127
             +L LLVS++ L C  ++ G+        R+Y+  PV  YF+R++    SL P   L   +
Sbjct:    92 MLSLLVSHSILKCRMIETGENGRTGKIERVYAAEPVCKYFLRDSDGTGSLVPLFMLLHTQ 151

Query:   128 VCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIVMEKVLES 187
             V    W  LK  +LEG  AFN AHGM+I++Y+  D  F ++FN  M   ++++M+KVL+ 
Sbjct:   152 VFFKTWTNLKDVILEGRDAFNSAHGMKIFEYINSDQPFAELFNRAMSEPSTMIMKKVLDV 211

Query:   188 YKGFEHXXXXXXXXXXXXITLNMIISKYPHIKGINYDLPYVIKDAPSYPG 237
             Y+GFE               L ++ SKYPHIKG+N+DL  V+  AP YPG
Sbjct:   212 YRGFEDVNTLVDVGGGNGTVLGLVTSKYPHIKGVNFDLAQVLTQAPFYPG 261

GO:0005634 "nucleus" evidence=ISM

GO:0008168 "methyltransferase activity" evidence=IEA

GO:0008171 "O-methyltransferase activity" evidence=IEA;ISS

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0009809 "lignin biosynthetic process" evidence=ISS

GO:0005829 "cytosol" evidence=TAS

TAIR|locus:2199582 IGMT4 "indole glucosinolate O-methyltransferase 4" [Arabidopsis thaliana (taxid:3702)]

 Score = 407 (148.3 bits), Expect = 5.5e-38, P = 5.5e-38
 Identities = 92/228 (40%), Positives = 138/228 (60%)

Query:    17 AMELASAIVLPAVMQAVVELDVFEII-SKAGPGAK-LSVAEIVAQIPLKDNNPEAAAMTL 74
             A+ LA+A   P V++A +EL VF+ + ++A      LS +EI +++P    NPEA  + L
Sbjct:    29 AVRLANAAAFPMVLKAALELGVFDTLYAEASRSDSFLSPSEIASKLPTTPRNPEAPVL-L 87

Query:    75 DRVLRLLVSYNALHCSFVD---GQRLYSLAPVSAYFVRNN-QNGASLSPYMALCLDKVCL 130
             DR+LRLL SY+ + C  V    G+R+Y   P+  +F+++N Q+  SL+  + +  D V L
Sbjct:    88 DRMLRLLASYSVVKCGKVSEGKGERVYRAEPICRFFLKDNIQDIGSLASQVIVNFDSVFL 147

Query:   131 DGWFGLKKQLLEGGIAFNKAHG-MQIYDYLGVDSRFNDVFNNGMLSHTSIVMEKVLESYK 189
             + W  LK  +LEGG AF +AHG M+++DY+G D RF+ +FN      T  V++K LE Y+
Sbjct:   148 NTWAQLKDVVLEGGDAFGRAHGGMKLFDYMGTDERFSKLFNQ--TGFTIAVVKKALEVYQ 205

Query:   190 GFEHXXXXXXXXXXXXITLNMIISKYPHIKGINYDLPYVIKDAPSYPG 237
             GF+              TL ++ SKYP+IKGIN+DL   +  APSYPG
Sbjct:   206 GFKGVNVLVDVGGGVGNTLGVVASKYPNIKGINFDLTCALAQAPSYPG 253

GO:0005634 "nucleus" evidence=ISM

GO:0008168 "methyltransferase activity" evidence=IEA

GO:0008171 "O-methyltransferase activity" evidence=IEA

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0005829 "cytosol" evidence=TAS

TAIR|locus:2030081 IGMT5 "indole glucosinolate O-methyltransferase 5" [Arabidopsis thaliana (taxid:3702)]

 Score = 407 (148.3 bits), Expect = 5.5e-38, P = 5.5e-38
 Identities = 90/238 (37%), Positives = 138/238 (57%)

Query:     8 EEETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKA------GPGAKLSVAEIVAQIP 61
             +EET     A+ LA+    P V +A +EL V + +  A      G  + L+ +EI  ++P
Sbjct:    10 DEETELGLAAVRLANCAAFPMVFKAAIELGVIDTLYLAARDDVTGSSSFLTPSEIAIRLP 69

Query:    62 LKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFVRNN--QNGASLSP 119
              K +NPEA A+ LDR+LRLL SY+ + C  +DG R+Y   P+  YF+++N  +   +L+ 
Sbjct:    70 TKPSNPEAPAL-LDRILRLLASYSMVKCQIIDGNRVYKAEPICRYFLKDNVDEELGTLAS 128

Query:   120 YMALCLDKVCLDGWFGLKKQLLEGGIAFNKAHG-MQIYDYLGVDSRFNDVFNNGMLSHTS 178
              + + LD V L+ W  LK  +LEGG+AF +A+G ++++DY+  D R + +FN    S   
Sbjct:   129 QLIVTLDTVFLNTWGELKNVVLEGGVAFGRANGGLKLFDYISKDERLSKLFNRTGFSVA- 187

Query:   179 IVMEKVLESYKGFEHXXXXXXXXXXXXITLNMIISKYPHIKGINYDLPYVIKDAPSYP 236
              V++K+L+ Y GFE              TL  + SKYP+IKGIN+DL   +  APSYP
Sbjct:   188 -VLKKILQVYSGFEGVNVLVDVGGGVGDTLGFVTSKYPNIKGINFDLTCALTQAPSYP 244

GO:0008168 "methyltransferase activity" evidence=IEA

GO:0008171 "O-methyltransferase activity" evidence=IEA

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0005829 "cytosol" evidence=TAS

TAIR|locus:2199587 IGMT2 "indole glucosinolate O-methyltransferase 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 402 (146.6 bits), Expect = 1.9e-37, P = 1.9e-37
 Identities = 92/228 (40%), Positives = 138/228 (60%)

Query:    17 AMELASAIVLPAVMQAVVELDVFEII-SKAG-PGAKLSVAEIVAQIPLKDNNPEAAAMTL 74
             A+ LA+A   P V++A +EL VF+ + ++A    + LS +EI +++P    NP A  + L
Sbjct:    29 AVRLANAAAFPMVLKASLELGVFDTLYAEASRTDSFLSPSEIASKLPTTPRNPGAPVL-L 87

Query:    75 DRVLRLLVSYNALHCSFVD---GQRLYSLAPVSAYFVRNN-QNGASLSPYMALCLDKVCL 130
             DR+LRLL SY+ + C  V    G+R+Y   P+  +F++NN Q+  SL+  + +  D V L
Sbjct:    88 DRMLRLLASYSMVKCEKVSVGKGERVYRAEPICRFFLKNNIQDIGSLASQVIVNFDSVFL 147

Query:   131 DGWFGLKKQLLEGGIAFNKAHG-MQIYDYLGVDSRFNDVFNNGMLSHTSIVMEKVLESYK 189
             + W  LK  +LEGG AF +AHG M+++DY+G D RF+ +FN      T  V++K LE Y+
Sbjct:   148 NTWAQLKDVVLEGGDAFGRAHGGMKLFDYMGTDERFSKLFNQ--TGFTIAVVKKALEVYQ 205

Query:   190 GFEHXXXXXXXXXXXXITLNMIISKYPHIKGINYDLPYVIKDAPSYPG 237
             GF+              TL ++ SKYP+IKGIN+DL   +  APSYPG
Sbjct:   206 GFKGVNVLVDVGGGVGNTLGVVTSKYPNIKGINFDLTCALAQAPSYPG 253

GO:0005634 "nucleus" evidence=ISM

GO:0008168 "methyltransferase activity" evidence=IEA;IDA

GO:0008171 "O-methyltransferase activity" evidence=IEA

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0042343 "indole glucosinolate metabolic process" evidence=IDA

GO:0005829 "cytosol" evidence=TAS

TAIR|locus:2199607 IGMT1 "indole glucosinolate O-methyltransferase 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 400 (145.9 bits), Expect = 3.0e-37, P = 3.0e-37
 Identities = 91/228 (39%), Positives = 134/228 (58%)

Query:    17 AMELASAIVLPAVMQAVVELDVFEIISKAGPGAK--LSVAEIVAQIPLKDNNPEAAAMTL 74
             A+ LA+A   P V++A +EL VF+ +  A       LS  EI +++P    NPEA  + L
Sbjct:    29 AVRLANAAAFPMVLKAALELGVFDTLYAAASRTDSFLSPYEIASKLPTTPRNPEAPVL-L 87

Query:    75 DRVLRLLVSYNALHCSFV---DGQRLYSLAPVSAYFVRNN-QNGASLSPYMALCLDKVCL 130
             DR+LRLL SY+ + C       G+R+Y   P+  +F+++N Q+  SL+  + +  D V L
Sbjct:    88 DRMLRLLASYSMVKCGKALSGKGERVYRAEPICRFFLKDNIQDIGSLASQVIVNFDSVFL 147

Query:   131 DGWFGLKKQLLEGGIAFNKAHG-MQIYDYLGVDSRFNDVFNNGMLSHTSIVMEKVLESYK 189
             + W  LK  +LEGG AF +AHG M+++DY+G D RF+ +FN      T  V++K LE Y+
Sbjct:   148 NTWAQLKDVVLEGGDAFGRAHGGMKLFDYMGTDERFSKLFNQ--TGFTIAVVKKALEVYE 205

Query:   190 GFEHXXXXXXXXXXXXITLNMIISKYPHIKGINYDLPYVIKDAPSYPG 237
             GF+              TL ++ SKYP+IKGIN+DL   +  APSYPG
Sbjct:   206 GFKGVKVLVDVGGGVGNTLGVVTSKYPNIKGINFDLTCALAQAPSYPG 253

GO:0005634 "nucleus" evidence=ISM

GO:0008168 "methyltransferase activity" evidence=IEA;IDA

GO:0008171 "O-methyltransferase activity" evidence=IEA

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0042343 "indole glucosinolate metabolic process" evidence=IDA

GO:0005829 "cytosol" evidence=TAS

TAIR|locus:2038026 AT1G33030 [Arabidopsis thaliana (taxid:3702)]

 Score = 399 (145.5 bits), Expect = 3.9e-37, P = 3.9e-37
 Identities = 87/234 (37%), Positives = 134/234 (57%)

Query:     9 EETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPE 68
             EE N  SYAM L+S+ VLP V++  ++L +F+I++++GP +   +  +++    K ++  
Sbjct:     2 EEQNLSSYAMILSSSSVLPMVLKTAIDLGLFDILAESGPSSASQIFSLLSNETKKHHD-- 59

Query:    69 AAAMTLDRVLRLLVSYNALHCSFVD--GQ--RLYSLAPVSAYFVRNNQNGASLSPYMALC 124
               +  ++R+LR L SY+ L CS     G+   +Y LAPV+ YF +N   G SL+P + L 
Sbjct:    60 --SSLVNRILRFLASYSILTCSVSTEHGEPFAIYGLAPVAKYFTKNQNGGGSLAPMVNLF 117

Query:   125 LDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIVMEKV 184
              DKV  D W+ LK  +LEGG+ FN  HG    + +G DSRF +VF + M     + +E+ 
Sbjct:   118 QDKVVTDMWYNLKDSVLEGGLPFNNTHGSSAVELVGSDSRFREVFQSSMKGFNEVFIEEF 177

Query:   185 LESYKGFEHXXXXXXXXXXXXITLNMIISKYPHI-KGINYDLPYVIKDAPSYPG 237
             L++Y GF+               L+ IISK+ HI K IN+DLP VI  +   PG
Sbjct:   178 LKNYNGFDGVKSLVDVGGGDGSLLSRIISKHTHIIKAINFDLPTVINTSLPSPG 231

GO:0008168 "methyltransferase activity" evidence=IEA

GO:0008171 "O-methyltransferase activity" evidence=IEA;ISS

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0005829 "cytosol" evidence=IDA;TAS

GO:0009809 "lignin biosynthetic process" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	2.1.1	0.766

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00037163001	SubName- Full=Chromosome chr16 scaffold_86, whole genome shotgun sequence; (364 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00022302001	SubName- Full=Chromosome chr6 scaffold_25, whole genome shotgun sequence; (155 aa)						•			0.899
	GSVIVG00022301001	SubName- Full=Chromosome chr6 scaffold_25, whole genome shotgun sequence; (217 aa)						•			0.899
	GSVIVG00022298001	SubName- Full=Chromosome chr6 scaffold_25, whole genome shotgun sequence; (508 aa)						•			0.899
	GSVIVG00022293001	SubName- Full=Chromosome chr6 scaffold_25, whole genome shotgun sequence; (508 aa)						•			0.899
	VvF3'h3	SubName- Full=Chromosome chr17 scaffold_12, whole genome shotgun sequence; (509 aa)						•			0.899
	VvF3'h1	SubName- Full=Putative uncharacterized protein (Chromosome chr17 scaffold_12, whole genome shot [...] (509 aa)						•			0.899
	GSVIVG00012074001	SubName- Full=Chromosome undetermined scaffold_2892, whole genome shotgun sequence; (508 aa)						•			0.899
	FLS4	SubName- Full=Chromosome chr18 scaffold_1, whole genome shotgun sequence; (335 aa)						•			0.800
	FLS2	SubName- Full=Putative uncharacterized protein (Chromosome chr18 scaffold_1, whole genome shotg [...] (335 aa)						•			0.800
	FLS3	SubName- Full=Chromosome chr18 scaffold_1, whole genome shotgun sequence; (271 aa)						•			0.800

---

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	244
pfam00891	239	pfam00891, Methyltransf_2, O-methyltransferase	2e-53
pfam08100	50	pfam08100, Dimerisation, Dimerisation domain	4e-10

>gnl|CDD|216177 pfam00891, Methyltransf_2, O-methyltransferase

 Score =  172 bits (437), Expect = 2e-53
 Identities = 63/145 (43%), Positives = 83/145 (57%), Gaps = 1/145 (0%)

Query: 93  DGQRLYSLAPVSAYFVRNNQNGASLSPYMALCLDKVCLDGWFGLKKQLLEGGIAFNKAHG 152
            G   Y L P S   V+   +  SL+P + +  D   L+ W  LK  + EGG  F +A G
Sbjct: 2   RGGEDYGLTPASKLLVKGE-DSPSLAPLLLMYADPTLLESWAHLKDAVREGGPPFERAFG 60

Query: 153 MQIYDYLGVDSRFNDVFNNGMLSHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMII 212
           M  ++YLG D  FN VFN  M +H+ +VM+K+LE+   F  +  LVDVGGG G     I+
Sbjct: 61  MPFFEYLGADPEFNRVFNRAMAAHSRLVMKKILETAFDFSGLSSLVDVGGGTGALAAAIV 120

Query: 213 SKYPHIKGINYDLPYVIKDAPSYPG 237
             YPHIKGI +DLP+VI DAPS   
Sbjct: 121 RAYPHIKGIVFDLPHVIADAPSADR 145

This family includes a range of O-methyltransferases. These enzymes utilise S-adenosyl methionine. Length = 239

>gnl|CDD|219719 pfam08100, Dimerisation, Dimerisation domain

 Score = 53.7 bits (130), Expect = 4e-10
 Identities = 23/54 (42%), Positives = 35/54 (64%), Gaps = 5/54 (9%)

Query: 29 VMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLV 82
          V++  +EL + +II+K   G  LS +E+ +++P    NPEA  M LDR+LRLL 
Sbjct: 2  VLKCAIELGIPDIIAKH--GKPLSPSELASKLPTV--NPEAPVM-LDRLLRLLA 50

This domain is found at the N-terminus of a variety of plant O-methyltransferases. It has been shown to mediate dimerisation of these proteins. Length = 50

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	244
KOG3178	342	consensus Hydroxyindole-O-methyltransferase and re	99.98
TIGR02716	306	C20_methyl_CrtF C-20 methyltransferase BchU. Membe	99.95
PF00891	241	Methyltransf_2: O-methyltransferase; InterPro: IPR	99.95
PF08100	51	Dimerisation: Dimerisation domain; InterPro: IPR01	99.09
PRK06922	677	hypothetical protein; Provisional	98.13
PF12847	112	Methyltransf_18: Methyltransferase domain; PDB: 3G	97.9
PRK14103	255	trans-aconitate 2-methyltransferase; Provisional	97.89
COG4106	257	Tam Trans-aconitate methyltransferase [General fun	97.78
PRK08287	187	cobalt-precorrin-6Y C(15)-methyltransferase; Valid	97.76
PRK01683	258	trans-aconitate 2-methyltransferase; Provisional	97.76
PF13847	152	Methyltransf_31: Methyltransferase domain; PDB: 3T	97.52
TIGR03587	204	Pse_Me-ase pseudaminic acid biosynthesis-associate	97.52
TIGR02469	124	CbiT precorrin-6Y C5,15-methyltransferase (decarbo	97.51
TIGR00091	194	tRNA (guanine-N(7)-)-methyltransferase. In E. coli	97.45
PRK00107	187	gidB 16S rRNA methyltransferase GidB; Reviewed	97.4
PRK15001	378	SAM-dependent 23S ribosomal RNA mG1835 methyltrans	97.39
TIGR02021	219	BchM-ChlM magnesium protoporphyrin O-methyltransfe	97.33
PRK04457	262	spermidine synthase; Provisional	97.33
PF08242	99	Methyltransf_12: Methyltransferase domain; InterPr	97.3
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	97.3
PRK00121	202	trmB tRNA (guanine-N(7)-)-methyltransferase; Revie	97.29
TIGR02752	231	MenG_heptapren 2-heptaprenyl-1,4-naphthoquinone me	97.26
COG2813	300	RsmC 16S RNA G1207 methylase RsmC [Translation, ri	97.24
TIGR00138	181	gidB 16S rRNA methyltransferase GidB. GidB (glucos	97.22
PRK06202	232	hypothetical protein; Provisional	97.22
PRK07402	196	precorrin-6B methylase; Provisional	97.22
PRK14121	390	tRNA (guanine-N(7)-)-methyltransferase; Provisiona	97.17
PF05175	170	MTS: Methyltransferase small domain; InterPro: IPR	97.15
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	97.08
TIGR00740	239	methyltransferase, putative. A simple BLAST search	97.06
PRK09489	342	rsmC 16S ribosomal RNA m2G1207 methyltransferase;	97.04
COG2242	187	CobL Precorrin-6B methylase 2 [Coenzyme metabolism	97.03
PRK11207	197	tellurite resistance protein TehB; Provisional	97.02
PRK15451	247	tRNA cmo(5)U34 methyltransferase; Provisional	97.01
PRK00274	272	ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1	96.96
PF02390	195	Methyltransf_4: Putative methyltransferase ; Inter	96.96
PRK08317	241	hypothetical protein; Provisional	96.91
COG2890	280	HemK Methylase of polypeptide chain release factor	96.88
PF13649	101	Methyltransf_25: Methyltransferase domain; PDB: 3B	96.87
COG2226	238	UbiE Methylase involved in ubiquinone/menaquinone	96.87
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	96.85
smart00650	169	rADc Ribosomal RNA adenine dimethylases.	96.84
PRK10258	251	biotin biosynthesis protein BioC; Provisional	96.81
TIGR03533	284	L3_gln_methyl protein-(glutamine-N5) methyltransfe	96.79
TIGR00477	195	tehB tellurite resistance protein TehB. Part of a	96.79
PRK11088	272	rrmA 23S rRNA methyltransferase A; Provisional	96.79
TIGR03704	251	PrmC_rel_meth putative protein-(glutamine-N5) meth	96.79
PRK11036	255	putative S-adenosyl-L-methionine-dependent methylt	96.78
TIGR02072	240	BioC biotin biosynthesis protein BioC. This enzyme	96.78
PRK11805	307	N5-glutamine S-adenosyl-L-methionine-dependent met	96.74
TIGR03534	251	RF_mod_PrmC protein-(glutamine-N5) methyltransfera	96.7
TIGR00080	215	pimt protein-L-isoaspartate(D-aspartate) O-methylt	96.69
COG2264	300	PrmA Ribosomal protein L11 methylase [Translation,	96.68
COG1414	246	IclR Transcriptional regulator [Transcription]	96.66
PRK00216	239	ubiE ubiquinone/menaquinone biosynthesis methyltra	96.64
PRK01581	374	speE spermidine synthase; Validated	96.63
PTZ00098	263	phosphoethanolamine N-methyltransferase; Provision	96.6
PLN02244	340	tocopherol O-methyltransferase	96.6
PRK07580	230	Mg-protoporphyrin IX methyl transferase; Validated	96.57
PRK14966	423	unknown domain/N5-glutamine S-adenosyl-L-methionin	96.55
COG2230	283	Cfa Cyclopropane fatty acid synthase and related m	96.55
PRK11188	209	rrmJ 23S rRNA methyltransferase J; Provisional	96.55
PLN02366	308	spermidine synthase	96.54
TIGR00536	284	hemK_fam HemK family putative methylases. The gene	96.51
PRK09328	275	N5-glutamine S-adenosyl-L-methionine-dependent met	96.5
PHA03411	279	putative methyltransferase; Provisional	96.49
PRK01544	506	bifunctional N5-glutamine S-adenosyl-L-methionine-	96.46
PRK11569	274	transcriptional repressor IclR; Provisional	96.43
PRK00811	283	spermidine synthase; Provisional	96.43
PRK04266	226	fibrillarin; Provisional	96.41
TIGR01934	223	MenG_MenH_UbiE ubiquinone/menaquinone biosynthesis	96.4
PLN02490	340	MPBQ/MSBQ methyltransferase	96.39
PRK10163	271	DNA-binding transcriptional repressor AllR; Provis	96.39
TIGR02431	248	pcaR_pcaU beta-ketoadipate pathway transcriptional	96.39
PRK05785	226	hypothetical protein; Provisional	96.39
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	96.36
PLN02233	261	ubiquinone biosynthesis methyltransferase	96.36
PRK13942	212	protein-L-isoaspartate O-methyltransferase; Provis	96.35
smart00138	264	MeTrc Methyltransferase, chemotaxis proteins. Meth	96.35
TIGR00438	188	rrmJ cell division protein FtsJ.	96.34
TIGR00755	253	ksgA dimethyladenosine transferase. Alternate name	96.33
PF13659	117	Methyltransf_26: Methyltransferase domain; PDB: 3G	96.32
PF01209	233	Ubie_methyltran: ubiE/COQ5 methyltransferase famil	96.32
PF06325	295	PrmA: Ribosomal protein L11 methyltransferase (Prm	96.31
PRK15090	257	DNA-binding transcriptional regulator KdgR; Provis	96.3
PF13679	141	Methyltransf_32: Methyltransferase domain	96.3
COG4123	248	Predicted O-methyltransferase [General function pr	96.3
PLN02336	475	phosphoethanolamine N-methyltransferase	96.29
PRK11705	383	cyclopropane fatty acyl phospholipid synthase; Pro	96.27
PRK14896	258	ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1	96.25
COG0220	227	Predicted S-adenosylmethionine-dependent methyltra	96.24
PRK09834	263	DNA-binding transcriptional activator MhpR; Provis	96.22
PRK13944	205	protein-L-isoaspartate O-methyltransferase; Provis	96.19
PF02082	83	Rrf2: Transcriptional regulator; InterPro: IPR0009	96.19
PF13489	161	Methyltransf_23: Methyltransferase domain; PDB: 3J	96.13
PF02353	273	CMAS: Mycolic acid cyclopropane synthetase; InterP	96.09
PRK00050	296	16S rRNA m(4)C1402 methyltranserfase; Provisional	96.08
PRK12335	287	tellurite resistance protein TehB; Provisional	96.07
PRK15068	322	tRNA mo(5)U34 methyltransferase; Provisional	96.07
TIGR00537	179	hemK_rel_arch HemK-related putative methylase. The	96.06
PRK03612	521	spermidine synthase; Provisional	96.03
TIGR01444	143	fkbM_fam methyltransferase, FkbM family. Members o	96.01
PRK00377	198	cbiT cobalt-precorrin-6Y C(15)-methyltransferase;	95.99
TIGR00406	288	prmA ribosomal protein L11 methyltransferase. Ribo	95.98
PHA03412	241	putative methyltransferase; Provisional	95.9
KOG1540	296	consensus Ubiquinone biosynthesis methyltransferas	95.9
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	95.89
PRK00517	250	prmA ribosomal protein L11 methyltransferase; Revi	95.87
PF08241	95	Methyltransf_11: Methyltransferase domain; InterPr	95.85
TIGR02081	194	metW methionine biosynthesis protein MetW. This pr	95.79
PRK00536	262	speE spermidine synthase; Provisional	95.72
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	95.67
TIGR03438	301	probable methyltransferase. This model represents	95.66
PRK14968	188	putative methyltransferase; Provisional	95.65
PLN03075	296	nicotianamine synthase; Provisional	95.61
TIGR00452	314	methyltransferase, putative. Known examples to dat	95.6
KOG2899	288	consensus Predicted methyltransferase [General fun	95.58
PLN02336	475	phosphoethanolamine N-methyltransferase	95.56
PLN02672	1082	methionine S-methyltransferase	95.55
PLN02396	322	hexaprenyldihydroxybenzoate methyltransferase	95.53
COG2227	243	UbiG 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-	95.49
COG3355	126	Predicted transcriptional regulator [Transcription	95.46
KOG2904	328	consensus Predicted methyltransferase [General fun	95.45
cd02440	107	AdoMet_MTases S-adenosylmethionine-dependent methy	95.44
TIGR00417	270	speE spermidine synthase. the SpeE subunit of sper	95.41
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	95.39
TIGR00478	228	tly hemolysin TlyA family protein. Hemolysins are	95.35
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	95.35
PRK11727	321	23S rRNA mA1618 methyltransferase; Provisional	95.33
PLN02585	315	magnesium protoporphyrin IX methyltransferase	95.33
PRK10141	117	DNA-binding transcriptional repressor ArsR; Provis	95.32
PRK11512	144	DNA-binding transcriptional repressor MarR; Provis	95.29
PTZ00338	294	dimethyladenosine transferase-like protein; Provis	95.26
COG1959	150	Predicted transcriptional regulator [Transcription	95.25
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	95.24
KOG1271	227	consensus Methyltransferases [General function pre	95.2
PRK11873	272	arsM arsenite S-adenosylmethyltransferase; Reviewe	95.08
PRK13943	322	protein-L-isoaspartate O-methyltransferase; Provis	95.0
COG0421	282	SpeE Spermidine synthase [Amino acid transport and	95.0
TIGR02010	135	IscR iron-sulfur cluster assembly transcription fa	94.99
PRK14967	223	putative methyltransferase; Provisional	94.96
TIGR03840	213	TMPT_Se_Te thiopurine S-methyltransferase, Se/Te d	94.92
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	94.9
PF07021	193	MetW: Methionine biosynthesis protein MetW; InterP	94.84
PF13601	80	HTH_34: Winged helix DNA-binding domain; PDB: 1UB9	94.81
PRK10857	164	DNA-binding transcriptional regulator IscR; Provis	94.8
PLN02823	336	spermine synthase	94.78
PRK13168	443	rumA 23S rRNA m(5)U1939 methyltransferase; Reviewe	94.76
COG2263	198	Predicted RNA methylase [Translation, ribosomal st	94.74
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	94.71
PF07757	112	AdoMet_MTase: Predicted AdoMet-dependent methyltra	94.71
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	94.67
PF08003	315	Methyltransf_9: Protein of unknown function (DUF16	94.66
PRK03522	315	rumB 23S rRNA methyluridine methyltransferase; Rev	94.64
PF09012	69	FeoC: FeoC like transcriptional regulator; InterPr	94.63
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	94.57
PRK04148	134	hypothetical protein; Provisional	94.54
PF03848	192	TehB: Tellurite resistance protein TehB; InterPro:	94.46
TIGR00738	132	rrf2_super rrf2 family protein (putative transcrip	94.44
PF14947	77	HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_	94.37
PRK06266	178	transcription initiation factor E subunit alpha; V	94.32
PLN02781	234	Probable caffeoyl-CoA O-methyltransferase	94.25
PRK00312	212	pcm protein-L-isoaspartate O-methyltransferase; Re	94.25
PRK10901	427	16S rRNA methyltransferase B; Provisional	94.14
PTZ00146	293	fibrillarin; Provisional	94.14
PF04703	62	FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.	94.1
PRK13255	218	thiopurine S-methyltransferase; Reviewed	94.08
PF05401	201	NodS: Nodulation protein S (NodS); InterPro: IPR00	94.04
KOG1270	282	consensus Methyltransferases [Coenzyme transport a	93.99
TIGR02337	118	HpaR homoprotocatechuate degradation operon regula	93.99
PRK10909	199	rsmD 16S rRNA m(2)G966-methyltransferase; Provisio	93.98
PRK05134	233	bifunctional 3-demethylubiquinone-9 3-methyltransf	93.94
TIGR02702	203	SufR_cyano iron-sulfur cluster biosynthesis transc	93.91
PF07381	90	DUF1495: Winged helix DNA-binding domain (DUF1495)	93.79
smart00347	101	HTH_MARR helix_turn_helix multiple antibiotic resi	93.73
PRK14902	444	16S rRNA methyltransferase B; Provisional	93.6
PF10294	173	Methyltransf_16: Putative methyltransferase; Inter	93.59
PF01135	209	PCMT: Protein-L-isoaspartate(D-aspartate) O-methyl	93.59
cd00090	78	HTH_ARSR Arsenical Resistance Operon Repressor and	93.49
TIGR02944	130	suf_reg_Xantho FeS assembly SUF system regulator,	93.47
PF01564	246	Spermine_synth: Spermine/spermidine synthase; Inte	93.47
TIGR00479	431	rumA 23S rRNA (uracil-5-)-methyltransferase RumA.	93.39
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	93.38
PF08461	66	HTH_12: Ribonuclease R winged-helix domain; InterP	93.36
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	93.34
KOG3010	261	consensus Methyltransferase [General function pred	93.31
COG4976	287	Predicted methyltransferase (contains TPR repeat)	93.19
TIGR01884	203	cas_HTH CRISPR locus-related DNA-binding protein.	93.12
TIGR01983	224	UbiG ubiquinone biosynthesis O-methyltransferase.	93.09
PF01638	90	HxlR: HxlR-like helix-turn-helix; InterPro: IPR002	93.09
PRK01544	506	bifunctional N5-glutamine S-adenosyl-L-methionine-	93.05
PF01728	181	FtsJ: FtsJ-like methyltransferase; InterPro: IPR00	92.96
PRK03902	142	manganese transport transcriptional regulator; Pro	92.94
TIGR00122	69	birA_repr_reg BirA biotin operon repressor domain.	92.75
TIGR02085	374	meth_trns_rumB 23S rRNA (uracil-5-)-methyltransfer	92.75
PHA00738	108	putative HTH transcription regulator	92.66
PRK11050	152	manganese transport regulator MntR; Provisional	92.62
TIGR00095	189	RNA methyltransferase, RsmD family. This model rep	92.39
PRK11920	153	rirA iron-responsive transcriptional regulator; Re	92.3
PRK11014	141	transcriptional repressor NsrR; Provisional	92.23
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	92.21
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	92.18
KOG3115	249	consensus Methyltransferase-like protein [General	92.1
KOG3420	185	consensus Predicted RNA methylase [Translation, ri	92.06
KOG1499	346	consensus Protein arginine N-methyltransferase PRM	91.9
COG4742	260	Predicted transcriptional regulator [Transcription	91.84
PF00398	262	RrnaAD: Ribosomal RNA adenine dimethylase; InterPr	91.6
PF06163	127	DUF977: Bacterial protein of unknown function (DUF	91.43
TIGR00563	426	rsmB ribosomal RNA small subunit methyltransferase	91.34
PF06080	204	DUF938: Protein of unknown function (DUF938); Inte	91.31
TIGR01889	109	Staph_reg_Sar staphylococcal accessory regulator f	91.07
KOG1541	270	consensus Predicted protein carboxyl methylase [Ge	91.06
PF14394	171	DUF4423: Domain of unknown function (DUF4423)	91.03
TIGR00373	158	conserved hypothetical protein TIGR00373. This fam	91.01
PRK03573	144	transcriptional regulator SlyA; Provisional	91.0
TIGR02143	353	trmA_only tRNA (uracil-5-)-methyltransferase. This	90.98
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	90.97
cd07153	116	Fur_like Ferric uptake regulator(Fur) and related	90.94
TIGR01177	329	conserved hypothetical protein TIGR01177. This fam	90.77
COG2518	209	Pcm Protein-L-isoaspartate carboxylmethyltransfera	90.66
PF05148	219	Methyltransf_8: Hypothetical methyltransferase; In	90.56
PRK11760	357	putative 23S rRNA C2498 ribose 2'-O-ribose methylt	90.52
COG2345	218	Predicted transcriptional regulator [Transcription	90.25
PF08123	205	DOT1: Histone methylation protein DOT1 ; InterPro:	90.18
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	89.92
PRK05031	362	tRNA (uracil-5-)-methyltransferase; Validated	89.76
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	89.6
COG1321	154	TroR Mn-dependent transcriptional regulator [Trans	89.55
PRK14165	217	winged helix-turn-helix domain-containing protein/	89.45
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	89.27
PF12147	311	Methyltransf_20: Putative methyltransferase; Inter	89.03
PHA02943	165	hypothetical protein; Provisional	88.98
PF05185	448	PRMT5: PRMT5 arginine-N-methyltransferase; InterPr	88.68
PF03291	331	Pox_MCEL: mRNA capping enzyme; InterPro: IPR004971	88.56
COG0357	215	GidB Predicted S-adenosylmethionine-dependent meth	88.54
COG4565	224	CitB Response regulator of citrate/malate metaboli	88.31
PF02527	184	GidB: rRNA small subunit methyltransferase G; Inte	88.3
COG4190	144	Predicted transcriptional regulator [Transcription	88.1
PF02002	105	TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024	87.98
COG2512	258	Predicted membrane-associated trancriptional regul	87.9
PRK15431	78	ferrous iron transport protein FeoC; Provisional	87.88
smart00529	96	HTH_DTXR Helix-turn-helix diphteria tox regulatory	87.74
PF01596	205	Methyltransf_3: O-methyltransferase; InterPro: IPR	87.66
COG4189	308	Predicted transcriptional regulator [Transcription	87.62
TIGR00006	305	S-adenosyl-methyltransferase MraW. Genetics paper	87.61
PRK14901	434	16S rRNA methyltransferase B; Provisional	87.52
PRK14903	431	16S rRNA methyltransferase B; Provisional	87.39
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	87.35
PF01795	310	Methyltransf_5: MraW methylase family; InterPro: I	87.32
PRK10870	176	transcriptional repressor MprA; Provisional	87.14
KOG2361	264	consensus Predicted methyltransferase [General fun	87.06
PRK11169	164	leucine-responsive transcriptional regulator; Prov	86.94
COG4262	508	Predicted spermidine synthase with an N-terminal m	86.92
COG5631	199	Predicted transcription regulator, contains HTH do	86.88
PF09243	274	Rsm22: Mitochondrial small ribosomal subunit Rsm22	86.8
COG3432	95	Predicted transcriptional regulator [Transcription	86.71
PF00392	64	GntR: Bacterial regulatory proteins, gntR family;	86.57
PF05724	218	TPMT: Thiopurine S-methyltransferase (TPMT); Inter	86.52
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	86.5
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	86.27
PRK14904	445	16S rRNA methyltransferase B; Provisional	86.08
cd07377	66	WHTH_GntR Winged helix-turn-helix (WHTH) DNA-bindi	85.99
PRK13256	226	thiopurine S-methyltransferase; Reviewed	85.96
COG1378	247	Predicted transcriptional regulators [Transcriptio	85.68
COG1522	154	Lrp Transcriptional regulators [Transcription]	85.68
PRK06474	178	hypothetical protein; Provisional	85.59
PF07789	155	DUF1627: Protein of unknown function (DUF1627); In	85.4
COG0030	259	KsgA Dimethyladenosine transferase (rRNA methylati	85.21
PRK04172	489	pheS phenylalanyl-tRNA synthetase subunit alpha; P	85.0
PF03141	506	Methyltransf_29: Putative S-adenosyl-L-methionine-	84.9
TIGR00446	264	nop2p NOL1/NOP2/sun family putative RNA methylase.	84.62
PRK04338	382	N(2),N(2)-dimethylguanosine tRNA methyltransferase	84.56
PF12793	115	SgrR_N: Sugar transport-related sRNA regulator N-t	84.48
PLN02853	492	Probable phenylalanyl-tRNA synthetase alpha chain	84.34
PRK15128	396	23S rRNA m(5)C1962 methyltransferase; Provisional	84.26
PF08784	102	RPA_C: Replication protein A C terminal; InterPro:	84.25
PF02319	71	E2F_TDP: E2F/DP family winged-helix DNA-binding do	84.17
PLN02476	278	O-methyltransferase	83.79
PRK04214	412	rbn ribonuclease BN/unknown domain fusion protein;	83.43
KOG4589	232	consensus Cell division protein FtsJ [Cell cycle c	83.06
TIGR02787	251	codY_Gpos GTP-sensing transcriptional pleiotropic	83.0
PF03444	78	HrcA_DNA-bdg: Winged helix-turn-helix transcriptio	82.36
PRK11783	702	rlmL 23S rRNA m(2)G2445 methyltransferase; Provisi	82.14
KOG1500	517	consensus Protein arginine N-methyltransferase CAR	81.62
PRK05638	442	threonine synthase; Validated	80.95
COG4122	219	Predicted O-methyltransferase [General function pr	80.8
PRK13509	251	transcriptional repressor UlaR; Provisional	80.74
COG1846	126	MarR Transcriptional regulators [Transcription]	80.56
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	80.42
PRK13777	185	transcriptional regulator Hpr; Provisional	80.41
PF04072	183	LCM: Leucine carboxyl methyltransferase; InterPro:	80.23

>KOG3178 consensus Hydroxyindole-O-methyltransferase and related SAM-dependent methyltransferases [General function prediction only]

Probab=99.98  E-value=2.1e-31  Score=228.96  Aligned_cols=226  Identities=47%  Similarity=0.832  Sum_probs=199.1

Q ss_pred             hhhchhHHHHHHHHhhhHHHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcc
Q 041256            8 EEETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNAL   87 (244)
Q Consensus         8 ~~~~~~~~~l~~~~~g~~~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll   87 (244)
                      ++|.++..+++++++++..+++|++|+||||||+|++.+   +  ..|+|..+.. |-+|.+|.. +.|+||.|++.+++
T Consensus         1 ~~e~~~~l~~~~l~~~~~~~~~lk~A~eL~v~d~l~~~~---~--p~~ia~~l~~-~~~~~~p~l-l~r~lr~L~s~~i~   73 (342)
T KOG3178|consen    1 DEENEASLRAMRLANGFALPMVLKAACELGVFDILANAG---S--PSEIASLLPT-PKNPEAPVL-LDRILRLLVSYSIL   73 (342)
T ss_pred             CchhHHHHHHHHHHhhhhhHHHHHHHHHcChHHHHHhCC---C--HHHHHHhccC-CCCCCChhH-HHHHHHHHHHhhhc
Confidence            367788899999999999999999999999999999963   2  7788877764 334555778 99999999999999


Q ss_pred             cceeecCCceeecCccccccccCCCCCCCHHHHHHHhcChhhhhhccchHHHHhcCCchhhhhhCCCchhhccCCchHHH
Q 041256           88 HCSFVDGQRLYSLAPVSAYFVRNNQNGASLSPYMALCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFND  167 (244)
Q Consensus        88 ~~~~~~~~~~y~~t~~s~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~g~~~~~~~~g~~~~e~~~~~~~~~~  167 (244)
                      ++...... .|++++.++++.++. +..++.+++...+++..++.|.++.++++.+..+|..++|+..|+|...++....
T Consensus        74 k~~~~~~~-~Y~~~~~~~~~l~~~-~~~S~a~~~~~~~~~v~~~~w~~l~dai~eg~~~~~~~~G~~l~~~~~~~~~~~~  151 (342)
T KOG3178|consen   74 KCRLVGGE-VYSATPVCKYFLKDS-GGGSLAPLVLLNTSKVIMNTWQFLKDAILEGGDAFATAHGMMLGGYGGADERFSK  151 (342)
T ss_pred             eeeeecce-eeeccchhhhheecC-CCCchhHHHHHhcccchhhhHHHHHHHHHhcccCCccccchhhhhhcccccccHH
Confidence            96432223 899999999777555 3458889888888888999999999999999999999999889999999998899


Q ss_pred             HHHHHHHhcchhhHHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCCC-CCceeec
Q 041256          168 VFNNGMLSHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSY-PGTLFIK  242 (244)
Q Consensus       168 ~f~~aM~~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~~-~~i~~~~  242 (244)
                      .|+++|...+....+.+++.|.+|++..+.||||||.|..+..++.+||+++++.+|+|.|++.++.+ |||+++.
T Consensus       152 ~~~~sm~~l~~~~~~~il~~~~Gf~~v~~avDvGgGiG~v~k~ll~~fp~ik~infdlp~v~~~a~~~~~gV~~v~  227 (342)
T KOG3178|consen  152 DFNGSMSFLSTLVMKKILEVYTGFKGVNVAVDVGGGIGRVLKNLLSKYPHIKGINFDLPFVLAAAPYLAPGVEHVA  227 (342)
T ss_pred             HHHHHHHHHHHHHHHhhhhhhcccccCceEEEcCCcHhHHHHHHHHhCCCCceeecCHHHHHhhhhhhcCCcceec
Confidence            99999999999988899999988999999999999999999999999999999999999999999998 9987653

>TIGR02716 C20_methyl_CrtF C-20 methyltransferase BchU

Probab=99.95  E-value=2.6e-27  Score=206.52  Aligned_cols=185  Identities=21%  Similarity=0.341  Sum_probs=138.3

Q ss_pred             HHHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccc
Q 041256           25 VLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVS  104 (244)
Q Consensus        25 ~~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s  104 (244)
                      ...++|++|++|||||+|++    +|+|++|||+++|++      ++. ++|+||+|+++|+|++   . +++|++|+.+
T Consensus         2 ~~~~~l~aa~~Lglfd~L~~----gp~t~~eLA~~~~~~------~~~-~~~lL~~L~~lgll~~---~-~~~y~~t~~~   66 (306)
T TIGR02716         2 IEFSCMKAAIELDLFSHMAE----GPKDLATLAADTGSV------PPR-LEMLLETLRQMRVINL---E-DGKWSLTEFA   66 (306)
T ss_pred             chHHHHHHHHHcCcHHHHhc----CCCCHHHHHHHcCCC------hHH-HHHHHHHHHhCCCeEe---c-CCcEecchhH
Confidence            35789999999999999987    799999999999997      678 9999999999999994   3 4899999999


Q ss_pred             cccccCCCCCC---CHHHHHHHhcChhhhhhccchHHHHhcCCchhhhhhCCCchhhccCCchHHHHHHHHHH-hcchhh
Q 041256          105 AYFVRNNQNGA---SLSPYMALCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGML-SHTSIV  180 (244)
Q Consensus       105 ~~l~~~~~~~~---~~~~~~~~~~~~~~~~~~~~l~~~l~~g~~~~~~~~g~~~~e~~~~~~~~~~~f~~aM~-~~~~~~  180 (244)
                      ..+..++ ++.   ++.++..+. .......|.+|.+++++ +++|..     .+++....++.. .|...|. ......
T Consensus        67 ~~~l~~~-~~~~~~~~~~~~~~~-~~~~~~~~~~l~~~~r~-~~~~~~-----~~~~~~~~~~~~-~~~~~~~~~~~~~~  137 (306)
T TIGR02716        67 DYMFSPT-PKEPNLHQTPVAKAM-AFLADDFYMGLSQAVRG-QKNFKG-----QVPYPPVTREDN-LYFEEIHRSNAKFA  137 (306)
T ss_pred             HhhccCC-ccchhhhcCchHHHH-HHHHHHHHHhHHHHhcC-Cccccc-----ccCCCCCCHHHH-HhHHHHHHhcchhH
Confidence            8555544 222   112333332 11223578999999974 444432     222322233333 3444444 444445


Q ss_pred             HHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCC
Q 041256          181 MEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPS  234 (244)
Q Consensus       181 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~  234 (244)
                      .+.+++.++ +++..+|||||||+|.+++.+++++|+++++++|+|++++.+++
T Consensus       138 ~~~l~~~~~-~~~~~~vlDiG~G~G~~~~~~~~~~p~~~~~~~D~~~~~~~a~~  190 (306)
T TIGR02716       138 IQLLLEEAK-LDGVKKMIDVGGGIGDISAAMLKHFPELDSTILNLPGAIDLVNE  190 (306)
T ss_pred             HHHHHHHcC-CCCCCEEEEeCCchhHHHHHHHHHCCCCEEEEEecHHHHHHHHH
Confidence            566778777 88889999999999999999999999999999999999988764

Members of this protein family are the S-adenosylmethionine-depenedent C-20 methyltransferase BchU, part of the pathway of bacteriochlorophyll c production in photosynthetic green sulfur bacteria. The position modified by this enzyme represents the difference between bacteriochlorophylls c and d; strains lacking this protein can only produced bacteriochlorophyll d.

>PF00891 Methyltransf_2: O-methyltransferase; InterPro: IPR001077 Methyl transfer from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals

Probab=99.95  E-value=1.5e-27  Score=201.16  Aligned_cols=147  Identities=27%  Similarity=0.517  Sum_probs=129.9

Q ss_pred             CceeecCccccccccCCCCCCCHHHHHHHhcChhhhhhccchHHHHhcCCchhhhhhCCCchhhccCCchHHHHHHHHHH
Q 041256           95 QRLYSLAPVSAYFVRNNQNGASLSPYMALCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGML  174 (244)
Q Consensus        95 ~~~y~~t~~s~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~g~~~~~~~~g~~~~e~~~~~~~~~~~f~~aM~  174 (244)
                      .++|+||+.|+.|+.++ ++.++..++.+...+..++.|.+|.+++++|+++|+..+|.++|+++.++|+..+.|+.+|+
T Consensus         3 ~~~y~~t~~s~~ll~~~-~~~~~~~~~~~~~~~~~~~~~~~L~~~v~~g~~~~~~~~g~~~~~~~~~~~~~~~~f~~~m~   81 (241)
T PF00891_consen    3 GDRYSLTPLSELLLSDH-SSPSMRGFVLFMISPELYPAWFRLTEAVRTGKPPFEKAFGTPFFEYLEEDPELAKRFNAAMA   81 (241)
T ss_dssp             TEEEEE-HHHHGGSTTT-TTTHHHHHHHHHTCHHHHHGGGGHHHHHHHSS-HHHHHHSS-HHHHHHCSHHHHHHHHHHHH
T ss_pred             CCEEeChHHHHHHhCCC-CcCcHHHHHHHhcCHHHHHHHHHHHhhhccCCCHHHHhcCCcHHHhhhhChHHHHHHHHHHH
Confidence            48999999999888776 33578888877668889999999999999999999999999999999999999999999999


Q ss_pred             hcchhhH-HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCCCCCceeecc
Q 041256          175 SHTSIVM-EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPGTLFIKF  243 (244)
Q Consensus       175 ~~~~~~~-~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~~~~i~~~~~  243 (244)
                      ..+.... +.+...++ |++.++|||||||+|.++.+++++||+++++++|+|+|++.+++.++|+++++
T Consensus        82 ~~~~~~~~~~~~~~~d-~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~~~~~~rv~~~~g  150 (241)
T PF00891_consen   82 EYSRLNAFDILLEAFD-FSGFKTVVDVGGGSGHFAIALARAYPNLRATVFDLPEVIEQAKEADRVEFVPG  150 (241)
T ss_dssp             HHHHHHHHHHHHHHST-TTTSSEEEEET-TTSHHHHHHHHHSTTSEEEEEE-HHHHCCHHHTTTEEEEES
T ss_pred             hhhhcchhhhhhcccc-ccCccEEEeccCcchHHHHHHHHHCCCCcceeeccHhhhhccccccccccccc
Confidence            9998877 77888888 99999999999999999999999999999999999999999988889998875

The reaction is catalysed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented. Three classes of DNA Mtases transfer the methyl group from AdoMet to the target base to form either N-6-methyladenine, or N-4-methylcytosine, or C-5- methylcytosine. In C-5-cytosine Mtases, ten conserved motifs are arranged in the same order []. Motif I (a glycine-rich or closely related consensus sequence; FAGxGG in M.HhaI []), shared by other AdoMet-Mtases [], is part of the cofactor binding site and motif IV (PCQ) is part of the catalytic site. In contrast, sequence comparison among N-6-adenine and N-4-cytosine Mtases indicated two of the conserved segments [], although more conserved segments may be present. One of them corresponds to motif I in C-5-cytosine Mtases, and the other is named (D/N/S)PP(Y/F). Crystal structures are known for a number of Mtases [, , , ]. The cofactor binding sites are almost identical and the essential catalytic amino acids coincide. The comparable protein folding and the existence of equivalent amino acids in similar secondary and tertiary positions indicate that many (if not all) AdoMet-Mtases have a common catalytic domain structure. This permits tertiary structure prediction of other DNA, RNA, protein, and small-molecule AdoMet-Mtases from their amino acid sequences []. This domain includes a range of O-methyltransferases some of which utilise S-adenosyl methionine as substrate []. In prokaryotes, the major role of DNA methylation is to protect host DNA against degradation by restriction enzymes. In eukaryotes, DNA methylation has been implicated in the control of several cellular processes, including differentiation, gene regulation, and embryonic development. O-methyltransferases have a common catalytic domain structure, which might be universal among S-adenosyl-L-methionine (AdoMet)-dependent methyltransferases []. Comparative analysis of the predicted amino acid sequences of a number of plant O-methyltransferase cDNA clones show that they share some 32-71% sequence identity, and can be grouped according to the different compounds they utilise as substrates [].; GO: 0008171 O-methyltransferase activity; PDB: 1FPQ_A 1FP1_D 3P9K_B 3P9I_D 3P9C_A 3I53_A 3I5U_A 3I64_A 3I58_A 1ZG3_A ....

>PF08100 Dimerisation: Dimerisation domain; InterPro: IPR012967 This domain is found at the N terminus of a variety of plant O-methyltransferases

Probab=99.09  E-value=2e-10  Score=72.80  Aligned_cols=51  Identities=49%  Similarity=0.821  Sum_probs=42.3

Q ss_pred             HHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHh
Q 041256           28 AVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLV   82 (244)
Q Consensus        28 ~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~   82 (244)
                      ++|++|+||||||+|++.| ++++|++||+.++...  +|.++.. +.|+||+|+
T Consensus         1 MaLk~aveLgI~dii~~~g-~~~ls~~eia~~l~~~--~p~~~~~-L~RimR~L~   51 (51)
T PF08100_consen    1 MALKCAVELGIPDIIHNAG-GGPLSLSEIAARLPTS--NPSAPPM-LDRIMRLLV   51 (51)
T ss_dssp             HHHHHHHHTTHHHHHHHHT-TS-BEHHHHHHTSTCT---TTHHHH-HHHHHHHHH
T ss_pred             CcHHHHHHcCcHHHHHHcC-CCCCCHHHHHHHcCCC--CcchHHH-HHHHHHHhC
Confidence            5899999999999999985 4699999999999832  4555678 999999985

It has been shown to mediate dimerisation of these proteins [].; GO: 0008168 methyltransferase activity, 0046983 protein dimerization activity; PDB: 1ZGJ_A 1ZG3_A 1ZHF_A 1ZGA_A 2QYO_A 1KYW_A 1KYZ_A 3REO_D 1FPX_A 1FP2_A ....

>PRK06922 hypothetical protein; Provisional

Probab=98.13  E-value=4.1e-06  Score=79.01  Aligned_cols=81  Identities=21%  Similarity=0.329  Sum_probs=62.1

Q ss_pred             CCchhhccCCchHHHHHHHHHHhcchhh--HHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHh
Q 041256          153 MQIYDYLGVDSRFNDVFNNGMLSHTSIV--MEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVI  229 (244)
Q Consensus       153 ~~~~e~~~~~~~~~~~f~~aM~~~~~~~--~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi  229 (244)
                      ..+|+++..+++..++|...|.......  .......++ +.+..+|||||||.|.++..+++++|+.+++.+|+ |.++
T Consensus       377 ~~~fd~fg~r~D~~dRf~~~~~yle~m~~~~~~k~~i~d-~~~g~rVLDIGCGTG~ls~~LA~~~P~~kVtGIDIS~~ML  455 (677)
T PRK06922        377 VLLFDFFGLRKDAYDRFHNEEVYLEHMNSSADDKRIILD-YIKGDTIVDVGAGGGVMLDMIEEETEDKRIYGIDISENVI  455 (677)
T ss_pred             hHHHHHhccChhhHhHHHhHHHHHHhccccHHHHHHHhh-hcCCCEEEEeCCCCCHHHHHHHHhCCCCEEEEEECCHHHH
Confidence            4678999988888889988776644332  112233445 66678999999999999999999999999999999 4557


Q ss_pred             hhCCC
Q 041256          230 KDAPS  234 (244)
Q Consensus       230 ~~a~~  234 (244)
                      +.+++
T Consensus       456 e~Ara  460 (677)
T PRK06922        456 DTLKK  460 (677)
T ss_pred             HHHHH
Confidence            76653

>PF12847 Methyltransf_18: Methyltransferase domain; PDB: 3G2Q_A 3G2O_A 3G2M_B 3G2P_B 3D2L_B 1IM8_B 3NJR_A 3E05_H 3EVZ_A 3HM2_A

Probab=97.90  E-value=7.7e-06  Score=60.07  Aligned_cols=41  Identities=20%  Similarity=0.355  Sum_probs=37.6

Q ss_pred             cceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+|+|||||+|.++..+++++|+.+++.+|. |+.++.+++
T Consensus         2 ~~~vLDlGcG~G~~~~~l~~~~~~~~v~gvD~s~~~~~~a~~   43 (112)
T PF12847_consen    2 GGRVLDLGCGTGRLSIALARLFPGARVVGVDISPEMLEIARE   43 (112)
T ss_dssp             TCEEEEETTTTSHHHHHHHHHHTTSEEEEEESSHHHHHHHHH
T ss_pred             CCEEEEEcCcCCHHHHHHHhcCCCCEEEEEeCCHHHHHHHHH
Confidence            36899999999999999999999999999999 888888764

...

>PRK14103 trans-aconitate 2-methyltransferase; Provisional

Probab=97.89  E-value=4.1e-05  Score=65.04  Aligned_cols=57  Identities=21%  Similarity=0.276  Sum_probs=47.2

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCCCCCcee
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPSYPGTLF  240 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~~~~i~~  240 (244)
                      ..+++.++ .....+|||||||+|.++..+++++|+.+++.+|+ |..++.+++. ++++
T Consensus        19 ~~ll~~l~-~~~~~~vLDlGcG~G~~~~~l~~~~p~~~v~gvD~s~~~~~~a~~~-~~~~   76 (255)
T PRK14103         19 YDLLARVG-AERARRVVDLGCGPGNLTRYLARRWPGAVIEALDSSPEMVAAARER-GVDA   76 (255)
T ss_pred             HHHHHhCC-CCCCCEEEEEcCCCCHHHHHHHHHCCCCEEEEEECCHHHHHHHHhc-CCcE
Confidence            46677776 56779999999999999999999999999999999 8888877652 3443

>COG4106 Tam Trans-aconitate methyltransferase [General function prediction only]

Probab=97.78  E-value=6.6e-05  Score=61.52  Aligned_cols=60  Identities=22%  Similarity=0.432  Sum_probs=51.7

Q ss_pred             HHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC-CCCceee
Q 041256          181 MEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS-YPGTLFI  241 (244)
Q Consensus       181 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~-~~~i~~~  241 (244)
                      ...++...+ ......|+|+|||.|....-|++++|+...+.+|- |..++.|++ .|+++|.
T Consensus        19 a~dLla~Vp-~~~~~~v~DLGCGpGnsTelL~~RwP~A~i~GiDsS~~Mla~Aa~rlp~~~f~   80 (257)
T COG4106          19 ARDLLARVP-LERPRRVVDLGCGPGNSTELLARRWPDAVITGIDSSPAMLAKAAQRLPDATFE   80 (257)
T ss_pred             HHHHHhhCC-ccccceeeecCCCCCHHHHHHHHhCCCCeEeeccCCHHHHHHHHHhCCCCcee
Confidence            357777788 78889999999999999999999999999999997 888888875 5776663

>PRK08287 cobalt-precorrin-6Y C(15)-methyltransferase; Validated

Probab=97.76  E-value=3.8e-05  Score=62.14  Aligned_cols=49  Identities=20%  Similarity=0.364  Sum_probs=41.8

Q ss_pred             HhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          185 LESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       185 ~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      +..++ .....+|+|||||+|.++..+++++|+.+++.+|. |..++.+++
T Consensus        24 ~~~l~-~~~~~~vLDiG~G~G~~~~~la~~~~~~~v~~vD~s~~~~~~a~~   73 (187)
T PRK08287         24 LSKLE-LHRAKHLIDVGAGTGSVSIEAALQFPSLQVTAIERNPDALRLIKE   73 (187)
T ss_pred             HHhcC-CCCCCEEEEECCcCCHHHHHHHHHCCCCEEEEEECCHHHHHHHHH
Confidence            34455 56678999999999999999999999999999999 788887764

>PRK01683 trans-aconitate 2-methyltransferase; Provisional

Probab=97.76  E-value=6.2e-05  Score=63.87  Aligned_cols=59  Identities=24%  Similarity=0.482  Sum_probs=48.6

Q ss_pred             HHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC-CCCcee
Q 041256          181 MEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS-YPGTLF  240 (244)
Q Consensus       181 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~-~~~i~~  240 (244)
                      ...++..++ ..+..+|+|||||.|.++..+++++|+.+++.+|+ |..++.+++ .+++++
T Consensus        20 ~~~ll~~~~-~~~~~~vLDiGcG~G~~~~~la~~~~~~~v~gvD~s~~~i~~a~~~~~~~~~   80 (258)
T PRK01683         20 ARDLLARVP-LENPRYVVDLGCGPGNSTELLVERWPAARITGIDSSPAMLAEARSRLPDCQF   80 (258)
T ss_pred             HHHHHhhCC-CcCCCEEEEEcccCCHHHHHHHHHCCCCEEEEEECCHHHHHHHHHhCCCCeE
Confidence            346677776 67778999999999999999999999999999999 788887765 345554

>PF13847 Methyltransf_31: Methyltransferase domain; PDB: 3T0I_B 3SVZ_B 3SXJ_A 3F4K_A 3GU3_B 2GH1_A 1R8Y_E 1R8X_B 2B3T_A 1T43_A

Probab=97.52  E-value=9.8e-05  Score=57.57  Aligned_cols=42  Identities=31%  Similarity=0.354  Sum_probs=36.8

Q ss_pred             CcceEEEecCCccHHHHHHH-HHCCCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMII-SKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~-~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      +..+|+|+|||+|.++..++ +.+|..+.+.+|+ |+.++.|++
T Consensus         3 ~~~~iLDlGcG~G~~~~~l~~~~~~~~~i~gvD~s~~~i~~a~~   46 (152)
T PF13847_consen    3 SNKKILDLGCGTGRLLIQLAKELNPGAKIIGVDISEEMIEYAKK   46 (152)
T ss_dssp             TTSEEEEET-TTSHHHHHHHHHSTTTSEEEEEESSHHHHHHHHH
T ss_pred             CCCEEEEecCcCcHHHHHHHHhcCCCCEEEEEECcHHHHHHhhc
Confidence            45799999999999999999 5689999999999 889988875

...

>TIGR03587 Pse_Me-ase pseudaminic acid biosynthesis-associated methylase

Probab=97.52  E-value=0.00017  Score=59.41  Aligned_cols=49  Identities=14%  Similarity=0.405  Sum_probs=41.8

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC-CCCcee
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS-YPGTLF  240 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~-~~~i~~  240 (244)
                      ....+|+|||||+|.++..+++..|+.+.+.+|+ |+.++.|++ .+++++
T Consensus        42 ~~~~~VLDiGCG~G~~~~~L~~~~~~~~v~giDiS~~~l~~A~~~~~~~~~   92 (204)
T TIGR03587        42 PKIASILELGANIGMNLAALKRLLPFKHIYGVEINEYAVEKAKAYLPNINI   92 (204)
T ss_pred             CCCCcEEEEecCCCHHHHHHHHhCCCCeEEEEECCHHHHHHHHhhCCCCcE
Confidence            4557899999999999999999999999999998 889998876 455544

Members of this small clade are methyltransferases of the pfam08241 family and are observed within operons for the biosynthesis of pseudaminic acid, a component of exopolysaccharide and flagellin glycosyl modifications. Notable among these genomes is Pseudomonas fluorescens PfO-1. Possibly one of the two hydroxyl groups of pseudaminic acid, at positions 4 and 8 is converted to a methoxy group by this enzyme

>TIGR02469 CbiT precorrin-6Y C5,15-methyltransferase (decarboxylating), CbiT subunit

Probab=97.51  E-value=0.0002  Score=53.18  Aligned_cols=49  Identities=16%  Similarity=0.175  Sum_probs=40.0

Q ss_pred             HHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256          184 VLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       184 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~  233 (244)
                      +++.++ .....+|+|+|||.|.++..+++++|+.+++.+|. +..++.++
T Consensus        11 ~~~~~~-~~~~~~vldlG~G~G~~~~~l~~~~~~~~v~~vD~s~~~~~~a~   60 (124)
T TIGR02469        11 TLSKLR-LRPGDVLWDIGAGSGSITIEAARLVPNGRVYAIERNPEALRLIE   60 (124)
T ss_pred             HHHHcC-CCCCCEEEEeCCCCCHHHHHHHHHCCCceEEEEcCCHHHHHHHH
Confidence            444555 45557999999999999999999999999999998 66666654

This model recognizes the CbiT methylase which is responsible, in part (along with CbiE), for methylating precorrin-6y (or cobalt-precorrin-6y) at both the 5 and 15 positions as well as the concomitant decarbozylation at C-12. In many organisms, this protein is fused to the CbiE subunit. The fused protein, when found in organisms catalyzing the oxidative version of the cobalamin biosynthesis pathway, is called CobL.

>TIGR00091 tRNA (guanine-N(7)-)-methyltransferase

Probab=97.45  E-value=0.0002  Score=58.31  Aligned_cols=41  Identities=15%  Similarity=0.219  Sum_probs=36.6

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~  233 (244)
                      ...++||||||.|.++..+++++|+.+++.+|+ +..++.++
T Consensus        16 ~~~~ilDiGcG~G~~~~~la~~~p~~~v~gvD~~~~~l~~a~   57 (194)
T TIGR00091        16 KAPLHLEIGCGKGRFLIDMAKQNPDKNFLGIEIHTPIVLAAN   57 (194)
T ss_pred             CCceEEEeCCCccHHHHHHHHhCCCCCEEEEEeeHHHHHHHH
Confidence            457999999999999999999999999999999 77776664

In E. coli, this protein flanks the DNA repair protein MutY, also called micA.

>PRK00107 gidB 16S rRNA methyltransferase GidB; Reviewed

Probab=97.40  E-value=0.00038  Score=56.49  Aligned_cols=42  Identities=21%  Similarity=0.159  Sum_probs=37.1

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...+|+|||||+|..+..+++++|+.+++.+|. |..++.+++
T Consensus        45 ~g~~VLDiGcGtG~~al~la~~~~~~~V~giD~s~~~l~~A~~   87 (187)
T PRK00107         45 GGERVLDVGSGAGFPGIPLAIARPELKVTLVDSLGKKIAFLRE   87 (187)
T ss_pred             CCCeEEEEcCCCCHHHHHHHHHCCCCeEEEEeCcHHHHHHHHH
Confidence            368999999999999999999999999999998 777776654

>PRK15001 SAM-dependent 23S ribosomal RNA mG1835 methyltransferase; Provisional

Probab=97.39  E-value=0.00022  Score=64.01  Aligned_cols=51  Identities=20%  Similarity=0.271  Sum_probs=41.9

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      -+++.+| .....+|+|+|||+|.++..+++++|+.+++.+|. +..++.+++
T Consensus       219 llL~~lp-~~~~~~VLDLGCGtGvi~i~la~~~P~~~V~~vD~S~~Av~~A~~  270 (378)
T PRK15001        219 FFMQHLP-ENLEGEIVDLGCGNGVIGLTLLDKNPQAKVVFVDESPMAVASSRL  270 (378)
T ss_pred             HHHHhCC-cccCCeEEEEeccccHHHHHHHHhCCCCEEEEEECCHHHHHHHHH
Confidence            3455665 33346999999999999999999999999999999 577777764

>TIGR02021 BchM-ChlM magnesium protoporphyrin O-methyltransferase

Probab=97.33  E-value=0.00048  Score=57.04  Aligned_cols=78  Identities=12%  Similarity=0.063  Sum_probs=48.8

Q ss_pred             chhhccCCchHHHHHHHHHHhcchhhHHHHHhhcCC-CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhC
Q 041256          155 IYDYLGVDSRFNDVFNNGMLSHTSIVMEKVLESYKG-FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDA  232 (244)
Q Consensus       155 ~~e~~~~~~~~~~~f~~aM~~~~~~~~~~~~~~~~~-~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a  232 (244)
                      -|+.+...+.....+...|..........+++.++. ..+..+|+|||||.|.++..+++.  +.+.+.+|. |+.++.+
T Consensus        16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~vLDiGcG~G~~~~~la~~--~~~v~gvD~s~~~i~~a   93 (219)
T TIGR02021        16 RWARIYGSGDPVSRVRQTVREGRAAMRRKLLDWLPKDPLKGKRVLDAGCGTGLLSIELAKR--GAIVKAVDISEQMVQMA   93 (219)
T ss_pred             HHHHhhCCchhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCEEEEEeCCCCHHHHHHHHC--CCEEEEEECCHHHHHHH
Confidence            344444444444455555533222222334433331 335689999999999999999886  447888898 7888777


Q ss_pred             CC
Q 041256          233 PS  234 (244)
Q Consensus       233 ~~  234 (244)
                      ++
T Consensus        94 ~~   95 (219)
T TIGR02021        94 RN   95 (219)
T ss_pred             HH
Confidence            64

This model represents the S-adenosylmethionine-dependent O-methyltransferase responsible for methylation of magnesium protoporphyrin IX. This step is essentiasl for the biosynthesis of both chlorophyll and bacteriochlorophyll. This model encompasses two closely related clades, from cyanobacteria (and plants) where it is called ChlM and other photosynthetic bacteria where it is known as BchM.

>PRK04457 spermidine synthase; Provisional

Probab=97.33  E-value=0.00019  Score=61.32  Aligned_cols=43  Identities=21%  Similarity=0.356  Sum_probs=39.6

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      +.+++|+|||||.|.++..+++.+|+.+++++|+ |+|++.|++
T Consensus        65 ~~~~~vL~IG~G~G~l~~~l~~~~p~~~v~~VEidp~vi~~A~~  108 (262)
T PRK04457         65 PRPQHILQIGLGGGSLAKFIYTYLPDTRQTAVEINPQVIAVARN  108 (262)
T ss_pred             CCCCEEEEECCCHhHHHHHHHHhCCCCeEEEEECCHHHHHHHHH
Confidence            4568899999999999999999999999999999 999998874

>PF08242 Methyltransf_12: Methyltransferase domain; InterPro: IPR013217 Methyl transfer from the ubiquitous donor S-adenosyl-L-methionine (SAM) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals

Probab=97.30  E-value=6.5e-05  Score=54.04  Aligned_cols=37  Identities=24%  Similarity=0.522  Sum_probs=31.9

Q ss_pred             EEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          198 VDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       198 vDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ||||||+|.++..+++++|..+.+..|. |..++.+++
T Consensus         1 LdiGcG~G~~~~~l~~~~~~~~~~~~D~s~~~l~~a~~   38 (99)
T PF08242_consen    1 LDIGCGTGRLLRALLEELPDARYTGVDISPSMLERARE   38 (99)
T ss_dssp             -EESTTTS-TTTTHHHHC-EEEEEEEESSSSTTSTTCC
T ss_pred             CEeCccChHHHHHHHHhCCCCEEEEEECCHHHHHHHHH
Confidence            7999999999999999999999999999 888888876

The reaction is catalyzed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented. This entry represents a methyltransferase domain found in a large variety of SAM-dependent methyltransferases including, but not limited to: Hexaprenyldihydroxybenzoate methyltransferase (2.1.1.114 from EC), a mitochodrial enzyme involved in ubiquinone biosynthesis [] Fatty acid synthase (2.3.1.85 from EC), a biosynthetic enzyme catalysing the formation of long-chain fatty acids Glycine N-methyltransferase (2.1.1.20 from EC) which catalyses the SAM-dependent methylation of glycine to form sarcosine and may play a role in regulating the methylation potential of the cell [] Enniatin synthetase, involved in non-ribosomal biosynthesis of cyclohexadepsipeptidase, enniatin [] Histamine N-methyltransferase (2.1.1.8 from EC), a SAM-dependent histamine-inactivating enzyme [] A probable cobalt-precorrin-6Y C(15)-methyltransferase thought to be involved in adenosylcobalamin biosynthesis [] Structural studies show that this domain forms the Rossman-like alpha-beta fold typical of SAM-dependent methyltransferases [, , ].; PDB: 2VZ8_A 2VZ9_A.

>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities

Probab=97.30  E-value=9.9e-05  Score=46.95  Aligned_cols=45  Identities=24%  Similarity=0.448  Sum_probs=37.9

Q ss_pred             cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      +.|++.|.+.+  ++.|+.|||+++|++      ..- +.|+|..|+..|++.+
T Consensus         6 l~iL~~l~~~~--~~~t~~eia~~~gl~------~st-v~r~L~tL~~~g~v~~   50 (52)
T PF09339_consen    6 LRILEALAESG--GPLTLSEIARALGLP------KST-VHRLLQTLVEEGYVER   50 (52)
T ss_dssp             HHHHHCHHCTB--SCEEHHHHHHHHTS-------HHH-HHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHcCC--CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCcCeec
Confidence            45788888875  678999999999996      345 9999999999999995

One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.

>PRK00121 trmB tRNA (guanine-N(7)-)-methyltransferase; Reviewed

Probab=97.29  E-value=0.00043  Score=56.80  Aligned_cols=49  Identities=18%  Similarity=0.173  Sum_probs=40.3

Q ss_pred             HHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          184 VLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       184 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      |.+.+.  ....+|+|||||.|.++..+++.+|+.+.+.+|. |+.++.+++
T Consensus        33 ~~~~~~--~~~~~VLDiGcGtG~~~~~la~~~p~~~v~gVD~s~~~i~~a~~   82 (202)
T PRK00121         33 WAELFG--NDAPIHLEIGFGKGEFLVEMAKANPDINFIGIEVHEPGVGKALK   82 (202)
T ss_pred             HHHHcC--CCCCeEEEEccCCCHHHHHHHHHCCCccEEEEEechHHHHHHHH
Confidence            444444  2558999999999999999999999999999998 777777653

>TIGR02752 MenG_heptapren 2-heptaprenyl-1,4-naphthoquinone methyltransferase

Probab=97.26  E-value=0.00057  Score=56.91  Aligned_cols=50  Identities=12%  Similarity=0.084  Sum_probs=40.3

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHC-CCCeEEEccc-hHHhhhCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKY-PHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~vi~~a~  233 (244)
                      .++..++ .....+|||||||+|.++..+++.+ |+.+++.+|+ |..++.++
T Consensus        36 ~~l~~l~-~~~~~~vLDiGcG~G~~~~~la~~~~~~~~v~gvD~s~~~~~~a~   87 (231)
T TIGR02752        36 DTMKRMN-VQAGTSALDVCCGTADWSIALAEAVGPEGHVIGLDFSENMLSVGR   87 (231)
T ss_pred             HHHHhcC-CCCCCEEEEeCCCcCHHHHHHHHHhCCCCEEEEEECCHHHHHHHH
Confidence            3444555 5566899999999999999999986 7789999999 77776665

MenG is a generic term for a methyltransferase that catalyzes the last step in menaquinone biosynthesis; the exact enzymatic activity differs for different MenG because the menaquinone differ in their prenoid side chains in different species. Members of this MenG protein family are 2-heptaprenyl-1,4-naphthoquinone methyltransferase, and are found together in operons with the two subunits of the heptaprenyl diphosphate synthase in Bacillus subtilis and related species.

>COG2813 RsmC 16S RNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]

Probab=97.24  E-value=0.00051  Score=59.24  Aligned_cols=52  Identities=23%  Similarity=0.292  Sum_probs=44.2

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      +-+++.++ .....+|+|+|||.|.+++.+++.+|+.+.+..|. ...++.+++
T Consensus       148 ~lLl~~l~-~~~~~~vlDlGCG~Gvlg~~la~~~p~~~vtmvDvn~~Av~~ar~  200 (300)
T COG2813         148 RLLLETLP-PDLGGKVLDLGCGYGVLGLVLAKKSPQAKLTLVDVNARAVESARK  200 (300)
T ss_pred             HHHHHhCC-ccCCCcEEEeCCCccHHHHHHHHhCCCCeEEEEecCHHHHHHHHH
Confidence            45677777 44445999999999999999999999999999998 678888875

>TIGR00138 gidB 16S rRNA methyltransferase GidB

Probab=97.22  E-value=0.00033  Score=56.55  Aligned_cols=40  Identities=20%  Similarity=0.186  Sum_probs=34.3

Q ss_pred             cceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256          194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~  233 (244)
                      ..+|+|||||+|.++..++..+|+.+++.+|. |..++.++
T Consensus        43 ~~~vLDiGcGtG~~s~~la~~~~~~~V~~iD~s~~~~~~a~   83 (181)
T TIGR00138        43 GKKVIDIGSGAGFPGIPLAIARPELKLTLLESNHKKVAFLR   83 (181)
T ss_pred             CCeEEEecCCCCccHHHHHHHCCCCeEEEEeCcHHHHHHHH
Confidence            47999999999999999999999999999998 55555543

GidB (glucose-inhibited division protein B) appears to be present and in a single copy in nearly all complete eubacterial genomes. It is missing only from some obligate intracellular species of various lineages (Chlamydiae, Ehrlichia, Wolbachia, Anaplasma, Buchnera, etc.). GidB shows a methytransferase fold in its the crystal structure, and acts as a 7-methylguanosine (m(7)G) methyltransferase, apparently specific to 16S rRNA.

>PRK06202 hypothetical protein; Provisional

Probab=97.22  E-value=0.0012  Score=55.12  Aligned_cols=43  Identities=19%  Similarity=0.120  Sum_probs=36.4

Q ss_pred             CCcceEEEecCCccHHHHHHHHH----CCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISK----YPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~----~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+..+|+|||||.|.++..+++.    .|+.+.+.+|+ |..++.+++
T Consensus        59 ~~~~~iLDlGcG~G~~~~~L~~~~~~~g~~~~v~gvD~s~~~l~~a~~  106 (232)
T PRK06202         59 DRPLTLLDIGCGGGDLAIDLARWARRDGLRLEVTAIDPDPRAVAFARA  106 (232)
T ss_pred             CCCcEEEEeccCCCHHHHHHHHHHHhCCCCcEEEEEcCCHHHHHHHHh
Confidence            45689999999999998888763    56789999999 888888875

>PRK07402 precorrin-6B methylase; Provisional

Probab=97.22  E-value=0.00048  Score=56.10  Aligned_cols=50  Identities=18%  Similarity=0.155  Sum_probs=42.0

Q ss_pred             HHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          184 VLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       184 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ++..++ .....+|+|+|||+|.++..+++..|+.+++.+|+ |..++.+++
T Consensus        32 l~~~l~-~~~~~~VLDiG~G~G~~~~~la~~~~~~~V~~vD~s~~~~~~a~~   82 (196)
T PRK07402         32 LISQLR-LEPDSVLWDIGAGTGTIPVEAGLLCPKGRVIAIERDEEVVNLIRR   82 (196)
T ss_pred             HHHhcC-CCCCCEEEEeCCCCCHHHHHHHHHCCCCEEEEEeCCHHHHHHHHH
Confidence            345555 55668999999999999999999999999999999 888887764

>PRK14121 tRNA (guanine-N(7)-)-methyltransferase; Provisional

Probab=97.17  E-value=0.00072  Score=60.71  Aligned_cols=50  Identities=20%  Similarity=0.208  Sum_probs=39.4

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~  233 (244)
                      .+++.+. -.....+||||||.|.++..+++++|+..++.+|+ +..++.+.
T Consensus       113 ~~~~~~~-~~~~p~vLEIGcGsG~~ll~lA~~~P~~~~iGIEI~~~~i~~a~  163 (390)
T PRK14121        113 NFLDFIS-KNQEKILIEIGFGSGRHLLYQAKNNPNKLFIGIEIHTPSIEQVL  163 (390)
T ss_pred             HHHHHhc-CCCCCeEEEEcCcccHHHHHHHHhCCCCCEEEEECCHHHHHHHH
Confidence            3454554 23457999999999999999999999999999998 55555553

>PF05175 MTS: Methyltransferase small domain; InterPro: IPR007848 This domain is found in ribosomal RNA small subunit methyltransferase C and in other methyltransferases

Probab=97.15  E-value=0.00025  Score=56.51  Aligned_cols=42  Identities=21%  Similarity=0.329  Sum_probs=37.8

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...+++|+|||+|.++..+++++|+.+++..|. |.+++.+++
T Consensus        31 ~~~~vLDlG~G~G~i~~~la~~~~~~~v~~vDi~~~a~~~a~~   73 (170)
T PF05175_consen   31 KGGRVLDLGCGSGVISLALAKRGPDAKVTAVDINPDALELAKR   73 (170)
T ss_dssp             TTCEEEEETSTTSHHHHHHHHTSTCEEEEEEESBHHHHHHHHH
T ss_pred             cCCeEEEecCChHHHHHHHHHhCCCCEEEEEcCCHHHHHHHHH
Confidence            457899999999999999999999999999998 888887764

; GO: 0008168 methyltransferase activity; PDB: 1WY7_A 1DUS_A 2OZV_A 2PJD_A 1VQ1_A 1NV9_A 1SG9_C 1NV8_A 3Q87_B 3DMF_A ....

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=97.08  E-value=0.00091  Score=47.30  Aligned_cols=58  Identities=21%  Similarity=0.336  Sum_probs=46.2

Q ss_pred             cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccc
Q 041256           36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVS  104 (244)
Q Consensus        36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s  104 (244)
                      +.|++.|.+.+  ++.|+.|||+.+|++      ..- +.|+|+.|...|++.++  ...+.|++++..
T Consensus         8 ~~Il~~l~~~~--~~~t~~~ia~~l~i~------~~t-v~r~l~~L~~~g~l~~~--~~~~~y~l~~~~   65 (91)
T smart00346        8 LAVLRALAEEP--GGLTLAELAERLGLS------KST-AHRLLNTLQELGYVEQD--GQNGRYRLGPKV   65 (91)
T ss_pred             HHHHHHHHhCC--CCcCHHHHHHHhCCC------HHH-HHHHHHHHHHCCCeeec--CCCCceeecHHH
Confidence            56788888753  589999999999996      445 99999999999999963  234678887753

>TIGR00740 methyltransferase, putative

Probab=97.06  E-value=0.00058  Score=57.33  Aligned_cols=43  Identities=16%  Similarity=0.167  Sum_probs=37.5

Q ss_pred             CCcceEEEecCCccHHHHHHHHH--CCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISK--YPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~--~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ....+|||||||.|.++..++++  +|+.+.+.+|+ |..++.|++
T Consensus        52 ~~~~~iLDlGcG~G~~~~~l~~~~~~p~~~v~gvD~s~~ml~~a~~   97 (239)
T TIGR00740        52 TPDSNVYDLGCSRGAATLSARRNINQPNVKIIGIDNSQPMVERCRQ   97 (239)
T ss_pred             CCCCEEEEecCCCCHHHHHHHHhcCCCCCeEEEEeCCHHHHHHHHH
Confidence            34578999999999999999997  48899999999 888888764

A simple BLAST search finds all members of this family and weaker hits to a large number of known and predicted methyltransferases. A single iteration with PSI-BLAST, keeping only clear members of the family, leads to a large number of highly significant hits to a set of known and predicted methyltransferases with a large repertoire of different specifities. This model is restricted to a subfamily found so far only in the Proteobacteria, sharing consistent length, full-length homology, and on average better than 35 % identity. It is reasonable to predict equivalent function within this subfamily.

>PRK09489 rsmC 16S ribosomal RNA m2G1207 methyltransferase; Provisional

Probab=97.04  E-value=0.00087  Score=59.51  Aligned_cols=50  Identities=20%  Similarity=0.332  Sum_probs=40.0

Q ss_pred             HHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          184 VLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       184 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      +++.++ .....+|+|+|||.|.++..+++++|+.+++..|. +..++.+++
T Consensus       188 Ll~~l~-~~~~g~VLDlGCG~G~ls~~la~~~p~~~v~~vDis~~Al~~A~~  238 (342)
T PRK09489        188 LLSTLT-PHTKGKVLDVGCGAGVLSAVLARHSPKIRLTLSDVSAAALESSRA  238 (342)
T ss_pred             HHHhcc-ccCCCeEEEeccCcCHHHHHHHHhCCCCEEEEEECCHHHHHHHHH
Confidence            445454 23345899999999999999999999999999998 677777654

>COG2242 CobL Precorrin-6B methylase 2 [Coenzyme metabolism]

Probab=97.03  E-value=0.0013  Score=52.89  Aligned_cols=48  Identities=15%  Similarity=0.073  Sum_probs=40.2

Q ss_pred             hhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          186 ESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       186 ~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+. ..+..+++|||||+|.++++++...|..+++.+|. ++.++..++
T Consensus        28 s~L~-~~~g~~l~DIGaGtGsi~iE~a~~~p~~~v~AIe~~~~a~~~~~~   76 (187)
T COG2242          28 SKLR-PRPGDRLWDIGAGTGSITIEWALAGPSGRVIAIERDEEALELIER   76 (187)
T ss_pred             HhhC-CCCCCEEEEeCCCccHHHHHHHHhCCCceEEEEecCHHHHHHHHH
Confidence            3444 56678999999999999999999999999999997 777766653

>PRK11207 tellurite resistance protein TehB; Provisional

Probab=97.02  E-value=0.00084  Score=54.84  Aligned_cols=50  Identities=24%  Similarity=0.309  Sum_probs=39.7

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      +.+++.++ .....+|+|+|||.|.++..++++  ..+++.+|+ |..++.+++
T Consensus        20 ~~l~~~l~-~~~~~~vLDiGcG~G~~a~~La~~--g~~V~gvD~S~~~i~~a~~   70 (197)
T PRK11207         20 SEVLEAVK-VVKPGKTLDLGCGNGRNSLYLAAN--GFDVTAWDKNPMSIANLER   70 (197)
T ss_pred             HHHHHhcc-cCCCCcEEEECCCCCHHHHHHHHC--CCEEEEEeCCHHHHHHHHH
Confidence            46666666 455689999999999999999986  468899999 777776653

>PRK15451 tRNA cmo(5)U34 methyltransferase; Provisional

Probab=97.01  E-value=0.00062  Score=57.60  Aligned_cols=43  Identities=21%  Similarity=0.225  Sum_probs=37.6

Q ss_pred             CCcceEEEecCCccHHHHHHHH--HCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIIS--KYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~--~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ....+|+|||||+|..+..+++  .+|+.+++.+|. |..++.|++
T Consensus        55 ~~~~~vLDlGcGtG~~~~~l~~~~~~~~~~v~gvD~S~~ml~~A~~  100 (247)
T PRK15451         55 QPGTQVYDLGCSLGAATLSVRRNIHHDNCKIIAIDNSPAMIERCRR  100 (247)
T ss_pred             CCCCEEEEEcccCCHHHHHHHHhcCCCCCeEEEEeCCHHHHHHHHH
Confidence            3457899999999999999988  479999999998 889988864

>PRK00274 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed

Probab=96.96  E-value=0.0016  Score=56.01  Aligned_cols=57  Identities=12%  Similarity=0.208  Sum_probs=41.9

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCCC---CCceee
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPSY---PGTLFI  241 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~~---~~i~~~  241 (244)
                      ..+++.++ .....+|+|||||.|.++..++++.+  +++.+|. |..++.+++.   ++++++
T Consensus        32 ~~i~~~l~-~~~~~~VLEiG~G~G~lt~~L~~~~~--~v~avE~d~~~~~~~~~~~~~~~v~~i   92 (272)
T PRK00274         32 DKIVDAAG-PQPGDNVLEIGPGLGALTEPLLERAA--KVTAVEIDRDLAPILAETFAEDNLTII   92 (272)
T ss_pred             HHHHHhcC-CCCcCeEEEeCCCccHHHHHHHHhCC--cEEEEECCHHHHHHHHHhhccCceEEE
Confidence            34555555 56668999999999999999999987  6777776 7777776542   355543

>PF02390 Methyltransf_4: Putative methyltransferase ; InterPro: IPR003358 This entry represents tRNA (guanine-N-7) methyltransferase (2

Probab=96.96  E-value=0.0012  Score=54.01  Aligned_cols=47  Identities=19%  Similarity=0.316  Sum_probs=36.6

Q ss_pred             ceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC------CCCCceee
Q 041256          195 KKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP------SYPGTLFI  241 (244)
Q Consensus       195 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~------~~~~i~~~  241 (244)
                      ..+||||||.|.++.++++++|+...+.+|. +..+..+.      .+++|.++
T Consensus        19 ~l~lEIG~G~G~~l~~~A~~~Pd~n~iGiE~~~~~v~~a~~~~~~~~l~Nv~~~   72 (195)
T PF02390_consen   19 PLILEIGCGKGEFLIELAKRNPDINFIGIEIRKKRVAKALRKAEKRGLKNVRFL   72 (195)
T ss_dssp             EEEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHHTTSSEEEE
T ss_pred             CeEEEecCCCCHHHHHHHHHCCCCCEEEEecchHHHHHHHHHHHhhcccceEEE
Confidence            5999999999999999999999999999997 44544442      14566554

1.1.33 from EC), which catalyses the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA. Capping of the pre-mRNA 5' end by addition a monomethylated guanosine cap (m(7)G) is an essential and the earliest modification in the biogenesis of mRNA []. The reaction is catalysed by three enzymes: triphosphatase, guanylyltransferase, and tRNA (guanine-N-7) methyltransferase [, ].; GO: 0008176 tRNA (guanine-N7-)-methyltransferase activity, 0006400 tRNA modification; PDB: 3DXZ_A 3DXY_A 3DXX_A 3CKK_A 3P2I_B 3P2K_D 3P2E_A 3MTE_B 3PB3_B 1YZH_B ....

>PRK08317 hypothetical protein; Provisional

Probab=96.91  E-value=0.0018  Score=53.63  Aligned_cols=50  Identities=18%  Similarity=0.242  Sum_probs=40.2

Q ss_pred             HHhhcCCCCCcceEEEecCCccHHHHHHHHHC-CCCeEEEccc-hHHhhhCCC
Q 041256          184 VLESYKGFEHVKKLVDVGGGLGITLNMIISKY-PHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       184 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      +.+.++ +....+|||||||.|.++..+++.+ |..+.+.+|+ |..++.+++
T Consensus        11 ~~~~~~-~~~~~~vLdiG~G~G~~~~~~a~~~~~~~~v~~~d~~~~~~~~a~~   62 (241)
T PRK08317         11 TFELLA-VQPGDRVLDVGCGPGNDARELARRVGPEGRVVGIDRSEAMLALAKE   62 (241)
T ss_pred             HHHHcC-CCCCCEEEEeCCCCCHHHHHHHHhcCCCcEEEEEeCCHHHHHHHHH
Confidence            445555 6677899999999999999999998 8889999998 565665543

>COG2890 HemK Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis]

Probab=96.88  E-value=0.00071  Score=58.42  Aligned_cols=39  Identities=23%  Similarity=0.376  Sum_probs=37.0

Q ss_pred             eEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          196 KLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       196 ~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      +|+|||+|+|..++++++++|+.+++..|+ |.+++.|++
T Consensus       113 ~ilDlGTGSG~iai~la~~~~~~~V~a~Dis~~Al~~A~~  152 (280)
T COG2890         113 RILDLGTGSGAIAIALAKEGPDAEVIAVDISPDALALARE  152 (280)
T ss_pred             cEEEecCChHHHHHHHHhhCcCCeEEEEECCHHHHHHHHH
Confidence            899999999999999999999999999999 899988875

>PF13649 Methyltransf_25: Methyltransferase domain; PDB: 3BXO_B 3GGD_A 3PX2_A 3PX3_A 3PFH_D 3PFG_A 1Y8C_A

Probab=96.87  E-value=0.00069  Score=48.92  Aligned_cols=38  Identities=24%  Similarity=0.503  Sum_probs=30.4

Q ss_pred             EEEecCCccHHHHHHHHHC---CCCeEEEccc-hHHhhhCCC
Q 041256          197 LVDVGGGLGITLNMIISKY---PHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       197 vvDVGGG~G~~~~~l~~~~---P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      |+|+|||+|..+..+++.+   |+.+.+.+|+ |+.++.+++
T Consensus         1 ILDlgcG~G~~~~~l~~~~~~~~~~~~~gvD~s~~~l~~~~~   42 (101)
T PF13649_consen    1 ILDLGCGTGRVTRALARRFDAGPSSRVIGVDISPEMLELAKK   42 (101)
T ss_dssp             -EEET-TTSHHHHHHHHHS-----SEEEEEES-HHHHHHHHH
T ss_pred             CEEeecCCcHHHHHHHHHhhhcccceEEEEECCHHHHHHHHH
Confidence            7999999999999999997   6789999998 777777764

>COG2226 UbiE Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]

Probab=96.87  E-value=0.0019  Score=54.34  Aligned_cols=42  Identities=17%  Similarity=0.170  Sum_probs=38.5

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...+|+|||||+|-++..+++..+..++++.|. +..++.+++
T Consensus        51 ~g~~vLDva~GTGd~a~~~~k~~g~g~v~~~D~s~~ML~~a~~   93 (238)
T COG2226          51 PGDKVLDVACGTGDMALLLAKSVGTGEVVGLDISESMLEVARE   93 (238)
T ss_pred             CCCEEEEecCCccHHHHHHHHhcCCceEEEEECCHHHHHHHHH
Confidence            568999999999999999999999999999998 788888875

>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases

Probab=96.85  E-value=0.0025  Score=42.91  Aligned_cols=60  Identities=17%  Similarity=0.222  Sum_probs=46.6

Q ss_pred             HHhcChhhHHhhcCCCC-CCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCc
Q 041256           33 VVELDVFEIISKAGPGA-KLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAP  102 (244)
Q Consensus        33 a~~lgifd~L~~~~~~g-~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~  102 (244)
                      ..+-.|+..|.+.|  + ++|+.|||+.+|++      ... +.|+|.-|...|++..... .++.|..+.
T Consensus         6 ~~~~~IL~~L~~~g--~~~~ta~eLa~~lgl~------~~~-v~r~L~~L~~~G~V~~~~~-~~~~W~i~~   66 (68)
T smart00550        6 SLEEKILEFLENSG--DETSTALQLAKNLGLP------KKE-VNRVLYSLEKKGKVCKQGG-TPPLWKLTD   66 (68)
T ss_pred             HHHHHHHHHHHHCC--CCCcCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEecCC-CCCceEeec
Confidence            34567888898874  3 39999999999997      456 9999999999999986321 247787764

Helix-turn-helix-containing domain. Also known as Zab.

>smart00650 rADc Ribosomal RNA adenine dimethylases

Probab=96.84  E-value=0.0023  Score=50.81  Aligned_cols=50  Identities=10%  Similarity=0.300  Sum_probs=38.9

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+++.++ +....+++|||||.|.++..++++  ..+++.+|. |..++.+++
T Consensus         3 ~~i~~~~~-~~~~~~vLEiG~G~G~lt~~l~~~--~~~v~~vE~~~~~~~~~~~   53 (169)
T smart00650        3 DKIVRAAN-LRPGDTVLEIGPGKGALTEELLER--AARVTAIEIDPRLAPRLRE   53 (169)
T ss_pred             HHHHHhcC-CCCcCEEEEECCCccHHHHHHHhc--CCeEEEEECCHHHHHHHHH
Confidence            34566666 666689999999999999999998  467888887 566666543

>PRK10258 biotin biosynthesis protein BioC; Provisional

Probab=96.81  E-value=0.0038  Score=52.71  Aligned_cols=50  Identities=18%  Similarity=0.251  Sum_probs=38.6

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+++.++ .....+|+|||||+|.++..+.+.  ..+++..|+ |..++.+++
T Consensus        32 ~~l~~~l~-~~~~~~vLDiGcG~G~~~~~l~~~--~~~v~~~D~s~~~l~~a~~   82 (251)
T PRK10258         32 DALLAMLP-QRKFTHVLDAGCGPGWMSRYWRER--GSQVTALDLSPPMLAQARQ   82 (251)
T ss_pred             HHHHHhcC-ccCCCeEEEeeCCCCHHHHHHHHc--CCeEEEEECCHHHHHHHHh
Confidence            44555555 345689999999999998888764  467899999 888877765

>TIGR03533 L3_gln_methyl protein-(glutamine-N5) methyltransferase, ribosomal protein L3-specific

Probab=96.79  E-value=0.0012  Score=57.07  Aligned_cols=42  Identities=21%  Similarity=0.269  Sum_probs=38.1

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      +..+|+|+|||+|.++..+++++|+.+++.+|. |..++.|++
T Consensus       121 ~~~~vLDlG~GsG~i~~~la~~~~~~~v~avDis~~al~~A~~  163 (284)
T TIGR03533       121 PVKRILDLCTGSGCIAIACAYAFPEAEVDAVDISPDALAVAEI  163 (284)
T ss_pred             CCCEEEEEeCchhHHHHHHHHHCCCCEEEEEECCHHHHHHHHH
Confidence            447899999999999999999999999999999 888888764

Members of this protein family methylate ribosomal protein L3 on a glutamine side chain. This family is related to HemK, a protein-glutamine methyltranferase for peptide chain release factors.

>TIGR00477 tehB tellurite resistance protein TehB

Probab=96.79  E-value=0.0025  Score=51.97  Aligned_cols=49  Identities=22%  Similarity=0.149  Sum_probs=38.1

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~  233 (244)
                      ..+++.++ .....+|+|||||.|.++..++++  +.+++.+|. |..++.++
T Consensus        20 ~~l~~~~~-~~~~~~vLDiGcG~G~~a~~la~~--g~~V~~iD~s~~~l~~a~   69 (195)
T TIGR00477        20 SAVREAVK-TVAPCKTLDLGCGQGRNSLYLSLA--GYDVRAWDHNPASIASVL   69 (195)
T ss_pred             HHHHHHhc-cCCCCcEEEeCCCCCHHHHHHHHC--CCeEEEEECCHHHHHHHH
Confidence            35556665 445689999999999999999985  568899998 77777654

Part of a tellurite-reducing operon tehA and tehB

>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional

Probab=96.79  E-value=0.0028  Score=54.31  Aligned_cols=48  Identities=29%  Similarity=0.497  Sum_probs=38.1

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCC---eEEEccc-hHHhhhCCC-CCCcee
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHI---KGINYDL-PYVIKDAPS-YPGTLF  240 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l---~~~v~Dl-p~vi~~a~~-~~~i~~  240 (244)
                      ...+|+|||||+|.++..+++.+|..   +++.+|+ |..++.|++ .+++.+
T Consensus        85 ~~~~vLDiGcG~G~~~~~l~~~~~~~~~~~v~giD~s~~~l~~A~~~~~~~~~  137 (272)
T PRK11088         85 KATALLDIGCGEGYYTHALADALPEITTMQLFGLDISKVAIKYAAKRYPQVTF  137 (272)
T ss_pred             CCCeEEEECCcCCHHHHHHHHhcccccCCeEEEECCCHHHHHHHHHhCCCCeE
Confidence            44789999999999999999998864   5799998 777877754 355544

>TIGR03704 PrmC_rel_meth putative protein-(glutamine-N5) methyltransferase, unknown substrate-specific

Probab=96.79  E-value=0.0021  Score=54.65  Aligned_cols=41  Identities=20%  Similarity=0.184  Sum_probs=37.4

Q ss_pred             cceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+++|+|||+|.++..+++++|..+++.+|. |..++.+++
T Consensus        87 ~~~vLDlg~GsG~i~l~la~~~~~~~v~~vDis~~al~~A~~  128 (251)
T TIGR03704        87 TLVVVDLCCGSGAVGAALAAALDGIELHAADIDPAAVRCARR  128 (251)
T ss_pred             CCEEEEecCchHHHHHHHHHhCCCCEEEEEECCHHHHHHHHH
Confidence            45899999999999999999999999999999 888888765

This protein family is closely related to two different families of protein-(glutamine-N5) methyltransferase. The first is PrmB, which modifies ribosomal protein L3 in some bacteria. The second is PrmC (HemK), which modifies peptide chain release factors 1 and 2 in most bacteria and also in eukaryotes. The glutamine side chain-binding motif NPPY shared by PrmB and PrmC is N[VAT]PY in this family. The protein substrate is unknown.

>PRK11036 putative S-adenosyl-L-methionine-dependent methyltransferase; Provisional

Probab=96.78  E-value=0.0026  Score=53.98  Aligned_cols=48  Identities=25%  Similarity=0.311  Sum_probs=37.9

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+++.++  ....+|+|||||.|.++..++++  ..+++.+|+ |+.++.|++
T Consensus        36 ~~l~~l~--~~~~~vLDiGcG~G~~a~~la~~--g~~v~~vD~s~~~l~~a~~   84 (255)
T PRK11036         36 RLLAELP--PRPLRVLDAGGGEGQTAIKLAEL--GHQVILCDLSAEMIQRAKQ   84 (255)
T ss_pred             HHHHhcC--CCCCEEEEeCCCchHHHHHHHHc--CCEEEEEECCHHHHHHHHH
Confidence            3444444  44579999999999999999987  467899999 888888764

>TIGR02072 BioC biotin biosynthesis protein BioC

Probab=96.78  E-value=0.0018  Score=53.72  Aligned_cols=42  Identities=19%  Similarity=0.423  Sum_probs=35.6

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...+|||||||.|.++..+++.+|+.+++..|. |..++.+++
T Consensus        34 ~~~~vLDlG~G~G~~~~~l~~~~~~~~~~~~D~~~~~~~~~~~   76 (240)
T TIGR02072        34 IPASVLDIGCGTGYLTRALLKRFPQAEFIALDISAGMLAQAKT   76 (240)
T ss_pred             CCCeEEEECCCccHHHHHHHHhCCCCcEEEEeChHHHHHHHHH
Confidence            347899999999999999999999999999998 566655543

This enzyme, which is found in biotin biosynthetic gene clusters in proteobacteria, firmicutes, green-sulfur bacteria, fusobacterium and bacteroides, is believed to carry out an enzymatic step prior to the formation of pimeloyl-CoA (although attribution of this annotation is not traceable). The enzyme appears related to methyltransferases by homology.

>PRK11805 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional

Probab=96.74  E-value=0.0012  Score=57.81  Aligned_cols=40  Identities=18%  Similarity=0.238  Sum_probs=37.3

Q ss_pred             ceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          195 KKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       195 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+|+|+|||+|.++..+++++|+.+++.+|+ |..++.|++
T Consensus       135 ~~VLDlG~GsG~iai~la~~~p~~~V~avDis~~al~~A~~  175 (307)
T PRK11805        135 TRILDLCTGSGCIAIACAYAFPDAEVDAVDISPDALAVAEI  175 (307)
T ss_pred             CEEEEEechhhHHHHHHHHHCCCCEEEEEeCCHHHHHHHHH
Confidence            6899999999999999999999999999999 888888865

>TIGR03534 RF_mod_PrmC protein-(glutamine-N5) methyltransferase, release factor-specific

Probab=96.70  E-value=0.0028  Score=53.18  Aligned_cols=42  Identities=19%  Similarity=0.299  Sum_probs=37.2

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...+|+|+|||+|.++..+++.+|+.+++.+|. |..++.+++
T Consensus        87 ~~~~ilDig~G~G~~~~~l~~~~~~~~v~~iD~~~~~~~~a~~  129 (251)
T TIGR03534        87 GPLRVLDLGTGSGAIALALAKERPDARVTAVDISPEALAVARK  129 (251)
T ss_pred             CCCeEEEEeCcHhHHHHHHHHHCCCCEEEEEECCHHHHHHHHH
Confidence            346899999999999999999999999999998 777877754

Members of this protein family are HemK (PrmC), a protein once thought to be involved in heme biosynthesis but now recognized to be a protein-glutamine methyltransferase that modifies the peptide chain release factors. All members of the seed alignment are encoded next to the release factor 1 gene (prfA) and confirmed by phylogenetic analysis. SIMBAL analysis (manuscript in prep.) shows the motif [LIV]PRx[DE]TE (in Escherichia coli, IPRPDTE) confers specificity for the release factors rather than for ribosomal protein L3.

>TIGR00080 pimt protein-L-isoaspartate(D-aspartate) O-methyltransferase

Probab=96.69  E-value=0.0042  Score=51.32  Aligned_cols=51  Identities=14%  Similarity=0.189  Sum_probs=40.3

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCC-CCeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYP-HIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+++.++ .....+|+|||||+|.++..+++..+ +.+++.+|. |+.++.|++
T Consensus        68 ~~~~~l~-~~~~~~VLDiG~GsG~~a~~la~~~~~~g~V~~vD~~~~~~~~A~~  120 (215)
T TIGR00080        68 MMTELLE-LKPGMKVLEIGTGSGYQAAVLAEIVGRDGLVVSIERIPELAEKAER  120 (215)
T ss_pred             HHHHHhC-CCCcCEEEEECCCccHHHHHHHHHhCCCCEEEEEeCCHHHHHHHHH
Confidence            4455555 56678999999999999999999865 567888886 888887764

Among the prokaryotes, the gene name is pcm. Among eukaryotes, pimt.

>COG2264 PrmA Ribosomal protein L11 methylase [Translation, ribosomal structure and biogenesis]

Probab=96.68  E-value=0.0012  Score=57.11  Aligned_cols=63  Identities=27%  Similarity=0.379  Sum_probs=44.3

Q ss_pred             HHHHHHHhcchhhHHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          168 VFNNGMLSHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       168 ~f~~aM~~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .|..+-...+.+.. .+++.+.  .+.++++|||||+|.++++.++--.. +++.+|+ |..++.+++
T Consensus       140 AFGTG~HpTT~lcL-~~Le~~~--~~g~~vlDvGcGSGILaIAa~kLGA~-~v~g~DiDp~AV~aa~e  203 (300)
T COG2264         140 AFGTGTHPTTSLCL-EALEKLL--KKGKTVLDVGCGSGILAIAAAKLGAK-KVVGVDIDPQAVEAARE  203 (300)
T ss_pred             ccCCCCChhHHHHH-HHHHHhh--cCCCEEEEecCChhHHHHHHHHcCCc-eEEEecCCHHHHHHHHH
Confidence            45444444444433 4455554  47799999999999999998876443 5677787 888888875

>COG1414 IclR Transcriptional regulator [Transcription]

Probab=96.66  E-value=0.0024  Score=54.13  Aligned_cols=59  Identities=22%  Similarity=0.381  Sum_probs=47.5

Q ss_pred             cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcccc
Q 041256           36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSA  105 (244)
Q Consensus        36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~  105 (244)
                      +.|++.|.+.+  .++++.|||+++|++      ..- +.|+|..|+..||+.+++  ..++|++++..-
T Consensus         7 l~iL~~l~~~~--~~l~l~ela~~~glp------ksT-~~RlL~tL~~~G~v~~d~--~~g~Y~Lg~~~~   65 (246)
T COG1414           7 LAILDLLAEGP--GGLSLAELAERLGLP------KST-VHRLLQTLVELGYVEQDP--EDGRYRLGPRLL   65 (246)
T ss_pred             HHHHHHHHhCC--CCCCHHHHHHHhCcC------HHH-HHHHHHHHHHCCCEEEcC--CCCcEeehHHHH
Confidence            56788888743  457899999999995      345 999999999999999742  257899998753

>PRK00216 ubiE ubiquinone/menaquinone biosynthesis methyltransferase; Reviewed

Probab=96.64  E-value=0.0031  Score=52.31  Aligned_cols=51  Identities=12%  Similarity=0.081  Sum_probs=40.1

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCC-CCeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYP-HIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .++..+. .....+|+|||||.|.++..+++.+| +.+++++|+ |..++.+++
T Consensus        42 ~~~~~~~-~~~~~~vldiG~G~G~~~~~l~~~~~~~~~v~~~D~s~~~~~~a~~   94 (239)
T PRK00216         42 KTIKWLG-VRPGDKVLDLACGTGDLAIALAKAVGKTGEVVGLDFSEGMLAVGRE   94 (239)
T ss_pred             HHHHHhC-CCCCCeEEEeCCCCCHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHH
Confidence            3444444 44557999999999999999999998 789999998 666666654

>PRK01581 speE spermidine synthase; Validated

Probab=96.63  E-value=0.0027  Score=56.54  Aligned_cols=43  Identities=23%  Similarity=0.265  Sum_probs=37.1

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .++++|++||||.|..+.++++..|..+.++.|+ |+|++.|++
T Consensus       149 ~~PkrVLIIGgGdG~tlrelLk~~~v~~It~VEIDpeVIelAr~  192 (374)
T PRK01581        149 IDPKRVLILGGGDGLALREVLKYETVLHVDLVDLDGSMINMARN  192 (374)
T ss_pred             CCCCEEEEECCCHHHHHHHHHhcCCCCeEEEEeCCHHHHHHHHh
Confidence            5668999999999999999997656678999998 889998874

>PTZ00098 phosphoethanolamine N-methyltransferase; Provisional

Probab=96.60  E-value=0.0031  Score=53.92  Aligned_cols=51  Identities=25%  Similarity=0.366  Sum_probs=41.1

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+++.++ +....+|||||||.|..+..+++++ +.+++.+|+ |..++.+++
T Consensus        42 ~~~l~~l~-l~~~~~VLDiGcG~G~~a~~la~~~-~~~v~giD~s~~~~~~a~~   93 (263)
T PTZ00098         42 TKILSDIE-LNENSKVLDIGSGLGGGCKYINEKY-GAHVHGVDICEKMVNIAKL   93 (263)
T ss_pred             HHHHHhCC-CCCCCEEEEEcCCCChhhHHHHhhc-CCEEEEEECCHHHHHHHHH
Confidence            45666676 6777899999999999999998876 678999998 666666654

>PLN02244 tocopherol O-methyltransferase

Probab=96.60  E-value=0.0031  Score=55.91  Aligned_cols=41  Identities=29%  Similarity=0.412  Sum_probs=34.5

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~  233 (244)
                      ....+|||||||.|.++..+++++ +.+++.+|+ |..++.++
T Consensus       117 ~~~~~VLDiGCG~G~~~~~La~~~-g~~v~gvD~s~~~i~~a~  158 (340)
T PLN02244        117 KRPKRIVDVGCGIGGSSRYLARKY-GANVKGITLSPVQAARAN  158 (340)
T ss_pred             CCCCeEEEecCCCCHHHHHHHHhc-CCEEEEEECCHHHHHHHH
Confidence            456899999999999999999988 778999998 66666554

>PRK07580 Mg-protoporphyrin IX methyl transferase; Validated

Probab=96.57  E-value=0.0034  Score=52.00  Aligned_cols=41  Identities=20%  Similarity=0.311  Sum_probs=33.8

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ....+|+|||||.|.++..++++.+  +++..|+ |..++.+++
T Consensus        62 ~~~~~vLDvGcG~G~~~~~l~~~~~--~v~~~D~s~~~i~~a~~  103 (230)
T PRK07580         62 LTGLRILDAGCGVGSLSIPLARRGA--KVVASDISPQMVEEARE  103 (230)
T ss_pred             CCCCEEEEEeCCCCHHHHHHHHcCC--EEEEEECCHHHHHHHHH
Confidence            4557999999999999999998865  4888898 777777764

>PRK14966 unknown domain/N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase fusion protein; Provisional

Probab=96.55  E-value=0.0022  Score=58.15  Aligned_cols=42  Identities=19%  Similarity=0.245  Sum_probs=38.1

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...+++|||||+|.++..+++++|+.+++.+|. |..++.+++
T Consensus       251 ~~~rVLDLGcGSG~IaiaLA~~~p~a~VtAVDiS~~ALe~Are  293 (423)
T PRK14966        251 ENGRVWDLGTGSGAVAVTVALERPDAFVRASDISPPALETARK  293 (423)
T ss_pred             CCCEEEEEeChhhHHHHHHHHhCCCCEEEEEECCHHHHHHHHH
Confidence            346899999999999999999999999999999 888888875

>COG2230 Cfa Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]

Probab=96.55  E-value=0.0049  Score=52.96  Aligned_cols=50  Identities=20%  Similarity=0.254  Sum_probs=41.9

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~  233 (244)
                      ..+.+.+. +++..+|||||||-|.+++-.+++| +.+++.+++ ++-.+.++
T Consensus        62 ~~~~~kl~-L~~G~~lLDiGCGWG~l~~~aA~~y-~v~V~GvTlS~~Q~~~~~  112 (283)
T COG2230          62 DLILEKLG-LKPGMTLLDIGCGWGGLAIYAAEEY-GVTVVGVTLSEEQLAYAE  112 (283)
T ss_pred             HHHHHhcC-CCCCCEEEEeCCChhHHHHHHHHHc-CCEEEEeeCCHHHHHHHH
Confidence            45677777 8899999999999999999999999 999999998 44444443

>PRK11188 rrmJ 23S rRNA methyltransferase J; Provisional

Probab=96.55  E-value=0.0082  Score=49.51  Aligned_cols=45  Identities=20%  Similarity=0.178  Sum_probs=34.1

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHC-CCCeEEEccchH
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKY-PHIKGINYDLPY  227 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dlp~  227 (244)
                      .+.+.|..+....+|||||||+|.++..++++. |..+++.+|+-+
T Consensus        41 ~~~~~~~~~~~~~~VLDlG~GtG~~t~~l~~~~~~~~~V~aVDi~~   86 (209)
T PRK11188         41 EIQQSDKLFKPGMTVVDLGAAPGGWSQYAVTQIGDKGRVIACDILP   86 (209)
T ss_pred             HHHHHhccCCCCCEEEEEcccCCHHHHHHHHHcCCCceEEEEeccc
Confidence            334444434566799999999999999999987 456888888744

>PLN02366 spermidine synthase

Probab=96.54  E-value=0.0024  Score=55.83  Aligned_cols=42  Identities=26%  Similarity=0.247  Sum_probs=35.2

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCC-CeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPH-IKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dl-p~vi~~a~~  234 (244)
                      ++.++|++||||.|..+..+++. |. .+++++|+ |.|++.+++
T Consensus        90 ~~pkrVLiIGgG~G~~~rellk~-~~v~~V~~VEiD~~Vi~~ar~  133 (308)
T PLN02366         90 PNPKKVLVVGGGDGGVLREIARH-SSVEQIDICEIDKMVIDVSKK  133 (308)
T ss_pred             CCCCeEEEEcCCccHHHHHHHhC-CCCCeEEEEECCHHHHHHHHH
Confidence            46789999999999999999865 65 57889998 678888865

>TIGR00536 hemK_fam HemK family putative methylases

Probab=96.51  E-value=0.0021  Score=55.49  Aligned_cols=40  Identities=23%  Similarity=0.405  Sum_probs=36.9

Q ss_pred             ceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          195 KKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       195 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+|+|+|||+|.++..+++.+|+.+++..|. |..++.+++
T Consensus       116 ~~vLDlG~GsG~i~l~la~~~~~~~v~avDis~~al~~a~~  156 (284)
T TIGR00536       116 LHILDLGTGSGCIALALAYEFPNAEVIAVDISPDALAVAEE  156 (284)
T ss_pred             CEEEEEeccHhHHHHHHHHHCCCCEEEEEECCHHHHHHHHH
Confidence            6899999999999999999999999999998 888887765

The gene hemK from E. coli was found to contribute to heme biosynthesis and originally suggested to be protoporphyrinogen oxidase (Medline 95189105). Functional analysis of the nearest homolog in Saccharomyces cerevisiae, YNL063w, finds it is not protoporphyrinogen oxidase and sequence analysis suggests that HemK homologs have S-adenosyl-methionine-dependent methyltransferase activity (Medline 99237242). Homologs are found, usually in a single copy, in nearly all completed genomes, but varying somewhat in apparent domain architecture. Both E. coli and H. influenzae have two members rather than one. The members from the Mycoplasmas have an additional C-terminal domain.

>PRK09328 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional

Probab=96.50  E-value=0.0041  Score=53.08  Aligned_cols=44  Identities=18%  Similarity=0.310  Sum_probs=37.8

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .....+|+|+|||+|.++..+++.+|..+++..|. |..++.+++
T Consensus       106 ~~~~~~vLDiG~GsG~~~~~la~~~~~~~v~~iDis~~~l~~a~~  150 (275)
T PRK09328        106 LKEPLRVLDLGTGSGAIALALAKERPDAEVTAVDISPEALAVARR  150 (275)
T ss_pred             ccCCCEEEEEcCcHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHH
Confidence            34557899999999999999999999999999998 677776654

>PHA03411 putative methyltransferase; Provisional

Probab=96.49  E-value=0.0036  Score=53.61  Aligned_cols=47  Identities=17%  Similarity=0.260  Sum_probs=39.3

Q ss_pred             cceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC-CCCcee
Q 041256          194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS-YPGTLF  240 (244)
Q Consensus       194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~-~~~i~~  240 (244)
                      ..+|+|+|||.|.++..++++.+..+++.+|+ |..++.+++ .+++++
T Consensus        65 ~grVLDLGcGsGilsl~la~r~~~~~V~gVDisp~al~~Ar~n~~~v~~  113 (279)
T PHA03411         65 TGKVLDLCAGIGRLSFCMLHRCKPEKIVCVELNPEFARIGKRLLPEAEW  113 (279)
T ss_pred             CCeEEEcCCCCCHHHHHHHHhCCCCEEEEEECCHHHHHHHHHhCcCCEE
Confidence            46899999999999999999988889999998 888887765 345554

>PRK01544 bifunctional N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase/tRNA (m7G46) methyltransferase; Reviewed

Probab=96.46  E-value=0.0024  Score=59.66  Aligned_cols=41  Identities=22%  Similarity=0.330  Sum_probs=37.5

Q ss_pred             cceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+|+|||||+|.++..+++++|+.+++.+|+ |.+++.|++
T Consensus       139 ~~~VLDlG~GsG~iai~la~~~p~~~v~avDis~~al~~A~~  180 (506)
T PRK01544        139 FLNILELGTGSGCIAISLLCELPNANVIATDISLDAIEVAKS  180 (506)
T ss_pred             CCEEEEccCchhHHHHHHHHHCCCCeEEEEECCHHHHHHHHH
Confidence            46899999999999999999999999999999 788888765

>PRK11569 transcriptional repressor IclR; Provisional

Probab=96.43  E-value=0.0042  Score=53.40  Aligned_cols=59  Identities=14%  Similarity=0.224  Sum_probs=47.4

Q ss_pred             cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcccc
Q 041256           36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSA  105 (244)
Q Consensus        36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~  105 (244)
                      +.|.+.|.+.+  ++.|+.|||+.+|++      ..- +.|+|.-|+..||+.++  ...++|++.+...
T Consensus        31 l~IL~~l~~~~--~~~~lseia~~lglp------ksT-v~RlL~tL~~~G~l~~~--~~~~~Y~lG~~l~   89 (274)
T PRK11569         31 LKLLEWIAESN--GSVALTELAQQAGLP------NST-THRLLTTMQQQGFVRQV--GELGHWAIGAHAF   89 (274)
T ss_pred             HHHHHHHHhCC--CCcCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEEc--CCCCeEecCHHHH
Confidence            56777887753  689999999999996      345 99999999999999863  2358899987653

>PRK00811 spermidine synthase; Provisional

Probab=96.43  E-value=0.0028  Score=54.84  Aligned_cols=43  Identities=21%  Similarity=0.244  Sum_probs=36.8

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      +++++|+|||||.|..+..++++.+.-+++++|+ |.|++.+++
T Consensus        75 ~~p~~VL~iG~G~G~~~~~~l~~~~~~~V~~VEid~~vv~~a~~  118 (283)
T PRK00811         75 PNPKRVLIIGGGDGGTLREVLKHPSVEKITLVEIDERVVEVCRK  118 (283)
T ss_pred             CCCCEEEEEecCchHHHHHHHcCCCCCEEEEEeCCHHHHHHHHH
Confidence            4568999999999999999997655568999998 899988875

>PRK04266 fibrillarin; Provisional

Probab=96.41  E-value=0.0078  Score=50.31  Aligned_cols=53  Identities=13%  Similarity=0.154  Sum_probs=40.0

Q ss_pred             cCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHh----hhCCCCCCceee
Q 041256          188 YKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVI----KDAPSYPGTLFI  241 (244)
Q Consensus       188 ~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi----~~a~~~~~i~~~  241 (244)
                      ++ .....+|+|+|||+|.++..+++..+.-+++.+|+ |+.+    +.+++.++|+++
T Consensus        68 l~-i~~g~~VlD~G~G~G~~~~~la~~v~~g~V~avD~~~~ml~~l~~~a~~~~nv~~i  125 (226)
T PRK04266         68 FP-IKKGSKVLYLGAASGTTVSHVSDIVEEGVVYAVEFAPRPMRELLEVAEERKNIIPI  125 (226)
T ss_pred             CC-CCCCCEEEEEccCCCHHHHHHHHhcCCCeEEEEECCHHHHHHHHHHhhhcCCcEEE
Confidence            55 56678999999999999999999998667888998 5433    344444555543

>TIGR01934 MenG_MenH_UbiE ubiquinone/menaquinone biosynthesis methyltransferases

Probab=96.40  E-value=0.0049  Score=50.54  Aligned_cols=51  Identities=18%  Similarity=0.147  Sum_probs=40.0

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCC-CeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPH-IKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+++... .....+|+|+|||.|.++..+++++|. .+.+.+|. |..++.+++
T Consensus        30 ~~~~~~~-~~~~~~vldiG~G~G~~~~~~~~~~~~~~~~~~iD~~~~~~~~~~~   82 (223)
T TIGR01934        30 RAVKLIG-VFKGQKVLDVACGTGDLAIELAKSAPDRGKVTGVDFSSEMLEVAKK   82 (223)
T ss_pred             HHHHHhc-cCCCCeEEEeCCCCChhHHHHHHhcCCCceEEEEECCHHHHHHHHH
Confidence            3344444 446689999999999999999999998 78999998 666666543

Note that a number of non-orthologous genes which are members of pfam03737 have been erroneously annotated as MenG methyltransferases.

>PLN02490 MPBQ/MSBQ methyltransferase

Probab=96.39  E-value=0.0075  Score=53.44  Aligned_cols=42  Identities=31%  Similarity=0.340  Sum_probs=36.7

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...+|||||||+|.++..+++++|..+++.+|+ |+.++.+++
T Consensus       113 ~~~~VLDLGcGtG~~~l~La~~~~~~~VtgVD~S~~mL~~A~~  155 (340)
T PLN02490        113 RNLKVVDVGGGTGFTTLGIVKHVDAKNVTILDQSPHQLAKAKQ  155 (340)
T ss_pred             CCCEEEEEecCCcHHHHHHHHHCCCCEEEEEECCHHHHHHHHH
Confidence            347999999999999999999999999999998 777777764

>PRK10163 DNA-binding transcriptional repressor AllR; Provisional

Probab=96.39  E-value=0.0047  Score=53.05  Aligned_cols=59  Identities=15%  Similarity=0.211  Sum_probs=47.3

Q ss_pred             cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcccc
Q 041256           36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSA  105 (244)
Q Consensus        36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~  105 (244)
                      +.|++.|.+.+  +++|+.|||+.+|++      ..- +.|+|.-|+..||+.++.  ..++|+++....
T Consensus        28 l~IL~~~~~~~--~~~tl~eIa~~lglp------kSt-v~RlL~tL~~~G~l~~~~--~~~~Y~lG~~l~   86 (271)
T PRK10163         28 IAILQYLEKSG--GSSSVSDISLNLDLP------LST-TFRLLKVLQAADFVYQDS--QLGWWHIGLGVF   86 (271)
T ss_pred             HHHHHHHHhCC--CCcCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEEcC--CCCeEEecHHHH
Confidence            56778887754  579999999999996      445 999999999999998642  357899987643

>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family

Probab=96.39  E-value=0.0043  Score=52.47  Aligned_cols=59  Identities=25%  Similarity=0.363  Sum_probs=47.6

Q ss_pred             cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcccccc
Q 041256           36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYF  107 (244)
Q Consensus        36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l  107 (244)
                      +.|.+.|.+.+  .+.|+.|||+.+|++      ..- +.|+|.-|+..||+.+   + .++|++.+....|
T Consensus        12 l~IL~~l~~~~--~~~~l~eia~~lglp------ksT-~~RlL~tL~~~G~l~~---~-~~~Y~lG~~~~~l   70 (248)
T TIGR02431        12 LAVIEAFGAER--PRLTLTDVAEATGLT------RAA-ARRFLLTLVELGYVTS---D-GRLFWLTPRVLRL   70 (248)
T ss_pred             HHHHHHHhcCC--CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEe---C-CCEEEecHHHHHH
Confidence            56778887653  689999999999995      345 9999999999999994   3 4789998875433

Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.

>PRK05785 hypothetical protein; Provisional

Probab=96.39  E-value=0.004  Score=52.04  Aligned_cols=40  Identities=20%  Similarity=0.194  Sum_probs=34.8

Q ss_pred             cceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+|+|||||+|.++..+++++ +.+++.+|. |+.++.+++
T Consensus        52 ~~~VLDlGcGtG~~~~~l~~~~-~~~v~gvD~S~~Ml~~a~~   92 (226)
T PRK05785         52 PKKVLDVAAGKGELSYHFKKVF-KYYVVALDYAENMLKMNLV   92 (226)
T ss_pred             CCeEEEEcCCCCHHHHHHHHhc-CCEEEEECCCHHHHHHHHh
Confidence            5799999999999999999988 678999998 777777654

>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis

Probab=96.36  E-value=0.0026  Score=42.63  Aligned_cols=56  Identities=16%  Similarity=0.201  Sum_probs=42.9

Q ss_pred             HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeec
Q 041256           34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSL  100 (244)
Q Consensus        34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~  100 (244)
                      .+..|+..|...   |+.|+.|||+.+|++      ... +.+.|+-|...|++.+... .+..|..
T Consensus         9 ~E~~vy~~Ll~~---~~~t~~eIa~~l~i~------~~~-v~~~L~~L~~~GlV~~~~~-~~~~Y~a   64 (68)
T PF01978_consen    9 NEAKVYLALLKN---GPATAEEIAEELGIS------RST-VYRALKSLEEKGLVEREEG-RPKVYRA   64 (68)
T ss_dssp             HHHHHHHHHHHH---CHEEHHHHHHHHTSS------HHH-HHHHHHHHHHTTSEEEEEE-CCEEEEE
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEEEcC-ceEEEEE
Confidence            345567777654   799999999999996      456 9999999999999997532 2445554

TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.

>PLN02233 ubiquinone biosynthesis methyltransferase

Probab=96.36  E-value=0.0086  Score=51.11  Aligned_cols=43  Identities=16%  Similarity=0.123  Sum_probs=36.0

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHC-CCCeEEEccc-hHHhhhCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKY-PHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~vi~~a~  233 (244)
                      .....+|+|||||+|.++..+++++ |+.+++.+|. |+.++.|+
T Consensus        71 ~~~~~~VLDlGcGtG~~~~~la~~~~~~~~V~gvD~S~~ml~~A~  115 (261)
T PLN02233         71 AKMGDRVLDLCCGSGDLAFLLSEKVGSDGKVMGLDFSSEQLAVAA  115 (261)
T ss_pred             CCCCCEEEEECCcCCHHHHHHHHHhCCCCEEEEEECCHHHHHHHH
Confidence            4456799999999999999999885 6789999998 77777764

>PRK13942 protein-L-isoaspartate O-methyltransferase; Provisional

Probab=96.35  E-value=0.01  Score=49.04  Aligned_cols=51  Identities=16%  Similarity=0.224  Sum_probs=40.5

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHC-CCCeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKY-PHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+++.++ .....+|+|||||+|.++..+++.. ++.+++.+|. |+.++.+++
T Consensus        67 ~~~~~l~-~~~g~~VLdIG~GsG~~t~~la~~~~~~~~V~~vE~~~~~~~~a~~  119 (212)
T PRK13942         67 IMCELLD-LKEGMKVLEIGTGSGYHAAVVAEIVGKSGKVVTIERIPELAEKAKK  119 (212)
T ss_pred             HHHHHcC-CCCcCEEEEECCcccHHHHHHHHhcCCCCEEEEEeCCHHHHHHHHH
Confidence            4455666 6777899999999999998888875 4568888987 788877764

>smart00138 MeTrc Methyltransferase, chemotaxis proteins

Probab=96.35  E-value=0.023  Score=48.56  Aligned_cols=52  Identities=13%  Similarity=0.215  Sum_probs=38.5

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccH----HHHHHHHHCC-----CCeEEEccc-hHHhhhCCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGI----TLNMIISKYP-----HIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~----~~~~l~~~~P-----~l~~~v~Dl-p~vi~~a~~  234 (244)
                      +.+++.-+ .....+|+|+|||+|.    +++.+++.+|     +.+.+..|+ |.+++.|++
T Consensus        89 p~l~~~~~-~~~~~ri~d~GCgtGee~YslA~~l~e~~~~~~~~~~~I~g~Dis~~~L~~Ar~  150 (264)
T smart00138       89 PLLIASRR-HGRRVRIWSAGCSTGEEPYSLAMLLAETLPKAREPDVKILATDIDLKALEKARA  150 (264)
T ss_pred             HHHHHhcC-CCCCEEEEeccccCChHHHHHHHHHHHHhhhcCCCCeEEEEEECCHHHHHHHHc
Confidence            44444333 3455799999999996    5667777765     578899998 888988875

Methylates methyl-accepting chemotaxis proteins to form gamma-glutamyl methyl ester residues.

>TIGR00438 rrmJ cell division protein FtsJ

Probab=96.34  E-value=0.01  Score=47.85  Aligned_cols=44  Identities=16%  Similarity=0.168  Sum_probs=34.7

Q ss_pred             HHhhcCCCCCcceEEEecCCccHHHHHHHHHC-CCCeEEEccchH
Q 041256          184 VLESYKGFEHVKKLVDVGGGLGITLNMIISKY-PHIKGINYDLPY  227 (244)
Q Consensus       184 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dlp~  227 (244)
                      +.+.+.......+|+|+|||+|.++..+++++ +..+.+.+|+.+
T Consensus        23 ~~~~~~~i~~g~~VLDiG~GtG~~~~~l~~~~~~~~~v~~vDis~   67 (188)
T TIGR00438        23 LNQKFKLIKPGDTVLDLGAAPGGWSQVAVEQVGGKGRVIAVDLQP   67 (188)
T ss_pred             HHHHhcccCCCCEEEEecCCCCHHHHHHHHHhCCCceEEEEeccc
Confidence            44445445667899999999999999999887 667888888844

>TIGR00755 ksgA dimethyladenosine transferase

Probab=96.33  E-value=0.0074  Score=51.21  Aligned_cols=49  Identities=14%  Similarity=0.287  Sum_probs=37.6

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~  233 (244)
                      ..+++..+ +.+..+|+|||||.|.++..++++.+.  ++.+|. +..++.++
T Consensus        19 ~~i~~~~~-~~~~~~VLEiG~G~G~lt~~L~~~~~~--v~~iE~d~~~~~~l~   68 (253)
T TIGR00755        19 QKIVEAAN-VLEGDVVLEIGPGLGALTEPLLKRAKK--VTAIEIDPRLAEILR   68 (253)
T ss_pred             HHHHHhcC-CCCcCEEEEeCCCCCHHHHHHHHhCCc--EEEEECCHHHHHHHH
Confidence            45566666 667789999999999999999999976  666665 55555554

Alternate name: S-adenosylmethionine--6-N',N'-adenosyl (rRNA) dimethyltransferase

>PF13659 Methyltransf_26: Methyltransferase domain; PDB: 3GJY_A 3LPM_B 2NP6_D 1AQI_B 2ADM_B 2IH2_A 2JG3_A 2IBS_D 2NP7_A 2IBT_A

Probab=96.32  E-value=0.0047  Score=45.45  Aligned_cols=39  Identities=21%  Similarity=0.292  Sum_probs=34.9

Q ss_pred             ceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          195 KKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       195 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+|+|+|||.|.++..++++. ..+++.+|+ |..++.++.
T Consensus         2 ~~vlD~~~G~G~~~~~~~~~~-~~~~~gvdi~~~~~~~a~~   41 (117)
T PF13659_consen    2 DRVLDPGCGSGTFLLAALRRG-AARVTGVDIDPEAVELARR   41 (117)
T ss_dssp             EEEEEETSTTCHHHHHHHHHC-TCEEEEEESSHHHHHHHHH
T ss_pred             CEEEEcCcchHHHHHHHHHHC-CCeEEEEEECHHHHHHHHH
Confidence            589999999999999999999 888999998 888887764

...

>PF01209 Ubie_methyltran: ubiE/COQ5 methyltransferase family; InterPro: IPR004033 A number of methyltransferases have been shown to share regions of similarities []

Probab=96.32  E-value=0.0036  Score=52.61  Aligned_cols=44  Identities=20%  Similarity=0.319  Sum_probs=31.9

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHC-CCCeEEEccc-hHHhhhCCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKY-PHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .....+|+|||||+|.++..++++. |+.+++..|. |..++.|++
T Consensus        45 ~~~g~~vLDv~~GtG~~~~~l~~~~~~~~~v~~vD~s~~ML~~a~~   90 (233)
T PF01209_consen   45 LRPGDRVLDVACGTGDVTRELARRVGPNGKVVGVDISPGMLEVARK   90 (233)
T ss_dssp             --S--EEEEET-TTSHHHHHHGGGSS---EEEEEES-HHHHHHHHH
T ss_pred             CCCCCEEEEeCCChHHHHHHHHHHCCCccEEEEecCCHHHHHHHHH
Confidence            3456799999999999999999885 6789999998 888888764

Apart from the ubiquinone/menaquinone biosynthesis methyltransferases (for example, the C-methyltransferase from the ubiE gene of Escherichia coli), the ubiquinone biosynthesis methyltransferases (for example, the C-methyltransferase from the COQ5 gene of Saccharomyces cerevisiae) and the menaquinone biosynthesis methyltransferases (for example, the C-methyltransferase from the MENH gene of Bacillus subtilis), this family also includes methyltransferases involved in biotin and sterol biosynthesis and in phosphatidylethanolamine methylation.; GO: 0008168 methyltransferase activity; PDB: 1VL5_C.

>PF06325 PrmA: Ribosomal protein L11 methyltransferase (PrmA); InterPro: IPR010456 This family consists of several Ribosomal protein L11 methyltransferase sequences

Probab=96.31  E-value=0.0022  Score=55.67  Aligned_cols=63  Identities=27%  Similarity=0.427  Sum_probs=43.6

Q ss_pred             HHHHHHHhcchhhHHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          168 VFNNGMLSHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       168 ~f~~aM~~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .|..+-..++++.. .+++.+.  .+..+|+|||||+|.++++.++.... +++.+|. |..++.+++
T Consensus       139 AFGTG~H~TT~lcl-~~l~~~~--~~g~~vLDvG~GSGILaiaA~klGA~-~v~a~DiDp~Av~~a~~  202 (295)
T PF06325_consen  139 AFGTGHHPTTRLCL-ELLEKYV--KPGKRVLDVGCGSGILAIAAAKLGAK-KVVAIDIDPLAVEAARE  202 (295)
T ss_dssp             SS-SSHCHHHHHHH-HHHHHHS--STTSEEEEES-TTSHHHHHHHHTTBS-EEEEEESSCHHHHHHHH
T ss_pred             cccCCCCHHHHHHH-HHHHHhc--cCCCEEEEeCCcHHHHHHHHHHcCCC-eEEEecCCHHHHHHHHH
Confidence            45555555555544 3444454  34479999999999999999987553 6888888 888888765

Its genetic determinant is prmA, which forms a bifunctional operon with the downstream panF gene []. The role of L11 methylation in ribosome function is, as yet, unknown. Deletion of the prmA gene in Escherichia coli showed no obvious effect [] except for the production of undermethylated forms of L11 []. Methylation is the most common post-transcriptional modification to ribosomal proteins in all organisms. PrmA is the only bacterial enzyme that catalyses the methylation of a ribosomal protein [].; GO: 0008276 protein methyltransferase activity, 0006479 protein methylation, 0005737 cytoplasm; PDB: 3GRZ_B 1F3L_A 2NXJ_B 3CJT_I 3CJQ_G 2NXE_A 2NXC_A 2ZBP_A 3EGV_A 3CJS_A ....

>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional

Probab=96.30  E-value=0.005  Score=52.38  Aligned_cols=58  Identities=10%  Similarity=0.243  Sum_probs=46.3

Q ss_pred             cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcccc
Q 041256           36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSA  105 (244)
Q Consensus        36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~  105 (244)
                      +.|.+.|.+.   ++.|+.|||+.+|++      ..- +.|+|+-|+..||+.++  ...++|++++...
T Consensus        17 l~IL~~l~~~---~~l~l~eia~~lgl~------kst-v~Rll~tL~~~G~l~~~--~~~~~Y~lG~~~~   74 (257)
T PRK15090         17 FGILQALGEE---REIGITELSQRVMMS------KST-VYRFLQTMKTLGYVAQE--GESEKYSLTLKLF   74 (257)
T ss_pred             HHHHHHhhcC---CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEEc--CCCCcEEecHHHH
Confidence            4567777664   589999999999996      345 99999999999999863  2358899998754

>PF13679 Methyltransf_32: Methyltransferase domain

Probab=96.30  E-value=0.0053  Score=47.33  Aligned_cols=43  Identities=19%  Similarity=0.336  Sum_probs=34.6

Q ss_pred             CCCcceEEEecCCccHHHHHHHHH----CCCCeEEEccc-hHHhhhCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISK----YPHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~----~P~l~~~v~Dl-p~vi~~a~  233 (244)
                      -.+..+|||+|+|.|+++..+...    .|+++++.+|. |+.++.+.
T Consensus        23 ~~~~~~vvD~GsG~GyLs~~La~~l~~~~~~~~v~~iD~~~~~~~~a~   70 (141)
T PF13679_consen   23 SKRCITVVDLGSGKGYLSRALAHLLCNSSPNLRVLGIDCNESLVESAQ   70 (141)
T ss_pred             cCCCCEEEEeCCChhHHHHHHHHHHHhcCCCCeEEEEECCcHHHHHHH
Confidence            356799999999999999999982    38899999997 55555553

>COG4123 Predicted O-methyltransferase [General function prediction only]

Probab=96.30  E-value=0.0042  Score=52.44  Aligned_cols=44  Identities=14%  Similarity=0.206  Sum_probs=38.1

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ....++|+|+|+|.|..+..+++++++.+.+.+|+ +...+.|++
T Consensus        42 ~~~~~~IlDlGaG~G~l~L~la~r~~~a~I~~VEiq~~~a~~A~~   86 (248)
T COG4123          42 VPKKGRILDLGAGNGALGLLLAQRTEKAKIVGVEIQEEAAEMAQR   86 (248)
T ss_pred             cccCCeEEEecCCcCHHHHHHhccCCCCcEEEEEeCHHHHHHHHH
Confidence            44579999999999999999999999999999999 666666654

>PLN02336 phosphoethanolamine N-methyltransferase

Probab=96.29  E-value=0.0059  Score=56.54  Aligned_cols=51  Identities=20%  Similarity=0.321  Sum_probs=40.2

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+++.++ ++...+|+|||||.|..+..+++++ +.+++.+|+ |..++.|++
T Consensus       256 e~l~~~~~-~~~~~~vLDiGcG~G~~~~~la~~~-~~~v~gvDiS~~~l~~A~~  307 (475)
T PLN02336        256 KEFVDKLD-LKPGQKVLDVGCGIGGGDFYMAENF-DVHVVGIDLSVNMISFALE  307 (475)
T ss_pred             HHHHHhcC-CCCCCEEEEEeccCCHHHHHHHHhc-CCEEEEEECCHHHHHHHHH
Confidence            34555555 5667899999999999999888876 779999999 677776643

>PRK11705 cyclopropane fatty acyl phospholipid synthase; Provisional

Probab=96.27  E-value=0.0065  Score=54.80  Aligned_cols=50  Identities=14%  Similarity=0.200  Sum_probs=40.0

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+++.++ .....+|||||||.|.++..+++++ +.+++.+|+ |+.++.+++
T Consensus       158 ~l~~~l~-l~~g~rVLDIGcG~G~~a~~la~~~-g~~V~giDlS~~~l~~A~~  208 (383)
T PRK11705        158 LICRKLQ-LKPGMRVLDIGCGWGGLARYAAEHY-GVSVVGVTISAEQQKLAQE  208 (383)
T ss_pred             HHHHHhC-CCCCCEEEEeCCCccHHHHHHHHHC-CCEEEEEeCCHHHHHHHHH
Confidence            4555555 6667899999999999999998876 678999998 777777654

>PRK14896 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Provisional

Probab=96.25  E-value=0.0086  Score=51.00  Aligned_cols=50  Identities=14%  Similarity=0.222  Sum_probs=37.8

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+++..+ .....+|+|||||.|.++..++++.  .+.+.+|+ +..++.+++
T Consensus        19 ~~iv~~~~-~~~~~~VLEIG~G~G~lt~~L~~~~--~~v~~vEid~~~~~~l~~   69 (258)
T PRK14896         19 DRIVEYAE-DTDGDPVLEIGPGKGALTDELAKRA--KKVYAIELDPRLAEFLRD   69 (258)
T ss_pred             HHHHHhcC-CCCcCeEEEEeCccCHHHHHHHHhC--CEEEEEECCHHHHHHHHH
Confidence            45555555 5566899999999999999999984  46788887 566666543

>COG0220 Predicted S-adenosylmethionine-dependent methyltransferase [General function prediction only]

Probab=96.24  E-value=0.0084  Score=50.11  Aligned_cols=38  Identities=16%  Similarity=0.240  Sum_probs=32.8

Q ss_pred             cceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhh
Q 041256          194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKD  231 (244)
Q Consensus       194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~  231 (244)
                      ...+|+||+|.|.++..+++++|+...+.++. ..++..
T Consensus        49 ~pi~lEIGfG~G~~l~~~A~~nP~~nfiGiEi~~~~v~~   87 (227)
T COG0220          49 APIVLEIGFGMGEFLVEMAKKNPEKNFLGIEIRVPGVAK   87 (227)
T ss_pred             CcEEEEECCCCCHHHHHHHHHCCCCCEEEEEEehHHHHH
Confidence            47999999999999999999999999999997 444433

>PRK09834 DNA-binding transcriptional activator MhpR; Provisional

Probab=96.22  E-value=0.0066  Score=51.84  Aligned_cols=61  Identities=15%  Similarity=0.153  Sum_probs=48.3

Q ss_pred             cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcccccc
Q 041256           36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYF  107 (244)
Q Consensus        36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l  107 (244)
                      +.|++.|.+.+  +++|+.|||+.+|++      ..- +.|+|+.|+..|++.+++  .++.|++++....+
T Consensus        14 l~iL~~l~~~~--~~ls~~eia~~lgl~------kst-v~RlL~tL~~~g~v~~~~--~~~~Y~Lg~~~~~l   74 (263)
T PRK09834         14 LMVLRALNRLD--GGATVGLLAELTGLH------RTT-VRRLLETLQEEGYVRRSA--SDDSFRLTLKVRQL   74 (263)
T ss_pred             HHHHHHHHhcC--CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEEec--CCCcEEEcHHHHHH
Confidence            55777787653  569999999999996      345 999999999999999642  35789998876433

>PRK13944 protein-L-isoaspartate O-methyltransferase; Provisional

Probab=96.19  E-value=0.0096  Score=48.88  Aligned_cols=50  Identities=16%  Similarity=0.105  Sum_probs=38.3

Q ss_pred             HHhhcCCCCCcceEEEecCCccHHHHHHHHHCC-CCeEEEccc-hHHhhhCCC
Q 041256          184 VLESYKGFEHVKKLVDVGGGLGITLNMIISKYP-HIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       184 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~vi~~a~~  234 (244)
                      +++.++ .....+|+|||||+|.++..+++..+ .-+++.+|. |+.++.+++
T Consensus        64 ~~~~l~-~~~~~~VLDiG~GsG~~~~~la~~~~~~g~V~~iD~~~~~~~~a~~  115 (205)
T PRK13944         64 MCELIE-PRPGMKILEVGTGSGYQAAVCAEAIERRGKVYTVEIVKELAIYAAQ  115 (205)
T ss_pred             HHHhcC-CCCCCEEEEECcCccHHHHHHHHhcCCCCEEEEEeCCHHHHHHHHH
Confidence            444444 45557999999999999999998875 557888998 777776654

>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp

Probab=96.19  E-value=0.0098  Score=41.52  Aligned_cols=52  Identities=23%  Similarity=0.337  Sum_probs=38.8

Q ss_pred             hhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecC-CceeecCcc
Q 041256           43 SKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDG-QRLYSLAPV  103 (244)
Q Consensus        43 ~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~-~~~y~~t~~  103 (244)
                      +..+.+++.|.+|||+.++++      +.. ++++|..|...|+++..  .| .|.|.++.-
T Consensus        18 a~~~~~~~~s~~eiA~~~~i~------~~~-l~kil~~L~~~Gli~s~--~G~~GGy~L~~~   70 (83)
T PF02082_consen   18 ARHPDGKPVSSKEIAERLGIS------PSY-LRKILQKLKKAGLIESS--RGRGGGYRLARP   70 (83)
T ss_dssp             HCTTTSC-BEHHHHHHHHTS-------HHH-HHHHHHHHHHTTSEEEE--TSTTSEEEESS-
T ss_pred             HhCCCCCCCCHHHHHHHHCcC------HHH-HHHHHHHHhhCCeeEec--CCCCCceeecCC
Confidence            433333569999999999997      678 99999999999999853  23 477888764

(strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.

>PF13489 Methyltransf_23: Methyltransferase domain; PDB: 3JWJ_A 3JWH_B 2AOV_B 2AOT_A 1JQD_B 2AOX_A 1JQE_A 2AOU_B 2AOW_A 3DLI_C

Probab=96.13  E-value=0.018  Score=44.46  Aligned_cols=39  Identities=23%  Similarity=0.399  Sum_probs=30.7

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhh
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKD  231 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~  231 (244)
                      .....+|||||||.|.++..+.+..+  +.+.+|. |..++.
T Consensus        20 ~~~~~~vLDiGcG~G~~~~~l~~~~~--~~~g~D~~~~~~~~   59 (161)
T PF13489_consen   20 LKPGKRVLDIGCGTGSFLRALAKRGF--EVTGVDISPQMIEK   59 (161)
T ss_dssp             TTTTSEEEEESSTTSHHHHHHHHTTS--EEEEEESSHHHHHH
T ss_pred             cCCCCEEEEEcCCCCHHHHHHHHhCC--EEEEEECCHHHHhh
Confidence            35668999999999999999966644  8889998 555533

...

>PF02353 CMAS: Mycolic acid cyclopropane synthetase; InterPro: IPR003333 This entry represents mycolic acid cyclopropane synthases and related enzymes, including CmaA1, CmaA2 (cyclopropane mycolic acid synthase A1 and A2) and MmaA1-4 (methoxymycolic acid synthase A1-4)

Probab=96.09  E-value=0.0081  Score=51.67  Aligned_cols=49  Identities=16%  Similarity=0.181  Sum_probs=34.4

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDA  232 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a  232 (244)
                      ..+++..+ .++..+|||||||-|.++..++++| +++++.+.+ ++-.+.+
T Consensus        52 ~~~~~~~~-l~~G~~vLDiGcGwG~~~~~~a~~~-g~~v~gitlS~~Q~~~a  101 (273)
T PF02353_consen   52 DLLCEKLG-LKPGDRVLDIGCGWGGLAIYAAERY-GCHVTGITLSEEQAEYA  101 (273)
T ss_dssp             HHHHTTTT---TT-EEEEES-TTSHHHHHHHHHH---EEEEEES-HHHHHHH
T ss_pred             HHHHHHhC-CCCCCEEEEeCCCccHHHHHHHHHc-CcEEEEEECCHHHHHHH
Confidence            45677776 7888999999999999999999999 889888887 4434433

All are thought to be S-adenosyl-L-methionine (SAM) utilising methyltransferases []. Mycolic acid cyclopropane synthase or cyclopropane-fatty-acyl-phospholipid synthase (CFA synthase) 2.1.1.79 from EC catalyses the reaction: S-adenosyl-L-methionine + phospholipid olefinic fatty acid -> S-adenosyl-L-homocysteine + phospholipid cyclopropane fatty acid. The major mycolic acid produced by Mycobacterium tuberculosis contains two cis-cyclopropanes in the meromycolate chain. Cyclopropanation may contribute to the structural integrity of the cell wall complex [].; GO: 0008610 lipid biosynthetic process; PDB: 3HA5_A 2FK8_A 3HA7_A 3HA3_A 2FK7_A 1KPG_D 1KP9_B 1KPH_D 3VC2_E 3VC1_D ....

>PRK00050 16S rRNA m(4)C1402 methyltranserfase; Provisional

Probab=96.08  E-value=0.011  Score=51.29  Aligned_cols=53  Identities=21%  Similarity=0.183  Sum_probs=44.6

Q ss_pred             HHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCC-CCeEEEccc-hHHhhhCCC
Q 041256          181 MEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYP-HIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       181 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...+++.+. .....++||+++|.|.++..+++++| +.+++.+|. |++++.+++
T Consensus         8 l~Evl~~L~-~~pg~~vlD~TlG~GGhS~~il~~~~~~g~VigiD~D~~al~~ak~   62 (296)
T PRK00050          8 LDEVVDALA-IKPDGIYVDGTFGGGGHSRAILERLGPKGRLIAIDRDPDAIAAAKD   62 (296)
T ss_pred             HHHHHHhhC-CCCCCEEEEeCcCChHHHHHHHHhCCCCCEEEEEcCCHHHHHHHHH
Confidence            356677665 45557999999999999999999996 789999998 899988875

>PRK12335 tellurite resistance protein TehB; Provisional

Probab=96.07  E-value=0.0069  Score=52.40  Aligned_cols=49  Identities=18%  Similarity=0.198  Sum_probs=36.7

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .++..++ .....+|+|||||.|..+..++++  +.+++.+|. |..++.+++
T Consensus       111 ~~~~~~~-~~~~~~vLDlGcG~G~~~~~la~~--g~~V~avD~s~~ai~~~~~  160 (287)
T PRK12335        111 EVLEAVQ-TVKPGKALDLGCGQGRNSLYLALL--GFDVTAVDINQQSLENLQE  160 (287)
T ss_pred             HHHHHhh-ccCCCCEEEeCCCCCHHHHHHHHC--CCEEEEEECCHHHHHHHHH
Confidence            3444444 334469999999999999999885  578999998 677776643

>PRK15068 tRNA mo(5)U34 methyltransferase; Provisional

Probab=96.07  E-value=0.012  Score=51.89  Aligned_cols=40  Identities=18%  Similarity=0.246  Sum_probs=31.5

Q ss_pred             HhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccch
Q 041256          185 LESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLP  226 (244)
Q Consensus       185 ~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  226 (244)
                      ...++.+ ..++|+|||||.|.++..+++..|. +++.+|..
T Consensus       115 ~~~l~~l-~g~~VLDIGCG~G~~~~~la~~g~~-~V~GiD~S  154 (322)
T PRK15068        115 LPHLSPL-KGRTVLDVGCGNGYHMWRMLGAGAK-LVVGIDPS  154 (322)
T ss_pred             HHhhCCC-CCCEEEEeccCCcHHHHHHHHcCCC-EEEEEcCC
Confidence            4444323 3489999999999999999999877 48999963

>TIGR00537 hemK_rel_arch HemK-related putative methylase

Probab=96.06  E-value=0.0058  Score=48.90  Aligned_cols=39  Identities=18%  Similarity=0.394  Sum_probs=33.7

Q ss_pred             cceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+|+|+|||+|.++..+.+..+  +++.+|+ |..++.+++
T Consensus        20 ~~~vLdlG~G~G~~~~~l~~~~~--~v~~vD~s~~~~~~a~~   59 (179)
T TIGR00537        20 PDDVLEIGAGTGLVAIRLKGKGK--CILTTDINPFAVKELRE   59 (179)
T ss_pred             CCeEEEeCCChhHHHHHHHhcCC--EEEEEECCHHHHHHHHH
Confidence            36899999999999999999987  7888898 887777664

The gene hemK from E. coli was found to contribute to heme biosynthesis and originally suggested to be protoporphyrinogen oxidase (Medline 95189105). Functional analysis of the nearest homolog in Saccharomyces cerevisiae, YNL063w, finds it is not protoporphyrinogen oxidase and sequence analysis suggests that HemK homologs have S-adenosyl-methionine-dependent methyltransferase activity (Medline 99237242). Homologs are found, usually in a single copy, in nearly all completed genomes, but varying somewhat in apparent domain architecture. This model represents an archaeal and eukaryotic protein family that lacks an N-terminal domain found in HemK and its eubacterial homologs. It is found in a single copy in the first six completed archaeal and eukaryotic genomes.

>PRK03612 spermidine synthase; Provisional

Probab=96.03  E-value=0.0091  Score=56.04  Aligned_cols=42  Identities=26%  Similarity=0.498  Sum_probs=37.0

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCC-CeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPH-IKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dl-p~vi~~a~~  234 (244)
                      ++.++|+|||||.|..+.++++ +|. -+++++|+ |++++.+++
T Consensus       296 ~~~~rVL~IG~G~G~~~~~ll~-~~~v~~v~~VEid~~vi~~ar~  339 (521)
T PRK03612        296 ARPRRVLVLGGGDGLALREVLK-YPDVEQVTLVDLDPAMTELART  339 (521)
T ss_pred             CCCCeEEEEcCCccHHHHHHHh-CCCcCeEEEEECCHHHHHHHHh
Confidence            4568999999999999999996 566 68999999 999999876

>TIGR01444 fkbM_fam methyltransferase, FkbM family

Probab=96.01  E-value=0.0061  Score=46.60  Aligned_cols=39  Identities=21%  Similarity=0.221  Sum_probs=34.2

Q ss_pred             eEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          196 KLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       196 ~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      +++|||+|.|.++..+++.+|..+++.+|. |...+.+++
T Consensus         1 ~vlDiGa~~G~~~~~~~~~~~~~~v~~~E~~~~~~~~l~~   40 (143)
T TIGR01444         1 VVIDVGANIGDTSLYFARKGAEGRVIAFEPLPDAYEILEE   40 (143)
T ss_pred             CEEEccCCccHHHHHHHHhCCCCEEEEEecCHHHHHHHHH
Confidence            589999999999999999999999999997 777766553

Members of this family are characterized by two well-conserved short regions separated by a variable in both sequence and length. The first of the two regions is found in a large number of proteins outside this subfamily, a number of which have been characterized as methyltransferases. One member of the present family, FkbM, was shown to be required for a specific methylation in the biosynthesis of the immunosuppressant FK506 in Streptomyces strain MA6548.

>PRK00377 cbiT cobalt-precorrin-6Y C(15)-methyltransferase; Provisional

Probab=95.99  E-value=0.011  Score=48.16  Aligned_cols=47  Identities=15%  Similarity=0.040  Sum_probs=38.4

Q ss_pred             hcCCCCCcceEEEecCCccHHHHHHHHH-CCCCeEEEccc-hHHhhhCCC
Q 041256          187 SYKGFEHVKKLVDVGGGLGITLNMIISK-YPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       187 ~~~~~~~~~~vvDVGGG~G~~~~~l~~~-~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .++ .....+|+|+|||+|.++..+++. .|..+++.+|. |..++.+++
T Consensus        35 ~l~-~~~~~~vlDlG~GtG~~s~~~a~~~~~~~~v~avD~~~~~~~~a~~   83 (198)
T PRK00377         35 KLR-LRKGDMILDIGCGTGSVTVEASLLVGETGKVYAVDKDEKAINLTRR   83 (198)
T ss_pred             HcC-CCCcCEEEEeCCcCCHHHHHHHHHhCCCCEEEEEECCHHHHHHHHH
Confidence            344 566689999999999999999886 46789999999 888876653

>TIGR00406 prmA ribosomal protein L11 methyltransferase

Probab=95.98  E-value=0.0059  Score=52.90  Aligned_cols=41  Identities=27%  Similarity=0.396  Sum_probs=32.8

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...+|+|||||+|.++..+++. +.-+++.+|+ |..++.+++
T Consensus       159 ~g~~VLDvGcGsG~lai~aa~~-g~~~V~avDid~~al~~a~~  200 (288)
T TIGR00406       159 KDKNVIDVGCGSGILSIAALKL-GAAKVVGIDIDPLAVESARK  200 (288)
T ss_pred             CCCEEEEeCCChhHHHHHHHHc-CCCeEEEEECCHHHHHHHHH
Confidence            4489999999999999888764 4458899998 677777654

Ribosomal protein L11 methyltransferase is an S-adenosyl-L-methionine-dependent methyltransferase required for the modification of ribosomal protein L11. This protein is found in bacteria and (with a probable transit peptide) in Arabidopsis.

