Citrus Sinensis ID: 039903

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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---
Protein Sequence
MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLNRDGVSLCPSRPWLETKPYEIYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAILIK
Secondary Structure (PSIPRED)
cccccccHHHHHHHHHHHHcHHHHHHHccccccccHHHHHHcccccccccHHHHHHHHHHHHHcccEEEEEccccccccccccccccccccccccccccccHHHHcccccccccccccccccHHcccccHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHccccccccEEEEEccccHHHHHHHHHHcccccEEEcccHHHHHccccccccEEEccccccccccccEEEcc
Secondary Structure Prediction (SSPRO)
HHHHcccHHHHHHHHHHHccHHHHHHcccccccEcHHHHHcccccccccHHHHHHHHHHHHHHcccEEEEccccEEEEEEEcHHHHHHcccccccccccccHHHHcHHccHHHHHHHcccHHHHHHcccHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccEEEEccccccHHHHHHcccccccEEEEEcHHHHccccccccEEEEEcccccccccccEEEcc
Coil and Loop (DISEMBL)
MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAaqmpssnpnAAVMLDRILRLLVTHRVLrctsagddqrlYGLAHVAKYFVLnrdgvslcpsrpwletkpyeIYDAVLEGGIsfnkvhgtgfyeyagndfrfnGVFNKAMLNHTSIVtnriidsskGFEQIKQLVDVGGGLGVNVNIIISNYlhikgvnfdlshviqdsssysgvkHIGGIMleripkgdailik
Flexible Loop (DISEMBL)
MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCtsagddqrlyGLAHVAKYFVLNRDGVSLCPSRPWLETKPYEIYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSysgvkhiggimleripkgdailik
Low Complexity Region (SEG)
MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLNRDGVSLCPSRPWLETKPYEIYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIKQlvdvggglgvnvnIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAILIK
Disordered region (IsUnstruct)
*******VLPAAMQAASELGVFEIIAKAGPTAKISAVEIAA*******NAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLNRDGVSLCPSRPWLETKPYEIYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAI***
Disordered Region (DISOPRED)
MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLNRDGVSLCPSRPWLETKPYEIYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAILIK
Disordered Region (DISEMBL)
MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLNRDGVSLCPSRPWLETKPYEIYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAILIK
Disordered Region (DISPRO)
MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLNRDGVSLCPSRPWLETKPYEIYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAILIK
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLNRDGVSLCPSRPWLETKPYEIYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAILIK
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	233	2.2.26 [Sep-21-2011]
A9X7L0	364	Anthranilate N-methyltran	N/A	no	0.995	0.637	0.523	2e-65
P28002	365	Caffeic acid 3-O-methyltr	N/A	no	1.0	0.638	0.524	1e-64
Q9SWC2	313	Caffeic acid 3-O-methyltr	N/A	no	0.995	0.741	0.497	1e-63
Q8LL87	350	Caffeic acid 3-O-methyltr	N/A	no	1.0	0.665	0.5	2e-62
Q00763	365	Caffeic acid 3-O-methyltr	N/A	no	0.995	0.635	0.493	1e-61
Q9FQY8	359	Caffeic acid 3-O-methyltr	N/A	no	0.995	0.646	0.493	2e-61
Q43046	365	Caffeic acid 3-O-methyltr	N/A	no	0.995	0.635	0.493	2e-61
Q8W013	363	Caffeic acid 3-O-methyltr	N/A	no	0.995	0.639	0.489	3e-61
Q9XGW0	361	Caffeic acid 3-O-methyltr	N/A	no	0.995	0.642	0.481	3e-61
Q43609	365	Caffeic acid 3-O-methyltr	N/A	no	0.995	0.635	0.485	6e-61

>sp|A9X7L0|ANMT_RUTGR Anthranilate N-methyltransferase OS=Ruta graveolens PE=1 SV=1

 Score =  248 bits (634), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 125/239 (52%), Positives = 171/239 (71%), Gaps = 7/239 (2%)

Query: 1   MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRL 60
           MQ +M+IVLP A Q+A +LGVFEIIAKA P  ++SA EIA  + + NP A VMLDR+LRL
Sbjct: 29  MQLSMAIVLPMATQSAIQLGVFEIIAKA-PGGRLSASEIATILQAQNPKAPVMLDRMLRL 87

Query: 61  LVTHRVLRCTSAGD-DQRLYGLAHVAKYFVLNRDGVSL-----CPSRPWLETKPYEIYDA 114
           LV+HRVL C+ +G   +RLYGL  V+KYFV ++DG SL      P           +  A
Sbjct: 88  LVSHRVLDCSVSGPAGERLYGLTSVSKYFVPDQDGASLGNFMALPLDKVFMESWMGVKGA 147

Query: 115 VLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIKQLVD 174
           V+EGGI FN+VHG   +EYA ++ +F+  +++AM NH++I   RI++  KGFE + +LVD
Sbjct: 148 VMEGGIPFNRVHGMHIFEYASSNSKFSDTYHRAMFNHSTIALKRILEHYKGFENVTKLVD 207

Query: 175 VGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAILIK 233
           VGGGLGV +++I S Y HI+ +NFDL HV+QD++SY GV+H+GG M E +P+GDAIL+K
Sbjct: 208 VGGGLGVTLSMIASKYPHIQAINFDLPHVVQDAASYPGVEHVGGNMFESVPEGDAILMK 266

Involved in the biosynthesis of acridine alkaloids. N-methyltransferase with a strict substrate specificity for anthranilate. No activity with anthranilic acid methyl ester, anthraniloyl CoA, 3- or 4-amino-benzoic acid, salicylic acid, catechol, eugenol, caffeic acid, quercetin, theobromin, theophyllin, putrescine and nicotinic acid among others.
Ruta graveolens (taxid: 37565)
EC: 2EC: .EC: 1EC: .EC: 1EC: .EC: 1EC: 1EC: 1

>sp|P28002|COMT1_MEDSA Caffeic acid 3-O-methyltransferase OS=Medicago sativa PE=1 SV=1

 Score =  245 bits (626), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 127/242 (52%), Positives = 164/242 (67%), Gaps = 9/242 (3%)

Query: 1   MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRL 60
           MQ A + VLP  +++A EL + EIIAKAGP A+IS +EIA+Q+P++NP+A VMLDR+LRL
Sbjct: 24  MQLASASVLPMILKSALELDLLEIIAKAGPGAQISPIEIASQLPTTNPDAPVMLDRMLRL 83

Query: 61  LVTHRVLRCT----SAGDDQRLYGLAHVAKYFVLNRDGVS-----LCPSRPWLETKPYEI 111
           L  + +L C+      G  QRLYGLA VAKY V N DGVS     L      L    Y +
Sbjct: 84  LACYIILTCSVRTQQDGKVQRLYGLATVAKYLVKNEDGVSISALNLMNQDKVLMESWYHL 143

Query: 112 YDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIKQ 171
            DAVL+GGI FNK +G   +EY G D RFN VFNK M +H++I   +I+++  GFE +K 
Sbjct: 144 KDAVLDGGIPFNKAYGMTAFEYHGTDPRFNKVFNKGMSDHSTITMKKILETYTGFEGLKS 203

Query: 172 LVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAIL 231
           LVDVGGG G  +N I+S Y  IKG+NFDL HVI+D+ SY GV+H+GG M   IPK DA+ 
Sbjct: 204 LVDVGGGTGAVINTIVSKYPTIKGINFDLPHVIEDAPSYPGVEHVGGDMFVSIPKADAVF 263

Query: 232 IK 233
           +K
Sbjct: 264 MK 265

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.

Medicago sativa (taxid: 3879)

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 =  243 bits (619), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 121/243 (49%), Positives = 168/243 (69%), Gaps = 11/243 (4%)

Query: 1   MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRL 60
           MQ A + VLPA + AA EL + EI+A+AGP A ++  E+A+Q+P+ NP+A VMLDRI RL
Sbjct: 6   MQLATASVLPAVLTAAIELDLLEIMARAGPGAYLTPGEVASQLPTQNPDAPVMLDRIFRL 65

Query: 61  LVTHRVLRCT----SAGDDQRLYGLAHVAKYFVLNRDGVSLCP------SRPWLETKPYE 110
           L ++ VL CT      G  +RLYGLA + K+ V N DGVSL P       R +LE+  Y 
Sbjct: 66  LASYSVLTCTLCDLPEGKVERLYGLAPLCKFLVKNEDGVSLAPLRLIDQDRVFLESW-YY 124

Query: 111 IYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIK 170
           + DA+LEGGI F+K HG   ++Y G D RFN +FN+AM +H++I+  +I+++  GFE +K
Sbjct: 125 MKDAILEGGIPFHKAHGMTAFDYPGTDPRFNKIFNRAMSDHSTIMMKKILETYNGFEGLK 184

Query: 171 QLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAI 230
            +VDVGGG G  +N+I++ Y  IKG+NFDL HVI+D+ SY GV+H+GG M   IP GDA+
Sbjct: 185 TVVDVGGGTGAILNMIVAKYPSIKGINFDLPHVIEDAPSYPGVEHVGGDMFVNIPNGDAV 244

Query: 231 LIK 233
            +K
Sbjct: 245 FMK 247

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

 Score =  238 bits (608), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 121/242 (50%), Positives = 162/242 (66%), Gaps = 9/242 (3%)

Query: 1   MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRL 60
           M  A + VLP  +++A EL + E+IAKAGP A +S  E+AAQ+P+ NP A +MLDRILRL
Sbjct: 11  MSLASASVLPMVLKSAIELDLLELIAKAGPGAYVSPSELAAQLPTHNPEAPIMLDRILRL 70

Query: 61  LVTHRVLRCT----SAGDDQRLYGLAHVAKYFVLNRDGVSLCP-----SRPWLETKPYEI 111
           L T+ VL C     + G  +RLYGLA V K+   N DGVS+ P         L    Y +
Sbjct: 71  LATYSVLDCKLNNLADGGVERLYGLAPVCKFLTKNADGVSMAPLLLMNQDKVLMESWYHL 130

Query: 112 YDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIKQ 171
            DAVL+GGI FNK +G   +EY G D RFN VFN+ M NH++I   +I++  +GFE +K 
Sbjct: 131 KDAVLDGGIPFNKAYGMTAFEYHGTDPRFNKVFNQGMSNHSTITMKKILEVYRGFEGLKT 190

Query: 172 LVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAIL 231
           +VDVGGG G  +N+IIS Y  IKG+NF+L HV++D+ S+SGV+H+GG M   +PKGDAI 
Sbjct: 191 VVDVGGGTGATLNMIISKYPTIKGINFELPHVVEDAPSHSGVEHVGGDMFVSVPKGDAIF 250

Query: 232 IK 233
           +K
Sbjct: 251 MK 252

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

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

 Score =  236 bits (602), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 120/243 (49%), Positives = 162/243 (66%), Gaps = 11/243 (4%)

Query: 1   MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRL 60
           MQ A + VLP  ++ A EL + EI+AKAGP A +S  EIA+ +P+ NP+A VMLDRILRL
Sbjct: 24  MQLASASVLPMILKTAIELDLLEIMAKAGPGAFLSTSEIASHLPTKNPDAPVMLDRILRL 83

Query: 61  LVTHRVLRCT----SAGDDQRLYGLAHVAKYFVLNRDGVSLCP------SRPWLETKPYE 110
           L ++ +L C+      G  +RLYGLA V K+   N DGVS+ P       +  +E+  Y 
Sbjct: 84  LASYSILTCSLKDLPDGKVERLYGLAPVCKFLTKNEDGVSVSPLCLMNQDKVLMESW-YY 142

Query: 111 IYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIK 170
           + DA+L+GGI FNK +G   +EY G D RFN VFNK M +H++I   +I+++ KGFE + 
Sbjct: 143 LKDAILDGGIPFNKAYGMTAFEYHGTDPRFNKVFNKGMSDHSTITMKKILETYKGFEGLT 202

Query: 171 QLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAI 230
            LVDVGGG G  VN I+S Y  IKG+NFDL HVI+D+ SY GV+H+GG M   +PK DA+
Sbjct: 203 SLVDVGGGTGAVVNTIVSKYPSIKGINFDLPHVIEDAPSYPGVEHVGGDMFVSVPKADAV 262

Query: 231 LIK 233
            +K
Sbjct: 263 FMK 265

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

 Score =  235 bits (600), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 120/243 (49%), Positives = 161/243 (66%), Gaps = 11/243 (4%)

Query: 1   MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRL 60
           MQ A + VLP  +++A EL + EI+AKAGP A IS  E+AAQ+P+ NP A VMLDR+LRL
Sbjct: 20  MQLASASVLPMVLKSALELDLLEIMAKAGPGAAISPSELAAQLPTKNPEAPVMLDRMLRL 79

Query: 61  LVTHRVLRCT----SAGDDQRLYGLAHVAKYFVLNRDGVSLCP------SRPWLETKPYE 110
           L T+ VL CT      G  +RLY LA V K    N DGVS+ P       +  +E+  Y 
Sbjct: 80  LATYSVLNCTLRTLPDGRVERLYSLAPVCKLLTKNADGVSVAPLLLMNQDKVLMESW-YH 138

Query: 111 IYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIK 170
           + DAVL+GG+ FNK +G   +EY G D RFN VFN+ M +H+++   +I++  KGFE + 
Sbjct: 139 LTDAVLDGGVPFNKAYGMTAFEYHGTDPRFNKVFNRGMSDHSTMTMKKILEDYKGFEGLN 198

Query: 171 QLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAI 230
            +VDVGGG G  VN+I+S Y  IKG+NFDLSHVI+D+ +Y GV+H+G  M   +PK DAI
Sbjct: 199 SIVDVGGGTGATVNMIVSKYPSIKGINFDLSHVIEDAPAYPGVEHVGRDMFVSVPKADAI 258

Query: 231 LIK 233
            +K
Sbjct: 259 FMK 261

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

 Score =  235 bits (599), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 120/243 (49%), Positives = 161/243 (66%), Gaps = 11/243 (4%)

Query: 1   MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRL 60
           MQ A + VLP  ++ A EL + EI+AKAGP A +S  EIA+ +P+ NP+A VMLDRILRL
Sbjct: 24  MQLASASVLPMILKTAIELDLLEIMAKAGPGAFLSTSEIASHLPTKNPDAPVMLDRILRL 83

Query: 61  LVTHRVLRCT----SAGDDQRLYGLAHVAKYFVLNRDGVSLCP------SRPWLETKPYE 110
           L ++ +L C+      G  +RLYGLA V K+   N DGVS+ P       +  +E+  Y 
Sbjct: 84  LASYSILTCSLKDLPDGKVERLYGLAPVCKFLTKNEDGVSVSPLCLMNQDKVLMESW-YY 142

Query: 111 IYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIK 170
           + DA+LEGGI FNK +G   +EY G D RFN VFNK M +H++I   +I+++ KGFE + 
Sbjct: 143 LKDAILEGGIPFNKAYGMTAFEYHGTDPRFNKVFNKGMSDHSTITMKKILETYKGFEGLT 202

Query: 171 QLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAI 230
            LVDVGGG G  VN I+S Y  IKG+NFDL HVI+D+ SY GV+H+GG M   +P  DA+
Sbjct: 203 SLVDVGGGTGAVVNTIVSKYPSIKGINFDLPHVIEDAPSYPGVEHVGGDMFVSVPNADAV 262

Query: 231 LIK 233
            +K
Sbjct: 263 FMK 265

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

 Score =  234 bits (598), Expect = 3e-61,   Method: Compositional matrix adjust.
 Identities = 119/243 (48%), Positives = 163/243 (67%), Gaps = 11/243 (4%)

Query: 1   MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRL 60
           M+ A + VLP  +++A EL + E+I K+GP A +S  E+AAQ+P+ NP+A VMLDRILRL
Sbjct: 24  MRLASASVLPMVLKSAIELDLLELIKKSGPGAYVSPSELAAQLPTQNPDAPVMLDRILRL 83

Query: 61  LVTHRVLRCT----SAGDDQRLYGLAHVAKYFVLNRDGVSLCP------SRPWLETKPYE 110
           L ++ VL CT      G  +RLY LA V K+   N DGVS+         +  +E+  Y 
Sbjct: 84  LASYSVLNCTLKDLPDGGIERLYSLAPVCKFLTKNEDGVSMAALLLMNQDKVLMESW-YH 142

Query: 111 IYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIK 170
           + DAVLEGGI FNK +G   +EY G D RFN VFN+ M NH++I+  +I++  +GF+ +K
Sbjct: 143 LKDAVLEGGIPFNKAYGMTAFEYHGKDPRFNKVFNQGMSNHSTIIMKKILEIYQGFQGLK 202

Query: 171 QLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAI 230
            +VDVGGG G  +N+I+S Y  IKG+NFDL HVI+D+ SY GV H+GG M   +PKGDAI
Sbjct: 203 TVVDVGGGTGATLNMIVSKYPSIKGINFDLPHVIEDAPSYPGVDHVGGDMFVSVPKGDAI 262

Query: 231 LIK 233
            +K
Sbjct: 263 FMK 265

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

 Score =  234 bits (597), Expect = 3e-61,   Method: Compositional matrix adjust.
 Identities = 117/243 (48%), Positives = 165/243 (67%), Gaps = 11/243 (4%)

Query: 1   MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRL 60
           MQ A + VLP  +++A EL + E+I K+G  A +S V++AAQ+P++NP+A VMLDRILRL
Sbjct: 22  MQLASASVLPMVLKSAIELDLLELIKKSGAGAFVSPVDLAAQLPTTNPDAHVMLDRILRL 81

Query: 61  LVTHRVLRCT----SAGDDQRLYGLAHVAKYFVLNRDGVSLCP------SRPWLETKPYE 110
           L ++ +L C       G  +RLYGLA V K+   N DGVS+ P       +  +E+  Y 
Sbjct: 82  LTSYAILECRLKTLPDGGVERLYGLAPVCKFLTKNEDGVSMAPLTLMNQDKVLMESW-YH 140

Query: 111 IYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIK 170
           + DAV++GGI FNK +G   +EY G D RFN VFN+ M NH++I   +I+++  GF+ +K
Sbjct: 141 LSDAVVDGGIPFNKAYGMTAFEYHGTDPRFNKVFNQGMSNHSTITMKKILETYTGFDGLK 200

Query: 171 QLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAI 230
            +VDVGGG G  +N+I+S Y  IKG+NFDL HVI+D+ SY GV+H+GG M   +PKGDAI
Sbjct: 201 TVVDVGGGTGATLNMIVSKYPSIKGINFDLPHVIEDAPSYPGVEHVGGDMFVSVPKGDAI 260

Query: 231 LIK 233
            +K
Sbjct: 261 FMK 263

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

 Score =  233 bits (595), Expect = 6e-61,   Method: Compositional matrix adjust.
 Identities = 118/243 (48%), Positives = 163/243 (67%), Gaps = 11/243 (4%)

Query: 1   MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRL 60
           MQ A + VLP  ++AA EL + EI+AKAGP   +S  +IA+Q+P+ NP+A VMLDR+LRL
Sbjct: 24  MQLASASVLPMVLKAAIELDLLEIMAKAGPGVFLSPTDIASQLPTKNPDAPVMLDRMLRL 83

Query: 61  LVTHRVL----RCTSAGDDQRLYGLAHVAKYFVLNRDGVSLCP------SRPWLETKPYE 110
           L ++ +L    R  + G  +RLYGL  V K+   N +GVS+ P       +  LE+  Y 
Sbjct: 84  LASYSILTYSLRTLADGKVERLYGLGPVCKFLTKNEEGVSIAPLCLMNQDKVLLESW-YH 142

Query: 111 IYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIK 170
           + DAVLEGGI FNK +G   +EY G D RFN VFN+ M +H++I   +I+++ KGFE + 
Sbjct: 143 LKDAVLEGGIPFNKAYGMTAFEYHGTDPRFNKVFNRGMADHSTITMKKILETYKGFEGLT 202

Query: 171 QLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAI 230
            +VDVGGG G  +N+I+S Y  IKG+NFDL HVI+D+  Y GV+H+GG M   +PKGDAI
Sbjct: 203 SVVDVGGGTGAVLNMIVSKYPSIKGINFDLPHVIEDAPQYPGVEHVGGDMFVSVPKGDAI 262

Query: 231 LIK 233
            +K
Sbjct: 263 FMK 265

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

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	233
224128073	358	catechol o-methyltransferase related [Po	0.995	0.648	0.525	2e-65
225453640	359	PREDICTED: quercetin 3-O-methyltransfera	0.987	0.640	0.512	1e-64
97974173	364	Caffeic acid 3-O-methyltransferase [Ipom	0.995	0.637	0.522	2e-64
388494808	362	unknown [Medicago truncatula]	1.0	0.643	0.528	3e-64
97974184	364	Caffeic acid 3-O-methyltransferase [Ipom	0.995	0.637	0.518	4e-64
357512657	362	Caffeic acid 3-O-methyltransferase [Medi	1.0	0.643	0.524	4e-64
255548061	359	o-methyltransferase, putative [Ricinus c	0.995	0.646	0.527	1e-63
342161927	364	RecName: Full=Anthranilate N-methyltrans	0.995	0.637	0.523	1e-63
357464229	365	Caffeic acid O-methyltransferase [Medica	1.0	0.638	0.528	2e-63
388502338	365	unknown [Medicago truncatula]	1.0	0.638	0.528	2e-63

>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 =  254 bits (649), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 125/238 (52%), Positives = 172/238 (72%), Gaps = 6/238 (2%)

Query: 1   MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRL 60
           MQ A+S VLP  M +A +LG+FEIIAKAGP AK+SA ++AAQ+P+ NP+A +MLDRILRL
Sbjct: 24  MQLALSSVLPMTMYSAIQLGIFEIIAKAGPDAKLSASDVAAQLPTKNPDAPMMLDRILRL 83

Query: 61  LVTHRVLRCTSAGDDQRLYGLAHVAKYFVLNRDGVSLCPSRPWLETKPY-----EIYDAV 115
           L +H VL C+  G  +RLY LA V+K++V N+DGVSL P    ++   +     ++ DAV
Sbjct: 84  LASHDVLGCSVDGS-ERLYSLAPVSKHYVRNKDGVSLGPFMALIQDNVFLQSWSQLKDAV 142

Query: 116 LEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIKQLVDV 175
           LEGG++F++VHG   +EY G D RFN VFN AM N T++V   ++++  GF+ +KQLV++
Sbjct: 143 LEGGVAFDRVHGAHAFEYPGLDPRFNQVFNTAMYNQTTVVLENMLEAYTGFKNLKQLVEI 202

Query: 176 GGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAILIK 233
           GGG+G  +  IIS Y  IKG+NFDL HVI+ + S  GV+H+GG M E +PKGDAI +K
Sbjct: 203 GGGMGHTIKAIISKYPQIKGINFDLPHVIEHAPSCPGVEHVGGDMFESVPKGDAIFLK 260

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225453640|ref|XP_002267179.1| PREDICTED: quercetin 3-O-methyltransferase 1 isoform 1 [Vitis vinifera] gi|147785074|emb|CAN75449.1| hypothetical protein VITISV_028011 [Vitis vinifera]

 Score =  251 bits (642), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 122/238 (51%), Positives = 168/238 (70%), Gaps = 8/238 (3%)

Query: 1   MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRL 60
           MQ   S VLP  MQ + ELG+F+IIAK G   + SA EIA+++P+ NP A +MLDR+L L
Sbjct: 27  MQLVTSSVLPMVMQTSIELGLFDIIAKLG---QASASEIASRLPTKNPEAPIMLDRMLYL 83

Query: 61  LVTHRVLRCTSAGDDQRLYGLAHVAKYFVLNRDGVSLCPSRPWLETKPY-----EIYDAV 115
           L TH VL C++   D+R+Y L  V+KYF  N+DGVS  P    ++ K +     ++ +A+
Sbjct: 84  LTTHSVLSCSAIDGDERVYALTPVSKYFASNQDGVSFGPLLALIQDKVFMDSWSQLKNAI 143

Query: 116 LEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIKQLVDV 175
           +EGGI FN+VHG+  +EY G D RFN VFN AM NHT+I+ N+I++S KGFE + ++VDV
Sbjct: 144 IEGGIPFNRVHGSHAFEYPGKDPRFNQVFNTAMFNHTTIIVNKILESYKGFEHLTRVVDV 203

Query: 176 GGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAILIK 233
           GGGLG  ++II S Y HI+ +NFDL HVI+ + ++ GV+HIGG M E +PKGDAI +K
Sbjct: 204 GGGLGTTLSIITSKYPHIEAINFDLPHVIEHAVAFPGVEHIGGDMFESVPKGDAIFMK 261

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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 =  251 bits (641), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 127/243 (52%), Positives = 167/243 (68%), Gaps = 11/243 (4%)

Query: 1   MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRL 60
           MQ A + VLP  +++A EL + E+IAKAGP A +S  E+AAQ+P++NP+AAVMLDRILRL
Sbjct: 25  MQLASASVLPMVLKSAIELDLLELIAKAGPGAAVSPSELAAQLPTTNPDAAVMLDRILRL 84

Query: 61  LVTHRVLRCT----SAGDDQRLYGLAHVAKYFVLNRDGVSLCP------SRPWLETKPYE 110
           L T+ VL C+      G  +RLY LA V KY   N DGVS+ P       +  +E+  Y 
Sbjct: 85  LCTYSVLNCSLRTLPDGRVERLYSLAPVCKYLTKNGDGVSMAPLLLMNQDKVLMESW-YH 143

Query: 111 IYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIK 170
           + DAVLEGGI FNK +G   +EY G D RFN VFN+ M +H++I   +I+D  KGFE +K
Sbjct: 144 LKDAVLEGGIPFNKAYGMTAFEYHGTDPRFNKVFNRGMSDHSTITMKKILDDYKGFEGLK 203

Query: 171 QLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAI 230
            LVDVGGG G  +N+I+S Y +IKG+NFDL HVI+DS  Y G++H+GG M   +PKGDAI
Sbjct: 204 SLVDVGGGTGATLNMILSKYPNIKGINFDLPHVIEDSPKYPGIEHVGGDMFVSVPKGDAI 263

Query: 231 LIK 233
            +K
Sbjct: 264 FMK 266

Source: Ipomoea nil

Species: Ipomoea nil

Genus: Ipomoea

Family: Convolvulaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388494808|gb|AFK35470.1| unknown [Medicago truncatula]

 Score =  250 bits (639), Expect = 3e-64,   Method: Compositional matrix adjust.
 Identities = 129/244 (52%), Positives = 168/244 (68%), Gaps = 11/244 (4%)

Query: 1   MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRL 60
           +Q + SIVL  A+Q+A ELGVFE++ KAG    +S+ EIA+++  +NP+A  MLDRIL L
Sbjct: 21  VQLSNSIVLSMALQSAIELGVFEVLQKAGRDTPLSSDEIASRLSCTNPDAPKMLDRILAL 80

Query: 61  LVTHRVLRCTSAGDDQ------RLYGLAHVAKYFVLNRDGVSLCPSRPWLETKPY----- 109
           L +H VL C+   D        RLY +  VAK+F  N DGVSL P     + K Y     
Sbjct: 81  LASHSVLNCSVHPDQHNLGSFHRLYAMTSVAKFFAPNSDGVSLGPLIALHQDKIYLQSWS 140

Query: 110 EIYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQI 169
           ++ DA+ EGGI FN+V+GT  +EYA  D RFN VFN AM+NHT+IV N+++ S KGFE +
Sbjct: 141 QLKDAIREGGIPFNRVYGTNDFEYASIDSRFNQVFNTAMINHTTIVMNKVLQSYKGFEDV 200

Query: 170 KQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDA 229
           K+LVDVGGGLGVNVN+I S + HI G+NFDL HVIQ + SY GV+H+GG M E +PK DA
Sbjct: 201 KRLVDVGGGLGVNVNLITSKHPHIHGINFDLPHVIQHAPSYPGVEHVGGDMFETVPKADA 260

Query: 230 ILIK 233
           I +K
Sbjct: 261 IFMK 264

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  250 bits (638), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 126/243 (51%), Positives = 167/243 (68%), Gaps = 11/243 (4%)

Query: 1   MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRL 60
           MQ A + VLP  +++A EL + E+IAKAGP A +S  E+AAQ+P++NP+AAVMLDRILRL
Sbjct: 25  MQLASASVLPMVLKSAIELDLLELIAKAGPGAAVSPSELAAQLPTTNPDAAVMLDRILRL 84

Query: 61  LVTHRVLRCT----SAGDDQRLYGLAHVAKYFVLNRDGVSLCP------SRPWLETKPYE 110
           L T+ VL C+      G  +RLY LA V KY   N DGVS+ P       +  +E+  Y 
Sbjct: 85  LCTYSVLNCSLRTLPDGRVERLYSLAPVCKYLTKNGDGVSMAPLLLMNQDKVLMESW-YH 143

Query: 111 IYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIK 170
           + DAVLEGGI FNK +G   +EY G D RFN VFN+ M +H++I   +I+D  KGFE +K
Sbjct: 144 LKDAVLEGGIPFNKAYGMTAFEYHGTDPRFNKVFNRGMSDHSTITMKKILDDYKGFEGLK 203

Query: 171 QLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAI 230
            LVDVGGG G  +N+I+S Y +IKG+NFDL HVI+D+  Y G++H+GG M   +PKGDAI
Sbjct: 204 SLVDVGGGTGATLNMILSKYPNIKGINFDLPHVIEDAPKYPGIEHVGGDMFVSVPKGDAI 263

Query: 231 LIK 233
            +K
Sbjct: 264 FMK 266

Source: Ipomoea nil

Species: Ipomoea nil

Genus: Ipomoea

Family: Convolvulaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357512657|ref|XP_003626617.1| Caffeic acid 3-O-methyltransferase [Medicago truncatula] gi|87240860|gb|ABD32718.1| O-methyltransferase, family 2; Dimerisation [Medicago truncatula] gi|355501632|gb|AES82835.1| Caffeic acid 3-O-methyltransferase [Medicago truncatula]

 Score =  250 bits (638), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 128/244 (52%), Positives = 168/244 (68%), Gaps = 11/244 (4%)

Query: 1   MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRL 60
           +Q + SIVL  A+Q+A ELGVFE++ KAG    +S+ EIA+++  +NP+A  MLDRIL L
Sbjct: 21  VQLSNSIVLSMALQSAIELGVFEVLQKAGRDTPLSSDEIASRLSCTNPDAPKMLDRILAL 80

Query: 61  LVTHRVLRCTSAGDDQ------RLYGLAHVAKYFVLNRDGVSLCPSRPWLETKPY----- 109
           L +H VL C+   D        RLY +  VAK+F  N DGVSL P     + K Y     
Sbjct: 81  LASHSVLNCSVHPDQHNLGSFHRLYAMTSVAKFFAPNSDGVSLGPLIALHQDKIYLQSWS 140

Query: 110 EIYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQI 169
           ++ DA+ EGGI FN+V+GT  +EYA  D RFN VFN AM+NHT+IV N+++ S KGFE +
Sbjct: 141 QLKDAIREGGIPFNRVYGTNDFEYASIDSRFNQVFNTAMINHTTIVMNKVLQSYKGFEDV 200

Query: 170 KQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDA 229
           K+LVDVGGGLGVN+N+I S + HI G+NFDL HVIQ + SY GV+H+GG M E +PK DA
Sbjct: 201 KRLVDVGGGLGVNINLITSKHPHIHGINFDLPHVIQHAPSYPGVEHVGGDMFETVPKADA 260

Query: 230 ILIK 233
           I +K
Sbjct: 261 IFMK 264

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  248 bits (634), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 126/239 (52%), Positives = 171/239 (71%), Gaps = 7/239 (2%)

Query: 1   MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPS-SNPNAAVMLDRILR 59
           MQ A+   LP ++ AA ELGVFEIIAKAGP +K+SA EI A++P   NP+AA+ LDR+LR
Sbjct: 24  MQLALGSALPMSLHAAIELGVFEIIAKAGPESKLSASEITAEIPDVQNPDAAITLDRVLR 83

Query: 60  LLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLNRDGVSLCPSRPWLETKPY-----EIYDA 114
           LL +H VL C+  G  +RLY L  V+KYFV N+DG+SL P    ++ K +     ++ DA
Sbjct: 84  LLASHNVLGCSLNGL-ERLYSLNPVSKYFVPNQDGISLGPFMALIQDKVFLDSWTKLKDA 142

Query: 115 VLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIKQLVD 174
           VLEGG  FNK HGT  + Y+G D RFN VFN AM +HT++V  +I+++ KGF+Q+KQL+D
Sbjct: 143 VLEGGSPFNKFHGTHCFGYSGLDSRFNHVFNTAMFHHTNLVITKILETYKGFKQLKQLID 202

Query: 175 VGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAILIK 233
           VGGGLG  +  IIS Y H+KG+NFDL HV++ + +  GV+H+ G M E +PKG+AI +K
Sbjct: 203 VGGGLGHTLKAIISKYPHLKGINFDLPHVVKYAPAIPGVEHVAGDMFESVPKGEAIFMK 261

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|342161927|sp|A9X7L0.1|ANMT_RUTGR RecName: Full=Anthranilate N-methyltransferase; Short=RgANMT gi|115315700|gb|ABI93949.1| anthranilate N-methyltransferase [Ruta graveolens]

 Score =  248 bits (634), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 125/239 (52%), Positives = 171/239 (71%), Gaps = 7/239 (2%)

Query: 1   MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRL 60
           MQ +M+IVLP A Q+A +LGVFEIIAKA P  ++SA EIA  + + NP A VMLDR+LRL
Sbjct: 29  MQLSMAIVLPMATQSAIQLGVFEIIAKA-PGGRLSASEIATILQAQNPKAPVMLDRMLRL 87

Query: 61  LVTHRVLRCTSAGD-DQRLYGLAHVAKYFVLNRDGVSL-----CPSRPWLETKPYEIYDA 114
           LV+HRVL C+ +G   +RLYGL  V+KYFV ++DG SL      P           +  A
Sbjct: 88  LVSHRVLDCSVSGPAGERLYGLTSVSKYFVPDQDGASLGNFMALPLDKVFMESWMGVKGA 147

Query: 115 VLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIKQLVD 174
           V+EGGI FN+VHG   +EYA ++ +F+  +++AM NH++I   RI++  KGFE + +LVD
Sbjct: 148 VMEGGIPFNRVHGMHIFEYASSNSKFSDTYHRAMFNHSTIALKRILEHYKGFENVTKLVD 207

Query: 175 VGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAILIK 233
           VGGGLGV +++I S Y HI+ +NFDL HV+QD++SY GV+H+GG M E +P+GDAIL+K
Sbjct: 208 VGGGLGVTLSMIASKYPHIQAINFDLPHVVQDAASYPGVEHVGGNMFESVPEGDAILMK 266

Source: Ruta graveolens

Species: Ruta graveolens

Genus: Ruta

Family: Rutaceae

Order: Sapindales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357464229|ref|XP_003602396.1| Caffeic acid O-methyltransferase [Medicago truncatula] gi|355491444|gb|AES72647.1| Caffeic acid O-methyltransferase [Medicago truncatula]

 Score =  248 bits (632), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 128/242 (52%), Positives = 163/242 (67%), Gaps = 9/242 (3%)

Query: 1   MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRL 60
           MQ A + VLP  +++A EL + EIIAKAGP A+IS +EIA+Q+P++NP A VMLDRILRL
Sbjct: 24  MQLASASVLPMVLKSALELDLLEIIAKAGPGAQISPIEIASQLPTTNPEAPVMLDRILRL 83

Query: 61  LVTHRVLRCT----SAGDDQRLYGLAHVAKYFVLNRDGVS-----LCPSRPWLETKPYEI 111
           L  + +L C+      G  QRLYGLA VAKY V N DGVS     L      L    Y +
Sbjct: 84  LACYNILTCSVRTQQDGKVQRLYGLATVAKYLVKNEDGVSISALNLMNQDKVLMESWYHL 143

Query: 112 YDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIKQ 171
            DAVL+GGI FNK +G   +EY G D RFN VFNK M +H++I   +I+++  GFE +K 
Sbjct: 144 KDAVLDGGIPFNKAYGMTAFEYHGTDPRFNKVFNKGMSDHSTITMKKILETYTGFEGLKS 203

Query: 172 LVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAIL 231
           LVDVGGG G  +N I+S Y  IKG+NFDL HVI+D+ SY GV+H+GG M   IPK DA+ 
Sbjct: 204 LVDVGGGTGAVINTIVSKYPTIKGINFDLPHVIEDAPSYPGVEHVGGDMFVSIPKADAVF 263

Query: 232 IK 233
           +K
Sbjct: 264 MK 265

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388502338|gb|AFK39235.1| unknown [Medicago truncatula]

 Score =  248 bits (632), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 128/242 (52%), Positives = 163/242 (67%), Gaps = 9/242 (3%)

Query: 1   MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRL 60
           MQ A + VLP  +++A EL + EIIAKAGP A+IS +EIA+Q+P++NP A VMLDRILRL
Sbjct: 24  MQLASASVLPMVLKSALELDLLEIIAKAGPGAQISPIEIASQLPTTNPEAPVMLDRILRL 83

Query: 61  LVTHRVLRCT----SAGDDQRLYGLAHVAKYFVLNRDGVS-----LCPSRPWLETKPYEI 111
           L  + +L C+      G  QRLYGLA VAKY V N DGVS     L      L    Y +
Sbjct: 84  LACYNILTCSVRTQQDGKVQRLYGLATVAKYLVKNEDGVSISALNLMNQDKVLMESWYHL 143

Query: 112 YDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIKQ 171
            DAVL+GGI FNK +G   +EY G D RFN VFNK M +H++I   +I+++  GFE +K 
Sbjct: 144 KDAVLDGGIPFNKAYGMTAFEYHGTDPRFNKVFNKGMSDHSTITMKKILETYTGFEGLKS 203

Query: 172 LVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAIL 231
           LVDVGGG G  +N I+S Y  IKG+NFDL HVI+D+ SY GV+H+GG M   IPK DA+ 
Sbjct: 204 LVDVGGGTGAVINTIVSKYPTIKGINFDLPHVIEDAPSYPGVEHVGGDMFVSIPKADAVF 263

Query: 232 IK 233
           +K
Sbjct: 264 MK 265

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	233
TAIR|locus:2153423	363	OMT1 "AT5G54160" [Arabidopsis	0.987	0.633	0.448	6.7e-49
UNIPROTKB|Q84N28	360	OMT1 "Flavone O-methyltransfer	0.995	0.644	0.411	6.6e-42
UNIPROTKB|Q6ZD89	368	ROMT-9 "Flavone 3'-O-methyltra	1.0	0.633	0.388	6.8e-40
TAIR|locus:2204680	381	AT1G77520 [Arabidopsis thalian	0.978	0.598	0.360	2.4e-37
TAIR|locus:2204695	381	AT1G77530 [Arabidopsis thalian	0.974	0.595	0.351	6.5e-35
TAIR|locus:2034016	363	AT1G51990 [Arabidopsis thalian	0.965	0.619	0.355	2.2e-34
UNIPROTKB|P93324	372	P93324 "Isoliquiritigenin 2'-O	0.957	0.599	0.369	3.7e-32
TAIR|locus:2038026	352	AT1G33030 [Arabidopsis thalian	0.974	0.644	0.340	6e-32
UNIPROTKB|A8QW52	376	EOMT "Eugenol O-methyltransfer	0.974	0.603	0.331	4.2e-31
TAIR|locus:2015223	381	AT1G63140 [Arabidopsis thalian	0.974	0.595	0.346	4.2e-31

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

 Score = 510 (184.6 bits), Expect = 6.7e-49, P = 6.7e-49
 Identities = 109/243 (44%), Positives = 156/243 (64%)

Query:     1 MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRL 60
             MQ A + VLP A+++A EL + EI+AK G  + +S  EIA+++P+ NP A VMLDRILRL
Sbjct:    24 MQLASASVLPMALKSALELDLLEIMAKNG--SPMSPTEIASKLPTKNPEAPVMLDRILRL 81

Query:    61 LVTHRVLRCTS---AGDD-QRLYGLAHVAKYFVLNRDGVS---LC---PSRPWLETKPYE 110
             L ++ VL C++   +GD  +R+YGL  V KY   N DGVS   LC     +  +E+  Y 
Sbjct:    82 LTSYSVLTCSNRKLSGDGVERIYGLGPVCKYLTKNEDGVSIAALCLMNQDKVLMESW-YH 140

Query:   111 IYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIK 170
             + DA+L+GGI FNK +G   +EY G D RFN VFN  M NH++I   +I+++ KGFE + 
Sbjct:   141 LKDAILDGGIPFNKAYGMSAFEYHGTDPRFNKVFNNGMSNHSTITMKKILETYKGFEGLT 200

Query:   171 QXXXXXXXXXXXXXIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAI 230
                           +I+S Y ++KG+NFDL HVI+D+ S+ G++H+GG M   +PKGDAI
Sbjct:   201 SLVDVGGGIGATLKMIVSKYPNLKGINFDLPHVIEDAPSHPGIEHVGGDMFVSVPKGDAI 260