>PHA03412 putative methyltransferase; Provisional

Probab=95.90  E-value=0.0098  Score=49.90  Aligned_cols=47  Identities=15%  Similarity=0.133  Sum_probs=37.6

Q ss_pred             cceEEEecCCccHHHHHHHHHC---CCCeEEEccc-hHHhhhCCC-CCCcee
Q 041256          194 VKKLVDVGGGLGITLNMIISKY---PHIKGINYDL-PYVIKDAPS-YPGTLF  240 (244)
Q Consensus       194 ~~~vvDVGGG~G~~~~~l~~~~---P~l~~~v~Dl-p~vi~~a~~-~~~i~~  240 (244)
                      ..+|||+|||+|.++..++++.   +..+.+.+|+ |..++.|++ .+++++
T Consensus        50 ~grVLDlG~GSG~Lalala~~~~~~~~~~V~aVEID~~Al~~Ar~n~~~~~~  101 (241)
T PHA03412         50 SGSVVDLCAGIGGLSFAMVHMMMYAKPREIVCVELNHTYYKLGKRIVPEATW  101 (241)
T ss_pred             CCEEEEccChHHHHHHHHHHhcccCCCcEEEEEECCHHHHHHHHhhccCCEE
Confidence            4799999999999999999885   4678899999 788888875 244443

>KOG1540 consensus Ubiquinone biosynthesis methyltransferase COQ5 [Coenzyme transport and metabolism]

Probab=95.90  E-value=0.021  Score=48.26  Aligned_cols=42  Identities=24%  Similarity=0.272  Sum_probs=37.1

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCC------CeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPH------IKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~------l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..-++|||+||+|-++..|+++-++      -+++|.|. |+.++.+++
T Consensus       100 ~~m~~lDvaGGTGDiaFril~~v~s~~~~~~~~V~v~Dinp~mL~vgkq  148 (296)
T KOG1540|consen  100 KGMKVLDVAGGTGDIAFRILRHVKSQFGDRESKVTVLDINPHMLAVGKQ  148 (296)
T ss_pred             CCCeEEEecCCcchhHHHHHHhhccccCCCCceEEEEeCCHHHHHHHHH
Confidence            4489999999999999999999988      78999998 888887764

>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A

Probab=95.89  E-value=0.011  Score=36.57  Aligned_cols=45  Identities=9%  Similarity=0.305  Sum_probs=36.5

Q ss_pred             HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCccc
Q 041256           34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALH   88 (244)
Q Consensus        34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~   88 (244)
                      .+..|+..|.+.   +++|..|||+.+|++      ... +.+.|+-|...|+++
T Consensus         4 ~~~~Il~~l~~~---~~~t~~ela~~~~is------~~t-v~~~l~~L~~~g~I~   48 (48)
T PF13412_consen    4 TQRKILNYLREN---PRITQKELAEKLGIS------RST-VNRYLKKLEEKGLIE   48 (48)
T ss_dssp             HHHHHHHHHHHC---TTS-HHHHHHHHTS-------HHH-HHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHhCCC------HHH-HHHHHHHHHHCcCcC
Confidence            355688889886   579999999999997      456 999999999999874

...

>PRK00517 prmA ribosomal protein L11 methyltransferase; Reviewed

Probab=95.87  E-value=0.0069  Score=51.30  Aligned_cols=42  Identities=26%  Similarity=0.282  Sum_probs=33.6

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ....+|+|||||+|.+++.+++..+. +++.+|. |..++.+++
T Consensus       118 ~~~~~VLDiGcGsG~l~i~~~~~g~~-~v~giDis~~~l~~A~~  160 (250)
T PRK00517        118 LPGKTVLDVGCGSGILAIAAAKLGAK-KVLAVDIDPQAVEAARE  160 (250)
T ss_pred             CCCCEEEEeCCcHHHHHHHHHHcCCC-eEEEEECCHHHHHHHHH
Confidence            35589999999999999887776554 6888998 778877764

>PF08241 Methyltransf_11: Methyltransferase domain; InterPro: IPR013216 Methyl transfer from the ubiquitous S-adenosyl-L-methionine (SAM) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals

Probab=95.85  E-value=0.0063  Score=42.49  Aligned_cols=36  Identities=17%  Similarity=0.267  Sum_probs=30.4

Q ss_pred             EEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          198 VDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       198 vDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ||||||.|..+..+.++ |..+.+..|. +..++.+++
T Consensus         1 LdiG~G~G~~~~~l~~~-~~~~v~~~D~~~~~~~~~~~   37 (95)
T PF08241_consen    1 LDIGCGTGRFAAALAKR-GGASVTGIDISEEMLEQARK   37 (95)
T ss_dssp             EEET-TTSHHHHHHHHT-TTCEEEEEES-HHHHHHHHH
T ss_pred             CEecCcCCHHHHHHHhc-cCCEEEEEeCCHHHHHHHHh
Confidence            79999999999999999 9999999998 565766654

The reaction is catalyzed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented. This entry represents a methyltransferase domain found in a large variety of SAM-dependent methyltransferases including, but not limited to: Arsenite methyltransferase (2.1.1.137 from EC) which converts arsenical compounds to their methylated forms [] Biotin synthesis protein bioC, which is involved in the early stages of biotin biosyntheis [] Arginine N-methyltransferase 1, an arginine-methylating enzyme which acts on residues present in a glycine and argine-rich domain and can methylate histones [] Hexaprenyldihydroxybenzoate methyltransferase (2.1.1.114 from EC), a mitochodrial enzyme involved in ubiquinone biosynthesis [] A probable cobalt-precorrin-6Y C(15)-methyltransferase thought to be involved in adenosylcobalamin biosynthesis [] Sterol 24-C-methyltransferase (2.1.1.41 from EC), shown to participate in ergosterol biosynthesis [] 3-demethylubiquinone-9 3-methyltransferase (2.1.1.64 from EC) involved in ubiquinone biosynthesis [] Structural studies show that this domain forms the Rossman-like alpha-beta fold typical of SAM-dependent methyltransferases [, , ]. ; GO: 0008168 methyltransferase activity, 0008152 metabolic process; PDB: 3CGG_B 3CCF_B 3BKW_B 2PXX_A 3I9F_A 2YQZ_B 2YR0_A 3BUS_A 3EGE_A 3G5L_B ....

>TIGR02081 metW methionine biosynthesis protein MetW

Probab=95.79  E-value=0.013  Score=47.49  Aligned_cols=40  Identities=15%  Similarity=0.314  Sum_probs=30.3

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~  233 (244)
                      ...+|+|||||.|.++..+++. ...+++.+|. |+.++.++
T Consensus        13 ~~~~iLDiGcG~G~~~~~l~~~-~~~~~~giD~s~~~i~~a~   53 (194)
T TIGR02081        13 PGSRVLDLGCGDGELLALLRDE-KQVRGYGIEIDQDGVLACV   53 (194)
T ss_pred             CCCEEEEeCCCCCHHHHHHHhc-cCCcEEEEeCCHHHHHHHH
Confidence            4468999999999999888765 4566788887 55555543

This protein is found alongside MetX, of the enzyme that acylates homoserine as a first step toward methionine biosynthesis, in many species. It appears to act in methionine biosynthesis but is not fully characterized.

>PRK00536 speE spermidine synthase; Provisional

Probab=95.72  E-value=0.012  Score=50.31  Aligned_cols=41  Identities=10%  Similarity=-0.074  Sum_probs=36.4

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+++|+=||||.|..++++++. |. +++..|+ ++|++.+++
T Consensus        71 ~~pk~VLIiGGGDGg~~REvLkh-~~-~v~mVeID~~Vv~~~k~  112 (262)
T PRK00536         71 KELKEVLIVDGFDLELAHQLFKY-DT-HVDFVQADEKILDSFIS  112 (262)
T ss_pred             CCCCeEEEEcCCchHHHHHHHCc-CC-eeEEEECCHHHHHHHHH
Confidence            56799999999999999999987 55 8999998 889988876

>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A

Probab=95.67  E-value=0.02  Score=37.98  Aligned_cols=48  Identities=10%  Similarity=0.284  Sum_probs=34.1

Q ss_pred             CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCC---ceeecCcc
Q 041256           49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQ---RLYSLAPV  103 (244)
Q Consensus        49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~---~~y~~t~~  103 (244)
                      ++.|..+|++.++++      ... +.+.++.|...|++++.....+   ..|++|+.
T Consensus        17 ~~~t~~~l~~~~~~~------~~~-vs~~i~~L~~~glv~~~~~~~d~R~~~~~LT~~   67 (68)
T PF13463_consen   17 GPMTQSDLAERLGIS------KST-VSRIIKKLEEKGLVEKERDPHDKRSKRYRLTPA   67 (68)
T ss_dssp             S-BEHHHHHHHTT--------HHH-HHHHHHHHHHTTSEEEEEESSCTTSEEEEE-HH
T ss_pred             CCcCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEecCCCCcCCeeEEEeCCC
Confidence            799999999999997      456 9999999999999975422212   34777764

>TIGR03438 probable methyltransferase

Probab=95.66  E-value=0.011  Score=51.49  Aligned_cols=41  Identities=15%  Similarity=0.293  Sum_probs=34.3

Q ss_pred             CcceEEEecCCccHHHHHHHHHCC-CCeEEEccc-hHHhhhCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYP-HIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~vi~~a~  233 (244)
                      ...+|||+|||+|.....|+++.+ ..+.+.+|+ ++.++.+.
T Consensus        63 ~~~~iLELGcGtG~~t~~Ll~~l~~~~~~~~iDiS~~mL~~a~  105 (301)
T TIGR03438        63 AGCELVELGSGSSRKTRLLLDALRQPARYVPIDISADALKESA  105 (301)
T ss_pred             CCCeEEecCCCcchhHHHHHHhhccCCeEEEEECCHHHHHHHH
Confidence            346899999999999999999998 688999999 55555554

This model represents a distinct set of uncharacterized proteins found in the bacteria. Analysis by PSI-BLAST shows remote sequence homology to methyltransferases

>PRK14968 putative methyltransferase; Provisional

Probab=95.65  E-value=0.012  Score=46.92  Aligned_cols=40  Identities=25%  Similarity=0.448  Sum_probs=33.8

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~  233 (244)
                      .+.++++|+|||.|.++..++++  ..+++.+|+ |++++.++
T Consensus        22 ~~~~~vLd~G~G~G~~~~~l~~~--~~~v~~~D~s~~~~~~a~   62 (188)
T PRK14968         22 KKGDRVLEVGTGSGIVAIVAAKN--GKKVVGVDINPYAVECAK   62 (188)
T ss_pred             cCCCEEEEEccccCHHHHHHHhh--cceEEEEECCHHHHHHHH
Confidence            44578999999999999999998  578899998 77777764

>PLN03075 nicotianamine synthase; Provisional

Probab=95.61  E-value=0.017  Score=50.18  Aligned_cols=43  Identities=21%  Similarity=0.165  Sum_probs=34.1

Q ss_pred             CCcceEEEecCCccHH--HHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGIT--LNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~--~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+++|+|||||.|-+  .....+.+|+.+++.+|. |+.++.|++
T Consensus       122 ~~p~~VldIGcGpgpltaiilaa~~~p~~~~~giD~d~~ai~~Ar~  167 (296)
T PLN03075        122 GVPTKVAFVGSGPLPLTSIVLAKHHLPTTSFHNFDIDPSANDVARR  167 (296)
T ss_pred             CCCCEEEEECCCCcHHHHHHHHHhcCCCCEEEEEeCCHHHHHHHHH
Confidence            4779999999998844  333445789999999999 888887764

>TIGR00452 methyltransferase, putative

Probab=95.60  E-value=0.025  Score=49.69  Aligned_cols=40  Identities=20%  Similarity=0.246  Sum_probs=31.2

Q ss_pred             HHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc
Q 041256          184 VLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL  225 (244)
Q Consensus       184 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  225 (244)
                      ++..+. ..+.++|+|||||+|.++..++...+. +++.+|.
T Consensus       113 ~l~~l~-~~~g~~VLDvGCG~G~~~~~~~~~g~~-~v~GiDp  152 (314)
T TIGR00452       113 VLPHLS-PLKGRTILDVGCGSGYHMWRMLGHGAK-SLVGIDP  152 (314)
T ss_pred             HHHhcC-CCCCCEEEEeccCCcHHHHHHHHcCCC-EEEEEcC
Confidence            344443 234489999999999999999998775 6888996

Known examples to date are restricted to the proteobacteria.

>KOG2899 consensus Predicted methyltransferase [General function prediction only]

Probab=95.58  E-value=0.012  Score=49.24  Aligned_cols=52  Identities=19%  Similarity=0.287  Sum_probs=43.4

Q ss_pred             HHHhhcC-CCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYK-GFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~-~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+..++ +|-..+.++||||+.|.+...+++.|-....+.+|+ |.-|..|++
T Consensus        47 ~rLk~L~~~~f~~~~~LDIGCNsG~lt~~iak~F~~r~iLGvDID~~LI~~Ark  100 (288)
T KOG2899|consen   47 PRLKVLEKDWFEPKQALDIGCNSGFLTLSIAKDFGPRRILGVDIDPVLIQRARK  100 (288)
T ss_pred             hhhhhccccccCcceeEeccCCcchhHHHHHHhhccceeeEeeccHHHHHHHHH
Confidence            4444443 366789999999999999999999999999999998 788888865

>PLN02336 phosphoethanolamine N-methyltransferase

Probab=95.56  E-value=0.027  Score=52.16  Aligned_cols=49  Identities=22%  Similarity=0.280  Sum_probs=37.1

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~  233 (244)
                      +.+++.++ .....+|+|||||.|.++..+++.+.  +++.+|. |..++.++
T Consensus        27 ~~il~~l~-~~~~~~vLDlGcG~G~~~~~la~~~~--~v~giD~s~~~l~~a~   76 (475)
T PLN02336         27 PEILSLLP-PYEGKSVLELGAGIGRFTGELAKKAG--QVIALDFIESVIKKNE   76 (475)
T ss_pred             hHHHhhcC-ccCCCEEEEeCCCcCHHHHHHHhhCC--EEEEEeCCHHHHHHHH
Confidence            45566665 44557999999999999999999864  5788887 66666554

>PLN02672 methionine S-methyltransferase

Probab=95.55  E-value=0.01  Score=59.73  Aligned_cols=40  Identities=28%  Similarity=0.285  Sum_probs=36.6

Q ss_pred             ceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          195 KKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       195 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+|+|||||+|.+++.+++++|..+++..|+ |..++.|++
T Consensus       120 ~~VLDlG~GSG~Iai~La~~~~~~~v~avDis~~Al~~A~~  160 (1082)
T PLN02672        120 KTVAELGCGNGWISIAIAEKWLPSKVYGLDINPRAVKVAWI  160 (1082)
T ss_pred             CEEEEEecchHHHHHHHHHHCCCCEEEEEECCHHHHHHHHH
Confidence            6899999999999999999999999999999 888888753

>PLN02396 hexaprenyldihydroxybenzoate methyltransferase

Probab=95.53  E-value=0.014  Score=51.33  Aligned_cols=39  Identities=21%  Similarity=0.131  Sum_probs=32.3

Q ss_pred             cceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+|||||||.|.++..+++  ++.+++.+|. |+.++.|++
T Consensus       132 g~~ILDIGCG~G~~s~~La~--~g~~V~GID~s~~~i~~Ar~  171 (322)
T PLN02396        132 GLKFIDIGCGGGLLSEPLAR--MGATVTGVDAVDKNVKIARL  171 (322)
T ss_pred             CCEEEEeeCCCCHHHHHHHH--cCCEEEEEeCCHHHHHHHHH
Confidence            46899999999999988876  4778999998 777777753

>COG2227 UbiG 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase [Coenzyme metabolism]

Probab=95.49  E-value=0.011  Score=49.32  Aligned_cols=39  Identities=23%  Similarity=0.117  Sum_probs=34.2

Q ss_pred             cceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+|||||||-|.++..+++..  .+++..|+ ++-|+.|+.
T Consensus        60 g~~vLDvGCGgG~Lse~mAr~G--a~VtgiD~se~~I~~Ak~   99 (243)
T COG2227          60 GLRVLDVGCGGGILSEPLARLG--ASVTGIDASEKPIEVAKL   99 (243)
T ss_pred             CCeEEEecCCccHhhHHHHHCC--CeeEEecCChHHHHHHHH
Confidence            3899999999999999999997  77888898 788888874

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=95.46  E-value=0.029  Score=42.32  Aligned_cols=46  Identities=15%  Similarity=0.283  Sum_probs=37.5

Q ss_pred             hcChhhHHh-hcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           35 ELDVFEIIS-KAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        35 ~lgifd~L~-~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      +..++-+|- .+   +|.|+++||+.++.+      ..- +.|-|+-|...|++.++
T Consensus        29 Dv~v~~~LL~~~---~~~tvdelae~lnr~------rSt-v~rsl~~L~~~GlV~Re   75 (126)
T COG3355          29 DVEVYKALLEEN---GPLTVDELAEILNRS------RST-VYRSLQNLLEAGLVERE   75 (126)
T ss_pred             HHHHHHHHHhhc---CCcCHHHHHHHHCcc------HHH-HHHHHHHHHHcCCeeee
Confidence            344666666 43   799999999999996      445 99999999999999974

>KOG2904 consensus Predicted methyltransferase [General function prediction only]

Probab=95.45  E-value=0.019  Score=48.95  Aligned_cols=44  Identities=20%  Similarity=0.270  Sum_probs=37.6

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      +.+...++|+|||+|.++..++..-|..+++..|. +.++..|.+
T Consensus       146 ~~~~~~ildlgtGSGaIslsll~~L~~~~v~AiD~S~~Ai~La~e  190 (328)
T KOG2904|consen  146 HSKHTHILDLGTGSGAISLSLLHGLPQCTVTAIDVSKAAIKLAKE  190 (328)
T ss_pred             hcccceEEEecCCccHHHHHHHhcCCCceEEEEeccHHHHHHHHH
Confidence            44556899999999999999999999999999998 666666654

>cd02440 AdoMet_MTases S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)

Probab=95.44  E-value=0.015  Score=40.44  Aligned_cols=37  Identities=24%  Similarity=0.376  Sum_probs=30.6

Q ss_pred             eEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256          196 KLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       196 ~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~  233 (244)
                      +++|+|+|.|.++..+++ .+..+.+.+|+ +..+..++
T Consensus         1 ~ildig~G~G~~~~~~~~-~~~~~~~~~d~~~~~~~~~~   38 (107)
T cd02440           1 RVLDLGCGTGALALALAS-GPGARVTGVDISPVALELAR   38 (107)
T ss_pred             CeEEEcCCccHHHHHHhc-CCCCEEEEEeCCHHHHHHHH
Confidence            589999999999999998 78889999998 45555444

There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).

>TIGR00417 speE spermidine synthase

Probab=95.41  E-value=0.014  Score=49.99  Aligned_cols=43  Identities=23%  Similarity=0.281  Sum_probs=35.9

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      +++++|++||||.|.++..+++..+..+.++.|+ |++++.+++
T Consensus        71 ~~p~~VL~iG~G~G~~~~~ll~~~~~~~v~~veid~~vi~~a~~  114 (270)
T TIGR00417        71 PNPKHVLVIGGGDGGVLREVLKHKSVEKATLVDIDEKVIELSKK  114 (270)
T ss_pred             CCCCEEEEEcCCchHHHHHHHhCCCcceEEEEeCCHHHHHHHHH
Confidence            4567999999999999999998776778888888 788777764

the SpeE subunit of spermidine synthase catalysesthe reaction (putrescine + S-adenosylmethioninamine = spermidine + 5'-methylthioadenosine) and is involved in polyamine biosynthesis and in the biosynthesis of spermidine from arganine. The region between residues 77 and 120 of the seed alignment is thought to be involved in binding to decarboxylated SAM.

>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities

Probab=95.39  E-value=0.013  Score=36.22  Aligned_cols=43  Identities=19%  Similarity=0.389  Sum_probs=36.6

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCccc
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALH   88 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~   88 (244)
                      ++.|...|.+    ||.++.||++.+|++      ... +.+-|+.|...|+++
T Consensus         4 R~~Il~~L~~----~~~~~~el~~~l~~s------~~~-vs~hL~~L~~~glV~   46 (47)
T PF01022_consen    4 RLRILKLLSE----GPLTVSELAEELGLS------QST-VSHHLKKLREAGLVE   46 (47)
T ss_dssp             HHHHHHHHTT----SSEEHHHHHHHHTS-------HHH-HHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHh----CCCchhhHHHhcccc------chH-HHHHHHHHHHCcCee
Confidence            4567778877    799999999999997      456 999999999999986

One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....

>TIGR00478 tly hemolysin TlyA family protein

Probab=95.35  E-value=0.06  Score=45.08  Aligned_cols=56  Identities=16%  Similarity=0.119  Sum_probs=38.2

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccch--HHhhhCCCCCCc
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLP--YVIKDAPSYPGT  238 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp--~vi~~a~~~~~i  238 (244)
                      ..+++.++...+.++++|||||+|.++..++++ +--+++.+|..  ......++.++|
T Consensus        64 ~~~l~~~~~~~~~~~vlDiG~gtG~~t~~l~~~-ga~~v~avD~~~~~l~~~l~~~~~v  121 (228)
T TIGR00478        64 KEALEEFNIDVKNKIVLDVGSSTGGFTDCALQK-GAKEVYGVDVGYNQLAEKLRQDERV  121 (228)
T ss_pred             HHHHHhcCCCCCCCEEEEcccCCCHHHHHHHHc-CCCEEEEEeCCHHHHHHHHhcCCCe
Confidence            345555541135579999999999999999986 44578889983  344444444444

Hemolysins are exotoxins that attack blood cell membranes and cause cell rupture, often by forming a pore in the membrane. At least two members of this protein family have been characterized indirectly as pore-forming hemolysins, one from the spirochete Serpula (Treponema) hyodysenteriae and one from Mycobacterium tuberculosis. However, homology domains in this protein suggest methyltransferase activity (pfam01728) and RNA-binding activity (pfam01479).

>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family

Probab=95.35  E-value=0.037  Score=36.38  Aligned_cols=44  Identities=23%  Similarity=0.326  Sum_probs=36.6

Q ss_pred             CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCc
Q 041256           49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAP  102 (244)
Q Consensus        49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~  102 (244)
                      +++|..+||+.+|++      ... +.|+|+.|...|++..   ...+.|.+++
T Consensus        24 ~~~s~~ela~~~g~s------~~t-v~r~l~~L~~~g~i~~---~~~~~~~l~~   67 (67)
T cd00092          24 LPLTRQEIADYLGLT------RET-VSRTLKELEEEGLISR---RGRGKYRVNP   67 (67)
T ss_pred             CCcCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEe---cCCCeEEeCC
Confidence            689999999999997      456 9999999999999995   2236787764

>PRK11727 23S rRNA mA1618 methyltransferase; Provisional

Probab=95.33  E-value=0.015  Score=51.05  Aligned_cols=42  Identities=17%  Similarity=0.221  Sum_probs=37.1

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...++||||+|+|.+..-++.+.|+.+++..|+ |..++.|++
T Consensus       114 ~~~~vLDIGtGag~I~~lLa~~~~~~~~~atDId~~Al~~A~~  156 (321)
T PRK11727        114 ANVRVLDIGVGANCIYPLIGVHEYGWRFVGSDIDPQALASAQA  156 (321)
T ss_pred             CCceEEEecCCccHHHHHHHhhCCCCEEEEEeCCHHHHHHHHH
Confidence            458999999999998888899999999999998 888888764

>PLN02585 magnesium protoporphyrin IX methyltransferase

Probab=95.33  E-value=0.015  Score=51.08  Aligned_cols=39  Identities=15%  Similarity=0.109  Sum_probs=32.7

Q ss_pred             cceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+|+|||||+|.++..++++  +.+++.+|+ |..++.+++
T Consensus       145 ~~~VLDlGcGtG~~a~~la~~--g~~V~gvD~S~~ml~~A~~  184 (315)
T PLN02585        145 GVTVCDAGCGTGSLAIPLALE--GAIVSASDISAAMVAEAER  184 (315)
T ss_pred             CCEEEEecCCCCHHHHHHHHC--CCEEEEEECCHHHHHHHHH
Confidence            479999999999999999986  568999998 667766654

>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional

Probab=95.32  E-value=0.036  Score=41.45  Aligned_cols=68  Identities=18%  Similarity=0.243  Sum_probs=51.5

Q ss_pred             HHHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCc
Q 041256           25 VLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAP  102 (244)
Q Consensus        25 ~~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~  102 (244)
                      ..+.+|.--.++.|+..|.+.   ++.++.||++.++++      +.. +.+-|+.|...|+++...+...-.|++++
T Consensus         8 ~~fkaLadptRl~IL~~L~~~---~~~~v~ela~~l~ls------qst-vS~HL~~L~~AGLV~~~r~Gr~~~Y~l~~   75 (117)
T PRK10141          8 QLFKILSDETRLGIVLLLRES---GELCVCDLCTALDQS------QPK-ISRHLALLRESGLLLDRKQGKWVHYRLSP   75 (117)
T ss_pred             HHHHHhCCHHHHHHHHHHHHc---CCcCHHHHHHHHCcC------HHH-HHHHHHHHHHCCceEEEEEcCEEEEEECc
Confidence            445667777889999999764   589999999999997      445 99999999999999864321122366654

>PRK11512 DNA-binding transcriptional repressor MarR; Provisional

Probab=95.29  E-value=0.11  Score=39.95  Aligned_cols=44  Identities=23%  Similarity=0.195  Sum_probs=36.6

Q ss_pred             ChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           37 DVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        37 gifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      .|+-.|...   +++|..+||+.++++      +.. +.++++-|...|++.+.
T Consensus        44 ~vL~~l~~~---~~~t~~eLa~~l~i~------~~t-vsr~l~~Le~~GlI~R~   87 (144)
T PRK11512         44 KVLCSIRCA---ACITPVELKKVLSVD------LGA-LTRMLDRLVCKGWVERL   87 (144)
T ss_pred             HHHHHHHHc---CCCCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEec
Confidence            356666654   589999999999997      456 99999999999999964

>PTZ00338 dimethyladenosine transferase-like protein; Provisional

Probab=95.26  E-value=0.039  Score=47.97  Aligned_cols=49  Identities=16%  Similarity=0.371  Sum_probs=36.5

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~  233 (244)
                      ..+++..+ .....+|+|||||.|.+...++++..  +++.+|+ +..++.++
T Consensus        26 ~~Iv~~~~-~~~~~~VLEIG~G~G~LT~~Ll~~~~--~V~avEiD~~li~~l~   75 (294)
T PTZ00338         26 DKIVEKAA-IKPTDTVLEIGPGTGNLTEKLLQLAK--KVIAIEIDPRMVAELK   75 (294)
T ss_pred             HHHHHhcC-CCCcCEEEEecCchHHHHHHHHHhCC--cEEEEECCHHHHHHHH
Confidence            35555555 56668999999999999999999864  5677776 55665554

>COG1959 Predicted transcriptional regulator [Transcription]

Probab=95.25  E-value=0.036  Score=43.31  Aligned_cols=54  Identities=22%  Similarity=0.276  Sum_probs=42.2

Q ss_pred             HHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecC-CceeecCcc
Q 041256           41 IISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDG-QRLYSLAPV  103 (244)
Q Consensus        41 ~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~-~~~y~~t~~  103 (244)
                      .|+..+.+++.|+++||+..+++      +.+ |.++|..|...|+++-.  .| .|.|+++.-
T Consensus        16 ~LA~~~~~~~~s~~~IA~~~~is------~~~-L~kil~~L~kaGlV~S~--rG~~GGy~Lar~   70 (150)
T COG1959          16 YLALLPGGGPVSSAEIAERQGIS------PSY-LEKILSKLRKAGLVKSV--RGKGGGYRLARP   70 (150)
T ss_pred             HHHhCCCCCcccHHHHHHHhCcC------HHH-HHHHHHHHHHcCCEEee--cCCCCCccCCCC
Confidence            44544433489999999999997      679 99999999999999853  23 577888663

>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B

Probab=95.24  E-value=0.021  Score=37.32  Aligned_cols=52  Identities=10%  Similarity=0.281  Sum_probs=42.2

Q ss_pred             HHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           28 AVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        28 ~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      .+|.--.++.|++.|...   +|.|+.|||+.+|++      +.. +.+-|+.|...|+++.
T Consensus         5 ~aL~~p~R~~Il~~L~~~---~~~t~~ela~~l~~~------~~t-~s~hL~~L~~aGli~~   56 (61)
T PF12840_consen    5 KALSDPTRLRILRLLASN---GPMTVSELAEELGIS------QST-VSYHLKKLEEAGLIEV   56 (61)
T ss_dssp             HHHTSHHHHHHHHHHHHC---STBEHHHHHHHHTS-------HHH-HHHHHHHHHHTTSEEE
T ss_pred             HHhCCHHHHHHHHHHhcC---CCCCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCeEE
Confidence            445555678888889443   699999999999996      456 9999999999999985

...

>KOG1271 consensus Methyltransferases [General function prediction only]

Probab=95.20  E-value=0.026  Score=45.34  Aligned_cols=39  Identities=21%  Similarity=0.410  Sum_probs=28.4

Q ss_pred             CcceEEEecCCccHHHHHHHHH-CCC-CeEEEccc-hHHhhhCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISK-YPH-IKGINYDL-PYVIKDAP  233 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~-~P~-l~~~v~Dl-p~vi~~a~  233 (244)
                      ...+|||+|||.|+++..|++. ||+ |+|  .|- +..++.|+
T Consensus        67 ~A~~VlDLGtGNG~~L~~L~~egf~~~L~G--vDYs~~AV~LA~  108 (227)
T KOG1271|consen   67 QADRVLDLGTGNGHLLFQLAKEGFQSKLTG--VDYSEKAVELAQ  108 (227)
T ss_pred             cccceeeccCCchHHHHHHHHhcCCCCccc--cccCHHHHHHHH
Confidence            3459999999999999999986 555 554  444 55555554

>PRK11873 arsM arsenite S-adenosylmethyltransferase; Reviewed

Probab=95.08  E-value=0.027  Score=48.13  Aligned_cols=44  Identities=23%  Similarity=0.362  Sum_probs=36.1

Q ss_pred             CCCcceEEEecCCccHHHHHHHHH-CCCCeEEEccc-hHHhhhCCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISK-YPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~-~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .....+|||||||.|..+..+++. .|+.+++.+|+ |..++.+++
T Consensus        75 ~~~g~~VLDiG~G~G~~~~~~a~~~g~~~~v~gvD~s~~~l~~A~~  120 (272)
T PRK11873         75 LKPGETVLDLGSGGGFDCFLAARRVGPTGKVIGVDMTPEMLAKARA  120 (272)
T ss_pred             CCCCCEEEEeCCCCCHHHHHHHHHhCCCCEEEEECCCHHHHHHHHH
Confidence            456689999999999988877776 46678999998 787887764

>PRK13943 protein-L-isoaspartate O-methyltransferase; Provisional

Probab=95.00  E-value=0.044  Score=48.26  Aligned_cols=51  Identities=12%  Similarity=0.177  Sum_probs=38.6

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCC-CeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPH-IKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+++..+ ..+..+|+|||||+|.++..+++..+. -+++.+|. |+.++.|++
T Consensus        71 ~ll~~L~-i~~g~~VLDIG~GtG~~a~~LA~~~~~~g~VvgVDis~~~l~~Ar~  123 (322)
T PRK13943         71 LFMEWVG-LDKGMRVLEIGGGTGYNAAVMSRVVGEKGLVVSVEYSRKICEIAKR  123 (322)
T ss_pred             HHHHhcC-CCCCCEEEEEeCCccHHHHHHHHhcCCCCEEEEEECCHHHHHHHHH
Confidence            3444444 556689999999999999999998874 46788887 777766653

>COG0421 SpeE Spermidine synthase [Amino acid transport and metabolism]

Probab=95.00  E-value=0.025  Score=48.84  Aligned_cols=44  Identities=27%  Similarity=0.389  Sum_probs=39.9

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+.+++|+=||||.|..+.++++..|--+.++.|+ |.|++.+++
T Consensus        74 h~~pk~VLiiGgGdG~tlRevlkh~~ve~i~~VEID~~Vi~~ar~  118 (282)
T COG0421          74 HPNPKRVLIIGGGDGGTLREVLKHLPVERITMVEIDPAVIELARK  118 (282)
T ss_pred             CCCCCeEEEECCCccHHHHHHHhcCCcceEEEEEcCHHHHHHHHH
Confidence            34568999999999999999999999889999999 999999875

>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR

Probab=94.99  E-value=0.052  Score=41.50  Aligned_cols=46  Identities=13%  Similarity=0.185  Sum_probs=37.3

Q ss_pred             CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCc
Q 041256           49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAP  102 (244)
Q Consensus        49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~  102 (244)
                      ++.|.++||+.++++      +.. ++++|+.|...|++... +...|.|.++.
T Consensus        24 ~~~s~~~ia~~~~ip------~~~-l~kil~~L~~~glv~s~-~G~~Ggy~l~~   69 (135)
T TIGR02010        24 GPVTLADISERQGIS------LSY-LEQLFAKLRKAGLVKSV-RGPGGGYQLGR   69 (135)
T ss_pred             CcCcHHHHHHHHCcC------HHH-HHHHHHHHHHCCceEEE-eCCCCCEeccC
Confidence            589999999999997      678 99999999999999742 22245677755

This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.

>PRK14967 putative methyltransferase; Provisional

Probab=94.96  E-value=0.032  Score=46.34  Aligned_cols=43  Identities=12%  Similarity=0.093  Sum_probs=33.3

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .....+|+|+|||+|.++..+++. +..+++.+|+ |..++.+++
T Consensus        34 ~~~~~~vLDlGcG~G~~~~~la~~-~~~~v~~vD~s~~~l~~a~~   77 (223)
T PRK14967         34 LGPGRRVLDLCTGSGALAVAAAAA-GAGSVTAVDISRRAVRSARL   77 (223)
T ss_pred             cCCCCeEEEecCCHHHHHHHHHHc-CCCeEEEEECCHHHHHHHHH
Confidence            444579999999999999998876 3347899998 666765543

>TIGR03840 TMPT_Se_Te thiopurine S-methyltransferase, Se/Te detoxification family

Probab=94.92  E-value=0.053  Score=44.88  Aligned_cols=39  Identities=8%  Similarity=0.079  Sum_probs=33.1

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDA  232 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a  232 (244)
                      ....+++|+|||.|..+..|+++  +.+++.+|+ |..++.+
T Consensus        33 ~~~~rvLd~GCG~G~da~~LA~~--G~~V~gvD~S~~Ai~~~   72 (213)
T TIGR03840        33 PAGARVFVPLCGKSLDLAWLAEQ--GHRVLGVELSEIAVEQF   72 (213)
T ss_pred             CCCCeEEEeCCCchhHHHHHHhC--CCeEEEEeCCHHHHHHH
Confidence            44579999999999999999976  778999999 7777764

Members of this family are thiopurine S-methyltransferase from a branch in which at least some member proteins can perform selenium methylation as a means to detoxify selenium, or perform a related detoxification of tellurium. Note that the EC number definition does not specify a particular thiopurine, but rather represents a class of activity.

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=94.90  E-value=0.046  Score=33.33  Aligned_cols=41  Identities=17%  Similarity=0.180  Sum_probs=34.0

Q ss_pred             CCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecC
Q 041256           50 KLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLA  101 (244)
Q Consensus        50 ~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t  101 (244)
                      +.|..+||+.++++      ... +.+.|+.|...|++..   . .+.|..+
T Consensus         8 ~~s~~~la~~l~~s------~~t-v~~~l~~L~~~g~l~~---~-~~~~~i~   48 (48)
T smart00419        8 PLTRQEIAELLGLT------RET-VSRTLKRLEKEGLISR---E-GGRIVIL   48 (48)
T ss_pred             ccCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEE---e-CCEEEEC
Confidence            78999999999997      456 9999999999999984   3 3667643

>PF07021 MetW: Methionine biosynthesis protein MetW; InterPro: IPR010743 This family consists of several bacterial and one archaeal methionine biosynthesis MetW proteins

Probab=94.84  E-value=0.032  Score=45.23  Aligned_cols=33  Identities=21%  Similarity=0.432  Sum_probs=27.0

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL  225 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  225 (244)
                      +...+|+|+|||.|.++..|.+. -++++..+|+
T Consensus        12 ~pgsrVLDLGCGdG~LL~~L~~~-k~v~g~GvEi   44 (193)
T PF07021_consen   12 EPGSRVLDLGCGDGELLAYLKDE-KQVDGYGVEI   44 (193)
T ss_pred             CCCCEEEecCCCchHHHHHHHHh-cCCeEEEEec
Confidence            34589999999999999777775 5888877776

Biosynthesis of methionine from homoserine in Pseudomonas putida takes place in three steps. The first step is the acylation of homoserine to yield an acyl-L-homoserine. This reaction is catalysed by the products of the metXW genes and is equivalent to the first step in enterobacteria, Gram-positive bacteria and fungi, except that in these microorganisms the reaction is catalysed by a single polypeptide (the product of the metA gene in Escherichia coli and the met5 gene product in Neurospora crassa). In P. putida, as in Gram-positive bacteria and certain fungi, the second and third steps are a direct sulphydrylation that converts the O-acyl-L-homoserine into homocysteine and further methylation to yield methionine. The latter reaction can be mediated by either of the two methionine synthetases present in the cells [].

>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A

Probab=94.81  E-value=0.029  Score=38.97  Aligned_cols=62  Identities=18%  Similarity=0.233  Sum_probs=45.2

Q ss_pred             HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc----eeecCcccc
Q 041256           34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR----LYSLAPVSA  105 (244)
Q Consensus        34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~----~y~~t~~s~  105 (244)
                      ++++|...|...   +..+..+|.+.+|++      ... +.+-|+.|...|+++...+...+    .|++|+.++
T Consensus         1 vRl~Il~~L~~~---~~~~f~~L~~~l~lt------~g~-Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~~lT~~Gr   66 (80)
T PF13601_consen    1 VRLAILALLYAN---EEATFSELKEELGLT------DGN-LSKHLKKLEEAGYVEVEKEFEGRRPRTWYSLTDKGR   66 (80)
T ss_dssp             HHHHHHHHHHHH---SEEEHHHHHHHTT--------HHH-HHHHHHHHHHTTSEEEEEE-SSS--EEEEEE-HHHH
T ss_pred             CHHHHHHHHhhc---CCCCHHHHHHHhCcC------HHH-HHHHHHHHHHCCCEEEEEeccCCCCeEEEEECHHHH
Confidence            467788888875   589999999999997      456 99999999999999865332111    377777664

>PRK10857 DNA-binding transcriptional regulator IscR; Provisional

Probab=94.80  E-value=0.063  Score=42.61  Aligned_cols=46  Identities=13%  Similarity=0.165  Sum_probs=37.6

Q ss_pred             CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCc
Q 041256           49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAP  102 (244)
Q Consensus        49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~  102 (244)
                      ++.|+++||+.++++      +.. +.++|+.|...|++... ....|.|.+..
T Consensus        24 ~~vs~~eIA~~~~ip------~~~-l~kIl~~L~~aGLv~s~-rG~~GGy~Lar   69 (164)
T PRK10857         24 GPVPLADISERQGIS------LSY-LEQLFSRLRKNGLVSSV-RGPGGGYLLGK   69 (164)
T ss_pred             CcCcHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEeC-CCCCCCeeccC
Confidence            589999999999997      678 99999999999999842 12246687754

>PLN02823 spermine synthase

Probab=94.78  E-value=0.03  Score=49.62  Aligned_cols=43  Identities=21%  Similarity=0.234  Sum_probs=37.9

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .++++|+-||||.|..+..+++..+..+.+++|+ |.|++.+++
T Consensus       102 ~~pk~VLiiGgG~G~~~re~l~~~~~~~v~~VEiD~~vv~lar~  145 (336)
T PLN02823        102 PNPKTVFIMGGGEGSTAREVLRHKTVEKVVMCDIDQEVVDFCRK  145 (336)
T ss_pred             CCCCEEEEECCCchHHHHHHHhCCCCCeEEEEECCHHHHHHHHH
Confidence            3568999999999999999998777778999998 999999875

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

Probab=94.76  E-value=0.031  Score=51.40  Aligned_cols=49  Identities=14%  Similarity=0.112  Sum_probs=37.7

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+++.++ ..+..+|+|+|||+|.++..+++..  .+++.+|. |+.++.|++
T Consensus       288 ~vl~~l~-~~~~~~VLDlgcGtG~~sl~la~~~--~~V~gvD~s~~al~~A~~  337 (443)
T PRK13168        288 RALEWLD-PQPGDRVLDLFCGLGNFTLPLARQA--AEVVGVEGVEAMVERARE  337 (443)
T ss_pred             HHHHHhc-CCCCCEEEEEeccCCHHHHHHHHhC--CEEEEEeCCHHHHHHHHH
Confidence            3344444 3455799999999999999999886  47888998 788887764

>COG2263 Predicted RNA methylase [Translation, ribosomal structure and biogenesis]

Probab=94.74  E-value=0.026  Score=45.52  Aligned_cols=41  Identities=22%  Similarity=0.255  Sum_probs=33.5

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..++|+|+|||+|.++++.+-..|. +++.+|. |+.++.+++
T Consensus        45 ~g~~V~DlG~GTG~La~ga~~lGa~-~V~~vdiD~~a~ei~r~   86 (198)
T COG2263          45 EGKTVLDLGAGTGILAIGAALLGAS-RVLAVDIDPEALEIARA   86 (198)
T ss_pred             CCCEEEEcCCCcCHHHHHHHhcCCc-EEEEEecCHHHHHHHHH
Confidence            3488999999999999998887766 5666676 888888875

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=94.71  E-value=0.077  Score=34.06  Aligned_cols=42  Identities=14%  Similarity=0.326  Sum_probs=34.2

Q ss_pred             hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      |+..|..    ++.|..+|++.++++      ... +.+.|+.|...|++...
T Consensus         2 il~~l~~----~~~~~~~i~~~l~is------~~~-v~~~l~~L~~~g~i~~~   43 (66)
T smart00418        2 ILKLLAE----GELCVCELAEILGLS------QST-VSHHLKKLREAGLVESR   43 (66)
T ss_pred             HHHHhhc----CCccHHHHHHHHCCC------HHH-HHHHHHHHHHCCCeeee
Confidence            4455552    689999999999997      345 99999999999999853

>PF07757 AdoMet_MTase: Predicted AdoMet-dependent methyltransferase; InterPro: IPR011671 tRNA (uracil-O(2)-)-methyltransferase catalyses the formation of O(2)-methyl-uracil at position 44 (m2U44) in tRNA(Ser) []

Probab=94.71  E-value=0.041  Score=40.28  Aligned_cols=44  Identities=23%  Similarity=0.357  Sum_probs=30.4

Q ss_pred             hhHHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc
Q 041256          179 IVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL  225 (244)
Q Consensus       179 ~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  225 (244)
                      +.+.-|.+.+. -.....+||||||+|.+.--|.+.  +.+|..+|.
T Consensus        45 yLi~LW~~~~~-~~~~~~FVDlGCGNGLLV~IL~~E--Gy~G~GiD~   88 (112)
T PF07757_consen   45 YLIELWRDMYG-EQKFQGFVDLGCGNGLLVYILNSE--GYPGWGIDA   88 (112)
T ss_pred             HHHHHHhcccC-CCCCCceEEccCCchHHHHHHHhC--CCCcccccc
Confidence            33445555555 356789999999999988777665  445666663

; GO: 0008168 methyltransferase activity

>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B

Probab=94.67  E-value=0.037  Score=35.93  Aligned_cols=48  Identities=10%  Similarity=0.272  Sum_probs=37.1

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      +..++-.|...+. .++|..|||+.++++      +.. +.++++.|...|++++.
T Consensus         7 q~~vL~~l~~~~~-~~~t~~~la~~l~~~------~~~-vs~~v~~L~~~Glv~r~   54 (62)
T PF12802_consen    7 QFRVLMALARHPG-EELTQSELAERLGIS------KST-VSRIVKRLEKKGLVERE   54 (62)
T ss_dssp             HHHHHHHHHHSTT-SGEEHHHHHHHHTS-------HHH-HHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHCCC-CCcCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEEe
Confidence            3445666777531 128999999999997      566 99999999999999964

...

>PF08003 Methyltransf_9: Protein of unknown function (DUF1698); InterPro: IPR010017 Methyl transfer from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals

Probab=94.66  E-value=0.057  Score=46.88  Aligned_cols=40  Identities=18%  Similarity=0.286  Sum_probs=29.7

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEcc
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYD  224 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~D  224 (244)
                      .+...++.+++ ++|+|||||+|.++...+++.|.. ++.+|
T Consensus       106 rl~p~l~~L~g-k~VLDIGC~nGY~~frM~~~GA~~-ViGiD  145 (315)
T PF08003_consen  106 RLLPHLPDLKG-KRVLDIGCNNGYYSFRMLGRGAKS-VIGID  145 (315)
T ss_pred             HHHhhhCCcCC-CEEEEecCCCcHHHHHHhhcCCCE-EEEEC
Confidence            34444432444 899999999999999999997763 56666

The reaction is catalysed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented. Three classes of DNA Mtases transfer the methyl group from AdoMet to the target base to form either N-6-methyladenine, or N-4-methylcytosine, or C-5- methylcytosine. In C-5-cytosine Mtases, ten conserved motifs are arranged in the same order []. Motif I (a glycine-rich or closely related consensus sequence; FAGxGG in M.HhaI []), shared by other AdoMet-Mtases [], is part of the cofactor binding site and motif IV (PCQ) is part of the catalytic site. In contrast, sequence comparison among N-6-adenine and N-4-cytosine Mtases indicated two of the conserved segments [], although more conserved segments may be present. One of them corresponds to motif I in C-5-cytosine Mtases, and the other is named (D/N/S)PP(Y/F). Crystal structures are known for a number of Mtases [, , , ]. The cofactor binding sites are almost identical and the essential catalytic amino acids coincide. The comparable protein folding and the existence of equivalent amino acids in similar secondary and tertiary positions indicate that many (if not all) AdoMet-Mtases have a common catalytic domain structure. This permits tertiary structure prediction of other DNA, RNA, protein, and small-molecule AdoMet-Mtases from their amino acid sequences []. This entry represents a set of bacterial AdoMet-dependent tRNA (mo5U34)-methyltransferases. These enzymes catalyse the conversion of 5-hydroxyuridine (ho5U) to 5-methoxyuridine (mo5U) at the wobble position (34) of tRNA []. The 5-methoxyuridine is subsequently converted to uridine-5-oxyacetic acid, a modified nucleoside that is apparently necessary for the efficient decoding of G-ending Pro, Ala, and Val codons in these organisms [].; GO: 0016300 tRNA (uracil) methyltransferase activity, 0002098 tRNA wobble uridine modification

>PRK03522 rumB 23S rRNA methyluridine methyltransferase; Reviewed

Probab=94.64  E-value=0.056  Score=47.38  Aligned_cols=39  Identities=13%  Similarity=0.019  Sum_probs=33.2

Q ss_pred             cceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+|+|+|||.|.++..++++  ..+++.+|. |..++.|++
T Consensus       174 ~~~VLDl~cG~G~~sl~la~~--~~~V~gvD~s~~av~~A~~  213 (315)
T PRK03522        174 PRSMWDLFCGVGGFGLHCATP--GMQLTGIEISAEAIACAKQ  213 (315)
T ss_pred             CCEEEEccCCCCHHHHHHHhc--CCEEEEEeCCHHHHHHHHH
Confidence            479999999999999999984  467899998 888887764

>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif

Probab=94.63  E-value=0.044  Score=36.77  Aligned_cols=43  Identities=12%  Similarity=0.288  Sum_probs=35.2

Q ss_pred             hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      |-+.|.+.   +..|..|||..++++      ++. +..+|..|+..|.+.+.
T Consensus         5 i~~~l~~~---~~~S~~eLa~~~~~s------~~~-ve~mL~~l~~kG~I~~~   47 (69)
T PF09012_consen    5 IRDYLRER---GRVSLAELAREFGIS------PEA-VEAMLEQLIRKGYIRKV   47 (69)
T ss_dssp             HHHHHHHS----SEEHHHHHHHTT--------HHH-HHHHHHHHHCCTSCEEE
T ss_pred             HHHHHHHc---CCcCHHHHHHHHCcC------HHH-HHHHHHHHHHCCcEEEe
Confidence            56778775   689999999999997      677 99999999999999963

FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.

>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance

Probab=94.57  E-value=0.029  Score=36.13  Aligned_cols=45  Identities=9%  Similarity=0.310  Sum_probs=36.4

Q ss_pred             cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      +.+...|.+.   +++|..+||+.++++      ... +.++++-|...||+++.
T Consensus         6 ~~iL~~l~~~---~~~~~~~la~~~~~~------~~~-~t~~i~~L~~~g~I~r~   50 (59)
T PF01047_consen    6 FRILRILYEN---GGITQSELAEKLGIS------RST-VTRIIKRLEKKGLIERE   50 (59)
T ss_dssp             HHHHHHHHHH---SSEEHHHHHHHHTS-------HHH-HHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHc---CCCCHHHHHHHHCCC------hhH-HHHHHHHHHHCCCEEec
Confidence            3445556665   589999999999997      456 99999999999999964

This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....

>PRK04148 hypothetical protein; Provisional

Probab=94.54  E-value=0.063  Score=41.06  Aligned_cols=48  Identities=21%  Similarity=0.302  Sum_probs=34.3

Q ss_pred             HHhhcCCCCCcceEEEecCCccH-HHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          184 VLESYKGFEHVKKLVDVGGGLGI-TLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       184 ~~~~~~~~~~~~~vvDVGGG~G~-~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      +.+.++ -.+..+++|||+|.|. ++..|.+.  +..++..|. |..++.+++
T Consensus         8 l~~~~~-~~~~~kileIG~GfG~~vA~~L~~~--G~~ViaIDi~~~aV~~a~~   57 (134)
T PRK04148          8 IAENYE-KGKNKKIVELGIGFYFKVAKKLKES--GFDVIVIDINEKAVEKAKK   57 (134)
T ss_pred             HHHhcc-cccCCEEEEEEecCCHHHHHHHHHC--CCEEEEEECCHHHHHHHHH
Confidence            445555 2345789999999996 77777754  568899998 777776643

>PF03848 TehB: Tellurite resistance protein TehB; InterPro: IPR015985 Tellurite resistance protein TehB is part of a tellurite-reducing operon tehA and tehB

Probab=94.46  E-value=0.09  Score=42.81  Aligned_cols=48  Identities=23%  Similarity=0.318  Sum_probs=35.1

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDA  232 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a  232 (244)
                      ..+++.++ .-+..++||+|||.|..+.-|+++  +..++.+|. +..++.+
T Consensus        20 s~v~~a~~-~~~~g~~LDlgcG~GRNalyLA~~--G~~VtAvD~s~~al~~l   68 (192)
T PF03848_consen   20 SEVLEAVP-LLKPGKALDLGCGEGRNALYLASQ--GFDVTAVDISPVALEKL   68 (192)
T ss_dssp             HHHHHHCT-TS-SSEEEEES-TTSHHHHHHHHT--T-EEEEEESSHHHHHHH
T ss_pred             HHHHHHHh-hcCCCcEEEcCCCCcHHHHHHHHC--CCeEEEEECCHHHHHHH
Confidence            35666777 556789999999999999999998  667888887 4455443

When present in high copy number, TehB is responsible for potassium tellurite resistance, probably by increasing the reduction rate of tellurite to metallic tellurium within the bacterium. TehB is a cytoplasmic protein which possesses three conserved motifs (I, II, and III) found in S-adenosyl-L-methionine (SAM)-dependent non-nucleic acid methyltransferases []. Conformational changes in TehB are observed upon binding of both tellurite and SAM, suggesting that TehB utilises a methyltransferase activity in the detoxification of tellurite. This entry represents the methyltransferase domain found in all TehB proteins.; PDB: 2KW5_A 3MER_B 3M70_A 2I6G_A 4DQ0_D 2XVA_B 2XVM_A.

>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator)

Probab=94.44  E-value=0.07  Score=40.37  Aligned_cols=46  Identities=24%  Similarity=0.275  Sum_probs=36.3

Q ss_pred             CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCc
Q 041256           49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAP  102 (244)
Q Consensus        49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~  102 (244)
                      ++.|.++||+.++++      +.. ++++|+.|...|++.... ...|.|.++.
T Consensus        24 ~~~s~~eia~~~~i~------~~~-v~~il~~L~~~gli~~~~-g~~ggy~l~~   69 (132)
T TIGR00738        24 GPVSVKEIAERQGIS------RSY-LEKILRTLRRAGLVESVR-GPGGGYRLAR   69 (132)
T ss_pred             CcCcHHHHHHHHCcC------HHH-HHHHHHHHHHCCcEEecc-CCCCCccCCC
Confidence            589999999999996      567 999999999999998421 1235577654

This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.

>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A

Probab=94.37  E-value=0.043  Score=37.77  Aligned_cols=49  Identities=18%  Similarity=0.205  Sum_probs=37.6

Q ss_pred             CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccccccc
Q 041256           49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFV  108 (244)
Q Consensus        49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l~  108 (244)
                      ++.+..+|+..++++      ... +.+.|+.|...|++..    +++.|.+|+.+..+.
T Consensus        18 ~~~~~t~i~~~~~L~------~~~-~~~yL~~L~~~gLI~~----~~~~Y~lTekG~~~l   66 (77)
T PF14947_consen   18 GGAKKTEIMYKANLN------YST-LKKYLKELEEKGLIKK----KDGKYRLTEKGKEFL   66 (77)
T ss_dssp             T-B-HHHHHTTST--------HHH-HHHHHHHHHHTTSEEE----ETTEEEE-HHHHHHH
T ss_pred             CCCCHHHHHHHhCcC------HHH-HHHHHHHHHHCcCeeC----CCCEEEECccHHHHH
Confidence            689999999999996      556 9999999999999973    368999999886443

>PRK06266 transcription initiation factor E subunit alpha; Validated

Probab=94.32  E-value=0.18  Score=40.53  Aligned_cols=44  Identities=18%  Similarity=0.266  Sum_probs=38.6

Q ss_pred             cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      ..|+++|...   |++|.++||+.+|++      ... ++++|..|...|++..
T Consensus        25 ~~Vl~~L~~~---g~~tdeeLA~~Lgi~------~~~-VRk~L~~L~e~gLv~~   68 (178)
T PRK06266         25 FEVLKALIKK---GEVTDEEIAEQTGIK------LNT-VRKILYKLYDARLADY   68 (178)
T ss_pred             hHHHHHHHHc---CCcCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCeEE
Confidence            3488889886   699999999999997      456 9999999999999984

>PLN02781 Probable caffeoyl-CoA O-methyltransferase

Probab=94.25  E-value=0.084  Score=44.31  Aligned_cols=44  Identities=14%  Similarity=0.091  Sum_probs=37.0

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCC-CCeEEEccc-hHHhhhCCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYP-HIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+.++|+|||+|.|..+..+++..| +-+++.+|. |+.++.|++
T Consensus        66 ~~~~~~vLEiGt~~G~s~l~la~~~~~~g~v~tiD~d~~~~~~A~~  111 (234)
T PLN02781         66 IMNAKNTLEIGVFTGYSLLTTALALPEDGRITAIDIDKEAYEVGLE  111 (234)
T ss_pred             HhCCCEEEEecCcccHHHHHHHHhCCCCCEEEEEECCHHHHHHHHH
Confidence            45678999999999999999998865 678999998 777777764

>PRK00312 pcm protein-L-isoaspartate O-methyltransferase; Reviewed

Probab=94.25  E-value=0.088  Score=43.22  Aligned_cols=48  Identities=10%  Similarity=0.189  Sum_probs=34.5

Q ss_pred             HHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          184 VLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       184 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      +++.++ .....+|+|||||+|.++..+++...  +.+.+|. |..++.+++
T Consensus        70 l~~~l~-~~~~~~VLeiG~GsG~~t~~la~~~~--~v~~vd~~~~~~~~a~~  118 (212)
T PRK00312         70 MTELLE-LKPGDRVLEIGTGSGYQAAVLAHLVR--RVFSVERIKTLQWEAKR  118 (212)
T ss_pred             HHHhcC-CCCCCEEEEECCCccHHHHHHHHHhC--EEEEEeCCHHHHHHHHH
Confidence            344444 56668999999999999887777654  5667776 676666643

>PRK10901 16S rRNA methyltransferase B; Provisional

Probab=94.14  E-value=0.061  Score=49.25  Aligned_cols=50  Identities=10%  Similarity=0.131  Sum_probs=40.2

Q ss_pred             HHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          184 VLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       184 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ++..++ .....+|+|+|||.|..+..+++..++.+++.+|. |..++.+++
T Consensus       236 ~~~~l~-~~~g~~VLDlgaG~G~~t~~la~~~~~~~v~a~D~s~~~l~~~~~  286 (427)
T PRK10901        236 AATLLA-PQNGERVLDACAAPGGKTAHILELAPQAQVVALDIDAQRLERVRE  286 (427)
T ss_pred             HHHHcC-CCCCCEEEEeCCCCChHHHHHHHHcCCCEEEEEeCCHHHHHHHHH
Confidence            334444 45568999999999999999999998888999998 777766653

>PTZ00146 fibrillarin; Provisional

Probab=94.14  E-value=0.11  Score=45.14  Aligned_cols=51  Identities=16%  Similarity=0.169  Sum_probs=38.2

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHC-CCCeEEEccchH-----HhhhCCCCCCceee
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKY-PHIKGINYDLPY-----VIKDAPSYPGTLFI  241 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dlp~-----vi~~a~~~~~i~~~  241 (244)
                      +....+|||+|||+|.++..+++.. |.=+++.+|..+     .++.+++.++|.++
T Consensus       130 IkpG~~VLDLGaG~G~~t~~lAdiVG~~G~VyAVD~s~r~~~dLl~~ak~r~NI~~I  186 (293)
T PTZ00146        130 IKPGSKVLYLGAASGTTVSHVSDLVGPEGVVYAVEFSHRSGRDLTNMAKKRPNIVPI  186 (293)
T ss_pred             cCCCCEEEEeCCcCCHHHHHHHHHhCCCCEEEEEECcHHHHHHHHHHhhhcCCCEEE
Confidence            4566899999999999999999987 345788888743     55666555666554

>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A

Probab=94.10  E-value=0.056  Score=35.61  Aligned_cols=45  Identities=20%  Similarity=0.191  Sum_probs=35.0

Q ss_pred             ChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           37 DVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        37 gifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      .|.+.|.+..  +|.|..|||+.+|++      ... .+++|..|...|.+...
T Consensus         4 ~Il~~i~~~~--~p~~T~eiA~~~gls------~~~-aR~yL~~Le~eG~V~~~   48 (62)
T PF04703_consen    4 KILEYIKEQN--GPLKTREIADALGLS------IYQ-ARYYLEKLEKEGKVERS   48 (62)
T ss_dssp             CHHHHHHHHT--S-EEHHHHHHHHTS-------HHH-HHHHHHHHHHCTSEEEE
T ss_pred             HHHHHHHHcC--CCCCHHHHHHHhCCC------HHH-HHHHHHHHHHCCCEEEe
Confidence            3566666632  799999999999997      445 99999999999999853

>PRK13255 thiopurine S-methyltransferase; Reviewed

Probab=94.08  E-value=0.11  Score=43.14  Aligned_cols=39  Identities=5%  Similarity=0.058  Sum_probs=32.8

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDA  232 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a  232 (244)
                      ....+|+|+|||.|..+..|+++  +.+++.+|+ |..++.+
T Consensus        36 ~~~~rvL~~gCG~G~da~~LA~~--G~~V~avD~s~~Ai~~~   75 (218)
T PRK13255         36 PAGSRVLVPLCGKSLDMLWLAEQ--GHEVLGVELSELAVEQF   75 (218)
T ss_pred             CCCCeEEEeCCCChHhHHHHHhC--CCeEEEEccCHHHHHHH
Confidence            44579999999999999999875  778999999 6767754

>PF05401 NodS: Nodulation protein S (NodS); InterPro: IPR008715 This entry consists of nodulation S (NodS) proteins

Probab=94.04  E-value=0.043  Score=44.66  Aligned_cols=52  Identities=15%  Similarity=0.355  Sum_probs=40.1

Q ss_pred             hcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC----CCCceee
Q 041256          187 SYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS----YPGTLFI  241 (244)
Q Consensus       187 ~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~----~~~i~~~  241 (244)
                      .+| -....++++||||.|.+...|+.++-  +.++.|. |..++.|++    .++|+++
T Consensus        38 aLp-~~ry~~alEvGCs~G~lT~~LA~rCd--~LlavDis~~Al~~Ar~Rl~~~~~V~~~   94 (201)
T PF05401_consen   38 ALP-RRRYRRALEVGCSIGVLTERLAPRCD--RLLAVDISPRALARARERLAGLPHVEWI   94 (201)
T ss_dssp             HHT-TSSEEEEEEE--TTSHHHHHHGGGEE--EEEEEES-HHHHHHHHHHTTT-SSEEEE
T ss_pred             hcC-ccccceeEecCCCccHHHHHHHHhhC--ceEEEeCCHHHHHHHHHhcCCCCCeEEE
Confidence            456 56778999999999999999999963  5788898 899999875    4677765

The products of the rhizobial nodulation genes are involved in the biosynthesis of lipochitin oligosaccharides (LCOs), which are host-specific signal molecules required for nodule formation. NodS is an S-adenosyl-L-methionine (SAM)-dependent methyltransferase involved in N methylation of LCOs. NodS uses N-deacetylated chitooligosaccharides, the products of the NodBC proteins, as its methyl acceptors [].; GO: 0008757 S-adenosylmethionine-dependent methyltransferase activity, 0009312 oligosaccharide biosynthetic process, 0009877 nodulation; PDB: 3OFK_D 3OFJ_A.

>KOG1270 consensus Methyltransferases [Coenzyme transport and metabolism]

Probab=93.99  E-value=0.036  Score=47.01  Aligned_cols=38  Identities=21%  Similarity=0.201  Sum_probs=32.5

Q ss_pred             ceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          195 KKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       195 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+|||||||.|.++.-|++..  ..++..|. +..|+.|++
T Consensus        91 ~~ilDvGCGgGLLSepLArlg--a~V~GID~s~~~V~vA~~  129 (282)
T KOG1270|consen   91 MKILDVGCGGGLLSEPLARLG--AQVTGIDASDDMVEVANE  129 (282)
T ss_pred             ceEEEeccCccccchhhHhhC--CeeEeecccHHHHHHHHH
Confidence            679999999999999999986  55777888 788888875

>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR

Probab=93.99  E-value=0.14  Score=37.98  Aligned_cols=65  Identities=12%  Similarity=0.175  Sum_probs=47.1

Q ss_pred             HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCccccccc
Q 041256           34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSAYFV  108 (244)
Q Consensus        34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~~l~  108 (244)
                      .+..++..|...   +++|..+||+.++++      ... +.++++-|...|++++.+...+.   .+.+|+.+..+.
T Consensus        29 ~q~~iL~~l~~~---~~~t~~ela~~~~~~------~~t-vs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT~~G~~~~   96 (118)
T TIGR02337        29 QQWRILRILAEQ---GSMEFTQLANQACIL------RPS-LTGILARLERDGLVTRLKASNDQRRVYISLTPKGQALY   96 (118)
T ss_pred             HHHHHHHHHHHc---CCcCHHHHHHHhCCC------chh-HHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHH
Confidence            344477777765   689999999999997      345 99999999999999963211122   477777665443

This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.

>PRK10909 rsmD 16S rRNA m(2)G966-methyltransferase; Provisional

Probab=93.98  E-value=0.078  Score=43.43  Aligned_cols=40  Identities=15%  Similarity=0.110  Sum_probs=32.0

Q ss_pred             cceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+++|+|||+|.++.+.+.+.. .+++.+|. |.+++.+++
T Consensus        54 ~~~vLDl~~GsG~l~l~~lsr~a-~~V~~vE~~~~a~~~a~~   94 (199)
T PRK10909         54 DARCLDCFAGSGALGLEALSRYA-AGATLLEMDRAVAQQLIK   94 (199)
T ss_pred             CCEEEEcCCCccHHHHHHHHcCC-CEEEEEECCHHHHHHHHH
Confidence            46899999999999998776654 57888887 777777654

>PRK05134 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional

Probab=93.94  E-value=0.1  Score=43.42  Aligned_cols=39  Identities=26%  Similarity=0.199  Sum_probs=30.4

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~  233 (244)
                      ...+|+|||||.|.++..+.+.  ..+++..|. |..++.++
T Consensus        48 ~~~~vLdiG~G~G~~~~~l~~~--~~~v~~iD~s~~~~~~a~   87 (233)
T PRK05134         48 FGKRVLDVGCGGGILSESMARL--GADVTGIDASEENIEVAR   87 (233)
T ss_pred             CCCeEEEeCCCCCHHHHHHHHc--CCeEEEEcCCHHHHHHHH
Confidence            4578999999999999988876  456888887 55555554

>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR

Probab=93.91  E-value=0.12  Score=42.28  Aligned_cols=62  Identities=16%  Similarity=0.231  Sum_probs=45.6

Q ss_pred             cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceee-cCCce----eecCcccccc
Q 041256           36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFV-DGQRL----YSLAPVSAYF  107 (244)
Q Consensus        36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~-~~~~~----y~~t~~s~~l  107 (244)
                      ..|+..|...   ++.|..+||+.++++      +.. +.+.|+.|...|++++... .+.|+    |++|+.+..+
T Consensus         4 ~~IL~~L~~~---~~~t~~eLA~~lgis------~~t-V~~~L~~Le~~GlV~r~~~~~~~gRp~~~y~LT~~G~~~   70 (203)
T TIGR02702         4 EDILSYLLKQ---GQATAAALAEALAIS------PQA-VRRHLKDLETEGLIEYEAVVQGMGRPQYHYQLSRQGREQ   70 (203)
T ss_pred             HHHHHHHHHc---CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCeEEeecccCCCCCceEEEECcchhhh
Confidence            3467777765   689999999999997      456 9999999999999986311 11222    6777766533

All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.

>PF07381 DUF1495: Winged helix DNA-binding domain (DUF1495); InterPro: IPR010863 This family consists of several hypothetical archaeal proteins of around 110 residues in length

Probab=93.79  E-value=0.11  Score=36.81  Aligned_cols=68  Identities=19%  Similarity=0.176  Sum_probs=48.1

Q ss_pred             HHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHH----------HHhhCCcc-cceeecCCceeec
Q 041256           32 AVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLR----------LLVSYNAL-HCSFVDGQRLYSL  100 (244)
Q Consensus        32 ~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr----------~L~~~gll-~~~~~~~~~~y~~  100 (244)
                      .=++..|+..|.+..+ .+.++.|||..++++      +.. +.--|+          .|+.+|++ .+....+...|++
T Consensus         8 S~~R~~vl~~L~~~yp-~~~~~~eIar~v~~~------~sn-V~GaL~G~g~rY~~e~SLv~lGLV~~~~~~~g~k~Y~l   79 (90)
T PF07381_consen    8 SKVRKKVLEYLCSIYP-EPAYPSEIARSVGSD------YSN-VLGALRGDGKRYNKEDSLVGLGLVEEEEEKGGFKYYRL   79 (90)
T ss_pred             HHHHHHHHHHHHHcCC-CcCCHHHHHHHHCCC------HHH-HHHHHhcCCCCcCcchhHHHcCCeeEeeecCCeeEEEe
Confidence            5567788999998843 589999999999997      333 444443          58899999 4322233457999


Q ss_pred             Ccccccc
Q 041256          101 APVSAYF  107 (244)
Q Consensus       101 t~~s~~l  107 (244)
                      |+.+..+
T Consensus        80 T~~G~~~   86 (90)
T PF07381_consen   80 TEKGKRI   86 (90)
T ss_pred             ChhhhhH
Confidence            8876543

The function of this family is unknown, although one sequence (Q8U3W1 from SWISSPROT) is described as a putative HTH transcription regulator.

>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein

Probab=93.73  E-value=0.1  Score=36.92  Aligned_cols=45  Identities=22%  Similarity=0.339  Sum_probs=38.0

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      ++.|+..|...   ++.|..+||+.++++      ... +.+.++-|...|++..
T Consensus        12 ~~~il~~l~~~---~~~~~~~la~~~~~s------~~~-i~~~l~~L~~~g~v~~   56 (101)
T smart00347       12 QFLVLRILYEE---GPLSVSELAKRLGVS------PST-VTRVLDRLEKKGLIRR   56 (101)
T ss_pred             HHHHHHHHHHc---CCcCHHHHHHHHCCC------chh-HHHHHHHHHHCCCeEe
Confidence            55677788765   579999999999997      445 9999999999999985

>PRK14902 16S rRNA methyltransferase B; Provisional

Probab=93.60  E-value=0.089  Score=48.39  Aligned_cols=50  Identities=14%  Similarity=0.030  Sum_probs=39.7

Q ss_pred             HHhhcCCCCCcceEEEecCCccHHHHHHHHHC-CCCeEEEccc-hHHhhhCCC
Q 041256          184 VLESYKGFEHVKKLVDVGGGLGITLNMIISKY-PHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       184 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      +...++ ..+..+|+|+|||.|..+..+++.. |..+++.+|+ +..++.+++
T Consensus       242 v~~~l~-~~~g~~VLDlgaG~G~~t~~la~~~~~~~~v~avDi~~~~l~~~~~  293 (444)
T PRK14902        242 VAPALD-PKGGDTVLDACAAPGGKTTHIAELLKNTGKVVALDIHEHKLKLIEE  293 (444)
T ss_pred             HHHHhC-CCCCCEEEEeCCCCCHHHHHHHHHhCCCCEEEEEeCCHHHHHHHHH
Confidence            334444 4556899999999999999999986 6789999999 777776654

>PF10294 Methyltransf_16: Putative methyltransferase; InterPro: IPR019410 There are a number of unidentified genes that have a high probability of coding for methyltransferases

Probab=93.59  E-value=0.098  Score=41.76  Aligned_cols=42  Identities=14%  Similarity=0.158  Sum_probs=32.3

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAP  233 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~  233 (244)
                      ...++|+++|+|.|..++.+++.++..++++-|.|++++..+
T Consensus        44 ~~~~~VLELGaG~Gl~gi~~a~~~~~~~Vv~TD~~~~l~~l~   85 (173)
T PF10294_consen   44 FRGKRVLELGAGTGLPGIAAAKLFGAARVVLTDYNEVLELLR   85 (173)
T ss_dssp             TTTSEEEETT-TTSHHHHHHHHT-T-SEEEEEE-S-HHHHHH
T ss_pred             cCCceEEEECCccchhHHHHHhccCCceEEEeccchhhHHHH
Confidence            456899999999999999999998888899999988877654

They make up approximately 0.6-1.6% of the genes in the yeast, human, mouse, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana, and Escherichia coli genomes []. This entry represents putative nicotinamide N-methyltransferases involved in rDNA silencing and in lifespan determination. ; PDB: 3BZB_A.

>PF01135 PCMT: Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT); InterPro: IPR000682 Protein-L-isoaspartate(D-aspartate) O-methyltransferase (2

Probab=93.59  E-value=0.11  Score=42.84  Aligned_cols=51  Identities=16%  Similarity=0.346  Sum_probs=37.2

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHC-CCCeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKY-PHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+++.++ .....+|+|||+|+|+++.-++... +.-+++.+|. |..++.|++
T Consensus        63 ~~l~~L~-l~pg~~VLeIGtGsGY~aAlla~lvg~~g~Vv~vE~~~~l~~~A~~  115 (209)
T PF01135_consen   63 RMLEALD-LKPGDRVLEIGTGSGYQAALLAHLVGPVGRVVSVERDPELAERARR  115 (209)
T ss_dssp             HHHHHTT-C-TT-EEEEES-TTSHHHHHHHHHHSTTEEEEEEESBHHHHHHHHH
T ss_pred             HHHHHHh-cCCCCEEEEecCCCcHHHHHHHHhcCccceEEEECccHHHHHHHHH
Confidence            4566676 7778999999999999999888864 4445677775 888888765

1.1.77 from EC) (PCMT) [] (which is also known as L-isoaspartyl protein carboxyl methyltransferase) is an enzyme that catalyses the transfer of a methyl group from S-adenosylmethionine to the free carboxyl groups of D-aspartyl or L-isoaspartyl residues in a variety of peptides and proteins. The enzyme does not act on normal L-aspartyl residues L-isoaspartyl and D-aspartyl are the products of the spontaneous deamidation and/or isomerisation of normal L-aspartyl and L-asparaginyl residues in proteins. PCMT plays a role in the repair and/or degradation of these damaged proteins; the enzymatic methyl esterification of the abnormal residues can lead to their conversion to normal L-aspartyl residues. The SAM domain is present in most of these proteins.; GO: 0004719 protein-L-isoaspartate (D-aspartate) O-methyltransferase activity, 0006464 protein modification process; PDB: 3LBF_A 1DL5_B 1JG3_B 1JG2_A 1JG1_A 1JG4_A 2YXE_A 2PBF_B 1VBF_C 1R18_A ....

>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors

Probab=93.49  E-value=0.2  Score=33.03  Aligned_cols=56  Identities=20%  Similarity=0.334  Sum_probs=40.2

Q ss_pred             cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCc
Q 041256           36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAP  102 (244)
Q Consensus        36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~  102 (244)
                      ..|+..+..    ++.+..||++.++++      ... +.+.|+.|...|++..........|+.++
T Consensus        10 ~~il~~l~~----~~~~~~ei~~~~~i~------~~~-i~~~l~~L~~~g~i~~~~~~~~~~~~~~~   65 (78)
T cd00090          10 LRILRLLLE----GPLTVSELAERLGLS------QST-VSRHLKKLEEAGLVESRREGRRVYYSLTD   65 (78)
T ss_pred             HHHHHHHHH----CCcCHHHHHHHHCcC------HhH-HHHHHHHHHHCCCeEEEEeccEEEEEeCC
Confidence            345666666    349999999999996      445 99999999999999853211124455554

ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.

>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial

Probab=93.47  E-value=0.11  Score=39.36  Aligned_cols=46  Identities=26%  Similarity=0.269  Sum_probs=36.4

Q ss_pred             CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCc
Q 041256           49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAP  102 (244)
Q Consensus        49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~  102 (244)
                      ++.|+.|||+.++++      +.. +.++|+.|...|++.... ...+.|.+..
T Consensus        24 ~~~s~~eia~~l~is------~~~-v~~~l~~L~~~Gli~~~~-g~~ggy~l~~   69 (130)
T TIGR02944        24 QPYSAAEIAEQTGLN------APT-VSKILKQLSLAGIVTSKR-GVEGGYTLAR   69 (130)
T ss_pred             CCccHHHHHHHHCcC------HHH-HHHHHHHHHHCCcEEecC-CCCCChhhcC
Confidence            689999999999997      567 999999999999997421 1235677644

The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.

>PF01564 Spermine_synth: Spermine/spermidine synthase; InterPro: IPR001045 Synonym(s): Spermidine aminopropyltransferase A group of polyamine biosynthetic enzymes involved in the fifth (last) step in the biosynthesis of spermidine from arginine and methionine which includes; spermidine synthase (2

Probab=93.47  E-value=0.06  Score=45.58  Aligned_cols=43  Identities=23%  Similarity=0.302  Sum_probs=36.2

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      +++++|+=||||.|..+.++++..|-.+.+++|+ |.|++.+++
T Consensus        75 ~~p~~VLiiGgG~G~~~~ell~~~~~~~i~~VEiD~~Vv~~a~~  118 (246)
T PF01564_consen   75 PNPKRVLIIGGGDGGTARELLKHPPVESITVVEIDPEVVELARK  118 (246)
T ss_dssp             SST-EEEEEESTTSHHHHHHTTSTT-SEEEEEES-HHHHHHHHH
T ss_pred             CCcCceEEEcCCChhhhhhhhhcCCcceEEEEecChHHHHHHHH
Confidence            4679999999999999999997777778999999 999998864

5.1.16 from EC), spermine synthase (2.5.1.22 from EC) and putrescine N-methyltransferase (2.1.1.53 from EC) []. The Thermotoga maritima spermidine synthase monomer consists of two domains: an N-terminal domain composed of six beta-strands, and a Rossmann-like C- terminal domain []. The larger C-terminal catalytic core domain consists of a seven-stranded beta-sheet flanked by nine alpha helices. This domain resembles a topology observed in a number of nucleotide and dinucleotide-binding enzymes, and in S-adenosyl-L-methionine (AdoMet)- dependent methyltransferase (MTases) [].; GO: 0003824 catalytic activity; PDB: 2E5W_C 2ZSU_E 2O0L_B 2O05_B 2O06_B 2O07_B 3RW9_B 2PWP_A 2HTE_B 3RIE_B ....

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

Probab=93.39  E-value=0.1  Score=47.81  Aligned_cols=47  Identities=17%  Similarity=0.249  Sum_probs=37.0

Q ss_pred             HhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          185 LESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       185 ~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+... ..+..+|+|+|||.|.++..+++...  +++.+|. |..++.|++
T Consensus       285 ~~~l~-~~~~~~vLDl~cG~G~~sl~la~~~~--~V~~vE~~~~av~~a~~  332 (431)
T TIGR00479       285 LEALE-LQGEELVVDAYCGVGTFTLPLAKQAK--SVVGIEVVPESVEKAQQ  332 (431)
T ss_pred             HHHhc-cCCCCEEEEcCCCcCHHHHHHHHhCC--EEEEEEcCHHHHHHHHH
Confidence            33334 45567999999999999999998753  6788888 888888775

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.

>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism

Probab=93.38  E-value=0.19  Score=32.33  Aligned_cols=42  Identities=19%  Similarity=0.331  Sum_probs=36.5

Q ss_pred             hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      |.+.|.+.   +..|++|||+.++++      +.- ++|=|..|...|++.+
T Consensus         5 Il~~l~~~---~~~s~~ela~~~~VS------~~T-iRRDl~~L~~~g~i~r   46 (57)
T PF08220_consen    5 ILELLKEK---GKVSVKELAEEFGVS------EMT-IRRDLNKLEKQGLIKR   46 (57)
T ss_pred             HHHHHHHc---CCEEHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEE
Confidence            56778775   699999999999997      445 9999999999999985

This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular

>PF08461 HTH_12: Ribonuclease R winged-helix domain; InterPro: IPR013668 This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea

Probab=93.36  E-value=0.13  Score=34.24  Aligned_cols=61  Identities=11%  Similarity=0.196  Sum_probs=43.7

Q ss_pred             hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcccc
Q 041256           38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSA  105 (244)
Q Consensus        38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~  105 (244)
                      |.+.|.+.+  +|++..+|++.++..+.+-. ++. ++|.|++|...|++.+   .+.+.+.+|+.+.
T Consensus         3 IL~~L~~~~--~P~g~~~l~~~L~~~g~~~s-e~a-vRrrLr~me~~Glt~~---~g~~G~~iT~~G~   63 (66)
T PF08461_consen    3 ILRILAESD--KPLGRKQLAEELKLRGEELS-EEA-VRRRLRAMERDGLTRK---VGRQGRIITEKGL   63 (66)
T ss_pred             HHHHHHHcC--CCCCHHHHHHHHHhcChhhh-HHH-HHHHHHHHHHCCCccc---cCCcccccCHHHH
Confidence            567788775  79999999999976522221 356 9999999999997774   3334456776543

>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=93.34  E-value=0.12  Score=32.87  Aligned_cols=32  Identities=16%  Similarity=0.459  Sum_probs=28.1

Q ss_pred             HHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCC
Q 041256           26 LPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLK   63 (244)
Q Consensus        26 ~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~   63 (244)
                      +-.+|.+|+++|-||.=.      ..|..|||+.+|++
T Consensus         5 Q~e~L~~A~~~GYfd~PR------~~tl~elA~~lgis   36 (53)
T PF04967_consen    5 QREILKAAYELGYFDVPR------RITLEELAEELGIS   36 (53)
T ss_pred             HHHHHHHHHHcCCCCCCC------cCCHHHHHHHhCCC
Confidence            457899999999999753      58999999999997

This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.

>KOG3010 consensus Methyltransferase [General function prediction only]

Probab=93.31  E-value=0.085  Score=44.21  Aligned_cols=44  Identities=27%  Similarity=0.273  Sum_probs=33.9

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCCCCCc
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPSYPGT  238 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~~~~i  238 (244)
                      ..+.++|||||+|..++.++..|-+  +|..|. +..++.+++.+++
T Consensus        33 ~h~~a~DvG~G~Gqa~~~iae~~k~--VIatD~s~~mL~~a~k~~~~   77 (261)
T KOG3010|consen   33 GHRLAWDVGTGNGQAARGIAEHYKE--VIATDVSEAMLKVAKKHPPV   77 (261)
T ss_pred             CcceEEEeccCCCcchHHHHHhhhh--heeecCCHHHHHHhhcCCCc
Confidence            4469999999999888888888766  566787 7778888775443

>COG4976 Predicted methyltransferase (contains TPR repeat) [General function prediction only]

Probab=93.19  E-value=0.083  Score=44.07  Aligned_cols=64  Identities=14%  Similarity=0.346  Sum_probs=41.4

Q ss_pred             HHHHHHHHHhcchhhHHH----HHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhC
Q 041256          166 NDVFNNGMLSHTSIVMEK----VLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDA  232 (244)
Q Consensus       166 ~~~f~~aM~~~~~~~~~~----~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a  232 (244)
                      +++|.+.....-.+..|.    .+...+ ...+++|+|+|||+|..+.+|...--.++|  +|+ ...++.|
T Consensus        95 Ae~Fd~~LVdkL~Y~vP~~l~emI~~~~-~g~F~~~lDLGCGTGL~G~~lR~~a~~ltG--vDiS~nMl~kA  163 (287)
T COG4976          95 AERFDHILVDKLGYSVPELLAEMIGKAD-LGPFRRMLDLGCGTGLTGEALRDMADRLTG--VDISENMLAKA  163 (287)
T ss_pred             HHHHHHHHHHHhcCccHHHHHHHHHhcc-CCccceeeecccCcCcccHhHHHHHhhccC--CchhHHHHHHH
Confidence            457777665544333333    333444 445899999999999999998887666555  566 3344444

>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein

Probab=93.12  E-value=0.18  Score=41.33  Aligned_cols=58  Identities=24%  Similarity=0.290  Sum_probs=45.1

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcc
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPV  103 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~  103 (244)
                      ++.+...|.+.   ++.+..+||+.++++      +.. +.|.|..|...|++.+... ....|.+|+.
T Consensus       145 ~~~IL~~l~~~---g~~s~~eia~~l~is------~st-v~r~L~~Le~~GlI~r~~~-r~~~~~lT~~  202 (203)
T TIGR01884       145 ELKVLEVLKAE---GEKSVKNIAKKLGKS------LST-ISRHLRELEKKGLVEQKGR-KGKRYSLTKL  202 (203)
T ss_pred             HHHHHHHHHHc---CCcCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEEEcC-CccEEEeCCC
Confidence            44567777764   579999999999997      455 9999999999999996421 3456888765

Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.

>TIGR01983 UbiG ubiquinone biosynthesis O-methyltransferase

Probab=93.09  E-value=0.099  Score=43.03  Aligned_cols=39  Identities=21%  Similarity=0.130  Sum_probs=30.7

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~  233 (244)
                      ...+|+|+|||.|.++..+++..+  +++..|+ |..++.++
T Consensus        45 ~~~~vLdlG~G~G~~~~~l~~~~~--~v~~iD~s~~~~~~a~   84 (224)
T TIGR01983        45 FGLRVLDVGCGGGLLSEPLARLGA--NVTGIDASEENIEVAK   84 (224)
T ss_pred             CCCeEEEECCCCCHHHHHHHhcCC--eEEEEeCCHHHHHHHH
Confidence            357999999999999999988765  4888888 55666554

This model represents an O-methyltransferase believed to act at two points in the ubiquinone biosynthetic pathway in bacteria (UbiG) and fungi (COQ3). A separate methylase (MenG/UbiE) catalyzes the single C-methylation step. The most commonly used names for genes in this family do not indicate whether this gene is an O-methyl, or C-methyl transferase.

>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure

Probab=93.09  E-value=0.12  Score=36.49  Aligned_cols=60  Identities=12%  Similarity=0.185  Sum_probs=42.9

Q ss_pred             hhhHHhhcCCCCCCCHHHHHHhC-CCCCCCCcchhccHHHHHHHHhhCCcccceeecCC---ceeecCccccccc
Q 041256           38 VFEIISKAGPGAKLSVAEIVAQI-PLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQ---RLYSLAPVSAYFV  108 (244)
Q Consensus        38 ifd~L~~~~~~g~~t~~eLA~~~-~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~---~~y~~t~~s~~l~  108 (244)
                      |...|..    |+....||.+.+ +++      +.. |.+-|+.|...|++++......   -.|++|+.+..|.
T Consensus        10 IL~~l~~----g~~rf~el~~~l~~is------~~~-L~~~L~~L~~~GLv~r~~~~~~p~~v~Y~LT~~G~~l~   73 (90)
T PF01638_consen   10 ILRALFQ----GPMRFSELQRRLPGIS------PKV-LSQRLKELEEAGLVERRVYPEVPPRVEYSLTEKGKELL   73 (90)
T ss_dssp             HHHHHTT----SSEEHHHHHHHSTTS-------HHH-HHHHHHHHHHTTSEEEEEESSSSSEEEEEE-HHHHHHH
T ss_pred             HHHHHHh----CCCcHHHHHHhcchhH------HHH-HHHHHHHHHHcchhhcccccCCCCCCccCCCcCHHHHH
Confidence            4455655    699999999999 786      556 9999999999999986422111   2488888776554

The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.

>PRK01544 bifunctional N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase/tRNA (m7G46) methyltransferase; Reviewed

Probab=93.05  E-value=0.11  Score=48.59  Aligned_cols=33  Identities=18%  Similarity=0.238  Sum_probs=31.1

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL  225 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  225 (244)
                      +...+||||||.|.++..+++++|+...+.+|.
T Consensus       347 ~~p~~lEIG~G~G~~~~~~A~~~p~~~~iGiE~  379 (506)
T PRK01544        347 KRKVFLEIGFGMGEHFINQAKMNPDALFIGVEV  379 (506)
T ss_pred             CCceEEEECCCchHHHHHHHHhCCCCCEEEEEe
Confidence            468999999999999999999999999999997

>PF01728 FtsJ: FtsJ-like methyltransferase; InterPro: IPR002877 RrmJ (FtsJ) is a well conserved heat shock protein present in prokaryotes, archaea, and eukaryotes

Probab=92.96  E-value=0.14  Score=40.93  Aligned_cols=47  Identities=19%  Similarity=0.251  Sum_probs=36.7

Q ss_pred             HHHHhhcCCCC--CcceEEEecCCccHHHHHHHHHC-CCCeEEEccchHH
Q 041256          182 EKVLESYKGFE--HVKKLVDVGGGLGITLNMIISKY-PHIKGINYDLPYV  228 (244)
Q Consensus       182 ~~~~~~~~~~~--~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dlp~v  228 (244)
                      .++.+.|+.++  +..++||+|++.|.++..++++. +..+++.+|+...
T Consensus        10 ~ei~~~~~~~~~~~~~~vlDlG~aPGGws~~~~~~~~~~~~v~avDl~~~   59 (181)
T PF01728_consen   10 YEIDEKFKIFKPGKGFTVLDLGAAPGGWSQVLLQRGGPAGRVVAVDLGPM   59 (181)
T ss_dssp             HHHHHTTSSS-TTTTEEEEEET-TTSHHHHHHHTSTTTEEEEEEEESSST
T ss_pred             HHHHHHCCCCCcccccEEEEcCCcccceeeeeeecccccceEEEEecccc
Confidence            45666666333  45999999999999999999998 7888999998654

RrmJ is responsible for methylating 23 S rRNA at position U2552 in the aminoacyl (A)1-site of the ribosome []. U2552 is one of the five universally conserved A-loop residues and has been shown to be methylated at the ribose 2'-OH group in the majority of organisms investigated so far. This suggests that this modification plays an important role in the A-loop function. RrmJ recognises its methylation target only when the 23 S rRNA is present in 50 S ribosomal subunits. This suggests that the RrmJ-mediated methylation must occur late in the maturation process of the ribosome. This is in contrast to other known 23 S rRNA modifications that occur in earlier maturation steps. The 1.5 A crystal structure of RrmJ in complex with its cofactor S-adenosylmethionine revealed that RrmJ has a methyltransferase fold. The active site of RrmJ appears to be formed by a catalytic triad consisting of two lysine residues and the negatively charged aspartate residue. Another highly conserved glutamate residue that is present in the active site of RrmJ appears to play only a minor role in the methyltransfer reaction in vivo []. ; GO: 0003676 nucleic acid binding, 0008168 methyltransferase activity, 0032259 methylation; PDB: 3GCZ_A 2PLW_A 2NYU_A 2OXT_C 3EMD_A 3ELY_A 3ELW_A 3ELU_A 3ELD_A 3EMB_A ....

>PRK03902 manganese transport transcriptional regulator; Provisional

Probab=92.94  E-value=0.19  Score=38.65  Aligned_cols=49  Identities=14%  Similarity=0.175  Sum_probs=40.4

Q ss_pred             CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcccccc
Q 041256           49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYF  107 (244)
Q Consensus        49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l  107 (244)
                      ++.++.+||+.++++      +.. +.+.++.|...|++.+.   ..+.|++|+.+..+
T Consensus        21 ~~~~~~ela~~l~vs------~~s-vs~~l~~L~~~Gli~~~---~~~~i~LT~~G~~~   69 (142)
T PRK03902         21 GYARVSDIAEALSVH------PSS-VTKMVQKLDKDEYLIYE---KYRGLVLTPKGKKI   69 (142)
T ss_pred             CCcCHHHHHHHhCCC------hhH-HHHHHHHHHHCCCEEEe---cCceEEECHHHHHH
Confidence            689999999999997      445 99999999999999852   24668998887644

>TIGR00122 birA_repr_reg BirA biotin operon repressor domain

Probab=92.75  E-value=0.26  Score=32.85  Aligned_cols=56  Identities=11%  Similarity=0.221  Sum_probs=41.8

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccc
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVS  104 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s  104 (244)
                      ++.++..|.+    ++.|..+||+.+|++      ... +.+-++.|...|+....  . ...|...+..
T Consensus         2 ~~~il~~L~~----~~~~~~eLa~~l~vS------~~t-v~~~l~~L~~~g~~i~~--~-~~g~~l~~~~   57 (69)
T TIGR00122         2 PLRLLALLAD----NPFSGEKLGEALGMS------RTA-VNKHIQTLREWGVDVLT--V-GKGYRLPPPI   57 (69)
T ss_pred             hHHHHHHHHc----CCcCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCeEEe--c-CCceEecCcc
Confidence            3456777876    588999999999997      445 99999999999996532  2 3456665543

This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.

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

Probab=92.75  E-value=0.12  Score=46.43  Aligned_cols=39  Identities=15%  Similarity=0.037  Sum_probs=32.4

Q ss_pred             cceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+|+|+|||+|.++..++..  ..+++.+|. |..++.+++
T Consensus       234 ~~~vLDL~cG~G~~~l~la~~--~~~v~~vE~~~~av~~a~~  273 (374)
T TIGR02085       234 VTQMWDLFCGVGGFGLHCAGP--DTQLTGIEIESEAIACAQQ  273 (374)
T ss_pred             CCEEEEccCCccHHHHHHhhc--CCeEEEEECCHHHHHHHHH
Confidence            368999999999999999854  467888997 888887764

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.

>PHA00738 putative HTH transcription regulator

Probab=92.66  E-value=0.26  Score=36.00  Aligned_cols=60  Identities=15%  Similarity=0.115  Sum_probs=44.7

Q ss_pred             HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcc
Q 041256           34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPV  103 (244)
Q Consensus        34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~  103 (244)
                      .++.|++.|.+.   ++.++.+|++.++++      ... +-+-|+.|...|++....+...-.|++++-
T Consensus        13 tRr~IL~lL~~~---e~~~V~eLae~l~lS------Qpt-VS~HLKvLreAGLV~srK~Gr~vyY~Ln~~   72 (108)
T PHA00738         13 LRRKILELIAEN---YILSASLISHTLLLS------YTT-VLRHLKILNEQGYIELYKEGRTLYAKIREN   72 (108)
T ss_pred             HHHHHHHHHHHc---CCccHHHHHHhhCCC------HHH-HHHHHHHHHHCCceEEEEECCEEEEEECCC
Confidence            467788889873   479999999999997      345 999999999999999643211224555553

>PRK11050 manganese transport regulator MntR; Provisional

Probab=92.62  E-value=0.76  Score=35.85  Aligned_cols=57  Identities=14%  Similarity=0.243  Sum_probs=43.5

Q ss_pred             hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcccccc
Q 041256           38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYF  107 (244)
Q Consensus        38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l  107 (244)
                      |...+...   ++.+..+||+.++++      ... +.+.++.|...|++...  . ...+.+|+.+..+
T Consensus        42 I~~~l~~~---~~~t~~eLA~~l~is------~st-Vsr~l~~Le~~GlI~r~--~-~~~v~LT~~G~~l   98 (152)
T PRK11050         42 IADLIAEV---GEARQVDIAARLGVS------QPT-VAKMLKRLARDGLVEMR--P-YRGVFLTPEGEKL   98 (152)
T ss_pred             HHHHHHhc---CCCCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEEe--c-CCceEECchHHHH
Confidence            55566653   689999999999997      456 99999999999999852  2 3457777766544

>TIGR00095 RNA methyltransferase, RsmD family

Probab=92.39  E-value=0.13  Score=41.77  Aligned_cols=40  Identities=15%  Similarity=0.036  Sum_probs=32.9

Q ss_pred             cceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+++|++||+|.++.+++.+... +++.+|. +.+++.+++
T Consensus        50 g~~vLDLfaGsG~lglea~srga~-~v~~vE~~~~a~~~~~~   90 (189)
T TIGR00095        50 GAHLLDVFAGSGLLGEEALSRGAK-VAFLEEDDRKANQTLKE   90 (189)
T ss_pred             CCEEEEecCCCcHHHHHHHhCCCC-EEEEEeCCHHHHHHHHH
Confidence            378999999999999999999774 6788887 677766653

This model represents a family of uncharacterized bacterial proteins. Members are present in nearly every complete bacterial genome, always in a single copy. PSI-BLAST analysis shows homology to several families of SAM-dependent methyltransferases, including ribosomal RNA adenine dimethylases.

>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed

Probab=92.30  E-value=0.22  Score=39.02  Aligned_cols=46  Identities=15%  Similarity=0.095  Sum_probs=37.6

Q ss_pred             CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCc
Q 041256           49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAP  102 (244)
Q Consensus        49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~  102 (244)
                      ++.|..+||+..+++      +.+ |.++|..|...|++.-.. ...|.|+++.
T Consensus        23 ~~~s~~eIA~~~~is------~~~-L~kIl~~L~~aGlv~S~r-G~~GGy~La~   68 (153)
T PRK11920         23 KLSRIPEIARAYGVS------ELF-LFKILQPLVEAGLVETVR-GRNGGVRLGR   68 (153)
T ss_pred             CcCcHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEeec-CCCCCeeecC
Confidence            578999999999997      678 999999999999998532 2246788755

>PRK11014 transcriptional repressor NsrR; Provisional

Probab=92.23  E-value=0.28  Score=37.72  Aligned_cols=46  Identities=9%  Similarity=0.052  Sum_probs=36.4

Q ss_pred             CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCc
Q 041256           49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAP  102 (244)
Q Consensus        49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~  102 (244)
                      .+.+..+||+..|++      +.. ++++|+.|...|++...+ ...|.|.+..
T Consensus        24 ~~~s~~~ia~~~~is------~~~-vrk~l~~L~~~Glv~s~~-G~~GG~~l~~   69 (141)
T PRK11014         24 RMTSISEVTEVYGVS------RNH-MVKIINQLSRAGYVTAVR-GKNGGIRLGK   69 (141)
T ss_pred             CccCHHHHHHHHCcC------HHH-HHHHHHHHHhCCEEEEec-CCCCCeeecC
Confidence            478999999999997      567 999999999999998532 1135677653

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=92.21  E-value=0.21  Score=36.30  Aligned_cols=45  Identities=18%  Similarity=0.376  Sum_probs=39.0

Q ss_pred             HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCccc
Q 041256           34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALH   88 (244)
Q Consensus        34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~   88 (244)
                      .+..|+..|.+.   ++.|..+||+.+|++      +.. +.+.++.|...|++.
T Consensus         4 ~D~~il~~L~~~---~~~~~~~la~~l~~s------~~t-v~~~l~~L~~~g~i~   48 (108)
T smart00344        4 IDRKILEELQKD---ARISLAELAKKVGLS------PST-VHNRVKRLEEEGVIK   48 (108)
T ss_pred             HHHHHHHHHHHh---CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCee
Confidence            456788888875   689999999999997      556 999999999999998

AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=92.18  E-value=0.31  Score=29.98  Aligned_cols=42  Identities=21%  Similarity=0.337  Sum_probs=35.0

Q ss_pred             hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      +++.|.+.   ++.|..+|++.++++      +.. +.+.|..|...|++.+
T Consensus         5 il~~l~~~---~~~s~~~l~~~l~~s------~~t-v~~~l~~L~~~g~i~~   46 (53)
T smart00420        5 ILELLAQQ---GKVSVEELAELLGVS------EMT-IRRDLNKLEEQGLLTR   46 (53)
T ss_pred             HHHHHHHc---CCcCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEE
Confidence            45666654   579999999999997      455 9999999999999985

>KOG3115 consensus Methyltransferase-like protein [General function prediction only]

Probab=92.10  E-value=0.078  Score=43.36  Aligned_cols=32  Identities=22%  Similarity=0.419  Sum_probs=28.1

Q ss_pred             cceEEEecCCccHHHHHHHHHCCCCeEEEccc
Q 041256          194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL  225 (244)
Q Consensus       194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  225 (244)
                      -..++|||||-|.+++.|...||+--.+..++
T Consensus        61 kvefaDIGCGyGGLlv~Lsp~fPdtLiLGmEI   92 (249)
T KOG3115|consen   61 KVEFADIGCGYGGLLMKLAPKFPDTLILGMEI   92 (249)
T ss_pred             cceEEeeccCccchhhhccccCccceeeeehh
Confidence            47799999999999999999999977766665

>KOG3420 consensus Predicted RNA methylase [Translation, ribosomal structure and biogenesis]

Probab=92.06  E-value=0.11  Score=40.39  Aligned_cols=48  Identities=27%  Similarity=0.449  Sum_probs=36.0

Q ss_pred             HHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCe-EEEccc-hHHhhhCCC
Q 041256          184 VLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIK-GINYDL-PYVIKDAPS  234 (244)
Q Consensus       184 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~-~~v~Dl-p~vi~~a~~  234 (244)
                      +-+-|.+++ .+++.|+|||.|.++  +.-.+|..+ ++.+|+ |+.++.+.+
T Consensus        40 Ih~TygdiE-gkkl~DLgcgcGmLs--~a~sm~~~e~vlGfDIdpeALEIf~r   89 (185)
T KOG3420|consen   40 IHNTYGDIE-GKKLKDLGCGCGMLS--IAFSMPKNESVLGFDIDPEALEIFTR   89 (185)
T ss_pred             HHhhhcccc-CcchhhhcCchhhhH--HHhhcCCCceEEeeecCHHHHHHHhh
Confidence            334454344 389999999999999  556777765 688998 888888765

>KOG1499 consensus Protein arginine N-methyltransferase PRMT1 and related enzymes [Posttranslational modification, protein turnover, chaperones; Transcription; Signal transduction mechanisms]

Probab=91.90  E-value=0.15  Score=44.88  Aligned_cols=40  Identities=23%  Similarity=0.145  Sum_probs=33.6

Q ss_pred             cceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCC
Q 041256          194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPS  234 (244)
Q Consensus       194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~  234 (244)
                      .++|+|||||+|.+++-.+++. .-++..+|-.++++.|.+
T Consensus        61 dK~VlDVGcGtGILS~F~akAG-A~~V~aVe~S~ia~~a~~  100 (346)
T KOG1499|consen   61 DKTVLDVGCGTGILSMFAAKAG-ARKVYAVEASSIADFARK  100 (346)
T ss_pred             CCEEEEcCCCccHHHHHHHHhC-cceEEEEechHHHHHHHH
Confidence            4899999999999999988887 667888888877776654

>COG4742 Predicted transcriptional regulator [Transcription]

Probab=91.84  E-value=0.28  Score=41.75  Aligned_cols=67  Identities=12%  Similarity=0.219  Sum_probs=55.6

Q ss_pred             HHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccccccc
Q 041256           29 VMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFV  108 (244)
Q Consensus        29 ~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l~  108 (244)
                      .+...-+.+|+=.|.+    ||+|.+||-..++++      +.. +..=++-|...|++.+   . ++.|++|..+..++
T Consensus         9 if~SekRk~lLllL~e----gPkti~EI~~~l~vs------~~a-i~pqiKkL~~~~LV~~---~-~~~Y~LS~~G~iiv   73 (260)
T COG4742           9 LFLSEKRKDLLLLLKE----GPKTIEEIKNELNVS------SSA-ILPQIKKLKDKGLVVQ---E-GDRYSLSSLGKIIV   73 (260)
T ss_pred             HHccHHHHHHHHHHHh----CCCCHHHHHHHhCCC------cHH-HHHHHHHHhhCCCEEe---c-CCEEEecchHHHHH
Confidence            3445567788888888    799999999999997      456 8888899999999995   3 59999999999877


Q ss_pred             cC
Q 041256          109 RN  110 (244)
Q Consensus       109 ~~  110 (244)
                      ..
T Consensus        74 ~k   75 (260)
T COG4742          74 EK   75 (260)
T ss_pred             HH
Confidence            55

>PF00398 RrnaAD: Ribosomal RNA adenine dimethylase; InterPro: IPR001737 This family of proteins include rRNA adenine dimethylases (e

Probab=91.60  E-value=0.23  Score=42.38  Aligned_cols=58  Identities=16%  Similarity=0.346  Sum_probs=41.8

Q ss_pred             HHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC----CCCceee
Q 041256          181 MEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS----YPGTLFI  241 (244)
Q Consensus       181 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~----~~~i~~~  241 (244)
                      ...+++..+ ..+...|+|||.|.|.+...|++..  -+.+++|. |.-++..++    .++++++
T Consensus        19 ~~~Iv~~~~-~~~~~~VlEiGpG~G~lT~~L~~~~--~~v~~vE~d~~~~~~L~~~~~~~~~~~vi   81 (262)
T PF00398_consen   19 ADKIVDALD-LSEGDTVLEIGPGPGALTRELLKRG--KRVIAVEIDPDLAKHLKERFASNPNVEVI   81 (262)
T ss_dssp             HHHHHHHHT-CGTTSEEEEESSTTSCCHHHHHHHS--SEEEEEESSHHHHHHHHHHCTTCSSEEEE
T ss_pred             HHHHHHhcC-CCCCCEEEEeCCCCccchhhHhccc--CcceeecCcHhHHHHHHHHhhhcccceee
Confidence            456777776 6778999999999999999999998  55666665 554444432    3455544

g. KsgA) and the Erythromycin resistance methylases (Erm). The bacterial enzyme KsgA catalyses the transfer of a total of four methyl groups from S-adenosyl-l-methionine (S-AdoMet) to two adjacent adenosine bases in 16S rRNA. This enzyme and the resulting modified adenosine bases appear to be conserved in all species of eubacteria, eukaryotes, and archaea, and in eukaryotic organelles. Bacterial resistance to the aminoglycoside antibiotic kasugamycin involves inactivation of KsgA and resulting loss of the dimethylations, with modest consequences to the overall fitness of the organism. In contrast, the yeast ortholog, Dim1, is essential. In Saccharomyces cerevisiae (Baker's yeast), and presumably in other eukaryotes, the enzyme performs a vital role in pre-rRNA processing in addition to its methylating activity. The best conserved region in these enzymes is located in the N-terminal section and corresponds to a region that is probably involved in S-adenosyl methionine (SAM) binding domain. The crystal structure of KsgA from Escherichia coli has been solved to a resolution of 2.1A. It bears a strong similarity to the crystal structure of ErmC' from Bacillus stearothermophilus and a lesser similarity to the yeast mitochondrial transcription factor, sc-mtTFB []. The Erm family of RNA methyltransferases, which methylate a single adenosine base in 23S rRNA confer resistance to the MLS-B group of antibiotics. Despite their sequence similarity, the two enzyme families have strikingly different levels of regulation that remain to be elucidated. Other orthologs, of this family include the yeast and Homo sapiens (Human) mitochondrial transcription factors (MTF1 and h-mtTFB respectively), which are nuclear encoded []. Human-mtTFB is able to stimulate transcription in vitro independently of its S-adenosylmethionine binding and rRNA methyltransferase activity [].; GO: 0000179 rRNA (adenine-N6,N6-)-dimethyltransferase activity, 0008649 rRNA methyltransferase activity, 0000154 rRNA modification; PDB: 3FTF_A 3R9X_B 3FTE_A 3FTC_A 3FTD_A 3GRY_A 3FYC_A 3GRU_A 3FYD_A 3GRV_A ....

>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function

Probab=91.43  E-value=0.44  Score=35.80  Aligned_cols=49  Identities=18%  Similarity=0.337  Sum_probs=41.0

Q ss_pred             HHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           31 QAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        31 ~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      +..+...|.+.+.++   |.+|..+++..+|++      -.. +.+.++.|++.|-|..
T Consensus        10 r~eLk~rIvElVRe~---GRiTi~ql~~~TGas------R~T-vk~~lreLVa~G~l~~   58 (127)
T PF06163_consen   10 REELKARIVELVREH---GRITIKQLVAKTGAS------RNT-VKRYLRELVARGDLYR   58 (127)
T ss_pred             HHHHHHHHHHHHHHc---CCccHHHHHHHHCCC------HHH-HHHHHHHHHHcCCeEe
Confidence            345667788888887   799999999999996      234 9999999999998884

>TIGR00563 rsmB ribosomal RNA small subunit methyltransferase RsmB

Probab=91.34  E-value=0.24  Score=45.32  Aligned_cols=50  Identities=14%  Similarity=0.139  Sum_probs=39.7

Q ss_pred             HHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          184 VLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       184 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      +...++ .....+|+|+|+|.|..+..+++..|+.+.+..|. ++.++.+++
T Consensus       230 ~~~~L~-~~~g~~VLDlcag~G~kt~~la~~~~~~~v~a~D~~~~~l~~~~~  280 (426)
T TIGR00563       230 VATWLA-PQNEETILDACAAPGGKTTHILELAPQAQVVALDIHEHRLKRVYE  280 (426)
T ss_pred             HHHHhC-CCCCCeEEEeCCCccHHHHHHHHHcCCCeEEEEeCCHHHHHHHHH
Confidence            344455 45568999999999999999999998778899998 777766653

The seed alignment is built from bacterial sequences only. Eukaryotic homologs include Nop2, a protein required for processing pre-rRNA, that is likely also a rRNA methyltransferase, although the fine specificity may differ. Cutoff scores are set to avoid treating archaeal and eukaroytic homologs automatically as functionally equivalent, although they may have very similar roles.

>PF06080 DUF938: Protein of unknown function (DUF938); InterPro: IPR010342 This family consists of several hypothetical proteins from both prokaryotes and eukaryotes

Probab=91.31  E-value=0.38  Score=39.49  Aligned_cols=34  Identities=15%  Similarity=0.267  Sum_probs=27.9

Q ss_pred             CCcc-eEEEecCCccHHHHHHHHHCCCCeEEEccc
Q 041256          192 EHVK-KLVDVGGGLGITLNMIISKYPHIKGINYDL  225 (244)
Q Consensus       192 ~~~~-~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  225 (244)
                      .... +|+.||.|+|..+..+++++|+++--==|.
T Consensus        23 ~~~~~~vLEiaSGtGqHa~~FA~~lP~l~WqPSD~   57 (204)
T PF06080_consen   23 PDSGTRVLEIASGTGQHAVYFAQALPHLTWQPSDP   57 (204)
T ss_pred             CccCceEEEEcCCccHHHHHHHHHCCCCEEcCCCC
Confidence            4444 599999999999999999999998644454

The function of this family is unknown.

>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family

Probab=91.07  E-value=0.3  Score=35.79  Aligned_cols=48  Identities=23%  Similarity=0.350  Sum_probs=37.0

Q ss_pred             hcChhhHHh--hcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           35 ELDVFEIIS--KAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        35 ~lgifd~L~--~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      ++.++..|.  ... ++++|..+||+.++++      ... +.++++.|...|++.+.
T Consensus        27 q~~vL~~l~~~~~~-~~~~t~~eL~~~l~~~------~st-vs~~i~~Le~kg~I~r~   76 (109)
T TIGR01889        27 ELLILYYLGKLENN-EGKLTLKEIIKEILIK------QSA-LVKIIKKLSKKGYLSKE   76 (109)
T ss_pred             HHHHHHHHHhhhcc-CCcCcHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEecc
Confidence            344555555  211 1689999999999997      456 99999999999999964

This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.

>KOG1541 consensus Predicted protein carboxyl methylase [General function prediction only]

Probab=91.06  E-value=0.11  Score=43.15  Aligned_cols=40  Identities=20%  Similarity=0.386  Sum_probs=32.1

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ....|+|||||+|..+..+...  +...+.+|. |..++.|.+
T Consensus        50 ~~~~iLDIGCGsGLSg~vL~~~--Gh~wiGvDiSpsML~~a~~   90 (270)
T KOG1541|consen   50 KSGLILDIGCGSGLSGSVLSDS--GHQWIGVDISPSMLEQAVE   90 (270)
T ss_pred             CCcEEEEeccCCCcchheeccC--CceEEeecCCHHHHHHHHH
Confidence            5799999999999988776554  467789998 888887763

>PF14394 DUF4423: Domain of unknown function (DUF4423)

Probab=91.03  E-value=1.2  Score=35.57  Aligned_cols=64  Identities=14%  Similarity=0.120  Sum_probs=47.5

Q ss_pred             hhHHHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhC--CCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeec
Q 041256           23 AIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQI--PLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSL  100 (244)
Q Consensus        23 g~~~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~--~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~  100 (244)
                      ..|...+++..+.+.=          +.-++++||+++  +++      +.. ++.-|..|..+|++++   .++|.|..
T Consensus        22 ~~W~~~~ir~l~~l~~----------~~~d~~~iak~l~p~is------~~e-v~~sL~~L~~~gli~k---~~~g~y~~   81 (171)
T PF14394_consen   22 SSWYHPAIRELLPLMP----------FAPDPEWIAKRLRPKIS------AEE-VRDSLEFLEKLGLIKK---DGDGKYVQ   81 (171)
T ss_pred             hhhHHHHHHHHhhcCC----------CCCCHHHHHHHhcCCCC------HHH-HHHHHHHHHHCCCeEE---CCCCcEEE
Confidence            5566666665544321          233899999999  886      556 9999999999999995   45689999


Q ss_pred             Cccccc
Q 041256          101 APVSAY  106 (244)
Q Consensus       101 t~~s~~  106 (244)
                      |..+-.
T Consensus        82 t~~~l~   87 (171)
T PF14394_consen   82 TDKSLT   87 (171)
T ss_pred             ecceee
Confidence            876544

>TIGR00373 conserved hypothetical protein TIGR00373

Probab=91.01  E-value=0.35  Score=38.13  Aligned_cols=44  Identities=14%  Similarity=0.074  Sum_probs=37.5

Q ss_pred             cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      ..|+++|...   +.+|-+|||+.+|++      ... ++++|..|...|++..
T Consensus        17 v~Vl~aL~~~---~~~tdEeLa~~Lgi~------~~~-VRk~L~~L~e~~Lv~~   60 (158)
T TIGR00373        17 GLVLFSLGIK---GEFTDEEISLELGIK------LNE-VRKALYALYDAGLADY   60 (158)
T ss_pred             HHHHHHHhcc---CCCCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCcee
Confidence            3478888765   689999999999997      455 9999999999999964

This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.

>PRK03573 transcriptional regulator SlyA; Provisional

Probab=91.00  E-value=0.43  Score=36.58  Aligned_cols=44  Identities=16%  Similarity=0.145  Sum_probs=35.3

Q ss_pred             hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      ++..|...+  ++.|..+||+.++++      +.. +.++++-|...|++++.
T Consensus        36 vL~~l~~~~--~~~t~~eLa~~l~~~------~~t-vt~~v~~Le~~GlV~r~   79 (144)
T PRK03573         36 TLHNIHQLP--PEQSQIQLAKAIGIE------QPS-LVRTLDQLEEKGLISRQ   79 (144)
T ss_pred             HHHHHHHcC--CCCCHHHHHHHhCCC------hhh-HHHHHHHHHHCCCEeee
Confidence            455665532  468999999999997      445 99999999999999964

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

Probab=90.98  E-value=0.3  Score=43.57  Aligned_cols=38  Identities=11%  Similarity=0.134  Sum_probs=32.2

Q ss_pred             ceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          195 KKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       195 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+++|++||+|.++..+.+...  +++.+|. ++.++.+++
T Consensus       199 ~~vlDl~~G~G~~sl~la~~~~--~v~~vE~~~~av~~a~~  237 (353)
T TIGR02143       199 GDLLELYCGNGNFSLALAQNFR--RVLATEIAKPSVNAAQY  237 (353)
T ss_pred             CcEEEEeccccHHHHHHHHhCC--EEEEEECCHHHHHHHHH
Confidence            4699999999999999998874  7888887 788887765

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.

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=90.97  E-value=0.5  Score=29.85  Aligned_cols=34  Identities=24%  Similarity=0.245  Sum_probs=29.5

Q ss_pred             CCC-CHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           49 AKL-SVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        49 g~~-t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      ..+ |..+||+.++++      ... +++.|+.|...|++..
T Consensus        18 ~~l~s~~~la~~~~vs------~~t-v~~~l~~L~~~g~i~~   52 (60)
T smart00345       18 DKLPSERELAAQLGVS------RTT-VREALSRLEAEGLVQR   52 (60)
T ss_pred             CcCcCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEE
Confidence            345 899999999997      456 9999999999999985

>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators

Probab=90.94  E-value=0.54  Score=34.53  Aligned_cols=51  Identities=24%  Similarity=0.365  Sum_probs=37.5

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCc-chhccHHHHHHHHhhCCcccce
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPE-AAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~-~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      +.-|++.|.+.+  ++.|++||.+.+.-.  .|. ...- ++|.|+.|+..|++.+.
T Consensus         3 R~~Il~~l~~~~--~~~sa~ei~~~l~~~--~~~i~~~T-VYR~L~~L~~~Gli~~~   54 (116)
T cd07153           3 RLAILEVLLESD--GHLTAEEIYERLRKK--GPSISLAT-VYRTLELLEEAGLVREI   54 (116)
T ss_pred             HHHHHHHHHhCC--CCCCHHHHHHHHHhc--CCCCCHHH-HHHHHHHHHhCCCEEEE
Confidence            345788888754  689999999998432  111 0233 99999999999999864

Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.

>TIGR01177 conserved hypothetical protein TIGR01177

Probab=90.77  E-value=0.46  Score=41.86  Aligned_cols=47  Identities=17%  Similarity=0.036  Sum_probs=34.8

Q ss_pred             HHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256          184 VLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       184 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~  233 (244)
                      ++.... +....+|+|+|||+|.++.+.+.  ...+.+..|. |..+..++
T Consensus       174 ~~~l~~-~~~g~~vLDp~cGtG~~lieaa~--~~~~v~g~Di~~~~~~~a~  221 (329)
T TIGR01177       174 MVNLAR-VTEGDRVLDPFCGTGGFLIEAGL--MGAKVIGCDIDWKMVAGAR  221 (329)
T ss_pred             HHHHhC-CCCcCEEEECCCCCCHHHHHHHH--hCCeEEEEcCCHHHHHHHH
Confidence            333334 66668999999999999988655  3667888898 77776654

This family is found exclusively in the Archaea.

>COG2518 Pcm Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]

Probab=90.66  E-value=0.49  Score=38.93  Aligned_cols=49  Identities=10%  Similarity=0.259  Sum_probs=38.0

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+++.+. .+...+|++||+|+|..+.-+.+---  +++-+|+ ++.++.|++
T Consensus        63 ~m~~~L~-~~~g~~VLEIGtGsGY~aAvla~l~~--~V~siEr~~~L~~~A~~  112 (209)
T COG2518          63 RMLQLLE-LKPGDRVLEIGTGSGYQAAVLARLVG--RVVSIERIEELAEQARR  112 (209)
T ss_pred             HHHHHhC-CCCCCeEEEECCCchHHHHHHHHHhC--eEEEEEEcHHHHHHHHH
Confidence            4456666 77889999999999999888777655  6777776 777777764

>PF05148 Methyltransf_8: Hypothetical methyltransferase; InterPro: IPR007823 This family consists of uncharacterised eukaryotic proteins which are related to S-adenosyl-L-methionine-dependent methyltransferases

Probab=90.56  E-value=0.55  Score=38.71  Aligned_cols=66  Identities=15%  Similarity=0.191  Sum_probs=34.8

Q ss_pred             hhccCCchHHHHHHH----HHHhcchhhHHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc
Q 041256          157 DYLGVDSRFNDVFNN----GMLSHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL  225 (244)
Q Consensus       157 e~~~~~~~~~~~f~~----aM~~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  225 (244)
                      +.+.++|+....++.    .+..|-......+++.+...++...|.|.|||.+.++.++.+   ..++.-|||
T Consensus        32 ~lf~~dP~~F~~YH~Gfr~Qv~~WP~nPvd~iI~~l~~~~~~~viaD~GCGdA~la~~~~~---~~~V~SfDL  101 (219)
T PF05148_consen   32 KLFQEDPELFDIYHEGFRQQVKKWPVNPVDVIIEWLKKRPKSLVIADFGCGDAKLAKAVPN---KHKVHSFDL  101 (219)
T ss_dssp             HHHHH-HHHHHHHHHHHHHHHCTSSS-HHHHHHHHHCTS-TTS-EEEES-TT-HHHHH--S------EEEEES
T ss_pred             HHHHhCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHHHhcCCCEEEEECCCchHHHHHhccc---CceEEEeec
Confidence            344556665554444    444444445566777665334557999999999999976642   246677776

; GO: 0008168 methyltransferase activity; PDB: 2ZFU_B.

>PRK11760 putative 23S rRNA C2498 ribose 2'-O-ribose methyltransferase; Provisional

Probab=90.52  E-value=0.5  Score=41.89  Aligned_cols=48  Identities=10%  Similarity=-0.006  Sum_probs=37.7

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCCCCCceee
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPGTLFI  241 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~~~~i~~~  241 (244)
                      ....++||||++.|.+...++++  +.+++.+|.-..-+.....++|+++
T Consensus       210 ~~g~~vlDLGAsPGGWT~~L~~r--G~~V~AVD~g~l~~~L~~~~~V~h~  257 (357)
T PRK11760        210 APGMRAVDLGAAPGGWTYQLVRR--GMFVTAVDNGPMAQSLMDTGQVEHL  257 (357)
T ss_pred             CCCCEEEEeCCCCcHHHHHHHHc--CCEEEEEechhcCHhhhCCCCEEEE
Confidence            45689999999999999999998  5689999976665555555666554

>COG2345 Predicted transcriptional regulator [Transcription]

Probab=90.25  E-value=0.41  Score=39.68  Aligned_cols=59  Identities=19%  Similarity=0.318  Sum_probs=44.9

Q ss_pred             hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecC-----CceeecCccccc
Q 041256           38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDG-----QRLYSLAPVSAY  106 (244)
Q Consensus        38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~-----~~~y~~t~~s~~  106 (244)
                      |...|.+.   +|.|+.|||+++|++      +.. ++|-|..|++.|+++.....+     .-.|++|..+..
T Consensus        16 il~lL~~~---g~~sa~elA~~Lgis------~~a-vR~HL~~Le~~Glv~~~~~~~g~GRP~~~y~Lt~~g~~   79 (218)
T COG2345          16 ILELLKKS---GPVSADELAEELGIS------PMA-VRRHLDDLEAEGLVEVERQQGGRGRPAKLYRLTEKGRE   79 (218)
T ss_pred             HHHHHhcc---CCccHHHHHHHhCCC------HHH-HHHHHHHHHhCcceeeeeccCCCCCCceeeeecccchh
Confidence            44556655   799999999999997      567 999999999999998532211     124888888764

>PF08123 DOT1: Histone methylation protein DOT1 ; InterPro: IPR013110 The DOT1 domain regulates gene expression by methylating histone H3 []

Probab=90.18  E-value=0.53  Score=38.72  Aligned_cols=49  Identities=18%  Similarity=0.282  Sum_probs=32.2

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDA  232 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a  232 (244)
                      .+++.+. +....+++|||+|.|....+.+-.++--+++.+++ |...+.|
T Consensus        33 ~il~~~~-l~~~dvF~DlGSG~G~~v~~aal~~~~~~~~GIEi~~~~~~~a   82 (205)
T PF08123_consen   33 KILDELN-LTPDDVFYDLGSGVGNVVFQAALQTGCKKSVGIEILPELHDLA   82 (205)
T ss_dssp             HHHHHTT---TT-EEEEES-TTSHHHHHHHHHH--SEEEEEE-SHHHHHHH
T ss_pred             HHHHHhC-CCCCCEEEECCCCCCHHHHHHHHHcCCcEEEEEEechHHHHHH
Confidence            4555565 66678999999999999998888887666888887 5555444

H3 methylation by DOT1 has been shown to be required for the DNA damage checkpoint in yeast [].; GO: 0018024 histone-lysine N-methyltransferase activity; PDB: 4ER3_A 4ER6_A 4EQZ_A 1NW3_A 3UWP_A 4ER5_A 3QOX_A 3SX0_A 4ER7_A 3SR4_A ....

>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets

Probab=89.92  E-value=0.66  Score=29.21  Aligned_cols=42  Identities=7%  Similarity=0.283  Sum_probs=32.1

Q ss_pred             ChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcc
Q 041256           37 DVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNAL   87 (244)
Q Consensus        37 gifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll   87 (244)
                      .|+..|.+.+  +++|.++||+.++++      ..- +.+-+..|...|+.
T Consensus         4 ~il~~L~~~~--~~it~~eLa~~l~vS------~rT-i~~~i~~L~~~~~~   45 (55)
T PF08279_consen    4 QILKLLLESK--EPITAKELAEELGVS------RRT-IRRDIKELREWGIP   45 (55)
T ss_dssp             HHHHHHHHTT--TSBEHHHHHHHCTS-------HHH-HHHHHHHHHHTT-E
T ss_pred             HHHHHHHHcC--CCcCHHHHHHHhCCC------HHH-HHHHHHHHHHCCCe
Confidence            3566675443  579999999999997      445 99999999999933

The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....

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

Probab=89.76  E-value=0.38  Score=43.06  Aligned_cols=38  Identities=11%  Similarity=0.127  Sum_probs=31.8

Q ss_pred             ceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          195 KKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       195 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+++|++||+|.++..+.+...  +++.+|. +..++.+++
T Consensus       208 ~~vLDl~~G~G~~sl~la~~~~--~v~~vE~~~~ai~~a~~  246 (362)
T PRK05031        208 GDLLELYCGNGNFTLALARNFR--RVLATEISKPSVAAAQY  246 (362)
T ss_pred             CeEEEEeccccHHHHHHHhhCC--EEEEEECCHHHHHHHHH
Confidence            4699999999999999998875  6788887 777777764

>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain

Probab=89.60  E-value=0.66  Score=33.16  Aligned_cols=44  Identities=7%  Similarity=0.105  Sum_probs=36.4

Q ss_pred             CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecC
Q 041256           49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLA  101 (244)
Q Consensus        49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t  101 (244)
                      .++|-.|||+.+|++      ..- +.|.|..|...|++...  .+-+.|+.|
T Consensus        46 ~~is~~eLa~~~g~s------r~t-Vsr~L~~Le~~GlI~r~--~~~~~~~~n   89 (95)
T TIGR01610        46 DRVTATVIAELTGLS------RTH-VSDAIKSLARRRIIFRQ--GMMGIVGVN   89 (95)
T ss_pred             CccCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCeeee--cCCceeecC
Confidence            589999999999997      445 99999999999999962  234777776

This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.

>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]

Probab=89.55  E-value=0.62  Score=36.54  Aligned_cols=52  Identities=8%  Similarity=0.072  Sum_probs=43.1

Q ss_pred             CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccccccccC
Q 041256           49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFVRN  110 (244)
Q Consensus        49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l~~~  110 (244)
                      ++....+||+.++++      |.- +...++-|...|++++.  . .+.+.+|+.+...+..
T Consensus        23 ~~~~~~diA~~L~Vs------p~s-Vt~ml~rL~~~GlV~~~--~-y~gi~LT~~G~~~a~~   74 (154)
T COG1321          23 GFARTKDIAERLKVS------PPS-VTEMLKRLERLGLVEYE--P-YGGVTLTEKGREKAKE   74 (154)
T ss_pred             CcccHHHHHHHhCCC------cHH-HHHHHHHHHHCCCeEEe--c-CCCeEEChhhHHHHHH
Confidence            799999999999997      445 88999999999999973  3 4779999987755544

>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional

Probab=89.45  E-value=0.49  Score=39.26  Aligned_cols=53  Identities=15%  Similarity=0.187  Sum_probs=41.3

Q ss_pred             CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccccccc
Q 041256           49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFV  108 (244)
Q Consensus        49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l~  108 (244)
                      ..+|..+||+.++++      +.. +.|.|+.|...|++++........+++|+.+..+.
T Consensus        20 ~~IS~~eLA~~L~iS------~~T-vsr~Lk~LEe~GlI~R~~~~r~~~v~LTekG~~ll   72 (217)
T PRK14165         20 VKISSSEFANHTGTS------SKT-AARILKQLEDEGYITRTIVPRGQLITITEKGLDVL   72 (217)
T ss_pred             CCcCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEEEEcCCceEEEECHHHHHHH
Confidence            469999999999997      456 99999999999999864322245678888776443

>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family

Probab=89.27  E-value=0.73  Score=30.02  Aligned_cols=34  Identities=9%  Similarity=0.236  Sum_probs=30.2

Q ss_pred             CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      ++.+..+||+.++++      +.- +...++-|...|+++.
T Consensus        21 ~~v~~~~iA~~L~vs------~~t-vt~ml~~L~~~GlV~~   54 (60)
T PF01325_consen   21 GPVRTKDIAERLGVS------PPT-VTEMLKRLAEKGLVEY   54 (60)
T ss_dssp             SSBBHHHHHHHHTS-------HHH-HHHHHHHHHHTTSEEE
T ss_pred             CCccHHHHHHHHCCC------hHH-HHHHHHHHHHCCCEEe
Confidence            799999999999997      445 8999999999999996

The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....

>PF12147 Methyltransf_20: Putative methyltransferase; InterPro: IPR022744 This C-terminal region is found in bacteria and eukaryotes and is approximately 110 amino acids in length

Probab=89.03  E-value=0.44  Score=41.20  Aligned_cols=43  Identities=16%  Similarity=0.243  Sum_probs=36.2

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCC--CeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPH--IKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~--l~~~v~Dl-p~vi~~a~~  234 (244)
                      ....+||||.||+|.+...+++.+|.  ..+.+.|. |.-|+..++
T Consensus       134 g~pvrIlDIAaG~GRYvlDal~~~~~~~~~i~LrDys~~Nv~~g~~  179 (311)
T PF12147_consen  134 GRPVRILDIAAGHGRYVLDALEKHPERPDSILLRDYSPINVEKGRA  179 (311)
T ss_pred             CCceEEEEeccCCcHHHHHHHHhCCCCCceEEEEeCCHHHHHHHHH
Confidence            36799999999999999999999998  67788887 666666653

It is found in association with PF00561 from PFAM. Many members are annotated as being lysophospholipases, and others as alpha-beta hydrolase fold-containing proteins. This domain belongs to the S-adenosyl-L-methionine-dependent methyltransferases superfamily.

>PHA02943 hypothetical protein; Provisional

Probab=88.98  E-value=0.92  Score=35.28  Aligned_cols=42  Identities=10%  Similarity=0.157  Sum_probs=34.8

Q ss_pred             ChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           37 DVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        37 gifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      .|.+.|..    |..|..|||+++|++      -.. .+-.|..|...|.+.+
T Consensus        15 eILE~Lk~----G~~TtseIAkaLGlS------~~q-a~~~LyvLErEG~Vkr   56 (165)
T PHA02943         15 KTLRLLAD----GCKTTSRIANKLGVS------HSM-ARNALYQLAKEGMVLK   56 (165)
T ss_pred             HHHHHHhc----CCccHHHHHHHHCCC------HHH-HHHHHHHHHHcCceEE
Confidence            45666733    789999999999997      345 8899999999999995

>PF05185 PRMT5: PRMT5 arginine-N-methyltransferase; InterPro: IPR007857 The human homologue of Saccharomyces cerevisiae Skb1 (Shk1 kinase-binding protein 1) is a protein methyltransferase []

Probab=88.68  E-value=0.86  Score=42.08  Aligned_cols=69  Identities=17%  Similarity=0.231  Sum_probs=43.1

Q ss_pred             CchhhccCCchHHHHHHHHHHhcchhhHHHHHhhcCCC---CCcceEEEecCCccHHHHHHHHHC----CCCeEEEccc-
Q 041256          154 QIYDYLGVDSRFNDVFNNGMLSHTSIVMEKVLESYKGF---EHVKKLVDVGGGLGITLNMIISKY----PHIKGINYDL-  225 (244)
Q Consensus       154 ~~~e~~~~~~~~~~~f~~aM~~~~~~~~~~~~~~~~~~---~~~~~vvDVGGG~G~~~~~l~~~~----P~l~~~v~Dl-  225 (244)
                      .-||.+++|+..-+.+.+|+..       .+.+....-   .+.+.|+|||+|+|-++...+++.    -..++..++- 
T Consensus       151 ~tYe~fE~D~vKY~~Ye~AI~~-------al~D~~~~~~~~~~~~vVldVGAGrGpL~~~al~A~~~~~~a~~VyAVEkn  223 (448)
T PF05185_consen  151 QTYEVFEKDPVKYDQYERAIEE-------ALKDRVRKNSYSSKDKVVLDVGAGRGPLSMFALQAGARAGGAVKVYAVEKN  223 (448)
T ss_dssp             HHHHHHCC-HHHHHHHHHHHHH-------HHHHHHTTS-SEETT-EEEEES-TTSHHHHHHHHTTHHHCCESEEEEEESS
T ss_pred             ccHhhHhcCHHHHHHHHHHHHH-------HHHhhhhhccccccceEEEEeCCCccHHHHHHHHHHHHhCCCeEEEEEcCC
Confidence            3578888899877888887632       223222211   135889999999999987776654    4567777765 


Q ss_pred             hHHh
Q 041256          226 PYVI  229 (244)
Q Consensus       226 p~vi  229 (244)
                      |..+
T Consensus       224 ~~A~  227 (448)
T PF05185_consen  224 PNAV  227 (448)
T ss_dssp             THHH
T ss_pred             HhHH
Confidence            4443

These proteins seem to play a role in Jak signalling.; GO: 0008168 methyltransferase activity, 0005737 cytoplasm; PDB: 2Y1W_C 2Y1X_D 2V7E_B 2V74_H 3R0Q_G 3B3F_B 3B3J_A 3B3G_A 3UA3_A 3UA4_B ....

>PF03291 Pox_MCEL: mRNA capping enzyme; InterPro: IPR004971 This is a family of viral mRNA capping enzymes

Probab=88.56  E-value=0.51  Score=41.79  Aligned_cols=61  Identities=20%  Similarity=0.161  Sum_probs=39.1

Q ss_pred             HHHHHHHHHhcchhhHHHHHhhcC----CCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          166 NDVFNNGMLSHTSIVMEKVLESYK----GFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       166 ~~~f~~aM~~~~~~~~~~~~~~~~----~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+.|+.++.+       .++..|-    .-....+|+|+|||.|..+....++.+. ..+..|+ ++.|+.|++
T Consensus        38 lR~fNNwvKs-------~LI~~~~~~~~~~~~~~~VLDl~CGkGGDL~Kw~~~~i~-~~vg~Dis~~si~ea~~  103 (331)
T PF03291_consen   38 LRNFNNWVKS-------VLIQKYAKKVKQNRPGLTVLDLCCGKGGDLQKWQKAKIK-HYVGIDISEESIEEARE  103 (331)
T ss_dssp             HHHHHHHHHH-------HHHHHHCHCCCCTTTT-EEEEET-TTTTTHHHHHHTT-S-EEEEEES-HHHHHHHHH
T ss_pred             HHHHhHHHHH-------HHHHHHHHhhhccCCCCeEEEecCCCchhHHHHHhcCCC-EEEEEeCCHHHHHHHHH
Confidence            5788888865       2333331    0115689999999999999888887332 3577888 666666643

The enzyme catalyses the first two reactions in the mRNA cap formation pathway. It is a heterodimer consisting of a large and small subunit. This entry is the large subunit. ; GO: 0006370 mRNA capping; PDB: 3EPP_A 3BGV_C 2VDW_C 1RI5_A 1RI3_A 1RI1_A 1Z3C_A 1RI2_A 2HV9_A 1RI4_A.

>COG0357 GidB Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]

Probab=88.54  E-value=0.44  Score=39.46  Aligned_cols=32  Identities=22%  Similarity=0.423  Sum_probs=29.8

Q ss_pred             cceEEEecCCccHHHHHHHHHCCCCeEEEccc
Q 041256          194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL  225 (244)
Q Consensus       194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  225 (244)
                      ..+++|||-|.|.=++=++=.+|+++.+++|-
T Consensus        68 ~~~~~DIGSGaGfPGipLAI~~p~~~vtLles   99 (215)
T COG0357          68 AKRVLDIGSGAGFPGIPLAIAFPDLKVTLLES   99 (215)
T ss_pred             CCEEEEeCCCCCCchhhHHHhccCCcEEEEcc
Confidence            68999999999999998889999999999994

>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]

Probab=88.31  E-value=0.69  Score=38.13  Aligned_cols=43  Identities=23%  Similarity=0.330  Sum_probs=34.2

Q ss_pred             hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      |.+.|...  +.+.|++|||+++|++      -.- .+|.|.+|++.|++.-
T Consensus       163 i~~~~~~~--~~~~Taeela~~~giS------RvT-aRRYLeyl~~~~~l~a  205 (224)
T COG4565         163 VREALKEP--DQELTAEELAQALGIS------RVT-ARRYLEYLVSNGILEA  205 (224)
T ss_pred             HHHHHhCc--CCccCHHHHHHHhCcc------HHH-HHHHHHHHHhcCeeeE
Confidence            45556522  2689999999999996      233 8999999999999984

>PF02527 GidB: rRNA small subunit methyltransferase G; InterPro: IPR003682 This entry represents a rRNA small subunit methyltransferase G

Probab=88.30  E-value=0.53  Score=38.07  Aligned_cols=30  Identities=20%  Similarity=0.313  Sum_probs=27.5

Q ss_pred             eEEEecCCccHHHHHHHHHCCCCeEEEccc
Q 041256          196 KLVDVGGGLGITLNMIISKYPHIKGINYDL  225 (244)
Q Consensus       196 ~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  225 (244)
                      +++|||.|.|.=++-++=.+|+++++++|-
T Consensus        51 ~~lDiGSGaGfPGipLaI~~p~~~~~LvEs   80 (184)
T PF02527_consen   51 KVLDIGSGAGFPGIPLAIARPDLQVTLVES   80 (184)
T ss_dssp             EEEEETSTTTTTHHHHHHH-TTSEEEEEES
T ss_pred             eEEecCCCCCChhHHHHHhCCCCcEEEEeC
Confidence            799999999999999999999999999994

Previously identified as a glucose-inhibited division protein B that appears to be present and in a single copy in all complete eubacterial genomes so far sequenced. Specifically methylates the N7 position of a guanosine in 16S rRNA [, , ].; GO: 0008649 rRNA methyltransferase activity, 0006364 rRNA processing, 0005737 cytoplasm; PDB: 1XDZ_A 3G88_A 3G8A_B 3G89_B 3G8B_B 1JSX_A.

>COG4190 Predicted transcriptional regulator [Transcription]

Probab=88.10  E-value=0.87  Score=34.50  Aligned_cols=51  Identities=16%  Similarity=0.264  Sum_probs=42.3

Q ss_pred             HHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           29 VMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        29 ~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      .+.+=-.+.+...|+..   +|.|..|||+.+|-+      +.. +.|-|+.|.-.|++.-
T Consensus        60 ~vLsp~nleLl~~Ia~~---~P~Si~ElAe~vgRd------v~n-vhr~Ls~l~~~GlI~f  110 (144)
T COG4190          60 RVLSPRNLELLELIAQE---EPASINELAELVGRD------VKN-VHRTLSTLADLGLIFF  110 (144)
T ss_pred             HHhChhHHHHHHHHHhc---CcccHHHHHHHhCcc------hHH-HHHHHHHHHhcCeEEE
Confidence            33344457788889886   699999999999986      566 9999999999999986

>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors

Probab=87.98  E-value=0.49  Score=34.35  Aligned_cols=42  Identities=12%  Similarity=0.282  Sum_probs=31.7

Q ss_pred             hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      |++.|...   |.++-++||+.++++      +.- ++++|..|...||+..
T Consensus        18 Il~~L~~~---~~l~de~la~~~~l~------~~~-vRkiL~~L~~~~lv~~   59 (105)
T PF02002_consen   18 ILDALLRK---GELTDEDLAKKLGLK------PKE-VRKILYKLYEDGLVSY   59 (105)
T ss_dssp             HHHHHHHH-----B-HHHHHHTT-S-------HHH-HHHHHHHHHHHSS-EE
T ss_pred             HHHHHHHc---CCcCHHHHHHHhCCC------HHH-HHHHHHHHHHCCCeEE
Confidence            68888865   689999999999997      456 9999999999999975

Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.

>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]

Probab=87.90  E-value=0.73  Score=39.30  Aligned_cols=48  Identities=21%  Similarity=0.391  Sum_probs=40.9

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCccccee
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSF   91 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~   91 (244)
                      +..+.++|.+.|  |-++-+||.+++|.+      ..- +.|+|+-|...|++++.+
T Consensus       197 e~~il~~i~~~G--Gri~Q~eL~r~lgls------ktT-vsR~L~~LEk~GlIe~~K  244 (258)
T COG2512         197 EKEILDLIRERG--GRITQAELRRALGLS------KTT-VSRILRRLEKRGLIEKEK  244 (258)
T ss_pred             HHHHHHHHHHhC--CEEeHHHHHHhhCCC------hHH-HHHHHHHHHhCCceEEEE
Confidence            456888898876  779999999999996      334 999999999999999753

>PRK15431 ferrous iron transport protein FeoC; Provisional

Probab=87.88  E-value=1  Score=30.97  Aligned_cols=43  Identities=16%  Similarity=0.244  Sum_probs=37.3

Q ss_pred             hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      |=|.|...   |..++.+||..++++      +.. ++.+|..++..|-+++.
T Consensus         7 lRd~l~~~---gr~s~~~Ls~~~~~p------~~~-VeaMLe~l~~kGkverv   49 (78)
T PRK15431          7 VRDLLALR---GRMEAAQISQTLNTP------QPM-INAMLQQLESMGKAVRI   49 (78)
T ss_pred             HHHHHHHc---CcccHHHHHHHHCcC------HHH-HHHHHHHHHHCCCeEee
Confidence            44778876   689999999999997      678 99999999999999963

>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element

Probab=87.74  E-value=0.71  Score=32.61  Aligned_cols=46  Identities=13%  Similarity=0.197  Sum_probs=35.9

Q ss_pred             HHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccccccc
Q 041256           53 VAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFV  108 (244)
Q Consensus        53 ~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l~  108 (244)
                      +.+||+.++++      +.. +.+.++.|...|++..   ..+..|.+|+.+..+.
T Consensus         2 ~~ela~~l~is------~st-vs~~l~~L~~~glI~r---~~~~~~~lT~~g~~~~   47 (96)
T smart00529        2 TSEIAERLNVS------PPT-VTQMLKKLEKDGLVEY---EPYRGITLTEKGRRLA   47 (96)
T ss_pred             HHHHHHHhCCC------hHH-HHHHHHHHHHCCCEEE---cCCCceEechhHHHHH
Confidence            46899999997      455 9999999999999996   2235688888765443

iron dependent repressor

>PF01596 Methyltransf_3: O-methyltransferase; InterPro: IPR002935 Members of this family are O-methyltransferases

Probab=87.66  E-value=0.56  Score=38.59  Aligned_cols=43  Identities=16%  Similarity=0.196  Sum_probs=35.9

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCC-CCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYP-HIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .++++||+||.+.|.-+..+++..| +.+.+.+|. |+-.+.|++
T Consensus        44 ~~~k~vLEIGt~~GySal~la~~l~~~g~i~tiE~~~~~~~~A~~   88 (205)
T PF01596_consen   44 TRPKRVLEIGTFTGYSALWLAEALPEDGKITTIEIDPERAEIARE   88 (205)
T ss_dssp             HT-SEEEEESTTTSHHHHHHHHTSTTTSEEEEEESSHHHHHHHHH
T ss_pred             cCCceEEEeccccccHHHHHHHhhcccceEEEecCcHHHHHHHHH
Confidence            4679999999999999999999987 588998988 767776654

The family includes also bacterial O-methyltransferases that may be involved in antibiotic production [].; GO: 0008171 O-methyltransferase activity; PDB: 1SUI_C 1SUS_D 3CBG_A 2GPY_B 3TR6_A 2AVD_A 3DUL_B 3DUW_B 2ZTH_A 1VID_A ....

>COG4189 Predicted transcriptional regulator [Transcription]

Probab=87.62  E-value=1  Score=37.67  Aligned_cols=54  Identities=13%  Similarity=0.317  Sum_probs=46.5

Q ss_pred             HHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           26 LPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        26 ~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      ..++|...+++.|.+.|+..   +|+.+.|||+++|++      ..- +..=+..|...|++.-
T Consensus        16 v~kalaS~vRv~Il~lL~~k---~plNvneiAe~lgLp------qst-~s~~ik~Le~aGlirT   69 (308)
T COG4189          16 VLKALASKVRVAILQLLHRK---GPLNVNEIAEALGLP------QST-MSANIKVLEKAGLIRT   69 (308)
T ss_pred             HHHHHHHHHHHHHHHHHHHh---CCCCHHHHHHHhCCc------hhh-hhhhHHHHHhcCceee
Confidence            45788899999999999986   699999999999996      334 7788999999999974

>TIGR00006 S-adenosyl-methyltransferase MraW

Probab=87.61  E-value=1.1  Score=39.19  Aligned_cols=52  Identities=21%  Similarity=0.215  Sum_probs=43.9

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+++.+. ......+||.=.|.|..+.+++++.|+.+.+.+|. |.+++.+++
T Consensus        10 ~Evl~~L~-~~~ggiyVD~TlG~GGHS~~iL~~l~~g~vigiD~D~~Al~~ak~   62 (305)
T TIGR00006        10 DEVVEGLN-IKPDGIYIDCTLGFGGHSKAILEQLGTGRLIGIDRDPQAIAFAKE   62 (305)
T ss_pred             HHHHHhcC-cCCCCEEEEeCCCChHHHHHHHHhCCCCEEEEEcCCHHHHHHHHH
Confidence            46666665 45567999999999999999999998889999998 888888765

Genetics paper in 1972 links mra cluster to peptidoglycan biosynthesis in E. coli. Seems to be common in proteobacteria.wn.

>PRK14901 16S rRNA methyltransferase B; Provisional

Probab=87.52  E-value=0.93  Score=41.61  Aligned_cols=49  Identities=10%  Similarity=-0.067  Sum_probs=37.3

Q ss_pred             HhhcCCCCCcceEEEecCCccHHHHHHHHHCC-CCeEEEccc-hHHhhhCCC
Q 041256          185 LESYKGFEHVKKLVDVGGGLGITLNMIISKYP-HIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       185 ~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...++ .....+|+|+|+|.|..+..+++..+ .-+.+.+|. ++-++.+++
T Consensus       245 ~~~l~-~~~g~~VLDl~ag~G~kt~~la~~~~~~g~v~a~D~~~~rl~~~~~  295 (434)
T PRK14901        245 APLLD-PQPGEVILDACAAPGGKTTHIAELMGDQGEIWAVDRSASRLKKLQE  295 (434)
T ss_pred             HHHhC-CCCcCEEEEeCCCCchhHHHHHHHhCCCceEEEEcCCHHHHHHHHH
Confidence            33444 45568999999999999999999864 468899998 666666653

>PRK14903 16S rRNA methyltransferase B; Provisional

Probab=87.39  E-value=0.82  Score=41.98  Aligned_cols=44  Identities=16%  Similarity=0.064  Sum_probs=35.8

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHC-CCCeEEEccc-hHHhhhCCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKY-PHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .....+|+|+|+|.|..+..+++.. +.-+++.+|+ +.-++.+++
T Consensus       235 ~~~g~~VLD~cagpGgkt~~la~~~~~~g~V~a~Dis~~rl~~~~~  280 (431)
T PRK14903        235 LEPGLRVLDTCAAPGGKTTAIAELMKDQGKILAVDISREKIQLVEK  280 (431)
T ss_pred             CCCCCEEEEeCCCccHHHHHHHHHcCCCCEEEEEECCHHHHHHHHH
Confidence            4556799999999999999999876 5678999998 676766653

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=87.35  E-value=0.86  Score=35.49  Aligned_cols=45  Identities=11%  Similarity=0.216  Sum_probs=39.4

Q ss_pred             HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCccc
Q 041256           34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALH   88 (244)
Q Consensus        34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~   88 (244)
                      .+..|.+.|...   +..|..+||+++|++      +.. +.+=++-|...|++.
T Consensus        10 ~D~~Il~~Lq~d---~R~s~~eiA~~lglS------~~t-V~~Ri~rL~~~GvI~   54 (153)
T PRK11179         10 LDRGILEALMEN---ARTPYAELAKQFGVS------PGT-IHVRVEKMKQAGIIT   54 (153)
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCee
Confidence            567788999885   689999999999997      455 889999999999997

>PF01795 Methyltransf_5: MraW methylase family; InterPro: IPR002903 This is a family of S-adenosyl-L-methionine-dependent methyltransferases, which are found primarily, though not exclusively, in bacteria

Probab=87.32  E-value=0.96  Score=39.59  Aligned_cols=53  Identities=26%  Similarity=0.262  Sum_probs=40.8

Q ss_pred             HHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          181 MEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       181 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...+++.+. ......+||.==|.|..+.++++++|+.+.+.+|. |.+++.+++
T Consensus         9 l~Evl~~L~-~~~~g~~vD~T~G~GGHS~aiL~~~~~~~li~~DrD~~a~~~a~~   62 (310)
T PF01795_consen    9 LKEVLEALN-PKPGGIYVDCTFGGGGHSKAILEKLPNGRLIGIDRDPEALERAKE   62 (310)
T ss_dssp             HHHHHHHHT---TT-EEEETT-TTSHHHHHHHHT-TT-EEEEEES-HHHHHHHHC
T ss_pred             HHHHHHhhC-cCCCceEEeecCCcHHHHHHHHHhCCCCeEEEecCCHHHHHHHHH
Confidence            356677776 56678999999999999999999999999999999 999987765

The Escherichia coli protein is essential and has been linked to peptidoglycan biosynthesis [, ].; GO: 0008168 methyltransferase activity; PDB: 1N2X_A 1M6Y_A 1WG8_A 3TKA_A.

>PRK10870 transcriptional repressor MprA; Provisional

Probab=87.14  E-value=0.72  Score=36.91  Aligned_cols=62  Identities=11%  Similarity=0.090  Sum_probs=42.4

Q ss_pred             hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCcccccc
Q 041256           38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSAYF  107 (244)
Q Consensus        38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~~l  107 (244)
                      +.-.|...+ ++++|..|||+.++++      ... +.|++.-|...|++++.....+.   ...+|+.+..+
T Consensus        60 iL~~L~~~~-~~~it~~eLa~~l~l~------~~t-vsr~v~rLe~kGlV~R~~~~~DrR~~~v~LT~~G~~~  124 (176)
T PRK10870         60 ALITLESQE-NHSIQPSELSCALGSS------RTN-ATRIADELEKRGWIERRESDNDRRCLHLQLTEKGHEF  124 (176)
T ss_pred             HHHHHhcCC-CCCcCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHH
Confidence            455554321 2579999999999997      445 99999999999999974322222   34555555433

>KOG2361 consensus Predicted methyltransferase [General function prediction only]

Probab=87.06  E-value=0.82  Score=38.49  Aligned_cols=41  Identities=24%  Similarity=0.448  Sum_probs=36.7

Q ss_pred             cceEEEecCCccHHHHHHHHHCCC--CeEEEccc-hHHhhhCCC
Q 041256          194 VKKLVDVGGGLGITLNMIISKYPH--IKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       194 ~~~vvDVGGG~G~~~~~l~~~~P~--l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+|+.||||.|...--+++.+|+  ++....|- |..|+..++
T Consensus        72 ~~~ilEvGCGvGNtvfPll~~~~n~~l~v~acDfsp~Ai~~vk~  115 (264)
T KOG2361|consen   72 AETILEVGCGVGNTVFPLLKTSPNNRLKVYACDFSPRAIELVKK  115 (264)
T ss_pred             hhhheeeccCCCcccchhhhcCCCCCeEEEEcCCChHHHHHHHh
Confidence            348999999999999999999999  99999997 888888775

>PRK11169 leucine-responsive transcriptional regulator; Provisional

Probab=86.94  E-value=0.78  Score=36.21  Aligned_cols=46  Identities=13%  Similarity=0.213  Sum_probs=40.0

Q ss_pred             HHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCccc
Q 041256           33 VVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALH   88 (244)
Q Consensus        33 a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~   88 (244)
                      .++..|..+|.+.   +.+|..+||+++|++      +.. +.+=++-|...|++.
T Consensus        14 ~~D~~IL~~Lq~d---~R~s~~eiA~~lglS------~~t-v~~Ri~rL~~~GvI~   59 (164)
T PRK11169         14 RIDRNILNELQKD---GRISNVELSKRVGLS------PTP-CLERVRRLERQGFIQ   59 (164)
T ss_pred             HHHHHHHHHhccC---CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCeE
Confidence            3677899999885   799999999999997      455 889999999999997

>COG4262 Predicted spermidine synthase with an N-terminal membrane domain [General function prediction only]

Probab=86.92  E-value=1  Score=40.33  Aligned_cols=41  Identities=32%  Similarity=0.550  Sum_probs=35.0

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCC-CeEEEccc-hHHhhhCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPH-IKGINYDL-PYVIKDAP  233 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dl-p~vi~~a~  233 (244)
                      .+.++++-+|||.|.-+.+++ +||+ -+.+..|| |.+|+.++
T Consensus       288 ~~a~~vLvlGGGDGLAlRell-kyP~~~qI~lVdLDP~miela~  330 (508)
T COG4262         288 RGARSVLVLGGGDGLALRELL-KYPQVEQITLVDLDPRMIELAS  330 (508)
T ss_pred             cccceEEEEcCCchHHHHHHH-hCCCcceEEEEecCHHHHHHhh
Confidence            457899999999999998876 5885 56788898 99999987

>COG5631 Predicted transcription regulator, contains HTH domain (MarR family) [Transcription]

Probab=86.88  E-value=3.7  Score=32.27  Aligned_cols=76  Identities=17%  Similarity=0.158  Sum_probs=53.9

Q ss_pred             HhhhHHHHHHHHHHhcC-------hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeec
Q 041256           21 ASAIVLPAVMQAVVELD-------VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVD   93 (244)
Q Consensus        21 ~~g~~~~~~L~~a~~lg-------ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~   93 (244)
                      .++.|...|+.++.+.+       |..++.-.+  .|+++++|+..++.+  |   ... +..-||-|...|+++.....
T Consensus        64 Af~rW~vrCmAaag~~~ls~~e~l~lH~irhrd--R~K~laDic~~ln~e--D---th~-itYslrKL~k~gLit~t~~g  135 (199)
T COG5631          64 AFGRWQVRCMAAAGEFSLSGPENLLLHIIRHRD--RPKSLADICQMLNRE--D---THN-ITYSLRKLLKGGLITRTGSG  135 (199)
T ss_pred             HHHHHHHHHHHHhcCCCCcchHHHHHHHHhhcC--chhhHHHHHHHhccc--c---chh-HHHHHHHHHhccceecCCCC
Confidence            55788888998887766       344554443  699999999999997  3   235 78889999999999942111


Q ss_pred             CCceeecCccc
Q 041256           94 GQRLYSLAPVS  104 (244)
Q Consensus        94 ~~~~y~~t~~s  104 (244)
                      ..-+|..|+.+
T Consensus       136 kevTy~vTa~G  146 (199)
T COG5631         136 KEVTYEVTALG  146 (199)
T ss_pred             ceEEEEEecch
Confidence            12347776654

>PF09243 Rsm22: Mitochondrial small ribosomal subunit Rsm22; InterPro: IPR015324 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=86.80  E-value=1.2  Score=38.32  Aligned_cols=50  Identities=22%  Similarity=0.348  Sum_probs=35.9

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCe-EEEccc-hHHhhhCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIK-GINYDL-PYVIKDAP  233 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~-~~v~Dl-p~vi~~a~  233 (244)
                      .+....|+| .+++|+|+|+|.|..+-++...+|++. .+.+|. +...+.++
T Consensus        24 El~~r~p~f-~P~~vLD~GsGpGta~wAa~~~~~~~~~~~~vd~s~~~~~l~~   75 (274)
T PF09243_consen   24 ELRKRLPDF-RPRSVLDFGSGPGTALWAAREVWPSLKEYTCVDRSPEMLELAK   75 (274)
T ss_pred             HHHHhCcCC-CCceEEEecCChHHHHHHHHHHhcCceeeeeecCCHHHHHHHH
Confidence            334344533 457999999999999999999999764 578887 55555443

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Rsm22 has been identified as a mitochondrial small ribosomal subunit [] and is a methyltransferase. In Schizosaccharomyces pombe (Fission yeast), Rsm22 is tandemly fused to Cox11 (a factor required for copper insertion into cytochrome oxidase) and the two proteins are proteolytically cleaved after import into the mitochondria []. This entry consists of mitochondrial Rsm22 and homologous sequences from bacteria.; GO: 0008168 methyltransferase activity, 0006412 translation

>COG3432 Predicted transcriptional regulator [Transcription]

Probab=86.71  E-value=0.51  Score=33.77  Aligned_cols=62  Identities=15%  Similarity=0.287  Sum_probs=44.4

Q ss_pred             hhhHHh-hcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccccccc
Q 041256           38 VFEIIS-KAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFV  108 (244)
Q Consensus        38 ifd~L~-~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l~  108 (244)
                      +||+|. ..+  +++...-|.-.++++      -.. ...+++.|+..|++..........|.+|+.+..|.
T Consensus        20 i~dIL~~~~~--~~~~~Tri~y~aNln------y~~-~~~yi~~L~~~Gli~~~~~~~~~~y~lT~KG~~fl   82 (95)
T COG3432          20 IFDILKAISE--GGIGITRIIYGANLN------YKR-AQKYIEMLVEKGLIIKQDNGRRKVYELTEKGKRFL   82 (95)
T ss_pred             HHHHHHHhcC--CCCCceeeeeecCcC------HHH-HHHHHHHHHhCCCEEeccCCccceEEEChhHHHHH
Confidence            567776 222  688888899999986      456 89999999999966642111112699999887554

>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities

Probab=86.57  E-value=1  Score=29.45  Aligned_cols=34  Identities=18%  Similarity=0.220  Sum_probs=28.2

Q ss_pred             CCC-CHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           49 AKL-SVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        49 g~~-t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      ..+ |..+||+..+++      ..- +++.|+.|...|++..
T Consensus        22 ~~lps~~~la~~~~vs------r~t-vr~al~~L~~~g~i~~   56 (64)
T PF00392_consen   22 DRLPSERELAERYGVS------RTT-VREALRRLEAEGLIER   56 (64)
T ss_dssp             SBE--HHHHHHHHTS-------HHH-HHHHHHHHHHTTSEEE
T ss_pred             CEeCCHHHHHHHhccC------CcH-HHHHHHHHHHCCcEEE
Confidence            467 999999999996      345 9999999999999986

The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....