Query:   231 LIK 233
              +K
Sbjct:   261 FMK 263

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

 Score = 444 (161.4 bits), Expect = 6.6e-42, P = 6.6e-42
 Identities = 100/243 (41%), Positives = 142/243 (58%)

Query:     1 MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSS-NPNAAVMLDRILR 59
             +Q   S +LP  ++ A ELG+ E +  AG    ++  E+AA++PS+ NP AA M+DR+LR
Sbjct:    21 LQLVSSSILPMTLKNAIELGLLETLVAAGGKL-LTPAEVAAKLPSTANPAAADMVDRMLR 79

Query:    60 LLVTHRVLRCT-SAGDDQRL---YGLAHVAKYFVLNRDGVSLCPSRPWLETKP-----YE 110
             LL ++ V+ CT   G D RL   Y  A V K+   N DGVS+       + K      Y 
Sbjct:    80 LLASYNVVSCTMEEGKDGRLSRRYRAAPVCKFLTPNEDGVSMAALALMNQDKVLMESWYY 139

Query:   111 IYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIK 170
             + DAVL+GGI FNK +G   +EY G D RFN VFN+ M NH+ I+T ++++  KGFE + 
Sbjct:   140 LKDAVLDGGIPFNKAYGMSAFEYHGTDPRFNRVFNEGMKNHSIIITKKLLEVYKGFEGLG 199

Query:   171 QXXXXXXXXXXXXXIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAI 230
                            I + Y  IKG+NFDL HVI ++  + GV H+GG M +++P GDAI
Sbjct:   200 TIVDVGGGVGATVGAITAAYPAIKGINFDLPHVISEAQPFPGVTHVGGDMFQKVPSGDAI 259

Query:   231 LIK 233
             L+K
Sbjct:   260 LMK 262

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

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

 Score = 425 (154.7 bits), Expect = 6.8e-40, P = 6.8e-40
 Identities = 97/250 (38%), Positives = 143/250 (57%)

Query:     1 MQPAMSIVLPAAMQAASELGVFEIIAKA------GPTAKISAVEIAAQMPS-SNPNAAVM 53
             +Q A S +LP  ++ A ELG+ E +  A      G  A ++  E+A ++PS +NP AA M
Sbjct:    21 LQLASSSILPMTLKNAIELGLLETLQSAAVAGGGGKAALLTPAEVADKLPSKANPAAADM 80

Query:    54 LDRILRLLVTHRVLRCT-SAGDDQRL---YGLAHVAKYFVLNRDGVSLCPSRPWLETKP- 108
             +DR+LRLL ++ V+RC    G D +L   Y  A V K+   N DGVS+       + K  
Sbjct:    81 VDRMLRLLASYNVVRCEMEEGADGKLSRRYAAAPVCKWLTPNEDGVSMAALALMNQDKVL 140

Query:   109 ----YEIYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSK 164
                 Y + DAVL+GGI FNK +G   +EY G D RFN VFN+ M NH+ I+T +++D   
Sbjct:   141 MESWYYLKDAVLDGGIPFNKAYGMTAFEYHGTDARFNRVFNEGMKNHSVIITKKLLDLYT 200

Query:   165 GFEQIKQXXXXXXXXXXXXXIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERI 224
             GF+                  ++S + HI+G+N+DL HVI ++  + GV+H+GG M   +
Sbjct:   201 GFDAASTVVDVGGGVGATVAAVVSRHPHIRGINYDLPHVISEAPPFPGVEHVGGDMFASV 260

Query:   225 PKG-DAILIK 233
             P+G DAIL+K
Sbjct:   261 PRGGDAILMK 270

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

GO:0032259 "methylation" evidence=IDA

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

 Score = 401 (146.2 bits), Expect = 2.4e-37, P = 2.4e-37
 Identities = 88/244 (36%), Positives = 136/244 (55%)

Query:     6 SIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPS--SNPNAAVMLDRILRLLVT 63
             ++  P  ++AA ELGV + IA AG    +S  EIA  +P+  +NP A V+LDR+L LLV+
Sbjct:    39 TVAFPMVLKAAFELGVIDTIAAAGNDTWLSPCEIACSLPTKPTNPEAPVLLDRMLSLLVS 98

Query:    64 HRVLRCT--SAGDD------QRLYGLAHVAKYFVLNRDGV-SLCPSRPWLETKPY----- 109
             H +L+C     G++      +R+Y    V KYF+ + DG  SL P    L T+ +     
Sbjct:    99 HSILKCRMIETGENGRTGKIERVYAAEPVCKYFLRDSDGTGSLVPLFMLLHTQVFFKTWT 158

Query:   110 EIYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQI 169
              + D +LEG  +FN  HG   +EY  +D  F  +FN+AM   ++++  +++D  +GFE +
Sbjct:   159 NLKDVILEGRDAFNSAHGMKIFEYINSDQPFAELFNRAMSEPSTMIMKKVLDVYRGFEDV 218

Query:   170 KQXXXXXXXXXXXXXIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDA 229
                            ++ S Y HIKGVNFDL+ V+  +  Y GV+H+ G M   +PKGDA
Sbjct:   219 NTLVDVGGGNGTVLGLVTSKYPHIKGVNFDLAQVLTQAPFYPGVEHVSGDMFVEVPKGDA 278

Query:   230 ILIK 233
             + +K
Sbjct:   279 VFMK 282

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:2204695 AT1G77530 [Arabidopsis thaliana (taxid:3702)]

 Score = 378 (138.1 bits), Expect = 6.5e-35, P = 6.5e-35
 Identities = 86/245 (35%), Positives = 135/245 (55%)

Query:     6 SIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPS--SNPNAAVMLDRILRLLVT 63
             ++  P  ++AA ELGV + IA A     +S  EIA  +P+  +NP A V+LDR+LRLLV+
Sbjct:    39 AVAFPMVLKAALELGVIDTIAAASNGTWLSPSEIAVSLPNKPTNPEAPVLLDRMLRLLVS 98

Query:    64 HRVLRCT--------SAGDDQRLYGLAHVAKYFVLNRDG-------VSLCPSRPWLETKP 108
             H +L+C           G  +R+Y    + KYF+ + DG       + L  S+  L+T  
Sbjct:    99 HSILKCCMVESRENGQTGKIERVYAAEPICKYFLKDSDGSGSLSSLLLLLHSQVILKTWT 158

Query:   109 YEIYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQ 168
               + D +LEG  +F+  H    +EY  +D +F+ +F++AM   +++V  ++++  +GFE 
Sbjct:   159 -NLKDVILEGKDAFSSAHDMRLFEYISSDDQFSKLFHRAMSESSTMVMKKVLEEYRGFED 217

Query:   169 IKQXXXXXXXXXXXXXIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGD 228
             +               +I S Y HIKGVNFDL+ V+  +  Y GVKH+ G M   +PKGD
Sbjct:   218 VNTLVDVGGGIGTILGLITSKYPHIKGVNFDLAQVLTQAPFYPGVKHVSGDMFIEVPKGD 277

Query:   229 AILIK 233
             AI +K
Sbjct:   278 AIFMK 282

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:2034016 AT1G51990 [Arabidopsis thaliana (taxid:3702)]

 Score = 373 (136.4 bits), Expect = 2.2e-34, P = 2.2e-34
 Identities = 84/236 (35%), Positives = 131/236 (55%)

Query:     9 LPAAMQAASELGVFEIIAKAGPTAK-ISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVL 67
             +P  ++ A EL +FEI+AKA P    +S V++A+     NP+A +M+DR+LR LV + V 
Sbjct:    28 VPYIVKTARELDLFEIMAKARPLGSYLSPVDLASMAAPKNPHAPMMIDRLLRFLVAYSVC 87

Query:    68 RCTSAGDDQ----RLYGLAHVAKYFVLNRDGVSLCPSRPWLETKPYE-----IYDAVLEG 118
              C    D++    R YGL  V K  + + DG S+ P      TK        + +A+ EG
Sbjct:    88 TCKLVKDEEGRESRAYGLGKVGKKLIKDEDGFSIAPYVLAGCTKAKGGVWSYLTEAIQEG 147

Query:   119 GIS-FNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIKQXXXXXX 177
             G S + + +    +EY   +     +FN++M NHTSIV  +I+++  GFE +        
Sbjct:   148 GASAWERANEALIFEYMKKNENLKKIFNESMTNHTSIVMKKILENYIGFEGVSDFVDVGG 207

Query:   178 XXXXXXXIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAILIK 233
                     I+S Y HIKG+NFDL H+++++    GV+HIGG M + IP+G+ IL+K
Sbjct:   208 SLGSNLAQILSKYPHIKGINFDLPHIVKEAPQIHGVEHIGGDMFDEIPRGEVILMK 263

GO:0008168 "methyltransferase activity" evidence=IEA

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

GO:0009507 "chloroplast" evidence=ISM

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0009809 "lignin biosynthetic process" evidence=ISS

GO:0005829 "cytosol" evidence=TAS

UNIPROTKB|P93324 P93324 "Isoliquiritigenin 2'-O-methyltransferase" [Medicago sativa (taxid:3879)]

 Score = 352 (129.0 bits), Expect = 3.7e-32, P = 3.7e-32
 Identities = 91/246 (36%), Positives = 141/246 (57%)

Query:     6 SIVLPAAMQAASELGVFEIIAKAGPT-AKISAVEIAAQMPSSNPNAAV--MLDRILRLLV 62
             ++V PA + AA +L +FEIIAKA P  A +S  EIA+++P+S  ++ +   LDR+LRLL 
Sbjct:    34 NLVYPAVLNAAIDLNLFEIIAKATPPGAFMSPSEIASKLPASTQHSDLPNRLDRMLRLLA 93

Query:    63 THRVLRCTSA----GDDQRLYGLAHVAKYFVLNRD-G------VSLC-PS--RPWLETKP 108
             ++ VL  T+     G  +R+YGL+ V KY V +   G        LC P+  + W+  K 
Sbjct:    94 SYSVLTSTTRTIEDGGAERVYGLSMVGKYLVPDESRGYLASFTTFLCYPALLQVWMNFK- 152

Query:   109 YEIYDAVLEGGIS-FNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFE 167
                 +AV++  I  F  VHG   YE+ G D + N +FNK+M++  +    R+++   GFE
Sbjct:   153 ----EAVVDEDIDLFKNVHGVTKYEFMGKDKKMNQIFNKSMVDVCATEMKRMLEIYTGFE 208

Query:   168 QIKQXXXXXXXXXXXXXIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKG 227
              I               +IIS Y  IKG+NFDL  VI+++   SG++H+GG M   +P+G
Sbjct:   209 GISTLVDVGGGSGRNLELIISKYPLIKGINFDLPQVIENAPPLSGIEHVGGDMFASVPQG 268

Query:   228 DAILIK 233
             DA+++K
Sbjct:   269 DAMILK 274

GO:0030751 "licodione 2'-O-methyltransferase activity" evidence=IDA

GO:0033802 "isoliquiritigenin 2'-O-methyltransferase activity" evidence=IDA

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

 Score = 350 (128.3 bits), Expect = 6.0e-32, P = 6.0e-32
 Identities = 81/238 (34%), Positives = 126/238 (52%)

Query:     6 SIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHR 65
             S VLP  ++ A +LG+F+I+A++GP++      + +     + +++ +++RILR L ++ 
Sbjct:    16 SSVLPMVLKTAIDLGLFDILAESGPSSASQIFSLLSNETKKHHDSS-LVNRILRFLASYS 74

Query:    66 VLRC---TSAGDDQRLYGLAHVAKYFVLNRDGV-SLCPSRPWLETKP-----YEIYDAVL 116
             +L C   T  G+   +YGLA VAKYF  N++G  SL P     + K      Y + D+VL
Sbjct:    75 ILTCSVSTEHGEPFAIYGLAPVAKYFTKNQNGGGSLAPMVNLFQDKVVTDMWYNLKDSVL 134

Query:   117 EGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIKQXXXXX 176
             EGG+ FN  HG+   E  G+D RF  VF  +M     +     + +  GF+ +K      
Sbjct:   135 EGGLPFNNTHGSSAVELVGSDSRFREVFQSSMKGFNEVFIEEFLKNYNGFDGVKSLVDVG 194

Query:   177 XXXXXXXXIIISNYLHI-KGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAILIK 233
                      IIS + HI K +NFDL  VI  S    G++H+ G M    PKG+AI +K
Sbjct:   195 GGDGSLLSRIISKHTHIIKAINFDLPTVINTSLPSPGIEHVAGDMFTNTPKGEAIFMK 252

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

UNIPROTKB|A8QW52 EOMT "Eugenol O-methyltransferase" [Sorghum bicolor (taxid:4558)]

 Score = 342 (125.4 bits), Expect = 4.2e-31, P = 4.2e-31
 Identities = 80/241 (33%), Positives = 124/241 (51%)

Query:     7 IVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAV-MLDRILRLLVTHR 65
             + +P  ++A  ELG+ +++  A       A+  A   P+  P AA  M+DR+LR L +H 
Sbjct:    36 LAVPFTIKAVIELGIMDLLLAADRAMTAEALTAALLCPAPAPAAAAAMVDRMLRFLASHG 95

Query:    66 VLRCTSA----GDDQ----RLYGLAHVAKYFVLNRDGVSLCPSRPWLETKP-----YEIY 112
             V+RC +     G D     R Y  A V K+F       S+ P   W+ +       + I 
Sbjct:    96 VVRCATESEELGSDDGKSCRRYAAAPVCKWFARGGGVESVVPMGFWMTSTTNMETWHNIK 155

Query:   113 DAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIKQX 172
             D VL G   F+K +G   +EY G +   N +FN+AM +H+ I+T R+++  +GFE     
Sbjct:   156 DGVLAGETPFDKAYGMPVFEYLGANGTMNTLFNEAMASHSMIITKRLLEVFRGFENYSVL 215

Query:   173 XXXXXXXXXXXXIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAILI 232
                         +I S Y +I G+N+DL HVI  +S   GV+H+ G M + IP+GDAI++
Sbjct:   216 VDVGGGNGTTMQMIRSQYENISGINYDLPHVIAQASPIEGVEHVAGNMFDNIPRGDAIIL 275

Query:   233 K 233
             K
Sbjct:   276 K 276

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

GO:0008757 "S-adenosylmethionine-dependent methyltransferase activity" evidence=IDA

GO:0032259 "methylation" evidence=IDA

TAIR|locus:2015223 AT1G63140 [Arabidopsis thaliana (taxid:3702)]

 Score = 342 (125.4 bits), Expect = 4.2e-31, P = 4.2e-31
 Identities = 85/245 (34%), Positives = 133/245 (54%)

Query:     6 SIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPS--SNPNAAVMLDRILRLLVT 63
             ++  P  ++ A ELGV ++I        +S  EIA  +P+  +NP A V+LDR+L LL +
Sbjct:    39 AMTFPMVLKTALELGVIDMITSVDDGVWLSPSEIALGLPTKPTNPEAPVLLDRMLVLLAS 98

Query:    64 HRVL--RCTSAGDD------QRLYGLAHVAKYFVLNR-DGV-SLCPSRPWLE----TKPY 109
             H +L  R    GD+      +R+Y    V  +F LNR DG+ SL      L+     KP+
Sbjct:    99 HSILKYRTVETGDNIGSRKTERVYAAEPVCTFF-LNRGDGLGSLATLFMVLQGEVCMKPW 157

Query:   110 E-IYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQ 168
             E + D +LEG  +F   HG  F+E  G++ +F  +FN+AM   ++++  ++++  KGFE 
Sbjct:   158 EHLKDMILEGKDAFTSAHGMRFFELIGSNEQFAEMFNRAMSEASTLIMKKVLEVYKGFED 217

Query:   169 IKQXXXXXXXXXXXXXIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGD 228
             +                + S Y HIKG+NFDL+ V+  +    GV+H+ G M + IPKGD
Sbjct:   218 VNTLVDVGGGIGTIIGQVTSKYPHIKGINFDLASVLAHAPFNKGVEHVSGDMFKEIPKGD 277

Query:   229 AILIK 233
             AI +K
Sbjct:   278 AIFMK 282

GO:0005737 "cytoplasm" 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

---

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: COMT4 SubName- Full=Putative uncharacterized protein; (358 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	233
pfam00891	239	pfam00891, Methyltransf_2, O-methyltransferase	1e-51
pfam08100	50	pfam08100, Dimerisation, Dimerisation domain	3e-14

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

 Score =  167 bits (425), Expect = 1e-51
 Identities = 66/171 (38%), Positives = 87/171 (50%), Gaps = 15/171 (8%)

Query: 73  GDDQRLYGLAHVAKYFVLNRDGVSLCPS----------RPWLETKPYEIYDAVLEGGISF 122
                 YGL   +K  V   D  SL P             W       + DAV EGG  F
Sbjct: 1   TRGGEDYGLTPASKLLVKGEDSPSLAPLLLMYADPTLLESW-----AHLKDAVREGGPPF 55

Query: 123 NKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIKQLVDVGGGLGVN 182
            +  G  F+EY G D  FN VFN+AM  H+ +V  +I++++  F  +  LVDVGGG G  
Sbjct: 56  ERAFGMPFFEYLGADPEFNRVFNRAMAAHSRLVMKKILETAFDFSGLSSLVDVGGGTGAL 115

Query: 183 VNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAILIK 233
              I+  Y HIKG+ FDL HVI D+ S   V+ +GG   E +P+ DAIL+K
Sbjct: 116 AAAIVRAYPHIKGIVFDLPHVIADAPSADRVEFVGGDFFESVPEADAILLK 166

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

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

 Score = 64.5 bits (158), Expect = 3e-14
 Identities = 25/51 (49%), Positives = 36/51 (70%), Gaps = 2/51 (3%)

Query: 12 AMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLV 62
           ++ A ELG+ +IIAK G    +S  E+A+++P+ NP A VMLDR+LRLL 
Sbjct: 2  VLKCAIELGIPDIIAKHG--KPLSPSELASKLPTVNPEAPVMLDRLLRLLA 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	233
KOG3178	342	consensus Hydroxyindole-O-methyltransferase and re	100.0
TIGR02716	306	C20_methyl_CrtF C-20 methyltransferase BchU. Membe	100.0
PF00891	241	Methyltransf_2: O-methyltransferase; InterPro: IPR	100.0
PF08100	51	Dimerisation: Dimerisation domain; InterPro: IPR01	99.16
PF12847	112	Methyltransf_18: Methyltransferase domain; PDB: 3G	98.87
PRK06922	677	hypothetical protein; Provisional	98.74
PRK08287	187	cobalt-precorrin-6Y C(15)-methyltransferase; Valid	98.68
PRK14103	255	trans-aconitate 2-methyltransferase; Provisional	98.55
PF13847	152	Methyltransf_31: Methyltransferase domain; PDB: 3T	98.54
COG4106	257	Tam Trans-aconitate methyltransferase [General fun	98.53
TIGR03587	204	Pse_Me-ase pseudaminic acid biosynthesis-associate	98.52
PRK01683	258	trans-aconitate 2-methyltransferase; Provisional	98.48
PF05175	170	MTS: Methyltransferase small domain; InterPro: IPR	98.47
TIGR02752	231	MenG_heptapren 2-heptaprenyl-1,4-naphthoquinone me	98.47
PRK04457	262	spermidine synthase; Provisional	98.44
PRK15451	247	tRNA cmo(5)U34 methyltransferase; Provisional	98.4
TIGR03533	284	L3_gln_methyl protein-(glutamine-N5) methyltransfe	98.4
TIGR00740	239	methyltransferase, putative. A simple BLAST search	98.39
PRK11805	307	N5-glutamine S-adenosyl-L-methionine-dependent met	98.38
PRK15001	378	SAM-dependent 23S ribosomal RNA mG1835 methyltrans	98.36
COG2226	238	UbiE Methylase involved in ubiquinone/menaquinone	98.34
PTZ00098	263	phosphoethanolamine N-methyltransferase; Provision	98.31
COG2890	280	HemK Methylase of polypeptide chain release factor	98.31
COG2242	187	CobL Precorrin-6B methylase 2 [Coenzyme metabolism	98.31
TIGR00536	284	hemK_fam HemK family putative methylases. The gene	98.3
PLN02244	340	tocopherol O-methyltransferase	98.3
TIGR02469	124	CbiT precorrin-6Y C5,15-methyltransferase (decarbo	98.28
PRK00107	187	gidB 16S rRNA methyltransferase GidB; Reviewed	98.25
PRK11207	197	tellurite resistance protein TehB; Provisional	98.23
TIGR03534	251	RF_mod_PrmC protein-(glutamine-N5) methyltransfera	98.23
smart00828	224	PKS_MT Methyltransferase in polyketide synthase (P	98.23
TIGR00091	194	tRNA (guanine-N(7)-)-methyltransferase. In E. coli	98.22
TIGR00138	181	gidB 16S rRNA methyltransferase GidB. GidB (glucos	98.21
PF13649	101	Methyltransf_25: Methyltransferase domain; PDB: 3B	98.19
PRK14966	423	unknown domain/N5-glutamine S-adenosyl-L-methionin	98.19
TIGR02021	219	BchM-ChlM magnesium protoporphyrin O-methyltransfe	98.19
PLN02336	475	phosphoethanolamine N-methyltransferase	98.17
PRK01544	506	bifunctional N5-glutamine S-adenosyl-L-methionine-	98.16
PF01209	233	Ubie_methyltran: ubiE/COQ5 methyltransferase famil	98.16
COG2813	300	RsmC 16S RNA G1207 methylase RsmC [Translation, ri	98.14
PLN02233	261	ubiquinone biosynthesis methyltransferase	98.14
PRK10258	251	biotin biosynthesis protein BioC; Provisional	98.13
PRK11088	272	rrmA 23S rRNA methyltransferase A; Provisional	98.12
PRK08317	241	hypothetical protein; Provisional	98.12
PRK00121	202	trmB tRNA (guanine-N(7)-)-methyltransferase; Revie	98.12
PF08242	99	Methyltransf_12: Methyltransferase domain; InterPr	98.12
PRK13942	212	protein-L-isoaspartate O-methyltransferase; Provis	98.12
TIGR02072	240	BioC biotin biosynthesis protein BioC. This enzyme	98.11
TIGR00080	215	pimt protein-L-isoaspartate(D-aspartate) O-methylt	98.11
PRK09328	275	N5-glutamine S-adenosyl-L-methionine-dependent met	98.11
PRK07402	196	precorrin-6B methylase; Provisional	98.11
smart00650	169	rADc Ribosomal RNA adenine dimethylases.	98.11
PRK14121	390	tRNA (guanine-N(7)-)-methyltransferase; Provisiona	98.11
PRK00216	239	ubiE ubiquinone/menaquinone biosynthesis methyltra	98.1
PF08241	95	Methyltransf_11: Methyltransferase domain; InterPr	98.09
TIGR03704	251	PrmC_rel_meth putative protein-(glutamine-N5) meth	98.09
PRK09489	342	rsmC 16S ribosomal RNA m2G1207 methyltransferase;	98.08
PRK13944	205	protein-L-isoaspartate O-methyltransferase; Provis	98.07
PRK11036	255	putative S-adenosyl-L-methionine-dependent methylt	98.06
TIGR01934	223	MenG_MenH_UbiE ubiquinone/menaquinone biosynthesis	98.06
PLN02490	340	MPBQ/MSBQ methyltransferase	98.03
PLN03075	296	nicotianamine synthase; Provisional	98.02
smart00138	264	MeTrc Methyltransferase, chemotaxis proteins. Meth	98.02
PRK06202	232	hypothetical protein; Provisional	98.02
PF13659	117	Methyltransf_26: Methyltransferase domain; PDB: 3G	98.01
COG4123	248	Predicted O-methyltransferase [General function pr	98.0
PRK14896	258	ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1	98.0
PRK00274	272	ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1	97.98
PHA03411	279	putative methyltransferase; Provisional	97.97
PLN02366	308	spermidine synthase	97.96
KOG1540	296	consensus Ubiquinone biosynthesis methyltransferas	97.92
TIGR00537	179	hemK_rel_arch HemK-related putative methylase. The	97.89
PRK07580	230	Mg-protoporphyrin IX methyl transferase; Validated	97.87
PRK00811	283	spermidine synthase; Provisional	97.85
PRK05785	226	hypothetical protein; Provisional	97.85
PRK11188	209	rrmJ 23S rRNA methyltransferase J; Provisional	97.82
TIGR00477	195	tehB tellurite resistance protein TehB. Part of a	97.81
TIGR00755	253	ksgA dimethyladenosine transferase. Alternate name	97.81
PRK11873	272	arsM arsenite S-adenosylmethyltransferase; Reviewe	97.8
PHA03412	241	putative methyltransferase; Provisional	97.79
PF05401	201	NodS: Nodulation protein S (NodS); InterPro: IPR00	97.78
PRK01581	374	speE spermidine synthase; Validated	97.75
PRK15068	322	tRNA mo(5)U34 methyltransferase; Provisional	97.74
COG2230	283	Cfa Cyclopropane fatty acid synthase and related m	97.74
PRK00377	198	cbiT cobalt-precorrin-6Y C(15)-methyltransferase;	97.73
PRK14967	223	putative methyltransferase; Provisional	97.71
PRK00312	212	pcm protein-L-isoaspartate O-methyltransferase; Re	97.71
PF02353	273	CMAS: Mycolic acid cyclopropane synthetase; InterP	97.71
PLN02672	1082	methionine S-methyltransferase	97.7
PRK14968	188	putative methyltransferase; Provisional	97.69
PRK00050	296	16S rRNA m(4)C1402 methyltranserfase; Provisional	97.67
PRK12335	287	tellurite resistance protein TehB; Provisional	97.63
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	97.63
PLN02396	322	hexaprenyldihydroxybenzoate methyltransferase	97.63
PRK13943	322	protein-L-isoaspartate O-methyltransferase; Provis	97.63
PTZ00338	294	dimethyladenosine transferase-like protein; Provis	97.62
PRK03612	521	spermidine synthase; Provisional	97.61
PRK04266	226	fibrillarin; Provisional	97.61
TIGR00438	188	rrmJ cell division protein FtsJ.	97.6
PF02390	195	Methyltransf_4: Putative methyltransferase ; Inter	97.59
PLN02336	475	phosphoethanolamine N-methyltransferase	97.59
PLN02781	234	Probable caffeoyl-CoA O-methyltransferase	97.58
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	97.57
TIGR03438	301	probable methyltransferase. This model represents	97.54
PRK04148	134	hypothetical protein; Provisional	97.51
PF07021	193	MetW: Methionine biosynthesis protein MetW; InterP	97.51
PF01135	209	PCMT: Protein-L-isoaspartate(D-aspartate) O-methyl	97.5
cd02440	107	AdoMet_MTases S-adenosylmethionine-dependent methy	97.49
TIGR03840	213	TMPT_Se_Te thiopurine S-methyltransferase, Se/Te d	97.45
TIGR02081	194	metW methionine biosynthesis protein MetW. This pr	97.45
KOG2904	328	consensus Predicted methyltransferase [General fun	97.44
PRK13168	443	rumA 23S rRNA m(5)U1939 methyltransferase; Reviewe	97.42
PRK10909	199	rsmD 16S rRNA m(2)G966-methyltransferase; Provisio	97.39
COG0421	282	SpeE Spermidine synthase [Amino acid transport and	97.39
PLN02823	336	spermine synthase	97.39
PRK11705	383	cyclopropane fatty acyl phospholipid synthase; Pro	97.38
TIGR00452	314	methyltransferase, putative. Known examples to dat	97.38
COG1414	246	IclR Transcriptional regulator [Transcription]	97.38
PF03848	192	TehB: Tellurite resistance protein TehB; InterPro:	97.37
TIGR00417	270	speE spermidine synthase. the SpeE subunit of sper	97.36
TIGR00406	288	prmA ribosomal protein L11 methyltransferase. Ribo	97.36
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	97.34
COG2263	198	Predicted RNA methylase [Translation, ribosomal st	97.32
PRK03522	315	rumB 23S rRNA methyluridine methyltransferase; Rev	97.32
PF06325	295	PrmA: Ribosomal protein L11 methyltransferase (Prm	97.32
PRK14902	444	16S rRNA methyltransferase B; Provisional	97.28
PRK11569	274	transcriptional repressor IclR; Provisional	97.24
PF09445	163	Methyltransf_15: RNA cap guanine-N2 methyltransfer	97.23
PRK10163	271	DNA-binding transcriptional repressor AllR; Provis	97.2
COG2264	300	PrmA Ribosomal protein L11 methylase [Translation,	97.2
COG2518	209	Pcm Protein-L-isoaspartate carboxylmethyltransfera	97.17
PRK11727	321	23S rRNA mA1618 methyltransferase; Provisional	97.17
KOG1271	227	consensus Methyltransferases [General function pre	97.16
PLN02585	315	magnesium protoporphyrin IX methyltransferase	97.15
TIGR02431	248	pcaR_pcaU beta-ketoadipate pathway transcriptional	97.15
PRK13255	218	thiopurine S-methyltransferase; Reviewed	97.15
PRK00536	262	speE spermidine synthase; Provisional	97.14
PRK09834	263	DNA-binding transcriptional activator MhpR; Provis	97.13
KOG2899	288	consensus Predicted methyltransferase [General fun	97.12
PRK15090	257	DNA-binding transcriptional regulator KdgR; Provis	97.12
TIGR01177	329	conserved hypothetical protein TIGR01177. This fam	97.1
PRK00517	250	prmA ribosomal protein L11 methyltransferase; Revi	97.08
PTZ00146	293	fibrillarin; Provisional	97.08
PF14947	77	HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_	97.08
PF02082	83	Rrf2: Transcriptional regulator; InterPro: IPR0009	97.05
PF05185	448	PRMT5: PRMT5 arginine-N-methyltransferase; InterPr	97.02
KOG1499	346	consensus Protein arginine N-methyltransferase PRM	97.01
PF08123	205	DOT1: Histone methylation protein DOT1 ; InterPro:	97.01
PRK10901	427	16S rRNA methyltransferase B; Provisional	97.0
KOG1500	517	consensus Protein arginine N-methyltransferase CAR	96.99
TIGR02085	374	meth_trns_rumB 23S rRNA (uracil-5-)-methyltransfer	96.96
PF13489	161	Methyltransf_23: Methyltransferase domain; PDB: 3J	96.96
KOG0820	315	consensus Ribosomal RNA adenine dimethylase [RNA p	96.96
COG0220	227	Predicted S-adenosylmethionine-dependent methyltra	96.92
PF01564	246	Spermine_synth: Spermine/spermidine synthase; Inte	96.91
PF01596	205	Methyltransf_3: O-methyltransferase; InterPro: IPR	96.91
PF13679	141	Methyltransf_32: Methyltransferase domain	96.9
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	96.9
TIGR00479	431	rumA 23S rRNA (uracil-5-)-methyltransferase RumA.	96.88
PLN02476	278	O-methyltransferase	96.87
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	96.86
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	96.85
TIGR01444	143	fkbM_fam methyltransferase, FkbM family. Members o	96.82
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	96.82
PRK05134	233	bifunctional 3-demethylubiquinone-9 3-methyltransf	96.74
KOG3420	185	consensus Predicted RNA methylase [Translation, ri	96.74
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	96.72
PRK10141	117	DNA-binding transcriptional repressor ArsR; Provis	96.64
PF04816	205	DUF633: Family of unknown function (DUF633) ; Inte	96.62
PRK14904	445	16S rRNA methyltransferase B; Provisional	96.6
PF00398	262	RrnaAD: Ribosomal RNA adenine dimethylase; InterPr	96.58
COG2227	243	UbiG 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-	96.57
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	96.56
TIGR01983	224	UbiG ubiquinone biosynthesis O-methyltransferase.	96.56
PF13601	80	HTH_34: Winged helix DNA-binding domain; PDB: 1UB9	96.55
smart00347	101	HTH_MARR helix_turn_helix multiple antibiotic resi	96.5
PF05724	218	TPMT: Thiopurine S-methyltransferase (TPMT); Inter	96.49
KOG1541	270	consensus Predicted protein carboxyl methylase [Ge	96.48
PRK11783	702	rlmL 23S rRNA m(2)G2445 methyltransferase; Provisi	96.46
TIGR00095	189	RNA methyltransferase, RsmD family. This model rep	96.45
PRK15128	396	23S rRNA m(5)C1962 methyltransferase; Provisional	96.44
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	96.43
COG4262	508	Predicted spermidine synthase with an N-terminal m	96.41
PRK10857	164	DNA-binding transcriptional regulator IscR; Provis	96.38
PRK03902	142	manganese transport transcriptional regulator; Pro	96.37
PF09012	69	FeoC: FeoC like transcriptional regulator; InterPr	96.37
PRK11760	357	putative 23S rRNA C2498 ribose 2'-O-ribose methylt	96.34
PF01170	179	UPF0020: Putative RNA methylase family UPF0020; In	96.34
PF01795	310	Methyltransf_5: MraW methylase family; InterPro: I	96.34
PRK01544	506	bifunctional N5-glutamine S-adenosyl-L-methionine-	96.33
COG1959	150	Predicted transcriptional regulator [Transcription	96.33
PRK13256	226	thiopurine S-methyltransferase; Reviewed	96.32
TIGR02010	135	IscR iron-sulfur cluster assembly transcription fa	96.32
COG2519	256	GCD14 tRNA(1-methyladenosine) methyltransferase an	96.31
PRK14901	434	16S rRNA methyltransferase B; Provisional	96.3
KOG1270	282	consensus Methyltransferases [Coenzyme transport a	96.29
TIGR02337	118	HpaR homoprotocatechuate degradation operon regula	96.27
TIGR00563	426	rsmB ribosomal RNA small subunit methyltransferase	96.26
TIGR02143	353	trmA_only tRNA (uracil-5-)-methyltransferase. This	96.25
COG3355	126	Predicted transcriptional regulator [Transcription	96.2
PF07381	90	DUF1495: Winged helix DNA-binding domain (DUF1495)	96.18
COG0030	259	KsgA Dimethyladenosine transferase (rRNA methylati	96.16
TIGR00738	132	rrf2_super rrf2 family protein (putative transcrip	96.15
TIGR00478	228	tly hemolysin TlyA family protein. Hemolysins are	96.14
PF08461	66	HTH_12: Ribonuclease R winged-helix domain; InterP	96.13
PRK14903	431	16S rRNA methyltransferase B; Provisional	96.07
TIGR00006	305	S-adenosyl-methyltransferase MraW. Genetics paper	96.06
TIGR02702	203	SufR_cyano iron-sulfur cluster biosynthesis transc	96.05
COG1321	154	TroR Mn-dependent transcriptional regulator [Trans	95.99
PRK11050	152	manganese transport regulator MntR; Provisional	95.93
PF04703	62	FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.	95.9
PF12147	311	Methyltransf_20: Putative methyltransferase; Inter	95.89
PRK05031	362	tRNA (uracil-5-)-methyltransferase; Validated	95.87
PF08003	315	Methyltransf_9: Protein of unknown function (DUF16	95.87
PLN02589	247	caffeoyl-CoA O-methyltransferase	95.81
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	95.75
COG4976	287	Predicted methyltransferase (contains TPR repeat)	95.74
COG4742	260	Predicted transcriptional regulator [Transcription	95.73
PF05148	219	Methyltransf_8: Hypothetical methyltransferase; In	95.71
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	95.7
TIGR00446	264	nop2p NOL1/NOP2/sun family putative RNA methylase.	95.67
COG3432	95	Predicted transcriptional regulator [Transcription	95.66
PF01638	90	HxlR: HxlR-like helix-turn-helix; InterPro: IPR002	95.64
PHA00738	108	putative HTH transcription regulator	95.64
PF10294	173	Methyltransf_16: Putative methyltransferase; Inter	95.63
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	95.6
TIGR02944	130	suf_reg_Xantho FeS assembly SUF system regulator,	95.59
cd00090	78	HTH_ARSR Arsenical Resistance Operon Repressor and	95.58
cd07153	116	Fur_like Ferric uptake regulator(Fur) and related	95.52
COG4122	219	Predicted O-methyltransferase [General function pr	95.48
PF01728	181	FtsJ: FtsJ-like methyltransferase; InterPro: IPR00	95.47
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	95.46
TIGR01884	203	cas_HTH CRISPR locus-related DNA-binding protein.	95.35
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	95.32
COG2345	218	Predicted transcriptional regulator [Transcription	95.28
PRK04338	382	N(2),N(2)-dimethylguanosine tRNA methyltransferase	95.22
KOG3115	249	consensus Methyltransferase-like protein [General	95.16
TIGR00122	69	birA_repr_reg BirA biotin operon repressor domain.	95.15
PF02475	200	Met_10: Met-10+ like-protein; InterPro: IPR003402	95.1
smart00529	96	HTH_DTXR Helix-turn-helix diphteria tox regulatory	95.08
PRK11920	153	rirA iron-responsive transcriptional regulator; Re	95.03
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	95.03
PRK11512	144	DNA-binding transcriptional repressor MarR; Provis	95.0
PF08704	247	GCD14: tRNA methyltransferase complex GCD14 subuni	94.97
PRK03573	144	transcriptional regulator SlyA; Provisional	94.82
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	94.8
PF07757	112	AdoMet_MTase: Predicted AdoMet-dependent methyltra	94.76
COG0293	205	FtsJ 23S rRNA methylase [Translation, ribosomal st	94.71
COG0275	314	Predicted S-adenosylmethionine-dependent methyltra	94.71
PF10007	92	DUF2250: Uncharacterized protein conserved in arch	94.7
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	94.53
TIGR01889	109	Staph_reg_Sar staphylococcal accessory regulator f	94.52
PRK15431	78	ferrous iron transport protein FeoC; Provisional	94.43
cd07377	66	WHTH_GntR Winged helix-turn-helix (WHTH) DNA-bindi	94.4
KOG1661	237	consensus Protein-L-isoaspartate(D-aspartate) O-me	94.37
PRK11783	702	rlmL 23S rRNA m(2)G2445 methyltransferase; Provisi	94.36
KOG3010	261	consensus Methyltransferase [General function pred	94.29
PRK14165	217	winged helix-turn-helix domain-containing protein/	94.12
KOG2361	264	consensus Predicted methyltransferase [General fun	94.11
KOG2730	263	consensus Methylase [General function prediction o	94.09
COG4076	252	Predicted RNA methylase [General function predicti	94.07
PF06080	204	DUF938: Protein of unknown function (DUF938); Inte	94.04
COG2384	226	Predicted SAM-dependent methyltransferase [General	93.98
PRK11014	141	transcriptional repressor NsrR; Provisional	93.97
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	93.94
KOG3191	209	consensus Predicted N6-DNA-methyltransferase [Tran	93.79
PF07091	251	FmrO: Ribosomal RNA methyltransferase (FmrO); PDB:	93.7
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	93.68
PRK04172	489	pheS phenylalanyl-tRNA synthetase subunit alpha; P	93.67
PF06163	127	DUF977: Bacterial protein of unknown function (DUF	93.64
PF01739	196	CheR: CheR methyltransferase, SAM binding domain;	93.63
COG4189	308	Predicted transcriptional regulator [Transcription	93.49
PRK06266	178	transcription initiation factor E subunit alpha; V	93.42
COG4190	144	Predicted transcriptional regulator [Transcription	93.41
PHA02943	165	hypothetical protein; Provisional	93.39
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	93.38
PRK06474	178	hypothetical protein; Provisional	93.29
PRK05638	442	threonine synthase; Validated	93.08
PF14394	171	DUF4423: Domain of unknown function (DUF4423)	92.78
TIGR00373	158	conserved hypothetical protein TIGR00373. This fam	92.63
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	92.49
PLN02853	492	Probable phenylalanyl-tRNA synthetase alpha chain	92.4
COG3963	194	Phospholipid N-methyltransferase [Lipid metabolism	92.36
PRK10870	176	transcriptional repressor MprA; Provisional	92.32
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	92.27
KOG3045	325	consensus Predicted RNA methylase involved in rRNA	92.07
COG1352	268	CheR Methylase of chemotaxis methyl-accepting prot	91.84
COG1846	126	MarR Transcriptional regulators [Transcription]	91.67
PF07789	155	DUF1627: Protein of unknown function (DUF1627); In	91.54
PF02527	184	GidB: rRNA small subunit methyltransferase G; Inte	91.46
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	91.42
COG0357	215	GidB Predicted S-adenosylmethionine-dependent meth	91.4
PF03444	78	HrcA_DNA-bdg: Winged helix-turn-helix transcriptio	91.12
PF01475	120	FUR: Ferric uptake regulator family; InterPro: IPR	91.03
PF04182	75	B-block_TFIIIC: B-block binding subunit of TFIIIC;	90.96
PRK11169	164	leucine-responsive transcriptional regulator; Prov	90.86
COG1522	154	Lrp Transcriptional regulators [Transcription]	90.8
PTZ00326	494	phenylalanyl-tRNA synthetase alpha chain; Provisio	90.69
COG5459	484	Predicted rRNA methylase [Translation, ribosomal s	90.64
COG1378	247	Predicted transcriptional regulators [Transcriptio	90.54
PRK13509	251	transcriptional repressor UlaR; Provisional	90.53
PF02002	105	TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024	90.46
PRK13777	185	transcriptional regulator Hpr; Provisional	90.3
PF04672	267	Methyltransf_19: S-adenosyl methyltransferase; Int	90.16
COG1733	120	Predicted transcriptional regulators [Transcriptio	90.11
COG2512	258	Predicted membrane-associated trancriptional regul	90.08
PF04072	183	LCM: Leucine carboxyl methyltransferase; InterPro:	89.99
PF05732	165	RepL: Firmicute plasmid replication protein (RepL)	89.83
PRK04214	412	rbn ribonuclease BN/unknown domain fusion protein;	89.77
COG2521	287	Predicted archaeal methyltransferase [General func	89.73
PF12793	115	SgrR_N: Sugar transport-related sRNA regulator N-t	89.72
PF13545	76	HTH_Crp_2: Crp-like helix-turn-helix domain; PDB:	89.7
KOG4589	232	consensus Cell division protein FtsJ [Cell cycle c	89.69
PRK10611	287	chemotaxis methyltransferase CheR; Provisional	89.56
TIGR00498	199	lexA SOS regulatory protein LexA. LexA acts as a h	89.2
PF03602	183	Cons_hypoth95: Conserved hypothetical protein 95;	89.04
PRK10411	240	DNA-binding transcriptional activator FucR; Provis	88.97
PF08784	102	RPA_C: Replication protein A C terminal; InterPro:	88.92
TIGR02147	271	Fsuc_second hypothetical protein, TIGR02147. This	88.78
PF09243	274	Rsm22: Mitochondrial small ribosomal subunit Rsm22	88.69
PF00126	60	HTH_1: Bacterial regulatory helix-turn-helix prote	88.42
PF03291	331	Pox_MCEL: mRNA capping enzyme; InterPro: IPR004971	88.33
PF08221	62	HTH_9: RNA polymerase III subunit RPC82 helix-turn	88.32
COG4565	224	CitB Response regulator of citrate/malate metaboli	88.08
PRK10906	252	DNA-binding transcriptional repressor GlpR; Provis	88.06
PF03141	506	Methyltransf_29: Putative S-adenosyl-L-methionine-	88.02
PF00392	64	GntR: Bacterial regulatory proteins, gntR family;	87.77
PRK09802	269	DNA-binding transcriptional regulator AgaR; Provis	87.71
COG5631	199	Predicted transcription regulator, contains HTH do	87.51
PF09821	120	AAA_assoc_C: C-terminal AAA-associated domain; Int	87.49
PF13730	55	HTH_36: Helix-turn-helix domain	87.32
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	87.21
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	87.17
PF02384	311	N6_Mtase: N-6 DNA Methylase; InterPro: IPR003356 T	87.05
TIGR00308	374	TRM1 tRNA(guanine-26,N2-N2) methyltransferase. Thi	86.9
PF02319	71	E2F_TDP: E2F/DP family winged-helix DNA-binding do	86.81
PF14338	92	Mrr_N: Mrr N-terminal domain	86.78
PRK09462	148	fur ferric uptake regulator; Provisional	86.69
COG0735	145	Fur Fe2+/Zn2+ uptake regulation proteins [Inorgani	86.66
TIGR02987	524	met_A_Alw26 type II restriction m6 adenine DNA met	86.48
PF05958	352	tRNA_U5-meth_tr: tRNA (Uracil-5-)-methyltransferas	86.43
COG3413	215	Predicted DNA binding protein [General function pr	86.19
KOG2187	534	consensus tRNA uracil-5-methyltransferase and rela	86.19
PF09929	118	DUF2161: Uncharacterized conserved protein (DUF216	85.92
PF05584	72	Sulfolobus_pRN: Sulfolobus plasmid regulatory prot	85.83
PRK11639	169	zinc uptake transcriptional repressor; Provisional	85.56
COG1349	253	GlpR Transcriptional regulators of sugar metabolis	85.45
PRK10742	250	putative methyltransferase; Provisional	85.26
PRK10434	256	srlR DNA-bindng transcriptional repressor SrlR; Pr	85.15
PF01861	243	DUF43: Protein of unknown function DUF43; InterPro	85.0
KOG1975	389	consensus mRNA cap methyltransferase [RNA processi	84.86
PRK11886	319	bifunctional biotin--[acetyl-CoA-carboxylase] synt	84.71
COG0116	381	Predicted N6-adenine-specific DNA methylase [DNA r	84.63
PF13384	50	HTH_23: Homeodomain-like domain; PDB: 2X48_C.	84.63
COG1497	260	Predicted transcriptional regulator [Transcription	83.84
TIGR01321	94	TrpR trp operon repressor, proteobacterial. This m	83.44
PF13518	52	HTH_28: Helix-turn-helix domain	83.41
COG2265	432	TrmA SAM-dependent methyltransferases related to t	83.33
PF09681	121	Phage_rep_org_N: N-terminal phage replisome organi	83.29
KOG0822	649	consensus Protein kinase inhibitor [Cell cycle con	82.98
KOG1709	271	consensus Guanidinoacetate methyltransferase and r	82.96
PRK10046	225	dpiA two-component response regulator DpiA; Provis	82.84
KOG1562	337	consensus Spermidine synthase [Amino acid transpor	82.8
TIGR02698	130	CopY_TcrY copper transport repressor, CopY/TcrY fa	81.92
PRK11642	813	exoribonuclease R; Provisional	81.58
PF13814	191	Replic_Relax: Replication-relaxation	81.39
PF08280	59	HTH_Mga: M protein trans-acting positive regulator	81.07
PF10668	60	Phage_terminase: Phage terminase small subunit; In	81.05
PF06969	66	HemN_C: HemN C-terminal domain; InterPro: IPR01072	81.0
PRK04424	185	fatty acid biosynthesis transcriptional regulator;	80.93
KOG2651	476	consensus rRNA adenine N-6-methyltransferase [RNA	80.91
COG1092	393	Predicted SAM-dependent methyltransferases [Genera	80.64
COG1568	354	Predicted methyltransferases [General function pre	80.63
PF12324	77	HTH_15: Helix-turn-helix domain of alkylmercury ly	80.47
PRK11161	235	fumarate/nitrate reduction transcriptional regulat	80.07