>PF05724 TPMT: Thiopurine S-methyltransferase (TPMT); InterPro: IPR008854 This family consists of thiopurine S-methyltransferase proteins from both eukaryotes and prokaryotes

Probab=86.52  E-value=1.1  Score=37.13  Aligned_cols=40  Identities=20%  Similarity=0.300  Sum_probs=34.6

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDA  232 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a  232 (244)
                      .....+|++.|||.|+.+..|+++  +.+++.+|+ |..|+.+
T Consensus        35 ~~~~~rvLvPgCG~g~D~~~La~~--G~~VvGvDls~~Ai~~~   75 (218)
T PF05724_consen   35 LKPGGRVLVPGCGKGYDMLWLAEQ--GHDVVGVDLSPTAIEQA   75 (218)
T ss_dssp             TSTSEEEEETTTTTSCHHHHHHHT--TEEEEEEES-HHHHHHH
T ss_pred             CCCCCeEEEeCCCChHHHHHHHHC--CCeEEEEecCHHHHHHH
Confidence            455679999999999999999987  578999999 7788776

Thiopurine S-methyltransferase (TPMT) is a cytosolic enzyme that catalyses S-methylation of aromatic and heterocyclic sulphydryl compounds, including anticancer and immunosuppressive thiopurines [].; GO: 0008119 thiopurine S-methyltransferase activity, 0008152 metabolic process, 0005737 cytoplasm; PDB: 1PJZ_A 2H11_A 2BZG_A 3LCC_A 3BGD_A 2GB4_A 3BGI_B.

>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria

Probab=86.50  E-value=1  Score=29.83  Aligned_cols=40  Identities=25%  Similarity=0.321  Sum_probs=30.1

Q ss_pred             HhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           42 ISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        42 L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      +.+.|  -|-|+.|||+.+|+.   .  +.. +.+.|+.|...|++.+
T Consensus        19 ~~~~G--~~Pt~rEIa~~~g~~---S--~~t-v~~~L~~Le~kG~I~r   58 (65)
T PF01726_consen   19 IEENG--YPPTVREIAEALGLK---S--TST-VQRHLKALERKGYIRR   58 (65)
T ss_dssp             HHHHS--S---HHHHHHHHTSS---S--HHH-HHHHHHHHHHTTSEEE
T ss_pred             HHHcC--CCCCHHHHHHHhCCC---C--hHH-HHHHHHHHHHCcCccC
Confidence            34444  477999999999995   2  445 9999999999999995

The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.

>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=86.27  E-value=0.8  Score=25.87  Aligned_cols=31  Identities=16%  Similarity=0.295  Sum_probs=24.2

Q ss_pred             CCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcc
Q 041256           50 KLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNAL   87 (244)
Q Consensus        50 ~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll   87 (244)
                      |+|-+|||..+|+.      .+- +.|+|..|...|++
T Consensus         2 ~mtr~diA~~lG~t------~ET-VSR~l~~l~~~glI   32 (32)
T PF00325_consen    2 PMTRQDIADYLGLT------RET-VSRILKKLERQGLI   32 (32)
T ss_dssp             E--HHHHHHHHTS-------HHH-HHHHHHHHHHTTSE
T ss_pred             CcCHHHHHHHhCCc------HHH-HHHHHHHHHHcCCC
Confidence            57889999999997      455 99999999988874

These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....

>PRK14904 16S rRNA methyltransferase B; Provisional

Probab=86.08  E-value=0.95  Score=41.68  Aligned_cols=44  Identities=11%  Similarity=0.040  Sum_probs=34.5

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCC-CCeEEEccc-hHHhhhCCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYP-HIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .....+|+|+|||.|..+..+++..+ .-+++.+|+ +..++.+++
T Consensus       248 ~~~g~~VLDlgaG~G~kt~~la~~~~~~~~V~avD~s~~~l~~~~~  293 (445)
T PRK14904        248 PQPGSTVLDLCAAPGGKSTFMAELMQNRGQITAVDRYPQKLEKIRS  293 (445)
T ss_pred             CCCCCEEEEECCCCCHHHHHHHHHhCCCcEEEEEECCHHHHHHHHH
Confidence            34457999999999999998888764 457899998 777766654

>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators

Probab=85.99  E-value=2.2  Score=27.34  Aligned_cols=32  Identities=16%  Similarity=0.166  Sum_probs=28.1

Q ss_pred             CCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           51 LSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        51 ~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      .|..+||+.++++      ... +.+.|..|...|+++.
T Consensus        26 ~~~~~la~~~~is------~~~-v~~~l~~L~~~G~i~~   57 (66)
T cd07377          26 PSERELAEELGVS------RTT-VREALRELEAEGLVER   57 (66)
T ss_pred             CCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEe
Confidence            3599999999997      456 9999999999999984

This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is

>PRK13256 thiopurine S-methyltransferase; Reviewed

Probab=85.96  E-value=0.77  Score=38.37  Aligned_cols=39  Identities=18%  Similarity=0.145  Sum_probs=33.1

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDA  232 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a  232 (244)
                      ....+|++.|||.|..+..|+++  +.+++.+|+ |..|+.+
T Consensus        42 ~~~~rvLvPgCGkg~D~~~LA~~--G~~V~GvDlS~~Ai~~~   81 (226)
T PRK13256         42 NDSSVCLIPMCGCSIDMLFFLSK--GVKVIGIELSEKAVLSF   81 (226)
T ss_pred             CCCCeEEEeCCCChHHHHHHHhC--CCcEEEEecCHHHHHHH
Confidence            34579999999999999999886  667999999 7777775

>COG1378 Predicted transcriptional regulators [Transcription]

Probab=85.68  E-value=1.6  Score=37.00  Aligned_cols=63  Identities=16%  Similarity=0.146  Sum_probs=47.3

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccccccc
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFV  108 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l~  108 (244)
                      |..++-+|-..   |+.|+.|||+..|++    +  .. ++.+|+-|...|++... ...+..|+.-+....+.
T Consensus        18 Ea~vY~aLl~~---g~~tA~eis~~sgvP----~--~k-vY~vl~sLe~kG~v~~~-~g~P~~y~av~p~~~i~   80 (247)
T COG1378          18 EAKVYLALLCL---GEATAKEISEASGVP----R--PK-VYDVLRSLEKKGLVEVI-EGRPKKYRAVPPEELIE   80 (247)
T ss_pred             HHHHHHHHHHh---CCccHHHHHHHcCCC----c--hh-HHHHHHHHHHCCCEEee-CCCCceEEeCCHHHHHH
Confidence            34456666665   699999999999995    3  35 99999999999999853 23467888877655443

>COG1522 Lrp Transcriptional regulators [Transcription]

Probab=85.68  E-value=1.1  Score=34.43  Aligned_cols=46  Identities=15%  Similarity=0.331  Sum_probs=39.5

Q ss_pred             HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      ++..|.+.|.+.   ++.+..+||+++|++      +.. +.+-++-|...|++..
T Consensus         9 ~D~~IL~~L~~d---~r~~~~eia~~lglS------~~~-v~~Ri~~L~~~GiI~~   54 (154)
T COG1522           9 IDRRILRLLQED---ARISNAELAERVGLS------PST-VLRRIKRLEEEGVIKG   54 (154)
T ss_pred             HHHHHHHHHHHh---CCCCHHHHHHHHCCC------HHH-HHHHHHHHHHCCceee
Confidence            466788889885   689999999999997      455 8999999999999983

>PRK06474 hypothetical protein; Provisional

Probab=85.59  E-value=1.3  Score=35.60  Aligned_cols=71  Identities=18%  Similarity=0.302  Sum_probs=50.9

Q ss_pred             HHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhC-CCCCCCCcchhccHHHHHHHHhhCCcccceeec--C---CceeecC
Q 041256           28 AVMQAVVELDVFEIISKAGPGAKLSVAEIVAQI-PLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVD--G---QRLYSLA  101 (244)
Q Consensus        28 ~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~-~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~--~---~~~y~~t  101 (244)
                      .+|.--.++.|++.|...+  ++.|+.+|++.+ +++      ..- +.|-|+.|...|++......  +   ...|+.+
T Consensus         6 ~~La~p~R~~Il~~L~~~~--~~~ta~el~~~l~~is------~aT-vYrhL~~L~e~GLI~~~~~~~~~~~~ek~y~~~   76 (178)
T PRK06474          6 EILMHPVRMKICQVLMRNK--EGLTPLELVKILKDVP------QAT-LYRHLQTMVDSGILHVVKEKKVRSVSEKYYAIN   76 (178)
T ss_pred             HhhCCHHHHHHHHHHHhCC--CCCCHHHHHHHhcCCC------HHH-HHHHHHHHHHCCCEEEeecccccCceeEEEEec
Confidence            4556667888999998753  359999999999 564      234 89999999999999964221  1   1247777


Q ss_pred             cccccc
Q 041256          102 PVSAYF  107 (244)
Q Consensus       102 ~~s~~l  107 (244)
                      +.+..+
T Consensus        77 ~~~~~~   82 (178)
T PRK06474         77 EEDAKI   82 (178)
T ss_pred             cceeee
Confidence            765443

>PF07789 DUF1627: Protein of unknown function (DUF1627); InterPro: IPR012432 This is a group of sequences found in hypothetical proteins predicted to be expressed in a number of bacterial species

Probab=85.40  E-value=1.4  Score=34.06  Aligned_cols=46  Identities=11%  Similarity=0.192  Sum_probs=35.5

Q ss_pred             CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecC
Q 041256           49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLA  101 (244)
Q Consensus        49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t  101 (244)
                      |++|.+|||.+.|++      .+. +.--|-++++.|-+.+....+.=+|..+
T Consensus         5 Ga~T~eELA~~FGvt------tRk-vaStLa~~ta~Grl~Rv~q~gkfRy~iP   50 (155)
T PF07789_consen    5 GAKTAEELAGKFGVT------TRK-VASTLAMVTATGRLIRVNQNGKFRYCIP   50 (155)
T ss_pred             CcccHHHHHHHhCcc------hhh-hHHHHHHHHhcceeEEecCCCceEEeCC
Confidence            899999999999997      556 8889999999999886432222345553

The region in question is approximately 150 amino acid residues long.

>COG0030 KsgA Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]

Probab=85.21  E-value=2.1  Score=36.54  Aligned_cols=43  Identities=19%  Similarity=0.475  Sum_probs=35.3

Q ss_pred             HHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEcc
Q 041256          181 MEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYD  224 (244)
Q Consensus       181 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~D  224 (244)
                      ...+++..+ ......|+.||.|.|.+...|+++...+.++=.|
T Consensus        19 ~~kIv~~a~-~~~~d~VlEIGpG~GaLT~~Ll~~~~~v~aiEiD   61 (259)
T COG0030          19 IDKIVEAAN-ISPGDNVLEIGPGLGALTEPLLERAARVTAIEID   61 (259)
T ss_pred             HHHHHHhcC-CCCCCeEEEECCCCCHHHHHHHhhcCeEEEEEeC
Confidence            456777666 5557899999999999999999999887776666

>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional

Probab=85.00  E-value=1  Score=42.04  Aligned_cols=67  Identities=12%  Similarity=0.182  Sum_probs=51.4

Q ss_pred             HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccccccccCC
Q 041256           34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFVRNN  111 (244)
Q Consensus        34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l~~~~  111 (244)
                      .+..+...|...   ++.|..+||+.++++      +.. +.+.++-|.+.|+++...+ ....|.+|+.++.+....
T Consensus         7 ~e~~vL~~L~~~---~~~s~~eLA~~l~l~------~~t-Vt~~i~~Le~kGlV~~~~~-~~~~i~LTeeG~~~~~~g   73 (489)
T PRK04172          7 NEKKVLKALKEL---KEATLEELAEKLGLP------PEA-VMRAAEWLEEKGLVKVEER-VEEVYVLTEEGKKYAEEG   73 (489)
T ss_pred             HHHHHHHHHHhC---CCCCHHHHHHHhCcC------HHH-HHHHHHHHHhCCCEEEEee-eEEEEEECHHHHHHHHhc
Confidence            344556667664   589999999999997      456 9999999999999996432 236799999998665544

>PF03141 Methyltransf_29: Putative S-adenosyl-L-methionine-dependent methyltransferase; InterPro: IPR004159 Members of this family of hypothetical plant proteins are putative methyltransferases

Probab=84.90  E-value=0.83  Score=42.33  Aligned_cols=24  Identities=17%  Similarity=0.336  Sum_probs=21.7

Q ss_pred             CCcceEEEecCCccHHHHHHHHHC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKY  215 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~  215 (244)
                      ...++++|||||.|.++..++++.
T Consensus       116 g~iR~~LDvGcG~aSF~a~l~~r~  139 (506)
T PF03141_consen  116 GGIRTALDVGCGVASFGAYLLERN  139 (506)
T ss_pred             CceEEEEeccceeehhHHHHhhCC
Confidence            357999999999999999999985

; GO: 0008168 methyltransferase activity

>TIGR00446 nop2p NOL1/NOP2/sun family putative RNA methylase

Probab=84.62  E-value=1.5  Score=37.35  Aligned_cols=43  Identities=9%  Similarity=0.033  Sum_probs=34.3

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCC-CeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPH-IKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dl-p~vi~~a~~  234 (244)
                      ....+|+|+|+|.|..+..+++..++ -+++..|. +..++.+++
T Consensus        70 ~~g~~VLDl~ag~G~kt~~la~~~~~~g~v~a~D~~~~~l~~~~~  114 (264)
T TIGR00446        70 DPPERVLDMAAAPGGKTTQISALMKNEGAIVANEFSKSRTKVLIA  114 (264)
T ss_pred             CCcCEEEEECCCchHHHHHHHHHcCCCCEEEEEcCCHHHHHHHHH
Confidence            45578999999999999999988754 57888998 666666553

>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional

Probab=84.56  E-value=0.98  Score=40.82  Aligned_cols=40  Identities=15%  Similarity=0.013  Sum_probs=35.2

Q ss_pred             ceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          195 KKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       195 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+|+|+++|+|.+++.++.+.+-.+++..|. |..++.+++
T Consensus        59 ~~vLDl~aGsG~~~l~~a~~~~~~~V~a~Din~~Av~~a~~   99 (382)
T PRK04338         59 ESVLDALSASGIRGIRYALETGVEKVTLNDINPDAVELIKK   99 (382)
T ss_pred             CEEEECCCcccHHHHHHHHHCCCCEEEEEeCCHHHHHHHHH
Confidence            5899999999999999999888667899998 888888764

>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term

Probab=84.48  E-value=1.4  Score=32.78  Aligned_cols=40  Identities=8%  Similarity=0.097  Sum_probs=33.6

Q ss_pred             CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCce
Q 041256           49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRL   97 (244)
Q Consensus        49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~   97 (244)
                      .++|++|||+.+.++      ++. ++.+|+-|...|+++-.  ++.|+
T Consensus        18 ~~vtl~elA~~l~cS------~Rn-~r~lLkkm~~~gWi~W~--pg~GR   57 (115)
T PF12793_consen   18 VEVTLDELAELLFCS------RRN-ARTLLKKMQEEGWITWQ--PGRGR   57 (115)
T ss_pred             cceeHHHHHHHhCCC------HHH-HHHHHHHHHHCCCeeee--CCCCC
Confidence            578999999999998      567 99999999999999963  34454

>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain

Probab=84.34  E-value=1  Score=41.79  Aligned_cols=68  Identities=10%  Similarity=0.161  Sum_probs=53.9

Q ss_pred             HHhcChhhHHhhcCCCCC-CCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccccccccCC
Q 041256           33 VVELDVFEIISKAGPGAK-LSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFVRNN  111 (244)
Q Consensus        33 a~~lgifd~L~~~~~~g~-~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l~~~~  111 (244)
                      +++..|...|.+.   ++ .+..+||+.+|++      .+. +.+.+..|.+.|+++...+ ....|.+|+.++.++..+
T Consensus         3 ~~e~~iL~~l~~~---~~~~~~~~la~~~g~~------~~~-v~~~~~~L~~kg~v~~~~~-~~~~~~LT~eG~~~l~~G   71 (492)
T PLN02853          3 MAEEALLGALSNN---EEISDSGQFAASHGLD------HNE-VVGVIKSLHGFRYVDAQDI-KRETWVLTEEGKKYAAEG   71 (492)
T ss_pred             hHHHHHHHHHHhc---CCCCCHHHHHHHcCCC------HHH-HHHHHHHHHhCCCEEEEEE-EEEEEEECHHHHHHHHcC
Confidence            4567788888874   44 7999999999997      456 9999999999999986533 357899999998555544

>PRK15128 23S rRNA m(5)C1962 methyltransferase; Provisional

Probab=84.26  E-value=0.97  Score=41.05  Aligned_cols=42  Identities=10%  Similarity=-0.071  Sum_probs=32.8

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+.++|+|+|||+|.++...+.. ...+++.+|+ |..++.+++
T Consensus       219 ~~g~rVLDlfsgtG~~~l~aa~~-ga~~V~~VD~s~~al~~a~~  261 (396)
T PRK15128        219 VENKRVLNCFSYTGGFAVSALMG-GCSQVVSVDTSQEALDIARQ  261 (396)
T ss_pred             cCCCeEEEeccCCCHHHHHHHhC-CCCEEEEEECCHHHHHHHHH
Confidence            34589999999999998876643 3457899998 788877765

>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A)

Probab=84.25  E-value=1.4  Score=31.70  Aligned_cols=48  Identities=17%  Similarity=0.281  Sum_probs=36.4

Q ss_pred             HhcChhhHHhh-cCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCccc
Q 041256           34 VELDVFEIISK-AGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALH   88 (244)
Q Consensus        34 ~~lgifd~L~~-~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~   88 (244)
                      +.-.|++.|.. ...+.++++.+|+++++++      +.. ++..|+.|+..|++-
T Consensus        48 ~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~------~~~-v~~al~~L~~eG~IY   96 (102)
T PF08784_consen   48 LQDKVLNFIKQQPNSEEGVHVDEIAQQLGMS------ENE-VRKALDFLSNEGHIY   96 (102)
T ss_dssp             HHHHHHHHHHC----TTTEEHHHHHHHSTS-------HHH-HHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHhcCCCCCcccHHHHHHHhCcC------HHH-HHHHHHHHHhCCeEe
Confidence            45557777776 2123579999999999996      456 999999999999886

RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.

>PF02319 E2F_TDP: E2F/DP family winged-helix DNA-binding domain; InterPro: IPR003316 The mammalian transcription factor E2F plays an important role in regulating the expression of genes that are required for passage through the cell cycle

Probab=84.17  E-value=0.56  Score=31.65  Aligned_cols=36  Identities=17%  Similarity=0.290  Sum_probs=30.4

Q ss_pred             CCCCHHHHHHhC---CCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           49 AKLSVAEIVAQI---PLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        49 g~~t~~eLA~~~---~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      +.+++.++|+.+   +..  +.  .++ ++-++.+|.++|++++
T Consensus        23 ~~i~l~~ia~~l~~~~~k--~~--~RR-lYDI~NVLealgli~K   61 (71)
T PF02319_consen   23 KSISLNEIADKLISENVK--TQ--RRR-LYDIINVLEALGLIEK   61 (71)
T ss_dssp             TEEEHHHHHHHCHHHCCH--HH--CHH-HHHHHHHHHHCTSEEE
T ss_pred             CcccHHHHHHHHcccccc--cc--cch-hhHHHHHHHHhCceee
Confidence            689999999999   872  11  456 9999999999999995

Multiple E2F family members have been identified that bind to DNA as heterodimers, interacting with proteins known as DP - the dimerisation partners [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005667 transcription factor complex; PDB: 1CF7_B.

>PLN02476 O-methyltransferase

Probab=83.79  E-value=1.3  Score=38.22  Aligned_cols=44  Identities=11%  Similarity=0.046  Sum_probs=36.5

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCC-CCeEEEccc-hHHhhhCCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYP-HIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..++++||+||.+.|..++.+++..| +-+.+-+|. |+..+.|++
T Consensus       116 ~~~ak~VLEIGT~tGySal~lA~al~~~G~V~TiE~d~e~~~~Ar~  161 (278)
T PLN02476        116 ILGAERCIEVGVYTGYSSLAVALVLPESGCLVACERDSNSLEVAKR  161 (278)
T ss_pred             hcCCCeEEEecCCCCHHHHHHHHhCCCCCEEEEEECCHHHHHHHHH
Confidence            45789999999999999999999876 567788888 666777754

>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed

Probab=83.43  E-value=1.8  Score=39.53  Aligned_cols=43  Identities=26%  Similarity=0.235  Sum_probs=35.6

Q ss_pred             CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecC
Q 041256           49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLA  101 (244)
Q Consensus        49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t  101 (244)
                      .|.|.++|++.++++      ++. ++++|+.|...|++.+   .+++.|.+.
T Consensus       309 ~~~t~~~La~~l~~~------~~~-v~~iL~~L~~agLI~~---~~~g~~~l~  351 (412)
T PRK04214        309 KALDVDEIRRLEPMG------YDE-LGELLCELARIGLLRR---GERGQWVLA  351 (412)
T ss_pred             CCCCHHHHHHHhCCC------HHH-HHHHHHHHHhCCCeEe---cCCCceEec
Confidence            689999999999996      567 9999999999999984   344556553

>KOG4589 consensus Cell division protein FtsJ [Cell cycle control, cell division, chromosome partitioning]

Probab=83.06  E-value=2  Score=34.87  Aligned_cols=45  Identities=16%  Similarity=0.228  Sum_probs=35.1

Q ss_pred             HhhcCCCCCcceEEEecCCccHHHHHHHHHC-CCCeEEEccchHHh
Q 041256          185 LESYKGFEHVKKLVDVGGGLGITLNMIISKY-PHIKGINYDLPYVI  229 (244)
Q Consensus       185 ~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dlp~vi  229 (244)
                      -+.|..+....+|+|+|+-.|..+.-..++. |+-.+...||-++.
T Consensus        61 ndKy~~l~p~~~VlD~G~APGsWsQVavqr~~p~g~v~gVDllh~~  106 (232)
T KOG4589|consen   61 NDKYRFLRPEDTVLDCGAAPGSWSQVAVQRVNPNGMVLGVDLLHIE  106 (232)
T ss_pred             hhhccccCCCCEEEEccCCCChHHHHHHHhhCCCceEEEEeeeecc
Confidence            3445545667999999999999998877776 99888888985544

>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY

Probab=83.00  E-value=4.2  Score=34.22  Aligned_cols=63  Identities=19%  Similarity=0.272  Sum_probs=45.2

Q ss_pred             HHHHHHhhhHHHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           16 YAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        16 ~l~~~~~g~~~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      .+.+++.+.....=|.+.-  .|++.|...  +|-++..+||+++|++      ... +++-+|.|.+.|+++-
T Consensus       168 a~Vq~Ai~tLSySEleAv~--~IL~~L~~~--egrlse~eLAerlGVS------Rs~-ireAlrkLE~aGvIe~  230 (251)
T TIGR02787       168 AAVQMAINTLSYSELEAVE--HIFEELDGN--EGLLVASKIADRVGIT------RSV-IVNALRKLESAGVIES  230 (251)
T ss_pred             HHHHHHHHhccHhHHHHHH--HHHHHhccc--cccccHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEe
Confidence            4444544544444343322  478888762  2689999999999997      456 9999999999999984

This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.

>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress

Probab=82.36  E-value=3.1  Score=28.61  Aligned_cols=47  Identities=6%  Similarity=-0.024  Sum_probs=37.2

Q ss_pred             CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecC-CceeecCccc
Q 041256           49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDG-QRLYSLAPVS  104 (244)
Q Consensus        49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~-~~~y~~t~~s  104 (244)
                      .|+...+||+.++.+      +.- ++-.|..|..+||++..  ++ .+.|..|..+
T Consensus        22 ~PVgSk~ia~~l~~s------~aT-IRN~M~~Le~lGlve~~--p~~s~GriPT~~a   69 (78)
T PF03444_consen   22 EPVGSKTIAEELGRS------PAT-IRNEMADLEELGLVESQ--PHPSGGRIPTDKA   69 (78)
T ss_pred             CCcCHHHHHHHHCCC------hHH-HHHHHHHHHHCCCccCC--CCCCCCCCcCHHH
Confidence            699999999999997      445 99999999999999841  22 3557777665

Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent

>PRK11783 rlmL 23S rRNA m(2)G2445 methyltransferase; Provisional

Probab=82.14  E-value=1.3  Score=43.37  Aligned_cols=41  Identities=10%  Similarity=-0.059  Sum_probs=34.1

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      +.++|+|+|||+|.++..+++. ..-+++.+|+ +..++.+++
T Consensus       538 ~g~rVLDlf~gtG~~sl~aa~~-Ga~~V~~vD~s~~al~~a~~  579 (702)
T PRK11783        538 KGKDFLNLFAYTGTASVHAALG-GAKSTTTVDMSNTYLEWAER  579 (702)
T ss_pred             CCCeEEEcCCCCCHHHHHHHHC-CCCEEEEEeCCHHHHHHHHH
Confidence            4589999999999999999986 3336899998 888888775

>KOG1500 consensus Protein arginine N-methyltransferase CARM1 [Posttranslational modification, protein turnover, chaperones; Transcription]

Probab=81.62  E-value=2.2  Score=37.77  Aligned_cols=31  Identities=32%  Similarity=0.502  Sum_probs=21.6

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHH
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISK  214 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~  214 (244)
                      .+++.-.+|++ +.|||||+|+|.++.-.+++
T Consensus       168 Ail~N~sDF~~-kiVlDVGaGSGILS~FAaqA  198 (517)
T KOG1500|consen  168 AILENHSDFQD-KIVLDVGAGSGILSFFAAQA  198 (517)
T ss_pred             HHHhcccccCC-cEEEEecCCccHHHHHHHHh
Confidence            44443322555 89999999999988765554

>PRK05638 threonine synthase; Validated

Probab=80.95  E-value=2.1  Score=39.43  Aligned_cols=58  Identities=17%  Similarity=0.256  Sum_probs=42.0

Q ss_pred             hhhHHhhcCCCCCCCHHHHHHhCC--CCCCCCcchhccHHHHHHHHhhCCcccceeecC-CceeecCccccc
Q 041256           38 VFEIISKAGPGAKLSVAEIVAQIP--LKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDG-QRLYSLAPVSAY  106 (244)
Q Consensus        38 ifd~L~~~~~~g~~t~~eLA~~~~--~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~-~~~y~~t~~s~~  106 (244)
                      |+..|.+    ++.+.-||++.++  ++      ... +.+.|+.|...|+++...+.+ .-.|++|+.+..
T Consensus       376 IL~~L~~----~~~~~~el~~~l~~~~s------~~~-v~~hL~~Le~~GLV~~~~~~g~~~~Y~Lt~~g~~  436 (442)
T PRK05638        376 ILKILSE----REMYGYEIWKALGKPLK------YQA-VYQHIKELEELGLIEEAYRKGRRVYYKLTEKGRR  436 (442)
T ss_pred             HHHHHhh----CCccHHHHHHHHcccCC------cch-HHHHHHHHHHCCCEEEeecCCCcEEEEECcHHHH
Confidence            5555654    6899999999998  54      345 999999999999997421122 234888887753

>COG4122 Predicted O-methyltransferase [General function prediction only]

Probab=80.80  E-value=2  Score=35.77  Aligned_cols=44  Identities=11%  Similarity=0.154  Sum_probs=38.9

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCC-CCeEEEccc-hHHhhhCCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYP-HIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+++++++.||.+.|.-++.++..-| +-+.+-+|+ |+-++.|++
T Consensus        57 ~~~~k~iLEiGT~~GySal~mA~~l~~~g~l~tiE~~~e~~~~A~~  102 (219)
T COG4122          57 LSGPKRILEIGTAIGYSALWMALALPDDGRLTTIERDEERAEIARE  102 (219)
T ss_pred             hcCCceEEEeecccCHHHHHHHhhCCCCCeEEEEeCCHHHHHHHHH
Confidence            56889999999999999999999999 778888998 777777765

>PRK13509 transcriptional repressor UlaR; Provisional

Probab=80.74  E-value=2.7  Score=35.59  Aligned_cols=43  Identities=14%  Similarity=0.251  Sum_probs=37.4

Q ss_pred             ChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           37 DVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        37 gifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      .|.+.|.+.   +..++.|||+.+|++      +.- ++|-|+.|...|++.+
T Consensus         9 ~Il~~l~~~---~~~~~~ela~~l~vS------~~T-irRdL~~Le~~g~i~r   51 (251)
T PRK13509          9 ILLELLAQL---GFVTVEKVIERLGIS------PAT-ARRDINKLDESGKLKK   51 (251)
T ss_pred             HHHHHHHHc---CCcCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEE
Confidence            477888875   689999999999997      445 9999999999999985

>COG1846 MarR Transcriptional regulators [Transcription]

Probab=80.56  E-value=2.7  Score=30.44  Aligned_cols=65  Identities=17%  Similarity=0.203  Sum_probs=44.5

Q ss_pred             HHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCcccccc
Q 041256           33 VVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSAYF  107 (244)
Q Consensus        33 a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~~l  107 (244)
                      -.+..+...|...   ++.+..+||+.++++      ... +.++++-|...|++.+.....+.   .+.+|+.+..+
T Consensus        22 ~~q~~~L~~l~~~---~~~~~~~la~~l~i~------~~~-vt~~l~~Le~~glv~r~~~~~DrR~~~l~lT~~G~~~   89 (126)
T COG1846          22 PPQYQVLLALYEA---GGITVKELAERLGLD------RST-VTRLLKRLEDKGLIERLRDPEDRRAVLVRLTEKGREL   89 (126)
T ss_pred             HHHHHHHHHHHHh---CCCcHHHHHHHHCCC------HHH-HHHHHHHHHHCCCeeecCCccccceeeEEECccHHHH
Confidence            3455566677775   344449999999997      456 99999999999999964222122   35666665533

>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B

Probab=80.42  E-value=2.2  Score=25.56  Aligned_cols=27  Identities=15%  Similarity=0.409  Sum_probs=20.8

Q ss_pred             HhcChhhHHhhcCCCCCCCHHHHHHhCCCC
Q 041256           34 VELDVFEIISKAGPGAKLSVAEIVAQIPLK   63 (244)
Q Consensus        34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~   63 (244)
                      ++..|.+.|.+.   +..+.++||+.+|++
T Consensus         4 ~D~~Il~~Lq~d---~r~s~~~la~~lglS   30 (42)
T PF13404_consen    4 LDRKILRLLQED---GRRSYAELAEELGLS   30 (42)
T ss_dssp             HHHHHHHHHHH----TTS-HHHHHHHHTS-
T ss_pred             HHHHHHHHHHHc---CCccHHHHHHHHCcC
Confidence            456688889885   689999999999997

...

>PRK13777 transcriptional regulator Hpr; Provisional

Probab=80.41  E-value=3.8  Score=33.13  Aligned_cols=44  Identities=16%  Similarity=0.040  Sum_probs=35.9

Q ss_pred             ChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           37 DVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        37 gifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      .+.-.|...   +++|..+||+.++++      ..- +.++++-|...|++.+.
T Consensus        49 ~iL~~L~~~---~~itq~eLa~~l~l~------~sT-vtr~l~rLE~kGlI~R~   92 (185)
T PRK13777         49 HILWIAYHL---KGASISEIAKFGVMH------VST-AFNFSKKLEERGYLTFS   92 (185)
T ss_pred             HHHHHHHhC---CCcCHHHHHHHHCCC------Hhh-HHHHHHHHHHCCCEEec
Confidence            455666664   589999999999986      345 89999999999999964

>PF04072 LCM: Leucine carboxyl methyltransferase; InterPro: IPR007213 This entry represents a group of leucine carboxymethyltransferases which methylate the carboxyl group of leucine residues to form alpha-leucine ester residues

Probab=80.23  E-value=3.8  Score=32.76  Aligned_cols=42  Identities=21%  Similarity=0.290  Sum_probs=33.0

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAP  233 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~  233 (244)
                      ++...||-+|+|-=.....+...+++++.+=+|+|+|++.-+
T Consensus        77 ~~~~qvV~LGaGlDTr~~Rl~~~~~~~~~~evD~p~v~~~K~  118 (183)
T PF04072_consen   77 PGARQVVNLGAGLDTRAYRLDNPAGGVRWFEVDLPEVIALKR  118 (183)
T ss_dssp             TTESEEEEET-TT--HHHHHHHTTTTEEEEEEE-HHHHHHHH
T ss_pred             CCCcEEEEcCCCCCchHHHhhccccceEEEEeCCHHHHHHHH
Confidence            345699999999999999999999999999999999987643

It includes LCTM1 which regulates the activity of serine/threonine phosphatase 2A (PP2A) through methylation of the C-terminal leucine residue of the catalytic subunit of PP2A [, , ]. This affects the heteromultimeric composition of PP2A which in turn affects protein recognition and substrate specificity. Like many other methyltransferases LCTM1 uses S-adenosylmethionine (SAM) as the methyl donor. LCTM1 contains the common SAM-dependent methyltransferase core fold, with various insertions and additions creating a specific PP2A binding site []. This entry also contains LCTM2, a homologue of LCTM1 which is not necessary for PP2A methylation and whose function is not clear.; GO: 0008168 methyltransferase activity; PDB: 2UYQ_A 2CKD_B 2UYO_A 2ZZK_B 2ZWA_B 2ZW9_B 1RJE_C 2OB2_B 1RJF_A 1RJD_A ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	244
1kyw_A	365	Crystal Structure Analysis Of Caffeic Acid5-Hydroxy		2e-59
3reo_A	368	Monolignol O-Methyltransferase (Momt) Length = 368		4e-55
3p9c_A	364	Crystal Structure Of Perennial Ryegrass Lpomt1 Boun		1e-45
1fp1_D	372	Crystal Structure Analysis Of Chalcone O-Methyltran		6e-33
1fpq_A	372	Crystal Structure Analysis Of Selenomethionine Subs		2e-24
1fp2_A	352	Crystal Structure Analysis Of Isoflavone O-Methyltr		8e-06
1fpx_A	352	Crystal Structure Analysis Of Selenomethionine Subs		2e-04

>pdb|1KYW|A Chain A, Crystal Structure Analysis Of Caffeic Acid5-Hydroxyferulic Acid 35-O-Methyltransferase In Complex With 5- Hydroxyconiferaldehyde Length = 365

Iteration: 1
 Score =  225 bits (573), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 120/235 (51%), Positives = 159/235 (67%), Gaps = 11/235 (4%)
Query: 8   EEETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNP 67
           +EE N F  AM+LASA VLP ++++ +ELD+ EII+KAGPGA++S  EI +Q+P    NP
Sbjct: 16  DEEANLF--AMQLASASVLPMILKSALELDLLEIIAKAGPGAQISPIEIASQLPT--TNP 71
Query: 68  EAAAMTLDRVLRLLVSYNALHCSF---VDG--QRLYSLAPVSAYFVRNNQNGASLSPYMA 122
           +A  M LDR+LRLL  Y  L CS     DG  QRLY LA V+ Y V+N ++G S+S    
Sbjct: 72  DAPVM-LDRMLRLLACYIILTCSVRTQQDGKVQRLYGLATVAKYLVKN-EDGVSISALNL 129
Query: 123 LCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIVME 182
           +  DKV ++ W+ LK  +L+GGI FNKA+GM  ++Y G D RFN VFN GM  H++I M+
Sbjct: 130 MNQDKVLMESWYHLKDAVLDGGIPFNKAYGMTAFEYHGTDPRFNKVFNKGMSDHSTITMK 189
Query: 183 KVLESYKGFEHXXXXXXXXXXXXITLNMIISKYPHIKGINYDLPYVIKDAPSYPG 237
           K+LE+Y GFE               +N I+SKYP IKGIN+DLP+VI+DAPSYPG
Sbjct: 190 KILETYTGFEGLKSLVDVGGGTGAVINTIVSKYPTIKGINFDLPHVIEDAPSYPG 244

>pdb|3REO|A Chain A, Monolignol O-Methyltransferase (Momt) Length = 368

Iteration: 1
 Score =  211 bits (536), Expect = 4e-55,   Method: Compositional matrix adjust.
 Identities = 116/236 (49%), Positives = 154/236 (65%), Gaps = 12/236 (5%)
Query: 8   EEETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKA-GPGAKLSVAEIVAQIPLKDNN 66
           +EE N F  AM+LASA VLP  ++A +ELDV EI++K+  P   +S AEI AQ+P    N
Sbjct: 18  DEEANLF--AMQLASAAVLPMALKAAIELDVLEIMAKSVPPSGYISPAEIAAQLP--TTN 73
Query: 67  PEAAAMTLDRVLRLLVSYNALHCSFVD-----GQRLYSLAPVSAYFVRNNQNGASLSPYM 121
           PEA  M LDRVLRLL SY+ +  +  +      +RLY LAPV   F+  N++G SL+P++
Sbjct: 74  PEAPVM-LDRVLRLLASYSVVTYTLRELPSGKVERLYGLAPVCK-FLTKNEDGVSLAPFL 131
Query: 122 ALCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIVM 181
            L  DKV L+ WF LK  +LEGGI FNKA+GM I+DY G D R N VFN GM S+++I M
Sbjct: 132 LLATDKVLLEPWFYLKDAILEGGIPFNKAYGMNIFDYHGTDHRINKVFNKGMSSNSTITM 191
Query: 182 EKVLESYKGFEHXXXXXXXXXXXXITLNMIISKYPHIKGINYDLPYVIKDAPSYPG 237
           +K+LE Y GFE                +MI++KYP I  IN+DLP+VI+DAP++ G
Sbjct: 192 KKILEMYNGFEGLTTIVDVGGGTGAVASMIVAKYPSINAINFDLPHVIQDAPAFSG 247

>pdb|3P9C|A Chain A, Crystal Structure Of Perennial Ryegrass Lpomt1 Bound To Sah Length = 364

Iteration: 1
 Score =  179 bits (454), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 100/246 (40%), Positives = 147/246 (59%), Gaps = 13/246 (5%)
Query: 1   MASIADREEETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQI 60
           MA+ AD +       +A++LAS+ VLP  ++  +EL + EI+  AG G  L+  E+ A++
Sbjct: 12  MAASADEDA----CMFALQLASSSVLPMTLKNAIELGLLEILVAAG-GKSLTPTEVAAKL 66
Query: 61  PLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQ-----RLYSLAPVSAYFVRNNQNGA 115
           P    NPEA  M +DR+LRLL SYN + C   +G+     R Y  APV   F+  N++G 
Sbjct: 67  P-SAANPEAPDM-VDRILRLLASYNVVTCLVEEGKDGRLSRSYGAAPVCK-FLTPNEDGV 123
Query: 116 SLSPYMALCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLS 175
           S++    +  DKV ++ W+ LK  +L+GGI FNKA+GM  ++Y G D RFN VFN GM +
Sbjct: 124 SMAALALMNQDKVLMESWYYLKDAVLDGGIPFNKAYGMSAFEYHGTDPRFNRVFNEGMKN 183
Query: 176 HTSIVMEKVLESYKGFEHXXXXXXXXXXXXITLNMIISKYPHIKGINYDLPYVIKDAPSY 235
           H+ I+ +K+LE Y GFE              T+  I + YP IKG+N+DLP+VI +AP +
Sbjct: 184 HSIIITKKLLELYHGFEGLGTLVDVGGGVGATVAAIAAHYPTIKGVNFDLPHVISEAPQF 243
Query: 236 PGTLFI 241
           PG   +
Sbjct: 244 PGVTHV 249

>pdb|1FP1|D Chain D, Crystal Structure Analysis Of Chalcone O-Methyltransferase Length = 372

Iteration: 1
 Score =  137 bits (345), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 87/244 (35%), Positives = 137/244 (56%), Gaps = 10/244 (4%)
Query: 1   MASIADREEETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGP-GAKLSVAEIVAQ 59
           +++ +++ E++   S AM L + +V PAV+ A ++L++FEII+KA P GA +S +EI ++
Sbjct: 13  ISATSEQTEDSACLS-AMVLTTNLVYPAVLNAAIDLNLFEIIAKATPPGAFMSPSEIASK 71
Query: 60  IPLKDNNPEAAAMTLDRVLRLLVSYNALHCS---FVDG--QRLYSLAPVSAYFVRNNQNG 114
           +P    + +     LDR+LRLL SY+ L  +     DG  +R+Y L+ V  Y V +   G
Sbjct: 72  LPASTQHSDLPN-RLDRMLRLLASYSVLTSTTRTIEDGGAERVYGLSMVGKYLVPDESRG 130
Query: 115 ASLSPYMALCLDKVCLDGWFGLKKQLLEGGIA-FNKAHGMQIYDYLGVDSRFNDVFNNGM 173
              S    LC   + L  W   K+ +++  I  F   HG+  Y+++G D + N +FN  M
Sbjct: 131 YLASFTTFLCYPAL-LQVWMNFKEAVVDEDIDLFKNVHGVTKYEFMGKDKKMNQIFNKSM 189
Query: 174 LSHTSIVMEKVLESYKGFEHXXXXXXXXXXXXITLNMIISKYPHIKGINYDLPYVIKDAP 233
           +   +  M+++LE Y GFE               L +IISKYP IKGIN+DLP VI++AP
Sbjct: 190 VDVCATEMKRMLEIYTGFEGISTLVDVGGGSGRNLELIISKYPLIKGINFDLPQVIENAP 249
Query: 234 SYPG 237
              G
Sbjct: 250 PLSG 253

>pdb|1FPQ|A Chain A, Crystal Structure Analysis Of Selenomethionine Substituted Chalcone O- Methyltransferase Length = 372

Iteration: 1
 Score =  109 bits (272), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 82/244 (33%), Positives = 128/244 (52%), Gaps = 10/244 (4%)
Query: 1   MASIADREEETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGP-GAKLSVAEIVAQ 59
           +++ +++ E++   S A  L + +V PAV+ A ++L++FEII+KA P GA  S +EI ++
Sbjct: 13  ISATSEQTEDSACLS-AXVLTTNLVYPAVLNAAIDLNLFEIIAKATPPGAFXSPSEIASK 71
Query: 60  IPLKDNNPEAAAMTLDRVLRLLVSYNALHCS---FVDG--QRLYSLAPVSAYFVRNNQNG 114
           +P    + +       R LRLL SY+ L  +     DG  +R+Y L+ V  Y V +   G
Sbjct: 72  LPASTQHSDLPNRLD-RXLRLLASYSVLTSTTRTIEDGGAERVYGLSXVGKYLVPDESRG 130
Query: 115 ASLSPYMALCLDKVCLDGWFGLKKQLLEGGIA-FNKAHGMQIYDYLGVDSRFNDVFNNGM 173
              S    LC   + L  W   K+ +++  I  F   HG+  Y++ G D + N +FN   
Sbjct: 131 YLASFTTFLCYPAL-LQVWXNFKEAVVDEDIDLFKNVHGVTKYEFXGKDKKXNQIFNKSX 189
Query: 174 LSHTSIVMEKVLESYKGFEHXXXXXXXXXXXXITLNMIISKYPHIKGINYDLPYVIKDAP 233
           +   +   ++ LE Y GFE               L +IISKYP IKGIN+DLP VI++AP
Sbjct: 190 VDVCATEXKRXLEIYTGFEGISTLVDVGGGSGRNLELIISKYPLIKGINFDLPQVIENAP 249
Query: 234 SYPG 237
              G
Sbjct: 250 PLSG 253

>pdb|1FP2|A Chain A, Crystal Structure Analysis Of Isoflavone O-Methyltransferase Length = 352

Iteration: 1
 Score = 47.4 bits (111), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 44/203 (21%), Positives = 83/203 (40%), Gaps = 10/203 (4%)
Query: 30  MQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC 89
           ++  VE+++  II   G    LS    + Q+P       +    + R++R L ++N    
Sbjct: 33  LKWAVEMNIPNIIQNHGKPISLSNLVSILQVP------SSKIGNVRRLMRYL-AHNGFFE 85
Query: 90  SFVDGQRLYSLAPVSAYFVRNNQNGASLSPYMALCLDKVCLDGWFGLKKQLLEGGIA-FN 148
                +  Y+L   S   VR +     L+P +   LD      +  LKK + E  +  F 
Sbjct: 86  IITKEEESYALTVASELLVRGSD--LCLAPMVECVLDPTLSGSYHELKKWIYEEDLTLFG 143
Query: 149 KAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIVMEKVLESYKGFEHXXXXXXXXXXXXITL 208
              G   +D+L  +  +N  FN+ M S + ++   + +    F+              T 
Sbjct: 144 VTLGSGFWDFLDKNPEYNTSFNDAMASDSKLINLALRDCDFVFDGLESIVDVGGGTGTTA 203
Query: 209 NMIISKYPHIKGINYDLPYVIKD 231
            +I   +P +K I +D P V+++
Sbjct: 204 KIICETFPKLKCIVFDRPQVVEN 226

>pdb|1FPX|A Chain A, Crystal Structure Analysis Of Selenomethionine Substituted Isoflavone O-Methyltransferase Length = 352

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 44/210 (20%), Positives = 82/210 (39%), Gaps = 10/210 (4%)
Query: 23  AIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLV 82
           A +    ++  VE ++  II   G    LS    + Q+P       +    + R+ R L 
Sbjct: 26  AFIDSXSLKWAVEXNIPNIIQNHGKPISLSNLVSILQVP------SSKIGNVRRLXRYL- 78
Query: 83  SYNALHCSFVDGQRLYSLAPVSAYFVRNNQNGASLSPYMALCLDKVCLDGWFGLKKQLLE 142
           ++N         +  Y+L   S   VR +     L+P +   LD      +  LKK + E
Sbjct: 79  AHNGFFEIITKEEESYALTVASELLVRGSD--LCLAPXVECVLDPTLSGSYHELKKWIYE 136
Query: 143 GGIA-FNKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIVMEKVLESYKGFEHXXXXXXXX 201
             +  F    G   +D+L  +  +N  FN+   S + ++   + +    F+         
Sbjct: 137 EDLTLFGVTLGSGFWDFLDKNPEYNTSFNDAXASDSKLINLALRDCDFVFDGLESIVDVG 196
Query: 202 XXXXITLNMIISKYPHIKGINYDLPYVIKD 231
                T  +I   +P +K I +D P V+++
Sbjct: 197 GGTGTTAKIICETFPKLKCIVFDRPQVVEN 226

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	244
3reo_A	368	(ISO)eugenol O-methyltransferase; directed evoluti	1e-76
3p9c_A	364	Caffeic acid O-methyltransferase; S-adenosylmethio	1e-73
1fp1_D	372	Isoliquiritigenin 2'-O-methyltransferase; protein-	3e-73
1fp2_A	352	Isoflavone O-methyltransferase; protein-product co	1e-70
1zg3_A	358	Isoflavanone 4'-O-methyltransferase; rossman fold,	3e-66
3gwz_A	369	MMCR; methyltransferase, mitomycin, S-adenosyl met	2e-64
3lst_A	348	CALO1 methyltransferase; calicheamicin, enediyne,	4e-64
3i53_A	332	O-methyltransferase; CO-complex, rossmann-like fol	2e-62
1qzz_A	374	RDMB, aclacinomycin-10-hydroxylase; anthracycline,	3e-61
1tw3_A	360	COMT, carminomycin 4-O-methyltransferase; anthracy	4e-60
2ip2_A	334	Probable phenazine-specific methyltransferase; pyo	4e-58
2r3s_A	335	Uncharacterized protein; methyltransferase domain,	6e-48
3dp7_A	363	SAM-dependent methyltransferase; structural genomi	3e-46
1x19_A	359	CRTF-related protein; methyltransferase, bacterioc	8e-45
3mcz_A	352	O-methyltransferase; adomet_mtases, S-adenosylmeth	1e-40

>3reo_A (ISO)eugenol O-methyltransferase; directed evolution, saturation mutagenesis, regioselectivity transferase; HET: SAH EUG; 1.90A {Clarkia breweri} PDB: 1kyz_A* 1kyw_A* Length = 368

 Score =  235 bits (600), Expect = 1e-76
 Identities = 115/247 (46%), Positives = 160/247 (64%), Gaps = 10/247 (4%)

Query: 1   MASIADREEETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAG-PGAKLSVAEIVAQ 59
           +  I     +     +AM+LASA VLP  ++A +ELDV EI++K+  P   +S AEI AQ
Sbjct: 9   IQIIPTHSSDEEANLFAMQLASAAVLPMALKAAIELDVLEIMAKSVPPSGYISPAEIAAQ 68

Query: 60  IPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVD-----GQRLYSLAPVSAYFVRNNQNG 114
           +P        A + LDRVLRLL SY+ +  +  +      +RLY LAPV  +  +N ++G
Sbjct: 69  LPT---TNPEAPVMLDRVLRLLASYSVVTYTLRELPSGKVERLYGLAPVCKFLTKN-EDG 124

Query: 115 ASLSPYMALCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGML 174
            SL+P++ L  DKV L+ WF LK  +LEGGI FNKA+GM I+DY G D R N VFN GM 
Sbjct: 125 VSLAPFLLLATDKVLLEPWFYLKDAILEGGIPFNKAYGMNIFDYHGTDHRINKVFNKGMS 184

Query: 175 SHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPS 234
           S+++I M+K+LE Y GFE +  +VDVGGG G   +MI++KYP I  IN+DLP+VI+DAP+
Sbjct: 185 SNSTITMKKILEMYNGFEGLTTIVDVGGGTGAVASMIVAKYPSINAINFDLPHVIQDAPA 244

Query: 235 YPGTLFI 241
           + G   +
Sbjct: 245 FSGVEHL 251

>3p9c_A Caffeic acid O-methyltransferase; S-adenosylmethionine dependent O-methyltransferase; HET: SAH; 1.80A {Lolium perenne} PDB: 3p9i_A* 3p9k_A* Length = 364

 Score =  227 bits (580), Expect = 1e-73
 Identities = 105/249 (42%), Positives = 154/249 (61%), Gaps = 12/249 (4%)

Query: 1   MASIADR---EEETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIV 57
           M S A       + +   +A++LAS+ VLP  ++  +EL + EI+  AG  + L+  E+ 
Sbjct: 5   MGSTAADMAASADEDACMFALQLASSSVLPMTLKNAIELGLLEILVAAGGKS-LTPTEVA 63

Query: 58  AQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQ-----RLYSLAPVSAYFVRNNQ 112
           A++P    NPEA  M +DR+LRLL SYN + C   +G+     R Y  APV  +   N  
Sbjct: 64  AKLPS-AANPEAPDM-VDRILRLLASYNVVTCLVEEGKDGRLSRSYGAAPVCKFLTPNE- 120

Query: 113 NGASLSPYMALCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNG 172
           +G S++    +  DKV ++ W+ LK  +L+GGI FNKA+GM  ++Y G D RFN VFN G
Sbjct: 121 DGVSMAALALMNQDKVLMESWYYLKDAVLDGGIPFNKAYGMSAFEYHGTDPRFNRVFNEG 180

Query: 173 MLSHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDA 232
           M +H+ I+ +K+LE Y GFE +  LVDVGGG+G T+  I + YP IKG+N+DLP+VI +A
Sbjct: 181 MKNHSIIITKKLLELYHGFEGLGTLVDVGGGVGATVAAIAAHYPTIKGVNFDLPHVISEA 240

Query: 233 PSYPGTLFI 241
           P +PG   +
Sbjct: 241 PQFPGVTHV 249

>1fp1_D Isoliquiritigenin 2'-O-methyltransferase; protein-substrate, protein-product complex; HET: SAH HCC; 1.82A {Medicago sativa} SCOP: a.4.5.29 c.66.1.12 PDB: 1fpq_A* Length = 372

 Score =  226 bits (578), Expect = 3e-73
 Identities = 92/249 (36%), Positives = 140/249 (56%), Gaps = 12/249 (4%)

Query: 3   SIADREEETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAG-PGAKLSVAEIVAQIP 61
           S    + E +    AM L + +V PAV+ A ++L++FEII+KA  PGA +S +EI +++P
Sbjct: 14  SATSEQTEDSACLSAMVLTTNLVYPAVLNAAIDLNLFEIIAKATPPGAFMSPSEIASKLP 73

Query: 62  LKDNNPEAAAMTLDRVLRLLVSYNALHCSFV-----DGQRLYSLAPVSAYFVRNNQNGAS 116
               + +     LDR+LRLL SY+ L  +         +R+Y L+ V  Y V +  +   
Sbjct: 74  ASTQHSDLPNR-LDRMLRLLASYSVLTSTTRTIEDGGAERVYGLSMVGKYLVPDE-SRGY 131

Query: 117 LSPYMALCLDKVCLDGWFGLKKQLLEGGI-AFNKAHGMQIYDYLGVDSRFNDVFNNGMLS 175
           L+ +         L  W   K+ +++  I  F   HG+  Y+++G D + N +FN  M+ 
Sbjct: 132 LASFTTFLCYPALLQVWMNFKEAVVDEDIDLFKNVHGVTKYEFMGKDKKMNQIFNKSMVD 191

Query: 176 HTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSY 235
             +  M+++LE Y GFE +  LVDVGGG G  L +IISKYP IKGIN+DLP VI++AP  
Sbjct: 192 VCATEMKRMLEIYTGFEGISTLVDVGGGSGRNLELIISKYPLIKGINFDLPQVIENAPPL 251

Query: 236 PGTLFIKFV 244
            G   I+ V
Sbjct: 252 SG---IEHV 257

>1fp2_A Isoflavone O-methyltransferase; protein-product complex; HET: SAH HMO; 1.40A {Medicago sativa} SCOP: a.4.5.29 c.66.1.12 PDB: 1fpx_A* 2qyo_A* Length = 352

 Score =  219 bits (559), Expect = 1e-70
 Identities = 56/248 (22%), Positives = 106/248 (42%), Gaps = 16/248 (6%)

Query: 1   MASIADREEETNNF---SYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIV 57
           MAS  +  + +  F   +   +   A +    ++  VE+++  II   G    LS   +V
Sbjct: 1   MASSINGRKPSEIFKAQALLYKHIYAFIDSMSLKWAVEMNIPNIIQNHGKPISLS--NLV 58

Query: 58  AQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFVRNNQNGASL 117
           + + +    P +    + R++R L             +  Y+L   S   VR +     L
Sbjct: 59  SILQV----PSSKIGNVRRLMRYLAHNGFFEII-TKEEESYALTVASELLVRGS--DLCL 111

Query: 118 SPYMALCLDKVCLDGWFGLKKQLLEGGI-AFNKAHGMQIYDYLGVDSRFNDVFNNGMLSH 176
           +P +   LD      +  LKK + E  +  F    G   +D+L  +  +N  FN+ M S 
Sbjct: 112 APMVECVLDPTLSGSYHELKKWIYEEDLTLFGVTLGSGFWDFLDKNPEYNTSFNDAMASD 171

Query: 177 TSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYP 236
           + ++   + +    F+ ++ +VDVGGG G T  +I   +P +K I +D P V+++     
Sbjct: 172 SKLINLALRDCDFVFDGLESIVDVGGGTGTTAKIICETFPKLKCIVFDRPQVVENLSGSN 231

Query: 237 GTLFIKFV 244
               + +V
Sbjct: 232 N---LTYV 236

>1zg3_A Isoflavanone 4'-O-methyltransferase; rossman fold, plant Pro transferase; HET: 2HI SAH; 2.35A {Medicago truncatula} PDB: 1zga_A* 1zhf_A* 1zgj_A* Length = 358

 Score =  208 bits (530), Expect = 3e-66
 Identities = 58/237 (24%), Positives = 96/237 (40%), Gaps = 19/237 (8%)

Query: 16  YAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLD 75
           +  +     V    +++ +EL + + I   G     +++E+ + + L      +    L 
Sbjct: 13  HLYKHVYNFVSSMALKSAMELGIADAIHNHGKPM--TLSELASSLKL----HPSKVNILH 66

Query: 76  RVLRLLVSYNALHCSFVDG-------QRLYSLAPVSAYFVRNNQNGASLSPYMALCLDKV 128
           R LRLL        + V G       +  YSL P S   +        LS  +   L   
Sbjct: 67  RFLRLLTHNGFFAKTIVKGKEGDEEEEIAYSLTPPSKLLISGKPT--CLSSIVKGALHPS 124

Query: 129 CLDGWFGLKKQLLEGG--IAFNKAHGMQIYDYLGVDSRFN--DVFNNGMLSHTSIVMEKV 184
            LD W   KK   E      F  A G   +D+L  DS  +   +F + M S + +    +
Sbjct: 125 SLDMWSSSKKWFNEDKEQTLFECATGESFWDFLNKDSESSTLSMFQDAMASDSRMFKLVL 184

Query: 185 LESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPGTLFI 241
            E+ + FE ++ LVDVGGG G    +I   +PH+K   +D P V+ +        F+
Sbjct: 185 QENKRVFEGLESLVDVGGGTGGVTKLIHEIFPHLKCTVFDQPQVVGNLTGNENLNFV 241

>3gwz_A MMCR; methyltransferase, mitomycin, S-adenosyl methionine, transferase; HET: MSE SAH; 1.91A {Streptomyces lavendulae} PDB: 3gxo_A* Length = 369

 Score =  203 bits (519), Expect = 2e-64
 Identities = 41/219 (18%), Positives = 83/219 (37%), Gaps = 16/219 (7%)

Query: 17  AMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDR 76
             ++         +   VEL V E++ + GP    +   +         + +     L R
Sbjct: 42  VNDILQGAWKARAIHVAVELGVPELLQE-GP---RTATALAEATGA---HEQT----LRR 90

Query: 77  VLRLLVSYNALHCSFVDGQRLYSLAPVSAYFVRNNQNGASLSPYMALCLDKVCLDGWFGL 136
           +LRLL +        +    L++   +SA  + +    + ++              W  L
Sbjct: 91  LLRLLATVGVFDD--LGHDDLFAQNALSAVLLPDP--ASPVATDARFQAAPWHWRAWEQL 146

Query: 137 KKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIVMEKVLESYKGFEHVKK 196
              +  G  +F+ A+G   +     D +  ++FN  M S +     +V  +Y  F     
Sbjct: 147 THSVRTGEASFDVANGTSFWQLTHEDPKARELFNRAMGSVSLTEAGQVAAAYD-FSGAAT 205

Query: 197 LVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSY 235
            VD+GGG G  +  ++  +P ++G   + P V ++A   
Sbjct: 206 AVDIGGGRGSLMAAVLDAFPGLRGTLLERPPVAEEAREL 244

>3lst_A CALO1 methyltransferase; calicheamicin, enediyne, SAH, STRU genomics, PSI-2, protein structure initiative; HET: SAH; 2.40A {Micromonospora echinospora} Length = 348

 Score =  202 bits (516), Expect = 4e-64
 Identities = 46/240 (19%), Positives = 86/240 (35%), Gaps = 22/240 (9%)

Query: 2   ASIADREEETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIP 61
           +      +   +     E A      A ++A   + V + +   GP    + AE+ A   
Sbjct: 11  SRAGGDMDRLQSALALYEEAMGYTYAAALRAAAAVGVADHL-VDGP---RTPAELAAATG 66

Query: 62  LKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFVRNNQNGASLSPYM 121
               + +A    L RVLRLL   + +  S       ++L    A    ++         +
Sbjct: 67  T---DADA----LRRVLRLLAVRDVVRES----DGRFALTDKGAALRSDS--PVPARAGI 113

Query: 122 ALCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIVM 181
            +  D +       +   L     AF    G  +  Y   D+    ++  GM + ++   
Sbjct: 114 LMFTDTMFWTMSHRVASALGPERPAFADIFGSSLDAYFDGDAEVEALYYEGMETVSAAEH 173

Query: 182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVI----KDAPSYPG 237
             +  +   F     + DVGGG G  L  ++ ++P ++G+  D   V+     DAP   G
Sbjct: 174 LILARAG-DFPATGTVADVGGGRGGFLLTVLREHPGLQGVLLDRAEVVARHRLDAPDVAG 232

>3i53_A O-methyltransferase; CO-complex, rossmann-like fold; HET: SAH; 2.08A {Streptomyces carzinostaticus subsp} PDB: 3i58_A* 3i5u_A* 3i64_A* Length = 332

 Score =  197 bits (504), Expect = 2e-62
 Identities = 47/221 (21%), Positives = 86/221 (38%), Gaps = 18/221 (8%)

Query: 16  YAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLD 75
             +   + +  P  ++    L V + I+ AG     + AEI +       + ++    LD
Sbjct: 8   IGLRALADLATPMAVRVAATLRVADHIA-AGH---RTAAEIASAAGA---HADS----LD 56

Query: 76  RVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFVRNNQNGASLSPYMALCLDKVCLD-GWF 134
           R+LR LV+         DGQ +Y L         ++   A    ++ +       D G+ 
Sbjct: 57  RLLRHLVAVGLFTR---DGQGVYGLTEFGEQLRDDH--AAGKRKWLDMNSAVGRGDLGFV 111

Query: 135 GLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIVMEKVLESYKGFEHV 194
            L   +  G  A+   +G   ++ LG D   +  F+  M  H  +    +   Y  +  +
Sbjct: 112 ELAHSIRTGQPAYPVRYGTSFWEDLGSDPVLSASFDTLMSHHLELDYTGIAAKYD-WAAL 170

Query: 195 KKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSY 235
             +VDVGGG G  L+ +++ +  + G   DL      A   
Sbjct: 171 GHVVDVGGGSGGLLSALLTAHEDLSGTVLDLQGPASAAHRR 211

>1qzz_A RDMB, aclacinomycin-10-hydroxylase; anthracycline, methyltransferase, polyketide, tailoring enzymes, structural proteomics in E spine; HET: SAM; 2.10A {Streptomyces purpurascens} SCOP: a.4.5.29 c.66.1.12 PDB: 1r00_A* 1xds_A* 1xdu_A* Length = 374

 Score =  196 bits (499), Expect = 3e-61
 Identities = 45/239 (18%), Positives = 87/239 (36%), Gaps = 19/239 (7%)

Query: 1   MASIADRE---EETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIV 57
           M+S +  E       +    ++    +V P  ++    L + + +  AG     ++A + 
Sbjct: 1   MSSSSPGEPLEPTDQDLDVLLKNLGNLVTPMALRVAATLRLVDHLL-AGA---DTLAGLA 56

Query: 58  AQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFVRNNQNGASL 117
            +      +P+A    L R++R L     L        R      +       +   A  
Sbjct: 57  DRTDT---HPQA----LSRLVRHLTVVGVLEGG-EKQGRPLRPTRLGMLLADGH--PAQQ 106

Query: 118 SPYMALCLD-KVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSH 176
             ++ L          + GL   +  G  A+   +G   ++ L  D    D F+  M   
Sbjct: 107 RAWLDLNGAVSHADLAFTGLLDVVRTGRPAYAGRYGRPFWEDLSADVALADSFDALMSCD 166

Query: 177 TSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSY 235
             +  E   ++Y  +  V+ ++DVGGG G  L  I  + PH++G   +L    + A   
Sbjct: 167 EDLAYEAPADAYD-WSAVRHVLDVGGGNGGMLAAIALRAPHLRGTLVELAGPAERARRR 224

>1tw3_A COMT, carminomycin 4-O-methyltransferase; anthracycline, methylate, tailoring enzyme, polyketide, S-adenosyl-L-homocystein; HET: SAH ERT; 2.35A {Streptomyces peucetius} SCOP: a.4.5.29 c.66.1.12 PDB: 1tw2_A* Length = 360

 Score =  192 bits (490), Expect = 4e-60
 Identities = 41/220 (18%), Positives = 80/220 (36%), Gaps = 18/220 (8%)

Query: 17  AMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDR 76
            +    ++  P V++    L + + I  AG     +V  + A+       PEA    L R
Sbjct: 23  TLIRLGSLHTPMVVRTAATLRLVDHIL-AGA---RTVKALAARTDT---RPEA----LLR 71

Query: 77  VLRLLVSYNALHCSFVDGQRLYSLAPVSAYFVRNNQNGASLSPYMALCL-DKVCLDGWFG 135
           ++R LV+   L     D    +    V      ++   A+   +  L          +  
Sbjct: 72  LIRHLVAIGLLEE---DAPGEFVPTEVGELLADDH--PAAQRAWHDLTQAVARADISFTR 126

Query: 136 LKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIVMEKVLESYKGFEHVK 195
           L   +  G   +   +G   Y+ L         F++ +     +  +    +Y  + +V+
Sbjct: 127 LPDAIRTGRPTYESIYGKPFYEDLAGRPDLRASFDSLLACDQDVAFDAPAAAY-DWTNVR 185

Query: 196 KLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSY 235
            ++DVGGG G     I  + PH+     ++   +  A SY
Sbjct: 186 HVLDVGGGKGGFAAAIARRAPHVSATVLEMAGTVDTARSY 225

>2ip2_A Probable phenazine-specific methyltransferase; pyocyanin, phenazine-1-carboxy PHZM; 1.80A {Pseudomonas aeruginosa} Length = 334

 Score =  186 bits (474), Expect = 4e-58
 Identities = 43/218 (19%), Positives = 73/218 (33%), Gaps = 21/218 (9%)

Query: 18  MELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRV 77
           +++ +       +     L + ++I   G     S   + A +     + E     + R+
Sbjct: 13  IQVVTGEWKSRCVYVATRLGLADLIES-GI---DSDETLAAAVGS---DAER----IHRL 61

Query: 78  LRLLVSYNALHCSFVDGQRLYSLAPVSAYFVRNNQNGASLSPYMALCLDKVCLDGWFGLK 137
           +RLLV++        D +  Y+  P S           S    M L   +     W    
Sbjct: 62  MRLLVAFEIFQG---DTRDGYANTPTSHLLRDVEG---SFRD-MVLFYGEEFHAAWTPAC 114

Query: 138 KQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIVMEKVLESYKGFEHVKKL 197
           + LL G   F  A G   Y YL         F   M   +++   ++      F   +  
Sbjct: 115 EALLSGTPGFELAFGEDFYSYLKRCPDAGRRFLLAM-KASNLAFHEIPRLL-DFRG-RSF 171

Query: 198 VDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSY 235
           VDVGGG G     I+   P  +G+  D    +  A   
Sbjct: 172 VDVGGGSGELTKAILQAEPSARGVMLDREGSLGVARDN 209

>2r3s_A Uncharacterized protein; methyltransferase domain, structural genomics, joint center structural genomics, JCSG, protein structure initiative; HET: MSE; 2.15A {Nostoc punctiforme} Length = 335

 Score =  160 bits (406), Expect = 6e-48
 Identities = 38/220 (17%), Positives = 77/220 (35%), Gaps = 21/220 (9%)

Query: 18  MELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRV 77
               +A    A ++A VEL+VF  IS+ G     S   +  +      +       +  +
Sbjct: 11  FNTVNAYQRSAAIKAAVELNVFTAISQ-GI---ESSQSLAQKCQT---SERG----MRML 59

Query: 78  LRLLVSYNALHCSFVDGQRLYSLAPVSAYFVRNNQNGASLSPYMALCLDKVCLDGWFGLK 137
              LV    +       +  Y L   SA F+    +   +   +   L  +  +G+  L 
Sbjct: 60  CDYLVIIGFMTK---QAEG-YRLTSDSAMFLDRQ-SKFYVGDAIEFLLSPMITNGFNDLT 114

Query: 138 KQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIVMEKVLESYKGFEHVKKL 197
             +L+GG A +    +       V  +F    +  M +   ++ + V E+        K+
Sbjct: 115 AAVLKGGTAISSEGTL--SPEHPVWVQFAKAMSPMMANPAQLIAQLVNEN---KIEPLKV 169

Query: 198 VDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPG 237
           +D+    G+    +    P+ +    D   V++ A     
Sbjct: 170 LDISASHGLFGIAVAQHNPNAEIFGVDWASVLEVAKENAR 209

>3dp7_A SAM-dependent methyltransferase; structural genomics, protein structure initiative, NEW YORK structural genomix research; 2.33A {Bacteroides vulgatus} Length = 363

 Score =  156 bits (397), Expect = 3e-46
 Identities = 42/224 (18%), Positives = 81/224 (36%), Gaps = 22/224 (9%)

Query: 17  AMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDR 76
           A E+A   V+  V + +++  +F+++S    G   ++ EI  +  L      A       
Sbjct: 19  AQEIAFGPVVFQVSRLMLKFGIFQLLSGKREG--YTLQEISGRTGL---TRYA----AQV 69

Query: 77  VLRLLVSYNALHCSFVDGQRLYSLAPVSAYFVRNNQNGASLSPYMALCLDKVCLDGWFGL 136
           +L   ++   +     +  R Y LA    + + +      ++         V   G F L
Sbjct: 70  LLEASLTIGTILL---EEDR-YVLAKAGWFLLND-----KMARVNMEFNHDVNYQGLFHL 120

Query: 137 KKQLLEGGIAFNKAHGMQ--IYDYLG-VDSRFNDVFNNGMLSHTSIVMEKVLESYKGFEH 193
           ++ LL G     K  G    IY+ L  +  +    +      ++     K LE      H
Sbjct: 121 EEALLNGRPEGLKVFGEWPTIYEGLSQLPEQVQKSWFGFDHFYSDQSFGKALEIV-FSHH 179

Query: 194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPG 237
            K+L+D+GG  G      +     ++    DLP  ++       
Sbjct: 180 PKRLLDIGGNTGKWATQCVQYNKEVEVTIVDLPQQLEMMRKQTA 223

>1x19_A CRTF-related protein; methyltransferase, bacteriochllochlorophyll, BCHU, SAM, SAH, adenosylmethyonine, S-adenosylhomocysteine, ADO-Met; 2.27A {Chlorobium tepidum} PDB: 1x1a_A* 1x1b_A* 1x1c_A* 1x1d_A* Length = 359

 Score =  152 bits (387), Expect = 8e-45
 Identities = 45/218 (20%), Positives = 81/218 (37%), Gaps = 21/218 (9%)

Query: 20  LASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLR 79
           +   ++  + M+A +ELD+F  +++ GP     +A + A        P      L+ +L 
Sbjct: 38  VFKGLIEFSCMKAAIELDLFSHMAE-GP---KDLATLAADTGS---VPPR----LEMLLE 86

Query: 80  LLVSYNALHCSFVDGQRLYSLAPVSAYFVRNNQNGASLSPYMALCLDKVCLDGWFGLKKQ 139
            L     ++    DG+  +SL   + Y         +L             D ++    Q
Sbjct: 87  TLRQMRVINLE--DGK--WSLTEFADYMFSPTPKEPNLHQTPVAKAMAFLADDFYMGLSQ 142

Query: 140 LLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIVMEKVLESYKGFEHVKKLVD 199
            + G   F          Y  V    N  F     S+    ++ +LE  K  + VKK++D
Sbjct: 143 AVRGQKNFKGQ-----VPYPPVTREDNLYFEEIHRSNAKFAIQLLLEEAK-LDGVKKMID 196

Query: 200 VGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPG 237
           VGGG+G     ++  +P +     +LP  I        
Sbjct: 197 VGGGIGDISAAMLKHFPELDSTILNLPGAIDLVNENAA 234

>3mcz_A O-methyltransferase; adomet_mtases, S-adenosylmethionine-dependent methyltransfer structural genomics, PSI-2; HET: MSE; 1.90A {Burkholderia thailandensis} Length = 352

 Score =  141 bits (358), Expect = 1e-40
 Identities = 38/237 (16%), Positives = 82/237 (34%), Gaps = 25/237 (10%)

Query: 1   MASIADREEETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQI 60
           +    + +    +    ++L+      A++   V   +F++          + AE+ A  
Sbjct: 12  IYESTEDKAALTSVVDLVKLSDQYRQSAILHYAVADKLFDLTQTG-----RTPAEVAASF 66

Query: 61  PLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFVRNNQNGASLSPY 120
            +              +L  L +   L     +G   +    ++  ++        + P 
Sbjct: 67  GM---VEGK----AAILLHALAALGLLTK---EGDA-FRNTALTERYLTTTSAD-YIGPI 114

Query: 121 MALCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIV 180
           +      +  D W  L + L        K    Q       D+R  D FN+ M+  +  +
Sbjct: 115 VEH--QYLQWDNWPRLGEILRSE-----KPLAFQQESRFAHDTRARDAFNDAMVRLSQPM 167

Query: 181 MEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPG 237
           ++ V E    F   + ++D+ GG G  L  ++ ++P + G  +DLP     A     
Sbjct: 168 VDVVSELG-VFARARTVIDLAGGHGTYLAQVLRRHPQLTGQIWDLPTTRDAARKTIH 223

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	244
4a6d_A	353	Hydroxyindole O-methyltransferase; melatonin, circ	100.0
3p9c_A	364	Caffeic acid O-methyltransferase; S-adenosylmethio	100.0
3reo_A	368	(ISO)eugenol O-methyltransferase; directed evoluti	100.0
1zg3_A	358	Isoflavanone 4'-O-methyltransferase; rossman fold,	100.0
1fp2_A	352	Isoflavone O-methyltransferase; protein-product co	100.0
3lst_A	348	CALO1 methyltransferase; calicheamicin, enediyne,	100.0
1fp1_D	372	Isoliquiritigenin 2'-O-methyltransferase; protein-	100.0
3gwz_A	369	MMCR; methyltransferase, mitomycin, S-adenosyl met	100.0
3i53_A	332	O-methyltransferase; CO-complex, rossmann-like fol	100.0
2ip2_A	334	Probable phenazine-specific methyltransferase; pyo	100.0
3dp7_A	363	SAM-dependent methyltransferase; structural genomi	100.0
1qzz_A	374	RDMB, aclacinomycin-10-hydroxylase; anthracycline,	99.97
1tw3_A	360	COMT, carminomycin 4-O-methyltransferase; anthracy	99.97
1x19_A	359	CRTF-related protein; methyltransferase, bacterioc	99.97
2r3s_A	335	Uncharacterized protein; methyltransferase domain,	99.96
3mcz_A	352	O-methyltransferase; adomet_mtases, S-adenosylmeth	99.96
2qm3_A	373	Predicted methyltransferase; putative methyltransf	98.75
1ve3_A	227	Hypothetical protein PH0226; dimer, riken structur	97.9
2fca_A	213	TRNA (guanine-N(7)-)-methyltransferase; 2.10A {Bac	97.67
3ege_A	261	Putative methyltransferase from antibiotic biosyn	97.66
3dtn_A	234	Putative methyltransferase MM_2633; structural gen	97.66
3e05_A	204	Precorrin-6Y C5,15-methyltransferase (decarboxyla;	97.63
3mq2_A	218	16S rRNA methyltransferase; methyltranferase, ribo	97.61
1yzh_A	214	TRNA (guanine-N(7)-)-methyltransferase; alpha-beta	97.61
3dxy_A	218	TRNA (guanine-N(7)-)-methyltransferase; rossmann f	97.6
4dzr_A	215	Protein-(glutamine-N5) methyltransferase, release	97.53
2qe6_A	274	Uncharacterized protein TFU_2867; putative methylt	97.49
2p35_A	259	Trans-aconitate 2-methyltransferase; SAM dependent	97.49
3g07_A	292	7SK snRNA methylphosphate capping enzyme; structur	97.46
3ckk_A	235	TRNA (guanine-N(7)-)-methyltransferase; mettl1, S-	97.45
3hm2_A	178	Precorrin-6Y C5,15-methyltransferase; alpha-beta-s	97.45
1jg1_A	235	PIMT;, protein-L-isoaspartate O-methyltransferase;	97.44
3ou2_A	218	SAM-dependent methyltransferase; O-methyltransfera	97.44
3vc1_A	312	Geranyl diphosphate 2-C-methyltransferase; rossman	97.42
3dlc_A	219	Putative S-adenosyl-L-methionine-dependent methylt	97.41
3g5t_A	299	Trans-aconitate 3-methyltransferase; structural ge	97.41
2plw_A	201	Ribosomal RNA methyltransferase, putative; malaria	97.4
3p2e_A	225	16S rRNA methylase; methyltransferase, transferase	97.39
3gjy_A	317	Spermidine synthase; APC62791, structural genomics	97.39
3mgg_A	276	Methyltransferase; NYSGXRC, PSI-II, protein struct	97.37
1yb2_A	275	Hypothetical protein TA0852; structural genomics,	97.36
3dli_A	240	Methyltransferase; PSI-II, NYSGXRC, structural gen	97.35
3dh0_A	219	SAM dependent methyltransferase; cystal structure,	97.34
2vdv_E	246	TRNA (guanine-N(7)-)-methyltransferase; S-adenosyl	97.33
3g5l_A	253	Putative S-adenosylmethionine dependent methyltran	97.33
4gek_A	261	TRNA (CMO5U34)-methyltransferase; structural genom	97.32
4hg2_A	257	Methyltransferase type 11; structural genomics, PS	97.31
3ujc_A	266	Phosphoethanolamine N-methyltransferase; parasite;	97.31
1vl5_A	260	Unknown conserved protein BH2331; putative methylt	97.31
3kkz_A	267	Uncharacterized protein Q5LES9; putative methyltra	97.3
3jwh_A	217	HEN1; methyltransferase; HET: SAH; 2.20A {Anabaena	97.3
3orh_A	236	Guanidinoacetate N-methyltransferase; structura ge	97.3
1jsx_A	207	Glucose-inhibited division protein B; methyltransf	97.29
3mb5_A	255	SAM-dependent methyltransferase; RNA methyltransfe	97.27
2yxd_A	183	Probable cobalt-precorrin-6Y C(15)-methyltransfer	97.26
3g89_A	249	Ribosomal RNA small subunit methyltransferase G; 1	97.25
1fbn_A	230	MJ fibrillarin homologue; MJ proteins, ribosomal R	97.24
3jwg_A	219	HEN1, methyltransferase type 12; 1.90A {Clostridiu	97.23
1pjz_A	203	Thiopurine S-methyltransferase; polymorphism, S-ad	97.2
3bkw_A	243	MLL3908 protein, S-adenosylmethionine dependent me	97.19
3cgg_A	195	SAM-dependent methyltransferase; NP_600671.1, meth	97.18
1nkv_A	256	Hypothetical protein YJHP; structural genomics, PS	97.18
1xdz_A	240	Methyltransferase GIDB; MCSG, protein structure in	97.18
3hem_A	302	Cyclopropane-fatty-acyl-phospholipid synthase 2; p	97.14
2pwy_A	258	TRNA (adenine-N(1)-)-methyltransferase; mtase, ado	97.14
2b3t_A	276	Protein methyltransferase HEMK; translation termin	97.13
3gu3_A	284	Methyltransferase; alpha-beta protein, structural	97.13
3mti_A	185	RRNA methylase; SAM-dependent, PSI, MCSG, structur	97.13
3f4k_A	257	Putative methyltransferase; structural genomics, P	97.11
1xxl_A	239	YCGJ protein; structural genomics, protein structu	97.11
3ccf_A	279	Cyclopropane-fatty-acyl-phospholipid synthase; YP_	97.1
2o57_A	297	Putative sarcosine dimethylglycine methyltransfera	97.08
4dcm_A	375	Ribosomal RNA large subunit methyltransferase G; 2	97.08
3adn_A	294	Spermidine synthase; aminopropyltransferase, polya	97.08
2esr_A	177	Methyltransferase; structural genomics, hypothetic	97.07
3bkx_A	275	SAM-dependent methyltransferase; YP_807781.1, cycl	97.07
1kpg_A	287	CFA synthase;, cyclopropane-fatty-acyl-phospholipi	97.06
3i9f_A	170	Putative type 11 methyltransferase; structural gen	97.06
3njr_A	204	Precorrin-6Y methylase; methyltransferase, decarbo	97.05
1xtp_A	254	LMAJ004091AAA; SGPP, structural genomics, PSI, pro	97.04
1nt2_A	210	Fibrillarin-like PRE-rRNA processing protein; adeM	97.03
3e8s_A	227	Putative SAM dependent methyltransferase; NP_74470	97.03
3bus_A	273	REBM, methyltransferase; rebeccamycin synthesis; H	97.02
3eey_A	197	Putative rRNA methylase; rRNA methylation, S-adeno	97.02
3cc8_A	230	Putative methyltransferase; structural genomics, j	97.02
2avd_A	229	Catechol-O-methyltransferase; structural genomics,	97.01
1m6y_A	301	S-adenosyl-methyltransferase MRAW; SAM-dependent m	97.01
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	97.01
2fk8_A	318	Methoxy mycolic acid synthase 4; S-adenosylmethion	97.0
3b3j_A	480	Histone-arginine methyltransferase CARM1; protein	97.0
3fzg_A	200	16S rRNA methylase; methyltransferase, plasmid, tr	97.0
2ipx_A	233	RRNA 2'-O-methyltransferase fibrillarin; FBL, stru	96.99
2gpy_A	233	O-methyltransferase; structural genomics, PSI, pro	96.99
3ggd_A	245	SAM-dependent methyltransferase; YP_325210.1, stru	96.98
3fpf_A	298	Mtnas, putative uncharacterized protein; thermonic	96.98
2nyu_A	196	Putative ribosomal RNA methyltransferase 2; SAM, s	96.97
2ozv_A	260	Hypothetical protein ATU0636; structural genomics,	96.96
3kr9_A	225	SAM-dependent methyltransferase; class I rossmann-	96.95
1xmk_A	79	Double-stranded RNA-specific adenosine deaminase;	96.95
2bm8_A	236	Cephalosporin hydroxylase CMCI; cephamycin biosynt	96.95
1i9g_A	280	Hypothetical protein RV2118C; mtase, adoMet, cryst	96.94
4htf_A	285	S-adenosylmethionine-dependent methyltransferase;	96.94
3hnr_A	220	Probable methyltransferase BT9727_4108; structural	96.92
1nv8_A	284	HEMK protein; class I adoMet-dependent methyltrans	96.91
1iy9_A	275	Spermidine synthase; rossmann fold, structural gen	96.91
3pfg_A	263	N-methyltransferase; N,N-dimethyltransferase, SAM	96.91
2yqz_A	263	Hypothetical protein TTHA0223; RNA methyltransfera	96.91
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	96.91
3ftd_A	249	Dimethyladenosine transferase; KSGA, rossmann-like	96.91
3ntv_A	232	MW1564 protein; rossmann fold, putative methyltran	96.89
3gnl_A	244	Uncharacterized protein, DUF633, LMOF2365_1472; st	96.89
3tfw_A	248	Putative O-methyltransferase; PSI-biology, nysgrc,	96.88
2pjd_A	343	Ribosomal RNA small subunit methyltransferase C; g	96.88
1y0u_A	96	Arsenical resistance operon repressor, putative; s	96.87
1qam_A	244	ERMC' methyltransferase; rRNA methyltransferase ER	96.87
3q87_B	170	N6 adenine specific DNA methylase; SAM-methyltrans	96.86
3iv6_A	261	Putative Zn-dependent alcohol dehydrogenase; alpha	96.85
3lec_A	230	NADB-rossmann superfamily protein; PSI, MCSG, stru	96.84
2p7i_A	250	Hypothetical protein; putative methyltransferase,	96.82
4fsd_A	383	Arsenic methyltransferase; rossmann fold; 1.75A {C	96.81
3dou_A	191	Ribosomal RNA large subunit methyltransferase J; c	96.81
2h00_A	254	Methyltransferase 10 domain containing protein; st	96.8
2fhp_A	187	Methylase, putative; alpha-beta-alpha sandwich, st	96.8
1o54_A	277	SAM-dependent O-methyltransferase; TM0748, structu	96.8
2yxe_A	215	Protein-L-isoaspartate O-methyltransferase; rossma	96.8
1g8a_A	227	Fibrillarin-like PRE-rRNA processing protein; rRNA	96.8
3bxo_A	239	N,N-dimethyltransferase; desosamine, sugar, carboh	96.78
3bwc_A	304	Spermidine synthase; SAM, SGPP, structura genomics	96.78
3lbf_A	210	Protein-L-isoaspartate O-methyltransferase; modifi	96.78
1u2z_A	433	Histone-lysine N-methyltransferase, H3 lysine-79 s	96.78
3uwp_A	438	Histone-lysine N-methyltransferase, H3 lysine-79;	96.78
3b73_A	111	PHIH1 repressor-like protein; winged-helix-turn-he	96.77
3g2m_A	299	PCZA361.24; SAM-dependent methyltransferase, glyco	96.77
3duw_A	223	OMT, O-methyltransferase, putative; alternating of	96.76
2xvm_A	199	Tellurite resistance protein TEHB; antibiotic resi	96.76
3h2b_A	203	SAM-dependent methyltransferase; alpha-beta protei	96.76
1o9g_A	250	RRNA methyltransferase; antibiotic resistance, Se-	96.75
1dus_A	194	MJ0882; hypothetical protein, methanococcus jannas	96.75
3m33_A	226	Uncharacterized protein; structural genomics, PSI-	96.74
1xj5_A	334	Spermidine synthase 1; structural genomics, protei	96.74
1p91_A	269	Ribosomal RNA large subunit methyltransferase A; R	96.74
3e23_A	211	Uncharacterized protein RPA2492; alpha-beta protei	96.74
2fyt_A	340	Protein arginine N-methyltransferase 3; structural	96.71
3tr6_A	225	O-methyltransferase; cellular processes; HET: SAH;	96.71
3c3p_A	210	Methyltransferase; NP_951602.1, structural genomic	96.71
2pt6_A	321	Spermidine synthase; transferase, structural genom	96.7
3uzu_A	279	Ribosomal RNA small subunit methyltransferase A; s	96.69
2i7c_A	283	Spermidine synthase; transferase, structural genom	96.69
3l8d_A	242	Methyltransferase; structural genomics, PSI, nysgr	96.68
1inl_A	296	Spermidine synthase; beta-barrel, rossman fold, st	96.68
2pxx_A	215	Uncharacterized protein MGC2408; structural genomi	96.68
1uir_A	314	Polyamine aminopropyltransferase; spermidien synth	96.66
3mq0_A	275	Transcriptional repressor of the blcabc operon; he	96.66
2o07_A	304	Spermidine synthase; structural genomics, structur	96.65
1wzn_A	252	SAM-dependent methyltransferase; structural genomi	96.65
2b2c_A	314	Spermidine synthase; beta-alpha, transferase; 2.50	96.64
2cmg_A	262	Spermidine synthase; transferase, putrescine amino	96.64
1mjf_A	281	Spermidine synthase; spermidine synthetase, struct	96.62
1ws6_A	171	Methyltransferase; structural genomics, riken stru	96.62
1dl5_A	317	Protein-L-isoaspartate O-methyltransferase; isoasp	96.61
1yub_A	245	Ermam, rRNA methyltransferase; MLS antibiotics; NM	96.6
2y1w_A	348	Histone-arginine methyltransferase CARM1; histone	96.59
3lpm_A	259	Putative methyltransferase; structural genomics, p	96.58
3thr_A	293	Glycine N-methyltransferase; GNMT, folate, methylt	96.58
3tma_A	354	Methyltransferase; thump domain; 2.05A {Thermus th	96.58
3u81_A	221	Catechol O-methyltransferase; neurotransmitter deg	96.57
2hnk_A	239	SAM-dependent O-methyltransferase; modified rossma	96.56
2nxc_A	254	L11 mtase, ribosomal protein L11 methyltransferase	96.55
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	96.55
1l3i_A	192	Precorrin-6Y methyltransferase/putative decarboxyl	96.52
1ne2_A	200	Hypothetical protein TA1320; structural genomics,	96.51
1sui_A	247	Caffeoyl-COA O-methyltransferase; rossmann fold, p	96.49
3d2l_A	243	SAM-dependent methyltransferase; ZP_00538691.1, st	96.49
3p9n_A	189	Possible methyltransferase (methylase); RV2966C, a	96.48
1zx0_A	236	Guanidinoacetate N-methyltransferase; structural g	96.47
3gru_A	295	Dimethyladenosine transferase; rossman fold, ribos	96.47
1ej0_A	180	FTSJ; methyltransferase, adoMet, adenosyl methioni	96.47
3a27_A	272	TYW2, uncharacterized protein MJ1557; wybutosine m	96.47
3ofk_A	216	Nodulation protein S; NODS, N-methyltransferase, S	96.46
4e2x_A	416	TCAB9; kijanose, tetronitrose, tetradeoxy sugar, s	96.44
2b25_A	336	Hypothetical protein; structural genomics, methyl	96.43
2ift_A	201	Putative methylase HI0767; NESG, Y767_haein, struc	96.43
3r3h_A	242	O-methyltransferase, SAM-dependent; structural gen	96.42
3bgv_A	313	MRNA CAP guanine-N7 methyltransferase; alternative	96.41
3ocj_A	305	Putative exported protein; structural genomics, PS	96.4
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	96.38
3tqs_A	255	Ribosomal RNA small subunit methyltransferase A; p	96.38
1qyr_A	252	KSGA, high level kasugamycin resistance protein, S	96.37
3grz_A	205	L11 mtase, ribosomal protein L11 methyltransferase	96.36
1vbf_A	231	231AA long hypothetical protein-L-isoaspartate O-	96.36
3c3y_A	237	Pfomt, O-methyltransferase; plant secondary metabo	96.36
4df3_A	233	Fibrillarin-like rRNA/TRNA 2'-O-methyltransferase;	96.31
3sm3_A	235	SAM-dependent methyltransferases; NESG, structural	96.28
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	96.27
3dr5_A	221	Putative O-methyltransferase; Q8NRD3, CGL1119, PF0	96.27
3jth_A	98	Transcription activator HLYU; transcription factor	96.27
2aot_A	292	HMT, histamine N-methyltransferase; classic methyl	96.25
3f6o_A	118	Probable transcriptional regulator, ARSR family pr	96.24
2ex4_A	241	Adrenal gland protein AD-003; methyltransferase, s	96.23
1u2w_A	122	CADC repressor, cadmium efflux system accessory pr	96.22
3cbg_A	232	O-methyltransferase; cyanobacterium; HET: SAH FER	96.21
3q7e_A	349	Protein arginine N-methyltransferase 1; HET: SAH;	96.21
3m70_A	286	Tellurite resistance protein TEHB homolog; structu	96.19
2xrn_A	241	HTH-type transcriptional regulator TTGV; DNA-bindi	96.19
2pbf_A	227	Protein-L-isoaspartate O-methyltransferase beta-A	96.17
2yvl_A	248	TRMI protein, hypothetical protein; tRNA, methyltr	96.17
1zq9_A	285	Probable dimethyladenosine transferase; SGC, struc	96.16
3fut_A	271	Dimethyladenosine transferase; methyltransferase,	96.09
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	96.08
1mkm_A	249	ICLR transcriptional regulator; structural genomic	96.08
3lcc_A	235	Putative methyl chloride transferase; halide methy	96.08
2ih2_A	421	Modification methylase TAQI; DNA, DNA methyltransf	96.06
3r4k_A	260	Transcriptional regulator, ICLR family; DNA/RNA-bi	96.06
3hp7_A	291	Hemolysin, putative; structural genomics, APC64019	96.05
3opn_A	232	Putative hemolysin; structural genomics, PSI-2, pr	96.04
2y75_A	129	HTH-type transcriptional regulator CYMR; DNA bindi	96.0
2gb4_A	252	Thiopurine S-methyltransferase; 18204406, thiopuri	95.99
3evz_A	230	Methyltransferase; NYSGXRC, NEW YORK SGX research	95.98
1ixk_A	315	Methyltransferase; open beta sheet; 1.90A {Pyrococ	95.95
3htx_A	950	HEN1; HEN1, small RNA methyltransferase, protein-R	95.92
1y8c_A	246	S-adenosylmethionine-dependent methyltransferase;	95.92
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	95.91
1wy7_A	207	Hypothetical protein PH1948; seven-stranded beta s	95.91
1ub9_A	100	Hypothetical protein PH1061; helix-turn-helix moti	95.91
1i1n_A	226	Protein-L-isoaspartate O-methyltransferase; S-aden	95.89
2fpo_A	202	Methylase YHHF; structural genomics, putative meth	95.89
2qfm_A	364	Spermine synthase; spermidine aminopropyltransfera	95.88
2frn_A	278	Hypothetical protein PH0793; structural genomics,	95.87
2jsc_A	118	Transcriptional regulator RV1994C/MT2050; cadmium,	95.84
2hzt_A	107	Putative HTH-type transcriptional regulator YTCD;	95.83
3gdh_A	241	Trimethylguanosine synthase homolog; M7G, CAP, dim	95.81
3bzb_A	281	Uncharacterized protein; RED ALGA, protein structu	95.79
2kko_A	108	Possible transcriptional regulatory protein (possi	95.79
3id6_C	232	Fibrillarin-like rRNA/TRNA 2'-O-methyltransferase;	95.77
3tm4_A	373	TRNA (guanine N2-)-methyltransferase TRM14; rossma	95.72
3ajd_A	274	Putative methyltransferase MJ0026; tRNA, M5C, ross	95.68
2kw5_A	202	SLR1183 protein; structural genomics, northeast st	95.68
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	95.67
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	95.66
2avn_A	260	Ubiquinone/menaquinone biosynthesis methyltransfe	95.66
2h1r_A	299	Dimethyladenosine transferase, putative; SGC toron	95.65
4azs_A	569	Methyltransferase WBDD; kinase; HET: AMP SAM; 2.15	95.61
3f6v_A	151	Possible transcriptional regulator, ARSR family pr	95.61
1vlm_A	219	SAM-dependent methyltransferase; possible histamin	95.58
1g6q_1	328	HnRNP arginine N-methyltransferase; SAM-binding do	95.58
1tbx_A	99	ORF F-93, hypothetical 11.0 kDa protein; sulfolobu	95.56
1ri5_A	298	MRNA capping enzyme; methyltransferase, M7G, messe	95.56
1r18_A	227	Protein-L-isoaspartate(D-aspartate)-O-methyltrans;	95.54
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	95.54
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	95.53
2wa2_A	276	Non-structural protein 5; transferase, S-adenosyl-	95.48
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	95.46
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	95.46
2oxt_A	265	Nucleoside-2'-O-methyltransferase; flavivirus, vir	95.43
3df8_A	111	Possible HXLR family transcriptional factor; APC89	95.42
2o0y_A	260	Transcriptional regulator; ICLR-family, structural	95.39
2p8j_A	209	S-adenosylmethionine-dependent methyltransferase;	95.35
2g7u_A	257	Transcriptional regulator; ICLR family, structural	95.33
1uwv_A	433	23S rRNA (uracil-5-)-methyltransferase RUMA; RNA m	95.32
4a5n_A	131	Uncharacterized HTH-type transcriptional regulato;	95.31
2gs9_A	211	Hypothetical protein TT1324; methyl transferase, s	95.29
3giw_A	277	Protein of unknown function DUF574; rossmann-fold	95.26
3t8r_A	143	Staphylococcus aureus CYMR; transcriptional regula	95.19
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	95.17
3lwf_A	159	LIN1550 protein, putative transcriptional regulato	95.17
2vdw_A	302	Vaccinia virus capping enzyme D1 subunit; nucleoti	95.14
3o4f_A	294	Spermidine synthase; aminopropyltransferase, polya	95.14
3r0q_C	376	Probable protein arginine N-methyltransferase 4.2;	95.13
2ia2_A	265	Putative transcriptional regulator; SAD, PSI-2, st	95.11
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	95.07
3frh_A	253	16S rRNA methylase; methyltransferase domain, heli	95.06
2wte_A	244	CSA3; antiviral protein, viral resistance, winged	95.05
1z7u_A	112	Hypothetical protein EF0647; winged-helix-turn-hel	95.02
2gxg_A	146	146AA long hypothetical transcriptional regulator;	94.97
2zfu_A	215	Nucleomethylin, cerebral protein 1; nucleolar prot	94.97
3f3x_A	144	Transcriptional regulator, MARR family, putative;	94.96
1wg8_A	285	Predicted S-adenosylmethionine-dependent methyltra	94.92
3lcv_B	281	Sisomicin-gentamicin resistance methylase SGM; ant	94.85
1ylf_A	149	RRF2 family protein; structural genomics, transcri	94.84
2g72_A	289	Phenylethanolamine N-methyltransferase; HET: SAM F	94.84
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	94.82
1on2_A	142	Transcriptional regulator MNTR; helix-turn-helix,	94.77
2nnn_A	140	Probable transcriptional regulator; structural gen	94.72
2i62_A	265	Nicotinamide N-methyltransferase; structural genom	94.71
3bja_A	139	Transcriptional regulator, MARR family, putative;	94.7
2yxl_A	450	PH0851 protein, 450AA long hypothetical FMU protei	94.68
4hc4_A	376	Protein arginine N-methyltransferase 6; HRMT1L6, S	94.68
2fsw_A	107	PG_0823 protein; alpha-beta structure, helix-turn-	94.57
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	94.57
3ldu_A	385	Putative methylase; structural genomics, PSI-2, pr	94.57
3fm5_A	150	Transcriptional regulator; MCSG, PF04017, PSI, MAR	94.56
2nyx_A	168	Probable transcriptional regulatory protein, RV14;	94.54
1af7_A	274	Chemotaxis receptor methyltransferase CHER; chemot	94.53
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	94.49
3k0l_A	162	Repressor protein; helix-turn-helix, structural ge	94.42
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	94.4
3k0b_A	393	Predicted N6-adenine-specific DNA methylase; methy	94.37
3r0a_A	123	Putative transcriptional regulator; structural gen	94.33
2hr3_A	147	Probable transcriptional regulator; MCSG, structur	94.32
2igt_A	332	SAM dependent methyltransferase; alpha-beta sandwi	94.32
2f2e_A	146	PA1607; transcription factor, helix-TRUN-helix, AP	94.32
3dmg_A	381	Probable ribosomal RNA small subunit methyltransf;	94.31
3e6m_A	161	MARR family transcriptional regulator; APC88769, s	94.29
3cdh_A	155	Transcriptional regulator, MARR family; helix-turn	94.28
3g3z_A	145	NMB1585, transcriptional regulator, MARR family; t	94.2
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	94.18
2r6z_A	258	UPF0341 protein in RSP 3' region; alpha-beta prote	94.15
1yyv_A	131	Putative transcriptional regulator; reductive meth	94.15
2fbi_A	142	Probable transcriptional regulator; MARR, APC5816,	94.13
3k69_A	162	Putative transcription regulator; putative transcr	94.11
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	94.1
3sso_A	419	Methyltransferase; macrolide, natural product, ros	93.97
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	93.95
2zkz_A	99	Transcriptional repressor PAGR; protein-DNA, HTH m	93.91
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	93.88
2p41_A	305	Type II methyltransferase; vizier, viral enzymes i	93.86
1s3j_A	155	YUSO protein; structural genomics, MARR transcript	93.85
2a61_A	145	Transcriptional regulator TM0710; APC4350, MCSG, m	93.8
2eth_A	154	Transcriptional regulator, putative, MAR family; M	93.79
1lj9_A	144	Transcriptional regulator SLYA; HTH DNA binding pr	93.78
1r7j_A	95	Conserved hypothetical protein SSO10A; winged heli	93.76
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	93.7
2f8l_A	344	Hypothetical protein LMO1582; structural genomics,	93.69
1sqg_A	429	SUN protein, FMU protein; rossmann-fold, mixed bet	93.63
3ldg_A	384	Putative uncharacterized protein SMU.472; YPSC, me	93.61
1xd7_A	145	YWNA; structural genomics, protein structure initi	93.53
2dul_A	378	N(2),N(2)-dimethylguanosine tRNA methyltransferas;	93.43
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	93.4
1z91_A	147	Organic hydroperoxide resistance transcriptional;	93.39
3kp7_A	151	Transcriptional regulator TCAR; multiple drug resi	93.38
3cjn_A	162	Transcriptional regulator, MARR family; silicibact	93.37
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	93.35
3s2w_A	159	Transcriptional regulator, MARR family; structural	93.27
3hsr_A	140	HTH-type transcriptional regulator SARZ; helix-tur	93.23
2bv6_A	142	MGRA, HTH-type transcriptional regulator MGRA; mul	93.21
2a14_A	263	Indolethylamine N-methyltransferase; SGC,INMT, str	93.18
3deu_A	166	Transcriptional regulator SLYA; MARR, WING-helix,	93.14
2oyr_A	258	UPF0341 protein YHIQ; alpha-beta protein, structur	93.12
1sfx_A	109	Conserved hypothetical protein AF2008; structural	93.1
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	93.09
3bj6_A	152	Transcriptional regulator, MARR family; helix-turn	93.09
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	93.0
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	92.9
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	92.89
2pex_A	153	Transcriptional regulator OHRR; transcription regu	92.87
3bt7_A	369	TRNA (uracil-5-)-methyltransferase; methyluridine,	92.83
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	92.77
3k6r_A	278	Putative transferase PH0793; structural genomics,	92.77
1wxx_A	382	TT1595, hypothetical protein TTHA1280; thermus the	92.77
3boq_A	160	Transcriptional regulator, MARR family; MARR famil	92.72
1p6r_A	82	Penicillinase repressor; transcription regulation,	92.72
3tka_A	347	Ribosomal RNA small subunit methyltransferase H; H	92.71
2lnb_A	80	Z-DNA-binding protein 1; structural genomics, nort	92.63
4aik_A	151	Transcriptional regulator SLYA; transcription, tra	92.53
3m6w_A	464	RRNA methylase; rRNA methyltransferase, 5-methylcy	92.31
2p4w_A	202	Transcriptional regulatory protein ARSR family; ar	92.25
2frh_A	127	SARA, staphylococcal accessory regulator A; winged	92.24
4dmg_A	393	Putative uncharacterized protein TTHA1493; rRNA, m	92.15
2okc_A	445	Type I restriction enzyme stysji M protein; NP_813	92.14
3ll7_A	410	Putative methyltransferase; methytransferase, stru	92.13
2as0_A	396	Hypothetical protein PH1915; RNA methyltransferase	92.11
2yx1_A	336	Hypothetical protein MJ0883; methyl transferase, t	92.06
2k4b_A	99	Transcriptional regulator; DNA binding protein, wi	92.04
3c6k_A	381	Spermine synthase; spermidine aminopropyltransfera	91.88
2jjq_A	425	Uncharacterized RNA methyltransferase pyrab10780;	91.83
3c0k_A	396	UPF0064 protein YCCW; PUA domain, adoMet dependent	91.74
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	91.63
2h09_A	155	Transcriptional regulator MNTR; transcription regu	91.61
2b78_A	385	Hypothetical protein SMU.776; structure genomics,	91.57
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	91.56
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	91.56
2vn2_A	128	DNAD, chromosome replication initiation protein; D	91.53
1sfu_A	75	34L protein; protein/Z-DNA complex, DNA binding pr	91.46
3m4x_A	456	NOL1/NOP2/SUN family protein; mtase domain, PUA do	91.4
1bja_A	95	Transcription regulatory protein MOTA; activation	91.37
2w25_A	150	Probable transcriptional regulatory protein; trans	91.35
3gcz_A	282	Polyprotein; flavivirus, RNA capping, methyltransf	91.11
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	91.11
3nqo_A	189	MARR-family transcriptional regulator; structural	91.04
3u2r_A	168	Regulatory protein MARR; structural genomics, PSI-	90.92
3b5i_A	374	S-adenosyl-L-methionine:salicylic acid carboxyl me	90.64
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	90.6
2v79_A	135	DNA replication protein DNAD; primosome, DNA-bindi	90.59
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	90.59
3jw4_A	148	Transcriptional regulator, MARR/EMRR family; DNA-b	90.55
3v97_A	703	Ribosomal RNA large subunit methyltransferase L; Y	90.54
2frx_A	479	Hypothetical protein YEBU; rossmann-type S-adenosy	90.45
2b9e_A	309	NOL1/NOP2/SUN domain family, member 5 isoform 2; m	90.4
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	90.35
2fbk_A	181	Transcriptional regulator, MARR family; winged-hel	90.29
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	90.25
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	90.24
1rjd_A	334	PPM1P, carboxy methyl transferase for protein phos	90.18
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	90.02
2fxa_A	207	Protease production regulatory protein HPR; protea	89.85
2qlz_A	232	Transcription factor PF0095; 2.50A {Pyrococcus fur	89.81
1uly_A	192	Hypothetical protein PH1932; helix-turn-helix, str	89.75
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	89.75
1ku9_A	152	Hypothetical protein MJ223; putative transcription	89.72
4auk_A	375	Ribosomal RNA large subunit methyltransferase M; Y	89.69
4b8x_A	147	SCO5413, possible MARR-transcriptional regulator;	89.58
2pg4_A	95	Uncharacterized protein; structural genomics, join	89.51
3hrs_A	214	Metalloregulator SCAR; DTXR/MNTR family member, tr	89.41
2o03_A	131	Probable zinc uptake regulation protein FURB; DNA-	89.4
3ua3_A	745	Protein arginine N-methyltransferase 5; TIM-barrel	89.37
2k4m_A	153	TR8_protein, UPF0146 protein MTH_1000; alpha+beta,	89.31
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	89.27
3evf_A	277	RNA-directed RNA polymerase NS5; NS5 methyltransfe	89.12
3u1d_A	151	Uncharacterized protein; GNTR-superfamily, structu	89.03
2fe3_A	145	Peroxide operon regulator; oxidative stress regula	88.95
2zig_A	297	TTHA0409, putative modification methylase; methylt	88.9
2esh_A	118	Conserved hypothetical protein TM0937; APC5794, st	88.9
2efj_A	384	3,7-dimethylxanthine methyltransferase; SAM-depend	87.81
1cf7_A	76	Protein (transcription factor E2F-4); E2F, winged-	87.57
2dk5_A	91	DNA-directed RNA polymerase III 39 kDa polypeptide	87.54
4gqb_A	637	Protein arginine N-methyltransferase 5; TIM barrel	87.53
4esf_A	117	PADR-like transcriptional regulator; PADR family,	87.42
1okr_A	123	MECI, methicillin resistance regulatory protein ME	86.33
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	86.29
3v97_A	703	Ribosomal RNA large subunit methyltransferase L; Y	86.27
1v4r_A	102	Transcriptional repressor; helix-turn-helix, winge	85.81
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	85.81
2ar0_A	541	M.ecoki, type I restriction enzyme ecoki M protein	85.63
3mwm_A	139	ZUR, putative metal uptake regulation protein; FUR	85.62
1j5y_A	187	Transcriptional regulator, biotin repressor famil;	85.33
2g9w_A	138	Conserved hypothetical protein; DNA-binding domain	84.92
2xig_A	150	Ferric uptake regulation protein; hpfur, transcrip	84.84
3cta_A	230	Riboflavin kinase; structural genomics, transferas	84.74
1z6r_A	406	MLC protein; transcriptional repressor, ROK family	84.6
3axs_A	392	Probable N(2),N(2)-dimethylguanosine tRNA methylt	84.46
1jhg_A	101	Trp operon repressor; complex (regulatory protein-	84.22
2xvc_A	59	ESCRT-III, SSO0910; cell cycle, cell division, cyt	84.07
3s1s_A	878	Restriction endonuclease bpusi; PD--(D/E)XK cataly	84.02
3l7w_A	108	Putative uncharacterized protein SMU.1704; PADR, t	84.01
1sd4_A	126	Penicillinase repressor; BLAI, MECI, methicillin,	83.84
3eld_A	300	Methyltransferase; flavivirus, RNA capping, guanyl	83.6
2obp_A	96	Putative DNA-binding protein; structural genomics,	83.5
2hoe_A	380	N-acetylglucosamine kinase; TM1224, structural gen	83.48
3f8b_A	116	Transcriptional regulator, PADR-like family; winge	83.19
3hhh_A	116	Transcriptional regulator, PADR family; PF03551, s	83.16
3p8z_A	267	Mtase, non-structural protein 5; methyltransferase	82.76
1hsj_A	487	Fusion protein consisting of staphylococcus access	82.73
2py6_A	409	Methyltransferase FKBM; YP_546752.1, structural ge	82.09
1m6e_X	359	S-adenosyl-L-methionnine:salicylic acid carboxyl m	82.07
1mzb_A	136	Ferric uptake regulation protein; ferric uptake re	81.35
1yg2_A	179	Gene activator APHA; virulence factor, winged heli	80.96
2ek5_A	129	Predicted transcriptional regulators; helix-turn-h	80.54
1fx7_A	230	Iron-dependent repressor IDER; DTXR, iron-dependen	80.33

>4a6d_A Hydroxyindole O-methyltransferase; melatonin, circadian clock; HET: SAM; 2.40A {Homo sapiens} PDB: 4a6e_A*

Probab=100.00  E-value=6.5e-40  Score=289.80  Aligned_cols=222  Identities=21%  Similarity=0.297  Sum_probs=198.1

Q ss_pred             hhchhHHHHHHHHhhhHHHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCccc
Q 041256            9 EETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALH   88 (244)
Q Consensus         9 ~~~~~~~~l~~~~~g~~~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~   88 (244)
                      .+++++..|++++.||+.+++|++|++|||||+|.+.+  +|+|++|||+++|++      +.. +.|+||+|++.|+|.
T Consensus         4 ~e~~~~~~L~~l~~Gf~~s~~L~aa~eLglfd~L~~~~--~p~t~~eLA~~~g~~------~~~-l~rlLr~L~~~gll~   74 (353)
T 4a6d_A            4 SEDQAYRLLNDYANGFMVSQVLFAACELGVFDLLAEAP--GPLDVAAVAAGVRAS------AHG-TELLLDICVSLKLLK   74 (353)
T ss_dssp             TSCHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHSS--SCBCHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEE
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHcCHHHHHhcCC--CCCCHHHHHHhhCcC------HHH-HHHHHHHHHHCCCEE
Confidence            46689999999999999999999999999999999864  799999999999997      678 999999999999998


Q ss_pred             ceeecCCceeecCcccc-ccccCCCCCCCHHHHHHHhcChhhhhhccchHHHHhcCCchhhhhhC---CCchhhccCCch
Q 041256           89 CSFVDGQRLYSLAPVSA-YFVRNNQNGASLSPYMALCLDKVCLDGWFGLKKQLLEGGIAFNKAHG---MQIYDYLGVDSR  164 (244)
Q Consensus        89 ~~~~~~~~~y~~t~~s~-~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~g~~~~~~~~g---~~~~e~~~~~~~  164 (244)
                      +..+.++++|++|+.+. ++.+++  +.++++++.+. .+..++.|.+|.+++++++++|...+|   .++|+++.++|+
T Consensus        75 ~~~~~~~~~y~~t~~s~~~l~~~~--~~~~~~~~~~~-~~~~~~~~~~L~~~vr~g~~~~~~~~g~~~~~~~~~~~~~~~  151 (353)
T 4a6d_A           75 VETRGGKAFYRNTELSSDYLTTVS--PTSQCSMLKYM-GRTSYRCWGHLADAVREGRNQYLETFGVPAEELFTAIYRSEG  151 (353)
T ss_dssp             EEEETTEEEEEECHHHHHHHSTTS--TTCCHHHHHHH-HHTHHHHHTTHHHHHHHTSCCHHHHHSCCCSSHHHHHTSSHH
T ss_pred             EeccCccceeeCCHHHHHHhhcCC--chHHHHHHHHh-CHHHHHHHHHHHHHHhcCCChhHHhcCCChHHHHHHHhhCHH
Confidence            65444567899999997 455555  67889888776 456788999999999999999999888   468999999999


Q ss_pred             HHHHHHHHHHhcchhhHHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCC------CCCc
Q 041256          165 FNDVFNNGMLSHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPS------YPGT  238 (244)
Q Consensus       165 ~~~~f~~aM~~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~------~~~i  238 (244)
                      ....|+++|...+....+.+++.++ |++.++|||||||+|.++.+++++||+++++++|+|+|++.+++      .++|
T Consensus       152 ~~~~f~~aM~~~~~~~~~~~~~~~~-~~~~~~v~DvGgG~G~~~~~l~~~~p~~~~~~~dlp~v~~~a~~~~~~~~~~rv  230 (353)
T 4a6d_A          152 ERLQFMQALQEVWSVNGRSVLTAFD-LSVFPLMCDLGGGAGALAKECMSLYPGCKITVFDIPEVVWTAKQHFSFQEEEQI  230 (353)
T ss_dssp             HHHHHHHHHHTTHHHHHHHHHHSSC-GGGCSEEEEETCTTSHHHHHHHHHCSSCEEEEEECHHHHHHHHHHSCC--CCSE
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcC-cccCCeEEeeCCCCCHHHHHHHHhCCCceeEeccCHHHHHHHHHhhhhcccCce
Confidence            9999999999998888889999999 99999999999999999999999999999999999999998864      3578


Q ss_pred             eeecc
Q 041256          239 LFIKF  243 (244)
Q Consensus       239 ~~~~~  243 (244)
                      +++.+
T Consensus       231 ~~~~g  235 (353)
T 4a6d_A          231 DFQEG  235 (353)
T ss_dssp             EEEES
T ss_pred             eeecC
Confidence            88865

>3p9c_A Caffeic acid O-methyltransferase; S-adenosylmethionine dependent O-methyltransferase; HET: SAH; 1.80A {Lolium perenne} PDB: 3p9i_A* 3p9k_A*

Probab=100.00  E-value=5.3e-39  Score=285.04  Aligned_cols=231  Identities=44%  Similarity=0.830  Sum_probs=204.6

Q ss_pred             hhhhchhHHHHHHHHhhhHHHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCC--CCCCCcchhccHHHHHHHHhhC
Q 041256            7 REEETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPL--KDNNPEAAAMTLDRVLRLLVSY   84 (244)
Q Consensus         7 ~~~~~~~~~~l~~~~~g~~~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~--~~~~~~~~~~~l~rlLr~L~~~   84 (244)
                      ..++.+++..+++++++++.+++|++|++|||||+|.+.| ++|+|++|||+++|+  +   |+++.. |+|+||+|++.
T Consensus        14 ~~~~~~~~~~~~~l~~~~~~~~~l~~a~~Lgifd~L~~~g-~~~~t~~eLA~~~g~~~~---~~~~~~-l~rlLr~L~~~   88 (364)
T 3p9c_A           14 ASADEDACMFALQLASSSVLPMTLKNAIELGLLEILVAAG-GKSLTPTEVAAKLPSAAN---PEAPDM-VDRILRLLASY   88 (364)
T ss_dssp             HHHHHHHHHHHHHHTTTTHHHHHHHHHHHHTHHHHHHHTT-TCCBCHHHHHHTTTCTTC---TTHHHH-HHHHHHHHHHT
T ss_pred             chHHHHHHHHHHHHHHhHHHHHHHHHHHHCChHHHHhhcC-CCCCCHHHHHHhcCCCCC---ccchhh-HHHHHHHHHhC
Confidence            4568889999999999999999999999999999999853 259999999999997  5   432348 99999999999


Q ss_pred             Ccccceeec---C--CceeecCccccccccCCCCCCCHHHHHHHhcChhhhhhccchHHHHhcCCchhhhhhCCCchhhc
Q 041256           85 NALHCSFVD---G--QRLYSLAPVSAYFVRNNQNGASLSPYMALCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYL  159 (244)
Q Consensus        85 gll~~~~~~---~--~~~y~~t~~s~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~g~~~~~~~~g~~~~e~~  159 (244)
                      |+|+++.+.   +  +++|++|+.++.|+.+. ++.++++++.+..++.++..|.+|.+++++|.++|+..+|.++|+|+
T Consensus        89 g~l~~~~~~~~~g~~~~~y~~t~~s~~l~~~~-~~~~~~~~~~~~~~~~~~~~~~~L~~~~r~g~~~~~~~~g~~~~~~~  167 (364)
T 3p9c_A           89 NVVTCLVEEGKDGRLSRSYGAAPVCKFLTPNE-DGVSMAALALMNQDKVLMESWYYLKDAVLDGGIPFNKAYGMSAFEYH  167 (364)
T ss_dssp             TSEEEEEEECSSSCEEEEEEECGGGGGSSCCT-TSCCTHHHHHHHTSHHHHGGGGGHHHHHHHCSCHHHHHHSSCHHHHH
T ss_pred             CCEEEeccccCCCCcCCEEecCHHHHHHcCCC-CCCCHHHHHHHhcCHHHHHHHhCHHHHHhhCCChHHHhcCCCHHHHH
Confidence            999964211   1  36899999999887765 46789999887767788999999999999999999999999999999


Q ss_pred             cCCchHHHHHHHHHHhcchhhHHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCCCCCce
Q 041256          160 GVDSRFNDVFNNGMLSHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPGTL  239 (244)
Q Consensus       160 ~~~~~~~~~f~~aM~~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~~~~i~  239 (244)
                      .++|+..+.|+++|...+....+.+++.++.|++..+|||||||+|.++..+++++|+++++++|+|++++.+++.++|+
T Consensus       168 ~~~~~~~~~f~~~m~~~~~~~~~~~~~~~~~~~~~~~vlDvG~G~G~~~~~l~~~~p~~~~~~~D~~~~~~~a~~~~~v~  247 (364)
T 3p9c_A          168 GTDPRFNRVFNEGMKNHSIIITKKLLELYHGFEGLGTLVDVGGGVGATVAAIAAHYPTIKGVNFDLPHVISEAPQFPGVT  247 (364)
T ss_dssp             TTCHHHHHHHHHHHHHHHHHHHHHHHHHCCTTTTCSEEEEETCTTSHHHHHHHHHCTTCEEEEEECHHHHTTCCCCTTEE
T ss_pred             HhCHHHHHHHHHHHHHhhHHHHHHHHHhcccccCCCEEEEeCCCCCHHHHHHHHHCCCCeEEEecCHHHHHhhhhcCCeE
Confidence            99999999999999998887778899988768888999999999999999999999999999999999999999888999


Q ss_pred             eecc
Q 041256          240 FIKF  243 (244)
Q Consensus       240 ~~~~  243 (244)
                      ++.+
T Consensus       248 ~~~~  251 (364)
T 3p9c_A          248 HVGG  251 (364)
T ss_dssp             EEEC
T ss_pred             EEeC
Confidence            8764

>3reo_A (ISO)eugenol O-methyltransferase; directed evolution, saturation mutagenesis, regioselectivity transferase; HET: SAH EUG; 1.90A {Clarkia breweri} PDB: 3tky_A* 1kyz_A* 1kyw_A*

Probab=100.00  E-value=8.3e-39  Score=284.14  Aligned_cols=231  Identities=52%  Similarity=0.889  Sum_probs=203.5

Q ss_pred             hhchhHHHHHHHHhhhHHHHHHHHHHhcChhhHHhhc-CCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcc
Q 041256            9 EETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKA-GPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNAL   87 (244)
Q Consensus         9 ~~~~~~~~l~~~~~g~~~~~~L~~a~~lgifd~L~~~-~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll   87 (244)
                      ++.+++..++++++|++.+++|++|++|||||+|++. |+++|+|++|||+++|..  +|+++.. |+|+||+|++.|+|
T Consensus        17 ~~~~~~~~~~~l~~~~~~~~~l~~a~~Lglfd~L~~~~gp~~~~t~~eLA~~~~~~--~~~~~~~-l~rlLr~L~~~gll   93 (368)
T 3reo_A           17 SDEEANLFAMQLASAAVLPMALKAAIELDVLEIMAKSVPPSGYISPAEIAAQLPTT--NPEAPVM-LDRVLRLLASYSVV   93 (368)
T ss_dssp             CHHHHHHHHHHHHTTTHHHHHHHHHHHTTHHHHHHHHCCTTCCBCHHHHHTTSSCC--CTTHHHH-HHHHHHHHHHTTSE
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCchhHHhhcCCCCCCcCHHHHHHhcCcC--CCcchhh-HHHHHHHHHhCCCe
Confidence            6888999999999999999999999999999999985 434689999999999842  2433457 99999999999999


Q ss_pred             cceee---cC--CceeecCccccccccCCCCCCCHHHHHHHhcChhhhhhccchHHHHhcCCchhhhhhCCCchhhccCC
Q 041256           88 HCSFV---DG--QRLYSLAPVSAYFVRNNQNGASLSPYMALCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVD  162 (244)
Q Consensus        88 ~~~~~---~~--~~~y~~t~~s~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~g~~~~~~~~g~~~~e~~~~~  162 (244)
                      ++...   .+  +++|++|+.++.|+.+. ++.++++++.+..++.++..|.+|.+++++|.++|+..+|.++|+|+.++
T Consensus        94 ~~~~~~~~~g~~~~~y~~t~~s~~l~~~~-~~~~~~~~~~~~~~~~~~~~~~~l~~~~r~g~~~~~~~~g~~~~~~~~~~  172 (368)
T 3reo_A           94 TYTLRELPSGKVERLYGLAPVCKFLTKNE-DGVSLAPFLLLATDKVLLEPWFYLKDAILEGGIPFNKAYGMNIFDYHGTD  172 (368)
T ss_dssp             EEEEEECTTSCEEEEEEECTTHHHHSCCT-TSCCSHHHHHHHTCHHHHGGGGGHHHHHHHCSCHHHHHSSSCHHHHHTTC
T ss_pred             EEecccCCCCcccceeCcCHHHHHHhCCC-CCCCHHHHHHHhcCHHHHhhhhchHHHHhcCCCHHHHHhCCCHHHHHhhC
Confidence            96311   11  36899999999887665 46789999887767788899999999999999999999999999999999


Q ss_pred             chHHHHHHHHHHhcchhhHHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCCCCCceeec
Q 041256          163 SRFNDVFNNGMLSHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPGTLFIK  242 (244)
Q Consensus       163 ~~~~~~f~~aM~~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~~~~i~~~~  242 (244)
                      |+..+.|+++|...+....+.+++.+++|++..+|||||||+|.++..+++++|+++++++|+|++++.+++.++|+++.
T Consensus       173 ~~~~~~f~~~m~~~~~~~~~~~~~~~~~~~~~~~vlDvG~G~G~~~~~l~~~~p~~~~~~~D~~~~~~~a~~~~~v~~~~  252 (368)
T 3reo_A          173 HRINKVFNKGMSSNSTITMKKILEMYNGFEGLTTIVDVGGGTGAVASMIVAKYPSINAINFDLPHVIQDAPAFSGVEHLG  252 (368)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTCCTTTTCSEEEEETCTTSHHHHHHHHHCTTCEEEEEECHHHHTTCCCCTTEEEEE
T ss_pred             HHHHHHHHHHHHhhhhhHHHHHHHhcccccCCCEEEEeCCCcCHHHHHHHHhCCCCEEEEEehHHHHHhhhhcCCCEEEe
Confidence            99999999999998887778889988768888999999999999999999999999999999999999999888998875


Q ss_pred             c
Q 041256          243 F  243 (244)
Q Consensus       243 ~  243 (244)
                      +
T Consensus       253 ~  253 (368)
T 3reo_A          253 G  253 (368)
T ss_dssp             C
T ss_pred             c
Confidence            4

>1zg3_A Isoflavanone 4'-O-methyltransferase; rossman fold, plant Pro transferase; HET: 2HI SAH; 2.35A {Medicago truncatula} PDB: 1zga_A* 1zhf_A* 1zgj_A*

Probab=100.00  E-value=3.4e-36  Score=266.09  Aligned_cols=228  Identities=27%  Similarity=0.411  Sum_probs=199.6

Q ss_pred             hhhhchhHHHHHHHHhhhHHHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCc
Q 041256            7 REEETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNA   86 (244)
Q Consensus         7 ~~~~~~~~~~l~~~~~g~~~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gl   86 (244)
                      .++..++...+++++++++.+++|++++++||||+|++.+  +|+|++|||+++|++   |++++. ++|+||+|++.|+
T Consensus         4 ~~~~~~~~~~l~~~~~~~~~~~~l~~a~~lgif~~L~~~~--~~~t~~eLA~~~g~~---~~~~~~-l~rlLr~L~~~gl   77 (358)
T 1zg3_A            4 ESELYHAQIHLYKHVYNFVSSMALKSAMELGIADAIHNHG--KPMTLSELASSLKLH---PSKVNI-LHRFLRLLTHNGF   77 (358)
T ss_dssp             TSCCTTHHHHHHHHHTTHHHHHHHHHHHHHTHHHHHHHHT--SCEEHHHHHHHTTCC---TTTHHH-HHHHHHHHHHTTS
T ss_pred             hHHhhhHHHHHHHHHHHHHHHHHHHHHHHCChHhHHhhcC--CCcCHHHHHHhcCCC---CcchHH-HHHHHHHHhhCCc
Confidence            4678899999999999999999999999999999999853  599999999999995   333567 9999999999999


Q ss_pred             ccceee---c-C---CceeecCccccccccCCCCCCCHHHHHHHhcChhhhhhccchHHHHhcC--CchhhhhhCCCchh
Q 041256           87 LHCSFV---D-G---QRLYSLAPVSAYFVRNNQNGASLSPYMALCLDKVCLDGWFGLKKQLLEG--GIAFNKAHGMQIYD  157 (244)
Q Consensus        87 l~~~~~---~-~---~~~y~~t~~s~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~g--~~~~~~~~g~~~~e  157 (244)
                      |++...   . +   +++|++|+.++.|++++  +.++++++.+..++.+++.|.+|+++++++  .++|+.++|.++|+
T Consensus        78 l~~~~~~~~~~~g~~~~~y~~t~~s~~l~~~~--~~~~~~~~~~~~~~~~~~~~~~L~~~l~~g~~~~~~~~~~g~~~~~  155 (358)
T 1zg3_A           78 FAKTIVKGKEGDEEEEIAYSLTPPSKLLISGK--PTCLSSIVKGALHPSSLDMWSSSKKWFNEDKEQTLFECATGESFWD  155 (358)
T ss_dssp             EEEEEECCSSSSCCCEEEEEECHHHHTTCTTS--TTCCHHHHHHHTSHHHHGGGGGHHHHHHCSCCCCHHHHHHSSCHHH
T ss_pred             EEEecccccccCCCCCCEEeCCHHHHHHhCCC--CccHHHHHHHhcCcHHHHHHHHHHHHHhCCCCCChHHHHhCCCHHH
Confidence            996300   1 1   47999999999888776  568999998876777889999999999998  78999999999999


Q ss_pred             hccCCchHHH--HHHHHHHhcchhhHHHHHhhcC-CCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCC
Q 041256          158 YLGVDSRFND--VFNNGMLSHTSIVMEKVLESYK-GFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPS  234 (244)
Q Consensus       158 ~~~~~~~~~~--~f~~aM~~~~~~~~~~~~~~~~-~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~  234 (244)
                      ++.++|+..+  .|+++|...+.... .+++.++ .|++..+|||||||+|.++..+++++|+++++++|+|.+++.+++
T Consensus       156 ~~~~~p~~~~~~~f~~~m~~~~~~~~-~~~~~~~~~~~~~~~vlDvG~G~G~~~~~l~~~~p~~~~~~~D~~~~~~~a~~  234 (358)
T 1zg3_A          156 FLNKDSESSTLSMFQDAMASDSRMFK-LVLQENKRVFEGLESLVDVGGGTGGVTKLIHEIFPHLKCTVFDQPQVVGNLTG  234 (358)
T ss_dssp             HHTSGGGHHHHHHHHHHHHHHHHTHH-HHHHHTHHHHHTCSEEEEETCTTSHHHHHHHHHCTTSEEEEEECHHHHSSCCC
T ss_pred             HHhcChhhhhHHHHHHHHhcccHHHH-HHHHhcchhccCCCEEEEECCCcCHHHHHHHHHCCCCeEEEeccHHHHhhccc
Confidence            9999999999  99999999887766 7888882 277889999999999999999999999999999999999999998


Q ss_pred             CCCceeecc
Q 041256          235 YPGTLFIKF  243 (244)
Q Consensus       235 ~~~i~~~~~  243 (244)
                      .++|+++.+
T Consensus       235 ~~~v~~~~~  243 (358)
T 1zg3_A          235 NENLNFVGG  243 (358)
T ss_dssp             CSSEEEEEC
T ss_pred             CCCcEEEeC
Confidence            888887753

>1fp2_A Isoflavone O-methyltransferase; protein-product complex; HET: SAH HMO; 1.40A {Medicago sativa} SCOP: a.4.5.29 c.66.1.12 PDB: 1fpx_A* 2qyo_A*

Probab=100.00  E-value=6.5e-36  Score=263.75  Aligned_cols=227  Identities=22%  Similarity=0.384  Sum_probs=200.5

Q ss_pred             chhhhchhHHHHHHHHhhhHHHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCC
Q 041256            6 DREEETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYN   85 (244)
Q Consensus         6 ~~~~~~~~~~~l~~~~~g~~~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~g   85 (244)
                      +.++..++...+++++++++.+++|++++++||||+|++.+  +|+|++|||+++|++   |++++. ++|+||+|++.|
T Consensus         9 ~~~~~~~a~~~l~~~~~~~~~~~~l~~a~~lgif~~L~~~~--~~~t~~ela~~~~~~---~~~~~~-l~rlLr~L~~~g   82 (352)
T 1fp2_A            9 KPSEIFKAQALLYKHIYAFIDSMSLKWAVEMNIPNIIQNHG--KPISLSNLVSILQVP---SSKIGN-VRRLMRYLAHNG   82 (352)
T ss_dssp             CSTHHHHHHHHHHHHHTTHHHHHHHHHHHHTTHHHHHHHHT--SCEEHHHHHHHHTCC---GGGHHH-HHHHHHHHHHTT
T ss_pred             ChHHHhhHHHHHHHHHHHHHHHHHHHHHHHCChhhhhhhcC--CCccHHHHHHHhCcC---CCChHH-HHHHHHHHHhCC
Confidence            34678889999999999999999999999999999999853  599999999999995   444668 999999999999


Q ss_pred             cccceeecCCceeecCccccccccCCCCCCCHHHHHHHhcChhhhhhccchHHHHh-cCCchhhhhhCCCchhhccCCch
Q 041256           86 ALHCSFVDGQRLYSLAPVSAYFVRNNQNGASLSPYMALCLDKVCLDGWFGLKKQLL-EGGIAFNKAHGMQIYDYLGVDSR  164 (244)
Q Consensus        86 ll~~~~~~~~~~y~~t~~s~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~-~g~~~~~~~~g~~~~e~~~~~~~  164 (244)
                      +|++.. .+++.|++|+.|+.|++++  +.++++++.+..++.++..|.+|+++++ +|+++|+..+|.++|+++.++|+
T Consensus        83 ll~~~~-~~~~~y~~t~~s~~L~~~~--~~~~~~~~~~~~~~~~~~~~~~L~~~l~~~g~~~~~~~~g~~~~~~~~~~~~  159 (352)
T 1fp2_A           83 FFEIIT-KEEESYALTVASELLVRGS--DLCLAPMVECVLDPTLSGSYHELKKWIYEEDLTLFGVTLGSGFWDFLDKNPE  159 (352)
T ss_dssp             SEEEEE-SSSEEEEECHHHHTTSTTS--SSCCHHHHHHHTCHHHHHGGGGHHHHHTCSSCCHHHHHHSSCHHHHHHHCHH
T ss_pred             eEEEec-CCCCeEeCCHHHHHHhCCC--CccHHHHHHHhcCchHHHHHHHHHHHHHhcCCChHHHHcCCCHHHHHHhChH
Confidence            999521 1358999999999888776  5689999888766777889999999999 88899999999999999999999


Q ss_pred             HHHHHHHHHHhcchhhHHHHHhhc--CCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCCCCCceeec
Q 041256          165 FNDVFNNGMLSHTSIVMEKVLESY--KGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPGTLFIK  242 (244)
Q Consensus       165 ~~~~f~~aM~~~~~~~~~~~~~~~--~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~~~~i~~~~  242 (244)
                      ..+.|+++|...+....+. ++.|  + |++..+|||||||+|.++..+++++|+++++++|+|.+++.+++.++|+++.
T Consensus       160 ~~~~f~~~m~~~~~~~~~~-~~~~~~~-~~~~~~vlDvG~G~G~~~~~l~~~~p~~~~~~~D~~~~~~~a~~~~~v~~~~  237 (352)
T 1fp2_A          160 YNTSFNDAMASDSKLINLA-LRDCDFV-FDGLESIVDVGGGTGTTAKIICETFPKLKCIVFDRPQVVENLSGSNNLTYVG  237 (352)
T ss_dssp             HHHHHHHHHHHTHHHHHHH-HHTCHHH-HTTCSEEEEETCTTSHHHHHHHHHCTTCEEEEEECHHHHTTCCCBTTEEEEE
T ss_pred             HHHHHHHHHHhcchhhhhH-HHhcccc-cccCceEEEeCCCccHHHHHHHHHCCCCeEEEeeCHHHHhhcccCCCcEEEe
Confidence            9999999999988776666 7777  4 7788999999999999999999999999999999999999999877888765


Q ss_pred             c
Q 041256          243 F  243 (244)
Q Consensus       243 ~  243 (244)
                      +
T Consensus       238 ~  238 (352)
T 1fp2_A          238 G  238 (352)
T ss_dssp             C
T ss_pred             c
Confidence            3

>3lst_A CALO1 methyltransferase; calicheamicin, enediyne, SAH, STRU genomics, PSI-2, protein structure initiative; HET: SAH; 2.40A {Micromonospora echinospora}

Probab=100.00  E-value=1.4e-35  Score=261.24  Aligned_cols=216  Identities=18%  Similarity=0.202  Sum_probs=193.6

Q ss_pred             hhchhHHHHHHHHhhhHHHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCccc
Q 041256            9 EETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALH   88 (244)
Q Consensus         9 ~~~~~~~~l~~~~~g~~~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~   88 (244)
                      ...++...++++++|++.+++|++++++||||+|.+    ||+|++|||+++|++      ++. ++|+||+|++.|+|+
T Consensus        18 ~~~~~~~~l~~~~~~~~~~~~l~~a~~lglf~~l~~----g~~t~~elA~~~g~~------~~~-l~rlLr~l~~~g~l~   86 (348)
T 3lst_A           18 DRLQSALALYEEAMGYTYAAALRAAAAVGVADHLVD----GPRTPAELAAATGTD------ADA-LRRVLRLLAVRDVVR   86 (348)
T ss_dssp             CHHHHHHHHHHHHTTHHHHHHHHHHHHHTGGGGGTT----SCBCHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEE
T ss_pred             CCchHHHHHHHHHHHHHHHHHHHHHHHcCchhHhhC----CCCCHHHHHHHhCcC------HHH-HHHHHHHHHhCCCEE
Confidence            445788899999999999999999999999999986    699999999999997      678 999999999999999


Q ss_pred             ceeecCCceeecCccccccccCCCCCCCHHHHHHHhcChhhhhhccchHHHHhcCCchhhhhhCCCchhhccCCchHHHH
Q 041256           89 CSFVDGQRLYSLAPVSAYFVRNNQNGASLSPYMALCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDV  168 (244)
Q Consensus        89 ~~~~~~~~~y~~t~~s~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~g~~~~~~~~g~~~~e~~~~~~~~~~~  168 (244)
                      +    ++++|++|+.|..|++++  +.++++++.+..++.+++.|.+|++++++|+++|+..+|.++|+|+.++|+..+.
T Consensus        87 ~----~~~~y~~t~~s~~l~~~~--~~~~~~~~~~~~~~~~~~~~~~l~~~l~~g~~~~~~~~g~~~~~~~~~~~~~~~~  160 (348)
T 3lst_A           87 E----SDGRFALTDKGAALRSDS--PVPARAGILMFTDTMFWTMSHRVASALGPERPAFADIFGSSLDAYFDGDAEVEAL  160 (348)
T ss_dssp             E----ETTEEEECTTTGGGSTTS--SSCSHHHHHHHTSHHHHHHHHTHHHHTCTTCCCHHHHHSSCHHHHHTTCHHHHHH
T ss_pred             e----cCCEEecCHHHHHHhcCC--CccHHHHHHHhcCHHHHHHHHHHHHHHhcCCChhhHHhCCCHHHHHHhCHHHHHH
Confidence            4    368999999999887765  5688888887667667889999999999999999999999999999999999999


Q ss_pred             HHHHHHhcchhhHHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCC-----CCCceeec
Q 041256          169 FNNGMLSHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPS-----YPGTLFIK  242 (244)
Q Consensus       169 f~~aM~~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~-----~~~i~~~~  242 (244)
                      |+++|...+....+.+++.++ |++..+|||||||+|.++..+++++|+++++++|+|.++...+.     .++|+++.
T Consensus       161 f~~~m~~~~~~~~~~~~~~~~-~~~~~~vLDvG~G~G~~~~~l~~~~p~~~~~~~D~~~~~~~~~~~~~~~~~~v~~~~  238 (348)
T 3lst_A          161 YYEGMETVSAAEHLILARAGD-FPATGTVADVGGGRGGFLLTVLREHPGLQGVLLDRAEVVARHRLDAPDVAGRWKVVE  238 (348)
T ss_dssp             HHHHHHHHHHTTHHHHHHHSC-CCSSEEEEEETCTTSHHHHHHHHHCTTEEEEEEECHHHHTTCCCCCGGGTTSEEEEE
T ss_pred             HHHHHHHhhhhhHHHHHHhCC-ccCCceEEEECCccCHHHHHHHHHCCCCEEEEecCHHHhhcccccccCCCCCeEEEe
Confidence            999999998888889999998 99999999999999999999999999999999999999883321     13577764

>1fp1_D Isoliquiritigenin 2'-O-methyltransferase; protein-substrate, protein-product complex; HET: SAH HCC; 1.82A {Medicago sativa} SCOP: a.4.5.29 c.66.1.12 PDB: 1fpq_A*

Probab=100.00  E-value=3.6e-35  Score=260.89  Aligned_cols=232  Identities=38%  Similarity=0.688  Sum_probs=185.4

Q ss_pred             cccchhhhchhHHHHH--HHHhhhHHHHHHHHHHhcChhhHHhhcCCCCC---CCHHHHHHhCCC---CCCCCcchhccH
Q 041256            3 SIADREEETNNFSYAM--ELASAIVLPAVMQAVVELDVFEIISKAGPGAK---LSVAEIVAQIPL---KDNNPEAAAMTL   74 (244)
Q Consensus         3 ~~~~~~~~~~~~~~l~--~~~~g~~~~~~L~~a~~lgifd~L~~~~~~g~---~t~~eLA~~~~~---~~~~~~~~~~~l   74 (244)
                      .+.+.++..+++..++  +++.+++.+++|++++++||||+|++.+  +|   +|++|||+++|+   +   |.+++. +
T Consensus        12 ~~~~~~~~~~~~~~l~~~~l~~~~~~~~~l~~a~~lgif~~L~~~g--~pg~~~t~~eLA~~~~~~~~~---~~~~~~-l   85 (372)
T 1fp1_D           12 QISATSEQTEDSACLSAMVLTTNLVYPAVLNAAIDLNLFEIIAKAT--PPGAFMSPSEIASKLPASTQH---SDLPNR-L   85 (372)
T ss_dssp             -------CCHHHHHHHHHHHHHTTHHHHHHHHHHHTTHHHHHHTCS--STTCCBCHHHHHTTSCGGGCC---TTHHHH-H
T ss_pred             ccCchhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHCChHHHHHhcC--CCCCCcCHHHHHHhcCCCCCC---CcChHH-H
Confidence            3556777888999999  9999999999999999999999999742  15   999999999998   4   322567 9


Q ss_pred             HHHHHHHhhCCccccee---ecC--CceeecCccccccccCCCCC-CCHHHHHHHhcChhhhhhccchHHHHhcC-Cchh
Q 041256           75 DRVLRLLVSYNALHCSF---VDG--QRLYSLAPVSAYFVRNNQNG-ASLSPYMALCLDKVCLDGWFGLKKQLLEG-GIAF  147 (244)
Q Consensus        75 ~rlLr~L~~~gll~~~~---~~~--~~~y~~t~~s~~l~~~~~~~-~~~~~~~~~~~~~~~~~~~~~l~~~l~~g-~~~~  147 (244)
                      +|+||+|++.|+|++..   +.+  +++|++|+.+..|++++  + .++++++.+..++.+++.|.+|+++++++ .++|
T Consensus        86 ~rlLr~L~~~gll~~~~~~~~~g~~~~~y~~t~~s~~L~~~~--~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~g~~~~~  163 (372)
T 1fp1_D           86 DRMLRLLASYSVLTSTTRTIEDGGAERVYGLSMVGKYLVPDE--SRGYLASFTTFLCYPALLQVWMNFKEAVVDEDIDLF  163 (372)
T ss_dssp             HHHHHHHHHTTSEEEEEEECTTSCEEEEEEECTTGGGGSTTC--TTCCCTHHHHHHTCHHHHHHHTTHHHHHHSCC----
T ss_pred             HHHHHHHhhCCceEecccccCCCCcCCeEecCHHHHHHhCCC--CCCCHHHHHHHhcCchHHHHHHHHHHHHHcCCCChh
Confidence            99999999999999631   011  36999999999888776  4 57899988876777788999999999998 8899


Q ss_pred             hhhhCCCchhhccCCchHHHHHHHHHHhcchhhHHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccchH
Q 041256          148 NKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPY  227 (244)
Q Consensus       148 ~~~~g~~~~e~~~~~~~~~~~f~~aM~~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~  227 (244)
                      +..+|.++|+++.++|+..+.|+++|...+....+.+++.++.+++..+|||||||+|.++..+++++|+++++++|+|.
T Consensus       164 ~~~~g~~~~~~~~~~~~~~~~f~~~m~~~~~~~~~~l~~~~~~~~~~~~vLDvG~G~G~~~~~l~~~~~~~~~~~~D~~~  243 (372)
T 1fp1_D          164 KNVHGVTKYEFMGKDKKMNQIFNKSMVDVCATEMKRMLEIYTGFEGISTLVDVGGGSGRNLELIISKYPLIKGINFDLPQ  243 (372)
T ss_dssp             ----------CCSSCHHHHHHHHHHHHHHHHHHHHHHHHHCCTTTTCSEEEEETCTTSHHHHHHHHHCTTCEEEEEECHH
T ss_pred             HHHhCCCHHHHHHhCHHHHHHHHHHHHhhhHHHHHHHHHHhhccCCCCEEEEeCCCCcHHHHHHHHHCCCCeEEEeChHH
Confidence            99999999999999999999999999998887778889988667888999999999999999999999999999999999


Q ss_pred             HhhhCCCCCCceeec
Q 041256          228 VIKDAPSYPGTLFIK  242 (244)
Q Consensus       228 vi~~a~~~~~i~~~~  242 (244)
                      +++.+++.++|+++.
T Consensus       244 ~~~~a~~~~~v~~~~  258 (372)
T 1fp1_D          244 VIENAPPLSGIEHVG  258 (372)
T ss_dssp             HHTTCCCCTTEEEEE
T ss_pred             HHHhhhhcCCCEEEe
Confidence            999999888888775

>3gwz_A MMCR; methyltransferase, mitomycin, S-adenosyl methionine, transferase; HET: MSE SAH; 1.91A {Streptomyces lavendulae} PDB: 3gxo_A*

Probab=100.00  E-value=3e-35  Score=261.22  Aligned_cols=216  Identities=18%  Similarity=0.300  Sum_probs=194.8

Q ss_pred             hchhHHHHHHHHhhhHHHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           10 ETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        10 ~~~~~~~l~~~~~g~~~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      ..+...+++++++|++.+++|++++++||||+|.+    +|+|++|||+++|++      ++. ++|+||+|++.|+|++
T Consensus        35 ~~~~~~~l~~l~~~~~~~~~l~~a~~lglf~~l~~----g~~t~~eLA~~~g~~------~~~-l~rlLr~L~~~g~l~~  103 (369)
T 3gwz_A           35 RAAAEETVNDILQGAWKARAIHVAVELGVPELLQE----GPRTATALAEATGAH------EQT-LRRLLRLLATVGVFDD  103 (369)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHTTGGGGTT----SCEEHHHHHHHHTCC------HHH-HHHHHHHHHHTTSSEE
T ss_pred             CChHHHHHHHHHHHHHHHHHHHHHHHCChhhhhcC----CCCCHHHHHHHHCcC------HHH-HHHHHHHHHhCCCEEE
Confidence            34667889999999999999999999999999985    699999999999997      678 9999999999999994


Q ss_pred             eeecCCce-eecCccccccccCCCCCCCHHHHHHHhcChhhhhhccchHHHHhcCCchhhhhhCCCchhhccCCchHHHH
Q 041256           90 SFVDGQRL-YSLAPVSAYFVRNNQNGASLSPYMALCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDV  168 (244)
Q Consensus        90 ~~~~~~~~-y~~t~~s~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~g~~~~~~~~g~~~~e~~~~~~~~~~~  168 (244)
                         .++++ |++|+.++.|.+++  +.++.+++.+..++..+..|.+|.++++++.++|...+|.++|+|+.++|+..+.
T Consensus       104 ---~~~~~~y~~t~~s~~L~~~~--~~~~~~~~~~~~~~~~~~~~~~l~~~l~~g~~~~~~~~g~~~~~~~~~~~~~~~~  178 (369)
T 3gwz_A          104 ---LGHDDLFAQNALSAVLLPDP--ASPVATDARFQAAPWHWRAWEQLTHSVRTGEASFDVANGTSFWQLTHEDPKAREL  178 (369)
T ss_dssp             ---CSSTTEEECCHHHHTTSCCT--TCHHHHHHHHHHSHHHHHHHHTHHHHHHHSSCSHHHHHSSCHHHHHHHCHHHHHH
T ss_pred             ---eCCCceEecCHHHHHHhcCC--chhHHHHHHHcCCHHHHHHHHhHHHHHhCCCChhHhhcCCCHHHHHHhCHHHHHH
Confidence               44688 99999999887765  5678888887766667789999999999999999999999999999999999999


Q ss_pred             HHHHHHhcchhhHHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCC-------CCCceee
Q 041256          169 FNNGMLSHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPS-------YPGTLFI  241 (244)
Q Consensus       169 f~~aM~~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~-------~~~i~~~  241 (244)
                      |+++|...+....+.+++.++ +++..+|||||||+|.++..+++++|+++++++|+|.+++.+++       .++|+++
T Consensus       179 f~~~m~~~~~~~~~~l~~~~~-~~~~~~vlDvG~G~G~~~~~l~~~~p~~~~~~~D~~~~~~~a~~~~~~~~l~~~v~~~  257 (369)
T 3gwz_A          179 FNRAMGSVSLTEAGQVAAAYD-FSGAATAVDIGGGRGSLMAAVLDAFPGLRGTLLERPPVAEEARELLTGRGLADRCEIL  257 (369)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSC-CTTCSEEEEETCTTSHHHHHHHHHCTTCEEEEEECHHHHHHHHHHHHHTTCTTTEEEE
T ss_pred             HHHHHHHHHhhhHHHHHHhCC-CccCcEEEEeCCCccHHHHHHHHHCCCCeEEEEcCHHHHHHHHHhhhhcCcCCceEEe
Confidence            999999988887888999998 89999999999999999999999999999999999999998874       2467776


Q ss_pred             c
Q 041256          242 K  242 (244)
Q Consensus       242 ~  242 (244)
                      .
T Consensus       258 ~  258 (369)
T 3gwz_A          258 P  258 (369)
T ss_dssp             E
T ss_pred             c
Confidence            5

>3i53_A O-methyltransferase; CO-complex, rossmann-like fold; HET: SAH; 2.08A {Streptomyces carzinostaticus subsp} PDB: 3i58_A* 3i5u_A* 3i64_A*

Probab=100.00  E-value=3.2e-35  Score=257.19  Aligned_cols=213  Identities=21%  Similarity=0.296  Sum_probs=188.8

Q ss_pred             HHHHHHHHhhhHHHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeec
Q 041256           14 FSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVD   93 (244)
Q Consensus        14 ~~~l~~~~~g~~~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~   93 (244)
                      ...+++++.|++.+++|++|+++||||+|.+    ||+|++|||+++|++      ++. ++|+||+|++.|++.+   .
T Consensus         6 ~~~l~~~~~g~~~~~~l~~a~~lglf~~l~~----g~~t~~elA~~~~~~------~~~-l~rlLr~l~~~gl~~~---~   71 (332)
T 3i53_A            6 AHIGLRALADLATPMAVRVAATLRVADHIAA----GHRTAAEIASAAGAH------ADS-LDRLLRHLVAVGLFTR---D   71 (332)
T ss_dssp             CSSCHHHHTCCHHHHHHHHHHHHTHHHHHHT----TCCBHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEE---C
T ss_pred             HHHHHHHHHhhHHHHHHHHHHHcChHHHHhc----CCCCHHHHHHHHCcC------HHH-HHHHHHHHHhCCcEEe---c
Confidence            3457899999999999999999999999986    699999999999997      678 9999999999999994   4


Q ss_pred             CCceeecCccccccccCCCCCCCHHHHHHHhcChhhh-hhccchHHHHhcCCchhhhhhCCCchhhccCCchHHHHHHHH
Q 041256           94 GQRLYSLAPVSAYFVRNNQNGASLSPYMALCLDKVCL-DGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNG  172 (244)
Q Consensus        94 ~~~~y~~t~~s~~l~~~~~~~~~~~~~~~~~~~~~~~-~~~~~l~~~l~~g~~~~~~~~g~~~~e~~~~~~~~~~~f~~a  172 (244)
                      ++++|.+|+.++.|.+++  +.++.+++.+..++..+ ..|.+|.+++++++++|+..+|.++|+++.++|+..+.|+++
T Consensus        72 ~~~~y~~t~~s~~l~~~~--~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~g~~~~~~~~~~~~~~~~f~~~  149 (332)
T 3i53_A           72 GQGVYGLTEFGEQLRDDH--AAGKRKWLDMNSAVGRGDLGFVELAHSIRTGQPAYPVRYGTSFWEDLGSDPVLSASFDTL  149 (332)
T ss_dssp             TTSBEEECTTGGGGSTTC--TTCCHHHHCTTSHHHHHGGGGGGHHHHHHHSSCSHHHHHSSCHHHHHHHCHHHHHHHHHH
T ss_pred             CCCeEEcCHhHHHHhcCC--chhHHHHHHHcCCHhHHHHHHHHhHHHHhcCCCHHHHhhCCCHHHHHHhCHHHHHHHHHH
Confidence            568999999999887665  56788888776444455 789999999999999999999989999999999999999999


Q ss_pred             HHhcchhhHHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCC-------CCCceeecc
Q 041256          173 MLSHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPS-------YPGTLFIKF  243 (244)
Q Consensus       173 M~~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~-------~~~i~~~~~  243 (244)
                      |...+....+.+++.++ |++..+|||||||+|.++..+++++|+++++++|+|.+++.+++       .++|+++.+
T Consensus       150 m~~~~~~~~~~~~~~~~-~~~~~~vlDvG~G~G~~~~~l~~~~p~~~~~~~D~~~~~~~a~~~~~~~~~~~~v~~~~~  226 (332)
T 3i53_A          150 MSHHLELDYTGIAAKYD-WAALGHVVDVGGGSGGLLSALLTAHEDLSGTVLDLQGPASAAHRRFLDTGLSGRAQVVVG  226 (332)
T ss_dssp             HHHHHHHHHTTGGGSSC-CGGGSEEEEETCTTSHHHHHHHHHCTTCEEEEEECHHHHHHHHHHHHHTTCTTTEEEEEC
T ss_pred             HHHhHHhhHHHHHHhCC-CCCCCEEEEeCCChhHHHHHHHHHCCCCeEEEecCHHHHHHHHHhhhhcCcCcCeEEecC
Confidence            99988776777888888 88889999999999999999999999999999999999999874       246777653

>2ip2_A Probable phenazine-specific methyltransferase; pyocyanin, phenazine-1-carboxy PHZM; 1.80A {Pseudomonas aeruginosa}

Probab=100.00  E-value=5.6e-34  Score=249.28  Aligned_cols=210  Identities=19%  Similarity=0.285  Sum_probs=188.1

Q ss_pred             hhHHHHHHHHhhhHHHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCccccee
Q 041256           12 NNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSF   91 (244)
Q Consensus        12 ~~~~~l~~~~~g~~~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~   91 (244)
                      .+...++++++|++.+++|++++++||||+|.+    +|+|++|||+++|++      ++. ++|+||+|++.|+|++  
T Consensus         7 ~~~~~l~~~~~~~~~~~~l~~~~~lgi~~~l~~----~~~t~~ela~~~~~~------~~~-l~r~Lr~L~~~g~l~~--   73 (334)
T 2ip2_A            7 AAARNLIQVVTGEWKSRCVYVATRLGLADLIES----GIDSDETLAAAVGSD------AER-IHRLMRLLVAFEIFQG--   73 (334)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHT----TCCSHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEE--
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHcCcHHHHhC----CCCCHHHHHHHhCcC------HHH-HHHHHHHHHhCCceEe--
Confidence            567889999999999999999999999999976    699999999999997      678 9999999999999995  