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

Probab=100.00  E-value=1.7e-34  Score=243.10  Aligned_cols=226  Identities=42%  Similarity=0.706  Sum_probs=201.2

Q ss_pred             CcccccchHHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCC-CCCCChhhHHHHHHHHhcCCceeeeccCCCCCce
Q 039903            1 MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPS-SNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLY   79 (233)
Q Consensus         1 ~~~~~~~~~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~-~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y   79 (233)
                      +++++++..+++|.+|+|||+||+|++.+   +  ..|||..+.. .+|.++..++|+||.|++.++++...-. .+ .|
T Consensus        11 ~~l~~~~~~~~~lk~A~eL~v~d~l~~~~---~--p~~ia~~l~~~~~~~~p~ll~r~lr~L~s~~i~k~~~~~-~~-~Y   83 (342)
T KOG3178|consen   11 MRLANGFALPMVLKAACELGVFDILANAG---S--PSEIASLLPTPKNPEAPVLLDRILRLLVSYSILKCRLVG-GE-VY   83 (342)
T ss_pred             HHHHhhhhhHHHHHHHHHcChHHHHHhCC---C--HHHHHHhccCCCCCCChhHHHHHHHHHHHhhhceeeeec-ce-ee
Confidence            36788999999999999999999999963   2  8888888885 3567899999999999999999986321 12 89


Q ss_pred             eccHhhhHhhcCCCCCCccchhccccC-----chhhHHHHHHcCCcchhhhhCCccccccccCchHHHHHHHHHHhcchh
Q 039903           80 GLAHVAKYFVLNRDGVSLCPSRPWLET-----KPYEIYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSI  154 (233)
Q Consensus        80 ~lt~~s~~l~~~~~~~~~~~~~~~~~~-----~~~~L~~~l~~g~~~~~~~~g~~~~~~~~~~~~~~~~f~~am~~~~~~  154 (233)
                      +++|.++.+..+....|+.+++....+     .|..|.++++.++.+|..++|+..|+|...++.....|+++|...+..
T Consensus        84 ~~~~~~~~~l~~~~~~S~a~~~~~~~~~v~~~~w~~l~dai~eg~~~~~~~~G~~l~~~~~~~~~~~~~~~~sm~~l~~~  163 (342)
T KOG3178|consen   84 SATPVCKYFLKDSGGGSLAPLVLLNTSKVIMNTWQFLKDAILEGGDAFATAHGMMLGGYGGADERFSKDFNGSMSFLSTL  163 (342)
T ss_pred             eccchhhhheecCCCCchhHHHHHhcccchhhhHHHHHHHHHhcccCCccccchhhhhhcccccccHHHHHHHHHHHHHH
Confidence            999999998855444578888776543     899999999999999999999888999999998889999999999999


Q ss_pred             cHHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCC-CCceEEecCcCCCCCCCCEEEeC
Q 039903          155 VTNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSY-SGVKHIGGIMLERIPKGDAILIK  233 (233)
Q Consensus       155 ~~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~-~ri~~~~gD~f~~~P~~D~~~lk  233 (233)
                      ..+.+++.|.+|++..++||||||.|..+..++.+||+++++.+|+|.+++.+... +.|+++.||+|+..|++|+|+||
T Consensus       164 ~~~~il~~~~Gf~~v~~avDvGgGiG~v~k~ll~~fp~ik~infdlp~v~~~a~~~~~gV~~v~gdmfq~~P~~daI~mk  243 (342)
T KOG3178|consen  164 VMKKILEVYTGFKGVNVAVDVGGGIGRVLKNLLSKYPHIKGINFDLPFVLAAAPYLAPGVEHVAGDMFQDTPKGDAIWMK  243 (342)
T ss_pred             HHHhhhhhhcccccCceEEEcCCcHhHHHHHHHHhCCCCceeecCHHHHHhhhhhhcCCcceecccccccCCCcCeEEEE
Confidence            88888999888999999999999999999999999999999999999999999888 88999999999999999999986

>TIGR02716 C20_methyl_CrtF C-20 methyltransferase BchU

Probab=100.00  E-value=7.5e-33  Score=236.88  Aligned_cols=205  Identities=20%  Similarity=0.298  Sum_probs=159.7

Q ss_pred             hHHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhH
Q 039903            8 VLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKY   87 (233)
Q Consensus         8 ~~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~   87 (233)
                      +.+++|++|++|||||.|.+    +|.|++|||+++++    +++.++||||+|+++|+|++.     +++|+||+.++.
T Consensus         2 ~~~~~l~aa~~Lglfd~L~~----gp~t~~eLA~~~~~----~~~~~~~lL~~L~~lgll~~~-----~~~y~~t~~~~~   68 (306)
T TIGR02716         2 IEFSCMKAAIELDLFSHMAE----GPKDLATLAADTGS----VPPRLEMLLETLRQMRVINLE-----DGKWSLTEFADY   68 (306)
T ss_pred             chHHHHHHHHHcCcHHHHhc----CCCCHHHHHHHcCC----ChHHHHHHHHHHHhCCCeEec-----CCcEecchhHHh
Confidence            46789999999999999987    69999999999999    999999999999999999984     689999999998


Q ss_pred             hhcCCCCC---Cccchhcccc----CchhhHHHHHHcCCcchhhhhCCccccccccCchHHHHHHHHHH-hcchhcHHHH
Q 039903           88 FVLNRDGV---SLCPSRPWLE----TKPYEIYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAML-NHTSIVTNRI  159 (233)
Q Consensus        88 l~~~~~~~---~~~~~~~~~~----~~~~~L~~~l~~g~~~~~~~~g~~~~~~~~~~~~~~~~f~~am~-~~~~~~~~~~  159 (233)
                      ++.+++..   ++.++..+..    ..|.+|+++++ ++++|...     +++....++.. .|...|. .......+.+
T Consensus        69 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~r-~~~~~~~~-----~~~~~~~~~~~-~~~~~~~~~~~~~~~~~l  141 (306)
T TIGR02716        69 MFSPTPKEPNLHQTPVAKAMAFLADDFYMGLSQAVR-GQKNFKGQ-----VPYPPVTREDN-LYFEEIHRSNAKFAIQLL  141 (306)
T ss_pred             hccCCccchhhhcCchHHHHHHHHHHHHHhHHHHhc-CCcccccc-----cCCCCCCHHHH-HhHHHHHHhcchhHHHHH
Confidence            77655421   1223333221    26899999997 44444332     22222333333 3444554 3333445667


Q ss_pred             HHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCC-------CCceEEecCcCC-CCCCCCEEE
Q 039903          160 IDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSY-------SGVKHIGGIMLE-RIPKGDAIL  231 (233)
Q Consensus       160 ~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~-------~ri~~~~gD~f~-~~P~~D~~~  231 (233)
                      ++.++ +++..+|+|||||+|.+++.+++++|+++++++|+|++++.++++       +||+++.+|+|+ ++|.+|+|+
T Consensus       142 ~~~~~-~~~~~~vlDiG~G~G~~~~~~~~~~p~~~~~~~D~~~~~~~a~~~~~~~gl~~rv~~~~~d~~~~~~~~~D~v~  220 (306)
T TIGR02716       142 LEEAK-LDGVKKMIDVGGGIGDISAAMLKHFPELDSTILNLPGAIDLVNENAAEKGVADRMRGIAVDIYKESYPEADAVL  220 (306)
T ss_pred             HHHcC-CCCCCEEEEeCCchhHHHHHHHHHCCCCEEEEEecHHHHHHHHHHHHhCCccceEEEEecCccCCCCCCCCEEE
Confidence            77777 888899999999999999999999999999999999999887642       689999999997 778789998


Q ss_pred             eC
Q 039903          232 IK  233 (233)
Q Consensus       232 lk  233 (233)
                      ++
T Consensus       221 ~~  222 (306)
T TIGR02716       221 FC  222 (306)
T ss_pred             eE
Confidence            63

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=100.00  E-value=4.6e-33  Score=230.54  Aligned_cols=158  Identities=24%  Similarity=0.438  Sum_probs=138.3

Q ss_pred             CCCceeccHhhhHhhcCCCCCCccchhccccC-----chhhHHHHHHcCCcchhhhhCCccccccccCchHHHHHHHHHH
Q 039903           75 DQRLYGLAHVAKYFVLNRDGVSLCPSRPWLET-----KPYEIYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAML  149 (233)
Q Consensus        75 ~~~~y~lt~~s~~l~~~~~~~~~~~~~~~~~~-----~~~~L~~~l~~g~~~~~~~~g~~~~~~~~~~~~~~~~f~~am~  149 (233)
                      ++++|+||+.|+.|+.+++..++..++.+...     .|.+|++++++|+++|+..+|.++|+|+.++|+..+.|+++|.
T Consensus         2 ~~~~y~~t~~s~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~v~~g~~~~~~~~g~~~~~~~~~~~~~~~~f~~~m~   81 (241)
T PF00891_consen    2 EGDRYSLTPLSELLLSDHSSPSMRGFVLFMISPELYPAWFRLTEAVRTGKPPFEKAFGTPFFEYLEEDPELAKRFNAAMA   81 (241)
T ss_dssp             STEEEEE-HHHHGGSTTTTTTHHHHHHHHHTCHHHHHGGGGHHHHHHHSS-HHHHHHSS-HHHHHHCSHHHHHHHHHHHH
T ss_pred             CCCEEeChHHHHHHhCCCCcCcHHHHHHHhcCHHHHHHHHHHHhhhccCCCHHHHhcCCcHHHhhhhChHHHHHHHHHHH
Confidence            57999999999999888763356666655332     8999999999999999999998899999999999999999999


Q ss_pred             hcchhcH-HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCCCCceEEecCcCCCCCCCC
Q 039903          150 NHTSIVT-NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGD  228 (233)
Q Consensus       150 ~~~~~~~-~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~~ri~~~~gD~f~~~P~~D  228 (233)
                      ..+.... +.+++.++ |++.++|||||||+|.++.+++++||+++++++|+|+|++.+++.+||++++||||+++|++|
T Consensus        82 ~~~~~~~~~~~~~~~d-~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~~~~~~rv~~~~gd~f~~~P~~D  160 (241)
T PF00891_consen   82 EYSRLNAFDILLEAFD-FSGFKTVVDVGGGSGHFAIALARAYPNLRATVFDLPEVIEQAKEADRVEFVPGDFFDPLPVAD  160 (241)
T ss_dssp             HHHHHHHHHHHHHHST-TTTSSEEEEET-TTSHHHHHHHHHSTTSEEEEEE-HHHHCCHHHTTTEEEEES-TTTCCSSES
T ss_pred             hhhhcchhhhhhcccc-ccCccEEEeccCcchHHHHHHHHHCCCCcceeeccHhhhhccccccccccccccHHhhhcccc
Confidence            9998887 77888888 999999999999999999999999999999999999999998888999999999999999999


Q ss_pred             EEEeC
Q 039903          229 AILIK  233 (233)
Q Consensus       229 ~~~lk  233 (233)
                      +|+||
T Consensus       161 ~~~l~  165 (241)
T PF00891_consen  161 VYLLR  165 (241)
T ss_dssp             EEEEE
T ss_pred             ceeee
Confidence            99985

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=99.16  E-value=5.9e-11  Score=73.63  Aligned_cols=51  Identities=55%  Similarity=0.813  Sum_probs=43.4

Q ss_pred             HHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHh
Q 039903           11 AAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLV   62 (233)
Q Consensus        11 ~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~   62 (233)
                      ++|++|++|||||+|+..| ++++|++||++++...+|.++..++|+||+|+
T Consensus         1 MaLk~aveLgI~dii~~~g-~~~ls~~eia~~l~~~~p~~~~~L~RimR~L~   51 (51)
T PF08100_consen    1 MALKCAVELGIPDIIHNAG-GGPLSLSEIAARLPTSNPSAPPMLDRIMRLLV   51 (51)
T ss_dssp             HHHHHHHHTTHHHHHHHHT-TS-BEHHHHHHTSTCT-TTHHHHHHHHHHHHH
T ss_pred             CcHHHHHHcCcHHHHHHcC-CCCCCHHHHHHHcCCCCcchHHHHHHHHHHhC
Confidence            5899999999999999985 36999999999999446667889999999986

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 ....

>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=98.87  E-value=5.4e-09  Score=75.77  Aligned_cols=64  Identities=13%  Similarity=0.227  Sum_probs=53.3

Q ss_pred             cceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCc-CC-CCCCC-CEEEe
Q 039903          169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIM-LE-RIPKG-DAILI  232 (233)
Q Consensus       169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~-f~-~~P~~-D~~~l  232 (233)
                      ..+|+|||||+|.++..+++++|..+++.+|. |+.++.++++       +||+++.+|+ +. ..+.. |++++
T Consensus         2 ~~~vLDlGcG~G~~~~~l~~~~~~~~v~gvD~s~~~~~~a~~~~~~~~~~~~i~~~~~d~~~~~~~~~~~D~v~~   76 (112)
T PF12847_consen    2 GGRVLDLGCGTGRLSIALARLFPGARVVGVDISPEMLEIARERAAEEGLSDRITFVQGDAEFDPDFLEPFDLVIC   76 (112)
T ss_dssp             TCEEEEETTTTSHHHHHHHHHHTTSEEEEEESSHHHHHHHHHHHHHTTTTTTEEEEESCCHGGTTTSSCEEEEEE
T ss_pred             CCEEEEEcCcCCHHHHHHHhcCCCCEEEEEeCCHHHHHHHHHHHHhcCCCCCeEEEECccccCcccCCCCCEEEE
Confidence            36899999999999999999999999999998 5677766542       7999999999 44 34444 98875

...

>PRK06922 hypothetical protein; Provisional

Probab=98.74  E-value=3.6e-08  Score=90.88  Aligned_cols=104  Identities=18%  Similarity=0.205  Sum_probs=77.7

Q ss_pred             CccccccccCchHHHHHHHHHHhcchhc--HHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HH
Q 039903          128 TGFYEYAGNDFRFNGVFNKAMLNHTSIV--TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VI  204 (233)
Q Consensus       128 ~~~~~~~~~~~~~~~~f~~am~~~~~~~--~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~  204 (233)
                      ..+|+++..+++..++|.+.|.......  .......++ +.+..+|+|||||+|.++..+++++|+.+++++|+++ ++
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            4578899888888888887776643332  111223344 6667899999999999999999999999999999975 57


Q ss_pred             hhccCC-----CCceEEecCcCC-C--CCCC--CEEEe
Q 039903          205 QDSSSY-----SGVKHIGGIMLE-R--IPKG--DAILI  232 (233)
Q Consensus       205 ~~a~~~-----~ri~~~~gD~f~-~--~P~~--D~~~l  232 (233)
                      +.+++.     .+++++.+|..+ +  +|.+  |+|+.
T Consensus       456 e~Ararl~~~g~~ie~I~gDa~dLp~~fedeSFDvVVs  493 (677)
T PRK06922        456 DTLKKKKQNEGRSWNVIKGDAINLSSSFEKESVDTIVY  493 (677)
T ss_pred             HHHHHHhhhcCCCeEEEEcchHhCccccCCCCEEEEEE
Confidence            766542     468888999876 3  5543  99875

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

Probab=98.68  E-value=5.3e-08  Score=77.45  Aligned_cols=71  Identities=20%  Similarity=0.285  Sum_probs=57.6

Q ss_pred             HhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCCCCCCC-CEEEe
Q 039903          161 DSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLERIPKG-DAILI  232 (233)
Q Consensus       161 ~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~~P~~-D~~~l  232 (233)
                      ..++ .....+++|||||+|.++..+++++|+.+++.+|. |+.++.++++      ++|+++.+|...+++.. |++++
T Consensus        25 ~~l~-~~~~~~vLDiG~G~G~~~~~la~~~~~~~v~~vD~s~~~~~~a~~n~~~~~~~~i~~~~~d~~~~~~~~~D~v~~  103 (187)
T PRK08287         25 SKLE-LHRAKHLIDVGAGTGSVSIEAALQFPSLQVTAIERNPDALRLIKENRQRFGCGNIDIIPGEAPIELPGKADAIFI  103 (187)
T ss_pred             HhcC-CCCCCEEEEECCcCCHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHhCCCCeEEEecCchhhcCcCCCEEEE
Confidence            4444 56678999999999999999999999999999999 5677776542      57999999986656553 98875

>PRK14103 trans-aconitate 2-methyltransferase; Provisional

Probab=98.55  E-value=3.4e-07  Score=76.43  Aligned_cols=74  Identities=18%  Similarity=0.263  Sum_probs=60.5

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCCCCceEEecCcCCCCCC--CCEEEe
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSYSGVKHIGGIMLERIPK--GDAILI  232 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~~ri~~~~gD~f~~~P~--~D~~~l  232 (233)
                      ..+++.++ .....+|||||||+|.++..+++++|+.+++.+|+ |..++.+++ .+++++.+|+.+..|.  .|+|+.
T Consensus        19 ~~ll~~l~-~~~~~~vLDlGcG~G~~~~~l~~~~p~~~v~gvD~s~~~~~~a~~-~~~~~~~~d~~~~~~~~~fD~v~~   95 (255)
T PRK14103         19 YDLLARVG-AERARRVVDLGCGPGNLTRYLARRWPGAVIEALDSSPEMVAAARE-RGVDARTGDVRDWKPKPDTDVVVS   95 (255)
T ss_pred             HHHHHhCC-CCCCCEEEEEcCCCCHHHHHHHHHCCCCEEEEEECCHHHHHHHHh-cCCcEEEcChhhCCCCCCceEEEE
Confidence            45667666 66678999999999999999999999999999999 568887776 4799999998763333  399875

>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=98.54  E-value=2e-07  Score=71.56  Aligned_cols=65  Identities=18%  Similarity=0.263  Sum_probs=53.1

Q ss_pred             CcceEEEecCCccHHHHHHH-HHcCCCcEEEeec-hHHHhhccC------CCCceEEecCcCC-C--CCC-CCEEEe
Q 039903          168 QIKQLVDVGGGLGVNVNIII-SNYLHIKGVNFDL-SHVIQDSSS------YSGVKHIGGIMLE-R--IPK-GDAILI  232 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~-~~~P~l~~~v~Dl-p~v~~~a~~------~~ri~~~~gD~f~-~--~P~-~D~~~l  232 (233)
                      +..+|+|+|||+|.++..++ +.+|..+++.+|+ |+.++.|++      .++++|+.+|+++ +  ++. .|+++.
T Consensus         3 ~~~~iLDlGcG~G~~~~~l~~~~~~~~~i~gvD~s~~~i~~a~~~~~~~~~~ni~~~~~d~~~l~~~~~~~~D~I~~   79 (152)
T PF13847_consen    3 SNKKILDLGCGTGRLLIQLAKELNPGAKIIGVDISEEMIEYAKKRAKELGLDNIEFIQGDIEDLPQELEEKFDIIIS   79 (152)
T ss_dssp             TTSEEEEET-TTSHHHHHHHHHSTTTSEEEEEESSHHHHHHHHHHHHHTTSTTEEEEESBTTCGCGCSSTTEEEEEE
T ss_pred             CCCEEEEecCcCcHHHHHHHHhcCCCCEEEEEECcHHHHHHhhcccccccccccceEEeehhccccccCCCeeEEEE
Confidence            45789999999999999999 5689999999998 568887765      2689999999999 4  333 398875

...

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

Probab=98.53  E-value=2.5e-07  Score=73.91  Aligned_cols=81  Identities=12%  Similarity=0.217  Sum_probs=66.5

Q ss_pred             HhcchhcHHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-CCceEEecCcCCCCCC
Q 039903          149 LNHTSIVTNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-SGVKHIGGIMLERIPK  226 (233)
Q Consensus       149 ~~~~~~~~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-~ri~~~~gD~f~~~P~  226 (233)
                      ...+++ +..++...+ ......|+|+|||.|.....|+++||....+.+|- |+.++.|+.. +.++|..+|.-+-.|+
T Consensus        13 ~eRtRP-a~dLla~Vp-~~~~~~v~DLGCGpGnsTelL~~RwP~A~i~GiDsS~~Mla~Aa~rlp~~~f~~aDl~~w~p~   90 (257)
T COG4106          13 DERTRP-ARDLLARVP-LERPRRVVDLGCGPGNSTELLARRWPDAVITGIDSSPAMLAKAAQRLPDATFEEADLRTWKPE   90 (257)
T ss_pred             HhccCc-HHHHHhhCC-ccccceeeecCCCCCHHHHHHHHhCCCCeEeeccCCHHHHHHHHHhCCCCceecccHhhcCCC
Confidence            444444 456777777 78889999999999999999999999999999997 6788887664 8999999999986564


Q ss_pred             --CCEEE
Q 039903          227 --GDAIL  231 (233)
Q Consensus       227 --~D~~~  231 (233)
                        .|+++
T Consensus        91 ~~~dllf   97 (257)
T COG4106          91 QPTDLLF   97 (257)
T ss_pred             Cccchhh
Confidence              37654

>TIGR03587 Pse_Me-ase pseudaminic acid biosynthesis-associated methylase

Probab=98.52  E-value=4.1e-07  Score=73.47  Aligned_cols=67  Identities=13%  Similarity=0.372  Sum_probs=56.9

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-CCceEEecCcCCCCCCC--CEEEe
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-SGVKHIGGIMLERIPKG--DAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-~ri~~~~gD~f~~~P~~--D~~~l  232 (233)
                      ..+..+|+|||||+|.++..+++..|..+++.+|+ |+.++.|++. +++++..+|+++++|.+  |+++.
T Consensus        41 ~~~~~~VLDiGCG~G~~~~~L~~~~~~~~v~giDiS~~~l~~A~~~~~~~~~~~~d~~~~~~~~sfD~V~~  111 (204)
T TIGR03587        41 LPKIASILELGANIGMNLAALKRLLPFKHIYGVEINEYAVEKAKAYLPNINIIQGSLFDPFKDNFFDLVLT  111 (204)
T ss_pred             cCCCCcEEEEecCCCHHHHHHHHhCCCCeEEEEECCHHHHHHHHhhCCCCcEEEeeccCCCCCCCEEEEEE
Confidence            34567899999999999999999989999999998 4688888763 77899999999877653  98875

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

>PRK01683 trans-aconitate 2-methyltransferase; Provisional

Probab=98.48  E-value=1.2e-06  Score=73.11  Aligned_cols=76  Identities=14%  Similarity=0.288  Sum_probs=61.6

Q ss_pred             HHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-CCceEEecCcCCCCCC--CCEEE
Q 039903          156 TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-SGVKHIGGIMLERIPK--GDAIL  231 (233)
Q Consensus       156 ~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-~ri~~~~gD~f~~~P~--~D~~~  231 (233)
                      ...++..++ .++..+|+|||||+|.++..+++++|..+++.+|+ |..++.+++. ++++++.+|+.+..|.  .|+++
T Consensus        20 ~~~ll~~~~-~~~~~~vLDiGcG~G~~~~~la~~~~~~~v~gvD~s~~~i~~a~~~~~~~~~~~~d~~~~~~~~~fD~v~   98 (258)
T PRK01683         20 ARDLLARVP-LENPRYVVDLGCGPGNSTELLVERWPAARITGIDSSPAMLAEARSRLPDCQFVEADIASWQPPQALDLIF   98 (258)
T ss_pred             HHHHHhhCC-CcCCCEEEEEcccCCHHHHHHHHHCCCCEEEEEECCHHHHHHHHHhCCCCeEEECchhccCCCCCccEEE
Confidence            345667666 67778999999999999999999999999999999 5578777664 7899999999763333  38886


Q ss_pred             e
Q 039903          232 I  232 (233)
Q Consensus       232 l  232 (233)
                      .
T Consensus        99 ~   99 (258)
T PRK01683         99 A   99 (258)
T ss_pred             E
Confidence            4

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

Probab=98.47  E-value=3.2e-07  Score=71.92  Aligned_cols=66  Identities=18%  Similarity=0.258  Sum_probs=55.4

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC------CCceEEecCcCCCCCC-C-CEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY------SGVKHIGGIMLERIPK-G-DAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~------~ri~~~~gD~f~~~P~-~-D~~~l  232 (233)
                      ....+++|+|||+|..+..+++++|+.+++.+|.. .+++.++++      +.|+++.+|+++.++. . |+|+.
T Consensus        30 ~~~~~vLDlG~G~G~i~~~la~~~~~~~v~~vDi~~~a~~~a~~n~~~n~~~~v~~~~~d~~~~~~~~~fD~Iv~  104 (170)
T PF05175_consen   30 HKGGRVLDLGCGSGVISLALAKRGPDAKVTAVDINPDALELAKRNAERNGLENVEVVQSDLFEALPDGKFDLIVS  104 (170)
T ss_dssp             HTTCEEEEETSTTSHHHHHHHHTSTCEEEEEEESBHHHHHHHHHHHHHTTCTTEEEEESSTTTTCCTTCEEEEEE
T ss_pred             ccCCeEEEecCChHHHHHHHHHhCCCCEEEEEcCCHHHHHHHHHHHHhcCccccccccccccccccccceeEEEE
Confidence            35678999999999999999999999999999984 577777653      3499999999998774 3 99875

; 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 ....

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

Probab=98.47  E-value=5.9e-07  Score=73.63  Aligned_cols=74  Identities=12%  Similarity=0.129  Sum_probs=58.3

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHc-CCCcEEEeec-hHHHhhccC------CCCceEEecCcCC-CCCCC-
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNY-LHIKGVNFDL-SHVIQDSSS------YSGVKHIGGIMLE-RIPKG-  227 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~v~~~a~~------~~ri~~~~gD~f~-~~P~~-  227 (233)
                      .++..++ .....+|||||||+|.++..+++.+ |+.+++.+|+ |+.++.+++      .++++++.+|+.+ ++|.+ 
T Consensus        36 ~~l~~l~-~~~~~~vLDiGcG~G~~~~~la~~~~~~~~v~gvD~s~~~~~~a~~~~~~~~~~~v~~~~~d~~~~~~~~~~  114 (231)
T TIGR02752        36 DTMKRMN-VQAGTSALDVCCGTADWSIALAEAVGPEGHVIGLDFSENMLSVGRQKVKDAGLHNVELVHGNAMELPFDDNS  114 (231)
T ss_pred             HHHHhcC-CCCCCEEEEeCCCcCHHHHHHHHHhCCCCEEEEEECCHHHHHHHHHHHHhcCCCceEEEEechhcCCCCCCC
Confidence            3445555 5666899999999999999999986 6789999999 567666553      2689999999988 66653 


Q ss_pred             -CEEEe
Q 039903          228 -DAILI  232 (233)
Q Consensus       228 -D~~~l  232 (233)
                       |++++
T Consensus       115 fD~V~~  120 (231)
T TIGR02752       115 FDYVTI  120 (231)
T ss_pred             ccEEEE
Confidence             98875

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.

>PRK04457 spermidine synthase; Provisional

Probab=98.44  E-value=3.7e-07  Score=76.56  Aligned_cols=66  Identities=17%  Similarity=0.209  Sum_probs=56.0

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCC---CCCCC-CEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLE---RIPKG-DAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~---~~P~~-D~~~l  232 (233)
                      ++.++++|||||.|.++..+++.+|+.+++++|+ |++++.++++       +|++++.+|..+   ..|.. |+|++
T Consensus        65 ~~~~~vL~IG~G~G~l~~~l~~~~p~~~v~~VEidp~vi~~A~~~f~~~~~~~rv~v~~~Da~~~l~~~~~~yD~I~~  142 (262)
T PRK04457         65 PRPQHILQIGLGGGSLAKFIYTYLPDTRQTAVEINPQVIAVARNHFELPENGERFEVIEADGAEYIAVHRHSTDVILV  142 (262)
T ss_pred             CCCCEEEEECCCHhHHHHHHHHhCCCCeEEEEECCHHHHHHHHHHcCCCCCCCceEEEECCHHHHHHhCCCCCCEEEE
Confidence            4567899999999999999999999999999999 7898887652       689999999875   34544 99875

>PRK15451 tRNA cmo(5)U34 methyltransferase; Provisional

Probab=98.40  E-value=5.3e-07  Score=74.93  Aligned_cols=66  Identities=18%  Similarity=0.224  Sum_probs=54.7

Q ss_pred             cCcceEEEecCCccHHHHHHHH--HcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCC-CCCCCCEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIIS--NYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLE-RIPKGDAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~--~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~-~~P~~D~~~l  232 (233)
                      .+..+|+|||||+|..+..+++  .+|+.+++.+|. |+.++.|+++       .+|+++.+|+.+ ++|..|++++
T Consensus        55 ~~~~~vLDlGcGtG~~~~~l~~~~~~~~~~v~gvD~S~~ml~~A~~~~~~~~~~~~v~~~~~d~~~~~~~~~D~vv~  131 (247)
T PRK15451         55 QPGTQVYDLGCSLGAATLSVRRNIHHDNCKIIAIDNSPAMIERCRRHIDAYKAPTPVDVIEGDIRDIAIENASMVVL  131 (247)
T ss_pred             CCCCEEEEEcccCCHHHHHHHHhcCCCCCeEEEEeCCHHHHHHHHHHHHhcCCCCCeEEEeCChhhCCCCCCCEEeh
Confidence            4557899999999999999988  469999999998 6788877652       489999999987 6666688764

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

Probab=98.40  E-value=6.3e-07  Score=76.04  Aligned_cols=65  Identities=15%  Similarity=0.209  Sum_probs=55.4

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCCCCCC-C-CEEEe
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLERIPK-G-DAILI  232 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~~P~-~-D~~~l  232 (233)
                      +..+++|+|||+|.++..+++++|+.+++.+|+ +.+++.|+++       ++|+++.+|+++++|. . |+++.
T Consensus       121 ~~~~vLDlG~GsG~i~~~la~~~~~~~v~avDis~~al~~A~~n~~~~~~~~~i~~~~~D~~~~~~~~~fD~Iv~  195 (284)
T TIGR03533       121 PVKRILDLCTGSGCIAIACAYAFPEAEVDAVDISPDALAVAEINIERHGLEDRVTLIQSDLFAALPGRKYDLIVS  195 (284)
T ss_pred             CCCEEEEEeCchhHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHcCCCCcEEEEECchhhccCCCCccEEEE
Confidence            346899999999999999999999999999999 5677777653       5799999999987765 3 98874

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.

>TIGR00740 methyltransferase, putative

Probab=98.39  E-value=7.1e-07  Score=73.71  Aligned_cols=66  Identities=12%  Similarity=0.142  Sum_probs=54.5

Q ss_pred             cCcceEEEecCCccHHHHHHHHH--cCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCC-CCCCCCEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISN--YLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLE-RIPKGDAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~--~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~-~~P~~D~~~l  232 (233)
                      ....+|||||||+|.++..++++  +|+.+++.+|+ |++++.|++.       .+|+++.+|+.+ ++|..|+++.
T Consensus        52 ~~~~~iLDlGcG~G~~~~~l~~~~~~p~~~v~gvD~s~~ml~~a~~~~~~~~~~~~v~~~~~d~~~~~~~~~d~v~~  128 (239)
T TIGR00740        52 TPDSNVYDLGCSRGAATLSARRNINQPNVKIIGIDNSQPMVERCRQHIAAYHSEIPVEILCNDIRHVEIKNASMVIL  128 (239)
T ss_pred             CCCCEEEEecCCCCHHHHHHHHhcCCCCCeEEEEeCCHHHHHHHHHHHHhcCCCCCeEEEECChhhCCCCCCCEEee
Confidence            45578999999999999999997  48899999999 6788777542       479999999998 6776787653

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.