Q ss_pred             ecCCceeecCccccccccCCCCCCCHHHHHHHhcChhhhhhccchHHHHhcCCchhhhhhCCCchhhccCCchHHHHHHH
Q 041256           92 VDGQRLYSLAPVSAYFVRNNQNGASLSPYMALCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNN  171 (244)
Q Consensus        92 ~~~~~~y~~t~~s~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~g~~~~~~~~g~~~~e~~~~~~~~~~~f~~  171 (244)
                       .+++.|++|+.+..|+ ++  +.++++++.+..++.+ ..|.+|.+++++++++|+..+|.++|+++.++|+..+.|++
T Consensus        74 -~~~~~y~~t~~s~~l~-~~--~~~~~~~~~~~~~~~~-~~~~~l~~~l~~~~~~~~~~~g~~~~~~~~~~~~~~~~f~~  148 (334)
T 2ip2_A           74 -DTRDGYANTPTSHLLR-DV--EGSFRDMVLFYGEEFH-AAWTPACEALLSGTPGFELAFGEDFYSYLKRCPDAGRRFLL  148 (334)
T ss_dssp             -ETTTEEEECHHHHTTS-SS--TTCSHHHHHHHTTHHH-HHTTTHHHHHHHCCCHHHHHHSSCHHHHHHHCHHHHHHHHH
T ss_pred             -cCCCeEecCHHHHHHh-CC--CccHHHHHHHhcCchh-hHHHHHHHHHhcCCChhhhhcCCCHHHHHhhChHHHHHHHH
Confidence             4468999999999888 65  5688998887756544 89999999999999999999999999999999999999999


Q ss_pred             HHHhcchhhHHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCCC-------CCceeec
Q 041256          172 GMLSHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSY-------PGTLFIK  242 (244)
Q Consensus       172 aM~~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~~-------~~i~~~~  242 (244)
                      +| ..+....+.+++.++ |++ .+|||||||+|.++..+++++|+++++++|+|.+++.+++.       ++|+++.
T Consensus       149 ~m-~~~~~~~~~~~~~~~-~~~-~~vlDvG~G~G~~~~~l~~~~p~~~~~~~D~~~~~~~a~~~~~~~~~~~~v~~~~  223 (334)
T 2ip2_A          149 AM-KASNLAFHEIPRLLD-FRG-RSFVDVGGGSGELTKAILQAEPSARGVMLDREGSLGVARDNLSSLLAGERVSLVG  223 (334)
T ss_dssp             HH-GGGHHHHHHHHHHSC-CTT-CEEEEETCTTCHHHHHHHHHCTTCEEEEEECTTCTHHHHHHTHHHHHTTSEEEEE
T ss_pred             HH-HHHHHHHHHHHHhCC-CCC-CEEEEeCCCchHHHHHHHHHCCCCEEEEeCcHHHHHHHHHHHhhcCCCCcEEEec
Confidence            99 887777788999998 888 99999999999999999999999999999999999888652       3577654

>3dp7_A SAM-dependent methyltransferase; structural genomics, protein structure initiative, NEW YORK structural genomix research; 2.33A {Bacteroides vulgatus}

Probab=100.00  E-value=2.9e-33  Score=247.91  Aligned_cols=215  Identities=19%  Similarity=0.209  Sum_probs=179.1

Q ss_pred             chhhhchhHHHHHHHHhhhHHHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCC
Q 041256            6 DREEETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYN   85 (244)
Q Consensus         6 ~~~~~~~~~~~l~~~~~g~~~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~g   85 (244)
                      ++.++.++...++++++|++.+++|++++++||||+|++.+  +|+|++|||+++|++      ++. ++|+||+|++.|
T Consensus         8 ~~~~~~~a~~~l~~l~~g~~~~~~l~~a~~lgifd~L~~~~--~~~t~~eLA~~~g~~------~~~-l~rlLr~l~~~g   78 (363)
T 3dp7_A            8 EQCTAAEAQRLAQEIAFGPVVFQVSRLMLKFGIFQLLSGKR--EGYTLQEISGRTGLT------RYA-AQVLLEASLTIG   78 (363)
T ss_dssp             SCCCSTTHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHTCT--TCBCHHHHHHHHTCC------HHH-HHHHHHHHHHHT
T ss_pred             CchhHHHHHHHHHHHHhhHHHHHHHHHHHHhCHHHHHHhcC--CCCCHHHHHHHhCcC------HHH-HHHHHHHHhhCC
Confidence            45678899999999999999999999999999999999843  699999999999997      678 999999999999


Q ss_pred             cccceeecCCceeecCccccccccCCCCCCCHHHHHHHhcChhhhhhccchHHHHhcCCchhhhhhC--CCchhhccCCc
Q 041256           86 ALHCSFVDGQRLYSLAPVSAYFVRNNQNGASLSPYMALCLDKVCLDGWFGLKKQLLEGGIAFNKAHG--MQIYDYLGVDS  163 (244)
Q Consensus        86 ll~~~~~~~~~~y~~t~~s~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~g~~~~~~~~g--~~~~e~~~~~~  163 (244)
                      +|++   . +++|++|+.|.+|++++  +  ...++.+. .+..++.|.+|++++++|.+++...+|  .++|+++.++|
T Consensus        79 ~l~~---~-~~~y~~t~~s~~L~~~~--~--~~~~~~~~-~~~~~~~~~~L~~~lr~g~~~~~~~~g~~~~~~~~~~~~~  149 (363)
T 3dp7_A           79 TILL---E-EDRYVLAKAGWFLLNDK--M--ARVNMEFN-HDVNYQGLFHLEEALLNGRPEGLKVFGEWPTIYEGLSQLP  149 (363)
T ss_dssp             SEEE---E-TTEEEECHHHHHHHHCH--H--HHHHHHHH-HHTTHHHHTTHHHHHHHSSCGGGGGTCCCSSHHHHGGGSC
T ss_pred             CeEe---c-CCEEecccchHHhhCCC--c--ccchheee-cHHhhhhHHHHHHHHhcCCCccccccCchHhHHHHHhhCH
Confidence            9984   3 58999999999888775  2  22333333 456788999999999999998888888  68999999999


Q ss_pred             hHHH----HHHHHHHhcchhhHHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCCC----
Q 041256          164 RFND----VFNNGMLSHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSY----  235 (244)
Q Consensus       164 ~~~~----~f~~aM~~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~~----  235 (244)
                      +..+    .|+.+|.....   ..++..+. ..+..+|||||||+|.++..+++++|+++++++|+|.+++.+++.    
T Consensus       150 ~~~~~~~~~f~~~~~~~~~---~~~l~~~~-~~~~~~vlDvG~G~G~~~~~l~~~~p~~~~~~~D~~~~~~~a~~~~~~~  225 (363)
T 3dp7_A          150 EQVQKSWFGFDHFYSDQSF---GKALEIVF-SHHPKRLLDIGGNTGKWATQCVQYNKEVEVTIVDLPQQLEMMRKQTAGL  225 (363)
T ss_dssp             HHHHHHHHHHHHHTTCCCC---HHHHHHHG-GGCCSEEEEESCTTCHHHHHHHHHSTTCEEEEEECHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHhhhhhH---HHHHHHhc-ccCCCEEEEeCCCcCHHHHHHHHhCCCCEEEEEeCHHHHHHHHHHHHhc
Confidence            8766    37777765432   23444443 357799999999999999999999999999999999999988752    


Q ss_pred             ---CCceeec
Q 041256          236 ---PGTLFIK  242 (244)
Q Consensus       236 ---~~i~~~~  242 (244)
                         ++|+++.
T Consensus       226 ~~~~~v~~~~  235 (363)
T 3dp7_A          226 SGSERIHGHG  235 (363)
T ss_dssp             TTGGGEEEEE
T ss_pred             CcccceEEEE
Confidence               3577664

>1qzz_A RDMB, aclacinomycin-10-hydroxylase; anthracycline, methyltransferase, polyketide, tailoring enzymes, structural proteomics in E spine; HET: SAM; 2.10A {Streptomyces purpurascens} SCOP: a.4.5.29 c.66.1.12 PDB: 1r00_A* 1xds_A* 1xdu_A*

Probab=99.97  E-value=6.7e-32  Score=239.39  Aligned_cols=207  Identities=18%  Similarity=0.281  Sum_probs=185.3

Q ss_pred             chhHHHHHHHHhhhHHHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           11 TNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        11 ~~~~~~l~~~~~g~~~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      .+....+++++.+++.+++|++++++||||.|.+    +|+|++|||+++|++      +.. +.|+||+|++.|+|++ 
T Consensus        14 ~~~~~~l~~~~~~~~~~~~l~~~~~l~i~~~l~~----~~~t~~eLA~~~g~~------~~~-l~r~Lr~L~~~Gll~~-   81 (374)
T 1qzz_A           14 DQDLDVLLKNLGNLVTPMALRVAATLRLVDHLLA----GADTLAGLADRTDTH------PQA-LSRLVRHLTVVGVLEG-   81 (374)
T ss_dssp             HHHHHHHHHTTTCCHHHHHHHHHHHTTHHHHHHT----TCCSHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEC-
T ss_pred             chHHHHHHHHHHhhHHHHHHHHHHHcChHHHHhC----CCCCHHHHHHHhCcC------HHH-HHHHHHHHhhCCCEEE-
Confidence            4566789999999999999999999999999965    699999999999997      678 9999999999999995 


Q ss_pred             eecCCc--eeecCccccccccCCCCCCCHHHHHHHhcChhhh-hhccchHHHHhcCCchhhhhhCCCchhhccCCchHHH
Q 041256           91 FVDGQR--LYSLAPVSAYFVRNNQNGASLSPYMALCLDKVCL-DGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFND  167 (244)
Q Consensus        91 ~~~~~~--~y~~t~~s~~l~~~~~~~~~~~~~~~~~~~~~~~-~~~~~l~~~l~~g~~~~~~~~g~~~~e~~~~~~~~~~  167 (244)
                        ..++  .|++|+.+..|++++  +.++++++.+..++..+ ..|.+|.++++++.++|+..+|.++|+++..+|+..+
T Consensus        82 --~~~~~~~y~~t~~s~~l~~~~--~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~g~~~~~~~~~~~~~~~  157 (374)
T 1qzz_A           82 --GEKQGRPLRPTRLGMLLADGH--PAQQRAWLDLNGAVSHADLAFTGLLDVVRTGRPAYAGRYGRPFWEDLSADVALAD  157 (374)
T ss_dssp             --CCC-CCCCEECTTGGGGSTTC--TTCHHHHHCTTSHHHHHHGGGGGHHHHHHHSCCSHHHHHSSCHHHHHHHCHHHHH
T ss_pred             --eCCCCeEEEEChHHHhhcCCC--cccHHHHHHHcCChhhHHHHHHHHHHHHhcCCChhhhhhCCCHHHHHhhChHHHH
Confidence              3456  899999999888776  66899988776544556 8999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcchhhHHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCC
Q 041256          168 VFNNGMLSHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPS  234 (244)
Q Consensus       168 ~f~~aM~~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~  234 (244)
                      .|+.+|........+.+++.++ +++..+|||||||+|.++..+++++|+++++.+|+|.+++.+++
T Consensus       158 ~f~~~~~~~~~~~~~~~~~~~~-~~~~~~vlDvG~G~G~~~~~l~~~~~~~~~~~~D~~~~~~~a~~  223 (374)
T 1qzz_A          158 SFDALMSCDEDLAYEAPADAYD-WSAVRHVLDVGGGNGGMLAAIALRAPHLRGTLVELAGPAERARR  223 (374)
T ss_dssp             HHHHTCGGGSTTTTHHHHHTSC-CTTCCEEEEETCTTSHHHHHHHHHCTTCEEEEEECHHHHHHHHH
T ss_pred             HHHHHHHHhhHhHHHHHHHhCC-CCCCCEEEEECCCcCHHHHHHHHHCCCCEEEEEeCHHHHHHHHH
Confidence            9999999887777778899888 88889999999999999999999999999999999999998864

>1tw3_A COMT, carminomycin 4-O-methyltransferase; anthracycline, methylate, tailoring enzyme, polyketide, S-adenosyl-L-homocystein; HET: SAH ERT; 2.35A {Streptomyces peucetius} SCOP: a.4.5.29 c.66.1.12 PDB: 1tw2_A*

Probab=99.97  E-value=7.4e-31  Score=231.64  Aligned_cols=205  Identities=17%  Similarity=0.275  Sum_probs=184.2

Q ss_pred             hHHHHHHHHhhhHHHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceee
Q 041256           13 NFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFV   92 (244)
Q Consensus        13 ~~~~l~~~~~g~~~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~   92 (244)
                      ...++++++.+++.+++|.+++++|||+.|.+    +|+|++|||+++|++      +.. +.|+||+|++.|+|.+   
T Consensus        19 ~~~~~~~~~~~~~~~~~l~~~~~l~i~~~l~~----~~~t~~ela~~~~~~------~~~-l~r~L~~L~~~g~~~~---   84 (360)
T 1tw3_A           19 DALRTLIRLGSLHTPMVVRTAATLRLVDHILA----GARTVKALAARTDTR------PEA-LLRLIRHLVAIGLLEE---   84 (360)
T ss_dssp             HHHHHHHHHHCSHHHHHHHHHHHTTHHHHHHT----TCCBHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEE---
T ss_pred             chHHHHHHHHhHHHHHHHHHHHHhCHHHHHhC----CCCCHHHHHHHhCcC------HHH-HHHHHHHHHHCCCEEe---
Confidence            35788999999999999999999999999965    699999999999997      677 9999999999999995   


Q ss_pred             cCCceeecCccccccccCCCCCCCHHHHHHHhcChh-hhhhccchHHHHhcCCchhhhhhCCCchhhccCCchHHHHHHH
Q 041256           93 DGQRLYSLAPVSAYFVRNNQNGASLSPYMALCLDKV-CLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNN  171 (244)
Q Consensus        93 ~~~~~y~~t~~s~~l~~~~~~~~~~~~~~~~~~~~~-~~~~~~~l~~~l~~g~~~~~~~~g~~~~e~~~~~~~~~~~f~~  171 (244)
                      .++++|++|+.+..|++++  +.+++.++.+...+. .+..|.+|.+.+++|.++|+..+|.++|+++..+|+....|..
T Consensus        85 ~~~g~y~~t~~s~~l~~~~--~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~g~~~~~~~~g~~~~~~~~~~p~~~~~f~~  162 (360)
T 1tw3_A           85 DAPGEFVPTEVGELLADDH--PAAQRAWHDLTQAVARADISFTRLPDAIRTGRPTYESIYGKPFYEDLAGRPDLRASFDS  162 (360)
T ss_dssp             EETTEEEECTTGGGGSTTS--TTCHHHHTCTTSHHHHHGGGGGGHHHHHHHCCCCHHHHHSSCHHHHHHTCHHHHHHHHH
T ss_pred             cCCCeEEeCHHHHHHhcCC--chhHHHHHHHhcCchhHHHHHHHHHHHHHcCCCHHHHhcCCCHHHHHHhChHHHHHHHH
Confidence            2468999999999898776  678888887764443 5789999999999999999999999999999999999999999


Q ss_pred             HHHhcchhhHHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCC
Q 041256          172 GMLSHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPS  234 (244)
Q Consensus       172 aM~~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~  234 (244)
                      +|...+....+.+++.++ +++..+|||||||+|.++..+++++|+++++.+|+|.+++.+++
T Consensus       163 ~~~~~~~~~~~~l~~~~~-~~~~~~vLDvG~G~G~~~~~l~~~~~~~~~~~~D~~~~~~~a~~  224 (360)
T 1tw3_A          163 LLACDQDVAFDAPAAAYD-WTNVRHVLDVGGGKGGFAAAIARRAPHVSATVLEMAGTVDTARS  224 (360)
T ss_dssp             HHTTTTTTTTHHHHHHSC-CTTCSEEEEETCTTSHHHHHHHHHCTTCEEEEEECTTHHHHHHH
T ss_pred             HHHHHHHHhHHHHHHhCC-CccCcEEEEeCCcCcHHHHHHHHhCCCCEEEEecCHHHHHHHHH
Confidence            999888777788899988 88889999999999999999999999999999999999988764

>1x19_A CRTF-related protein; methyltransferase, bacteriochllochlorophyll, BCHU, SAM, SAH, adenosylmethyonine, S-adenosylhomocysteine, ADO-Met; 2.27A {Chlorobium tepidum} PDB: 1x1a_A* 1x1b_A* 1x1c_A* 1x1d_A*

Probab=99.97  E-value=3.9e-30  Score=227.21  Aligned_cols=207  Identities=19%  Similarity=0.271  Sum_probs=179.4

Q ss_pred             hhhhchhHHHHHHHHh-hhHHHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCC
Q 041256            7 REEETNNFSYAMELAS-AIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYN   85 (244)
Q Consensus         7 ~~~~~~~~~~l~~~~~-g~~~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~g   85 (244)
                      ..+..++..+++++++ |++.+++|++++++||||.|.+    +|+|++|||+++|++      ++. ++|+||+|++.|
T Consensus        24 ~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~lgif~~L~~----~~~t~~eLA~~~g~~------~~~-l~rlLr~L~~~g   92 (359)
T 1x19_A           24 NNDLLNYYHRANELVFKGLIEFSCMKAAIELDLFSHMAE----GPKDLATLAADTGSV------PPR-LEMLLETLRQMR   92 (359)
T ss_dssp             CCHHHHHHHHHHHHHTHHHHHHHHHHHHHHHTHHHHHTT----CCBCHHHHHHHHTCC------HHH-HHHHHHHHHHTT
T ss_pred             ccccCCcchHHHHHHHHHHHHHHHHHHHHHcCcHHHHcC----CCCCHHHHHHHhCcC------hHH-HHHHHHHHHhCC
Confidence            3456778889999997 8999999999999999999986    699999999999997      678 999999999999


Q ss_pred             cccceeecCCceeecCccc-cccccCCCCC---CCHHHHHHHhcChhhhhhccchHHHHhcCCchhhhhhCCCchhhccC
Q 041256           86 ALHCSFVDGQRLYSLAPVS-AYFVRNNQNG---ASLSPYMALCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGV  161 (244)
Q Consensus        86 ll~~~~~~~~~~y~~t~~s-~~l~~~~~~~---~~~~~~~~~~~~~~~~~~~~~l~~~l~~g~~~~~~~~g~~~~e~~~~  161 (244)
                      +|++   . +++|++|+.+ .++++++  +   .++++++.+. .+.+++.|.+|+++++++.+          |+++.+
T Consensus        93 ll~~---~-~~~y~~t~~~~~~l~~~~--~~~~~~~~~~~~~~-~~~~~~~~~~L~~~l~~g~~----------~~~~~~  155 (359)
T 1x19_A           93 VINL---E-DGKWSLTEFADYMFSPTP--KEPNLHQTPVAKAM-AFLADDFYMGLSQAVRGQKN----------FKGQVP  155 (359)
T ss_dssp             SEEE---E-TTEEEECHHHHHHSSSSC--SBTTBCCHHHHHHH-HHHHHHTGGGHHHHHTTSCC----------CCCSSC
T ss_pred             CeEe---e-CCeEecCHHHHHHhcCCC--CCccccHHHHHHHH-HHHHHHHHHHHHHHHhcCCC----------Cccccc
Confidence            9995   3 3699999975 5777665  5   5788888776 45678899999999988654          778888


Q ss_pred             Cch---HHHHHHHHHHhcch-hhHHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCC---
Q 041256          162 DSR---FNDVFNNGMLSHTS-IVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPS---  234 (244)
Q Consensus       162 ~~~---~~~~f~~aM~~~~~-~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~---  234 (244)
                      +|+   ..+.|..+|...+. ...+.+++.++ +++..+|||||||+|.++..+++++|+++++++|+|.+++.+++   
T Consensus       156 ~p~~~~~~~~f~~~m~~~~~~~~~~~l~~~~~-~~~~~~vLDvG~G~G~~~~~l~~~~p~~~~~~~D~~~~~~~a~~~~~  234 (359)
T 1x19_A          156 YPPVTREDNLYFEEIHRSNAKFAIQLLLEEAK-LDGVKKMIDVGGGIGDISAAMLKHFPELDSTILNLPGAIDLVNENAA  234 (359)
T ss_dssp             SSCCSHHHHHHHHHHHHTTCHHHHHHHHHHCC-CTTCCEEEEESCTTCHHHHHHHHHCTTCEEEEEECGGGHHHHHHHHH
T ss_pred             CchhhHHHHHHHHHHHHhccchhHHHHHHhcC-CCCCCEEEEECCcccHHHHHHHHHCCCCeEEEEecHHHHHHHHHHHH
Confidence            999   99999999999988 77788999998 88889999999999999999999999999999999999998864   


Q ss_pred             ---CC-Cceeec
Q 041256          235 ---YP-GTLFIK  242 (244)
Q Consensus       235 ---~~-~i~~~~  242 (244)
                         .+ +|+++.
T Consensus       235 ~~~~~~~v~~~~  246 (359)
T 1x19_A          235 EKGVADRMRGIA  246 (359)
T ss_dssp             HTTCTTTEEEEE
T ss_pred             hcCCCCCEEEEe
Confidence               22 477654

>2r3s_A Uncharacterized protein; methyltransferase domain, structural genomics, joint center structural genomics, JCSG, protein structure initiative; HET: MSE; 2.15A {Nostoc punctiforme}

Probab=99.96  E-value=1.6e-29  Score=220.68  Aligned_cols=198  Identities=17%  Similarity=0.179  Sum_probs=176.2

Q ss_pred             hHHHHHHHHhhhHHHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceee
Q 041256           13 NFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFV   92 (244)
Q Consensus        13 ~~~~l~~~~~g~~~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~   92 (244)
                      ....+++++.|++.+++|++++++||||+|++    +|+|++|||+++|++      ++. ++|+||+|++.|+|++   
T Consensus         6 ~~~~l~~~~~~~~~~~~l~~~~~l~i~~~l~~----~~~t~~ela~~~~~~------~~~-l~r~L~~L~~~g~l~~---   71 (335)
T 2r3s_A            6 SPALFFNTVNAYQRSAAIKAAVELNVFTAISQ----GIESSQSLAQKCQTS------ERG-MRMLCDYLVIIGFMTK---   71 (335)
T ss_dssp             CSHHHHHHHTTHHHHHHHHHHHHTTHHHHHTT----SEECHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEE---
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHcChHHHHhc----CCCCHHHHHHHhCCC------chH-HHHHHHHHHhcCCeEe---
Confidence            34689999999999999999999999999986    699999999999997      678 9999999999999984   


Q ss_pred             cCCceeecCccc-cccccCCCCCCCHHHHHHHhcChhhhhhccchHHHHhcCCchhhhhhCCCchhhccCCchHHHHHHH
Q 041256           93 DGQRLYSLAPVS-AYFVRNNQNGASLSPYMALCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNN  171 (244)
Q Consensus        93 ~~~~~y~~t~~s-~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~g~~~~~~~~g~~~~e~~~~~~~~~~~f~~  171 (244)
                      . +++|++|+.+ ..|.+++  +.++++++.+..++..++.|.+|.++++++.++|+     + |+++.++++....|..
T Consensus        72 ~-~~~y~~t~~~~~~l~~~~--~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~-----~-~~~~~~~~~~~~~~~~  142 (335)
T 2r3s_A           72 Q-AEGYRLTSDSAMFLDRQS--KFYVGDAIEFLLSPMITNGFNDLTAAVLKGGTAIS-----S-EGTLSPEHPVWVQFAK  142 (335)
T ss_dssp             E-TTEEEECHHHHHHTCTTS--TTCCGGGHHHHTCHHHHGGGTTHHHHHHHTSCCST-----T-TGGGSTTCTHHHHHHH
T ss_pred             c-CCEEecCHHHHHHhccCC--cHHHHHHHHHhcchhhHHHHHhHHHHHhcCCCCCC-----C-cccccCCHHHHHHHHH
Confidence            3 5899999999 5777766  56788888877555678899999999999887764     3 8888899999999999


Q ss_pred             HHHhcchhhHHHHHhhcCCC--CCcceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCC
Q 041256          172 GMLSHTSIVMEKVLESYKGF--EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPS  234 (244)
Q Consensus       172 aM~~~~~~~~~~~~~~~~~~--~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~  234 (244)
                      +|..........+++.++ +  .+..+|+|||||+|.++..+++++|+.+++++|++.+++.+++
T Consensus       143 ~~~~~~~~~~~~~~~~~~-~~~~~~~~vlDvG~G~G~~~~~l~~~~p~~~~~~~D~~~~~~~a~~  206 (335)
T 2r3s_A          143 AMSPMMANPAQLIAQLVN-ENKIEPLKVLDISASHGLFGIAVAQHNPNAEIFGVDWASVLEVAKE  206 (335)
T ss_dssp             HSGGGGHHHHHHHHHHHT-C--CCCSEEEEETCTTCHHHHHHHHHCTTCEEEEEECHHHHHHHHH
T ss_pred             HHHHHHhhhHHHHHHhcc-cccCCCCEEEEECCCcCHHHHHHHHHCCCCeEEEEecHHHHHHHHH
Confidence            999988877778888888 7  7889999999999999999999999999999999988888765

>3mcz_A O-methyltransferase; adomet_mtases, S-adenosylmethionine-dependent methyltransfer structural genomics, PSI-2; HET: MSE; 1.90A {Burkholderia thailandensis}

Probab=99.96  E-value=6.9e-29  Score=218.39  Aligned_cols=209  Identities=19%  Similarity=0.314  Sum_probs=169.8

Q ss_pred             cchhhhchhHHHHHHHHhhhHHHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhC
Q 041256            5 ADREEETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSY   84 (244)
Q Consensus         5 ~~~~~~~~~~~~l~~~~~g~~~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~   84 (244)
                      .|..++ +....+++++.+++.+++|++++++||||+|.     +|+|++|||+++|++      ++. ++|+||+|++.
T Consensus        17 ~~~~~l-~~p~~l~~~~~~~~~~~~l~~a~~lgif~~l~-----~~~t~~elA~~~~~~------~~~-l~rlLr~L~~~   83 (352)
T 3mcz_A           17 EDKAAL-TSVVDLVKLSDQYRQSAILHYAVADKLFDLTQ-----TGRTPAEVAASFGMV------EGK-AAILLHALAAL   83 (352)
T ss_dssp             CSCCCC-CSHHHHHHHHHTHHHHHHHHHHHHTTHHHHTT-----SCBCHHHHHHHHTCC------HHH-HHHHHHHHHHT
T ss_pred             cCCCCC-CCHHHHHHHHHHHHHHHHHHHHHHCChHHHhC-----CCCCHHHHHHHhCcC------hHH-HHHHHHHHHHC
Confidence            344444 44555999999999999999999999999995     389999999999997      678 99999999999


Q ss_pred             CcccceeecCCceeecCcccc-ccccCCCCCCCHHHHHHHhcChhhhhhccchHHHHhcCCch-hhhhhCCCchhhccCC
Q 041256           85 NALHCSFVDGQRLYSLAPVSA-YFVRNNQNGASLSPYMALCLDKVCLDGWFGLKKQLLEGGIA-FNKAHGMQIYDYLGVD  162 (244)
Q Consensus        85 gll~~~~~~~~~~y~~t~~s~-~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~g~~~-~~~~~g~~~~e~~~~~  162 (244)
                      |+|++   .+ ++|++|+.+. ++.++.  +.+++.++.+.  ...++.|.+|.+++++|.+. |+..      .++.++
T Consensus        84 gll~~---~~-~~y~~t~~s~~~l~~~~--~~~~~~~~~~~--~~~~~~~~~l~~~l~~g~~~~f~~~------~~~~~~  149 (352)
T 3mcz_A           84 GLLTK---EG-DAFRNTALTERYLTTTS--ADYIGPIVEHQ--YLQWDNWPRLGEILRSEKPLAFQQE------SRFAHD  149 (352)
T ss_dssp             TSEEE---ET-TEEEECHHHHHHHSTTC--TTCCHHHHHHH--HTTTTTGGGHHHHHTCSSCCTTSHH------HHTTTC
T ss_pred             CCeEe---cC-CeeecCHHHHhhccCCC--hhhHHHHHHHh--HHHHHHHHHHHHHHhCCCCCCcccc------cccccC
Confidence            99995   43 7899999998 455554  67888887654  34678999999999998653 3322      123578


Q ss_pred             chHHHHHHHHHHhcchhhHHHHHhhcCCCCC-cceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCCC------
Q 041256          163 SRFNDVFNNGMLSHTSIVMEKVLESYKGFEH-VKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSY------  235 (244)
Q Consensus       163 ~~~~~~f~~aM~~~~~~~~~~~~~~~~~~~~-~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~~------  235 (244)
                      |+..+.|..+|...... ...+++.++ +.+ ..+|||||||+|.++..+++++|+++++++|+|.+++.+++.      
T Consensus       150 ~~~~~~f~~~m~~~~~~-~~~~l~~~~-~~~~~~~vlDvG~G~G~~~~~l~~~~p~~~~~~~D~~~~~~~a~~~~~~~~~  227 (352)
T 3mcz_A          150 TRARDAFNDAMVRLSQP-MVDVVSELG-VFARARTVIDLAGGHGTYLAQVLRRHPQLTGQIWDLPTTRDAARKTIHAHDL  227 (352)
T ss_dssp             HHHHHHHHHHHHHHHHH-HHHHHHTCG-GGTTCCEEEEETCTTCHHHHHHHHHCTTCEEEEEECGGGHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHhhhhh-HHHHHHhCC-CcCCCCEEEEeCCCcCHHHHHHHHhCCCCeEEEEECHHHHHHHHHHHHhcCC
Confidence            99999999999983332 237888888 777 899999999999999999999999999999999999887641      


Q ss_pred             -CCceeec
Q 041256          236 -PGTLFIK  242 (244)
Q Consensus       236 -~~i~~~~  242 (244)
                       ++|+++.
T Consensus       228 ~~~v~~~~  235 (352)
T 3mcz_A          228 GGRVEFFE  235 (352)
T ss_dssp             GGGEEEEE
T ss_pred             CCceEEEe
Confidence             2476654

>2qm3_A Predicted methyltransferase; putative methyltransferase, structural genomics, pyrococcus PSI-2, protein structure initiative; HET: MSE; 2.05A {Pyrococcus furiosus dsm 3638}

Probab=98.75  E-value=9.2e-09  Score=90.87  Aligned_cols=159  Identities=10%  Similarity=0.020  Sum_probs=95.1

Q ss_pred             ChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcccc-ccccCCCCCC
Q 041256           37 DVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSA-YFVRNNQNGA  115 (244)
Q Consensus        37 gifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~-~l~~~~~~~~  115 (244)
                      ++|..| .    +|.|+.|||..++++      +.. +.++|+.|.+.|+++.   .+ + |++|+.+. ++...+  +.
T Consensus        47 ~ll~~L-~----~~~t~~eLa~~~g~~------~~~-v~~~L~~l~~~gll~~---~~-~-~~lt~~~~~~l~~~~--~~  107 (373)
T 2qm3_A           47 NVLSAV-L----ASDDIWRIVDLSEEP------LPL-VVAILESLNELGYVTF---ED-G-VKLTEKGEELVAEYG--IG  107 (373)
T ss_dssp             HHHHHH-H----HCSCHHHHHHHHTSC------HHH-HHHHHHHHHHTTSEEC---SS-S-SEECHHHHHHHHHHT--CC
T ss_pred             HHHHHh-c----CCCCHHHHHHHhCCC------hHH-HHHHHHHHhhCCcEEE---CC-C-EEECHHHHHHHHhcC--cc
Confidence            789999 5    589999999999997      667 9999999999999984   22 5 99999876 444322  11


Q ss_pred             CHHHHHH-HhcC-h----hhhhhccchHHHHhcCCchhhhhhCCCchhhccCCchHHHHHHHHHHhcchhhHHHHHhhcC
Q 041256          116 SLSPYMA-LCLD-K----VCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIVMEKVLESYK  189 (244)
Q Consensus       116 ~~~~~~~-~~~~-~----~~~~~~~~l~~~l~~g~~~~~~~~g~~~~e~~~~~~~~~~~f~~aM~~~~~~~~~~~~~~~~  189 (244)
                      +..+.+. ...+ .    .+...|..+.+.++....+.      ..|+.....++  ......+         .... .+
T Consensus       108 ~~~~~~~~~~~g~g~~~~~~~~~~~~l~~~~~~~~~~~------~~~~~~~~~~~--~~~~~~l---------~~~~-~~  169 (373)
T 2qm3_A          108 KRYDFTCPHCQGKTVDLQAFADLLEQFREIVKDRPEPL------HEFDQAYVTPE--TTVARVI---------LMHT-RG  169 (373)
T ss_dssp             CCCC------------CGGGHHHHHHHHHHHTTCCCCC------GGGTCCCBCHH--HHHHHHH---------HHHH-TT
T ss_pred             ccccccchhhcCCCcchhhhHHHHHHHHHHHhcCCccc------hhcCCeecCHH--HHHHHHH---------HHhh-cC
Confidence            1111110 0000 1    11112334444444321110      11111001111  1111111         0011 11


Q ss_pred             CCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          190 GFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       190 ~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                       .....+|+||| |+|.++..+++..|+.+++.+|+ |.+++.+++
T Consensus       170 -~~~~~~VLDlG-G~G~~~~~la~~~~~~~v~~vDi~~~~l~~a~~  213 (373)
T 2qm3_A          170 -DLENKDIFVLG-DDDLTSIALMLSGLPKRIAVLDIDERLTKFIEK  213 (373)
T ss_dssp             -CSTTCEEEEES-CTTCHHHHHHHHTCCSEEEEECSCHHHHHHHHH
T ss_pred             -CCCCCEEEEEC-CCCHHHHHHHHhCCCCEEEEEECCHHHHHHHHH
Confidence             12458999999 99999999999999999999999 899998875

>1ve3_A Hypothetical protein PH0226; dimer, riken structural genomics/proteomics initiative, RSGI, structural genomics, unknown function, NPPSFA; HET: SAM; 2.10A {Pyrococcus horikoshii} SCOP: c.66.1.43

Probab=97.90  E-value=4.7e-06  Score=67.34  Aligned_cols=40  Identities=18%  Similarity=0.176  Sum_probs=34.7

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...+|+|||||.|.++..+++++|  +++.+|+ |..++.+++
T Consensus        38 ~~~~vLDlG~G~G~~~~~l~~~~~--~v~~vD~s~~~~~~a~~   78 (227)
T 1ve3_A           38 KRGKVLDLACGVGGFSFLLEDYGF--EVVGVDISEDMIRKARE   78 (227)
T ss_dssp             SCCEEEEETCTTSHHHHHHHHTTC--EEEEEESCHHHHHHHHH
T ss_pred             CCCeEEEEeccCCHHHHHHHHcCC--EEEEEECCHHHHHHHHH
Confidence            367999999999999999999988  7888888 888877754

>2fca_A TRNA (guanine-N(7)-)-methyltransferase; 2.10A {Bacillus subtilis} SCOP: c.66.1.53

Probab=97.67  E-value=4.1e-05  Score=61.85  Aligned_cols=42  Identities=26%  Similarity=0.324  Sum_probs=37.3

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...+|||||||+|.++..+++++|+.+++.+|. |..++.|++
T Consensus        38 ~~~~vLDiGcG~G~~~~~la~~~p~~~v~giD~s~~~l~~a~~   80 (213)
T 2fca_A           38 DNPIHIEVGTGKGQFISGMAKQNPDINYIGIELFKSVIVTAVQ   80 (213)
T ss_dssp             CCCEEEEECCTTSHHHHHHHHHCTTSEEEEECSCHHHHHHHHH
T ss_pred             CCceEEEEecCCCHHHHHHHHHCCCCCEEEEEechHHHHHHHH
Confidence            457899999999999999999999999999998 777777653

>3ege_A Putative methyltransferase from antibiotic biosyn pathway; YP_324569.1, putative methyltransferase from antibiotic BIOS pathway; 2.40A {Anabaena variabilis atcc 29413}

Probab=97.66  E-value=9.6e-05  Score=61.35  Aligned_cols=57  Identities=11%  Similarity=0.125  Sum_probs=46.1

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCCCCCceee
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPSYPGTLFI  241 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~~~~i~~~  241 (244)
                      ..+.+.++ .....+|||||||+|.++..+++  |+.+++.+|+ |..++.+++.++++++
T Consensus        24 ~~l~~~~~-~~~~~~vLDiGcG~G~~~~~l~~--~~~~v~gvD~s~~~~~~a~~~~~~~~~   81 (261)
T 3ege_A           24 NAIINLLN-LPKGSVIADIGAGTGGYSVALAN--QGLFVYAVEPSIVMRQQAVVHPQVEWF   81 (261)
T ss_dssp             HHHHHHHC-CCTTCEEEEETCTTSHHHHHHHT--TTCEEEEECSCHHHHHSSCCCTTEEEE
T ss_pred             HHHHHHhC-CCCCCEEEEEcCcccHHHHHHHh--CCCEEEEEeCCHHHHHHHHhccCCEEE
Confidence            34555555 56778999999999999999998  7889999999 7888888776666654

>3dtn_A Putative methyltransferase MM_2633; structural genomics, unknown function, PSI-2, protein structure initiative; 2.09A {Methanosarcina mazei}

Probab=97.66  E-value=6.9e-05  Score=60.85  Aligned_cols=52  Identities=17%  Similarity=0.256  Sum_probs=42.1

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+.+.++...+..+|||||||.|.++..+++++|+.+++.+|+ |..++.+++
T Consensus        34 ~~~~~~~~~~~~~~vLDiG~G~G~~~~~l~~~~~~~~v~~vD~s~~~~~~a~~   86 (234)
T 3dtn_A           34 VSVSIASVDTENPDILDLGAGTGLLSAFLMEKYPEATFTLVDMSEKMLEIAKN   86 (234)
T ss_dssp             HHHHTCCCSCSSCEEEEETCTTSHHHHHHHHHCTTCEEEEEESCHHHHHHHHH
T ss_pred             HHHHHhhcCCCCCeEEEecCCCCHHHHHHHHhCCCCeEEEEECCHHHHHHHHH
Confidence            3444444234568999999999999999999999999999999 878777654

>3e05_A Precorrin-6Y C5,15-methyltransferase (decarboxyla; porphyrin metabolism, S-adenosyl-methionine; 1.80A {Geobacter metallireducens} SCOP: c.66.1.0

Probab=97.63  E-value=6.2e-05  Score=59.99  Aligned_cols=51  Identities=12%  Similarity=0.098  Sum_probs=43.5

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .++..++ .....+|+|||||+|.++..+++.+|..+++.+|. |..++.+++
T Consensus        31 ~~l~~l~-~~~~~~vLDiG~G~G~~~~~la~~~~~~~v~~vD~s~~~~~~a~~   82 (204)
T 3e05_A           31 VTLSKLR-LQDDLVMWDIGAGSASVSIEASNLMPNGRIFALERNPQYLGFIRD   82 (204)
T ss_dssp             HHHHHTT-CCTTCEEEEETCTTCHHHHHHHHHCTTSEEEEEECCHHHHHHHHH
T ss_pred             HHHHHcC-CCCCCEEEEECCCCCHHHHHHHHHCCCCEEEEEeCCHHHHHHHHH
Confidence            4455555 66778999999999999999999999999999999 888887764

>3mq2_A 16S rRNA methyltransferase; methyltranferase, ribosomal, antibiotic resistance, aminoglycoside, S-adenosyl-L-methionine; HET: SAH; 1.69A {Streptomyces SP}

Probab=97.61  E-value=8.2e-05  Score=59.82  Aligned_cols=40  Identities=18%  Similarity=0.159  Sum_probs=35.0

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhh
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIK  230 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~  230 (244)
                      .....+|||||||.|.++..+++++|+.+++.+|+ |..++
T Consensus        25 ~~~~~~vLDiGcG~G~~~~~la~~~p~~~v~gvD~s~~~l~   65 (218)
T 3mq2_A           25 SQYDDVVLDVGTGDGKHPYKVARQNPSRLVVALDADKSRME   65 (218)
T ss_dssp             TTSSEEEEEESCTTCHHHHHHHHHCTTEEEEEEESCGGGGH
T ss_pred             ccCCCEEEEecCCCCHHHHHHHHHCCCCEEEEEECCHHHHH
Confidence            45668999999999999999999999999999999 55344

>1yzh_A TRNA (guanine-N(7)-)-methyltransferase; alpha-beta-alpha sandwich, S-adenosylmeth dependent, structural genomics, PSI; 2.02A {Streptococcus pneumoniae} SCOP: c.66.1.53

Probab=97.61  E-value=5.8e-05  Score=60.74  Aligned_cols=42  Identities=26%  Similarity=0.326  Sum_probs=37.8

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...+|+|||||.|.++..+++++|+.+++.+|. |..++.+++
T Consensus        41 ~~~~vLDiGcG~G~~~~~la~~~p~~~v~gvD~s~~~l~~a~~   83 (214)
T 1yzh_A           41 DNPIHVEVGSGKGAFVSGMAKQNPDINYIGIDIQKSVLSYALD   83 (214)
T ss_dssp             CCCEEEEESCTTSHHHHHHHHHCTTSEEEEEESCHHHHHHHHH
T ss_pred             CCCeEEEEccCcCHHHHHHHHHCCCCCEEEEEcCHHHHHHHHH
Confidence            457899999999999999999999999999998 888887754

>3dxy_A TRNA (guanine-N(7)-)-methyltransferase; rossmann fold methyltransferase, tRNA modification, S-adenosyl-L-methionine, TR processing; HET: SAM; 1.50A {Escherichia coli} PDB: 3dxx_A* 3dxz_A*

Probab=97.60  E-value=5.9e-05  Score=61.34  Aligned_cols=49  Identities=10%  Similarity=0.189  Sum_probs=40.6

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC------CCCceee
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS------YPGTLFI  241 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~------~~~i~~~  241 (244)
                      ...+|||||||.|.++..+++++|+.+++.+|. |..++.+++      .++|+++
T Consensus        34 ~~~~vLDiGcG~G~~~~~lA~~~p~~~v~giD~s~~~l~~a~~~~~~~~l~nv~~~   89 (218)
T 3dxy_A           34 EAPVTLEIGFGMGASLVAMAKDRPEQDFLGIEVHSPGVGACLASAHEEGLSNLRVM   89 (218)
T ss_dssp             CCCEEEEESCTTCHHHHHHHHHCTTSEEEEECSCHHHHHHHHHHHHHTTCSSEEEE
T ss_pred             CCCeEEEEeeeChHHHHHHHHHCCCCeEEEEEecHHHHHHHHHHHHHhCCCcEEEE
Confidence            457999999999999999999999999999998 777766643      3456654

>4dzr_A Protein-(glutamine-N5) methyltransferase, release specific; structural genomics, PSI-biology; 2.55A {Alicyclobacillus acidocaldarius subsp}

Probab=97.53  E-value=0.0001  Score=58.59  Aligned_cols=52  Identities=21%  Similarity=0.233  Sum_probs=35.9

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+++.++......+|+|||||+|.++..+++++|+.+++.+|+ |..++.+++
T Consensus        20 ~~~~~l~~~~~~~~vLDiG~G~G~~~~~l~~~~~~~~v~~vD~~~~~~~~a~~   72 (215)
T 4dzr_A           20 EAIRFLKRMPSGTRVIDVGTGSGCIAVSIALACPGVSVTAVDLSMDALAVARR   72 (215)
T ss_dssp             HHHHHHTTCCTTEEEEEEESSBCHHHHHHHHHCTTEEEEEEECC---------
T ss_pred             HHHHHhhhcCCCCEEEEecCCHhHHHHHHHHhCCCCeEEEEECCHHHHHHHHH
Confidence            3444444225678999999999999999999999999999999 888888876

>2qe6_A Uncharacterized protein TFU_2867; putative methyltransferase, structural genomics, joint cente structural genomics, JCSG; HET: NEP SAM; 1.95A {Thermobifida fusca}

Probab=97.49  E-value=0.00011  Score=61.75  Aligned_cols=50  Identities=24%  Similarity=0.428  Sum_probs=41.8

Q ss_pred             CCcceEEEecCCc---cHHHHHHHHHCCCCeEEEccc-hHHhhhCCC----CCCceee
Q 041256          192 EHVKKLVDVGGGL---GITLNMIISKYPHIKGINYDL-PYVIKDAPS----YPGTLFI  241 (244)
Q Consensus       192 ~~~~~vvDVGGG~---G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~----~~~i~~~  241 (244)
                      .+..+|||||||.   |.++..+.+.+|+.+++.+|+ |.+++.+++    .++|+++
T Consensus        76 ~~~~~vLDlGcG~pt~G~~~~~~~~~~p~~~v~~vD~sp~~l~~Ar~~~~~~~~v~~~  133 (274)
T 2qe6_A           76 AGISQFLDLGSGLPTVQNTHEVAQSVNPDARVVYVDIDPMVLTHGRALLAKDPNTAVF  133 (274)
T ss_dssp             TCCCEEEEETCCSCCSSCHHHHHHHHCTTCEEEEEESSHHHHHHHHHHHTTCTTEEEE
T ss_pred             cCCCEEEEECCCCCCCChHHHHHHHhCCCCEEEEEECChHHHHHHHHhcCCCCCeEEE
Confidence            3458999999999   999888888999999999999 999988864    2456654

>2p35_A Trans-aconitate 2-methyltransferase; SAM dependent methyltrans agrobacterium tumefaciens, structural genomics, PSI-2; HET: SAH; 1.95A {Agrobacterium tumefaciens str}

Probab=97.49  E-value=8e-05  Score=61.27  Aligned_cols=57  Identities=23%  Similarity=0.313  Sum_probs=45.6

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC-CCCcee
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS-YPGTLF  240 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~-~~~i~~  240 (244)
                      .+++.++ .....+|+|||||.|.++..+++++|..+++.+|+ |..++.+++ .+++++
T Consensus        24 ~l~~~~~-~~~~~~vLdiG~G~G~~~~~l~~~~~~~~v~~~D~s~~~~~~a~~~~~~~~~   82 (259)
T 2p35_A           24 DLLAQVP-LERVLNGYDLGCGPGNSTELLTDRYGVNVITGIDSDDDMLEKAADRLPNTNF   82 (259)
T ss_dssp             HHHTTCC-CSCCSSEEEETCTTTHHHHHHHHHHCTTSEEEEESCHHHHHHHHHHSTTSEE
T ss_pred             HHHHhcC-CCCCCEEEEecCcCCHHHHHHHHhCCCCEEEEEECCHHHHHHHHHhCCCcEE
Confidence            4555555 56668999999999999999999999999999998 777777654 344544

>3g07_A 7SK snRNA methylphosphate capping enzyme; structural genomics consortium (SGC), methyltransferase, phosphoprotein, S-adenosyl-L-methionine; HET: SAM; 2.65A {Homo sapiens}

Probab=97.46  E-value=9e-05  Score=62.80  Aligned_cols=42  Identities=19%  Similarity=0.306  Sum_probs=37.8

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...+|||||||.|.++..+++++|..+++.+|+ |..++.|++
T Consensus        46 ~~~~VLDiGCG~G~~~~~la~~~~~~~v~gvDis~~~i~~A~~   88 (292)
T 3g07_A           46 RGRDVLDLGCNVGHLTLSIACKWGPSRMVGLDIDSRLIHSARQ   88 (292)
T ss_dssp             TTSEEEEESCTTCHHHHHHHHHTCCSEEEEEESCHHHHHHHHH
T ss_pred             CCCcEEEeCCCCCHHHHHHHHHcCCCEEEEECCCHHHHHHHHH
Confidence            568999999999999999999999999999999 777877754

>3ckk_A TRNA (guanine-N(7)-)-methyltransferase; mettl1, S-adenosyl-L-methionine, tRNA Pro structural genomics, structural genomics consortium, SGC; HET: SAM; 1.55A {Homo sapiens}

Probab=97.45  E-value=0.00013  Score=60.10  Aligned_cols=41  Identities=17%  Similarity=0.246  Sum_probs=35.6

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDA  232 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a  232 (244)
                      .+..+|||||||.|.++..+++++|+.+++.+|+ +..++.|
T Consensus        45 ~~~~~vLDiGcG~G~~~~~la~~~p~~~v~GiDis~~~l~~A   86 (235)
T 3ckk_A           45 QAQVEFADIGCGYGGLLVELSPLFPDTLILGLEIRVKVSDYV   86 (235)
T ss_dssp             -CCEEEEEETCTTCHHHHHHGGGSTTSEEEEEESCHHHHHHH
T ss_pred             CCCCeEEEEccCCcHHHHHHHHHCCCCeEEEEECCHHHHHHH
Confidence            4557899999999999999999999999999998 6666644

>3hm2_A Precorrin-6Y C5,15-methyltransferase; alpha-beta-sandwich, structural genomics, PSI-2, protein structure initiative; 2.21A {Corynebacterium diphtheriae}

Probab=97.45  E-value=9.1e-05  Score=57.26  Aligned_cols=51  Identities=16%  Similarity=0.227  Sum_probs=42.4

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+++.++ .....+|+|||||.|.++..+++++|..+++.+|+ |..++.+++
T Consensus        16 ~~~~~~~-~~~~~~vldiG~G~G~~~~~l~~~~~~~~v~~vD~~~~~~~~a~~   67 (178)
T 3hm2_A           16 LAISALA-PKPHETLWDIGGGSGSIAIEWLRSTPQTTAVCFEISEERRERILS   67 (178)
T ss_dssp             HHHHHHC-CCTTEEEEEESTTTTHHHHHHHTTSSSEEEEEECSCHHHHHHHHH
T ss_pred             HHHHHhc-ccCCCeEEEeCCCCCHHHHHHHHHCCCCeEEEEeCCHHHHHHHHH
Confidence            3444555 56668999999999999999999999999999999 777777763

>1jg1_A PIMT;, protein-L-isoaspartate O-methyltransferase; rossmann methyltransferase, protein repair isomerization; HET: SAH; 1.20A {Pyrococcus furiosus} SCOP: c.66.1.7 PDB: 1jg2_A* 1jg3_A* 1jg4_A*

Probab=97.44  E-value=5.2e-05  Score=61.95  Aligned_cols=52  Identities=17%  Similarity=0.219  Sum_probs=42.7

Q ss_pred             HHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          181 MEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       181 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...+++.++ .....+|+|||||.|.++..+++..| .+++.+|. |..++.+++
T Consensus        80 ~~~~~~~l~-~~~~~~vLdiG~G~G~~~~~la~~~~-~~v~~vD~~~~~~~~a~~  132 (235)
T 1jg1_A           80 VAIMLEIAN-LKPGMNILEVGTGSGWNAALISEIVK-TDVYTIERIPELVEFAKR  132 (235)
T ss_dssp             HHHHHHHHT-CCTTCCEEEECCTTSHHHHHHHHHHC-SCEEEEESCHHHHHHHHH
T ss_pred             HHHHHHhcC-CCCCCEEEEEeCCcCHHHHHHHHHhC-CEEEEEeCCHHHHHHHHH
Confidence            345556665 66778999999999999999999998 88999996 788877764

>3ou2_A SAM-dependent methyltransferase; O-methyltransferase, SAH; HET: SAH; 1.50A {Streptomyces luridus} PDB: 3ou6_A* 3ou7_A*

Probab=97.44  E-value=0.00027  Score=56.31  Aligned_cols=58  Identities=14%  Similarity=0.095  Sum_probs=43.2

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC--CCCceee
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS--YPGTLFI  241 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~--~~~i~~~  241 (244)
                      ..+++.+.......+|+|||||.|.++..++++  ..+++.+|+ |..++.+++  .++|+++
T Consensus        35 ~~~~~~l~~~~~~~~vLdiG~G~G~~~~~l~~~--~~~v~~~D~s~~~~~~a~~~~~~~~~~~   95 (218)
T 3ou2_A           35 PAALERLRAGNIRGDVLELASGTGYWTRHLSGL--ADRVTALDGSAEMIAEAGRHGLDNVEFR   95 (218)
T ss_dssp             HHHHHHHTTTTSCSEEEEESCTTSHHHHHHHHH--SSEEEEEESCHHHHHHHGGGCCTTEEEE
T ss_pred             HHHHHHHhcCCCCCeEEEECCCCCHHHHHHHhc--CCeEEEEeCCHHHHHHHHhcCCCCeEEE
Confidence            344554443455679999999999999999999  668999998 888887765  2455543

>3vc1_A Geranyl diphosphate 2-C-methyltransferase; rossmann fold, methyltransferase fold, SAM-dependent methyltransferase; HET: SAH GST GOL; 1.82A {Streptomyces coelicolor} PDB: 3vc2_A* 4f84_A* 4f85_A 4f86_A*

Probab=97.42  E-value=0.00023  Score=60.66  Aligned_cols=65  Identities=17%  Similarity=0.125  Sum_probs=46.7

Q ss_pred             HHHHHHHhcchhhHHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          168 VFNNGMLSHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       168 ~f~~aM~~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .|.. +..........+++.++.+....+|||||||.|.++..+++++ +.+++.+|+ |..++.+++
T Consensus        93 ~f~~-~~~~~~~~~~~l~~~l~~~~~~~~vLDiGcG~G~~~~~la~~~-~~~v~gvD~s~~~~~~a~~  158 (312)
T 3vc1_A           93 VIAE-LHRLESAQAEFLMDHLGQAGPDDTLVDAGCGRGGSMVMAHRRF-GSRVEGVTLSAAQADFGNR  158 (312)
T ss_dssp             HHHH-HHHHHHHHHHHHHTTSCCCCTTCEEEEESCTTSHHHHHHHHHH-CCEEEEEESCHHHHHHHHH
T ss_pred             HHhh-hhhHHHHHHHHHHHHhccCCCCCEEEEecCCCCHHHHHHHHHc-CCEEEEEeCCHHHHHHHHH
Confidence            4443 3333333334566665435667899999999999999999986 678999998 788877754

>3dlc_A Putative S-adenosyl-L-methionine-dependent methyltransferase; structural genomics, joint center for structural genomics; HET: MSE SAM; 1.15A {Methanococcus maripaludis}

Probab=97.41  E-value=7.4e-05  Score=59.58  Aligned_cols=50  Identities=14%  Similarity=0.203  Sum_probs=40.4

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+++.++ .... +|||||||.|.++..++++ |+.+++.+|+ |..++.+++
T Consensus        34 ~~~~~~~~-~~~~-~vLdiG~G~G~~~~~l~~~-~~~~v~~~D~s~~~~~~a~~   84 (219)
T 3dlc_A           34 ENIINRFG-ITAG-TCIDIGSGPGALSIALAKQ-SDFSIRALDFSKHMNEIALK   84 (219)
T ss_dssp             HHHHHHHC-CCEE-EEEEETCTTSHHHHHHHHH-SEEEEEEEESCHHHHHHHHH
T ss_pred             HHHHHhcC-CCCC-EEEEECCCCCHHHHHHHHc-CCCeEEEEECCHHHHHHHHH
Confidence            34455555 4444 9999999999999999999 8899999998 888877764

>3g5t_A Trans-aconitate 3-methyltransferase; structural genomics, protein structure initiative, PSI, center for eukaryotic structural genomics; HET: MSE SAH T8N; 1.12A {Saccharomyces cerevisiae}

Probab=97.41  E-value=0.00024  Score=60.08  Aligned_cols=43  Identities=35%  Similarity=0.378  Sum_probs=38.3

Q ss_pred             CCcceEEEecCCccHHHHHHHHHC-CCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKY-PHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ....+|||||||.|.++..+++++ |..+++.+|+ |..++.+++
T Consensus        35 ~~~~~vLDiGcG~G~~~~~la~~~~~~~~v~gvD~s~~~~~~a~~   79 (299)
T 3g5t_A           35 GERKLLVDVGCGPGTATLQMAQELKPFEQIIGSDLSATMIKTAEV   79 (299)
T ss_dssp             SCCSEEEEETCTTTHHHHHHHHHSSCCSEEEEEESCHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCHHHHHHHHhCCCCCEEEEEeCCHHHHHHHHH
Confidence            466899999999999999999997 9999999999 778877754

>2plw_A Ribosomal RNA methyltransferase, putative; malaria, SAM, structural genomics, structural genomics consortium, SGC; HET: SAM; 1.70A {Plasmodium falciparum}

Probab=97.40  E-value=0.00029  Score=55.72  Aligned_cols=45  Identities=20%  Similarity=0.185  Sum_probs=37.2

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCC--CCeEEEccchH
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYP--HIKGINYDLPY  227 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P--~l~~~v~Dlp~  227 (244)
                      .+.+.|..+....+|+|||||+|.++..+++++|  +.+++.+|+.+
T Consensus        12 ~~~~~~~~~~~~~~vLDlGcG~G~~~~~l~~~~~~~~~~v~gvD~s~   58 (201)
T 2plw_A           12 ELDNKYLFLKKNKIILDIGCYPGSWCQVILERTKNYKNKIIGIDKKI   58 (201)
T ss_dssp             HHHHHHCCCCTTEEEEEESCTTCHHHHHHHHHTTTSCEEEEEEESSC
T ss_pred             HHHHHcCCCCCCCEEEEeCCCCCHHHHHHHHHcCCCCceEEEEeCCc
Confidence            4555665345668999999999999999999998  68899999855

>3p2e_A 16S rRNA methylase; methyltransferase, transferase, NPMA; HET: SAH; 1.68A {Escherichia coli} PDB: 3p2i_A 3p2k_A* 3pb3_A* 3mte_A*

Probab=97.39  E-value=0.00019  Score=58.57  Aligned_cols=46  Identities=15%  Similarity=0.133  Sum_probs=36.6

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccch-HHh
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLP-YVI  229 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp-~vi  229 (244)
                      ..+.+.+.  ....+|||||||.|.++..+++++|+.+++.+|+. +.+
T Consensus        15 ~~~~~~~~--~~~~~vLDiGCG~G~~~~~la~~~~~~~v~GvD~s~~~m   61 (225)
T 3p2e_A           15 DELTEIIG--QFDRVHIDLGTGDGRNIYKLAINDQNTFYIGIDPVKENL   61 (225)
T ss_dssp             HHHHHHHT--TCSEEEEEETCTTSHHHHHHHHTCTTEEEEEECSCCGGG
T ss_pred             HHHHHHhC--CCCCEEEEEeccCcHHHHHHHHhCCCCEEEEEeCCHHHH
Confidence            34444443  44579999999999999999999999999999994 444

>3gjy_A Spermidine synthase; APC62791, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.47A {Corynebacterium glutamicum atcc 13032}

Probab=97.39  E-value=0.00012  Score=63.06  Aligned_cols=41  Identities=15%  Similarity=0.291  Sum_probs=37.8

Q ss_pred             cceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+|||||||.|.++..+++++|+.+.+++|+ |.+++.+++
T Consensus        90 ~~rVLdIG~G~G~la~~la~~~p~~~v~~VEidp~vi~~Ar~  131 (317)
T 3gjy_A           90 KLRITHLGGGACTMARYFADVYPQSRNTVVELDAELARLSRE  131 (317)
T ss_dssp             GCEEEEESCGGGHHHHHHHHHSTTCEEEEEESCHHHHHHHHH
T ss_pred             CCEEEEEECCcCHHHHHHHHHCCCcEEEEEECCHHHHHHHHH
Confidence            34999999999999999999999999999999 999998874

>3mgg_A Methyltransferase; NYSGXRC, PSI-II, protein structure initiative, structural genomics, NEW YORK SGX research center for structural genomics; 1.86A {Methanosarcina mazei}

Probab=97.37  E-value=0.00015  Score=60.35  Aligned_cols=44  Identities=18%  Similarity=0.386  Sum_probs=39.3

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      +....+|||||||.|.++..+++++|+.+++.+|. |..++.+++
T Consensus        35 ~~~~~~vLDiG~G~G~~~~~l~~~~~~~~v~~vD~s~~~~~~a~~   79 (276)
T 3mgg_A           35 YPPGAKVLEAGCGIGAQTVILAKNNPDAEITSIDISPESLEKARE   79 (276)
T ss_dssp             CCTTCEEEETTCTTSHHHHHHHHHCTTSEEEEEESCHHHHHHHHH
T ss_pred             CCCCCeEEEecCCCCHHHHHHHHhCCCCEEEEEECCHHHHHHHHH
Confidence            56678999999999999999999999999999998 777777654

>1yb2_A Hypothetical protein TA0852; structural genomics, methyltransferase, thermoplasma acidoph midwest center for structural genomics, MCSG; 2.01A {Thermoplasma acidophilum} SCOP: c.66.1.13

Probab=97.36  E-value=9.4e-05  Score=62.04  Aligned_cols=51  Identities=14%  Similarity=0.060  Sum_probs=40.1

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHH-CCCCeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISK-YPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~-~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .++..++ +....+|+|+|||.|.++..+++. +|..+++.+|+ |..++.+++
T Consensus       101 ~~~~~~~-~~~~~~VLD~G~G~G~~~~~la~~~~~~~~v~~vD~s~~~~~~a~~  153 (275)
T 1yb2_A          101 YIIMRCG-LRPGMDILEVGVGSGNMSSYILYALNGKGTLTVVERDEDNLKKAMD  153 (275)
T ss_dssp             -----CC-CCTTCEEEEECCTTSHHHHHHHHHHTTSSEEEEECSCHHHHHHHHH
T ss_pred             HHHHHcC-CCCcCEEEEecCCCCHHHHHHHHHcCCCCEEEEEECCHHHHHHHHH
Confidence            4455555 667789999999999999999998 89999999999 888777653

>3dli_A Methyltransferase; PSI-II, NYSGXRC, structural genomics, protein structure initiative; 2.46A {Archaeoglobus fulgidus}

Probab=97.35  E-value=0.00032  Score=57.23  Aligned_cols=49  Identities=22%  Similarity=0.337  Sum_probs=37.1

Q ss_pred             HHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          184 VLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       184 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      +...++.+....+|||||||.|.++..++++  +.+++.+|+ |..++.+++
T Consensus        32 ~~~~l~~~~~~~~vLDiGcG~G~~~~~l~~~--~~~v~gvD~s~~~~~~a~~   81 (240)
T 3dli_A           32 LRRYIPYFKGCRRVLDIGCGRGEFLELCKEE--GIESIGVDINEDMIKFCEG   81 (240)
T ss_dssp             HGGGGGGTTTCSCEEEETCTTTHHHHHHHHH--TCCEEEECSCHHHHHHHHT
T ss_pred             HHHHHhhhcCCCeEEEEeCCCCHHHHHHHhC--CCcEEEEECCHHHHHHHHh
Confidence            3333443456689999999999999999998  456888898 777777654

>3dh0_A SAM dependent methyltransferase; cystal structure, PSI-2, NYSGXRC, structural genomics, protein structure initiative; HET: SAM; 2.72A {Aquifex aeolicus}

Probab=97.34  E-value=0.00014  Score=58.37  Aligned_cols=52  Identities=25%  Similarity=0.295  Sum_probs=43.7

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHC-CCCeEEEccc-hHHhhhCCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKY-PHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+++.++ .....+|||||||.|.++..+++.. |+.+++.+|. |..++.+++
T Consensus        27 ~~~~~~~~-~~~~~~vLDiG~G~G~~~~~l~~~~~~~~~v~~vD~s~~~~~~a~~   80 (219)
T 3dh0_A           27 EKVLKEFG-LKEGMTVLDVGTGAGFYLPYLSKMVGEKGKVYAIDVQEEMVNYAWE   80 (219)
T ss_dssp             HHHHHHHT-CCTTCEEEESSCTTCTTHHHHHHHHTTTCEEEEEESCHHHHHHHHH
T ss_pred             HHHHHHhC-CCCCCEEEEEecCCCHHHHHHHHHhCCCcEEEEEECCHHHHHHHHH
Confidence            45566666 6777899999999999999999997 8899999998 787777754

>2vdv_E TRNA (guanine-N(7)-)-methyltransferase; S-adenosyl-L-methionine, phosphorylation, M7G, spout MT, tRNA processing; HET: SAM; 2.30A {Saccharomyces cerevisiae} PDB: 2vdu_E

Probab=97.33  E-value=0.0002  Score=58.88  Aligned_cols=41  Identities=15%  Similarity=0.233  Sum_probs=36.3

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDA  232 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a  232 (244)
                      +...+|||||||.|.++..+++.+|+.+++.+|. +.+++.+
T Consensus        48 ~~~~~vLDiGcG~G~~~~~la~~~~~~~v~gvD~s~~~l~~a   89 (246)
T 2vdv_E           48 TKKVTIADIGCGFGGLMIDLSPAFPEDLILGMEIRVQVTNYV   89 (246)
T ss_dssp             SCCEEEEEETCTTSHHHHHHHHHSTTSEEEEEESCHHHHHHH
T ss_pred             CCCCEEEEEcCCCCHHHHHHHHhCCCCCEEEEEcCHHHHHHH
Confidence            4568999999999999999999999999999997 6776655

>3g5l_A Putative S-adenosylmethionine dependent methyltransferase; structural genomics, PSI-2, protein structure initiative; 2.35A {Listeria monocytogenes str}

Probab=97.33  E-value=0.00027  Score=58.04  Aligned_cols=57  Identities=18%  Similarity=0.206  Sum_probs=43.2

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC---CCCceee
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS---YPGTLFI  241 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~---~~~i~~~  241 (244)
                      .+.+.++ .....+|||||||.|.++..++++.+. +++.+|+ |..++.+++   .++|+++
T Consensus        35 ~l~~~~~-~~~~~~vLD~GcG~G~~~~~l~~~~~~-~v~~vD~s~~~~~~a~~~~~~~~~~~~   95 (253)
T 3g5l_A           35 ELKKMLP-DFNQKTVLDLGCGFGWHCIYAAEHGAK-KVLGIDLSERMLTEAKRKTTSPVVCYE   95 (253)
T ss_dssp             HHHTTCC-CCTTCEEEEETCTTCHHHHHHHHTTCS-EEEEEESCHHHHHHHHHHCCCTTEEEE
T ss_pred             HHHHhhh-ccCCCEEEEECCCCCHHHHHHHHcCCC-EEEEEECCHHHHHHHHHhhccCCeEEE
Confidence            4455555 446689999999999999999999776 8899998 777777754   2345543

>4gek_A TRNA (CMO5U34)-methyltransferase; structural genomics, PSI-biology, NEW YORK structural genomi research consortium, nysgrc, rossmann fold; HET: GEK; 1.50A {Escherichia coli} PDB: 1im8_A*

Probab=97.32  E-value=0.00017  Score=60.36  Aligned_cols=43  Identities=21%  Similarity=0.238  Sum_probs=37.3

Q ss_pred             CCcceEEEecCCccHHHHHHHHHC--CCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKY--PHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~--P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      +...+|+|||||+|.++..+++++  |+++++.+|+ |..++.|++
T Consensus        69 ~~~~~vLDlGcGtG~~~~~la~~~~~~~~~v~gvD~s~~ml~~A~~  114 (261)
T 4gek_A           69 QPGTQVYDLGCSLGAATLSVRRNIHHDNCKIIAIDNSPAMIERCRR  114 (261)
T ss_dssp             CTTCEEEEETCTTTHHHHHHHHTCCSSSCEEEEEESCHHHHHHHHH
T ss_pred             CCCCEEEEEeCCCCHHHHHHHHhcCCCCCEEEEEECCHHHHHHHHH
Confidence            556899999999999999999985  6789999998 888887764

>4hg2_A Methyltransferase type 11; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; HET: MES; 1.60A {Anaeromyxobacter dehalogenans}

Probab=97.31  E-value=0.00021  Score=59.65  Aligned_cols=47  Identities=17%  Similarity=0.145  Sum_probs=40.1

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCCCCCceee
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPSYPGTLFI  241 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~~~~i~~~  241 (244)
                      ...+|||||||+|.++..+++++.  +++.+|+ |..++.|++.++|+++
T Consensus        39 ~~~~vLDvGcGtG~~~~~l~~~~~--~v~gvD~s~~ml~~a~~~~~v~~~   86 (257)
T 4hg2_A           39 ARGDALDCGCGSGQASLGLAEFFE--RVHAVDPGEAQIRQALRHPRVTYA   86 (257)
T ss_dssp             CSSEEEEESCTTTTTHHHHHTTCS--EEEEEESCHHHHHTCCCCTTEEEE
T ss_pred             CCCCEEEEcCCCCHHHHHHHHhCC--EEEEEeCcHHhhhhhhhcCCceee
Confidence            346899999999999999999875  5788898 7889999888888765

>3ujc_A Phosphoethanolamine N-methyltransferase; parasite; HET: PC; 1.19A {Plasmodium falciparum} PDB: 3uj9_A* 3uj6_A* 3uj7_A* 3uj8_A* 3uja_A 3ujb_A* 4fgz_A* 3ujd_A*

Probab=97.31  E-value=0.00017  Score=59.36  Aligned_cols=58  Identities=24%  Similarity=0.377  Sum_probs=44.9

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCCC----CCceee
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPSY----PGTLFI  241 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~~----~~i~~~  241 (244)
                      ..+++.++ .....+|||||||.|.++..+++++ +.+++.+|+ |..++.+++.    ++|+++
T Consensus        45 ~~~~~~~~-~~~~~~vLdiG~G~G~~~~~l~~~~-~~~v~~vD~s~~~~~~a~~~~~~~~~~~~~  107 (266)
T 3ujc_A           45 KKILSDIE-LNENSKVLDIGSGLGGGCMYINEKY-GAHTHGIDICSNIVNMANERVSGNNKIIFE  107 (266)
T ss_dssp             HHHTTTCC-CCTTCEEEEETCTTSHHHHHHHHHH-CCEEEEEESCHHHHHHHHHTCCSCTTEEEE
T ss_pred             HHHHHhcC-CCCCCEEEEECCCCCHHHHHHHHHc-CCEEEEEeCCHHHHHHHHHHhhcCCCeEEE
Confidence            34555555 6677899999999999999999998 789999998 7777776542    455543

>1vl5_A Unknown conserved protein BH2331; putative methyltransferase, structural genomics, joint cente structural genomics, JCSG; HET: MSE; 1.95A {Bacillus halodurans} SCOP: c.66.1.41

Probab=97.31  E-value=0.00015  Score=59.98  Aligned_cols=50  Identities=22%  Similarity=0.297  Sum_probs=40.7

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+++.++ .....+|||||||.|.++..++++.+  +++.+|+ |..++.+++
T Consensus        27 ~~l~~~l~-~~~~~~vLDiGcG~G~~~~~l~~~~~--~v~gvD~s~~~l~~a~~   77 (260)
T 1vl5_A           27 AKLMQIAA-LKGNEEVLDVATGGGHVANAFAPFVK--KVVAFDLTEDILKVARA   77 (260)
T ss_dssp             HHHHHHHT-CCSCCEEEEETCTTCHHHHHHGGGSS--EEEEEESCHHHHHHHHH
T ss_pred             HHHHHHhC-CCCCCEEEEEeCCCCHHHHHHHHhCC--EEEEEeCCHHHHHHHHH
Confidence            45566666 56778999999999999999999987  7899998 777777653

>3kkz_A Uncharacterized protein Q5LES9; putative methyltransferase, BFR250, NESG, structural genomics, PSI-2; HET: SAM; 1.68A {Bacteroides fragilis nctc 9343} PDB: 3e7p_A 3t7s_A* 3t7r_A* 3t7t_A*

Probab=97.30  E-value=0.00019  Score=59.62  Aligned_cols=50  Identities=14%  Similarity=0.109  Sum_probs=40.2

Q ss_pred             HHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          184 VLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       184 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      +++.++......+|||||||.|.++..++++ |..+++.+|+ |..++.+++
T Consensus        37 ~l~~l~~~~~~~~vLDiGcG~G~~~~~la~~-~~~~v~gvD~s~~~~~~a~~   87 (267)
T 3kkz_A           37 ALSFIDNLTEKSLIADIGCGTGGQTMVLAGH-VTGQVTGLDFLSGFIDIFNR   87 (267)
T ss_dssp             HHTTCCCCCTTCEEEEETCTTCHHHHHHHTT-CSSEEEEEESCHHHHHHHHH
T ss_pred             HHHhcccCCCCCEEEEeCCCCCHHHHHHHhc-cCCEEEEEeCCHHHHHHHHH
Confidence            3444433456789999999999999999998 8899999999 777777654

>3jwh_A HEN1; methyltransferase; HET: SAH; 2.20A {Anabaena variabilis} PDB: 3jwj_A

Probab=97.30  E-value=0.00015  Score=58.24  Aligned_cols=43  Identities=16%  Similarity=0.268  Sum_probs=37.8

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ....+|||||||.|.++..+++++|..+++.+|+ |..++.+++
T Consensus        28 ~~~~~vLDiGcG~G~~~~~l~~~~~~~~v~gvD~s~~~~~~a~~   71 (217)
T 3jwh_A           28 SNARRVIDLGCGQGNLLKILLKDSFFEQITGVDVSYRSLEIAQE   71 (217)
T ss_dssp             TTCCEEEEETCTTCHHHHHHHHCTTCSEEEEEESCHHHHHHHHH
T ss_pred             cCCCEEEEeCCCCCHHHHHHHhhCCCCEEEEEECCHHHHHHHHH
Confidence            4457999999999999999999999999999998 787777754

>3orh_A Guanidinoacetate N-methyltransferase; structura genomics, structural genomics consortium, SGC; HET: SAH; 1.86A {Homo sapiens} PDB: 1xcj_A* 1xcl_A* 1p1c_A* 1p1b_A* 1khh_A*

Probab=97.30  E-value=7.7e-05  Score=61.25  Aligned_cols=42  Identities=12%  Similarity=0.111  Sum_probs=36.0

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ....+|||||||.|..+..++++.|. +.+++|+ |.+++.|++
T Consensus        59 ~~G~rVLdiG~G~G~~~~~~~~~~~~-~v~~id~~~~~~~~a~~  101 (236)
T 3orh_A           59 SKGGRVLEVGFGMAIAASKVQEAPID-EHWIIECNDGVFQRLRD  101 (236)
T ss_dssp             TTCEEEEEECCTTSHHHHHHTTSCEE-EEEEEECCHHHHHHHHH
T ss_pred             cCCCeEEEECCCccHHHHHHHHhCCc-EEEEEeCCHHHHHHHHH
Confidence            34589999999999999999988885 6788898 899998864

>1jsx_A Glucose-inhibited division protein B; methyltransferase fold, structural genomics, PSI, protein structure initiative; 2.40A {Escherichia coli} SCOP: c.66.1.20

Probab=97.29  E-value=6.1e-05  Score=59.96  Aligned_cols=41  Identities=17%  Similarity=0.120  Sum_probs=36.8

Q ss_pred             cceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+|+|||||+|.++..+++.+|+.+++.+|. |..++.+++
T Consensus        66 ~~~vLDiG~G~G~~~~~l~~~~~~~~v~~vD~s~~~~~~a~~  107 (207)
T 1jsx_A           66 GERFIDVGTGPGLPGIPLSIVRPEAHFTLLDSLGKRVRFLRQ  107 (207)
T ss_dssp             SSEEEEETCTTTTTHHHHHHHCTTSEEEEEESCHHHHHHHHH
T ss_pred             CCeEEEECCCCCHHHHHHHHHCCCCEEEEEeCCHHHHHHHHH
Confidence            47999999999999999999999999999998 777777653

>3mb5_A SAM-dependent methyltransferase; RNA methyltransferase, M1A, TRMI, intermolecular contacts, R specificity, tetramer, disulfide bond; HET: SAM; 1.60A {Pyrococcus abyssi} PDB: 3lga_A* 3lhd_C*

Probab=97.27  E-value=9.6e-05  Score=60.89  Aligned_cols=52  Identities=15%  Similarity=0.130  Sum_probs=44.2

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHH-CCCCeEEEccc-hHHhhhCCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISK-YPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~-~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..++..++ .....+|+|+|||+|.++..+++. .|..+++.+|+ |..++.|++
T Consensus        83 ~~i~~~~~-~~~~~~vldiG~G~G~~~~~l~~~~~~~~~v~~~D~~~~~~~~a~~  136 (255)
T 3mb5_A           83 ALIVAYAG-ISPGDFIVEAGVGSGALTLFLANIVGPEGRVVSYEIREDFAKLAWE  136 (255)
T ss_dssp             HHHHHHTT-CCTTCEEEEECCTTSHHHHHHHHHHCTTSEEEEECSCHHHHHHHHH
T ss_pred             HHHHHhhC-CCCCCEEEEecCCchHHHHHHHHHhCCCeEEEEEecCHHHHHHHHH
Confidence            34555666 667789999999999999999999 89999999999 788888764

>2yxd_A Probable cobalt-precorrin-6Y C(15)-methyltransfer [decarboxylating]; alpha and beta protein (A/B) class; HET: MES; 2.30A {Methanocaldococcus jannaschii}

Probab=97.26  E-value=0.00026  Score=54.62  Aligned_cols=49  Identities=18%  Similarity=0.079  Sum_probs=39.7

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+++.++ .....+|+|||||.|.++..+++  +..+++.+|. |..++.+++
T Consensus        26 ~~~~~~~-~~~~~~vLdiG~G~G~~~~~l~~--~~~~v~~vD~~~~~~~~a~~   75 (183)
T 2yxd_A           26 VSIGKLN-LNKDDVVVDVGCGSGGMTVEIAK--RCKFVYAIDYLDGAIEVTKQ   75 (183)
T ss_dssp             HHHHHHC-CCTTCEEEEESCCCSHHHHHHHT--TSSEEEEEECSHHHHHHHHH
T ss_pred             HHHHHcC-CCCCCEEEEeCCCCCHHHHHHHh--cCCeEEEEeCCHHHHHHHHH
Confidence            3444455 55668999999999999999998  8889999998 777777764

>3g89_A Ribosomal RNA small subunit methyltransferase G; 16S rRNA methyltransferase, translation, cytoplasm, rRNA processing; HET: HIC SAM AMP; 1.50A {Thermus thermophilus} PDB: 3g88_A* 3g8a_A* 3g8b_A*

Probab=97.25  E-value=0.00018  Score=59.65  Aligned_cols=43  Identities=14%  Similarity=0.129  Sum_probs=38.1

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ....+|+|||||+|..+..++..+|+.+++.+|. +..++.+++
T Consensus        79 ~~~~~vLDiG~G~G~~~i~la~~~~~~~v~~vD~s~~~~~~a~~  122 (249)
T 3g89_A           79 QGPLRVLDLGTGAGFPGLPLKIVRPELELVLVDATRKKVAFVER  122 (249)
T ss_dssp             CSSCEEEEETCTTTTTHHHHHHHCTTCEEEEEESCHHHHHHHHH
T ss_pred             CCCCEEEEEcCCCCHHHHHHHHHCCCCEEEEEECCHHHHHHHHH
Confidence            4568999999999999999999999999999997 777777654

>1fbn_A MJ fibrillarin homologue; MJ proteins, ribosomal RNA processing, snoRNP, structural genomics, BSGC structure funded by NIH; 1.60A {Methanocaldococcus jannaschii} SCOP: c.66.1.3 PDB: 1g8s_A

Probab=97.24  E-value=0.00053  Score=55.70  Aligned_cols=51  Identities=12%  Similarity=0.165  Sum_probs=40.3

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhC----CCCCCceee
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDA----PSYPGTLFI  241 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a----~~~~~i~~~  241 (244)
                      +....+|+|||||+|.++..+++.+|..+++.+|. |..++.+    +..++|+++
T Consensus        72 ~~~~~~VLDlGcG~G~~~~~la~~~~~~~v~gvD~s~~~~~~a~~~~~~~~~v~~~  127 (230)
T 1fbn_A           72 IKRDSKILYLGASAGTTPSHVADIADKGIVYAIEYAPRIMRELLDACAERENIIPI  127 (230)
T ss_dssp             CCTTCEEEEESCCSSHHHHHHHHHTTTSEEEEEESCHHHHHHHHHHTTTCTTEEEE
T ss_pred             CCCCCEEEEEcccCCHHHHHHHHHcCCcEEEEEECCHHHHHHHHHHhhcCCCeEEE
Confidence            55668999999999999999999999888999998 6666543    334556553

>3jwg_A HEN1, methyltransferase type 12; 1.90A {Clostridium thermocellum} PDB: 3jwi_A

Probab=97.23  E-value=0.00017  Score=57.84  Aligned_cols=43  Identities=23%  Similarity=0.343  Sum_probs=38.1

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ....+|||||||.|.++..+++++|..+++.+|+ |..++.+++
T Consensus        28 ~~~~~vLDiGcG~G~~~~~l~~~~~~~~v~gvD~s~~~~~~a~~   71 (219)
T 3jwg_A           28 VNAKKVIDLGCGEGNLLSLLLKDKSFEQITGVDVSYSVLERAKD   71 (219)
T ss_dssp             TTCCEEEEETCTTCHHHHHHHTSTTCCEEEEEESCHHHHHHHHH
T ss_pred             cCCCEEEEecCCCCHHHHHHHhcCCCCEEEEEECCHHHHHHHHH
Confidence            3457999999999999999999999999999998 788877764

>1pjz_A Thiopurine S-methyltransferase; polymorphism, S-adenosylmethionine, drug metabolism; NMR {Pseudomonas syringae PV} SCOP: c.66.1.36

Probab=97.20  E-value=0.0003  Score=56.20  Aligned_cols=48  Identities=6%  Similarity=-0.006  Sum_probs=38.4

Q ss_pred             HHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          184 VLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       184 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      +++.+. .....+|+|||||+|..+..++++  +.+++.+|+ |..++.|++
T Consensus        14 ~~~~l~-~~~~~~vLD~GCG~G~~~~~la~~--g~~V~gvD~S~~~l~~a~~   62 (203)
T 1pjz_A           14 YWSSLN-VVPGARVLVPLCGKSQDMSWLSGQ--GYHVVGAELSEAAVERYFT   62 (203)
T ss_dssp             HHHHHC-CCTTCEEEETTTCCSHHHHHHHHH--CCEEEEEEECHHHHHHHHH
T ss_pred             HHHhcc-cCCCCEEEEeCCCCcHhHHHHHHC--CCeEEEEeCCHHHHHHHHH
Confidence            344444 556689999999999999999997  568999998 788887753

>3bkw_A MLL3908 protein, S-adenosylmethionine dependent methyltransferase; NP_104914.1; HET: MSE; 1.60A {Mesorhizobium loti}

Probab=97.19  E-value=0.00042  Score=56.22  Aligned_cols=50  Identities=16%  Similarity=0.110  Sum_probs=38.7

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+...++ .....+|+|||||.|.++..++++.+ .+++.+|+ |..++.+++
T Consensus        34 ~l~~~~~-~~~~~~vLdiG~G~G~~~~~l~~~~~-~~v~~vD~s~~~~~~a~~   84 (243)
T 3bkw_A           34 ALRAMLP-EVGGLRIVDLGCGFGWFCRWAHEHGA-SYVLGLDLSEKMLARARA   84 (243)
T ss_dssp             HHHHHSC-CCTTCEEEEETCTTCHHHHHHHHTTC-SEEEEEESCHHHHHHHHH
T ss_pred             HHHHhcc-ccCCCEEEEEcCcCCHHHHHHHHCCC-CeEEEEcCCHHHHHHHHH
Confidence            4555555 45668999999999999999998843 27888898 777777754

>3cgg_A SAM-dependent methyltransferase; NP_600671.1, methyltransferase domain, structural genomics; HET: NHE CIT; 2.00A {Corynebacterium glutamicum atcc 13032}

Probab=97.18  E-value=0.0003  Score=54.83  Aligned_cols=54  Identities=20%  Similarity=0.366  Sum_probs=40.1

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC-CCCcee
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS-YPGTLF  240 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~-~~~i~~  240 (244)
                      .++..+  .....+|+|||||.|.++..+++.  +.+++.+|. |..++.+++ .+++++
T Consensus        38 ~~l~~~--~~~~~~vLdiG~G~G~~~~~l~~~--~~~v~~~D~~~~~~~~a~~~~~~~~~   93 (195)
T 3cgg_A           38 RLIDAM--APRGAKILDAGCGQGRIGGYLSKQ--GHDVLGTDLDPILIDYAKQDFPEARW   93 (195)
T ss_dssp             HHHHHH--SCTTCEEEEETCTTTHHHHHHHHT--TCEEEEEESCHHHHHHHHHHCTTSEE
T ss_pred             HHHHHh--ccCCCeEEEECCCCCHHHHHHHHC--CCcEEEEcCCHHHHHHHHHhCCCCcE
Confidence            455555  356689999999999999999988  568888898 777776654 234443

>1nkv_A Hypothetical protein YJHP; structural genomics, PSI, protein structure initiative, northeast structural genomics consortium, NESG; 2.90A {Escherichia coli} SCOP: c.66.1.21

Probab=97.18  E-value=0.00039  Score=57.04  Aligned_cols=51  Identities=18%  Similarity=0.274  Sum_probs=41.5

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+++.++ .....+|||||||.|.++..+++++ +.+++.+|+ |..++.+++
T Consensus        26 ~~l~~~~~-~~~~~~VLDiGcG~G~~~~~la~~~-~~~v~gvD~s~~~l~~a~~   77 (256)
T 1nkv_A           26 ATLGRVLR-MKPGTRILDLGSGSGEMLCTWARDH-GITGTGIDMSSLFTAQAKR   77 (256)
T ss_dssp             HHHHHHTC-CCTTCEEEEETCTTCHHHHHHHHHT-CCEEEEEESCHHHHHHHHH
T ss_pred             HHHHHhcC-CCCCCEEEEECCCCCHHHHHHHHhc-CCeEEEEeCCHHHHHHHHH
Confidence            34555555 6677899999999999999999998 678999998 777777753

>1xdz_A Methyltransferase GIDB; MCSG, protein structure initiative, structural genomics, methyltransferase fold, PSI; 1.60A {Bacillus subtilis} SCOP: c.66.1.20

Probab=97.18  E-value=0.00019  Score=58.75  Aligned_cols=44  Identities=27%  Similarity=0.336  Sum_probs=38.2

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      +....+|+|||||+|.++..++...|+.+++.+|. |..++.+++
T Consensus        68 ~~~~~~vLDiG~G~G~~~~~la~~~~~~~v~~vD~s~~~~~~a~~  112 (240)
T 1xdz_A           68 FNQVNTICDVGAGAGFPSLPIKICFPHLHVTIVDSLNKRITFLEK  112 (240)
T ss_dssp             GGGCCEEEEECSSSCTTHHHHHHHCTTCEEEEEESCHHHHHHHHH
T ss_pred             cCCCCEEEEecCCCCHHHHHHHHhCCCCEEEEEeCCHHHHHHHHH
Confidence            34568999999999999999999999999999998 777777654

>3hem_A Cyclopropane-fatty-acyl-phospholipid synthase 2; protein-ligand complex, cytoplasm, lipid synthesis, methyltransferase; HET: D22; 2.39A {Mycobacterium tuberculosis} SCOP: c.66.1.18 PDB: 1kpi_A*

Probab=97.14  E-value=0.00032  Score=59.36  Aligned_cols=51  Identities=22%  Similarity=0.372  Sum_probs=42.8

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+++.++ .....+|||||||.|.++..+++++| .+++.+|+ |..++.+++
T Consensus        62 ~~~~~~~~-~~~~~~vLDiGcG~G~~~~~la~~~~-~~v~gvD~s~~~~~~a~~  113 (302)
T 3hem_A           62 KLALDKLN-LEPGMTLLDIGCGWGSTMRHAVAEYD-VNVIGLTLSENQYAHDKA  113 (302)
T ss_dssp             HHHHHTTC-CCTTCEEEEETCTTSHHHHHHHHHHC-CEEEEEECCHHHHHHHHH
T ss_pred             HHHHHHcC-CCCcCEEEEeeccCcHHHHHHHHhCC-CEEEEEECCHHHHHHHHH
Confidence            35566666 66778999999999999999999988 89999999 788877764

>2pwy_A TRNA (adenine-N(1)-)-methyltransferase; mtase, adoMet, TRMI, tRNA-M1A58; HET: SAH; 1.70A {Thermus thermophilus}

Probab=97.14  E-value=0.00018  Score=59.19  Aligned_cols=51  Identities=12%  Similarity=0.121  Sum_probs=43.3

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHH-CCCCeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISK-YPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~-~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .++..++ +....+|||+|||.|.++..+++. .|..+++.+|. |..++.+++
T Consensus        87 ~~~~~~~-~~~~~~vLdiG~G~G~~~~~l~~~~~~~~~v~~~D~~~~~~~~a~~  139 (258)
T 2pwy_A           87 AMVTLLD-LAPGMRVLEAGTGSGGLTLFLARAVGEKGLVESYEARPHHLAQAER  139 (258)
T ss_dssp             HHHHHTT-CCTTCEEEEECCTTSHHHHHHHHHHCTTSEEEEEESCHHHHHHHHH
T ss_pred             HHHHHcC-CCCCCEEEEECCCcCHHHHHHHHHhCCCCEEEEEeCCHHHHHHHHH
Confidence            4566666 677789999999999999999999 78999999998 888777754

>2b3t_A Protein methyltransferase HEMK; translation termination, methylation, conformational changes; HET: SAH; 3.10A {Escherichia coli} SCOP: c.66.1.30 PDB: 1t43_A*

Probab=97.13  E-value=0.00059  Score=57.06  Aligned_cols=50  Identities=24%  Similarity=0.323  Sum_probs=41.0

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+++.++  ....+|+|||||+|.++..+++.+|+.+++..|. |..++.+++
T Consensus       101 ~~l~~~~--~~~~~vLDlG~GsG~~~~~la~~~~~~~v~~vD~s~~~l~~a~~  151 (276)
T 2b3t_A          101 QALARLP--EQPCRILDLGTGTGAIALALASERPDCEIIAVDRMPDAVSLAQR  151 (276)
T ss_dssp             HHHHHSC--SSCCEEEEETCTTSHHHHHHHHHCTTSEEEEECSSHHHHHHHHH
T ss_pred             HHHHhcc--cCCCEEEEecCCccHHHHHHHHhCCCCEEEEEECCHHHHHHHHH
Confidence            3444443  3457999999999999999999999999999998 788877764

>3gu3_A Methyltransferase; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative, northeast structural genomics consortium, NESG; HET: SAH; 2.30A {Bacillus cereus} SCOP: c.66.1.49 PDB: 2gh1_A

Probab=97.13  E-value=0.00035  Score=58.68  Aligned_cols=51  Identities=18%  Similarity=0.234  Sum_probs=40.6

Q ss_pred             HHhhcCCCCCcceEEEecCCccHHHHHHHHHCCC-CeEEEccc-hHHhhhCCC
Q 041256          184 VLESYKGFEHVKKLVDVGGGLGITLNMIISKYPH-IKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       184 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dl-p~vi~~a~~  234 (244)
                      +++.+....+..+|||||||+|.++..+++.+|. .+++.+|+ |..++.+++
T Consensus        13 ~~~~~~~~~~~~~vLDiGcG~G~~~~~l~~~~~~~~~v~gvD~s~~~~~~a~~   65 (284)
T 3gu3_A           13 LVNTVWKITKPVHIVDYGCGYGYLGLVLMPLLPEGSKYTGIDSGETLLAEARE   65 (284)
T ss_dssp             HHHTTSCCCSCCEEEEETCTTTHHHHHHTTTSCTTCEEEEEESCHHHHHHHHH
T ss_pred             HHHHHhccCCCCeEEEecCCCCHHHHHHHHhCCCCCEEEEEECCHHHHHHHHH
Confidence            3333322567799999999999999999999995 89999998 777766543

>3mti_A RRNA methylase; SAM-dependent, PSI, MCSG, structural genomics, midwest cente structural genomics, protein structure initiative; 1.95A {Streptococcus thermophilus} PDB: 3lby_A*

Probab=97.13  E-value=0.00033  Score=54.65  Aligned_cols=42  Identities=14%  Similarity=0.191  Sum_probs=36.3

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .....+|+|||||+|.++..++++  ..+++.+|+ |..++.|++
T Consensus        20 ~~~~~~vLDiGcG~G~~~~~la~~--~~~v~~vD~s~~~l~~a~~   62 (185)
T 3mti_A           20 LDDESIVVDATMGNGNDTAFLAGL--SKKVYAFDVQEQALGKTSQ   62 (185)
T ss_dssp             CCTTCEEEESCCTTSHHHHHHHTT--SSEEEEEESCHHHHHHHHH
T ss_pred             CCCCCEEEEEcCCCCHHHHHHHHh--CCEEEEEECCHHHHHHHHH
Confidence            455689999999999999999988  788999998 888887764

>3f4k_A Putative methyltransferase; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 2.30A {Bacteroides thetaiotaomicron} PDB: 3t0i_A* 3svz_A* 3sxj_A*

Probab=97.11  E-value=0.00055  Score=56.15  Aligned_cols=51  Identities=20%  Similarity=0.194  Sum_probs=40.6

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .++..+.......+|||||||.|.++..+++++|. +++.+|+ |..++.+++
T Consensus        36 ~~l~~l~~~~~~~~vLDiG~G~G~~~~~l~~~~~~-~v~~vD~s~~~~~~a~~   87 (257)
T 3f4k_A           36 KAVSFINELTDDAKIADIGCGTGGQTLFLADYVKG-QITGIDLFPDFIEIFNE   87 (257)
T ss_dssp             HHHTTSCCCCTTCEEEEETCTTSHHHHHHHHHCCS-EEEEEESCHHHHHHHHH
T ss_pred             HHHHHHhcCCCCCeEEEeCCCCCHHHHHHHHhCCC-eEEEEECCHHHHHHHHH
Confidence            34444433556689999999999999999999997 8999998 777776653

>1xxl_A YCGJ protein; structural genomics, protein structure initiative, PSI, NEW YORK SGX research center for structural genomics, nysgxrc; 2.10A {Bacillus subtilis} SCOP: c.66.1.41 PDB: 2glu_A*

Probab=97.11  E-value=0.00037  Score=56.89  Aligned_cols=50  Identities=18%  Similarity=0.243  Sum_probs=40.7

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+++..+ .....+|+|||||.|.++..+++..+  +++.+|+ |..++.+++
T Consensus        11 ~~~~~~~~-~~~~~~vLDiGcG~G~~~~~l~~~~~--~v~~vD~s~~~~~~a~~   61 (239)
T 1xxl_A           11 GLMIKTAE-CRAEHRVLDIGAGAGHTALAFSPYVQ--ECIGVDATKEMVEVASS   61 (239)
T ss_dssp             HHHHHHHT-CCTTCEEEEESCTTSHHHHHHGGGSS--EEEEEESCHHHHHHHHH
T ss_pred             chHHHHhC-cCCCCEEEEEccCcCHHHHHHHHhCC--EEEEEECCHHHHHHHHH
Confidence            45566666 67789999999999999999999986  7888898 777776653

>3ccf_A Cyclopropane-fatty-acyl-phospholipid synthase; YP_321342.1, putative methyltransferase; 1.90A {Anabaena variabilis atcc 29413}

Probab=97.10  E-value=0.00047  Score=57.60  Aligned_cols=55  Identities=22%  Similarity=0.295  Sum_probs=42.2

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC-CCCcee
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS-YPGTLF  240 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~-~~~i~~  240 (244)
                      .+++.++ .....+|||||||.|.++..+++  |..+++.+|+ |..++.+++ .+++++
T Consensus        48 ~l~~~l~-~~~~~~vLDiGcG~G~~~~~l~~--~~~~v~gvD~s~~~~~~a~~~~~~~~~  104 (279)
T 3ccf_A           48 DLLQLLN-PQPGEFILDLGCGTGQLTEKIAQ--SGAEVLGTDNAATMIEKARQNYPHLHF  104 (279)
T ss_dssp             HHHHHHC-CCTTCEEEEETCTTSHHHHHHHH--TTCEEEEEESCHHHHHHHHHHCTTSCE
T ss_pred             HHHHHhC-CCCCCEEEEecCCCCHHHHHHHh--CCCeEEEEECCHHHHHHHHhhCCCCEE
Confidence            4555555 56668999999999999999998  8889999998 777776654 244443

>2o57_A Putative sarcosine dimethylglycine methyltransferase; structural genomics, protein structure initiative, PSI-2; 1.95A {Galdieria sulphuraria} SCOP: c.66.1.18

Probab=97.08  E-value=0.00025  Score=59.69  Aligned_cols=51  Identities=18%  Similarity=0.271  Sum_probs=40.1

Q ss_pred             HHHHhhc----CCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          182 EKVLESY----KGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       182 ~~~~~~~----~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+++.+    + +....+|||||||.|.++..+++++ +.+++.+|+ |..++.+++
T Consensus        68 ~~l~~~l~~~~~-~~~~~~vLDiGcG~G~~~~~l~~~~-~~~v~gvD~s~~~~~~a~~  123 (297)
T 2o57_A           68 EWLASELAMTGV-LQRQAKGLDLGAGYGGAARFLVRKF-GVSIDCLNIAPVQNKRNEE  123 (297)
T ss_dssp             HHHHHHHHHTTC-CCTTCEEEEETCTTSHHHHHHHHHH-CCEEEEEESCHHHHHHHHH
T ss_pred             HHHHHHhhhccC-CCCCCEEEEeCCCCCHHHHHHHHHh-CCEEEEEeCCHHHHHHHHH
Confidence            3455555    4 6677899999999999999999987 458999998 677766643

>4dcm_A Ribosomal RNA large subunit methyltransferase G; 23S rRNA (guanine1835-N2)-methyltransferase; HET: SAM; 2.30A {Escherichia coli}

Probab=97.08  E-value=0.00048  Score=60.62  Aligned_cols=51  Identities=20%  Similarity=0.271  Sum_probs=42.7

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+++.++ .....+|+|+|||.|.++..+++++|..+++.+|. |..++.+++
T Consensus       213 ~ll~~l~-~~~~~~VLDlGcG~G~~s~~la~~~p~~~V~gvD~s~~al~~Ar~  264 (375)
T 4dcm_A          213 FFMQHLP-ENLEGEIVDLGCGNGVIGLTLLDKNPQAKVVFVDESPMAVASSRL  264 (375)
T ss_dssp             HHHHTCC-CSCCSEEEEETCTTCHHHHHHHHHCTTCEEEEEESCHHHHHHHHH
T ss_pred             HHHHhCc-ccCCCeEEEEeCcchHHHHHHHHHCCCCEEEEEECcHHHHHHHHH
Confidence            3456665 34448999999999999999999999999999998 778877764

>2esr_A Methyltransferase; structural genomics, hypothetical protein, streptococcus PYO PSI, protein structure initiative; HET: GLC; 1.80A {Streptococcus pyogenes} SCOP: c.66.1.46

Probab=97.07  E-value=0.00063  Score=52.59  Aligned_cols=42  Identities=10%  Similarity=-0.053  Sum_probs=36.1

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ....+|+|||||.|.++..++++ +..+++.+|+ |..++.+++
T Consensus        30 ~~~~~vLDlGcG~G~~~~~l~~~-~~~~v~~vD~~~~~~~~a~~   72 (177)
T 2esr_A           30 FNGGRVLDLFAGSGGLAIEAVSR-GMSAAVLVEKNRKAQAIIQD   72 (177)
T ss_dssp             CCSCEEEEETCTTCHHHHHHHHT-TCCEEEEECCCHHHHHHHHH
T ss_pred             cCCCeEEEeCCCCCHHHHHHHHc-CCCEEEEEECCHHHHHHHHH
Confidence            45579999999999999999987 7778999999 888887764

>3bkx_A SAM-dependent methyltransferase; YP_807781.1, cyclopropane-fatty-acyl-phospholipid synthase-L protein, methyltransferase domain; 1.85A {Lactobacillus casei}

Probab=97.07  E-value=0.00029  Score=58.49  Aligned_cols=44  Identities=14%  Similarity=0.265  Sum_probs=37.2

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHC-CCCeEEEccchH
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKY-PHIKGINYDLPY  227 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dlp~  227 (244)
                      .+++.++ .....+|+|||||.|.++..+++++ |+.+++.+|+..
T Consensus        34 ~l~~~~~-~~~~~~vLDiGcG~G~~~~~l~~~~g~~~~v~gvD~s~   78 (275)
T 3bkx_A           34 AIAEAWQ-VKPGEKILEIGCGQGDLSAVLADQVGSSGHVTGIDIAS   78 (275)
T ss_dssp             HHHHHHT-CCTTCEEEEESCTTSHHHHHHHHHHCTTCEEEEECSSC
T ss_pred             HHHHHcC-CCCCCEEEEeCCCCCHHHHHHHHHhCCCCEEEEEECCc
Confidence            4566666 6677899999999999999999996 889999999843

>1kpg_A CFA synthase;, cyclopropane-fatty-acyl-phospholipid synthase 1; mixed alpha beta fold, structural genomics, PSI; HET: SAH 16A; 2.00A {Mycobacterium tuberculosis} SCOP: c.66.1.18 PDB: 1kp9_A* 1kph_A* 1tpy_A* 1l1e_A*

Probab=97.06  E-value=0.00044  Score=57.90  Aligned_cols=51  Identities=22%  Similarity=0.298  Sum_probs=40.9

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+++.++ .....+|||||||.|.++..++++++. +++.+|+ |..++.+++
T Consensus        54 ~~~~~~~~-~~~~~~vLDiGcG~G~~~~~l~~~~~~-~v~gvd~s~~~~~~a~~  105 (287)
T 1kpg_A           54 DLALGKLG-LQPGMTLLDVGCGWGATMMRAVEKYDV-NVVGLTLSKNQANHVQQ  105 (287)
T ss_dssp             HHHHTTTT-CCTTCEEEEETCTTSHHHHHHHHHHCC-EEEEEESCHHHHHHHHH
T ss_pred             HHHHHHcC-CCCcCEEEEECCcccHHHHHHHHHcCC-EEEEEECCHHHHHHHHH
Confidence            34556565 566789999999999999999988765 9999998 777777654

>3i9f_A Putative type 11 methyltransferase; structural genomics, PSI-2, protein structure initiative; 2.50A {Sulfolobus solfataricus}

Probab=97.06  E-value=0.00016  Score=55.66  Aligned_cols=54  Identities=17%  Similarity=0.201  Sum_probs=42.3

Q ss_pred             HhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC-CCCceee
Q 041256          185 LESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS-YPGTLFI  241 (244)
Q Consensus       185 ~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~-~~~i~~~  241 (244)
                      ++.++ .....+|+|||||.|.++..+++++.  +++.+|+ |..++.+++ .++|+++
T Consensus        10 ~~~~~-~~~~~~vLDiG~G~G~~~~~l~~~~~--~v~~vD~s~~~~~~a~~~~~~v~~~   65 (170)
T 3i9f_A           10 LPNIF-EGKKGVIVDYGCGNGFYCKYLLEFAT--KLYCIDINVIALKEVKEKFDSVITL   65 (170)
T ss_dssp             HHHHH-SSCCEEEEEETCTTCTTHHHHHTTEE--EEEEECSCHHHHHHHHHHCTTSEEE
T ss_pred             HHhcC-cCCCCeEEEECCCCCHHHHHHHhhcC--eEEEEeCCHHHHHHHHHhCCCcEEE
Confidence            44444 56678999999999999999999985  8899998 777777765 4566654

>3njr_A Precorrin-6Y methylase; methyltransferase, decarboxylase, transferase; HET: SAH PG4; 2.70A {Rhodobacter capsulatus}

Probab=97.05  E-value=0.00055  Score=54.78  Aligned_cols=48  Identities=19%  Similarity=0.149  Sum_probs=39.5

Q ss_pred             HHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          184 VLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       184 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ++..++ .....+|+|||||.|.++..++++  ..+++.+|+ |..++.|++
T Consensus        47 ~l~~l~-~~~~~~vLDlGcG~G~~~~~la~~--~~~v~~vD~s~~~~~~a~~   95 (204)
T 3njr_A           47 TLAALA-PRRGELLWDIGGGSGSVSVEWCLA--GGRAITIEPRADRIENIQK   95 (204)
T ss_dssp             HHHHHC-CCTTCEEEEETCTTCHHHHHHHHT--TCEEEEEESCHHHHHHHHH
T ss_pred             HHHhcC-CCCCCEEEEecCCCCHHHHHHHHc--CCEEEEEeCCHHHHHHHHH
Confidence            344455 566689999999999999999998  788999998 888887764

>1xtp_A LMAJ004091AAA; SGPP, structural genomics, PSI, protein structure initiative dependent methyltransferase; HET: SAI; 1.94A {Leishmania major} SCOP: c.66.1.42

Probab=97.04  E-value=0.00019  Score=58.80  Aligned_cols=51  Identities=14%  Similarity=0.211  Sum_probs=40.5

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+++.++ .....+|||||||.|.++..++++. ..+++.+|. |..++.+++
T Consensus        83 ~~~l~~l~-~~~~~~vLDiG~G~G~~~~~l~~~~-~~~v~~vD~s~~~~~~a~~  134 (254)
T 1xtp_A           83 RNFIASLP-GHGTSRALDCGAGIGRITKNLLTKL-YATTDLLEPVKHMLEEAKR  134 (254)
T ss_dssp             HHHHHTST-TCCCSEEEEETCTTTHHHHHTHHHH-CSEEEEEESCHHHHHHHHH
T ss_pred             HHHHHhhc-ccCCCEEEEECCCcCHHHHHHHHhh-cCEEEEEeCCHHHHHHHHH
Confidence            35566665 5567899999999999999999987 557889997 777777654

>1nt2_A Fibrillarin-like PRE-rRNA processing protein; adeMet, binding motif, RNA binding protein; HET: SAM; 2.90A {Archaeoglobus fulgidus} SCOP: c.66.1.3

Probab=97.03  E-value=0.00056  Score=55.09  Aligned_cols=50  Identities=6%  Similarity=0.029  Sum_probs=37.8

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hH----HhhhCCCCCCcee
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PY----VIKDAPSYPGTLF  240 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~----vi~~a~~~~~i~~  240 (244)
                      .....+|+|||||+|.++..+++..|+-+++.+|+ |.    .++.+++.++|.+
T Consensus        55 ~~~g~~VLDlGcGtG~~~~~la~~~~~~~V~gvD~s~~~l~~~~~~a~~~~~v~~  109 (210)
T 1nt2_A           55 LRGDERVLYLGAASGTTVSHLADIVDEGIIYAVEYSAKPFEKLLELVRERNNIIP  109 (210)
T ss_dssp             CCSSCEEEEETCTTSHHHHHHHHHTTTSEEEEECCCHHHHHHHHHHHHHCSSEEE
T ss_pred             CCCCCEEEEECCcCCHHHHHHHHHcCCCEEEEEECCHHHHHHHHHHHhcCCCeEE
Confidence            45667999999999999999999998778999998 43    3344443444443

>3e8s_A Putative SAM dependent methyltransferase; NP_744700.1, structural genomics, joint center for structural genom JCSG; HET: SAH; 2.10A {Pseudomonas putida KT2440}

Probab=97.03  E-value=0.00037  Score=55.74  Aligned_cols=54  Identities=17%  Similarity=0.225  Sum_probs=40.7

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCCCCCce
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPSYPGTL  239 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~~~~i~  239 (244)
                      .+++.+. .....+|||||||.|.++..++++  +.+++.+|+ |..++.+++.+.++
T Consensus        43 ~~~~~~~-~~~~~~vLdiG~G~G~~~~~l~~~--~~~v~~vD~s~~~~~~a~~~~~~~   97 (227)
T 3e8s_A           43 AILLAIL-GRQPERVLDLGCGEGWLLRALADR--GIEAVGVDGDRTLVDAARAAGAGE   97 (227)
T ss_dssp             HHHHHHH-HTCCSEEEEETCTTCHHHHHHHTT--TCEEEEEESCHHHHHHHHHTCSSC
T ss_pred             HHHHHhh-cCCCCEEEEeCCCCCHHHHHHHHC--CCEEEEEcCCHHHHHHHHHhcccc
Confidence            3444444 344589999999999999999998  568899998 77787776554443

>3bus_A REBM, methyltransferase; rebeccamycin synthesis; HET: SAH; 2.65A {Lechevalieria aerocolonigenes}

Probab=97.02  E-value=0.00083  Score=55.64  Aligned_cols=50  Identities=12%  Similarity=0.265  Sum_probs=41.4

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~  233 (244)
                      ..+++.++ .....+|||||||.|.++..+++++ +.+++.+|+ |..++.++
T Consensus        51 ~~l~~~~~-~~~~~~vLDiGcG~G~~~~~l~~~~-~~~v~gvD~s~~~~~~a~  101 (273)
T 3bus_A           51 DEMIALLD-VRSGDRVLDVGCGIGKPAVRLATAR-DVRVTGISISRPQVNQAN  101 (273)
T ss_dssp             HHHHHHSC-CCTTCEEEEESCTTSHHHHHHHHHS-CCEEEEEESCHHHHHHHH
T ss_pred             HHHHHhcC-CCCCCEEEEeCCCCCHHHHHHHHhc-CCEEEEEeCCHHHHHHHH
Confidence            45666666 6677899999999999999999987 689999998 77776665

>3eey_A Putative rRNA methylase; rRNA methylation, S-adenosyl-methionine, structural genomics structure initiative, PSI; HET: SAM; 2.20A {Clostridium thermocellum atcc 27405}

Probab=97.02  E-value=0.00026  Score=55.81  Aligned_cols=44  Identities=16%  Similarity=0.212  Sum_probs=37.6

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHC-CCCeEEEccc-hHHhhhCCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKY-PHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .....+|+|+|||.|.++..+++++ |..+++.+|+ |..++.+++
T Consensus        20 ~~~~~~vLDlGcG~G~~~~~l~~~~~~~~~v~~vD~s~~~~~~a~~   65 (197)
T 3eey_A           20 VKEGDTVVDATCGNGNDTAFLASLVGENGRVFGFDIQDKAIANTTK   65 (197)
T ss_dssp             CCTTCEEEESCCTTSHHHHHHHHHHCTTCEEEEECSCHHHHHHHHH
T ss_pred             CCCCCEEEEcCCCCCHHHHHHHHHhCCCCEEEEEECCHHHHHHHHH
Confidence            3455799999999999999999986 7889999998 788877764

>3cc8_A Putative methyltransferase; structural genomics, joint center for structural genomics, JCSG, protein structure initiative, PS transferase; 1.64A {Bacillus cereus}

Probab=97.02  E-value=0.00042  Score=55.51  Aligned_cols=49  Identities=18%  Similarity=0.234  Sum_probs=38.6

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+++.++  ....+|+|||||.|.++..+++. + .+++.+|. |..++.+++
T Consensus        23 ~~l~~~~~--~~~~~vLdiG~G~G~~~~~l~~~-~-~~~~~~D~~~~~~~~~~~   72 (230)
T 3cc8_A           23 PNLLKHIK--KEWKEVLDIGCSSGALGAAIKEN-G-TRVSGIEAFPEAAEQAKE   72 (230)
T ss_dssp             HHHHTTCC--TTCSEEEEETCTTSHHHHHHHTT-T-CEEEEEESSHHHHHHHHT
T ss_pred             HHHHHHhc--cCCCcEEEeCCCCCHHHHHHHhc-C-CeEEEEeCCHHHHHHHHH
Confidence            45566554  45689999999999999999998 5 88999998 666666543

>2avd_A Catechol-O-methyltransferase; structural genomics, structural genomics consortium, SGC; HET: SAM; 1.70A {Homo sapiens} SCOP: c.66.1.1

Probab=97.01  E-value=0.00027  Score=57.09  Aligned_cols=43  Identities=14%  Similarity=0.118  Sum_probs=37.5

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCC-CCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYP-HIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+..+|+|||||.|..+..+++..| +.+++.+|. |..++.+++
T Consensus        68 ~~~~~vLdiG~G~G~~~~~la~~~~~~~~v~~vD~~~~~~~~a~~  112 (229)
T 2avd_A           68 IQAKKALDLGTFTGYSALALALALPADGRVVTCEVDAQPPELGRP  112 (229)
T ss_dssp             TTCCEEEEECCTTSHHHHHHHTTSCTTCEEEEEESCSHHHHHHHH
T ss_pred             cCCCEEEEEcCCccHHHHHHHHhCCCCCEEEEEECCHHHHHHHHH
Confidence            4557999999999999999999988 789999998 888877764

>1m6y_A S-adenosyl-methyltransferase MRAW; SAM-dependent methyltransferase fold, protein-cofactor product complex, structural genomics, PSI; HET: SAH; 1.90A {Thermotoga maritima} SCOP: a.60.13.1 c.66.1.23 PDB: 1n2x_A*

Probab=97.01  E-value=0.00056  Score=58.41  Aligned_cols=52  Identities=27%  Similarity=0.288  Sum_probs=43.7

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+++.++ .....+|||+|||.|.++..+++++|+.+++.+|. |..++.|++
T Consensus        16 ~e~l~~L~-~~~g~~vLD~g~G~G~~s~~la~~~~~~~VigvD~d~~al~~A~~   68 (301)
T 1m6y_A           16 REVIEFLK-PEDEKIILDCTVGEGGHSRAILEHCPGCRIIGIDVDSEVLRIAEE   68 (301)
T ss_dssp             HHHHHHHC-CCTTCEEEETTCTTSHHHHHHHHHCTTCEEEEEESCHHHHHHHHH
T ss_pred             HHHHHhcC-CCCCCEEEEEeCCcCHHHHHHHHHCCCCEEEEEECCHHHHHHHHH
Confidence            44555555 55668999999999999999999999999999998 888888764

>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A

Probab=97.01  E-value=0.00041  Score=45.59  Aligned_cols=55  Identities=16%  Similarity=0.372  Sum_probs=44.0

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecC
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLA  101 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t  101 (244)
                      +..|.+.|.+.+  .++|..|||+.+|++      ... +.+.|..|...|++..   ...+.|+++
T Consensus        12 ~~~IL~~L~~~~--~~~s~~eLA~~lgls------r~t-v~~~l~~L~~~G~I~~---~~~G~y~lg   66 (67)
T 2heo_A           12 EQKILQVLSDDG--GPVAIFQLVKKCQVP------KKT-LNQVLYRLKKEDRVSS---PSPKYWSIG   66 (67)
T ss_dssp             HHHHHHHHHHHC--SCEEHHHHHHHHCSC------HHH-HHHHHHHHHHTTSEEE---EETTEEEEC
T ss_pred             HHHHHHHHHHcC--CCcCHHHHHHHHCcC------HHH-HHHHHHHHHHCCcEec---CCCceEeeC
Confidence            456888887753  589999999999996      456 9999999999999874   234788764

>2fk8_A Methoxy mycolic acid synthase 4; S-adenosylmethionine-dependent methyltransferase fold, trans; HET: SAM; 2.00A {Mycobacterium tuberculosis} SCOP: c.66.1.18 PDB: 2fk7_A* 3ha3_A* 3ha5_A* 3ha7_A*

Probab=97.00  E-value=0.00052  Score=58.44  Aligned_cols=51  Identities=18%  Similarity=0.333  Sum_probs=41.6

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+++.++ .....+|||||||.|.++..+++++ +.+++.+|+ |..++.+++
T Consensus        80 ~~~~~~~~-~~~~~~vLDiGcG~G~~~~~la~~~-~~~v~gvD~s~~~~~~a~~  131 (318)
T 2fk8_A           80 DLNLDKLD-LKPGMTLLDIGCGWGTTMRRAVERF-DVNVIGLTLSKNQHARCEQ  131 (318)
T ss_dssp             HHHHTTSC-CCTTCEEEEESCTTSHHHHHHHHHH-CCEEEEEESCHHHHHHHHH
T ss_pred             HHHHHhcC-CCCcCEEEEEcccchHHHHHHHHHC-CCEEEEEECCHHHHHHHHH
Confidence            45566665 5667899999999999999999987 569999998 777777754

>3b3j_A Histone-arginine methyltransferase CARM1; protein arginine methyltransferase 4, APO catalytic domain, regulator, mRNA processing; 2.55A {Rattus norvegicus}

Probab=97.00  E-value=0.00053  Score=62.36  Aligned_cols=51  Identities=20%  Similarity=0.109  Sum_probs=40.0

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPS  234 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~  234 (244)
                      ..+++.++ ..+..+|+|||||.|.++..+++ .|..+++.+|+...++.|++
T Consensus       148 ~~il~~l~-~~~~~~VLDiGcGtG~la~~la~-~~~~~V~gvD~s~~l~~A~~  198 (480)
T 3b3j_A          148 RAILQNHT-DFKDKIVLDVGCGSGILSFFAAQ-AGARKIYAVEASTMAQHAEV  198 (480)
T ss_dssp             HHHHHTGG-GTTTCEEEEESCSTTHHHHHHHH-TTCSEEEEEECHHHHHHHHH
T ss_pred             HHHHHhhh-hcCCCEEEEecCcccHHHHHHHH-cCCCEEEEEEcHHHHHHHHH
Confidence            45566555 44568999999999999998877 68889999999777666653

>3fzg_A 16S rRNA methylase; methyltransferase, plasmid, transferase; HET: SAM; 2.00A {Escherichia coli}

Probab=97.00  E-value=0.00038  Score=55.59  Aligned_cols=43  Identities=23%  Similarity=0.225  Sum_probs=38.8

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ....+|+|+|||.|-++..++...|+.+.+..|. +..++.+++
T Consensus        48 ~~~~~VLDlGCG~GplAl~l~~~~p~a~~~A~Di~~~~leiar~   91 (200)
T 3fzg_A           48 KHVSSILDFGCGFNPLALYQWNENEKIIYHAYDIDRAEIAFLSS   91 (200)
T ss_dssp             CCCSEEEEETCTTHHHHHHHHCSSCCCEEEEECSCHHHHHHHHH
T ss_pred             CCCCeEEEecCCCCHHHHHHHhcCCCCEEEEEeCCHHHHHHHHH
Confidence            4568999999999999999999999999999998 788887764

>2ipx_A RRNA 2'-O-methyltransferase fibrillarin; FBL, structural genomics, structural genomics consortium, SGC; HET: MTA; 1.82A {Homo sapiens}

Probab=96.99  E-value=0.00033  Score=57.02  Aligned_cols=51  Identities=14%  Similarity=0.131  Sum_probs=39.1

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHC-CCCeEEEccc-hH----HhhhCCCCCCceee
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKY-PHIKGINYDL-PY----VIKDAPSYPGTLFI  241 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~----vi~~a~~~~~i~~~  241 (244)
                      +....+|+|||||+|.++..+++++ |+.+++.+|+ |.    .++.+++.++|+++
T Consensus        75 ~~~~~~vLDlG~G~G~~~~~la~~~g~~~~v~gvD~s~~~i~~~~~~a~~~~~v~~~  131 (233)
T 2ipx_A           75 IKPGAKVLYLGAASGTTVSHVSDIVGPDGLVYAVEFSHRSGRDLINLAKKRTNIIPV  131 (233)
T ss_dssp             CCTTCEEEEECCTTSHHHHHHHHHHCTTCEEEEECCCHHHHHHHHHHHHHCTTEEEE
T ss_pred             CCCCCEEEEEcccCCHHHHHHHHHhCCCcEEEEEECCHHHHHHHHHHhhccCCeEEE
Confidence            4566899999999999999999997 7889999998 33    34444444555543

>2gpy_A O-methyltransferase; structural genomics, PSI, protein structure initiative, NEW research center for structural genomics, nysgxrc; HET: MSE; 1.90A {Bacillus halodurans}

Probab=96.99  E-value=0.00046  Score=56.06  Aligned_cols=42  Identities=10%  Similarity=0.232  Sum_probs=37.6

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...+|||||||.|..+..+++.+|+.+++.+|. |..++.+++
T Consensus        54 ~~~~vLdiG~G~G~~~~~la~~~~~~~v~~vD~~~~~~~~a~~   96 (233)
T 2gpy_A           54 APARILEIGTAIGYSAIRMAQALPEATIVSIERDERRYEEAHK   96 (233)
T ss_dssp             CCSEEEEECCTTSHHHHHHHHHCTTCEEEEECCCHHHHHHHHH
T ss_pred             CCCEEEEecCCCcHHHHHHHHHCCCCEEEEEECCHHHHHHHHH
Confidence            457999999999999999999999999999999 788877764

>3ggd_A SAM-dependent methyltransferase; YP_325210.1, structural GEN joint center for structural genomics, JCSG; HET: SAH; 2.11A {Anabaena variabilis atcc 29413}

Probab=96.98  E-value=0.00084  Score=54.73  Aligned_cols=49  Identities=18%  Similarity=0.296  Sum_probs=38.8

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC---CCCceee
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS---YPGTLFI  241 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~---~~~i~~~  241 (244)
                      .....+|||||||+|.++..++++++  +++.+|. |..++.+++   ..+|+++
T Consensus        54 ~~~~~~vLD~GcG~G~~~~~la~~~~--~v~gvD~s~~~~~~a~~~~~~~~~~~~  106 (245)
T 3ggd_A           54 FNPELPLIDFACGNGTQTKFLSQFFP--RVIGLDVSKSALEIAAKENTAANISYR  106 (245)
T ss_dssp             SCTTSCEEEETCTTSHHHHHHHHHSS--CEEEEESCHHHHHHHHHHSCCTTEEEE
T ss_pred             cCCCCeEEEEcCCCCHHHHHHHHhCC--CEEEEECCHHHHHHHHHhCcccCceEE
Confidence            34567899999999999999999999  6888888 778877754   2355554

>3fpf_A Mtnas, putative uncharacterized protein; thermonicotianamine, nicotianamine, biosynthetic protein; HET: TNA MTA; 1.66A {Methanothermobacter thermautotrophicusorganism_taxid} PDB: 3fpe_A* 3fph_A* 3fpg_A* 3fpj_A* 3o31_A*

Probab=96.98  E-value=0.00056  Score=58.26  Aligned_cols=44  Identities=16%  Similarity=0.221  Sum_probs=39.1

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .....+|+|||||.|.++..++.+.|+.+++.+|+ |+.++.|++
T Consensus       120 l~~g~rVLDIGcG~G~~ta~~lA~~~ga~V~gIDis~~~l~~Ar~  164 (298)
T 3fpf_A          120 FRRGERAVFIGGGPLPLTGILLSHVYGMRVNVVEIEPDIAELSRK  164 (298)
T ss_dssp             CCTTCEEEEECCCSSCHHHHHHHHTTCCEEEEEESSHHHHHHHHH
T ss_pred             CCCcCEEEEECCCccHHHHHHHHHccCCEEEEEECCHHHHHHHHH
Confidence            67779999999999988877778889999999999 899998875

>2nyu_A Putative ribosomal RNA methyltransferase 2; SAM, structural genomics, structural genomics consortium, SGC; HET: SAM; 1.76A {Homo sapiens}

Probab=96.97  E-value=0.0012  Score=51.85  Aligned_cols=45  Identities=18%  Similarity=0.096  Sum_probs=36.2

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCC---------CeEEEccchH
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPH---------IKGINYDLPY  227 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~---------l~~~v~Dlp~  227 (244)
                      .+.+.++.+....+|||||||.|.++..+++++|.         .+++.+|+.+
T Consensus        12 ~l~~~~~~~~~~~~vLDlGcG~G~~~~~la~~~~~~~~~~~~~~~~v~~vD~s~   65 (196)
T 2nyu_A           12 EVNERHQILRPGLRVLDCGAAPGAWSQVAVQKVNAAGTDPSSPVGFVLGVDLLH   65 (196)
T ss_dssp             HHHHHHCCCCTTCEEEEETCCSCHHHHHHHHHTTTTCCCTTSCCCEEEEECSSC
T ss_pred             HHHHhcCCCCCCCEEEEeCCCCCHHHHHHHHHhccccccccCCCceEEEEechh
Confidence            34445553456689999999999999999999875         7899999855

>2ozv_A Hypothetical protein ATU0636; structural genomics, predicted transferase, predicted O-methyltransferase, PFAM PF05175; HET: MSE; 1.70A {Agrobacterium tumefaciens str}

Probab=96.96  E-value=0.00061  Score=56.66  Aligned_cols=44  Identities=14%  Similarity=0.182  Sum_probs=38.6

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .....+|||||||+|.++..+++++|+.+++.+|+ |..++.+++
T Consensus        34 ~~~~~~VLDlG~G~G~~~l~la~~~~~~~v~gvDi~~~~~~~a~~   78 (260)
T 2ozv_A           34 DDRACRIADLGAGAGAAGMAVAARLEKAEVTLYERSQEMAEFARR   78 (260)
T ss_dssp             CCSCEEEEECCSSSSHHHHHHHHHCTTEEEEEEESSHHHHHHHHH
T ss_pred             ccCCCEEEEeCChHhHHHHHHHHhCCCCeEEEEECCHHHHHHHHH
Confidence            45568999999999999999999999999999999 777777653

>3kr9_A SAM-dependent methyltransferase; class I rossmann-like methyltransferase fold; 2.00A {Streptococcus pneumoniae} PDB: 3ku1_A*

Probab=96.95  E-value=0.00036  Score=57.09  Aligned_cols=43  Identities=14%  Similarity=0.056  Sum_probs=38.2

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ....+|+|||||+|.+++.+++.+|..+++..|. |..++.|++
T Consensus        14 ~~g~~VlDIGtGsG~l~i~la~~~~~~~V~avDi~~~al~~A~~   57 (225)
T 3kr9_A           14 SQGAILLDVGSDHAYLPIELVERGQIKSAIAGEVVEGPYQSAVK   57 (225)
T ss_dssp             CTTEEEEEETCSTTHHHHHHHHTTSEEEEEEEESSHHHHHHHHH
T ss_pred             CCCCEEEEeCCCcHHHHHHHHHhCCCCEEEEEECCHHHHHHHHH
Confidence            3447999999999999999999999999999998 788888764

>1xmk_A Double-stranded RNA-specific adenosine deaminase; winged helix-turn-helix, RNA editing, interferon, ADAR1, hydrolase; 0.97A {Homo sapiens} SCOP: a.4.5.19

Probab=96.95  E-value=0.00052  Score=46.62  Aligned_cols=61  Identities=11%  Similarity=0.114  Sum_probs=48.5

Q ss_pred             HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchh-ccHHHHHHHHhhCCcccceeecCCceeecCcccc
Q 041256           34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAA-MTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSA  105 (244)
Q Consensus        34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~-~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~  105 (244)
                      .+-.|.+.|...   ||.|+.+||+.+|++      +. . +++.|..|...|++..... +.-.|++|+.++
T Consensus        12 ~~~~IL~~Lk~~---g~~ta~eiA~~Lgit------~~~a-Vr~hL~~Le~eGlV~~~~~-gRP~w~LT~~g~   73 (79)
T 1xmk_A           12 IKEKICDYLFNV---SDSSALNLAKNIGLT------KARD-INAVLIDMERQGDVYRQGT-TPPIWHLTDKKR   73 (79)
T ss_dssp             HHHHHHHHHHHT---CCEEHHHHHHHHCGG------GHHH-HHHHHHHHHHTTSEEEECS-SSCEEEECHHHH
T ss_pred             HHHHHHHHHHHc---CCcCHHHHHHHcCCC------cHHH-HHHHHHHHHHCCCEEecCC-CCCCeEeCHhHH
Confidence            345677888886   699999999999997      55 6 9999999999999985322 223899988764

>2bm8_A Cephalosporin hydroxylase CMCI; cephamycin biosynthesis; 2.5A {Streptomyces clavuligerus} SCOP: c.66.1.50 PDB: 2bm9_A* 2br5_A* 2br4_A* 2br3_A*

Probab=96.95  E-value=0.00072  Score=55.47  Aligned_cols=48  Identities=15%  Similarity=-0.003  Sum_probs=39.3

Q ss_pred             cceEEEecCCccHHHHHHHHH----CCCCeEEEccc-hHHhhhCCC-CCCceee
Q 041256          194 VKKLVDVGGGLGITLNMIISK----YPHIKGINYDL-PYVIKDAPS-YPGTLFI  241 (244)
Q Consensus       194 ~~~vvDVGGG~G~~~~~l~~~----~P~l~~~v~Dl-p~vi~~a~~-~~~i~~~  241 (244)
                      ..+|||||||+|..+..+++.    +|+.+++.+|+ |..++.|+. .++|+++
T Consensus        82 ~~~VLDiG~GtG~~t~~la~~~~~~~~~~~V~gvD~s~~~l~~a~~~~~~v~~~  135 (236)
T 2bm8_A           82 PRTIVELGVYNGGSLAWFRDLTKIMGIDCQVIGIDRDLSRCQIPASDMENITLH  135 (236)
T ss_dssp             CSEEEEECCTTSHHHHHHHHHHHHTTCCCEEEEEESCCTTCCCCGGGCTTEEEE
T ss_pred             CCEEEEEeCCCCHHHHHHHHhhhhcCCCCEEEEEeCChHHHHHHhccCCceEEE
Confidence            469999999999999999998    79999999998 777777754 2456554

>1i9g_A Hypothetical protein RV2118C; mtase, adoMet, crystal, structural genomics, protein structure initiative; HET: SAM; 1.98A {Mycobacterium tuberculosis} SCOP: c.66.1.13

Probab=96.94  E-value=0.00086  Score=55.87  Aligned_cols=52  Identities=13%  Similarity=0.183  Sum_probs=42.5

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHH-CCCCeEEEccc-hHHhhhCCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISK-YPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~-~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..++..++ .....+|+|||||+|.++..++++ .|..+++.+|. |..++.+++
T Consensus        89 ~~i~~~~~-~~~~~~vLdiG~G~G~~~~~l~~~~~~~~~v~~vD~~~~~~~~a~~  142 (280)
T 1i9g_A           89 AQIVHEGD-IFPGARVLEAGAGSGALTLSLLRAVGPAGQVISYEQRADHAEHARR  142 (280)
T ss_dssp             HHHHHHTT-CCTTCEEEEECCTTSHHHHHHHHHHCTTSEEEEECSCHHHHHHHHH
T ss_pred             HHHHHHcC-CCCCCEEEEEcccccHHHHHHHHHhCCCCEEEEEeCCHHHHHHHHH
Confidence            34556666 667789999999999999999996 68899999998 877776653

>4htf_A S-adenosylmethionine-dependent methyltransferase; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; HET: MSE SAM; 1.60A {Escherichia coli}

Probab=96.94  E-value=0.00047  Score=57.69  Aligned_cols=48  Identities=27%  Similarity=0.353  Sum_probs=38.3

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .++..++  .+..+|||||||.|.++..++++  +.+++.+|+ |..++.+++
T Consensus        60 ~~l~~~~--~~~~~vLDiGcG~G~~~~~l~~~--~~~v~gvD~s~~~~~~a~~  108 (285)
T 4htf_A           60 RVLAEMG--PQKLRVLDAGGGEGQTAIKMAER--GHQVILCDLSAQMIDRAKQ  108 (285)
T ss_dssp             HHHHHTC--SSCCEEEEETCTTCHHHHHHHHT--TCEEEEEESCHHHHHHHHH
T ss_pred             HHHHhcC--CCCCEEEEeCCcchHHHHHHHHC--CCEEEEEECCHHHHHHHHH
Confidence            4455554  23579999999999999999998  678999998 778877764

>3hnr_A Probable methyltransferase BT9727_4108; structural genomics, PSI-2, protein structure initiative; 2.80A {Bacillus thuringiensis serovarkonkukian}

Probab=96.92  E-value=0.00061  Score=54.49  Aligned_cols=49  Identities=14%  Similarity=0.091  Sum_probs=37.7

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+++.++ .....+|||||||.|.++..++++  +.+++.+|. |..++.+++
T Consensus        36 ~~l~~~~-~~~~~~vLDiGcG~G~~~~~l~~~--~~~v~~vD~s~~~~~~a~~   85 (220)
T 3hnr_A           36 DILEDVV-NKSFGNVLEFGVGTGNLTNKLLLA--GRTVYGIEPSREMRMIAKE   85 (220)
T ss_dssp             HHHHHHH-HTCCSEEEEECCTTSHHHHHHHHT--TCEEEEECSCHHHHHHHHH
T ss_pred             HHHHHhh-ccCCCeEEEeCCCCCHHHHHHHhC--CCeEEEEeCCHHHHHHHHH
Confidence            3344443 345689999999999999999998  668999998 777776654

>1nv8_A HEMK protein; class I adoMet-dependent methyltransferase; HET: SAM MEQ; 2.20A {Thermotoga maritima} SCOP: c.66.1.30 PDB: 1nv9_A* 1vq1_A* 1sg9_A*

Probab=96.91  E-value=0.0005  Score=58.09  Aligned_cols=41  Identities=17%  Similarity=0.176  Sum_probs=37.1

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...+|+|||||+|.++..+++. |+.+++.+|+ |..++.|++
T Consensus       123 ~~~~vLDlG~GsG~~~~~la~~-~~~~v~~vDis~~al~~A~~  164 (284)
T 1nv8_A          123 GIKTVADIGTGSGAIGVSVAKF-SDAIVFATDVSSKAVEIARK  164 (284)
T ss_dssp             TCCEEEEESCTTSHHHHHHHHH-SSCEEEEEESCHHHHHHHHH
T ss_pred             CCCEEEEEeCchhHHHHHHHHC-CCCEEEEEECCHHHHHHHHH
Confidence            3468999999999999999999 9999999999 888888864

>1iy9_A Spermidine synthase; rossmann fold, structural genomics, PSI, protein structure initiative, northeast structural genomics consortium, NESG; 2.30A {Bacillus subtilis} SCOP: c.66.1.17

Probab=96.91  E-value=0.00034  Score=58.88  Aligned_cols=42  Identities=24%  Similarity=0.273  Sum_probs=37.6

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..++|+|||||.|.++..+++++|..+++++|+ |.+++.+++
T Consensus        75 ~~~~VLdiG~G~G~~~~~l~~~~~~~~v~~vEid~~~v~~ar~  117 (275)
T 1iy9_A           75 NPEHVLVVGGGDGGVIREILKHPSVKKATLVDIDGKVIEYSKK  117 (275)
T ss_dssp             SCCEEEEESCTTCHHHHHHTTCTTCSEEEEEESCHHHHHHHHH
T ss_pred             CCCEEEEECCchHHHHHHHHhCCCCceEEEEECCHHHHHHHHH
Confidence            458999999999999999999888889999999 889888764

>3pfg_A N-methyltransferase; N,N-dimethyltransferase, SAM binding, DTDP-linked sugar BIND transferase; HET: SAM TLO; 1.35A {Streptomyces fradiae} PDB: 3pfh_A* 3px3_A* 3px2_A*

Probab=96.91  E-value=0.0012  Score=54.40  Aligned_cols=48  Identities=19%  Similarity=0.308  Sum_probs=38.3

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC-CCCceee
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS-YPGTLFI  241 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~-~~~i~~~  241 (244)
                      .+..+|||||||.|.++..++++.+  +++.+|+ |..++.+++ .++|+++
T Consensus        49 ~~~~~vLDiGcG~G~~~~~l~~~~~--~v~gvD~s~~~~~~a~~~~~~~~~~   98 (263)
T 3pfg_A           49 PKAASLLDVACGTGMHLRHLADSFG--TVEGLELSADMLAIARRRNPDAVLH   98 (263)
T ss_dssp             TTCCEEEEETCTTSHHHHHHTTTSS--EEEEEESCHHHHHHHHHHCTTSEEE
T ss_pred             CCCCcEEEeCCcCCHHHHHHHHcCC--eEEEEECCHHHHHHHHhhCCCCEEE
Confidence            3458999999999999999999865  6888898 888888765 3455544

>2yqz_A Hypothetical protein TTHA0223; RNA methyltransferase, SAM, structural genomics, NPPSFA; HET: SAM; 1.80A {Thermus thermophilus} PDB: 2yr0_A

Probab=96.91  E-value=0.00098  Score=54.68  Aligned_cols=41  Identities=15%  Similarity=0.148  Sum_probs=34.1

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~  233 (244)
                      .....+|+|||||.|.++..++++  +.+++.+|. |..++.++
T Consensus        37 ~~~~~~vLDiG~G~G~~~~~l~~~--~~~v~~vD~s~~~~~~a~   78 (263)
T 2yqz_A           37 KGEEPVFLELGVGTGRIALPLIAR--GYRYIALDADAAMLEVFR   78 (263)
T ss_dssp             SSSCCEEEEETCTTSTTHHHHHTT--TCEEEEEESCHHHHHHHH
T ss_pred             CCCCCEEEEeCCcCCHHHHHHHHC--CCEEEEEECCHHHHHHHH
Confidence            556789999999999999999987  567888998 67776654

>1qbj_A Protein (double-stranded RNA specific adenosine D (ADAR1)); protein-Z-DNA complex, hydrolase-DNA complex; HET: DNA; 2.10A {Homo sapiens} SCOP: a.4.5.19 PDB: 3f21_A* 3f22_A* 3f23_A* 3irr_A* 3irq_D* 2gxb_A 2acj_A 2l54_A

Probab=96.91  E-value=0.0011  Score=45.23  Aligned_cols=68  Identities=15%  Similarity=0.252  Sum_probs=47.1

Q ss_pred             HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcccccccc
Q 041256           34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFVR  109 (244)
Q Consensus        34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l~~  109 (244)
                      .+..|.+.|.+.+++.++|+.|||+++|++      ... +.+.|.-|...|++.... ..++.|...+....+..
T Consensus        11 ~~~~IL~~L~~~~pg~~~t~~eLA~~Lgvs------r~t-V~~~L~~Le~~G~I~~~g-~~~~~W~i~~~~~~~~~   78 (81)
T 1qbj_A           11 QEQRILKFLEELGEGKATTAHDLSGKLGTP------KKE-INRVLYSLAKKGKLQKEA-GTPPLWKIAVSTQAWNQ   78 (81)
T ss_dssp             HHHHHHHHHHHHCTTCCBCHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEEES-SSSCEEEEC--------
T ss_pred             HHHHHHHHHHHcCCCCCcCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEecC-CCCCeeEEeCcHHhccC
Confidence            455678888886433479999999999996      445 999999999999998632 23578888877665543

>3ftd_A Dimethyladenosine transferase; KSGA, rossmann-like fold, RNA methyltransferase, mtase, anti resistance, methyltransferase, RNA-binding; 1.44A {Aquifex aeolicus} PDB: 3ftc_A 3fte_A 3ftf_A* 3r9x_B*

Probab=96.91  E-value=0.0012  Score=54.67  Aligned_cols=52  Identities=25%  Similarity=0.405  Sum_probs=41.7

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPSY  235 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~~  235 (244)
                      ..+++..+ .....+|+|||||.|.++..++++ +..+++.+|+ |..++.+++.
T Consensus        21 ~~iv~~~~-~~~~~~VLDiG~G~G~lt~~L~~~-~~~~v~avEid~~~~~~~~~~   73 (249)
T 3ftd_A           21 KKIAEELN-IEEGNTVVEVGGGTGNLTKVLLQH-PLKKLYVIELDREMVENLKSI   73 (249)
T ss_dssp             HHHHHHTT-CCTTCEEEEEESCHHHHHHHHTTS-CCSEEEEECCCHHHHHHHTTS
T ss_pred             HHHHHhcC-CCCcCEEEEEcCchHHHHHHHHHc-CCCeEEEEECCHHHHHHHHhc
Confidence            45566665 566689999999999999999987 5678899998 7777777654

>3ntv_A MW1564 protein; rossmann fold, putative methyltransferase, transferase; HET: MSE; 1.55A {Staphylococcus aureus}

Probab=96.89  E-value=0.00046  Score=56.28  Aligned_cols=43  Identities=19%  Similarity=0.264  Sum_probs=38.5

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+..+|||||||.|..+..+++.+|+.+++.+|+ |..++.|++
T Consensus        70 ~~~~~vLDiG~G~G~~~~~la~~~~~~~v~~vD~~~~~~~~a~~  113 (232)
T 3ntv_A           70 NNVKNILEIGTAIGYSSMQFASISDDIHVTTIERNETMIQYAKQ  113 (232)
T ss_dssp             HTCCEEEEECCSSSHHHHHHHTTCTTCEEEEEECCHHHHHHHHH
T ss_pred             cCCCEEEEEeCchhHHHHHHHHhCCCCEEEEEECCHHHHHHHHH
Confidence            4568999999999999999999999999999998 888887764

>3gnl_A Uncharacterized protein, DUF633, LMOF2365_1472; structural genomics, PSI-2, protein structure initiative; 1.50A {Listeria monocytogenes str}

Probab=96.89  E-value=0.00038  Score=57.66  Aligned_cols=43  Identities=9%  Similarity=0.105  Sum_probs=38.2

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+..+|+|||||+|.+++.+++..|..+++..|. |..++.|++
T Consensus        20 ~~g~~VlDIGtGsG~l~i~la~~~~~~~V~avDi~~~al~~A~~   63 (244)
T 3gnl_A           20 TKNERIADIGSDHAYLPCFAVKNQTASFAIAGEVVDGPFQSAQK   63 (244)
T ss_dssp             CSSEEEEEETCSTTHHHHHHHHTTSEEEEEEEESSHHHHHHHHH
T ss_pred             CCCCEEEEECCccHHHHHHHHHhCCCCEEEEEECCHHHHHHHHH
Confidence            3457999999999999999999999999999998 788888764

>3tfw_A Putative O-methyltransferase; PSI-biology, nysgrc, structural genomics, NEW YORK structura genomics research consortium; 1.88A {Klebsiella pneumoniae subsp}

Probab=96.88  E-value=0.00052  Score=56.59  Aligned_cols=43  Identities=12%  Similarity=0.159  Sum_probs=38.2

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCC-CCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYP-HIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+..+|||||||.|..+..+++.+| +.+++.+|+ |..++.|++
T Consensus        62 ~~~~~VLdiG~G~G~~~~~la~~~~~~~~v~~vD~s~~~~~~a~~  106 (248)
T 3tfw_A           62 TQAKRILEIGTLGGYSTIWMARELPADGQLLTLEADAHHAQVARE  106 (248)
T ss_dssp             HTCSEEEEECCTTSHHHHHHHTTSCTTCEEEEEECCHHHHHHHHH
T ss_pred             cCCCEEEEecCCchHHHHHHHHhCCCCCEEEEEECCHHHHHHHHH
Confidence            4568999999999999999999998 899999999 888887764

>2pjd_A Ribosomal RNA small subunit methyltransferase C; gene duplication, RNA modification, SAM binding; 2.10A {Escherichia coli}

Probab=96.88  E-value=0.00051  Score=59.51  Aligned_cols=52  Identities=19%  Similarity=0.279  Sum_probs=42.2

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+++.++ .....+|+|||||.|.++..+++++|+.+++.+|. |..++.+++
T Consensus       186 ~~ll~~l~-~~~~~~VLDlGcG~G~~~~~la~~~~~~~v~~vD~s~~~l~~a~~  238 (343)
T 2pjd_A          186 QLLLSTLT-PHTKGKVLDVGCGAGVLSVAFARHSPKIRLTLCDVSAPAVEASRA  238 (343)
T ss_dssp             HHHHHHSC-TTCCSBCCBTTCTTSHHHHHHHHHCTTCBCEEEESBHHHHHHHHH
T ss_pred             HHHHHhcC-cCCCCeEEEecCccCHHHHHHHHHCCCCEEEEEECCHHHHHHHHH
Confidence            44566664 34457899999999999999999999999999999 667777654

>1y0u_A Arsenical resistance operon repressor, putative; structural genomics, protein structure initiative, PSI; HET: MSE; 1.60A {Archaeoglobus fulgidus} SCOP: a.4.5.5

Probab=96.87  E-value=0.0011  Score=46.50  Aligned_cols=62  Identities=16%  Similarity=0.215  Sum_probs=49.6

Q ss_pred             HHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcccc
Q 041256           28 AVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSA  105 (244)
Q Consensus        28 ~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~  105 (244)
                      .++..-.++.|+..| .    ++.|..|||+.++++      ... +.+.|+.|...|++.+   .. +.|++++.+.
T Consensus        26 ~~l~~~~r~~Il~~L-~----~~~~~~eLa~~l~is------~~t-v~~~L~~L~~~Glv~~---~~-g~y~l~~~g~   87 (96)
T 1y0u_A           26 YAVTNPVRRKILRML-D----KGRSEEEIMQTLSLS------KKQ-LDYHLKVLEAGFCIER---VG-ERWVVTDAGK   87 (96)
T ss_dssp             HHHSCHHHHHHHHHH-H----TTCCHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEE---ET-TEEEECTTTC
T ss_pred             HHhCCHHHHHHHHHH-c----CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEE---EC-CEEEECCCch
Confidence            344444567788888 5    689999999999997      455 9999999999999995   33 6899988754

>1qam_A ERMC' methyltransferase; rRNA methyltransferase ERMC', cofactor analogs; 2.20A {Bacillus subtilis} SCOP: c.66.1.24 PDB: 1qan_A* 1qao_A* 1qaq_A* 2erc_A

Probab=96.87  E-value=0.0013  Score=54.16  Aligned_cols=50  Identities=10%  Similarity=0.254  Sum_probs=39.5

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+++..+ .....+|+|||||.|.++..++++.  .+++.+|+ |..++.+++
T Consensus        20 ~~i~~~~~-~~~~~~VLDiG~G~G~lt~~l~~~~--~~v~~vD~~~~~~~~a~~   70 (244)
T 1qam_A           20 DKIMTNIR-LNEHDNIFEIGSGKGHFTLELVQRC--NFVTAIEIDHKLCKTTEN   70 (244)
T ss_dssp             HHHHTTCC-CCTTCEEEEECCTTSHHHHHHHHHS--SEEEEECSCHHHHHHHHH
T ss_pred             HHHHHhCC-CCCCCEEEEEeCCchHHHHHHHHcC--CeEEEEECCHHHHHHHHH
Confidence            45566665 5666899999999999999999997  67888888 777766553

>3q87_B N6 adenine specific DNA methylase; SAM-methyltransferase, methyltransferase, methylation, trans activator-transferase complex; HET: SAM; 2.00A {Encephalitozoon cuniculi}

Probab=96.86  E-value=0.0011  Score=51.35  Aligned_cols=36  Identities=17%  Similarity=0.326  Sum_probs=31.0

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhh
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKD  231 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~  231 (244)
                      ...+|+|||||+|.++..++++.   +++.+|+ |..++.
T Consensus        23 ~~~~vLD~GcG~G~~~~~l~~~~---~v~gvD~s~~~~~~   59 (170)
T 3q87_B           23 EMKIVLDLGTSTGVITEQLRKRN---TVVSTDLNIRALES   59 (170)
T ss_dssp             CSCEEEEETCTTCHHHHHHTTTS---EEEEEESCHHHHHT
T ss_pred             CCCeEEEeccCccHHHHHHHhcC---cEEEEECCHHHHhc
Confidence            34699999999999999999988   8899998 666665

>3iv6_A Putative Zn-dependent alcohol dehydrogenase; alpha/beta fold, rossmann-fold, structural genomics, PSI-2, structure initiative; HET: SAM; 2.70A {Rhodobacter sphaeroides}

Probab=96.85  E-value=0.00078  Score=56.35  Aligned_cols=50  Identities=8%  Similarity=0.083  Sum_probs=39.5

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+++..+ .....+|+|||||+|.++..++++  ..+++.+|+ |..++.+++
T Consensus        35 ~~il~~l~-l~~g~~VLDlGcGtG~~a~~La~~--g~~V~gvD~S~~ml~~Ar~   85 (261)
T 3iv6_A           35 ENDIFLEN-IVPGSTVAVIGASTRFLIEKALER--GASVTVFDFSQRMCDDLAE   85 (261)
T ss_dssp             HHHHHTTT-CCTTCEEEEECTTCHHHHHHHHHT--TCEEEEEESCHHHHHHHHH
T ss_pred             HHHHHhcC-CCCcCEEEEEeCcchHHHHHHHhc--CCEEEEEECCHHHHHHHHH
Confidence            34555565 666789999999999999999987  457889998 777777653

>3lec_A NADB-rossmann superfamily protein; PSI, MCSG, structural genomics, midwest CENT structural genomics, protein structure initiative; 1.80A {Streptococcus agalactiae}

Probab=96.84  E-value=0.00044  Score=56.74  Aligned_cols=43  Identities=14%  Similarity=0.015  Sum_probs=38.2

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+..+|+|||||+|.+++.+++..|..+++..|. |..++.|++
T Consensus        20 ~~g~~VlDIGtGsG~l~i~la~~~~~~~V~AvDi~~~al~~A~~   63 (230)
T 3lec_A           20 PKGARLLDVGSDHAYLPIFLLQMGYCDFAIAGEVVNGPYQSALK   63 (230)
T ss_dssp             CTTEEEEEETCSTTHHHHHHHHTTCEEEEEEEESSHHHHHHHHH
T ss_pred             CCCCEEEEECCchHHHHHHHHHhCCCCEEEEEECCHHHHHHHHH
Confidence            3458999999999999999999999999999998 788888764

>2p7i_A Hypothetical protein; putative methyltransferase, structural genomics, joint cente structural genomics, JCSG; 1.74A {Pectobacterium atrosepticum SCRI1043} SCOP: c.66.1.41 PDB: 2p7h_A

Probab=96.82  E-value=0.00066  Score=55.00  Aligned_cols=40  Identities=13%  Similarity=0.093  Sum_probs=33.0

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...+|||||||.|.++..++++++  +++.+|+ |..++.+++
T Consensus        42 ~~~~vLDiGcG~G~~~~~l~~~~~--~v~gvD~s~~~~~~a~~   82 (250)
T 2p7i_A           42 RPGNLLELGSFKGDFTSRLQEHFN--DITCVEASEEAISHAQG   82 (250)
T ss_dssp             CSSCEEEESCTTSHHHHHHTTTCS--CEEEEESCHHHHHHHHH
T ss_pred             CCCcEEEECCCCCHHHHHHHHhCC--cEEEEeCCHHHHHHHHH
Confidence            446899999999999999999988  5777787 677776654

>4fsd_A Arsenic methyltransferase; rossmann fold; 1.75A {Cyanidioschyzon SP} PDB: 4fr0_A* 4fs8_A 3p7e_A 3qnh_A 3qhu_A

Probab=96.81  E-value=0.00071  Score=59.51  Aligned_cols=42  Identities=21%  Similarity=0.234  Sum_probs=37.2

Q ss_pred             CcceEEEecCCccHHHHHHHHHC-CCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKY-PHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...+|||||||+|.++..+++.+ |+.+++.+|+ |..++.+++
T Consensus        83 ~~~~VLDlGcG~G~~~~~la~~~~~~~~v~gvD~s~~~l~~a~~  126 (383)
T 4fsd_A           83 EGATVLDLGCGTGRDVYLASKLVGEHGKVIGVDMLDNQLEVARK  126 (383)
T ss_dssp             TTCEEEEESCTTSHHHHHHHHHHTTTCEEEEEECCHHHHHHHHH
T ss_pred             CCCEEEEecCccCHHHHHHHHHhCCCCEEEEEECCHHHHHHHHH
Confidence            45799999999999999999997 8999999999 778877764

>3dou_A Ribosomal RNA large subunit methyltransferase J; cell division, structural genomics, protein structure initiative, PSI; HET: SAM; 1.45A {Thermoplasma volcanium} SCOP: c.66.1.0

Probab=96.81  E-value=0.0014  Score=51.86  Aligned_cols=44  Identities=23%  Similarity=0.265  Sum_probs=35.8

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccchH
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPY  227 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~  227 (244)
                      ..+.+.|..+....+|||+|||+|.++..++++  ..+++.+|+-+
T Consensus        14 ~ei~~~~~~~~~g~~VLDlG~G~G~~s~~la~~--~~~V~gvD~~~   57 (191)
T 3dou_A           14 EFLLDRYRVVRKGDAVIEIGSSPGGWTQVLNSL--ARKIISIDLQE   57 (191)
T ss_dssp             HHHHHHHCCSCTTCEEEEESCTTCHHHHHHTTT--CSEEEEEESSC
T ss_pred             HHHHHHcCCCCCCCEEEEEeecCCHHHHHHHHc--CCcEEEEeccc
Confidence            456666664566789999999999999999988  77889999843

>2h00_A Methyltransferase 10 domain containing protein; structural genomics, structural genomics consortium, SGC; HET: SAH; 2.00A {Homo sapiens} SCOP: c.66.1.54

Probab=96.80  E-value=0.00049  Score=56.63  Aligned_cols=42  Identities=10%  Similarity=0.146  Sum_probs=37.5

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...+|+|||||+|.++..+++++|+.+++.+|+ |..++.|++
T Consensus        65 ~~~~vLDlG~G~G~~~~~la~~~~~~~v~gvD~s~~~~~~a~~  107 (254)
T 2h00_A           65 TLRRGIDIGTGASCIYPLLGATLNGWYFLATEVDDMCFNYAKK  107 (254)
T ss_dssp             CCCEEEEESCTTTTHHHHHHHHHHCCEEEEEESCHHHHHHHHH
T ss_pred             CCCEEEEeCCChhHHHHHHHHhCCCCeEEEEECCHHHHHHHHH
Confidence            457999999999999999999999999999998 888887764

>2fhp_A Methylase, putative; alpha-beta-alpha sandwich, structural genomics, PSI, protein structure initiative; HET: MSE; 1.60A {Enterococcus faecalis} SCOP: c.66.1.46

Probab=96.80  E-value=0.0016  Score=50.49  Aligned_cols=43  Identities=16%  Similarity=-0.026  Sum_probs=35.9

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .....+|+|+|||.|.++..+++ .+..+++.+|+ |..++.+++
T Consensus        42 ~~~~~~vLD~GcG~G~~~~~~~~-~~~~~v~~vD~~~~~~~~a~~   85 (187)
T 2fhp_A           42 YFDGGMALDLYSGSGGLAIEAVS-RGMDKSICIEKNFAALKVIKE   85 (187)
T ss_dssp             CCSSCEEEETTCTTCHHHHHHHH-TTCSEEEEEESCHHHHHHHHH
T ss_pred             hcCCCCEEEeCCccCHHHHHHHH-cCCCEEEEEECCHHHHHHHHH
Confidence            34557999999999999999887 56778999999 888887764

>1o54_A SAM-dependent O-methyltransferase; TM0748, structural genomi PSI, protein structure initiative, joint center for structu genomics; 1.65A {Thermotoga maritima} SCOP: c.66.1.13

Probab=96.80  E-value=0.0015  Score=54.47  Aligned_cols=52  Identities=17%  Similarity=0.146  Sum_probs=43.5