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

Probab=98.38  E-value=5.4e-07  Score=77.23  Aligned_cols=63  Identities=14%  Similarity=0.169  Sum_probs=54.7

Q ss_pred             ceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCCCCCC--CCEEEe
Q 039903          170 KQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLERIPK--GDAILI  232 (233)
Q Consensus       170 ~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~~P~--~D~~~l  232 (233)
                      .+++|+|||+|.++..+++++|+.+++.+|+ |.+++.|+++       +||+++.+|+++.+|.  .|+++.
T Consensus       135 ~~VLDlG~GsG~iai~la~~~p~~~V~avDis~~al~~A~~n~~~~~l~~~i~~~~~D~~~~l~~~~fDlIvs  207 (307)
T PRK11805        135 TRILDLCTGSGCIAIACAYAFPDAEVDAVDISPDALAVAEINIERHGLEDRVTLIESDLFAALPGRRYDLIVS  207 (307)
T ss_pred             CEEEEEechhhHHHHHHHHHCCCCEEEEEeCCHHHHHHHHHHHHHhCCCCcEEEEECchhhhCCCCCccEEEE
Confidence            6899999999999999999999999999999 6688777653       5799999999987765  399874

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

Probab=98.36  E-value=1e-06  Score=77.42  Aligned_cols=73  Identities=19%  Similarity=0.162  Sum_probs=57.7

Q ss_pred             HHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC---------CCceEEecCcCCCCCC-C
Q 039903          159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY---------SGVKHIGGIMLERIPK-G  227 (233)
Q Consensus       159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~---------~ri~~~~gD~f~~~P~-~  227 (233)
                      +++.++ .....+|+|+|||+|.+++.+++++|..+++.+|.. .+++.++++         ++++++.+|.++.++. .
T Consensus       220 lL~~lp-~~~~~~VLDLGCGtGvi~i~la~~~P~~~V~~vD~S~~Av~~A~~N~~~n~~~~~~~v~~~~~D~l~~~~~~~  298 (378)
T PRK15001        220 FMQHLP-ENLEGEIVDLGCGNGVIGLTLLDKNPQAKVVFVDESPMAVASSRLNVETNMPEALDRCEFMINNALSGVEPFR  298 (378)
T ss_pred             HHHhCC-cccCCeEEEEeccccHHHHHHHHhCCCCEEEEEECCHHHHHHHHHHHHHcCcccCceEEEEEccccccCCCCC
Confidence            455555 333368999999999999999999999999999996 467766542         3789999999986654 3


Q ss_pred             -CEEEe
Q 039903          228 -DAILI  232 (233)
Q Consensus       228 -D~~~l  232 (233)
                       |+|+.
T Consensus       299 fDlIls  304 (378)
T PRK15001        299 FNAVLC  304 (378)
T ss_pred             EEEEEE
Confidence             98875

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

Probab=98.34  E-value=1.8e-06  Score=71.04  Aligned_cols=65  Identities=20%  Similarity=0.253  Sum_probs=57.1

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC------CCceEEecCcCC-CCCCC--CEEEe
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY------SGVKHIGGIMLE-RIPKG--DAILI  232 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~------~ri~~~~gD~f~-~~P~~--D~~~l  232 (233)
                      ...++||||||+|-++..+++..+..+++++|.. ..++.|++.      ..|+|+.+|..+ |+|..  |+|.+
T Consensus        51 ~g~~vLDva~GTGd~a~~~~k~~g~g~v~~~D~s~~ML~~a~~k~~~~~~~~i~fv~~dAe~LPf~D~sFD~vt~  125 (238)
T COG2226          51 PGDKVLDVACGTGDMALLLAKSVGTGEVVGLDISESMLEVAREKLKKKGVQNVEFVVGDAENLPFPDNSFDAVTI  125 (238)
T ss_pred             CCCEEEEecCCccHHHHHHHHhcCCceEEEEECCHHHHHHHHHHhhccCccceEEEEechhhCCCCCCccCEEEe
Confidence            5689999999999999999999999999999985 588888763      239999999999 99984  99876

>PTZ00098 phosphoethanolamine N-methyltransferase; Provisional

Probab=98.31  E-value=2.3e-06  Score=71.85  Aligned_cols=74  Identities=18%  Similarity=0.358  Sum_probs=59.0

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccC----CCCceEEecCcCC-CCCCC--C
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSS----YSGVKHIGGIMLE-RIPKG--D  228 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~----~~ri~~~~gD~f~-~~P~~--D  228 (233)
                      ..++..++ ..+..+|||||||+|..+..+++.+ ..+++.+|+. ..++.+++    .++|+++.+|+.+ ++|.+  |
T Consensus        42 ~~~l~~l~-l~~~~~VLDiGcG~G~~a~~la~~~-~~~v~giD~s~~~~~~a~~~~~~~~~i~~~~~D~~~~~~~~~~FD  119 (263)
T PTZ00098         42 TKILSDIE-LNENSKVLDIGSGLGGGCKYINEKY-GAHVHGVDICEKMVNIAKLRNSDKNKIEFEANDILKKDFPENTFD  119 (263)
T ss_pred             HHHHHhCC-CCCCCEEEEEcCCCChhhHHHHhhc-CCEEEEEECCHHHHHHHHHHcCcCCceEEEECCcccCCCCCCCeE
Confidence            45666666 7777899999999999999998875 6789999984 56666654    2689999999997 78764  9


Q ss_pred             EEEe
Q 039903          229 AILI  232 (233)
Q Consensus       229 ~~~l  232 (233)
                      +++.
T Consensus       120 ~V~s  123 (263)
T PTZ00098        120 MIYS  123 (263)
T ss_pred             EEEE
Confidence            9874

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

Probab=98.31  E-value=9.1e-07  Score=74.86  Aligned_cols=62  Identities=15%  Similarity=0.204  Sum_probs=53.4

Q ss_pred             eEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCCCCCCC-CEEEe
Q 039903          171 QLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLERIPKG-DAILI  232 (233)
Q Consensus       171 ~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~~P~~-D~~~l  232 (233)
                      +++|||+|+|..++++++++|+.+++..|+ |++++.|+.+      .|+.++.+|+|++++.. |+++.
T Consensus       113 ~ilDlGTGSG~iai~la~~~~~~~V~a~Dis~~Al~~A~~Na~~~~l~~~~~~~~dlf~~~~~~fDlIVs  182 (280)
T COG2890         113 RILDLGTGSGAIAIALAKEGPDAEVIAVDISPDALALARENAERNGLVRVLVVQSDLFEPLRGKFDLIVS  182 (280)
T ss_pred             cEEEecCChHHHHHHHHhhCcCCeEEEEECCHHHHHHHHHHHHHcCCccEEEEeeecccccCCceeEEEe
Confidence            799999999999999999999999999998 5688877654      56777777999988764 98874

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

Probab=98.31  E-value=2.4e-06  Score=67.16  Aligned_cols=71  Identities=17%  Similarity=0.156  Sum_probs=58.0

Q ss_pred             HhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCCC---CCCCCEE
Q 039903          161 DSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLER---IPKGDAI  230 (233)
Q Consensus       161 ~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~---~P~~D~~  230 (233)
                      ..+. ..+..+++|||||+|..+++++..+|+.|++.+|. ++.++..+.+      ++++.+.||.-+.   .|..|.+
T Consensus        28 s~L~-~~~g~~l~DIGaGtGsi~iE~a~~~p~~~v~AIe~~~~a~~~~~~N~~~fg~~n~~vv~g~Ap~~L~~~~~~dai  106 (187)
T COG2242          28 SKLR-PRPGDRLWDIGAGTGSITIEWALAGPSGRVIAIERDEEALELIERNAARFGVDNLEVVEGDAPEALPDLPSPDAI  106 (187)
T ss_pred             HhhC-CCCCCEEEEeCCCccHHHHHHHHhCCCceEEEEecCHHHHHHHHHHHHHhCCCcEEEEeccchHhhcCCCCCCEE
Confidence            4454 66778999999999999999999999999999997 4566655543      8999999998874   4445998


Q ss_pred             Ee
Q 039903          231 LI  232 (233)
Q Consensus       231 ~l  232 (233)
                      ++
T Consensus       107 FI  108 (187)
T COG2242         107 FI  108 (187)
T ss_pred             EE
Confidence            86

>TIGR00536 hemK_fam HemK family putative methylases

Probab=98.30  E-value=2.2e-06  Score=72.71  Aligned_cols=63  Identities=16%  Similarity=0.286  Sum_probs=54.1

Q ss_pred             ceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCCCCCC-C-CEEEe
Q 039903          170 KQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLERIPK-G-DAILI  232 (233)
Q Consensus       170 ~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~~P~-~-D~~~l  232 (233)
                      .+++|+|||+|.++..+++.+|+.+++.+|+ +..++.++++       +||+++.+|+++++|. . |+++.
T Consensus       116 ~~vLDlG~GsG~i~l~la~~~~~~~v~avDis~~al~~a~~n~~~~~~~~~v~~~~~d~~~~~~~~~fDlIvs  188 (284)
T TIGR00536       116 LHILDLGTGSGCIALALAYEFPNAEVIAVDISPDALAVAEENAEKNQLEHRVEFIQSNLFEPLAGQKIDIIVS  188 (284)
T ss_pred             CEEEEEeccHhHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHcCCCCcEEEEECchhccCcCCCccEEEE
Confidence            6899999999999999999999999999998 5577777653       4699999999997765 3 88874

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.

>PLN02244 tocopherol O-methyltransferase

Probab=98.30  E-value=2.6e-06  Score=74.16  Aligned_cols=65  Identities=22%  Similarity=0.284  Sum_probs=52.7

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC-------CCceEEecCcCC-CCCCC--CEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY-------SGVKHIGGIMLE-RIPKG--DAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~-------~ri~~~~gD~f~-~~P~~--D~~~l  232 (233)
                      +...+|||||||.|.++..+++++ ..+++.+|+. ..++.+++.       ++|+++.+|+.+ ++|.+  |+|+.
T Consensus       117 ~~~~~VLDiGCG~G~~~~~La~~~-g~~v~gvD~s~~~i~~a~~~~~~~g~~~~v~~~~~D~~~~~~~~~~FD~V~s  192 (340)
T PLN02244        117 KRPKRIVDVGCGIGGSSRYLARKY-GANVKGITLSPVQAARANALAAAQGLSDKVSFQVADALNQPFEDGQFDLVWS  192 (340)
T ss_pred             CCCCeEEEecCCCCHHHHHHHHhc-CCEEEEEECCHHHHHHHHHHHHhcCCCCceEEEEcCcccCCCCCCCccEEEE
Confidence            456899999999999999999988 7789999985 455555431       589999999988 77764  98874

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

Probab=98.28  E-value=4.2e-06  Score=61.34  Aligned_cols=73  Identities=14%  Similarity=0.089  Sum_probs=54.7

Q ss_pred             HHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccC------CCCceEEecCcCC---CCCC-C
Q 039903          159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSS------YSGVKHIGGIMLE---RIPK-G  227 (233)
Q Consensus       159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~------~~ri~~~~gD~f~---~~P~-~  227 (233)
                      +++.+. .....+++|+|||.|.++..+++++|+.+++.+|.. ..++.++.      .++++++.+|...   ..+. .
T Consensus        11 ~~~~~~-~~~~~~vldlG~G~G~~~~~l~~~~~~~~v~~vD~s~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   89 (124)
T TIGR02469        11 TLSKLR-LRPGDVLWDIGAGSGSITIEAARLVPNGRVYAIERNPEALRLIERNARRFGVSNIVIVEGDAPEALEDSLPEP   89 (124)
T ss_pred             HHHHcC-CCCCCEEEEeCCCCCHHHHHHHHHCCCceEEEEcCCHHHHHHHHHHHHHhCCCceEEEeccccccChhhcCCC
Confidence            344444 455579999999999999999999999999999984 46665543      2678999898764   2233 3


Q ss_pred             CEEEe
Q 039903          228 DAILI  232 (233)
Q Consensus       228 D~~~l  232 (233)
                      |++++
T Consensus        90 D~v~~   94 (124)
T TIGR02469        90 DRVFI   94 (124)
T ss_pred             CEEEE
Confidence            88875

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.

>PRK00107 gidB 16S rRNA methyltransferase GidB; Reviewed

Probab=98.25  E-value=3.5e-06  Score=67.08  Aligned_cols=66  Identities=18%  Similarity=0.090  Sum_probs=53.0

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCC-CCCC-CCEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLE-RIPK-GDAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~-~~P~-~D~~~l  232 (233)
                      +...+++|||||+|..+..+++++|..+++.+|. ++.++.++++      ++|+++.+|..+ +.+. .|+++.
T Consensus        44 ~~g~~VLDiGcGtG~~al~la~~~~~~~V~giD~s~~~l~~A~~~~~~~~l~~i~~~~~d~~~~~~~~~fDlV~~  118 (187)
T PRK00107         44 PGGERVLDVGSGAGFPGIPLAIARPELKVTLVDSLGKKIAFLREVAAELGLKNVTVVHGRAEEFGQEEKFDVVTS  118 (187)
T ss_pred             CCCCeEEEEcCCCCHHHHHHHHHCCCCeEEEEeCcHHHHHHHHHHHHHcCCCCEEEEeccHhhCCCCCCccEEEE
Confidence            3468999999999999999999999999999998 4567666542      469999999877 3332 398875

>PRK11207 tellurite resistance protein TehB; Provisional

Probab=98.23  E-value=3.7e-06  Score=67.53  Aligned_cols=73  Identities=16%  Similarity=0.184  Sum_probs=55.7

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCC-CCCCC-
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLE-RIPKG-  227 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~-~~P~~-  227 (233)
                      +.+++.++ .....++||+|||.|.++..++++  ..+++.+|+ |..++.+++.      .+|+++..|+.+ +++.. 
T Consensus        20 ~~l~~~l~-~~~~~~vLDiGcG~G~~a~~La~~--g~~V~gvD~S~~~i~~a~~~~~~~~~~~v~~~~~d~~~~~~~~~f   96 (197)
T PRK11207         20 SEVLEAVK-VVKPGKTLDLGCGNGRNSLYLAAN--GFDVTAWDKNPMSIANLERIKAAENLDNLHTAVVDLNNLTFDGEY   96 (197)
T ss_pred             HHHHHhcc-cCCCCcEEEECCCCCHHHHHHHHC--CCEEEEEeCCHHHHHHHHHHHHHcCCCcceEEecChhhCCcCCCc
Confidence            45666666 555689999999999999999986  468999999 5566666542      458899999987 55554 


Q ss_pred             CEEEe
Q 039903          228 DAILI  232 (233)
Q Consensus       228 D~~~l  232 (233)
                      |+|+.
T Consensus        97 D~I~~  101 (197)
T PRK11207         97 DFILS  101 (197)
T ss_pred             CEEEE
Confidence            98863

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

Probab=98.23  E-value=3.6e-06  Score=69.65  Aligned_cols=65  Identities=15%  Similarity=0.204  Sum_probs=54.0

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCCCCCC--CCEEEe
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLERIPK--GDAILI  232 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~~P~--~D~~~l  232 (233)
                      +..+++|+|||+|.++..+++.+|+.+++.+|. +..++.++.+      ++++++.+|++++++.  .|+++.
T Consensus        87 ~~~~ilDig~G~G~~~~~l~~~~~~~~v~~iD~~~~~~~~a~~~~~~~~~~~~~~~~~d~~~~~~~~~fD~Vi~  160 (251)
T TIGR03534        87 GPLRVLDLGTGSGAIALALAKERPDARVTAVDISPEALAVARKNAARLGLDNVTFLQSDWFEPLPGGKFDLIVS  160 (251)
T ss_pred             CCCeEEEEeCcHhHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHcCCCeEEEEECchhccCcCCceeEEEE
Confidence            346899999999999999999999999999997 5577766542      5799999999987654  388864

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.

>smart00828 PKS_MT Methyltransferase in polyketide synthase (PKS) enzymes

Probab=98.23  E-value=2.8e-06  Score=69.32  Aligned_cols=62  Identities=15%  Similarity=0.243  Sum_probs=50.6

Q ss_pred             ceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccC-------CCCceEEecCcCC-CCCCC-CEEE
Q 039903          170 KQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSS-------YSGVKHIGGIMLE-RIPKG-DAIL  231 (233)
Q Consensus       170 ~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~-------~~ri~~~~gD~f~-~~P~~-D~~~  231 (233)
                      ++|||||||.|.++..+++.+|+.+++.+|+. +.++.+++       .++|+++.+|+.+ +.|.. |+++
T Consensus         1 ~~vLDiGcG~G~~~~~la~~~~~~~v~gid~s~~~~~~a~~~~~~~gl~~~i~~~~~d~~~~~~~~~fD~I~   72 (224)
T smart00828        1 KRVLDFGCGYGSDLIDLAERHPHLQLHGYTISPEQAEVGRERIRALGLQGRIRIFYRDSAKDPFPDTYDLVF   72 (224)
T ss_pred             CeEEEECCCCCHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHhcCCCcceEEEecccccCCCCCCCCEee
Confidence            47999999999999999999999999999985 45555544       2689999999987 55554 8876

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

Probab=98.22  E-value=1.9e-06  Score=68.96  Aligned_cols=65  Identities=11%  Similarity=0.221  Sum_probs=51.9

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCC-C---CCCC--CEEEe
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLE-R---IPKG--DAILI  232 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~-~---~P~~--D~~~l  232 (233)
                      ...+++|||||+|.++..+++++|+.+++.+|+ +..++.+.+.      ++|+++.+|+.+ .   +|.+  |.+++
T Consensus        16 ~~~~ilDiGcG~G~~~~~la~~~p~~~v~gvD~~~~~l~~a~~~~~~~~l~ni~~i~~d~~~~~~~~~~~~~~d~v~~   93 (194)
T TIGR00091        16 KAPLHLEIGCGKGRFLIDMAKQNPDKNFLGIEIHTPIVLAANNKANKLGLKNLHVLCGDANELLDKFFPDGSLSKVFL   93 (194)
T ss_pred             CCceEEEeCCCccHHHHHHHHhCCCCCEEEEEeeHHHHHHHHHHHHHhCCCCEEEEccCHHHHHHhhCCCCceeEEEE
Confidence            457899999999999999999999999999998 4566665432      689999999975 1   4442  77654

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

>TIGR00138 gidB 16S rRNA methyltransferase GidB

Probab=98.21  E-value=2.5e-06  Score=67.64  Aligned_cols=64  Identities=17%  Similarity=0.171  Sum_probs=50.4

Q ss_pred             cceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccC------CCCceEEecCcCC-CCCC-CCEEEe
Q 039903          169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSS------YSGVKHIGGIMLE-RIPK-GDAILI  232 (233)
Q Consensus       169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~------~~ri~~~~gD~f~-~~P~-~D~~~l  232 (233)
                      ..+++|||||+|.++..++..+|+.+++.+|..+ .++.+++      .++|+++.+|+.+ +... .|+|+.
T Consensus        43 ~~~vLDiGcGtG~~s~~la~~~~~~~V~~iD~s~~~~~~a~~~~~~~~~~~i~~i~~d~~~~~~~~~fD~I~s  115 (181)
T TIGR00138        43 GKKVIDIGSGAGFPGIPLAIARPELKLTLLESNHKKVAFLREVKAELGLNNVEIVNGRAEDFQHEEQFDVITS  115 (181)
T ss_pred             CCeEEEecCCCCccHHHHHHHCCCCeEEEEeCcHHHHHHHHHHHHHhCCCCeEEEecchhhccccCCccEEEe
Confidence            5799999999999999999999999999999864 5544432      2579999999977 3222 398874

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.

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

Probab=98.19  E-value=2e-06  Score=61.33  Aligned_cols=61  Identities=13%  Similarity=0.261  Sum_probs=46.5

Q ss_pred             EEEecCCccHHHHHHHHHc---CCCcEEEeech-HHHhhccCC-----CCceEEecCcCC-CCCC--CCEEEe
Q 039903          172 LVDVGGGLGVNVNIIISNY---LHIKGVNFDLS-HVIQDSSSY-----SGVKHIGGIMLE-RIPK--GDAILI  232 (233)
Q Consensus       172 vvDvGGG~G~~~~~l~~~~---P~l~~~v~Dlp-~v~~~a~~~-----~ri~~~~gD~f~-~~P~--~D~~~l  232 (233)
                      |+|+|||+|..+..+++.+   |..+.+.+|+. +.++.+++.     .+++++..|+.+ +++.  .|+|+.
T Consensus         1 ILDlgcG~G~~~~~l~~~~~~~~~~~~~gvD~s~~~l~~~~~~~~~~~~~~~~~~~D~~~l~~~~~~~D~v~~   73 (101)
T PF13649_consen    1 ILDLGCGTGRVTRALARRFDAGPSSRVIGVDISPEMLELAKKRFSEDGPKVRFVQADARDLPFSDGKFDLVVC   73 (101)
T ss_dssp             -EEET-TTSHHHHHHHHHS-----SEEEEEES-HHHHHHHHHHSHHTTTTSEEEESCTTCHHHHSSSEEEEEE
T ss_pred             CEEeecCCcHHHHHHHHHhhhcccceEEEEECCHHHHHHHHHhchhcCCceEEEECCHhHCcccCCCeeEEEE
Confidence            6999999999999999997   66899999984 577776653     489999999987 5444  388875

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

Probab=98.19  E-value=4.8e-06  Score=73.63  Aligned_cols=65  Identities=15%  Similarity=0.194  Sum_probs=54.2

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-----CCceEEecCcCCC-CCC---CCEEEe
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-----SGVKHIGGIMLER-IPK---GDAILI  232 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-----~ri~~~~gD~f~~-~P~---~D~~~l  232 (233)
                      +..+++|||||+|.++..+++++|+.+++.+|+ |++++.++++     .+|+++.+|+++. .|.   -|+++.
T Consensus       251 ~~~rVLDLGcGSG~IaiaLA~~~p~a~VtAVDiS~~ALe~AreNa~~~g~rV~fi~gDl~e~~l~~~~~FDLIVS  325 (423)
T PRK14966        251 ENGRVWDLGTGSGAVAVTVALERPDAFVRASDISPPALETARKNAADLGARVEFAHGSWFDTDMPSEGKWDIIVS  325 (423)
T ss_pred             CCCEEEEEeChhhHHHHHHHHhCCCCEEEEEECCHHHHHHHHHHHHHcCCcEEEEEcchhccccccCCCccEEEE
Confidence            346899999999999999999999999999999 6688877653     4799999999973 442   288875

>TIGR02021 BchM-ChlM magnesium protoporphyrin O-methyltransferase

Probab=98.19  E-value=8.9e-06  Score=66.22  Aligned_cols=100  Identities=11%  Similarity=0.051  Sum_probs=64.5

Q ss_pred             ccccccCchHHHHHHHHHHhcchhcHHHHHHhccc-ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhcc
Q 039903          131 YEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKG-FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSS  208 (233)
Q Consensus       131 ~~~~~~~~~~~~~f~~am~~~~~~~~~~~~~~~~~-~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~  208 (233)
                      |+.+..++.....+...|..........+++.+.. ..+..+++|||||+|.++..+++.  ..+++.+|. |+.++.|+
T Consensus        17 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~vLDiGcG~G~~~~~la~~--~~~v~gvD~s~~~i~~a~   94 (219)
T TIGR02021        17 WARIYGSGDPVSRVRQTVREGRAAMRRKLLDWLPKDPLKGKRVLDAGCGTGLLSIELAKR--GAIVKAVDISEQMVQMAR   94 (219)
T ss_pred             HHHhhCCchhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCEEEEEeCCCCHHHHHHHHC--CCEEEEEECCHHHHHHHH
Confidence            44444444444455555533333333444444331 334689999999999999999886  447899998 55777765


Q ss_pred             CC-------CCceEEecCcCCCCCCCCEEEe
Q 039903          209 SY-------SGVKHIGGIMLERIPKGDAILI  232 (233)
Q Consensus       209 ~~-------~ri~~~~gD~f~~~P~~D~~~l  232 (233)
                      +.       +++++..+|+.+....-|+++.
T Consensus        95 ~~~~~~~~~~~i~~~~~d~~~~~~~fD~ii~  125 (219)
T TIGR02021        95 NRAQGRDVAGNVEFEVNDLLSLCGEFDIVVC  125 (219)
T ss_pred             HHHHhcCCCCceEEEECChhhCCCCcCEEEE
Confidence            42       4899999998763233488764

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.

>PLN02336 phosphoethanolamine N-methyltransferase

Probab=98.17  E-value=6.2e-06  Score=74.89  Aligned_cols=74  Identities=22%  Similarity=0.313  Sum_probs=58.0

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC-----CCceEEecCcCC-CCCCC--
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY-----SGVKHIGGIMLE-RIPKG--  227 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~-----~ri~~~~gD~f~-~~P~~--  227 (233)
                      ..+++.+. .++..+|+|||||+|..+..+++++ +.+++.+|+. +.++.|+++     .+|+++.+|+++ ++|.+  
T Consensus       256 e~l~~~~~-~~~~~~vLDiGcG~G~~~~~la~~~-~~~v~gvDiS~~~l~~A~~~~~~~~~~v~~~~~d~~~~~~~~~~f  333 (475)
T PLN02336        256 KEFVDKLD-LKPGQKVLDVGCGIGGGDFYMAENF-DVHVVGIDLSVNMISFALERAIGRKCSVEFEVADCTKKTYPDNSF  333 (475)
T ss_pred             HHHHHhcC-CCCCCEEEEEeccCCHHHHHHHHhc-CCEEEEEECCHHHHHHHHHHhhcCCCceEEEEcCcccCCCCCCCE
Confidence            34555555 5667899999999999999998876 7799999995 567666542     589999999998 67763  


Q ss_pred             CEEEe
Q 039903          228 DAILI  232 (233)
Q Consensus       228 D~~~l  232 (233)
                      |+|+.
T Consensus       334 D~I~s  338 (475)
T PLN02336        334 DVIYS  338 (475)
T ss_pred             EEEEE
Confidence            98874

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

Probab=98.16  E-value=3.3e-06  Score=77.20  Aligned_cols=64  Identities=19%  Similarity=0.243  Sum_probs=54.5

Q ss_pred             cceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCCCCCC--CCEEEe
Q 039903          169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLERIPK--GDAILI  232 (233)
Q Consensus       169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~~P~--~D~~~l  232 (233)
                      ..+|+|||||+|.+++.+++++|+.+++.+|+ |.+++.|+++       ++|+++.+|+++.++.  -|+++.
T Consensus       139 ~~~VLDlG~GsG~iai~la~~~p~~~v~avDis~~al~~A~~N~~~~~l~~~v~~~~~D~~~~~~~~~fDlIvs  212 (506)
T PRK01544        139 FLNILELGTGSGCIAISLLCELPNANVIATDISLDAIEVAKSNAIKYEVTDRIQIIHSNWFENIEKQKFDFIVS  212 (506)
T ss_pred             CCEEEEccCchhHHHHHHHHHCCCCeEEEEECCHHHHHHHHHHHHHcCCccceeeeecchhhhCcCCCccEEEE
Confidence            46899999999999999999999999999999 5677777653       5899999999987664  388874

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

Probab=98.16  E-value=3.8e-06  Score=69.24  Aligned_cols=67  Identities=16%  Similarity=0.238  Sum_probs=47.3

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHc-CCCcEEEeec-hHHHhhccCC------CCceEEecCcCC-CCCCC--CEEEe
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNY-LHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLE-RIPKG--DAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~-~~P~~--D~~~l  232 (233)
                      .....+|+|||||+|.++..++++. |+.+++++|. ++.++.|++.      .+|+++.+|..+ |+|..  |++++
T Consensus        45 ~~~g~~vLDv~~GtG~~~~~l~~~~~~~~~v~~vD~s~~ML~~a~~k~~~~~~~~i~~v~~da~~lp~~d~sfD~v~~  122 (233)
T PF01209_consen   45 LRPGDRVLDVACGTGDVTRELARRVGPNGKVVGVDISPGMLEVARKKLKREGLQNIEFVQGDAEDLPFPDNSFDAVTC  122 (233)
T ss_dssp             --S--EEEEET-TTSHHHHHHGGGSS---EEEEEES-HHHHHHHHHHHHHTT--SEEEEE-BTTB--S-TT-EEEEEE
T ss_pred             CCCCCEEEEeCCChHHHHHHHHHHCCCccEEEEecCCHHHHHHHHHHHHhhCCCCeeEEEcCHHHhcCCCCceeEEEH
Confidence            4556799999999999999999875 6789999998 4588877652      589999999999 89874  98875

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.

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

Probab=98.14  E-value=8.5e-06  Score=68.71  Aligned_cols=74  Identities=14%  Similarity=0.183  Sum_probs=58.6

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccCC------CCceEEecCcCCCCCCC-CE
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSSY------SGVKHIGGIMLERIPKG-DA  229 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~~------~ri~~~~gD~f~~~P~~-D~  229 (233)
                      -+++.++ .....+|+|+|||.|.+++.+++.+|+.+.+.+|... +++.++++      ++..+...|.+++...- |+
T Consensus       149 lLl~~l~-~~~~~~vlDlGCG~Gvlg~~la~~~p~~~vtmvDvn~~Av~~ar~Nl~~N~~~~~~v~~s~~~~~v~~kfd~  227 (300)
T COG2813         149 LLLETLP-PDLGGKVLDLGCGYGVLGLVLAKKSPQAKLTLVDVNARAVESARKNLAANGVENTEVWASNLYEPVEGKFDL  227 (300)
T ss_pred             HHHHhCC-ccCCCcEEEeCCCccHHHHHHHHhCCCCeEEEEecCHHHHHHHHHhHHHcCCCccEEEEecccccccccccE
Confidence            4667777 4444599999999999999999999999999999864 88888775      33367788999876653 87


Q ss_pred             EEe
Q 039903          230 ILI  232 (233)
Q Consensus       230 ~~l  232 (233)
                      |+.
T Consensus       228 Iis  230 (300)
T COG2813         228 IIS  230 (300)
T ss_pred             EEe
Confidence            764

>PLN02233 ubiquinone biosynthesis methyltransferase

Probab=98.14  E-value=1e-05  Score=67.85  Aligned_cols=67  Identities=19%  Similarity=0.229  Sum_probs=54.2

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHc-CCCcEEEeech-HHHhhccC---------CCCceEEecCcCC-CCCCC--CEEE
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNY-LHIKGVNFDLS-HVIQDSSS---------YSGVKHIGGIMLE-RIPKG--DAIL  231 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~-P~l~~~v~Dlp-~v~~~a~~---------~~ri~~~~gD~f~-~~P~~--D~~~  231 (233)
                      ..+..+|+|||||+|.++..+++++ |+.+++.+|.. +.++.|++         .++|+++.+|+.+ |+|.+  |+++
T Consensus        71 ~~~~~~VLDlGcGtG~~~~~la~~~~~~~~V~gvD~S~~ml~~A~~r~~~~~~~~~~~i~~~~~d~~~lp~~~~sfD~V~  150 (261)
T PLN02233         71 AKMGDRVLDLCCGSGDLAFLLSEKVGSDGKVMGLDFSSEQLAVAASRQELKAKSCYKNIEWIEGDATDLPFDDCYFDAIT  150 (261)
T ss_pred             CCCCCEEEEECCcCCHHHHHHHHHhCCCCEEEEEECCHHHHHHHHHHhhhhhhccCCCeEEEEcccccCCCCCCCEeEEE
Confidence            4556799999999999999999885 67899999984 57776643         2589999999988 78763  9887


Q ss_pred             e
Q 039903          232 I  232 (233)
Q Consensus       232 l  232 (233)
                      +
T Consensus       151 ~  151 (261)
T PLN02233        151 M  151 (261)
T ss_pred             E
Confidence            5

>PRK10258 biotin biosynthesis protein BioC; Provisional

Probab=98.13  E-value=1.8e-05  Score=65.80  Aligned_cols=74  Identities=11%  Similarity=0.155  Sum_probs=55.5

Q ss_pred             HHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-CCceEEecCcCC-CCCCC--CEE
Q 039903          156 TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-SGVKHIGGIMLE-RIPKG--DAI  230 (233)
Q Consensus       156 ~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-~ri~~~~gD~f~-~~P~~--D~~  230 (233)
                      +..+++.++ .....+|+|||||+|.++..+.+.  ..+++.+|+ |..++.++.. ..+.++.+|+.+ ++|..  |++
T Consensus        31 a~~l~~~l~-~~~~~~vLDiGcG~G~~~~~l~~~--~~~v~~~D~s~~~l~~a~~~~~~~~~~~~d~~~~~~~~~~fD~V  107 (251)
T PRK10258         31 ADALLAMLP-QRKFTHVLDAGCGPGWMSRYWRER--GSQVTALDLSPPMLAQARQKDAADHYLAGDIESLPLATATFDLA  107 (251)
T ss_pred             HHHHHHhcC-ccCCCeEEEeeCCCCHHHHHHHHc--CCeEEEEECCHHHHHHHHhhCCCCCEEEcCcccCcCCCCcEEEE
Confidence            344555555 345689999999999999888774  467999999 6688877764 456788999977 66653  888


Q ss_pred             Ee
Q 039903          231 LI  232 (233)
Q Consensus       231 ~l  232 (233)
                      +.
T Consensus       108 ~s  109 (251)
T PRK10258        108 WS  109 (251)
T ss_pred             EE
Confidence            63

>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional

Probab=98.12  E-value=1e-05  Score=68.21  Aligned_cols=64  Identities=19%  Similarity=0.251  Sum_probs=52.6

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCC---cEEEeec-hHHHhhccCC-CCceEEecCcCC-CCCCC--CEEE
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHI---KGVNFDL-SHVIQDSSSY-SGVKHIGGIMLE-RIPKG--DAIL  231 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l---~~~v~Dl-p~v~~~a~~~-~ri~~~~gD~f~-~~P~~--D~~~  231 (233)
                      +..+|+|||||+|.++..+++.+|..   +++.+|+ +..++.|++. +++++..+|..+ +++.+  |+|+
T Consensus        85 ~~~~vLDiGcG~G~~~~~l~~~~~~~~~~~v~giD~s~~~l~~A~~~~~~~~~~~~d~~~lp~~~~sfD~I~  156 (272)
T PRK11088         85 KATALLDIGCGEGYYTHALADALPEITTMQLFGLDISKVAIKYAAKRYPQVTFCVASSHRLPFADQSLDAII  156 (272)
T ss_pred             CCCeEEEECCcCCHHHHHHHHhcccccCCeEEEECCCHHHHHHHHHhCCCCeEEEeecccCCCcCCceeEEE
Confidence            44789999999999999999998864   6799998 4577777654 789999999988 77763  8876

>PRK08317 hypothetical protein; Provisional

Probab=98.12  E-value=1.2e-05  Score=65.73  Aligned_cols=73  Identities=19%  Similarity=0.233  Sum_probs=57.1

Q ss_pred             HHHhcccccCcceEEEecCCccHHHHHHHHHc-CCCcEEEeech-HHHhhccCC-----CCceEEecCcCC-CCCCC--C
Q 039903          159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNY-LHIKGVNFDLS-HVIQDSSSY-----SGVKHIGGIMLE-RIPKG--D  228 (233)
Q Consensus       159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~-P~l~~~v~Dlp-~v~~~a~~~-----~ri~~~~gD~f~-~~P~~--D  228 (233)
                      +++.++ .....+|||||||.|.++..+++.+ |..+++.+|+. ..++.+++.     ++++++.+|+.+ +++.+  |
T Consensus        11 ~~~~~~-~~~~~~vLdiG~G~G~~~~~~a~~~~~~~~v~~~d~~~~~~~~a~~~~~~~~~~~~~~~~d~~~~~~~~~~~D   89 (241)
T PRK08317         11 TFELLA-VQPGDRVLDVGCGPGNDARELARRVGPEGRVVGIDRSEAMLALAKERAAGLGPNVEFVRGDADGLPFPDGSFD   89 (241)
T ss_pred             HHHHcC-CCCCCEEEEeCCCCCHHHHHHHHhcCCCcEEEEEeCCHHHHHHHHHHhhCCCCceEEEecccccCCCCCCCce
Confidence            445555 6677899999999999999999998 78899999985 455555442     679999999887 66653  8


Q ss_pred             EEEe
Q 039903          229 AILI  232 (233)
Q Consensus       229 ~~~l  232 (233)
                      +++.
T Consensus        90 ~v~~   93 (241)
T PRK08317         90 AVRS   93 (241)
T ss_pred             EEEE
Confidence            8775

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

Probab=98.12  E-value=5.6e-06  Score=66.74  Aligned_cols=65  Identities=15%  Similarity=0.241  Sum_probs=51.7

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC------CCceEEecCcCC--C--CCCC--CEEEe
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY------SGVKHIGGIMLE--R--IPKG--DAILI  232 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~------~ri~~~~gD~f~--~--~P~~--D~~~l  232 (233)
                      ...+|+|||||+|.++..+++.+|+.+++.+|.. +.++.+++.      ++|+++.+|+.+  +  ++.+  |++++
T Consensus        40 ~~~~VLDiGcGtG~~~~~la~~~p~~~v~gVD~s~~~i~~a~~~~~~~~~~~v~~~~~d~~~~l~~~~~~~~~D~V~~  117 (202)
T PRK00121         40 DAPIHLEIGFGKGEFLVEMAKANPDINFIGIEVHEPGVGKALKKIEEEGLTNLRLLCGDAVEVLLDMFPDGSLDRIYL  117 (202)
T ss_pred             CCCeEEEEccCCCHHHHHHHHHCCCccEEEEEechHHHHHHHHHHHHcCCCCEEEEecCHHHHHHHHcCccccceEEE
Confidence            4578999999999999999999999999999984 567666532      689999999933  3  4443  77764

>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=98.12  E-value=9.5e-07  Score=62.63  Aligned_cols=60  Identities=12%  Similarity=0.244  Sum_probs=40.2

Q ss_pred             EEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC---------CCceEEecCcCCCCCC-C-CEEEe
Q 039903          173 VDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY---------SGVKHIGGIMLERIPK-G-DAILI  232 (233)
Q Consensus       173 vDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~---------~ri~~~~gD~f~~~P~-~-D~~~l  232 (233)
                      ||||||+|.++..+++++|..+.+.+|. |..++.+++.         .++++...|.++..+. . |+|++
T Consensus         1 LdiGcG~G~~~~~l~~~~~~~~~~~~D~s~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fD~V~~   72 (99)
T PF08242_consen    1 LDIGCGTGRLLRALLEELPDARYTGVDISPSMLERARERLAELGNDNFERLRFDVLDLFDYDPPESFDLVVA   72 (99)
T ss_dssp             -EESTTTS-TTTTHHHHC-EEEEEEEESSSSTTSTTCCCHHHCT---EEEEE--SSS---CCC----SEEEE
T ss_pred             CEeCccChHHHHHHHHhCCCCEEEEEECCHHHHHHHHHHhhhcCCcceeEEEeecCChhhcccccccceehh
Confidence            7999999999999999999999999998 4578777664         2456666666664443 3 98875

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.

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

Probab=98.12  E-value=1.4e-05  Score=64.91  Aligned_cols=74  Identities=14%  Similarity=0.172  Sum_probs=56.8

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHc-CCCcEEEeec-hHHHhhccCC------CCceEEecCcCCCCC-CC-
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNY-LHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLERIP-KG-  227 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~~P-~~-  227 (233)
                      .+++.++ ..+..+++|||||+|.++..+++.. ++.+++.+|. |+.++.++++      ++|+++.+|.++..| .+ 
T Consensus        67 ~~~~~l~-~~~g~~VLdIG~GsG~~t~~la~~~~~~~~V~~vE~~~~~~~~a~~~l~~~g~~~v~~~~gd~~~~~~~~~~  145 (212)
T PRK13942         67 IMCELLD-LKEGMKVLEIGTGSGYHAAVVAEIVGKSGKVVTIERIPELAEKAKKTLKKLGYDNVEVIVGDGTLGYEENAP  145 (212)
T ss_pred             HHHHHcC-CCCcCEEEEECCcccHHHHHHHHhcCCCCEEEEEeCCHHHHHHHHHHHHHcCCCCeEEEECCcccCCCcCCC
Confidence            4455555 6777899999999999999988875 4568899997 5577766552      589999999988443 33 


Q ss_pred             -CEEEe
Q 039903          228 -DAILI  232 (233)
Q Consensus       228 -D~~~l  232 (233)
                       |+|++
T Consensus       146 fD~I~~  151 (212)
T PRK13942        146 YDRIYV  151 (212)
T ss_pred             cCEEEE
Confidence             99875

>TIGR02072 BioC biotin biosynthesis protein BioC

Probab=98.11  E-value=7.3e-06  Score=67.03  Aligned_cols=64  Identities=17%  Similarity=0.325  Sum_probs=52.6

Q ss_pred             cceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC--CCceEEecCcCC-CCCCC--CEEEe
Q 039903          169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY--SGVKHIGGIMLE-RIPKG--DAILI  232 (233)
Q Consensus       169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~--~ri~~~~gD~f~-~~P~~--D~~~l  232 (233)
                      ..+|||||||+|.++..+++.+|+.+++.+|.. ..++.++..  ++++++.+|+.+ ++|..  |+++.
T Consensus        35 ~~~vLDlG~G~G~~~~~l~~~~~~~~~~~~D~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~fD~vi~  104 (240)
T TIGR02072        35 PASVLDIGCGTGYLTRALLKRFPQAEFIALDISAGMLAQAKTKLSENVQFICGDAEKLPLEDSSFDLIVS  104 (240)
T ss_pred             CCeEEEECCCccHHHHHHHHhCCCCcEEEEeChHHHHHHHHHhcCCCCeEEecchhhCCCCCCceeEEEE
Confidence            478999999999999999999999999999985 455555543  589999999987 65553  98874

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.

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

Probab=98.11  E-value=1.3e-05  Score=65.19  Aligned_cols=74  Identities=12%  Similarity=0.112  Sum_probs=56.8

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcC-CCcEEEeec-hHHHhhccCC------CCceEEecCcCCCCCC---
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLERIPK---  226 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~~P~---  226 (233)
                      .+++.++ .+...+++|||||+|.++..+++..+ +.+++.+|. |+.++.|+++      ++|+++.+|..+..+.   
T Consensus        68 ~~~~~l~-~~~~~~VLDiG~GsG~~a~~la~~~~~~g~V~~vD~~~~~~~~A~~~~~~~g~~~v~~~~~d~~~~~~~~~~  146 (215)
T TIGR00080        68 MMTELLE-LKPGMKVLEIGTGSGYQAAVLAEIVGRDGLVVSIERIPELAEKAERRLRKLGLDNVIVIVGDGTQGWEPLAP  146 (215)
T ss_pred             HHHHHhC-CCCcCEEEEECCCccHHHHHHHHHhCCCCEEEEEeCCHHHHHHHHHHHHHCCCCCeEEEECCcccCCcccCC
Confidence            4445555 56678999999999999999999865 567899997 5677776542      6799999999874432   


Q ss_pred             CCEEEe
Q 039903          227 GDAILI  232 (233)
Q Consensus       227 ~D~~~l  232 (233)
                      -|++++
T Consensus       147 fD~Ii~  152 (215)
T TIGR00080       147 YDRIYV  152 (215)
T ss_pred             CCEEEE
Confidence            398875

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

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

Probab=98.11  E-value=1e-05  Score=68.03  Aligned_cols=67  Identities=18%  Similarity=0.260  Sum_probs=54.8

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC------CCceEEecCcCCCCCC--CCEEEe
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY------SGVKHIGGIMLERIPK--GDAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~------~ri~~~~gD~f~~~P~--~D~~~l  232 (233)
                      ..+..+++|+|||+|.++..+++.+|..+++.+|.. ..++.++++      .+++++.+|++++++.  .|+++.
T Consensus       106 ~~~~~~vLDiG~GsG~~~~~la~~~~~~~v~~iDis~~~l~~a~~n~~~~~~~~i~~~~~d~~~~~~~~~fD~Iv~  181 (275)
T PRK09328        106 LKEPLRVLDLGTGSGAIALALAKERPDAEVTAVDISPEALAVARRNAKHGLGARVEFLQGDWFEPLPGGRFDLIVS  181 (275)
T ss_pred             ccCCCEEEEEcCcHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHhCCCCcEEEEEccccCcCCCCceeEEEE
Confidence            345578999999999999999999999999999985 466666542      5899999999987663  388864

>PRK07402 precorrin-6B methylase; Provisional

Probab=98.11  E-value=9.9e-06  Score=64.86  Aligned_cols=63  Identities=19%  Similarity=0.137  Sum_probs=51.4

Q ss_pred             HHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCC
Q 039903          159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLE  222 (233)
Q Consensus       159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~  222 (233)
                      +++.++ .....+|+|+|||+|.++..+++..|..+++.+|+ |+.++.++++      ++|+++.+|..+
T Consensus        32 l~~~l~-~~~~~~VLDiG~G~G~~~~~la~~~~~~~V~~vD~s~~~~~~a~~n~~~~~~~~v~~~~~d~~~  101 (196)
T PRK07402         32 LISQLR-LEPDSVLWDIGAGTGTIPVEAGLLCPKGRVIAIERDEEVVNLIRRNCDRFGVKNVEVIEGSAPE  101 (196)
T ss_pred             HHHhcC-CCCCCEEEEeCCCCCHHHHHHHHHCCCCEEEEEeCCHHHHHHHHHHHHHhCCCCeEEEECchHH
Confidence            445554 55668999999999999999999999999999998 6677776542      579999998865

>smart00650 rADc Ribosomal RNA adenine dimethylases

Probab=98.11  E-value=1.1e-05  Score=63.04  Aligned_cols=72  Identities=13%  Similarity=0.283  Sum_probs=55.4

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccCC----CCceEEecCcCC-CCCCC--C
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSSY----SGVKHIGGIMLE-RIPKG--D  228 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~~----~ri~~~~gD~f~-~~P~~--D  228 (233)
                      ..+++.++ ..+..+++|||||.|.++..++++  ..+++.+|+.. .++.++++    ++++++.+|+++ +.+..  |
T Consensus         3 ~~i~~~~~-~~~~~~vLEiG~G~G~lt~~l~~~--~~~v~~vE~~~~~~~~~~~~~~~~~~v~ii~~D~~~~~~~~~~~d   79 (169)
T smart00650        3 DKIVRAAN-LRPGDTVLEIGPGKGALTEELLER--AARVTAIEIDPRLAPRLREKFAAADNLTVIHGDALKFDLPKLQPY   79 (169)
T ss_pred             HHHHHhcC-CCCcCEEEEECCCccHHHHHHHhc--CCeEEEEECCHHHHHHHHHHhccCCCEEEEECchhcCCccccCCC
Confidence            34556665 666789999999999999999998  46789999864 66655442    689999999998 66652  7


Q ss_pred             EEE
Q 039903          229 AIL  231 (233)
Q Consensus       229 ~~~  231 (233)
                      .++
T Consensus        80 ~vi   82 (169)
T smart00650       80 KVV   82 (169)
T ss_pred             EEE
Confidence            665

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

Probab=98.11  E-value=8.8e-06  Score=71.44  Aligned_cols=73  Identities=18%  Similarity=0.192  Sum_probs=54.4

Q ss_pred             HHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccC------CCCceEEecCcC---CCCCCC-
Q 039903          159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSS------YSGVKHIGGIML---ERIPKG-  227 (233)
Q Consensus       159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~------~~ri~~~~gD~f---~~~P~~-  227 (233)
                      +++.+. -.....+||||||+|.++..+++++|+..++++|+. ..++.+..      .++|.++.+|..   +.+|.+ 
T Consensus       114 ~~~~~~-~~~~p~vLEIGcGsG~~ll~lA~~~P~~~~iGIEI~~~~i~~a~~ka~~~gL~NV~~i~~DA~~ll~~~~~~s  192 (390)
T PRK14121        114 FLDFIS-KNQEKILIEIGFGSGRHLLYQAKNNPNKLFIGIEIHTPSIEQVLKQIELLNLKNLLIINYDARLLLELLPSNS  192 (390)
T ss_pred             HHHHhc-CCCCCeEEEEcCcccHHHHHHHHhCCCCCEEEEECCHHHHHHHHHHHHHcCCCcEEEEECCHHHhhhhCCCCc
Confidence            444443 233468999999999999999999999999999984 45554432      268999999974   356654 


Q ss_pred             -CEEEe
Q 039903          228 -DAILI  232 (233)
Q Consensus       228 -D~~~l  232 (233)
                       |.+++
T Consensus       193 ~D~I~l  198 (390)
T PRK14121        193 VEKIFV  198 (390)
T ss_pred             eeEEEE
Confidence             77764

>PRK00216 ubiE ubiquinone/menaquinone biosynthesis methyltransferase; Reviewed

Probab=98.10  E-value=1.6e-05  Score=65.04  Aligned_cols=74  Identities=18%  Similarity=0.180  Sum_probs=56.5

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcC-CCcEEEeech-HHHhhccCC-------CCceEEecCcCC-CCCCC
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDLS-HVIQDSSSY-------SGVKHIGGIMLE-RIPKG  227 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dlp-~v~~~a~~~-------~ri~~~~gD~f~-~~P~~  227 (233)
                      .+++.+. ..+..+|+|||||.|.++..+++.+| +.+++++|+. ..++.+++.       .+++++.+|+.+ +.+.+
T Consensus        42 ~~~~~~~-~~~~~~vldiG~G~G~~~~~l~~~~~~~~~v~~~D~s~~~~~~a~~~~~~~~~~~~~~~~~~d~~~~~~~~~  120 (239)
T PRK00216         42 KTIKWLG-VRPGDKVLDLACGTGDLAIALAKAVGKTGEVVGLDFSEGMLAVGREKLRDLGLSGNVEFVQGDAEALPFPDN  120 (239)
T ss_pred             HHHHHhC-CCCCCeEEEeCCCCCHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHhhcccccccCeEEEecccccCCCCCC
Confidence            3444444 44557999999999999999999998 7899999984 466665542       579999999987 55443


Q ss_pred             --CEEEe
Q 039903          228 --DAILI  232 (233)
Q Consensus       228 --D~~~l  232 (233)
                        |+|++
T Consensus       121 ~~D~I~~  127 (239)
T PRK00216        121 SFDAVTI  127 (239)
T ss_pred             CccEEEE
Confidence              88864

>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=98.09  E-value=8e-06  Score=56.67  Aligned_cols=59  Identities=19%  Similarity=0.317  Sum_probs=47.2

Q ss_pred             EEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccCC---CCceEEecCcCC-CCCCC--CEEEe
Q 039903          173 VDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSSY---SGVKHIGGIMLE-RIPKG--DAILI  232 (233)
Q Consensus       173 vDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~~---~ri~~~~gD~f~-~~P~~--D~~~l  232 (233)
                      ||||||.|..+..++++ |..+++.+|..+ .++.+++.   .+++++.+|+.+ ++|..  |+++.
T Consensus         1 LdiG~G~G~~~~~l~~~-~~~~v~~~D~~~~~~~~~~~~~~~~~~~~~~~d~~~l~~~~~sfD~v~~   66 (95)
T PF08241_consen    1 LDIGCGTGRFAAALAKR-GGASVTGIDISEEMLEQARKRLKNEGVSFRQGDAEDLPFPDNSFDVVFS   66 (95)
T ss_dssp             EEET-TTSHHHHHHHHT-TTCEEEEEES-HHHHHHHHHHTTTSTEEEEESBTTSSSS-TT-EEEEEE
T ss_pred             CEecCcCCHHHHHHHhc-cCCEEEEEeCCHHHHHHHHhcccccCchheeehHHhCcccccccccccc
Confidence            79999999999999999 999999999854 57766652   567899999998 88874  88874

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 ....

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

Probab=98.09  E-value=1.1e-05  Score=67.28  Aligned_cols=64  Identities=16%  Similarity=0.145  Sum_probs=52.9

Q ss_pred             cceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC---CCceEEecCcCCCCC----C-CCEEEe
Q 039903          169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY---SGVKHIGGIMLERIP----K-GDAILI  232 (233)
Q Consensus       169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~---~ri~~~~gD~f~~~P----~-~D~~~l  232 (233)
                      ..+++|+|||+|.++..+++++|..+++.+|. |.+++.++++   .+++++.+|+++.++    . -|+++.
T Consensus        87 ~~~vLDlg~GsG~i~l~la~~~~~~~v~~vDis~~al~~A~~N~~~~~~~~~~~D~~~~l~~~~~~~fDlVv~  159 (251)
T TIGR03704        87 TLVVVDLCCGSGAVGAALAAALDGIELHAADIDPAAVRCARRNLADAGGTVHEGDLYDALPTALRGRVDILAA  159 (251)
T ss_pred             CCEEEEecCchHHHHHHHHHhCCCCEEEEEECCHHHHHHHHHHHHHcCCEEEEeechhhcchhcCCCEeEEEE
Confidence            45899999999999999999999999999998 6788877764   347899999987554    2 288774

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.

>PRK09489 rsmC 16S ribosomal RNA m2G1207 methyltransferase; Provisional

Probab=98.08  E-value=1.3e-05  Score=69.66  Aligned_cols=73  Identities=18%  Similarity=0.216  Sum_probs=55.1

Q ss_pred             HHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC-----CCceEEecCcCCCCCCC-CEEE
Q 039903          159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY-----SGVKHIGGIMLERIPKG-DAIL  231 (233)
Q Consensus       159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~-----~ri~~~~gD~f~~~P~~-D~~~  231 (233)
                      +++.++ -....+|+|+|||.|.++..+++++|+.+++.+|.. .+++.++.+     -..+++.+|.++..+.. |+|+
T Consensus       188 Ll~~l~-~~~~g~VLDlGCG~G~ls~~la~~~p~~~v~~vDis~~Al~~A~~nl~~n~l~~~~~~~D~~~~~~~~fDlIv  266 (342)
T PRK09489        188 LLSTLT-PHTKGKVLDVGCGAGVLSAVLARHSPKIRLTLSDVSAAALESSRATLAANGLEGEVFASNVFSDIKGRFDMII  266 (342)
T ss_pred             HHHhcc-ccCCCeEEEeccCcCHHHHHHHHhCCCCEEEEEECCHHHHHHHHHHHHHcCCCCEEEEcccccccCCCccEEE
Confidence            344444 223358999999999999999999999999999985 477766542     24567889998865554 9887


Q ss_pred             e
Q 039903          232 I  232 (233)
Q Consensus       232 l  232 (233)
                      .
T Consensus       267 s  267 (342)
T PRK09489        267 S  267 (342)
T ss_pred             E
Confidence            4

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

Probab=98.07  E-value=1.8e-05  Score=63.98  Aligned_cols=73  Identities=15%  Similarity=0.125  Sum_probs=54.4

Q ss_pred             HHHhcccccCcceEEEecCCccHHHHHHHHHcC-CCcEEEeech-HHHhhccCC-------CCceEEecCcCCCCCC---
Q 039903          159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDLS-HVIQDSSSY-------SGVKHIGGIMLERIPK---  226 (233)
Q Consensus       159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dlp-~v~~~a~~~-------~ri~~~~gD~f~~~P~---  226 (233)
                      +++.++ .....+++|||||+|.++..+++..+ .-+++.+|.. +.++.++++       ++++++.+|+.+.+|.   
T Consensus        64 ~~~~l~-~~~~~~VLDiG~GsG~~~~~la~~~~~~g~V~~iD~~~~~~~~a~~~l~~~~~~~~v~~~~~d~~~~~~~~~~  142 (205)
T PRK13944         64 MCELIE-PRPGMKILEVGTGSGYQAAVCAEAIERRGKVYTVEIVKELAIYAAQNIERLGYWGVVEVYHGDGKRGLEKHAP  142 (205)
T ss_pred             HHHhcC-CCCCCEEEEECcCccHHHHHHHHhcCCCCEEEEEeCCHHHHHHHHHHHHHcCCCCcEEEEECCcccCCccCCC
Confidence            444444 45567999999999999999998865 5678999984 566666542       4699999999885543   


Q ss_pred             CCEEEe
Q 039903          227 GDAILI  232 (233)
Q Consensus       227 ~D~~~l  232 (233)
                      .|++++
T Consensus       143 fD~Ii~  148 (205)
T PRK13944        143 FDAIIV  148 (205)
T ss_pred             ccEEEE
Confidence            298875

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

Probab=98.06  E-value=1.2e-05  Score=67.02  Aligned_cols=71  Identities=20%  Similarity=0.253  Sum_probs=53.3

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCC--CCCC-
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLE--RIPK-  226 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~--~~P~-  226 (233)
                      .+++.++  ++..+|+|||||+|.++..+++.  ..+++.+|+ |+.++.|++.       ++++++.+|+.+  +++. 
T Consensus        36 ~~l~~l~--~~~~~vLDiGcG~G~~a~~la~~--g~~v~~vD~s~~~l~~a~~~~~~~g~~~~v~~~~~d~~~l~~~~~~  111 (255)
T PRK11036         36 RLLAELP--PRPLRVLDAGGGEGQTAIKLAEL--GHQVILCDLSAEMIQRAKQAAEAKGVSDNMQFIHCAAQDIAQHLET  111 (255)
T ss_pred             HHHHhcC--CCCCEEEEeCCCchHHHHHHHHc--CCEEEEEECCHHHHHHHHHHHHhcCCccceEEEEcCHHHHhhhcCC
Confidence            3444443  44579999999999999999987  467899998 5677777642       579999999976  3443 


Q ss_pred             -CCEEEe
Q 039903          227 -GDAILI  232 (233)
Q Consensus       227 -~D~~~l  232 (233)
                       .|++++
T Consensus       112 ~fD~V~~  118 (255)
T PRK11036        112 PVDLILF  118 (255)
T ss_pred             CCCEEEe
Confidence             398875

>TIGR01934 MenG_MenH_UbiE ubiquinone/menaquinone biosynthesis methyltransferases

Probab=98.06  E-value=1.6e-05  Score=64.37  Aligned_cols=74  Identities=16%  Similarity=0.129  Sum_probs=57.0

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcCC-CcEEEeec-hHHHhhccCC----CCceEEecCcCC-CCCCC--C
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLH-IKGVNFDL-SHVIQDSSSY----SGVKHIGGIMLE-RIPKG--D  228 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~-l~~~v~Dl-p~v~~~a~~~----~ri~~~~gD~f~-~~P~~--D  228 (233)
                      .+++... ..+..+|+|+|||.|.++..+++++|. .+++++|. |..++.+++.    ++++++.+|+.+ +++.+  |
T Consensus        30 ~~~~~~~-~~~~~~vldiG~G~G~~~~~~~~~~~~~~~~~~iD~~~~~~~~~~~~~~~~~~i~~~~~d~~~~~~~~~~~D  108 (223)
T TIGR01934        30 RAVKLIG-VFKGQKVLDVACGTGDLAIELAKSAPDRGKVTGVDFSSEMLEVAKKKSELPLNIEFIQADAEALPFEDNSFD  108 (223)
T ss_pred             HHHHHhc-cCCCCeEEEeCCCCChhHHHHHHhcCCCceEEEEECCHHHHHHHHHHhccCCCceEEecchhcCCCCCCcEE
Confidence            3444444 446689999999999999999999997 88999998 4566666542    579999999998 55543  8


Q ss_pred             EEEe
Q 039903          229 AILI  232 (233)
Q Consensus       229 ~~~l  232 (233)
                      ++++
T Consensus       109 ~i~~  112 (223)
T TIGR01934       109 AVTI  112 (223)
T ss_pred             EEEE
Confidence            8764

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=98.03  E-value=1.8e-05  Score=68.64  Aligned_cols=65  Identities=23%  Similarity=0.278  Sum_probs=54.1

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC---CCceEEecCcCC-CCCCC--CEEEe
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY---SGVKHIGGIMLE-RIPKG--DAILI  232 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~---~ri~~~~gD~f~-~~P~~--D~~~l  232 (233)
                      ...+|||||||+|.++..+++.+|..+++++|+ ++.++.+++.   .+++++.+|+.+ +++.+  |+|+.
T Consensus       113 ~~~~VLDLGcGtG~~~l~La~~~~~~~VtgVD~S~~mL~~A~~k~~~~~i~~i~gD~e~lp~~~~sFDvVIs  184 (340)
T PLN02490        113 RNLKVVDVGGGTGFTTLGIVKHVDAKNVTILDQSPHQLAKAKQKEPLKECKIIEGDAEDLPFPTDYADRYVS  184 (340)
T ss_pred             CCCEEEEEecCCcHHHHHHHHHCCCCEEEEEECCHHHHHHHHHhhhccCCeEEeccHHhCCCCCCceeEEEE
Confidence            346899999999999999999999899999998 5567777653   579999999987 67653  98874

>PLN03075 nicotianamine synthase; Provisional

Probab=98.02  E-value=1.9e-05  Score=67.00  Aligned_cols=66  Identities=12%  Similarity=0.081  Sum_probs=50.5

Q ss_pred             cCcceEEEecCCccHH--HHHHHHHcCCCcEEEeech-HHHhhccCC--------CCceEEecCcCCCCC--CC-CEEEe
Q 039903          167 EQIKQLVDVGGGLGVN--VNIIISNYLHIKGVNFDLS-HVIQDSSSY--------SGVKHIGGIMLERIP--KG-DAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~--~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~--------~ri~~~~gD~f~~~P--~~-D~~~l  232 (233)
                      .+.++|+|||||.|-+  ...+++.+|+.+++.+|.. +.++.|++.        +||+|+.+|..+..+  .. |+|++
T Consensus       122 ~~p~~VldIGcGpgpltaiilaa~~~p~~~~~giD~d~~ai~~Ar~~~~~~~gL~~rV~F~~~Da~~~~~~l~~FDlVF~  201 (296)
T PLN03075        122 GVPTKVAFVGSGPLPLTSIVLAKHHLPTTSFHNFDIDPSANDVARRLVSSDPDLSKRMFFHTADVMDVTESLKEYDVVFL  201 (296)
T ss_pred             CCCCEEEEECCCCcHHHHHHHHHhcCCCCEEEEEeCCHHHHHHHHHHhhhccCccCCcEEEECchhhcccccCCcCEEEE
Confidence            4779999999998854  3334457899999999984 577666542        689999999998433  23 99986

>smart00138 MeTrc Methyltransferase, chemotaxis proteins

Probab=98.02  E-value=8.4e-05  Score=62.42  Aligned_cols=66  Identities=15%  Similarity=0.215  Sum_probs=50.4

Q ss_pred             cCcceEEEecCCccH----HHHHHHHHcC-----CCcEEEeech-HHHhhccCC--------------------------
Q 039903          167 EQIKQLVDVGGGLGV----NVNIIISNYL-----HIKGVNFDLS-HVIQDSSSY--------------------------  210 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~----~~~~l~~~~P-----~l~~~v~Dlp-~v~~~a~~~--------------------------  210 (233)
                      .+..+|+|+|||+|.    +++.+++.+|     +.+++..|+. ++++.|++.                          
T Consensus        98 ~~~~ri~d~GCgtGee~YslA~~l~e~~~~~~~~~~~I~g~Dis~~~L~~Ar~~~y~~~~~~~~~~~~~~~yf~~~~~~~  177 (264)
T smart00138       98 GRRVRIWSAGCSTGEEPYSLAMLLAETLPKAREPDVKILATDIDLKALEKARAGIYPERELEDLPKALLARYFSRVEDKY  177 (264)
T ss_pred             CCCEEEEeccccCChHHHHHHHHHHHHhhhcCCCCeEEEEEECCHHHHHHHHcCCCCHHHHhcCCHHHHhhhEEeCCCeE
Confidence            445799999999996    5666777765     5789999985 578877652                          


Q ss_pred             -------CCceEEecCcCC-CCCCC--CEEEe
Q 039903          211 -------SGVKHIGGIMLE-RIPKG--DAILI  232 (233)
Q Consensus       211 -------~ri~~~~gD~f~-~~P~~--D~~~l  232 (233)
                             ++|+|..+|+.+ +.|.+  |+|+.
T Consensus       178 ~v~~~ir~~V~F~~~dl~~~~~~~~~fD~I~c  209 (264)
T smart00138      178 RVKPELKERVRFAKHNLLAESPPLGDFDLIFC  209 (264)
T ss_pred             EEChHHhCcCEEeeccCCCCCCccCCCCEEEe
Confidence                   379999999999 44443  99875

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

>PRK06202 hypothetical protein; Provisional

Probab=98.02  E-value=4e-05  Score=62.95  Aligned_cols=66  Identities=17%  Similarity=0.107  Sum_probs=47.3

Q ss_pred             cCcceEEEecCCccHHHHHHHHH----cCCCcEEEeec-hHHHhhccCC---CCceEEecCcCC-CCCC--CCEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISN----YLHIKGVNFDL-SHVIQDSSSY---SGVKHIGGIMLE-RIPK--GDAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~----~P~l~~~v~Dl-p~v~~~a~~~---~ri~~~~gD~f~-~~P~--~D~~~l  232 (233)
                      .+..+|+|||||+|.++..|++.    .|+.+++.+|+ |+.++.+++.   .++++..+|.-. +.+.  .|+++.
T Consensus        59 ~~~~~iLDlGcG~G~~~~~L~~~~~~~g~~~~v~gvD~s~~~l~~a~~~~~~~~~~~~~~~~~~l~~~~~~fD~V~~  135 (232)
T PRK06202         59 DRPLTLLDIGCGGGDLAIDLARWARRDGLRLEVTAIDPDPRAVAFARANPRRPGVTFRQAVSDELVAEGERFDVVTS  135 (232)
T ss_pred             CCCcEEEEeccCCCHHHHHHHHHHHhCCCCcEEEEEcCCHHHHHHHHhccccCCCeEEEEecccccccCCCccEEEE
Confidence            45689999999999998888764    46789999998 5688877654   456665554322 2233  388875

>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=98.01  E-value=7.4e-06  Score=59.62  Aligned_cols=62  Identities=19%  Similarity=0.296  Sum_probs=51.2

Q ss_pred             ceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC-------CCceEEecCcCC-C--CCCC--CEEEe
Q 039903          170 KQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY-------SGVKHIGGIMLE-R--IPKG--DAILI  232 (233)
Q Consensus       170 ~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~-------~ri~~~~gD~f~-~--~P~~--D~~~l  232 (233)
                      .+|+|+|||+|.++..+++.. ..+++.+|+. ..++.++.+       +|++++.+|+++ .  ++..  |+|+.
T Consensus         2 ~~vlD~~~G~G~~~~~~~~~~-~~~~~gvdi~~~~~~~a~~~~~~~~~~~~~~~~~~D~~~~~~~~~~~~~D~Iv~   76 (117)
T PF13659_consen    2 DRVLDPGCGSGTFLLAALRRG-AARVTGVDIDPEAVELARRNLPRNGLDDRVEVIVGDARDLPEPLPDGKFDLIVT   76 (117)
T ss_dssp             EEEEEETSTTCHHHHHHHHHC-TCEEEEEESSHHHHHHHHHHCHHCTTTTTEEEEESHHHHHHHTCTTT-EEEEEE
T ss_pred             CEEEEcCcchHHHHHHHHHHC-CCeEEEEEECHHHHHHHHHHHHHccCCceEEEEECchhhchhhccCceeEEEEE
Confidence            579999999999999999998 8899999984 566766542       689999999997 3  5543  88875

...

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

Probab=98.00  E-value=1e-05  Score=66.78  Aligned_cols=74  Identities=14%  Similarity=0.180  Sum_probs=57.5

Q ss_pred             HHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccCC-------CCceEEecCcCC---CCCCC
Q 039903          159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSSY-------SGVKHIGGIMLE---RIPKG  227 (233)
Q Consensus       159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~~-------~ri~~~~gD~f~---~~P~~  227 (233)
                      ++..+.......+|+|+|+|.|..+..+++++++.+++.+|+.+ .++.|+++       +||+++..|+-+   ..+.+
T Consensus        35 LL~~~~~~~~~~~IlDlGaG~G~l~L~la~r~~~a~I~~VEiq~~~a~~A~~nv~ln~l~~ri~v~~~Di~~~~~~~~~~  114 (248)
T COG4123          35 LLAAFAPVPKKGRILDLGAGNGALGLLLAQRTEKAKIVGVEIQEEAAEMAQRNVALNPLEERIQVIEADIKEFLKALVFA  114 (248)
T ss_pred             HHHhhcccccCCeEEEecCCcCHHHHHHhccCCCCcEEEEEeCHHHHHHHHHHHHhCcchhceeEehhhHHHhhhccccc
Confidence            33443313447999999999999999999999999999999964 66677653       899999999987   23333


Q ss_pred             --CEEEe
Q 039903          228 --DAILI  232 (233)
Q Consensus       228 --D~~~l  232 (233)
                        |+|+.
T Consensus       115 ~fD~Ii~  121 (248)
T COG4123         115 SFDLIIC  121 (248)
T ss_pred             ccCEEEe
Confidence              78764

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

Probab=98.00  E-value=2.2e-05  Score=65.74  Aligned_cols=72  Identities=17%  Similarity=0.267  Sum_probs=54.8

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccC----CCCceEEecCcCC-CCCCCCEE
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSS----YSGVKHIGGIMLE-RIPKGDAI  230 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~----~~ri~~~~gD~f~-~~P~~D~~  230 (233)
                      ..+++.++ ..+..+++|||||.|.++..++++.  .+++++|+. ..++.+++    .++|+++.+|+++ ++|..|.+
T Consensus        19 ~~iv~~~~-~~~~~~VLEIG~G~G~lt~~L~~~~--~~v~~vEid~~~~~~l~~~~~~~~~v~ii~~D~~~~~~~~~d~V   95 (258)
T PRK14896         19 DRIVEYAE-DTDGDPVLEIGPGKGALTDELAKRA--KKVYAIELDPRLAEFLRDDEIAAGNVEIIEGDALKVDLPEFNKV   95 (258)
T ss_pred             HHHHHhcC-CCCcCeEEEEeCccCHHHHHHHHhC--CEEEEEECCHHHHHHHHHHhccCCCEEEEEeccccCCchhceEE
Confidence            44555555 5566899999999999999999984  478999986 45655543    3689999999998 66665665


Q ss_pred             E
Q 039903          231 L  231 (233)
Q Consensus       231 ~  231 (233)
                      +
T Consensus        96 v   96 (258)
T PRK14896         96 V   96 (258)
T ss_pred             E
Confidence            4

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

Probab=97.98  E-value=2.1e-05  Score=66.37  Aligned_cols=66  Identities=15%  Similarity=0.286  Sum_probs=51.7

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC---CCceEEecCcCC-CCC
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY---SGVKHIGGIMLE-RIP  225 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~---~ri~~~~gD~f~-~~P  225 (233)
                      ..+++.++ .....+|+|||||+|.++..++++.+  +++.+|.. ..++.+++.   ++++++.+|+.+ +++
T Consensus        32 ~~i~~~l~-~~~~~~VLEiG~G~G~lt~~L~~~~~--~v~avE~d~~~~~~~~~~~~~~~v~~i~~D~~~~~~~  102 (272)
T PRK00274         32 DKIVDAAG-PQPGDNVLEIGPGLGALTEPLLERAA--KVTAVEIDRDLAPILAETFAEDNLTIIEGDALKVDLS  102 (272)
T ss_pred             HHHHHhcC-CCCcCeEEEeCCCccHHHHHHHHhCC--cEEEEECCHHHHHHHHHhhccCceEEEEChhhcCCHH
Confidence            34555555 66668999999999999999999987  78889884 466666543   689999999987 544

>PHA03411 putative methyltransferase; Provisional

Probab=97.97  E-value=2.1e-05  Score=65.86  Aligned_cols=64  Identities=14%  Similarity=0.124  Sum_probs=53.1

Q ss_pred             cceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-CCceEEecCcCCCC-CC-CCEEEe
Q 039903          169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-SGVKHIGGIMLERI-PK-GDAILI  232 (233)
Q Consensus       169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-~ri~~~~gD~f~~~-P~-~D~~~l  232 (233)
                      ..+|+|+|||+|.++..++++.+..+++.+|+ |..++.++++ ++++++.+|+++.. +. -|+|+.
T Consensus        65 ~grVLDLGcGsGilsl~la~r~~~~~V~gVDisp~al~~Ar~n~~~v~~v~~D~~e~~~~~kFDlIIs  132 (279)
T PHA03411         65 TGKVLDLCAGIGRLSFCMLHRCKPEKIVCVELNPEFARIGKRLLPEAEWITSDVFEFESNEKFDVVIS  132 (279)
T ss_pred             CCeEEEcCCCCCHHHHHHHHhCCCCEEEEEECCHHHHHHHHHhCcCCEEEECchhhhcccCCCcEEEE
Confidence            46899999999999999999988889999998 4577777764 78999999999843 33 388875

>PLN02366 spermidine synthase

Probab=97.96  E-value=1.6e-05  Score=68.20  Aligned_cols=65  Identities=26%  Similarity=0.288  Sum_probs=51.6

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCC-CcEEEeechH-HHhhccCC----------CCceEEecCcCC---CCCC-C-CE
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLH-IKGVNFDLSH-VIQDSSSY----------SGVKHIGGIMLE---RIPK-G-DA  229 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~-l~~~v~Dlp~-v~~~a~~~----------~ri~~~~gD~f~---~~P~-~-D~  229 (233)
                      ++.++||+||||.|..+.++++. |. .+++++|+.+ |++.++++          +|++++.+|.++   ..|. . |+
T Consensus        90 ~~pkrVLiIGgG~G~~~rellk~-~~v~~V~~VEiD~~Vi~~ar~~f~~~~~~~~dpRv~vi~~Da~~~l~~~~~~~yDv  168 (308)
T PLN02366         90 PNPKKVLVVGGGDGGVLREIARH-SSVEQIDICEIDKMVIDVSKKFFPDLAVGFDDPRVNLHIGDGVEFLKNAPEGTYDA  168 (308)
T ss_pred             CCCCeEEEEcCCccHHHHHHHhC-CCCCeEEEEECCHHHHHHHHHhhhhhccccCCCceEEEEChHHHHHhhccCCCCCE
Confidence            56789999999999999999865 65 5789999865 78877652          699999999764   4444 3 99


Q ss_pred             EEe
Q 039903          230 ILI  232 (233)
Q Consensus       230 ~~l  232 (233)
                      |++
T Consensus       169 Ii~  171 (308)
T PLN02366        169 IIV  171 (308)
T ss_pred             EEE
Confidence            875

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

Probab=97.92  E-value=6.7e-05  Score=61.67  Aligned_cols=64  Identities=23%  Similarity=0.262  Sum_probs=54.9

Q ss_pred             cceEEEecCCccHHHHHHHHHcCC------CcEEEeec-hHHHhhccCC---------CCceEEecCcCC-CCCCC--CE
Q 039903          169 IKQLVDVGGGLGVNVNIIISNYLH------IKGVNFDL-SHVIQDSSSY---------SGVKHIGGIMLE-RIPKG--DA  229 (233)
Q Consensus       169 ~~~vvDvGGG~G~~~~~l~~~~P~------l~~~v~Dl-p~v~~~a~~~---------~ri~~~~gD~f~-~~P~~--D~  229 (233)
                      .-++|||+||+|..+-.+++.-+.      -+++++|+ |+.++.+++.         .|+.++.+|.-+ |+|..  |.
T Consensus       101 ~m~~lDvaGGTGDiaFril~~v~s~~~~~~~~V~v~Dinp~mL~vgkqRa~~~~l~~~~~~~w~~~dAE~LpFdd~s~D~  180 (296)
T KOG1540|consen  101 GMKVLDVAGGTGDIAFRILRHVKSQFGDRESKVTVLDINPHMLAVGKQRAKKRPLKASSRVEWVEGDAEDLPFDDDSFDA  180 (296)
T ss_pred             CCeEEEecCCcchhHHHHHHhhccccCCCCceEEEEeCCHHHHHHHHHHHhhcCCCcCCceEEEeCCcccCCCCCCccee
Confidence            378999999999999999999888      78999998 6777766542         469999999999 99984  99


Q ss_pred             EEe
Q 039903          230 ILI  232 (233)
Q Consensus       230 ~~l  232 (233)
                      |.+
T Consensus       181 yTi  183 (296)
T KOG1540|consen  181 YTI  183 (296)
T ss_pred             EEE
Confidence            986

>TIGR00537 hemK_rel_arch HemK-related putative methylase

Probab=97.89  E-value=3.7e-05  Score=60.61  Aligned_cols=63  Identities=13%  Similarity=0.207  Sum_probs=49.8

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-----CCceEEecCcCCCCCC-CCEEEe
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-----SGVKHIGGIMLERIPK-GDAILI  232 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-----~ri~~~~gD~f~~~P~-~D~~~l  232 (233)
                      +..+++|+|||+|.++..+++..+  +++.+|+ |..++.++.+     -+++++.+|+++..+. .|+++.
T Consensus        19 ~~~~vLdlG~G~G~~~~~l~~~~~--~v~~vD~s~~~~~~a~~~~~~~~~~~~~~~~d~~~~~~~~fD~Vi~   88 (179)
T TIGR00537        19 KPDDVLEIGAGTGLVAIRLKGKGK--CILTTDINPFAVKELRENAKLNNVGLDVVMTDLFKGVRGKFDVILF   88 (179)
T ss_pred             CCCeEEEeCCChhHHHHHHHhcCC--EEEEEECCHHHHHHHHHHHHHcCCceEEEEcccccccCCcccEEEE
Confidence            346899999999999999999887  7999998 5677766553     3688899999884443 488874

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.

>PRK07580 Mg-protoporphyrin IX methyl transferase; Validated

Probab=97.87  E-value=4.7e-05  Score=62.15  Aligned_cols=63  Identities=17%  Similarity=0.196  Sum_probs=47.4

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCCCCCC-CCEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLERIPK-GDAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~~P~-~D~~~l  232 (233)
                      .+..+|+|||||+|.++..++++.+  +++.+|+ +..++.+++.       ++|+++.+| ++..+. -|+++.
T Consensus        62 ~~~~~vLDvGcG~G~~~~~l~~~~~--~v~~~D~s~~~i~~a~~~~~~~~~~~~i~~~~~d-~~~~~~~fD~v~~  133 (230)
T PRK07580         62 LTGLRILDAGCGVGSLSIPLARRGA--KVVASDISPQMVEEARERAPEAGLAGNITFEVGD-LESLLGRFDTVVC  133 (230)
T ss_pred             CCCCEEEEEeCCCCHHHHHHHHcCC--EEEEEECCHHHHHHHHHHHHhcCCccCcEEEEcC-chhccCCcCEEEE
Confidence            4557999999999999999998765  4999998 4577766542       489999999 443233 387763

>PRK00811 spermidine synthase; Provisional

Probab=97.85  E-value=2.4e-05  Score=66.32  Aligned_cols=66  Identities=17%  Similarity=0.236  Sum_probs=52.0

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccC-----------CCCceEEecCcCCCC--CC-C-CEE
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSS-----------YSGVKHIGGIMLERI--PK-G-DAI  230 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~-----------~~ri~~~~gD~f~~~--P~-~-D~~  230 (233)
                      ++.++|+|||||.|..+..+++..+..+++++|+ |.+++.+++           .+||+++.+|.++-+  +. . |+|
T Consensus        75 ~~p~~VL~iG~G~G~~~~~~l~~~~~~~V~~VEid~~vv~~a~~~~~~~~~~~~~d~rv~v~~~Da~~~l~~~~~~yDvI  154 (283)
T PRK00811         75 PNPKRVLIIGGGDGGTLREVLKHPSVEKITLVEIDERVVEVCRKYLPEIAGGAYDDPRVELVIGDGIKFVAETENSFDVI  154 (283)
T ss_pred             CCCCEEEEEecCchHHHHHHHcCCCCCEEEEEeCCHHHHHHHHHHhHHhccccccCCceEEEECchHHHHhhCCCcccEE
Confidence            4568999999999999999997645568999998 457777764           268999999988722  33 3 998


Q ss_pred             Ee
Q 039903          231 LI  232 (233)
Q Consensus       231 ~l  232 (233)
                      ++
T Consensus       155 i~  156 (283)
T PRK00811        155 IV  156 (283)
T ss_pred             EE
Confidence            75

>PRK05785 hypothetical protein; Provisional

Probab=97.85  E-value=3.8e-05  Score=63.04  Aligned_cols=62  Identities=15%  Similarity=0.180  Sum_probs=50.1

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCCCCceEEecCcCC-CCCCC--CEEEe
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSYSGVKHIGGIMLE-RIPKG--DAILI  232 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~~ri~~~~gD~f~-~~P~~--D~~~l  232 (233)
                      ...+|+|||||+|.++..+++++ +.+++.+|. ++.++.|++.  ..++.+|+.+ |+|..  |+++.
T Consensus        51 ~~~~VLDlGcGtG~~~~~l~~~~-~~~v~gvD~S~~Ml~~a~~~--~~~~~~d~~~lp~~d~sfD~v~~  116 (226)
T PRK05785         51 RPKKVLDVAAGKGELSYHFKKVF-KYYVVALDYAENMLKMNLVA--DDKVVGSFEALPFRDKSFDVVMS  116 (226)
T ss_pred             CCCeEEEEcCCCCHHHHHHHHhc-CCEEEEECCCHHHHHHHHhc--cceEEechhhCCCCCCCEEEEEe
Confidence            35799999999999999999987 678999998 5688877653  3567888887 77764  98874

>PRK11188 rrmJ 23S rRNA methyltransferase J; Provisional

Probab=97.82  E-value=0.0001  Score=59.75  Aligned_cols=60  Identities=20%  Similarity=0.234  Sum_probs=46.2

Q ss_pred             HHHhcccccCcceEEEecCCccHHHHHHHHHc-CCCcEEEeechHHHhhccCCCCceEEecCcCC
Q 039903          159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNY-LHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLE  222 (233)
Q Consensus       159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~-P~l~~~v~Dlp~v~~~a~~~~ri~~~~gD~f~  222 (233)
                      +.+.+..+++..+|||||||+|.++..++++. |..+++.+|+.+.    ...++|+++.+|+.+
T Consensus        42 ~~~~~~~~~~~~~VLDlG~GtG~~t~~l~~~~~~~~~V~aVDi~~~----~~~~~v~~i~~D~~~  102 (209)
T PRK11188         42 IQQSDKLFKPGMTVVDLGAAPGGWSQYAVTQIGDKGRVIACDILPM----DPIVGVDFLQGDFRD  102 (209)
T ss_pred             HHHHhccCCCCCEEEEEcccCCHHHHHHHHHcCCCceEEEEecccc----cCCCCcEEEecCCCC
Confidence            33444424566799999999999999999987 4578999998662    223579999999987

>TIGR00477 tehB tellurite resistance protein TehB

Probab=97.81  E-value=9.6e-05  Score=59.20  Aligned_cols=73  Identities=14%  Similarity=0.074  Sum_probs=51.6

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC-----CCceEEecCcCC-CCCCC-C
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY-----SGVKHIGGIMLE-RIPKG-D  228 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~-----~ri~~~~gD~f~-~~P~~-D  228 (233)
                      ..+++.++ .....+++|||||+|.++..++++  ..+++.+|+. ..++.+++.     -++++..+|+.. +++.. |
T Consensus        20 ~~l~~~~~-~~~~~~vLDiGcG~G~~a~~la~~--g~~V~~iD~s~~~l~~a~~~~~~~~~~v~~~~~d~~~~~~~~~fD   96 (195)
T TIGR00477        20 SAVREAVK-TVAPCKTLDLGCGQGRNSLYLSLA--GYDVRAWDHNPASIASVLDMKARENLPLRTDAYDINAAALNEDYD   96 (195)
T ss_pred             HHHHHHhc-cCCCCcEEEeCCCCCHHHHHHHHC--CCeEEEEECCHHHHHHHHHHHHHhCCCceeEeccchhccccCCCC
Confidence            34555555 445679999999999999999986  5689999984 466655431     247777888765 44443 8


Q ss_pred             EEEe
Q 039903          229 AILI  232 (233)
Q Consensus       229 ~~~l  232 (233)
                      +++.
T Consensus        97 ~I~~  100 (195)
T TIGR00477        97 FIFS  100 (195)
T ss_pred             EEEE
Confidence            8763

Part of a tellurite-reducing operon tehA and tehB

>TIGR00755 ksgA dimethyladenosine transferase

Probab=97.81  E-value=6.3e-05  Score=62.72  Aligned_cols=69  Identities=14%  Similarity=0.305  Sum_probs=52.7

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccC----CCCceEEecCcCC-CCCCCC
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSS----YSGVKHIGGIMLE-RIPKGD  228 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~----~~ri~~~~gD~f~-~~P~~D  228 (233)
                      ..+++.++ ..+..+|+|||||.|.++..++++.+.  ++.+|.. ..++.++.    .++++++.+|+.+ +++..|
T Consensus        19 ~~i~~~~~-~~~~~~VLEiG~G~G~lt~~L~~~~~~--v~~iE~d~~~~~~l~~~~~~~~~v~v~~~D~~~~~~~~~d   93 (253)
T TIGR00755        19 QKIVEAAN-VLEGDVVLEIGPGLGALTEPLLKRAKK--VTAIEIDPRLAEILRKLLSLYERLEVIEGDALKVDLPDFP   93 (253)
T ss_pred             HHHHHhcC-CCCcCEEEEeCCCCCHHHHHHHHhCCc--EEEEECCHHHHHHHHHHhCcCCcEEEEECchhcCChhHcC
Confidence            45556665 667789999999999999999999875  8888874 45555543    3689999999998 665434

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

>PRK11873 arsM arsenite S-adenosylmethyltransferase; Reviewed

Probab=97.80  E-value=5.3e-05  Score=63.75  Aligned_cols=67  Identities=15%  Similarity=0.243  Sum_probs=53.2

Q ss_pred             ccCcceEEEecCCccHHHHHHHHH-cCCCcEEEeec-hHHHhhccCC------CCceEEecCcCC-CCCCC--CEEEe
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISN-YLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLE-RIPKG--DAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~-~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~-~~P~~--D~~~l  232 (233)
                      .....+|||||||+|..+..+++. .|+.+++.+|+ |..++.++++      ++++++.+|+.+ ++|.+  |+++.
T Consensus        75 ~~~g~~VLDiG~G~G~~~~~~a~~~g~~~~v~gvD~s~~~l~~A~~~~~~~g~~~v~~~~~d~~~l~~~~~~fD~Vi~  152 (272)
T PRK11873         75 LKPGETVLDLGSGGGFDCFLAARRVGPTGKVIGVDMTPEMLAKARANARKAGYTNVEFRLGEIEALPVADNSVDVIIS  152 (272)
T ss_pred             CCCCCEEEEeCCCCCHHHHHHHHHhCCCCEEEEECCCHHHHHHHHHHHHHcCCCCEEEEEcchhhCCCCCCceeEEEE
Confidence            556689999999999988877776 46678999998 5677777652      689999999887 67653  88863

>PHA03412 putative methyltransferase; Provisional

Probab=97.79  E-value=5.8e-05  Score=61.89  Aligned_cols=64  Identities=14%  Similarity=0.074  Sum_probs=52.0

Q ss_pred             cceEEEecCCccHHHHHHHHHc---CCCcEEEeech-HHHhhccCC-CCceEEecCcCC-CCCC-CCEEEe
Q 039903          169 IKQLVDVGGGLGVNVNIIISNY---LHIKGVNFDLS-HVIQDSSSY-SGVKHIGGIMLE-RIPK-GDAILI  232 (233)
Q Consensus       169 ~~~vvDvGGG~G~~~~~l~~~~---P~l~~~v~Dlp-~v~~~a~~~-~ri~~~~gD~f~-~~P~-~D~~~l  232 (233)
                      ..+|||+|||+|.++..++++.   +..+++.+|+. .+++.|+.+ .++.++.+|++. +++. -|+|+.
T Consensus        50 ~grVLDlG~GSG~Lalala~~~~~~~~~~V~aVEID~~Al~~Ar~n~~~~~~~~~D~~~~~~~~~FDlIIs  120 (241)
T PHA03412         50 SGSVVDLCAGIGGLSFAMVHMMMYAKPREIVCVELNHTYYKLGKRIVPEATWINADALTTEFDTLFDMAIS  120 (241)
T ss_pred             CCEEEEccChHHHHHHHHHHhcccCCCcEEEEEECCHHHHHHHHhhccCCEEEEcchhcccccCCccEEEE
Confidence            4699999999999999999875   46789999995 477778765 789999999987 4443 398874

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

Probab=97.78  E-value=4.1e-05  Score=60.80  Aligned_cols=68  Identities=18%  Similarity=0.289  Sum_probs=52.0

Q ss_pred             hcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccC----CCCceEEecCcCCCCCCC--CEEEe
Q 039903          162 SSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSS----YSGVKHIGGIMLERIPKG--DAILI  232 (233)
Q Consensus       162 ~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~----~~ri~~~~gD~f~~~P~~--D~~~l  232 (233)
                      .++ -..+.++++||||.|.++..|+.++-  +.++.|. |.+++.|++    .++|+++..|+-+..|.+  |+|++
T Consensus        38 aLp-~~ry~~alEvGCs~G~lT~~LA~rCd--~LlavDis~~Al~~Ar~Rl~~~~~V~~~~~dvp~~~P~~~FDLIV~  112 (201)
T PF05401_consen   38 ALP-RRRYRRALEVGCSIGVLTERLAPRCD--RLLAVDISPRALARARERLAGLPHVEWIQADVPEFWPEGRFDLIVL  112 (201)
T ss_dssp             HHT-TSSEEEEEEE--TTSHHHHHHGGGEE--EEEEEES-HHHHHHHHHHTTT-SSEEEEES-TTT---SS-EEEEEE
T ss_pred             hcC-ccccceeEecCCCccHHHHHHHHhhC--ceEEEeCCHHHHHHHHHhcCCCCCeEEEECcCCCCCCCCCeeEEEE
Confidence            456 56778999999999999999999973  5899998 668888865    378999999998888875  99986

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.