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHH-CCCCeEEEccc-hHHhhhCCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISK-YPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~-~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..++..++ +....+|||+|||+|.++..++++ .|..+++.+|. |..++.+++
T Consensus       102 ~~i~~~~~-~~~~~~VLDiG~G~G~~~~~la~~~~~~~~v~~vD~s~~~~~~a~~  155 (277)
T 1o54_A          102 SFIAMMLD-VKEGDRIIDTGVGSGAMCAVLARAVGSSGKVFAYEKREEFAKLAES  155 (277)
T ss_dssp             HHHHHHTT-CCTTCEEEEECCTTSHHHHHHHHHTTTTCEEEEECCCHHHHHHHHH
T ss_pred             HHHHHHhC-CCCCCEEEEECCcCCHHHHHHHHHhCCCcEEEEEECCHHHHHHHHH
Confidence            34556666 667789999999999999999999 78999999998 888877764

>2yxe_A Protein-L-isoaspartate O-methyltransferase; rossman-type fold, alpha/beta/alpha sandwich structure, STRU genomics, NPPSFA; 2.00A {Methanocaldococcus jannaschii}

Probab=96.80  E-value=0.0011  Score=52.86  Aligned_cols=51  Identities=14%  Similarity=0.170  Sum_probs=41.0

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHC-CCCeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKY-PHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+++.+. .....+|+|||||.|.++..+++.. |+.+++.+|. |..++.+++
T Consensus        68 ~~~~~~~-~~~~~~vLdiG~G~G~~~~~l~~~~~~~~~v~~vD~~~~~~~~a~~  120 (215)
T 2yxe_A           68 MMCELLD-LKPGMKVLEIGTGCGYHAAVTAEIVGEDGLVVSIERIPELAEKAER  120 (215)
T ss_dssp             HHHHHTT-CCTTCEEEEECCTTSHHHHHHHHHHCTTSEEEEEESCHHHHHHHHH
T ss_pred             HHHHhhC-CCCCCEEEEECCCccHHHHHHHHHhCCCCEEEEEeCCHHHHHHHHH
Confidence            3444454 5666899999999999999999988 7789999998 777777654

>1g8a_A Fibrillarin-like PRE-rRNA processing protein; rRNA binding, RNA binding, structural genomics, BSGC structure funded by NIH; 1.40A {Pyrococcus horikoshii} SCOP: c.66.1.3 PDB: 2nnw_B 3nmu_F* 3nvk_I* 3nvm_B 1pry_A

Probab=96.80  E-value=0.0013  Score=53.12  Aligned_cols=51  Identities=16%  Similarity=0.097  Sum_probs=38.1

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHC-CCCeEEEccc-hHHhh----hCCCCCCceee
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKY-PHIKGINYDL-PYVIK----DAPSYPGTLFI  241 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~vi~----~a~~~~~i~~~  241 (244)
                      +....+|+|+|||+|.++..++++. |+.+++.+|. |..++    .+++.++|+++
T Consensus        71 ~~~~~~vLDlG~G~G~~~~~la~~~~~~~~v~~vD~s~~~~~~~~~~~~~~~~v~~~  127 (227)
T 1g8a_A           71 IKPGKSVLYLGIASGTTASHVSDIVGWEGKIFGIEFSPRVLRELVPIVEERRNIVPI  127 (227)
T ss_dssp             CCTTCEEEEETTTSTTHHHHHHHHHCTTSEEEEEESCHHHHHHHHHHHSSCTTEEEE
T ss_pred             CCCCCEEEEEeccCCHHHHHHHHHhCCCeEEEEEECCHHHHHHHHHHHhccCCCEEE
Confidence            4566799999999999999999985 6788999998 54333    33334566553

>3bxo_A N,N-dimethyltransferase; desosamine, sugar, carbohydrate, antibiotic, SAM, adoMet; HET: SAM UPP; 2.00A {Streptomyces venezuelae}

Probab=96.78  E-value=0.00079  Score=54.43  Aligned_cols=48  Identities=19%  Similarity=0.335  Sum_probs=38.4

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC-CCCceee
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS-YPGTLFI  241 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~-~~~i~~~  241 (244)
                      .+..+|+|||||.|.++..++++++  +++.+|+ |..++.+++ .++++++
T Consensus        39 ~~~~~vLdiG~G~G~~~~~l~~~~~--~v~~~D~s~~~~~~a~~~~~~~~~~   88 (239)
T 3bxo_A           39 PEASSLLDVACGTGTHLEHFTKEFG--DTAGLELSEDMLTHARKRLPDATLH   88 (239)
T ss_dssp             TTCCEEEEETCTTSHHHHHHHHHHS--EEEEEESCHHHHHHHHHHCTTCEEE
T ss_pred             CCCCeEEEecccCCHHHHHHHHhCC--cEEEEeCCHHHHHHHHHhCCCCEEE
Confidence            4558999999999999999999987  7888998 888877764 3455543

>3bwc_A Spermidine synthase; SAM, SGPP, structura genomics, PSI, protein structure initiative, structural GEN pathogenic protozoa consortium; HET: MSE SAM; 2.30A {Trypanosoma cruzi} PDB: 3bwb_A*

Probab=96.78  E-value=0.00059  Score=58.21  Aligned_cols=43  Identities=16%  Similarity=0.200  Sum_probs=38.0

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ....+|+|||||.|.++..+++..|..+++.+|+ |.+++.+++
T Consensus        94 ~~~~~VLdiG~G~G~~~~~l~~~~~~~~v~~vDid~~~i~~a~~  137 (304)
T 3bwc_A           94 PKPERVLIIGGGDGGVLREVLRHGTVEHCDLVDIDGEVMEQSKQ  137 (304)
T ss_dssp             SSCCEEEEEECTTSHHHHHHHTCTTCCEEEEEESCHHHHHHHHH
T ss_pred             CCCCeEEEEcCCCCHHHHHHHhCCCCCEEEEEECCHHHHHHHHH
Confidence            4568999999999999999999888899999999 888887764

>3lbf_A Protein-L-isoaspartate O-methyltransferase; modified rossman-type fold, S-adenosyl-L- methionine; HET: SAH; 1.80A {Escherichia coli}

Probab=96.78  E-value=0.002  Score=51.20  Aligned_cols=49  Identities=10%  Similarity=0.140  Sum_probs=39.4

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+++.++ .....+|+|||||.|.++..+++.  ..+++.+|. |..++.+++
T Consensus        68 ~~~~~l~-~~~~~~vLdiG~G~G~~~~~la~~--~~~v~~vD~~~~~~~~a~~  117 (210)
T 3lbf_A           68 RMTELLE-LTPQSRVLEIGTGSGYQTAILAHL--VQHVCSVERIKGLQWQARR  117 (210)
T ss_dssp             HHHHHTT-CCTTCEEEEECCTTSHHHHHHHHH--SSEEEEEESCHHHHHHHHH
T ss_pred             HHHHhcC-CCCCCEEEEEcCCCCHHHHHHHHh--CCEEEEEecCHHHHHHHHH
Confidence            3445555 567789999999999999999998  678899998 777777764

>1u2z_A Histone-lysine N-methyltransferase, H3 lysine-79 specific; histone methyltransferase, nucleosome; HET: SAH; 2.20A {Saccharomyces cerevisiae} SCOP: c.66.1.31

Probab=96.78  E-value=0.0015  Score=58.63  Aligned_cols=49  Identities=10%  Similarity=0.173  Sum_probs=40.1

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDA  232 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a  232 (244)
                      .+++.++ .....+|||||||.|.++..+++.+|..+++.+|+ |..++.|
T Consensus       233 ~ml~~l~-l~~g~~VLDLGCGsG~la~~LA~~~g~~~V~GVDis~~~l~~A  282 (433)
T 1u2z_A          233 DVYQQCQ-LKKGDTFMDLGSGVGNCVVQAALECGCALSFGCEIMDDASDLT  282 (433)
T ss_dssp             HHHHHTT-CCTTCEEEEESCTTSHHHHHHHHHHCCSEEEEEECCHHHHHHH
T ss_pred             HHHHhcC-CCCCCEEEEeCCCcCHHHHHHHHHCCCCEEEEEeCCHHHHHHH
Confidence            4455555 66778999999999999999999999889999998 5555555

>3uwp_A Histone-lysine N-methyltransferase, H3 lysine-79; epigenetics, tubercidin, structu genomics, structural genomics consortium, SGC; HET: 5ID; 2.05A {Homo sapiens} PDB: 4eqz_A* 3sx0_A* 4er0_A* 4er7_A* 1nw3_A* 4er6_A* 4er5_A* 3qow_A* 3qox_A* 4ek9_A* 4ekg_A* 4eki_A* 4er3_A* 3sr4_A*

Probab=96.78  E-value=0.0016  Score=57.95  Aligned_cols=51  Identities=16%  Similarity=0.211  Sum_probs=41.2

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~  233 (244)
                      ..+++.++ .....+|+|||||.|.++..++..++.-+++.+|+ |..++.|+
T Consensus       163 ~~il~~l~-l~~gd~VLDLGCGtG~l~l~lA~~~g~~kVvGIDiS~~~lelAr  214 (438)
T 3uwp_A          163 AQMIDEIK-MTDDDLFVDLGSGVGQVVLQVAAATNCKHHYGVEKADIPAKYAE  214 (438)
T ss_dssp             HHHHHHHC-CCTTCEEEEESCTTSHHHHHHHHHCCCSEEEEEECCHHHHHHHH
T ss_pred             HHHHHhcC-CCCCCEEEEeCCCCCHHHHHHHHHCCCCEEEEEeCCHHHHHHHH
Confidence            34556566 67778999999999999999999998878999999 55665554

>3b73_A PHIH1 repressor-like protein; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 2.12A {Haloarcula marismortui atcc 43049}

Probab=96.77  E-value=0.0011  Score=48.09  Aligned_cols=63  Identities=16%  Similarity=0.229  Sum_probs=51.6

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhC--CCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccccccccC
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQI--PLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFVRN  110 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~--~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l~~~  110 (244)
                      +..|++.|.+.   |++|+.+||+.+  +++      +.. +.+-|+.|...|+++.   .+.+.|++|+.+..+...
T Consensus        15 d~~IL~~L~~~---g~~s~~eLA~~l~~giS------~~a-Vs~rL~~Le~~GLV~~---~~rg~Y~LT~~G~~~l~~   79 (111)
T 3b73_A           15 DDRILEIIHEE---GNGSPKELEDRDEIRIS------KSS-VSRRLKKLADHDLLQP---LANGVYVITEEGEAYLNG   79 (111)
T ss_dssp             HHHHHHHHHHH---SCBCHHHHHTSTTCCSC------HHH-HHHHHHHHHHTTSEEE---CSTTCEEECHHHHHHHTT
T ss_pred             HHHHHHHHHHc---CCCCHHHHHHHHhcCCC------HHH-HHHHHHHHHHCCCEEe---cCCceEEECchHHHHHHH
Confidence            45678888775   699999999999  887      567 9999999999999995   244689999998755444

>3g2m_A PCZA361.24; SAM-dependent methyltransferase, glycopeptide antibiotics biosynthesis, structural genomics; 2.00A {Amycolatopsis orientalis} PDB: 3g2o_A* 3g2p_A* 3g2q_A*

Probab=96.77  E-value=0.0007  Score=57.15  Aligned_cols=50  Identities=8%  Similarity=0.042  Sum_probs=39.1

Q ss_pred             HHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          181 MEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       181 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...+++.++ . ...+|||||||.|.++..++++  +.+++.+|+ |..++.+++
T Consensus        72 ~~~~~~~~~-~-~~~~vLDlGcG~G~~~~~l~~~--~~~v~gvD~s~~~~~~a~~  122 (299)
T 3g2m_A           72 AREFATRTG-P-VSGPVLELAAGMGRLTFPFLDL--GWEVTALELSTSVLAAFRK  122 (299)
T ss_dssp             HHHHHHHHC-C-CCSCEEEETCTTTTTHHHHHTT--TCCEEEEESCHHHHHHHHH
T ss_pred             HHHHHHhhC-C-CCCcEEEEeccCCHHHHHHHHc--CCeEEEEECCHHHHHHHHH
Confidence            345566655 2 3349999999999999999998  567899998 788887764

>3duw_A OMT, O-methyltransferase, putative; alternating of alpha and beta with complex SAH; HET: SAH; 1.20A {Bacillus cereus} PDB: 3dul_A*

Probab=96.76  E-value=0.00071  Score=54.42  Aligned_cols=43  Identities=9%  Similarity=0.064  Sum_probs=37.8

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCC-CCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYP-HIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ....+|+|||||.|..+..+++++| +.+++.+|+ |..++.+++
T Consensus        57 ~~~~~vLdiG~G~G~~~~~la~~~~~~~~v~~vD~~~~~~~~a~~  101 (223)
T 3duw_A           57 QGARNILEIGTLGGYSTIWLARGLSSGGRVVTLEASEKHADIARS  101 (223)
T ss_dssp             HTCSEEEEECCTTSHHHHHHHTTCCSSCEEEEEESCHHHHHHHHH
T ss_pred             hCCCEEEEecCCccHHHHHHHHhCCCCCEEEEEECCHHHHHHHHH
Confidence            4558999999999999999999999 789999998 888877753

>2xvm_A Tellurite resistance protein TEHB; antibiotic resistance, transferase; HET: SAH; 1.48A {Escherichia coli} PDB: 2xva_A* 4dq0_A* 2i6g_A*

Probab=96.76  E-value=0.0015  Score=51.06  Aligned_cols=49  Identities=22%  Similarity=0.240  Sum_probs=39.0

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+++.++ .....+|+|||||.|.++..++++  +.+++.+|. |..++.+++
T Consensus        23 ~l~~~~~-~~~~~~vLdiG~G~G~~~~~l~~~--~~~v~~vD~s~~~~~~a~~   72 (199)
T 2xvm_A           23 EVLEAVK-VVKPGKTLDLGCGNGRNSLYLAAN--GYDVDAWDKNAMSIANVER   72 (199)
T ss_dssp             HHHHHTT-TSCSCEEEEETCTTSHHHHHHHHT--TCEEEEEESCHHHHHHHHH
T ss_pred             HHHHHhh-ccCCCeEEEEcCCCCHHHHHHHHC--CCeEEEEECCHHHHHHHHH
Confidence            4455555 455679999999999999999988  668999998 777777654

>3h2b_A SAM-dependent methyltransferase; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; HET: SAH; 2.00A {Corynebacterium glutamicum atcc 13032}

Probab=96.76  E-value=0.00082  Score=53.08  Aligned_cols=46  Identities=20%  Similarity=0.167  Sum_probs=37.1

Q ss_pred             cceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC-CCCceee
Q 041256          194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS-YPGTLFI  241 (244)
Q Consensus       194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~-~~~i~~~  241 (244)
                      ..+|||||||.|.++..++++  +.+++.+|+ |..++.+++ .++|+++
T Consensus        42 ~~~vLDiGcG~G~~~~~l~~~--~~~v~gvD~s~~~~~~a~~~~~~~~~~   89 (203)
T 3h2b_A           42 DGVILDVGSGTGRWTGHLASL--GHQIEGLEPATRLVELARQTHPSVTFH   89 (203)
T ss_dssp             CSCEEEETCTTCHHHHHHHHT--TCCEEEECCCHHHHHHHHHHCTTSEEE
T ss_pred             CCeEEEecCCCCHHHHHHHhc--CCeEEEEeCCHHHHHHHHHhCCCCeEE
Confidence            478999999999999999998  558899998 777777765 4555554

>1o9g_A RRNA methyltransferase; antibiotic resistance, Se-MAD; 1.5A {Streptomyces viridochromogenes} SCOP: c.66.1.29 PDB: 1o9h_A

Probab=96.75  E-value=0.00088  Score=55.05  Aligned_cols=50  Identities=20%  Similarity=0.088  Sum_probs=40.5

Q ss_pred             HHhhcCCCCCcceEEEecCCccHHHHHHHHH--CCCCeEEEccc-hHHhhhCCC
Q 041256          184 VLESYKGFEHVKKLVDVGGGLGITLNMIISK--YPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       184 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~--~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      +++.++ -....+|+|+|||+|.++..+++.  +|..+++.+|+ |..++.|++
T Consensus        43 ~l~~~~-~~~~~~vLD~gcGsG~~~~~la~~~~~~~~~v~gvDis~~~l~~A~~   95 (250)
T 1o9g_A           43 ALARLP-GDGPVTLWDPCCGSGYLLTVLGLLHRRSLRQVIASDVDPAPLELAAK   95 (250)
T ss_dssp             HHHTSS-CCSCEEEEETTCTTSHHHHHHHHHTGGGEEEEEEEESCHHHHHHHHH
T ss_pred             HHHhcc-cCCCCeEEECCCCCCHHHHHHHHHhccCCCeEEEEECCHHHHHHHHH
Confidence            344443 235579999999999999999998  88889999999 888888763

>1dus_A MJ0882; hypothetical protein, methanococcus jannaschii, structural genomics, BSGC structure funded by NIH; 1.80A {Methanocaldococcus jannaschii} SCOP: c.66.1.4

Probab=96.75  E-value=0.0014  Score=50.78  Aligned_cols=49  Identities=18%  Similarity=0.219  Sum_probs=39.8

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+++.++ .....+|+|||||.|.++..++++  ..+++.+|+ |..++.+++
T Consensus        43 ~l~~~~~-~~~~~~vLdiG~G~G~~~~~~~~~--~~~v~~~D~~~~~~~~a~~   92 (194)
T 1dus_A           43 ILVENVV-VDKDDDILDLGCGYGVIGIALADE--VKSTTMADINRRAIKLAKE   92 (194)
T ss_dssp             HHHHHCC-CCTTCEEEEETCTTSHHHHHHGGG--SSEEEEEESCHHHHHHHHH
T ss_pred             HHHHHcc-cCCCCeEEEeCCCCCHHHHHHHHc--CCeEEEEECCHHHHHHHHH
Confidence            4455555 566689999999999999999998  778999998 777777654

>3m33_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, MCSG, midwest center for structural genomics; 2.19A {Deinococcus radiodurans}

Probab=96.74  E-value=0.00093  Score=54.03  Aligned_cols=48  Identities=19%  Similarity=0.257  Sum_probs=38.6

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC-CCCceee
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS-YPGTLFI  241 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~-~~~i~~~  241 (244)
                      ....+|+|||||+|.++..++++  +.+++.+|+ |..++.+++ .++|+++
T Consensus        47 ~~~~~vLDiGcG~G~~~~~l~~~--~~~v~~vD~s~~~~~~a~~~~~~~~~~   96 (226)
T 3m33_A           47 TPQTRVLEAGCGHGPDAARFGPQ--AARWAAYDFSPELLKLARANAPHADVY   96 (226)
T ss_dssp             CTTCEEEEESCTTSHHHHHHGGG--SSEEEEEESCHHHHHHHHHHCTTSEEE
T ss_pred             CCCCeEEEeCCCCCHHHHHHHHc--CCEEEEEECCHHHHHHHHHhCCCceEE
Confidence            44579999999999999999998  568999998 788877765 3555554

>1xj5_A Spermidine synthase 1; structural genomics, protein structure initiative, CESG, AT1G23820, putrescine aminopropyl transferase, SPDS1; 2.70A {Arabidopsis thaliana} SCOP: c.66.1.17 PDB: 2q41_A

Probab=96.74  E-value=0.00059  Score=59.14  Aligned_cols=43  Identities=19%  Similarity=0.198  Sum_probs=38.5

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...++|+|||||.|.++..++++.|..+++.+|+ |.+++.|++
T Consensus       119 ~~~~~VLdIG~G~G~~a~~la~~~~~~~V~~VDis~~~l~~Ar~  162 (334)
T 1xj5_A          119 PNPKKVLVIGGGDGGVLREVARHASIEQIDMCEIDKMVVDVSKQ  162 (334)
T ss_dssp             SCCCEEEEETCSSSHHHHHHTTCTTCCEEEEEESCHHHHHHHHH
T ss_pred             CCCCEEEEECCCccHHHHHHHHcCCCCEEEEEECCHHHHHHHHH
Confidence            4568999999999999999999988999999999 888888764

>1p91_A Ribosomal RNA large subunit methyltransferase A; RLMA, RRMA, 23S rRNA, NESG, structural genomics, PSI, protein structure initiative; HET: SAM; 2.80A {Escherichia coli} SCOP: c.66.1.33

Probab=96.74  E-value=0.00085  Score=55.56  Aligned_cols=43  Identities=23%  Similarity=0.415  Sum_probs=36.9

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ....+|+|||||.|.++..+++++|+.+++.+|. |..++.+++
T Consensus        84 ~~~~~vLdiG~G~G~~~~~l~~~~~~~~v~~vD~s~~~~~~a~~  127 (269)
T 1p91_A           84 DKATAVLDIGCGEGYYTHAFADALPEITTFGLDVSKVAIKAAAK  127 (269)
T ss_dssp             TTCCEEEEETCTTSTTHHHHHHTCTTSEEEEEESCHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCHHHHHHHHhCCCCeEEEEeCCHHHHHHHHH
Confidence            3457999999999999999999999999999998 666666653

>3e23_A Uncharacterized protein RPA2492; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; HET: SAM; 1.60A {Rhodopseudomonas palustris}

Probab=96.74  E-value=0.00081  Score=53.54  Aligned_cols=42  Identities=17%  Similarity=0.256  Sum_probs=34.7

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      +....+|||||||.|.++..++++  +.+++.+|+ |..++.+++
T Consensus        41 ~~~~~~vLDiGcG~G~~~~~l~~~--~~~v~~vD~s~~~~~~a~~   83 (211)
T 3e23_A           41 LPAGAKILELGCGAGYQAEAMLAA--GFDVDATDGSPELAAEASR   83 (211)
T ss_dssp             SCTTCEEEESSCTTSHHHHHHHHT--TCEEEEEESCHHHHHHHHH
T ss_pred             cCCCCcEEEECCCCCHHHHHHHHc--CCeEEEECCCHHHHHHHHH
Confidence            445679999999999999999988  568899998 777776654

>2fyt_A Protein arginine N-methyltransferase 3; structural genomics, structural genomics consortium, SGC; HET: SAH; 2.00A {Homo sapiens} SCOP: c.66.1.6 PDB: 3smq_A* 1f3l_A*

Probab=96.71  E-value=0.0013  Score=56.89  Aligned_cols=50  Identities=20%  Similarity=0.175  Sum_probs=37.6

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~  234 (244)
                      .+.+... ..+..+|+|||||+|.++..++++ +..+++.+|..+.++.+++
T Consensus        55 ~i~~~~~-~~~~~~VLDiGcGtG~ls~~la~~-g~~~v~gvD~s~~~~~a~~  104 (340)
T 2fyt_A           55 FIYQNPH-IFKDKVVLDVGCGTGILSMFAAKA-GAKKVLGVDQSEILYQAMD  104 (340)
T ss_dssp             HHHHCGG-GTTTCEEEEETCTTSHHHHHHHHT-TCSEEEEEESSTHHHHHHH
T ss_pred             HHHhhhh-hcCCCEEEEeeccCcHHHHHHHHc-CCCEEEEEChHHHHHHHHH
Confidence            3344444 455689999999999999999887 5568999998667776653

>3tr6_A O-methyltransferase; cellular processes; HET: SAH; 2.70A {Coxiella burnetii} SCOP: c.66.1.0

Probab=96.71  E-value=0.00083  Score=54.03  Aligned_cols=42  Identities=21%  Similarity=0.166  Sum_probs=37.0

Q ss_pred             CcceEEEecCCccHHHHHHHHHCC-CCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYP-HIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...+|||||||.|..+..+++++| +.+.+.+|. |..++.+++
T Consensus        64 ~~~~vLdiG~G~G~~~~~la~~~~~~~~v~~vD~~~~~~~~a~~  107 (225)
T 3tr6_A           64 QAKKVIDIGTFTGYSAIAMGLALPKDGTLITCDVDEKSTALAKE  107 (225)
T ss_dssp             TCSEEEEECCTTSHHHHHHHTTCCTTCEEEEEESCHHHHHHHHH
T ss_pred             CCCEEEEeCCcchHHHHHHHHhCCCCCEEEEEeCCHHHHHHHHH
Confidence            457999999999999999999998 889999998 777777754

>3c3p_A Methyltransferase; NP_951602.1, structural genomics, joint for structural genomics, JCSG, protein structure initiative transferase; 1.90A {Geobacter sulfurreducens pca}

Probab=96.71  E-value=0.0008  Score=53.70  Aligned_cols=42  Identities=17%  Similarity=0.124  Sum_probs=37.0

Q ss_pred             CcceEEEecCCccHHHHHHHHHCC-CCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYP-HIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~vi~~a~~  234 (244)
                      +..+|||||||.|..+..+++..| +.+++.+|. |..++.+++
T Consensus        56 ~~~~vLdiG~G~G~~~~~la~~~~~~~~v~~vD~~~~~~~~a~~   99 (210)
T 3c3p_A           56 QPQLVVVPGDGLGCASWWFARAISISSRVVMIDPDRDNVEHARR   99 (210)
T ss_dssp             CCSEEEEESCGGGHHHHHHHTTSCTTCEEEEEESCHHHHHHHHH
T ss_pred             CCCEEEEEcCCccHHHHHHHHhCCCCCEEEEEECCHHHHHHHHH
Confidence            457999999999999999999998 889999998 788877764

>2pt6_A Spermidine synthase; transferase, structural genomics consor SGC,dcadoMet complex; HET: S4M 1PG; 2.00A {Plasmodium falciparum} PDB: 2pss_A* 2pt9_A*

Probab=96.70  E-value=0.00061  Score=58.69  Aligned_cols=42  Identities=19%  Similarity=0.122  Sum_probs=37.6

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...+|+|||||.|.++..+++..|..+++.+|+ |.+++.+++
T Consensus       116 ~~~~VLdiG~G~G~~~~~l~~~~~~~~v~~vDis~~~l~~ar~  158 (321)
T 2pt6_A          116 EPKNVLVVGGGDGGIIRELCKYKSVENIDICEIDETVIEVSKI  158 (321)
T ss_dssp             SCCEEEEEECTTCHHHHHHTTCTTCCEEEEEESCHHHHHHHHH
T ss_pred             CCCEEEEEcCCccHHHHHHHHcCCCCEEEEEECCHHHHHHHHH
Confidence            458999999999999999999888999999999 888888764

>3uzu_A Ribosomal RNA small subunit methyltransferase A; ssgcid, seattle structural genomics center for infectio disease; 1.75A {Burkholderia pseudomallei}

Probab=96.69  E-value=0.00064  Score=57.44  Aligned_cols=51  Identities=18%  Similarity=0.288  Sum_probs=39.6

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCC--CeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPH--IKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~--l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+++..+ .....+|+|||||.|.++..++++.+.  .+++.+|+ |..++.+++
T Consensus        33 ~iv~~~~-~~~~~~VLEIG~G~G~lt~~La~~~~~~~~~V~avDid~~~l~~a~~   86 (279)
T 3uzu_A           33 AIVAAIR-PERGERMVEIGPGLGALTGPVIARLATPGSPLHAVELDRDLIGRLEQ   86 (279)
T ss_dssp             HHHHHHC-CCTTCEEEEECCTTSTTHHHHHHHHCBTTBCEEEEECCHHHHHHHHH
T ss_pred             HHHHhcC-CCCcCEEEEEccccHHHHHHHHHhCCCcCCeEEEEECCHHHHHHHHH
Confidence            4555555 566689999999999999999998765  55788887 677766654

>2i7c_A Spermidine synthase; transferase, structural genomics consor; HET: AAT 1PG; 1.71A {Plasmodium falciparum} PDB: 2hte_A* 3b7p_A* 3rie_A* 2pwp_A*

Probab=96.69  E-value=0.00064  Score=57.40  Aligned_cols=43  Identities=19%  Similarity=0.129  Sum_probs=38.2

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...++|+|||||.|..+..+++..|..+++++|+ |.+++.+++
T Consensus        77 ~~~~~VLdiG~G~G~~~~~l~~~~~~~~v~~vDid~~~i~~a~~  120 (283)
T 2i7c_A           77 KEPKNVLVVGGGDGGIIRELCKYKSVENIDICEIDETVIEVSKI  120 (283)
T ss_dssp             SSCCEEEEEECTTSHHHHHHTTCTTCCEEEEEESCHHHHHHHHH
T ss_pred             CCCCeEEEEeCCcCHHHHHHHHcCCCCEEEEEECCHHHHHHHHH
Confidence            4568999999999999999999888899999999 888887764

>3l8d_A Methyltransferase; structural genomics, PSI, nysgrc, protein structure initiative, NEW YORK SGX research center for STRU genomics; 1.70A {Bacillus thuringiensis}

Probab=96.68  E-value=0.0027  Score=51.37  Aligned_cols=48  Identities=23%  Similarity=0.364  Sum_probs=38.2

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCCC---CCceee
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPSY---PGTLFI  241 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~~---~~i~~~  241 (244)
                      ....+|||||||.|.++..++++  +.+++.+|+ |..++.+++.   ++|+++
T Consensus        52 ~~~~~vLDiG~G~G~~~~~l~~~--~~~v~~vD~s~~~~~~a~~~~~~~~~~~~  103 (242)
T 3l8d_A           52 KKEAEVLDVGCGDGYGTYKLSRT--GYKAVGVDISEVMIQKGKERGEGPDLSFI  103 (242)
T ss_dssp             CTTCEEEEETCTTSHHHHHHHHT--TCEEEEEESCHHHHHHHHTTTCBTTEEEE
T ss_pred             CCCCeEEEEcCCCCHHHHHHHHc--CCeEEEEECCHHHHHHHHhhcccCCceEE
Confidence            35579999999999999999998  568899998 7788777653   455543

>1inl_A Spermidine synthase; beta-barrel, rossman fold, structural genomics, PSI, protein structure initiative; 1.50A {Thermotoga maritima} SCOP: c.66.1.17 PDB: 1jq3_A*

Probab=96.68  E-value=0.00065  Score=57.75  Aligned_cols=42  Identities=31%  Similarity=0.381  Sum_probs=37.4

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...+|+|||||.|.++..+++..|..+++.+|+ |.+++.+++
T Consensus        90 ~~~~VLdiG~G~G~~~~~l~~~~~~~~v~~vDid~~~~~~a~~  132 (296)
T 1inl_A           90 NPKKVLIIGGGDGGTLREVLKHDSVEKAILCEVDGLVIEAARK  132 (296)
T ss_dssp             SCCEEEEEECTTCHHHHHHTTSTTCSEEEEEESCHHHHHHHHH
T ss_pred             CCCEEEEEcCCcCHHHHHHHhcCCCCEEEEEECCHHHHHHHHH
Confidence            447999999999999999999888899999999 888887764

>2pxx_A Uncharacterized protein MGC2408; structural genomics consortium, SGC, methyltransferase, LOC84291, transferase; HET: SAH; 1.30A {Homo sapiens}

Probab=96.68  E-value=0.0008  Score=53.32  Aligned_cols=42  Identities=10%  Similarity=0.030  Sum_probs=35.2

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ....+|+|||||.|.++..++++.+. +++.+|. |..++.+++
T Consensus        41 ~~~~~vLdiGcG~G~~~~~l~~~~~~-~v~~~D~s~~~~~~a~~   83 (215)
T 2pxx_A           41 RPEDRILVLGCGNSALSYELFLGGFP-NVTSVDYSSVVVAAMQA   83 (215)
T ss_dssp             CTTCCEEEETCTTCSHHHHHHHTTCC-CEEEEESCHHHHHHHHH
T ss_pred             CCCCeEEEECCCCcHHHHHHHHcCCC-cEEEEeCCHHHHHHHHH
Confidence            45579999999999999999999776 8899998 777776653

>1uir_A Polyamine aminopropyltransferase; spermidien synthase, spermine synthase, riken STR genomics/proteomics initiative, RSGI; 2.00A {Thermus thermophilus} SCOP: c.66.1.17 PDB: 3anx_A*

Probab=96.66  E-value=0.00068  Score=58.12  Aligned_cols=43  Identities=26%  Similarity=0.352  Sum_probs=37.8

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...++|+|||||.|.++..++++.|..+++.+|+ |.+++.+++
T Consensus        76 ~~~~~VLdiG~G~G~~~~~l~~~~~~~~v~~vDid~~~i~~ar~  119 (314)
T 1uir_A           76 PEPKRVLIVGGGEGATLREVLKHPTVEKAVMVDIDGELVEVAKR  119 (314)
T ss_dssp             SCCCEEEEEECTTSHHHHHHTTSTTCCEEEEEESCHHHHHHHHH
T ss_pred             CCCCeEEEEcCCcCHHHHHHHhcCCCCEEEEEECCHHHHHHHHH
Confidence            3458999999999999999999888899999999 888887753

>3mq0_A Transcriptional repressor of the blcabc operon; helix-turn-helix, GAF fold, transcription repressor; 1.79A {Agrobacterium tumefaciens}

Probab=96.66  E-value=0.0012  Score=55.55  Aligned_cols=58  Identities=16%  Similarity=0.299  Sum_probs=47.3

Q ss_pred             cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcccc
Q 041256           36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSA  105 (244)
Q Consensus        36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~  105 (244)
                      +.|++.|.+.+  +++|+.|||+.+|++      ..- +.|+|+-|+..||+.++   .+++|++++...
T Consensus        33 l~IL~~l~~~~--~~ltl~eia~~lgl~------ksT-v~RlL~tL~~~G~v~~~---~~~~Y~LG~~~~   90 (275)
T 3mq0_A           33 VRILDLVAGSP--RDLTAAELTRFLDLP------KSS-AHGLLAVMTELDLLARS---ADGTLRIGPHSL   90 (275)
T ss_dssp             HHHHHHHHHCS--SCEEHHHHHHHHTCC--------C-HHHHHHHHHHTTSEEEC---TTSEEEECTHHH
T ss_pred             HHHHHHHhhCC--CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEEC---CCCcEEehHHHH
Confidence            56888998864  589999999999996      345 99999999999999963   347899988754

>2o07_A Spermidine synthase; structural genomics, structural genomics consortium, SGC, transferase; HET: SPD MTA; 1.89A {Homo sapiens} SCOP: c.66.1.17 PDB: 2o06_A* 2o05_A* 2o0l_A* 3rw9_A*

Probab=96.65  E-value=0.0007  Score=57.85  Aligned_cols=43  Identities=19%  Similarity=0.283  Sum_probs=38.4

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...++|+|||||.|.++..++++.|..+++.+|+ |.+++.+++
T Consensus        94 ~~~~~VLdiG~G~G~~~~~l~~~~~~~~v~~vDid~~~i~~ar~  137 (304)
T 2o07_A           94 PNPRKVLIIGGGDGGVLREVVKHPSVESVVQCEIDEDVIQVSKK  137 (304)
T ss_dssp             SSCCEEEEEECTTSHHHHHHTTCTTCCEEEEEESCHHHHHHHHH
T ss_pred             CCCCEEEEECCCchHHHHHHHHcCCCCEEEEEECCHHHHHHHHH
Confidence            4568999999999999999999988899999999 888887764

>1wzn_A SAM-dependent methyltransferase; structural genomics, riken structural genomics/proteomics initiative, RSGI; HET: SAH; 1.90A {Pyrococcus horikoshii} SCOP: c.66.1.43

Probab=96.65  E-value=0.004  Score=50.74  Aligned_cols=49  Identities=16%  Similarity=0.303  Sum_probs=38.1

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .++.... .....+|+|||||+|.++..++++  +.+++.+|+ |..++.+++
T Consensus        32 ~~~~~~~-~~~~~~vLDlGcG~G~~~~~l~~~--~~~v~gvD~s~~~l~~a~~   81 (252)
T 1wzn_A           32 EIFKEDA-KREVRRVLDLACGTGIPTLELAER--GYEVVGLDLHEEMLRVARR   81 (252)
T ss_dssp             HHHHHTC-SSCCCEEEEETCTTCHHHHHHHHT--TCEEEEEESCHHHHHHHHH
T ss_pred             HHHHHhc-ccCCCEEEEeCCCCCHHHHHHHHC--CCeEEEEECCHHHHHHHHH
Confidence            3444443 345689999999999999999987  568999998 777777653

>2b2c_A Spermidine synthase; beta-alpha, transferase; 2.50A {Caenorhabditis elegans} SCOP: c.66.1.17

Probab=96.64  E-value=0.00076  Score=57.90  Aligned_cols=43  Identities=23%  Similarity=0.268  Sum_probs=38.1

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...++|+|||||.|..+..+++..|..+++.+|+ |.+++.|++
T Consensus       107 ~~~~~VLdIG~G~G~~~~~l~~~~~~~~v~~vDid~~~i~~Ar~  150 (314)
T 2b2c_A          107 PDPKRVLIIGGGDGGILREVLKHESVEKVTMCEIDEMVIDVAKK  150 (314)
T ss_dssp             SSCCEEEEESCTTSHHHHHHTTCTTCCEEEEECSCHHHHHHHHH
T ss_pred             CCCCEEEEEcCCcCHHHHHHHHcCCCCEEEEEECCHHHHHHHHH
Confidence            3458999999999999999999888999999999 888888764

>2cmg_A Spermidine synthase; transferase, putrescine aminopropyltransferase, spermidine biosynthesis, polyamine biosynthesis, SPEE; 2.0A {Helicobacter pylori} PDB: 2cmh_A

Probab=96.64  E-value=0.0014  Score=54.75  Aligned_cols=41  Identities=10%  Similarity=-0.087  Sum_probs=36.9

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...++|+|||||.|.++..++++ + .+++..|+ |.+++.|++
T Consensus        71 ~~~~~VL~iG~G~G~~~~~ll~~-~-~~v~~veid~~~i~~ar~  112 (262)
T 2cmg_A           71 KELKEVLIVDGFDLELAHQLFKY-D-THIDFVQADEKILDSFIS  112 (262)
T ss_dssp             SCCCEEEEESSCCHHHHHHHTTS-S-CEEEEECSCHHHHGGGTT
T ss_pred             CCCCEEEEEeCCcCHHHHHHHhC-C-CEEEEEECCHHHHHHHHH
Confidence            35589999999999999999998 8 89999998 899999876

>1mjf_A Spermidine synthase; spermidine synthetase, structural genomics, PSI, protein structure initiative; 1.80A {Pyrococcus furiosus} SCOP: c.66.1.17 PDB: 2e5w_A* 2zsu_A*

Probab=96.62  E-value=0.00072  Score=56.98  Aligned_cols=40  Identities=23%  Similarity=0.282  Sum_probs=36.0

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~  233 (244)
                      ..++|+|||||.|.++..++++ |..+++.+|+ |.+++.++
T Consensus        75 ~~~~VLdiG~G~G~~~~~l~~~-~~~~v~~vDid~~~i~~ar  115 (281)
T 1mjf_A           75 KPKRVLVIGGGDGGTVREVLQH-DVDEVIMVEIDEDVIMVSK  115 (281)
T ss_dssp             CCCEEEEEECTTSHHHHHHTTS-CCSEEEEEESCHHHHHHHH
T ss_pred             CCCeEEEEcCCcCHHHHHHHhC-CCCEEEEEECCHHHHHHHH
Confidence            4579999999999999999998 8889999999 88888765

>1ws6_A Methyltransferase; structural genomics, riken structural genomics/proteomics initiative, RSGI; 2.50A {Thermus thermophilus} SCOP: c.66.1.46

Probab=96.62  E-value=0.0012  Score=50.42  Aligned_cols=40  Identities=13%  Similarity=0.016  Sum_probs=34.7

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...+|+|+|||.|.++..++++.++  ++.+|+ |..++.+++
T Consensus        41 ~~~~vLD~GcG~G~~~~~l~~~~~~--v~~vD~~~~~~~~a~~   81 (171)
T 1ws6_A           41 RRGRFLDPFAGSGAVGLEAASEGWE--AVLVEKDPEAVRLLKE   81 (171)
T ss_dssp             TCCEEEEETCSSCHHHHHHHHTTCE--EEEECCCHHHHHHHHH
T ss_pred             CCCeEEEeCCCcCHHHHHHHHCCCe--EEEEeCCHHHHHHHHH
Confidence            4578999999999999999999877  889998 788877764

>1dl5_A Protein-L-isoaspartate O-methyltransferase; isoaspartyl residues, protein repair, deamidation, post-translational modification; HET: SAH; 1.80A {Thermotoga maritima} SCOP: c.66.1.7 d.197.1.1

Probab=96.61  E-value=0.0018  Score=55.33  Aligned_cols=51  Identities=12%  Similarity=0.178  Sum_probs=41.0

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCC-CCeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYP-HIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+++..+ .....+|+|||||.|.++..+++..+ +.+++.+|+ |+.++.+++
T Consensus        66 ~l~~~l~-~~~~~~VLDiGcG~G~~~~~la~~~~~~~~v~gvD~s~~~~~~a~~  118 (317)
T 1dl5_A           66 LFMEWVG-LDKGMRVLEIGGGTGYNAAVMSRVVGEKGLVVSVEYSRKICEIAKR  118 (317)
T ss_dssp             HHHHHTT-CCTTCEEEEECCTTSHHHHHHHHHHCTTCEEEEEESCHHHHHHHHH
T ss_pred             HHHHhcC-CCCcCEEEEecCCchHHHHHHHHhcCCCCEEEEEECCHHHHHHHHH
Confidence            4445555 56668999999999999999999988 488999998 777777764

>1yub_A Ermam, rRNA methyltransferase; MLS antibiotics; NMR {Streptococcus pneumoniae} SCOP: c.66.1.24

Probab=96.60  E-value=0.0013  Score=54.12  Aligned_cols=50  Identities=8%  Similarity=0.216  Sum_probs=41.0

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+++..+ .....+|+|||||.|.++..++++.  .+++.+|+ |..++.+++
T Consensus        19 ~~i~~~~~-~~~~~~VLDiG~G~G~~~~~l~~~~--~~v~~id~~~~~~~~a~~   69 (245)
T 1yub_A           19 NQIIKQLN-LKETDTVYEIGTGKGHLTTKLAKIS--KQVTSIELDSHLFNLSSE   69 (245)
T ss_dssp             HHHHHHCC-CCSSEEEEECSCCCSSCSHHHHHHS--SEEEESSSSCSSSSSSSC
T ss_pred             HHHHHhcC-CCCCCEEEEEeCCCCHHHHHHHHhC--CeEEEEECCHHHHHHHHH
Confidence            45566666 5667899999999999999999986  78899998 777777765

>2y1w_A Histone-arginine methyltransferase CARM1; histone modification; HET: SFG 849; 2.10A {Homo sapiens} PDB: 2y1x_A* 3b3f_A* 3b3g_A 2v74_B* 2v7e_A

Probab=96.59  E-value=0.0011  Score=57.58  Aligned_cols=49  Identities=20%  Similarity=0.129  Sum_probs=37.1

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAP  233 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~  233 (244)
                      .+.+.+. ..+..+|||||||.|.++..++++ +..+++.+|..+.++.++
T Consensus        41 ~i~~~l~-~~~~~~VLDiGcGtG~ls~~la~~-g~~~V~~vD~s~~~~~a~   89 (348)
T 2y1w_A           41 AILQNHT-DFKDKIVLDVGCGSGILSFFAAQA-GARKIYAVEASTMAQHAE   89 (348)
T ss_dssp             HHHHTGG-GTTTCEEEEETCTTSHHHHHHHHT-TCSEEEEEECSTHHHHHH
T ss_pred             HHHhccc-cCCcCEEEEcCCCccHHHHHHHhC-CCCEEEEECCHHHHHHHH
Confidence            4455554 445689999999999999988875 667899999865655554

>3lpm_A Putative methyltransferase; structural genomics, protein structure initiative, NEW YORK structural genomix research consortium, nysgxrc; 2.40A {Listeria monocytogenes}

Probab=96.58  E-value=0.0018  Score=53.59  Aligned_cols=43  Identities=16%  Similarity=0.240  Sum_probs=37.5

Q ss_pred             CC-CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          191 FE-HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       191 ~~-~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .. ...+|+|||||+|.++..++++.+. +++.+|+ |..++.|++
T Consensus        46 ~~~~~~~vLDlG~G~G~~~~~la~~~~~-~v~gvDi~~~~~~~a~~   90 (259)
T 3lpm_A           46 LPIRKGKIIDLCSGNGIIPLLLSTRTKA-KIVGVEIQERLADMAKR   90 (259)
T ss_dssp             CCSSCCEEEETTCTTTHHHHHHHTTCCC-EEEEECCSHHHHHHHHH
T ss_pred             CCCCCCEEEEcCCchhHHHHHHHHhcCC-cEEEEECCHHHHHHHHH
Confidence            55 6789999999999999999999887 8999998 788877754

>3thr_A Glycine N-methyltransferase; GNMT, folate, methyltransferase binding, liver cytosol, transferase-transferase inhibitor C; HET: C2F TAM; 2.00A {Rattus norvegicus} SCOP: c.66.1.5 PDB: 3ths_A* 1xva_A* 1d2c_A 1kia_A* 1nbh_A* 1bhj_A* 2idj_A 2idk_A* 1d2g_A 1d2h_A* 1nbi_A* 1r8x_A 1r8y_A 1r74_A* 2azt_A*

Probab=96.58  E-value=0.0016  Score=54.55  Aligned_cols=40  Identities=20%  Similarity=0.235  Sum_probs=33.5

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~  233 (244)
                      ....+|||||||+|.++..++++.+  +++.+|+ |..++.++
T Consensus        56 ~~~~~vLDiGcG~G~~~~~l~~~~~--~v~gvD~s~~~l~~a~   96 (293)
T 3thr_A           56 HGCHRVLDVACGTGVDSIMLVEEGF--SVTSVDASDKMLKYAL   96 (293)
T ss_dssp             TTCCEEEETTCTTSHHHHHHHHTTC--EEEEEESCHHHHHHHH
T ss_pred             cCCCEEEEecCCCCHHHHHHHHCCC--eEEEEECCHHHHHHHH
Confidence            4557999999999999999999854  8899998 67777664

>3tma_A Methyltransferase; thump domain; 2.05A {Thermus thermophilus}

Probab=96.58  E-value=0.0016  Score=56.49  Aligned_cols=52  Identities=17%  Similarity=0.024  Sum_probs=44.3

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHC-CCCeEEEccc-hHHhhhCCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKY-PHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..++.... |....+|+|+|||+|.+++.++... |+.+++..|. |..++.|++
T Consensus       193 ~~l~~~~~-~~~~~~vLD~gcGsG~~~ie~a~~~~~~~~v~g~Di~~~~i~~a~~  246 (354)
T 3tma_A          193 QALLRLAD-ARPGMRVLDPFTGSGTIALEAASTLGPTSPVYAGDLDEKRLGLARE  246 (354)
T ss_dssp             HHHHHHTT-CCTTCCEEESSCTTSHHHHHHHHHHCTTSCEEEEESCHHHHHHHHH
T ss_pred             HHHHHHhC-CCCCCEEEeCCCCcCHHHHHHHHhhCCCceEEEEECCHHHHHHHHH
Confidence            34555555 7778899999999999999999998 9999999998 888888764

>3u81_A Catechol O-methyltransferase; neurotransmitter degradation, transferase transferase inhibitor complex; HET: SAH; 1.13A {Rattus norvegicus} SCOP: c.66.1.1 PDB: 3nwe_A* 3oe5_A* 3ozr_A* 3oe4_A* 3ozt_A* 3ozs_A* 3r6t_A* 3hvi_A* 1jr4_A* 1vid_A* 1h1d_A* 2cl5_A* 3hvh_A* 3hvj_A* 3hvk_A* 3nw9_A* 3nwb_A* 3s68_A* 2zlb_A 2zth_A* ...

Probab=96.57  E-value=0.0013  Score=52.90  Aligned_cols=43  Identities=7%  Similarity=0.077  Sum_probs=37.3

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCC-CCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYP-HIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+..+|||||||.|..+..++++.| +.+++.+|+ |..++.|++
T Consensus        57 ~~~~~vLdiG~G~G~~~~~la~~~~~~~~v~~vD~~~~~~~~a~~  101 (221)
T 3u81_A           57 YSPSLVLELGAYCGYSAVRMARLLQPGARLLTMEINPDCAAITQQ  101 (221)
T ss_dssp             HCCSEEEEECCTTSHHHHHHHTTSCTTCEEEEEESCHHHHHHHHH
T ss_pred             cCCCEEEEECCCCCHHHHHHHHhCCCCCEEEEEeCChHHHHHHHH
Confidence            3558999999999999999999875 889999998 888887764

>2hnk_A SAM-dependent O-methyltransferase; modified rossman fold; HET: SAH; 2.30A {Leptospira interrogans}

Probab=96.56  E-value=0.0021  Score=52.36  Aligned_cols=43  Identities=19%  Similarity=0.166  Sum_probs=37.5

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCC-CCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYP-HIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ....+|+|||||.|..+..+++.+| ..+++.+|. |..++.+++
T Consensus        59 ~~~~~VLdiG~G~G~~~~~la~~~~~~~~v~~vD~~~~~~~~a~~  103 (239)
T 2hnk_A           59 SGAKRIIEIGTFTGYSSLCFASALPEDGKILCCDVSEEWTNVARK  103 (239)
T ss_dssp             HTCSEEEEECCTTCHHHHHHHHHSCTTCEEEEEESCHHHHHHHHH
T ss_pred             hCcCEEEEEeCCCCHHHHHHHHhCCCCCEEEEEECCHHHHHHHHH
Confidence            3457999999999999999999998 789999998 888877764

>2nxc_A L11 mtase, ribosomal protein L11 methyltransferase; transferase S-adenosly-L-methionine dependent methyltransfer posttranslational modification; 1.59A {Thermus thermophilus} SCOP: c.66.1.39 PDB: 1ufk_A 2nxe_A* 2nxj_A 2nxn_A 2zbp_A* 2zbq_A* 2zbr_A* 3cjq_A* 3cjr_A* 3cju_A* 3egv_A* 3cjt_A*

Probab=96.55  E-value=0.0016  Score=53.90  Aligned_cols=41  Identities=24%  Similarity=0.348  Sum_probs=35.1

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ....+|+|||||+|.++..+++..+  +++..|. |..++.+++
T Consensus       119 ~~~~~VLDiGcG~G~l~~~la~~g~--~v~gvDi~~~~v~~a~~  160 (254)
T 2nxc_A          119 RPGDKVLDLGTGSGVLAIAAEKLGG--KALGVDIDPMVLPQAEA  160 (254)
T ss_dssp             CTTCEEEEETCTTSHHHHHHHHTTC--EEEEEESCGGGHHHHHH
T ss_pred             CCCCEEEEecCCCcHHHHHHHHhCC--eEEEEECCHHHHHHHHH
Confidence            4557999999999999999999877  8899998 888877764

>1qgp_A Protein (double stranded RNA adenosine deaminase); Z-alpha-Z-DNA binding domain, RNA-editing, Z-DNA recognition, ADAR1, helix- turn-helix; NMR {Homo sapiens} SCOP: a.4.5.19

Probab=96.55  E-value=0.0016  Score=43.98  Aligned_cols=61  Identities=16%  Similarity=0.275  Sum_probs=46.7

Q ss_pred             HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCc
Q 041256           34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAP  102 (244)
Q Consensus        34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~  102 (244)
                      .+..|++.|.+.+++.++|+.|||+++|++      ... +.+.|+-|...|++.... ..++.|..++
T Consensus        15 ~~~~IL~~L~~~~~~~~~t~~eLA~~Lgvs------~~t-V~~~L~~L~~~G~I~~~g-~~~~~W~i~~   75 (77)
T 1qgp_A           15 QEQRILKFLEELGEGKATTAHDLSGKLGTP------KKE-INRVLYSLAKKGKLQKEA-GTPPLWKIAV   75 (77)
T ss_dssp             HHHHHHHHHHHHCSSSCEEHHHHHHHHCCC------HHH-HHHHHHHHHHHTSEEEEC-SSSCEEEECC
T ss_pred             HHHHHHHHHHHcCCCCCcCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEecC-CCCCceEecC
Confidence            356688888886433489999999999996      445 999999999999998632 2356777665

>1l3i_A Precorrin-6Y methyltransferase/putative decarboxylase; structural genomics, beta barrel, rossmann fold, tetramer; HET: SAH; 1.95A {Methanothermobacterthermautotrophicus} SCOP: c.66.1.22 PDB: 1kxz_A 1l3b_A 1f38_A 1l3c_A*

Probab=96.52  E-value=0.0027  Score=49.06  Aligned_cols=48  Identities=19%  Similarity=0.127  Sum_probs=38.8

Q ss_pred             HHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          184 VLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       184 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      +++.++ .....+|+|+|||.|.++..+++..  .+++.+|. |..++.+++
T Consensus        25 ~~~~~~-~~~~~~vldiG~G~G~~~~~l~~~~--~~v~~~D~~~~~~~~a~~   73 (192)
T 1l3i_A           25 IMCLAE-PGKNDVAVDVGCGTGGVTLELAGRV--RRVYAIDRNPEAISTTEM   73 (192)
T ss_dssp             HHHHHC-CCTTCEEEEESCTTSHHHHHHHTTS--SEEEEEESCHHHHHHHHH
T ss_pred             HHHhcC-CCCCCEEEEECCCCCHHHHHHHHhc--CEEEEEECCHHHHHHHHH
Confidence            344445 5666899999999999999999988  78899998 777777654

>1ne2_A Hypothetical protein TA1320; structural genomics, conserved hypothetical protein, PSI, protein structure initiative; 1.75A {Thermoplasma acidophilum} SCOP: c.66.1.32

Probab=96.51  E-value=0.0017  Score=51.20  Aligned_cols=48  Identities=23%  Similarity=0.231  Sum_probs=37.8

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCCC-CCcee
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPSY-PGTLF  240 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~~-~~i~~  240 (244)
                      ....+|+|+|||.|.++..+++. +..+++.+|+ |..++.+++. +++++
T Consensus        50 ~~~~~vlD~gcG~G~~~~~l~~~-~~~~v~~vD~~~~~~~~a~~~~~~~~~   99 (200)
T 1ne2_A           50 IGGRSVIDAGTGNGILACGSYLL-GAESVTAFDIDPDAIETAKRNCGGVNF   99 (200)
T ss_dssp             SBTSEEEEETCTTCHHHHHHHHT-TBSEEEEEESCHHHHHHHHHHCTTSEE
T ss_pred             CCCCEEEEEeCCccHHHHHHHHc-CCCEEEEEECCHHHHHHHHHhcCCCEE
Confidence            45579999999999999999887 5567999998 8888877642 24444

>1sui_A Caffeoyl-COA O-methyltransferase; rossmann fold, protein-cofactor-substrate complex; HET: SAH FRE; 2.70A {Medicago sativa} SCOP: c.66.1.1 PDB: 1sus_A*

Probab=96.49  E-value=0.0015  Score=53.96  Aligned_cols=43  Identities=16%  Similarity=0.091  Sum_probs=37.5

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCC-CCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYP-HIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+.++|||||||.|..+..+++..| +.+++.+|. |..++.+++
T Consensus        78 ~~~~~VLeiG~G~G~~~~~la~~~~~~~~v~~iD~s~~~~~~a~~  122 (247)
T 1sui_A           78 INAKNTMEIGVYTGYSLLATALAIPEDGKILAMDINKENYELGLP  122 (247)
T ss_dssp             TTCCEEEEECCGGGHHHHHHHHHSCTTCEEEEEESCCHHHHHHHH
T ss_pred             hCcCEEEEeCCCcCHHHHHHHHhCCCCCEEEEEECCHHHHHHHHH
Confidence            3457999999999999999999998 789999998 777777764

>3d2l_A SAM-dependent methyltransferase; ZP_00538691.1, structural G joint center for structural genomics, JCSG; HET: MSE; 1.90A {Exiguobacterium sibiricum 255-15}

Probab=96.49  E-value=0.0026  Score=51.40  Aligned_cols=39  Identities=21%  Similarity=0.308  Sum_probs=33.2

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...+|||||||.|.++..++++   .+++.+|+ |..++.+++
T Consensus        33 ~~~~vLdiG~G~G~~~~~l~~~---~~v~~vD~s~~~~~~a~~   72 (243)
T 3d2l_A           33 PGKRIADIGCGTGTATLLLADH---YEVTGVDLSEEMLEIAQE   72 (243)
T ss_dssp             TTCEEEEESCTTCHHHHHHTTT---SEEEEEESCHHHHHHHHH
T ss_pred             CCCeEEEecCCCCHHHHHHhhC---CeEEEEECCHHHHHHHHH
Confidence            3479999999999999999887   78999998 777777654

>3p9n_A Possible methyltransferase (methylase); RV2966C, adoMet binding, RNA methylase, RSMD, SAM-fold, RNA methyltransferase; 1.90A {Mycobacterium tuberculosis}

Probab=96.48  E-value=0.0023  Score=50.07  Aligned_cols=41  Identities=10%  Similarity=-0.062  Sum_probs=34.3

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...+|+|+|||+|.++..++++ +..+++.+|+ |..++.+++
T Consensus        44 ~~~~vLDlgcG~G~~~~~~~~~-~~~~v~~vD~~~~~~~~a~~   85 (189)
T 3p9n_A           44 TGLAVLDLYAGSGALGLEALSR-GAASVLFVESDQRSAAVIAR   85 (189)
T ss_dssp             TTCEEEEETCTTCHHHHHHHHT-TCSEEEEEECCHHHHHHHHH
T ss_pred             CCCEEEEeCCCcCHHHHHHHHC-CCCeEEEEECCHHHHHHHHH
Confidence            4478999999999999987774 6668999998 888888764

>1zx0_A Guanidinoacetate N-methyltransferase; structural genomics, structural genomics consortium; HET: SAH; 1.86A {Homo sapiens} PDB: 3orh_A* 1xcj_A* 1xcl_A* 1p1c_A* 1p1b_A* 1khh_A*

Probab=96.47  E-value=0.0012  Score=53.72  Aligned_cols=42  Identities=12%  Similarity=0.111  Sum_probs=33.7

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ....+|||||||+|.++..+++..+. +++.+|+ |..++.|++
T Consensus        59 ~~~~~vLDiGcGtG~~~~~l~~~~~~-~v~gvD~s~~~l~~a~~  101 (236)
T 1zx0_A           59 SKGGRVLEVGFGMAIAASKVQEAPID-EHWIIECNDGVFQRLRD  101 (236)
T ss_dssp             TTCEEEEEECCTTSHHHHHHHTSCEE-EEEEEECCHHHHHHHHH
T ss_pred             CCCCeEEEEeccCCHHHHHHHhcCCC-eEEEEcCCHHHHHHHHH
Confidence            34579999999999999999665554 7899998 777777764

>3gru_A Dimethyladenosine transferase; rossman fold, ribosomal assem adenosyl-L-methionine, rRNA, methyltransferase, RNA-binding processing; HET: AMP; 1.60A {Methanocaldococcus jannaschii} PDB: 3grr_A* 3grv_A* 3gry_A* 3fyd_A 3fyc_A*

Probab=96.47  E-value=0.0036  Score=53.24  Aligned_cols=57  Identities=19%  Similarity=0.220  Sum_probs=42.2

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC----CCCceee
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS----YPGTLFI  241 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~----~~~i~~~  241 (244)
                      ..+++..+ .....+|+|||||.|.++..++++  .-+++.+|+ |..++.+++    .++++++
T Consensus        40 ~~Iv~~l~-~~~~~~VLEIG~G~G~lT~~La~~--~~~V~aVEid~~li~~a~~~~~~~~~v~vi  101 (295)
T 3gru_A           40 NKAVESAN-LTKDDVVLEIGLGKGILTEELAKN--AKKVYVIEIDKSLEPYANKLKELYNNIEII  101 (295)
T ss_dssp             HHHHHHTT-CCTTCEEEEECCTTSHHHHHHHHH--SSEEEEEESCGGGHHHHHHHHHHCSSEEEE
T ss_pred             HHHHHhcC-CCCcCEEEEECCCchHHHHHHHhc--CCEEEEEECCHHHHHHHHHHhccCCCeEEE
Confidence            45566665 566689999999999999999998  457888887 666666653    2455543

>1ej0_A FTSJ; methyltransferase, adoMet, adenosyl methionine, heat shock proteins, 23S ribosomal RNA; HET: SAM; 1.50A {Escherichia coli} SCOP: c.66.1.2 PDB: 1eiz_A*

Probab=96.47  E-value=0.0043  Score=47.05  Aligned_cols=45  Identities=22%  Similarity=0.200  Sum_probs=35.9

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHC-CCCeEEEccchH
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKY-PHIKGINYDLPY  227 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dlp~  227 (244)
                      .+++.+.......+|+|||||.|.++..+++++ |+.+++..|+..
T Consensus        12 ~~~~~~~~~~~~~~vLd~G~G~G~~~~~l~~~~~~~~~v~~~D~~~   57 (180)
T 1ej0_A           12 EIQQSDKLFKPGMTVVDLGAAPGGWSQYVVTQIGGKGRIIACDLLP   57 (180)
T ss_dssp             HHHHHHCCCCTTCEEEEESCTTCHHHHHHHHHHCTTCEEEEEESSC
T ss_pred             HHHHHhCCCCCCCeEEEeCCCCCHHHHHHHHHhCCCCeEEEEECcc
Confidence            445555424556799999999999999999995 788999999855

>3a27_A TYW2, uncharacterized protein MJ1557; wybutosine modification, transferase; HET: SAM; 2.00A {Methanocaldococcus jannaschii}

Probab=96.47  E-value=0.0017  Score=54.42  Aligned_cols=44  Identities=11%  Similarity=-0.029  Sum_probs=39.2

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      +.+..+|+|+|||.|.++..++++.+..+++.+|+ |..++.+++
T Consensus       117 ~~~~~~VLDlgcG~G~~s~~la~~~~~~~V~~vD~s~~av~~a~~  161 (272)
T 3a27_A          117 SNENEVVVDMFAGIGYFTIPLAKYSKPKLVYAIEKNPTAYHYLCE  161 (272)
T ss_dssp             CCTTCEEEETTCTTTTTHHHHHHHTCCSEEEEEECCHHHHHHHHH
T ss_pred             cCCCCEEEEecCcCCHHHHHHHHhCCCCEEEEEeCCHHHHHHHHH
Confidence            45668999999999999999999999889999999 888888764

>3ofk_A Nodulation protein S; NODS, N-methyltransferase, SAH, SAM, NOD factor, fixation, symbiosis, alpha/beta structure; HET: SAH; 1.85A {Bradyrhizobium SP} PDB: 3ofj_A*

Probab=96.46  E-value=0.002  Score=51.36  Aligned_cols=42  Identities=17%  Similarity=0.149  Sum_probs=34.8

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .....+|||||||.|.++..++++.  .+++.+|. |..++.+++
T Consensus        49 ~~~~~~vLDiGcG~G~~~~~l~~~~--~~v~~vD~s~~~~~~a~~   91 (216)
T 3ofk_A           49 SGAVSNGLEIGCAAGAFTEKLAPHC--KRLTVIDVMPRAIGRACQ   91 (216)
T ss_dssp             TSSEEEEEEECCTTSHHHHHHGGGE--EEEEEEESCHHHHHHHHH
T ss_pred             cCCCCcEEEEcCCCCHHHHHHHHcC--CEEEEEECCHHHHHHHHH
Confidence            4566899999999999999999986  37888998 777777654

>4e2x_A TCAB9; kijanose, tetronitrose, tetradeoxy sugar, sugar methylation, transferase; HET: SAH TYD; 1.40A {Micromonospora chalcea} PDB: 3ndi_A* 3ndj_A* 4e32_A* 4e33_A* 4e2y_A* 4e31_A* 4e2w_A* 4e2z_A* 4e30_A*

Probab=96.44  E-value=0.0017  Score=57.51  Aligned_cols=52  Identities=17%  Similarity=0.172  Sum_probs=41.3

Q ss_pred             HHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCCC
Q 041256          181 MEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPSY  235 (244)
Q Consensus       181 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~~  235 (244)
                      ...+++.++ .....+|||||||.|.++..++++.  .+++.+|+ +..++.+++.
T Consensus        96 ~~~l~~~~~-~~~~~~VLDiGcG~G~~~~~l~~~g--~~v~gvD~s~~~~~~a~~~  148 (416)
T 4e2x_A           96 ARDFLATEL-TGPDPFIVEIGCNDGIMLRTIQEAG--VRHLGFEPSSGVAAKAREK  148 (416)
T ss_dssp             HHHHHHTTT-CSSSCEEEEETCTTTTTHHHHHHTT--CEEEEECCCHHHHHHHHTT
T ss_pred             HHHHHHHhC-CCCCCEEEEecCCCCHHHHHHHHcC--CcEEEECCCHHHHHHHHHc
Confidence            345666666 6677899999999999999999874  48899998 6777777653

>2b25_A Hypothetical protein; structural genomics, methyl transferase, SAM, structural GEN consortium, SGC, transferase; HET: SAM; 2.50A {Homo sapiens} SCOP: c.66.1.13

Probab=96.43  E-value=0.0028  Score=54.52  Aligned_cols=51  Identities=12%  Similarity=0.115  Sum_probs=41.6

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHH-CCCCeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISK-YPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~-~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .++..++ .....+|||||||+|.++..+++. .|+.+++.+|+ |..++.|++
T Consensus        96 ~~l~~l~-~~~g~~VLDiG~G~G~~~~~la~~~g~~~~v~~vD~~~~~~~~a~~  148 (336)
T 2b25_A           96 MILSMMD-INPGDTVLEAGSGSGGMSLFLSKAVGSQGRVISFEVRKDHHDLAKK  148 (336)
T ss_dssp             HHHHHHT-CCTTCEEEEECCTTSHHHHHHHHHHCTTCEEEEEESSHHHHHHHHH
T ss_pred             HHHHhcC-CCCCCEEEEeCCCcCHHHHHHHHHhCCCceEEEEeCCHHHHHHHHH
Confidence            4555555 566789999999999999999998 58899999998 777776653

>2ift_A Putative methylase HI0767; NESG, Y767_haein, structural genomics, PSI-2, protein structure initiative; 2.30A {Haemophilus influenzae} SCOP: c.66.1.46

Probab=96.43  E-value=0.0016  Score=51.75  Aligned_cols=40  Identities=18%  Similarity=0.017  Sum_probs=33.3

Q ss_pred             cceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+|||+|||+|.++..++++.+ .+++.+|+ |..++.+++
T Consensus        54 ~~~vLDlGcGtG~~~~~~~~~~~-~~v~gvD~s~~~l~~a~~   94 (201)
T 2ift_A           54 QSECLDGFAGSGSLGFEALSRQA-KKVTFLELDKTVANQLKK   94 (201)
T ss_dssp             TCEEEETTCTTCHHHHHHHHTTC-SEEEEECSCHHHHHHHHH
T ss_pred             CCeEEEcCCccCHHHHHHHHccC-CEEEEEECCHHHHHHHHH
Confidence            36899999999999999887754 57899998 788887764

>3r3h_A O-methyltransferase, SAM-dependent; structural genomics, PSI-biology, NEW YORK structural genomi research consortium, nysgrc; 2.65A {Legionella pneumophila subsp}

Probab=96.42  E-value=0.0012  Score=54.42  Aligned_cols=43  Identities=21%  Similarity=0.200  Sum_probs=36.8

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCC-CCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYP-HIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+.++|||||||.|..+..+++..| +.+++.+|+ |+.++.|++
T Consensus        59 ~~~~~VLDiG~G~G~~t~~la~~~~~~~~v~~iD~~~~~~~~a~~  103 (242)
T 3r3h_A           59 TRAKKVLELGTFTGYSALAMSLALPDDGQVITCDINEGWTKHAHP  103 (242)
T ss_dssp             HTCSEEEEEESCCSHHHHHHHHTSCTTCEEEEEECCCSSCCCSHH
T ss_pred             cCcCEEEEeeCCcCHHHHHHHHhCCCCCEEEEEECCHHHHHHHHH
Confidence            3457999999999999999999997 789999998 777777654

>3bgv_A MRNA CAP guanine-N7 methyltransferase; alternative splicing, mRNA capping, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: SAH; 2.30A {Homo sapiens} PDB: 3epp_A*

Probab=96.41  E-value=0.0028  Score=53.80  Aligned_cols=64  Identities=23%  Similarity=0.151  Sum_probs=42.6

Q ss_pred             HHHHHHHHHhcchhhHHHHHhhcC-CCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256          166 NDVFNNGMLSHTSIVMEKVLESYK-GFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       166 ~~~f~~aM~~~~~~~~~~~~~~~~-~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~  233 (244)
                      .+.|++++...-   ...+++.+. ......+|+|||||.|.++..+++ .+..+.+..|+ |..++.++
T Consensus         9 lr~~~~~~k~~l---~~~~~~~l~~~~~~~~~VLDlGcG~G~~~~~l~~-~~~~~v~gvD~s~~~l~~a~   74 (313)
T 3bgv_A            9 LRNFNNWMKSVL---IGEFLEKVRQKKKRDITVLDLGCGKGGDLLKWKK-GRINKLVCTDIADVSVKQCQ   74 (313)
T ss_dssp             HHHHHHHHHHHH---HHHHHHHHHHTC--CCEEEEETCTTTTTHHHHHH-TTCSEEEEEESCHHHHHHHH
T ss_pred             hhhccHHHHHHH---HHHHHHHhhhccCCCCEEEEECCCCcHHHHHHHh-cCCCEEEEEeCCHHHHHHHH
Confidence            456777766522   223333222 023567999999999999999988 46778999998 66666654

>3ocj_A Putative exported protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; HET: PLM; 1.39A {Bordetella parapertussis}

Probab=96.40  E-value=0.00096  Score=56.55  Aligned_cols=44  Identities=18%  Similarity=0.164  Sum_probs=38.3

Q ss_pred             CCCcceEEEecCCccHHHHHHH-HHCCCCeEEEccc-hHHhhhCCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMII-SKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~-~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .....+|+|||||.|.++..++ ..+|+.+++.+|+ |..++.+++
T Consensus       116 l~~~~~vLDiGcG~G~~~~~la~~~~~~~~v~gvD~s~~~~~~a~~  161 (305)
T 3ocj_A          116 LRPGCVVASVPCGWMSELLALDYSACPGVQLVGIDYDPEALDGATR  161 (305)
T ss_dssp             CCTTCEEEETTCTTCHHHHTSCCTTCTTCEEEEEESCHHHHHHHHH
T ss_pred             CCCCCEEEEecCCCCHHHHHHHHhcCCCCeEEEEECCHHHHHHHHH
Confidence            4566899999999999999996 7899999999999 888887764

>3pqk_A Biofilm growth-associated repressor; helix-turn-helix motif, winged-helix fold, transcriptional R DNA binding, transcription; 2.09A {Xylella fastidiosa} PDB: 3pqj_A

Probab=96.38  E-value=0.0038  Score=44.01  Aligned_cols=50  Identities=20%  Similarity=0.254  Sum_probs=40.2

Q ss_pred             HHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           29 VMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        29 ~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      +|.--.++.|+..|.+    ++.|+.|||+.+|++      ... +.+-|+.|...|++..
T Consensus        19 ~l~~~~r~~Il~~L~~----~~~~~~ela~~l~is------~~t-vs~~L~~L~~~Glv~~   68 (102)
T 3pqk_A           19 TLSHPVRLMLVCTLVE----GEFSVGELEQQIGIG------QPT-LSQQLGVLRESGIVET   68 (102)
T ss_dssp             HHCSHHHHHHHHHHHT----CCBCHHHHHHHHTCC------TTH-HHHHHHHHHHTTSEEE
T ss_pred             HcCCHHHHHHHHHHHh----CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCeEE
Confidence            3334455667777865    689999999999997      345 9999999999999985

>3tqs_A Ribosomal RNA small subunit methyltransferase A; protein synthesis; 1.98A {Coxiella burnetii} SCOP: c.66.1.0

Probab=96.38  E-value=0.0018  Score=53.97  Aligned_cols=50  Identities=12%  Similarity=0.228  Sum_probs=39.1

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+++..+ .....+|+|||||.|.++..++++.  .+++.+|+ |..++.+++
T Consensus        19 ~~iv~~~~-~~~~~~VLEIG~G~G~lt~~La~~~--~~V~avEid~~~~~~~~~   69 (255)
T 3tqs_A           19 QKIVSAIH-PQKTDTLVEIGPGRGALTDYLLTEC--DNLALVEIDRDLVAFLQK   69 (255)
T ss_dssp             HHHHHHHC-CCTTCEEEEECCTTTTTHHHHTTTS--SEEEEEECCHHHHHHHHH
T ss_pred             HHHHHhcC-CCCcCEEEEEcccccHHHHHHHHhC--CEEEEEECCHHHHHHHHH
Confidence            34566665 5667899999999999999999986  57888887 777776653

>1qyr_A KSGA, high level kasugamycin resistance protein, S-adenosylMet; adenosine dimethyltransferase, rRNA modification, transferase, translation; 2.10A {Escherichia coli} SCOP: c.66.1.24 PDB: 4adv_V 3tpz_A

Probab=96.37  E-value=0.003  Score=52.46  Aligned_cols=50  Identities=10%  Similarity=0.096  Sum_probs=37.9

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+++..+ .....+|+|||||.|.++. + ++.+..+++.+|+ |..++.+++
T Consensus        11 ~~iv~~~~-~~~~~~VLEIG~G~G~lt~-l-~~~~~~~v~avEid~~~~~~a~~   61 (252)
T 1qyr_A           11 DSIVSAIN-PQKGQAMVEIGPGLAALTE-P-VGERLDQLTVIELDRDLAARLQT   61 (252)
T ss_dssp             HHHHHHHC-CCTTCCEEEECCTTTTTHH-H-HHTTCSCEEEECCCHHHHHHHHT
T ss_pred             HHHHHhcC-CCCcCEEEEECCCCcHHHH-h-hhCCCCeEEEEECCHHHHHHHHH
Confidence            45566665 5666799999999999999 5 4555545888998 788877765

>3grz_A L11 mtase, ribosomal protein L11 methyltransferase; methylase, SAM-binding domain, PSI-2, nysgxrc; 2.00A {Lactobacillus delbrueckii subsp}

Probab=96.36  E-value=0.0023  Score=50.64  Aligned_cols=42  Identities=19%  Similarity=0.137  Sum_probs=35.2

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ....+|+|||||.|.++..+++ +|..+++.+|. |..++.+++
T Consensus        59 ~~~~~vLDiG~G~G~~~~~l~~-~~~~~v~~vD~s~~~~~~a~~  101 (205)
T 3grz_A           59 VKPLTVADVGTGSGILAIAAHK-LGAKSVLATDISDESMTAAEE  101 (205)
T ss_dssp             SSCCEEEEETCTTSHHHHHHHH-TTCSEEEEEESCHHHHHHHHH
T ss_pred             cCCCEEEEECCCCCHHHHHHHH-CCCCEEEEEECCHHHHHHHHH
Confidence            4557999999999999999775 67789999998 788877764

>1vbf_A 231AA long hypothetical protein-L-isoaspartate O- methyltransferase; trimeric coiled coil assembly; 2.80A {Sulfolobus tokodaii} SCOP: c.66.1.7

Probab=96.36  E-value=0.0047  Score=49.72  Aligned_cols=49  Identities=16%  Similarity=0.297  Sum_probs=39.0

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+++.++ .....+|+|||||.|.++..+++..  .+++.+|. |..++.+++
T Consensus        61 ~~~~~~~-~~~~~~vLdiG~G~G~~~~~l~~~~--~~v~~vD~~~~~~~~a~~  110 (231)
T 1vbf_A           61 FMLDELD-LHKGQKVLEIGTGIGYYTALIAEIV--DKVVSVEINEKMYNYASK  110 (231)
T ss_dssp             HHHHHTT-CCTTCEEEEECCTTSHHHHHHHHHS--SEEEEEESCHHHHHHHHH
T ss_pred             HHHHhcC-CCCCCEEEEEcCCCCHHHHHHHHHc--CEEEEEeCCHHHHHHHHH
Confidence            4455555 5666899999999999999999987  67888887 777777654

>3c3y_A Pfomt, O-methyltransferase; plant secondary metabolism; HET: SAH; 1.37A {Mesembryanthemum crystallinum}

Probab=96.36  E-value=0.0022  Score=52.47  Aligned_cols=43  Identities=21%  Similarity=0.132  Sum_probs=37.7

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCC-CCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYP-HIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+.++|||||||.|..+..++++.| +.+.+.+|. |..++.+++
T Consensus        69 ~~~~~VLeiG~G~G~~~~~la~~~~~~~~v~~iD~~~~~~~~a~~  113 (237)
T 3c3y_A           69 VNAKKTIEVGVFTGYSLLLTALSIPDDGKITAIDFDREAYEIGLP  113 (237)
T ss_dssp             TTCCEEEEECCTTSHHHHHHHHHSCTTCEEEEEESCHHHHHHHHH
T ss_pred             hCCCEEEEeCCCCCHHHHHHHHhCCCCCEEEEEECCHHHHHHHHH
Confidence            4567999999999999999999988 789999999 888877764

>4df3_A Fibrillarin-like rRNA/TRNA 2'-O-methyltransferase; NADP rossmann superfamily, S-adenosyl-L-M (SAM) binding, nucleolus; HET: SAM; 1.73A {Aeropyrum pernix}

Probab=96.31  E-value=0.0021  Score=52.74  Aligned_cols=51  Identities=16%  Similarity=0.196  Sum_probs=41.1

Q ss_pred             CCCcceEEEecCCccHHHHHHHHH-CCCCeEEEccc-hHHhhhC----CCCCCceee
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISK-YPHIKGINYDL-PYVIKDA----PSYPGTLFI  241 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~-~P~l~~~v~Dl-p~vi~~a----~~~~~i~~~  241 (244)
                      ++...+|+|+|||+|.++..+++. -|+=+++.+|. |+.++.+    ++.++|.++
T Consensus        75 ikpG~~VldlG~G~G~~~~~la~~VG~~G~V~avD~s~~~~~~l~~~a~~~~ni~~V  131 (233)
T 4df3_A           75 VKEGDRILYLGIASGTTASHMSDIIGPRGRIYGVEFAPRVMRDLLTVVRDRRNIFPI  131 (233)
T ss_dssp             CCTTCEEEEETCTTSHHHHHHHHHHCTTCEEEEEECCHHHHHHHHHHSTTCTTEEEE
T ss_pred             CCCCCEEEEecCcCCHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhHhhcCeeEE
Confidence            567799999999999999999998 49989999998 6666554    345666655

>3sm3_A SAM-dependent methyltransferases; NESG, structural genomics, PSI-biology, protein structure in northeast structural genomics; 2.20A {Methanosarcina mazei}

Probab=96.28  E-value=0.0029  Score=50.73  Aligned_cols=41  Identities=22%  Similarity=0.260  Sum_probs=34.6

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ....+|||||||.|.++..++++  +.+++.+|+ |..++.+++
T Consensus        29 ~~~~~vLdiG~G~G~~~~~l~~~--~~~v~~vD~s~~~~~~a~~   70 (235)
T 3sm3_A           29 QEDDEILDIGCGSGKISLELASK--GYSVTGIDINSEAIRLAET   70 (235)
T ss_dssp             CTTCEEEEETCTTSHHHHHHHHT--TCEEEEEESCHHHHHHHHH
T ss_pred             CCCCeEEEECCCCCHHHHHHHhC--CCeEEEEECCHHHHHHHHH
Confidence            45579999999999999999998  668999998 777776653

>3cuo_A Uncharacterized HTH-type transcriptional regulato; DNA-binding transcriptional regulator, structural genomics, MCSG; 2.00A {Escherichia coli K12}

Probab=96.27  E-value=0.003  Score=43.95  Aligned_cols=48  Identities=15%  Similarity=0.120  Sum_probs=39.8

Q ss_pred             HHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           33 VVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        33 a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      -.++.|+..|.+.   ++.|..|||+.+|++      +.. +.+.|+.|...|++...
T Consensus        24 ~~~~~il~~l~~~---~~~s~~ela~~l~is------~~t-vs~~l~~L~~~glv~~~   71 (99)
T 3cuo_A           24 PKRLLILCMLSGS---PGTSAGELTRITGLS------ASA-TSQHLARMRDEGLIDSQ   71 (99)
T ss_dssp             HHHHHHHHHHTTC---CSEEHHHHHHHHCCC------HHH-HHHHHHHHHHTTSEEEE
T ss_pred             hHHHHHHHHHHhC---CCcCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEEE
Confidence            4556677788663   589999999999997      456 99999999999999863

>3dr5_A Putative O-methyltransferase; Q8NRD3, CGL1119, PF01596, CGR117, NESG, structural genomics, PSI-2, protein structure initiative; 2.25A {Corynebacterium glutamicum}

Probab=96.27  E-value=0.0022  Score=51.96  Aligned_cols=40  Identities=10%  Similarity=0.043  Sum_probs=35.1

Q ss_pred             ceEEEecCCccHHHHHHHHHCC-CCeEEEccc-hHHhhhCCC
Q 041256          195 KKLVDVGGGLGITLNMIISKYP-HIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       195 ~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+|||||||.|..+..++++.| +.+++.+|+ |+.++.|++
T Consensus        58 ~~vLdiG~G~G~~~~~la~~~~~~~~v~~vD~~~~~~~~a~~   99 (221)
T 3dr5_A           58 TGAIAITPAAGLVGLYILNGLADNTTLTCIDPESEHQRQAKA   99 (221)
T ss_dssp             CEEEEESTTHHHHHHHHHHHSCTTSEEEEECSCHHHHHHHHH
T ss_pred             CCEEEEcCCchHHHHHHHHhCCCCCEEEEEECCHHHHHHHHH
Confidence            4999999999999999999986 889999998 777777754

>3jth_A Transcription activator HLYU; transcription factor, RTXA, DNA-binding, transcription regulation; 2.00A {Vibrio vulnificus}

Probab=96.27  E-value=0.0026  Score=44.57  Aligned_cols=63  Identities=21%  Similarity=0.277  Sum_probs=45.7

Q ss_pred             HHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCc
Q 041256           29 VMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAP  102 (244)
Q Consensus        29 ~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~  102 (244)
                      +|.--.++.|+..|.+    ++.|+.|||+.+|++      ... +.+.|+.|...|++........-.|++++
T Consensus        19 ~l~~~~r~~Il~~L~~----~~~~~~ela~~l~is------~~t-vs~~L~~L~~~Glv~~~~~g~~~~y~l~~   81 (98)
T 3jth_A           19 AMANERRLQILCMLHN----QELSVGELCAKLQLS------QSA-LSQHLAWLRRDGLVTTRKEAQTVYYTLKS   81 (98)
T ss_dssp             HHCSHHHHHHHHHTTT----SCEEHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEEECCTTCCEEEECC
T ss_pred             HcCCHHHHHHHHHHhc----CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCeEEEEeCCEEEEEECH
Confidence            3444456677888876    589999999999997      455 99999999999999863211122355544

>2aot_A HMT, histamine N-methyltransferase; classic methyltransferase fold, protein-drug complex; HET: CSO 2PM SAH; 1.90A {Homo sapiens} SCOP: c.66.1.19 PDB: 1jqd_A* 2aou_A* 2aov_A* 2aox_A* 1jqe_A* 2aow_A*

Probab=96.25  E-value=0.0036  Score=52.63  Aligned_cols=41  Identities=20%  Similarity=0.214  Sum_probs=30.8

Q ss_pred             CcceEEEecCCccHHHH----HHHHHCCCCeE--EEccc-hHHhhhCC
Q 041256          193 HVKKLVDVGGGLGITLN----MIISKYPHIKG--INYDL-PYVIKDAP  233 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~----~l~~~~P~l~~--~v~Dl-p~vi~~a~  233 (244)
                      ...+|||||||+|.++.    .++.++|+.++  +..|. ++.++.++
T Consensus        52 ~~~~VLDiG~GtG~~~~~~l~~l~~~~~~~~v~~~~vD~S~~ml~~a~   99 (292)
T 2aot_A           52 SEIKILSIGGGAGEIDLQILSKVQAQYPGVCINNEVVEPSAEQIAKYK   99 (292)
T ss_dssp             SEEEEEEETCTTSHHHHHHHHHHHHHSTTCEEEEEEECSCHHHHHHHH
T ss_pred             CCCeEEEEcCCCCHHHHHHHHHHHhhCCCceeeEEEEeCCHHHHHHHH
Confidence            45799999999997544    55667899854  99997 66666554

>3f6o_A Probable transcriptional regulator, ARSR family protein; transcriptional regulator,RHA00566,MCSG, structural genomics, PSI-2; 1.90A {Rhodococcus SP}

Probab=96.24  E-value=0.0033  Score=45.78  Aligned_cols=65  Identities=9%  Similarity=0.113  Sum_probs=48.2

Q ss_pred             HHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcc
Q 041256           28 AVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPV  103 (244)
Q Consensus        28 ~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~  103 (244)
                      .+|.--.++.|+..|.+    +|.|+.|||+.+|++      ... +.+.|+.|...|++........-.|++++.
T Consensus        13 ~al~~~~R~~Il~~L~~----~~~~~~eLa~~l~is------~~t-vs~hL~~L~~~GlV~~~~~gr~~~y~l~~~   77 (118)
T 3f6o_A           13 QALADPTRRAVLGRLSR----GPATVSELAKPFDMA------LPS-FMKHIHFLEDSGWIRTHKQGRVRTCAIEKE   77 (118)
T ss_dssp             HHHTSHHHHHHHHHHHT----CCEEHHHHHTTCCSC------HHH-HHHHHHHHHHTTSEEEEEETTEEEEEECSH
T ss_pred             HHhCCHHHHHHHHHHHh----CCCCHHHHHHHhCcC------HHH-HHHHHHHHHHCCCeEEEecCCEEEEEECHH
Confidence            44455567778888875    699999999999997      455 999999999999998642211234666553

>2ex4_A Adrenal gland protein AD-003; methyltransferase, structural genomics, SGC, structural genomics consortium; HET: SAH; 1.75A {Homo sapiens} SCOP: c.66.1.42

Probab=96.23  E-value=0.002  Score=52.48  Aligned_cols=41  Identities=15%  Similarity=0.164  Sum_probs=35.1

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...+|||||||.|.++..+++++ ..+++.+|+ |..++.+++
T Consensus        79 ~~~~vLDiGcG~G~~~~~l~~~~-~~~v~~vD~s~~~~~~a~~  120 (241)
T 2ex4_A           79 GTSCALDCGAGIGRITKRLLLPL-FREVDMVDITEDFLVQAKT  120 (241)
T ss_dssp             CCSEEEEETCTTTHHHHHTTTTT-CSEEEEEESCHHHHHHHHH
T ss_pred             CCCEEEEECCCCCHHHHHHHHhc-CCEEEEEeCCHHHHHHHHH
Confidence            46899999999999999999987 568899998 777777654

>1u2w_A CADC repressor, cadmium efflux system accessory protein; LEAD, SOFT metal ION resistance, ARSR/SM family, DNA binding protein; 1.90A {Staphylococcus aureus} SCOP: a.4.5.5 PDB: 3f72_A

Probab=96.22  E-value=0.0046  Score=45.28  Aligned_cols=53  Identities=13%  Similarity=0.141  Sum_probs=43.4

Q ss_pred             HHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           27 PAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        27 ~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      ..+|.--.++.|+..|...   ++.|+.|||+.+|++      ... +.+.|+.|...|++..
T Consensus        36 ~~al~~~~rl~IL~~L~~~---~~~s~~eLa~~l~is------~st-vs~~L~~L~~~Glv~~   88 (122)
T 1u2w_A           36 LKAIADENRAKITYALCQD---EELCVCDIANILGVT------IAN-ASHHLRTLYKQGVVNF   88 (122)
T ss_dssp             HHHHHSHHHHHHHHHHHHS---SCEEHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEE
T ss_pred             HHHhCCHHHHHHHHHHHHC---CCcCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCeEE
Confidence            3444445677889999854   689999999999997      456 9999999999999985

>3cbg_A O-methyltransferase; cyanobacterium; HET: SAH FER 4FE; 2.00A {Synechocystis SP}

Probab=96.21  E-value=0.0031  Score=51.29  Aligned_cols=42  Identities=19%  Similarity=0.180  Sum_probs=36.5

Q ss_pred             CcceEEEecCCccHHHHHHHHHCC-CCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYP-HIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~vi~~a~~  234 (244)
                      +..+|||||||.|..+..+++..| +.+.+.+|. |..++.|++
T Consensus        72 ~~~~vLdiG~G~G~~~~~la~~~~~~~~v~~iD~~~~~~~~a~~  115 (232)
T 3cbg_A           72 GAKQVLEIGVFRGYSALAMALQLPPDGQIIACDQDPNATAIAKK  115 (232)
T ss_dssp             TCCEEEEECCTTSHHHHHHHTTSCTTCEEEEEESCHHHHHHHHH
T ss_pred             CCCEEEEecCCCCHHHHHHHHhCCCCCEEEEEECCHHHHHHHHH
Confidence            457999999999999999999998 789999998 777777654

>3q7e_A Protein arginine N-methyltransferase 1; HET: SAH; 2.20A {Rattus norvegicus} PDB: 1orh_A* 1ori_A* 1or8_A*

Probab=96.21  E-value=0.0019  Score=56.07  Aligned_cols=41  Identities=24%  Similarity=0.219  Sum_probs=34.5

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~  234 (244)
                      +..+|||||||.|.++..++++ +..+++.+|..+.++.|++
T Consensus        66 ~~~~VLDvGcG~G~~~~~la~~-g~~~v~gvD~s~~l~~a~~  106 (349)
T 3q7e_A           66 KDKVVLDVGSGTGILCMFAAKA-GARKVIGIECSSISDYAVK  106 (349)
T ss_dssp             TTCEEEEESCTTSHHHHHHHHT-TCSEEEEEECSTHHHHHHH
T ss_pred             CCCEEEEEeccchHHHHHHHHC-CCCEEEEECcHHHHHHHHH
Confidence            4579999999999999999988 7778999999767776653

>3m70_A Tellurite resistance protein TEHB homolog; structural genomics, PSI-2, protein ST initiative; 1.95A {Haemophilus influenzae}

Probab=96.19  E-value=0.003  Score=52.71  Aligned_cols=49  Identities=18%  Similarity=0.136  Sum_probs=38.1

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+++.++ .....+|||||||.|.++..++++  +.+++.+|. |..++.+++
T Consensus       111 ~~~~~~~-~~~~~~vLD~GcG~G~~~~~l~~~--g~~v~~vD~s~~~~~~a~~  160 (286)
T 3m70_A          111 DVVDAAK-IISPCKVLDLGCGQGRNSLYLSLL--GYDVTSWDHNENSIAFLNE  160 (286)
T ss_dssp             HHHHHHH-HSCSCEEEEESCTTCHHHHHHHHT--TCEEEEEESCHHHHHHHHH
T ss_pred             HHHHHhh-ccCCCcEEEECCCCCHHHHHHHHC--CCeEEEEECCHHHHHHHHH
Confidence            4444444 345689999999999999999998  568999998 777777654

>2xrn_A HTH-type transcriptional regulator TTGV; DNA-binding protein, tetramer gene regulator, cooperative DN binding, multidrug binding protein; 2.90A {Pseudomonas putida} PDB: 2xro_A

Probab=96.19  E-value=0.003  Score=51.99  Aligned_cols=59  Identities=15%  Similarity=0.180  Sum_probs=46.6

Q ss_pred             cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcccc
Q 041256           36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSA  105 (244)
Q Consensus        36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~  105 (244)
                      +.|++.|.+.+  +++|+.|||+.+|++      ..- +.|+|+.|...|++.+++  ..++|++++...
T Consensus         9 l~iL~~l~~~~--~~~s~~ela~~~gl~------~st-v~r~l~~L~~~G~v~~~~--~~~~Y~lg~~~~   67 (241)
T 2xrn_A            9 ASIMRALGSHP--HGLSLAAIAQLVGLP------RST-VQRIINALEEEFLVEALG--PAGGFRLGPALG   67 (241)
T ss_dssp             HHHHHHHHTCT--TCEEHHHHHHHTTSC------HHH-HHHHHHHHHTTTSEEECG--GGCEEEECSHHH
T ss_pred             HHHHHHHHhCC--CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEEeC--CCCeEEECHHHH
Confidence            45677787653  479999999999996      445 999999999999999632  237899987654

>2pbf_A Protein-L-isoaspartate O-methyltransferase beta-A methyltransferase; protein repair, isoaspartyl formation, P. falciparum; HET: SAH; 2.00A {Plasmodium falciparum}

Probab=96.17  E-value=0.006  Score=48.97  Aligned_cols=44  Identities=16%  Similarity=0.163  Sum_probs=37.0

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHC-----CCCeEEEccc-hHHhhhCCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKY-----PHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~-----P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .....+|+|||||.|.++..+++..     |+.+++.+|. |..++.+++
T Consensus        78 ~~~~~~VLdiG~G~G~~~~~la~~~~~~~~~~~~v~~vD~~~~~~~~a~~  127 (227)
T 2pbf_A           78 LKPGSRAIDVGSGSGYLTVCMAIKMNVLENKNSYVIGLERVKDLVNFSLE  127 (227)
T ss_dssp             SCTTCEEEEESCTTSHHHHHHHHHTTTTTCTTCEEEEEESCHHHHHHHHH
T ss_pred             CCCCCEEEEECCCCCHHHHHHHHHhcccCCCCCEEEEEeCCHHHHHHHHH
Confidence            4556899999999999999999986     6789999998 777777654

>2yvl_A TRMI protein, hypothetical protein; tRNA, methyltransferase, S-adenosylmethionine, structural GE NPPSFA; HET: SAM; 2.20A {Aquifex aeolicus}

Probab=96.17  E-value=0.0079  Score=48.78  Aligned_cols=49  Identities=14%  Similarity=0.211  Sum_probs=39.6

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .++...+ .....+|+|+|||.|.++..++++  ..+++.+|. |..++.+++
T Consensus        82 ~~~~~~~-~~~~~~vldiG~G~G~~~~~l~~~--~~~v~~vD~~~~~~~~a~~  131 (248)
T 2yvl_A           82 YIALKLN-LNKEKRVLEFGTGSGALLAVLSEV--AGEVWTFEAVEEFYKTAQK  131 (248)
T ss_dssp             HHHHHTT-CCTTCEEEEECCTTSHHHHHHHHH--SSEEEEECSCHHHHHHHHH
T ss_pred             HHHHhcC-CCCCCEEEEeCCCccHHHHHHHHh--CCEEEEEecCHHHHHHHHH
Confidence            4455555 566789999999999999999999  778999997 777776654

>1zq9_A Probable dimethyladenosine transferase; SGC, structural genomics, structural genomics consortium; HET: SAM; 1.90A {Homo sapiens} SCOP: c.66.1.24

Probab=96.16  E-value=0.0047  Score=52.05  Aligned_cols=49  Identities=16%  Similarity=0.350  Sum_probs=38.6

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~  233 (244)
                      ..+++.++ .....+|+|||||.|.++..++++..  +++.+|+ |..++.++
T Consensus        18 ~~i~~~~~-~~~~~~VLDiG~G~G~lt~~L~~~~~--~v~~vD~~~~~~~~a~   67 (285)
T 1zq9_A           18 NSIIDKAA-LRPTDVVLEVGPGTGNMTVKLLEKAK--KVVACELDPRLVAELH   67 (285)
T ss_dssp             HHHHHHTC-CCTTCEEEEECCTTSTTHHHHHHHSS--EEEEEESCHHHHHHHH
T ss_pred             HHHHHhcC-CCCCCEEEEEcCcccHHHHHHHhhCC--EEEEEECCHHHHHHHH
Confidence            45566666 56678999999999999999999864  6788887 66666654

>3fut_A Dimethyladenosine transferase; methyltransferase, dimethyltransferase, dual-specific methyltransferase, 16S rRNA methyltransferase; 1.52A {Thermus thermophilus} PDB: 3fuu_A* 3fuv_A 3fuw_A* 3fux_A*

Probab=96.09  E-value=0.0042  Score=52.12  Aligned_cols=49  Identities=12%  Similarity=0.108  Sum_probs=37.1

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+++..+ .... +|+|||||.|.++..++++.  .+++.+|+ |..++.+++
T Consensus        37 ~~Iv~~~~-~~~~-~VLEIG~G~G~lt~~L~~~~--~~V~avEid~~~~~~l~~   86 (271)
T 3fut_A           37 RRIVEAAR-PFTG-PVFEVGPGLGALTRALLEAG--AEVTAIEKDLRLRPVLEE   86 (271)
T ss_dssp             HHHHHHHC-CCCS-CEEEECCTTSHHHHHHHHTT--CCEEEEESCGGGHHHHHH
T ss_pred             HHHHHhcC-CCCC-eEEEEeCchHHHHHHHHHcC--CEEEEEECCHHHHHHHHH
Confidence            34566555 5555 99999999999999999986  46777777 666666543

>2oqg_A Possible transcriptional regulator, ARSR family P; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 1.54A {Rhodococcus SP}

Probab=96.08  E-value=0.0055  Score=43.85  Aligned_cols=59  Identities=12%  Similarity=0.235  Sum_probs=43.2

Q ss_pred             HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcc
Q 041256           34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPV  103 (244)
Q Consensus        34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~  103 (244)
                      .++.|+..|..    ++.|..|||+.+|++      +.. +.+.|+.|...|++..........|++|+.
T Consensus        22 ~r~~IL~~L~~----~~~~~~ela~~l~is------~~t-v~~~l~~L~~~gli~~~~~gr~~~y~l~~~   80 (114)
T 2oqg_A           22 TRWEILTELGR----ADQSASSLATRLPVS------RQA-IAKHLNALQACGLVESVKVGREIRYRALGA   80 (114)
T ss_dssp             HHHHHHHHHHH----SCBCHHHHHHHSSSC------HHH-HHHHHHHHHHTTSEEEEEETTEEEEEECSH
T ss_pred             HHHHHHHHHHc----CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCeeEEecCCEEEEEechH
Confidence            45667777844    689999999999997      456 999999999999998532111123666554

>1mkm_A ICLR transcriptional regulator; structural genomics, winged helix-turn-helix, PSI, protein structure initiative; 2.20A {Thermotoga maritima} SCOP: a.4.5.33 d.110.2.2

Probab=96.08  E-value=0.0064  Score=50.15  Aligned_cols=57  Identities=14%  Similarity=0.196  Sum_probs=46.2

Q ss_pred             cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccc
Q 041256           36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVS  104 (244)
Q Consensus        36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s  104 (244)
                      +.|++.|.+.+  +++|+.|||+.+|++      ..- +.|+|+.|...|++.++   ..+.|++++..
T Consensus        11 l~iL~~l~~~~--~~~~~~ela~~~gl~------~st-v~r~l~~L~~~G~v~~~---~~~~Y~lg~~~   67 (249)
T 1mkm_A           11 FEILDFIVKNP--GDVSVSEIAEKFNMS------VSN-AYKYMVVLEEKGFVLRK---KDKRYVPGYKL   67 (249)
T ss_dssp             HHHHHHHHHCS--SCBCHHHHHHHTTCC------HHH-HHHHHHHHHHTTSEEEC---TTSCEEECTHH
T ss_pred             HHHHHHHHhCC--CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCcEEEC---CCCcEEECHHH
Confidence            45677887653  479999999999996      445 99999999999999962   35789998754

>3lcc_A Putative methyl chloride transferase; halide methyltransferase; HET: SAH; 1.80A {Arabidopsis thaliana}

Probab=96.08  E-value=0.0028  Score=51.29  Aligned_cols=38  Identities=18%  Similarity=0.211  Sum_probs=32.6

Q ss_pred             ceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          195 KKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       195 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+|||||||.|.++..+++  ++.+++.+|+ |..++.+++
T Consensus        68 ~~vLDiGcG~G~~~~~l~~--~~~~v~gvD~s~~~~~~a~~  106 (235)
T 3lcc_A           68 GRALVPGCGGGHDVVAMAS--PERFVVGLDISESALAKANE  106 (235)
T ss_dssp             EEEEEETCTTCHHHHHHCB--TTEEEEEECSCHHHHHHHHH
T ss_pred             CCEEEeCCCCCHHHHHHHh--CCCeEEEEECCHHHHHHHHH
Confidence            5999999999999999976  6778999998 777877754

>2ih2_A Modification methylase TAQI; DNA, DNA methyltransferase, target base partner, 5-methylpyr 2(1H)-ONE, base flipping; HET: 5PY 6MA NEA; 1.61A {Thermus aquaticus} SCOP: c.66.1.27 d.287.1.1 PDB: 2ibs_A* 2ibt_A* 2ih4_A* 2ih5_A* 2jg3_A* 2np6_A* 2np7_A* 1aqj_A* 1aqi_A* 2adm_A* 1g38_A*

Probab=96.06  E-value=0.0079  Score=53.02  Aligned_cols=48  Identities=6%  Similarity=0.065  Sum_probs=37.4

Q ss_pred             HHhhcCCCCCcceEEEecCCccHHHHHHHHHC-CCCeEEEccc-hHHhhhC
Q 041256          184 VLESYKGFEHVKKLVDVGGGLGITLNMIISKY-PHIKGINYDL-PYVIKDA  232 (244)
Q Consensus       184 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~vi~~a  232 (244)
                      +++.++ .....+|+|+|||+|.++..+++++ +..+.+.+|+ |..++.|
T Consensus        31 ~~~~~~-~~~~~~vLD~gcGtG~~~~~~~~~~~~~~~i~gvDi~~~~~~~a   80 (421)
T 2ih2_A           31 MVSLAE-APRGGRVLEPACAHGPFLRAFREAHGTAYRFVGVEIDPKALDLP   80 (421)
T ss_dssp             HHHHCC-CCTTCEEEEETCTTCHHHHHHHHHHCSCSEEEEEESCTTTCCCC
T ss_pred             HHHhhc-cCCCCEEEECCCCChHHHHHHHHHhCCCCeEEEEECCHHHHHhC
Confidence            344444 3344699999999999999999988 7788999998 6666655

>3r4k_A Transcriptional regulator, ICLR family; DNA/RNA-binding 3-helical bundle, profilin-like, structural joint center for structural genomics, JCSG; 2.46A {Ruegeria SP}

Probab=96.06  E-value=0.0017  Score=54.12  Aligned_cols=59  Identities=15%  Similarity=0.286  Sum_probs=46.3

Q ss_pred             cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcccc
Q 041256           36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSA  105 (244)
Q Consensus        36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~  105 (244)
                      +.|++.|.+.+  +++|+.|||+++|++      ..- +.|+|+-|+..||+.++  .+.++|++++...
T Consensus         9 l~IL~~l~~~~--~~lsl~eia~~lgl~------ksT-~~RlL~tL~~~G~v~~~--~~~~~Y~lG~~~~   67 (260)
T 3r4k_A            9 LTLLTYFNHGR--LEIGLSDLTRLSGMN------KAT-VYRLMSELQEAGFVEQV--EGARSYRLGPQVL   67 (260)
T ss_dssp             HHHHTTCBTTB--SEEEHHHHHHHHCSC------HHH-HHHHHHHHHHTTSEEEC--SSSSEEEECTTHH
T ss_pred             HHHHHHHhhCC--CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEEc--CCCCcEEcCHHHH
Confidence            34667776543  689999999999996      445 99999999999999963  2237899988643

>3hp7_A Hemolysin, putative; structural genomics, APC64019, PSI-2, protein STR initiative, midwest center for structural genomics, MCSG; HET: MSE; 1.53A {Streptococcus thermophilus}

Probab=96.05  E-value=0.0072  Score=51.23  Aligned_cols=47  Identities=13%  Similarity=0.147  Sum_probs=34.8

Q ss_pred             HHHhhcCCCC-CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhh
Q 041256          183 KVLESYKGFE-HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKD  231 (244)
Q Consensus       183 ~~~~~~~~~~-~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~  231 (244)
                      .+++.+. .. ...+++|||||+|.++..++++ +.-+++.+|. |..++.
T Consensus        75 ~~l~~~~-~~~~g~~vLDiGcGTG~~t~~L~~~-ga~~V~aVDvs~~mL~~  123 (291)
T 3hp7_A           75 KALAVFN-LSVEDMITIDIGASTGGFTDVMLQN-GAKLVYAVDVGTNQLVW  123 (291)
T ss_dssp             HHHHHTT-CCCTTCEEEEETCTTSHHHHHHHHT-TCSEEEEECSSSSCSCH
T ss_pred             HHHHhcC-CCccccEEEecCCCccHHHHHHHhC-CCCEEEEEECCHHHHHH
Confidence            4455665 43 4579999999999999988886 5568899998 444443

>3opn_A Putative hemolysin; structural genomics, PSI-2, protein structure initiative, NE SGX research center for structural genomics, nysgxrc; 2.05A {Lactococcus lactis subsp}

Probab=96.04  E-value=0.011  Score=48.34  Aligned_cols=48  Identities=17%  Similarity=0.236  Sum_probs=35.0

Q ss_pred             HHHhhcCCCC-CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhC
Q 041256          183 KVLESYKGFE-HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDA  232 (244)
Q Consensus       183 ~~~~~~~~~~-~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a  232 (244)
                      .+++.++ .. ...+|+|||||+|.++..++++ ...+++.+|+ |..++.+
T Consensus        27 ~~L~~~~-~~~~g~~VLDiGcGtG~~t~~la~~-g~~~V~gvDis~~ml~~a   76 (232)
T 3opn_A           27 KALKEFH-LEINGKTCLDIGSSTGGFTDVMLQN-GAKLVYALDVGTNQLAWK   76 (232)
T ss_dssp             HHHHHTT-CCCTTCEEEEETCTTSHHHHHHHHT-TCSEEEEECSSCCCCCHH
T ss_pred             HHHHHcC-CCCCCCEEEEEccCCCHHHHHHHhc-CCCEEEEEcCCHHHHHHH
Confidence            4455555 33 4579999999999999999988 3348999998 5555543

>2y75_A HTH-type transcriptional regulator CYMR; DNA binding protein; 2.00A {Bacillus subtilis}

Probab=96.00  E-value=0.0082  Score=44.24  Aligned_cols=45  Identities=18%  Similarity=0.198  Sum_probs=36.2

Q ss_pred             CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecC-CceeecCc
Q 041256           49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDG-QRLYSLAP  102 (244)
Q Consensus        49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~-~~~y~~t~  102 (244)
                      ++.|..+||+.++++      +.. ++++|+.|...|++...  .+ .|.|.++.
T Consensus        25 ~~~s~~ela~~~~i~------~~~-v~~il~~L~~~Glv~~~--~g~~ggy~L~~   70 (129)
T 2y75_A           25 GPTSLKSIAQTNNLS------EHY-LEQLVSPLRNAGLVKSI--RGAYGGYVLGS   70 (129)
T ss_dssp             CCBCHHHHHHHTTSC------HHH-HHHHHHHHHHTTSEEEC------CCEEESS
T ss_pred             CcCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCceEec--CCCCCceEeCC
Confidence            689999999999997      567 99999999999999852  22 36688765

>2gb4_A Thiopurine S-methyltransferase; 18204406, thiopurine methyltransferase, structural genomics, PSI, protein structure initiative; HET: SAH; 1.25A {Mus musculus} PDB: 3bgi_A* 3bgd_A* 2bzg_A* 2h11_A*

Probab=95.99  E-value=0.0047  Score=51.13  Aligned_cols=40  Identities=8%  Similarity=0.026  Sum_probs=34.1

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~  233 (244)
                      ....+|+|||||.|..+..|+++  +.+++.+|+ |..++.|+
T Consensus        67 ~~~~~vLD~GCG~G~~~~~La~~--G~~V~gvD~S~~~i~~a~  107 (252)
T 2gb4_A           67 QSGLRVFFPLCGKAIEMKWFADR--GHTVVGVEISEIGIREFF  107 (252)
T ss_dssp             CCSCEEEETTCTTCTHHHHHHHT--TCEEEEECSCHHHHHHHH
T ss_pred             CCCCeEEEeCCCCcHHHHHHHHC--CCeEEEEECCHHHHHHHH
Confidence            34579999999999999999987  568999998 78887764

>3evz_A Methyltransferase; NYSGXRC, NEW YORK SGX research CE structural genomics, protein structure initiative, pyrococc furiosus, PSI-2; 2.20A {Pyrococcus furiosus}

Probab=95.98  E-value=0.0045  Score=49.77  Aligned_cols=43  Identities=12%  Similarity=0.115  Sum_probs=36.9

Q ss_pred             CCCcceEEEecCC-ccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          191 FEHVKKLVDVGGG-LGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       191 ~~~~~~vvDVGGG-~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .....+|+||||| +|.++..+++.+ ..+++.+|. |..++.+++
T Consensus        53 ~~~~~~vLDlG~G~~G~~~~~la~~~-~~~v~~vD~s~~~~~~a~~   97 (230)
T 3evz_A           53 LRGGEVALEIGTGHTAMMALMAEKFF-NCKVTATEVDEEFFEYARR   97 (230)
T ss_dssp             CCSSCEEEEECCTTTCHHHHHHHHHH-CCEEEEEECCHHHHHHHHH
T ss_pred             cCCCCEEEEcCCCHHHHHHHHHHHhc-CCEEEEEECCHHHHHHHHH
Confidence            3566899999999 999999999987 788999998 788877764

>1ixk_A Methyltransferase; open beta sheet; 1.90A {Pyrococcus horikoshii} SCOP: c.66.1.38

Probab=95.95  E-value=0.0086  Score=51.17  Aligned_cols=49  Identities=6%  Similarity=0.000  Sum_probs=39.0

Q ss_pred             HhhcCCCCCcceEEEecCCccHHHHHHHHHCC-CCeEEEccc-hHHhhhCCC
Q 041256          185 LESYKGFEHVKKLVDVGGGLGITLNMIISKYP-HIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       185 ~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...++ .....+|+|+|||.|..+..+++..+ ..+++.+|+ |..++.+++
T Consensus       111 ~~~l~-~~~g~~VLDlg~G~G~~t~~la~~~~~~~~v~avD~s~~~l~~a~~  161 (315)
T 1ixk_A          111 PVALD-PKPGEIVADMAAAPGGKTSYLAQLMRNDGVIYAFDVDENRLRETRL  161 (315)
T ss_dssp             HHHHC-CCTTCEEEECCSSCSHHHHHHHHHTTTCSEEEEECSCHHHHHHHHH
T ss_pred             HHHhC-CCCCCEEEEeCCCCCHHHHHHHHHhCCCCEEEEEcCCHHHHHHHHH
Confidence            34444 56668999999999999999999975 488999998 676776654

>3htx_A HEN1; HEN1, small RNA methyltransferase, protein-RNA complex; HET: SAH; 3.10A {Arabidopsis thaliana}

Probab=95.92  E-value=0.0033  Score=60.47  Aligned_cols=43  Identities=26%  Similarity=0.319  Sum_probs=36.8

Q ss_pred             CCcceEEEecCCccHHHHHHHHHC-CCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKY-PHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ....+|||||||.|.++..+++.. |..+++.+|+ |..++.|++
T Consensus       720 ~~g~rVLDVGCGTG~lai~LAr~g~p~a~VtGVDIS~emLe~ARe  764 (950)
T 3htx_A          720 SSASTLVDFGCGSGSLLDSLLDYPTSLQTIIGVDISPKGLARAAK  764 (950)
T ss_dssp             SCCSEEEEETCSSSHHHHHHTSSCCCCCEEEEEESCHHHHHHHHH
T ss_pred             cCCCEEEEECCCCCHHHHHHHHhCCCCCeEEEEECCHHHHHHHHH
Confidence            356899999999999999999998 6679999998 777777743

>1y8c_A S-adenosylmethionine-dependent methyltransferase; structural genomics, protein structure initiative, PSI; 2.50A {Clostridium acetobutylicum} SCOP: c.66.1.43

Probab=95.92  E-value=0.0061  Score=49.13  Aligned_cols=40  Identities=18%  Similarity=0.223  Sum_probs=33.6

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...+|+|||||.|.++..++++  ..+++.+|. |..++.+++
T Consensus        37 ~~~~vLdiG~G~G~~~~~l~~~--~~~~~~~D~s~~~~~~a~~   77 (246)
T 1y8c_A           37 VFDDYLDLACGTGNLTENLCPK--FKNTWAVDLSQEMLSEAEN   77 (246)
T ss_dssp             CTTEEEEETCTTSTTHHHHGGG--SSEEEEECSCHHHHHHHHH
T ss_pred             CCCeEEEeCCCCCHHHHHHHHC--CCcEEEEECCHHHHHHHHH
Confidence            4579999999999999999998  457899998 777777654

>1r1u_A CZRA, repressor protein; zinc, DNA binding, transcriptional regulation, winged HTH protein, transcription repressor; 2.00A {Staphylococcus aureus} SCOP: a.4.5.5 PDB: 1r1v_A 2kjb_A 2kjc_A

Probab=95.91  E-value=0.0057  Score=43.52  Aligned_cols=50  Identities=22%  Similarity=0.343  Sum_probs=40.4

Q ss_pred             HHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           30 MQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        30 L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      |..-.++.|+..|..    ++.|+.|||+.+|++      ... +.+.|+.|...|++...
T Consensus        23 l~~~~r~~IL~~L~~----~~~~~~ela~~l~is------~st-vs~~L~~L~~~Glv~~~   72 (106)
T 1r1u_A           23 LGDYNRIRIMELLSV----SEASVGHISHQLNLS------QSN-VSHQLKLLKSVHLVKAK   72 (106)
T ss_dssp             TCSHHHHHHHHHHHH----CCBCHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEEE
T ss_pred             hCCHHHHHHHHHHHh----CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCeEEE
Confidence            333455667777875    689999999999997      456 99999999999999853

>1wy7_A Hypothetical protein PH1948; seven-stranded beta sheet, methyltransferase fold, structura genomics, transferase; HET: SAH; 2.20A {Pyrococcus horikoshii} SCOP: c.66.1.32

Probab=95.91  E-value=0.0054  Score=48.44  Aligned_cols=42  Identities=14%  Similarity=0.062  Sum_probs=34.5

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ....+|+|+|||.|.++..+++..+ -+++.+|. |..++.+++
T Consensus        48 ~~~~~vlD~g~G~G~~~~~l~~~~~-~~v~~vD~~~~~~~~a~~   90 (207)
T 1wy7_A           48 IEGKVVADLGAGTGVLSYGALLLGA-KEVICVEVDKEAVDVLIE   90 (207)
T ss_dssp             STTCEEEEETCTTCHHHHHHHHTTC-SEEEEEESCHHHHHHHHH
T ss_pred             CCcCEEEEeeCCCCHHHHHHHHcCC-CEEEEEECCHHHHHHHHH
Confidence            3457999999999999999998743 37899998 788877764

>1ub9_A Hypothetical protein PH1061; helix-turn-helix motif, winged helix motif, structural genom transcription; 2.05A {Pyrococcus horikoshii} SCOP: a.4.5.28

Probab=95.91  E-value=0.0049  Score=42.86  Aligned_cols=67  Identities=15%  Similarity=0.199  Sum_probs=48.4

Q ss_pred             HHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCC---ceeecCccc
Q 041256           28 AVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQ---RLYSLAPVS  104 (244)
Q Consensus        28 ~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~---~~y~~t~~s  104 (244)
                      .++..-.++.|+..|...   ++.|..+||+.++++      ... +.+.|+.|...|++......++   ..|++|+.+
T Consensus        11 ~~l~~~~~~~iL~~L~~~---~~~~~~ela~~l~is------~~t-vs~~l~~L~~~gli~~~~~~~~~r~~~~~lt~~g   80 (100)
T 1ub9_A           11 HILGNPVRLGIMIFLLPR---RKAPFSQIQKVLDLT------PGN-LDSHIRVLERNGLVKTYKVIADRPRTVVEITDFG   80 (100)
T ss_dssp             HHHHSHHHHHHHHHHHHH---SEEEHHHHHHHTTCC------HHH-HHHHHHHHHHTTSEEEEEECSSSCEEEEEECHHH
T ss_pred             cccCChHHHHHHHHHHhc---CCcCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEEEecCCCcceEEEEECHHH
Confidence            344555677788888654   589999999999997      456 9999999999999985321111   246666654

>1i1n_A Protein-L-isoaspartate O-methyltransferase; S-adenosyl homocysteine, protein repair; HET: SAH; 1.50A {Homo sapiens} SCOP: c.66.1.7 PDB: 1kr5_A*

Probab=95.89  E-value=0.0053  Score=49.26  Aligned_cols=42  Identities=26%  Similarity=0.235  Sum_probs=35.8

Q ss_pred             CCcceEEEecCCccHHHHHHHHHC-CCCeEEEccc-hHHhhhCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKY-PHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~vi~~a~  233 (244)
                      ....+|+|||||.|.++..+++.. |+.+++.+|. |..++.++
T Consensus        76 ~~~~~vLDiG~G~G~~~~~la~~~~~~~~v~~vD~s~~~~~~a~  119 (226)
T 1i1n_A           76 HEGAKALDVGSGSGILTACFARMVGCTGKVIGIDHIKELVDDSV  119 (226)
T ss_dssp             CTTCEEEEETCTTSHHHHHHHHHHCTTCEEEEEESCHHHHHHHH
T ss_pred             CCCCEEEEEcCCcCHHHHHHHHHhCCCcEEEEEeCCHHHHHHHH
Confidence            455799999999999999999985 7789999998 77777665

>2fpo_A Methylase YHHF; structural genomics, putative methyltransferase, PSI, protei structure initiative; HET: MSE; 2.05A {Escherichia coli} SCOP: c.66.1.46

Probab=95.89  E-value=0.0052  Score=48.83  Aligned_cols=40  Identities=15%  Similarity=0.086  Sum_probs=33.3

Q ss_pred             cceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+|+|+|||+|.++..++++.. -+++.+|+ |..++.+++
T Consensus        55 ~~~vLDlgcG~G~~~~~l~~~~~-~~V~~vD~s~~~l~~a~~   95 (202)
T 2fpo_A           55 DAQCLDCFAGSGALGLEALSRYA-AGATLIEMDRAVSQQLIK   95 (202)
T ss_dssp             TCEEEETTCTTCHHHHHHHHTTC-SEEEEECSCHHHHHHHHH
T ss_pred             CCeEEEeCCCcCHHHHHHHhcCC-CEEEEEECCHHHHHHHHH
Confidence            36899999999999999888754 37899998 788887764

>2frn_A Hypothetical protein PH0793; structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; 2.10A {Pyrococcus horikoshii OT3} PDB: 3k6r_A 3a25_A* 3a26_A*

Probab=95.87  E-value=0.0036  Score=52.51  Aligned_cols=42  Identities=24%  Similarity=0.150  Sum_probs=36.6

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ....+|+|+|||+|.++..++++.+. +++..|+ |..++.+++
T Consensus       124 ~~~~~VLDlgcG~G~~~~~la~~~~~-~V~~vD~s~~~~~~a~~  166 (278)
T 2frn_A          124 KPDELVVDMFAGIGHLSLPIAVYGKA-KVIAIEKDPYTFKFLVE  166 (278)
T ss_dssp             CTTCEEEETTCTTTTTHHHHHHHTCC-EEEEECCCHHHHHHHHH
T ss_pred             CCCCEEEEecccCCHHHHHHHHhCCC-EEEEEECCHHHHHHHHH
Confidence            44589999999999999999999887 8999998 788887764

>2hzt_A Putative HTH-type transcriptional regulator YTCD; DNA-binding protein, HTH-type transcription regulators, structural genomics, PSI-2; HET: CSU MSE; 2.00A {Bacillus subtilis} SCOP: a.4.5.69

Probab=95.83  E-value=0.013  Score=41.73  Aligned_cols=52  Identities=17%  Similarity=0.190  Sum_probs=39.8

Q ss_pred             CCCCHHHHHHhC-CCCCCCCcchhccHHHHHHHHhhCCcccceeecCC---ceeecCcccccc
Q 041256           49 AKLSVAEIVAQI-PLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQ---RLYSLAPVSAYF  107 (244)
Q Consensus        49 g~~t~~eLA~~~-~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~---~~y~~t~~s~~l  107 (244)
                      ++.+..||++.+ +++      +.. +.+.|+.|...|++++.....+   -.|++|+.+..+
T Consensus        26 ~~~~~~eLa~~l~~is------~~t-ls~~L~~Le~~GlI~r~~~~~d~r~~~y~LT~~G~~l   81 (107)
T 2hzt_A           26 GKKRTSELKRLMPNIT------QKM-LTQQLRELEADGVINRIVYNQVPPKVEYELSEYGRSL   81 (107)
T ss_dssp             CCBCHHHHHHHCTTSC------HHH-HHHHHHHHHHTTSEEEEEECSSSCEEEEEECTTGGGG
T ss_pred             CCCCHHHHHHHhcCCC------HHH-HHHHHHHHHHCCCEEEeecCCCCCeEEEEECccHHHH
Confidence            689999999999 997      456 9999999999999986432211   247777766433

>3gdh_A Trimethylguanosine synthase homolog; M7G, CAP, dimethyltransferase, usnRNA, snoRNA, telomerase, cytoplasm, methyltransferase, nucleus; HET: MGP SAH; 2.00A {Homo sapiens} PDB: 3egi_A*

Probab=95.81  E-value=0.0055  Score=49.71  Aligned_cols=40  Identities=23%  Similarity=0.181  Sum_probs=34.3

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...+|+|||||+|.++..+++..  .+++.+|+ |..++.+++
T Consensus        78 ~~~~vLD~gcG~G~~~~~la~~~--~~v~~vD~s~~~~~~a~~  118 (241)
T 3gdh_A           78 KCDVVVDAFCGVGGNTIQFALTG--MRVIAIDIDPVKIALARN  118 (241)
T ss_dssp             CCSEEEETTCTTSHHHHHHHHTT--CEEEEEESCHHHHHHHHH
T ss_pred             CCCEEEECccccCHHHHHHHHcC--CEEEEEECCHHHHHHHHH
Confidence            45799999999999999999975  78899998 778877764

>3bzb_A Uncharacterized protein; RED ALGA, protein structure initiat center for eukaryotic structural genomics, CESG, structural genomics; 2.79A {Cyanidioschyzon merolae}

Probab=95.79  E-value=0.0081  Score=50.35  Aligned_cols=42  Identities=17%  Similarity=0.215  Sum_probs=33.5

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc--hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL--PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl--p~vi~~a~~  234 (244)
                      ....+|+|||||+|.++..+++.. ..+++..|+  |..++.+++
T Consensus        78 ~~~~~vLDlG~G~G~~~~~~a~~~-~~~v~~~D~s~~~~~~~a~~  121 (281)
T 3bzb_A           78 IAGKTVCELGAGAGLVSIVAFLAG-ADQVVATDYPDPEILNSLES  121 (281)
T ss_dssp             TTTCEEEETTCTTSHHHHHHHHTT-CSEEEEEECSCHHHHHHHHH
T ss_pred             cCCCeEEEecccccHHHHHHHHcC-CCEEEEEeCCCHHHHHHHHH
Confidence            345799999999999999888763 348999999  677777653

>2kko_A Possible transcriptional regulatory protein (possibly ARSR-family); NESG, DNA-binding, transcription regulation, WHTH, homodimer; NMR {Mycobacterium bovis} PDB: 3gw2_A

Probab=95.79  E-value=0.003  Score=45.25  Aligned_cols=46  Identities=13%  Similarity=0.226  Sum_probs=38.0

Q ss_pred             HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      .++.|+..|.+    ++.|+.|||+.+|++      +.. +.+.|+.|...|++...
T Consensus        26 ~r~~IL~~L~~----~~~s~~eLa~~lgis------~st-vs~~L~~L~~~GlV~~~   71 (108)
T 2kko_A           26 RRLQILDLLAQ----GERAVEAIATATGMN------LTT-ASANLQALKSGGLVEAR   71 (108)
T ss_dssp             TTHHHHHHHTT----CCEEHHHHHHHHTCC------HHH-HHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHHHc----CCcCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCeEEE
Confidence            34556667765    689999999999997      456 99999999999999853

>3id6_C Fibrillarin-like rRNA/TRNA 2'-O-methyltransferase; C/D guide RNA, 2'-O-methylation, coiled-coil, methyltransfer binding, rRNA processing; HET: SAM; 2.60A {Sulfolobus solfataricus} SCOP: c.66.1.0 PDB: 3id5_B* 3pla_E*

Probab=95.77  E-value=0.0099  Score=48.69  Aligned_cols=51  Identities=18%  Similarity=0.230  Sum_probs=37.9

Q ss_pred             CCCcceEEEecCCccHHHHHHHHH-CCCCeEEEccc-hHH----hhhCCCCCCceee
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISK-YPHIKGINYDL-PYV----IKDAPSYPGTLFI  241 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~-~P~l~~~v~Dl-p~v----i~~a~~~~~i~~~  241 (244)
                      +....+|+|+|||+|.++..+++. .|+-+++.+|+ |..    ++.++++++|+++
T Consensus        74 l~~g~~VLDlG~GtG~~t~~la~~v~~~G~V~avD~s~~~l~~l~~~a~~r~nv~~i  130 (232)
T 3id6_C           74 IRKGTKVLYLGAASGTTISHVSDIIELNGKAYGVEFSPRVVRELLLVAQRRPNIFPL  130 (232)
T ss_dssp             CCTTCEEEEETCTTSHHHHHHHHHHTTTSEEEEEECCHHHHHHHHHHHHHCTTEEEE
T ss_pred             CCCCCEEEEEeecCCHHHHHHHHHhCCCCEEEEEECcHHHHHHHHHHhhhcCCeEEE
Confidence            556789999999999999999886 47888999998 433    3444444555543

>3tm4_A TRNA (guanine N2-)-methyltransferase TRM14; rossmann fold, thump domain, tRNA methyltransferase; HET: SAM; 1.95A {Pyrococcus furiosus} PDB: 3tlj_A* 3tm5_A*

Probab=95.72  E-value=0.006  Score=53.42  Aligned_cols=44  Identities=14%  Similarity=-0.074  Sum_probs=38.5

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      |....+|+|+|||+|.+++.+++..+..+++.+|+ |..++.|++
T Consensus       215 ~~~~~~vLD~gCGsG~~~i~~a~~~~~~~v~g~Dis~~~l~~A~~  259 (373)
T 3tm4_A          215 ELDGGSVLDPMCGSGTILIELALRRYSGEIIGIEKYRKHLIGAEM  259 (373)
T ss_dssp             TCCSCCEEETTCTTCHHHHHHHHTTCCSCEEEEESCHHHHHHHHH
T ss_pred             cCCCCEEEEccCcCcHHHHHHHHhCCCCeEEEEeCCHHHHHHHHH
Confidence            45668999999999999999999998778999998 888888764

>3ajd_A Putative methyltransferase MJ0026; tRNA, M5C, rossmann fold, structural genomics, riken structu genomics/proteomics initiative; 1.27A {Methanocaldococcus jannaschii} PDB: 3a4t_A

Probab=95.68  E-value=0.0083  Score=50.08  Aligned_cols=44  Identities=9%  Similarity=-0.028  Sum_probs=37.0

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCCC-CeEEEccc-hHHhhhCCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYPH-IKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dl-p~vi~~a~~  234 (244)
                      .....+|+|+|||.|..+..+++..++ .+++.+|. |..++.+++
T Consensus        81 ~~~g~~VLDlgaG~G~~t~~la~~~~~~~~v~avD~~~~~l~~~~~  126 (274)
T 3ajd_A           81 PREDDFILDMCAAPGGKTTHLAQLMKNKGTIVAVEISKTRTKALKS  126 (274)
T ss_dssp             CCTTCEEEETTCTTCHHHHHHHHHTTTCSEEEEEESCHHHHHHHHH
T ss_pred             CCCcCEEEEeCCCccHHHHHHHHHcCCCCEEEEECCCHHHHHHHHH
Confidence            455679999999999999999999887 88999998 666766653

>2kw5_A SLR1183 protein; structural genomics, northeast structural genomics consortium (NESG), PSI-2, protein structure initiative, unknown function; NMR {Synechocystis} PDB: 3mer_A

Probab=95.68  E-value=0.006  Score=47.94  Aligned_cols=37  Identities=16%  Similarity=0.120  Sum_probs=31.7

Q ss_pred             eEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          196 KLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       196 ~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      +|+|||||.|.++..+++.  +.+++.+|. |..++.+++
T Consensus        32 ~vLdiGcG~G~~~~~l~~~--~~~v~~vD~s~~~~~~a~~   69 (202)
T 2kw5_A           32 KILCLAEGEGRNACFLASL--GYEVTAVDQSSVGLAKAKQ   69 (202)
T ss_dssp             EEEECCCSCTHHHHHHHTT--TCEEEEECSSHHHHHHHHH
T ss_pred             CEEEECCCCCHhHHHHHhC--CCeEEEEECCHHHHHHHHH
Confidence            9999999999999999987  568999998 777776654

>2htj_A P fimbrial regulatory protein KS71A; winged helix-turn-helix, PAP PILI, transcription activator; NMR {Escherichia coli} SCOP: a.4.5.73

Probab=95.67  E-value=0.013  Score=39.43  Aligned_cols=43  Identities=16%  Similarity=0.200  Sum_probs=36.8

Q ss_pred             ChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           37 DVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        37 gifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      .|++.|.+.   ++.|..|||+.+|++      ..- +.+.|+.|...|++..
T Consensus         4 ~Il~~L~~~---~~~s~~eLa~~lgvs------~~t-v~r~L~~L~~~GlI~~   46 (81)
T 2htj_A            4 EILEFLNRH---NGGKTAEIAEALAVT------DYQ-ARYYLLLLEKAGMVQR   46 (81)
T ss_dssp             HHHHHHHHS---CCCCHHHHHHHHTSC------HHH-HHHHHHHHHHHTSEEE
T ss_pred             HHHHHHHHc---CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEE
Confidence            467777765   689999999999997      455 9999999999999984

>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19

Probab=95.66  E-value=0.0091  Score=40.66  Aligned_cols=59  Identities=12%  Similarity=0.126  Sum_probs=44.5

Q ss_pred             HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccc
Q 041256           34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVS  104 (244)
Q Consensus        34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s  104 (244)
                      ....|.+.|.+.   | .|+.|||+++|++      ... +++.|.-|...|++.... ..+-.|+++..+
T Consensus        18 ~~~~IL~lL~~~---g-~sa~eLAk~LgiS------k~a-Vr~~L~~Le~eG~I~~~~-~~PP~W~~~~~~   76 (82)
T 1oyi_A           18 IVCEAIKTIGIE---G-ATAAQLTRQLNME------KRE-VNKALYDLQRSAMVYSSD-DIPPRWFMTTEA   76 (82)
T ss_dssp             HHHHHHHHHSSS---T-EEHHHHHHHSSSC------HHH-HHHHHHHHHHHTSSEECS-SSSCEEESCC--
T ss_pred             HHHHHHHHHHHc---C-CCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEeCC-CCCCcceeccCc
Confidence            445677788763   4 9999999999997      556 999999999999998632 225677776654

>2avn_A Ubiquinone/menaquinone biosynthesis methyltransfe related protein; ubiquinone/menaquinone biosynthesis methyltransferase-relate protein; HET: SAI; 2.35A {Thermotoga maritima} SCOP: c.66.1.41

Probab=95.66  E-value=0.0068  Score=49.89  Aligned_cols=39  Identities=18%  Similarity=0.250  Sum_probs=32.8

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~  233 (244)
                      ...+|||||||.|.++..++++  ..+++.+|. |..++.++
T Consensus        54 ~~~~vLDiGcG~G~~~~~l~~~--~~~v~gvD~s~~~l~~a~   93 (260)
T 2avn_A           54 NPCRVLDLGGGTGKWSLFLQER--GFEVVLVDPSKEMLEVAR   93 (260)
T ss_dssp             SCCEEEEETCTTCHHHHHHHTT--TCEEEEEESCHHHHHHHH
T ss_pred             CCCeEEEeCCCcCHHHHHHHHc--CCeEEEEeCCHHHHHHHH
Confidence            5579999999999999999987  568899998 77776654

>2h1r_A Dimethyladenosine transferase, putative; SGC toronto dimethyladenosine transferase, structural genomics, structural genomics consortium; 1.89A {Plasmodium falciparum}

Probab=95.65  E-value=0.0068  Score=51.43  Aligned_cols=50  Identities=18%  Similarity=0.310  Sum_probs=38.6

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+++..+ .....+|+|||||.|.++..++++  ..+++.+|+ |..++.+++
T Consensus        32 ~~i~~~~~-~~~~~~VLDiG~G~G~lt~~La~~--~~~v~~vDi~~~~~~~a~~   82 (299)
T 2h1r_A           32 DKIIYAAK-IKSSDIVLEIGCGTGNLTVKLLPL--AKKVITIDIDSRMISEVKK   82 (299)
T ss_dssp             HHHHHHHC-CCTTCEEEEECCTTSTTHHHHTTT--SSEEEEECSCHHHHHHHHH
T ss_pred             HHHHHhcC-CCCcCEEEEEcCcCcHHHHHHHhc--CCEEEEEECCHHHHHHHHH
Confidence            34555555 566689999999999999999987  457888998 777766653

>4azs_A Methyltransferase WBDD; kinase; HET: AMP SAM; 2.15A {Escherichia coli} PDB: 4azt_A* 4azv_A* 4azw_A*

Probab=95.61  E-value=0.0069  Score=56.06  Aligned_cols=41  Identities=17%  Similarity=0.140  Sum_probs=34.7

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ....+|||||||.|.++..+++.  +.+++.+|+ |..|+.|+.
T Consensus        65 ~~~~~vLDvGCG~G~~~~~la~~--ga~V~giD~~~~~i~~a~~  106 (569)
T 4azs_A           65 GRPLNVLDLGCAQGFFSLSLASK--GATIVGIDFQQENINVCRA  106 (569)
T ss_dssp             TSCCEEEEETCTTSHHHHHHHHT--TCEEEEEESCHHHHHHHHH
T ss_pred             CCCCeEEEECCCCcHHHHHHHhC--CCEEEEECCCHHHHHHHHH
Confidence            34578999999999999999997  678999998 778887763

>3f6v_A Possible transcriptional regulator, ARSR family protein; probable transcriptional repressor ARSR family, structural genomics, PSI-2; 1.48A {Rhodococcus SP}

Probab=95.61  E-value=0.0083  Score=45.78  Aligned_cols=67  Identities=16%  Similarity=0.250  Sum_probs=50.2

Q ss_pred             HHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcc
Q 041256           26 LPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPV  103 (244)
Q Consensus        26 ~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~  103 (244)
                      ...+|.--.++.|+..|.+    ++.|+.|||+.+|++      ... +.+-|+.|...|++........-.|++|+.
T Consensus        51 ~l~aL~~p~R~~IL~~L~~----~~~t~~eLa~~lgls------~st-vs~hL~~L~~aGlV~~~~~Gr~~~y~lt~~  117 (151)
T 3f6v_A           51 QLEVAAEPTRRRLVQLLTS----GEQTVNNLAAHFPAS------RSA-ISQHLRVLTEAGLVTPRKDGRFRYYRLDPQ  117 (151)
T ss_dssp             HHHHHTSHHHHHHHHHGGG----CCEEHHHHHTTSSSC------HHH-HHHHHHHHHHTTSEEEEEETTEEEEEECHH
T ss_pred             HHHHhCCHHHHHHHHHHHh----CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEEEecCCEEEEEEChH
Confidence            3456666678889999985    699999999999997      456 999999999999998632111124666553

>1vlm_A SAM-dependent methyltransferase; possible histamine methyltransferase, structural genomics, JCSG, protein struc initiative, PSI; 2.20A {Thermotoga maritima} SCOP: c.66.1.41

Probab=95.58  E-value=0.0064  Score=48.63  Aligned_cols=35  Identities=20%  Similarity=0.122  Sum_probs=27.8

Q ss_pred             cceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+|+|||||.|.++..++++      +.+|. |..++.+++
T Consensus        48 ~~~vLDiG~G~G~~~~~l~~~------~~vD~s~~~~~~a~~   83 (219)
T 1vlm_A           48 EGRGVEIGVGTGRFAVPLKIK------IGVEPSERMAEIARK   83 (219)
T ss_dssp             SSCEEEETCTTSTTHHHHTCC------EEEESCHHHHHHHHH
T ss_pred             CCcEEEeCCCCCHHHHHHHHH------hccCCCHHHHHHHHh
Confidence            579999999999999988765      77787 666665543

>1g6q_1 HnRNP arginine N-methyltransferase; SAM-binding domain, beta-barrel, mixed alpha-beta, hexamer; 2.90A {Saccharomyces cerevisiae} SCOP: c.66.1.6

Probab=95.58  E-value=0.0045  Score=53.17  Aligned_cols=41  Identities=27%  Similarity=0.290  Sum_probs=33.0

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~  234 (244)
                      +..+|+|||||+|.++..++++ +..+++.+|....++.+++
T Consensus        38 ~~~~VLDiGcGtG~ls~~la~~-g~~~v~~vD~s~~~~~a~~   78 (328)
T 1g6q_1           38 KDKIVLDVGCGTGILSMFAAKH-GAKHVIGVDMSSIIEMAKE   78 (328)
T ss_dssp             TTCEEEEETCTTSHHHHHHHHT-CCSEEEEEESSTHHHHHHH
T ss_pred             CCCEEEEecCccHHHHHHHHHC-CCCEEEEEChHHHHHHHHH
Confidence            3479999999999999988886 5568999998766666543

>1tbx_A ORF F-93, hypothetical 11.0 kDa protein; sulfolobus spindle virus, winged helix, fusellovirus; 2.70A {Sulfolobus virus 1} SCOP: a.4.5.48

Probab=95.56  E-value=0.008  Score=41.98  Aligned_cols=63  Identities=13%  Similarity=0.202  Sum_probs=45.6

Q ss_pred             cChhhHHhhcCCCCCCCHHHH----HHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccccccc
Q 041256           36 LDVFEIISKAGPGAKLSVAEI----VAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFV  108 (244)
Q Consensus        36 lgifd~L~~~~~~g~~t~~eL----A~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l~  108 (244)
                      +.++..|.+.   ++.|..+|    |+.++++      +.. +.++++.|...|++.+........|.+|+.++.+.
T Consensus        11 ~~iL~~l~~~---~~~~~~el~~~la~~l~is------~~t-vs~~l~~Le~~gli~r~~~~r~~~~~LT~~G~~~~   77 (99)
T 1tbx_A           11 AIVLAYLYDN---EGIATYDLYKKVNAEFPMS------TAT-FYDAKKFLIQEGFVKERQERGEKRLYLTEKGKLFA   77 (99)
T ss_dssp             HHHHHHHTTC---TTCBHHHHHHHHHTTSCCC------HHH-HHHHHHHHHHTTSEEEEEETTEEEEEECHHHHHHH
T ss_pred             HHHHHHHHHc---CCcCHHHHHHHHHHHcCCC------HHH-HHHHHHHHHHCCCEEEEecCCceEEEECHHHHHHH
Confidence            4456666654   68999999    9999997      456 99999999999999864322223466777665443

>1ri5_A MRNA capping enzyme; methyltransferase, M7G, messenger RNA CAP, structural genomics, PSI, protein structure initiative; 2.10A {Encephalitozoon cuniculi} SCOP: c.66.1.34 PDB: 1ri2_A* 1ri3_A* 1ri1_A* 1ri4_A 1z3c_A* 2hv9_A*

Probab=95.56  E-value=0.011  Score=49.12  Aligned_cols=42  Identities=21%  Similarity=0.148  Sum_probs=34.2

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ....+|||||||.|.++..+++. +..+++.+|+ |..++.+++
T Consensus        63 ~~~~~vLDiGcG~G~~~~~l~~~-~~~~v~gvD~s~~~~~~a~~  105 (298)
T 1ri5_A           63 KRGDSVLDLGCGKGGDLLKYERA-GIGEYYGVDIAEVSINDARV  105 (298)
T ss_dssp             CTTCEEEEETCTTTTTHHHHHHH-TCSEEEEEESCHHHHHHHHH
T ss_pred             CCCCeEEEECCCCCHHHHHHHHC-CCCEEEEEECCHHHHHHHHH
Confidence            45589999999999999997776 5668999998 777776653

>1r18_A Protein-L-isoaspartate(D-aspartate)-O-methyltrans; methyltransferase, isomerization, protein repair, S-adenosyl homocysteine; HET: SAH; 2.20A {Drosophila melanogaster} SCOP: c.66.1.7

Probab=95.54  E-value=0.0073  Score=48.62  Aligned_cols=44  Identities=11%  Similarity=0.246  Sum_probs=35.5

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCC------CCeEEEccc-hHHhhhCCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYP------HIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P------~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .....+|+|||||.|.++..+++..+      ..+++.+|. |..++.+++
T Consensus        82 ~~~~~~VLdiG~G~G~~~~~la~~~~~~~~~~~~~v~~vD~~~~~~~~a~~  132 (227)
T 1r18_A           82 LKPGARILDVGSGSGYLTACFYRYIKAKGVDADTRIVGIEHQAELVRRSKA  132 (227)
T ss_dssp             CCTTCEEEEESCTTSHHHHHHHHHHHHSCCCTTCEEEEEESCHHHHHHHHH
T ss_pred             CCCCCEEEEECCCccHHHHHHHHhcccccCCccCEEEEEEcCHHHHHHHHH
Confidence            34557999999999999999999765      368899997 777776653

>2k02_A Ferrous iron transport protein C; FEOC, iron-sulfur, metal-binding, metal binding protein; NMR {Klebsiella pneumoniae subsp}

Probab=95.54  E-value=0.013  Score=40.36  Aligned_cols=43  Identities=9%  Similarity=0.251  Sum_probs=37.8

Q ss_pred             hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      |.+.|.+.   |.+|+.|||+.++++      +.- ++|.|..|...|++.+.
T Consensus         7 Il~~L~~~---g~vsv~eLA~~l~VS------~~T-IRrDL~~Le~~G~l~R~   49 (87)
T 2k02_A            7 VRDMLALQ---GRMEAKQLSARLQTP------QPL-IDAMLERMEAMGKVVRI   49 (87)
T ss_dssp             HHHHHHHS---CSEEHHHHHHHTTCC------HHH-HHHHHHHHHTTCCSEEE
T ss_pred             HHHHHHHc---CCCcHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEEE
Confidence            66778776   799999999999997      556 99999999999999964

>1xn7_A Hypothetical protein YHGG; alpha+beta, GFT structural genomics, protein structure initiative, PSI, NESG; NMR {Escherichia coli} SCOP: a.4.5.62

Probab=95.53  E-value=0.014  Score=39.34  Aligned_cols=42  Identities=17%  Similarity=0.264  Sum_probs=37.3

Q ss_pred             hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      |.+.|.+.   |.+++.|||+.++++      +.- ++|.|..|...|++.+
T Consensus         7 Il~~L~~~---g~vsv~eLa~~l~VS------~~T-IRrdL~~Le~~G~l~R   48 (78)
T 1xn7_A            7 VRDLLALR---GRMEAAQISQTLNTP------QPM-INAMLQQLESMGKAVR   48 (78)
T ss_dssp             HHHHHHHS---CSBCHHHHHHHTTCC------HHH-HHHHHHHHHHHTSEEE
T ss_pred             HHHHHHHc---CCCcHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEE
Confidence            66778776   699999999999997      556 9999999999999986

>2wa2_A Non-structural protein 5; transferase, S-adenosyl-L- methionine, virion, membrane, flavivirus, N7-methyltransferase, 2'-O-methyltransferase; HET: SAM; 1.80A {Modoc virus} PDB: 2wa1_A*

Probab=95.48  E-value=0.012  Score=49.38  Aligned_cols=39  Identities=18%  Similarity=0.041  Sum_probs=31.0

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDA  232 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a  232 (244)
                      +....+|||||||+|.++..++++   -+++.+|+-..+..+
T Consensus        80 ~~~g~~VLDlGcGtG~~s~~la~~---~~V~gVD~s~m~~~a  118 (276)
T 2wa2_A           80 VELKGTVVDLGCGRGSWSYYAASQ---PNVREVKAYTLGTSG  118 (276)
T ss_dssp             CCCCEEEEEESCTTCHHHHHHHTS---TTEEEEEEECCCCTT
T ss_pred             CCCCCEEEEeccCCCHHHHHHHHc---CCEEEEECchhhhhh
Confidence            456689999999999999999988   578889985543333

>3ech_A MEXR, multidrug resistance operon repressor; winged helix, helix-turn-helix, protein-peptide complex; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28 PDB: 1lnw_A 3mex_A

Probab=95.46  E-value=0.02  Score=42.35  Aligned_cols=48  Identities=19%  Similarity=0.293  Sum_probs=38.0

Q ss_pred             HHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           33 VVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        33 a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      ..++.++..|...   +++|..+||+.++++      +.. +.++++.|...|++++.
T Consensus        37 ~~~~~vL~~l~~~---~~~t~~eLa~~l~~~------~~t-vs~~l~~L~~~Glv~r~   84 (142)
T 3ech_A           37 PPDVHVLKLIDEQ---RGLNLQDLGRQMCRD------KAL-ITRKIRELEGRNLVRRE   84 (142)
T ss_dssp             HHHHHHHHHHHHT---TTCCHHHHHHHHC---------CH-HHHHHHHHHHTTSEEC-
T ss_pred             HHHHHHHHHHHhC---CCcCHHHHHHHhCCC------HHH-HHHHHHHHHHCCCEeec
Confidence            4556688888876   589999999999997      455 99999999999999963

>1r1t_A Transcriptional repressor SMTB; zinc, transcriptional regulation, winged HTH protein, DNA binding, transcription repressor; 1.70A {Synechococcus elongatus pcc 7942} SCOP: a.4.5.5 PDB: 1r23_A 1smt_A 1r22_A

Probab=95.46  E-value=0.012  Score=43.22  Aligned_cols=50  Identities=14%  Similarity=0.314  Sum_probs=41.0

Q ss_pred             HHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           30 MQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        30 L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      |.--.++.|+..|.+    ++.++.+||+.+|++      ... +.+.|+.|...|++...
T Consensus        43 L~~~~rl~IL~~L~~----~~~s~~ela~~lgis------~st-vs~~L~~Le~~Glv~~~   92 (122)
T 1r1t_A           43 LADPNRLRLLSLLAR----SELCVGDLAQAIGVS------ESA-VSHQLRSLRNLRLVSYR   92 (122)
T ss_dssp             HCCHHHHHHHHHHTT----CCBCHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEEE
T ss_pred             hCCHHHHHHHHHHHc----CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCeEEE
Confidence            333356778888875    689999999999997      456 99999999999999853

>2oxt_A Nucleoside-2'-O-methyltransferase; flavivirus, viral enzyme, RNA capping, S-adenosyl-L-methionine, viral protein; HET: SAM; 2.90A {Meaban virus}

Probab=95.43  E-value=0.014  Score=48.62  Aligned_cols=36  Identities=19%  Similarity=0.108  Sum_probs=29.9

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccchHHh
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVI  229 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi  229 (244)
                      +....+|||||||+|.++..++++   -+++.+|+-..+
T Consensus        72 ~~~g~~VLDlGcGtG~~s~~la~~---~~V~gvD~s~m~  107 (265)
T 2oxt_A           72 VELTGRVVDLGCGRGGWSYYAASR---PHVMDVRAYTLG  107 (265)
T ss_dssp             CCCCEEEEEESCTTSHHHHHHHTS---TTEEEEEEECCC
T ss_pred             CCCCCEEEEeCcCCCHHHHHHHHc---CcEEEEECchhh
Confidence            456689999999999999998887   578899985443

>3df8_A Possible HXLR family transcriptional factor; APC89000, structural genomics, midwest center for structural genomics, MCSG; 1.65A {Thermoplasma volcanium} SCOP: a.4.5.0

Probab=95.42  E-value=0.011  Score=42.50  Aligned_cols=75  Identities=11%  Similarity=0.138  Sum_probs=53.1

Q ss_pred             hHHHHHHHHhhhHHHHHHHHHHhcChhhHHhhcCCCCCCC--HHHHHHhC-CCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           13 NFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLS--VAEIVAQI-PLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        13 ~~~~l~~~~~g~~~~~~L~~a~~lgifd~L~~~~~~g~~t--~~eLA~~~-~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      +...+++.+.+.|....|         ..|..    |+.+  +.||++.+ |++      +.. +.+.|+.|...|++++
T Consensus        16 ~~~~~l~~l~~~wrl~IL---------~~L~~----g~~~~~~~eL~~~l~gis------~~~-ls~~L~~Le~~GlV~r   75 (111)
T 3df8_A           16 PSESVLHLLGKKYTMLII---------SVLGN----GSTRQNFNDIRSSIPGIS------STI-LSRRIKDLIDSGLVER   75 (111)
T ss_dssp             TTSSTHHHHHSTTHHHHH---------HHHTS----SSSCBCHHHHHHTSTTCC------HHH-HHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHcCccHHHHH---------HHHhc----CCCCCCHHHHHHHccCCC------HHH-HHHHHHHHHHCCCEEE
Confidence            344555666666655544         34543    5777  99999999 897      456 9999999999999996


Q ss_pred             eeecCCceeecCccccccc
Q 041256           90 SFVDGQRLYSLAPVSAYFV  108 (244)
Q Consensus        90 ~~~~~~~~y~~t~~s~~l~  108 (244)
                      ... ..-.|++|+.++.+.
T Consensus        76 ~~~-r~~~y~LT~~G~~l~   93 (111)
T 3df8_A           76 RSG-QITTYALTEKGMNVR   93 (111)
T ss_dssp             EES-SSEEEEECHHHHHHH
T ss_pred             eec-CcEEEEECccHHHHH
Confidence            422 235688888776544

>2o0y_A Transcriptional regulator; ICLR-family, structural genomics, protein structure initiative, midwest center for structural genomics, MCSG; 2.00A {Rhodococcus SP}

Probab=95.39  E-value=0.007  Score=50.33  Aligned_cols=57  Identities=23%  Similarity=0.360  Sum_probs=44.0

Q ss_pred             cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccc
Q 041256           36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVS  104 (244)
Q Consensus        36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s  104 (244)
                      +.|++.|...+  +++|+.|||+.+|++      ..- +.|+|+.|...||+.++   ..++|++++..
T Consensus        26 l~iL~~l~~~~--~~~~~~eia~~~gl~------kst-v~r~l~tL~~~G~v~~~---~~~~Y~lg~~~   82 (260)
T 2o0y_A           26 IDLLELFDAAH--PTRSLKELVEGTKLP------KTT-VVRLVATMCARSVLTSR---ADGSYSLGPEM   82 (260)
T ss_dssp             HHHHTTCBTTB--SSBCHHHHHHHHCCC------HHH-HHHHHHHHHHTTSEEEC---TTSCEEECHHH
T ss_pred             HHHHHHHhhCC--CCcCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEEC---CCCeEEecHHH
Confidence            34566665432  689999999999996      445 99999999999999963   23489998764

>2p8j_A S-adenosylmethionine-dependent methyltransferase; NP_349143.1; HET: PGE GOL; 2.00A {Clostridium acetobutylicum}

Probab=95.35  E-value=0.0074  Score=47.54  Aligned_cols=41  Identities=20%  Similarity=0.233  Sum_probs=31.5

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~  233 (244)
                      ....+|+|||||.|.+...++.+ ++.+++.+|. |..++.++
T Consensus        22 ~~~~~vLDiGcG~G~~~~~~~~~-~~~~v~~vD~s~~~~~~a~   63 (209)
T 2p8j_A           22 NLDKTVLDCGAGGDLPPLSIFVE-DGYKTYGIEISDLQLKKAE   63 (209)
T ss_dssp             SSCSEEEEESCCSSSCTHHHHHH-TTCEEEEEECCHHHHHHHH
T ss_pred             CCCCEEEEECCCCCHHHHHHHHh-CCCEEEEEECCHHHHHHHH
Confidence            44579999999999986555544 6679999998 77776654

>2g7u_A Transcriptional regulator; ICLR family, structural genomics, PSI, protein structure initiative, midwest center for struc genomics; 2.30A {Rhodococcus SP}

Probab=95.33  E-value=0.0067  Score=50.34  Aligned_cols=60  Identities=17%  Similarity=0.187  Sum_probs=47.1

Q ss_pred             cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccccccc
Q 041256           36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFV  108 (244)
Q Consensus        36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l~  108 (244)
                      +.|++.|.+.+  ++.|+.|||+.+|++      ..- +.|+|+.|...|++.+   . ++.|++++....|.
T Consensus        17 l~iL~~l~~~~--~~~~~~eia~~~gl~------~st-v~r~l~~L~~~G~v~~---~-~~~Y~Lg~~~~~l~   76 (257)
T 2g7u_A           17 FAVLLAFDAQR--PNPTLAELATEAGLS------RPA-VRRILLTLQKLGYVAG---S-GGRWSLTPRVLSIG   76 (257)
T ss_dssp             HHHHHTCSSSC--SSCBHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEE---E-TTEEEECGGGHHHH
T ss_pred             HHHHHHHHhCC--CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEe---C-CCEEEEcHHHHHHH
Confidence            34566666532  589999999999996      445 9999999999999995   3 48999998765444

>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=95.32  E-value=0.012  Score=52.48  Aligned_cols=49  Identities=12%  Similarity=0.207  Sum_probs=38.8

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+++.++ .....+|+|+|||.|.++..++++  ..+++.+|. |..++.|++
T Consensus       277 ~~~~~l~-~~~~~~VLDlgcG~G~~~~~la~~--~~~V~gvD~s~~al~~A~~  326 (433)
T 1uwv_A          277 RALEWLD-VQPEDRVLDLFCGMGNFTLPLATQ--AASVVGVEGVPALVEKGQQ  326 (433)
T ss_dssp             HHHHHHT-CCTTCEEEEESCTTTTTHHHHHTT--SSEEEEEESCHHHHHHHHH
T ss_pred             HHHHhhc-CCCCCEEEECCCCCCHHHHHHHhh--CCEEEEEeCCHHHHHHHHH
Confidence            3344444 455679999999999999999988  678899998 788888764

>4a5n_A Uncharacterized HTH-type transcriptional regulato; activator, DNA binding, MARR-like; 1.81A {Bacillus subtilis} PDB: 4a5m_A

Probab=95.31  E-value=0.031  Score=41.52  Aligned_cols=75  Identities=15%  Similarity=0.127  Sum_probs=53.0