>PRK01581 speE spermidine synthase; Validated

Probab=97.75  E-value=6e-05  Score=65.58  Aligned_cols=67  Identities=19%  Similarity=0.163  Sum_probs=52.8

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccC-------------CCCceEEecCcCCCC---CCC-
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSS-------------YSGVKHIGGIMLERI---PKG-  227 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~-------------~~ri~~~~gD~f~~~---P~~-  227 (233)
                      ..+.++|++||||.|..+.++++..|..+++++|+. ++++.|++             .+|++++.+|.++-+   +.. 
T Consensus       148 h~~PkrVLIIGgGdG~tlrelLk~~~v~~It~VEIDpeVIelAr~~~~L~~~~~~~~~DpRV~vvi~Da~~fL~~~~~~Y  227 (374)
T PRK01581        148 VIDPKRVLILGGGDGLALREVLKYETVLHVDLVDLDGSMINMARNVPELVSLNKSAFFDNRVNVHVCDAKEFLSSPSSLY  227 (374)
T ss_pred             CCCCCEEEEECCCHHHHHHHHHhcCCCCeEEEEeCCHHHHHHHHhccccchhccccCCCCceEEEECcHHHHHHhcCCCc
Confidence            356789999999999999999986556789999984 57887774             279999999999732   223 


Q ss_pred             CEEEe
Q 039903          228 DAILI  232 (233)
Q Consensus       228 D~~~l  232 (233)
                      |+|++
T Consensus       228 DVIIv  232 (374)
T PRK01581        228 DVIII  232 (374)
T ss_pred             cEEEE
Confidence            88875

>PRK15068 tRNA mo(5)U34 methyltransferase; Provisional

Probab=97.74  E-value=0.00012  Score=63.19  Aligned_cols=71  Identities=14%  Similarity=0.119  Sum_probs=50.8

Q ss_pred             HHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhcc-------CCCCceEEecCcCC-CCCCC-CE
Q 039903          160 IDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSS-------SYSGVKHIGGIMLE-RIPKG-DA  229 (233)
Q Consensus       160 ~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~-------~~~ri~~~~gD~f~-~~P~~-D~  229 (233)
                      +..++.++ .++|+|||||+|.++..+++..|. +++++|... .+..++       ...+|+++.+|+.+ +.+.. |+
T Consensus       115 ~~~l~~l~-g~~VLDIGCG~G~~~~~la~~g~~-~V~GiD~S~~~l~q~~a~~~~~~~~~~i~~~~~d~e~lp~~~~FD~  192 (322)
T PRK15068        115 LPHLSPLK-GRTVLDVGCGNGYHMWRMLGAGAK-LVVGIDPSQLFLCQFEAVRKLLGNDQRAHLLPLGIEQLPALKAFDT  192 (322)
T ss_pred             HHhhCCCC-CCEEEEeccCCcHHHHHHHHcCCC-EEEEEcCCHHHHHHHHHHHHhcCCCCCeEEEeCCHHHCCCcCCcCE
Confidence            34443233 479999999999999999999877 499999654 222211       12589999999877 55554 98


Q ss_pred             EEe
Q 039903          230 ILI  232 (233)
Q Consensus       230 ~~l  232 (233)
                      |+.
T Consensus       193 V~s  195 (322)
T PRK15068        193 VFS  195 (322)
T ss_pred             EEE
Confidence            874

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

Probab=97.74  E-value=0.0001  Score=61.99  Aligned_cols=64  Identities=17%  Similarity=0.158  Sum_probs=52.3

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccC-------CCCceEEecCcCC
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSS-------YSGVKHIGGIMLE  222 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~-------~~ri~~~~gD~f~  222 (233)
                      ..+++.+. +++..+|||||||-|.+++..+++| +.+++.+++.+ ..+.+++       .++|++...|+-+
T Consensus        62 ~~~~~kl~-L~~G~~lLDiGCGWG~l~~~aA~~y-~v~V~GvTlS~~Q~~~~~~r~~~~gl~~~v~v~l~d~rd  133 (283)
T COG2230          62 DLILEKLG-LKPGMTLLDIGCGWGGLAIYAAEEY-GVTVVGVTLSEEQLAYAEKRIAARGLEDNVEVRLQDYRD  133 (283)
T ss_pred             HHHHHhcC-CCCCCEEEEeCCChhHHHHHHHHHc-CCEEEEeeCCHHHHHHHHHHHHHcCCCcccEEEeccccc
Confidence            45677777 8999999999999999999999999 99999999853 4444443       1578888888765

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

Probab=97.73  E-value=0.00012  Score=58.78  Aligned_cols=71  Identities=20%  Similarity=0.124  Sum_probs=53.7

Q ss_pred             HhcccccCcceEEEecCCccHHHHHHHHHc-CCCcEEEeec-hHHHhhccCC-------CCceEEecCcCCC---CCC-C
Q 039903          161 DSSKGFEQIKQLVDVGGGLGVNVNIIISNY-LHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLER---IPK-G  227 (233)
Q Consensus       161 ~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~---~P~-~  227 (233)
                      ..++ .....+++|+|||+|.++..+++.. |..+++.+|+ |+.++.++++       ++++++.+|+.+.   .+. .
T Consensus        34 ~~l~-~~~~~~vlDlG~GtG~~s~~~a~~~~~~~~v~avD~~~~~~~~a~~n~~~~g~~~~v~~~~~d~~~~l~~~~~~~  112 (198)
T PRK00377         34 SKLR-LRKGDMILDIGCGTGSVTVEASLLVGETGKVYAVDKDEKAINLTRRNAEKFGVLNNIVLIKGEAPEILFTINEKF  112 (198)
T ss_pred             HHcC-CCCcCEEEEeCCcCCHHHHHHHHHhCCCCEEEEEECCHHHHHHHHHHHHHhCCCCCeEEEEechhhhHhhcCCCC
Confidence            3344 5666899999999999999998864 6789999998 6677766432       5789999999762   222 4


Q ss_pred             CEEEe
Q 039903          228 DAILI  232 (233)
Q Consensus       228 D~~~l  232 (233)
                      |++++
T Consensus       113 D~V~~  117 (198)
T PRK00377        113 DRIFI  117 (198)
T ss_pred             CEEEE
Confidence            88875

>PRK14967 putative methyltransferase; Provisional

Probab=97.71  E-value=8.8e-05  Score=60.62  Aligned_cols=66  Identities=12%  Similarity=0.081  Sum_probs=50.4

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC-----CCceEEecCcCCCCCC-C-CEEEe
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY-----SGVKHIGGIMLERIPK-G-DAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~-----~ri~~~~gD~f~~~P~-~-D~~~l  232 (233)
                      .....+++|+|||+|.++..+++. +..+++.+|+. ..++.++++     -+++++.+|+++.++. . |+|+.
T Consensus        34 ~~~~~~vLDlGcG~G~~~~~la~~-~~~~v~~vD~s~~~l~~a~~n~~~~~~~~~~~~~d~~~~~~~~~fD~Vi~  107 (223)
T PRK14967         34 LGPGRRVLDLCTGSGALAVAAAAA-GAGSVTAVDISRRAVRSARLNALLAGVDVDVRRGDWARAVEFRPFDVVVS  107 (223)
T ss_pred             cCCCCeEEEecCCHHHHHHHHHHc-CCCeEEEEECCHHHHHHHHHHHHHhCCeeEEEECchhhhccCCCeeEEEE
Confidence            455579999999999999998876 44588999985 466655542     3588899999886664 3 98875

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

Probab=97.71  E-value=0.00017  Score=58.37  Aligned_cols=71  Identities=13%  Similarity=0.208  Sum_probs=52.3

Q ss_pred             HHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCCCCCC-C--C
Q 039903          159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLERIPK-G--D  228 (233)
Q Consensus       159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~~P~-~--D  228 (233)
                      ++..++ ..+..+|+|||||+|.++..+++...  +++.+|. |+.++.++++      .+|+++.+|+++.+|. +  |
T Consensus        70 l~~~l~-~~~~~~VLeiG~GsG~~t~~la~~~~--~v~~vd~~~~~~~~a~~~~~~~~~~~v~~~~~d~~~~~~~~~~fD  146 (212)
T PRK00312         70 MTELLE-LKPGDRVLEIGTGSGYQAAVLAHLVR--RVFSVERIKTLQWEAKRRLKQLGLHNVSVRHGDGWKGWPAYAPFD  146 (212)
T ss_pred             HHHhcC-CCCCCEEEEECCCccHHHHHHHHHhC--EEEEEeCCHHHHHHHHHHHHHCCCCceEEEECCcccCCCcCCCcC
Confidence            344444 56678999999999999988887754  6788887 4566666542      5699999999886553 2  9


Q ss_pred             EEEe
Q 039903          229 AILI  232 (233)
Q Consensus       229 ~~~l  232 (233)
                      ++++
T Consensus       147 ~I~~  150 (212)
T PRK00312        147 RILV  150 (212)
T ss_pred             EEEE
Confidence            8875

>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=97.71  E-value=7.8e-05  Score=62.88  Aligned_cols=73  Identities=15%  Similarity=0.082  Sum_probs=47.6

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccC-------CCCceEEecCcCCCCCCCC
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSS-------YSGVKHIGGIMLERIPKGD  228 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~-------~~ri~~~~gD~f~~~P~~D  228 (233)
                      ..+++.++ .+...+|||||||-|.+++.++++| +++++.+.+.+ -.+.+++       .++|++...|+.+--+.-|
T Consensus        52 ~~~~~~~~-l~~G~~vLDiGcGwG~~~~~~a~~~-g~~v~gitlS~~Q~~~a~~~~~~~gl~~~v~v~~~D~~~~~~~fD  129 (273)
T PF02353_consen   52 DLLCEKLG-LKPGDRVLDIGCGWGGLAIYAAERY-GCHVTGITLSEEQAEYARERIREAGLEDRVEVRLQDYRDLPGKFD  129 (273)
T ss_dssp             HHHHTTTT---TT-EEEEES-TTSHHHHHHHHHH---EEEEEES-HHHHHHHHHHHHCSTSSSTEEEEES-GGG---S-S
T ss_pred             HHHHHHhC-CCCCCEEEEeCCCccHHHHHHHHHc-CcEEEEEECCHHHHHHHHHHHHhcCCCCceEEEEeeccccCCCCC
Confidence            45667776 7888999999999999999999999 88999999854 4444432       2789999999876222236


Q ss_pred             EEE
Q 039903          229 AIL  231 (233)
Q Consensus       229 ~~~  231 (233)
                      .|+
T Consensus       130 ~Iv  132 (273)
T PF02353_consen  130 RIV  132 (273)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            654

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 ....

>PLN02672 methionine S-methyltransferase

Probab=97.70  E-value=5.1e-05  Score=74.39  Aligned_cols=62  Identities=19%  Similarity=0.202  Sum_probs=51.0

Q ss_pred             ceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC----------------------CCceEEecCcCCCCCC
Q 039903          170 KQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY----------------------SGVKHIGGIMLERIPK  226 (233)
Q Consensus       170 ~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~----------------------~ri~~~~gD~f~~~P~  226 (233)
                      .+|+|||||+|..++.+++++|+.+++.+|+ |.+++.|+++                      +||+++.+|+++.++.
T Consensus       120 ~~VLDlG~GSG~Iai~La~~~~~~~v~avDis~~Al~~A~~Na~~n~l~~~~~~~~~~~~~~l~~rV~f~~sDl~~~~~~  199 (1082)
T PLN02672        120 KTVAELGCGNGWISIAIAEKWLPSKVYGLDINPRAVKVAWINLYLNALDDDGLPVYDGEGKTLLDRVEFYESDLLGYCRD  199 (1082)
T ss_pred             CEEEEEecchHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHcCcccccccccccccccccccEEEEECchhhhccc
Confidence            5899999999999999999999999999998 4577666321                      4799999999986642


Q ss_pred             ----CCEEE
Q 039903          227 ----GDAIL  231 (233)
Q Consensus       227 ----~D~~~  231 (233)
                          -|+|+
T Consensus       200 ~~~~fDlIV  208 (1082)
T PLN02672        200 NNIELDRIV  208 (1082)
T ss_pred             cCCceEEEE
Confidence                27765

>PRK14968 putative methyltransferase; Provisional

Probab=97.69  E-value=0.00011  Score=57.86  Aligned_cols=64  Identities=22%  Similarity=0.295  Sum_probs=50.3

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CC-ceEEecCcCCCCCC--CCEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SG-VKHIGGIMLERIPK--GDAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~r-i~~~~gD~f~~~P~--~D~~~l  232 (233)
                      .+..+++|+|||+|.++..++++  ..+++.+|+ |++++.++++       ++ +.++.+|++++++.  .|+++.
T Consensus        22 ~~~~~vLd~G~G~G~~~~~l~~~--~~~v~~~D~s~~~~~~a~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~d~vi~   96 (188)
T PRK14968         22 KKGDRVLEVGTGSGIVAIVAAKN--GKKVVGVDINPYAVECAKCNAKLNNIRNNGVEVIRSDLFEPFRGDKFDVILF   96 (188)
T ss_pred             cCCCEEEEEccccCHHHHHHHhh--cceEEEEECCHHHHHHHHHHHHHcCCCCcceEEEeccccccccccCceEEEE
Confidence            45578999999999999999998  578999998 4577766432       23 89999999987665  388764

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

Probab=97.67  E-value=0.00012  Score=62.32  Aligned_cols=76  Identities=16%  Similarity=0.161  Sum_probs=59.0

Q ss_pred             HHHHHHhcccccCcceEEEecCCccHHHHHHHHHcC-CCcEEEeec-hHHHhhccCC----CCceEEecCcCC---CCCC
Q 039903          156 TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDL-SHVIQDSSSY----SGVKHIGGIMLE---RIPK  226 (233)
Q Consensus       156 ~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~v~~~a~~~----~ri~~~~gD~f~---~~P~  226 (233)
                      ..++++.+. -....++||++||.|.++..++++.| +.+++.+|. |++++.+++.    +||+++.+||-+   ..+.
T Consensus         8 l~Evl~~L~-~~pg~~vlD~TlG~GGhS~~il~~~~~~g~VigiD~D~~al~~ak~~L~~~~ri~~i~~~f~~l~~~l~~   86 (296)
T PRK00050          8 LDEVVDALA-IKPDGIYVDGTFGGGGHSRAILERLGPKGRLIAIDRDPDAIAAAKDRLKPFGRFTLVHGNFSNLKEVLAE   86 (296)
T ss_pred             HHHHHHhhC-CCCCCEEEEeCcCChHHHHHHHHhCCCCCEEEEEcCCHHHHHHHHHhhccCCcEEEEeCCHHHHHHHHHc
Confidence            456667665 44557999999999999999999996 789999998 5677777652    589999999986   1322


Q ss_pred             ----CCEEEe
Q 039903          227 ----GDAILI  232 (233)
Q Consensus       227 ----~D~~~l  232 (233)
                          -|.+++
T Consensus        87 ~~~~vDgIl~   96 (296)
T PRK00050         87 GLGKVDGILL   96 (296)
T ss_pred             CCCccCEEEE
Confidence                377765

>PRK12335 tellurite resistance protein TehB; Provisional

Probab=97.63  E-value=0.00015  Score=61.55  Aligned_cols=72  Identities=14%  Similarity=0.150  Sum_probs=52.2

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC-----CCceEEecCcCC-CCCCC-CE
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY-----SGVKHIGGIMLE-RIPKG-DA  229 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~-----~ri~~~~gD~f~-~~P~~-D~  229 (233)
                      .++..++ ..+..++||||||+|.++..++++  ..+++.+|.. .+++.+++.     -++++..+|+.. .++.. |+
T Consensus       111 ~~~~~~~-~~~~~~vLDlGcG~G~~~~~la~~--g~~V~avD~s~~ai~~~~~~~~~~~l~v~~~~~D~~~~~~~~~fD~  187 (287)
T PRK12335        111 EVLEAVQ-TVKPGKALDLGCGQGRNSLYLALL--GFDVTAVDINQQSLENLQEIAEKENLNIRTGLYDINSASIQEEYDF  187 (287)
T ss_pred             HHHHHhh-ccCCCCEEEeCCCCCHHHHHHHHC--CCEEEEEECCHHHHHHHHHHHHHcCCceEEEEechhcccccCCccE
Confidence            4445444 344569999999999999999885  5789999985 566655432     368888889877 44443 98


Q ss_pred             EEe
Q 039903          230 ILI  232 (233)
Q Consensus       230 ~~l  232 (233)
                      ++.
T Consensus       188 I~~  190 (287)
T PRK12335        188 ILS  190 (287)
T ss_pred             EEE
Confidence            864

>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=97.63  E-value=2.8e-05  Score=48.58  Aligned_cols=46  Identities=24%  Similarity=0.386  Sum_probs=40.4

Q ss_pred             hChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           19 LGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        19 lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      +.|++.|...+  ++.|+.|||+++|+    +...+.|+|..|+..|+++++
T Consensus         6 l~iL~~l~~~~--~~~t~~eia~~~gl----~~stv~r~L~tL~~~g~v~~d   51 (52)
T PF09339_consen    6 LRILEALAESG--GPLTLSEIARALGL----PKSTVHRLLQTLVEEGYVERD   51 (52)
T ss_dssp             HHHHHCHHCTB--SCEEHHHHHHHHTS-----HHHHHHHHHHHHHTTSEEEC
T ss_pred             HHHHHHHHcCC--CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCcCeecC
Confidence            45788888875  57899999999999    999999999999999999984

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.

>PLN02396 hexaprenyldihydroxybenzoate methyltransferase

Probab=97.63  E-value=8.1e-05  Score=64.20  Aligned_cols=62  Identities=15%  Similarity=0.091  Sum_probs=47.8

Q ss_pred             cceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC-------CCceEEecCcCC-CCCC--CCEEEe
Q 039903          169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY-------SGVKHIGGIMLE-RIPK--GDAILI  232 (233)
Q Consensus       169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~-------~ri~~~~gD~f~-~~P~--~D~~~l  232 (233)
                      ..+|||||||.|.++..+++  ++.+++.+|.. +.++.|+.+       .+|+++.+|+-+ +.+.  .|+++.
T Consensus       132 g~~ILDIGCG~G~~s~~La~--~g~~V~GID~s~~~i~~Ar~~~~~~~~~~~i~~~~~dae~l~~~~~~FD~Vi~  204 (322)
T PLN02396        132 GLKFIDIGCGGGLLSEPLAR--MGATVTGVDAVDKNVKIARLHADMDPVTSTIEYLCTTAEKLADEGRKFDAVLS  204 (322)
T ss_pred             CCEEEEeeCCCCHHHHHHHH--cCCEEEEEeCCHHHHHHHHHHHHhcCcccceeEEecCHHHhhhccCCCCEEEE
Confidence            36899999999999998886  46789999984 577766532       479999999865 4444  298874

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

Probab=97.63  E-value=0.00021  Score=61.62  Aligned_cols=73  Identities=16%  Similarity=0.259  Sum_probs=54.0

Q ss_pred             HHHhcccccCcceEEEecCCccHHHHHHHHHcCC-CcEEEeech-HHHhhccC------CCCceEEecCcCCCCCC---C
Q 039903          159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLH-IKGVNFDLS-HVIQDSSS------YSGVKHIGGIMLERIPK---G  227 (233)
Q Consensus       159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~-l~~~v~Dlp-~v~~~a~~------~~ri~~~~gD~f~~~P~---~  227 (233)
                      +++.++ .++..+|+|||||+|.++..+++..+. -+++.+|.. +.++.|++      .++|+++.+|..+..+.   .
T Consensus        72 ll~~L~-i~~g~~VLDIG~GtG~~a~~LA~~~~~~g~VvgVDis~~~l~~Ar~~l~~~g~~nV~~i~gD~~~~~~~~~~f  150 (322)
T PRK13943         72 FMEWVG-LDKGMRVLEIGGGTGYNAAVMSRVVGEKGLVVSVEYSRKICEIAKRNVRRLGIENVIFVCGDGYYGVPEFAPY  150 (322)
T ss_pred             HHHhcC-CCCCCEEEEEeCCccHHHHHHHHhcCCCCEEEEEECCHHHHHHHHHHHHHcCCCcEEEEeCChhhcccccCCc
Confidence            344444 556689999999999999999998874 468889974 56665554      26799999998874442   3


Q ss_pred             CEEEe
Q 039903          228 DAILI  232 (233)
Q Consensus       228 D~~~l  232 (233)
                      |++++
T Consensus       151 D~Ii~  155 (322)
T PRK13943        151 DVIFV  155 (322)
T ss_pred             cEEEE
Confidence            88875

>PTZ00338 dimethyladenosine transferase-like protein; Provisional

Probab=97.62  E-value=0.0002  Score=61.02  Aligned_cols=72  Identities=15%  Similarity=0.321  Sum_probs=53.5

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccC-------CCCceEEecCcCC-CCCCC
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSS-------YSGVKHIGGIMLE-RIPKG  227 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~-------~~ri~~~~gD~f~-~~P~~  227 (233)
                      ..+++... .....+|+|||||.|.++..++++..  +++.+|+. ..++.+++       .++++++.+|+.+ ..|..
T Consensus        26 ~~Iv~~~~-~~~~~~VLEIG~G~G~LT~~Ll~~~~--~V~avEiD~~li~~l~~~~~~~~~~~~v~ii~~Dal~~~~~~~  102 (294)
T PTZ00338         26 DKIVEKAA-IKPTDTVLEIGPGTGNLTEKLLQLAK--KVIAIEIDPRMVAELKKRFQNSPLASKLEVIEGDALKTEFPYF  102 (294)
T ss_pred             HHHHHhcC-CCCcCEEEEecCchHHHHHHHHHhCC--cEEEEECCHHHHHHHHHHHHhcCCCCcEEEEECCHhhhccccc
Confidence            34555555 56668999999999999999999854  58888885 35555443       3689999999998 56555


Q ss_pred             CEEE
Q 039903          228 DAIL  231 (233)
Q Consensus       228 D~~~  231 (233)
                      |.++
T Consensus       103 d~Vv  106 (294)
T PTZ00338        103 DVCV  106 (294)
T ss_pred             CEEE
Confidence            7654

>PRK03612 spermidine synthase; Provisional

Probab=97.61  E-value=0.00012  Score=67.28  Aligned_cols=65  Identities=15%  Similarity=0.332  Sum_probs=52.9

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCC-CcEEEeec-hHHHhhccCC-------------CCceEEecCcCC---CCCCC-
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLH-IKGVNFDL-SHVIQDSSSY-------------SGVKHIGGIMLE---RIPKG-  227 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~-l~~~v~Dl-p~v~~~a~~~-------------~ri~~~~gD~f~---~~P~~-  227 (233)
                      ++.++|+|||||+|..+.++++ +|. -+++++|+ |++++.++++             +|++++.+|.++   ..+.. 
T Consensus       296 ~~~~rVL~IG~G~G~~~~~ll~-~~~v~~v~~VEid~~vi~~ar~~~~l~~~~~~~~~dprv~vi~~Da~~~l~~~~~~f  374 (521)
T PRK03612        296 ARPRRVLVLGGGDGLALREVLK-YPDVEQVTLVDLDPAMTELARTSPALRALNGGALDDPRVTVVNDDAFNWLRKLAEKF  374 (521)
T ss_pred             CCCCeEEEEcCCccHHHHHHHh-CCCcCeEEEEECCHHHHHHHHhCCcchhhhccccCCCceEEEEChHHHHHHhCCCCC
Confidence            4568999999999999999997 576 78999999 6788887761             689999999887   23444 


Q ss_pred             CEEEe
Q 039903          228 DAILI  232 (233)
Q Consensus       228 D~~~l  232 (233)
                      |+|++
T Consensus       375 DvIi~  379 (521)
T PRK03612        375 DVIIV  379 (521)
T ss_pred             CEEEE
Confidence            99875

>PRK04266 fibrillarin; Provisional

Probab=97.61  E-value=0.0003  Score=57.71  Aligned_cols=68  Identities=9%  Similarity=0.047  Sum_probs=51.8

Q ss_pred             cccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHh----hccCCCCceEEecCcCCC-----CCCC-CEEE
Q 039903          163 SKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQ----DSSSYSGVKHIGGIMLER-----IPKG-DAIL  231 (233)
Q Consensus       163 ~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~----~a~~~~ri~~~~gD~f~~-----~P~~-D~~~  231 (233)
                      ++ .++..+|+|+|||+|.++..+++..+.-+++.+|+. +.++    .+++.++|.++.+|..++     ++.. |+++
T Consensus        68 l~-i~~g~~VlD~G~G~G~~~~~la~~v~~g~V~avD~~~~ml~~l~~~a~~~~nv~~i~~D~~~~~~~~~l~~~~D~i~  146 (226)
T PRK04266         68 FP-IKKGSKVLYLGAASGTTVSHVSDIVEEGVVYAVEFAPRPMRELLEVAEERKNIIPILADARKPERYAHVVEKVDVIY  146 (226)
T ss_pred             CC-CCCCCEEEEEccCCCHHHHHHHHhcCCCeEEEEECCHHHHHHHHHHhhhcCCcEEEECCCCCcchhhhccccCCEEE
Confidence            44 667789999999999999999999986688999984 3443    444447899999998753     2333 8876

>TIGR00438 rrmJ cell division protein FtsJ

Probab=97.60  E-value=0.00031  Score=55.83  Aligned_cols=58  Identities=16%  Similarity=0.170  Sum_probs=45.8

Q ss_pred             HhcccccCcceEEEecCCccHHHHHHHHHc-CCCcEEEeechHHHhhccCCCCceEEecCcCC
Q 039903          161 DSSKGFEQIKQLVDVGGGLGVNVNIIISNY-LHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLE  222 (233)
Q Consensus       161 ~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~-P~l~~~v~Dlp~v~~~a~~~~ri~~~~gD~f~  222 (233)
                      +.+....+..+|+|+|||+|.++..+++++ +..+++.+|+.+..    ..++++++.+|+.+
T Consensus        25 ~~~~~i~~g~~VLDiG~GtG~~~~~l~~~~~~~~~v~~vDis~~~----~~~~i~~~~~d~~~   83 (188)
T TIGR00438        25 QKFKLIKPGDTVLDLGAAPGGWSQVAVEQVGGKGRVIAVDLQPMK----PIENVDFIRGDFTD   83 (188)
T ss_pred             HHhcccCCCCEEEEecCCCCHHHHHHHHHhCCCceEEEEeccccc----cCCCceEEEeeCCC
Confidence            334434667899999999999999999887 66789999997643    23678999999876

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

Probab=97.59  E-value=0.00011  Score=58.89  Aligned_cols=53  Identities=13%  Similarity=0.230  Sum_probs=42.1

Q ss_pred             ceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccC------CCCceEEecCcCC
Q 039903          170 KQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSS------YSGVKHIGGIMLE  222 (233)
Q Consensus       170 ~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~------~~ri~~~~gD~f~  222 (233)
                      ..+||||||.|.++.++++++|+..++++|+- ..+..+..      .+++.++.+|...
T Consensus        19 ~l~lEIG~G~G~~l~~~A~~~Pd~n~iGiE~~~~~v~~a~~~~~~~~l~Nv~~~~~da~~   78 (195)
T PF02390_consen   19 PLILEIGCGKGEFLIELAKRNPDINFIGIEIRKKRVAKALRKAEKRGLKNVRFLRGDARE   78 (195)
T ss_dssp             EEEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHHTTSSEEEEES-CTT
T ss_pred             CeEEEecCCCCHHHHHHHHHCCCCCEEEEecchHHHHHHHHHHHhhcccceEEEEccHHH
Confidence            49999999999999999999999999999974 34444432      3899999999876

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 ....

>PLN02336 phosphoethanolamine N-methyltransferase

Probab=97.59  E-value=0.00023  Score=64.68  Aligned_cols=74  Identities=22%  Similarity=0.310  Sum_probs=54.4

Q ss_pred             HHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccC----CCCceEEecCcCC---CCCCC
Q 039903          156 TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSS----YSGVKHIGGIMLE---RIPKG  227 (233)
Q Consensus       156 ~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~----~~ri~~~~gD~f~---~~P~~  227 (233)
                      .+.+++.++ ..+..+++|||||+|.++..+++.+.  +++.+|.. +.++.+..    .++++++.+|+.+   ++|..
T Consensus        26 ~~~il~~l~-~~~~~~vLDlGcG~G~~~~~la~~~~--~v~giD~s~~~l~~a~~~~~~~~~i~~~~~d~~~~~~~~~~~  102 (475)
T PLN02336         26 RPEILSLLP-PYEGKSVLELGAGIGRFTGELAKKAG--QVIALDFIESVIKKNESINGHYKNVKFMCADVTSPDLNISDG  102 (475)
T ss_pred             hhHHHhhcC-ccCCCEEEEeCCCcCHHHHHHHhhCC--EEEEEeCCHHHHHHHHHHhccCCceEEEEecccccccCCCCC
Confidence            345566655 44557999999999999999999864  68999974 56665542    2689999999964   45543


Q ss_pred             --CEEEe
Q 039903          228 --DAILI  232 (233)
Q Consensus       228 --D~~~l  232 (233)
                        |+|+.
T Consensus       103 ~fD~I~~  109 (475)
T PLN02336        103 SVDLIFS  109 (475)
T ss_pred             CEEEEeh
Confidence              88874

>PLN02781 Probable caffeoyl-CoA O-methyltransferase

Probab=97.58  E-value=0.00022  Score=58.78  Aligned_cols=67  Identities=12%  Similarity=0.108  Sum_probs=53.0

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcC-CCcEEEeech-HHHhhccCC-------CCceEEecCcCCCCC-------C--C
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDLS-HVIQDSSSY-------SGVKHIGGIMLERIP-------K--G  227 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dlp-~v~~~a~~~-------~ri~~~~gD~f~~~P-------~--~  227 (233)
                      ..+.++++|||+|+|.-+..+++..| +.+++.+|.. +.++.|+++       ++|+++.||..+.+|       .  -
T Consensus        66 ~~~~~~vLEiGt~~G~s~l~la~~~~~~g~v~tiD~d~~~~~~A~~n~~~~gl~~~i~~~~gda~~~L~~l~~~~~~~~f  145 (234)
T PLN02781         66 IMNAKNTLEIGVFTGYSLLTTALALPEDGRITAIDIDKEAYEVGLEFIKKAGVDHKINFIQSDALSALDQLLNNDPKPEF  145 (234)
T ss_pred             HhCCCEEEEecCcccHHHHHHHHhCCCCCEEEEEECCHHHHHHHHHHHHHcCCCCcEEEEEccHHHHHHHHHhCCCCCCC
Confidence            45678999999999999999998865 7899999985 566666653       689999999987321       2  3


Q ss_pred             CEEEe
Q 039903          228 DAILI  232 (233)
Q Consensus       228 D~~~l  232 (233)
                      |++++
T Consensus       146 D~Vfi  150 (234)
T PLN02781        146 DFAFV  150 (234)
T ss_pred             CEEEE
Confidence            88875

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=97.57  E-value=0.00022  Score=49.55  Aligned_cols=60  Identities=17%  Similarity=0.212  Sum_probs=50.4

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhh
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAK   86 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~   86 (233)
                      -+.|++.|...+  ++.|..|||+.+++    +...+.|+|+.|+..|++.+..   .++.|++++...
T Consensus         7 ~~~Il~~l~~~~--~~~t~~~ia~~l~i----~~~tv~r~l~~L~~~g~l~~~~---~~~~y~l~~~~~   66 (91)
T smart00346        7 GLAVLRALAEEP--GGLTLAELAERLGL----SKSTAHRLLNTLQELGYVEQDG---QNGRYRLGPKVL   66 (91)
T ss_pred             HHHHHHHHHhCC--CCcCHHHHHHHhCC----CHHHHHHHHHHHHHCCCeeecC---CCCceeecHHHH
Confidence            456888888763  48999999999999    9999999999999999999852   357899887543

>TIGR03438 probable methyltransferase

Probab=97.54  E-value=0.00011  Score=62.81  Aligned_cols=55  Identities=18%  Similarity=0.274  Sum_probs=44.4

Q ss_pred             CcceEEEecCCccHHHHHHHHHcC-CCcEEEeechH-HHhhccCC-----C--CceEEecCcCC
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDLSH-VIQDSSSY-----S--GVKHIGGIMLE  222 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dlp~-v~~~a~~~-----~--ri~~~~gD~f~  222 (233)
                      ...+|||+|||+|..+..|+++.+ ..+++.+|+.+ .++.+.+.     +  +|.++.+||++
T Consensus        63 ~~~~iLELGcGtG~~t~~Ll~~l~~~~~~~~iDiS~~mL~~a~~~l~~~~p~~~v~~i~gD~~~  126 (301)
T TIGR03438        63 AGCELVELGSGSSRKTRLLLDALRQPARYVPIDISADALKESAAALAADYPQLEVHGICADFTQ  126 (301)
T ss_pred             CCCeEEecCCCcchhHHHHHHhhccCCeEEEEECCHHHHHHHHHHHHhhCCCceEEEEEEcccc
Confidence            446899999999999999999988 68999999965 55555432     3  46778999987

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

>PRK04148 hypothetical protein; Provisional

Probab=97.51  E-value=0.00045  Score=51.80  Aligned_cols=69  Identities=12%  Similarity=0.195  Sum_probs=50.0

Q ss_pred             HHHhcccccCcceEEEecCCccH-HHHHHHHHcCCCcEEEeec-hHHHhhccCCCCceEEecCcCCCCCC----CCEEE
Q 039903          159 IIDSSKGFEQIKQLVDVGGGLGV-NVNIIISNYLHIKGVNFDL-SHVIQDSSSYSGVKHIGGIMLERIPK----GDAIL  231 (233)
Q Consensus       159 ~~~~~~~~~~~~~vvDvGGG~G~-~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~~ri~~~~gD~f~~~P~----~D~~~  231 (233)
                      +.+.++ -.+..+++|||+|.|. ++..|.+.  +..++.+|. |..++.+++ ..++++.+|.|++-+.    +|++.
T Consensus         8 l~~~~~-~~~~~kileIG~GfG~~vA~~L~~~--G~~ViaIDi~~~aV~~a~~-~~~~~v~dDlf~p~~~~y~~a~liy   82 (134)
T PRK04148          8 IAENYE-KGKNKKIVELGIGFYFKVAKKLKES--GFDVIVIDINEKAVEKAKK-LGLNAFVDDLFNPNLEIYKNAKLIY   82 (134)
T ss_pred             HHHhcc-cccCCEEEEEEecCCHHHHHHHHHC--CCEEEEEECCHHHHHHHHH-hCCeEEECcCCCCCHHHHhcCCEEE
Confidence            444444 2234789999999996 77777765  568999998 457777765 3689999999996554    37653

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

Probab=97.51  E-value=0.0002  Score=56.75  Aligned_cols=64  Identities=20%  Similarity=0.371  Sum_probs=48.8

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHH-HhhccCCCCceEEecCcCC---CCCCC--CEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHV-IQDSSSYSGVKHIGGIMLE---RIPKG--DAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v-~~~a~~~~ri~~~~gD~f~---~~P~~--D~~~l  232 (233)
                      +...+|+|+|||.|.++..|.+. .++++..+|+.+. +..+-+ ..++.+.+|.-+   .+|..  |.++|
T Consensus        12 ~pgsrVLDLGCGdG~LL~~L~~~-k~v~g~GvEid~~~v~~cv~-rGv~Viq~Dld~gL~~f~d~sFD~VIl   81 (193)
T PF07021_consen   12 EPGSRVLDLGCGDGELLAYLKDE-KQVDGYGVEIDPDNVAACVA-RGVSVIQGDLDEGLADFPDQSFDYVIL   81 (193)
T ss_pred             CCCCEEEecCCCchHHHHHHHHh-cCCeEEEEecCHHHHHHHHH-cCCCEEECCHHHhHhhCCCCCccEEeh
Confidence            44589999999999999888875 6999999998543 333322 478899999887   46653  98886

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 [].

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

Probab=97.50  E-value=0.00022  Score=57.80  Aligned_cols=75  Identities=15%  Similarity=0.263  Sum_probs=54.0

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcC-CCcEEEeec-hHHHhhccCC------CCceEEecCcCCCCCC-C
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLERIPK-G  227 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~~P~-~  227 (233)
                      ..+++.++ .+...+++|||+|+|.++..+++-.- .-+++.+|. |+.++.|+++      .+|+++.||-....|. +
T Consensus        62 a~~l~~L~-l~pg~~VLeIGtGsGY~aAlla~lvg~~g~Vv~vE~~~~l~~~A~~~l~~~~~~nv~~~~gdg~~g~~~~a  140 (209)
T PF01135_consen   62 ARMLEALD-LKPGDRVLEIGTGSGYQAALLAHLVGPVGRVVSVERDPELAERARRNLARLGIDNVEVVVGDGSEGWPEEA  140 (209)
T ss_dssp             HHHHHHTT-C-TT-EEEEES-TTSHHHHHHHHHHSTTEEEEEEESBHHHHHHHHHHHHHHTTHSEEEEES-GGGTTGGG-
T ss_pred             HHHHHHHh-cCCCCEEEEecCCCcHHHHHHHHhcCccceEEEECccHHHHHHHHHHHHHhccCceeEEEcchhhccccCC
Confidence            34566666 77889999999999999999988754 445777786 5677777653      5899999999987765 4


Q ss_pred             --CEEEe
Q 039903          228 --DAILI  232 (233)
Q Consensus       228 --D~~~l  232 (233)
                        |.|++
T Consensus       141 pfD~I~v  147 (209)
T PF01135_consen  141 PFDRIIV  147 (209)
T ss_dssp             SEEEEEE
T ss_pred             CcCEEEE
Confidence              88875

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 ....

>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=97.49  E-value=0.00033  Score=48.44  Aligned_cols=61  Identities=20%  Similarity=0.173  Sum_probs=47.6

Q ss_pred             eEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhcc------CCCCceEEecCcCCCC---CC-CCEEEe
Q 039903          171 QLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSS------SYSGVKHIGGIMLERI---PK-GDAILI  232 (233)
Q Consensus       171 ~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~------~~~ri~~~~gD~f~~~---P~-~D~~~l  232 (233)
                      +++|+|||.|.++..+++ .+..+++.+|+.+ .+..++      ...+++++.+|+.+..   +. .|+++.
T Consensus         1 ~ildig~G~G~~~~~~~~-~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~i~~   72 (107)
T cd02440           1 RVLDLGCGTGALALALAS-GPGARVTGVDISPVALELARKAAAALLADNVEVLKGDAEELPPEADESFDVIIS   72 (107)
T ss_pred             CeEEEcCCccHHHHHHhc-CCCCEEEEEeCCHHHHHHHHHHHhcccccceEEEEcChhhhccccCCceEEEEE
Confidence            589999999999999999 7888999999864 555444      1268999999999843   23 388875

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.).

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

Probab=97.45  E-value=0.00057  Score=55.57  Aligned_cols=54  Identities=7%  Similarity=0.083  Sum_probs=43.4

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccC------------------CCCceEEecCcCC
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSS------------------YSGVKHIGGIMLE  222 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~------------------~~ri~~~~gD~f~  222 (233)
                      ....+++|+|||.|..+..|+++  ..+++.+|+.+ .++.+..                  ..+|+++.+|+|+
T Consensus        33 ~~~~rvLd~GCG~G~da~~LA~~--G~~V~gvD~S~~Ai~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~D~~~  105 (213)
T TIGR03840        33 PAGARVFVPLCGKSLDLAWLAEQ--GHRVLGVELSEIAVEQFFAENGLTPTVTQQGEFTRYRAGNIEIFCGDFFA  105 (213)
T ss_pred             CCCCeEEEeCCCchhHHHHHHhC--CCeEEEEeCCHHHHHHHHHHcCCCcceeccccceeeecCceEEEEccCCC
Confidence            34579999999999999999986  77899999954 5665311                  2479999999998

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.

>TIGR02081 metW methionine biosynthesis protein MetW

Probab=97.45  E-value=0.00049  Score=54.91  Aligned_cols=64  Identities=19%  Similarity=0.361  Sum_probs=47.9

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCCCCceEEecCcCC---CCCC--CCEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSYSGVKHIGGIMLE---RIPK--GDAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~~ri~~~~gD~f~---~~P~--~D~~~l  232 (233)
                      +...+++|||||+|.++..+++. ...+++.+|.. +.++.++. .+++++.+|+.+   +++.  .|++++
T Consensus        12 ~~~~~iLDiGcG~G~~~~~l~~~-~~~~~~giD~s~~~i~~a~~-~~~~~~~~d~~~~l~~~~~~sfD~Vi~   81 (194)
T TIGR02081        12 PPGSRVLDLGCGDGELLALLRDE-KQVRGYGIEIDQDGVLACVA-RGVNVIQGDLDEGLEAFPDKSFDYVIL   81 (194)
T ss_pred             CCCCEEEEeCCCCCHHHHHHHhc-cCCcEEEEeCCHHHHHHHHH-cCCeEEEEEhhhcccccCCCCcCEEEE
Confidence            34468999999999999988875 45678899984 46666654 468899999875   2443  398875

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.

>KOG2904 consensus Predicted methyltransferase [General function prediction only]

Probab=97.44  E-value=0.00041  Score=57.67  Aligned_cols=60  Identities=15%  Similarity=0.219  Sum_probs=48.1

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccCC-------CCceEE----ecCcCCCCC
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSSY-------SGVKHI----GGIMLERIP  225 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~~-------~ri~~~----~gD~f~~~P  225 (233)
                      +.....++|+|||+|..+..+++.-|..+++..|... ++..|.++       +||..+    .+|.+.+.|
T Consensus       146 ~~~~~~ildlgtGSGaIslsll~~L~~~~v~AiD~S~~Ai~La~eN~qr~~l~g~i~v~~~~me~d~~~~~~  217 (328)
T KOG2904|consen  146 HSKHTHILDLGTGSGAISLSLLHGLPQCTVTAIDVSKAAIKLAKENAQRLKLSGRIEVIHNIMESDASDEHP  217 (328)
T ss_pred             hcccceEEEecCCccHHHHHHHhcCCCceEEEEeccHHHHHHHHHHHHHHhhcCceEEEecccccccccccc
Confidence            4455689999999999999999999999999999865 56666554       777776    677777544

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

Probab=97.42  E-value=0.00017  Score=65.01  Aligned_cols=72  Identities=14%  Similarity=0.113  Sum_probs=53.2

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC------CCceEEecCcCCCC-----C
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY------SGVKHIGGIMLERI-----P  225 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~------~ri~~~~gD~f~~~-----P  225 (233)
                      .+++.+. ..+..+++|+|||+|.++..+++..  .+++.+|.. +.++.|+++      ++++++.+|+.+.+     +
T Consensus       288 ~vl~~l~-~~~~~~VLDlgcGtG~~sl~la~~~--~~V~gvD~s~~al~~A~~n~~~~~~~~v~~~~~d~~~~l~~~~~~  364 (443)
T PRK13168        288 RALEWLD-PQPGDRVLDLFCGLGNFTLPLARQA--AEVVGVEGVEAMVERARENARRNGLDNVTFYHANLEEDFTDQPWA  364 (443)
T ss_pred             HHHHHhc-CCCCCEEEEEeccCCHHHHHHHHhC--CEEEEEeCCHHHHHHHHHHHHHcCCCceEEEEeChHHhhhhhhhh
Confidence            3444443 3455799999999999999999886  578999984 577777653      57999999997532     2


Q ss_pred             C--CCEEEe
Q 039903          226 K--GDAILI  232 (233)
Q Consensus       226 ~--~D~~~l  232 (233)
                      .  .|++++
T Consensus       365 ~~~fD~Vi~  373 (443)
T PRK13168        365 LGGFDKVLL  373 (443)
T ss_pred             cCCCCEEEE
Confidence            2  388875

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

Probab=97.39  E-value=0.0003  Score=56.57  Aligned_cols=63  Identities=13%  Similarity=0.127  Sum_probs=47.9

Q ss_pred             cceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCCCCC--C--CCEEEe
Q 039903          169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLERIP--K--GDAILI  232 (233)
Q Consensus       169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~~P--~--~D~~~l  232 (233)
                      ..+++|+|||+|.++.+++.+.. .+++.+|. |++++.++++      .+++++.+|+++.++  .  .|++++
T Consensus        54 ~~~vLDl~~GsG~l~l~~lsr~a-~~V~~vE~~~~a~~~a~~Nl~~~~~~~v~~~~~D~~~~l~~~~~~fDlV~~  127 (199)
T PRK10909         54 DARCLDCFAGSGALGLEALSRYA-AGATLLEMDRAVAQQLIKNLATLKAGNARVVNTNALSFLAQPGTPHNVVFV  127 (199)
T ss_pred             CCEEEEcCCCccHHHHHHHHcCC-CEEEEEECCHHHHHHHHHHHHHhCCCcEEEEEchHHHHHhhcCCCceEEEE
Confidence            46899999999999998666654 58899997 4566666553      579999999987432  2  388875

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

Probab=97.39  E-value=0.00033  Score=59.24  Aligned_cols=66  Identities=20%  Similarity=0.243  Sum_probs=55.8

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC----------CCceEEecCcCC---CCCC-CCEEE
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY----------SGVKHIGGIMLE---RIPK-GDAIL  231 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~----------~ri~~~~gD~f~---~~P~-~D~~~  231 (233)
                      +++++||=||||.|..++++++..|.-+.+++|+ |.|++.+++.          +|++.+.+|-++   ..+. .|+|+
T Consensus        75 ~~pk~VLiiGgGdG~tlRevlkh~~ve~i~~VEID~~Vi~~ar~~l~~~~~~~~dpRv~i~i~Dg~~~v~~~~~~fDvIi  154 (282)
T COG0421          75 PNPKRVLIIGGGDGGTLREVLKHLPVERITMVEIDPAVIELARKYLPEPSGGADDPRVEIIIDDGVEFLRDCEEKFDVII  154 (282)
T ss_pred             CCCCeEEEECCCccHHHHHHHhcCCcceEEEEEcCHHHHHHHHHhccCcccccCCCceEEEeccHHHHHHhCCCcCCEEE
Confidence            4557999999999999999999988889999999 5688888762          799999999887   3444 49988


Q ss_pred             e
Q 039903          232 I  232 (233)
Q Consensus       232 l  232 (233)
                      +
T Consensus       155 ~  155 (282)
T COG0421         155 V  155 (282)
T ss_pred             E
Confidence            5

>PLN02823 spermine synthase

Probab=97.39  E-value=0.0003  Score=61.00  Aligned_cols=66  Identities=18%  Similarity=0.165  Sum_probs=53.2

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC----------CCceEEecCcCCCC---CCC-CEEE
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY----------SGVKHIGGIMLERI---PKG-DAIL  231 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~----------~ri~~~~gD~f~~~---P~~-D~~~  231 (233)
                      .+.++++-||||.|..++.+++..+.-+++++|+ |.|++.++++          +|++++.+|.++-+   +.. |+|+
T Consensus       102 ~~pk~VLiiGgG~G~~~re~l~~~~~~~v~~VEiD~~vv~lar~~~~~~~~~~~dprv~v~~~Da~~~L~~~~~~yDvIi  181 (336)
T PLN02823        102 PNPKTVFIMGGGEGSTAREVLRHKTVEKVVMCDIDQEVVDFCRKHLTVNREAFCDKRLELIINDARAELEKRDEKFDVII  181 (336)
T ss_pred             CCCCEEEEECCCchHHHHHHHhCCCCCeEEEEECCHHHHHHHHHhcccccccccCCceEEEEChhHHHHhhCCCCccEEE
Confidence            4568999999999999999998766778999998 5688887652          69999999998732   233 8887


Q ss_pred             e
Q 039903          232 I  232 (233)
Q Consensus       232 l  232 (233)
                      +
T Consensus       182 ~  182 (336)
T PLN02823        182 G  182 (336)
T ss_pred             e
Confidence            5

>PRK11705 cyclopropane fatty acyl phospholipid synthase; Provisional

Probab=97.38  E-value=0.00062  Score=60.23  Aligned_cols=71  Identities=14%  Similarity=0.079  Sum_probs=52.0

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC---CCceEEecCcCCCCCC-CCEEE
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY---SGVKHIGGIMLERIPK-GDAIL  231 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~---~ri~~~~gD~f~~~P~-~D~~~  231 (233)
                      .+++.++ .+...+|||||||.|.++..+++++ +.+++.+|+ |+.++.+++.   ..|++..+|+.+. +. -|+++
T Consensus       158 ~l~~~l~-l~~g~rVLDIGcG~G~~a~~la~~~-g~~V~giDlS~~~l~~A~~~~~~l~v~~~~~D~~~l-~~~fD~Iv  233 (383)
T PRK11705        158 LICRKLQ-LKPGMRVLDIGCGWGGLARYAAEHY-GVSVVGVTISAEQQKLAQERCAGLPVEIRLQDYRDL-NGQFDRIV  233 (383)
T ss_pred             HHHHHhC-CCCCCEEEEeCCCccHHHHHHHHHC-CCEEEEEeCCHHHHHHHHHHhccCeEEEEECchhhc-CCCCCEEE
Confidence            3445555 6667899999999999999999876 678999998 4577766543   2478888887542 33 37765

>TIGR00452 methyltransferase, putative

Probab=97.38  E-value=0.00083  Score=57.78  Aligned_cols=72  Identities=11%  Similarity=0.037  Sum_probs=48.6

Q ss_pred             HHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhc---c----CCCCceEEecCcCC-CCCCC-C
Q 039903          159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDS---S----SYSGVKHIGGIMLE-RIPKG-D  228 (233)
Q Consensus       159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a---~----~~~ri~~~~gD~f~-~~P~~-D  228 (233)
                      ++..+. ..+.++|+|||||+|.++..++...++ +++.+|... .+..+   +    ...++.+..+|+-+ +.+.. |
T Consensus       113 ~l~~l~-~~~g~~VLDvGCG~G~~~~~~~~~g~~-~v~GiDpS~~ml~q~~~~~~~~~~~~~v~~~~~~ie~lp~~~~FD  190 (314)
T TIGR00452       113 VLPHLS-PLKGRTILDVGCGSGYHMWRMLGHGAK-SLVGIDPTVLFLCQFEAVRKLLDNDKRAILEPLGIEQLHELYAFD  190 (314)
T ss_pred             HHHhcC-CCCCCEEEEeccCCcHHHHHHHHcCCC-EEEEEcCCHHHHHHHHHHHHHhccCCCeEEEECCHHHCCCCCCcC
Confidence            344443 233489999999999999999988775 689999744 33322   1    12578888888755 32233 8


Q ss_pred             EEEe
Q 039903          229 AILI  232 (233)
Q Consensus       229 ~~~l  232 (233)
                      +|+.
T Consensus       191 ~V~s  194 (314)
T TIGR00452       191 TVFS  194 (314)
T ss_pred             EEEE
Confidence            8864

Known examples to date are restricted to the proteobacteria.

>COG1414 IclR Transcriptional regulator [Transcription]

Probab=97.38  E-value=0.00038  Score=57.87  Aligned_cols=61  Identities=18%  Similarity=0.293  Sum_probs=51.1

Q ss_pred             hChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHh
Q 039903           19 LGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYF   88 (233)
Q Consensus        19 lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l   88 (233)
                      +.|++.|...+  .+.++.|||+++|+    +...+.|+|..|+..|+++++.   ++++|++++....|
T Consensus         7 l~iL~~l~~~~--~~l~l~ela~~~gl----pksT~~RlL~tL~~~G~v~~d~---~~g~Y~Lg~~~~~l   67 (246)
T COG1414           7 LAILDLLAEGP--GGLSLAELAERLGL----PKSTVHRLLQTLVELGYVEQDP---EDGRYRLGPRLLEL   67 (246)
T ss_pred             HHHHHHHHhCC--CCCCHHHHHHHhCc----CHHHHHHHHHHHHHCCCEEEcC---CCCcEeehHHHHHH
Confidence            56888888853  45779999999999    9999999999999999999973   35789999865443

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

Probab=97.37  E-value=0.00062  Score=54.30  Aligned_cols=72  Identities=15%  Similarity=0.239  Sum_probs=50.2

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccC-----CCCceEEecCcCC-CCCCC-C
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSS-----YSGVKHIGGIMLE-RIPKG-D  228 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~-----~~ri~~~~gD~f~-~~P~~-D  228 (233)
                      +.+++..+ .-+..++||+|||.|..+.-|+++  +..++.+|... .++.+..     .-.|+....|+.+ .+|.. |
T Consensus        20 s~v~~a~~-~~~~g~~LDlgcG~GRNalyLA~~--G~~VtAvD~s~~al~~l~~~a~~~~l~i~~~~~Dl~~~~~~~~yD   96 (192)
T PF03848_consen   20 SEVLEAVP-LLKPGKALDLGCGEGRNALYLASQ--GFDVTAVDISPVALEKLQRLAEEEGLDIRTRVADLNDFDFPEEYD   96 (192)
T ss_dssp             HHHHHHCT-TS-SSEEEEES-TTSHHHHHHHHT--T-EEEEEESSHHHHHHHHHHHHHTT-TEEEEE-BGCCBS-TTTEE
T ss_pred             HHHHHHHh-hcCCCcEEEcCCCCcHHHHHHHHC--CCeEEEEECCHHHHHHHHHHHhhcCceeEEEEecchhccccCCcC
Confidence            45666666 556789999999999999999998  77799999864 4443322     2348899999988 66655 8


Q ss_pred             EEE
Q 039903          229 AIL  231 (233)
Q Consensus       229 ~~~  231 (233)
                      +|+
T Consensus        97 ~I~   99 (192)
T PF03848_consen   97 FIV   99 (192)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            875

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.

>TIGR00417 speE spermidine synthase

Probab=97.36  E-value=0.00032  Score=59.05  Aligned_cols=66  Identities=20%  Similarity=0.235  Sum_probs=50.7

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC----------CCceEEecCcCC--C-CCCC-CEEE
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY----------SGVKHIGGIMLE--R-IPKG-DAIL  231 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~----------~ri~~~~gD~f~--~-~P~~-D~~~  231 (233)
                      ++.++|++||||.|..+..+++..+..+++++|+. .+++.++++          +|++++.+|.++  . .+.. |+|+
T Consensus        71 ~~p~~VL~iG~G~G~~~~~ll~~~~~~~v~~veid~~vi~~a~~~~~~~~~~~~~~~v~i~~~D~~~~l~~~~~~yDvIi  150 (270)
T TIGR00417        71 PNPKHVLVIGGGDGGVLREVLKHKSVEKATLVDIDEKVIELSKKFLPSLAGSYDDPRVDLQIDDGFKFLADTENTFDVII  150 (270)
T ss_pred             CCCCEEEEEcCCchHHHHHHHhCCCcceEEEEeCCHHHHHHHHHHhHhhcccccCCceEEEECchHHHHHhCCCCccEEE
Confidence            45679999999999999999987667789999985 576766542          689999999876  2 2333 8887


Q ss_pred             e
Q 039903          232 I  232 (233)
Q Consensus       232 l  232 (233)
                      +
T Consensus       151 ~  151 (270)
T TIGR00417       151 V  151 (270)
T ss_pred             E
Confidence            5

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.

>TIGR00406 prmA ribosomal protein L11 methyltransferase

Probab=97.36  E-value=0.00034  Score=59.48  Aligned_cols=64  Identities=19%  Similarity=0.196  Sum_probs=45.0

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC-------CCceEEecCcCCCCCC-CCEEEe
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY-------SGVKHIGGIMLERIPK-GDAILI  232 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~-------~ri~~~~gD~f~~~P~-~D~~~l  232 (233)
                      +..+|+|||||+|.+++.+++. +.-+++.+|+. ..++.++++       +++.+..+|.....+. .|+++.
T Consensus       159 ~g~~VLDvGcGsG~lai~aa~~-g~~~V~avDid~~al~~a~~n~~~n~~~~~~~~~~~~~~~~~~~~fDlVva  231 (288)
T TIGR00406       159 KDKNVIDVGCGSGILSIAALKL-GAAKVVGIDIDPLAVESARKNAELNQVSDRLQVKLIYLEQPIEGKADVIVA  231 (288)
T ss_pred             CCCEEEEeCCChhHHHHHHHHc-CCCeEEEEECCHHHHHHHHHHHHHcCCCcceEEEecccccccCCCceEEEE
Confidence            4489999999999999888764 45689999985 466666553       4667666664332233 388864

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.

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

Probab=97.34  E-value=0.00061  Score=45.00  Aligned_cols=60  Identities=17%  Similarity=0.260  Sum_probs=49.2

Q ss_pred             HHhhChhHHHHhcCCCC-CCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903           16 ASELGVFEIIAKAGPTA-KISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH   83 (233)
Q Consensus        16 a~~lglfd~L~~~~~~~-~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~   83 (233)
                      ..+-.|++.|...|  + ++|+.|||+++|+    +...++|+|..|...|+++....  ....|+++.
T Consensus         6 ~~~~~IL~~L~~~g--~~~~ta~eLa~~lgl----~~~~v~r~L~~L~~~G~V~~~~~--~~~~W~i~~   66 (68)
T smart00550        6 SLEEKILEFLENSG--DETSTALQLAKNLGL----PKKEVNRVLYSLEKKGKVCKQGG--TPPLWKLTD   66 (68)
T ss_pred             HHHHHHHHHHHHCC--CCCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEecCC--CCCceEeec
Confidence            45667899999985  2 3999999999999    99999999999999999998531  136777654

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

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

Probab=97.32  E-value=0.00063  Score=53.65  Aligned_cols=63  Identities=14%  Similarity=0.148  Sum_probs=47.6

Q ss_pred             cceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-----CCceEEecCcCCCCCCCCEEEe
Q 039903          169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-----SGVKHIGGIMLERIPKGDAILI  232 (233)
Q Consensus       169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-----~ri~~~~gD~f~~~P~~D~~~l  232 (233)
                      .++|+|+|||+|.+++..+-..|+ +++.+|+ |+.++.++++     .+|+|+..|.-+--+.-|.++|
T Consensus        46 g~~V~DlG~GTG~La~ga~~lGa~-~V~~vdiD~~a~ei~r~N~~~l~g~v~f~~~dv~~~~~~~dtvim  114 (198)
T COG2263          46 GKTVLDLGAGTGILAIGAALLGAS-RVLAVDIDPEALEIARANAEELLGDVEFVVADVSDFRGKFDTVIM  114 (198)
T ss_pred             CCEEEEcCCCcCHHHHHHHhcCCc-EEEEEecCHHHHHHHHHHHHhhCCceEEEEcchhhcCCccceEEE
Confidence            378999999999999998876654 6777787 6688877765     6899999998763333355554

>PRK03522 rumB 23S rRNA methyluridine methyltransferase; Reviewed

Probab=97.32  E-value=0.00051  Score=59.17  Aligned_cols=62  Identities=11%  Similarity=0.046  Sum_probs=48.4

Q ss_pred             cceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCCC---CCC-CCEEEe
Q 039903          169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLER---IPK-GDAILI  232 (233)
Q Consensus       169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~---~P~-~D~~~l  232 (233)
                      ..+|+|+|||+|.++..+++.  ..+++.+|. ++.++.|+++      ++|+++.+|+.+-   ... .|++++
T Consensus       174 ~~~VLDl~cG~G~~sl~la~~--~~~V~gvD~s~~av~~A~~n~~~~~l~~v~~~~~D~~~~~~~~~~~~D~Vv~  246 (315)
T PRK03522        174 PRSMWDLFCGVGGFGLHCATP--GMQLTGIEISAEAIACAKQSAAELGLTNVQFQALDSTQFATAQGEVPDLVLV  246 (315)
T ss_pred             CCEEEEccCCCCHHHHHHHhc--CCEEEEEeCCHHHHHHHHHHHHHcCCCceEEEEcCHHHHHHhcCCCCeEEEE
Confidence            478999999999999999984  467999998 5577776543      5799999999762   222 388875

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

Probab=97.32  E-value=0.00028  Score=60.08  Aligned_cols=82  Identities=16%  Similarity=0.186  Sum_probs=50.9

Q ss_pred             HHHHHHHhcchhcHHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCce
Q 039903          143 VFNKAMLNHTSIVTNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVK  214 (233)
Q Consensus       143 ~f~~am~~~~~~~~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~  214 (233)
                      .|-.+-+.++++.... ++.+.  .+..+|+|||||+|.++++.++... -+++.+|. |.+++.|+++       +++.
T Consensus       139 AFGTG~H~TT~lcl~~-l~~~~--~~g~~vLDvG~GSGILaiaA~klGA-~~v~a~DiDp~Av~~a~~N~~~N~~~~~~~  214 (295)
T PF06325_consen  139 AFGTGHHPTTRLCLEL-LEKYV--KPGKRVLDVGCGSGILAIAAAKLGA-KKVVAIDIDPLAVEAARENAELNGVEDRIE  214 (295)
T ss_dssp             SS-SSHCHHHHHHHHH-HHHHS--STTSEEEEES-TTSHHHHHHHHTTB-SEEEEEESSCHHHHHHHHHHHHTT-TTCEE
T ss_pred             cccCCCCHHHHHHHHH-HHHhc--cCCCEEEEeCCcHHHHHHHHHHcCC-CeEEEecCCHHHHHHHHHHHHHcCCCeeEE
Confidence            3555555555554333 34443  3447999999999999999888644 47899998 4567777664       5565


Q ss_pred             EEecCcCCCCCC--CCEEE
Q 039903          215 HIGGIMLERIPK--GDAIL  231 (233)
Q Consensus       215 ~~~gD~f~~~P~--~D~~~  231 (233)
                      ..   .....+.  .|+|+
T Consensus       215 v~---~~~~~~~~~~dlvv  230 (295)
T PF06325_consen  215 VS---LSEDLVEGKFDLVV  230 (295)
T ss_dssp             ES---CTSCTCCS-EEEEE
T ss_pred             EE---EecccccccCCEEE
Confidence            42   1223333  38876

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 ....

>PRK14902 16S rRNA methyltransferase B; Provisional

Probab=97.28  E-value=0.00058  Score=61.63  Aligned_cols=71  Identities=14%  Similarity=0.054  Sum_probs=54.3

Q ss_pred             HhcccccCcceEEEecCCccHHHHHHHHHc-CCCcEEEeec-hHHHhhccCC------CCceEEecCcCCC---CCC-CC
Q 039903          161 DSSKGFEQIKQLVDVGGGLGVNVNIIISNY-LHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLER---IPK-GD  228 (233)
Q Consensus       161 ~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~---~P~-~D  228 (233)
                      ..++ ..+..+|+|+|||+|..+..+++.. |..+++.+|+ +..++.++++      ++|+++.+|+.+.   ++. .|
T Consensus       244 ~~l~-~~~g~~VLDlgaG~G~~t~~la~~~~~~~~v~avDi~~~~l~~~~~n~~~~g~~~v~~~~~D~~~~~~~~~~~fD  322 (444)
T PRK14902        244 PALD-PKGGDTVLDACAAPGGKTTHIAELLKNTGKVVALDIHEHKLKLIEENAKRLGLTNIETKALDARKVHEKFAEKFD  322 (444)
T ss_pred             HHhC-CCCCCEEEEeCCCCCHHHHHHHHHhCCCCEEEEEeCCHHHHHHHHHHHHHcCCCeEEEEeCCcccccchhcccCC
Confidence            3444 4556899999999999999999986 6789999999 5566666542      4699999999762   343 39


Q ss_pred             EEEe
Q 039903          229 AILI  232 (233)
Q Consensus       229 ~~~l  232 (233)
                      +|++
T Consensus       323 ~Vl~  326 (444)
T PRK14902        323 KILV  326 (444)
T ss_pred             EEEE
Confidence            8875

>PRK11569 transcriptional repressor IclR; Provisional

Probab=97.24  E-value=0.00064  Score=57.38  Aligned_cols=62  Identities=18%  Similarity=0.231  Sum_probs=51.7

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHh
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYF   88 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l   88 (233)
                      =+.|++.|.+.+  ++.|+.|||+.+|+    +..-+.|+|..|+..|+++++.   ..++|++.+....|
T Consensus        30 al~IL~~l~~~~--~~~~lseia~~lgl----pksTv~RlL~tL~~~G~l~~~~---~~~~Y~lG~~l~~L   91 (274)
T PRK11569         30 GLKLLEWIAESN--GSVALTELAQQAGL----PNSTTHRLLTTMQQQGFVRQVG---ELGHWAIGAHAFIV   91 (274)
T ss_pred             HHHHHHHHHhCC--CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEcC---CCCeEecCHHHHHH
Confidence            356788888754  58999999999999    9999999999999999999863   46899998765443

>PF09445 Methyltransf_15: RNA cap guanine-N2 methyltransferase; InterPro: IPR019012 RNA cap guanine-N2 methyltransferases such as Schizosaccharomyces pombe (Fission yeast) trimethylguanosine synthase (Tgs1) and Giardia lamblia (Giardia intestinalis) Tgs2, catalyse the methylation step(s) for the conversion of the 7-monomethylguanosine (m(7)G) caps of snRNAs and snoRNAs to a 2,2,7-trimethylguanosine (m(2,2,7)G) cap structure [, , ]

Probab=97.23  E-value=0.00023  Score=55.25  Aligned_cols=62  Identities=16%  Similarity=0.266  Sum_probs=44.8

Q ss_pred             ceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCCC---CC--C-CCEEEeC
Q 039903          170 KQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLER---IP--K-GDAILIK  233 (233)
Q Consensus       170 ~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~---~P--~-~D~~~lk  233 (233)
                      .+|+|+-||.|..++++++.+++  ++.+|+ |.-++.++.+       +||.++.||+++-   +.  . .|++++.
T Consensus         1 ~~vlD~fcG~GGNtIqFA~~~~~--Viaidid~~~~~~a~hNa~vYGv~~~I~~i~gD~~~~~~~~~~~~~~D~vFlS   76 (163)
T PF09445_consen    1 TTVLDAFCGVGGNTIQFARTFDR--VIAIDIDPERLECAKHNAEVYGVADNIDFICGDFFELLKRLKSNKIFDVVFLS   76 (163)
T ss_dssp             SEEEETT-TTSHHHHHHHHTT-E--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEES-HHHHGGGB------SEEEE-
T ss_pred             CEEEEeccCcCHHHHHHHHhCCe--EEEEECCHHHHHHHHHHHHHcCCCCcEEEEeCCHHHHHhhccccccccEEEEC
Confidence            47999999999999999999776  777787 4566666653       6999999999983   22  2 3888873

Trimethylguanosine synthase is specific for guanine, and N7 methylation must precede N2 methylation. This enzyme is required for pre-mRNA splicing, pre-rRNA processing and small ribosomal subunit synthesis. As such, this enzyme plays a role in transcriptional regulation. ; GO: 0008168 methyltransferase activity, 0001510 RNA methylation, 0009452 RNA capping; PDB: 3EGI_B 3GDH_A.

>PRK10163 DNA-binding transcriptional repressor AllR; Provisional

Probab=97.20  E-value=0.00077  Score=56.83  Aligned_cols=62  Identities=13%  Similarity=0.180  Sum_probs=52.0

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHh
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYF   88 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l   88 (233)
                      =+.|++.|...+  ++.|+.|||+.+|+    +...+.|+|..|+..|+|.++.   ..+.|++++....|
T Consensus        27 ~l~IL~~~~~~~--~~~tl~eIa~~lgl----pkStv~RlL~tL~~~G~l~~~~---~~~~Y~lG~~l~~L   88 (271)
T PRK10163         27 GIAILQYLEKSG--GSSSVSDISLNLDL----PLSTTFRLLKVLQAADFVYQDS---QLGWWHIGLGVFNV   88 (271)
T ss_pred             HHHHHHHHHhCC--CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEcC---CCCeEEecHHHHHH
Confidence            356888888764  57999999999999    9999999999999999999863   46889998765443

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

Probab=97.20  E-value=0.00073  Score=57.37  Aligned_cols=43  Identities=21%  Similarity=0.224  Sum_probs=34.8

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccCC
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSSY  210 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~~  210 (233)
                      .+..+++|||||+|.++++.++- -..+++.+|+.+ +++.|+++
T Consensus       161 ~~g~~vlDvGcGSGILaIAa~kL-GA~~v~g~DiDp~AV~aa~eN  204 (300)
T COG2264         161 KKGKTVLDVGCGSGILAIAAAKL-GAKKVVGVDIDPQAVEAAREN  204 (300)
T ss_pred             cCCCEEEEecCChhHHHHHHHHc-CCceEEEecCCHHHHHHHHHH
Confidence            46799999999999999998885 455689999854 67777664

>COG2518 Pcm Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]

Probab=97.17  E-value=0.002  Score=51.87  Aligned_cols=72  Identities=14%  Similarity=0.252  Sum_probs=56.7

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC------CCceEEecCcCCCCCC-C--
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY------SGVKHIGGIMLERIPK-G--  227 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~------~ri~~~~gD~f~~~P~-~--  227 (233)
                      .+++.+. .+...+||+||+|+|..+.-+++---  +++-+|+- +..+.|+++      .+|.++.||=.+-+|. +  
T Consensus        63 ~m~~~L~-~~~g~~VLEIGtGsGY~aAvla~l~~--~V~siEr~~~L~~~A~~~L~~lg~~nV~v~~gDG~~G~~~~aPy  139 (209)
T COG2518          63 RMLQLLE-LKPGDRVLEIGTGSGYQAAVLARLVG--RVVSIERIEELAEQARRNLETLGYENVTVRHGDGSKGWPEEAPY  139 (209)
T ss_pred             HHHHHhC-CCCCCeEEEECCCchHHHHHHHHHhC--eEEEEEEcHHHHHHHHHHHHHcCCCceEEEECCcccCCCCCCCc
Confidence            4556666 78889999999999999988888755  77778874 456667653      6799999999998887 5  


Q ss_pred             CEEEe
Q 039903          228 DAILI  232 (233)
Q Consensus       228 D~~~l  232 (233)
                      |.|++
T Consensus       140 D~I~V  144 (209)
T COG2518         140 DRIIV  144 (209)
T ss_pred             CEEEE
Confidence            98875

>PRK11727 23S rRNA mA1618 methyltransferase; Provisional

Probab=97.17  E-value=0.00072  Score=58.24  Aligned_cols=64  Identities=16%  Similarity=0.191  Sum_probs=47.7

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC--------CCceEEe----cCcCCCC--CCC--CEE
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY--------SGVKHIG----GIMLERI--PKG--DAI  230 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~--------~ri~~~~----gD~f~~~--P~~--D~~  230 (233)
                      ...++||||||+|.....++.+.|+.+++..|+. .+++.|+++        +||++..    .++|+.+  |..  |++
T Consensus       114 ~~~~vLDIGtGag~I~~lLa~~~~~~~~~atDId~~Al~~A~~Nv~~Np~l~~~I~~~~~~~~~~i~~~i~~~~~~fDli  193 (321)
T PRK11727        114 ANVRVLDIGVGANCIYPLIGVHEYGWRFVGSDIDPQALASAQAIISANPGLNGAIRLRLQKDSKAIFKGIIHKNERFDAT  193 (321)
T ss_pred             CCceEEEecCCccHHHHHHHhhCCCCEEEEEeCCHHHHHHHHHHHHhccCCcCcEEEEEccchhhhhhcccccCCceEEE
Confidence            3578999999999998888999999999999984 577777642        4777753    4566532  332  877


Q ss_pred             E
Q 039903          231 L  231 (233)
Q Consensus       231 ~  231 (233)
                      +
T Consensus       194 v  194 (321)
T PRK11727        194 L  194 (321)
T ss_pred             E
Confidence            6

>KOG1271 consensus Methyltransferases [General function prediction only]

Probab=97.16  E-value=0.001  Score=52.19  Aligned_cols=64  Identities=16%  Similarity=0.243  Sum_probs=45.9

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccC------C-CCceEEecCcCCC--CCCC-CEEE
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSS------Y-SGVKHIGGIMLER--IPKG-DAIL  231 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~------~-~ri~~~~gD~f~~--~P~~-D~~~  231 (233)
                      +..+|||+|||.|+++..|++.--.-+.+..|.. .+++.|+.      . +.|+|...|+++|  .+.. |+|+
T Consensus        67 ~A~~VlDLGtGNG~~L~~L~~egf~~~L~GvDYs~~AV~LA~niAe~~~~~n~I~f~q~DI~~~~~~~~qfdlvl  141 (227)
T KOG1271|consen   67 QADRVLDLGTGNGHLLFQLAKEGFQSKLTGVDYSEKAVELAQNIAERDGFSNEIRFQQLDITDPDFLSGQFDLVL  141 (227)
T ss_pred             cccceeeccCCchHHHHHHHHhcCCCCccccccCHHHHHHHHHHHHhcCCCcceeEEEeeccCCcccccceeEEe
Confidence            3459999999999999999987444345677764 35555542      2 4499999999984  3333 7776

>PLN02585 magnesium protoporphyrin IX methyltransferase

Probab=97.15  E-value=0.00092  Score=57.55  Aligned_cols=61  Identities=13%  Similarity=0.039  Sum_probs=45.6

Q ss_pred             cceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccCC-----------CCceEEecCcCCCCCC-CCEEEe
Q 039903          169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSSY-----------SGVKHIGGIMLERIPK-GDAILI  232 (233)
Q Consensus       169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~~-----------~ri~~~~gD~f~~~P~-~D~~~l  232 (233)
                      ..+|||||||+|.++..++++  ..+++.+|+.+ .++.++++           .+++|..+|+.+ ++. -|+|+.
T Consensus       145 ~~~VLDlGcGtG~~a~~la~~--g~~V~gvD~S~~ml~~A~~~~~~~~~~~~~~~~~~f~~~Dl~~-l~~~fD~Vv~  218 (315)
T PLN02585        145 GVTVCDAGCGTGSLAIPLALE--GAIVSASDISAAMVAEAERRAKEALAALPPEVLPKFEANDLES-LSGKYDTVTC  218 (315)
T ss_pred             CCEEEEecCCCCHHHHHHHHC--CCEEEEEECCHHHHHHHHHHHHhcccccccccceEEEEcchhh-cCCCcCEEEE
Confidence            479999999999999999986  56899999854 66666542           357888888753 233 387763

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

Probab=97.15  E-value=0.00082  Score=55.81  Aligned_cols=59  Identities=19%  Similarity=0.223  Sum_probs=50.6

Q ss_pred             hChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHh
Q 039903           19 LGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYF   88 (233)
Q Consensus        19 lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l   88 (233)
                      +.|.+.|...+  .+.|+.|||+.+|+    +...+.|+|..|+..|+++++     ++.|++.+.-..|
T Consensus        12 l~IL~~l~~~~--~~~~l~eia~~lgl----pksT~~RlL~tL~~~G~l~~~-----~~~Y~lG~~~~~l   70 (248)
T TIGR02431        12 LAVIEAFGAER--PRLTLTDVAEATGL----TRAAARRFLLTLVELGYVTSD-----GRLFWLTPRVLRL   70 (248)
T ss_pred             HHHHHHHhcCC--CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEeC-----CCEEEecHHHHHH
Confidence            56788887654  58999999999999    999999999999999999984     6889999865444

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.