Q ss_pred             HHHHHHHHhhhHHHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhC-CCCCCCCcchhccHHHHHHHHhhCCcccceee
Q 041256           14 FSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQI-PLKDNNPEAAAMTLDRVLRLLVSYNALHCSFV   92 (244)
Q Consensus        14 ~~~l~~~~~g~~~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~-~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~   92 (244)
                      ...+++++.+.|...+|.         .|..    |+.+..||++.+ |++      +.. |.+.|+.|...|++++...
T Consensus        16 i~~~l~~lg~kW~l~IL~---------~L~~----g~~rf~eL~~~l~gIs------~~~-Ls~~L~~Le~~GLV~R~~~   75 (131)
T 4a5n_A           16 VEFTLDVIGGKWKGILFY---------HMID----GKKRFNEFRRICPSIT------QRM-LTLQLRELEADGIVHREVY   75 (131)
T ss_dssp             HHHHHHHHCSSSHHHHHH---------HHTT----SCBCHHHHHHHCTTSC------HHH-HHHHHHHHHHTTSEEEEEE
T ss_pred             HHHHHHHHcCcCHHHHHH---------HHhc----CCcCHHHHHHHhcccC------HHH-HHHHHHHHHHCCCEEEEec
Confidence            445555555565555543         3433    699999999999 997      456 9999999999999996422


Q ss_pred             cCC---ceeecCccccccc
Q 041256           93 DGQ---RLYSLAPVSAYFV  108 (244)
Q Consensus        93 ~~~---~~y~~t~~s~~l~  108 (244)
                      ..+   -.|++|+.++.+.
T Consensus        76 ~~d~r~v~y~LT~~G~~l~   94 (131)
T 4a5n_A           76 HQVPPKVEYSLTEFGRTLE   94 (131)
T ss_dssp             CSSSCEEEEEECTTGGGGH
T ss_pred             CCCCCeEEEEECHhHHHHH
Confidence            111   2588888877554

>2gs9_A Hypothetical protein TT1324; methyl transferase, structural genomics, NPPSFA, national PR protein structural and functional analyses; HET: SAH; 2.60A {Thermus thermophilus}

Probab=95.29  E-value=0.0096  Score=47.08  Aligned_cols=45  Identities=16%  Similarity=0.254  Sum_probs=33.1

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCC-eEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHI-KGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l-~~~v~Dl-p~vi~~a~~  234 (244)
                      .++..+.  ....+|+|||||.|.++..+     +. +++.+|. |..++.+++
T Consensus        28 ~~l~~~~--~~~~~vLdiG~G~G~~~~~l-----~~~~v~~vD~s~~~~~~a~~   74 (211)
T 2gs9_A           28 RALKGLL--PPGESLLEVGAGTGYWLRRL-----PYPQKVGVEPSEAMLAVGRR   74 (211)
T ss_dssp             HHHHTTC--CCCSEEEEETCTTCHHHHHC-----CCSEEEEECCCHHHHHHHHH
T ss_pred             HHHHHhc--CCCCeEEEECCCCCHhHHhC-----CCCeEEEEeCCHHHHHHHHH
Confidence            3444443  25689999999999999887     44 7899998 666666553

>3giw_A Protein of unknown function DUF574; rossmann-fold protein, structural genomics, joint center for structural genomics, JCSG; HET: MSE UNL; 1.45A {Streptomyces avermitilis} PDB: 3go4_A*

Probab=95.26  E-value=0.016  Score=48.75  Aligned_cols=43  Identities=23%  Similarity=0.410  Sum_probs=34.1

Q ss_pred             CCcceEEEecCCc--cHHHHHH-HHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGL--GITLNMI-ISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~--G~~~~~l-~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+.++|||||||.  +....++ .+..|+.+++.+|. |.+++.+++
T Consensus        77 ~g~~q~LDLGcG~pT~~~~~~la~~~~P~arVv~VD~sp~mLa~Ar~  123 (277)
T 3giw_A           77 AGIRQFLDIGTGIPTSPNLHEIAQSVAPESRVVYVDNDPIVLTLSQG  123 (277)
T ss_dssp             SCCCEEEEESCCSCCSSCHHHHHHHHCTTCEEEEEECCHHHHHTTHH
T ss_pred             cCCCEEEEeCCCCCcccHHHHHHHHHCCCCEEEEEeCChHHHHHHHH
Confidence            3568999999997  3344444 45689999999999 999999875

>3t8r_A Staphylococcus aureus CYMR; transcriptional regulator protein, dimer, sulfenic acid, UNK function; 1.70A {Staphylococcus aureus} PDB: 3t8t_A

Probab=95.19  E-value=0.021  Score=43.06  Aligned_cols=46  Identities=15%  Similarity=0.176  Sum_probs=37.3

Q ss_pred             CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCc
Q 041256           49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAP  102 (244)
Q Consensus        49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~  102 (244)
                      ++.|.++||+.++++      +.. ++++|..|...|++.-. +...|.|.++.
T Consensus        27 ~~~s~~~IA~~~~i~------~~~-l~kil~~L~~aGlv~s~-rG~~GGy~Lar   72 (143)
T 3t8r_A           27 GCISLKSIAEENNLS------DLY-LEQLVGPLRNAGLIRSV-RGAKGGYQLRV   72 (143)
T ss_dssp             CCEEHHHHHHHTTCC------HHH-HHHHHHHHHHTTSEEEC-SSSSSEEEESS
T ss_pred             CCcCHHHHHHHHCcC------HHH-HHHHHHHHHHCCEEEec-CCCCCCeeecC
Confidence            589999999999997      678 99999999999999742 12246788755

>2qww_A Transcriptional regulator, MARR family; YP_013417.1, multiple antibiotic-resistance repressor (MARR) structural genomics; HET: MSE; 2.07A {Listeria monocytogenes str}

Probab=95.17  E-value=0.052  Score=40.54  Aligned_cols=62  Identities=13%  Similarity=0.183  Sum_probs=45.3

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc--eeecCCc---eeecCccccc
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC--SFVDGQR---LYSLAPVSAY  106 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~--~~~~~~~---~y~~t~~s~~  106 (244)
                      ++.++..|...   +++|..+||+.++++      +.. +.++++.|...|++.+  .....+.   .+.+|+.+..
T Consensus        43 ~~~iL~~l~~~---~~~t~~eLa~~l~~~------~~t-vs~~l~~Le~~Glv~r~~~~~~~d~R~~~~~LT~~G~~  109 (154)
T 2qww_A           43 QLAMINVIYST---PGISVADLTKRLIIT------GSS-AAANVDGLISLGLVVKLNKTIPNDSMDLTLKLSKKGED  109 (154)
T ss_dssp             HHHHHHHHHHS---TTEEHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEESCC--CTTCTTCEEEECHHHHH
T ss_pred             HHHHHHHHHHC---CCCCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEecCcCCCCCCceeEeEECHHHHH
Confidence            45577777775   589999999999997      456 9999999999999985  3212222   3666666553

>3lwf_A LIN1550 protein, putative transcriptional regulator; structural genomics, JOI for structural genomics, JCSG; HET: SO4; 2.06A {Listeria innocua}

Probab=95.17  E-value=0.026  Score=43.46  Aligned_cols=60  Identities=12%  Similarity=0.106  Sum_probs=44.0

Q ss_pred             CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccccccccCCCCCCCHHHHHHHh
Q 041256           49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFVRNNQNGASLSPYMALC  124 (244)
Q Consensus        49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l~~~~~~~~~~~~~~~~~  124 (244)
                      ++.|.++||+.++++      +.. ++++|..|...|++.-. +...|.|.++.-       . ..-+++..+...
T Consensus        43 ~~~s~~eIA~~~~i~------~~~-l~kil~~L~~aGlv~s~-rG~~GGy~Lar~-------p-~eItL~dVi~av  102 (159)
T 3lwf_A           43 GPISLRSIAQDKNLS------EHY-LEQLIGPLRNAGIVKSI-RGAHGGYVLNGD-------P-EKITAGDIIRTL  102 (159)
T ss_dssp             CCBCHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEEE-CSTTCEEEECSC-------T-TTCBHHHHHHHH
T ss_pred             CCcCHHHHHHHHCcC------HHH-HHHHHHHHHHCCeEEEe-cCCCCceEecCC-------H-HHCCHHHHHHHH
Confidence            689999999999997      678 99999999999999842 222466887542       2 122566666544

>2vdw_A Vaccinia virus capping enzyme D1 subunit; nucleotidyltransferase, S-adenosyl-L-methionine, RNA metabolism, mRNA processing, methyltransferase, poxvirus; HET: SAH; 2.70A {Vaccinia virus}

Probab=95.14  E-value=0.0098  Score=50.54  Aligned_cols=41  Identities=15%  Similarity=0.073  Sum_probs=32.3

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...+|||||||.|..+..+++.. ..+++.+|+ |..++.|++
T Consensus        48 ~~~~VLDlGCG~G~~l~~~~~~~-~~~v~GiD~S~~~l~~A~~   89 (302)
T 2vdw_A           48 NKRKVLAIDFGNGADLEKYFYGE-IALLVATDPDADAIARGNE   89 (302)
T ss_dssp             SCCEEEETTCTTTTTHHHHHHTT-CSEEEEEESCHHHHHHHHH
T ss_pred             CCCeEEEEecCCcHhHHHHHhcC-CCeEEEEECCHHHHHHHHH
Confidence            35799999999998777766543 457899998 788888764

>3o4f_A Spermidine synthase; aminopropyltransferase, polyamine synthase, rossmann fold, P biosynthesis, spermidine biosynthesis, transferase; 2.90A {Escherichia coli}

Probab=95.14  E-value=0.011  Score=50.11  Aligned_cols=43  Identities=19%  Similarity=0.203  Sum_probs=38.3

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+++|+=||||.|..+.++++..|--+.+++|+ |.|++.+++
T Consensus        82 p~pk~VLIiGgGdG~~~revlk~~~v~~v~~VEID~~Vv~~a~~  125 (294)
T 3o4f_A           82 GHAKHVLIIGGGDGAMLREVTRHKNVESITMVEIDAGVVSFCRQ  125 (294)
T ss_dssp             SCCCEEEEESCTTSHHHHHHHTCTTCCEEEEEESCHHHHHHHHH
T ss_pred             CCCCeEEEECCCchHHHHHHHHcCCcceEEEEcCCHHHHHHHHh
Confidence            5678999999999999999999888888999998 999988754

>3r0q_C Probable protein arginine N-methyltransferase 4.2; arginine methyltransferase, methylation; HET: SAH; 2.61A {Arabidopsis thaliana}

Probab=95.13  E-value=0.013  Score=51.35  Aligned_cols=43  Identities=21%  Similarity=0.111  Sum_probs=34.3

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPS  234 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~  234 (244)
                      .....+|||||||+|.++..++++. ..+++.+|....++.+++
T Consensus        61 ~~~~~~VLDlGcGtG~ls~~la~~g-~~~V~gvD~s~~~~~a~~  103 (376)
T 3r0q_C           61 HFEGKTVLDVGTGSGILAIWSAQAG-ARKVYAVEATKMADHARA  103 (376)
T ss_dssp             TTTTCEEEEESCTTTHHHHHHHHTT-CSEEEEEESSTTHHHHHH
T ss_pred             cCCCCEEEEeccCcCHHHHHHHhcC-CCEEEEEccHHHHHHHHH
Confidence            4556899999999999999999883 348899998766666653

>2ia2_A Putative transcriptional regulator; SAD, PSI-2, structural genomics, structure initiative, midwest center for structural genomic transcription; 2.10A {Rhodococcus SP}

Probab=95.11  E-value=0.0071  Score=50.43  Aligned_cols=58  Identities=19%  Similarity=0.246  Sum_probs=45.8

Q ss_pred             cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccccc
Q 041256           36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAY  106 (244)
Q Consensus        36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~  106 (244)
                      +.|++.|.+.+  +++|+.|||+.+|++      ..- +.|+|+.|...|++.+   . +++|++++....
T Consensus        24 l~iL~~l~~~~--~~~~~~eia~~~gl~------~st-v~r~l~tL~~~G~v~~---~-~~~Y~Lg~~~~~   81 (265)
T 2ia2_A           24 LAVIRCFDHRN--QRRTLSDVARATDLT------RAT-ARRFLLTLVELGYVAT---D-GSAFWLTPRVLE   81 (265)
T ss_dssp             HHHHHTCCSSC--SSEEHHHHHHHHTCC------HHH-HHHHHHHHHHHTSEEE---S-SSEEEECGGGGG
T ss_pred             HHHHHHHHhCC--CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEe---c-CCEEEEcHHHHH
Confidence            44566676432  589999999999996      445 9999999999999995   3 488999886543

>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2}

Probab=95.07  E-value=0.015  Score=39.12  Aligned_cols=44  Identities=18%  Similarity=0.224  Sum_probs=36.4

Q ss_pred             hhhHHhhc-----CCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           38 VFEIISKA-----GPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        38 ifd~L~~~-----~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      |++.|.+.     |  +|.|+.|||+.+|++      +.- +++-|..|...|++...
T Consensus         9 IL~~I~~~i~~~~g--~~psv~EIa~~lgvS------~~T-Vrr~L~~Le~kG~I~R~   57 (77)
T 2jt1_A            9 IISIVQERQNMDDG--APVKTRDIADAAGLS------IYQ-VRLYLEQLHDVGVLEKV   57 (77)
T ss_dssp             HHHHHHHHHHHHTT--SCEEHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHhhccC--CCcCHHHHHHHHCCC------HHH-HHHHHHHHHHCCcEEec
Confidence            45555554     4  699999999999997      556 99999999999999963

>3frh_A 16S rRNA methylase; methyltransferase domain, helical N-terminal domain, methyltransferase, plasmid, transferase; HET: SAH; 1.20A {Escherichia coli} PDB: 3fri_A* 3b89_A*

Probab=95.06  E-value=0.017  Score=47.72  Aligned_cols=41  Identities=12%  Similarity=0.005  Sum_probs=35.1

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      +..+.+|+|||||.|-++..+.   |..+.+.+|+ +..++.+++
T Consensus       103 ~~~p~~VLDlGCG~gpLal~~~---~~~~y~a~DId~~~i~~ar~  144 (253)
T 3frh_A          103 AETPRRVLDIACGLNPLALYER---GIASVWGCDIHQGLGDVITP  144 (253)
T ss_dssp             SCCCSEEEEETCTTTHHHHHHT---TCSEEEEEESBHHHHHHHHH
T ss_pred             CCCCCeEEEecCCccHHHHHhc---cCCeEEEEeCCHHHHHHHHH
Confidence            4557899999999999999888   9999999998 777777654

>2wte_A CSA3; antiviral protein, viral resistance, winged helix-turn-helix prnai nucleotide-binding domain; HET: MSE; 1.80A {Sulfolobus solfataricus}

Probab=95.05  E-value=0.013  Score=48.36  Aligned_cols=62  Identities=11%  Similarity=0.202  Sum_probs=48.7

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccccccc
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFV  108 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l~  108 (244)
                      ++.|...|.+.   +++|..|||+.+|++      ..- +.|.|+.|...|++.+.  .....|++|+.+..+.
T Consensus       154 ~~~IL~~L~~~---~~~s~~eLA~~lgls------ksT-v~r~L~~Le~~GlV~r~--~r~~~~~LT~~G~~l~  215 (244)
T 2wte_A          154 EMKLLNVLYET---KGTGITELAKMLDKS------EKT-LINKIAELKKFGILTQK--GKDRKVELNELGLNVI  215 (244)
T ss_dssp             HHHHHHHHHHH---TCBCHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEEE--TTTTEEEECHHHHHHH
T ss_pred             HHHHHHHHHHc---CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEEe--CCccEEEECHHHHHHH
Confidence            44566676654   589999999999997      455 99999999999999963  2346799998876553

>1z7u_A Hypothetical protein EF0647; winged-helix-turn-helix, MARR, structural genomics, PSI, Pro structure initiative; 2.20A {Enterococcus faecalis} SCOP: a.4.5.69

Probab=95.02  E-value=0.018  Score=41.34  Aligned_cols=59  Identities=14%  Similarity=0.196  Sum_probs=43.1

Q ss_pred             hhhHHhhcCCCCCCCHHHHHHhC-CCCCCCCcchhccHHHHHHHHhhCCcccceeecCC---ceeecCcccccc
Q 041256           38 VFEIISKAGPGAKLSVAEIVAQI-PLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQ---RLYSLAPVSAYF  107 (244)
Q Consensus        38 ifd~L~~~~~~g~~t~~eLA~~~-~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~---~~y~~t~~s~~l  107 (244)
                      |...|..    ++.+..|||+.+ +++      +.. +.+.|+.|...|++++.....+   -.|++|+.+..+
T Consensus        27 IL~~L~~----~~~~~~eLa~~l~~is------~~t-vs~~L~~Le~~GlI~r~~~~~d~r~~~~~LT~~G~~~   89 (112)
T 1z7u_A           27 LMDELFQ----GTKRNGELMRALDGIT------QRV-LTDRLREMEKDGLVHRESFNELPPRVEYTLTPEGYAL   89 (112)
T ss_dssp             HHHHHHH----SCBCHHHHHHHSTTCC------HHH-HHHHHHHHHHHTSEEEEEECCSSCEEEEEECHHHHHH
T ss_pred             HHHHHHh----CCCCHHHHHHHhccCC------HHH-HHHHHHHHHHCCCEEEeecCCCCCeEEEEECHhHHHH
Confidence            3444554    589999999999 997      456 9999999999999986432211   137887776533

>2gxg_A 146AA long hypothetical transcriptional regulator; winged helix; 1.45A {Sulfolobus tokodaii} PDB: 2eb7_A 2yr2_A 3gez_A 3gf2_A* 3gfi_A 3gfm_A 3gfj_A 3gfl_A

Probab=94.97  E-value=0.11  Score=38.23  Aligned_cols=60  Identities=10%  Similarity=0.058  Sum_probs=43.4

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCcccc
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSA  105 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~  105 (244)
                      ++.++..|. .   ++.|..+||+.++++      ... +.++++.|...|++.+.....+.   .+.+|+.+.
T Consensus        39 ~~~iL~~l~-~---~~~~~~ela~~l~~s------~~t-vs~~l~~Le~~glv~r~~~~~d~r~~~~~lT~~G~  101 (146)
T 2gxg_A           39 DFLVLRATS-D---GPKTMAYLANRYFVT------QSA-ITASVDKLEEMGLVVRVRDREDRRKILIEITEKGL  101 (146)
T ss_dssp             HHHHHHHHT-T---SCBCHHHHHHHTTCC------HHH-HHHHHHHHHHTTSEEEEECSSCTTCEEEEECHHHH
T ss_pred             HHHHHHHHh-c---CCcCHHHHHHHhCCC------chh-HHHHHHHHHHCCCEEeecCCCCCceEEEEECHHHH
Confidence            445667776 3   699999999999997      456 99999999999999864211122   255555544

>2zfu_A Nucleomethylin, cerebral protein 1; nucleolar protein, SAM-binding protein, protein structure, N phosphoprotein, nuclear protein; HET: SAH; 2.00A {Homo sapiens}

Probab=94.97  E-value=0.025  Score=44.80  Aligned_cols=39  Identities=15%  Similarity=0.083  Sum_probs=27.5

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccch
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLP  226 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  226 (244)
                      .+++.+.......+|+|||||.|.++..+.     .+++.+|+.
T Consensus        57 ~~~~~l~~~~~~~~vLDiG~G~G~~~~~l~-----~~v~~~D~s   95 (215)
T 2zfu_A           57 RIARDLRQRPASLVVADFGCGDCRLASSIR-----NPVHCFDLA   95 (215)
T ss_dssp             HHHHHHHTSCTTSCEEEETCTTCHHHHHCC-----SCEEEEESS
T ss_pred             HHHHHHhccCCCCeEEEECCcCCHHHHHhh-----ccEEEEeCC
Confidence            344444323456899999999999998873     567777763

>3f3x_A Transcriptional regulator, MARR family, putative; DNA binding protein, DNA-binding, transcription regulation; 1.90A {Sulfolobus solfataricus}

Probab=94.96  E-value=0.038  Score=40.90  Aligned_cols=64  Identities=8%  Similarity=0.167  Sum_probs=47.2

Q ss_pred             HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCccccccc
Q 041256           34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSAYFV  108 (244)
Q Consensus        34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~~l~  108 (244)
                      .++.++..|...   ++ |..+||+.++++      +.. +.++++.|...|++.+.....+.   .+.+|+.+..+.
T Consensus        38 ~~~~iL~~l~~~---~~-~~~~la~~l~~~------~~t-vs~~l~~Le~~Glv~r~~~~~D~R~~~~~LT~~G~~~~  104 (144)
T 3f3x_A           38 LDFSILKATSEE---PR-SMVYLANRYFVT------QSA-ITAAVDKLEAKGLVRRIRDSKDRRIVIVEITPKGRQVL  104 (144)
T ss_dssp             HHHHHHHHHHHS---CE-EHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHH
T ss_pred             HHHHHHHHHHHC---CC-CHHHHHHHHCCC------hhH-HHHHHHHHHHCCCEEeccCCCCCceEEEEECHHHHHHH
Confidence            355678888875   35 999999999997      556 99999999999999974322222   367777665443

>1wg8_A Predicted S-adenosylmethionine-dependent methyltransferase; S-adenosyl-methyltransferase, MRAW; HET: SAM; 2.00A {Thermus thermophilus} SCOP: a.60.13.1 c.66.1.23

Probab=94.92  E-value=0.021  Score=48.11  Aligned_cols=51  Identities=18%  Similarity=0.112  Sum_probs=42.9

Q ss_pred             HHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          181 MEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       181 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...+++.+. +.....+||.++|.|..+.+|+++  +.+.+.+|. |..++.+++
T Consensus        11 l~e~le~L~-~~~gg~~VD~T~G~GGHS~~il~~--~g~VigiD~Dp~Ai~~A~~   62 (285)
T 1wg8_A           11 YQEALDLLA-VRPGGVYVDATLGGAGHARGILER--GGRVIGLDQDPEAVARAKG   62 (285)
T ss_dssp             HHHHHHHHT-CCTTCEEEETTCTTSHHHHHHHHT--TCEEEEEESCHHHHHHHHH
T ss_pred             HHHHHHhhC-CCCCCEEEEeCCCCcHHHHHHHHC--CCEEEEEeCCHHHHHHHHh
Confidence            456777776 667789999999999999999998  778999998 888877653

>3lcv_B Sisomicin-gentamicin resistance methylase SGM; antibiotic resistance, methyltransferase, transferase; HET: SAM; 2.00A {Micromonospora zionensis} PDB: 3lcu_A*

Probab=94.85  E-value=0.004  Score=52.06  Aligned_cols=43  Identities=14%  Similarity=0.052  Sum_probs=37.8

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+.+|+|||||.|-++..+...+|..+.+.+|. +..++.+++
T Consensus       131 ~~p~~VLDLGCG~GpLAl~~~~~~p~a~y~a~DId~~~le~a~~  174 (281)
T 3lcv_B          131 PRPNTLRDLACGLNPLAAPWMGLPAETVYIASDIDARLVGFVDE  174 (281)
T ss_dssp             CCCSEEEETTCTTGGGCCTTTTCCTTCEEEEEESBHHHHHHHHH
T ss_pred             CCCceeeeeccCccHHHHHHHhhCCCCEEEEEeCCHHHHHHHHH
Confidence            3478999999999999999999999999999998 677776654

>1ylf_A RRF2 family protein; structural genomics, transcription regulator, P protein structure initiative; 2.50A {Bacillus cereus atcc 14579} SCOP: a.4.5.55

Probab=94.84  E-value=0.026  Score=42.79  Aligned_cols=63  Identities=6%  Similarity=0.050  Sum_probs=44.7

Q ss_pred             HHHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcc
Q 041256           25 VLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPV  103 (244)
Q Consensus        25 ~~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~  103 (244)
                      ....+|++.+.+...   ..    ++.|.++||+.++++      +.. ++++|..|...|++...  .|.|.|.++.-
T Consensus        12 ~~~yAl~~L~~La~~---~~----~~~~~~~iA~~~~i~------~~~-l~kil~~L~~~Glv~s~--rG~GGy~L~~~   74 (149)
T 1ylf_A           12 RFSIAVHILSILKNN---PS----SLCTSDYMAESVNTN------PVV-IRKIMSYLKQAGFVYVN--RGPGGAGLLKD   74 (149)
T ss_dssp             HHHHHHHHHHHHHHS---CG----GGCCHHHHHHHHTSC------HHH-HHHHHHHHHHTTSEEEC-----CCEEESSC
T ss_pred             HHHHHHHHHHHHHhC---CC----CCcCHHHHHHHHCcC------HHH-HHHHHHHHHHCCcEEEc--cCCCceEeCCC
Confidence            334466666655431   11    589999999999997      678 99999999999999842  23566877653

>2g72_A Phenylethanolamine N-methyltransferase; HET: SAM F21; 2.00A {Homo sapiens} SCOP: c.66.1.15 PDB: 1yz3_A* 2an4_A* 2an5_A* 2g70_A* 2g71_A* 2an3_A* 2g8n_A* 2ony_A* 3hcb_A* 3hcc_A* 3hcd_A* 3hcf_A* 3kpj_A* 3kpu_A* 3kpv_A* 3kpw_A* 3kpy_A* 3kqm_A* 3kqo_A* 3kqp_A* ...

Probab=94.84  E-value=0.0044  Score=51.88  Aligned_cols=40  Identities=13%  Similarity=0.150  Sum_probs=30.2

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~  233 (244)
                      ...+|||||||+|. ...++.+.+..+++.+|+ |..++.++
T Consensus        71 ~~~~vLDiGcG~G~-~~~l~~~~~~~~v~gvD~s~~~l~~a~  111 (289)
T 2g72_A           71 SGRTLIDIGSGPTV-YQLLSACSHFEDITMTDFLEVNRQELG  111 (289)
T ss_dssp             CCSEEEEETCTTCC-GGGTTGGGGCSEEEEECSCHHHHHHHH
T ss_pred             CCCeEEEECCCcCh-HHHHhhccCCCeEEEeCCCHHHHHHHH
Confidence            45799999999999 444455555668999998 77776554

>3bdd_A Regulatory protein MARR; putative multiple antibiotic-resistance repressor, structura genomics, joint center for structural genomics, JCSG; 2.20A {Streptococcus suis}

Probab=94.82  E-value=0.035  Score=40.73  Aligned_cols=65  Identities=14%  Similarity=0.131  Sum_probs=48.6

Q ss_pred             HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCccccccc
Q 041256           34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSAYFV  108 (244)
Q Consensus        34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~~l~  108 (244)
                      .++.++..|...   ++.|..+||+.++++      +.. +.+.++.|...|++.......++   .|.+|+.+..+.
T Consensus        32 ~~~~iL~~l~~~---~~~~~~ela~~l~is------~~~-vs~~l~~L~~~gli~~~~~~~d~r~~~~~lT~~G~~~~   99 (142)
T 3bdd_A           32 TRYSILQTLLKD---APLHQLALQERLQID------RAA-VTRHLKLLEESGYIIRKRNPDNQREVLVWPTEQAREAL   99 (142)
T ss_dssp             HHHHHHHHHHHH---CSBCHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEEEECSSSTTCEEEEECHHHHHHH
T ss_pred             HHHHHHHHHHhC---CCCCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHH
Confidence            345578888775   589999999999997      456 99999999999999864321112   477777776544

>1on2_A Transcriptional regulator MNTR; helix-turn-helix, DNA-binding protein, metalloregulatory protein; 1.61A {Bacillus subtilis} SCOP: a.4.5.24 a.76.1.1 PDB: 2ev0_A 1on1_A 2ev5_A 2ev6_A* 2f5c_A 2f5d_A 2f5e_A 2f5f_A 2hyf_A* 2hyg_D 3r60_A* 3r61_A*

Probab=94.77  E-value=0.025  Score=42.03  Aligned_cols=50  Identities=12%  Similarity=0.118  Sum_probs=41.4

Q ss_pred             CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccccccc
Q 041256           49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFV  108 (244)
Q Consensus        49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l~  108 (244)
                      ++.|..+||+.++++      +.. +.+.|+.|...|++.+   .....|.+|+.+..+.
T Consensus        21 ~~~~~~ela~~l~vs------~~t-vs~~l~~Le~~Glv~r---~~~~~~~LT~~g~~~~   70 (142)
T 1on2_A           21 GYARVSDIAEALAVH------PSS-VTKMVQKLDKDEYLIY---EKYRGLVLTSKGKKIG   70 (142)
T ss_dssp             SSCCHHHHHHHHTSC------HHH-HHHHHHHHHHTTSEEE---ETTTEEEECHHHHHHH
T ss_pred             CCCCHHHHHHHhCCC------HHH-HHHHHHHHHHCCCEEE---eeCceEEEchhHHHHH
Confidence            589999999999997      456 9999999999999995   2346789988876443

>2nnn_A Probable transcriptional regulator; structural genomics, PSI-2, protein structure initiative, M center for structural genomics, MCSG; 2.40A {Pseudomonas aeruginosa}

Probab=94.72  E-value=0.023  Score=41.67  Aligned_cols=61  Identities=15%  Similarity=0.149  Sum_probs=45.4

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCcccc
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSA  105 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~  105 (244)
                      ++.|+..|...   +++|..+||+.++++      ... +.++++.|...|++.+.....+.   .|.+|+.+.
T Consensus        40 ~~~iL~~l~~~---~~~t~~ela~~l~~~------~~t-vs~~l~~L~~~glv~r~~~~~d~R~~~~~lT~~G~  103 (140)
T 2nnn_A           40 QWAALVRLGET---GPCPQNQLGRLTAMD------AAT-IKGVVERLDKRGLIQRSADPDDGRRLLVSLSPAGR  103 (140)
T ss_dssp             HHHHHHHHHHH---SSBCHHHHHHHTTCC------HHH-HHHHHHHHHHTTCEEEEEETTEEEEEEEEECHHHH
T ss_pred             HHHHHHHHHHc---CCCCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEeeCCCCCCCeeeeEECHhHH
Confidence            45578888765   589999999999997      456 99999999999999863211122   256666554

>2i62_A Nicotinamide N-methyltransferase; structural genomics, structural genomics consortium, SGC; HET: SAH; 1.80A {Mus musculus} PDB: 2iip_A* 3rod_A*

Probab=94.71  E-value=0.0034  Score=51.44  Aligned_cols=41  Identities=17%  Similarity=0.080  Sum_probs=34.2

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~  233 (244)
                      .+..+|||||||.|.++..+++..+ .+++.+|. |..++.++
T Consensus        55 ~~~~~vLDlGcG~G~~~~~l~~~~~-~~v~gvD~s~~~l~~a~   96 (265)
T 2i62_A           55 VKGELLIDIGSGPTIYQLLSACESF-TEIIVSDYTDQNLWELQ   96 (265)
T ss_dssp             CCEEEEEEESCTTCCGGGTTGGGTE-EEEEEEESCHHHHHHHH
T ss_pred             cCCCEEEEECCCccHHHHHHhhccc-CeEEEecCCHHHHHHHH
Confidence            4568999999999999999988877 57889998 67777764

>3bja_A Transcriptional regulator, MARR family, putative; NP_978771.1, putative MARR-like transcription regulator, MAR structural genomics; 2.38A {Bacillus cereus}

Probab=94.70  E-value=0.022  Score=41.72  Aligned_cols=46  Identities=9%  Similarity=0.285  Sum_probs=38.5

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      ++.++..|...   +++|..+||+.++++      +.. +.+.++.|...|++.+.
T Consensus        35 ~~~iL~~l~~~---~~~~~~ela~~l~~~------~~t-vs~~l~~L~~~gli~r~   80 (139)
T 3bja_A           35 QFGVIQVLAKS---GKVSMSKLIENMGCV------PSN-MTTMIQRMKRDGYVMTE   80 (139)
T ss_dssp             HHHHHHHHHHS---CSEEHHHHHHHCSSC------CTT-HHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHc---CCcCHHHHHHHHCCC------hhH-HHHHHHHHHHCCCeeec
Confidence            45577778775   689999999999997      446 99999999999999863

>2yxl_A PH0851 protein, 450AA long hypothetical FMU protein; FMU-homolog, methyltransferase, structural genomics, NPPSFA; HET: SFG; 2.55A {Pyrococcus horikoshii}

Probab=94.68  E-value=0.031  Score=50.16  Aligned_cols=67  Identities=13%  Similarity=0.092  Sum_probs=45.6

Q ss_pred             HHHHHHHHHhcchhhHHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCC-CeEEEccc-hHHhhhCC
Q 041256          166 NDVFNNGMLSHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPH-IKGINYDL-PYVIKDAP  233 (244)
Q Consensus       166 ~~~f~~aM~~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dl-p~vi~~a~  233 (244)
                      ...|..+.-.........+...++ .....+|+|+|||.|..+..+++..++ .+++.+|. |..++.++
T Consensus       233 ~~~~~~G~~~~qd~~s~l~~~~l~-~~~g~~VLDlgaG~G~~t~~la~~~~~~~~v~a~D~s~~~l~~~~  301 (450)
T 2yxl_A          233 SSAFNEGKIIVQEEASAVASIVLD-PKPGETVVDLAAAPGGKTTHLAELMKNKGKIYAFDVDKMRMKRLK  301 (450)
T ss_dssp             CHHHHTTSEEECCHHHHHHHHHHC-CCTTCEEEESSCTTCHHHHHHHHHTTTCSEEEEECSCHHHHHHHH
T ss_pred             CchhhCceEEecCchhHHHHHhcC-CCCcCEEEEeCCCccHHHHHHHHHcCCCCEEEEEcCCHHHHHHHH
Confidence            345555443333222223334444 556679999999999999999999987 88999998 66566554

>4hc4_A Protein arginine N-methyltransferase 6; HRMT1L6, S-adenosyl-L-homocysteine, struc genomics, structural genomics consortium, SGC; HET: SAH; 1.97A {Homo sapiens}

Probab=94.68  E-value=0.019  Score=50.48  Aligned_cols=39  Identities=21%  Similarity=0.238  Sum_probs=29.8

Q ss_pred             ceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCC
Q 041256          195 KKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPS  234 (244)
Q Consensus       195 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~  234 (244)
                      ++|||||||+|.+++..+++.. -+++.+|..+.++.|++
T Consensus        85 k~VLDvG~GtGiLs~~Aa~aGA-~~V~ave~s~~~~~a~~  123 (376)
T 4hc4_A           85 KTVLDVGAGTGILSIFCAQAGA-RRVYAVEASAIWQQARE  123 (376)
T ss_dssp             CEEEEETCTTSHHHHHHHHTTC-SEEEEEECSTTHHHHHH
T ss_pred             CEEEEeCCCccHHHHHHHHhCC-CEEEEEeChHHHHHHHH
Confidence            7899999999999887776543 37888888666666553

>2fsw_A PG_0823 protein; alpha-beta structure, helix-turn-helix, winged-helix-turn-HE structural genomics, PSI, protein structure initiative; HET: MSE; 2.16A {Porphyromonas gingivalis} SCOP: a.4.5.69

Probab=94.57  E-value=0.034  Score=39.45  Aligned_cols=75  Identities=17%  Similarity=0.204  Sum_probs=51.0

Q ss_pred             hHHHHHHHHhhhHHHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCC-CCCCCCcchhccHHHHHHHHhhCCccccee
Q 041256           13 NFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIP-LKDNNPEAAAMTLDRVLRLLVSYNALHCSF   91 (244)
Q Consensus        13 ~~~~l~~~~~g~~~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~-~~~~~~~~~~~~l~rlLr~L~~~gll~~~~   91 (244)
                      ....+++++.+.+....|         ..|.+    ++.+..||++.++ ++      +.. +.+.|+.|...|++++..
T Consensus        14 ~~~~~l~~l~~~~~~~IL---------~~L~~----~~~~~~eL~~~l~gis------~~~-ls~~L~~Le~~GlV~r~~   73 (107)
T 2fsw_A           14 PVRKSMQIFAGKWTLLII---------FQINR----RIIRYGELKRAIPGIS------EKM-LIDELKFLCGKGLIKKKQ   73 (107)
T ss_dssp             HHHHHHHHHTSSSHHHHH---------HHHTT----SCEEHHHHHHHSTTCC------HHH-HHHHHHHHHHTTSEEEEE
T ss_pred             CHHHHHHHHcCccHHHHH---------HHHHh----CCcCHHHHHHHcccCC------HHH-HHHHHHHHHHCCCEEEee
Confidence            344555555555554443         34543    6899999999994 97      456 999999999999998643


Q ss_pred             ecCC---ceeecCcccccc
Q 041256           92 VDGQ---RLYSLAPVSAYF  107 (244)
Q Consensus        92 ~~~~---~~y~~t~~s~~l  107 (244)
                      ...+   -.|.+|+.++.+
T Consensus        74 ~~~d~r~~~y~LT~~G~~l   92 (107)
T 2fsw_A           74 YPEVPPRVEYSLTPLGEKV   92 (107)
T ss_dssp             ECSSSCEEEEEECHHHHTT
T ss_pred             cCCCCCeeEEEECccHHHH
Confidence            2211   248888877543

>2fu4_A Ferric uptake regulation protein; DNA binding domain, helix-turn-helix, DNA binding protein; 1.80A {Escherichia coli}

Probab=94.57  E-value=0.022  Score=38.37  Aligned_cols=48  Identities=15%  Similarity=0.290  Sum_probs=37.8

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhC-----CCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQI-----PLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~-----~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      +..|++.|.+.+ +++.|++||++.+     +++      ..- ++|.|+.|+..|++.+.
T Consensus        19 r~~IL~~l~~~~-~~~~s~~el~~~l~~~~~~is------~~T-VyR~L~~L~~~Glv~~~   71 (83)
T 2fu4_A           19 RLKILEVLQEPD-NHHVSAEDLYKRLIDMGEEIG------LAT-VYRVLNQFDDAGIVTRH   71 (83)
T ss_dssp             HHHHHHHHTSGG-GSSBCHHHHHHHHHHTTCCCC------HHH-HHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHHhCC-CCCCCHHHHHHHHHHhCCCCC------Hhh-HHHHHHHHHHCCCeEEE
Confidence            345788887641 0489999999999     775      344 99999999999999864

>3ldu_A Putative methylase; structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; HET: MSE GTP; 1.70A {Clostridium difficile}

Probab=94.57  E-value=0.027  Score=49.56  Aligned_cols=52  Identities=21%  Similarity=0.093  Sum_probs=40.8

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCC--------------------------------------CeEEEc
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPH--------------------------------------IKGINY  223 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~--------------------------------------l~~~v~  223 (244)
                      ..++.... |.....|+|++||+|.++++.+....+                                      .+++.+
T Consensus       185 a~ll~~~~-~~~~~~vlDp~CGSGt~lieaa~~~~~~apg~~R~f~f~~w~~~~~~~w~~~~~~a~~~~~~~~~~~V~Gv  263 (385)
T 3ldu_A          185 AGLIYLTP-WKAGRVLVDPMCGSGTILIEAAMIGINMAPGLNREFISEKWRTLDKKIWWDVRKDAFNKIDNESKFKIYGY  263 (385)
T ss_dssp             HHHHHTSC-CCTTSCEEETTCTTCHHHHHHHHHHTTCCTTTTSCCGGGGCTTSCHHHHHHHHHHHHHHSCCSCCCCEEEE
T ss_pred             HHHHHhhC-CCCCCeEEEcCCCCCHHHHHHHHHHhhhCCCcccccchhhcccCCHHHHHHHHHHHHHHhhccCCceEEEE
Confidence            34555555 777799999999999999998876332                                      578999


Q ss_pred             cc-hHHhhhCCC
Q 041256          224 DL-PYVIKDAPS  234 (244)
Q Consensus       224 Dl-p~vi~~a~~  234 (244)
                      |. |.+++.|++
T Consensus       264 Did~~ai~~Ar~  275 (385)
T 3ldu_A          264 DIDEESIDIARE  275 (385)
T ss_dssp             ESCHHHHHHHHH
T ss_pred             ECCHHHHHHHHH
Confidence            98 888888865

>3fm5_A Transcriptional regulator; MCSG, PF04017, PSI, MARR, structu genomics, protein structure initiative, midwest center for structural genomics; HET: GOL; 2.00A {Rhodococcus jostii}

Probab=94.56  E-value=0.084  Score=39.27  Aligned_cols=63  Identities=8%  Similarity=0.075  Sum_probs=42.7

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCce---eecCccccc
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRL---YSLAPVSAY  106 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~---y~~t~~s~~  106 (244)
                      ++.++..|...+  +++|..+||+.++++      +.. +.++++-|...|++++.....+.+   +.+|+.++.
T Consensus        41 q~~vL~~l~~~~--~~~t~~eLa~~l~i~------~~t-vs~~l~~Le~~Glv~r~~~~~D~R~~~~~LT~~G~~  106 (150)
T 3fm5_A           41 SYSVLVLACEQA--EGVNQRGVAATMGLD------PSQ-IVGLVDELEERGLVVRTLDPSDRRNKLIAATEEGRR  106 (150)
T ss_dssp             HHHHHHHHHHST--TCCCSHHHHHHHTCC------HHH-HHHHHHHHHTTTSEEC-----------CEECHHHHH
T ss_pred             HHHHHHHHHhCC--CCcCHHHHHHHHCCC------HhH-HHHHHHHHHHCCCEEeeCCccccchheeeECHHHHH
Confidence            445667776543  578999999999997      456 999999999999998632111221   555555543

>2nyx_A Probable transcriptional regulatory protein, RV14; alpha/beta, structural genomics, PSI-2; 2.30A {Mycobacterium tuberculosis}

Probab=94.54  E-value=0.069  Score=40.78  Aligned_cols=63  Identities=14%  Similarity=0.188  Sum_probs=46.6

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCcccccc
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSAYF  107 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~~l  107 (244)
                      ++.|+..|...   +++|..+||+.++++      ... +.++++.|...|++.+.....+.   .+.+|+.+..+
T Consensus        47 ~~~iL~~L~~~---~~~t~~eLa~~l~is------~~t-vs~~l~~Le~~GlV~r~~~~~DrR~~~~~LT~~G~~~  112 (168)
T 2nyx_A           47 QFRTLVILSNH---GPINLATLATLLGVQ------PSA-TGRMVDRLVGAELIDRLPHPTSRRELLAALTKRGRDV  112 (168)
T ss_dssp             HHHHHHHHHHH---CSEEHHHHHHHHTSC------HHH-HHHHHHHHHHTTSEEEEECSSCSSCEEEEECHHHHHH
T ss_pred             HHHHHHHHHHc---CCCCHHHHHHHhCCC------HHH-HHHHHHHHHHCCCEEeccCCCCCCeeEEEECHHHHHH
Confidence            45577788775   589999999999997      456 99999999999999864211122   26666666543

>1af7_A Chemotaxis receptor methyltransferase CHER; chemotaxis receptor methylation; HET: SAH; 2.00A {Salmonella typhimurium} SCOP: a.58.1.1 c.66.1.8 PDB: 1bc5_A*

Probab=94.53  E-value=0.016  Score=48.66  Aligned_cols=41  Identities=15%  Similarity=0.098  Sum_probs=33.4

Q ss_pred             cceEEEecCCccH----HHHHHHHHCC----CCeEEEccc-hHHhhhCCC
Q 041256          194 VKKLVDVGGGLGI----TLNMIISKYP----HIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       194 ~~~vvDVGGG~G~----~~~~l~~~~P----~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+|+|+|||+|.    +++.+++..|    +.+++..|+ |.+++.|++
T Consensus       106 ~~rIld~GCgTGee~ysiAi~L~e~~~~~~~~~~I~atDis~~~L~~Ar~  155 (274)
T 1af7_A          106 EYRVWSAAASTGEEPYSIAITLADALGMAPGRWKVFASDIDTEVLEKARS  155 (274)
T ss_dssp             CEEEEESCCTTTHHHHHHHHHHHHHHCSCTTSEEEEEEESCHHHHHHHHH
T ss_pred             CcEEEEeeccCChhHHHHHHHHHHhcccCCCCeEEEEEECCHHHHHHHHh
Confidence            4789999999998    6666777756    468899999 888888764

>3bpv_A Transcriptional regulator; MARR, DNA binding, transcription factor, winged helix motif, DNA-binding; 1.40A {Methanobacterium thermoautotrophicum} PDB: 3bpx_A*

Probab=94.49  E-value=0.023  Score=41.58  Aligned_cols=61  Identities=11%  Similarity=0.126  Sum_probs=44.3

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCce---eecCcccc
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRL---YSLAPVSA  105 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~---y~~t~~s~  105 (244)
                      ++.++..|...   ++.|..+||+.++++      ... +.++++.|...|++.+.....+++   +.+|+.+.
T Consensus        31 ~~~iL~~l~~~---~~~~~~ela~~l~~s------~~t-vs~~l~~L~~~glv~~~~~~~d~R~~~~~lT~~G~   94 (138)
T 3bpv_A           31 QVACLLRIHRE---PGIKQDELATFFHVD------KGT-IARTLRRLEESGFIEREQDPENRRRYILEVTRRGE   94 (138)
T ss_dssp             HHHHHHHHHHS---TTCBHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHH
T ss_pred             HHHHHHHHHHc---CCCCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEeecCCCCceeEEeeECHhHH
Confidence            44466777765   689999999999997      456 999999999999999642222222   55555544

>3k0l_A Repressor protein; helix-turn-helix, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; 2.35A {Acinetobacter SP}

Probab=94.42  E-value=0.038  Score=41.92  Aligned_cols=63  Identities=13%  Similarity=0.186  Sum_probs=46.3

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCcccccc
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSAYF  107 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~~l  107 (244)
                      ++.|+..|...   +++|..+||+.++++      +.. +.++++.|...|++++.....+.   .+.+|+.++.+
T Consensus        48 q~~iL~~l~~~---~~~t~~eLa~~l~~~------~~t-vs~~l~~Le~~Glv~r~~~~~DrR~~~l~LT~~G~~~  113 (162)
T 3k0l_A           48 QFTALSVLAAK---PNLSNAKLAERSFIK------PQS-ANKILQDLLANGWIEKAPDPTHGRRILVTVTPSGLDK  113 (162)
T ss_dssp             HHHHHHHHHHC---TTCCHHHHHHHHTSC------GGG-HHHHHHHHHHTTSEEEEECCSSSCCEEEEECHHHHHH
T ss_pred             HHHHHHHHHHC---CCCCHHHHHHHHCCC------HHH-HHHHHHHHHHCcCeEecCCCCcCCeeEeEECHhHHHH
Confidence            34577788775   689999999999997      456 99999999999999964322222   35666655533

>1jgs_A Multiple antibiotic resistance protein MARR; transcription regulation, DNA-binding, repressor, transcription; HET: SAL; 2.30A {Escherichia coli} SCOP: a.4.5.28

Probab=94.40  E-value=0.027  Score=41.31  Aligned_cols=63  Identities=21%  Similarity=0.174  Sum_probs=45.3

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCcccccc
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSAYF  107 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~~l  107 (244)
                      ++.++..|...   ++.|..+||+.++++      +.. +.++++.|...|++.+.....++   .+.+|+.+..+
T Consensus        36 ~~~iL~~l~~~---~~~~~~~la~~l~~~------~~t-vs~~l~~L~~~gli~r~~~~~d~R~~~~~lT~~G~~~  101 (138)
T 1jgs_A           36 QFKVLCSIRCA---ACITPVELKKVLSVD------LGA-LTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTGGAAI  101 (138)
T ss_dssp             HHHHHHHHHHH---SSBCHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEEEECTTCSSCEEEEECHHHHHH
T ss_pred             HHHHHHHHHhc---CCCCHHHHHHHHCCC------hHH-HHHHHHHHHHCCCEEecCCcccCceeEeEEChhHHHH
Confidence            44466777765   589999999999997      456 99999999999999864222222   25666655433

>3k0b_A Predicted N6-adenine-specific DNA methylase; methylase,PF01170, putative RNA methylase, PSI,MCSG, structu genomics; 1.50A {Listeria monocytogenes str}

Probab=94.37  E-value=0.033  Score=49.18  Aligned_cols=52  Identities=13%  Similarity=0.014  Sum_probs=40.9

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCC--------------------------------------CeEEEc
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPH--------------------------------------IKGINY  223 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~--------------------------------------l~~~v~  223 (244)
                      ..++.... |.....|+|.+||+|.++++.+....+                                      .+++.+
T Consensus       191 a~ll~l~~-~~~~~~vlDp~CGSGt~~ieaa~~~~~~apg~~R~f~f~~w~~~~~~~w~~~~~~a~~~~~~~~~~~V~Gv  269 (393)
T 3k0b_A          191 AALVLLTS-WHPDRPFYDPVCGSGTIPIEAALIGQNIAPGFNREFVSETWDWMPKQVWADARQEAEDLANYDQPLNIIGG  269 (393)
T ss_dssp             HHHHHHSC-CCTTSCEEETTCTTSHHHHHHHHHHTTCCTTTTSCCGGGGCTTSCHHHHHHHHHHHHHHCCTTCCCCEEEE
T ss_pred             HHHHHHhC-CCCCCeEEEcCCCCCHHHHHHHHHhcCcCCCccccchhhccccCCHHHHHHHHHHHHHhhcccCCceEEEE
Confidence            34555555 877789999999999999998876544                                      568999


Q ss_pred             cc-hHHhhhCCC
Q 041256          224 DL-PYVIKDAPS  234 (244)
Q Consensus       224 Dl-p~vi~~a~~  234 (244)
                      |. |.+++.|++
T Consensus       270 Did~~al~~Ar~  281 (393)
T 3k0b_A          270 DIDARLIEIAKQ  281 (393)
T ss_dssp             ESCHHHHHHHHH
T ss_pred             ECCHHHHHHHHH
Confidence            98 888888764

>3r0a_A Putative transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; 2.31A {Methanosarcina mazei}

Probab=94.33  E-value=0.031  Score=40.87  Aligned_cols=47  Identities=15%  Similarity=0.285  Sum_probs=38.6

Q ss_pred             hcChhhHHhhcCCCCC-CCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           35 ELDVFEIISKAGPGAK-LSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~-~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      +..|+..|.+.+  +| +|+.|||+.++++      ..- +.|.|+.|...|++.+.
T Consensus        28 e~~il~~L~~~~--~~~~t~~eLa~~l~~s------~sT-V~r~L~~L~~~GlV~r~   75 (123)
T 3r0a_A           28 DLNVMKSFLNEP--DRWIDTDALSKSLKLD------VST-VQRSVKKLHEKEILQRS   75 (123)
T ss_dssp             HHHHHHHHHHST--TCCEEHHHHHHHHTSC------HHH-HHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHCC--CCCcCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEee
Confidence            445777777754  56 9999999999997      455 99999999999999863

>2hr3_A Probable transcriptional regulator; MCSG, structural genomics, PSI-2, protein structure initiati midwest center for structural genomics; 2.40A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=94.32  E-value=0.039  Score=40.83  Aligned_cols=62  Identities=18%  Similarity=0.158  Sum_probs=44.5

Q ss_pred             HhcChhhHHhh-cCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCcccc
Q 041256           34 VELDVFEIISK-AGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSA  105 (244)
Q Consensus        34 ~~lgifd~L~~-~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~  105 (244)
                      .++.++..|.. .   ++.|..+||+.++++      ... +.++++.|...|++.+.....++   .+.+|+.+.
T Consensus        36 ~~~~iL~~l~~~~---~~~~~~~la~~l~i~------~~~-vs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~  101 (147)
T 2hr3_A           36 SQLVVLGAIDRLG---GDVTPSELAAAERMR------SSN-LAALLRELERGGLIVRHADPQDGRRTRVSLSSEGR  101 (147)
T ss_dssp             HHHHHHHHHHHTT---SCBCHHHHHHHTTCC------HHH-HHHHHHHHHHTTSEEEEC------CCEEEECHHHH
T ss_pred             HHHHHHHHHHHcC---CCCCHHHHHHHhCCC------hhh-HHHHHHHHHHCCCEeeCCCCCCCCceeeEECHHHH
Confidence            45667778876 4   689999999999997      456 99999999999999863211112   255665554

>2igt_A SAM dependent methyltransferase; alpha-beta sandwich, beta-barrel, structural genomics, PSI-2 structure initiative; HET: MSE SAM GOL; 1.89A {Agrobacterium tumefaciens str} SCOP: c.66.1.51

Probab=94.32  E-value=0.023  Score=48.93  Aligned_cols=40  Identities=15%  Similarity=0.034  Sum_probs=34.1

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      +..+|||+|||+|.++..+++...  +++.+|+ |..++.+++
T Consensus       153 ~~~~VLDlgcGtG~~sl~la~~ga--~V~~VD~s~~al~~a~~  193 (332)
T 2igt_A          153 RPLKVLNLFGYTGVASLVAAAAGA--EVTHVDASKKAIGWAKE  193 (332)
T ss_dssp             SCCEEEEETCTTCHHHHHHHHTTC--EEEEECSCHHHHHHHHH
T ss_pred             CCCcEEEcccccCHHHHHHHHcCC--EEEEEECCHHHHHHHHH
Confidence            446999999999999999999754  8999998 888887764

>2f2e_A PA1607; transcription factor, helix-TRUN-helix, APC5613, structural genomics, PSI, protein structure initiative; HET: GLC; 1.85A {Pseudomonas aeruginosa} SCOP: a.4.5.69

Probab=94.32  E-value=0.046  Score=41.24  Aligned_cols=52  Identities=17%  Similarity=0.186  Sum_probs=40.2

Q ss_pred             CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecC--CceeecCcccccc
Q 041256           49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDG--QRLYSLAPVSAYF  107 (244)
Q Consensus        49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~--~~~y~~t~~s~~l  107 (244)
                      |+.+..||++.++++      ... +.+.|+.|...|++++.....  .-.|++|+.++.+
T Consensus        36 g~~~~~eLa~~lgis------~~t-ls~~L~~Le~~GlI~r~~~~~d~~~~y~LT~~G~~l   89 (146)
T 2f2e_A           36 GLTRFGEFQKSLGLA------KNI-LAARLRNLVEHGVMVAVPAESGSHQEYRLTDKGRAL   89 (146)
T ss_dssp             TCCSHHHHHHHHCCC------HHH-HHHHHHHHHHTTSEEEEECSSSSCEEEEECHHHHTT
T ss_pred             CCCCHHHHHHHhCCC------HHH-HHHHHHHHHHCCCEEEEecCCCCeEEEEECchHHHH
Confidence            689999999999997      456 999999999999999632111  1268888876544

>3dmg_A Probable ribosomal RNA small subunit methyltransf; monomethyltranserase, 16S rRNA methyltransferase, N2 G1207 methyltransferase; HET: SAH; 1.55A {Thermus thermophilus} PDB: 3dmf_A* 3dmh_A* 2zul_A* 2zwv_A*

Probab=94.31  E-value=0.017  Score=50.84  Aligned_cols=40  Identities=10%  Similarity=0.127  Sum_probs=34.0

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...+|+|+|||.|.++..++++  +.+++.+|. |..++.+++
T Consensus       233 ~~~~VLDlGcG~G~~~~~la~~--g~~V~gvDis~~al~~A~~  273 (381)
T 3dmg_A          233 RGRQVLDLGAGYGALTLPLARM--GAEVVGVEDDLASVLSLQK  273 (381)
T ss_dssp             TTCEEEEETCTTSTTHHHHHHT--TCEEEEEESBHHHHHHHHH
T ss_pred             CCCEEEEEeeeCCHHHHHHHHc--CCEEEEEECCHHHHHHHHH
Confidence            4479999999999999999998  568899998 788877764

>3e6m_A MARR family transcriptional regulator; APC88769, silicibacter pomeroyi DSS, structural genomics, PSI-2, protein structure initiative; 2.20A {Silicibacter pomeroyi}

Probab=94.29  E-value=0.1  Score=39.41  Aligned_cols=62  Identities=16%  Similarity=0.177  Sum_probs=44.6

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCccccc
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSAY  106 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~~  106 (244)
                      ++.|+..|...   +++|..+||+.++++      +.. +.++++.|...|++++.....+.   .+.+|+.++.
T Consensus        55 q~~vL~~l~~~---~~~t~~eLa~~l~~~------~~~-vs~~l~~Le~~Glv~r~~~~~DrR~~~~~LT~~G~~  119 (161)
T 3e6m_A           55 KLRLLSSLSAY---GELTVGQLATLGVME------QST-TSRTVDQLVDEGLAARSISDADQRKRTVVLTRKGKK  119 (161)
T ss_dssp             HHHHHHHHHHH---SEEEHHHHHHHTTCC------HHH-HHHHHHHHHHTTSEEECC---CCCSCEEEECHHHHH
T ss_pred             HHHHHHHHHhC---CCCCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEeeCCcccCCeeEeeECHHHHH
Confidence            44477778765   589999999999997      456 99999999999999963211122   3556655543

>3cdh_A Transcriptional regulator, MARR family; helix-turn-hleix, structura genomics, PSI-2, protein structure initiative; 2.69A {Silicibacter pomeroyi dss-3}

Probab=94.28  E-value=0.13  Score=38.32  Aligned_cols=62  Identities=6%  Similarity=0.072  Sum_probs=43.6

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCccccc
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSAY  106 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~~  106 (244)
                      ++.|+..|...   +++|..+||+.++++      ... +.++++.|...|++.+.....++   .+.+|+.+..
T Consensus        45 ~~~iL~~l~~~---~~~t~~ela~~l~i~------~~t-vs~~l~~Le~~Glv~r~~~~~d~R~~~~~lT~~G~~  109 (155)
T 3cdh_A           45 EWRVLACLVDN---DAMMITRLAKLSLME------QSR-MTRIVDQMDARGLVTRVADAKDKRRVRVRLTDDGRA  109 (155)
T ss_dssp             HHHHHHHHSSC---SCBCHHHHHHHTTCC------HHH-HHHHHHHHHHTTSEEECC------CCCEEECHHHHH
T ss_pred             HHHHHHHHHHC---CCcCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEeccCCCcCCeeEeEECHHHHH
Confidence            34467777664   689999999999997      456 99999999999999853211112   2556665543

>3g3z_A NMB1585, transcriptional regulator, MARR family; transcription factor, structur genomics, oxford protein production facility; 2.10A {Neisseria meningitidis serogroup B}

Probab=94.20  E-value=0.03  Score=41.52  Aligned_cols=64  Identities=14%  Similarity=0.140  Sum_probs=46.3

Q ss_pred             HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCcccccc
Q 041256           34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSAYF  107 (244)
Q Consensus        34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~~l  107 (244)
                      .++.++..|...   +++|..+||+.++++      +.. +.++++.|...|++++.....+.   .+.+|+.+..+
T Consensus        32 ~q~~iL~~l~~~---~~~t~~eLa~~l~~~------~~t-vs~~l~~Le~~Glv~r~~~~~D~R~~~~~LT~~G~~~   98 (145)
T 3g3z_A           32 NLFAVLYTLATE---GSRTQKHIGEKWSLP------KQT-VSGVCKTLAGQGLIEWQEGEQDRRKRLLSLTETGKAY   98 (145)
T ss_dssp             HHHHHHHHHHHH---CSBCHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEECCCSSCGGGSCEEECHHHHHH
T ss_pred             HHHHHHHHHHHC---CCCCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEeeccCCCCCceeeeeEChhHHHH
Confidence            345577778775   589999999999997      456 99999999999999963211122   35666655433

>2rdp_A Putative transcriptional regulator MARR; PFAM PF01047, winged-helix binding motif, structural genomics, PSI-2; 2.30A {Geobacillus stearothermophilus}

Probab=94.18  E-value=0.031  Score=41.55  Aligned_cols=61  Identities=10%  Similarity=0.113  Sum_probs=43.9

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCcccc
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSA  105 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~  105 (244)
                      ++.++..|...   ++.|..+||+.++++      ... +.++++.|...|++.......++   .+.+|+.+.
T Consensus        44 ~~~iL~~l~~~---~~~t~~ela~~l~~~------~~t-vs~~l~~Le~~Glv~r~~~~~d~R~~~~~lT~~G~  107 (150)
T 2rdp_A           44 QFVALQWLLEE---GDLTVGELSNKMYLA------CST-TTDLVDRMERNGLVARVRDEHDRRVVRIRLLEKGE  107 (150)
T ss_dssp             HHHHHHHHHHH---CSBCHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEEEECCC---CEEEEECHHHH
T ss_pred             HHHHHHHHHHc---CCCCHHHHHHHHCCC------chh-HHHHHHHHHHCCCeeecCCCCCcceeEeEECHhHH
Confidence            34467777765   589999999999997      456 99999999999999863211122   255555554

>2r6z_A UPF0341 protein in RSP 3' region; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 1.80A {Neisseria gonorrhoeae}

Probab=94.15  E-value=0.031  Score=46.34  Aligned_cols=42  Identities=19%  Similarity=0.181  Sum_probs=33.3

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-h-------HHhhhCCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-P-------YVIKDAPS  234 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p-------~vi~~a~~  234 (244)
                      .....+|+|+|||.|.++..+++.  ..+++.+|+ |       ..++.+++
T Consensus        81 ~~~~~~VLDlgcG~G~~a~~lA~~--g~~V~~vD~s~~~~~ll~~~l~~a~~  130 (258)
T 2r6z_A           81 HTAHPTVWDATAGLGRDSFVLASL--GLTVTAFEQHPAVACLLSDGIRRALL  130 (258)
T ss_dssp             GGGCCCEEETTCTTCHHHHHHHHT--TCCEEEEECCHHHHHHHHHHHHHHHH
T ss_pred             cCCcCeEEEeeCccCHHHHHHHHh--CCEEEEEECChhhhHHHHHHHHHHHh
Confidence            344578999999999999999986  568999998 6       55665543

>1yyv_A Putative transcriptional regulator; reductive methylation, D lysine, structural genomics, PSI; HET: MLY; 2.35A {Salmonella typhimurium} SCOP: a.4.5.69

Probab=94.15  E-value=0.037  Score=40.98  Aligned_cols=76  Identities=12%  Similarity=0.073  Sum_probs=51.6

Q ss_pred             hHHHHHHHHhhhHHHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhC-CCCCCCCcchhccHHHHHHHHhhCCccccee
Q 041256           13 NFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQI-PLKDNNPEAAAMTLDRVLRLLVSYNALHCSF   91 (244)
Q Consensus        13 ~~~~l~~~~~g~~~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~-~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~   91 (244)
                      ....+++++.+.|...+         ...|..    |+++..||++.+ |++      +.. +.+.|+.|...|++++..
T Consensus        24 ~~~~~l~~l~~~w~l~I---------L~~L~~----g~~~~~eLa~~l~gis------~~t-ls~~L~~Le~~GlV~r~~   83 (131)
T 1yyv_A           24 PSREVLKHVTSRWGVLI---------LVALRD----GTHRFSDLRRXMGGVS------EXM-LAQSLQALEQDGFLNRVS   83 (131)
T ss_dssp             THHHHHHHHHSHHHHHH---------HHHGGG----CCEEHHHHHHHSTTCC------HHH-HHHHHHHHHHHTCEEEEE
T ss_pred             CHHHHHHHHcCCcHHHH---------HHHHHc----CCCCHHHHHHHhccCC------HHH-HHHHHHHHHHCCcEEEEe
Confidence            34455555555555443         334543    689999999999 797      456 999999999999999643


Q ss_pred             ecCC---ceeecCccccccc
Q 041256           92 VDGQ---RLYSLAPVSAYFV  108 (244)
Q Consensus        92 ~~~~---~~y~~t~~s~~l~  108 (244)
                      ...+   -.|++|+.++.+.
T Consensus        84 ~~~d~r~~~y~LT~~G~~l~  103 (131)
T 1yyv_A           84 YPVVPPHVEYSLTPLGEQVS  103 (131)
T ss_dssp             ECSSSCEEEEEECHHHHHHH
T ss_pred             cCCCCCeEEEEECccHHHHH
Confidence            2211   2588888765443

>2fbi_A Probable transcriptional regulator; MARR, APC5816, structural genomic protein structure initiative; 2.10A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=94.13  E-value=0.025  Score=41.57  Aligned_cols=62  Identities=11%  Similarity=0.083  Sum_probs=45.2

Q ss_pred             HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCce---eecCcccc
Q 041256           34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRL---YSLAPVSA  105 (244)
Q Consensus        34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~---y~~t~~s~  105 (244)
                      .++.++..|...   +++|..+||+.++++      ... +.++++.|...|++.+.....+.+   +.+|+.+.
T Consensus        37 ~~~~iL~~l~~~---~~~t~~ela~~l~~s------~~~-vs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~  101 (142)
T 2fbi_A           37 QQWRVIRILRQQ---GEMESYQLANQACIL------RPS-MTGVLARLERDGIVRRWKAPKDQRRVYVNLTEKGQ  101 (142)
T ss_dssp             HHHHHHHHHHHH---CSEEHHHHHHHTTCC------HHH-HHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHH
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHCCC------HhH-HHHHHHHHHHCCCEEeecCCCCCCeeEEEECHHHH
Confidence            355577777775   589999999999997      456 999999999999998642222222   55555544

>3k69_A Putative transcription regulator; putative transcriptional regulator, structural genomics, JOI for structural genomics, JCSG; HET: MSE; 1.95A {Lactobacillus plantarum} SCOP: a.4.5.0

Probab=94.11  E-value=0.085  Score=40.56  Aligned_cols=47  Identities=21%  Similarity=0.309  Sum_probs=38.0

Q ss_pred             CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcc
Q 041256           49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPV  103 (244)
Q Consensus        49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~  103 (244)
                      ++.|.++||+.++++      +.. ++++|..|...|++.-. +...|.|++..-
T Consensus        27 ~~~s~~~IA~~~~is------~~~-l~kil~~L~~aGlv~s~-rG~~GGy~Lar~   73 (162)
T 3k69_A           27 SKVASRELAQSLHLN------PVM-IRNILSVLHKHGYLTGT-VGKNGGYQLDLA   73 (162)
T ss_dssp             SCBCHHHHHHHHTSC------GGG-THHHHHHHHHTTSSEEE-CSTTCEEECCSC
T ss_pred             CCcCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEee-cCCCCCeEecCC
Confidence            589999999999997      568 99999999999999742 222467888653

>3nrv_A Putative transcriptional regulator (MARR/EMRR FAM; PSI-2, protein structure initiati structural genomics; HET: MSE; 2.00A {Acinetobacter SP}

Probab=94.10  E-value=0.027  Score=41.91  Aligned_cols=47  Identities=21%  Similarity=0.316  Sum_probs=39.1

Q ss_pred             HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      .++.++..|...   +++|..+||+.++++      +.. +.++++.|...|++.+.
T Consensus        41 ~~~~iL~~l~~~---~~~t~~ela~~l~~~------~~t-vs~~l~~Le~~Glv~r~   87 (148)
T 3nrv_A           41 TEWRIISVLSSA---SDCSVQKISDILGLD------KAA-VSRTVKKLEEKKYIEVN   87 (148)
T ss_dssp             HHHHHHHHHHHS---SSBCHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEC-
T ss_pred             HHHHHHHHHHcC---CCCCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEee
Confidence            345577778775   589999999999997      556 99999999999999863

>3sso_A Methyltransferase; macrolide, natural product, rossman fold; HET: SAH; 1.90A {Micromonospora griseorubida} PDB: 3ssn_A* 3ssm_A*

Probab=93.97  E-value=0.051  Score=48.17  Aligned_cols=47  Identities=13%  Similarity=0.080  Sum_probs=33.2

Q ss_pred             CcceEEEecCC------ccHHHHHHHHH-CCCCeEEEccchHHhhhCCCCCCceee
Q 041256          193 HVKKLVDVGGG------LGITLNMIISK-YPHIKGINYDLPYVIKDAPSYPGTLFI  241 (244)
Q Consensus       193 ~~~~vvDVGGG------~G~~~~~l~~~-~P~l~~~v~Dlp~vi~~a~~~~~i~~~  241 (244)
                      +..+|||||||      +|..+..++++ +|+.+++.+|+.+...  ...++|+++
T Consensus       216 ~~~rVLDIGCG~~~~~~TGG~Sl~la~~~fP~a~V~GVDiSp~m~--~~~~rI~fv  269 (419)
T 3sso_A          216 QQVRVLEIGVGGYKHPEWGGGSLRMWKSFFPRGQIYGLDIMDKSH--VDELRIRTI  269 (419)
T ss_dssp             SCCEEEEECCSCTTCSSCCCHHHHHHHHHCTTCEEEEEESSCCGG--GCBTTEEEE
T ss_pred             CCCEEEEEecCCCcCCCCCHHHHHHHHHhCCCCEEEEEECCHHHh--hcCCCcEEE
Confidence            45899999999      66667777765 5999999999943322  233566654

>3oop_A LIN2960 protein; protein structure initiative, PSI-2, structural genomics, MI center for structural genomics, MCSG, unknown function; 1.78A {Listeria innocua}

Probab=93.95  E-value=0.022  Score=42.17  Aligned_cols=63  Identities=19%  Similarity=0.210  Sum_probs=44.8

Q ss_pred             HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCccccc
Q 041256           34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSAY  106 (244)
Q Consensus        34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~~  106 (244)
                      .+..++..|...   +++|..+||+.++++      +.. +.++++.|...|++++.+...+.   .+.+|+.+..
T Consensus        38 ~~~~iL~~l~~~---~~~t~~eLa~~l~~~------~~~-vs~~l~~L~~~Glv~r~~~~~D~R~~~~~LT~~G~~  103 (143)
T 3oop_A           38 EQWSVLEGIEAN---EPISQKEIALWTKKD------TPT-VNRIVDVLLRKELIVREISTEDRRISLLSLTDKGRK  103 (143)
T ss_dssp             HHHHHHHHHHHH---SSEEHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEEEC----CCSCEEEECHHHHH
T ss_pred             HHHHHHHHHHHc---CCcCHHHHHHHHCCC------Hhh-HHHHHHHHHHCCCeeccCCCccCceeeeeECHHHHH
Confidence            344567777765   689999999999997      556 99999999999999863211122   3556665543

>2zkz_A Transcriptional repressor PAGR; protein-DNA, HTH motif, dimer, DN binding, transcription regulation; 2.00A {Bacillus anthracis}

Probab=93.91  E-value=0.053  Score=37.89  Aligned_cols=60  Identities=17%  Similarity=0.197  Sum_probs=41.5

Q ss_pred             HHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCc
Q 041256           32 AVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAP  102 (244)
Q Consensus        32 ~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~  102 (244)
                      --.++.|+..|...   ++.|+.|||+.+|++      ... +.+-|+.|... ++....+...-.|++++
T Consensus        26 ~~~Rl~IL~~l~~~---~~~~~~ela~~l~is------~st-vs~hL~~L~~~-lv~~~~~gr~~~y~l~~   85 (99)
T 2zkz_A           26 HPMRLKIVNELYKH---KALNVTQIIQILKLP------QST-VSQHLCKMRGK-VLKRNRQGLEIYYSINN   85 (99)
T ss_dssp             SHHHHHHHHHHHHH---SCEEHHHHHHHHTCC------HHH-HHHHHHHHBTT-TBEEEEETTEEEEECCC
T ss_pred             CHHHHHHHHHHHHC---CCcCHHHHHHHHCcC------HHH-HHHHHHHHHHH-hhhheEeCcEEEEEECh
Confidence            34556677544443   689999999999997      456 99999999999 88753221112355554

>2fbh_A Transcriptional regulator PA3341; MARR, transcription regulator, APC5857, structural genomics, protein structure initiative; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=93.88  E-value=0.044  Score=40.42  Aligned_cols=45  Identities=16%  Similarity=0.119  Sum_probs=37.1

Q ss_pred             cChhhHH-hhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           36 LDVFEII-SKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        36 lgifd~L-~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      +.++..| ...   ++.|..+||+.++++      +.. +.++++.|...|++...
T Consensus        40 ~~iL~~l~~~~---~~~t~~~la~~l~~s------~~~-vs~~l~~L~~~glv~r~   85 (146)
T 2fbh_A           40 WLVLLHLARHR---DSPTQRELAQSVGVE------GPT-LARLLDGLESQGLVRRL   85 (146)
T ss_dssp             HHHHHHHHHCS---SCCBHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHcC---CCCCHHHHHHHhCCC------hhh-HHHHHHHHHHCCCeeec
Confidence            3466777 443   689999999999997      456 99999999999999863

>2p41_A Type II methyltransferase; vizier, viral enzymes involved in replication, dengue virus methyltransferase, structural genomics; HET: G1G SAH CIT; 1.80A {Dengue virus 2} SCOP: c.66.1.25 PDB: 2p1d_A* 1l9k_A* 2p3o_A* 2p3q_A* 2p40_A* 2p3l_A* 1r6a_A*

Probab=93.86  E-value=0.036  Score=47.11  Aligned_cols=32  Identities=19%  Similarity=-0.036  Sum_probs=26.9

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL  225 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  225 (244)
                      +....+|||||||.|.++..++++   -+++.+|+
T Consensus        80 ~~~g~~VLDlGcG~G~~s~~la~~---~~V~gvD~  111 (305)
T 2p41_A           80 VTPEGKVVDLGCGRGGWSYYCGGL---KNVREVKG  111 (305)
T ss_dssp             SCCCEEEEEETCTTSHHHHHHHTS---TTEEEEEE
T ss_pred             CCCCCEEEEEcCCCCHHHHHHHhc---CCEEEEec
Confidence            455689999999999999999988   36777787

>1s3j_A YUSO protein; structural genomics, MARR transcriptional regulator family, PSI, protein structure initiative; HET: MSE; 2.25A {Bacillus subtilis} SCOP: a.4.5.28

Probab=93.85  E-value=0.15  Score=37.95  Aligned_cols=45  Identities=22%  Similarity=0.269  Sum_probs=38.0

Q ss_pred             cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      +.|+..|...   ++.|..+||+.++++      ... +.++++.|...|++.+.
T Consensus        40 ~~iL~~l~~~---~~~t~~ela~~l~~s------~~t-vs~~l~~Le~~glv~r~   84 (155)
T 1s3j_A           40 LFVLASLKKH---GSLKVSEIAERMEVK------PSA-VTLMADRLEQKNLIART   84 (155)
T ss_dssp             HHHHHHHHHH---SEEEHHHHHHHHTSC------HHH-HHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHc---CCCCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEeec
Confidence            4477777765   589999999999997      456 99999999999999863

>2a61_A Transcriptional regulator TM0710; APC4350, MCSG, midwest center for structural genomics, PSI, protein structure initiative, MARR; 1.80A {Thermotoga maritima} SCOP: a.4.5.28

Probab=93.80  E-value=0.034  Score=41.03  Aligned_cols=63  Identities=10%  Similarity=0.106  Sum_probs=45.7

Q ss_pred             HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCccccc
Q 041256           34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSAY  106 (244)
Q Consensus        34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~~  106 (244)
                      .++.++..|...   ++.|..+||+.++++      ... +.++++.|...|++.......+.   .|.+|+.+..
T Consensus        34 ~~~~iL~~l~~~---~~~~~~~la~~l~~s------~~t-vs~~l~~L~~~glv~r~~~~~d~r~~~~~lT~~G~~   99 (145)
T 2a61_A           34 AQFDILQKIYFE---GPKRPGELSVLLGVA------KST-VTGLVKRLEADGYLTRTPDPADRRAYFLVITRKGEE   99 (145)
T ss_dssp             HHHHHHHHHHHH---CCBCHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHH
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHCCC------chh-HHHHHHHHHHCCCeeecCCCCCCceEEEEECHHHHH
Confidence            345577777765   589999999999997      456 99999999999999964211122   2556665543

>2eth_A Transcriptional regulator, putative, MAR family; MARR family, structural genomics, joint center for structura genomics, JCSG; 2.30A {Thermotoga maritima} SCOP: a.4.5.28

Probab=93.79  E-value=0.05  Score=40.78  Aligned_cols=47  Identities=15%  Similarity=0.110  Sum_probs=39.4

Q ss_pred             HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      .++.|+..|...   +++|..+||+.++++      ... +.++++.|...|++.+.
T Consensus        45 ~~~~iL~~l~~~---~~~t~~ela~~l~is------~~t-vs~~l~~Le~~Gli~r~   91 (154)
T 2eth_A           45 TELYAFLYVALF---GPKKMKEIAEFLSTT------KSN-VTNVVDSLEKRGLVVRE   91 (154)
T ss_dssp             HHHHHHHHHHHH---CCBCHHHHHHHTTSC------HHH-HHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEee
Confidence            355677778765   589999999999997      456 99999999999999863

>1lj9_A Transcriptional regulator SLYA; HTH DNA binding protein, structural genomics, PSI, protein structure initiative; 1.60A {Enterococcus faecalis} SCOP: a.4.5.28

Probab=93.78  E-value=0.033  Score=41.10  Aligned_cols=60  Identities=7%  Similarity=-0.013  Sum_probs=43.8

Q ss_pred             cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCcccc
Q 041256           36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSA  105 (244)
Q Consensus        36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~  105 (244)
                      +.++..|...   +++|..+||+.++++      ... +.++++.|...|++.......+.   .+.+|+.+.
T Consensus        32 ~~iL~~l~~~---~~~t~~~la~~l~~s------~~~-vs~~l~~Le~~gli~r~~~~~d~R~~~~~lT~~G~   94 (144)
T 1lj9_A           32 YLYLVRVCEN---PGIIQEKIAELIKVD------RTT-AARAIKRLEEQGFIYRQEDASNKKIKRIYATEKGK   94 (144)
T ss_dssp             HHHHHHHHHS---TTEEHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEEEECSSCTTCEEEEECHHHH
T ss_pred             HHHHHHHHHC---cCcCHHHHHHHHCCC------HhH-HHHHHHHHHHCCCEEeecCCCCCceeeeEEChhHH
Confidence            4467777765   589999999999997      456 99999999999999864211122   255555554

>1r7j_A Conserved hypothetical protein SSO10A; winged helix-turn-helix, two-stranded antiparallel coiled CO structural genomics, PSI; 1.47A {Sulfolobus solfataricus} SCOP: a.4.5.49 PDB: 1xsx_A

Probab=93.76  E-value=0.047  Score=38.11  Aligned_cols=47  Identities=15%  Similarity=0.259  Sum_probs=40.9

Q ss_pred             CCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccccccc
Q 041256           51 LSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFV  108 (244)
Q Consensus        51 ~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l~  108 (244)
                      ++..+||..+|++      ++. +.+.++.|...|++.+   . .+.|.+|+.+..+.
T Consensus        21 ~~~t~La~~~~ls------~~~-~~~~l~~L~~~GLI~~---~-~~~~~LT~kG~~~l   67 (95)
T 1r7j_A           21 SPKTRIMYGANLS------YAL-TGRYIKMLMDLEIIRQ---E-GKQYMLTKKGEELL   67 (95)
T ss_dssp             BCHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEE---E-TTEEEECHHHHHHH
T ss_pred             CCHHHHHHHhCcC------HHH-HHHHHHHHHHCCCeEE---E-CCeeEEChhHHHHH
Confidence            8999999999997      667 9999999999999995   3 36699999987554

>2lkp_A Transcriptional regulator, ARSR family; symmetric homodimer, NI(II) binding protein, DNA binding Pro transcription regulator; NMR {Mycobacterium tuberculosis}

Probab=93.70  E-value=0.049  Score=39.19  Aligned_cols=46  Identities=15%  Similarity=0.271  Sum_probs=39.0

Q ss_pred             HHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           33 VVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        33 a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      -.++.|+..|.+    ++.|..+||+.++++      ... +.+.|+.|...|++..
T Consensus        32 ~~~~~il~~L~~----~~~s~~ela~~l~is------~st-vsr~l~~Le~~Glv~~   77 (119)
T 2lkp_A           32 PSRLMILTQLRN----GPLPVTDLAEAIGME------QSA-VSHQLRVLRNLGLVVG   77 (119)
T ss_dssp             HHHHHHHHHHHH----CCCCHHHHHHHHSSC------HHH-HHHHHHHHHHHCSEEE
T ss_pred             HHHHHHHHHHHH----CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEE
Confidence            456677788877    479999999999997      456 9999999999999985

>2f8l_A Hypothetical protein LMO1582; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE SAM; 2.20A {Listeria monocytogenes} SCOP: c.66.1.45

Probab=93.69  E-value=0.021  Score=49.16  Aligned_cols=43  Identities=16%  Similarity=0.197  Sum_probs=35.8

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCC-----CeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPH-----IKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~-----l~~~v~Dl-p~vi~~a~~  234 (244)
                      ....+|+|+|||+|.++..+++..|.     .+++.+|+ |..++.|+.
T Consensus       129 ~~~~~VlDp~cGsG~~l~~~~~~~~~~~~~~~~v~GiDi~~~~~~~a~~  177 (344)
T 2f8l_A          129 KKNVSILDPACGTANLLTTVINQLELKGDVDVHASGVDVDDLLISLALV  177 (344)
T ss_dssp             CSEEEEEETTCTTSHHHHHHHHHHHTTSSCEEEEEEEESCHHHHHHHHH
T ss_pred             CCCCEEEeCCCCccHHHHHHHHHHHHhcCCCceEEEEECCHHHHHHHHH
Confidence            35589999999999999999998875     67899998 777776653

>1sqg_A SUN protein, FMU protein; rossmann-fold, mixed beta sheet, methyltransferase-fold, RNA-binding domain; 1.65A {Escherichia coli} SCOP: a.79.1.3 c.66.1.38 PDB: 1sqf_A

Probab=93.63  E-value=0.027  Score=50.15  Aligned_cols=48  Identities=10%  Similarity=0.124  Sum_probs=38.3

Q ss_pred             HhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256          185 LESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       185 ~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~  233 (244)
                      ...++ .....+|+|+|||.|..+..+++..|+.+++.+|. |..++.++
T Consensus       239 ~~~l~-~~~g~~VLDlgaG~G~~t~~la~~~~~~~v~a~D~~~~~l~~~~  287 (429)
T 1sqg_A          239 MTWLA-PQNGEHILDLCAAPGGKTTHILEVAPEAQVVAVDIDEQRLSRVY  287 (429)
T ss_dssp             HHHHC-CCTTCEEEEESCTTCHHHHHHHHHCTTCEEEEEESSTTTHHHHH
T ss_pred             HHHcC-CCCcCeEEEECCCchHHHHHHHHHcCCCEEEEECCCHHHHHHHH
Confidence            33444 45567999999999999999999999988999998 55565554

>3ldg_A Putative uncharacterized protein SMU.472; YPSC, methyltransferase, transferase; HET: SAH; 1.96A {Streptococcus mutans}

Probab=93.61  E-value=0.055  Score=47.56  Aligned_cols=52  Identities=13%  Similarity=0.029  Sum_probs=40.6

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCC--------------------------------------CeEEEc
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPH--------------------------------------IKGINY  223 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~--------------------------------------l~~~v~  223 (244)
                      ..++.... |.....|+|.+||+|.++++.+....+                                      .+++.+
T Consensus       184 aall~l~~-~~~~~~llDp~CGSGt~lIEAa~~a~~iapg~~R~f~f~~w~~~~~~~w~~~~~~a~~~~~~~~~~~v~Gv  262 (384)
T 3ldg_A          184 AAIILLSN-WFPDKPFVDPTCGSGTFCIEAAMIGMNIAPGFNRDFAFEEWPWVDEALVTRVRNEADEQADYDIQLDISGF  262 (384)
T ss_dssp             HHHHHHTT-CCTTSCEEETTCTTSHHHHHHHHHHTTCCTTTTCCCGGGGCTTSCHHHHHHHHHHHHHHCCTTCCCCEEEE
T ss_pred             HHHHHHhC-CCCCCeEEEeCCcCCHHHHHHHHHhcCcCCCccccchhhhhccCCHHHHHHHHHHHHHhhhccCCceEEEE
Confidence            34555555 777789999999999999998875444                                      568999


Q ss_pred             cc-hHHhhhCCC
Q 041256          224 DL-PYVIKDAPS  234 (244)
Q Consensus       224 Dl-p~vi~~a~~  234 (244)
                      |. |.+++.|++
T Consensus       263 Did~~al~~Ar~  274 (384)
T 3ldg_A          263 DFDGRMVEIARK  274 (384)
T ss_dssp             ESCHHHHHHHHH
T ss_pred             ECCHHHHHHHHH
Confidence            98 888888764

>1xd7_A YWNA; structural genomics, protein structure initiative, winged HE binding, hypothetical protein, PSI; 2.30A {Bacillus subtilis subsp} SCOP: a.4.5.55

Probab=93.53  E-value=0.064  Score=40.34  Aligned_cols=42  Identities=21%  Similarity=0.226  Sum_probs=35.0

Q ss_pred             CHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCc
Q 041256           52 SVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAP  102 (244)
Q Consensus        52 t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~  102 (244)
                      |.++||+..+++      +.. ++++|..|...|++...  .|.|.|.++.
T Consensus        25 s~~~IA~~~~i~------~~~-l~kIl~~L~~aGlv~s~--rG~GGy~Lar   66 (145)
T 1xd7_A           25 SSEIIADSVNTN------PVV-VRRMISLLKKADILTSR--AGVPGASLKK   66 (145)
T ss_dssp             CHHHHHHHHTSC------HHH-HHHHHHHHHHTTSEECC--SSSSSCEESS
T ss_pred             CHHHHHHHHCcC------HHH-HHHHHHHHHHCCceEee--cCCCCceecC
Confidence            999999999997      678 99999999999999842  2356677755

>2dul_A N(2),N(2)-dimethylguanosine tRNA methyltransferas; tRNA modification enzyme, guanine 26, N(2),N(2)-dimethyltran structural genomics; 1.90A {Pyrococcus horikoshii} SCOP: c.66.1.58 PDB: 2ejt_A* 2eju_A* 2ytz_A*

Probab=93.43  E-value=0.045  Score=48.02  Aligned_cols=41  Identities=15%  Similarity=-0.023  Sum_probs=36.5

Q ss_pred             cceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+|+|+|+|+|..++.++++.|..+++..|+ |..++.+++
T Consensus        48 ~~~VLDl~aGtG~~~l~~a~~~~~~~V~avDi~~~av~~a~~   89 (378)
T 2dul_A           48 PKIVLDALSATGIRGIRFALETPAEEVWLNDISEDAYELMKR   89 (378)
T ss_dssp             CSEEEESSCTTSHHHHHHHHHSSCSEEEEEESCHHHHHHHHH
T ss_pred             CCEEEECCCchhHHHHHHHHhCCCCeEEEEECCHHHHHHHHH
Confidence            47899999999999999999999889999998 888777764

>2fa5_A Transcriptional regulator MARR/EMRR family; multiple antibiotics resistance repressor, XCC structural genomics, X-RAY diffraction; 1.80A {Xanthomonas campestris}

Probab=93.40  E-value=0.045  Score=41.30  Aligned_cols=45  Identities=16%  Similarity=0.220  Sum_probs=38.5

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      ++.|+..|...   +++|..+||+.++++      ... +.++++.|...|++.+
T Consensus        51 ~~~iL~~l~~~---~~~t~~ela~~l~is------~~t-vs~~l~~Le~~glv~r   95 (162)
T 2fa5_A           51 EWRVITILALY---PGSSASEVSDRTAMD------KVA-VSRAVARLLERGFIRR   95 (162)
T ss_dssp             HHHHHHHHHHS---TTCCHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEC
T ss_pred             HHHHHHHHHhC---CCCCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEee
Confidence            44577788775   689999999999997      456 9999999999999986

>1z91_A Organic hydroperoxide resistance transcriptional; OHRR, MARR family, bacterial transcription factor, DNA bindi protein; 2.50A {Bacillus subtilis} SCOP: a.4.5.28 PDB: 1z9c_A*

Probab=93.39  E-value=0.036  Score=41.07  Aligned_cols=66  Identities=15%  Similarity=0.165  Sum_probs=47.8

Q ss_pred             HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCcccccccc
Q 041256           34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSAYFVR  109 (244)
Q Consensus        34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~~l~~  109 (244)
                      .++.++..|...   ++.|..+||+.++++      ... +.++++.|...|++.+.....++   .+.+|+.+..+..
T Consensus        41 ~~~~iL~~l~~~---~~~~~~~la~~l~~~------~~t-vs~~l~~L~~~glv~r~~~~~d~R~~~~~LT~~G~~~~~  109 (147)
T 1z91_A           41 PQYLALLLLWEH---ETLTVKKMGEQLYLD------SGT-LTPMLKRMEQQGLITRKRSEEDERSVLISLTEDGALLKE  109 (147)
T ss_dssp             HHHHHHHHHHHH---SEEEHHHHHHTTTCC------HHH-HHHHHHHHHHHTSEECCBCSSCTTSBEEEECHHHHSGGG
T ss_pred             HHHHHHHHHHHC---CCCCHHHHHHHHCCC------cCc-HHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHHH
Confidence            345567777765   589999999999997      456 99999999999999863211112   3677777765443

>3kp7_A Transcriptional regulator TCAR; multiple drug resistance, biofilm, transcription regulation, binding, transcription regulator; 2.30A {Staphylococcus epidermidis RP62A} PDB: 3kp3_A* 3kp4_A* 3kp5_A* 3kp2_A* 3kp6_A

Probab=93.38  E-value=0.19  Score=37.31  Aligned_cols=43  Identities=16%  Similarity=0.298  Sum_probs=36.6

Q ss_pred             cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      ..++..| ..   +++|..+||+.++++      +.. +.++++.|...|++.+
T Consensus        41 ~~iL~~l-~~---~~~t~~eLa~~l~~~------~~~-vs~~l~~Le~~Glv~r   83 (151)
T 3kp7_A           41 SHVLNML-SI---EALTVGQITEKQGVN------KAA-VSRRVKKLLNAELVKL   83 (151)
T ss_dssp             HHHHHHH-HH---SCBCHHHHHHHHCSC------SSH-HHHHHHHHHHTTSEEC
T ss_pred             HHHHHHH-Hc---CCcCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEe
Confidence            3477778 54   699999999999997      345 9999999999999995

>3cjn_A Transcriptional regulator, MARR family; silicibacter pomeroy structural genomics, PSI-2, protein structure initiative; 1.95A {Silicibacter pomeroyi dss-3}

Probab=93.37  E-value=0.045  Score=41.36  Aligned_cols=47  Identities=15%  Similarity=0.189  Sum_probs=39.5

Q ss_pred             HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      .++.|+..|...   +++|..+||+.++++      ... +.++++.|...|++.+.
T Consensus        53 ~~~~iL~~l~~~---~~~t~~ela~~l~is------~~t-vs~~l~~Le~~Gli~r~   99 (162)
T 3cjn_A           53 AKMRALAILSAK---DGLPIGTLGIFAVVE------QST-LSRALDGLQADGLVRRE   99 (162)
T ss_dssp             HHHHHHHHHHHS---CSEEHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHC---CCCCHHHHHHHHCCC------hhH-HHHHHHHHHHCCCEEec
Confidence            345577888775   689999999999997      456 99999999999999863

>3eco_A MEPR; mutlidrug efflux pump regulator winged helix-turn-helix motif, DNA-binding, transcription, transcription regulation; 2.40A {Staphylococcus aureus} SCOP: a.4.5.0

Probab=93.35  E-value=0.043  Score=40.28  Aligned_cols=65  Identities=9%  Similarity=0.045  Sum_probs=45.2

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCcccccc
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSAYF  107 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~~l  107 (244)
                      ++.++..|...+. +++|..+||+.++++      +.. +.++++.|...|++++.....++   .+.+|+.+..+
T Consensus        33 ~~~vL~~l~~~~~-~~~t~~ela~~l~~~------~~t-vs~~l~~Le~~Gli~r~~~~~D~R~~~~~LT~~G~~~  100 (139)
T 3eco_A           33 QGHTLGYLYAHQQ-DGLTQNDIAKALQRT------GPT-VSNLLRNLERKKLIYRYVDAQDTRRKNIGLTTSGIKL  100 (139)
T ss_dssp             HHHHHHHHHHSTT-TCEEHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEEEECCC--CCEEEEECHHHHHH
T ss_pred             HHHHHHHHHhcCC-CCcCHHHHHHHhCCC------ccc-HHHHHHHHHHCCCEeecCCCCCCCeeeeEECHHHHHH
Confidence            4456777776521 489999999999997      456 99999999999999964222222   24555555433

>3s2w_A Transcriptional regulator, MARR family; structural genomics, PSI-biology, protein structure initiati midwest center for structural genomics; 2.45A {Methanosarcina mazei}

Probab=93.27  E-value=0.041  Score=41.55  Aligned_cols=61  Identities=8%  Similarity=0.069  Sum_probs=43.5

Q ss_pred             cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCccccc
Q 041256           36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSAY  106 (244)
Q Consensus        36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~~  106 (244)
                      +.++..|...   +++|..+||+.++++      +.. +.++++.|...|++++.....+.   .+.+|+.+..
T Consensus        53 ~~vL~~l~~~---~~~t~~eLa~~l~~~------~~t-vs~~l~~Le~~Glv~r~~~~~DrR~~~l~LT~~G~~  116 (159)
T 3s2w_A           53 FPFLMRLYRE---DGINQESLSDYLKID------KGT-TARAIQKLVDEGYVFRQRDEKDRRSYRVFLTEKGKK  116 (159)
T ss_dssp             HHHHHHHHHS---CSEEHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEEEECC---CCEEEEECHHHHH
T ss_pred             HHHHHHHHHC---CCCCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEEecCCCCCCeeEEEECHHHHH
Confidence            3456677665   689999999999997      556 99999999999999964211122   3556655543

>3hsr_A HTH-type transcriptional regulator SARZ; helix-turn-helix, cysteine disulfide, MARR-family transcript regulator, DNA-binding; 1.90A {Staphylococcus aureus subsp} PDB: 3hse_A 3hrm_A 4gxo_A

Probab=93.23  E-value=0.024  Score=41.93  Aligned_cols=62  Identities=16%  Similarity=0.158  Sum_probs=42.9

Q ss_pred             cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCcccccc
Q 041256           36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSAYF  107 (244)
Q Consensus        36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~~l  107 (244)
                      +.+...|...   +++|..+||+.++++      +.. +.++++.|...|++++.+...+.   .+.+|+.++.+
T Consensus        39 ~~vL~~l~~~---~~~t~~eLa~~l~~~------~~t-vs~~l~~L~~~Glv~r~~~~~D~R~~~~~LT~~G~~~  103 (140)
T 3hsr_A           39 YIVLMAIEND---EKLNIKKLGERVFLD------SGT-LTPLLKKLEKKDYVVRTREEKDERNLQISLTEQGKAI  103 (140)
T ss_dssp             HHHHHHSCTT---CEEEHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEEEC-------CEEEECHHHHHT
T ss_pred             HHHHHHHHHc---CCcCHHHHHHHHCCC------hhh-HHHHHHHHHHCCCeEecCCCCCcceeeeeEChHHHHH
Confidence            3355556543   689999999999997      556 99999999999999963211122   35666655533

>2bv6_A MGRA, HTH-type transcriptional regulator MGRA; multidrug resistance regulator, virulence determinant, transcriptional factors; 2.8A {Staphylococcus aureus} SCOP: a.4.5.28

Probab=93.21  E-value=0.055  Score=39.81  Aligned_cols=62  Identities=13%  Similarity=0.242  Sum_probs=45.0

Q ss_pred             HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCcccc
Q 041256           34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSA  105 (244)
Q Consensus        34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~  105 (244)
                      .++.|+..|...   +++|..+||+.++++      ... +.+.++.|...|++.......++   .+.+|+.+.
T Consensus        38 ~~~~iL~~l~~~---~~~~~~ela~~l~~~------~~t-vs~~l~~L~~~gli~r~~~~~d~R~~~~~lT~~G~  102 (142)
T 2bv6_A           38 PQFLVLTILWDE---SPVNVKKVVTELALD------TGT-VSPLLKRMEQVDLIKRERSEVDQREVFIHLTDKSE  102 (142)
T ss_dssp             HHHHHHHHHHHS---SEEEHHHHHHHTTCC------TTT-HHHHHHHHHHTTSEEEEECSSSTTCEEEEECHHHH
T ss_pred             HHHHHHHHHHHc---CCcCHHHHHHHHCCC------hhh-HHHHHHHHHHCCCEEeecCCCCcceEEEEEChHHH
Confidence            345577778775   589999999999997      445 99999999999999864211112   355565554

>2a14_A Indolethylamine N-methyltransferase; SGC,INMT, structural genomics, structural genomics consortium; HET: SAH; 1.70A {Homo sapiens} SCOP: c.66.1.15

Probab=93.18  E-value=0.012  Score=48.69  Aligned_cols=41  Identities=15%  Similarity=0.048  Sum_probs=29.2

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~  233 (244)
                      .+..+|||||||.|.++..++...- -+++..|+ |..++.++
T Consensus        54 ~~g~~vLDiGCG~G~~~~~~~~~~~-~~v~g~D~s~~~l~~a~   95 (263)
T 2a14_A           54 LQGDTLIDIGSGPTIYQVLAACDSF-QDITLSDFTDRNREELE   95 (263)
T ss_dssp             CCEEEEEESSCTTCCGGGTTGGGTE-EEEEEEESCHHHHHHHH
T ss_pred             CCCceEEEeCCCccHHHHHHHHhhh-cceeeccccHHHHHHHH
Confidence            4558999999999987765544322 25788998 77777654

>3deu_A Transcriptional regulator SLYA; MARR, WING-helix, transcription regulator, activator, DNA-binding, repressor; HET: SAL; 2.30A {Salmonella typhimurium} SCOP: a.4.5.28

Probab=93.14  E-value=0.051  Score=41.55  Aligned_cols=63  Identities=14%  Similarity=0.089  Sum_probs=43.6

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCccccc
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSAY  106 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~~  106 (244)
                      ++.|+..|...+  +++|..+||+.++++      ... +.++++.|...|++++.....+.   .+.+|+.++.
T Consensus        55 q~~vL~~L~~~~--~~~t~~eLa~~l~i~------~~t-vs~~l~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~  120 (166)
T 3deu_A           55 HWVTLHNIHQLP--PDQSQIQLAKAIGIE------QPS-LVRTLDQLEDKGLISRQTCASDRRAKRIKLTEKAEP  120 (166)
T ss_dssp             HHHHHHHHHHSC--SSEEHHHHHHHHTSC------HHH-HHHHHHHHHHTTSEEEC--------CEEEECGGGHH
T ss_pred             HHHHHHHHHHcC--CCCCHHHHHHHHCCC------Hhh-HHHHHHHHHHCCCEEeeCCCCCCCeeEEEECHHHHH
Confidence            445677777632  579999999999997      556 99999999999999963211122   3556665543

>2oyr_A UPF0341 protein YHIQ; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; HET: SAH; 2.00A {Shigella flexneri 2A} SCOP: c.66.1.55 PDB: 2pgx_A 2pkw_A

Probab=93.12  E-value=0.084  Score=43.82  Aligned_cols=42  Identities=17%  Similarity=0.101  Sum_probs=32.5

Q ss_pred             HHHhhcCCCCCc--ceEEEecCCccHHHHHHHHHCCCCeEEEccchH
Q 041256          183 KVLESYKGFEHV--KKLVDVGGGLGITLNMIISKYPHIKGINYDLPY  227 (244)
Q Consensus       183 ~~~~~~~~~~~~--~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~  227 (244)
                      .+.+... ..+.  .+|+|+|||.|..+..++++  +.+++.+|.-.
T Consensus        77 ~l~~al~-l~~g~~~~VLDl~~G~G~dal~lA~~--g~~V~~vE~~~  120 (258)
T 2oyr_A           77 AVAKAVG-IKGDYLPDVVDATAGLGRDAFVLASV--GCRVRMLERNP  120 (258)
T ss_dssp             HHHHHTT-CBTTBCCCEEETTCTTCHHHHHHHHH--TCCEEEEECCH
T ss_pred             HHHHHhc-ccCCCCCEEEEcCCcCCHHHHHHHHc--CCEEEEEECCH
Confidence            3444444 4444  79999999999999999998  55799999843

>1sfx_A Conserved hypothetical protein AF2008; structural genomics, HTH MOT protein structure initiative, midwest center for structural genomics; 1.55A {Archaeoglobus fulgidus} SCOP: a.4.5.50

Probab=93.10  E-value=0.063  Score=37.37  Aligned_cols=46  Identities=15%  Similarity=0.377  Sum_probs=38.1

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      ++.|+..|...   ++.|..+||+.++++      ... +.+.|+.|...|++...
T Consensus        22 ~~~il~~l~~~---~~~s~~ela~~l~is------~~t-v~~~l~~L~~~glv~~~   67 (109)
T 1sfx_A           22 DVRIYSLLLER---GGMRVSEIARELDLS------ARF-VRDRLKVLLKRGFVRRE   67 (109)
T ss_dssp             HHHHHHHHHHH---CCBCHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHc---CCCCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEEE
Confidence            44566777654   589999999999997      456 99999999999999863

>3bro_A Transcriptional regulator; helix_TURN_helix, multiple antibiotic resistance protein (MA structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.04A {Oenococcus oeni} SCOP: a.4.5.28

Probab=93.09  E-value=0.084  Score=38.62  Aligned_cols=63  Identities=8%  Similarity=0.160  Sum_probs=44.2

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCcccc
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSA  105 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~  105 (244)
                      ++.++..|...+ ++++|..+||+.++++      +.. +.++++.|...|++.+.+...+.   .+.+|+.+.
T Consensus        36 ~~~iL~~l~~~~-~~~~~~~ela~~l~~~------~~t-vs~~l~~Le~~Gli~r~~~~~d~R~~~i~lT~~G~  101 (141)
T 3bro_A           36 QMTIIDYLSRNK-NKEVLQRDLESEFSIK------SST-ATVLLQRMEIKKLLYRKVSGKDSRQKCLKLTKKAN  101 (141)
T ss_dssp             HHHHHHHHHHTT-TSCCBHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEEEECSSCTTSEEEEECHHHH
T ss_pred             HHHHHHHHHHCC-CCCcCHHHHHHHHCCC------cch-HHHHHHHHHHCCCEEeeCCCcCCCeeeeEECHHHH
Confidence            344677777753 1279999999999997      456 99999999999999864211122   355555544

>3bj6_A Transcriptional regulator, MARR family; helix-turn-helix, trasnscription regulator, STR genomics, PSI-2, protein structure initiative; 2.01A {Silicibacter pomeroyi dss-3}

Probab=93.09  E-value=0.046  Score=40.70  Aligned_cols=46  Identities=13%  Similarity=0.216  Sum_probs=38.8

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      ++.|+..|...   +++|..+||+.++++      ... +.++++.|...|++.+.
T Consensus        42 ~~~iL~~l~~~---~~~t~~ela~~l~~~------~~~-vs~~l~~Le~~Glv~r~   87 (152)
T 3bj6_A           42 QRAILEGLSLT---PGATAPQLGAALQMK------RQY-ISRILQEVQRAGLIERR   87 (152)
T ss_dssp             HHHHHHHHHHS---TTEEHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHhC---CCCCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCeeec
Confidence            44577778775   589999999999997      456 99999999999999963

>3tgn_A ADC operon repressor ADCR; helix-turn-helix, transcriptional regulator, transcription; 2.00A {Streptococcus pneumoniae}

Probab=93.00  E-value=0.066  Score=39.52  Aligned_cols=45  Identities=16%  Similarity=0.342  Sum_probs=37.2

Q ss_pred             HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      .+..|+..|...   + +|..+||+.++++      ... +.++++.|...|++.+
T Consensus        39 ~~~~iL~~l~~~---~-~t~~eLa~~l~~s------~~t-vs~~l~~L~~~Glv~r   83 (146)
T 3tgn_A           39 TQEHILMLLSEE---S-LTNSELARRLNVS------QAA-VTKAIKSLVKEGMLET   83 (146)
T ss_dssp             HHHHHHHHHTTC---C-CCHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEC
T ss_pred             HHHHHHHHHHhC---C-CCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCeEe
Confidence            345566777663   4 9999999999997      456 9999999999999986

>1q1h_A TFE, transcription factor E, TFE; TFIIE, transcription initiation, preinitiation complex, RNA polymerase II, transcription bubble; 2.90A {Sulfolobus solfataricus} SCOP: a.4.5.41

Probab=92.90  E-value=0.11  Score=36.85  Aligned_cols=46  Identities=24%  Similarity=0.374  Sum_probs=36.7

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      ++.|+..+...|  .+.|..+||+.+|++      ... +++.|+.|...|++..
T Consensus        20 ~l~Il~~l~~~g--~~~s~~eLa~~lgvs------~~t-V~~~L~~L~~~GlV~~   65 (110)
T 1q1h_A           20 VIDVLRILLDKG--TEMTDEEIANQLNIK------VND-VRKKLNLLEEQGFVSY   65 (110)
T ss_dssp             THHHHHHHHHHC--SCBCHHHHHHTTTSC------HHH-HHHHHHHHHHHTSCEE
T ss_pred             HHHHHHHHHHcC--CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEE
Confidence            345666665432  379999999999997      445 9999999999999985

>4hbl_A Transcriptional regulator, MARR family; HTH, transcription factor, DNA binding; 2.50A {Staphylococcus epidermidis}

Probab=92.89  E-value=0.038  Score=41.31  Aligned_cols=47  Identities=13%  Similarity=0.103  Sum_probs=38.9

Q ss_pred             HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      .++.|...|...   +++|..+||+.++++      +.. +.++++.|...|++++.
T Consensus        42 ~q~~iL~~l~~~---~~~~~~eLa~~l~~~------~~~-vs~~l~~L~~~Glv~r~   88 (149)
T 4hbl_A           42 SQYLVMLTLWEE---NPQTLNSIGRHLDLS------SNT-LTPMLKRLEQSGWVKRE   88 (149)
T ss_dssp             HHHHHHHHHHHS---SSEEHHHHHHHHTCC------HHH-HHHHHHHHHHHTSEEC-
T ss_pred             HHHHHHHHHHHC---CCCCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEeeC
Confidence            345577777765   689999999999997      556 99999999999999963

>2pex_A Transcriptional regulator OHRR; transcription regulator; 1.90A {Xanthomonas campestris} PDB: 2pfb_A

Probab=92.87  E-value=0.067  Score=39.93  Aligned_cols=65  Identities=17%  Similarity=0.189  Sum_probs=46.6

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCcccccccc
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSAYFVR  109 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~~l~~  109 (244)
                      ++.|+..|...   +++|..+||+.++++      ... +.++++.|...|++.+.....+.   .+.+|+.+..+..
T Consensus        49 ~~~iL~~l~~~---~~~t~~ela~~l~~s------~~t-vs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~~~  116 (153)
T 2pex_A           49 QYLVMLVLWET---DERSVSEIGERLYLD------SAT-LTPLLKRLQAAGLVTRTRAASDERQVIIALTETGRALRS  116 (153)
T ss_dssp             HHHHHHHHHHS---CSEEHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEEEC-------CEEEECHHHHHGGG
T ss_pred             HHHHHHHHHhC---CCcCHHHHHHHhCCC------ccc-HHHHHHHHHHCCCEeecCCcccCCeeEeeECHHHHHHHH
Confidence            44577777775   689999999999997      456 99999999999999863211112   4677777664443

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

Probab=92.83  E-value=0.12  Score=45.03  Aligned_cols=38  Identities=11%  Similarity=0.094  Sum_probs=32.0

Q ss_pred             ceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          195 KKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       195 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+|+|+|||.|.++..+++..  -+++.+|. |..++.|++
T Consensus       215 ~~vLDl~cG~G~~~l~la~~~--~~V~gvd~~~~ai~~a~~  253 (369)
T 3bt7_A          215 GDLLELYCGNGNFSLALARNF--DRVLATEIAKPSVAAAQY  253 (369)
T ss_dssp             SEEEEESCTTSHHHHHHGGGS--SEEEEECCCHHHHHHHHH
T ss_pred             CEEEEccCCCCHHHHHHHhcC--CEEEEEECCHHHHHHHHH
Confidence            679999999999999988754  46888998 888888764

>2x4h_A Hypothetical protein SSO2273; transcription; 2.30A {Sulfolobus solfataricus}

Probab=92.77  E-value=0.079  Score=39.01  Aligned_cols=48  Identities=4%  Similarity=-0.053  Sum_probs=39.6

Q ss_pred             CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcccccc
Q 041256           49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYF  107 (244)
Q Consensus        49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l  107 (244)
                      ++.|..+||+.++++      ... +.+.|+.|...|++.+   .. ..|.+|+.+..+
T Consensus        30 ~~~s~~ela~~l~is------~~t-v~~~l~~Le~~Gli~r---~~-~~~~Lt~~g~~~   77 (139)
T 2x4h_A           30 EGAKINRIAKDLKIA------PSS-VFEEVSHLEEKGLVKK---KE-DGVWITNNGTRS   77 (139)
T ss_dssp             SCBCHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEE---ET-TEEEECHHHHHH
T ss_pred             CCcCHHHHHHHhCCC------hHH-HHHHHHHHHHCCCEEe---cC-CeEEEChhHHHH
Confidence            689999999999997      456 9999999999999995   22 668888776543

>3k6r_A Putative transferase PH0793; structural genomics, PSI structure initiative, midwest center for structural genomic unknown function; 2.10A {Pyrococcus horikoshii} PDB: 3a25_A* 3a26_A*

Probab=92.77  E-value=0.043  Score=46.12  Aligned_cols=43  Identities=23%  Similarity=0.156  Sum_probs=35.9

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      +....+|+|+|||.|.+++.++++ ...+++..|+ |..++.+++
T Consensus       123 ~~~g~~VlD~~aG~G~~~i~~a~~-g~~~V~avD~np~a~~~~~~  166 (278)
T 3k6r_A          123 AKPDELVVDMFAGIGHLSLPIAVY-GKAKVIAIEKDPYTFKFLVE  166 (278)
T ss_dssp             CCTTCEEEETTCTTTTTTHHHHHH-TCCEEEEECCCHHHHHHHHH
T ss_pred             cCCCCEEEEecCcCcHHHHHHHHh-cCCeEEEEECCHHHHHHHHH
Confidence            345689999999999999999876 4568999999 888888764

>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=92.77  E-value=0.054  Score=47.37  Aligned_cols=40  Identities=13%  Similarity=-0.016  Sum_probs=34.9

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...+|+|+|||+|.++..+++.  ..+++.+|. |..++.+++
T Consensus       209 ~~~~VLDlg~G~G~~~~~la~~--~~~v~~vD~s~~~~~~a~~  249 (382)
T 1wxx_A          209 RGERALDVFSYAGGFALHLALG--FREVVAVDSSAEALRRAEE  249 (382)
T ss_dssp             CEEEEEEETCTTTHHHHHHHHH--EEEEEEEESCHHHHHHHHH
T ss_pred             CCCeEEEeeeccCHHHHHHHHh--CCEEEEEECCHHHHHHHHH
Confidence            5679999999999999999998  567899998 888888764

>3boq_A Transcriptional regulator, MARR family; MARR famil structural genomics, PSI-2, protein structure initiative; 2.39A {Silicibacter pomeroyi dss-3}

Probab=92.72  E-value=0.047  Score=41.06  Aligned_cols=46  Identities=9%  Similarity=0.211  Sum_probs=37.6

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      ++.|+..|...+  +++|..+||+.++++      ... +.++++.|...|++.+
T Consensus        49 ~~~iL~~L~~~~--~~~~~~ela~~l~i~------~~t-vs~~l~~Le~~Gli~r   94 (160)
T 3boq_A           49 KFDAMAQLARNP--DGLSMGKLSGALKVT------NGN-VSGLVNRLIKDGMVVK   94 (160)
T ss_dssp             HHHHHHHHHHCT--TCEEHHHHHHHCSSC------CSC-HHHHHHHHHHHTSEEE
T ss_pred             HHHHHHHHHHcC--CCCCHHHHHHHHCCC------hhh-HHHHHHHHHHCCCEEe
Confidence            455778884322  689999999999997      445 9999999999999986

>1p6r_A Penicillinase repressor; transcription regulation, DNA-binding, winged helix protein, bacterial resistance to antibiotics; NMR {Bacillus licheniformis} SCOP: a.4.5.39 PDB: 2p7c_B

Probab=92.72  E-value=0.064  Score=35.93  Aligned_cols=46  Identities=22%  Similarity=0.411  Sum_probs=36.7

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCC----CCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIP----LKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~----~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      +..|.+.|.+.   ++.|..||++.++    ++      +.- +.++|+.|...|++.+.
T Consensus        11 e~~vL~~L~~~---~~~t~~ei~~~l~~~~~~s------~~T-v~~~l~rL~~kGlv~r~   60 (82)
T 1p6r_A           11 ELEVMKVIWKH---SSINTNEVIKELSKTSTWS------PKT-IQTMLLRLIKKGALNHH   60 (82)
T ss_dssp             HHHHHHHHHTS---SSEEHHHHHHHHHHHSCCC------HHH-HHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHcC---CCCCHHHHHHHHhhcCCcc------HHH-HHHHHHHHHHCCCeEEE
Confidence            45566777664   6899999999997    43      345 99999999999999964

>3tka_A Ribosomal RNA small subunit methyltransferase H; HET: SAM CTN PG4; 2.25A {Escherichia coli}

Probab=92.71  E-value=0.24  Score=42.75  Aligned_cols=60  Identities=18%  Similarity=0.198  Sum_probs=47.9

Q ss_pred             HHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHC-CCCeEEEccc-hHHhhhCCCC--CCceee
Q 041256          181 MEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKY-PHIKGINYDL-PYVIKDAPSY--PGTLFI  241 (244)
Q Consensus       181 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~vi~~a~~~--~~i~~~  241 (244)
                      ...+++.+. ......+||...|.|..+.+|+++. |+.+.+.+|. |++++.++.+  ++++++
T Consensus        46 l~Evl~~L~-i~pggiyVD~TlG~GGHS~~iL~~lg~~GrVig~D~Dp~Al~~A~rL~~~Rv~lv  109 (347)
T 3tka_A           46 LDEAVNGLN-IRPDGIYIDGTFGRGGHSRLILSQLGEEGRLLAIDRDPQAIAVAKTIDDPRFSII  109 (347)
T ss_dssp             THHHHHHTC-CCTTCEEEESCCTTSHHHHHHHTTCCTTCEEEEEESCHHHHHHHTTCCCTTEEEE
T ss_pred             HHHHHHhhC-CCCCCEEEEeCcCCCHHHHHHHHhCCCCCEEEEEECCHHHHHHHHhhcCCcEEEE
Confidence            356777776 5667899999999999999999985 8899999998 8888887543  345443

>2lnb_A Z-DNA-binding protein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, immune system; NMR {Homo sapiens}

Probab=92.63  E-value=0.11  Score=34.63  Aligned_cols=55  Identities=16%  Similarity=0.299  Sum_probs=44.6

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecC
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLA  101 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t  101 (244)
                      +-.|++.|.+.|  .|++..+||+.+|++      ..- +.+.|..|-..|.+..   +..-.|.++
T Consensus        21 eekVLe~LkeaG--~PlkageIae~~Gvd------KKe-VdKaik~LKkEgkI~S---PkRCyw~~~   75 (80)
T 2lnb_A           21 EQRILQVLTEAG--SPVKLAQLVKECQAP------KRE-LNQVLYRMKKELKVSL---TSPATWCLG   75 (80)
T ss_dssp             HHHHHHHHHHHT--SCEEHHHHHHHHTSC------HHH-HHHHHHHHHHTTSEEE---EETTEEEES
T ss_pred             HHHHHHHHHHcC--CCCCHHHHHHHHCCC------HHH-HHHHHHHHHHcCCccC---CCCceeeCC
Confidence            456888999987  799999999999996      344 9999999999999884   234677765

>4aik_A Transcriptional regulator SLYA; transcription, transcription factor; 1.85A {Yersinia pseudotuberculosis} PDB: 4aih_A 4aij_A 3qpt_A* 3q5f_A*

Probab=92.53  E-value=0.13  Score=38.68  Aligned_cols=62  Identities=16%  Similarity=0.100  Sum_probs=43.5

Q ss_pred             ChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCcccccc
Q 041256           37 DVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSAYF  107 (244)
Q Consensus        37 gifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~~l  107 (244)
                      .+.-.|...+  ++.+..+||+.++++      +.. +.++++-|...|++.+.+.+.+.   ...+|+.+..+
T Consensus        35 ~vL~~L~~~~--~~~~~~eLa~~l~~~------~~t-vs~~v~~Le~~GlV~R~~~~~DrR~~~l~LT~~G~~~   99 (151)
T 4aik_A           35 VTLYNINRLP--PEQSQIQLAKAIGIE------QPS-LVRTLDQLEEKGLITRHTSANDRRAKRIKLTEQSSPI   99 (151)
T ss_dssp             HHHHHHHHSC--TTSCHHHHHHHHTSC------HHH-HHHHHHHHHHTTSEEEEECSSCTTCEEEEECGGGHHH
T ss_pred             HHHHHHHHcC--CCCcHHHHHHHHCcC------HHH-HHHHHHHHHhCCCeEeecCCCCCcchhhhcCHHHHHH
Confidence            3455565543  467889999999997      556 99999999999999864322223   25566655533

>3m6w_A RRNA methylase; rRNA methyltransferase, 5-methylcytidine, RSMF, adoMet, MULT specific, methyltransferase, transferase; HET: CXM SAM; 1.30A {Thermus thermophilus} PDB: 3m6v_A* 3m6u_A* 3m6x_A*

Probab=92.31  E-value=0.081  Score=47.69  Aligned_cols=44  Identities=5%  Similarity=0.006  Sum_probs=36.8

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCCC-CeEEEccc-hHHhhhCCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYPH-IKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dl-p~vi~~a~~  234 (244)
                      .....+|+|+|||.|..+..+++..++ .+++.+|+ |..++.+++
T Consensus        99 ~~~g~~VLDlgaGpG~kt~~LA~~~~~~g~V~AvDis~~~l~~a~~  144 (464)
T 3m6w_A           99 PKPGERVLDLAAAPGGKTTHLAARMGGKGLLLANEVDGKRVRGLLE  144 (464)
T ss_dssp             CCTTCEEEESSCTTCHHHHHHHHHTTTCSEEEEECSCHHHHHHHHH
T ss_pred             cCCCCEEEEEcCCcCHHHHHHHHhCCCCCEEEEEECCHHHHHHHHH
Confidence            455689999999999999999999876 68899998 777776654

>2p4w_A Transcriptional regulatory protein ARSR family; archaea, PHR, heat shock, transcriptional regulation, winged DNA binding; 2.60A {Pyrococcus furiosus} SCOP: a.4.5.64

Probab=92.25  E-value=0.13  Score=40.93  Aligned_cols=66  Identities=12%  Similarity=0.176  Sum_probs=47.2

Q ss_pred             HHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeec----C-CceeecCc
Q 041256           28 AVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVD----G-QRLYSLAP  102 (244)
Q Consensus        28 ~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~----~-~~~y~~t~  102 (244)
                      .+|..-.++.|+..|..    +|.|..+||+.+|++      ... +.+.|+.|...|++......    + .-.|++|+
T Consensus        10 kaL~~~~rl~IL~~L~~----~~~s~~eLa~~l~is------~st-vs~hLk~Le~~GLV~~~~~~~~~g~~~~~Y~Lt~   78 (202)
T 2p4w_A           10 DVLGNETRRRILFLLTK----RPYFVSELSRELGVG------QKA-VLEHLRILEEAGLIESRVEKIPRGRPRKYYMIKK   78 (202)
T ss_dssp             HHHHSHHHHHHHHHHHH----SCEEHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEEEECCBTTBCCCEEEEECT
T ss_pred             HHhCCHHHHHHHHHHHh----CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCceEEEeeccCCCCceEEEEECh
Confidence            34444455666777765    699999999999997      456 99999999999999864321    1 12466666


Q ss_pred             cc
Q 041256          103 VS  104 (244)
Q Consensus       103 ~s  104 (244)
                      ..
T Consensus        79 ~~   80 (202)
T 2p4w_A           79 GL   80 (202)
T ss_dssp             TE
T ss_pred             HH
Confidence            54

>2frh_A SARA, staphylococcal accessory regulator A; winged-helix protein, divalent metal binding, transcription; 2.50A {Staphylococcus aureus} SCOP: a.4.5.28 PDB: 2fnp_A 1fzp_D

Probab=92.24  E-value=0.078  Score=38.64  Aligned_cols=63  Identities=11%  Similarity=0.172  Sum_probs=43.9

Q ss_pred             cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCccccc
Q 041256           36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSAY  106 (244)
Q Consensus        36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~~  106 (244)
                      ..+...|...+ +++.|..+||+.++++      +.. +.++++-|...|++.+.+...+.   .+.+|+.++.
T Consensus        40 ~~vL~~l~~~~-~~~~t~~eLa~~l~~~------~~t-vs~~l~~Le~~Glv~r~~~~~D~R~~~i~LT~~G~~  105 (127)
T 2frh_A           40 FAVLTYISENK-EKEYYLKDIINHLNYK------QPQ-VVKAVKILSQEDYFDKKRNEHDERTVLILVNAQQRK  105 (127)
T ss_dssp             HHHHHHHHHTC-CSEEEHHHHHHHSSSH------HHH-HHHHHHHHHHTTSSCCBCCSSSSCCCEEECCSHHHH
T ss_pred             HHHHHHHHhcc-CCCcCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHH
Confidence            44666666541 1589999999999996      456 99999999999999863212222   2556665543

>4dmg_A Putative uncharacterized protein TTHA1493; rRNA, methyltransferase, S-adenosyl-methionine, 23S ribosoma transferase; HET: SAM; 1.70A {Thermus thermophilus}

Probab=92.15  E-value=0.065  Score=47.23  Aligned_cols=40  Identities=13%  Similarity=-0.066  Sum_probs=33.5

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...+|+|+|||+|.++..+++...  +++.+|+ |..++.+++
T Consensus       214 ~g~~VLDlg~GtG~~sl~~a~~ga--~V~avDis~~al~~a~~  254 (393)
T 4dmg_A          214 PGERVLDVYSYVGGFALRAARKGA--YALAVDKDLEALGVLDQ  254 (393)
T ss_dssp             TTCEEEEESCTTTHHHHHHHHTTC--EEEEEESCHHHHHHHHH
T ss_pred             CCCeEEEcccchhHHHHHHHHcCC--eEEEEECCHHHHHHHHH
Confidence            368999999999999999999754  4899998 777777764

>2okc_A Type I restriction enzyme stysji M protein; NP_813429.1, N-6 DNA methylase, type I restriction enzyme ST protein; HET: SAM; 2.20A {Bacteroides thetaiotaomicron vpi-5482} SCOP: c.66.1.45

Probab=92.14  E-value=0.068  Score=47.73  Aligned_cols=50  Identities=16%  Similarity=0.072  Sum_probs=37.1

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHC-------------CCCeEEEccc-hHHhhhCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKY-------------PHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-------------P~l~~~v~Dl-p~vi~~a~  233 (244)
                      .+++... .....+|+|.|||+|.++..+.+..             +..+.+.+|+ |..++.|+
T Consensus       162 ~mv~~l~-~~~~~~VlDpacGsG~fl~~~~~~l~~~~~~~~~~~~~~~~~i~G~Ei~~~~~~lA~  225 (445)
T 2okc_A          162 AMVDCIN-PQMGETVCDPACGTGGFLLTAYDYMKGQSASKEKRDFLRDKALHGVDNTPLVVTLAS  225 (445)
T ss_dssp             HHHHHHC-CCTTCCEEETTCTTCHHHHHHHHHHHTCC-CCHHHHHHHHTTEEEEESCHHHHHHHH
T ss_pred             HHHHHhC-CCCCCEEeccCCCcchHHHHHHHHHHHhcCCHHHHHhhcCeEEEEEeCCHHHHHHHH
Confidence            3344444 3445799999999999999988764             5567899998 77777664

>3ll7_A Putative methyltransferase; methytransferase, structural genomics, MCSG, PSI-2, protein initiative; HET: MSE; 1.80A {Porphyromonas gingivalis}

Probab=92.13  E-value=0.08  Score=46.95  Aligned_cols=39  Identities=33%  Similarity=0.422  Sum_probs=33.0

Q ss_pred             cceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+|+|+|||.|..+..+++..  .+++.+|. |..++.|++
T Consensus        94 g~~VLDLgcG~G~~al~LA~~g--~~V~~VD~s~~~l~~Ar~  133 (410)
T 3ll7_A           94 GTKVVDLTGGLGIDFIALMSKA--SQGIYIERNDETAVAARH  133 (410)
T ss_dssp             TCEEEESSCSSSHHHHHHHTTC--SEEEEEESCHHHHHHHHH
T ss_pred             CCEEEEeCCCchHHHHHHHhcC--CEEEEEECCHHHHHHHHH
Confidence            5899999999999999988874  58899998 777777754

>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=92.11  E-value=0.079  Score=46.49  Aligned_cols=41  Identities=20%  Similarity=0.009  Sum_probs=34.8

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...+|+|+|||.|.++..+++. +.-+++.+|+ |..++.+++
T Consensus       217 ~~~~VLDl~~G~G~~~~~la~~-g~~~v~~vD~s~~~l~~a~~  258 (396)
T 2as0_A          217 PGDRVLDVFTYTGGFAIHAAIA-GADEVIGIDKSPRAIETAKE  258 (396)
T ss_dssp             TTCEEEETTCTTTHHHHHHHHT-TCSEEEEEESCHHHHHHHHH
T ss_pred             CCCeEEEecCCCCHHHHHHHHC-CCCEEEEEeCCHHHHHHHHH
Confidence            5589999999999999999987 4457899998 888887764

>2yx1_A Hypothetical protein MJ0883; methyl transferase, tRNA modification enzyme, transferase; HET: SFG; 2.20A {Methanocaldococcus jannaschii} PDB: 2zzn_A* 3ay0_A* 2zzm_A*

Probab=92.06  E-value=0.063  Score=46.15  Aligned_cols=40  Identities=20%  Similarity=0.094  Sum_probs=34.0

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ....+|+|+|||+|.++.. ++  ...+++.+|+ |..++.+++
T Consensus       194 ~~~~~VLDlg~G~G~~~l~-a~--~~~~V~~vD~s~~ai~~a~~  234 (336)
T 2yx1_A          194 SLNDVVVDMFAGVGPFSIA-CK--NAKKIYAIDINPHAIELLKK  234 (336)
T ss_dssp             CTTCEEEETTCTTSHHHHH-TT--TSSEEEEEESCHHHHHHHHH
T ss_pred             CCCCEEEEccCccCHHHHh-cc--CCCEEEEEECCHHHHHHHHH
Confidence            3557999999999999999 76  5778999999 888888764

>2k4b_A Transcriptional regulator; DNA binding protein, winged helix; NMR {Lactococcus lactis subsp}

Probab=92.04  E-value=0.098  Score=36.81  Aligned_cols=50  Identities=32%  Similarity=0.305  Sum_probs=37.7

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      +..|...|-+.   +++|..||++.++.++ +. .+.- +.++|+-|+..|++.+.
T Consensus        37 e~~VL~~L~~~---~~~t~~eL~~~l~~~~-~~-s~sT-Vt~~L~rLe~KGlV~R~   86 (99)
T 2k4b_A           37 ELIVMRVIWSL---GEARVDEIYAQIPQEL-EW-SLAT-VKTLLGRLVKKEMLSTE   86 (99)
T ss_dssp             CSHHHHHHHHH---SCEEHHHHHHTCCGGG-CC-CHHH-HHHHHHHHHHTTSCEEE
T ss_pred             HHHHHHHHHhC---CCCCHHHHHHHHhccc-CC-CHhh-HHHHHHHHHHCCCEEEE
Confidence            45577888764   6899999999997520 00 0334 99999999999999964

>3c6k_A Spermine synthase; spermidine aminopropyltransferase, SPMSY, structural genomics, structural genomics consortium, SGC, phosphoprotein; HET: SPD MTA; 1.95A {Homo sapiens} PDB: 3c6m_A*

Probab=91.88  E-value=0.082  Score=46.34  Aligned_cols=41  Identities=22%  Similarity=0.205  Sum_probs=35.3

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+++|+=||||.|..+.++++. |.-+.+++|+ |.|++.+++
T Consensus       205 ~pkrVLIIGgGdG~~~revlkh-~~~~V~~VEIDp~VVe~ar~  246 (381)
T 3c6k_A          205 TGKDVLILGGGDGGILCEIVKL-KPKMVTMVEIDQMVIDGCKK  246 (381)
T ss_dssp             TTCEEEEEECTTCHHHHHHHTT-CCSEEEEEESCHHHHHHHHH
T ss_pred             CCCeEEEECCCcHHHHHHHHhc-CCceeEEEccCHHHHHHHHh
Confidence            4589999999999999999975 5578899998 999998764

>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=91.83  E-value=0.11  Score=46.16  Aligned_cols=41  Identities=17%  Similarity=0.228  Sum_probs=34.0

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+..+|+|+|||.|.++..+++.  ..+++.+|. |..++.|++
T Consensus       289 ~~~~~VLDlgcG~G~~sl~la~~--~~~V~gvD~s~~ai~~A~~  330 (425)
T 2jjq_A          289 VEGEKILDMYSGVGTFGIYLAKR--GFNVKGFDSNEFAIEMARR  330 (425)
T ss_dssp             CCSSEEEEETCTTTHHHHHHHHT--TCEEEEEESCHHHHHHHHH
T ss_pred             CCCCEEEEeeccchHHHHHHHHc--CCEEEEEECCHHHHHHHHH
Confidence            34579999999999999999987  447889998 788887764

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

Probab=91.74  E-value=0.082  Score=46.41  Aligned_cols=41  Identities=10%  Similarity=-0.077  Sum_probs=34.5

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      +..+|+|+|||+|.++..+++.. .-+++.+|+ |..++.+++
T Consensus       220 ~~~~VLDl~cG~G~~sl~la~~g-~~~V~~vD~s~~al~~a~~  261 (396)
T 3c0k_A          220 ENKRVLNCFSYTGGFAVSALMGG-CSQVVSVDTSQEALDIARQ  261 (396)
T ss_dssp             TTCEEEEESCTTCSHHHHHHHTT-CSEEEEEESCHHHHHHHHH
T ss_pred             CCCeEEEeeccCCHHHHHHHHCC-CCEEEEEECCHHHHHHHHH
Confidence            45799999999999999999875 457899998 788887764

>2pn6_A ST1022, 150AA long hypothetical transcriptional regulator; LRP/ASNC family Gln binding, structural genomics, NPPSFA; HET: GLN; 1.44A {Sulfolobus tokodaii} PDB: 2efn_A* 2e7x_A* 2e7w_A* 2yx4_A* 2efq_A* 2pmh_A* 2yx7_A* 2efp_A* 2efo_A*

Probab=91.63  E-value=0.14  Score=38.37  Aligned_cols=46  Identities=24%  Similarity=0.368  Sum_probs=39.1

Q ss_pred             HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      .+..|...|.+.   ++.|..|||+.+|++      +.. +.+.++.|...|++..
T Consensus         4 ~~~~il~~L~~~---~~~~~~ela~~lg~s------~~t-v~~~l~~L~~~G~i~~   49 (150)
T 2pn6_A            4 IDLRILKILQYN---AKYSLDEIAREIRIP------KAT-LSYRIKKLEKDGVIKG   49 (150)
T ss_dssp             HHHHHHHHHTTC---TTSCHHHHHHHHTSC------HHH-HHHHHHHHHHTTSSCC
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCcEEE
Confidence            355678888764   689999999999997      556 9999999999999984

>2h09_A Transcriptional regulator MNTR; transcription regulator, diphtheria toxin, manganese transport, structural genomics, NPPSFA; 2.10A {Escherichia coli}

Probab=91.61  E-value=0.095  Score=39.44  Aligned_cols=56  Identities=11%  Similarity=0.211  Sum_probs=42.3

Q ss_pred             hhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcccccc
Q 041256           39 FEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYF  107 (244)
Q Consensus        39 fd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l  107 (244)
                      ...|...   ++.|..+||+.++++      ... +.+.|+.|...|++..  +. ...+.+|+.+..+
T Consensus        46 ~~~l~~~---~~~~~~~la~~l~vs------~~t-vs~~l~~Le~~Glv~r--~~-~~~~~lT~~g~~~  101 (155)
T 2h09_A           46 SDLIREV---GEARQVDMAARLGVS------QPT-VAKMLKRLATMGLIEM--IP-WRGVFLTAEGEKL  101 (155)
T ss_dssp             HHHHHHH---SCCCHHHHHHHHTSC------HHH-HHHHHHHHHHTTCEEE--ET-TTEEEECHHHHHH
T ss_pred             HHHHHhC---CCcCHHHHHHHhCcC------HHH-HHHHHHHHHHCCCEEE--ec-CCceEEChhHHHH
Confidence            3355553   579999999999997      456 9999999999999985  22 3557777766543

>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=91.57  E-value=0.083  Score=46.30  Aligned_cols=42  Identities=7%  Similarity=-0.164  Sum_probs=34.4

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+..+|+|+|||+|.++..++++. .-+++.+|+ |..++.|++
T Consensus       211 ~~~~~VLDl~cGtG~~sl~la~~g-a~~V~~vD~s~~al~~A~~  253 (385)
T 2b78_A          211 AAGKTVLNLFSYTAAFSVAAAMGG-AMATTSVDLAKRSRALSLA  253 (385)
T ss_dssp             TBTCEEEEETCTTTHHHHHHHHTT-BSEEEEEESCTTHHHHHHH
T ss_pred             cCCCeEEEEeeccCHHHHHHHHCC-CCEEEEEECCHHHHHHHHH
Confidence            445799999999999999999863 237899998 888888764

>2cfx_A HTH-type transcriptional regulator LRPC; transcriptional regulation, DNA binding, FFRP; 2.4A {Bacillus subtilis} SCOP: a.4.5.32 d.58.4.2

Probab=91.56  E-value=0.15  Score=38.02  Aligned_cols=45  Identities=24%  Similarity=0.420  Sum_probs=38.5

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      +..|.+.|.+.   ++.|..|||+.+|++      +.. +.+.++.|...|++..
T Consensus         7 d~~il~~L~~~---~~~s~~ela~~lg~s------~~t-v~~~l~~L~~~G~i~~   51 (144)
T 2cfx_A            7 DLNIIEELKKD---SRLSMRELGRKIKLS------PPS-VTERVRQLESFGIIKQ   51 (144)
T ss_dssp             HHHHHHHHHHC---SCCCHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHc---CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCeEE
Confidence            44678888775   689999999999997      556 9999999999999984

>2qvo_A Uncharacterized protein AF_1382; PSI, structural genomics, southeast collaboratory for structural genomics; 1.85A {Archaeoglobus fulgidus dsm 4304} PDB: 3o3k_A 3ov8_A

Probab=91.56  E-value=0.11  Score=35.77  Aligned_cols=51  Identities=6%  Similarity=0.143  Sum_probs=38.0

Q ss_pred             CCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecC-CceeecCccccccc
Q 041256           50 KLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDG-QRLYSLAPVSAYFV  108 (244)
Q Consensus        50 ~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~-~~~y~~t~~s~~l~  108 (244)
                      ++|..+||+.++++      ... +.++++.|...|++. ++.++ ...|.+|+.+..+.
T Consensus        30 ~~t~~eLa~~l~i~------~~t-vs~~l~~Le~~Glv~-~~~d~R~~~v~LT~~G~~~~   81 (95)
T 2qvo_A           30 DVYIQYIASKVNSP------HSY-VWLIIKKFEEAKMVE-CELEGRTKIIRLTDKGQKIA   81 (95)
T ss_dssp             CEEHHHHHHHSSSC------HHH-HHHHHHHHHHTTSEE-EEEETTEEEEEECHHHHHHH
T ss_pred             CcCHHHHHHHHCcC------HHH-HHHHHHHHHHCcCcc-CCCCCCeEEEEEChhHHHHH
Confidence            49999999999997      456 999999999999994 22211 12478887765443

>2vn2_A DNAD, chromosome replication initiation protein; DNA replication, primosome; 2.3A {Geobacillus kaustophilus HTA426}

Probab=91.53  E-value=0.16  Score=37.23  Aligned_cols=33  Identities=18%  Similarity=0.185  Sum_probs=29.9

Q ss_pred             CCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           50 KLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        50 ~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      ..|..+||+.++++      +.- +.+.++.|...|++..
T Consensus        51 ~ps~~~LA~~l~~s------~~~-V~~~l~~Le~kGlI~~   83 (128)
T 2vn2_A           51 FPTPAELAERMTVS------AAE-CMEMVRRLLQKGMIAI   83 (128)
T ss_dssp             SCCHHHHHHTSSSC------HHH-HHHHHHHHHHTTSSEE
T ss_pred             CCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEE
Confidence            47999999999997      556 9999999999999986

>1sfu_A 34L protein; protein/Z-DNA complex, DNA binding protein/DNA complex; 2.00A {Yaba-like disease virus} SCOP: a.4.5.19

Probab=91.46  E-value=0.47  Score=31.44  Aligned_cols=52  Identities=4%  Similarity=0.019  Sum_probs=38.0

Q ss_pred             hhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecC
Q 041256           39 FEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLA  101 (244)
Q Consensus        39 fd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t  101 (244)
                      ++.|.+.   +..|+.+||+++|++      ..- +.|+|.-|...|.+...+. .+-+|..+
T Consensus        21 i~~L~~~---~~~Ta~~IAkkLg~s------K~~-vNr~LY~L~kkG~V~~~~~-~PP~W~~~   72 (75)
T 1sfu_A           21 VLSLNTN---DYTTAISLSNRLKIN------KKK-INQQLYKLQKEDTVKMVPS-NPPKWFKN   72 (75)
T ss_dssp             HHTSCTT---CEECHHHHHHHTTCC------HHH-HHHHHHHHHHTTSEEEECC-SSCEEEEC
T ss_pred             HHhCCCC---cchHHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEecCCC-CCCCccCC
Confidence            3455552   469999999999996      455 9999999999999986322 24455544

>3m4x_A NOL1/NOP2/SUN family protein; mtase domain, PUA domain, RRM motif, transferase; 2.28A {Enterococcus faecium}

Probab=91.40  E-value=0.14  Score=45.96  Aligned_cols=44  Identities=11%  Similarity=0.047  Sum_probs=36.0

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCCC-CeEEEccc-hHHhhhCCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYPH-IKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dl-p~vi~~a~~  234 (244)
                      .....+|+|+|+|.|..+..+++..++ -+++..|+ |..++.+++
T Consensus       103 ~~~g~~VLDlcaGpGgkt~~lA~~~~~~g~V~AvDis~~rl~~~~~  148 (456)
T 3m4x_A          103 AKPGEKVLDLCAAPGGKSTQLAAQMKGKGLLVTNEIFPKRAKILSE  148 (456)
T ss_dssp             CCTTCEEEESSCTTCHHHHHHHHHHTTCSEEEEECSSHHHHHHHHH
T ss_pred             CCCCCEEEEECCCcCHHHHHHHHHcCCCCEEEEEeCCHHHHHHHHH
Confidence            455689999999999999999998765 68899998 666666653

>1bja_A Transcription regulatory protein MOTA; activation domain, middle mode transcription, alpha helical structure, transcription regulation; 2.19A {Enterobacteria phage T4} SCOP: a.4.5.9 PDB: 1i1s_A

Probab=91.37  E-value=0.19  Score=35.02  Aligned_cols=60  Identities=13%  Similarity=0.207  Sum_probs=46.3

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHH-hCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccccccc
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVA-QIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFV  108 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~-~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l~  108 (244)
                      ++.|+-.|.+.   ++.|..+||+ ..+++      ... +.|=++.|...|+++.   .+++ +.+|+.++.+.
T Consensus        18 QfsiL~~L~~~---~~~t~~~Lae~~l~~d------rst-vsrnl~~L~r~GlVe~---~~~D-l~LT~~G~~~l   78 (95)
T 1bja_A           18 TATILITIAKK---DFITAAEVREVHPDLG------NAV-VNSNIGVLIKKGLVEK---SGDG-LIITGEAQDII   78 (95)
T ss_dssp             HHHHHHHHHHS---TTBCHHHHHHTCTTSC------HHH-HHHHHHHHHTTTSEEE---ETTE-EEECHHHHHHH
T ss_pred             HHHHHHHHHHC---CCCCHHHHHHHHhccc------HHH-HHHHHHHHHHCCCeec---CCCC-eeeCHhHHHHH
Confidence            34456667775   5899999999 99996      456 9999999999999982   3445 78888776444

>2w25_A Probable transcriptional regulatory protein; transcription regulation, mutant, RV3291C, Glu104Ala, DNA-binding; 2.15A {Mycobacterium tuberculosis} PDB: 2vbw_A* 2vbx_A* 2vby_A* 2vbz_A* 2vc0_A 2vc1_A 2w24_A 2ivm_A 2w29_A 2qz8_A

Probab=91.35  E-value=0.16  Score=38.08  Aligned_cols=45  Identities=11%  Similarity=0.191  Sum_probs=38.3

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      +..|...|.+.   ++.|..|||+.+|++      +.. +.+.++.|...|++.+
T Consensus         9 ~~~iL~~L~~~---~~~s~~ela~~lg~s------~~t-v~~~l~~L~~~G~i~~   53 (150)
T 2w25_A            9 DRILVRELAAD---GRATLSELATRAGLS------VSA-VQSRVRRLESRGVVQG   53 (150)
T ss_dssp             HHHHHHHHHHC---TTCCHHHHHHHHTSC------HHH-HHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHc---CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEE
Confidence            45677788775   689999999999997      556 9999999999999974

>3gcz_A Polyprotein; flavivirus, RNA capping, methyltransferase, viral enzyme STR ATP-binding, nucleotide-binding, RNA replication, structura genomics; HET: SAM; 1.70A {Yokose virus}

Probab=91.11  E-value=0.2  Score=42.01  Aligned_cols=44  Identities=20%  Similarity=0.086  Sum_probs=33.2

Q ss_pred             HHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc
Q 041256          181 MEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL  225 (244)
Q Consensus       181 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  225 (244)
                      ...+.+.+. +....+|||+|||.|.++.-.+++.|-..++.+|+
T Consensus        79 L~ei~eK~~-Lk~~~~VLDLGaAPGGWsQvAa~~~gv~sV~Gvdv  122 (282)
T 3gcz_A           79 LRWMEERGY-VKPTGIVVDLGCGRGGWSYYAASLKNVKKVMAFTL  122 (282)
T ss_dssp             HHHHHHTTS-CCCCEEEEEETCTTCHHHHHHHTSTTEEEEEEECC
T ss_pred             HHHHHHhcC-CCCCCEEEEeCCCCCHHHHHHHHhcCCCeeeeEEe
Confidence            345666664 67778999999999999999888777555555555

>2p5v_A Transcriptional regulator, LRP/ASNC family; NMB0573, structu genomics; 1.99A {Neisseria meningitidis} PDB: 2p6s_A 2p6t_A

Probab=91.11  E-value=0.17  Score=38.47  Aligned_cols=45  Identities=13%  Similarity=0.313  Sum_probs=38.5

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      +..|.+.|.+.   +++|..|||+.+|++      +.. +.+.++.|...|++..
T Consensus        12 ~~~il~~L~~~---~~~s~~ela~~lg~s------~~t-v~~~l~~L~~~G~i~~   56 (162)
T 2p5v_A           12 DIKILQVLQEN---GRLTNVELSERVALS------PSP-CLRRLKQLEDAGIVRQ   56 (162)
T ss_dssp             HHHHHHHHHHC---TTCCHHHHHHHHTSC------HHH-HHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHc---CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEee
Confidence            44677888775   689999999999997      556 9999999999999984

>3nqo_A MARR-family transcriptional regulator; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE PG4; 2.20A {Clostridium difficile}

Probab=91.04  E-value=0.15  Score=39.86  Aligned_cols=68  Identities=6%  Similarity=-0.015  Sum_probs=49.5

Q ss_pred             HHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCC---ceeecCccccccc
Q 041256           33 VVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQ---RLYSLAPVSAYFV  108 (244)
Q Consensus        33 a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~---~~y~~t~~s~~l~  108 (244)
                      ..++.|...|...+ ++++|..+||+.++++      ... +.++++.|...|++.+.....+   -.+.+|+.+..+.
T Consensus        41 ~~q~~vL~~L~~~~-~~~~t~~eLa~~l~is------~~t-vs~~l~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~  111 (189)
T 3nqo_A           41 SRQYMTILSILHLP-EEETTLNNIARKMGTS------KQN-INRLVANLEKNGYVDVIPSPHDKRAINVKVTDLGKKVM  111 (189)
T ss_dssp             HHHHHHHHHHHHSC-GGGCCHHHHHHHHTSC------HHH-HHHHHHHHHHTTSEEEEECSSCSSCEEEEECHHHHHHH
T ss_pred             HHHHHHHHHHHhcc-CCCcCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEeccCCCCCCeeEEEECHHHHHHH
Confidence            34566777777531 1689999999999997      456 9999999999999996432222   2477887776444

>3u2r_A Regulatory protein MARR; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, helix-turn-helix; 2.20A {Planctomyces limnophilus}

Probab=90.92  E-value=0.1  Score=39.71  Aligned_cols=65  Identities=9%  Similarity=0.131  Sum_probs=43.3

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCcccccc
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSAYF  107 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~~l  107 (244)
                      ++.|+..|...+ ++++|..+||+.++++      +.. +.++++.|...|++++.....+.   .+.+|+.++.+
T Consensus        48 q~~vL~~l~~~~-~~~~t~~eLa~~l~~~------~~t-vs~~l~~Le~~Glv~r~~~~~DrR~~~l~LT~~G~~~  115 (168)
T 3u2r_A           48 QYNTLRLLRSVH-PEGMATLQIADRLISR------APD-ITRLIDRLDDRGLVLRTRKPENRRVVEVALTDAGLKL  115 (168)
T ss_dssp             HHHHHHHHHHHT-TSCEEHHHHHHHC---------CTH-HHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHH
T ss_pred             HHHHHHHHHhcC-CCCcCHHHHHHHHCCC------hhh-HHHHHHHHHHCCCEeecCCCCCCCeeEeEECHHHHHH
Confidence            445677777642 1589999999999997      445 99999999999999974322222   35666655533

>3b5i_A S-adenosyl-L-methionine:salicylic acid carboxyl methyltransferase-like protein; sabath family, indole-3-acetic acid, S-AD methionine; HET: SAH; 2.75A {Arabidopsis thaliana}

Probab=90.64  E-value=0.2  Score=43.87  Aligned_cols=34  Identities=26%  Similarity=0.376  Sum_probs=27.4

Q ss_pred             cceEEEecCCccHHHHHH--------HHHC-------CCCeEEEccchH
Q 041256          194 VKKLVDVGGGLGITLNMI--------ISKY-------PHIKGINYDLPY  227 (244)
Q Consensus       194 ~~~vvDVGGG~G~~~~~l--------~~~~-------P~l~~~v~Dlp~  227 (244)
                      .-+|+|+|||+|..+..+        .+++       |++++..-|||.
T Consensus        53 ~~~IaDlGCssG~Nt~~~v~~ii~~i~~~~~~~~~~~pe~~v~~nDLp~  101 (374)
T 3b5i_A           53 PFTAVDLGCSSGANTVHIIDFIVKHISKRFDAAGIDPPEFTAFFSDLPS  101 (374)
T ss_dssp             CEEEEEETCCSSHHHHHHHHHHHHHHHHHHHHTTCCCCCEEEEEEECTT
T ss_pred             ceEEEecCCCCChhHHHHHHHHHHHHHHHHhhcCCCCCceeEEecCCCc
Confidence            588999999999877665        3344       888889989984

>2dbb_A Putative HTH-type transcriptional regulator PH006; ASNC family, helix-turn-helix (HTH) domain, structural genom NPPSFA; 2.00A {Pyrococcus horikoshii}

Probab=90.60  E-value=0.2  Score=37.57  Aligned_cols=46  Identities=15%  Similarity=0.299  Sum_probs=38.9

Q ss_pred             HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      .+..|...|.+.   ++.|..|||+.+|++      +.. +.+.++.|...|++..
T Consensus        10 ~d~~il~~L~~~---~~~s~~ela~~lg~s------~~t-v~~~l~~L~~~G~i~~   55 (151)
T 2dbb_A           10 VDMQLVKILSEN---SRLTYRELADILNTT------RQR-IARRIDKLKKLGIIRK   55 (151)
T ss_dssp             HHHHHHHHHHHC---TTCCHHHHHHHTTSC------HHH-HHHHHHHHHHHTSEEE
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEE
Confidence            345678888875   689999999999997      556 9999999999999983

>2v79_A DNA replication protein DNAD; primosome, DNA-binding protein; HET: DNA; 2.00A {Bacillus subtilis}

Probab=90.59  E-value=0.2  Score=37.28  Aligned_cols=35  Identities=9%  Similarity=0.098  Sum_probs=31.0

Q ss_pred             CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      ...|.++||+++|++      +.- +.++|+-|...||+...
T Consensus        50 ~~ps~~~LA~~~~~s------~~~-v~~~L~~L~~KGlI~i~   84 (135)
T 2v79_A           50 YFPTPNQLQEGMSIS------VEE-CTNRLRMFIQKGFLFIE   84 (135)
T ss_dssp             CSCCHHHHHTTSSSC------HHH-HHHHHHHHHHHTSCEEE
T ss_pred             CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEEE
Confidence            468999999999997      556 99999999999999963

>3i4p_A Transcriptional regulator, ASNC family; PSI, structural genom protein structure initiative, midwest center for structural genomics; 2.30A {Agrobacterium tumefaciens str}

Probab=90.59  E-value=0.2  Score=38.24  Aligned_cols=45  Identities=13%  Similarity=0.296  Sum_probs=39.0

Q ss_pred             HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCccc
Q 041256           34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALH   88 (244)
Q Consensus        34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~   88 (244)
                      .+..|.+.|.+.   +++|..+||+++|++      +.. +.+-++.|...|++.
T Consensus         4 ~d~~il~~L~~~---~~~s~~~la~~lg~s------~~t-v~~rl~~L~~~g~i~   48 (162)
T 3i4p_A            4 LDRKILRILQED---STLAVADLAKKVGLS------TTP-CWRRIQKMEEDGVIR   48 (162)
T ss_dssp             HHHHHHHHHTTC---SCSCHHHHHHHHTCC------HHH-HHHHHHHHHHTTSSC
T ss_pred             HHHHHHHHHHHC---CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCee
Confidence            355678888875   799999999999997      556 999999999999998

>3jw4_A Transcriptional regulator, MARR/EMRR family; DNA-binding protein, structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.10A {Clostridium acetobutylicum} SCOP: a.4.5.0

Probab=90.55  E-value=0.87  Score=33.43  Aligned_cols=47  Identities=9%  Similarity=0.040  Sum_probs=33.1

Q ss_pred             cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      ..++..|...+ ++++|..+||+.++++      +.. +.++++.|...|++.+.
T Consensus        44 ~~vL~~l~~~~-~~~~t~~eLa~~l~~~------~~~-vs~~l~~L~~~Glv~r~   90 (148)
T 3jw4_A           44 GRMIGYIYENQ-ESGIIQKDLAQFFGRR------GAS-ITSMLQGLEKKGYIERR   90 (148)
T ss_dssp             HHHHHHHHHHT-TTCCCHHHHHHC------------C-HHHHHHHHHHTTSBCCC
T ss_pred             HHHHHHHHhCC-CCCCCHHHHHHHHCCC------hhH-HHHHHHHHHHCCCEEee
Confidence            44666676642 1589999999999997      456 99999999999999863

>3v97_A Ribosomal RNA large subunit methyltransferase L; YCBY, RNA methyltransferase, ribosome RNA, SAH, RLML; HET: SAH OSU; 2.20A {Escherichia coli} PDB: 3v8v_A*

Probab=90.54  E-value=0.2  Score=47.46  Aligned_cols=52  Identities=17%  Similarity=0.030  Sum_probs=40.4

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHH------------------------------------------CCCCe
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISK------------------------------------------YPHIK  219 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~------------------------------------------~P~l~  219 (244)
                      ..++.... |.....|+|.+||+|.++++.+..                                          .|+.+
T Consensus       180 a~ll~~~~-~~~~~~llDP~CGSGt~lIeAa~~a~~~apG~~R~~f~fe~w~~~~~~~w~~~~~ea~~~~~~~~~~~~~~  258 (703)
T 3v97_A          180 AAIVMRSG-WQPGTPLLDPMCGSGTLLIEAAMLATDRAPGLHRGRWGFSGWAQHDEAIWQEVKAEAQTRARKGLAEYSSH  258 (703)
T ss_dssp             HHHHHHTT-CCTTSCEEETTCTTSHHHHHHHHHHTTCCTTTTCCCCTTTTBTTCCHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_pred             HHHHHhhC-CCCCCeEEecCCCCcHHHHHHHHHHhhcCCCCCccccchhhcccCCHHHHHHHHHHHHHHhhhccccCCcc
Confidence            34455555 777789999999999999987764                                          24467


Q ss_pred             EEEccc-hHHhhhCCC
Q 041256          220 GINYDL-PYVIKDAPS  234 (244)
Q Consensus       220 ~~v~Dl-p~vi~~a~~  234 (244)
                      ++.+|. |.+++.|++
T Consensus       259 i~G~Did~~av~~A~~  274 (703)
T 3v97_A          259 FYGSDSDARVIQRART  274 (703)
T ss_dssp             EEEEESCHHHHHHHHH
T ss_pred             EEEEECCHHHHHHHHH
Confidence            899998 888888764

>2frx_A Hypothetical protein YEBU; rossmann-type S-adenosylmethionine-dependent methyltransfera domain; 2.90A {Escherichia coli}

Probab=90.45  E-value=0.31  Score=44.00  Aligned_cols=42  Identities=12%  Similarity=0.127  Sum_probs=35.0

Q ss_pred             CcceEEEecCCccHHHHHHHHHCC-CCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYP-HIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...+|+|+|||.|..+..+++..+ .-+++..|+ +..++.+++
T Consensus       117 ~g~~VLDl~aGpG~kt~~lA~~~~~~g~V~avDis~~~l~~~~~  160 (479)
T 2frx_A          117 APQRVMDVAAAPGSKTTQISARMNNEGAILANEFSASRVKVLHA  160 (479)
T ss_dssp             CCSEEEESSCTTSHHHHHHHHHTTTCSEEEEECSSHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCHHHHHHHHhCCCCCEEEEEECCHHHHHHHHH
Confidence            567999999999999999999976 478999998 666666553

>2b9e_A NOL1/NOP2/SUN domain family, member 5 isoform 2; methytransferase, structural genomics, structural genomics consortium, SGC; HET: SAM; 1.65A {Homo sapiens} SCOP: c.66.1.38

Probab=90.40  E-value=0.25  Score=42.01  Aligned_cols=44  Identities=11%  Similarity=0.084  Sum_probs=35.7

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHC-CCCeEEEccc-hHHhhhCCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKY-PHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .....+|+|+|+|.|..+..+++.. +.-+++.+|+ |..++.+++
T Consensus       100 ~~~g~~VLDlcaG~G~kt~~la~~~~~~g~V~a~D~~~~~l~~~~~  145 (309)
T 2b9e_A          100 PPPGSHVIDACAAPGNKTSHLAALLKNQGKIFAFDLDAKRLASMAT  145 (309)
T ss_dssp             CCTTCEEEESSCTTCHHHHHHHHHHTTCSEEEEEESCHHHHHHHHH
T ss_pred             CCCCCEEEEeCCChhHHHHHHHHHhCCCCEEEEEeCCHHHHHHHHH
Confidence            4555799999999999999999985 5678999998 666666553

>2cyy_A Putative HTH-type transcriptional regulator PH151; structural genomics, pyrococcus horikosii OT3, NPPSFA; HET: MSE GLN; 1.80A {Pyrococcus horikoshii} SCOP: a.4.5.32 d.58.4.2

Probab=90.35  E-value=0.18  Score=37.90  Aligned_cols=45  Identities=16%  Similarity=0.243  Sum_probs=38.4

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      +..|.+.|.+.   ++.|..|||+.+|++      +.. +.+.++.|...|++..
T Consensus         9 ~~~il~~L~~~---~~~s~~ela~~lg~s------~~t-v~~~l~~L~~~G~i~~   53 (151)
T 2cyy_A            9 DKKIIKILQND---GKAPLREISKITGLA------EST-IHERIRKLRESGVIKK   53 (151)
T ss_dssp             HHHHHHHHHHC---TTCCHHHHHHHHCSC------HHH-HHHHHHHHHHHTSSCC
T ss_pred             HHHHHHHHHHc---CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCeEE
Confidence            45677888775   689999999999997      556 9999999999999983

>2fbk_A Transcriptional regulator, MARR family; winged-helix-turn-helix; 2.30A {Deinococcus radiodurans} SCOP: a.4.5.28

Probab=90.29  E-value=0.075  Score=41.11  Aligned_cols=48  Identities=13%  Similarity=0.172  Sum_probs=37.6

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      ++.|+..|...+..+++|..+||+.++++      ... +.++++.|...|++++
T Consensus        71 ~~~iL~~L~~~~~~~~~t~~eLa~~l~is------~~t-vs~~l~~Le~~GlV~r  118 (181)
T 2fbk_A           71 GWDLLLTLYRSAPPEGLRPTELSALAAIS------GPS-TSNRIVRLLEKGLIER  118 (181)
T ss_dssp             HHHHHHHHHHHCCSSCBCHHHHHHHCSCC------SGG-GSSHHHHHHHHTSEEC
T ss_pred             HHHHHHHHHHcCCCCCCCHHHHHHHHCCC------HHH-HHHHHHHHHHCcCEEe
Confidence            44577788775310139999999999997      345 8899999999999986

>2ia0_A Putative HTH-type transcriptional regulator PF086; ASNC, PSI, structural genomics, southeast collaboratory for structural genomics; 2.37A {Pyrococcus furiosus}

Probab=90.25  E-value=0.23  Score=38.38  Aligned_cols=46  Identities=13%  Similarity=0.330  Sum_probs=39.0

Q ss_pred             HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      .+..|.+.|.+.   +++|..|||+++|++      +.. +.+.++.|...|++..
T Consensus        18 ~d~~IL~~L~~~---~~~s~~eLA~~lglS------~~t-v~~~l~~L~~~G~I~~   63 (171)
T 2ia0_A           18 LDRNILRLLKKD---ARLTISELSEQLKKP------EST-IHFRIKKLQERGVIER   63 (171)
T ss_dssp             HHHHHHHHHHHC---TTCCHHHHHHHHTSC------HHH-HHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEe
Confidence            345678888875   689999999999997      556 9999999999999973

>1rjd_A PPM1P, carboxy methyl transferase for protein phosphatase 2A catalytic subunit; SAM dependent methyltransferase; HET: SAM; 1.80A {Saccharomyces cerevisiae} SCOP: c.66.1.37 PDB: 1rje_A* 1rjf_A 1rjg_A* 2ob2_A* 2ob1_A

Probab=90.18  E-value=0.31  Score=41.92  Aligned_cols=40  Identities=15%  Similarity=0.360  Sum_probs=36.4

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDA  232 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a  232 (244)
                      +...||.+|||.......+...+|+++.+=+|+|+|++.-
T Consensus        97 ~~~qVV~LGaGlDTr~~RL~~~~~~~~~~EvD~P~vi~~K  136 (334)
T 1rjd_A           97 EKVQVVNLGCGSDLRMLPLLQMFPHLAYVDIDYNESVELK  136 (334)
T ss_dssp             SSEEEEEETCTTCCTHHHHHHHCTTEEEEEEECHHHHHHH
T ss_pred             CCcEEEEeCCCCccHHHHhcCcCCCCEEEECCCHHHHHHH
Confidence            4589999999999999999999999999999999998763

>2cg4_A Regulatory protein ASNC; DNA binding, FFRP, LRP family, transcription, DNA- binding, transcription regulation; 2.4A {Escherichia coli} SCOP: a.4.5.32 d.58.4.2

Probab=90.02  E-value=0.19  Score=37.77  Aligned_cols=45  Identities=11%  Similarity=0.172  Sum_probs=38.5

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      +..|...|.+.   ++.|..|||+++|++      +.. +.+.++.|...|++..
T Consensus        10 d~~il~~L~~~---~~~s~~ela~~lg~s------~~t-v~~~l~~L~~~G~i~~   54 (152)
T 2cg4_A           10 DRGILEALMGN---ARTAYAELAKQFGVS------PET-IHVRVEKMKQAGIITG   54 (152)
T ss_dssp             HHHHHHHHHHC---TTSCHHHHHHHHTSC------HHH-HHHHHHHHHHHTSEEE
T ss_pred             HHHHHHHHHHc---CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHcCCcce
Confidence            44577888875   689999999999997      556 9999999999999984

>2fxa_A Protease production regulatory protein HPR; protease porduction, regulation, STR genomics, PSI, protein structure initiative; HET: PGE P6G 1PE; 2.40A {Bacillus subtilis} SCOP: a.4.5.28

Probab=89.85  E-value=0.12  Score=41.22  Aligned_cols=63  Identities=14%  Similarity=0.018  Sum_probs=45.0

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCcccccc
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSAYF  107 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~~l  107 (244)
                      ++.|+..|...   +++|..+||+.++++      ... +.++++.|...|++.+.....+.   .+.+|+.+..+
T Consensus        50 q~~iL~~L~~~---~~~t~~eLa~~l~i~------~st-vs~~l~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~  115 (207)
T 2fxa_A           50 EHHILWIAYQL---NGASISEIAKFGVMH------VST-AFNFSKKLEERGYLRFSKRLNDKRNTYVQLTEEGTEV  115 (207)
T ss_dssp             HHHHHHHHHHH---TSEEHHHHHHHTTCC------HHH-HHHHHHHHHHHTSEEEECC------CEEEECHHHHHH
T ss_pred             HHHHHHHHHHC---CCcCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEEecCCCCCceEEEEECHHHHHH
Confidence            34466777765   589999999999997      456 99999999999999863211122   46666666533

>2qlz_A Transcription factor PF0095; 2.50A {Pyrococcus furiosus} PDB: 2quf_A

Probab=89.81  E-value=0.1  Score=42.57  Aligned_cols=67  Identities=7%  Similarity=0.207  Sum_probs=48.6

Q ss_pred             HHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCC------ceeecC
Q 041256           28 AVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQ------RLYSLA  101 (244)
Q Consensus        28 ~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~------~~y~~t  101 (244)
                      .+|.--.++.|+..|..    +|+|+.+||+.+|++      ... +.+.|+.|...|++......+.      -.|+++
T Consensus         7 kaL~~~~R~~IL~~L~~----g~~s~~ELa~~lglS------~st-Vs~hL~~Le~aGLV~~~~~~gr~~GRp~~~Y~Lt   75 (232)
T 2qlz_A            7 YILGNKVRRDLLSHLTC----MECYFSLLSSKVSVS------STA-VAKHLKIMEREGVLQSYEKEERFIGPTKKYYKIS   75 (232)
T ss_dssp             HHHTSHHHHHHHHHHTT----TTTCSSSSCTTCCCC------HHH-HHHHHHHHHHTTSEEEEEECC-----CEEEEEEC
T ss_pred             HHhCCHHHHHHHHHHHh----CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEEeeecCCCCCCccEEEEEc
Confidence            34444556778888875    699999999999997      456 9999999999999985212211      137776


Q ss_pred             cccc
Q 041256          102 PVSA  105 (244)
Q Consensus       102 ~~s~  105 (244)
                      +.+.
T Consensus        76 ~~~~   79 (232)
T 2qlz_A           76 IAKS   79 (232)
T ss_dssp             CCEE
T ss_pred             cchh
Confidence            6543

>1uly_A Hypothetical protein PH1932; helix-turn-helix, structural genomics, DNA binding protein; 2.50A {Pyrococcus horikoshii} SCOP: a.4.5.58 PDB: 2cwe_A

Probab=89.75  E-value=0.29  Score=38.57  Aligned_cols=51  Identities=6%  Similarity=0.169  Sum_probs=41.6

Q ss_pred             HHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           29 VMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        29 ~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      ++....+..|...|.+    +++|..|||+.+|++      +.. +.+.|+.|...|++...
T Consensus        16 ~l~d~~~~~IL~~L~~----~~~s~~eLA~~lglS------~st-v~~~l~~Le~~GlI~~~   66 (192)
T 1uly_A           16 VMLEDTRRKILKLLRN----KEMTISQLSEILGKT------PQT-IYHHIEKLKEAGLVEVK   66 (192)
T ss_dssp             HHHSHHHHHHHHHHTT----CCBCHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEEE
T ss_pred             HhCCHHHHHHHHHHHc----CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEEE
Confidence            3334456678888874    689999999999997      556 99999999999999864

>1i1g_A Transcriptional regulator LRPA; helix-turn-helix, LRP/ASNC family; 2.90A {Pyrococcus furiosus} SCOP: a.4.5.32 d.58.4.2

Probab=89.75  E-value=0.21  Score=36.78  Aligned_cols=45  Identities=16%  Similarity=0.295  Sum_probs=37.5

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      +..|...|.+.   ++.|..|||+.+|++      +.. +.+.|+.|...|++..
T Consensus         6 ~~~il~~L~~~---~~~~~~ela~~lg~s------~~t-v~~~l~~L~~~G~i~~   50 (141)
T 1i1g_A            6 DKIILEILEKD---ARTPFTEIAKKLGIS------ETA-VRKRVKALEEKGIIEG   50 (141)
T ss_dssp             HHHHHHHHHHC---TTCCHHHHHHHHTSC------HHH-HHHHHHHHHHHTSSCC
T ss_pred             HHHHHHHHHHc---CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEec
Confidence            44567778764   689999999999997      456 9999999999999973

>1ku9_A Hypothetical protein MJ223; putative transcription factor, homodimeric winged-helix fold, structural genomics, PSI; 2.80A {Methanocaldococcus jannaschii} SCOP: a.4.5.36

Probab=89.72  E-value=0.24  Score=36.36  Aligned_cols=44  Identities=14%  Similarity=0.285  Sum_probs=35.2

Q ss_pred             hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      ++..|....  ++.|..|||+.+|++      ... +.++|+.|...|++.+.
T Consensus        31 il~~L~~~~--~~~t~~ela~~l~~~------~st-vs~~l~~L~~~G~v~r~   74 (152)
T 1ku9_A           31 VYAILYLSD--KPLTISDIMEELKIS------KGN-VSMSLKKLEELGFVRKV   74 (152)
T ss_dssp             HHHHHHHCS--SCEEHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHcC--CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEEE
Confidence            455554221  689999999999997      456 99999999999999963

>4auk_A Ribosomal RNA large subunit methyltransferase M; YGDE; HET: TLA PGE; 1.90A {Escherichia coli} PDB: 4atn_A* 4b17_A*

Probab=89.69  E-value=0.23  Score=43.39  Aligned_cols=49  Identities=10%  Similarity=0.026  Sum_probs=36.7

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCCCCCceee
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPGTLFI  241 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~~~~i~~~  241 (244)
                      +....++||+|++.|.++..++++  +.+++.+|.-+.-+.....++|+++
T Consensus       209 l~~G~~vlDLGAaPGGWT~~l~~r--g~~V~aVD~~~l~~~l~~~~~V~~~  257 (375)
T 4auk_A          209 LANGMWAVDLGACPGGWTYQLVKR--NMWVYSVDNGPMAQSLMDTGQVTWL  257 (375)
T ss_dssp             SCTTCEEEEETCTTCHHHHHHHHT--TCEEEEECSSCCCHHHHTTTCEEEE
T ss_pred             CCCCCEEEEeCcCCCHHHHHHHHC--CCEEEEEEhhhcChhhccCCCeEEE
Confidence            345689999999999999999988  6789999974433333345666654

>4b8x_A SCO5413, possible MARR-transcriptional regulator; winged helix motif; HET: CME; 1.25A {Streptomyces coelicolor}

Probab=89.58  E-value=0.11  Score=38.85  Aligned_cols=50  Identities=8%  Similarity=0.068  Sum_probs=36.8

Q ss_pred             CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCce---eecCcccc
Q 041256           49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRL---YSLAPVSA  105 (244)
Q Consensus        49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~---y~~t~~s~  105 (244)
                      +++|..+||+.++++      +.. +.++++-|...|++++.+...+.+   ..+|+.++
T Consensus        50 ~~~t~~eLa~~l~~~------~~t-vs~~v~~Le~~Glv~r~~~~~DrR~~~l~LT~~G~  102 (147)
T 4b8x_A           50 GELPMSKIGERLMVH------PTS-VTNTVDRLVRSGLVAKRPNPNDGRGTLATITDKGR  102 (147)
T ss_dssp             GEEEHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEEEECC----CEEEEECHHHH
T ss_pred             CCcCHHHHHHHHCCC------HHH-HHHHHHHHHhCCCEEEeecCCcCceeEEEECHHHH
Confidence            689999999999997      556 999999999999999743222222   45555554

>2pg4_A Uncharacterized protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2, DNA binding protein; HET: MSE CIT; 2.21A {Aeropyrum pernix} SCOP: a.4.5.48

Probab=89.51  E-value=0.14  Score=35.14  Aligned_cols=61  Identities=16%  Similarity=0.097  Sum_probs=41.5

Q ss_pred             hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhcc-HHHHHHHHhhCCcccceeecC-CceeecCcccccc
Q 041256           38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMT-LDRVLRLLVSYNALHCSFVDG-QRLYSLAPVSAYF  107 (244)
Q Consensus        38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~-l~rlLr~L~~~gll~~~~~~~-~~~y~~t~~s~~l  107 (244)
                      ++..|...+  ++.|..|||+.++++       ..+ +.++++.|...|++..++.+. .-.+.+|+.+..+
T Consensus        20 ~L~~l~~~~--~~~t~~eLa~~l~is-------~~t~vs~~l~~Le~~Glv~~~~~drR~~~~~LT~~G~~~   82 (95)
T 2pg4_A           20 TLLEFEKKG--YEPSLAEIVKASGVS-------EKTFFMGLKDRLIRAGLVKEETLSYRVKTLKLTEKGRRL   82 (95)
T ss_dssp             HHHHHHHTT--CCCCHHHHHHHHCCC-------HHHHHTTHHHHHHHTTSEEEEEEETTEEEEEECHHHHHH
T ss_pred             HHHHHHhcC--CCCCHHHHHHHHCCC-------chHHHHHHHHHHHHCCCeecCCCCCCeEEEEECHhHHHH
Confidence            444555542  379999999999996       233 689999999999998432211 1236667666533

>3hrs_A Metalloregulator SCAR; DTXR/MNTR family member, transcription; 2.70A {Streptococcus gordonii} PDB: 3hrt_A 3hru_A

Probab=89.41  E-value=0.26  Score=39.43  Aligned_cols=50  Identities=16%  Similarity=0.209  Sum_probs=42.3

Q ss_pred             CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccccccc
Q 041256           49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFV  108 (244)
Q Consensus        49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l~  108 (244)
                      ++.+..+||+.++++      +.. +.+.++.|...|++.+  + ....+.+|+.++.+.
T Consensus        19 ~~~~~~~lA~~l~vs------~~t-vs~~l~~Le~~GlV~r--~-~~~~i~LT~~G~~~~   68 (214)
T 3hrs_A           19 NKITNKEIAQLMQVS------PPA-VTEMMKKLLAEELLIK--D-KKAGYLLTDLGLKLV   68 (214)
T ss_dssp             SCCCHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEE--E-TTTEEEECHHHHHHH
T ss_pred             CCcCHHHHHHHHCCC------hhH-HHHHHHHHHHCCCEEE--e-cCCCeEECHHHHHHH
Confidence            789999999999997      456 9999999999999996  2 346789999887554

>2o03_A Probable zinc uptake regulation protein FURB; DNA-binding, helix-turn-helix, zinc binding, GE regulation; 2.70A {Mycobacterium tuberculosis}

Probab=89.40  E-value=0.46  Score=34.82  Aligned_cols=50  Identities=10%  Similarity=0.100  Sum_probs=39.5

Q ss_pred             HHHhcChhhHHhhcCCCCCCCHHHHHHhC-----CCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           32 AVVELDVFEIISKAGPGAKLSVAEIVAQI-----PLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        32 ~a~~lgifd~L~~~~~~g~~t~~eLA~~~-----~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      +--+.-|++.|.+.+  ++.|++||.+.+     +++      ..- ++|.|+.|+..|++.+.
T Consensus        10 T~qR~~Il~~l~~~~--~~~sa~ei~~~l~~~~~~is------~~T-VYR~L~~L~e~Glv~~~   64 (131)
T 2o03_A           10 TRQRAAISTLLETLD--DFRSAQELHDELRRRGENIG------LTT-VYRTLQSMASSGLVDTL   64 (131)
T ss_dssp             HHHHHHHHHHHHHCC--SCEEHHHHHHHHHHTTCCCC------HHH-HHHHHHHHHTTTSEEEE
T ss_pred             CHHHHHHHHHHHhCC--CCCCHHHHHHHHHHhCCCCC------Hhh-HHHHHHHHHHCCCEEEE
Confidence            344666888888653  689999999998     554      334 99999999999999864

>3ua3_A Protein arginine N-methyltransferase 5; TIM-barrel, rossmann fold, beta-barrel, symmetric arginine dimethylase, SAM binding; HET: SAH; 3.00A {Caenorhabditis elegans} PDB: 3ua4_A

Probab=89.37  E-value=0.38  Score=45.47  Aligned_cols=50  Identities=18%  Similarity=0.230  Sum_probs=33.4

Q ss_pred             chhhccCCchHHHHHHHHHHhcchhhHHHHHhhcCCCCCcceEEEecCCccHHHHHH
Q 041256          155 IYDYLGVDSRFNDVFNNGMLSHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMI  211 (244)
Q Consensus       155 ~~e~~~~~~~~~~~f~~aM~~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l  211 (244)
                      .||.+++|+-+-..|.+|+...       +.+.+++-.+.+.|+|||||+|-++...
T Consensus       378 tYe~fekD~vRy~~Y~~AI~~a-------l~d~~~~~~~~~VVldVGaGtGpLs~~a  427 (745)
T 3ua3_A          378 VYNTFEQDQIKYDVYGEAVVGA-------LKDLGADGRKTVVIYLLGGGRGPIGTKI  427 (745)
T ss_dssp             HHHHHHHCHHHHHHHHHHHHHH-------HHHHHTTCCSEEEEEEESCTTCHHHHHH
T ss_pred             HHHHHcCChhhHHHHHHHHHHH-------HHHhhcccCCCcEEEEECCCCCHHHHHH
Confidence            4677778887777888877541       2222221134579999999999997543

>2k4m_A TR8_protein, UPF0146 protein MTH_1000; alpha+beta, rossman fold, structural genomics, PSI-2; NMR {Methanothermobacterthermautotrophicus str}

Probab=89.31  E-value=0.25  Score=37.41  Aligned_cols=38  Identities=18%  Similarity=0.214  Sum_probs=27.5

Q ss_pred             CCcceEEEecCCccH-HHHHHHHHCCCCeEEEccc-hHHhh
Q 041256          192 EHVKKLVDVGGGLGI-TLNMIISKYPHIKGINYDL-PYVIK  230 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~-~~~~l~~~~P~l~~~v~Dl-p~vi~  230 (244)
                      ....++||||+|.|. .+..|+++ -+..++..|+ |..++
T Consensus        34 ~~~~rVlEVG~G~g~~vA~~La~~-~g~~V~atDInp~Av~   73 (153)
T 2k4m_A           34 GPGTRVVEVGAGRFLYVSDYIRKH-SKVDLVLTDIKPSHGG   73 (153)
T ss_dssp             CSSSEEEEETCTTCCHHHHHHHHH-SCCEEEEECSSCSSTT
T ss_pred             CCCCcEEEEccCCChHHHHHHHHh-CCCeEEEEECCccccc
Confidence            344799999999995 77666653 5677888887 54443

>2d1h_A ST1889, 109AA long hypothetical transcriptional regulator; helix-turn-helix, intermolecular and intramolecular S-S bond structural genomics; 2.05A {Sulfolobus tokodaii} SCOP: a.4.5.50

Probab=89.27  E-value=0.28  Score=33.90  Aligned_cols=35  Identities=11%  Similarity=0.237  Sum_probs=31.4

Q ss_pred             CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      ++.|..|||+.+|++      ..- +.|.|+.|...|++.+.
T Consensus        35 ~~~t~~ela~~l~is------~~t-v~~~l~~L~~~g~v~~~   69 (109)
T 2d1h_A           35 KPITSEELADIFKLS------KTT-VENSLKKLIELGLVVRT   69 (109)
T ss_dssp             SCEEHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEEE
T ss_pred             CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCeEee
Confidence            689999999999997      455 99999999999999963

>3evf_A RNA-directed RNA polymerase NS5; NS5 methyltransferase, RNA CAP binding, binding, capsid protein; HET: GTA SAH; 1.45A {Yellow fever virus} SCOP: c.66.1.0 PDB: 3evb_A* 3evc_A* 3evd_A* 3eve_A* 3eva_A*

Probab=89.12  E-value=0.36  Score=40.29  Aligned_cols=37  Identities=14%  Similarity=-0.022  Sum_probs=27.2

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeE
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKG  220 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~  220 (244)
                      .+.+..- +....+|||+|||.|.++..++++.|--.+
T Consensus        65 ei~ek~~-l~~~~~VLDLGaAPGGWSQvAa~~~~~~~v  101 (277)
T 3evf_A           65 WFHERGY-VKLEGRVIDLGCGRGGWCYYAAAQKEVSGV  101 (277)
T ss_dssp             HHHHTTS-SCCCEEEEEETCTTCHHHHHHHTSTTEEEE
T ss_pred             HHHHhCC-CCCCCEEEEecCCCCHHHHHHHHhcCCCcc
Confidence            4444433 566679999999999999988887664443

>3u1d_A Uncharacterized protein; GNTR-superfamily, structural genomics, PSI-biology, midwest for structural genomics, MCSG; 1.80A {Halomicrobium mukohataei}

Probab=89.03  E-value=0.51  Score=35.79  Aligned_cols=64  Identities=23%  Similarity=0.202  Sum_probs=45.7

Q ss_pred             HhcChhhHHhhcCCCCCCCHHHHHHhCC-CCCCCCcchhccHHHHHHHHhhCCcccceeec----CCc----eeecCccc
Q 041256           34 VELDVFEIISKAGPGAKLSVAEIVAQIP-LKDNNPEAAAMTLDRVLRLLVSYNALHCSFVD----GQR----LYSLAPVS  104 (244)
Q Consensus        34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~-~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~----~~~----~y~~t~~s  104 (244)
                      .++.|+..|...+ .+..|+++|++.++ ++      ..- ++|-|+.|+..|++.+....    +.|    .|++|+.+
T Consensus        30 tR~~IL~~Ll~~p-~~~~ta~eL~~~l~~lS------~aT-VyrhL~~L~eaGLV~~~~~~~~~~~rGrP~k~Y~LT~~G  101 (151)
T 3u1d_A           30 TRLDVLHQILAQP-DGVLSVEELLYRNPDET------EAN-LRYHVDELVDRGIVEKIPVPRAKSVDDPPTTFYAVTGEG  101 (151)
T ss_dssp             HHHHHHHHHHHST-TSCBCHHHHHHHCTTSC------HHH-HHHHHHHHHHTTSEEEEECCCCTTSSSCCCEEEEECHHH
T ss_pred             HHHHHHHHHHcCC-CCCCCHHHHHHhcCCCC------HHH-HHHHHHHHHHCCCeEEeecCcCcccCCCCceEEEECHHH
Confidence            4566677776643 24689999999998 76      345 99999999999999853111    012    57888877


Q ss_pred             c
Q 041256          105 A  105 (244)
Q Consensus       105 ~  105 (244)
                      +
T Consensus       102 r  102 (151)
T 3u1d_A          102 I  102 (151)
T ss_dssp             H
T ss_pred             H
Confidence            6

>2fe3_A Peroxide operon regulator; oxidative stress regulator, DNA binding protein; 1.75A {Bacillus subtilis} PDB: 3f8n_A 2rgv_A*

Probab=88.95  E-value=0.69  Score=34.54  Aligned_cols=48  Identities=13%  Similarity=0.148  Sum_probs=38.0

Q ss_pred             HhcChhhHHhhcCCCCCCCHHHHHHhC-----CCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           34 VELDVFEIISKAGPGAKLSVAEIVAQI-----PLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        34 ~~lgifd~L~~~~~~g~~t~~eLA~~~-----~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      -+.-|++.|.+.+  ++.|++||.+.+     +++      ..- ++|.|+.|+..|++.+.
T Consensus        23 qR~~Il~~L~~~~--~~~sa~ei~~~l~~~~~~is------~aT-VYR~L~~L~e~Glv~~~   75 (145)
T 2fe3_A           23 QRHAILEYLVNSM--AHPTADDIYKALEGKFPNMS------VAT-VYNNLRVFRESGLVKEL   75 (145)
T ss_dssp             HHHHHHHHHHHCS--SCCCHHHHHHHHGGGCTTCC------HHH-HHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHhCC--CCCCHHHHHHHHHHhCCCCC------hhh-HHHHHHHHHHCCCEEEE
Confidence            3455888887753  689999999998     443      334 99999999999999864

>2zig_A TTHA0409, putative modification methylase; methyltransferase, S- adenosylmethionine, structural genomics, NPPSFA; 2.10A {Thermus thermophilus} PDB: 2zie_A* 2zif_A

Probab=88.90  E-value=0.34  Score=40.71  Aligned_cols=49  Identities=18%  Similarity=0.179  Sum_probs=36.7

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+++.+.  .....|+|++||+|..+.++++.  +-+++.+|+ |..++.|++
T Consensus       226 ~~~i~~~~--~~~~~vlD~f~GsGt~~~~a~~~--g~~~~g~e~~~~~~~~a~~  275 (297)
T 2zig_A          226 ERLVRMFS--FVGDVVLDPFAGTGTTLIAAARW--GRRALGVELVPRYAQLAKE  275 (297)
T ss_dssp             HHHHHHHC--CTTCEEEETTCTTTHHHHHHHHT--TCEEEEEESCHHHHHHHHH
T ss_pred             HHHHHHhC--CCCCEEEECCCCCCHHHHHHHHc--CCeEEEEeCCHHHHHHHHH
Confidence            34555543  34478999999999999998886  457999998 677776653

>2esh_A Conserved hypothetical protein TM0937; APC5794, structural genomics, PSI, protein structure initiative; 2.30A {Thermotoga maritima} SCOP: a.4.5.61

Probab=88.90  E-value=0.74  Score=33.02  Aligned_cols=67  Identities=12%  Similarity=0.205  Sum_probs=47.1

Q ss_pred             HHHHHhcChhhHHhhcCCCCCCCHHHHHHhCC--------CCCCCCcch-hccHHHHHHHHhhCCcccceeec--CC--c
Q 041256           30 MQAVVELDVFEIISKAGPGAKLSVAEIVAQIP--------LKDNNPEAA-AMTLDRVLRLLVSYNALHCSFVD--GQ--R   96 (244)
Q Consensus        30 L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~--------~~~~~~~~~-~~~l~rlLr~L~~~gll~~~~~~--~~--~   96 (244)
                      +....++-|...|.+    +|.+.-+|++.++        ++      + .. +.+.|+-|...|+++.....  ++  -
T Consensus        10 ~~~~~~~~IL~~L~~----~~~~gyel~~~l~~~g~~~~~is------~~~t-ly~~L~~Le~~GlI~~~~~~~~~~~r~   78 (118)
T 2esh_A           10 RGWWLASTILLLVAE----KPSHGYELAERLAEFGIEIPGIG------HMGN-IYRVLADLEESGFLSTEWDTTVSPPRK   78 (118)
T ss_dssp             HHHHHHHHHHHHHHH----SCBCHHHHHHHHHTTCCSSTTCC------CCCC-HHHHHHHHHHTTSEEEEEECSSSSCEE
T ss_pred             ccchHHHHHHHHHHc----CCCCHHHHHHHHHHhCCcccCCC------Ccch-HHHHHHHHHHCCCeEEEeecCCCCCce
Confidence            334455667777776    5899999999883        44      4 45 99999999999999864321  11  2


Q ss_pred             eeecCcccccc
Q 041256           97 LYSLAPVSAYF  107 (244)
Q Consensus        97 ~y~~t~~s~~l  107 (244)
                      .|++|+.++.+
T Consensus        79 ~Y~LT~~G~~~   89 (118)
T 2esh_A           79 IYRITPQGKLY   89 (118)
T ss_dssp             EEEECHHHHHH
T ss_pred             EEEEChHHHHH
Confidence            47888877633

>2efj_A 3,7-dimethylxanthine methyltransferase; SAM-dependant methyltransferase, SAH, theobromine; HET: SAH 37T; 2.00A {Coffea canephora} PDB: 2eg5_A*

Probab=87.81  E-value=0.33  Score=42.58  Aligned_cols=33  Identities=24%  Similarity=0.178  Sum_probs=27.9

Q ss_pred             cceEEEecCCccHHHHHHHHH-----------------CCCCeEEEccch
Q 041256          194 VKKLVDVGGGLGITLNMIISK-----------------YPHIKGINYDLP  226 (244)
Q Consensus       194 ~~~vvDVGGG~G~~~~~l~~~-----------------~P~l~~~v~Dlp  226 (244)
                      .-+|+|+||++|..+..++..                 .|+++++.-|||
T Consensus        53 ~~~IaDlGCssG~NT~~~v~~ii~~i~~~~~~~~~~~~~pe~~v~~nDLp  102 (384)
T 2efj_A           53 CFKVGDLGCASGPNTFSTVRDIVQSIDKVGQEKKNELERPTIQIFLNDLF  102 (384)
T ss_dssp             EEEEEEETCCSSHHHHHHHHHHHHHHTCC----------CEEEEEEECCT
T ss_pred             ceEEEecCCCCCchHHHHHHHHHHHHHHHhhhcccCCCCCceEEEecCCC
Confidence            688999999999988877666                 578888888999

>1cf7_A Protein (transcription factor E2F-4); E2F, winged-helix, DNA-binding domain, cell cycle, transcription/DNA complex; HET: DNA; 2.60A {Homo sapiens} SCOP: a.4.5.17

Probab=87.57  E-value=0.53  Score=31.33  Aligned_cols=34  Identities=6%  Similarity=0.096  Sum_probs=30.9

Q ss_pred             CCCCHHHHHHhCCC-CCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           49 AKLSVAEIVAQIPL-KDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        49 g~~t~~eLA~~~~~-~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      +.+++.++|+.+++ .      -++ ++.++.+|.++|++++
T Consensus        29 ~~i~l~~aa~~L~v~~------kRR-iYDI~NVLe~igli~K   63 (76)
T 1cf7_A           29 GVLDLKLAADTLAVRQ------KRR-IYDITNVLEGIGLIEK   63 (76)
T ss_dssp             TEEEHHHHHHHTTTCC------THH-HHHHHHHHHHHTSEEE
T ss_pred             CcCcHHHHHHHhCCcc------cee-hhhHHHHHhHhcceee
Confidence            68999999999999 5      466 9999999999999995

>2dk5_A DNA-directed RNA polymerase III 39 kDa polypeptide; structural genomics, winged helix domain, NPPSFA; NMR {Homo sapiens} SCOP: a.4.5.85

Probab=87.54  E-value=0.38  Score=33.17  Aligned_cols=46  Identities=20%  Similarity=0.282  Sum_probs=37.0

Q ss_pred             cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      +.|+..|.+.+. .+++..|||++++++      ..- +.++|+.|...||+.+
T Consensus        23 ~~Vl~~I~~~g~-~gi~qkeLa~~~~l~------~~t-vt~iLk~LE~kglIkr   68 (91)
T 2dk5_A           23 KLVYQIIEDAGN-KGIWSRDVRYKSNLP------LTE-INKILKNLESKKLIKA   68 (91)
T ss_dssp             HHHHHHHHHHCT-TCEEHHHHHHHTTCC------HHH-HHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHcCC-CCcCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEE
Confidence            446677776421 479999999999997      345 9999999999999984

>4gqb_A Protein arginine N-methyltransferase 5; TIM barrel, beta-propeller, methyltransferase, methylation, transferase-protein binding complex; HET: 0XU; 2.06A {Homo sapiens} PDB: 4g56_A*

Probab=87.53  E-value=0.55  Score=43.92  Aligned_cols=71  Identities=15%  Similarity=0.141  Sum_probs=42.9

Q ss_pred             chhhccCCchHHHHHHHHHHhcchhhHHHHHhhcCC---CCCcceEEEecCCccHHHHHHHHHC----CCCeEEEccchH
Q 041256          155 IYDYLGVDSRFNDVFNNGMLSHTSIVMEKVLESYKG---FEHVKKLVDVGGGLGITLNMIISKY----PHIKGINYDLPY  227 (244)
Q Consensus       155 ~~e~~~~~~~~~~~f~~aM~~~~~~~~~~~~~~~~~---~~~~~~vvDVGGG~G~~~~~l~~~~----P~l~~~v~Dlp~  227 (244)
                      .||.+++|+-+-..+.+|+..       .+.+..+.   -.+.+.|+|||+|+|-++...+++-    -++++..++-..
T Consensus       323 tYevFEkD~vKy~~Ye~AI~~-------Al~d~~~~~~~~~~~~vVldVGaGrGpLv~~al~A~a~~~~~vkVyAVEknp  395 (637)
T 4gqb_A          323 TYEVFEKDPIKYSQYQQAIYK-------CLLDRVPEEEKDTNVQVLMVLGAGRGPLVNASLRAAKQADRRIKLYAVEKNP  395 (637)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHH-------HHHHHSCGGGTTTCEEEEEEESCTTSHHHHHHHHHHHHTTCEEEEEEEESCH
T ss_pred             hhhhhcCChhhHHHHHHHHHH-------HHHHhhhhccccCCCcEEEEECCCCcHHHHHHHHHHHhcCCCcEEEEEECCH
Confidence            477778898877888888753       22222210   2345789999999999854444432    224566666543


Q ss_pred             HhhhC
Q 041256          228 VIKDA  232 (244)
Q Consensus       228 vi~~a  232 (244)
                      ....+
T Consensus       396 ~A~~a  400 (637)
T 4gqb_A          396 NAVVT  400 (637)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            33333

>4esf_A PADR-like transcriptional regulator; PADR family, DNA binding protein, HTH fold; 2.20A {Bacillus cereus}

Probab=87.42  E-value=0.93  Score=32.61  Aligned_cols=67  Identities=21%  Similarity=0.239  Sum_probs=46.5

Q ss_pred             HHHHHHhcChhhHHhhcCCCCCCCHHHHHHhC------CCCCCCCcchhccHHHHHHHHhhCCcccceeec---CC--ce
Q 041256           29 VMQAVVELDVFEIISKAGPGAKLSVAEIVAQI------PLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVD---GQ--RL   97 (244)
Q Consensus        29 ~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~------~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~---~~--~~   97 (244)
                      .++-.+++=|...|.+    +|.+--+|++.+      +++      +.. +...|+-|...|+++.....   ++  -.
T Consensus         7 l~~g~l~~~IL~lL~~----~p~~Gyei~~~l~~~g~~~is------~gt-lY~~L~rLe~~GlI~~~~~~~~~g~~rk~   75 (117)
T 4esf_A            7 MLKGSLEGCVLEIISR----RETYGYEITRHLNDLGFTEVV------EGT-VYTILVRLEKKKLVNIEKKPSDMGPPRKF   75 (117)
T ss_dssp             HHHHHHHHHHHHHHHH----SCBCHHHHHHHHHHHTCTTCC------HHH-HHHHHHHHHHTTCEEEEEEC-----CEEE
T ss_pred             HHHChHHHHHHHHHHc----CCCCHHHHHHHHHHcCCCCCC------ccH-HHHHHHHHHHCCCEEEEeecCCCCCCceE
Confidence            3444455556667776    689999999987      565      456 99999999999999864321   11  24


Q ss_pred             eecCccccc
Q 041256           98 YSLAPVSAY  106 (244)
Q Consensus        98 y~~t~~s~~  106 (244)
                      |++|+.++.
T Consensus        76 Y~LT~~G~~   84 (117)
T 4esf_A           76 YSLNEAGRQ   84 (117)
T ss_dssp             EEECHHHHH
T ss_pred             EEECHHHHH
Confidence            778777653

>1okr_A MECI, methicillin resistance regulatory protein MECI; bacterial antibiotic resistance, MECI protein, transcriptional regulatory element; 2.4A {Staphylococcus aureus} SCOP: a.4.5.39 PDB: 1sax_A 1sd7_A 2d45_A 1sd6_A

Probab=86.33  E-value=0.21  Score=35.76  Aligned_cols=45  Identities=16%  Similarity=0.194  Sum_probs=35.7

Q ss_pred             cChhhHHhhcCCCCCCCHHHHHHhCC----CCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           36 LDVFEIISKAGPGAKLSVAEIVAQIP----LKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        36 lgifd~L~~~~~~g~~t~~eLA~~~~----~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      ..|...|...   ++.|..+||+.++    ++      ... +.++|+-|...|++.+.
T Consensus        13 ~~vL~~l~~~---~~~t~~ela~~l~~~~~~s------~~t-v~~~l~~L~~~Glv~r~   61 (123)
T 1okr_A           13 WEVMNIIWMK---KYASANNIIEEIQMQKDWS------PKT-IRTLITRLYKKGFIDRK   61 (123)
T ss_dssp             HHHHHHHHHH---SSEEHHHHHHHHHHHCCCC------HHH-HHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHhC---CCcCHHHHHHHHhccCCCc------Hhh-HHHHHHHHHHCCCeEEE
Confidence            3455566554   6899999999998    54      345 99999999999999964

>3k2z_A LEXA repressor; winged helix-turn-helix, SOS system, autoca cleavage, DNA damage, DNA repair, DNA replication, DNA-BIND hydrolase; 1.37A {Thermotoga maritima}

Probab=86.29  E-value=0.6  Score=36.62  Aligned_cols=41  Identities=24%  Similarity=0.135  Sum_probs=33.7

Q ss_pred             hHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           40 EIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        40 d~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      +.+.+.|  .|.|..|||+.+|++      ... +.+.|+.|...|++..
T Consensus        16 ~~~~~~g--~~~s~~eia~~lgl~------~~t-v~~~l~~Le~~G~i~~   56 (196)
T 3k2z_A           16 EFIEKNG--YPPSVREIARRFRIT------PRG-ALLHLIALEKKGYIER   56 (196)
T ss_dssp             HHHHHHS--SCCCHHHHHHHHTSC------HHH-HHHHHHHHHHTTSEEC
T ss_pred             HHHHHhC--CCCCHHHHHHHcCCC------cHH-HHHHHHHHHHCCCEEe
Confidence            3444543  489999999999997      345 9999999999999995

>3v97_A Ribosomal RNA large subunit methyltransferase L; YCBY, RNA methyltransferase, ribosome RNA, SAH, RLML; HET: SAH OSU; 2.20A {Escherichia coli} PDB: 3v8v_A*

Probab=86.27  E-value=0.4  Score=45.45  Aligned_cols=40  Identities=10%  Similarity=-0.114  Sum_probs=33.1

Q ss_pred             cceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+|||+|||+|.++..+++... -+++.+|+ |..++.+++
T Consensus       540 g~~VLDlg~GtG~~sl~aa~~ga-~~V~aVD~s~~al~~a~~  580 (703)
T 3v97_A          540 GKDFLNLFSYTGSATVHAGLGGA-RSTTTVDMSRTYLEWAER  580 (703)
T ss_dssp             TCEEEEESCTTCHHHHHHHHTTC-SEEEEEESCHHHHHHHHH
T ss_pred             CCcEEEeeechhHHHHHHHHCCC-CEEEEEeCCHHHHHHHHH
Confidence            47999999999999999988543 36899998 788887764

>1v4r_A Transcriptional repressor; helix-turn-helix, winged-helix, gene regulation; NMR {Streptomyces} SCOP: a.4.5.6

Probab=85.81  E-value=0.45  Score=33.10  Aligned_cols=34  Identities=35%  Similarity=0.382  Sum_probs=29.4

Q ss_pred             CCC-CHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           49 AKL-SVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        49 g~~-t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      ..+ |..+||+.+|++      ..- +++-|+.|...|++..
T Consensus        33 ~~lps~~eLa~~~~vS------r~t-vr~al~~L~~~Gli~~   67 (102)
T 1v4r_A           33 DTLPSVADIRAQFGVA------AKT-VSRALAVLKSEGLVSS   67 (102)
T ss_dssp             SBCCCHHHHHHHSSSC------TTH-HHHHTTTTTTSSCCEE
T ss_pred             CCCcCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEE
Confidence            355 999999999997      344 9999999999999985

>1p4x_A Staphylococcal accessory regulator A homologue; winged-helix protein, transcription; 2.20A {Staphylococcus aureus} SCOP: a.4.5.28 a.4.5.28

Probab=85.81  E-value=0.42  Score=39.30  Aligned_cols=64  Identities=16%  Similarity=0.143  Sum_probs=44.9

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCccccc
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSAY  106 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~~  106 (244)
                      +..|...|...+. +++|..|||+.++++      +.. +.++++-|...|++.+.+...+.   ...+|+.+..
T Consensus       160 q~~vL~~L~~~~~-~~~t~~eLa~~l~i~------~~t-vt~~v~rLe~~GlV~R~~~~~DrR~~~i~LT~~G~~  226 (250)
T 1p4x_A          160 EFTILAIITSQNK-NIVLLKDLIETIHHK------YPQ-TVRALNNLKKQGYLIKERSTEDERKILIHMDDAQQD  226 (250)
T ss_dssp             HHHHHHHHHTTTT-CCEEHHHHHHHSSSC------HHH-HHHHHHHHHHHTSSEEEECSSSTTCEEEECCHHHHH
T ss_pred             HHHHHHHHHhCCC-CCcCHHHHHHHHCCC------hhh-HHHHHHHHHHCCCEEeeCCCCCCCeEEEEECHHHHH
Confidence            3446677766531 259999999999997      456 99999999999999974322233   2455555543

>2ar0_A M.ecoki, type I restriction enzyme ecoki M protein; structural genomics, protein structure initiative, nysgxrc; 2.80A {Escherichia coli} SCOP: c.66.1.45 PDB: 2y7c_B 2y7h_B*

Probab=85.63  E-value=0.32  Score=44.61  Aligned_cols=49  Identities=18%  Similarity=0.034  Sum_probs=34.7

Q ss_pred             HHhhcCCCCCcceEEEecCCccHHHHHHHHHCC------------------CCeEEEccc-hHHhhhCC
Q 041256          184 VLESYKGFEHVKKLVDVGGGLGITLNMIISKYP------------------HIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       184 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P------------------~l~~~v~Dl-p~vi~~a~  233 (244)
                      +++... .....+|+|.+||+|.++..+.+...                  ..+...+|+ |..+..|+
T Consensus       161 mv~~l~-p~~~~~VlDPaCGSG~fLi~a~~~l~~~~~~~~~~~~~~~~~~~~~~i~GiEid~~~~~lA~  228 (541)
T 2ar0_A          161 IIHLLK-PQPREVVQDPAAGTAGFLIEADRYVKSQTNDLDDLDGDTQDFQIHRAFIGLELVPGTRRLAL  228 (541)
T ss_dssp             HHHHHC-CCTTCCEEETTCTTTHHHHHHHHHHHTTTTTTTTSCHHHHHHHHHTSEEEEESCHHHHHHHH
T ss_pred             HHHHhc-cCCCCeEecCCcccchHHHHHHHHHHHhhcccccCCHHHHhhhhcceEEEEcCCHHHHHHHH
Confidence            344444 34457999999999999998876532                  236788888 77776664

>3mwm_A ZUR, putative metal uptake regulation protein; FUR, regulatory metal, graded transcription regulation, transcription; 2.40A {Streptomyces coelicolor}

Probab=85.62  E-value=0.97  Score=33.47  Aligned_cols=64  Identities=14%  Similarity=0.123  Sum_probs=42.7

Q ss_pred             HHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCc-chhccHHHHHHHHhhCCcccceeec-CCceeecC
Q 041256           33 VVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPE-AAAMTLDRVLRLLVSYNALHCSFVD-GQRLYSLA  101 (244)
Q Consensus        33 a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~-~~~~~l~rlLr~L~~~gll~~~~~~-~~~~y~~t  101 (244)
                      .-+.-|++.|.+.+  ++.|++||.+.+.-.  .|. ...- ++|.|+.|+..|++.+..-. +..+|..+
T Consensus        14 ~qR~~Il~~L~~~~--~h~sa~eI~~~l~~~--~~~is~aT-VYR~L~~L~e~Glv~~~~~~~g~~~Y~~~   79 (139)
T 3mwm_A           14 RQRAAVSAALQEVE--EFRSAQELHDMLKHK--GDAVGLTT-VYRTLQSLADAGEVDVLRTAEGESVYRRC   79 (139)
T ss_dssp             HHHHHHHHHHTTCS--SCEEHHHHHHHHHHT--TCCCCHHH-HHHHHHHHHHTTSSEEEECTTSCEEEECC
T ss_pred             HHHHHHHHHHHhCC--CCCCHHHHHHHHHHh--CCCCCHHH-HHHHHHHHHHCCCEEEEEcCCCceEEEEC
Confidence            34566888888764  689999999988421  111 0233 99999999999999864211 12356653

>1j5y_A Transcriptional regulator, biotin repressor famil; structural genomics, TM1602, BIOT repressor family, JCSG, conserved hypothetical protein; 2.30A {Thermotoga maritima} SCOP: a.4.5.1 d.94.2.1

Probab=85.33  E-value=0.77  Score=35.76  Aligned_cols=58  Identities=16%  Similarity=0.200  Sum_probs=44.4

Q ss_pred             HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCc-ccceeecCCceeecCccc
Q 041256           34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNA-LHCSFVDGQRLYSLAPVS  104 (244)
Q Consensus        34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gl-l~~~~~~~~~~y~~t~~s  104 (244)
                      -...|.+.|.+.+  +++|..|||+.+|++      ..- ++|-++.|...|+ +..   . .+.|.+.+..
T Consensus        22 R~~~Il~~L~~~~--~~~s~~eLa~~l~vS------~~T-i~rdi~~L~~~G~~I~~---~-~~Gy~l~~~~   80 (187)
T 1j5y_A           22 RLKSIVRILERSK--EPVSGAQLAEELSVS------RQV-IVQDIAYLRSLGYNIVA---T-PRGYVLAGGK   80 (187)
T ss_dssp             HHHHHHHHHHHCS--SCBCHHHHHHHHTSC------HHH-HHHHHHHHHHHTCCCEE---E-TTEEECCTTT
T ss_pred             HHHHHHHHHHHcC--CCcCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCeEEE---E-CCEEEECCcc
Confidence            4556788887643  579999999999997      455 9999999999999 653   2 3568777654

>2g9w_A Conserved hypothetical protein; DNA-binding domain, bacterial transcription repressor, DNA B protein; 1.80A {Mycobacterium tuberculosis} SCOP: a.4.5.39

Probab=84.92  E-value=0.73  Score=33.89  Aligned_cols=46  Identities=17%  Similarity=0.153  Sum_probs=36.4

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCC----CCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIP----LKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~----~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      +..|...|.+..  +++|..||++.++    ++      ..- +.++|+-|...|++.+
T Consensus        11 e~~vL~~L~~~~--~~~t~~el~~~l~~~~~~~------~~T-vt~~l~rLe~kGlv~r   60 (138)
T 2g9w_A           11 ERAVMDHLWSRT--EPQTVRQVHEALSARRDLA------YTT-VMAVLQRLAKKNLVLQ   60 (138)
T ss_dssp             HHHHHHHHHTCS--SCEEHHHHHHHHTTTCCCC------HHH-HHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHhcC--CCCCHHHHHHHHhccCCCC------HHH-HHHHHHHHHHCCCEEE
Confidence            455666776521  5899999999997    44      345 9999999999999996

>2xig_A Ferric uptake regulation protein; hpfur, transcription, homeostasis; HET: CIT; 1.85A {Helicobacter pylori}

Probab=84.84  E-value=0.97  Score=33.95  Aligned_cols=50  Identities=22%  Similarity=0.297  Sum_probs=39.7

Q ss_pred             HHHhcChhhHHhhcCCCCCCCHHHHHHhC-----CCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           32 AVVELDVFEIISKAGPGAKLSVAEIVAQI-----PLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        32 ~a~~lgifd~L~~~~~~g~~t~~eLA~~~-----~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      +--+.-|++.|.+.+  ++.|++||.+.+     +++      ..- ++|.|+.|+..|++.+.
T Consensus        26 T~qR~~IL~~l~~~~--~~~sa~ei~~~l~~~~~~is------~aT-VYR~L~~L~e~Glv~~~   80 (150)
T 2xig_A           26 SKQREEVVSVLYRSG--THLSPEEITHSIRQKDKNTS------ISS-VYRILNFLEKENFISVL   80 (150)
T ss_dssp             HHHHHHHHHHHHHCS--SCBCHHHHHHHHHHHSTTCC------HHH-HHHHHHHHHHTTSEEEE
T ss_pred             CHHHHHHHHHHHhCC--CCCCHHHHHHHHHHhCCCCC------Hhh-HHHHHHHHHHCCcEEEE
Confidence            445566889998764  689999999998     453      334 99999999999999864

>3cta_A Riboflavin kinase; structural genomics, transferase, PSI-2, protein structure initiative; 2.20A {Thermoplasma acidophilum dsm 1728} SCOP: a.4.5.28 b.43.5.2

Probab=84.74  E-value=0.52  Score=37.94  Aligned_cols=54  Identities=7%  Similarity=0.106  Sum_probs=41.8

Q ss_pred             CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCcccccccc
Q 041256           49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFVR  109 (244)
Q Consensus        49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l~~  109 (244)
                      ++.|..++|+.++++      ... +.|.++.|...|+|.+........+.+|+.++.+..
T Consensus        26 ~~~s~s~aA~~L~is------q~a-vSr~I~~LE~~~L~~R~~~~R~~~v~LT~~G~~l~~   79 (230)
T 3cta_A           26 AYLTSSKLADMLGIS------QQS-ASRIIIDLEKNGYITRTVTKRGQILNITEKGLDVLY   79 (230)
T ss_dssp             EECCHHHHHHHHTSC------HHH-HHHHHHHHHHTTSEEEEEETTEEEEEECHHHHHHHH
T ss_pred             CCcCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEEEEcCCeEEEEECHHHHHHHH
Confidence            468999999999997      456 999999999999999632111356888888875553

>1z6r_A MLC protein; transcriptional repressor, ROK family protein, DNA binding P helix-turn-helix, phosphotransferase system; 2.70A {Escherichia coli} SCOP: a.4.5.63 c.55.1.10 c.55.1.10 PDB: 3bp8_A

Probab=84.60  E-value=0.87  Score=39.80  Aligned_cols=50  Identities=10%  Similarity=0.212  Sum_probs=40.9

Q ss_pred             HHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           30 MQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        30 L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      ++..-+..|++.|.+.   +++|..|||+.+|++      ..- +.++++.|...|++.+
T Consensus        13 ~r~~n~~~il~~l~~~---~~~sr~~la~~~~ls------~~t-v~~~v~~L~~~g~i~~   62 (406)
T 1z6r_A           13 IKQTNAGAVYRLIDQL---GPVSRIDLSRLAQLA------PAS-ITKIVHEMLEAHLVQE   62 (406)
T ss_dssp             HHHHHHHHHHHHHHSS---CSCCHHHHHHHTTCC------HHH-HHHHHHHHHHHTSEEE
T ss_pred             HHHhHHHHHHHHHHHc---CCcCHHHHHHHHCCC------HHH-HHHHHHHHHHCCcEEe
Confidence            3333445578888875   799999999999997      445 9999999999999985

>3axs_A Probable N(2),N(2)-dimethylguanosine tRNA methylt TRM1; structural genomics, riken structural genomics/proteomics in RSGI; HET: SFG; 2.16A {Aquifex aeolicus} PDB: 3axt_A*

Probab=84.46  E-value=0.54  Score=41.35  Aligned_cols=42  Identities=17%  Similarity=0.075  Sum_probs=35.9

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCC-CeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPH-IKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dl-p~vi~~a~~  234 (244)
                      +..+|+|+++|+|.+++.++++.++ -+++..|+ |..++.+++
T Consensus        52 ~g~~VLDlfaGtG~~sl~aa~~~~ga~~V~avDi~~~av~~~~~   95 (392)
T 3axs_A           52 RPVKVADPLSASGIRAIRFLLETSCVEKAYANDISSKAIEIMKE   95 (392)
T ss_dssp             SCEEEEESSCTTSHHHHHHHHHCSCEEEEEEECSCHHHHHHHHH
T ss_pred             CCCEEEECCCcccHHHHHHHHhCCCCCEEEEEECCHHHHHHHHH
Confidence            3478999999999999999998776 46788998 888888765

>1jhg_A Trp operon repressor; complex (regulatory protein-peptide), DNA-binding regulatory complex (regulatory protein-peptide) complex; HET: TRP; 1.30A {Escherichia coli} SCOP: a.4.12.1 PDB: 1co0_A* 1mi7_R 1p6z_R 1wrp_R* 1zt9_A* 2oz9_R* 3ssw_R 3wrp_A 1rcs_A* 1wrs_R* 1wrt_R 2xdi_A 3ssx_R* 1trr_A* 1tro_A*

Probab=84.22  E-value=0.94  Score=31.86  Aligned_cols=41  Identities=15%  Similarity=0.165  Sum_probs=33.0

Q ss_pred             HHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhh
Q 041256           32 AVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVS   83 (244)
Q Consensus        32 ~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~   83 (244)
                      .+.++||+..|..    |..|..|||+.+|++      ... +.|+=|.|-.
T Consensus        44 l~~R~~l~~~L~~----ge~TQREIA~~lGiS------~st-ISRi~r~L~~   84 (101)
T 1jhg_A           44 LGTRVRIIEELLR----GEMSQRELKNELGAG------IAT-ITRGSNSLKA   84 (101)
T ss_dssp             HHHHHHHHHHHHH----CCSCHHHHHHHHCCC------HHH-HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHc----CCcCHHHHHHHHCCC------hhh-hhHHHHHHHH
Confidence            3457899999987    689999999999997      456 8888776643

>2xvc_A ESCRT-III, SSO0910; cell cycle, cell division, cytokinesis, winged-helix; 2.15A {Sulfolobus solfataricus}

Probab=84.07  E-value=0.94  Score=28.20  Aligned_cols=46  Identities=13%  Similarity=0.221  Sum_probs=38.6

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      +-.|.+.+..+|  |-+.+...|++.|++      .+. +..+||-|..-|++..
T Consensus        12 e~~lL~yIr~sG--GildI~~~a~kygV~------kde-V~~~LrrLe~KGLI~l   57 (59)
T 2xvc_A           12 ERELLDYIVNNG--GFLDIEHFSKVYGVE------KQE-VVKLLEALKNKGLIAV   57 (59)
T ss_dssp             HHHHHHHHHHTT--SEEEHHHHHHHHCCC------HHH-HHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHcC--CEEeHHHHHHHhCCC------HHH-HHHHHHHHHHCCCeec
Confidence            345778888876  789999999999997      456 8999999999999873

>3s1s_A Restriction endonuclease bpusi; PD--(D/E)XK catalytic motif, gamma-N6M-adenosine methyltrans S-adenosyl-methionine binding, hydrolase; HET: SAH; 2.35A {Bacillus pumilus}

Probab=84.02  E-value=0.64  Score=44.71  Aligned_cols=42  Identities=12%  Similarity=0.153  Sum_probs=34.3

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCCC---CeEEEccc-hHHhhhC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYPH---IKGINYDL-PYVIKDA  232 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~---l~~~v~Dl-p~vi~~a  232 (244)
                      +....+|+|.|||+|.++.+++++.+.   .+...+|+ |..++.|
T Consensus       319 l~~g~rVLDPaCGSG~FLIaaA~~l~ei~~~~IyGvEIDp~Al~LA  364 (878)
T 3s1s_A          319 LTEDEVISDPAAGSGNLLATVSAGFNNVMPRQIWANDIETLFLELL  364 (878)
T ss_dssp             CCTTCEEEETTCTTSHHHHHHHHTSTTCCGGGEEEECSCGGGHHHH
T ss_pred             CCCCCEEEECCCCccHHHHHHHHHhcccCCCeEEEEECCHHHHHHH
Confidence            345679999999999999999998873   56889998 6666665

>3l7w_A Putative uncharacterized protein SMU.1704; PADR, transcriptional factor, transcription; HET: MSE; 2.20A {Streptococcus mutans} SCOP: a.4.5.0

Probab=84.01  E-value=0.85  Score=32.15  Aligned_cols=63  Identities=22%  Similarity=0.237  Sum_probs=43.0

Q ss_pred             HHhcChhhHHhhcCCCCCCCHHHHHHhC----CCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc----eeecCccc
Q 041256           33 VVELDVFEIISKAGPGAKLSVAEIVAQI----PLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR----LYSLAPVS  104 (244)
Q Consensus        33 a~~lgifd~L~~~~~~g~~t~~eLA~~~----~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~----~y~~t~~s  104 (244)
                      ..++-|...|.+    +|.+--+|++.+    +++      +.. +.+.|+-|...|+++......++    .|++|+.+
T Consensus         9 ~l~~~IL~~L~~----~~~~gyel~~~l~~~~~i~------~~t-ly~~L~~Le~~GlI~~~~~~~~~r~r~~y~LT~~G   77 (108)
T 3l7w_A            9 LIEYLILAIVSK----HDSYGYDISQTIKLIASIK------EST-LYPILKKLEKAGYLSTYTQEHQGRRRKYYHLTDSG   77 (108)
T ss_dssp             HHHHHHHHHHHH----SCEEHHHHHHHHTTTCCCC------HHH-HHHHHHHHHHTTSEEEEEEEETTEEEEEEEECHHH
T ss_pred             HHHHHHHHHHHc----CCCcHHHHHHHHHHHhCCC------cCh-HHHHHHHHHHCCCeEEEeecCCCCcceEEEECHHH
Confidence            345556667776    578877777774    675      456 99999999999999864321122    37777766


Q ss_pred             cc
Q 041256          105 AY  106 (244)
Q Consensus       105 ~~  106 (244)
                      +.
T Consensus        78 ~~   79 (108)
T 3l7w_A           78 EK   79 (108)
T ss_dssp             HH
T ss_pred             HH
Confidence            53

>1sd4_A Penicillinase repressor; BLAI, MECI, methicillin, B-lactam, DNA binding PR; 2.00A {Staphylococcus aureus} SCOP: a.4.5.39 PDB: 1xsd_A

Probab=83.84  E-value=0.56  Score=33.60  Aligned_cols=50  Identities=22%  Similarity=0.260  Sum_probs=36.9

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      +..|...|.+.   +|+|..|||+.++.+ .+. ++.- +.++|+-|...|++.+.
T Consensus        12 q~~vL~~L~~~---~~~t~~el~~~l~~~-~~~-~~~T-vt~~l~rLe~kGlv~R~   61 (126)
T 1sd4_A           12 EWDVMNIIWDK---KSVSANEIVVEIQKY-KEV-SDKT-IRTLITRLYKKEIIKRY   61 (126)
T ss_dssp             HHHHHHHHHHS---SSEEHHHHHHHHHTT-SCC-CHHH-HHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHhc---CCCCHHHHHHHHhhc-CCC-Chhh-HHHHHHHHHHCCceEEE
Confidence            44566677765   689999999999741 000 0345 99999999999999963

>3eld_A Methyltransferase; flavivirus, RNA capping, guanylyltransfer viral enzyme structure; HET: SFG; 1.90A {Wesselsbron virus} PDB: 3elu_A* 3elw_A* 3ely_A* 3emb_A* 3emd_A*

Probab=83.60  E-value=1.2  Score=37.64  Aligned_cols=42  Identities=17%  Similarity=0.132  Sum_probs=31.2

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL  225 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  225 (244)
                      .+.+. ..+....++||+||+.|.++.-++++.+-..++.+|+
T Consensus        72 ei~ek-~l~~~g~~vlDLGaaPGgWsqva~~~~gv~sV~Gvdl  113 (300)
T 3eld_A           72 WLHER-GYLRITGRVLDLGCGRGGWSYYAAAQKEVMSVKGYTL  113 (300)
T ss_dssp             HHHHH-TSCCCCEEEEEETCTTCHHHHHHHTSTTEEEEEEECC
T ss_pred             HHHHh-CCCCCCCEEEEcCCCCCHHHHHHHHhcCCceeeeEEe
Confidence            44444 4356779999999999999999998766545555565

>2obp_A Putative DNA-binding protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE; 1.70A {Ralstonia eutropha} SCOP: a.4.5.71

Probab=83.50  E-value=0.95  Score=31.50  Aligned_cols=49  Identities=24%  Similarity=0.220  Sum_probs=36.8

Q ss_pred             CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCce--eecCcccc
Q 041256           49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRL--YSLAPVSA  105 (244)
Q Consensus        49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~--y~~t~~s~  105 (244)
                      ++.+..+||+.++++      -.. |.|.|..|...|++..... .+++  ..+|+.++
T Consensus        35 ~~~s~~eLa~~l~l~------~st-LsR~l~rLe~~GLV~r~~~-~D~R~~v~LT~~G~   85 (96)
T 2obp_A           35 TPWSLPKIAKRAQLP------MSV-LRRVLTQLQAAGLADVSVE-ADGRGHASLTQEGA   85 (96)
T ss_dssp             CCCBHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEEEEC-TTSCEEEEECHHHH
T ss_pred             CCcCHHHHHHHhCCc------hhh-HHHHHHHHHHCCCEEeecC-CCCceeEEECHHHH
Confidence            679999999999996      345 9999999999999996432 2333  44454443

>2hoe_A N-acetylglucosamine kinase; TM1224, structural genomics, PSI-2, protein structure initiative, joint center structural genomics, JCSG; 2.46A {Thermotoga maritima} SCOP: a.4.5.63 c.55.1.10 c.55.1.10

Probab=83.48  E-value=0.61  Score=40.49  Aligned_cols=70  Identities=11%  Similarity=0.185  Sum_probs=46.7

Q ss_pred             HHHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecC------Ccee
Q 041256           25 VLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDG------QRLY   98 (244)
Q Consensus        25 ~~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~------~~~y   98 (244)
                      ..+++++..-+..|++.|. .   +++|..|||+.+|++      ..- +.++++.|...|++.+.....      +-.|
T Consensus        12 ~~~~~~~~~~~~~il~~l~-~---~~~sr~~la~~~gls------~~t-v~~~v~~L~~~gli~~~~~~~~~~GR~~~~l   80 (380)
T 2hoe_A           12 HMPKSVRAENISRILKRIM-K---SPVSRVELAEELGLT------KTT-VGEIAKIFLEKGIVVEEKDSPKGVGRPTKSL   80 (380)
T ss_dssp             ----------CCCSHHHHH-H---SCBCHHHHHHHHTCC------HHH-HHHHHHHHHHHTSEEEEECCC----CCCEEE
T ss_pred             cCchhHHHHHHHHHHHHHH-c---CCcCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEeecCCCCCCCCCceEE
Confidence            4567778888888999999 6   699999999999997      445 999999999999998532100      1236


Q ss_pred             ecCcccc
Q 041256           99 SLAPVSA  105 (244)
Q Consensus        99 ~~t~~s~  105 (244)
                      +.++-..
T Consensus        81 ~~~~~~~   87 (380)
T 2hoe_A           81 KISPNCA   87 (380)
T ss_dssp             EECGGGC
T ss_pred             EEccCCC
Confidence            7776654

>3f8b_A Transcriptional regulator, PADR-like family; winged helix turn helix, transcription regulator; 2.00A {Lactococcus lactis subsp} SCOP: a.4.5.0 PDB: 3f8c_A* 3f8f_A*

Probab=83.19  E-value=2  Score=30.65  Aligned_cols=68  Identities=18%  Similarity=0.305  Sum_probs=46.8

Q ss_pred             HHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhC--------CCCCCCCcchhccHHHHHHHHhhCCcccceeec-CC---
Q 041256           28 AVMQAVVELDVFEIISKAGPGAKLSVAEIVAQI--------PLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVD-GQ---   95 (244)
Q Consensus        28 ~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~--------~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~-~~---   95 (244)
                      +.++-..++=|...|.+    +|.+--+|.+.+        +++      +.. +.+.|+-|...|+++..... ..   
T Consensus         7 ~~~~g~l~~~IL~~L~~----~~~~Gyei~~~l~~~~~~~~~i~------~gt-ly~~L~rLe~~GlI~~~~~~~~~~~~   75 (116)
T 3f8b_A            7 EMLRAQTNVILLNVLKQ----GDNYVYGIIKQVKEASNGEMELN------EAT-LYTIFKRLEKDGIISSYWGDESQGGR   75 (116)
T ss_dssp             HHHHHHHHHHHHHHHHH----CCBCHHHHHHHHHHHTTTCCCCC------HHH-HHHHHHHHHHTTSEEEEEEC----CC
T ss_pred             HHHhchHHHHHHHHHHh----CCCCHHHHHHHHHHHhCCCCCCC------cch-HHHHHHHHHHCCCEEEEeeccCCCCC
Confidence            34444556666677776    689999998887        454      456 99999999999999864211 11   


Q ss_pred             -ceeecCccccc
Q 041256           96 -RLYSLAPVSAY  106 (244)
Q Consensus        96 -~~y~~t~~s~~  106 (244)
                       -.|++|+.++.
T Consensus        76 rk~Y~LT~~G~~   87 (116)
T 3f8b_A           76 RKYYRLTEIGHE   87 (116)
T ss_dssp             EEEEEECHHHHH
T ss_pred             ceEEEECHHHHH
Confidence             24778777653

>3hhh_A Transcriptional regulator, PADR family; PF03551, structural PSI-2, protein structure initiative, midwest center for STR genomics, MCSG; 2.70A {Enterococcus faecalis} SCOP: a.4.5.0

Probab=83.16  E-value=1.4  Score=31.57  Aligned_cols=68  Identities=15%  Similarity=0.169  Sum_probs=47.1

Q ss_pred             HHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhC------CCCCCCCcchhccHHHHHHHHhhCCcccceeecC-C----c
Q 041256           28 AVMQAVVELDVFEIISKAGPGAKLSVAEIVAQI------PLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDG-Q----R   96 (244)
Q Consensus        28 ~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~------~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~-~----~   96 (244)
                      +.++-..++=|...|.+    +|.+--+|++.+      +++      +.. +...|+-|...|+++...... .    -
T Consensus         8 ~l~~g~l~~~IL~lL~~----~p~~Gyei~~~l~~~g~~~is------~gt-lY~~L~rLe~~GlI~~~~~~~~~g~~rk   76 (116)
T 3hhh_A            8 ELLKGILEGLVLAIIQR----KETYGYEITKILNDQGFTEIV------EGT-VYTILLRLEKNQWVIAEKKPSEKGPMRK   76 (116)
T ss_dssp             HHHTTHHHHHHHHHHHH----SCBCHHHHHHHHHTTSCSSCC------HHH-HHHHHHHHHHTTSEEEEEEECC--CEEE
T ss_pred             HHHhhhHHHHHHHHHhc----CCCCHHHHHHHHHHcCCCCCC------ccH-HHHHHHHHHHCCCEEEEeeecCCCCCce
Confidence            34444455556677776    689999999987      454      456 999999999999998643211 1    1


Q ss_pred             eeecCccccc
Q 041256           97 LYSLAPVSAY  106 (244)
Q Consensus        97 ~y~~t~~s~~  106 (244)
                      .|++|+.++.
T Consensus        77 ~Y~lT~~G~~   86 (116)
T 3hhh_A           77 FYRLTSSGEA   86 (116)
T ss_dssp             EEEECHHHHH
T ss_pred             EEEECHHHHH
Confidence            4788877653

>3p8z_A Mtase, non-structural protein 5; methyltransferase, RNA, ER, transferase-transferase inhibito; HET: 36A SAH; 1.70A {Dengue virus 3} SCOP: c.66.1.25 PDB: 3p97_A* 2xbm_A* 3evg_A*

Probab=82.76  E-value=1.3  Score=36.33  Aligned_cols=44  Identities=14%  Similarity=0.059  Sum_probs=34.6

Q ss_pred             HHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc
Q 041256          181 MEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL  225 (244)
Q Consensus       181 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  225 (244)
                      ...+.+.+- +....+|||+||+.|.++.-.+....--++..+|+
T Consensus        67 L~ei~ek~~-l~~g~~VvDLGaapGGWSq~~a~~~g~~~V~avdv  110 (267)
T 3p8z_A           67 LQWFVERNM-VIPEGRVIDLGCGRGGWSYYCAGLKKVTEVRGYTK  110 (267)
T ss_dssp             HHHHHHTTS-SCCCEEEEEESCTTSHHHHHHHTSTTEEEEEEECC
T ss_pred             HHHHHHhcC-CCCCCEEEEcCCCCCcHHHHHHHhcCCCEEEEEec
Confidence            345666664 67678999999999999997777766557888887

>1hsj_A Fusion protein consisting of staphylococcus accessary regulator protein R and maltose...; novel fold for DNA binding; HET: GLC; 2.30A {Escherichia coli} SCOP: a.4.5.28 c.94.1.1

Probab=82.73  E-value=0.76  Score=40.98  Aligned_cols=47  Identities=19%  Similarity=0.236  Sum_probs=37.7

Q ss_pred             cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      ..|...|.+.+ ++++|..|||+.++++      ... +.|+++-|...|++++.
T Consensus       407 ~~vl~~l~~~~-~~~~~~~~l~~~~~~~------~~~-~t~~~~~le~~g~v~r~  453 (487)
T 1hsj_A          407 IYILNHILRSE-SNEISSKEIAKCSEFK------PYY-LTKALQKLKDLKLLSKK  453 (487)
T ss_dssp             HHHHHHHHTCS-CSEEEHHHHHHSSCCC------HHH-HHHHHHHHHTTTTSCCE
T ss_pred             HHHHHHHHhCC-CCCcCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEeec
Confidence            34666676641 1589999999999997      456 99999999999999974

>2py6_A Methyltransferase FKBM; YP_546752.1, structural genomics, JO center for structural genomics, JCSG, protein structure INI PSI-2; 2.15A {Methylobacillus flagellatus KT} SCOP: c.66.1.56

Probab=82.09  E-value=1.9  Score=37.96  Aligned_cols=42  Identities=17%  Similarity=0.201  Sum_probs=33.7

Q ss_pred             CCcceEEEecCCccHHHHHHH-HHCCC-CeEEEccc-hHHhhhCC
Q 041256          192 EHVKKLVDVGGGLGITLNMII-SKYPH-IKGINYDL-PYVIKDAP  233 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~-~~~P~-l~~~v~Dl-p~vi~~a~  233 (244)
                      .+..+++|||++.|.++..++ +..|. .+++.++- |...+..+
T Consensus       225 ~~~~~viDvGAn~G~~s~~~a~~~~~~~~~V~afEP~p~~~~~L~  269 (409)
T 2py6_A          225 SDSEKMVDCGASIGESLAGLIGVTKGKFERVWMIEPDRINLQTLQ  269 (409)
T ss_dssp             CSSCEEEEETCTTSHHHHHHHHHHTSCCSEEEEECCCHHHHHHHH
T ss_pred             CCCCEEEECCCCcCHHHHHHHHHhcCCCCEEEEEcCCHHHHHHHH
Confidence            456899999999999999988 67776 78999985 66655543

>1m6e_X S-adenosyl-L-methionnine:salicylic acid carboxyl methyltransferase; rossmann fold, protein-small molecule complex; HET: SAH SAL; 3.00A {Clarkia breweri} SCOP: c.66.1.35

Probab=82.07  E-value=0.48  Score=41.17  Aligned_cols=35  Identities=20%  Similarity=0.283  Sum_probs=25.6

Q ss_pred             CCcceEEEecCCccHHHHHHHHH----------------CCCCeEEEccch
Q 041256          192 EHVKKLVDVGGGLGITLNMIISK----------------YPHIKGINYDLP  226 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~----------------~P~l~~~v~Dlp  226 (244)
                      ++.-+|+|+||++|..+..++..                .|.++++.-|||
T Consensus        50 ~~~~~IaDlGCs~G~Nt~~~v~~ii~~i~~~~~~~~~~~~pe~~v~~nDLp  100 (359)
T 1m6e_X           50 TTRLAIADLGCSSGPNALFAVTELIKTVEELRKKMGRENSPEYQIFLNDLP  100 (359)
T ss_dssp             SSEECCEEESCCSSTTTTTGGGTTHHHHHHHHHSSSCSSCCEEEEEEEECT
T ss_pred             CCceEEEecCCCCCcchHHHHHHHHHHHHHHHHhcCCCCCCceEEEecCCC
Confidence            45688999999999754433322                577788888998

>1mzb_A Ferric uptake regulation protein; ferric uptake regulator, iron, DTXR, gene regulation; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.42

Probab=81.35  E-value=1.7  Score=31.85  Aligned_cols=48  Identities=13%  Similarity=0.234  Sum_probs=36.6

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhC-----CCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQI-----PLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~-----~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      +.-|++.|.+.+ +++.|++||.+.+     +++      ..- ++|.|+.|+..|++.+.
T Consensus        20 R~~Il~~L~~~~-~~~~sa~ei~~~l~~~~~~is------~aT-VYR~L~~L~e~Glv~~~   72 (136)
T 1mzb_A           20 RVKILQMLDSAE-QRHMSAEDVYKALMEAGEDVG------LAT-VYRVLTQFEAAGLVVRH   72 (136)
T ss_dssp             HHHHHHHHHCC--CCSBCHHHHHHHHHHTTCCCC------HHH-HHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHHhCC-CCCCCHHHHHHHHHhhCCCCC------HHH-HHHHHHHHHHCCcEEEE
Confidence            445788887642 1489999999998     443      334 99999999999999853

>1yg2_A Gene activator APHA; virulence factor, winged helix, transcripti factor, transcription; 2.20A {Vibrio cholerae} SCOP: a.4.5.61

Probab=80.96  E-value=1.2  Score=34.30  Aligned_cols=60  Identities=12%  Similarity=0.216  Sum_probs=44.2

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhC--------CCCCCCCcchhccHHHHHHHHhhCCcccceeecC-----CceeecC
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQI--------PLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDG-----QRLYSLA  101 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~--------~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~-----~~~y~~t  101 (244)
                      ++-|...|.+    +|.+.-||++.+        +++      +.. +++.|+-|...|+++......     .-.|++|
T Consensus         4 ~~~iL~lL~~----~~~~gyel~~~l~~~~~~~~~~s------~~~-ly~~L~~Le~~GlI~~~~~~~~~~~~r~~Y~lT   72 (179)
T 1yg2_A            4 PHVILTVLST----RDATGYDITKEFSASIGYFWKAS------HQQ-VYRELNKMGEQGLVTCVLEPQEGKPDRKVYSIT   72 (179)
T ss_dssp             HHHHHHHHHH----CCBCHHHHHHHHTTGGGGTCCCC------HHH-HHHHHHHHHHTTSEEECCC---------CEEEC
T ss_pred             HHHHHHHHhc----CCCCHHHHHHHHHHHhCCccCCC------cCc-HHHHHHHHHHCCCeEEEeecCCCCCCceEEEeC
Confidence            4456677776    699999999998        354      456 999999999999998532111     1259999


Q ss_pred             cccc
Q 041256          102 PVSA  105 (244)
Q Consensus       102 ~~s~  105 (244)
                      +.++
T Consensus        73 ~~G~   76 (179)
T 1yg2_A           73 QAGR   76 (179)
T ss_dssp             HHHH
T ss_pred             hHHH
Confidence            9986

>2ek5_A Predicted transcriptional regulators; helix-turn-helix, interwined alpha helices; 2.20A {Corynebacterium glutamicum atcc 13032} PDB: 2du9_A

Probab=80.54  E-value=2.3  Score=30.98  Aligned_cols=41  Identities=24%  Similarity=0.262  Sum_probs=32.3

Q ss_pred             CCC-CHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCcee
Q 041256           49 AKL-SVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLY   98 (244)
Q Consensus        49 g~~-t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y   98 (244)
                      ..+ |..+||+.+|++      ..- +++-|+.|...|++..  ..+.|.|
T Consensus        26 ~~LPse~~La~~~gvS------r~t-Vr~Al~~L~~~Gli~~--~~g~G~~   67 (129)
T 2ek5_A           26 QRVPSTNELAAFHRIN------PAT-ARNGLTLLVEAGILYK--KRGIGMF   67 (129)
T ss_dssp             SCBCCHHHHHHHTTCC------HHH-HHHHHHHHHTTTSEEE--ETTTEEE
T ss_pred             CcCcCHHHHHHHHCcC------HHH-HHHHHHHHHHCCcEEE--ecCCEEE
Confidence            356 899999999997      344 9999999999999985  3344544

>1fx7_A Iron-dependent repressor IDER; DTXR, iron-dependent regulator, signaling protein; 2.00A {Mycobacterium tuberculosis} SCOP: a.4.5.24 a.76.1.1 b.34.1.2 PDB: 1u8r_A

Probab=80.33  E-value=0.83  Score=36.78  Aligned_cols=47  Identities=13%  Similarity=0.160  Sum_probs=38.3

Q ss_pred             CHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccccccc
Q 041256           52 SVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFV  108 (244)
Q Consensus        52 t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l~  108 (244)
                      +..+||+.++++      ... +.++|+-|...|++++   ..+..+.+|+.++.+.
T Consensus        26 ~~~~La~~l~vs------~~t-vs~~l~~Le~~GlV~r---~~~~~v~LT~~G~~~~   72 (230)
T 1fx7_A           26 LRARIAERLDQS------GPT-VSQTVSRMERDGLLRV---AGDRHLELTEKGRALA   72 (230)
T ss_dssp             CHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEE---CTTSCEEECHHHHHHH
T ss_pred             cHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEE---eCCccEEECHHHHHHH
Confidence            449999999997      456 9999999999999996   2246788999887554

---

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	244
d1fp2a2	244	c.66.1.12 (A:109-352) Isoflavone O-methyltransfera	3e-36
d1kyza2	243	c.66.1.12 (A:120-362) Caffeic acid/5-hydroxyferuli	5e-36
d1fp1d2	244	c.66.1.12 (D:129-372) Chalcone O-methyltransferase	2e-35
d1fp1d1	110	a.4.5.29 (D:19-128) Chalcone O-methyltransferase {	9e-33
d1kyza1	107	a.4.5.29 (A:13-119) Caffeic acid/5-hydroxyferulic	2e-30
d1qzza2	256	c.66.1.12 (A:102-357) Aclacinomycin-10-hydroxylase	6e-22
d1tw3a2	253	c.66.1.12 (A:99-351) Carminomycin 4-O-methyltransf	8e-20
d1fp2a1	101	a.4.5.29 (A:8-108) Isoflavone O-methyltransferase	4e-13
d1tw3a1	85	a.4.5.29 (A:14-98) Carminomycin 4-O-methyltransfer	5e-08
d1qzza1	92	a.4.5.29 (A:10-101) Aclacinomycin-10-hydroxylase R	3e-06

>d1fp2a2 c.66.1.12 (A:109-352) Isoflavone O-methyltransferase {Alfalfa (Medicago sativa) [TaxId: 3879]} Length = 244

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Plant O-methyltransferase, C-terminal domain
domain: Isoflavone O-methyltransferase
species: Alfalfa (Medicago sativa) [TaxId: 3879]

 Score =  126 bits (317), Expect = 3e-36
 Identities = 33/127 (25%), Positives = 61/127 (48%), Gaps = 1/127 (0%)

Query: 116 SLSPYMALCLDKVCLDGWFGLKKQLLEGGI-AFNKAHGMQIYDYLGVDSRFNDVFNNGML 174
            L+P +   LD      +  LKK + E  +  F    G   +D+L  +  +N  FN+ M 
Sbjct: 2   CLAPMVECVLDPTLSGSYHELKKWIYEEDLTLFGVTLGSGFWDFLDKNPEYNTSFNDAMA 61

Query: 175 SHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPS 234
           S + ++   + +    F+ ++ +VDVGGG G T  +I   +P +K I +D P V+++   
Sbjct: 62  SDSKLINLALRDCDFVFDGLESIVDVGGGTGTTAKIICETFPKLKCIVFDRPQVVENLSG 121

Query: 235 YPGTLFI 241
                ++
Sbjct: 122 SNNLTYV 128

>d1kyza2 c.66.1.12 (A:120-362) Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase {Alfalfa (Medicago sativa) [TaxId: 3879]} Length = 243

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Plant O-methyltransferase, C-terminal domain
domain: Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase
species: Alfalfa (Medicago sativa) [TaxId: 3879]

 Score =  126 bits (316), Expect = 5e-36
 Identities = 72/129 (55%), Positives = 95/129 (73%)

Query: 113 NGASLSPYMALCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNG 172
           +G S+S    +  DKV ++ W+ LK  +L+GGI FNKA+GM  ++Y G D RFN VFN G
Sbjct: 1   DGVSISALNLMNQDKVLMESWYHLKDAVLDGGIPFNKAYGMTAFEYHGTDPRFNKVFNKG 60

Query: 173 MLSHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDA 232
           M  H++I M+K+LE+Y GFE +K LVDVGGG G  +N I+SKYP IKGIN+DLP+VI+DA
Sbjct: 61  MSDHSTITMKKILETYTGFEGLKSLVDVGGGTGAVINTIVSKYPTIKGINFDLPHVIEDA 120

Query: 233 PSYPGTLFI 241
           PSYPG   +
Sbjct: 121 PSYPGVEHV 129

>d1fp1d2 c.66.1.12 (D:129-372) Chalcone O-methyltransferase {Alfalfa (Medicago sativa) [TaxId: 3879]} Length = 244

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Plant O-methyltransferase, C-terminal domain
domain: Chalcone O-methyltransferase
species: Alfalfa (Medicago sativa) [TaxId: 3879]

 Score =  124 bits (312), Expect = 2e-35
 Identities = 50/127 (39%), Positives = 73/127 (57%), Gaps = 1/127 (0%)

Query: 116 SLSPYMALCLDKVCLDGWFGLKKQLLEGGI-AFNKAHGMQIYDYLGVDSRFNDVFNNGML 174
            L+ +         L  W   K+ +++  I  F   HG+  Y+++G D + N +FN  M+
Sbjct: 3   YLASFTTFLCYPALLQVWMNFKEAVVDEDIDLFKNVHGVTKYEFMGKDKKMNQIFNKSMV 62

Query: 175 SHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPS 234
              +  M+++LE Y GFE +  LVDVGGG G  L +IISKYP IKGIN+DLP VI++AP 
Sbjct: 63  DVCATEMKRMLEIYTGFEGISTLVDVGGGSGRNLELIISKYPLIKGINFDLPQVIENAPP 122

Query: 235 YPGTLFI 241
             G   +
Sbjct: 123 LSGIEHV 129

>d1fp1d1 a.4.5.29 (D:19-128) Chalcone O-methyltransferase {Alfalfa (Medicago sativa) [TaxId: 3879]} Length = 110

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Plant O-methyltransferase, N-terminal domain
domain: Chalcone O-methyltransferase
species: Alfalfa (Medicago sativa) [TaxId: 3879]

 Score =  113 bits (284), Expect = 9e-33
 Identities = 39/110 (35%), Positives = 63/110 (57%), Gaps = 7/110 (6%)

Query: 8   EEETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAG-PGAKLSVAEIVAQIPLKDNN 66
           + E +    AM L + +V PAV+ A ++L++FEII+KA  PGA +S +EI +++P    +
Sbjct: 1   QTEDSACLSAMVLTTNLVYPAVLNAAIDLNLFEIIAKATPPGAFMSPSEIASKLPASTQH 60

Query: 67  PEAAAMTLDRVLRLLVSYNALHCSFVDG-----QRLYSLAPVSAYFVRNN 111
            +     LDR+LRLL SY+ L  +         +R+Y L+ V  Y V + 
Sbjct: 61  SDLPNR-LDRMLRLLASYSVLTSTTRTIEDGGAERVYGLSMVGKYLVPDE 109

>d1kyza1 a.4.5.29 (A:13-119) Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase {Alfalfa (Medicago sativa) [TaxId: 3879]} Length = 107

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Plant O-methyltransferase, N-terminal domain
domain: Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase
species: Alfalfa (Medicago sativa) [TaxId: 3879]

 Score =  107 bits (268), Expect = 2e-30
 Identities = 51/107 (47%), Positives = 69/107 (64%), Gaps = 8/107 (7%)

Query: 9   EETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPE 68
            +     +AM+LASA VLP ++++ +ELD+ EII+KAGPGA++S  EI +Q+P    NP+
Sbjct: 3   SDEEANLFAMQLASASVLPMILKSALELDLLEIIAKAGPGAQISPIEIASQLPTT--NPD 60

Query: 69  AAAMTLDRVLRLLVSYNALHCSFV-----DGQRLYSLAPVSAYFVRN 110
           A  M LDR+LRLL  Y  L CS         QRLY LA V+ Y V+N
Sbjct: 61  APVM-LDRMLRLLACYIILTCSVRTQQDGKVQRLYGLATVAKYLVKN 106

>d1qzza2 c.66.1.12 (A:102-357) Aclacinomycin-10-hydroxylase RdmB {Streptomyces purpurascens [TaxId: 1924]} Length = 256

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Plant O-methyltransferase, C-terminal domain
domain: Aclacinomycin-10-hydroxylase RdmB
species: Streptomyces purpurascens [TaxId: 1924]

 Score = 88.9 bits (219), Expect = 6e-22
 Identities = 26/101 (25%), Positives = 45/101 (44%), Gaps = 1/101 (0%)

Query: 133 WFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIVMEKVLESYKGFE 192
           + GL   +  G  A+   +G   ++ L  D    D F+  M     +  E   ++Y  + 
Sbjct: 22  FTGLLDVVRTGRPAYAGRYGRPFWEDLSADVALADSFDALMSCDEDLAYEAPADAYD-WS 80

Query: 193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAP 233
            V+ ++DVGGG G  L  I  + PH++G   +L    + A 
Sbjct: 81  AVRHVLDVGGGNGGMLAAIALRAPHLRGTLVELAGPAERAR 121

>d1tw3a2 c.66.1.12 (A:99-351) Carminomycin 4-O-methyltransferase {Streptomyces peucetius [TaxId: 1950]} Length = 253

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Plant O-methyltransferase, C-terminal domain
domain: Carminomycin 4-O-methyltransferase
species: Streptomyces peucetius [TaxId: 1950]

 Score = 83.2 bits (204), Expect = 8e-20
 Identities = 20/103 (19%), Positives = 41/103 (39%), Gaps = 1/103 (0%)

Query: 133 WFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIVMEKVLESYKGFE 192
           +  L   +  G   +   +G   Y+ L         F++ +     +  +    +Y  + 
Sbjct: 21  FTRLPDAIRTGRPTYESIYGKPFYEDLAGRPDLRASFDSLLACDQDVAFDAPAAAYD-WT 79

Query: 193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSY 235
           +V+ ++DVGGG G     I  + PH+     ++   +  A SY
Sbjct: 80  NVRHVLDVGGGKGGFAAAIARRAPHVSATVLEMAGTVDTARSY 122

>d1fp2a1 a.4.5.29 (A:8-108) Isoflavone O-methyltransferase {Alfalfa (Medicago sativa) [TaxId: 3879]} Length = 101

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Plant O-methyltransferase, N-terminal domain
domain: Isoflavone O-methyltransferase
species: Alfalfa (Medicago sativa) [TaxId: 3879]

 Score = 61.5 bits (149), Expect = 4e-13
 Identities = 17/94 (18%), Positives = 38/94 (40%), Gaps = 7/94 (7%)

Query: 18  MELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRV 77
            +   A +    ++  VE+++  II   G    +S++ +V+ + +    P +    + R+
Sbjct: 14  YKHIYAFIDSMSLKWAVEMNIPNIIQNHGKP--ISLSNLVSILQV----PSSKIGNVRRL 67

Query: 78  LRLLVSYNALHCSFVDGQRLYSLAPVSAYFVRNN 111
           +R L           +    Y+L   S   VR +
Sbjct: 68  MRYLAHNGFFEIITKEE-ESYALTVASELLVRGS 100

>d1tw3a1 a.4.5.29 (A:14-98) Carminomycin 4-O-methyltransferase {Streptomyces peucetius [TaxId: 1950]} Length = 85

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Plant O-methyltransferase, N-terminal domain
domain: Carminomycin 4-O-methyltransferase
species: Streptomyces peucetius [TaxId: 1950]

 Score = 47.1 bits (112), Expect = 5e-08
 Identities = 16/93 (17%), Positives = 30/93 (32%), Gaps = 15/93 (16%)

Query: 18  MELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRV 77
           + L S +  P V++    L + + I         +V  + A+              L R+
Sbjct: 7   IRLGS-LHTPMVVRTAATLRLVDHILA----GARTVKALAARTD-------TRPEALLRL 54

Query: 78  LRLLVSYNALHCSFVDGQRLYSLAPVSAYFVRN 110
           +R LV+   L     D    +    V      +
Sbjct: 55  IRHLVAIGLLEE---DAPGEFVPTEVGELLADD 84

>d1qzza1 a.4.5.29 (A:10-101) Aclacinomycin-10-hydroxylase RdmB {Streptomyces purpurascens [TaxId: 1924]} Length = 92

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Plant O-methyltransferase, N-terminal domain
domain: Aclacinomycin-10-hydroxylase RdmB
species: Streptomyces purpurascens [TaxId: 1924]

 Score = 42.4 bits (100), Expect = 3e-06
 Identities = 14/101 (13%), Positives = 33/101 (32%), Gaps = 12/101 (11%)

Query: 8   EEETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNP 67
           E    +    ++    +V P  ++    L + + +  AG     ++A +  +      +P
Sbjct: 2   EPTDQDLDVLLKNLGNLVTPMALRVAATLRLVDHLL-AGA---DTLAGLADRTDT---HP 54

Query: 68  EAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFV 108
           +A +    R++R L     L        R      +     
Sbjct: 55  QALS----RLVRHLTVVGVLEGG-EKQGRPLRPTRLGMLLA 90

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	244
d1kyza2	243	Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltra	99.95
d1fp1d2	244	Chalcone O-methyltransferase {Alfalfa (Medicago sa	99.94
d1fp2a2	244	Isoflavone O-methyltransferase {Alfalfa (Medicago	99.92
d1qzza2	256	Aclacinomycin-10-hydroxylase RdmB {Streptomyces pu	99.87
d1tw3a2	253	Carminomycin 4-O-methyltransferase {Streptomyces p	99.83
d1fp2a1	101	Isoflavone O-methyltransferase {Alfalfa (Medicago	99.82
d1tw3a1	85	Carminomycin 4-O-methyltransferase {Streptomyces p	99.73
d1kyza1	107	Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltra	99.72
d1fp1d1	110	Chalcone O-methyltransferase {Alfalfa (Medicago sa	99.72
d1qzza1	92	Aclacinomycin-10-hydroxylase RdmB {Streptomyces pu	99.7
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	97.98
d2o57a1	282	Putative sarcosine dimethylglycine methyltransfera	97.91
d1p91a_	268	rRNA methyltransferase RlmA {Escherichia coli [Tax	97.75
d1nkva_	245	Hypothetical Protein YjhP {Escherichia coli [TaxId	97.74
d1im8a_	225	Hypothetical protein HI0319 (YecO) {Haemophilus in	97.66
d2fcaa1	204	tRNA (guanine-N(7)-)-methyltransferase TrmB {Bacil	97.66
d1yzha1	204	tRNA (guanine-N(7)-)-methyltransferase TrmB {Strep	97.66
d1vl5a_	231	Hypothetical protein BH2331 {Bacillus halodurans [	97.59
d1xxla_	234	Hypothetical protein YcgJ {Bacillus subtilis [TaxI	97.45
d1nt2a_	209	Fibrillarin homologue {Archaeon Archaeoglobus fulg	97.44
d2b3ta1	274	N5-glutamine methyltransferase, HemK {Escherichia	97.4
d1g8sa_	230	Fibrillarin homologue {Archaeon Methanococcus jann	97.39
d1l3ia_	186	Precorrin-6Y methyltransferase (CbiT) {Archaeon Me	97.33
d1m6ya2	192	TM0872, methyltransferase domain {Thermotoga marit	97.31
d1pjza_	201	Thiopurine S-methyltransferase {Pseudomonas syring	97.29
d1zx0a1	229	Guanidinoacetate methyltransferase {Human (Homo sa	97.28
d1wzna1	251	Hypothetical methyltransferase PH1305 {Archaeon Py	97.16
d2gh1a1	281	Methyltransferase BC2162 {Bacillus cereus [TaxId:	97.12
d1u2za_	406	Catalytic, N-terminal domain of histone methyltran	97.12
d1xtpa_	254	Hypothetical protein Lmaj004091aaa (LmjF30.0810) {	97.11
d1dusa_	194	Hypothetical protein MJ0882 {Archaeon Methanococcu	97.0
d2i6ga1	198	Putative methyltransferase TehB {Salmonella typhim	96.99
d1ne2a_	197	Hypothetical protein Ta1320 {Archaeon Thermoplasma	96.96
d2ex4a1	222	Adrenal gland protein AD-003 (C9orf32) {Human (Hom	96.95
d2p7ia1	225	Hypothetical protein ECA1738 {Erwinia carotovora [	96.92
d1ve3a1	226	Hypothetical protein PH0226 {Archaeon Pyrococcus h	96.9
d2nxca1	254	PrmA-like protein TTHA0656 (TT0836) {Thermus therm	96.88
d1nw3a_	328	Catalytic, N-terminal domain of histone methyltran	96.88
d2fk8a1	280	Methoxy mycolic acid synthase 4, Mma4 {Mycobacteri	96.84
d1dl5a1	213	Protein-L-isoaspartyl O-methyltransferase {Thermot	96.8
d1xvaa_	292	Glycine N-methyltransferase {Rat (Rattus norvegicu	96.78
d1ri5a_	252	mRNA cap (Guanine N-7) methyltransferase {Fungus (	96.78
d1y8ca_	246	Putative methyltransferase CAC2371 {Clostridium ac	96.78
d2avna1	246	Hypothetical methyltransferase TM1389 {Thermotoga	96.76
d1kpga_	285	CmaA1 {Mycobacterium tuberculosis [TaxId: 1773]}	96.56
d2bzga1	229	Thiopurine S-methyltransferase {Human (Homo sapien	96.53
d2h00a1	250	Methyltransferase 10 domain containing protein MET	96.45
d1o54a_	266	Hypothetical protein TM0748 {Thermotoga maritima [	96.43
d1yb2a1	250	Hypothetical protein Ta0852 {Thermoplasma acidophi	96.43
d1kpia_	291	CmaA2 {Mycobacterium tuberculosis [TaxId: 1773]}	96.43
d1jqea_	280	Histamine methyltransferase {Human (Homo sapiens)	96.37
d1i9ga_	264	Probable methyltransferase Rv2118c {Mycobacterium	96.34
d1vlma_	208	Possible histamine N-methyltransferase TM1293 {The	96.32
d1ub9a_	100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	96.31
d1wy7a1	201	Hypothetical protein PH1948 {Archaeon Pyrococcus h	96.1
d2esra1	152	Putative methyltransferase SPy1538 {Streptococcus	96.04
d2fyta1	311	Protein arginine N-methyltransferase 3, PRMT3 {Hum	95.99
d1r1ta_	98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	95.78
d1i1na_	224	Protein-L-isoaspartyl O-methyltransferase {Human (	95.69
d1lvaa3	64	C-terminal fragment of elongation factor SelB {Moo	95.69
d1oria_	316	Protein arginine N-methyltransferase 1, PRMT1 {Rat	95.67
d1g6q1_	328	Arginine methyltransferase, HMT1 {Baker's yeast (S	95.67
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	95.66
d2b25a1	324	Hypothetical protein FLJ20628 {Human (Homo sapiens	95.63
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	95.55
d1u2wa1	108	Cadmium efflux system accessory protein CadC {Stap	95.53
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	95.51
d1g8aa_	227	Fibrillarin homologue {Archaeon Pyrococcus horikos	95.51
d1r1ua_	94	Metal-sensing transcriptional repressor CzrA {Stap	95.5
d1uira_	312	Spermidine synthase {Thermus thermophilus [TaxId:	95.39
d2hoea1	62	N-acetylglucosamine kinase {Thermotoga maritima [T	95.21
d1nv8a_	271	N5-glutamine methyltransferase, HemK {Thermotoga m	95.12
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	95.07
d1s3ja_	143	Putative transcriptional regulator YusO {Bacillus	95.06
d1ws6a1	171	Methyltransferase TTHA0928 {Thermus thermophilus [	95.04
d1lnwa_	141	MexR repressor {Pseudomonas aeruginosa [TaxId: 287	95.04
d1z6ra1	70	Mlc protein N-terminal domain {Escherichia coli [T	95.03
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	95.02
d1vbfa_	224	Protein-L-isoaspartyl O-methyltransferase {Sulfolo	94.96
d1iy9a_	274	Spermidine synthase {Bacillus subtilis [TaxId: 142	94.84
d1xd7a_	127	Hypothetical protein ywnA {Bacillus subtilis [TaxI	94.77
d2o07a1	285	Spermidine synthase {Human (Homo sapiens) [TaxId:	94.76
d1ylfa1	138	Hypothetical protein BC1842 {Bacillus cereus [TaxI	94.71
d1mjfa_	276	Putative spermidine synthetase PF0127 (SpeE) {Arch	94.55
d2p4wa1	194	Transcriptional regulatory protein PF1790 {Pyrococ	94.55
d1inla_	295	Spermidine synthase {Thermotoga maritima [TaxId: 2	94.44
d2b2ca1	312	Spermidine synthase {Caenorhabditis elegans [TaxId	94.42
d2hr3a1	145	Probable transcriptional regulator PA3067 {Pseudom	94.33
d2etha1	140	Putative transcriptional regulator TM0816 {Thermot	94.3
d2a14a1	257	Indolethylamine N-methyltransferase, INMT {Human (	94.3
d2a61a1	139	Transcriptional regulator TM0710 {Thermotoga marit	94.26
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	94.21
d1jg1a_	215	Protein-L-isoaspartyl O-methyltransferase {Archaeo	94.13
d3ctaa1	85	Ta1064 (RFK), N-terminal domain {Thermoplasma acid	94.08
d1wg8a2	182	TM0872, methyltransferase domain {Thermus thermoph	93.94
d1yuba_	245	rRNA adenine dimethylase {Streptococcus pneumoniae	93.84
d1qama_	235	rRNA adenine dimethylase {Bacillus subtilis, Ermc'	93.79
d1xj5a_	290	Spermidine synthase {Thale cress (Arabidopsis thal	93.76
d2frna1	260	Hypothetical protein PH0793 {Pyrococcus horikoshii	93.72
d1dpua_	69	C-terminal domain of RPA32 {Human (Homo sapiens) [	93.65
d1ulya_	190	Hypothetical protein PH1932 {Pyrococcus horikoshii	93.61
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	93.56
d1r18a_	223	Protein-L-isoaspartyl O-methyltransferase {Fruit f	93.53
d2fpoa1	183	Methylase YhhF {Escherichia coli [TaxId: 562]}	93.16
d2bv6a1	136	Transcriptional regulator MgrA {Staphylococcus aur	93.16
d1r7ja_	90	Sso10a (SSO10449) {Archaeon Sulfolobus solfataricu	93.01
d2hzta1	95	Putative transcriptional regulator YtcD {Bacillus	92.88
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	92.69
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	92.67
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	92.62
d2fbha1	137	Transcriptional regulator PA3341 {Pseudomonas aeru	92.47
d2g72a1	263	Phenylethanolamine N-methyltransferase, PNMTase {H	92.34
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	92.14
d1ej0a_	180	RNA methyltransferase FtsJ {Escherichia coli [TaxI	92.13
d1jgsa_	138	Multiple antibiotic resistance repressor, MarR {Es	92.12
d2cl5a1	214	Catechol O-methyltransferase, COMT {Rat (Rattus no	91.91
d1z91a1	137	Organic hydroperoxide resistance transcriptional r	91.89
d2gxba1	59	Z-alpha domain of dsRNA-specific adenosine deamina	91.69
d1xdza_	239	Glucose-inhibited division protein B (GidB) {Bacil	91.59
d2ih2a1	223	DNA methylase TaqI, N-terminal domain {Thermus aqu	91.45
d2frha1	115	Pleiotropic regulator of virulence genes, SarA {St	91.31
d2fhpa1	182	Putative methylase EF2452 {Enterococcus faecalis [	91.29
d3deua1	140	Transcriptional regulator SlyA {Salmonella typhimu	90.87
d2fbia1	136	Probable transcriptional regulator PA4135 {Pseudom	90.82
d1hsja1	115	Staphylococcal accessory regulator A homolog, SarR	90.73
d1lj9a_	144	Transcriptional regulator SlyA {Enterococcus faeca	90.5
d1jsxa_	207	Glucose-inhibited division protein B (GidB) {Esche	90.45
d1j75a_	57	Dlm-1 {Mouse (Mus musculus) [TaxId: 10090]}	90.44
d2as0a2	324	Hypothetical protein PH1915, middle and C-terminal	89.83
d1q1ha_	88	Transcription factor E/IIe-alpha, N-terminal domai	89.59
d2fswa1	102	Hypothetical protein PG0823 {Porphyromonas gingiva	89.44
d2fxaa1	162	Protease production regulatory protein Hpr {Bacill	89.27
d2fbka1	172	Transcriptional regulator DR1159 {Deinococcus radi	89.21
d1xmka1	73	Z-alpha domain of dsRNA-specific adenosine deamina	89.2
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	89.08
d1z7ua1	108	Hypothetical protein EF0647 {Enterococcus faecalis	88.92
d1p4xa2	125	Staphylococcal accessory regulator A homolog, SarS	88.5
d2avda1	219	COMT domain-containing protein 1, COMTD1 {Human (H	88.44
d1yyva1	114	Putative transcriptional regulator YtfH {Salmonell	88.34
d2ev0a1	61	Manganese transport regulator MntR {Bacillus subti	88.3
d2f2ea1	142	Hypothetical protein PA1607 {Pseudomonas aeruginos	88.19
d1p4xa1	125	Staphylococcal accessory regulator A homolog, SarS	88.18
d3bwga1	78	Transcriptional regulator YydK {Bacillus subtilis	87.51
d1zq9a1	278	Probable dimethyladenosine transferase {Human (Hom	87.22
d1wxxa2	318	Hypothetical protein TTHA1280, middle and C-termin	87.18
d2hs5a1	69	Putative transcriptional regulator RHA1_ro03477 {R	86.84
d1qyra_	252	High level kasugamycin resistance protein KsgA {Es	86.53
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	86.29
d2p41a1	257	An RNA cap (nucleoside-2'-O-)-methyltransferase do	85.83
d1hw1a1	74	Fatty acid responsive transcription factor FadR, N	83.96
d2f8la1	328	Hypothetical protein Lmo1582 {Listeria monocytogen	83.52
d1bl0a1	54	MarA {Escherichia coli [TaxId: 562]}	83.12
d1sfua_	70	34L {Yaba-like disease virus, YLDV [TaxId: 132475]	83.06
d1susa1	227	Caffeoyl-CoA O-methyltransferase {Alfalfa (Medicag	81.64
d2igta1	309	Putative methyltransferase Atu0340 {Agrobacterium	81.53
d1nd9a_	49	N-terminal subdomain of bacterial translation init	80.02

>d1kyza2 c.66.1.12 (A:120-362) Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase {Alfalfa (Medicago sativa) [TaxId: 3879]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Plant O-methyltransferase, C-terminal domain
domain: Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase
species: Alfalfa (Medicago sativa) [TaxId: 3879]

Probab=99.95  E-value=7.3e-28  Score=200.22  Aligned_cols=130  Identities=55%  Similarity=0.988  Sum_probs=121.8

Q ss_pred             CCCHHHHHHHhcChhhhhhccchHHHHhcCCchhhhhhCCCchhhccCCchHHHHHHHHHHhcchhhHHHHHhhcCCCCC
Q 041256          114 GASLSPYMALCLDKVCLDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIVMEKVLESYKGFEH  193 (244)
Q Consensus       114 ~~~~~~~~~~~~~~~~~~~~~~l~~~l~~g~~~~~~~~g~~~~e~~~~~~~~~~~f~~aM~~~~~~~~~~~~~~~~~~~~  193 (244)
                      +.|+++++.+..++.+++.|.+|.+++|+|+++|+.++|.++|+|+.++|+..+.|+++|...+....+.+++.|+.+++
T Consensus         2 ~~s~~~~~~~~~~~~~~~~W~~L~~avrtG~~~f~~~~G~~~~~~~~~~p~~~~~F~~aM~~~~~~~~~~~~~~~~~~~~   81 (243)
T d1kyza2           2 GVSISALNLMNQDKVLMESWYHLKDAVLDGGIPFNKAYGMTAFEYHGTDPRFNKVFNKGMSDHSTITMKKILETYTGFEG   81 (243)
T ss_dssp             SCCTHHHHHHHTSHHHHGGGGGHHHHHHHCSCHHHHHHSSCHHHHGGGCHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSS
T ss_pred             CCcHHHHHHHhcCHHHHHHHHHHHHHHhhCCCHHHhhcCCCHHHHHHhCHHHHHHHHHHHhHhhhhHHHHHHHhcccccC
Confidence            35899999998898899999999999999999999999999999999999999999999999988888899999984466


Q ss_pred             cceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCCCCCceeecc
Q 041256          194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPGTLFIKF  243 (244)
Q Consensus       194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~~~~i~~~~~  243 (244)
                      .++|||||||+|.++++++++||+++++++|+|+|++.+++.+++++++|
T Consensus        82 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~~~~~~r~~~~~~  131 (243)
T d1kyza2          82 LKSLVDVGGGTGAVINTIVSKYPTIKGINFDLPHVIEDAPSYPGVEHVGG  131 (243)
T ss_dssp             CSEEEEETCTTSHHHHHHHHHCTTSEEEEEECTTTTTTCCCCTTEEEEEC
T ss_pred             CcEEEEecCCCcHHHHHHHHHCCCCeEEEcccHHhhhhcccCCceEEecc
Confidence            89999999999999999999999999999999999999999899998876

>d1fp1d2 c.66.1.12 (D:129-372) Chalcone O-methyltransferase {Alfalfa (Medicago sativa) [TaxId: 3879]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Plant O-methyltransferase, C-terminal domain
domain: Chalcone O-methyltransferase
species: Alfalfa (Medicago sativa) [TaxId: 3879]

Probab=99.94  E-value=2.2e-27  Score=197.22  Aligned_cols=128  Identities=38%  Similarity=0.732  Sum_probs=109.0

Q ss_pred             CHHHHHHHhcChhhhhhccchHHHHhcCC-chhhhhhCCCchhhccCCchHHHHHHHHHHhcchhhHHHHHhhcCCCCCc
Q 041256          116 SLSPYMALCLDKVCLDGWFGLKKQLLEGG-IAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIVMEKVLESYKGFEHV  194 (244)
Q Consensus       116 ~~~~~~~~~~~~~~~~~~~~l~~~l~~g~-~~~~~~~g~~~~e~~~~~~~~~~~f~~aM~~~~~~~~~~~~~~~~~~~~~  194 (244)
                      |+++++.++++|.+++.|.+|.+++++|. ++|+.++|.++|||+.+||+..+.|+++|.+.+....+.+++.|+.|++.
T Consensus         3 ~l~~~~~~~~~p~~~~~w~~l~~~v~~g~~~~f~~~~G~~~~e~l~~~p~~~~~F~~aM~~~s~~~~~~l~~~~~~f~~~   82 (244)
T d1fp1d2           3 YLASFTTFLCYPALLQVWMNFKEAVVDEDIDLFKNVHGVTKYEFMGKDKKMNQIFNKSMVDVCATEMKRMLEIYTGFEGI   82 (244)
T ss_dssp             CCTHHHHHHTCHHHHHHHTTHHHHHHSCC--------------CCSSCHHHHHHHHHHHHHHHHHHHHHHHHHCCTTTTC
T ss_pred             cHHHHHHHHhCHHHHHHHHHHHHHHhcCCCCHhHHhcCCCHHHHHhhCHHHHHHHHHHHHHHHHHHHHHHHHhcccccCC
Confidence            78999999999999999999999999865 67999999999999999999999999999999998889999999878999


Q ss_pred             ceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCCCCCceeecc
Q 041256          195 KKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPGTLFIKF  243 (244)
Q Consensus       195 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~~~~i~~~~~  243 (244)
                      ++|||||||+|.++++++++||++++|++|+|+|++.+...++|+++++
T Consensus        83 ~~vlDiGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~~~~~~ri~~~~g  131 (244)
T d1fp1d2          83 STLVDVGGGSGRNLELIISKYPLIKGINFDLPQVIENAPPLSGIEHVGG  131 (244)
T ss_dssp             SEEEEETCTTSHHHHHHHHHCTTCEEEEEECHHHHTTCCCCTTEEEEEC
T ss_pred             cEEEEecCCCcHHHHHHHHHCCCCeEEEecchhhhhccCCCCCeEEecC
Confidence            9999999999999999999999999999999999999988899999875

>d1fp2a2 c.66.1.12 (A:109-352) Isoflavone O-methyltransferase {Alfalfa (Medicago sativa) [TaxId: 3879]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Plant O-methyltransferase, C-terminal domain
domain: Isoflavone O-methyltransferase
species: Alfalfa (Medicago sativa) [TaxId: 3879]

Probab=99.92  E-value=2e-25  Score=185.40  Aligned_cols=127  Identities=26%  Similarity=0.508  Sum_probs=116.0

Q ss_pred             CHHHHHHHhcChhhhhhccchHHHHhcCC-chhhhhhCCCchhhccCCchHHHHHHHHHHhcchhhHHHHHhh-cCCCCC
Q 041256          116 SLSPYMALCLDKVCLDGWFGLKKQLLEGG-IAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIVMEKVLES-YKGFEH  193 (244)
Q Consensus       116 ~~~~~~~~~~~~~~~~~~~~l~~~l~~g~-~~~~~~~g~~~~e~~~~~~~~~~~f~~aM~~~~~~~~~~~~~~-~~~~~~  193 (244)
                      ++.+++.++.+|.++..|.+|.++++++. ++|+.++|+++|+|+.+||++.+.|+++|...+......+.+. ++ |++
T Consensus         2 s~ap~~~~~~~p~~~~~w~~l~~~~~~~~~~~f~~a~G~~~~e~l~~~pe~~~~F~~aM~~~s~~~~~~~~~~~~~-~~~   80 (244)
T d1fp2a2           2 CLAPMVECVLDPTLSGSYHELKKWIYEEDLTLFGVTLGSGFWDFLDKNPEYNTSFNDAMASDSKLINLALRDCDFV-FDG   80 (244)
T ss_dssp             CCHHHHHHHTCHHHHHGGGGHHHHHTCSSCCHHHHHHSSCHHHHHHHCHHHHHHHHHHHHHTHHHHHHHHHTCHHH-HTT
T ss_pred             ChHHHHHHHhCHHHHHHHHHHHHHHhcCCCCHHHHhhCCCHHHHHHhCHHHHHHHHHHhhhhhhhhhhhHhhhccc-ccC
Confidence            57889999889999999999999999874 6899999999999999999999999999999888766666653 35 788


Q ss_pred             cceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCCCCCceeecc
Q 041256          194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPSYPGTLFIKF  243 (244)
Q Consensus       194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~~~~i~~~~~  243 (244)
                      .++|||||||+|.++++++++||++++++||||+|++.+...++|++++|
T Consensus        81 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~~~~~~rv~~~~g  130 (244)
T d1fp2a2          81 LESIVDVGGGTGTTAKIICETFPKLKCIVFDRPQVVENLSGSNNLTYVGG  130 (244)
T ss_dssp             CSEEEEETCTTSHHHHHHHHHCTTCEEEEEECHHHHTTCCCBTTEEEEEC
T ss_pred             ceEEEEecCCccHHHHHHHHhCCCCeEEEecCHHHHHhCcccCceEEEec
Confidence            99999999999999999999999999999999999999998889999876

>d1qzza2 c.66.1.12 (A:102-357) Aclacinomycin-10-hydroxylase RdmB {Streptomyces purpurascens [TaxId: 1924]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Plant O-methyltransferase, C-terminal domain
domain: Aclacinomycin-10-hydroxylase RdmB
species: Streptomyces purpurascens [TaxId: 1924]

Probab=99.87  E-value=8e-23  Score=170.73  Aligned_cols=128  Identities=22%  Similarity=0.309  Sum_probs=113.0

Q ss_pred             CCCHHHHHHHhcChhhh-hhccchHHHHhcCCchhhhhhCCCchhhccCCchHHHHHHHHHHhcchhhHHHHHhhcCCCC
Q 041256          114 GASLSPYMALCLDKVCL-DGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIVMEKVLESYKGFE  192 (244)
Q Consensus       114 ~~~~~~~~~~~~~~~~~-~~~~~l~~~l~~g~~~~~~~~g~~~~e~~~~~~~~~~~f~~aM~~~~~~~~~~~~~~~~~~~  192 (244)
                      |.++++++.+....... .+|.+|.+++|+|.++|+..+|.++|+|+.++|+..+.|+++|...+....+.+++.+| |+
T Consensus         2 p~~~~~~~~l~~~~~~~~~~~~~L~~~~rtG~~~~~~~~G~~~~e~~~~~p~~~~~f~~~m~~~~~~~~~~~~~~~d-~~   80 (256)
T d1qzza2           2 PAQQRAWLDLNGAVSHADLAFTGLLDVVRTGRPAYAGRYGRPFWEDLSADVALADSFDALMSCDEDLAYEAPADAYD-WS   80 (256)
T ss_dssp             TTCHHHHHCTTSHHHHHHGGGGGHHHHHHHSCCSHHHHHSSCHHHHHHHCHHHHHHHHHTCGGGSTTTTHHHHHTSC-CT
T ss_pred             cHHHHHHHhhcCchhhhHhhHHHHHHHHHhCCchhhhhhCCCHHHHHHhCHHHHHHHHHHHHhhHHHHHHHHHhcCC-Cc
Confidence            45788888766333333 37999999999999999999999999999999999999999999999888899999999 99


Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCCC-------CCCceeec
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAPS-------YPGTLFIK  242 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~~-------~~~i~~~~  242 (244)
                      +.++|||||||+|.++.+++++||+++++++|+|++++.+++       .++|+++.
T Consensus        81 ~~~~vlDvG~G~G~~~~~l~~~~P~~~~~~~Dlp~~~~~a~~~~~~~~~~~ri~~~~  137 (256)
T d1qzza2          81 AVRHVLDVGGGNGGMLAAIALRAPHLRGTLVELAGPAERARRRFADAGLADRVTVAE  137 (256)
T ss_dssp             TCCEEEEETCTTSHHHHHHHHHCTTCEEEEEECHHHHHHHHHHHHHTTCTTTEEEEE
T ss_pred             cCCEEEEECCCCCHHHHHHHHhhcCcEEEEecChHHHHHHHHHHhhcCCcceeeeee
Confidence            999999999999999999999999999999999999988763       24566654

>d1tw3a2 c.66.1.12 (A:99-351) Carminomycin 4-O-methyltransferase {Streptomyces peucetius [TaxId: 1950]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Plant O-methyltransferase, C-terminal domain
domain: Carminomycin 4-O-methyltransferase
species: Streptomyces peucetius [TaxId: 1950]

Probab=99.83  E-value=2.5e-21  Score=161.10  Aligned_cols=112  Identities=17%  Similarity=0.310  Sum_probs=103.2

Q ss_pred             hhhccchHHHHhcCCchhhhhhCCCchhhccCCchHHHHHHHHHHhcchhhHHHHHhhcCCCCCcceEEEecCCccHHHH
Q 041256          130 LDGWFGLKKQLLEGGIAFNKAHGMQIYDYLGVDSRFNDVFNNGMLSHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLN  209 (244)
Q Consensus       130 ~~~~~~l~~~l~~g~~~~~~~~g~~~~e~~~~~~~~~~~f~~aM~~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~  209 (244)
                      ..+|.+|++++|+|+++|+.++|+++|+|+.++|+..+.|+.+|...+....+.+++.|| |++.++|||||||+|.++.
T Consensus        18 ~~~~~~L~~~vr~G~~~~~~~~G~~~~~~~~~~~~~~~~f~~~m~~~~~~~~~~~~~~~d-~~~~~~VLDvGcG~G~~~~   96 (253)
T d1tw3a2          18 DISFTRLPDAIRTGRPTYESIYGKPFYEDLAGRPDLRASFDSLLACDQDVAFDAPAAAYD-WTNVRHVLDVGGGKGGFAA   96 (253)
T ss_dssp             GGGGGGHHHHHHHCCCCHHHHHSSCHHHHHHTCHHHHHHHHHHHTTTTTTTTHHHHHHSC-CTTCSEEEEETCTTSHHHH
T ss_pred             cccHHHHHHHHHhCCchhhhccCCCHHHHHhhCHHHHHHHHHHHHHhHHHHHHHHHhhcC-CccCCEEEEeCCCCCHHHH
Confidence            348999999999999999999999999999999999999999999998888889999999 9999999999999999999


Q ss_pred             HHHHHCCCCeEEEccchHHhhhCCC-------CCCceeec
Q 041256          210 MIISKYPHIKGINYDLPYVIKDAPS-------YPGTLFIK  242 (244)
Q Consensus       210 ~l~~~~P~l~~~v~Dlp~vi~~a~~-------~~~i~~~~  242 (244)
                      .+++++|+++++++|+|++++.+++       .++|+++.
T Consensus        97 ~la~~~p~~~~~~~D~~~~~~~a~~~~~~~~~~~rv~~~~  136 (253)
T d1tw3a2          97 AIARRAPHVSATVLEMAGTVDTARSYLKDEGLSDRVDVVE  136 (253)
T ss_dssp             HHHHHCTTCEEEEEECTTHHHHHHHHHHHTTCTTTEEEEE
T ss_pred             HHHHhcceeEEEEccCHHHHHHHHHHHHHhhcccchhhcc
Confidence            9999999999999999999988764       24677664

>d1fp2a1 a.4.5.29 (A:8-108) Isoflavone O-methyltransferase {Alfalfa (Medicago sativa) [TaxId: 3879]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Plant O-methyltransferase, N-terminal domain
domain: Isoflavone O-methyltransferase
species: Alfalfa (Medicago sativa) [TaxId: 3879]

Probab=99.82  E-value=5.6e-21  Score=136.68  Aligned_cols=97  Identities=18%  Similarity=0.260  Sum_probs=84.9

Q ss_pred             hhhchhHHHHHHHHhhhHHHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcc
Q 041256            8 EEETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNAL   87 (244)
Q Consensus         8 ~~~~~~~~~l~~~~~g~~~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll   87 (244)
                      .|..+++..+|++++||+.+++|++|++|||||+|++.+  ||+|++|||++++++   +.+++. +.|+||+|++.|+|
T Consensus         4 ~e~~qaq~~l~~~~~gf~~s~aL~~aveLgi~d~l~~~~--~p~t~~eLa~~~~~~---~~~~~~-L~RlLR~L~~~gi~   77 (101)
T d1fp2a1           4 SEIFKAQALLYKHIYAFIDSMSLKWAVEMNIPNIIQNHG--KPISLSNLVSILQVP---SSKIGN-VRRLMRYLAHNGFF   77 (101)
T ss_dssp             THHHHHHHHHHHHHTTHHHHHHHHHHHHTTHHHHHHHHT--SCEEHHHHHHHHTCC---GGGHHH-HHHHHHHHHHTTSE
T ss_pred             HHHHHHHHHHHHHHHhHHHHHHHHHHHHcCcHHHHHHcC--CCCCHHHHHHHcCCC---CccchH-HHHHHHHHHhCCce
Confidence            466789999999999999999999999999999998765  799999999999996   433567 99999999999999


Q ss_pred             cceeecCCceeecCccccccccCC
Q 041256           88 HCSFVDGQRLYSLAPVSAYFVRNN  111 (244)
Q Consensus        88 ~~~~~~~~~~y~~t~~s~~l~~~~  111 (244)
                      .++. .++++|++|+.|++|++++
T Consensus        78 ~~~~-~~~~~Y~lt~~s~~Lv~~~  100 (101)
T d1fp2a1          78 EIIT-KEEESYALTVASELLVRGS  100 (101)
T ss_dssp             EEEE-SSSEEEEECHHHHTTSTTS
T ss_pred             eeec-CCCCeEecCHHHHHhhcCC
Confidence            8542 3457999999999998875

>d1tw3a1 a.4.5.29 (A:14-98) Carminomycin 4-O-methyltransferase {Streptomyces peucetius [TaxId: 1950]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Plant O-methyltransferase, N-terminal domain
domain: Carminomycin 4-O-methyltransferase
species: Streptomyces peucetius [TaxId: 1950]

Probab=99.73  E-value=3.7e-18  Score=118.29  Aligned_cols=83  Identities=17%  Similarity=0.246  Sum_probs=73.0

Q ss_pred             HHHHHHHHhhhHHHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeec
Q 041256           14 FSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVD   93 (244)
Q Consensus        14 ~~~l~~~~~g~~~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~   93 (244)
                      ..+ +..+.+++.+++|++|+++||||+|.+    ||+|++|||+++|++      ++. +.|+||+|++.|+|++   +
T Consensus         3 ~~~-l~~l~~~~~~~aL~~av~L~ifd~l~~----gp~s~~eLA~~~g~~------~~~-l~rlLr~l~a~gl~~e---~   67 (85)
T d1tw3a1           3 LRT-LIRLGSLHTPMVVRTAATLRLVDHILA----GARTVKALAARTDTR------PEA-LLRLIRHLVAIGLLEE---D   67 (85)
T ss_dssp             HHH-HHHHHCSHHHHHHHHHHHTTHHHHHHT----TCCBHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEE---E
T ss_pred             HHH-HHHHHchHHHHHHHHHHHcCcHHHhcc----CCCCHHHHHHHhCcC------hhH-HHHHHHHHHHCCCeEe---c
Confidence            344 444579999999999999999999976    799999999999997      678 9999999999999984   4


Q ss_pred             CCceeecCccccccccCC
Q 041256           94 GQRLYSLAPVSAYFVRNN  111 (244)
Q Consensus        94 ~~~~y~~t~~s~~l~~~~  111 (244)
                      +++.|++|+.|+.|.+|+
T Consensus        68 ~~~~y~lt~~s~~L~~Dh   85 (85)
T d1tw3a1          68 APGEFVPTEVGELLADDH   85 (85)
T ss_dssp             ETTEEEECTTGGGGSTTS
T ss_pred             CCCeEecCHHHHHhhcCC
Confidence            579999999999998774

>d1kyza1 a.4.5.29 (A:13-119) Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase {Alfalfa (Medicago sativa) [TaxId: 3879]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Plant O-methyltransferase, N-terminal domain
domain: Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase
species: Alfalfa (Medicago sativa) [TaxId: 3879]

Probab=99.72  E-value=8.2e-18  Score=120.45  Aligned_cols=100  Identities=50%  Similarity=0.828  Sum_probs=84.2

Q ss_pred             hhchhHHHHHHHHhhhHHHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCccc
Q 041256            9 EETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALH   88 (244)
Q Consensus         9 ~~~~~~~~l~~~~~g~~~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~   88 (244)
                      +++++....++++++++.+++|++|++|||||+|++.|.++++|..|||.++..+  ||+++.. |.|+||+|++.|+|.
T Consensus         3 ~dee~~l~a~~L~~~~v~pmaLk~AieLgI~DiI~~~G~~~~ls~~eia~~l~~~--~p~~~~~-L~RilR~Las~~vf~   79 (107)
T d1kyza1           3 SDEEANLFAMQLASASVLPMILKSALELDLLEIIAKAGPGAQISPIEIASQLPTT--NPDAPVM-LDRMLRLLACYIILT   79 (107)
T ss_dssp             CHHHHHHHHHHHHTTTHHHHHHHHHHHTTHHHHHHTTCTTCCBCHHHHHHTSSCC--CTTHHHH-HHHHHHHHHHTTSEE
T ss_pred             ccHHHHHHHHHHHHhhHHHHHHHHHHHcCCHHHHHHcCCCCCCCHHHHHHhcCCC--CCcchHH-HHHHHHHHHhcCceE
Confidence            3456667788999999999999999999999999998766789999999999987  6665678 999999999999997


Q ss_pred             ceeecC-C----ceeecCccccccccCC
Q 041256           89 CSFVDG-Q----RLYSLAPVSAYFVRNN  111 (244)
Q Consensus        89 ~~~~~~-~----~~y~~t~~s~~l~~~~  111 (244)
                      +..+.. +    .+|.+||.|++|+++.
T Consensus        80 ~~~~~~~dg~~~~~Y~LTpvsk~Lv~de  107 (107)
T d1kyza1          80 CSVRTQQDGKVQRLYGLATVAKYLVKNE  107 (107)
T ss_dssp             EEEEECTTSCEEEEEEECHHHHHHSCCT
T ss_pred             EeeecCCCCCeeeEEecchhHHhhcCCC
Confidence            542221 2    2699999999999873

>d1fp1d1 a.4.5.29 (D:19-128) Chalcone O-methyltransferase {Alfalfa (Medicago sativa) [TaxId: 3879]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Plant O-methyltransferase, N-terminal domain
domain: Chalcone O-methyltransferase
species: Alfalfa (Medicago sativa) [TaxId: 3879]

Probab=99.72  E-value=1.2e-17  Score=119.89  Aligned_cols=103  Identities=37%  Similarity=0.600  Sum_probs=85.3

Q ss_pred             hhhchhHHHHHHHHhhhHHHHHHHHHHhcChhhHHhhcC-CCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCc
Q 041256            8 EEETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAG-PGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNA   86 (244)
Q Consensus         8 ~~~~~~~~~l~~~~~g~~~~~~L~~a~~lgifd~L~~~~-~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gl   86 (244)
                      ++++++....++++++++.+++|++|++|||||+|+..| +++++|+.|||.++..++.||..+.. |.|+||+|++.|+
T Consensus         1 ~~~~~~~l~a~~L~~~~v~pMaLk~AieLgI~diI~~~G~~~~~ls~~ela~~lp~~~~~p~~~~~-L~RiLRlLas~~v   79 (110)
T d1fp1d1           1 QTEDSACLSAMVLTTNLVYPAVLNAAIDLNLFEIIAKATPPGAFMSPSEIASKLPASTQHSDLPNR-LDRMLRLLASYSV   79 (110)
T ss_dssp             CCHHHHHHHHHHHHHTTHHHHHHHHHHHTTHHHHHHTCSSTTCCBCHHHHHTTSCGGGCCTTHHHH-HHHHHHHHHHTTS
T ss_pred             CchHHHHHHHHHHHHhhHHHHHHHHHHHcCCHHHHHHcCCCCCCCCHHHHHHhCCCCCCCccHHHH-HHHHHHHHHHcCc
Confidence            467788899999999999999999999999999999876 23568999999998864345655668 9999999999999


Q ss_pred             ccceeecC-Cc----eeecCccccccccCC
Q 041256           87 LHCSFVDG-QR----LYSLAPVSAYFVRNN  111 (244)
Q Consensus        87 l~~~~~~~-~~----~y~~t~~s~~l~~~~  111 (244)
                      |.+..+.+ +|    +|.+||.|++|++++
T Consensus        80 f~~~~~~~~~g~~e~~Y~Ltpvsk~Lv~de  109 (110)
T d1fp1d1          80 LTSTTRTIEDGGAERVYGLSMVGKYLVPDE  109 (110)
T ss_dssp             EEEEEEECTTSCEEEEEEECTTGGGGSTTC
T ss_pred             cccccccCCCCCeeeEEecchhhHhhcCCC
Confidence            97543222 22    599999999999875

>d1qzza1 a.4.5.29 (A:10-101) Aclacinomycin-10-hydroxylase RdmB {Streptomyces purpurascens [TaxId: 1924]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Plant O-methyltransferase, N-terminal domain
domain: Aclacinomycin-10-hydroxylase RdmB
species: Streptomyces purpurascens [TaxId: 1924]

Probab=99.70  E-value=1.2e-17  Score=117.17  Aligned_cols=88  Identities=11%  Similarity=0.178  Sum_probs=77.6

Q ss_pred             hchhHHHHHHHHhhhHHHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           10 ETNNFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        10 ~~~~~~~l~~~~~g~~~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      .++....+++++.+++.+++|++|+++||||+|.+    ||+|++|||+++|++      ++. +.|+||+|+++|+|++
T Consensus         4 ~d~~~d~ll~~~~~~~~~~~L~~aveL~ifd~L~~----gp~t~~eLA~~~g~~------~~~-l~rLlr~L~a~gll~~   72 (92)
T d1qzza1           4 TDQDLDVLLKNLGNLVTPMALRVAATLRLVDHLLA----GADTLAGLADRTDTH------PQA-LSRLVRHLTVVGVLEG   72 (92)
T ss_dssp             CHHHHHHHHHTTTCCHHHHHHHHHHHTTHHHHHHT----TCCSHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEC
T ss_pred             cchhHHHHHHHHHchHHHHHHHHHHHcCchHHHhC----CCCCHHHHHHHHCcC------chH-HHHHHHHHHHCCCeee
Confidence            34678899999999999999999999999999986    799999999999997      678 9999999999999996


Q ss_pred             eeecCCceeecCcccccccc
Q 041256           90 SFVDGQRLYSLAPVSAYFVR  109 (244)
Q Consensus        90 ~~~~~~~~y~~t~~s~~l~~  109 (244)
                      +. .+.+.|++|+.+..|++
T Consensus        73 ~~-d~~~~~~~t~~g~lL~d   91 (92)
T d1qzza1          73 GE-KQGRPLRPTRLGMLLAD   91 (92)
T ss_dssp             CC-C-CCCCEECTTGGGGST
T ss_pred             ec-CCCceecccHHHHhccC
Confidence            42 23467999999998875

>d1mkma1 a.4.5.33 (A:1-75) Transcriptional regulator IclR, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcriptional regulator IclR, N-terminal domain
domain: Transcriptional regulator IclR, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=97.98  E-value=4.4e-06  Score=54.93  Aligned_cols=57  Identities=14%  Similarity=0.198  Sum_probs=47.5

Q ss_pred             cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccc
Q 041256           36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVS  104 (244)
Q Consensus        36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s  104 (244)
                      +.|.+.+.+.+  +|+|+.|||+.+|++      ..- +.|+|..|+..|++++   +.+++|++++..
T Consensus         8 l~IL~~~a~~~--~~~s~~eia~~~~~~------~st-~~rll~tL~~~g~l~~---~~~g~y~lG~~l   64 (75)
T d1mkma1           8 FEILDFIVKNP--GDVSVSEIAEKFNMS------VSN-AYKYMVVLEEKGFVLR---KKDKRYVPGYKL   64 (75)
T ss_dssp             HHHHHHHHHCS--SCBCHHHHHHHTTCC------HHH-HHHHHHHHHHTTSEEE---CTTSCEEECTHH
T ss_pred             HHHHHHHHhCC--CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEE---CCCCCEeecHHH
Confidence            45788888865  689999999999996      445 9999999999999996   346889998753

>d2o57a1 c.66.1.18 (A:16-297) Putative sarcosine dimethylglycine methyltransferase {Red algae (Galdieria sulphuraria) [TaxId: 130081]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Mycolic acid cyclopropane synthase
domain: Putative sarcosine dimethylglycine methyltransferase
species: Red algae (Galdieria sulphuraria) [TaxId: 130081]

Probab=97.91  E-value=3.7e-06  Score=68.95  Aligned_cols=65  Identities=14%  Similarity=0.207  Sum_probs=47.9

Q ss_pred             HHHHHHHhcchhhHHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          168 VFNNGMLSHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       168 ~f~~aM~~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+..++..........+....+ +++..+|||||||.|.++..+++++ +.+++.+|+ |..++.|++
T Consensus        43 ~~~~a~~~~~~~~~~~l~~~~~-l~~~~~vLDiGcG~G~~~~~la~~~-~~~v~gvD~s~~~i~~a~~  108 (282)
T d2o57a1          43 EIREASLRTDEWLASELAMTGV-LQRQAKGLDLGAGYGGAARFLVRKF-GVSIDCLNIAPVQNKRNEE  108 (282)
T ss_dssp             CHHHHHHHHHHHHHHHHHHTTC-CCTTCEEEEETCTTSHHHHHHHHHH-CCEEEEEESCHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHHhcC-CCCCCEEEEeCCCCcHHHhhhhccC-CcEEEEEeccchhhhhhhc
Confidence            3444444444444455666666 7888999999999999999999876 678999998 777776654

>d1p91a_ c.66.1.33 (A:) rRNA methyltransferase RlmA {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: rRNA methyltransferase RlmA
domain: rRNA methyltransferase RlmA
species: Escherichia coli [TaxId: 562]

Probab=97.75  E-value=1.1e-05  Score=65.83  Aligned_cols=50  Identities=26%  Similarity=0.484  Sum_probs=42.9

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC-CCCceee
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS-YPGTLFI  241 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~-~~~i~~~  241 (244)
                      .+..+|||||||+|.++..+++++|+.+++.+|+ |..++.|++ .++|+++
T Consensus        83 ~~~~~iLDiGcG~G~~~~~l~~~~~~~~~~giD~s~~~~~~a~~~~~~~~~~  134 (268)
T d1p91a_          83 DKATAVLDIGCGEGYYTHAFADALPEITTFGLDVSKVAIKAAAKRYPQVTFC  134 (268)
T ss_dssp             TTCCEEEEETCTTSTTHHHHHHTCTTSEEEEEESCHHHHHHHHHHCTTSEEE
T ss_pred             CCCCEEEEeCCCCcHHHHHHHHHCCCCEEEEecchHhhhhhhhcccccccce
Confidence            5668999999999999999999999999999998 778887765 5666653

>d1nkva_ c.66.1.21 (A:) Hypothetical Protein YjhP {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: Hypothetical Protein YjhP
domain: Hypothetical Protein YjhP
species: Escherichia coli [TaxId: 562]

Probab=97.74  E-value=1.8e-05  Score=63.25  Aligned_cols=51  Identities=18%  Similarity=0.273  Sum_probs=42.1

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+.+.+. +....+|||||||.|.++..++++++ .+++.+|+ |..++.+++
T Consensus        23 ~~l~~~~~-l~pg~~VLDiGCG~G~~~~~la~~~~-~~v~GvD~s~~~~~~ar~   74 (245)
T d1nkva_          23 ATLGRVLR-MKPGTRILDLGSGSGEMLCTWARDHG-ITGTGIDMSSLFTAQAKR   74 (245)
T ss_dssp             HHHHHHTC-CCTTCEEEEETCTTCHHHHHHHHHTC-CEEEEEESCHHHHHHHHH
T ss_pred             HHHHHHcC-CCCCCEEEEEcCCCCHHHHHHHHhcC-CEEEEEecccchhhHHHH
Confidence            35566666 77789999999999999999998876 79999999 777776654

>d1im8a_ c.66.1.14 (A:) Hypothetical protein HI0319 (YecO) {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Hypothetical protein HI0319 (YecO)
domain: Hypothetical protein HI0319 (YecO)
species: Haemophilus influenzae [TaxId: 727]

Probab=97.66  E-value=2.9e-05  Score=61.21  Aligned_cols=43  Identities=16%  Similarity=0.169  Sum_probs=37.8

Q ss_pred             CCcceEEEecCCccHHHHHHHHH--CCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISK--YPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~--~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ....+|||||||+|..+..+++.  +|+.+++.+|+ |..++.|++
T Consensus        38 ~~~~~vLDlGCGtG~~~~~l~~~~~~~~~~v~giD~S~~ml~~A~~   83 (225)
T d1im8a_          38 TADSNVYDLGCSRGAATLSARRNINQPNVKIIGIDNSQPMVERCRQ   83 (225)
T ss_dssp             CTTCEEEEESCTTCHHHHHHHHTCCCSSCEEEEECSCHHHHHHHHH
T ss_pred             CCCCEEEEeccchhhHHHHHHHhhcCCCCceEEeCCCHHHHHHHHH
Confidence            45579999999999999999986  58999999999 888888864

>d2fcaa1 c.66.1.53 (A:10-213) tRNA (guanine-N(7)-)-methyltransferase TrmB {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: TrmB-like
domain: tRNA (guanine-N(7)-)-methyltransferase TrmB
species: Bacillus subtilis [TaxId: 1423]

Probab=97.66  E-value=2.1e-05  Score=61.68  Aligned_cols=39  Identities=28%  Similarity=0.359  Sum_probs=34.4

Q ss_pred             cceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhC
Q 041256          194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDA  232 (244)
Q Consensus       194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a  232 (244)
                      ...|||||||.|.++..+++++|+...+.+|+ +..+..+
T Consensus        30 ~PlvLeIGcG~G~~~~~lA~~~p~~~~iGiD~~~~~i~~a   69 (204)
T d2fcaa1          30 NPIHIEVGTGKGQFISGMAKQNPDINYIGIELFKSVIVTA   69 (204)
T ss_dssp             CCEEEEECCTTSHHHHHHHHHCTTSEEEEECSCHHHHHHH
T ss_pred             CceEEEEEecCcHHHHHHHHhCCCCcEEEeecchHHHHHH
Confidence            46899999999999999999999999999997 6666554

>d1yzha1 c.66.1.53 (A:8-211) tRNA (guanine-N(7)-)-methyltransferase TrmB {Streptococcus pneumoniae [TaxId: 1313]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: TrmB-like
domain: tRNA (guanine-N(7)-)-methyltransferase TrmB
species: Streptococcus pneumoniae [TaxId: 1313]

Probab=97.66  E-value=2.1e-05  Score=61.61  Aligned_cols=49  Identities=24%  Similarity=0.341  Sum_probs=39.4

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC------CCCceee
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS------YPGTLFI  241 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~------~~~i~~~  241 (244)
                      ....+||||||.|.++..+++.+|+...+.+|. +..+..+.+      +++|.++
T Consensus        31 ~~plvLdIGcG~G~~~~~lA~~~p~~~~iGid~~~~~v~~a~~~~~~~~l~Ni~~~   86 (204)
T d1yzha1          31 DNPIHVEVGSGKGAFVSGMAKQNPDINYIGIDIQKSVLSYALDKVLEVGVPNIKLL   86 (204)
T ss_dssp             CCCEEEEESCTTSHHHHHHHHHCTTSEEEEEESCHHHHHHHHHHHHHHCCSSEEEE
T ss_pred             CCCeEEEEeccCCHHHHHHHHHCCCCceEEEeccHHHHHHHHHhhhhhccccceee
Confidence            346899999999999999999999999999997 665655532      4566654

>d1vl5a_ c.66.1.41 (A:) Hypothetical protein BH2331 {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: UbiE/COQ5-like
domain: Hypothetical protein BH2331
species: Bacillus halodurans [TaxId: 86665]

Probab=97.59  E-value=2.8e-05  Score=61.18  Aligned_cols=57  Identities=19%  Similarity=0.272  Sum_probs=43.9

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC------CCCceee
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS------YPGTLFI  241 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~------~~~i~~~  241 (244)
                      ..+++..+ +.+..+|+|||||.|.++..++++.+  +++.+|+ |..++.|++      .++|+++
T Consensus         5 ~~ll~~~~-l~~~~rVLDiGcG~G~~~~~l~~~~~--~v~gvD~s~~~i~~A~~~~~~~~~~~i~~~   68 (231)
T d1vl5a_           5 AKLMQIAA-LKGNEEVLDVATGGGHVANAFAPFVK--KVVAFDLTEDILKVARAFIEGNGHQQVEYV   68 (231)
T ss_dssp             HHHHHHHT-CCSCCEEEEETCTTCHHHHHHGGGSS--EEEEEESCHHHHHHHHHHHHHTTCCSEEEE
T ss_pred             HHHHHhcC-CCCcCEEEEecccCcHHHHHHHHhCC--EEEEEECCHHHHhhhhhccccccccccccc
Confidence            35666666 78889999999999999999999876  5677888 777776643      3566654

>d1xxla_ c.66.1.41 (A:) Hypothetical protein YcgJ {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: UbiE/COQ5-like
domain: Hypothetical protein YcgJ
species: Bacillus subtilis [TaxId: 1423]

Probab=97.45  E-value=4.3e-05  Score=60.47  Aligned_cols=49  Identities=18%  Similarity=0.253  Sum_probs=40.1

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      -+++..+ ++...+|||||||+|.++..++++.+  +++.+|+ +..++.|++
T Consensus         7 ~l~~~~~-~~~~~rILDiGcGtG~~~~~la~~~~--~v~gvD~S~~~l~~A~~   56 (234)
T d1xxla_           7 LMIKTAE-CRAEHRVLDIGAGAGHTALAFSPYVQ--ECIGVDATKEMVEVASS   56 (234)
T ss_dssp             HHHHHHT-CCTTCEEEEESCTTSHHHHHHGGGSS--EEEEEESCHHHHHHHHH
T ss_pred             HHHHHhC-CCCCCEEEEeCCcCcHHHHHHHHhCC--eEEEEeCChhhhhhhhh
Confidence            3567777 88889999999999999999999875  5788998 666666653

>d1nt2a_ c.66.1.3 (A:) Fibrillarin homologue {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Fibrillarin homologue
domain: Fibrillarin homologue
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=97.44  E-value=5.7e-05  Score=59.23  Aligned_cols=53  Identities=8%  Similarity=0.043  Sum_probs=44.4

Q ss_pred             cCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC----CCCceee
Q 041256          188 YKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS----YPGTLFI  241 (244)
Q Consensus       188 ~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~----~~~i~~~  241 (244)
                      ++ ++...+|||||||+|..+..+++..|+-+++.+|. |..++.+++    +++++++
T Consensus        52 l~-lkpg~~VLDlGcG~G~~~~~la~~v~~g~V~gvDis~~~i~~a~~~a~~~~ni~~i  109 (209)
T d1nt2a_          52 LK-LRGDERVLYLGAASGTTVSHLADIVDEGIIYAVEYSAKPFEKLLELVRERNNIIPL  109 (209)
T ss_dssp             CC-CCSSCEEEEETCTTSHHHHHHHHHTTTSEEEEECCCHHHHHHHHHHHHHCSSEEEE
T ss_pred             CC-CCCCCEEEEeCCcCCHHHHHHHHhccCCeEEEEeCCHHHHHHHHHHhhccCCceEE
Confidence            45 67789999999999999999999999999999999 888887753    4555554

>d2b3ta1 c.66.1.30 (A:2-275) N5-glutamine methyltransferase, HemK {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: N5-glutamine methyltransferase, HemK
domain: N5-glutamine methyltransferase, HemK
species: Escherichia coli [TaxId: 562]

Probab=97.40  E-value=9e-05  Score=60.50  Aligned_cols=43  Identities=26%  Similarity=0.339  Sum_probs=39.3

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ....+|+|+|||+|..++.+++++|+.+++..|. |..++.|++
T Consensus       107 ~~~~~vlDlGtGSG~I~i~la~~~p~~~v~avDis~~Al~~A~~  150 (274)
T d2b3ta1         107 EQPCRILDLGTGTGAIALALASERPDCEIIAVDRMPDAVSLAQR  150 (274)
T ss_dssp             SSCCEEEEETCTTSHHHHHHHHHCTTSEEEEECSSHHHHHHHHH
T ss_pred             ccccceeeeehhhhHHHHHHHhhCCcceeeeccchhHHHhHHHH
Confidence            4557899999999999999999999999999999 889988875

>d1g8sa_ c.66.1.3 (A:) Fibrillarin homologue {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Fibrillarin homologue
domain: Fibrillarin homologue
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=97.39  E-value=4.9e-05  Score=60.53  Aligned_cols=54  Identities=11%  Similarity=0.129  Sum_probs=43.7

Q ss_pred             hcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC----CCCCceee
Q 041256          187 SYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP----SYPGTLFI  241 (244)
Q Consensus       187 ~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~----~~~~i~~~  241 (244)
                      .++ +....+|+|||||+|..+..+++..|+-+++.+|+ |..++.++    +++++.++
T Consensus        69 ~l~-ikpG~~VLDlGcGsG~~~~~la~~~~~g~V~aVDiS~~~i~~a~~~a~~~~ni~~i  127 (230)
T d1g8sa_          69 VMP-IKRDSKILYLGASAGTTPSHVADIADKGIVYAIEYAPRIMRELLDACAERENIIPI  127 (230)
T ss_dssp             CCC-CCTTCEEEEESCCSSHHHHHHHHHTTTSEEEEEESCHHHHHHHHHHTTTCTTEEEE
T ss_pred             hCC-CCCCCEEEEeCEEcCHHHHHHHHhCCCCEEEEEeCcHHHHHHHHHHHhhhcccceE
Confidence            344 67779999999999999999999999999999998 76666554    35666554

>d1l3ia_ c.66.1.22 (A:) Precorrin-6Y methyltransferase (CbiT) {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Precorrin-6Y methyltransferase (CbiT)
domain: Precorrin-6Y methyltransferase (CbiT)
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=97.33  E-value=8.1e-05  Score=56.99  Aligned_cols=48  Identities=19%  Similarity=0.138  Sum_probs=39.1

Q ss_pred             HHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          184 VLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       184 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ++.... ..+..+|+|||||+|.+++.+++..+  +++.+|. |..++.|++
T Consensus        25 il~~l~-~~~g~~VLDiGcGsG~~s~~lA~~~~--~V~avD~~~~~l~~a~~   73 (186)
T d1l3ia_          25 IMCLAE-PGKNDVAVDVGCGTGGVTLELAGRVR--RVYAIDRNPEAISTTEM   73 (186)
T ss_dssp             HHHHHC-CCTTCEEEEESCTTSHHHHHHHTTSS--EEEEEESCHHHHHHHHH
T ss_pred             HHHhcC-CCCCCEEEEEECCeEcccccccccce--EEEEecCCHHHHHHHHH
Confidence            344455 56778999999999999999988765  6788898 888888875

>d1m6ya2 c.66.1.23 (A:2-114,A:216-294) TM0872, methyltransferase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: MraW-like putative methyltransferases
domain: TM0872, methyltransferase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=97.31  E-value=0.00012  Score=56.52  Aligned_cols=53  Identities=26%  Similarity=0.293  Sum_probs=45.9

Q ss_pred             HHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          181 MEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       181 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...+++.+. .....++||+++|.|.++..+++++|+.+.+.+|+ |+.++.+++
T Consensus        12 l~evi~~l~-~~~~~~~lD~t~G~Gghs~~il~~~~~~~vi~~D~d~~~l~~a~~   65 (192)
T d1m6ya2          12 VREVIEFLK-PEDEKIILDCTVGEGGHSRAILEHCPGCRIIGIDVDSEVLRIAEE   65 (192)
T ss_dssp             HHHHHHHHC-CCTTCEEEETTCTTSHHHHHHHHHCTTCEEEEEESCHHHHHHHHH
T ss_pred             HHHHHHhhC-CCCCCEEEEecCCCcHHHHHHHhcCCCCeEEEeechHHHHHHHHH
Confidence            356677666 56668999999999999999999999999999999 899988864

>d1pjza_ c.66.1.36 (A:) Thiopurine S-methyltransferase {Pseudomonas syringae [TaxId: 317]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Thiopurine S-methyltransferase
domain: Thiopurine S-methyltransferase
species: Pseudomonas syringae [TaxId: 317]

Probab=97.29  E-value=8.4e-05  Score=56.41  Aligned_cols=47  Identities=6%  Similarity=0.001  Sum_probs=38.6

Q ss_pred             HhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          185 LESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       185 ~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...+. ..+..+|||||||.|..+..|+++  +.+++.+|+ +..++.|++
T Consensus        13 ~~~l~-~~~~~rvLd~GCG~G~~a~~la~~--G~~V~gvD~S~~~i~~a~~   60 (201)
T d1pjza_          13 WSSLN-VVPGARVLVPLCGKSQDMSWLSGQ--GYHVVGAELSEAAVERYFT   60 (201)
T ss_dssp             HHHHC-CCTTCEEEETTTCCSHHHHHHHHH--CCEEEEEEECHHHHHHHHH
T ss_pred             HHHcC-CCCCCEEEEecCcCCHHHHHHHHc--CCceEeecccHHHHHHHHH
Confidence            33344 567789999999999999999987  688999998 778877764

>d1zx0a1 c.66.1.16 (A:8-236) Guanidinoacetate methyltransferase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Guanidinoacetate methyltransferase
domain: Guanidinoacetate methyltransferase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.28  E-value=4.7e-05  Score=60.36  Aligned_cols=42  Identities=12%  Similarity=0.111  Sum_probs=34.9

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ....+|||||||.|..+..++++.|. +.+++|+ |.+++.|++
T Consensus        52 ~~g~~VLdIGcG~G~~a~~~a~~~~~-~v~~id~s~~~~~~a~~   94 (229)
T d1zx0a1          52 SKGGRVLEVGFGMAIAASKVQEAPID-EHWIIECNDGVFQRLRD   94 (229)
T ss_dssp             TTCEEEEEECCTTSHHHHHHHTSCEE-EEEEEECCHHHHHHHHH
T ss_pred             cCCCeEEEeeccchHHHHHHHHcCCC-eEEEeCCCHHHHHHHHH
Confidence            34578999999999999999987664 6888898 888888764

>d1wzna1 c.66.1.43 (A:1-251) Hypothetical methyltransferase PH1305 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: CAC2371-like
domain: Hypothetical methyltransferase PH1305
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=97.16  E-value=0.00016  Score=57.31  Aligned_cols=49  Identities=16%  Similarity=0.269  Sum_probs=39.3

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .++..+. ..+.++|||||||+|.++..++++..  +++.+|+ |..++.|++
T Consensus        32 ~~~~~~~-~~~~~~iLDiGcGtG~~~~~l~~~~~--~v~gvD~s~~mi~~a~~   81 (251)
T d1wzna1          32 EIFKEDA-KREVRRVLDLACGTGIPTLELAERGY--EVVGLDLHEEMLRVARR   81 (251)
T ss_dssp             HHHHHTC-SSCCCEEEEETCTTCHHHHHHHHTTC--EEEEEESCHHHHHHHHH
T ss_pred             HHHHHhc-CCCCCEEEEeCCCCCccchhhcccce--EEEEEeecccccccccc
Confidence            4455555 56778999999999999999999764  6888898 778888764

>d2gh1a1 c.66.1.49 (A:13-293) Methyltransferase BC2162 {Bacillus cereus [TaxId: 1396]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: BC2162-like
domain: Methyltransferase BC2162
species: Bacillus cereus [TaxId: 1396]

Probab=97.12  E-value=0.00015  Score=59.12  Aligned_cols=52  Identities=17%  Similarity=0.209  Sum_probs=41.3

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCC-CeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPH-IKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+++....+.++.+|||||||.|.++..+++.+|. .+.+.+|+ |..++.|++
T Consensus        17 ~l~~~~~~~~~~~~ILDiGcG~G~~~~~la~~~~~~~~v~giD~s~~~l~~a~~   70 (281)
T d2gh1a1          17 FLVNTVWKITKPVHIVDYGCGYGYLGLVLMPLLPEGSKYTGIDSGETLLAEARE   70 (281)
T ss_dssp             HHHHTTSCCCSCCEEEEETCTTTHHHHHHTTTSCTTCEEEEEECCHHHHHHHHH
T ss_pred             HHHHHHhccCCcCEEEEecCcCCHHHHHHHHhCCCCCEEEEEecchhHhhhhhc
Confidence            34443322677899999999999999999999985 78999998 777877764

>d1u2za_ c.66.1.31 (A:) Catalytic, N-terminal domain of histone methyltransferase Dot1l {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Catalytic, N-terminal domain of histone methyltransferase Dot1l
domain: Catalytic, N-terminal domain of histone methyltransferase Dot1l
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.12  E-value=0.00019  Score=61.66  Aligned_cols=51  Identities=10%  Similarity=0.151  Sum_probs=43.2

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~  233 (244)
                      ..+++..+ +....+|||||||.|..+..+++++|.-+++.+|+ |..++.|+
T Consensus       206 ~~Il~~l~-Lkpgd~fLDLGCG~G~~vl~aA~~~g~~~v~GIDiS~~~i~~Ak  257 (406)
T d1u2za_         206 SDVYQQCQ-LKKGDTFMDLGSGVGNCVVQAALECGCALSFGCEIMDDASDLTI  257 (406)
T ss_dssp             HHHHHHTT-CCTTCEEEEESCTTSHHHHHHHHHHCCSEEEEEECCHHHHHHHH
T ss_pred             HHHHHHhC-CCCCCEEEeCCCCCcHHHHHHHHHcCCCeEEEEeCCHHHHHHHH
Confidence            45666666 77778999999999999999999999889999998 66666664

>d1xtpa_ c.66.1.42 (A:) Hypothetical protein Lmaj004091aaa (LmjF30.0810) {Leishmania major [TaxId: 5664]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: AD-003 protein-like
domain: Hypothetical protein Lmaj004091aaa (LmjF30.0810)
species: Leishmania major [TaxId: 5664]

Probab=97.11  E-value=0.00014  Score=58.56  Aligned_cols=51  Identities=14%  Similarity=0.205  Sum_probs=41.1

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+++.++ ..+..++||||||.|.++..+++++++ +++.+|. +..++.|++
T Consensus        83 ~~fl~~l~-~~~~~~vLD~GcG~G~~t~~ll~~~~~-~v~~vD~s~~~l~~a~~  134 (254)
T d1xtpa_          83 RNFIASLP-GHGTSRALDCGAGIGRITKNLLTKLYA-TTDLLEPVKHMLEEAKR  134 (254)
T ss_dssp             HHHHHTST-TCCCSEEEEETCTTTHHHHHTHHHHCS-EEEEEESCHHHHHHHHH
T ss_pred             HHHHhhCC-CCCCCeEEEecccCChhhHHHHhhcCc-eEEEEcCCHHHHHhhhc
Confidence            34566666 567789999999999999999988776 6778887 778888764

>d1dusa_ c.66.1.4 (A:) Hypothetical protein MJ0882 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Hypothetical protein MJ0882
domain: Hypothetical protein MJ0882
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=97.00  E-value=0.00018  Score=55.26  Aligned_cols=49  Identities=18%  Similarity=0.233  Sum_probs=38.7

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      -+++.++ ..+..+|+|||||+|.++..+++.+|+  +++.|+ |..++.+++
T Consensus        43 lLi~~l~-~~~~~~VLDiGcG~G~~~~~la~~~~~--v~~iD~s~~~i~~a~~   92 (194)
T d1dusa_          43 ILVENVV-VDKDDDILDLGCGYGVIGIALADEVKS--TTMADINRRAIKLAKE   92 (194)
T ss_dssp             HHHHHCC-CCTTCEEEEETCTTSHHHHHHGGGSSE--EEEEESCHHHHHHHHH
T ss_pred             HHHHhCC-cCCCCeEEEEeecCChhHHHHHhhccc--cceeeeccccchhHHH
Confidence            3455666 566789999999999999999999886  555676 888887764

>d2i6ga1 c.66.1.44 (A:1-198) Putative methyltransferase TehB {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: TehB-like
domain: Putative methyltransferase TehB
species: Salmonella typhimurium [TaxId: 90371]

Probab=96.99  E-value=0.0003  Score=53.96  Aligned_cols=48  Identities=19%  Similarity=0.200  Sum_probs=36.7

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~  233 (244)
                      .++.... +....+|||||||.|..+..++++.+  +++.+|+ +..++.++
T Consensus        21 ~~~~~~~-~~~~grvLDiGcG~G~~~~~la~~g~--~v~gvD~s~~~l~~a~   69 (198)
T d2i6ga1          21 DVLAAAK-VVAPGRTLDLGCGNGRNSLYLAANGY--DVTAWDKNPASMANLE   69 (198)
T ss_dssp             HHHHHHT-TSCSCEEEEETCTTSHHHHHHHHTTC--EEEEEESCHHHHHHHH
T ss_pred             HHHHHcc-cCCCCcEEEECCCCCHHHHHHHHHhh--hhccccCcHHHHHHHH
Confidence            3444444 55567999999999999999999864  6788898 66677654

>d1ne2a_ c.66.1.32 (A:) Hypothetical protein Ta1320 {Archaeon Thermoplasma acidophilum [TaxId: 2303]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Ta1320-like
domain: Hypothetical protein Ta1320
species: Archaeon Thermoplasma acidophilum [TaxId: 2303]

Probab=96.96  E-value=0.00024  Score=55.02  Aligned_cols=49  Identities=22%  Similarity=0.291  Sum_probs=37.4

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC-CCCceee
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS-YPGTLFI  241 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~-~~~i~~~  241 (244)
                      ++ .++|+|+|||+|.++++++...+. +++.+|. |..++.+++ .++++++
T Consensus        47 l~-Gk~VLDlGcGtG~l~i~a~~~ga~-~V~~vDid~~a~~~ar~N~~~~~~~   97 (197)
T d1ne2a_          47 IG-GRSVIDAGTGNGILACGSYLLGAE-SVTAFDIDPDAIETAKRNCGGVNFM   97 (197)
T ss_dssp             SB-TSEEEEETCTTCHHHHHHHHTTBS-EEEEEESCHHHHHHHHHHCTTSEEE
T ss_pred             CC-CCEEEEeCCCCcHHHHHHHHcCCC-cccccccCHHHHHHHHHccccccEE
Confidence            54 389999999999999888777665 6788887 888888775 3455543

>d2ex4a1 c.66.1.42 (A:2-224) Adrenal gland protein AD-003 (C9orf32) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: AD-003 protein-like
domain: Adrenal gland protein AD-003 (C9orf32)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.95  E-value=0.00014  Score=57.03  Aligned_cols=43  Identities=14%  Similarity=0.125  Sum_probs=36.0

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+..+|||||||.|.++..++++++. +++.+|+ |..++.|++
T Consensus        58 ~~~~~~vLDiGcG~G~~~~~l~~~~~~-~v~~vD~s~~~l~~ak~  101 (222)
T d2ex4a1          58 KTGTSCALDCGAGIGRITKRLLLPLFR-EVDMVDITEDFLVQAKT  101 (222)
T ss_dssp             CCCCSEEEEETCTTTHHHHHTTTTTCS-EEEEEESCHHHHHHHHH
T ss_pred             CCCCCEEEEeccCCCHhhHHHHHhcCC-EEEEeecCHHHhhcccc
Confidence            345689999999999999999888874 7888898 888887764

>d2p7ia1 c.66.1.41 (A:22-246) Hypothetical protein ECA1738 {Erwinia carotovora [TaxId: 554]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: UbiE/COQ5-like
domain: Hypothetical protein ECA1738
species: Erwinia carotovora [TaxId: 554]

Probab=96.92  E-value=0.00022  Score=56.01  Aligned_cols=49  Identities=16%  Similarity=0.172  Sum_probs=37.7

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC--CCCceee
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS--YPGTLFI  241 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~--~~~i~~~  241 (244)
                      +.+.++|||||||+|.++..++++..  +++.+|+ |..++.|++  ..+|+++
T Consensus        18 ~~~~~~VLDiGcG~G~~~~~l~~~g~--~v~giD~s~~~i~~a~~~~~~~~~~~   69 (225)
T d2p7ia1          18 FFRPGNLLELGSFKGDFTSRLQEHFN--DITCVEASEEAISHAQGRLKDGITYI   69 (225)
T ss_dssp             GCCSSCEEEESCTTSHHHHHHTTTCS--CEEEEESCHHHHHHHHHHSCSCEEEE
T ss_pred             hCCCCcEEEEeCCCcHHHHHHHHcCC--eEEEEeCcHHHhhhhhcccccccccc
Confidence            34557899999999999999998865  5888898 778888764  2345543

>d1ve3a1 c.66.1.43 (A:2-227) Hypothetical protein PH0226 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: CAC2371-like
domain: Hypothetical protein PH0226
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=96.90  E-value=0.00038  Score=53.88  Aligned_cols=48  Identities=19%  Similarity=0.295  Sum_probs=36.4

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .++..+  +.+..+|||||||+|.++..+++.  +.+++.+|+ +..++.|++
T Consensus        29 ~~~~~~--l~~~~~ILDiGcG~G~~~~~la~~--~~~v~giD~S~~~i~~ak~   77 (226)
T d1ve3a1          29 PLLMKY--MKKRGKVLDLACGVGGFSFLLEDY--GFEVVGVDISEDMIRKARE   77 (226)
T ss_dssp             HHHHHS--CCSCCEEEEETCTTSHHHHHHHHT--TCEEEEEESCHHHHHHHHH
T ss_pred             HHHHHh--cCCCCEEEEECCCcchhhhhHhhh--hcccccccccccchhhhhh
Confidence            344443  344478999999999999999985  567888998 777877754

>d2nxca1 c.66.1.39 (A:1-254) PrmA-like protein TTHA0656 (TT0836) {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Ribosomal protein L11 methyltransferase PrmA
domain: PrmA-like protein TTHA0656 (TT0836)
species: Thermus thermophilus [TaxId: 274]

Probab=96.88  E-value=0.00025  Score=57.17  Aligned_cols=62  Identities=21%  Similarity=0.322  Sum_probs=42.7

Q ss_pred             HHHHHHHhcchhhHHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          168 VFNNGMLSHTSIVMEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       168 ~f~~aM~~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .|..+-..+++.....+ ..+.  ....+|+|||||+|.+++++++.  +.+++.+|. |..++.|++
T Consensus        98 aFGTG~H~TT~l~l~~l-~~~~--~~g~~VLDiGcGsG~l~i~aa~~--g~~V~gvDis~~av~~A~~  160 (254)
T d2nxca1          98 AFGTGHHETTRLALKAL-ARHL--RPGDKVLDLGTGSGVLAIAAEKL--GGKALGVDIDPMVLPQAEA  160 (254)
T ss_dssp             ----CCSHHHHHHHHHH-HHHC--CTTCEEEEETCTTSHHHHHHHHT--TCEEEEEESCGGGHHHHHH
T ss_pred             ccCccccchhhHHHHHH-Hhhc--CccCEEEEcccchhHHHHHHHhc--CCEEEEEECChHHHHHHHH
Confidence            56666666665555443 3333  34589999999999999988775  457889998 888888874

>d1nw3a_ c.66.1.31 (A:) Catalytic, N-terminal domain of histone methyltransferase Dot1l {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Catalytic, N-terminal domain of histone methyltransferase Dot1l
domain: Catalytic, N-terminal domain of histone methyltransferase Dot1l
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.88  E-value=0.00055  Score=57.03  Aligned_cols=51  Identities=16%  Similarity=0.211  Sum_probs=42.9

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~  233 (244)
                      ..+++.+. ..+..+|+|||||.|.++..+++.+|..+++.+|+ |..++.|+
T Consensus       141 ~~~~~~~~-l~~~~~vlD~GcG~G~~~~~~a~~~~~~~~~Gid~s~~~~~~a~  192 (328)
T d1nw3a_         141 AQMIDEIK-MTDDDLFVDLGSGVGQVVLQVAAATNCKHHYGVEKADIPAKYAE  192 (328)
T ss_dssp             HHHHHHSC-CCTTCEEEEETCTTSHHHHHHHHHCCCSEEEEEECSHHHHHHHH
T ss_pred             HHHHHHcC-CCCCCEEEEcCCCCCHHHHHHHHHhCCCeEEEEeCCHHHHHHHH
Confidence            45666676 77778999999999999999999999999999998 66666553

>d2fk8a1 c.66.1.18 (A:22-301) Methoxy mycolic acid synthase 4, Mma4 {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Mycolic acid cyclopropane synthase
domain: Methoxy mycolic acid synthase 4, Mma4
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=96.84  E-value=0.00036  Score=56.94  Aligned_cols=50  Identities=18%  Similarity=0.331  Sum_probs=40.5

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~  233 (244)
                      ..+++.+. ++...+|||||||.|.++..++++++ .+++.+|+ ++-++.|+
T Consensus        42 ~~~~~~l~-l~~g~~VLDiGCG~G~~a~~~a~~~g-~~v~gi~ls~~q~~~a~   92 (280)
T d2fk8a1          42 DLNLDKLD-LKPGMTLLDIGCGWGTTMRRAVERFD-VNVIGLTLSKNQHARCE   92 (280)
T ss_dssp             HHHHTTSC-CCTTCEEEEESCTTSHHHHHHHHHHC-CEEEEEESCHHHHHHHH
T ss_pred             HHHHHHcC-CCCCCEEEEecCCchHHHHHHHHhCc-eeEEEecchHHHHHHHH
Confidence            46777777 78889999999999999999888886 58999988 55555554

>d1dl5a1 c.66.1.7 (A:1-213) Protein-L-isoaspartyl O-methyltransferase {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Protein-L-isoaspartyl O-methyltransferase
domain: Protein-L-isoaspartyl O-methyltransferase
species: Thermotoga maritima [TaxId: 2336]

Probab=96.80  E-value=0.00074  Score=52.69  Aligned_cols=51  Identities=12%  Similarity=0.186  Sum_probs=42.6

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHC-CCCeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKY-PHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+++.++ .+...+|+|||||+|.++..+++.. |+.+++.+|. |+.++.|++
T Consensus        66 ~~l~~l~-l~~g~~VLdiG~GtG~~s~~la~~~~~~g~V~~id~~~~~~~~a~~  118 (213)
T d1dl5a1          66 LFMEWVG-LDKGMRVLEIGGGTGYNAAVMSRVVGEKGLVVSVEYSRKICEIAKR  118 (213)
T ss_dssp             HHHHHTT-CCTTCEEEEECCTTSHHHHHHHHHHCTTCEEEEEESCHHHHHHHHH
T ss_pred             HHHHhhh-ccccceEEEecCccchhHHHHHHHhCCCCcEEEeecchhhHHHhhh
Confidence            4566666 7888999999999999999999876 7788999987 888888764

>d1xvaa_ c.66.1.5 (A:) Glycine N-methyltransferase {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Glycine N-methyltransferase
domain: Glycine N-methyltransferase
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=96.78  E-value=0.00041  Score=56.59  Aligned_cols=40  Identities=20%  Similarity=0.297  Sum_probs=33.7

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~  233 (244)
                      .+.++|||||||+|.++..|+++  +.+++.+|+ |..++.|+
T Consensus        55 ~~~~~vLD~GcG~G~~~~~la~~--g~~v~gvD~S~~ml~~A~   95 (292)
T d1xvaa_          55 HGCHRVLDVACGTGVDSIMLVEE--GFSVTSVDASDKMLKYAL   95 (292)
T ss_dssp             TTCCEEEESSCTTSHHHHHHHHT--TCEEEEEESCHHHHHHHH
T ss_pred             cCCCEEEEecCCCcHHHHHHHHc--CCeeeeccCchHHHHHHH
Confidence            44579999999999999999987  578999999 67776654

>d1ri5a_ c.66.1.34 (A:) mRNA cap (Guanine N-7) methyltransferase {Fungus (Encephalitozoon cuniculi) [TaxId: 6035]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: mRNA cap (Guanine N-7) methyltransferase
domain: mRNA cap (Guanine N-7) methyltransferase
species: Fungus (Encephalitozoon cuniculi) [TaxId: 6035]

Probab=96.78  E-value=0.00053  Score=54.66  Aligned_cols=48  Identities=21%  Similarity=0.194  Sum_probs=37.2

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~  233 (244)
                      .+++.|.  +...+|||||||+|..+..+++..+. +.+..|+ |..++.|+
T Consensus        16 ~lI~~~~--~~~~~VLDlGCG~G~~~~~~~~~~~~-~v~GiD~S~~~l~~A~   64 (252)
T d1ri5a_          16 CLIRLYT--KRGDSVLDLGCGKGGDLLKYERAGIG-EYYGVDIAEVSINDAR   64 (252)
T ss_dssp             HHHHHHC--CTTCEEEEETCTTTTTHHHHHHHTCS-EEEEEESCHHHHHHHH
T ss_pred             HHHHHhC--CCcCEEEEecccCcHHHHHHHHcCCC-eEEEecCCHHHHHHHH
Confidence            4556653  55689999999999999999887543 6788898 77777775

>d1y8ca_ c.66.1.43 (A:) Putative methyltransferase CAC2371 {Clostridium acetobutylicum [TaxId: 1488]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: CAC2371-like
domain: Putative methyltransferase CAC2371
species: Clostridium acetobutylicum [TaxId: 1488]

Probab=96.78  E-value=0.00019  Score=56.94  Aligned_cols=40  Identities=18%  Similarity=0.278  Sum_probs=33.5

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..++|||||||+|.++..++++..  +++.+|+ |..++.|++
T Consensus        37 ~~~~vLDiGCG~G~~~~~l~~~g~--~v~GvD~S~~ml~~A~~   77 (246)
T d1y8ca_          37 VFDDYLDLACGTGNLTENLCPKFK--NTWAVDLSQEMLSEAEN   77 (246)
T ss_dssp             CTTEEEEETCTTSTTHHHHGGGSS--EEEEECSCHHHHHHHHH
T ss_pred             CCCeEEEEeCcCCHHHHHHHHhCC--ccEeeccchhhhhhccc
Confidence            357899999999999999999876  5788898 677777754

>d2avna1 c.66.1.41 (A:1-246) Hypothetical methyltransferase TM1389 {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: UbiE/COQ5-like
domain: Hypothetical methyltransferase TM1389
species: Thermotoga maritima [TaxId: 2336]

Probab=96.76  E-value=0.00033  Score=55.02  Aligned_cols=41  Identities=17%  Similarity=0.249  Sum_probs=34.6

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+..+|||||||+|.++..++++  +.+++.+|+ |..++.|++
T Consensus        41 ~~~~~vLDiGcG~G~~~~~l~~~--~~~v~giD~s~~~l~~a~~   82 (246)
T d2avna1          41 KNPCRVLDLGGGTGKWSLFLQER--GFEVVLVDPSKEMLEVARE   82 (246)
T ss_dssp             CSCCEEEEETCTTCHHHHHHHTT--TCEEEEEESCHHHHHHHHH
T ss_pred             CCCCEEEEECCCCchhccccccc--ceEEEEeeccccccccccc
Confidence            45578999999999999999876  568899998 888887765

>d1kpga_ c.66.1.18 (A:) CmaA1 {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Mycolic acid cyclopropane synthase
domain: CmaA1
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=96.56  E-value=0.00073  Score=55.20  Aligned_cols=49  Identities=22%  Similarity=0.344  Sum_probs=39.4

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDA  232 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a  232 (244)
                      ..+++... .+...+|||||||.|.++..++++++ ++++.+++ |+-++.|
T Consensus        52 ~~~~~~l~-l~~G~~VLDiGCG~G~~a~~~a~~~g-~~v~git~s~~Q~~~a  101 (285)
T d1kpga_          52 DLALGKLG-LQPGMTLLDVGCGWGATMMRAVEKYD-VNVVGLTLSKNQANHV  101 (285)
T ss_dssp             HHHHTTTT-CCTTCEEEEETCTTSHHHHHHHHHHC-CEEEEEESCHHHHHHH
T ss_pred             HHHHHHcC-CCCCCEEEEecCcchHHHHHHHhcCC-cceEEEeccHHHHHHH
Confidence            45667776 78889999999999999999999995 79988888 4434433

>d2bzga1 c.66.1.36 (A:17-245) Thiopurine S-methyltransferase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Thiopurine S-methyltransferase
domain: Thiopurine S-methyltransferase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.53  E-value=0.00085  Score=52.64  Aligned_cols=41  Identities=5%  Similarity=-0.032  Sum_probs=34.8

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~  233 (244)
                      .....+|||+|||.|..+..|+++  +.+++.+|+ |..|+.++
T Consensus        43 ~~~~~rvLd~GCG~G~~a~~LA~~--G~~V~gvD~S~~ai~~a~   84 (229)
T d2bzga1          43 GKSGLRVFFPLCGKAVEMKWFADR--GHSVVGVEISELGIQEFF   84 (229)
T ss_dssp             TCCSCEEEETTCTTCTHHHHHHHT--TCEEEEECSCHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCcHHHHHHHhC--CCcEEEEeCCHHHHHHHH
Confidence            456689999999999999999986  668999999 77887654

>d2h00a1 c.66.1.54 (A:5-254) Methyltransferase 10 domain containing protein METT10D {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Methyltransferase 10 domain
domain: Methyltransferase 10 domain containing protein METT10D
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.45  E-value=0.00057  Score=54.79  Aligned_cols=43  Identities=9%  Similarity=0.144  Sum_probs=39.0

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      +...+++|||+|+|..+..|++++|+.+++..|. |+.++.|++
T Consensus        60 ~~~~~~LDiGtGsg~I~~~l~~~~~~~~~~~~Di~~~al~~A~~  103 (250)
T d2h00a1          60 STLRRGIDIGTGASCIYPLLGATLNGWYFLATEVDDMCFNYAKK  103 (250)
T ss_dssp             CCCCEEEEESCTTTTHHHHHHHHHHCCEEEEEESCHHHHHHHHH
T ss_pred             cccceEEEeCCCchHHHHHHHHhCCCccccceecCHHHHHHHHH
Confidence            3457999999999999999999999999999999 888888865

>d1o54a_ c.66.1.13 (A:) Hypothetical protein TM0748 {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: tRNA(1-methyladenosine) methyltransferase-like
domain: Hypothetical protein TM0748
species: Thermotoga maritima [TaxId: 2336]

Probab=96.43  E-value=0.0015  Score=52.73  Aligned_cols=66  Identities=20%  Similarity=0.129  Sum_probs=50.8

Q ss_pred             HHHHHHHhcchhh----HHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHC-CCCeEEEccc-hHHhhhCCC
Q 041256          168 VFNNGMLSHTSIV----MEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKY-PHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       168 ~f~~aM~~~~~~~----~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .|...|...++..    +.-++...+ .....+|+|+|||+|.++..+++.. |+-+.+.+|. |+.++.|++
T Consensus        75 d~~~~~~r~~qiiypkd~~~Ii~~l~-i~pG~~VLDiG~GsG~lt~~lA~~~~~~G~V~~vD~~~~~~~~A~~  146 (266)
T d1o54a_          75 DEIMNMKRRTQIVYPKDSSFIAMMLD-VKEGDRIIDTGVGSGAMCAVLARAVGSSGKVFAYEKREEFAKLAES  146 (266)
T ss_dssp             HHHHTCCC-CCCCCHHHHHHHHHHTT-CCTTCEEEEECCTTSHHHHHHHHHTTTTCEEEEECCCHHHHHHHHH
T ss_pred             HHHhhccCCccccchHHHHHHHHhhC-CCCCCEEEECCCCCCHHHHHHHHHhCCCcEEEEEeCCHHHHHHHHH
Confidence            3445666555532    234566677 7888999999999999999999875 8999999998 888888764

>d1yb2a1 c.66.1.13 (A:6-255) Hypothetical protein Ta0852 {Thermoplasma acidophilum [TaxId: 2303]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: tRNA(1-methyladenosine) methyltransferase-like
domain: Hypothetical protein Ta0852
species: Thermoplasma acidophilum [TaxId: 2303]

Probab=96.43  E-value=0.0011  Score=53.06  Aligned_cols=66  Identities=15%  Similarity=0.113  Sum_probs=42.3

Q ss_pred             HHHHHHHhcchhhH----HHHHhhcCCCCCcceEEEecCCccHHHHHHHHH-CCCCeEEEccc-hHHhhhCCC
Q 041256          168 VFNNGMLSHTSIVM----EKVLESYKGFEHVKKLVDVGGGLGITLNMIISK-YPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       168 ~f~~aM~~~~~~~~----~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~-~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .|...|...++...    ..++...+ .....+|+|+|||+|.++..+++. .|+-+.+.+|. ++.++.|++
T Consensus        57 ~~~~~~~r~~qiiypkD~~~Ii~~l~-i~pG~rVLEiG~GsG~lt~~la~~v~~~g~V~~vD~~e~~~~~A~~  128 (250)
T d1yb2a1          57 YFGRVIRRNTQIISEIDASYIIMRCG-LRPGMDILEVGVGSGNMSSYILYALNGKGTLTVVERDEDNLKKAMD  128 (250)
T ss_dssp             GHHHHC------------------CC-CCTTCEEEEECCTTSHHHHHHHHHHTTSSEEEEECSCHHHHHHHHH
T ss_pred             HHHhhCCCCCcccCHHHHHHHHHHcC-CCCcCEEEEeeeeCcHHHHHHHHHhCCCcEEEEEECCHHHHHHHHH
Confidence            45555665555432    23444455 667799999999999999999987 68999999998 667777653

>d1kpia_ c.66.1.18 (A:) CmaA2 {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Mycolic acid cyclopropane synthase
domain: CmaA2
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=96.43  E-value=0.0016  Score=53.20  Aligned_cols=42  Identities=26%  Similarity=0.482  Sum_probs=36.5

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL  225 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  225 (244)
                      ..+++... ++...+|||||||.|.++..++++++ .+++.+++
T Consensus        51 ~~~~~~l~-l~~G~~VLDiGCG~G~~~~~~a~~~g-~~v~git~   92 (291)
T d1kpia_          51 KLALDKLN-LEPGMTLLDIGCGWGSTMRHAVAEYD-VNVIGLTL   92 (291)
T ss_dssp             HHHHHTTC-CCTTCEEEEETCTTSHHHHHHHHHHC-CEEEEEES
T ss_pred             HHHHHhcC-CCCCCEEEEecCcchHHHHHHHHhcC-cceeeccc
Confidence            45677777 88889999999999999999999997 58888888

>d1jqea_ c.66.1.19 (A:) Histamine methyltransferase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Histamine methyltransferase
domain: Histamine methyltransferase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.37  E-value=0.0011  Score=53.43  Aligned_cols=52  Identities=17%  Similarity=0.243  Sum_probs=33.4

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHH----HHCCCCe--EEEccc-hHHhhhCC
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMII----SKYPHIK--GINYDL-PYVIKDAP  233 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~----~~~P~l~--~~v~Dl-p~vi~~a~  233 (244)
                      +.+++.+...+...+|||||||+|.++..++    .++|+..  .+.+|. +..++.++
T Consensus        29 ~~~l~~l~~~~~~~~VLDiGcG~G~~~~~ll~~l~~~~~~~~~~~~~vD~s~~~l~~a~   87 (280)
T d1jqea_          29 PGIIGRIGDTKSEIKILSIGGGAGEIDLQILSKVQAQYPGVCINNEVVEPSAEQIAKYK   87 (280)
T ss_dssp             HHHTTTTTTTCSEEEEEEETCTTSHHHHHHHHHHHHHSTTCEEEEEEECCCHHHHHHHH
T ss_pred             HHHHHHhccCCCCCeEEEEcCCCCHHHHHHHHHhhhhccCCceEEEEEeCcHHHHHHHH
Confidence            3444443212344579999999999866654    4577764  578887 55565553

>d1i9ga_ c.66.1.13 (A:) Probable methyltransferase Rv2118c {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: tRNA(1-methyladenosine) methyltransferase-like
domain: Probable methyltransferase Rv2118c
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=96.34  E-value=0.0018  Score=52.19  Aligned_cols=66  Identities=12%  Similarity=0.167  Sum_probs=51.4

Q ss_pred             HHHHHHHhcchhh----HHHHHhhcCCCCCcceEEEecCCccHHHHHHHHH-CCCCeEEEccc-hHHhhhCCC
Q 041256          168 VFNNGMLSHTSIV----MEKVLESYKGFEHVKKLVDVGGGLGITLNMIISK-YPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       168 ~f~~aM~~~~~~~----~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~-~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .|...|...++..    +.-++...+ .....+|||+|||+|.++..|++. .|+-+.+.+|. ++.++.|++
T Consensus        68 ~~~~~~~r~tqiiypkD~s~Ii~~l~-i~PG~~VLE~G~GsG~lt~~La~~vgp~G~V~~~d~~~~~~~~Ar~  139 (264)
T d1i9ga_          68 DYVMSMPRGPQVIYPKDAAQIVHEGD-IFPGARVLEAGAGSGALTLSLLRAVGPAGQVISYEQRADHAEHARR  139 (264)
T ss_dssp             HHHTTSCSCSCCCCHHHHHHHHHHTT-CCTTCEEEEECCTTSHHHHHHHHHHCTTSEEEEECSCHHHHHHHHH
T ss_pred             HHHhhccCCccccchHHHHHHHHHhC-CCCCCEEEecCcCCcHHHHHHHHhhCCCcEEEEecCCHHHHHHHHH
Confidence            4555666666543    334566666 788899999999999999999998 79999999998 777777753

>d1vlma_ c.66.1.41 (A:) Possible histamine N-methyltransferase TM1293 {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: UbiE/COQ5-like
domain: Possible histamine N-methyltransferase TM1293
species: Thermotoga maritima [TaxId: 2336]

Probab=96.32  E-value=0.001  Score=50.98  Aligned_cols=34  Identities=18%  Similarity=0.102  Sum_probs=27.2

Q ss_pred             ceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          195 KKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       195 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+|||||||+|.++..+.+      .+.+|+ |..++.+++
T Consensus        38 ~~vLDiGcG~G~~~~~~~~------~~giD~s~~~~~~a~~   72 (208)
T d1vlma_          38 GRGVEIGVGTGRFAVPLKI------KIGVEPSERMAEIARK   72 (208)
T ss_dssp             SCEEEETCTTSTTHHHHTC------CEEEESCHHHHHHHHH
T ss_pred             CeEEEECCCCcccccccce------EEEEeCChhhcccccc
Confidence            5799999999999887743      467788 888887764

>d1ub9a_ a.4.5.28 (A:) Hypothetical protein PH1061 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Hypothetical protein PH1061
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=96.31  E-value=0.0012  Score=44.89  Aligned_cols=63  Identities=17%  Similarity=0.213  Sum_probs=48.5

Q ss_pred             HHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCcccc
Q 041256           33 VVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSA  105 (244)
Q Consensus        33 a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~  105 (244)
                      -.++.|...|...   ++.|+.|||+.++++      ... +.+.|+.|...|+++......++   .|++|+.++
T Consensus        16 p~r~~IL~~L~~~---~~~~~~eLa~~l~is------~~~-vs~~l~~L~~~glV~~~~~~~d~r~~~~~LT~~G~   81 (100)
T d1ub9a_          16 PVRLGIMIFLLPR---RKAPFSQIQKVLDLT------PGN-LDSHIRVLERNGLVKTYKVIADRPRTVVEITDFGM   81 (100)
T ss_dssp             HHHHHHHHHHHHH---SEEEHHHHHHHTTCC------HHH-HHHHHHHHHHTTSEEEEEECSSSCEEEEEECHHHH
T ss_pred             HHHHHHHHHhccC---CCeeHHHHHHHHhhc------ccc-ccHHHHHHhhhceeEEEEcCcCCccccccCCHHHH
Confidence            3467788888765   689999999999997      456 99999999999999864222222   388887664

>d1wy7a1 c.66.1.32 (A:4-204) Hypothetical protein PH1948 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Ta1320-like
domain: Hypothetical protein PH1948
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=96.10  E-value=0.0015  Score=50.46  Aligned_cols=42  Identities=17%  Similarity=0.131  Sum_probs=33.6

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      +++ ++|+|+|||+|.++++++.+.+ .+++.+|. |..++.+++
T Consensus        45 l~g-~~vLDlg~GtG~l~i~a~~~g~-~~v~~vdi~~~~~~~a~~   87 (201)
T d1wy7a1          45 IEG-KVVADLGAGTGVLSYGALLLGA-KEVICVEVDKEAVDVLIE   87 (201)
T ss_dssp             STT-CEEEEETCTTCHHHHHHHHTTC-SEEEEEESCHHHHHHHHH
T ss_pred             CCC-CEEEECcCcchHHHHHHHHcCC-CEEEEEcCcHHHHHHHHH
Confidence            444 7999999999999998877644 58888998 777777754

>d2esra1 c.66.1.46 (A:28-179) Putative methyltransferase SPy1538 {Streptococcus pyogenes [TaxId: 1314]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: YhhF-like
domain: Putative methyltransferase SPy1538
species: Streptococcus pyogenes [TaxId: 1314]

Probab=96.04  E-value=0.0029  Score=46.36  Aligned_cols=41  Identities=10%  Similarity=-0.038  Sum_probs=34.7

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      +.++|||+|||+|.++++.+.+... +++.+|. |..++.+++
T Consensus        14 ~g~~vlDl~~GtG~~~iea~~rga~-~v~~ve~~~~a~~~~~~   55 (152)
T d2esra1          14 NGGRVLDLFAGSGGLAIEAVSRGMS-AAVLVEKNRKAQAIIQD   55 (152)
T ss_dssp             CSCEEEEETCTTCHHHHHHHHTTCC-EEEEECCCHHHHHHHHH
T ss_pred             CCCeEEEcCCccCHHHHHHHHhCcc-eeeeehhchhhhhhhhh
Confidence            4589999999999999999988775 8899998 888877654

>d2fyta1 c.66.1.6 (A:238-548) Protein arginine N-methyltransferase 3, PRMT3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Arginine methyltransferase
domain: Protein arginine N-methyltransferase 3, PRMT3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.99  E-value=0.0044  Score=50.71  Aligned_cols=38  Identities=24%  Similarity=0.198  Sum_probs=30.5

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhh
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIK  230 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~  230 (244)
                      .+.++|+|||||+|.+++.++++.+ -+++.+|..+...
T Consensus        34 ~~~~~VLDiGcG~G~lsl~aa~~Ga-~~V~aid~s~~~~   71 (311)
T d2fyta1          34 FKDKVVLDVGCGTGILSMFAAKAGA-KKVLGVDQSEILY   71 (311)
T ss_dssp             TTTCEEEEETCTTSHHHHHHHHTTC-SEEEEEESSTHHH
T ss_pred             CCcCEEEEECCCCCHHHHHHHHcCC-CEEEEEeCHHHHH
Confidence            3458999999999999999998866 3788889855443

>d1r1ta_ a.4.5.5 (A:) SmtB repressor {Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: SmtB repressor
species: Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]

Probab=95.78  E-value=0.0037  Score=42.46  Aligned_cols=52  Identities=17%  Similarity=0.339  Sum_probs=43.9

Q ss_pred             HHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           28 AVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        28 ~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      ++|.--.++.|+..|.+    ++.|+.|||+.+|++      ... +.+-|+.|...|++...
T Consensus        18 kaL~~p~Rl~Il~~L~~----~~~~v~ela~~l~is------~st-vS~HL~~L~~aglV~~~   69 (98)
T d1r1ta_          18 AVLADPNRLRLLSLLAR----SELCVGDLAQAIGVS------ESA-VSHQLRSLRNLRLVSYR   69 (98)
T ss_dssp             HHHCCHHHHHHHHHHTT----CCBCHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEEE
T ss_pred             HHhCCHHHHHHHHHHHc----CCcCHHHHHHHHCcC------HHH-HHHHHHHHHHCCceEEE
Confidence            45556677888888976    689999999999997      456 99999999999999864

>d1i1na_ c.66.1.7 (A:) Protein-L-isoaspartyl O-methyltransferase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Protein-L-isoaspartyl O-methyltransferase
domain: Protein-L-isoaspartyl O-methyltransferase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.69  E-value=0.0064  Score=47.51  Aligned_cols=52  Identities=25%  Similarity=0.185  Sum_probs=39.8

Q ss_pred             HHHhhcC-CCCCcceEEEecCCccHHHHHHHHH-CCCCeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYK-GFEHVKKLVDVGGGLGITLNMIISK-YPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~-~~~~~~~vvDVGGG~G~~~~~l~~~-~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+++.+. ..+...+|||||||+|..+..+++. .|.-+++.+|. |+.++.|++
T Consensus        65 ~~le~L~~~l~~g~~VLdiG~GsGy~ta~la~l~~~~g~V~~ie~~~~l~~~a~~  119 (224)
T d1i1na_          65 YALELLFDQLHEGAKALDVGSGSGILTACFARMVGCTGKVIGIDHIKELVDDSVN  119 (224)
T ss_dssp             HHHHHTTTTSCTTCEEEEETCTTSHHHHHHHHHHCTTCEEEEEESCHHHHHHHHH
T ss_pred             HHHHHHhhccCCCCeEEEecCCCCHHHHHHHHHhCCCceEEEEcCCHHHHHHHHH
Confidence            3455441 2566789999999999999888874 68889999997 778777653

>d1lvaa3 a.4.5.35 (A:511-574) C-terminal fragment of elongation factor SelB {Moorella thermoacetica [TaxId: 1525]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: C-terminal fragment of elongation factor SelB
domain: C-terminal fragment of elongation factor SelB
species: Moorella thermoacetica [TaxId: 1525]

Probab=95.69  E-value=0.01  Score=36.86  Aligned_cols=53  Identities=19%  Similarity=0.167  Sum_probs=40.8

Q ss_pred             ChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeec
Q 041256           37 DVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSL  100 (244)
Q Consensus        37 gifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~  100 (244)
                      .|-+++.+.|- .|-++.|||+.+|++      +.. ++.+|+.|+..|.+.+   ..++.|-|
T Consensus        11 ~I~~~~~~~g~-~PP~vrdl~~~l~~~------e~~-~~~lL~~l~~~G~lvk---I~~d~yfh   63 (64)
T d1lvaa3          11 DLEDKYRVSRW-QPPSFKEVAGSFNLD------PSE-LEELLHYLVREGVLVK---INDEFYWH   63 (64)
T ss_dssp             HHHHHHHHHTT-SCCBHHHHHHHTTCC------HHH-HHHHHHHHHHTTSEEE---SSSSBEEE
T ss_pred             HHHHHHHHcCC-CCCcHHHHHHHhCCC------HHH-HHHHHHHHHHCCCEEE---eccccccc
Confidence            34555655442 589999999999997      566 9999999999999995   34576643

>d1oria_ c.66.1.6 (A:) Protein arginine N-methyltransferase 1, PRMT1 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Arginine methyltransferase
domain: Protein arginine N-methyltransferase 1, PRMT1
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=95.67  E-value=0.0029  Score=52.05  Aligned_cols=38  Identities=26%  Similarity=0.260  Sum_probs=29.8

Q ss_pred             cceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhC
Q 041256          194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDA  232 (244)
Q Consensus       194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a  232 (244)
                      .++|||||||+|.++..++++.+. +++.+|..+....+
T Consensus        34 ~~~VLDiGcG~G~ls~~aa~~Ga~-~V~avd~s~~~~~a   71 (316)
T d1oria_          34 DKVVLDVGSGTGILCMFAAKAGAR-KVIGIECSSISDYA   71 (316)
T ss_dssp             TCEEEEETCTTSHHHHHHHHTTCS-EEEEEECSTTHHHH
T ss_pred             cCEEEEEecCCcHHHHHHHHhCCC-EEEEEcCcHHHhhh
Confidence            378999999999999988887554 78888986544443

>d1g6q1_ c.66.1.6 (1:) Arginine methyltransferase, HMT1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Arginine methyltransferase
domain: Arginine methyltransferase, HMT1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.67  E-value=0.0033  Score=51.95  Aligned_cols=39  Identities=28%  Similarity=0.310  Sum_probs=30.7

Q ss_pred             cceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhCC
Q 041256          194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDAP  233 (244)
Q Consensus       194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a~  233 (244)
                      .++|||||||+|.++..++++... +++..|..+.+..++
T Consensus        39 ~~~VLDlGcGtG~ls~~aa~~Ga~-~V~avd~s~~~~~a~   77 (328)
T d1g6q1_          39 DKIVLDVGCGTGILSMFAAKHGAK-HVIGVDMSSIIEMAK   77 (328)
T ss_dssp             TCEEEEETCTTSHHHHHHHHTCCS-EEEEEESSTHHHHHH
T ss_pred             cCEEEEeCCCCCHHHHHHHHhCCC-EEEEEeCCHHHHHHH
Confidence            379999999999999887776543 788889876665554

>d1sfxa_ a.4.5.50 (A:) Hypothetical protein AF2008 {Archaeoglobus fulgidus [TaxId: 2234]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: TrmB-like
domain: Hypothetical protein AF2008
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=95.66  E-value=0.0043  Score=42.86  Aligned_cols=44  Identities=16%  Similarity=0.360  Sum_probs=36.9

Q ss_pred             ChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           37 DVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        37 gifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      .|+-.|.+.   |+.|+.|||+.+|++      ... +.++|+-|...|++.+.
T Consensus        24 ~v~~~L~~~---g~~t~~eia~~~~i~------~~~-v~~~l~~L~~~GlV~r~   67 (109)
T d1sfxa_          24 RIYSLLLER---GGMRVSEIARELDLS------ARF-VRDRLKVLLKRGFVRRE   67 (109)
T ss_dssp             HHHHHHHHH---CCBCHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHhc---CCCCHHHHHHHhCCC------cch-HHHHHHHHHhCCCEEEE
Confidence            356667665   699999999999996      455 99999999999999853

>d2b25a1 c.66.1.13 (A:6-329) Hypothetical protein FLJ20628 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: tRNA(1-methyladenosine) methyltransferase-like
domain: Hypothetical protein FLJ20628
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.63  E-value=0.0053  Score=50.82  Aligned_cols=66  Identities=14%  Similarity=0.128  Sum_probs=50.6

Q ss_pred             HHHHHHHHhcchhh----HHHHHhhcCCCCCcceEEEecCCccHHHHHHHHH-CCCCeEEEccc-hHHhhhCC
Q 041256          167 DVFNNGMLSHTSIV----MEKVLESYKGFEHVKKLVDVGGGLGITLNMIISK-YPHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       167 ~~f~~aM~~~~~~~----~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~-~P~l~~~v~Dl-p~vi~~a~  233 (244)
                      ..|...|...++..    +..++...+ .....+|+|+|||+|.++..|++. .|+-+++.+|. |+.++.|+
T Consensus        69 ~d~~~~~~r~tqiiypkD~~~Il~~l~-i~pG~rVLE~GtGsG~lt~~LAr~vg~~G~V~t~E~~~~~~~~A~  140 (324)
T d2b25a1          69 EDYVVLMKRGTAITFPKDINMILSMMD-INPGDTVLEAGSGSGGMSLFLSKAVGSQGRVISFEVRKDHHDLAK  140 (324)
T ss_dssp             HHHHHHSCCSSCCCCHHHHHHHHHHHT-CCTTCEEEEECCTTSHHHHHHHHHHCTTCEEEEEESSHHHHHHHH
T ss_pred             HHHhhccCCCCcccccccHHHHHHHhC-CCCCCEEEEecccccHHHHHHHHHhCCCcEEEEecCCHHHHHHHH
Confidence            34556676666542    334666777 788899999999999999999987 69999999998 66666654

>d1z05a1 a.4.5.63 (A:10-80) Transcriptional regulator VC2007 N-terminal domain {Vibrio cholerae [TaxId: 666]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: Transcriptional regulator VC2007 N-terminal domain
species: Vibrio cholerae [TaxId: 666]

Probab=95.55  E-value=0.0064  Score=38.51  Aligned_cols=44  Identities=18%  Similarity=0.337  Sum_probs=38.4

Q ss_pred             cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      ..|+..|...   +++|..|||+.+|++      +.- +.++++.|...|++.+
T Consensus         9 ~~Il~~l~~~---g~~sr~eLa~~~glS------~~T-v~~~l~~L~~~Glv~e   52 (71)
T d1z05a1           9 GRVYKLIDQK---GPISRIDLSKESELA------PAS-ITKITRELIDAHLIHE   52 (71)
T ss_dssp             HHHHHHHHHH---CSBCHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHc---CCcCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEE
Confidence            3578888886   699999999999997      456 9999999999999984

>d1u2wa1 a.4.5.5 (A:12-119) Cadmium efflux system accessory protein CadC {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: Cadmium efflux system accessory protein CadC
species: Staphylococcus aureus [TaxId: 1280]

Probab=95.53  E-value=0.0063  Score=42.05  Aligned_cols=55  Identities=13%  Similarity=0.152  Sum_probs=46.7

Q ss_pred             HHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           26 LPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        26 ~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      .+.+|.--.++.|+..|...   ++.++.|||+.+|++      ... +.+-|+.|...|++...
T Consensus        24 ~~kaLadp~Rl~Il~~L~~~---~~~~v~ela~~l~~s------~s~-vS~HL~~L~~aGlv~~~   78 (108)
T d1u2wa1          24 ILKAIADENRAKITYALCQD---EELCVCDIANILGVT------IAN-ASHHLRTLYKQGVVNFR   78 (108)
T ss_dssp             HHHHHHSHHHHHHHHHHHHS---SCEEHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEEC
T ss_pred             HHHHhCCHHHHHHHHHHHhC---CCccHHHHHHHHccC------hhH-HHHHHHHHHHCCeeEEE
Confidence            45677777889999999764   689999999999997      456 99999999999999853

>d1biaa1 a.4.5.1 (A:1-63) Biotin repressor, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Biotin repressor, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=95.51  E-value=0.0096  Score=36.84  Aligned_cols=55  Identities=16%  Similarity=0.288  Sum_probs=42.1

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecC
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLA  101 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t  101 (244)
                      ++.|...|.+.   +..|.+|||+.+|++      ..- +++-+..|...|+..+. ..+ ..|++.
T Consensus         7 ~~~iL~~L~~~---~~~s~~eLa~~l~vS------~~t-i~r~i~~L~~~G~~I~~-~~g-~GY~L~   61 (63)
T d1biaa1           7 PLKLIALLANG---EFHSGEQLGETLGMS------RAA-INKHIQTLRDWGVDVFT-VPG-KGYSLP   61 (63)
T ss_dssp             HHHHHHHHTTS---SCBCHHHHHHHHTSC------HHH-HHHHHHHHHHTTCCCEE-ETT-TEEECS
T ss_pred             HHHHHHHHHHC---CcCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCcEEE-eCC-CeEEeC
Confidence            45677888764   689999999999997      455 99999999999985532 222 358875

>d1g8aa_ c.66.1.3 (A:) Fibrillarin homologue {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Fibrillarin homologue
domain: Fibrillarin homologue
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=95.51  E-value=0.0031  Score=49.55  Aligned_cols=43  Identities=16%  Similarity=0.150  Sum_probs=37.2

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHC-CCCeEEEccc-hHHhhhCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKY-PHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~vi~~a~  233 (244)
                      ++...+|+|+|||+|.+...+++.. |+-+++.+|. |..++.++
T Consensus        71 i~pG~~VLDlGaGsG~~t~~la~~VG~~G~V~aVD~s~~~l~~a~  115 (227)
T d1g8aa_          71 IKPGKSVLYLGIASGTTASHVSDIVGWEGKIFGIEFSPRVLRELV  115 (227)
T ss_dssp             CCTTCEEEEETTTSTTHHHHHHHHHCTTSEEEEEESCHHHHHHHH
T ss_pred             cCCCCEEEEeccCCCHHHHHHHHHhCCCCEEEEEeCcHHHHHHHH
Confidence            5677999999999999999999986 8889999998 77766654

>d1r1ua_ a.4.5.5 (A:) Metal-sensing transcriptional repressor CzrA {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: Metal-sensing transcriptional repressor CzrA
species: Staphylococcus aureus [TaxId: 1280]

Probab=95.50  E-value=0.005  Score=41.45  Aligned_cols=53  Identities=21%  Similarity=0.298  Sum_probs=44.2

Q ss_pred             HHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           27 PAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        27 ~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      +.+|.--.++.|+..|..    ++.++.||++.+|++      ... +.+-|+.|...|++...
T Consensus        12 fkaL~d~~Rl~Il~~L~~----~~~~v~el~~~l~~s------~~~-vS~HL~~L~~~glv~~~   64 (94)
T d1r1ua_          12 FKALGDYNRIRIMELLSV----SEASVGHISHQLNLS------QSN-VSHQLKLLKSVHLVKAK   64 (94)
T ss_dssp             HHHTCSHHHHHHHHHHHH----CCBCHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEEE
T ss_pred             HHHhCCHHHHHHHHHHHc----CCccHHHHHHHHCCC------HHH-HHHHHHHHHHCCceEEE
Confidence            345555577888898987    699999999999997      456 99999999999999864

>d1uira_ c.66.1.17 (A:) Spermidine synthase {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Spermidine synthase
domain: Spermidine synthase
species: Thermus thermophilus [TaxId: 274]

Probab=95.39  E-value=0.0037  Score=51.51  Aligned_cols=43  Identities=26%  Similarity=0.352  Sum_probs=38.4

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      +.+++|+.||||.|..+.++++..|..+.+++|+ |.|++.+++
T Consensus        76 ~~pk~VLiiG~G~G~~~~~ll~~~~~~~v~~VEiD~~Vi~~a~~  119 (312)
T d1uira_          76 PEPKRVLIVGGGEGATLREVLKHPTVEKAVMVDIDGELVEVAKR  119 (312)
T ss_dssp             SCCCEEEEEECTTSHHHHHHTTSTTCCEEEEEESCHHHHHHHHH
T ss_pred             CCcceEEEeCCCchHHHHHHHhcCCcceEEEecCCHHHHHHHHh
Confidence            5678999999999999999999888889999998 899987753

>d2hoea1 a.4.5.63 (A:10-71) N-acetylglucosamine kinase {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: N-acetylglucosamine kinase
species: Thermotoga maritima [TaxId: 2336]

Probab=95.21  E-value=0.0074  Score=37.28  Aligned_cols=42  Identities=12%  Similarity=0.264  Sum_probs=37.0

Q ss_pred             ChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           37 DVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        37 gifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      .|+..|.+    +|+|-.|||+.+|++      ..- +.++++.|...|++.+
T Consensus         3 ~Il~~i~~----~pisr~eLa~~~gls------~~T-Vs~~v~~L~~~GlV~e   44 (62)
T d2hoea1           3 RILKRIMK----SPVSRVELAEELGLT------KTT-VGEIAKIFLEKGIVVE   44 (62)
T ss_dssp             CSHHHHHH----SCBCHHHHHHHHTCC------HHH-HHHHHHHHHHHTSEEE
T ss_pred             HHHHHHHH----CCcCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEE
Confidence            47788876    699999999999997      455 9999999999999985

>d1nv8a_ c.66.1.30 (A:) N5-glutamine methyltransferase, HemK {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: N5-glutamine methyltransferase, HemK
domain: N5-glutamine methyltransferase, HemK
species: Thermotoga maritima [TaxId: 2336]

Probab=95.12  E-value=0.0045  Score=49.95  Aligned_cols=41  Identities=20%  Similarity=0.269  Sum_probs=36.0

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      +..+++|+|||+|..+..++ ++|+.+++..|. |+.++.|++
T Consensus       110 ~~~~vld~g~GsG~i~~~la-~~~~~~v~a~Dis~~Al~~A~~  151 (271)
T d1nv8a_         110 GIKTVADIGTGSGAIGVSVA-KFSDAIVFATDVSSKAVEIARK  151 (271)
T ss_dssp             TCCEEEEESCTTSHHHHHHH-HHSSCEEEEEESCHHHHHHHHH
T ss_pred             cccEEEEeeeeeehhhhhhh-hcccceeeechhhhhHHHHHHH
Confidence            45689999999999999987 579999999998 888888875

>d1j5ya1 a.4.5.1 (A:3-67) Putative transcriptional regulator TM1602, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Putative transcriptional regulator TM1602, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=95.07  E-value=0.017  Score=35.86  Aligned_cols=56  Identities=16%  Similarity=0.206  Sum_probs=42.2

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCc
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAP  102 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~  102 (244)
                      ...|.+.|.+..  +++|..+||+.++++      ..- ++|-+..|...|+-...  . .+.|.+.+
T Consensus         9 ~~~Il~~L~~~~--~~vs~~~La~~l~VS------~~T-I~rdi~~L~~~G~~I~~--~-~gGY~L~~   64 (65)
T d1j5ya1           9 LKSIVRILERSK--EPVSGAQLAEELSVS------RQV-IVQDIAYLRSLGYNIVA--T-PRGYVLAG   64 (65)
T ss_dssp             HHHHHHHHHHCS--SCBCHHHHHHHHTSC------HHH-HHHHHHHHHHHTCCCEE--E-TTEEECCT
T ss_pred             HHHHHHHHHHcC--CCCcHHHHHHHHCCC------HHH-HHHHHHHHHHCCCeEEE--e-CCCEEeCC
Confidence            456778887653  689999999999997      445 99999999999974321  2 35688754

>d1s3ja_ a.4.5.28 (A:) Putative transcriptional regulator YusO {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Putative transcriptional regulator YusO
species: Bacillus subtilis [TaxId: 1423]

Probab=95.06  E-value=0.025  Score=40.40  Aligned_cols=62  Identities=21%  Similarity=0.198  Sum_probs=45.4

Q ss_pred             cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCce---eecCcccccc
Q 041256           36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRL---YSLAPVSAYF  107 (244)
Q Consensus        36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~---y~~t~~s~~l  107 (244)
                      ..++..|...   ++.|..+||+.++++      +.. +.+++.-|+..|++++.+-..+.+   +.+|+.+..+
T Consensus        38 ~~iL~~l~~~---~~~t~~~la~~~~i~------~~~-vs~~l~~L~~~glv~r~~~~~D~R~~~v~lT~~G~~~  102 (143)
T d1s3ja_          38 LFVLASLKKH---GSLKVSEIAERMEVK------PSA-VTLMADRLEQKNLIARTHNTKDRRVIDLSLTDEGDIK  102 (143)
T ss_dssp             HHHHHHHHHH---SEEEHHHHHHHHTSC------HHH-HHHHHHHHHHTTSEEEEECSSCTTSEEEEECHHHHHH
T ss_pred             HHHHHHHHHC---CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHhhhheeeeecCCCCceEEEECHHHHHH
Confidence            3466777765   589999999999997      556 999999999999998642222232   6666665533

>d1ws6a1 c.66.1.46 (A:15-185) Methyltransferase TTHA0928 {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: YhhF-like
domain: Methyltransferase TTHA0928
species: Thermus thermophilus [TaxId: 274]

Probab=95.04  E-value=0.0069  Score=45.22  Aligned_cols=42  Identities=12%  Similarity=0.083  Sum_probs=34.2

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .....+|+|+|||+|.++++.+.+.  .+++.+|. |..++.+++
T Consensus        39 ~~~g~~vLDl~~G~G~~~i~a~~~g--a~vv~vD~~~~a~~~~~~   81 (171)
T d1ws6a1          39 YPRRGRFLDPFAGSGAVGLEAASEG--WEAVLVEKDPEAVRLLKE   81 (171)
T ss_dssp             CTTCCEEEEETCSSCHHHHHHHHTT--CEEEEECCCHHHHHHHHH
T ss_pred             ccCCCeEEEeccccchhhhhhhhcc--chhhhcccCHHHHhhhhH
Confidence            3455799999999999999988874  47778898 888887754

>d1lnwa_ a.4.5.28 (A:) MexR repressor {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: MexR repressor
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=95.04  E-value=0.031  Score=39.94  Aligned_cols=47  Identities=19%  Similarity=0.302  Sum_probs=38.1

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCccccee
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSF   91 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~   91 (244)
                      +..+...|...   +++|..+||+.++++      ... +.|+++.|+..|++++.+
T Consensus        38 q~~vL~~l~~~---~~~t~~~la~~l~~~------~~~-vsr~l~~L~~~G~v~r~~   84 (141)
T d1lnwa_          38 DVHVLKLIDEQ---RGLNLQDLGRQMCRD------KAL-ITRKIRELEGRNLVRRER   84 (141)
T ss_dssp             HHHHHHHHHSS---TTCBHHHHHHHTTCC------HHH-HHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHHC---CCCCHHHHHHHHCcc------HhH-HHHHHHHHHHhhceeeec
Confidence            34456666664   579999999999997      456 999999999999998643

>d1z6ra1 a.4.5.63 (A:12-81) Mlc protein N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: Mlc protein N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=95.03  E-value=0.013  Score=36.99  Aligned_cols=44  Identities=11%  Similarity=0.228  Sum_probs=38.3

Q ss_pred             cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      ..|+..|...   +++|-.|||+.+|++      ..- +.++++.|...|++.+
T Consensus         8 ~~Il~~i~~~---g~~sr~eLa~~~gLS------~~T-vs~iv~~L~~~glv~e   51 (70)
T d1z6ra1           8 GAVYRLIDQL---GPVSRIDLSRLAQLA------PAS-ITKIVHEMLEAHLVQE   51 (70)
T ss_dssp             HHHHHHHHSS---CSCCHHHHHHHTTCC------HHH-HHHHHHHHHHHTSEEE
T ss_pred             HHHHHHHHHc---CCcCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCEEe
Confidence            3478888876   799999999999997      445 9999999999999984

>d2d1ha1 a.4.5.50 (A:1-109) Hypothetical transcriptional regulator ST1889 {Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: TrmB-like
domain: Hypothetical transcriptional regulator ST1889
species: Sulfolobus tokodaii [TaxId: 111955]

Probab=95.02  E-value=0.0059  Score=42.01  Aligned_cols=44  Identities=11%  Similarity=0.201  Sum_probs=35.4

Q ss_pred             hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      |+..|...+  ||+|..+||+.++++      +.. +.++|+-|...|++.+.
T Consensus        26 iL~~L~~~~--~~~t~~eLa~~~~i~------~~t-vs~~l~~L~~~GlV~r~   69 (109)
T d2d1ha1          26 VLLKMVEIE--KPITSEELADIFKLS------KTT-VENSLKKLIELGLVVRT   69 (109)
T ss_dssp             HHHHHHHHC--SCEEHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHcC--CCCCHHHHHHHHCcc------HhH-HHHHHHHHHHCCCEEEe
Confidence            444444333  689999999999997      456 99999999999999864

>d1vbfa_ c.66.1.7 (A:) Protein-L-isoaspartyl O-methyltransferase {Sulfolobus tokodaii [TaxId: 111955]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Protein-L-isoaspartyl O-methyltransferase
domain: Protein-L-isoaspartyl O-methyltransferase
species: Sulfolobus tokodaii [TaxId: 111955]

Probab=94.96  E-value=0.01  Score=46.38  Aligned_cols=56  Identities=18%  Similarity=0.342  Sum_probs=40.4

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC----CCCceee
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS----YPGTLFI  241 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~----~~~i~~~  241 (244)
                      .+++.++ .....+|+|||||+|.++..+++...  +++.+|. |+.++.|++    .++|+++
T Consensus        61 ~ml~~L~-l~~g~~VLdIG~GsGy~ta~La~l~~--~V~aiE~~~~~~~~A~~~~~~~~nv~~~  121 (224)
T d1vbfa_          61 FMLDELD-LHKGQKVLEIGTGIGYYTALIAEIVD--KVVSVEINEKMYNYASKLLSYYNNIKLI  121 (224)
T ss_dssp             HHHHHTT-CCTTCEEEEECCTTSHHHHHHHHHSS--EEEEEESCHHHHHHHHHHHTTCSSEEEE
T ss_pred             HHHHHhh-hcccceEEEecCCCCHHHHHHHHHhc--ccccccccHHHHHHHHHHHhcccccccc
Confidence            3566677 78888999999999999888777654  5666665 777776654    3455543

>d1iy9a_ c.66.1.17 (A:) Spermidine synthase {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Spermidine synthase
domain: Spermidine synthase
species: Bacillus subtilis [TaxId: 1423]

Probab=94.84  E-value=0.0072  Score=48.77  Aligned_cols=43  Identities=23%  Similarity=0.263  Sum_probs=38.1

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+++|+-||||.|..+.++++..|..+.+++|+ |+|++.+++
T Consensus        74 ~~p~~vLiiGgG~G~~~~~~l~~~~~~~i~~VEID~~Vi~~a~~  117 (274)
T d1iy9a_          74 PNPEHVLVVGGGDGGVIREILKHPSVKKATLVDIDGKVIEYSKK  117 (274)
T ss_dssp             SSCCEEEEESCTTCHHHHHHTTCTTCSEEEEEESCHHHHHHHHH
T ss_pred             CCcceEEecCCCCcHHHHHHHhcCCcceEEEecCCHHHHHHHHH
Confidence            4678999999999999999998888889999998 999998753

>d1xd7a_ a.4.5.55 (A:) Hypothetical protein ywnA {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcriptional regulator Rrf2
domain: Hypothetical protein ywnA
species: Bacillus subtilis [TaxId: 1423]

Probab=94.77  E-value=0.017  Score=40.82  Aligned_cols=34  Identities=21%  Similarity=0.275  Sum_probs=31.4

Q ss_pred             CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      ++.|.++||+.++++      +.. ++++|+.|...|+++-
T Consensus        17 ~~~ss~~IA~~~~~~------~~~-v~kIl~~L~~aglV~s   50 (127)
T d1xd7a_          17 EKTSSEIIADSVNTN------PVV-VRRMISLLKKADILTS   50 (127)
T ss_dssp             SCCCHHHHHHHHTSC------HHH-HHHHHHHHHHTTSEEC
T ss_pred             CCCCHHHHHHHhCcC------HHH-HHHHHHHHHHhCcccc
Confidence            589999999999997      678 9999999999999984

>d2o07a1 c.66.1.17 (A:16-300) Spermidine synthase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Spermidine synthase
domain: Spermidine synthase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.76  E-value=0.0073  Score=49.01  Aligned_cols=44  Identities=18%  Similarity=0.276  Sum_probs=39.1

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      -..+++|+-||||.|..+.++++..|..+.++.|+ |.|++.+++
T Consensus        76 ~~~pk~vLiiGgG~G~~~~~~l~~~~~~~v~~vEiD~~Vv~~a~~  120 (285)
T d2o07a1          76 HPNPRKVLIIGGGDGGVLREVVKHPSVESVVQCEIDEDVIQVSKK  120 (285)
T ss_dssp             SSSCCEEEEEECTTSHHHHHHTTCTTCCEEEEEESCHHHHHHHHH
T ss_pred             CcCcCeEEEeCCCchHHHHHHHHcCCcceeeeccCCHHHHHHHHh
Confidence            35678999999999999999998888889999998 999999864

>d1ylfa1 a.4.5.55 (A:5-142) Hypothetical protein BC1842 {Bacillus cereus [TaxId: 1396]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcriptional regulator Rrf2
domain: Hypothetical protein BC1842
species: Bacillus cereus [TaxId: 1396]

Probab=94.71  E-value=0.014  Score=41.76  Aligned_cols=45  Identities=7%  Similarity=0.094  Sum_probs=35.8

Q ss_pred             CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCc
Q 041256           49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAP  102 (244)
Q Consensus        49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~  102 (244)
                      .+.|.++||+.++++      +.. ++++|+.|...|++.-.  .|.|.|.+..
T Consensus        22 ~~vss~~IA~~~~i~------~~~-l~kil~~L~~aGlv~S~--rG~GG~~L~~   66 (138)
T d1ylfa1          22 SLCTSDYMAESVNTN------PVV-IRKIMSYLKQAGFVYVN--RGPGGAGLLK   66 (138)
T ss_dssp             GGCCHHHHHHHHTSC------HHH-HHHHHHHHHHTTSEEEC-----CCEEESS
T ss_pred             CcCcHHHHHHHHCcC------HHH-HHHHHHHHHHCCCeEee--cCCCCceecC
Confidence            579999999999997      678 99999999999999842  3456676643

>d1mjfa_ c.66.1.17 (A:) Putative spermidine synthetase PF0127 (SpeE) {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Spermidine synthase
domain: Putative spermidine synthetase PF0127 (SpeE)
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=94.55  E-value=0.0094  Score=48.07  Aligned_cols=42  Identities=21%  Similarity=0.246  Sum_probs=36.3

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .++++|+-||||.|..+.++++ +|..+.+++|+ |.|++.+++
T Consensus        71 ~~p~~vLiiG~G~G~~~~~~l~-~~~~~v~~VEiD~~Vi~~a~~  113 (276)
T d1mjfa_          71 PKPKRVLVIGGGDGGTVREVLQ-HDVDEVIMVEIDEDVIMVSKD  113 (276)
T ss_dssp             SCCCEEEEEECTTSHHHHHHTT-SCCSEEEEEESCHHHHHHHHH
T ss_pred             CCCceEEEecCCchHHHHHHHH-hCCceEEEecCCHHHHHHHHH
Confidence            5678999999999999999986 56678889998 999998763

>d2p4wa1 a.4.5.64 (A:1-194) Transcriptional regulatory protein PF1790 {Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PF1790-like
domain: Transcriptional regulatory protein PF1790
species: Pyrococcus furiosus [TaxId: 2261]

Probab=94.55  E-value=0.015  Score=44.22  Aligned_cols=66  Identities=12%  Similarity=0.148  Sum_probs=49.0

Q ss_pred             HHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCC-----ceeecCcc
Q 041256           29 VMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQ-----RLYSLAPV  103 (244)
Q Consensus        29 ~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~-----~~y~~t~~  103 (244)
                      +|.-=.++.|+..|.+    +|.|+.|||+.+|++      +.. +.+-|+.|...|+++...+...     ..|+++..
T Consensus        11 ~l~~~~R~~Il~~L~~----~~~~~~ela~~l~~s------~~~-v~~HL~~L~~~Glv~~~~~~~~~G~~~~~y~l~~~   79 (194)
T d2p4wa1          11 VLGNETRRRILFLLTK----RPYFVSELSRELGVG------QKA-VLEHLRILEEAGLIESRVEKIPRGRPRKYYMIKKG   79 (194)
T ss_dssp             HHHSHHHHHHHHHHHH----SCEEHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEEEECCBTTBCCCEEEEECTT
T ss_pred             HhCCHHHHHHHHHHHh----CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCeEEEEeecCCCCceEEEEeccc
Confidence            3333456677888876    699999999999997      566 9999999999999985322111     25787776


Q ss_pred             cc
Q 041256          104 SA  105 (244)
Q Consensus       104 s~  105 (244)
                      +.
T Consensus        80 ~~   81 (194)
T d2p4wa1          80 LR   81 (194)
T ss_dssp             EE
T ss_pred             ce
Confidence            54

>d1inla_ c.66.1.17 (A:) Spermidine synthase {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Spermidine synthase
domain: Spermidine synthase
species: Thermotoga maritima [TaxId: 2336]

Probab=94.44  E-value=0.0096  Score=48.53  Aligned_cols=43  Identities=30%  Similarity=0.369  Sum_probs=38.3

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+++|+=||||.|..+.++++..|..+.+++|+ |.|++.+++
T Consensus        88 ~~pk~VLiiGgG~G~~~r~~l~~~~~~~i~~VEIDp~Vi~~a~~  131 (295)
T d1inla_          88 PNPKKVLIIGGGDGGTLREVLKHDSVEKAILCEVDGLVIEAARK  131 (295)
T ss_dssp             SSCCEEEEEECTTCHHHHHHTTSTTCSEEEEEESCHHHHHHHHH
T ss_pred             CCCceEEEecCCchHHHHHHHhcCCCceEEEecCCHHHHHHHHH
Confidence            4678999999999999999999888888999998 999998864

>d2b2ca1 c.66.1.17 (A:3-314) Spermidine synthase {Caenorhabditis elegans [TaxId: 6239]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Spermidine synthase
domain: Spermidine synthase
species: Caenorhabditis elegans [TaxId: 6239]

Probab=94.42  E-value=0.011  Score=48.64  Aligned_cols=43  Identities=23%  Similarity=0.268  Sum_probs=38.1

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..+++|+-||||.|..+.++++..|-.+.+++|+ |.|++.+++
T Consensus       105 ~~pk~VLIiGgG~G~~~rellk~~~v~~v~~VEID~~Vv~~a~~  148 (312)
T d2b2ca1         105 PDPKRVLIIGGGDGGILREVLKHESVEKVTMCEIDEMVIDVAKK  148 (312)
T ss_dssp             SSCCEEEEESCTTSHHHHHHTTCTTCCEEEEECSCHHHHHHHHH
T ss_pred             CCCCeEEEeCCCchHHHHHHHHcCCcceEEEEcccHHHHHHHHh
Confidence            5678999999999999999998777778999998 999998864

>d2hr3a1 a.4.5.28 (A:2-146) Probable transcriptional regulator PA3067 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Probable transcriptional regulator PA3067
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=94.33  E-value=0.021  Score=41.01  Aligned_cols=64  Identities=19%  Similarity=0.170  Sum_probs=44.6

Q ss_pred             HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCccccc
Q 041256           34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSAY  106 (244)
Q Consensus        34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~~  106 (244)
                      .++.+...|...+  |++|..+||+.++++      ... +.++++-|...|++++.+...+.   .+.+|+.+..
T Consensus        35 ~q~~vL~~L~~~~--g~~t~~~La~~~~~~------~~~-vs~~i~~L~~~glv~r~~~~~DrR~~~i~LT~~G~~  101 (145)
T d2hr3a1          35 SQLVVLGAIDRLG--GDVTPSELAAAERMR------SSN-LAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRR  101 (145)
T ss_dssp             HHHHHHHHHHHTT--SCBCHHHHHHHTTCC------HHH-HHHHHHHHHHTTSEEEEC------CCEEEECHHHHH
T ss_pred             HHHHHHHHHHHcC--CCCCHHHHHHHHCCC------HHH-HHHHHHHHHHcCCeEeeeCccchhHHHhccCHHHHH
Confidence            3455666676543  689999999999997      556 99999999999999863211111   3566665543

>d2etha1 a.4.5.28 (A:1-140) Putative transcriptional regulator TM0816 {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Putative transcriptional regulator TM0816
species: Thermotoga maritima [TaxId: 2336]

Probab=94.30  E-value=0.018  Score=41.07  Aligned_cols=62  Identities=15%  Similarity=0.075  Sum_probs=46.4

Q ss_pred             HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCcccc
Q 041256           34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSA  105 (244)
Q Consensus        34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~  105 (244)
                      -+.-++..|...   +++|..+||+.++++      ... +.++++.|...|++++.+.+.+.   ..++|+.+.
T Consensus        33 ~q~~iL~~l~~~---~~~t~~~La~~l~i~------~~~-vs~~v~~L~~~gli~r~~~~~D~R~~~l~lT~~G~   97 (140)
T d2etha1          33 TELYAFLYVALF---GPKKMKEIAEFLSTT------KSN-VTNVVDSLEKRGLVVREMDPVDRRTYRVVLTEKGK   97 (140)
T ss_dssp             HHHHHHHHHHHH---CCBCHHHHHHHTTSC------HHH-HHHHHHHHHHTTSEEEEECTTTSSCEEEEECHHHH
T ss_pred             HHHHHHHHHHHc---CCcCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCeeeeecccccchhhhhcCHHHH
Confidence            345577778776   589999999999997      556 99999999999999974322222   355555554

>d2a14a1 c.66.1.15 (A:5-261) Indolethylamine N-methyltransferase, INMT {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Arylamine N-methyltransferase
domain: Indolethylamine N-methyltransferase, INMT
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.30  E-value=0.0021  Score=50.67  Aligned_cols=42  Identities=14%  Similarity=0.048  Sum_probs=31.5

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+..+|||||||.|.++..+++... -+++..|+ |..++.|++
T Consensus        50 ~~g~~vLDlGcG~G~~~~~~~~~~~-~~v~giD~S~~~i~~a~~   92 (257)
T d2a14a1          50 LQGDTLIDIGSGPTIYQVLAACDSF-QDITLSDFTDRNREELEK   92 (257)
T ss_dssp             CCEEEEEESSCTTCCGGGTTGGGTE-EEEEEEESCHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCHhHHHHhcccc-CcEEEecCCHHHHHHHHH
Confidence            4568999999999988766655432 26899998 777777753

>d2a61a1 a.4.5.28 (A:5-143) Transcriptional regulator TM0710 {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator TM0710
species: Thermotoga maritima [TaxId: 2336]

Probab=94.26  E-value=0.042  Score=38.98  Aligned_cols=62  Identities=10%  Similarity=0.104  Sum_probs=44.4

Q ss_pred             ChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCccccccc
Q 041256           37 DVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSAYFV  108 (244)
Q Consensus        37 gifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~~l~  108 (244)
                      -+...|...   ++.|..+||+.++++      ... +.+++.-|...|++++.....++   .+.+|+.+..+.
T Consensus        34 ~iL~~i~~~---~~~t~~~la~~l~i~------~~t-vs~~l~~L~~~gli~r~~~~~D~R~~~i~LT~~G~~~~   98 (139)
T d2a61a1          34 DILQKIYFE---GPKRPGELSVLLGVA------KST-VTGLVKRLEADGYLTRTPDPADRRAYFLVITRKGEEVI   98 (139)
T ss_dssp             HHHHHHHHH---CCBCHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHH
T ss_pred             HHHHHHHHc---CCCCHHHHHHHhCCC------ccc-chHHHHHHHhcCeeeeeeccCCCCeEEEEECHHHHHHH
Confidence            355556554   589999999999997      456 99999999999999864322222   366666655433

>d1ku9a_ a.4.5.36 (A:) DNA-binding protein Mj223 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: DNA-binding protein Mj223
domain: DNA-binding protein Mj223
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=94.21  E-value=0.018  Score=41.51  Aligned_cols=45  Identities=13%  Similarity=0.276  Sum_probs=37.4

Q ss_pred             ChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           37 DVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        37 gifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      .|+-.|..++  +|+|..|||+.+|++      ... +.+.|+.|...|++.+.
T Consensus        30 ~i~~~L~~~~--~plt~~ela~~l~vs------k~~-vs~~l~~L~~~GlV~r~   74 (151)
T d1ku9a_          30 AVYAILYLSD--KPLTISDIMEELKIS------KGN-VSMSLKKLEELGFVRKV   74 (151)
T ss_dssp             HHHHHHHHCS--SCEEHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHhCC--CCcCHHHHHHHhCCC------cch-HHHHHHHHHHCCCEEEE
Confidence            4566665543  689999999999997      556 99999999999999864

>d1jg1a_ c.66.1.7 (A:) Protein-L-isoaspartyl O-methyltransferase {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Protein-L-isoaspartyl O-methyltransferase
domain: Protein-L-isoaspartyl O-methyltransferase
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=94.13  E-value=0.025  Score=43.74  Aligned_cols=50  Identities=18%  Similarity=0.225  Sum_probs=36.6

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+++.++ ..+..+|+|||+|+|..+.-+++-. +-+++.+|. |+.++.+++
T Consensus        69 ~ml~~L~-l~~g~~VLeIGsGsGY~taila~l~-g~~V~~ie~~~~l~~~a~~  119 (215)
T d1jg1a_          69 IMLEIAN-LKPGMNILEVGTGSGWNAALISEIV-KTDVYTIERIPELVEFAKR  119 (215)
T ss_dssp             HHHHHHT-CCTTCCEEEECCTTSHHHHHHHHHH-CSCEEEEESCHHHHHHHHH
T ss_pred             HHHHhhc-cCccceEEEecCCCChhHHHHHHhh-CceeEEEeccHHHHHHHHH
Confidence            4456666 7777899999999999998777654 344655655 777777764

>d3ctaa1 a.4.5.28 (A:5-89) Ta1064 (RFK), N-terminal domain {Thermoplasma acidophilum [TaxId: 2303]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Ta1064 (RFK), N-terminal domain
species: Thermoplasma acidophilum [TaxId: 2303]

Probab=94.08  E-value=0.0088  Score=39.35  Aligned_cols=49  Identities=8%  Similarity=0.131  Sum_probs=38.3

Q ss_pred             CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecC-CceeecCcccc
Q 041256           49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDG-QRLYSLAPVSA  105 (244)
Q Consensus        49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~-~~~y~~t~~s~  105 (244)
                      +++|..+||+.++++      +.. +.++|.-|...|++.+.. ++ .-.|.+|+.+.
T Consensus        20 ~~lt~~eLa~~l~i~------~~~-vs~~l~~Le~~GlV~r~~-D~R~~~i~LT~~G~   69 (85)
T d3ctaa1          20 AYLTSSKLADMLGIS------QQS-ASRIIIDLEKNGYITRTV-TKRGQILNITEKGL   69 (85)
T ss_dssp             EECCHHHHHHHHTSC------HHH-HHHHHHHHHHTTSEEEEE-ETTEEEEEECHHHH
T ss_pred             CCCCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCeeeec-ccccccceECHHHH
Confidence            689999999999997      556 999999999999999632 21 12366676655

>d1wg8a2 c.66.1.23 (A:5-108,A:207-284) TM0872, methyltransferase domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: MraW-like putative methyltransferases
domain: TM0872, methyltransferase domain
species: Thermus thermophilus [TaxId: 274]

Probab=93.94  E-value=0.034  Score=41.83  Aligned_cols=57  Identities=19%  Similarity=0.153  Sum_probs=44.3

Q ss_pred             HHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC--CCCcee
Q 041256          181 MEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS--YPGTLF  240 (244)
Q Consensus       181 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~--~~~i~~  240 (244)
                      ...+++.+. .....++||...|.|.++.++++++  .+++.+|+ |++++.+++  .+++.+
T Consensus         7 l~Evl~~l~-~~~g~~~vD~T~G~GGhs~~iL~~~--~~viaiD~D~~ai~~a~~~~~~~~~~   66 (182)
T d1wg8a2           7 YQEALDLLA-VRPGGVYVDATLGGAGHARGILERG--GRVIGLDQDPEAVARAKGLHLPGLTV   66 (182)
T ss_dssp             HHHHHHHHT-CCTTCEEEETTCTTSHHHHHHHHTT--CEEEEEESCHHHHHHHHHTCCTTEEE
T ss_pred             HHHHHHhcC-CCCCCEEEEeCCCCcHHHHHHhccc--CcEEEEhhhhhHHHHHhhccccceeE
Confidence            356666665 5667899999999999999999974  58899998 888888764  244443

>d1yuba_ c.66.1.24 (A:) rRNA adenine dimethylase {Streptococcus pneumoniae, Ermam [TaxId: 1313]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: rRNA adenine dimethylase-like
domain: rRNA adenine dimethylase
species: Streptococcus pneumoniae, Ermam [TaxId: 1313]

Probab=93.84  E-value=0.019  Score=45.34  Aligned_cols=51  Identities=8%  Similarity=0.240  Sum_probs=39.1

Q ss_pred             HHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          181 MEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       181 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...+++..+ .....+||+||+|.|.+...|+++..  +.+.+|. +.-++.+++
T Consensus        18 i~kIv~~~~-~~~~d~VLEIGpG~G~LT~~L~~~~~--~v~aIE~D~~l~~~l~~   69 (245)
T d1yuba_          18 LNQIIKQLN-LKETDTVYEIGTGKGHLTTKLAKISK--QVTSIELDSHLFNLSSE   69 (245)
T ss_dssp             HHHHHHHCC-CCSSEEEEECSCCCSSCSHHHHHHSS--EEEESSSSCSSSSSSSC
T ss_pred             HHHHHHhcC-CCCCCeEEEECCCccHHHHHHHhhcC--ceeEeeecccchhhhhh
Confidence            456777776 77789999999999999999999855  5666666 455555554

>d1qama_ c.66.1.24 (A:) rRNA adenine dimethylase {Bacillus subtilis, Ermc' [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: rRNA adenine dimethylase-like
domain: rRNA adenine dimethylase
species: Bacillus subtilis, Ermc' [TaxId: 1423]

Probab=93.79  E-value=0.061  Score=42.02  Aligned_cols=58  Identities=9%  Similarity=0.241  Sum_probs=41.0

Q ss_pred             HHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC----CCCCceee
Q 041256          181 MEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP----SYPGTLFI  241 (244)
Q Consensus       181 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~----~~~~i~~~  241 (244)
                      ...+++..+ .....+|++||+|.|.+...|+++...  .+.+|. +..++..+    +.++++++
T Consensus        10 ~~~iv~~~~-~~~~d~VlEIGpG~G~LT~~Ll~~~~~--v~avE~D~~l~~~l~~~~~~~~n~~i~   72 (235)
T d1qama_          10 IDKIMTNIR-LNEHDNIFEIGSGKGHFTLELVQRCNF--VTAIEIDHKLCKTTENKLVDHDNFQVL   72 (235)
T ss_dssp             HHHHHTTCC-CCTTCEEEEECCTTSHHHHHHHHHSSE--EEEECSCHHHHHHHHHHTTTCCSEEEE
T ss_pred             HHHHHHhcC-CCCCCeEEEECCCchHHHHHHHhCcCc--eEEEeeccchHHHHHHHhhcccchhhh
Confidence            456777776 778899999999999999999998655  555554 55554443    24555543

>d1xj5a_ c.66.1.17 (A:) Spermidine synthase {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Spermidine synthase
domain: Spermidine synthase
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=93.76  E-value=0.017  Score=46.87  Aligned_cols=43  Identities=19%  Similarity=0.198  Sum_probs=38.2

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      +++++|+=||||.|..+.++++..|-.+.+++|+ |+|++.+++
T Consensus        79 ~~pk~VLiiGgG~G~~~r~~l~~~~~~~i~~VEiD~~Vi~~~~~  122 (290)
T d1xj5a_          79 PNPKKVLVIGGGDGGVLREVARHASIEQIDMCEIDKMVVDVSKQ  122 (290)
T ss_dssp             SCCCEEEEETCSSSHHHHHHTTCTTCCEEEEEESCHHHHHHHHH
T ss_pred             CCCcceEEecCCchHHHHHHHhcccceeeEEecCCHHHHHHHHH
Confidence            5678999999999999999999778778999998 999998864

>d2frna1 c.66.1.47 (A:19-278) Hypothetical protein PH0793 {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Met-10+ protein-like
domain: Hypothetical protein PH0793
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=93.72  E-value=0.014  Score=46.54  Aligned_cols=42  Identities=24%  Similarity=0.178  Sum_probs=35.9

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+..+|||+|||.|.++..++++ +..+++..|+ |..++.+++
T Consensus       106 ~~g~~VlD~~aG~G~~~l~~a~~-~~~~V~avd~n~~a~~~~~~  148 (260)
T d2frna1         106 KPDELVVDMFAGIGHLSLPIAVY-GKAKVIAIEKDPYTFKFLVE  148 (260)
T ss_dssp             CTTCEEEETTCTTTTTHHHHHHH-TCCEEEEECCCHHHHHHHHH
T ss_pred             CCccEEEECcceEcHHHHHHHHh-CCcEEEEecCCHHHHHHHHH
Confidence            45689999999999999999986 4568999999 888888764

>d1dpua_ a.4.5.16 (A:) C-terminal domain of RPA32 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: C-terminal domain of RPA32
domain: C-terminal domain of RPA32
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.65  E-value=0.068  Score=33.43  Aligned_cols=58  Identities=9%  Similarity=0.176  Sum_probs=43.8

Q ss_pred             cChhhHHhhcCCCCCCCHHHHHHhC-CCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCc
Q 041256           36 LDVFEIISKAGPGAKLSVAEIVAQI-PLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAP  102 (244)
Q Consensus        36 lgifd~L~~~~~~g~~t~~eLA~~~-~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~  102 (244)
                      ..||+.|...+.+.++++.+|++++ +++      +.. ++..++.|+..|++--  ..+++.|..|.
T Consensus         9 ~~V~~~i~s~~~~eGi~~~el~~~l~~~~------~~~-i~~aid~L~~eG~IYs--TiDddHfkstd   67 (69)
T d1dpua_           9 NQVLNLIKACPRPEGLNFQDLKNQLKHMS------VSS-IKQAVDFLSNEGHIYS--TVDDDHFKSTD   67 (69)
T ss_dssp             HHHHHHHHHCCCTTTEEHHHHHHHSTTSC------HHH-HHHHHHHHHHTTSEEE--CSSTTEEEESS
T ss_pred             HHHHHHHHhCCCccCcCHHHHHHHccCCC------HHH-HHHHHHHHHhCCceec--ccccchhcccC
Confidence            3466666665545689999999998 686      556 9999999999998863  24567887664

>d1ulya_ a.4.5.58 (A:) Hypothetical protein PH1932 {Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Hypothetical protein PH1932
domain: Hypothetical protein PH1932
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=93.61  E-value=0.03  Score=42.11  Aligned_cols=68  Identities=6%  Similarity=0.136  Sum_probs=51.0

Q ss_pred             HHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeec-CC----ceeec
Q 041256           26 LPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVD-GQ----RLYSL  100 (244)
Q Consensus        26 ~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~-~~----~~y~~  100 (244)
                      ...+|.--.++.|++.|..    +|.|+.|||+.+|++      +.. +.+-|+.|...|++....+. ..    -.|.+
T Consensus        12 ~~~~l~~p~R~~Il~~L~~----~~~s~~ela~~lg~s------~~~-v~~hl~~L~~~glv~~~~~~~~~g~~~k~y~~   80 (190)
T d1ulya_          12 VIKVMLEDTRRKILKLLRN----KEMTISQLSEILGKT------PQT-IYHHIEKLKEAGLVEVKRTEMKGNLVEKYYGR   80 (190)
T ss_dssp             HHHHHHSHHHHHHHHHHTT----CCBCHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEEEEEEEETTEEEEEEEE
T ss_pred             HHHHhCCHHHHHHHHHHHh----CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCeEEEEeeccCCcceEEEEE
Confidence            3456666677888999975    799999999999997      556 99999999999999642111 11    23777


Q ss_pred             Cccc
Q 041256          101 APVS  104 (244)
Q Consensus       101 t~~s  104 (244)
                      |+.+
T Consensus        81 ~~~~   84 (190)
T d1ulya_          81 TADV   84 (190)
T ss_dssp             SSSE
T ss_pred             cccc
Confidence            7654

>d3broa1 a.4.5.28 (A:3-137) Transcriptional regulator OEOE1854 {Oenococcus oeni [TaxId: 1247]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator OEOE1854
species: Oenococcus oeni [TaxId: 1247]

Probab=93.56  E-value=0.031  Score=39.49  Aligned_cols=67  Identities=7%  Similarity=0.140  Sum_probs=47.4

Q ss_pred             HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCccccccc
Q 041256           34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSAYFV  108 (244)
Q Consensus        34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~~l~  108 (244)
                      .++.++..|...+ ++++|..|||+.++++      ... +.++++.|...|++.+.....+.   .+.+|+.+..+.
T Consensus        30 ~q~~vL~~l~~~~-~~~it~~ela~~~~~~------~~~-vs~~l~~L~~~g~v~r~~~~~D~R~~~i~lT~~G~~~~   99 (135)
T d3broa1          30 TQMTIIDYLSRNK-NKEVLQRDLESEFSIK------SST-ATVLLQRMEIKKLLYRKVSGKDSRQKCLKLTKKANKLE   99 (135)
T ss_dssp             HHHHHHHHHHHTT-TSCCBHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEEEECSSCTTSEEEEECHHHHTTH
T ss_pred             HHHHHHHHHHHcC-CCCCCHHHHHHHHCcC------HhH-HHHHHHHHHHHHHHHHHhhhhhhhhhhhcccHHHHHHH
Confidence            3444666677653 2579999999999997      456 99999999999999864222222   477777655433

>d1r18a_ c.66.1.7 (A:) Protein-L-isoaspartyl O-methyltransferase {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Protein-L-isoaspartyl O-methyltransferase
domain: Protein-L-isoaspartyl O-methyltransferase
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=93.53  E-value=0.047  Score=42.36  Aligned_cols=51  Identities=14%  Similarity=0.222  Sum_probs=36.9

Q ss_pred             HHHhhcC-CCCCcceEEEecCCccHHHHHHHHH------CCCCeEEEccc-hHHhhhCC
Q 041256          183 KVLESYK-GFEHVKKLVDVGGGLGITLNMIISK------YPHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       183 ~~~~~~~-~~~~~~~vvDVGGG~G~~~~~l~~~------~P~l~~~v~Dl-p~vi~~a~  233 (244)
                      .+++.+. +..+..+|||||+|+|.++..+.+.      ++..+++.+|. ++.++.++
T Consensus        69 ~~l~~L~~~l~~g~~VLeIGtGsGY~ta~la~l~g~~g~~~~~~V~~iE~~~~l~~~a~  127 (223)
T d1r18a_          69 FALEYLRDHLKPGARILDVGSGSGYLTACFYRYIKAKGVDADTRIVGIEHQAELVRRSK  127 (223)
T ss_dssp             HHHHHTTTTCCTTCEEEEESCTTSHHHHHHHHHHHHSCCCTTCEEEEEESCHHHHHHHH
T ss_pred             HHHHHHhhccCCCCeEEEecCCCCHHHHHHHHHhhhccCCcccEEEEEecCHHHHHHHH
Confidence            3455541 2667789999999999988777664      56678888876 66666664

>d2fpoa1 c.66.1.46 (A:10-192) Methylase YhhF {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: YhhF-like
domain: Methylase YhhF
species: Escherichia coli [TaxId: 562]

Probab=93.16  E-value=0.022  Score=42.77  Aligned_cols=39  Identities=15%  Similarity=0.113  Sum_probs=33.0

Q ss_pred             ceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          195 KKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       195 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .+|||++||+|.++.+.+.+... +++.+|. +.+++.+++
T Consensus        45 ~~vLDlfaGsG~~giealsrGa~-~v~~VE~~~~a~~~~k~   84 (183)
T d2fpoa1          45 AQCLDCFAGSGALGLEALSRYAA-GATLIEMDRAVSQQLIK   84 (183)
T ss_dssp             CEEEETTCTTCHHHHHHHHTTCS-EEEEECSCHHHHHHHHH
T ss_pred             hhhhhhhccccceeeeEEecCcc-eeEEEEEeechhhHHHH
Confidence            68999999999999999998876 7888887 777776653

>d2bv6a1 a.4.5.28 (A:5-140) Transcriptional regulator MgrA {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator MgrA
species: Staphylococcus aureus [TaxId: 1280]

Probab=93.16  E-value=0.033  Score=39.47  Aligned_cols=61  Identities=13%  Similarity=0.256  Sum_probs=44.9

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCcccc
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSA  105 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~  105 (244)
                      +..+...|...   ++.|..+||+.++++      ... +.|+++-|+..|++++...+.++   ...+|+.+.
T Consensus        36 q~~vL~~i~~~---~~~t~~~la~~l~~~------~~~-~s~~l~~L~~~Gli~r~~~~~D~R~~~l~lT~~G~   99 (136)
T d2bv6a1          36 QFLVLTILWDE---SPVNVKKVVTELALD------TGT-VSPLLKRMEQVDLIKRERSEVDQREVFIHLTDKSE   99 (136)
T ss_dssp             HHHHHHHHHHS---SEEEHHHHHHHTTCC------TTT-HHHHHHHHHHTTSEEEEECSSSTTCEEEEECHHHH
T ss_pred             HHHHHHHHHcC---CCCCHHHHHHHHCCC------HhH-HHHHHHHHHHCCCEEEeecCCcccchhhccCHHHH
Confidence            34466677775   589999999999997      456 99999999999999864322222   356666554

>d1r7ja_ a.4.5.49 (A:) Sso10a (SSO10449) {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Archaeal DNA-binding protein
domain: Sso10a (SSO10449)
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=93.01  E-value=0.037  Score=36.65  Aligned_cols=57  Identities=14%  Similarity=0.234  Sum_probs=44.4

Q ss_pred             hhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccccccc
Q 041256           39 FEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVSAYFV  108 (244)
Q Consensus        39 fd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s~~l~  108 (244)
                      +|+|....  ++.+...|...++++      ... +...|..|...|++.+   . ++.|.+|+.+..|.
T Consensus         9 ~DIL~~~~--~g~~kT~i~~~aNLs------~~~-~~kyl~~L~~~GLI~~---~-~~~Y~iT~kG~~~L   65 (90)
T d1r7ja_           9 QAILEACK--SGSPKTRIMYGANLS------YAL-TGRYIKMLMDLEIIRQ---E-GKQYMLTKKGEELL   65 (90)
T ss_dssp             HHHHHHHT--TCBCHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEE---E-TTEEEECHHHHHHH
T ss_pred             HHHHHHHh--CCCCccHHHHHcCCC------HHH-HHHHHHHHHHCCCeee---c-CCEEEECccHHHHH
Confidence            44444332  346789999999997      567 9999999999999984   3 58899999987554

>d2hzta1 a.4.5.69 (A:4-98) Putative transcriptional regulator YtcD {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: HxlR-like
domain: Putative transcriptional regulator YtcD
species: Bacillus subtilis [TaxId: 1423]

Probab=92.88  E-value=0.075  Score=35.42  Aligned_cols=53  Identities=17%  Similarity=0.182  Sum_probs=40.3

Q ss_pred             CCCCHHHHHHhC-CCCCCCCcchhccHHHHHHHHhhCCcccceeecC-C--ceeecCccccccc
Q 041256           49 AKLSVAEIVAQI-PLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDG-Q--RLYSLAPVSAYFV  108 (244)
Q Consensus        49 g~~t~~eLA~~~-~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~-~--~~y~~t~~s~~l~  108 (244)
                      |+....||.+.+ |++      +.. |.+=|+.|...|++++..... +  -.|++|+.+..|.
T Consensus        23 g~~rF~el~~~l~gis------~~~-Ls~rLk~Le~~glv~r~~~~~~p~~veY~LT~~G~~L~   79 (95)
T d2hzta1          23 GKKRTSELKRLMPNIT------QKM-LTQQLRELEADGVINRIVYNQVPPKVEYELSEYGRSLE   79 (95)
T ss_dssp             CCBCHHHHHHHCTTSC------HHH-HHHHHHHHHHTTSEEEEEECSSSCEEEEEECTTGGGGH
T ss_pred             CCCCHHHHHHHhhcCC------hhH-HHHHHHHHHHhHHHhheeccccccchhhhhhhhHHHHH
Confidence            689999999998 887      556 999999999999998642111 1  1388888776554

>d2cyya1 a.4.5.32 (A:5-64) Putative transcriptional regulator PH1519 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Putative transcriptional regulator PH1519
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=92.69  E-value=0.045  Score=33.16  Aligned_cols=45  Identities=16%  Similarity=0.287  Sum_probs=38.7

Q ss_pred             HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCccc
Q 041256           34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALH   88 (244)
Q Consensus        34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~   88 (244)
                      ++..|...|.+.   +.+|..|||+++|++      +.. +.+=++.|...|++.
T Consensus         4 ~D~~Il~~L~~n---~r~s~~eiA~~l~ls------~~~-v~~Ri~~L~~~giI~   48 (60)
T d2cyya1           4 IDKKIIKILQND---GKAPLREISKITGLA------EST-IHERIRKLRESGVIK   48 (60)
T ss_dssp             HHHHHHHHHHHC---TTCCHHHHHHHHCSC------HHH-HHHHHHHHHHHTSSC
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCeE
Confidence            456788889885   689999999999997      556 888999999999988

>d1i1ga1 a.4.5.32 (A:2-61) LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: LprA
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=92.67  E-value=0.042  Score=33.37  Aligned_cols=44  Identities=16%  Similarity=0.317  Sum_probs=37.6

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCccc
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALH   88 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~   88 (244)
                      +..|...|.+.   +.+|..+||+++|++      +.. +.+=++.|...|++.
T Consensus         5 D~kIl~~L~~n---~r~s~~~lA~~~gls------~~~-v~~Ri~~L~~~giI~   48 (60)
T d1i1ga1           5 DKIILEILEKD---ARTPFTEIAKKLGIS------ETA-VRKRVKALEEKGIIE   48 (60)
T ss_dssp             HHHHHHHHHHC---TTCCHHHHHHHHTSC------HHH-HHHHHHHHHHHTSSC
T ss_pred             HHHHHHHHHHc---CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCeE
Confidence            45677888885   689999999999997      556 888999999999987

>d2cfxa1 a.4.5.32 (A:1-63) Transcriptional regulator LrpC {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Transcriptional regulator LrpC
species: Bacillus subtilis [TaxId: 1423]

Probab=92.62  E-value=0.057  Score=33.08  Aligned_cols=45  Identities=24%  Similarity=0.460  Sum_probs=38.6

Q ss_pred             HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCccc
Q 041256           34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALH   88 (244)
Q Consensus        34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~   88 (244)
                      ++..|.+.|.+.   +.+|..+||+.+|++      +.- +.+=++-|...|++.
T Consensus         6 ~D~~IL~~L~~n---~r~s~~~iA~~lgis------~~t-v~~Ri~~L~~~giI~   50 (63)
T d2cfxa1           6 IDLNIIEELKKD---SRLSMRELGRKIKLS------PPS-VTERVRQLESFGIIK   50 (63)
T ss_dssp             HHHHHHHHHHHC---SCCCHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCee
Confidence            355678889885   689999999999997      455 889999999999997

>d2fbha1 a.4.5.28 (A:8-144) Transcriptional regulator PA3341 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator PA3341
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=92.47  E-value=0.048  Score=38.51  Aligned_cols=44  Identities=16%  Similarity=0.174  Sum_probs=35.4

Q ss_pred             hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      +.-.|...+  +++|..+||+.++++      ... +.++++-|+..|++++.
T Consensus        33 iL~~l~~~~--~~~t~~~la~~~~~~------~~~-vs~~v~~L~~~gli~r~   76 (137)
T d2fbha1          33 VLLHLARHR--DSPTQRELAQSVGVE------GPT-LARLLDGLESQGLVRRL   76 (137)
T ss_dssp             HHHHHHHCS--SCCBHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHcC--CCCcHHHHHHHHCCC------HHH-HHHHHHHHHHcCCcccc
Confidence            344555543  468999999999997      556 99999999999999964

>d2g72a1 c.66.1.15 (A:18-280) Phenylethanolamine N-methyltransferase, PNMTase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Arylamine N-methyltransferase
domain: Phenylethanolamine N-methyltransferase, PNMTase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.34  E-value=0.013  Score=46.66  Aligned_cols=41  Identities=12%  Similarity=0.060  Sum_probs=30.3

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~  233 (244)
                      .+..+|+|||||.|.+..-.+.++.. +++..|. |..++.++
T Consensus        53 ~~g~~vLDiGcG~g~~~~~~~~~~~~-~v~~~D~S~~~i~~~~   94 (263)
T d2g72a1          53 VSGRTLIDIGSGPTVYQLLSACSHFE-DITMTDFLEVNRQELG   94 (263)
T ss_dssp             SCCSEEEEETCTTCCGGGTTGGGGCS-EEEEECSCHHHHHHHH
T ss_pred             CCCcEEEEeccCCCHHHHHHhcccCC-eEEEEeCCHHHHHHHH
Confidence            45689999999999876544444433 6888898 77777664

>d2cg4a1 a.4.5.32 (A:4-66) Regulatory protein AsnC {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Regulatory protein AsnC
species: Escherichia coli [TaxId: 562]

Probab=92.14  E-value=0.051  Score=33.29  Aligned_cols=45  Identities=11%  Similarity=0.200  Sum_probs=38.4

Q ss_pred             HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCccc
Q 041256           34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALH   88 (244)
Q Consensus        34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~   88 (244)
                      ++..|...|.+.   +..|..|||+++|++      +.. +.+=++.|...|++.
T Consensus         6 ~D~~IL~~L~~~---~r~s~~eiA~~l~ls------~~~-v~~Ri~rL~~~GiI~   50 (63)
T d2cg4a1           6 LDRGILEALMGN---ARTAYAELAKQFGVS------PET-IHVRVEKMKQAGIIT   50 (63)
T ss_dssp             HHHHHHHHHHHC---TTSCHHHHHHHHTSC------HHH-HHHHHHHHHHHTSEE
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHCcC------HHH-HHHHHHHHHHCCCeE
Confidence            355678888885   689999999999997      556 889999999999998

>d1ej0a_ c.66.1.2 (A:) RNA methyltransferase FtsJ {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: RNA methyltransferase FtsJ
domain: RNA methyltransferase FtsJ
species: Escherichia coli [TaxId: 562]

Probab=92.13  E-value=0.14  Score=38.21  Aligned_cols=46  Identities=22%  Similarity=0.216  Sum_probs=36.2

Q ss_pred             HHHHhhcCCCCCcceEEEecCCccHHHHHHHHHC-CCCeEEEccchH
Q 041256          182 EKVLESYKGFEHVKKLVDVGGGLGITLNMIISKY-PHIKGINYDLPY  227 (244)
Q Consensus       182 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dlp~  227 (244)
                      .++-+.|+-+....+|||+|++.|.++..+.++. +.-+.+.+|+-.
T Consensus        11 ~EI~~k~~l~k~~~~vlDLg~aPGgw~q~~~~~~~~~~~v~~vDl~~   57 (180)
T d1ej0a_          11 DEIQQSDKLFKPGMTVVDLGAAPGGWSQYVVTQIGGKGRIIACDLLP   57 (180)
T ss_dssp             HHHHHHHCCCCTTCEEEEESCTTCHHHHHHHHHHCTTCEEEEEESSC
T ss_pred             HHHHHHhCccCCCCeEEEEeccCCcceEEEEeeccccceEEEeeccc
Confidence            3566677756777899999999999999888764 446788888743

>d1jgsa_ a.4.5.28 (A:) Multiple antibiotic resistance repressor, MarR {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Multiple antibiotic resistance repressor, MarR
species: Escherichia coli [TaxId: 562]

Probab=92.12  E-value=0.05  Score=38.58  Aligned_cols=63  Identities=21%  Similarity=0.174  Sum_probs=45.2

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCcccccc
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSAYF  107 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~~l  107 (244)
                      +..+...|...   ++.|..+||+.++++      ... +.+++..|...|++++.+...++   .+++|+.+..+
T Consensus        36 q~~vL~~l~~~---~~~t~~ela~~~~i~------~~~-vs~~v~~L~~~glv~r~~~~~D~R~~~i~lT~~G~~~  101 (138)
T d1jgsa_          36 QFKVLCSIRCA---ACITPVELKKVLSVD------LGA-LTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTGGAAI  101 (138)
T ss_dssp             HHHHHHHHHHH---SSBCHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEEEECTTCSSCEEEEECHHHHHH
T ss_pred             HHHHHHhHHhC---cCCCHHHHHHHHCCC------HhH-HHHHHHHHhhCCCEEEeeccCCCCeeEEEECHHHHHH
Confidence            34455566655   589999999999997      556 99999999999999864322233   36666655433

>d2cl5a1 c.66.1.1 (A:3-216) Catechol O-methyltransferase, COMT {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: COMT-like
domain: Catechol O-methyltransferase, COMT
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=91.91  E-value=0.058  Score=41.48  Aligned_cols=43  Identities=7%  Similarity=0.068  Sum_probs=36.0

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCC-CCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYP-HIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .++++||+||+|.|..+..++++.| +-+++.+|. |+..+.|++
T Consensus        55 ~kpk~ILEiGt~~G~Sti~la~al~~~g~v~sid~~~~~~~~a~~   99 (214)
T d2cl5a1          55 YSPSLVLELGAYCGYSAVRMARLLQPGARLLTMEMNPDYAAITQQ   99 (214)
T ss_dssp             HCCSEEEEECCTTSHHHHHHHTTCCTTCEEEEEESCHHHHHHHHH
T ss_pred             hCCCEEEEEccCchhHHHHHHHhCCCccEEEEEeccHHHHHHHHH
Confidence            3568999999999999999999875 578999998 666776653

>d1z91a1 a.4.5.28 (A:8-144) Organic hydroperoxide resistance transcriptional regulator OhrR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Organic hydroperoxide resistance transcriptional regulator OhrR
species: Bacillus subtilis [TaxId: 1423]

Probab=91.89  E-value=0.035  Score=39.35  Aligned_cols=61  Identities=15%  Similarity=0.164  Sum_probs=45.0

Q ss_pred             hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCce---eecCccccccc
Q 041256           38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRL---YSLAPVSAYFV  108 (244)
Q Consensus        38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~---y~~t~~s~~l~  108 (244)
                      +...|...   +++|..+||+.++++      +.. +.|++.-|+..|++.+.+.+.+.+   ..+|+.+..+.
T Consensus        38 vL~~l~~~---~~~t~~~La~~~~i~------~~~-vsr~i~~L~~~glv~r~~~~~D~R~~~i~lT~~G~~~~  101 (137)
T d1z91a1          38 ALLLLWEH---ETLTVKKMGEQLYLD------SGT-LTPMLKRMEQQGLITRKRSEEDERSVLISLTEDGALLK  101 (137)
T ss_dssp             HHHHHHHH---SEEEHHHHHHTTTCC------HHH-HHHHHHHHHHHTSEECCBCSSCTTSBEEEECHHHHSGG
T ss_pred             HHHHHHcC---CCCCHHHHHHHHCcC------HHH-HHHHHHHHhhccceEEeecCCCCCeEEEEECHHHHHHH
Confidence            45566654   589999999999997      456 999999999999998643222333   67777765443

>d2gxba1 a.4.5.19 (A:140-198) Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Z-DNA binding domain
domain: Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.69  E-value=0.14  Score=30.50  Aligned_cols=43  Identities=16%  Similarity=0.262  Sum_probs=34.3

Q ss_pred             hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      .+..|.+   ....|+.+||.+++++      ... +.|+|..|...|.+.+.
T Consensus         7 ~l~~lg~---~~~~tA~~LA~kl~vp------Kk~-iNr~LYsL~~kgkl~k~   49 (59)
T d2gxba1           7 FLEELGE---GKATTAHDLSGKLGTP------KKE-INRVLYSLAKKGKLQKE   49 (59)
T ss_dssp             HHHHHCT---TCCBCHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEEE
T ss_pred             HHHhcCC---ccchhHHHHHHHhCCc------HHH-HHHHHHHHHHccchhhc
Confidence            3444544   3689999999999995      345 99999999999999863

>d1xdza_ c.66.1.20 (A:) Glucose-inhibited division protein B (GidB) {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Glucose-inhibited division protein B (GidB)
domain: Glucose-inhibited division protein B (GidB)
species: Bacillus subtilis [TaxId: 1423]

Probab=91.59  E-value=0.057  Score=42.36  Aligned_cols=35  Identities=31%  Similarity=0.488  Sum_probs=31.3

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL  225 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  225 (244)
                      ++...+++|||.|.|.=++-++=.+|+++.+++|-
T Consensus        68 ~~~~~~ilDiGSGaGfPGi~laI~~p~~~v~Lves  102 (239)
T d1xdza_          68 FNQVNTICDVGAGAGFPSLPIKICFPHLHVTIVDS  102 (239)
T ss_dssp             GGGCCEEEEECSSSCTTHHHHHHHCTTCEEEEEES
T ss_pred             ccCCCeEEeecCCCchHHHHHHHhCCCccceeecc
Confidence            45668999999999999888888999999999994

>d2ih2a1 c.66.1.27 (A:21-243) DNA methylase TaqI, N-terminal domain {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: DNA methylase TaqI, N-terminal domain
domain: DNA methylase TaqI, N-terminal domain
species: Thermus aquaticus [TaxId: 271]

Probab=91.45  E-value=0.13  Score=38.80  Aligned_cols=46  Identities=7%  Similarity=0.086  Sum_probs=33.9

Q ss_pred             HHhhcCCCCCcceEEEecCCccHHHHHHHHHCCC-CeEEEccc-hHHhh
Q 041256          184 VLESYKGFEHVKKLVDVGGGLGITLNMIISKYPH-IKGINYDL-PYVIK  230 (244)
Q Consensus       184 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dl-p~vi~  230 (244)
                      +++... .....+|+|.|||+|.++.++.++++. .+...+|+ |..+.
T Consensus        11 m~~l~~-~~~~~~IlDp~~G~G~fl~~~~~~~~~~~~i~g~ei~~~~~~   58 (223)
T d2ih2a1          11 MVSLAE-APRGGRVLEPACAHGPFLRAFREAHGTAYRFVGVEIDPKALD   58 (223)
T ss_dssp             HHHHCC-CCTTCEEEEETCTTCHHHHHHHHHHCSCSEEEEEESCTTTCC
T ss_pred             HHHhcC-CCCcCEEEECCCchHHHHHHHHHhccccceEEeeecCHHHHh
Confidence            444444 455689999999999999999988776 45777787 44333

>d2frha1 a.4.5.28 (A:102-216) Pleiotropic regulator of virulence genes, SarA {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Pleiotropic regulator of virulence genes, SarA
species: Staphylococcus aureus [TaxId: 1280]

Probab=91.31  E-value=0.068  Score=36.77  Aligned_cols=60  Identities=12%  Similarity=0.182  Sum_probs=42.3

Q ss_pred             hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCcccc
Q 041256           38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSA  105 (244)
Q Consensus        38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~  105 (244)
                      +...|...+ ++++|..+||+.++++      ... +.++++.|...|++.+.+.+.+.   .+.+|+.++
T Consensus        38 vL~~l~~~~-~~~~t~~~la~~l~~~------~~t-vs~~i~~Le~~gli~r~~~~~D~R~~~i~LT~~G~  100 (115)
T d2frha1          38 VLTYISENK-EKEYYLKDIINHLNYK------QPQ-VVKAVKILSQEDYFDKKRNEHDERTVLILVNAQQR  100 (115)
T ss_dssp             HHHHHHHTC-CSEEEHHHHHHHSSSH------HHH-HHHHHHHHHHTTSSCCBCCSSSSCCCEEECCSHHH
T ss_pred             HHHHHHcCC-CCCCCHHHHHHHHCCC------HhH-HHHHHHHHHhhhhheeeecccCCceEEEEECHHHH
Confidence            344555542 2579999999999997      456 99999999999999964322222   256666554

>d2fhpa1 c.66.1.46 (A:1-182) Putative methylase EF2452 {Enterococcus faecalis [TaxId: 1351]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: YhhF-like
domain: Putative methylase EF2452
species: Enterococcus faecalis [TaxId: 1351]

Probab=91.29  E-value=0.093  Score=39.13  Aligned_cols=41  Identities=17%  Similarity=0.005  Sum_probs=33.4

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ...+|||+.+|+|.++.+.+.+... +++.+|. +.+++.+++
T Consensus        41 ~~~~vLDlfaGsG~~g~ea~srGa~-~v~~ve~~~~a~~~~~~   82 (182)
T d2fhpa1          41 DGGMALDLYSGSGGLAIEAVSRGMD-KSICIEKNFAALKVIKE   82 (182)
T ss_dssp             SSCEEEETTCTTCHHHHHHHHTTCS-EEEEEESCHHHHHHHHH
T ss_pred             CCCEEEEcccccccccceeeecchh-HHHHHHHHHHHHHHHHH
Confidence            4589999999999999999998755 6777887 777777653

>d3deua1 a.4.5.28 (A:2-141) Transcriptional regulator SlyA {Salmonella typhimurium [TaxId: 90371]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator SlyA
species: Salmonella typhimurium [TaxId: 90371]

Probab=90.87  E-value=0.091  Score=37.08  Aligned_cols=62  Identities=15%  Similarity=0.135  Sum_probs=42.2

Q ss_pred             hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCccccccc
Q 041256           38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSAYFV  108 (244)
Q Consensus        38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~~l~  108 (244)
                      +.-.|...+  +++|..+||+.++++      ... +.++++-|...|++++.+.+.++   .+.+|+.+..+.
T Consensus        36 ~L~~l~~~~--~~~t~~~la~~l~i~------~~~-vs~~l~~L~~~glI~~~~~~~D~R~~~l~lT~~G~~~~  100 (140)
T d3deua1          36 TLHNIHQLP--PDQSQIQLAKAIGIE------QPS-LVRTLDQLEDKGLISRQTCASDRRAKRIKLTEKAEPLI  100 (140)
T ss_dssp             HHHHHHHSC--SSEEHHHHHHHHTSC------HHH-HHHHHHHHHHTTSEEEC--------CEEEECGGGHHHH
T ss_pred             HHHHHHHcC--CCccHHHHHHHHCCC------HhH-HHHHHHHHHhCCCEEecccCCCCCceeeEECHHHHHHH
Confidence            445555432  479999999999997      456 99999999999999853222222   467777665433

>d2fbia1 a.4.5.28 (A:5-140) Probable transcriptional regulator PA4135 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Probable transcriptional regulator PA4135
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=90.82  E-value=0.16  Score=35.56  Aligned_cols=60  Identities=12%  Similarity=0.097  Sum_probs=44.0

Q ss_pred             cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCcccc
Q 041256           36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSA  105 (244)
Q Consensus        36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~  105 (244)
                      ..+...|...   ++.|..+||+.++++      ... +.++++-|...|++++.+...++   ...+|+.+.
T Consensus        33 ~~vL~~l~~~---~~~t~~~la~~~~i~------~~~-vs~~i~~L~~~gli~r~~~~~D~R~~~l~lT~~G~   95 (136)
T d2fbia1          33 WRVIRILRQQ---GEMESYQLANQACIL------RPS-MTGVLARLERDGIVRRWKAPKDQRRVYVNLTEKGQ   95 (136)
T ss_dssp             HHHHHHHHHH---CSEEHHHHHHHTTCC------HHH-HHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHH
T ss_pred             HHHHHHHHHc---CCCCHHHHHHHHCCC------HHH-HHHHHHHHHHCCCEEEeecCccCchhhhccCHHHH
Confidence            3455666665   689999999999997      556 99999999999999864322222   255666554

>d1hsja1 a.4.5.28 (A:373-487) Staphylococcal accessory regulator A homolog, SarR {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Staphylococcal accessory regulator A homolog, SarR
species: Staphylococcus aureus [TaxId: 1280]

Probab=90.73  E-value=0.087  Score=36.21  Aligned_cols=46  Identities=20%  Similarity=0.218  Sum_probs=35.7

Q ss_pred             hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCccccee
Q 041256           38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSF   91 (244)
Q Consensus        38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~   91 (244)
                      +...|...+ ++++|..+||+.++++      ... +.+++.-|...|++.+..
T Consensus        37 vL~~l~~~~-~~~~t~~ela~~l~~~------~~~-vs~~i~~Le~~gli~r~~   82 (115)
T d1hsja1          37 ILNHILRSE-SNEISSKEIAKCSEFK------PYY-LTKALQKLKDLKLLSKKR   82 (115)
T ss_dssp             HHHHHHTCS-CSEEEHHHHHHSSCCC------HHH-HHHHHHHHHTTTTSCCEE
T ss_pred             HHHHHHccC-CCCcCHHHHHHHHCCC------hhh-HHHHHHHHHHcCCeEEEe
Confidence            444454321 2589999999999997      456 999999999999999743

>d1lj9a_ a.4.5.28 (A:) Transcriptional regulator SlyA {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator SlyA
species: Enterococcus faecalis [TaxId: 1351]

Probab=90.50  E-value=0.11  Score=37.05  Aligned_cols=43  Identities=9%  Similarity=0.096  Sum_probs=35.7

Q ss_pred             hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      +...|.+.   +++|..+||+.++++      +.. +.++++-|...|++++.
T Consensus        34 iL~~i~~~---~~~t~~~la~~l~i~------~~t-vs~~l~~L~~~glI~r~   76 (144)
T d1lj9a_          34 YLVRVCEN---PGIIQEKIAELIKVD------RTT-AARAIKRLEEQGFIYRQ   76 (144)
T ss_dssp             HHHHHHHS---TTEEHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHhC---CCCCHHHHHHHHCcc------Hhh-HHHHHHHHHhhhccccc
Confidence            44456664   579999999999997      556 99999999999999864

>d1jsxa_ c.66.1.20 (A:) Glucose-inhibited division protein B (GidB) {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: Glucose-inhibited division protein B (GidB)
domain: Glucose-inhibited division protein B (GidB)
species: Escherichia coli [TaxId: 562]

Probab=90.45  E-value=0.12  Score=39.50  Aligned_cols=32  Identities=22%  Similarity=0.218  Sum_probs=29.4

Q ss_pred             cceEEEecCCccHHHHHHHHHCCCCeEEEccc
Q 041256          194 VKKLVDVGGGLGITLNMIISKYPHIKGINYDL  225 (244)
Q Consensus       194 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  225 (244)
                      ..+++|||.|.|.=++-++-.+|+++.+++|-
T Consensus        66 ~~~ilDiGsGaG~PGi~laI~~p~~~~~Lves   97 (207)
T d1jsxa_          66 GERFIDVGTGPGLPGIPLSIVRPEAHFTLLDS   97 (207)
T ss_dssp             SSEEEEETCTTTTTHHHHHHHCTTSEEEEEES
T ss_pred             CCceeeeeccCCceeeehhhhcccceEEEEec
Confidence            46899999999999888888999999999995

>d1j75a_ a.4.5.19 (A:) Dlm-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Z-DNA binding domain
domain: Dlm-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=90.44  E-value=0.1  Score=30.45  Aligned_cols=54  Identities=17%  Similarity=0.351  Sum_probs=43.3

Q ss_pred             hcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeec
Q 041256           35 ELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSL  100 (244)
Q Consensus        35 ~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~  100 (244)
                      |-.|...|.+.|  .|....+|+++++++      ... +.++|..|-..+=+..   .++.+|++
T Consensus         3 EQkILQVL~dag--spvk~~ql~k~cqVp------kk~-lNqVL~rlkke~kVsl---~~patW~l   56 (57)
T d1j75a_           3 EQKILQVLSDDG--GPVKIGQLVKKCQVP------KKT-LNQVLYRLKKEDRVSS---PEPATWSI   56 (57)
T ss_dssp             HHHHHHHHHHHC--SCEEHHHHHHHHCSC------HHH-HHHHHHHHHHTTSEEE---EETTEEEE
T ss_pred             HHHHHHHHHhcC--CchHHHHHHHHHCCC------HHH-HHHHHHHHHhcccccc---CCCccccC
Confidence            456888899887  799999999999995      334 9999999998888774   34677765

>d2as0a2 c.66.1.51 (A:73-396) Hypothetical protein PH1915, middle and C-terminal domains {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: hypothetical RNA methyltransferase
domain: Hypothetical protein PH1915, middle and C-terminal domains
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=89.83  E-value=0.085  Score=43.11  Aligned_cols=42  Identities=19%  Similarity=0.045  Sum_probs=35.7

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ++..+|+|+|||+|.+++.+++.... +++..|+ |..++.+++
T Consensus       144 ~~g~~VLDl~~g~G~~si~~a~~ga~-~V~~vD~s~~al~~a~~  186 (324)
T d2as0a2         144 QPGDRVLDVFTYTGGFAIHAAIAGAD-EVIGIDKSPRAIETAKE  186 (324)
T ss_dssp             CTTCEEEETTCTTTHHHHHHHHTTCS-EEEEEESCHHHHHHHHH
T ss_pred             CCCCeeecccCcccchhhhhhhcCCc-EEEeecCCHHHHHHHHH
Confidence            45689999999999999999988653 7899998 888888865

>d1q1ha_ a.4.5.41 (A:) Transcription factor E/IIe-alpha, N-terminal domain {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcription factor E/IIe-alpha, N-terminal domain
domain: Transcription factor E/IIe-alpha, N-terminal domain
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=89.59  E-value=0.2  Score=32.62  Aligned_cols=45  Identities=24%  Similarity=0.374  Sum_probs=37.2

Q ss_pred             ChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           37 DVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        37 gifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      .|++.|.+.+  +-.|=++||+.+|+.      ... ++++|..|...|+++..
T Consensus        22 ~v~~~L~~~~--~evtDe~iA~~tgi~------in~-VRk~Ly~L~~~~L~~y~   66 (88)
T d1q1ha_          22 DVLRILLDKG--TEMTDEEIANQLNIK------VND-VRKKLNLLEEQGFVSYR   66 (88)
T ss_dssp             HHHHHHHHHC--SCBCHHHHHHTTTSC------HHH-HHHHHHHHHHHTSCEEE
T ss_pred             HHHHHHHhcc--CcCCHHHHHHHhCCc------HHH-HHHHHHHHHhCCceEEE
Confidence            4788776542  479999999999997      556 99999999999999753

>d2fswa1 a.4.5.69 (A:3-104) Hypothetical protein PG0823 {Porphyromonas gingivalis [TaxId: 837]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: HxlR-like
domain: Hypothetical protein PG0823
species: Porphyromonas gingivalis [TaxId: 837]

Probab=89.44  E-value=0.12  Score=34.78  Aligned_cols=76  Identities=16%  Similarity=0.187  Sum_probs=53.9

Q ss_pred             hHHHHHHHHhhhHHHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhC-CCCCCCCcchhccHHHHHHHHhhCCccccee
Q 041256           13 NFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQI-PLKDNNPEAAAMTLDRVLRLLVSYNALHCSF   91 (244)
Q Consensus        13 ~~~~l~~~~~g~~~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~-~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~   91 (244)
                      +....++++-+-|....|..         |..    |+....||.+.+ |++      +.. |.+=|+.|...|++.+..
T Consensus         9 pv~~~l~ilg~kW~l~Il~~---------L~~----g~~rF~el~~~l~gIs------~~~-Ls~rLkeL~~~glv~r~~   68 (102)
T d2fswa1           9 PVRKSMQIFAGKWTLLIIFQ---------INR----RIIRYGELKRAIPGIS------EKM-LIDELKFLCGKGLIKKKQ   68 (102)
T ss_dssp             HHHHHHHHHTSSSHHHHHHH---------HTT----SCEEHHHHHHHSTTCC------HHH-HHHHHHHHHHTTSEEEEE
T ss_pred             CHHHHHHHHcCCCHHHHHHH---------Hcc----CCCCHHHHHhhCcccc------hhH-HHHHHHHHHHCCceeecc
Confidence            46667777777776655443         333    689999999998 787      556 899999999999998642


Q ss_pred             ecC-C--ceeecCccccccc
Q 041256           92 VDG-Q--RLYSLAPVSAYFV  108 (244)
Q Consensus        92 ~~~-~--~~y~~t~~s~~l~  108 (244)
                      ... +  -.|++|+.+..|.
T Consensus        69 ~~~~p~~veY~LT~~G~~L~   88 (102)
T d2fswa1          69 YPEVPPRVEYSLTPLGEKVL   88 (102)
T ss_dssp             ECSSSCEEEEEECHHHHTTH
T ss_pred             cCCCCCeehhhhhHhHHHHH
Confidence            111 1  1389988876554

>d2fxaa1 a.4.5.28 (A:6-167) Protease production regulatory protein Hpr {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Protease production regulatory protein Hpr
species: Bacillus subtilis [TaxId: 1423]

Probab=89.27  E-value=0.39  Score=34.87  Aligned_cols=58  Identities=14%  Similarity=0.023  Sum_probs=42.0

Q ss_pred             hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCcccc
Q 041256           38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSA  105 (244)
Q Consensus        38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~  105 (244)
                      +...|...   +++|..+||+.++++      ... +.++++-|...|++++.....+.   ...+|+.+.
T Consensus        46 vL~~l~~~---~~~t~~~la~~~~l~------~~t-vs~~i~rL~~~gli~r~~~~~D~R~~~l~lT~~G~  106 (162)
T d2fxaa1          46 ILWIAYQL---NGASISEIAKFGVMH------VST-AFNFSKKLEERGYLRFSKRLNDKRNTYVQLTEEGT  106 (162)
T ss_dssp             HHHHHHHH---TSEEHHHHHHHTTCC------HHH-HHHHHHHHHHHTSEEEECC------CEEEECHHHH
T ss_pred             HHhhhccC---CCcCHHHHHHHHcCC------chh-hHHHHHHHHHCCCceeecccccCeeeeeccCHhHH
Confidence            66677665   589999999999997      456 99999999999999963211122   355566554

>d2fbka1 a.4.5.28 (A:8-179) Transcriptional regulator DR1159 {Deinococcus radiodurans [TaxId: 1299]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator DR1159
species: Deinococcus radiodurans [TaxId: 1299]

Probab=89.21  E-value=0.056  Score=40.00  Aligned_cols=46  Identities=11%  Similarity=0.155  Sum_probs=35.6

Q ss_pred             hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      |.-.|...++++++|..+||+.++++      ... +.++++-|...|++++.
T Consensus        67 vL~~L~~~~~~~~lt~~eLa~~l~i~------~~t-vsr~l~~Le~~GlV~r~  112 (172)
T d2fbka1          67 LLLTLYRSAPPEGLRPTELSALAAIS------GPS-TSNRIVRLLEKGLIERR  112 (172)
T ss_dssp             HHHHHHHHCCSSCBCHHHHHHHCSCC------SGG-GSSHHHHHHHHTSEECC
T ss_pred             HHHHHHhhCCCCCcCHHHHHHHHCcC------HhH-HHHHHHHHHhCCCeeee
Confidence            44555544433458999999999997      445 88999999999999963

>d1xmka1 a.4.5.19 (A:294-366) Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Z-DNA binding domain
domain: Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.20  E-value=0.15  Score=32.11  Aligned_cols=61  Identities=11%  Similarity=0.123  Sum_probs=47.1

Q ss_pred             HhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeecCccc
Q 041256           34 VELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSLAPVS  104 (244)
Q Consensus        34 ~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~t~~s  104 (244)
                      .+..|.+.|...   |+.|+-.||+.+|++    . ..- +.+.|..|...|-+.+... .+-.|.++...
T Consensus         6 ~eekI~~~L~~~---g~~~Al~iak~lGl~----k-ake-VN~~LY~L~k~g~v~k~~~-tPP~W~L~~~~   66 (73)
T d1xmka1           6 IKEKICDYLFNV---SDSSALNLAKNIGLT----K-ARD-INAVLIDMERQGDVYRQGT-TPPIWHLTDKK   66 (73)
T ss_dssp             HHHHHHHHHHHT---CCEEHHHHHHHHCGG----G-HHH-HHHHHHHHHHTTSEEEECS-SSCEEEECHHH
T ss_pred             HHHHHHHHHHHc---CCchHHHHHHHhCCC----c-HHH-HhHHHHHHHHCCCeecCCC-CCCceeeecch
Confidence            456788899886   689999999999995    2 124 8999999999999986432 25678887654

>d1jhfa1 a.4.5.2 (A:2-72) LexA repressor, N-terminal DNA-binding domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: LexA repressor, N-terminal DNA-binding domain
domain: LexA repressor, N-terminal DNA-binding domain
species: Escherichia coli [TaxId: 562]

Probab=89.08  E-value=0.27  Score=30.64  Aligned_cols=35  Identities=14%  Similarity=0.218  Sum_probs=30.6

Q ss_pred             CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      -|-|+.|||+.+|+.   .  +.. +.+.|..|...|++.+
T Consensus        23 ~~Ps~rei~~~~g~~---S--~st-v~~~l~~Le~kG~I~r   57 (71)
T d1jhfa1          23 MPPTRAEIAQRLGFR---S--PNA-AEEHLKALARKGVIEI   57 (71)
T ss_dssp             SCCCHHHHHHHTTCS---S--HHH-HHHHHHHHHHTTSEEE
T ss_pred             CCCCHHHHHHHcCCC---C--HHH-HHHHHHHHHHCcCeec
Confidence            588999999999984   1  455 9999999999999995

>d1z7ua1 a.4.5.69 (A:1-108) Hypothetical protein EF0647 {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: HxlR-like
domain: Hypothetical protein EF0647
species: Enterococcus faecalis [TaxId: 1351]

Probab=88.92  E-value=0.15  Score=34.77  Aligned_cols=76  Identities=13%  Similarity=0.156  Sum_probs=51.6

Q ss_pred             hHHHHHHHHhhhHHHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhC-CCCCCCCcchhccHHHHHHHHhhCCccccee
Q 041256           13 NFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQI-PLKDNNPEAAAMTLDRVLRLLVSYNALHCSF   91 (244)
Q Consensus        13 ~~~~l~~~~~g~~~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~-~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~   91 (244)
                      +....++++-+-|....|.         .|..    |+....||.+.+ |++      +.. |.+=|+.|...|++.+..
T Consensus         8 ~i~~al~iig~kW~~~Il~---------~L~~----g~~RF~el~~~l~gIS------~~~-Ls~rLk~L~~~glv~R~~   67 (108)
T d1z7ua1           8 SINLALSTINGKWKLSLMD---------ELFQ----GTKRNGELMRALDGIT------QRV-LTDRLREMEKDGLVHRES   67 (108)
T ss_dssp             HHHHHHHTTCSTTHHHHHH---------HHHH----SCBCHHHHHHHSTTCC------HHH-HHHHHHHHHHHTSEEEEE
T ss_pred             cHHHHHHHHcCCCHHHHHH---------HHHc----CCCCHHHHHHHCcCCC------hhH-HHHHHHHHHHCCcceeec
Confidence            3444555555555555443         4544    689999999998 687      556 999999999999998632


Q ss_pred             ecC-C--ceeecCccccccc
Q 041256           92 VDG-Q--RLYSLAPVSAYFV  108 (244)
Q Consensus        92 ~~~-~--~~y~~t~~s~~l~  108 (244)
                      ... +  -.|++|+.+..|.
T Consensus        68 ~~~~p~~veY~LT~~G~~L~   87 (108)
T d1z7ua1          68 FNELPPRVEYTLTPEGYALY   87 (108)
T ss_dssp             ECCSSCEEEEEECHHHHHHH
T ss_pred             cCCCcceehhhhchhHHHHH
Confidence            111 1  1388888876554

>d1p4xa2 a.4.5.28 (A:126-250) Staphylococcal accessory regulator A homolog, SarS {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Staphylococcal accessory regulator A homolog, SarS
species: Staphylococcus aureus [TaxId: 1280]

Probab=88.50  E-value=0.13  Score=35.81  Aligned_cols=61  Identities=15%  Similarity=0.132  Sum_probs=42.6

Q ss_pred             ChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCc---eeecCcccc
Q 041256           37 DVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQR---LYSLAPVSA  105 (244)
Q Consensus        37 gifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~---~y~~t~~s~  105 (244)
                      .+...|...+ ++++|..+||+.++++      ... +.++++-|...|++.+..-..+.   ...+|+.++
T Consensus        37 ~vL~~l~~~~-~~~~~~~~ia~~l~~~------~~~-vs~~v~~L~~~glV~r~~~~~D~R~v~i~LT~~G~  100 (125)
T d1p4xa2          37 TILAIITSQN-KNIVLLKDLIETIHHK------YPQ-TVRALNNLKKQGYLIKERSTEDERKILIHMDDAQQ  100 (125)
T ss_dssp             HHHHHHHTTT-TCCEEHHHHHHHSSSC------HHH-HHHHHHHHHHHTSSEEEECSSSTTCEEEECCHHHH
T ss_pred             HHHHHHHHcc-CCCccHHHHHHHHCCC------cch-HHHHHHHHHhccCEeeeecCCCCCeEEEEECHHHH
Confidence            3566665432 2578999999999997      456 99999999999999864322222   255555544

>d2avda1 c.66.1.1 (A:44-262) COMT domain-containing protein 1, COMTD1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: COMT-like
domain: COMT domain-containing protein 1, COMTD1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.44  E-value=0.16  Score=39.06  Aligned_cols=44  Identities=14%  Similarity=0.131  Sum_probs=36.8

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCC-CCeEEEccc-hHHhhhCCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYP-HIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..++++||+||++.|.-+..+++.-| +-+.+.+|. |+..+.|++
T Consensus        57 ~~~~k~vLEiGt~~GyStl~~a~al~~~g~i~tie~~~~~~~~A~~  102 (219)
T d2avda1          57 LIQAKKALDLGTFTGYSALALALALPADGRVVTCEVDAQPPELGRP  102 (219)
T ss_dssp             HTTCCEEEEECCTTSHHHHHHHTTSCTTCEEEEEESCSHHHHHHHH
T ss_pred             ccCCCeEEEEechhhHHHHHHHHhCCCCceEEEEeechhHHHHHHH
Confidence            35679999999999999999999987 678888887 677666653

>d1yyva1 a.4.5.69 (A:9-122) Putative transcriptional regulator YtfH {Salmonella typhimurium [TaxId: 90371]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: HxlR-like
domain: Putative transcriptional regulator YtfH
species: Salmonella typhimurium [TaxId: 90371]

Probab=88.34  E-value=0.11  Score=35.70  Aligned_cols=76  Identities=13%  Similarity=0.106  Sum_probs=54.7

Q ss_pred             hHHHHHHHHhhhHHHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhC-CCCCCCCcchhccHHHHHHHHhhCCccccee
Q 041256           13 NFSYAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQI-PLKDNNPEAAAMTLDRVLRLLVSYNALHCSF   91 (244)
Q Consensus        13 ~~~~l~~~~~g~~~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~-~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~   91 (244)
                      +....++++.+-|....|..         |..    |+....||.+.+ |++      +.. |.+=|+.|...|++.+..
T Consensus        13 pv~~~l~~ig~kW~l~Il~~---------L~~----g~~RF~el~~~l~gis------~~~-Ls~rL~~Le~~glv~R~~   72 (114)
T d1yyva1          13 PSREVLKHVTSRWGVLILVA---------LRD----GTHRFSDLRRKMGGVS------EKM-LAQSLQALEQDGFLNRVS   72 (114)
T ss_dssp             THHHHHHHHHSHHHHHHHHH---------GGG----CCEEHHHHHHHSTTCC------HHH-HHHHHHHHHHHTCEEEEE
T ss_pred             CHHHHHHHHcCCCHHHHHHH---------Hhc----CCCCHHHHHHHccccc------hhH-HHHHHHHHHHHHHHhhcc
Confidence            35667777777777666543         334    688999999999 786      456 899999999999998642


Q ss_pred             ecC-C--ceeecCccccccc
Q 041256           92 VDG-Q--RLYSLAPVSAYFV  108 (244)
Q Consensus        92 ~~~-~--~~y~~t~~s~~l~  108 (244)
                      ... +  -.|++|+.+..|.
T Consensus        73 ~~~~p~~veY~LT~~G~~L~   92 (114)
T d1yyva1          73 YPVVPPHVEYSLTPLGEQVS   92 (114)
T ss_dssp             ECSSSCEEEEEECHHHHHHH
T ss_pred             cCCCCchhHhHhhHhHHHHH
Confidence            111 1  2388888876554

>d2ev0a1 a.4.5.24 (A:2-62) Manganese transport regulator MntR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Iron-dependent repressor protein
domain: Manganese transport regulator MntR
species: Bacillus subtilis [TaxId: 1423]

Probab=88.30  E-value=0.26  Score=29.77  Aligned_cols=34  Identities=12%  Similarity=0.191  Sum_probs=30.7

Q ss_pred             CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      ++.+..+||+.+|++      +.- +...++-|...|+++.
T Consensus        20 ~~v~~~~iA~~L~vs------~~S-Vs~mikrL~~~GlV~~   53 (61)
T d2ev0a1          20 GYARVSDIAEALAVH------PSS-VTKMVQKLDKDEYLIY   53 (61)
T ss_dssp             SSCCHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEC
T ss_pred             CCccHHHHHHHhCCC------chh-HHHHHHHHHHCCCEEE
Confidence            689999999999997      445 8999999999999996

>d2f2ea1 a.4.5.69 (A:5-146) Hypothetical protein PA1607 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: HxlR-like
domain: Hypothetical protein PA1607
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=88.19  E-value=0.29  Score=34.92  Aligned_cols=73  Identities=12%  Similarity=0.104  Sum_probs=49.2

Q ss_pred             HHHHHHhhhHHHHHHHHHHhcChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCC
Q 041256           16 YAMELASAIVLPAVMQAVVELDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQ   95 (244)
Q Consensus        16 ~l~~~~~g~~~~~~L~~a~~lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~   95 (244)
                      ..++++-.-|....|..         |..    |+....||.+.+|++      +.. |.+=|+.|...|++.+.....+
T Consensus        12 ~~l~ilg~kW~l~Il~~---------l~~----G~~rf~el~~~lgis------~~v-Ls~rL~~L~~~gLv~r~~~~~p   71 (142)
T d2f2ea1          12 RPLDVIGDGWSMLIVRD---------AFE----GLTRFGEFQKSLGLA------KNI-LAARLRNLVEHGVMVAVPAESG   71 (142)
T ss_dssp             TTHHHHCSSSHHHHHHH---------HHT----TCCSHHHHHHHHCCC------HHH-HHHHHHHHHHTTSEEEEECSSS
T ss_pred             HHHHHHcCCCHHHHHHH---------HHc----CCCCHHHHHHHhhcc------HHH-HHHHHHHHHHhcceeeecCCCC
Confidence            34445555555555444         223    699999999999997      456 8888999999999985211111


Q ss_pred             --ceeecCccccccc
Q 041256           96 --RLYSLAPVSAYFV  108 (244)
Q Consensus        96 --~~y~~t~~s~~l~  108 (244)
                        -.|++|+.+.-|.
T Consensus        72 ~r~~Y~LT~~G~~L~   86 (142)
T d2f2ea1          72 SHQEYRLTDKGRALF   86 (142)
T ss_dssp             SCEEEEECHHHHTTH
T ss_pred             CeeEEecCcCcchHH
Confidence              2488888765443

>d1p4xa1 a.4.5.28 (A:1-125) Staphylococcal accessory regulator A homolog, SarS {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Staphylococcal accessory regulator A homolog, SarS
species: Staphylococcus aureus [TaxId: 1280]

Probab=88.18  E-value=0.17  Score=35.10  Aligned_cols=47  Identities=15%  Similarity=0.185  Sum_probs=37.1

Q ss_pred             cChhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           36 LDVFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        36 lgifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      +-|...|...+ ++++|..|||+.++++      ... +.++++-|...|++.+.
T Consensus        37 ~~iL~~l~~~~-~~~~t~~eia~~~~~~------~~~-vs~~l~~L~~~g~v~r~   83 (125)
T d1p4xa1          37 FILLTYLFHQQ-ENTLPFKKIVSDLCYK------QSD-LVQHIKVLVKHSYISKV   83 (125)
T ss_dssp             HHHHHHHHSCS-CSEEEHHHHHHHSSSC------GGG-THHHHHHHHHTTSCEEE
T ss_pred             HHHHHHHHHhc-cCCcCHHHHHHHhCCC------cch-HHHHHHHHHHCCCceee
Confidence            33555665543 2689999999999997      456 99999999999999864

>d3bwga1 a.4.5.6 (A:5-82) Transcriptional regulator YydK {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Transcriptional regulator YydK
species: Bacillus subtilis [TaxId: 1423]

Probab=87.51  E-value=0.44  Score=30.03  Aligned_cols=43  Identities=23%  Similarity=0.384  Sum_probs=34.6

Q ss_pred             CCC-CHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeec
Q 041256           49 AKL-SVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSL  100 (244)
Q Consensus        49 g~~-t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~  100 (244)
                      ..+ |..+||+..+++      ..- +++-|+.|...|++..  ..+.|.|-.
T Consensus        20 ~~LPse~~La~~~~vS------r~t-vr~Al~~L~~~Gli~~--~~g~G~~V~   63 (78)
T d3bwga1          20 DKLPVLETLMAQFEVS------KST-ITKSLELLEQKGAIFQ--VRGSGIFVR   63 (78)
T ss_dssp             CBCCCHHHHHHHTTCC------HHH-HHHHHHHHHHTTSEEE--ETTTEEEEC
T ss_pred             CCCcCHHHHHHHHCCC------HHH-HHHHHHHHHHCCcEEE--EcCcEEEEc
Confidence            466 899999999997      344 9999999999999996  345566654

>d1zq9a1 c.66.1.24 (A:36-313) Probable dimethyladenosine transferase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: rRNA adenine dimethylase-like
domain: Probable dimethyladenosine transferase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.22  E-value=0.29  Score=39.03  Aligned_cols=43  Identities=14%  Similarity=0.321  Sum_probs=33.4

Q ss_pred             HHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEcc
Q 041256          181 MEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYD  224 (244)
Q Consensus       181 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~D  224 (244)
                      ...+++... .....+|++||.|.|.+...|+++.+.+.++=.|
T Consensus        10 ~~kIv~~~~-~~~~d~VlEIGPG~G~LT~~Ll~~~~~v~aiE~D   52 (278)
T d1zq9a1          10 INSIIDKAA-LRPTDVVLEVGPGTGNMTVKLLEKAKKVVACELD   52 (278)
T ss_dssp             HHHHHHHTC-CCTTCEEEEECCTTSTTHHHHHHHSSEEEEEESC
T ss_pred             HHHHHHHhC-CCCCCEEEEECCCchHHHHHHHhcCCcEEEEEEc
Confidence            456666666 6667899999999999999999997755554444

>d1wxxa2 c.66.1.51 (A:65-382) Hypothetical protein TTHA1280, middle and C-terminal domains {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: hypothetical RNA methyltransferase
domain: Hypothetical protein TTHA1280, middle and C-terminal domains
species: Thermus thermophilus [TaxId: 274]

Probab=87.18  E-value=0.15  Score=41.44  Aligned_cols=40  Identities=13%  Similarity=-0.016  Sum_probs=32.8

Q ss_pred             CcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          193 HVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       193 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      ..++|+|++||+|.+++++++.  .-+++..|. +..++.+++
T Consensus       145 ~g~rVLDl~~gtG~~s~~~a~g--~~~V~~vD~s~~al~~a~~  185 (318)
T d1wxxa2         145 RGERALDVFSYAGGFALHLALG--FREVVAVDSSAEALRRAEE  185 (318)
T ss_dssp             CEEEEEEETCTTTHHHHHHHHH--EEEEEEEESCHHHHHHHHH
T ss_pred             CCCeeeccCCCCcHHHHHHHhc--CCcEEeecchHHHHHHHHH
Confidence            4589999999999999998764  346788898 888888764

>d2hs5a1 a.4.5.6 (A:25-93) Putative transcriptional regulator RHA1_ro03477 {Rhodococcus sp. RHA1 [TaxId: 101510]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Putative transcriptional regulator RHA1 ro03477
species: Rhodococcus sp. RHA1 [TaxId: 101510]

Probab=86.84  E-value=0.37  Score=29.70  Aligned_cols=43  Identities=14%  Similarity=0.245  Sum_probs=34.3

Q ss_pred             CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceeec
Q 041256           49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYSL  100 (244)
Q Consensus        49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~~  100 (244)
                      ..++..+||+..|++      ..- +++-|+.|...|+++.  ..+.|.|-.
T Consensus        24 ~~l~~~~La~~~~vS------r~t-vr~Al~~L~~~Gli~~--~~~~G~~V~   66 (69)
T d2hs5a1          24 ARLSEPDICAALDVS------RNT-VREAFQILIEDRLVAH--ELNRGVFVR   66 (69)
T ss_dssp             CEECHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEE--ETTTEEEEC
T ss_pred             CccCHHHHHHHHCCC------HHH-HHHHHHHHHHCCcEEE--EcCCEEEec
Confidence            467899999999997      345 9999999999999996  344565543

>d1qyra_ c.66.1.24 (A:) High level kasugamycin resistance protein KsgA {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: rRNA adenine dimethylase-like
domain: High level kasugamycin resistance protein KsgA
species: Escherichia coli [TaxId: 562]

Probab=86.53  E-value=0.26  Score=38.65  Aligned_cols=50  Identities=12%  Similarity=0.253  Sum_probs=36.1

Q ss_pred             HHHHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccchHHhhhC
Q 041256          181 MEKVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDLPYVIKDA  232 (244)
Q Consensus       181 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~a  232 (244)
                      ...+++... ..+...|+.||+|.|.+...|+++...+.++=.| +.-++..
T Consensus        10 ~~~Iv~~~~-~~~~d~vlEIGpG~G~LT~~Ll~~~~~v~aiEiD-~~l~~~L   59 (252)
T d1qyra_          10 IDSIVSAIN-PQKGQAMVEIGPGLAALTEPVGERLDQLTVIELD-RDLAARL   59 (252)
T ss_dssp             HHHHHHHHC-CCTTCCEEEECCTTTTTHHHHHTTCSCEEEECCC-HHHHHHH
T ss_pred             HHHHHHhcC-CCCCCEEEEECCCchHHHHHHHccCCceEEEEec-cchhHHH
Confidence            456676666 6777899999999999999999987654444344 5544443

>d2isya1 a.4.5.24 (A:2-64) Iron-dependent regulator IdeR {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Iron-dependent repressor protein
domain: Iron-dependent regulator IdeR
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=86.29  E-value=0.71  Score=27.90  Aligned_cols=34  Identities=9%  Similarity=0.080  Sum_probs=30.7

Q ss_pred             CCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccc
Q 041256           49 AKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHC   89 (244)
Q Consensus        49 g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~   89 (244)
                      ++.+..+||+.+|++      +.- +.+.++-|...|++..
T Consensus        22 ~~v~~~~iA~~L~vs------~~S-Vt~mvkrL~~~Glv~~   55 (63)
T d2isya1          22 VTPLRARIAERLDQS------GPT-VSQTVSRMERDGLLRV   55 (63)
T ss_dssp             CCCCHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEE
T ss_pred             CCCcHHHHHHHhCCC------chh-HHHHHHHHHHCCCEEE
Confidence            689999999999997      445 8999999999999996

>d2p41a1 c.66.1.25 (A:8-264) An RNA cap (nucleoside-2'-O-)-methyltransferase domain of RNA polymerase NS5 {Dengue virus 2 [TaxId: 11060]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: mRNA cap methylase
domain: An RNA cap (nucleoside-2'-O-)-methyltransferase domain of RNA polymerase NS5
species: Dengue virus 2 [TaxId: 11060]

Probab=85.83  E-value=0.39  Score=37.57  Aligned_cols=42  Identities=17%  Similarity=-0.057  Sum_probs=30.8

Q ss_pred             HHHhhcCCCCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc
Q 041256          183 KVLESYKGFEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL  225 (244)
Q Consensus       183 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  225 (244)
                      .+.+.+- +....+|||+|||.|..+..+++..+..+...+++
T Consensus        57 ~~~~~~~-~~~~~~vvDlG~~pGgws~~~a~~~~v~~V~g~~i   98 (257)
T d2p41a1          57 WFVERNL-VTPEGKVVDLGCGRGGWSYYCGGLKNVREVKGLTK   98 (257)
T ss_dssp             HHHHTTS-SCCCEEEEEETCTTSHHHHHHHTSTTEEEEEEECC
T ss_pred             HHHHhcC-ccCCCeEEEecCCCChHHHHHHhhcCCCceeEEEe
Confidence            4455553 66667899999999999999998876655444443

>d1hw1a1 a.4.5.6 (A:5-78) Fatty acid responsive transcription factor FadR, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Fatty acid responsive transcription factor FadR, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=83.96  E-value=0.62  Score=29.08  Aligned_cols=42  Identities=21%  Similarity=0.173  Sum_probs=33.5

Q ss_pred             CCC-CHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccceeecCCceee
Q 041256           49 AKL-SVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCSFVDGQRLYS   99 (244)
Q Consensus        49 g~~-t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~y~   99 (244)
                      ..+ |..+||+.++++      ..- +++-++.|+..|++..  ..+.|.|-
T Consensus        25 ~~LPs~~eLa~~~~vS------r~t-vr~Al~~L~~~G~i~~--~~g~G~~V   67 (74)
T d1hw1a1          25 TILPAERELSELIGVT------RTT-LREVLQRLARDGWLTI--QHGKPTKV   67 (74)
T ss_dssp             SBCCCHHHHHHHHTCC------HHH-HHHHHHHHHHTTSEEE--ETTEEEEE
T ss_pred             CCCccHHHHHHHHCCC------HHH-HHHHHHHHHHCCcEEE--EeCceEEE
Confidence            456 899999999997      344 9999999999999996  34445554

>d2f8la1 c.66.1.45 (A:2-329) Hypothetical protein Lmo1582 {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: N-6 DNA Methylase-like
domain: Hypothetical protein Lmo1582
species: Listeria monocytogenes [TaxId: 1639]

Probab=83.52  E-value=0.53  Score=37.84  Aligned_cols=42  Identities=17%  Similarity=0.196  Sum_probs=32.5

Q ss_pred             CCcceEEEecCCccHHHHHHHHH-----CCCCeEEEccc-hHHhhhCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISK-----YPHIKGINYDL-PYVIKDAP  233 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~-----~P~l~~~v~Dl-p~vi~~a~  233 (244)
                      ....+|+|.+||+|.++.++.++     .++.+.+.+|. |..+..|+
T Consensus       116 ~~~~~vlDp~~GsG~~l~~~~~~l~~~~~~~~~~~g~di~~~~~~~a~  163 (328)
T d2f8la1         116 KKNVSILDPACGTANLLTTVINQLELKGDVDVHASGVDVDDLLISLAL  163 (328)
T ss_dssp             CSEEEEEETTCTTSHHHHHHHHHHHTTSSCEEEEEEEESCHHHHHHHH
T ss_pred             CCCCEEEeCCCCcchhHHHHHHHHHhccCccceEEEecccHHHHHHHH
Confidence            45689999999999999998764     45567788898 66666553

>d1bl0a1 a.4.1.8 (A:9-62) MarA {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: AraC type transcriptional activator
domain: MarA
species: Escherichia coli [TaxId: 562]

Probab=83.12  E-value=0.69  Score=26.68  Aligned_cols=42  Identities=12%  Similarity=0.116  Sum_probs=31.5

Q ss_pred             hhhHHhhcCCCCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcc
Q 041256           38 VFEIISKAGPGAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNAL   87 (244)
Q Consensus        38 ifd~L~~~~~~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll   87 (244)
                      +.+.|.+.- +.++|+++||+.+|++      +.. +.|+.+......+.
T Consensus         8 v~~yI~~~~-~~~~tl~~lA~~~~~s------~~~-l~r~Fk~~~g~tp~   49 (54)
T d1bl0a1           8 ILDWIEDNL-ESPLSLEKVSERSGYS------KWH-LQRMFKKETGHSLG   49 (54)
T ss_dssp             HHHHHHTTT-TSCCCCHHHHHHSSSC------HHH-HHHHHHHHHSSCHH
T ss_pred             HHHHHHhcc-CCCCCHHHHHHHHCcC------HHH-HHHHHHHHHCcCHH
Confidence            445565553 2689999999999997      667 99998887765543

>d1sfua_ a.4.5.19 (A:) 34L {Yaba-like disease virus, YLDV [TaxId: 132475]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Z-DNA binding domain
domain: 34L
species: Yaba-like disease virus, YLDV [TaxId: 132475]

Probab=83.06  E-value=1.5  Score=26.93  Aligned_cols=36  Identities=6%  Similarity=0.119  Sum_probs=31.2

Q ss_pred             CCCCCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCcccce
Q 041256           48 GAKLSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALHCS   90 (244)
Q Consensus        48 ~g~~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~   90 (244)
                      +..+|+.+||+.+|++      ... +-|.|.-|...|.+.+.
T Consensus        22 ~~~~tA~~LAk~Lg~~------Kk~-VNr~LY~L~~~G~v~~~   57 (70)
T d1sfua_          22 NDYTTAISLSNRLKIN------KKK-INQQLYKLQKEDTVKMV   57 (70)
T ss_dssp             TCEECHHHHHHHTTCC------HHH-HHHHHHHHHHTTSEEEE
T ss_pred             CCCchHHHHHHHhCCC------HHH-HHHHHHHHHHCCCeecC
Confidence            4689999999999996      345 99999999999999863

>d1susa1 c.66.1.1 (A:21-247) Caffeoyl-CoA O-methyltransferase {Alfalfa (Medicago sativa) [TaxId: 3879]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: COMT-like
domain: Caffeoyl-CoA O-methyltransferase
species: Alfalfa (Medicago sativa) [TaxId: 3879]

Probab=81.64  E-value=0.47  Score=36.49  Aligned_cols=43  Identities=16%  Similarity=0.091  Sum_probs=36.1

Q ss_pred             CCcceEEEecCCccHHHHHHHHHCC-CCeEEEccc-hHHhhhCCC
Q 041256          192 EHVKKLVDVGGGLGITLNMIISKYP-HIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       192 ~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .++++||+||.+.|.-+..+++..| +-+.+.+|. |+.++.|++
T Consensus        58 ~~~k~iLEiGT~~GyStl~la~al~~~g~v~tie~~~~~~~~A~~  102 (227)
T d1susa1          58 INAKNTMEIGVYTGYSLLATALAIPEDGKILAMDINKENYELGLP  102 (227)
T ss_dssp             HTCCEEEEECCGGGHHHHHHHHHSCTTCEEEEEESCCHHHHHHHH
T ss_pred             cCCCcEEEecchhhhhHHHHHhhCCCCcEEEEEeccchhHHHHHH
Confidence            4679999999999999999999987 578888887 776666654

>d2igta1 c.66.1.51 (A:1-309) Putative methyltransferase Atu0340 {Agrobacterium tumefaciens [TaxId: 358]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: hypothetical RNA methyltransferase
domain: Putative methyltransferase Atu0340
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=81.53  E-value=0.47  Score=38.28  Aligned_cols=42  Identities=14%  Similarity=0.027  Sum_probs=35.0

Q ss_pred             CCCcceEEEecCCccHHHHHHHHHCCCCeEEEccc-hHHhhhCCC
Q 041256          191 FEHVKKLVDVGGGLGITLNMIISKYPHIKGINYDL-PYVIKDAPS  234 (244)
Q Consensus       191 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-p~vi~~a~~  234 (244)
                      .++.++|||+.||+|.++..+++..  .+++.+|. +..++.|++
T Consensus       130 ~~~~~rVLdlf~~tG~~sl~aa~~G--A~V~~VD~s~~al~~a~~  172 (309)
T d2igta1         130 ADRPLKVLNLFGYTGVASLVAAAAG--AEVTHVDASKKAIGWAKE  172 (309)
T ss_dssp             SSSCCEEEEETCTTCHHHHHHHHTT--CEEEEECSCHHHHHHHHH
T ss_pred             ccCCCeEEEecCCCcHHHHHHHhCC--CeEEEEeChHHHHHHHHH
Confidence            4566899999999999999988764  57889998 788888864

>d1nd9a_ a.6.1.6 (A:) N-terminal subdomain of bacterial translation initiation factor IF2 {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: Putative DNA-binding domain
superfamily: Putative DNA-binding domain
family: N-terminal subdomain of bacterial translation initiation factor IF2
domain: N-terminal subdomain of bacterial translation initiation factor IF2
species: Escherichia coli [TaxId: 562]

Probab=80.02  E-value=0.32  Score=28.02  Aligned_cols=28  Identities=7%  Similarity=0.242  Sum_probs=24.7

Q ss_pred             CCHHHHHHhCCCCCCCCcchhccHHHHHHHHhhCCccc
Q 041256           51 LSVAEIVAQIPLKDNNPEAAAMTLDRVLRLLVSYNALH   88 (244)
Q Consensus        51 ~t~~eLA~~~~~~~~~~~~~~~~l~rlLr~L~~~gll~   88 (244)
                      +|++++|+.+|.+          ..|||..|...|+-.
T Consensus         3 vTVk~lA~~v~~~----------vd~Ll~Ql~~AGl~k   30 (49)
T d1nd9a_           3 VTIKTLAAERQTS----------VERLVQQFADAGIRK   30 (49)
T ss_dssp             ECTTHHHHHHSSS----------HHHHHHHHHHHTSCC
T ss_pred             ccHHHHHHHHCcC----------HHHHHHHHHHcCCCC
Confidence            6899999999996          778999999999843