>PRK13255 thiopurine S-methyltransferase; Reviewed

Probab=97.15  E-value=0.0018  Score=52.79  Aligned_cols=64  Identities=9%  Similarity=0.089  Sum_probs=47.8

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccC------------------CCCceEEecCcCCCCCC
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSS------------------YSGVKHIGGIMLERIPK  226 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~------------------~~ri~~~~gD~f~~~P~  226 (233)
                      ..+..+++|+|||.|..+..|+++  ..+++.+|+.+ .++.+..                  ..+|++..+|+|+..|.
T Consensus        35 ~~~~~rvL~~gCG~G~da~~LA~~--G~~V~avD~s~~Ai~~~~~~~~l~~~~~~~~~~~~~~~~~v~~~~~D~~~l~~~  112 (218)
T PRK13255         35 LPAGSRVLVPLCGKSLDMLWLAEQ--GHEVLGVELSELAVEQFFAENGLTPQTRQSGEFEHYQAGEITIYCGDFFALTAA  112 (218)
T ss_pred             CCCCCeEEEeCCCChHhHHHHHhC--CCeEEEEccCHHHHHHHHHHcCCCccccccccccccccCceEEEECcccCCCcc
Confidence            344579999999999999999985  77899999864 5554311                  15799999999984332


Q ss_pred             --C--CEEE
Q 039903          227 --G--DAIL  231 (233)
Q Consensus       227 --~--D~~~  231 (233)
                        +  |+++
T Consensus       113 ~~~~fd~v~  121 (218)
T PRK13255        113 DLADVDAVY  121 (218)
T ss_pred             cCCCeeEEE
Confidence              2  6665

>PRK00536 speE spermidine synthase; Provisional

Probab=97.14  E-value=0.001  Score=55.71  Aligned_cols=62  Identities=15%  Similarity=0.109  Sum_probs=48.7

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC----------CCceEEecCcCCCCC-CC-CEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY----------SGVKHIGGIMLERIP-KG-DAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~----------~ri~~~~gD~f~~~P-~~-D~~~l  232 (233)
                      +++++||=||||.|..++++++. |. +++.+|+. .|++.++++          +|++.+.  ++.+.. .- |+|++
T Consensus        71 ~~pk~VLIiGGGDGg~~REvLkh-~~-~v~mVeID~~Vv~~~k~~lP~~~~~~~DpRv~l~~--~~~~~~~~~fDVIIv  145 (262)
T PRK00536         71 KELKEVLIVDGFDLELAHQLFKY-DT-HVDFVQADEKILDSFISFFPHFHEVKNNKNFTHAK--QLLDLDIKKYDLIIC  145 (262)
T ss_pred             CCCCeEEEEcCCchHHHHHHHCc-CC-eeEEEECCHHHHHHHHHHCHHHHHhhcCCCEEEee--hhhhccCCcCCEEEE
Confidence            56799999999999999999995 66 99999995 588888762          7999886  344323 33 88875

>PRK09834 DNA-binding transcriptional activator MhpR; Provisional

Probab=97.13  E-value=0.0011  Score=55.70  Aligned_cols=64  Identities=13%  Similarity=0.123  Sum_probs=53.2

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhc
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVL   90 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~   90 (233)
                      -+.|++.|...+  ++.|+.|||+.+++    +...+.|+|+.|+..|+++++.   +.+.|++++....|..
T Consensus        13 al~iL~~l~~~~--~~ls~~eia~~lgl----~kstv~RlL~tL~~~g~v~~~~---~~~~Y~Lg~~~~~l~~   76 (263)
T PRK09834         13 GLMVLRALNRLD--GGATVGLLAELTGL----HRTTVRRLLETLQEEGYVRRSA---SDDSFRLTLKVRQLSE   76 (263)
T ss_pred             HHHHHHHHHhcC--CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEec---CCCcEEEcHHHHHHHH
Confidence            356788887754  46999999999999    9999999999999999999863   3678999987665543

>KOG2899 consensus Predicted methyltransferase [General function prediction only]

Probab=97.12  E-value=0.00063  Score=55.63  Aligned_cols=54  Identities=17%  Similarity=0.199  Sum_probs=45.0

Q ss_pred             HHHHHhcc-cccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccCC
Q 039903          157 NRIIDSSK-GFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSSY  210 (233)
Q Consensus       157 ~~~~~~~~-~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~~  210 (233)
                      +..++.++ +|-....+|||||++|.++..+++.|-....+.+|+.+ -|+.|+++
T Consensus        46 D~rLk~L~~~~f~~~~~LDIGCNsG~lt~~iak~F~~r~iLGvDID~~LI~~Ark~  101 (288)
T KOG2899|consen   46 DPRLKVLEKDWFEPKQALDIGCNSGFLTLSIAKDFGPRRILGVDIDPVLIQRARKE  101 (288)
T ss_pred             ChhhhhccccccCcceeEeccCCcchhHHHHHHhhccceeeEeeccHHHHHHHHHh
Confidence            45566665 36777999999999999999999999999999999966 56778764

>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional

Probab=97.12  E-value=0.00093  Score=55.83  Aligned_cols=60  Identities=13%  Similarity=0.234  Sum_probs=50.4

Q ss_pred             hChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHh
Q 039903           19 LGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYF   88 (233)
Q Consensus        19 lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l   88 (233)
                      +.|.+.|...   ++.|+.|||+.+|+    +...+.|+|+.|+..|+++++.   +++.|++.+....|
T Consensus        17 l~IL~~l~~~---~~l~l~eia~~lgl----~kstv~Rll~tL~~~G~l~~~~---~~~~Y~lG~~~~~l   76 (257)
T PRK15090         17 FGILQALGEE---REIGITELSQRVMM----SKSTVYRFLQTMKTLGYVAQEG---ESEKYSLTLKLFEL   76 (257)
T ss_pred             HHHHHHhhcC---CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEcC---CCCcEEecHHHHHH
Confidence            4577777764   48999999999999    9999999999999999999863   46889999765444

>TIGR01177 conserved hypothetical protein TIGR01177

Probab=97.10  E-value=0.0016  Score=56.40  Aligned_cols=71  Identities=13%  Similarity=0.050  Sum_probs=52.2

Q ss_pred             HHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCC-CCCC--CC
Q 039903          159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLE-RIPK--GD  228 (233)
Q Consensus       159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~-~~P~--~D  228 (233)
                      ++.... ++...+++|+|||+|.++++.+..  ..+++..|+ +..++.++.+      +.+.++.+|+.+ +++.  .|
T Consensus       174 ~~~l~~-~~~g~~vLDp~cGtG~~lieaa~~--~~~v~g~Di~~~~~~~a~~nl~~~g~~~i~~~~~D~~~l~~~~~~~D  250 (329)
T TIGR01177       174 MVNLAR-VTEGDRVLDPFCGTGGFLIEAGLM--GAKVIGCDIDWKMVAGARINLEHYGIEDFFVKRGDATKLPLSSESVD  250 (329)
T ss_pred             HHHHhC-CCCcCEEEECCCCCCHHHHHHHHh--CCeEEEEcCCHHHHHHHHHHHHHhCCCCCeEEecchhcCCcccCCCC
Confidence            333334 666789999999999999887653  677899998 4567665543      458899999998 6654  38


Q ss_pred             EEEe
Q 039903          229 AILI  232 (233)
Q Consensus       229 ~~~l  232 (233)
                      +++.
T Consensus       251 ~Iv~  254 (329)
T TIGR01177       251 AIAT  254 (329)
T ss_pred             EEEE
Confidence            8875

This family is found exclusively in the Archaea.

>PRK00517 prmA ribosomal protein L11 methyltransferase; Reviewed

Probab=97.08  E-value=0.00061  Score=56.70  Aligned_cols=42  Identities=19%  Similarity=0.216  Sum_probs=33.0

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccC
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSS  209 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~  209 (233)
                      ....+++|||||+|.+++.+++..+. +++.+|+. ..++.+++
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            45689999999999999987775544 68999984 56776665

>PTZ00146 fibrillarin; Provisional

Probab=97.08  E-value=0.0023  Score=54.22  Aligned_cols=67  Identities=13%  Similarity=0.058  Sum_probs=51.0

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcC-CCcEEEeechH-----HHhhccCCCCceEEecCcCCCC------CCCCEEEe
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDLSH-----VIQDSSSYSGVKHIGGIMLERI------PKGDAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dlp~-----v~~~a~~~~ri~~~~gD~f~~~------P~~D~~~l  232 (233)
                      ++...+|||+|||+|.++..+++... .=+++.+|+.+     .++.++..++|.++.+|...+.      +..|++++
T Consensus       130 IkpG~~VLDLGaG~G~~t~~lAdiVG~~G~VyAVD~s~r~~~dLl~~ak~r~NI~~I~~Da~~p~~y~~~~~~vDvV~~  208 (293)
T PTZ00146        130 IKPGSKVLYLGAASGTTVSHVSDLVGPEGVVYAVEFSHRSGRDLTNMAKKRPNIVPIIEDARYPQKYRMLVPMVDVIFA  208 (293)
T ss_pred             cCCCCEEEEeCCcCCHHHHHHHHHhCCCCEEEEEECcHHHHHHHHHHhhhcCCCEEEECCccChhhhhcccCCCCEEEE
Confidence            45668999999999999999999863 55788889764     4555555578999999987542      22498875

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

Probab=97.08  E-value=0.0014  Score=44.32  Aligned_cols=50  Identities=18%  Similarity=0.193  Sum_probs=41.2

Q ss_pred             CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhc
Q 039903           32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVL   90 (233)
Q Consensus        32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~   90 (233)
                      ++.+..+|+..+++    +...+.+.|+.|...|+++.     .++.|.+|+.|..++.
T Consensus        18 ~~~~~t~i~~~~~L----~~~~~~~yL~~L~~~gLI~~-----~~~~Y~lTekG~~~l~   67 (77)
T PF14947_consen   18 GGAKKTEIMYKANL----NYSTLKKYLKELEEKGLIKK-----KDGKYRLTEKGKEFLE   67 (77)
T ss_dssp             T-B-HHHHHTTST------HHHHHHHHHHHHHTTSEEE-----ETTEEEE-HHHHHHHH
T ss_pred             CCCCHHHHHHHhCc----CHHHHHHHHHHHHHCcCeeC-----CCCEEEECccHHHHHH
Confidence            68999999999999    99999999999999999977     4899999999987653

>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=97.05  E-value=0.0008  Score=46.20  Aligned_cols=55  Identities=22%  Similarity=0.265  Sum_probs=42.4

Q ss_pred             HHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903           23 EIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH   83 (233)
Q Consensus        23 d~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~   83 (233)
                      -.|+..+.+++.|..|||+.+++    ++..++++++.|...|+++....  .+|.|.++.
T Consensus        15 ~~la~~~~~~~~s~~eiA~~~~i----~~~~l~kil~~L~~~Gli~s~~G--~~GGy~L~~   69 (83)
T PF02082_consen   15 LYLARHPDGKPVSSKEIAERLGI----SPSYLRKILQKLKKAGLIESSRG--RGGGYRLAR   69 (83)
T ss_dssp             HHHHCTTTSC-BEHHHHHHHHTS-----HHHHHHHHHHHHHTTSEEEETS--TTSEEEESS
T ss_pred             HHHHhCCCCCCCCHHHHHHHHCc----CHHHHHHHHHHHhhCCeeEecCC--CCCceeecC
Confidence            33454433346999999999999    99999999999999999987642  468888875

(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.

>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=97.02  E-value=0.0019  Score=58.18  Aligned_cols=96  Identities=21%  Similarity=0.207  Sum_probs=61.1

Q ss_pred             ccccccccCchHHHHHHHHHHhcchhcHHHHHHhcccc---cCcceEEEecCCccHHHHHHHHH----cCCCcEEEeech
Q 039903          129 GFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGF---EQIKQLVDVGGGLGVNVNIIISN----YLHIKGVNFDLS  201 (233)
Q Consensus       129 ~~~~~~~~~~~~~~~f~~am~~~~~~~~~~~~~~~~~~---~~~~~vvDvGGG~G~~~~~l~~~----~P~l~~~v~Dlp  201 (233)
                      ..||.+++|+..-+.+.+|+..       .+.+....-   .+...|+|||+|+|-++...+++    .-..++..++-.
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            3577788888877778877642       222221111   13578999999999998666554    346788888864


Q ss_pred             H-HHhhc----cCC---CCceEEecCcCC-CCCC-CCEEE
Q 039903          202 H-VIQDS----SSY---SGVKHIGGIMLE-RIPK-GDAIL  231 (233)
Q Consensus       202 ~-v~~~a----~~~---~ri~~~~gD~f~-~~P~-~D~~~  231 (233)
                      + ++...    +.+   ++|+++.+|+-+ +.|+ +|+++
T Consensus       224 ~~A~~~l~~~v~~n~w~~~V~vi~~d~r~v~lpekvDIIV  263 (448)
T PF05185_consen  224 PNAVVTLQKRVNANGWGDKVTVIHGDMREVELPEKVDIIV  263 (448)
T ss_dssp             THHHHHHHHHHHHTTTTTTEEEEES-TTTSCHSS-EEEEE
T ss_pred             HhHHHHHHHHHHhcCCCCeEEEEeCcccCCCCCCceeEEE
Confidence            3 33221    222   899999999999 8887 59875

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 ....

>KOG1499 consensus Protein arginine N-methyltransferase PRMT1 and related enzymes [Posttranslational modification, protein turnover, chaperones; Transcription; Signal transduction mechanisms]

Probab=97.01  E-value=0.001  Score=57.13  Aligned_cols=62  Identities=21%  Similarity=0.227  Sum_probs=51.0

Q ss_pred             cceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccC----C---CCceEEecCcCC-CCCC-C-CEEE
Q 039903          169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSS----Y---SGVKHIGGIMLE-RIPK-G-DAIL  231 (233)
Q Consensus       169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~----~---~ri~~~~gD~f~-~~P~-~-D~~~  231 (233)
                      .++|+|||||+|.+++-.+++. ..++..+|-.++++.|.+    +   +.|+++.|..-+ ++|. . |+++
T Consensus        61 dK~VlDVGcGtGILS~F~akAG-A~~V~aVe~S~ia~~a~~iv~~N~~~~ii~vi~gkvEdi~LP~eKVDiIv  132 (346)
T KOG1499|consen   61 DKTVLDVGCGTGILSMFAAKAG-ARKVYAVEASSIADFARKIVKDNGLEDVITVIKGKVEDIELPVEKVDIIV  132 (346)
T ss_pred             CCEEEEcCCCccHHHHHHHHhC-cceEEEEechHHHHHHHHHHHhcCccceEEEeecceEEEecCccceeEEe
Confidence            4899999999999999999887 678899998887777654    2   679999998888 8883 4 8764

>PF08123 DOT1: Histone methylation protein DOT1 ; InterPro: IPR013110 The DOT1 domain regulates gene expression by methylating histone H3 []

Probab=97.01  E-value=0.0012  Score=53.38  Aligned_cols=74  Identities=19%  Similarity=0.253  Sum_probs=46.4

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccC---------------CCCceEEecCcC
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSS---------------YSGVKHIGGIML  221 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~---------------~~ri~~~~gD~f  221 (233)
                      .+++.+. .....+++|||+|.|....+.+-.++--+++++++- ...+.|..               ..+|++..|||+
T Consensus        33 ~il~~~~-l~~~dvF~DlGSG~G~~v~~aal~~~~~~~~GIEi~~~~~~~a~~~~~~~~~~~~~~g~~~~~v~l~~gdfl  111 (205)
T PF08123_consen   33 KILDELN-LTPDDVFYDLGSGVGNVVFQAALQTGCKKSVGIEILPELHDLAEELLEELKKRMKHYGKRPGKVELIHGDFL  111 (205)
T ss_dssp             HHHHHTT---TT-EEEEES-TTSHHHHHHHHHH--SEEEEEE-SHHHHHHHHHHHHHHHHHHHHCTB---EEEEECS-TT
T ss_pred             HHHHHhC-CCCCCEEEECCCCCCHHHHHHHHHcCCcEEEEEEechHHHHHHHHHHHHHHHHHHHhhcccccceeeccCcc
Confidence            4555555 666789999999999999888887776669999874 34433322               157899999999


Q ss_pred             C-C-----CCCCCEEEe
Q 039903          222 E-R-----IPKGDAILI  232 (233)
Q Consensus       222 ~-~-----~P~~D~~~l  232 (233)
                      + +     +..||++++
T Consensus       112 ~~~~~~~~~s~AdvVf~  128 (205)
T PF08123_consen  112 DPDFVKDIWSDADVVFV  128 (205)
T ss_dssp             THHHHHHHGHC-SEEEE
T ss_pred             ccHhHhhhhcCCCEEEE
Confidence            7 3     244798876

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 ....

>PRK10901 16S rRNA methyltransferase B; Provisional

Probab=97.00  E-value=0.002  Score=57.90  Aligned_cols=73  Identities=14%  Similarity=0.064  Sum_probs=54.4

Q ss_pred             HHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-----CCceEEecCcCCC---CCC--C
Q 039903          159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-----SGVKHIGGIMLER---IPK--G  227 (233)
Q Consensus       159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-----~ri~~~~gD~f~~---~P~--~  227 (233)
                      ++..++ .....+|+|+|||+|..+..+++..++.+++.+|+ ++.++.++++     -+++++.+|..+.   .+.  .
T Consensus       236 ~~~~l~-~~~g~~VLDlgaG~G~~t~~la~~~~~~~v~a~D~s~~~l~~~~~n~~~~g~~~~~~~~D~~~~~~~~~~~~f  314 (427)
T PRK10901        236 AATLLA-PQNGERVLDACAAPGGKTAHILELAPQAQVVALDIDAQRLERVRENLQRLGLKATVIVGDARDPAQWWDGQPF  314 (427)
T ss_pred             HHHHcC-CCCCCEEEEeCCCCChHHHHHHHHcCCCEEEEEeCCHHHHHHHHHHHHHcCCCeEEEEcCcccchhhcccCCC
Confidence            333444 45568999999999999999999998888999998 4566666543     2478899999862   222  3


Q ss_pred             CEEEe
Q 039903          228 DAILI  232 (233)
Q Consensus       228 D~~~l  232 (233)
                      |.|++
T Consensus       315 D~Vl~  319 (427)
T PRK10901        315 DRILL  319 (427)
T ss_pred             CEEEE
Confidence            88874

>KOG1500 consensus Protein arginine N-methyltransferase CARM1 [Posttranslational modification, protein turnover, chaperones; Transcription]

Probab=96.99  E-value=0.0019  Score=55.33  Aligned_cols=64  Identities=23%  Similarity=0.346  Sum_probs=50.7

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCC-------CCceEEecCcCC-CCCCC-CEEE
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSY-------SGVKHIGGIMLE-RIPKG-DAIL  231 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~-------~ri~~~~gD~f~-~~P~~-D~~~  231 (233)
                      |++ +.|||||+|+|.++.-.+++- .-++-.++-.+..+.|++.       +||+.++|-.-+ ++|+. |+++
T Consensus       176 F~~-kiVlDVGaGSGILS~FAaqAG-A~~vYAvEAS~MAqyA~~Lv~~N~~~~rItVI~GKiEdieLPEk~DviI  248 (517)
T KOG1500|consen  176 FQD-KIVLDVGAGSGILSFFAAQAG-AKKVYAVEASEMAQYARKLVASNNLADRITVIPGKIEDIELPEKVDVII  248 (517)
T ss_pred             cCC-cEEEEecCCccHHHHHHHHhC-cceEEEEehhHHHHHHHHHHhcCCccceEEEccCccccccCchhccEEE
Confidence            655 789999999999987776653 3456677777777777652       899999999998 99984 9875

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

Probab=96.96  E-value=0.00081  Score=59.34  Aligned_cols=62  Identities=11%  Similarity=0.050  Sum_probs=47.7

Q ss_pred             cceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCCCCC---C-CCEEEe
Q 039903          169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLERIP---K-GDAILI  232 (233)
Q Consensus       169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~~P---~-~D~~~l  232 (233)
                      ..+++|+|||+|.++..++.+  ..+++.+|. |+.++.|+++      ++++++.+|+.+..+   . .|++++
T Consensus       234 ~~~vLDL~cG~G~~~l~la~~--~~~v~~vE~~~~av~~a~~N~~~~~~~~~~~~~~d~~~~~~~~~~~~D~vi~  306 (374)
T TIGR02085       234 VTQMWDLFCGVGGFGLHCAGP--DTQLTGIEIESEAIACAQQSAQMLGLDNLSFAALDSAKFATAQMSAPELVLV  306 (374)
T ss_pred             CCEEEEccCCccHHHHHHhhc--CCeEEEEECCHHHHHHHHHHHHHcCCCcEEEEECCHHHHHHhcCCCCCEEEE
Confidence            468999999999999999964  467899997 5577766653      579999999976222   2 388875

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.

>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=96.96  E-value=0.0036  Score=47.62  Aligned_cols=39  Identities=21%  Similarity=0.373  Sum_probs=31.2

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhh
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQD  206 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~  206 (233)
                      .....+|||||||.|.++..+++..+  +++.+|..+ .++.
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  899999854 5544

...

>KOG0820 consensus Ribosomal RNA adenine dimethylase [RNA processing and modification]

Probab=96.96  E-value=0.0028  Score=52.80  Aligned_cols=73  Identities=15%  Similarity=0.336  Sum_probs=54.6

Q ss_pred             HHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccC----C---CCceEEecCcCC-CCCC
Q 039903          156 TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSS----Y---SGVKHIGGIMLE-RIPK  226 (233)
Q Consensus       156 ~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~----~---~ri~~~~gD~f~-~~P~  226 (233)
                      +..++..-+ .+....|+.||.|+|.+...++++  .-+++.+++ |..++...+    .   ...+.+.|||++ ++|-
T Consensus        47 ~~~I~~ka~-~k~tD~VLEvGPGTGnLT~~lLe~--~kkVvA~E~Dprmvael~krv~gtp~~~kLqV~~gD~lK~d~P~  123 (315)
T KOG0820|consen   47 IDQIVEKAD-LKPTDVVLEVGPGTGNLTVKLLEA--GKKVVAVEIDPRMVAELEKRVQGTPKSGKLQVLHGDFLKTDLPR  123 (315)
T ss_pred             HHHHHhccC-CCCCCEEEEeCCCCCHHHHHHHHh--cCeEEEEecCcHHHHHHHHHhcCCCccceeeEEecccccCCCcc
Confidence            345666656 778899999999999999999998  445777776 455544332    2   579999999999 8887


Q ss_pred             CCEEE
Q 039903          227 GDAIL  231 (233)
Q Consensus       227 ~D~~~  231 (233)
                      -|.++
T Consensus       124 fd~cV  128 (315)
T KOG0820|consen  124 FDGCV  128 (315)
T ss_pred             cceee
Confidence            65543

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

Probab=96.92  E-value=0.0014  Score=53.67  Aligned_cols=53  Identities=9%  Similarity=0.172  Sum_probs=42.0

Q ss_pred             ceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccC----C--CCceEEecCcCC
Q 039903          170 KQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSS----Y--SGVKHIGGIMLE  222 (233)
Q Consensus       170 ~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~----~--~ri~~~~gD~f~  222 (233)
                      ..+|+||||.|.+...+++++|+.-++++|.- .++..+..    .  ++|..+.+|.-+
T Consensus        50 pi~lEIGfG~G~~l~~~A~~nP~~nfiGiEi~~~~v~~~l~k~~~~~l~Nlri~~~DA~~  109 (227)
T COG0220          50 PIVLEIGFGMGEFLVEMAKKNPEKNFLGIEIRVPGVAKALKKIKELGLKNLRLLCGDAVE  109 (227)
T ss_pred             cEEEEECCCCCHHHHHHHHHCCCCCEEEEEEehHHHHHHHHHHHHcCCCcEEEEcCCHHH
Confidence            68999999999999999999999999999973 34433322    1  478888887665

>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=96.91  E-value=0.0011  Score=55.18  Aligned_cols=66  Identities=18%  Similarity=0.242  Sum_probs=51.3

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC----------CCceEEecCcCC---CCCC-C-CEE
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY----------SGVKHIGGIMLE---RIPK-G-DAI  230 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~----------~ri~~~~gD~f~---~~P~-~-D~~  230 (233)
                      ++.++||=||||.|..+.++++..|-.+++++|+ |.|++.+++.          +|++.+.+|-+.   ..+. . |+|
T Consensus        75 ~~p~~VLiiGgG~G~~~~ell~~~~~~~i~~VEiD~~Vv~~a~~~f~~~~~~~~d~r~~i~~~Dg~~~l~~~~~~~yDvI  154 (246)
T PF01564_consen   75 PNPKRVLIIGGGDGGTARELLKHPPVESITVVEIDPEVVELARKYFPEFSEGLDDPRVRIIIGDGRKFLKETQEEKYDVI  154 (246)
T ss_dssp             SST-EEEEEESTTSHHHHHHTTSTT-SEEEEEES-HHHHHHHHHHTHHHHTTGGSTTEEEEESTHHHHHHTSSST-EEEE
T ss_pred             CCcCceEEEcCCChhhhhhhhhcCCcceEEEEecChHHHHHHHHhchhhccccCCCceEEEEhhhHHHHHhccCCcccEE
Confidence            5689999999999999999998666778999999 5588877652          699999999875   4455 4 877


Q ss_pred             Ee
Q 039903          231 LI  232 (233)
Q Consensus       231 ~l  232 (233)
                      ++
T Consensus       155 i~  156 (246)
T PF01564_consen  155 IV  156 (246)
T ss_dssp             EE
T ss_pred             EE
Confidence            64

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 ....

>PF01596 Methyltransf_3: O-methyltransferase; InterPro: IPR002935 Members of this family are O-methyltransferases

Probab=96.91  E-value=0.0015  Score=52.78  Aligned_cols=67  Identities=18%  Similarity=0.275  Sum_probs=51.8

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcC-CCcEEEeech-HHHhhccCC-------CCceEEecCcCCCCC-------CC--
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDLS-HVIQDSSSY-------SGVKHIGGIMLERIP-------KG--  227 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dlp-~v~~~a~~~-------~ri~~~~gD~f~~~P-------~~--  227 (233)
                      ..+.+++|+||++.|.-+..+++..| +.+++-+|.. +-.+.|+++       +||+++.||..+.+|       .+  
T Consensus        43 ~~~~k~vLEIGt~~GySal~la~~l~~~g~i~tiE~~~~~~~~A~~~~~~ag~~~~I~~~~gda~~~l~~l~~~~~~~~f  122 (205)
T PF01596_consen   43 LTRPKRVLEIGTFTGYSALWLAEALPEDGKITTIEIDPERAEIARENFRKAGLDDRIEVIEGDALEVLPELANDGEEGQF  122 (205)
T ss_dssp             HHT-SEEEEESTTTSHHHHHHHHTSTTTSEEEEEESSHHHHHHHHHHHHHTTGGGGEEEEES-HHHHHHHHHHTTTTTSE
T ss_pred             hcCCceEEEeccccccHHHHHHHhhcccceEEEecCcHHHHHHHHHHHHhcCCCCcEEEEEeccHhhHHHHHhccCCCce
Confidence            46789999999999999999999987 5899999984 466666542       799999999986332       12  


Q ss_pred             CEEEe
Q 039903          228 DAILI  232 (233)
Q Consensus       228 D~~~l  232 (233)
                      |++++
T Consensus       123 D~VFi  127 (205)
T PF01596_consen  123 DFVFI  127 (205)
T ss_dssp             EEEEE
T ss_pred             eEEEE
Confidence            88876

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 ....

>PF13679 Methyltransf_32: Methyltransferase domain

Probab=96.90  E-value=0.0015  Score=49.47  Aligned_cols=57  Identities=14%  Similarity=0.255  Sum_probs=42.1

Q ss_pred             ccCcceEEEecCCccHHHHHHHHH----cCCCcEEEeech-HHHhhccCC---------CCceEEecCcCC
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISN----YLHIKGVNFDLS-HVIQDSSSY---------SGVKHIGGIMLE  222 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~----~P~l~~~v~Dlp-~v~~~a~~~---------~ri~~~~gD~f~  222 (233)
                      -.+..+|||+|||.|+++..++..    .|+++++.+|.. +.++.+.+.         .++++..+++..
T Consensus        23 ~~~~~~vvD~GsG~GyLs~~La~~l~~~~~~~~v~~iD~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~   93 (141)
T PF13679_consen   23 SKRCITVVDLGSGKGYLSRALAHLLCNSSPNLRVLGIDCNESLVESAQKRAQKLGSDLEKRLSFIQGDIAD   93 (141)
T ss_pred             cCCCCEEEEeCCChhHHHHHHHHHHHhcCCCCeEEEEECCcHHHHHHHHHHHHhcchhhccchhhccchhh
Confidence            366789999999999999999992    288999999974 344444331         456777766654

>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=96.90  E-value=0.0011  Score=42.75  Aligned_cols=54  Identities=13%  Similarity=0.246  Sum_probs=46.8

Q ss_pred             HHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           10 PAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        10 s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      ..+|..-.++.|++.|...   +|.|+.|||+.+++    ++..+.+-|+.|...|+++..
T Consensus         4 ~~aL~~p~R~~Il~~L~~~---~~~t~~ela~~l~~----~~~t~s~hL~~L~~aGli~~~   57 (61)
T PF12840_consen    4 FKALSDPTRLRILRLLASN---GPMTVSELAEELGI----SQSTVSYHLKKLEEAGLIEVE   57 (61)
T ss_dssp             HHHHTSHHHHHHHHHHHHC---STBEHHHHHHHHTS-----HHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHhCCHHHHHHHHHHhcC---CCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCeEEe
Confidence            4566667889999999554   69999999999999    999999999999999999986

...

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

Probab=96.88  E-value=0.0011  Score=59.67  Aligned_cols=65  Identities=15%  Similarity=0.284  Sum_probs=50.3

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCCCCC-----C--CCEEE
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLERIP-----K--GDAIL  231 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~~P-----~--~D~~~  231 (233)
                      ..+..+++|+|||+|.++..+++...  +++.+|. ++.++.|+++      ++|+++.+|+.+.+|     .  .|+++
T Consensus       290 ~~~~~~vLDl~cG~G~~sl~la~~~~--~V~~vE~~~~av~~a~~n~~~~~~~nv~~~~~d~~~~l~~~~~~~~~~D~vi  367 (431)
T TIGR00479       290 LQGEELVVDAYCGVGTFTLPLAKQAK--SVVGIEVVPESVEKAQQNAELNGIANVEFLAGTLETVLPKQPWAGQIPDVLL  367 (431)
T ss_pred             cCCCCEEEEcCCCcCHHHHHHHHhCC--EEEEEEcCHHHHHHHHHHHHHhCCCceEEEeCCHHHHHHHHHhcCCCCCEEE
Confidence            45567999999999999999998753  6899998 5678777653      689999999865221     1  38887


Q ss_pred             e
Q 039903          232 I  232 (233)
Q Consensus       232 l  232 (233)
                      +
T Consensus       368 ~  368 (431)
T TIGR00479       368 L  368 (431)
T ss_pred             E
Confidence            5

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.

>PLN02476 O-methyltransferase

Probab=96.87  E-value=0.0035  Score=52.92  Aligned_cols=67  Identities=13%  Similarity=0.111  Sum_probs=53.2

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcC-CCcEEEeech-HHHhhccCC-------CCceEEecCcCCCCC--------CC-
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDLS-HVIQDSSSY-------SGVKHIGGIMLERIP--------KG-  227 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dlp-~v~~~a~~~-------~ri~~~~gD~f~~~P--------~~-  227 (233)
                      ..+.+++|+||.+.|..+..+++..| +-+++-+|.. +..+.|+++       ++|+++.||..+.+|        .. 
T Consensus       116 ~~~ak~VLEIGT~tGySal~lA~al~~~G~V~TiE~d~e~~~~Ar~n~~~aGl~~~I~li~GdA~e~L~~l~~~~~~~~F  195 (278)
T PLN02476        116 ILGAERCIEVGVYTGYSSLAVALVLPESGCLVACERDSNSLEVAKRYYELAGVSHKVNVKHGLAAESLKSMIQNGEGSSY  195 (278)
T ss_pred             hcCCCeEEEecCCCCHHHHHHHHhCCCCCEEEEEECCHHHHHHHHHHHHHcCCCCcEEEEEcCHHHHHHHHHhcccCCCC
Confidence            56789999999999999999999876 6678889985 466666553       699999999987332        23 


Q ss_pred             CEEEe
Q 039903          228 DAILI  232 (233)
Q Consensus       228 D~~~l  232 (233)
                      |++++
T Consensus       196 D~VFI  200 (278)
T PLN02476        196 DFAFV  200 (278)
T ss_pred             CEEEE
Confidence            88876

>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=96.86  E-value=0.0027  Score=41.42  Aligned_cols=58  Identities=14%  Similarity=0.273  Sum_probs=41.5

Q ss_pred             hhHHHH-hcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhh
Q 039903           21 VFEIIA-KAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVA   85 (233)
Q Consensus        21 lfd~L~-~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s   85 (233)
                      |...|. ..   ++.+..+||+.+++    +...+.+.++.|...|++++..+..  ....|++|+.|
T Consensus         8 vL~~l~~~~---~~~t~~~l~~~~~~----~~~~vs~~i~~L~~~glv~~~~~~~d~R~~~~~LT~~G   68 (68)
T PF13463_consen    8 VLRALAHSD---GPMTQSDLAERLGI----SKSTVSRIIKKLEEKGLVEKERDPHDKRSKRYRLTPAG   68 (68)
T ss_dssp             HHHHHT--T---S-BEHHHHHHHTT------HHHHHHHHHHHHHTTSEEEEEESSCTTSEEEEE-HHH
T ss_pred             HHHHHHccC---CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEecCCCCcCCeeEEEeCCCC
Confidence            444555 32   69999999999999    9999999999999999998765431  22468888865

>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=96.85  E-value=0.00095  Score=43.93  Aligned_cols=48  Identities=21%  Similarity=0.236  Sum_probs=41.8

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeec
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTS   71 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~   71 (233)
                      .+..++..|...   ++.|..|||+.+++    +...+.+.|+.|...|++++..
T Consensus         9 ~E~~vy~~Ll~~---~~~t~~eIa~~l~i----~~~~v~~~L~~L~~~GlV~~~~   56 (68)
T PF01978_consen    9 NEAKVYLALLKN---GPATAEEIAEELGI----SRSTVYRALKSLEEKGLVEREE   56 (68)
T ss_dssp             HHHHHHHHHHHH---CHEEHHHHHHHHTS----SHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEEc
Confidence            355677777655   69999999999999    9999999999999999999874

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.

>TIGR01444 fkbM_fam methyltransferase, FkbM family

Probab=96.82  E-value=0.0018  Score=48.66  Aligned_cols=52  Identities=12%  Similarity=0.135  Sum_probs=39.4

Q ss_pred             eEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCC
Q 039903          171 QLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLE  222 (233)
Q Consensus       171 ~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~  222 (233)
                      +++|||||.|.++..+++.+|+.+++.+|. |...+.++++      ++++++...+..
T Consensus         1 ~vlDiGa~~G~~~~~~~~~~~~~~v~~~E~~~~~~~~l~~~~~~n~~~~v~~~~~al~~   59 (143)
T TIGR01444         1 VVIDVGANIGDTSLYFARKGAEGRVIAFEPLPDAYEILEENVKLNNLPNVVLLNAAVGD   59 (143)
T ss_pred             CEEEccCCccHHHHHHHHhCCCCEEEEEecCHHHHHHHHHHHHHcCCCcEEEEEeeeeC
Confidence            589999999999999999999999999996 4555544331      346666555543

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.

>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=96.82  E-value=0.0011  Score=40.31  Aligned_cols=44  Identities=11%  Similarity=0.277  Sum_probs=39.2

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceee
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRC   69 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~   69 (233)
                      ++.|...|.+    +|.++.|||+.+++    +...+.+-|+.|...|++++
T Consensus         4 R~~Il~~L~~----~~~~~~el~~~l~~----s~~~vs~hL~~L~~~glV~~   47 (47)
T PF01022_consen    4 RLRILKLLSE----GPLTVSELAEELGL----SQSTVSHHLKKLREAGLVEK   47 (47)
T ss_dssp             HHHHHHHHTT----SSEEHHHHHHHHTS-----HHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHh----CCCchhhHHHhccc----cchHHHHHHHHHHHCcCeeC
Confidence            5678888888    69999999999999    99999999999999999874

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 ....

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

Probab=96.74  E-value=0.005  Score=50.39  Aligned_cols=63  Identities=17%  Similarity=0.062  Sum_probs=45.1

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC-----CCceEEecCcCC-C-CC-CC-CEEEe
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY-----SGVKHIGGIMLE-R-IP-KG-DAILI  232 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~-----~ri~~~~gD~f~-~-~P-~~-D~~~l  232 (233)
                      +..+|+|||||.|.++..+++.  ..+++..|.. ..++.++++     .+++++.+|+.+ + .+ .. |++++
T Consensus        48 ~~~~vLdiG~G~G~~~~~l~~~--~~~v~~iD~s~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~fD~Ii~  120 (233)
T PRK05134         48 FGKRVLDVGCGGGILSESMARL--GADVTGIDASEENIEVARLHALESGLKIDYRQTTAEELAAEHPGQFDVVTC  120 (233)
T ss_pred             CCCeEEEeCCCCCHHHHHHHHc--CCeEEEEcCCHHHHHHHHHHHHHcCCceEEEecCHHHhhhhcCCCccEEEE
Confidence            4578999999999999988886  4578999985 455555432     357888888765 2 22 23 88864

>KOG3420 consensus Predicted RNA methylase [Translation, ribosomal structure and biogenesis]

Probab=96.74  E-value=0.0018  Score=48.99  Aligned_cols=68  Identities=22%  Similarity=0.283  Sum_probs=49.0

Q ss_pred             hcccccCcceEEEecCCccHHHHHHHHHcCCCc-EEEeec-hHHHhhccCC-----CCceEEecCcCCCCCCC---CEEE
Q 039903          162 SSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIK-GVNFDL-SHVIQDSSSY-----SGVKHIGGIMLERIPKG---DAIL  231 (233)
Q Consensus       162 ~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~-~~v~Dl-p~v~~~a~~~-----~ri~~~~gD~f~~~P~~---D~~~  231 (233)
                      -|.++++ +++.|+|||.|.++  ++-.+|..+ ++++|+ |++++..+.+     -+|.+..+|+.++.|.+   |..+
T Consensus        43 TygdiEg-kkl~DLgcgcGmLs--~a~sm~~~e~vlGfDIdpeALEIf~rNaeEfEvqidlLqcdildle~~~g~fDtav  119 (185)
T KOG3420|consen   43 TYGDIEG-KKLKDLGCGCGMLS--IAFSMPKNESVLGFDIDPEALEIFTRNAEEFEVQIDLLQCDILDLELKGGIFDTAV  119 (185)
T ss_pred             hhccccC-cchhhhcCchhhhH--HHhhcCCCceEEeeecCHHHHHHHhhchHHhhhhhheeeeeccchhccCCeEeeEE
Confidence            3443444 78999999999999  445566665 789998 6688877665     36788889988866652   5554


Q ss_pred             e
Q 039903          232 I  232 (233)
Q Consensus       232 l  232 (233)
                      +
T Consensus       120 i  120 (185)
T KOG3420|consen  120 I  120 (185)
T ss_pred             e
Confidence            3

>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=96.72  E-value=0.0027  Score=38.63  Aligned_cols=45  Identities=13%  Similarity=0.304  Sum_probs=38.7

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCcee
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLR   68 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~   68 (233)
                      .+..|+..|.+.|   ++|..|||+.+|+    +...+.+.++-|...|+++
T Consensus         4 ~~~~Il~~l~~~~---~~t~~ela~~~~i----s~~tv~~~l~~L~~~g~I~   48 (48)
T PF13412_consen    4 TQRKILNYLRENP---RITQKELAEKLGI----SRSTVNRYLKKLEEKGLIE   48 (48)
T ss_dssp             HHHHHHHHHHHCT---TS-HHHHHHHHTS-----HHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHHcC---CCCHHHHHHHhCC----CHHHHHHHHHHHHHCcCcC
Confidence            4667889999974   7999999999999    9999999999999999874

...

>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional

Probab=96.64  E-value=0.0038  Score=45.75  Aligned_cols=68  Identities=16%  Similarity=0.280  Sum_probs=55.9

Q ss_pred             hHHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903            8 VLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH   83 (233)
Q Consensus         8 ~~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~   83 (233)
                      ..+.+|.--.++.|+..|...   ++.++.|||+.+++    ++..+.+-|+.|...|+++....+ ..-.|++++
T Consensus         8 ~~fkaLadptRl~IL~~L~~~---~~~~v~ela~~l~l----sqstvS~HL~~L~~AGLV~~~r~G-r~~~Y~l~~   75 (117)
T PRK10141          8 QLFKILSDETRLGIVLLLRES---GELCVCDLCTALDQ----SQPKISRHLALLRESGLLLDRKQG-KWVHYRLSP   75 (117)
T ss_pred             HHHHHhCCHHHHHHHHHHHHc---CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCceEEEEEc-CEEEEEECc
Confidence            456777788899999999874   48999999999999    999999999999999999976421 233477765

>PF04816 DUF633: Family of unknown function (DUF633) ; InterPro: IPR006901 This is a family of uncharacterised bacterial proteins

Probab=96.62  E-value=0.0027  Score=51.26  Aligned_cols=61  Identities=20%  Similarity=0.221  Sum_probs=46.3

Q ss_pred             EEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCCCCCC---CCEEEe
Q 039903          172 LVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLERIPK---GDAILI  232 (233)
Q Consensus       172 vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~~P~---~D~~~l  232 (233)
                      |.||||-||.+.+.|+++...-+++..|+ |.-++.|+++       ++|++.-||=|+.++.   .|++++
T Consensus         1 vaDIGtDHgyLpi~L~~~~~~~~~ia~DI~~gpL~~A~~~i~~~~l~~~i~~rlgdGL~~l~~~e~~d~ivI   72 (205)
T PF04816_consen    1 VADIGTDHGYLPIYLLKNGKAPKAIAVDINPGPLEKAKENIAKYGLEDRIEVRLGDGLEVLKPGEDVDTIVI   72 (205)
T ss_dssp             EEEET-STTHHHHHHHHTTSEEEEEEEESSHHHHHHHHHHHHHTT-TTTEEEEE-SGGGG--GGG---EEEE
T ss_pred             CceeccchhHHHHHHHhcCCCCEEEEEeCCHHHHHHHHHHHHHcCCcccEEEEECCcccccCCCCCCCEEEE
Confidence            68999999999999999999999999998 4466666542       7999999999987765   367664

; GO: 0016429 tRNA (adenine-N1-)-methyltransferase activity; PDB: 3LEC_A 3KU1_G 3KR9_A 3GNL_B.

>PRK14904 16S rRNA methyltransferase B; Provisional

Probab=96.60  E-value=0.0053  Score=55.47  Aligned_cols=67  Identities=16%  Similarity=0.113  Sum_probs=50.3

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcC-CCcEEEeech-HHHhhccCC------CCceEEecCcCCCCCC--CCEEEe
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDLS-HVIQDSSSY------SGVKHIGGIMLERIPK--GDAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dlp-~v~~~a~~~------~ri~~~~gD~f~~~P~--~D~~~l  232 (233)
                      .....+|+|+|||+|..+..+++..+ .-+++.+|+. +.++.++++      ++|+++.+|..+..|.  .|+|++
T Consensus       248 ~~~g~~VLDlgaG~G~kt~~la~~~~~~~~V~avD~s~~~l~~~~~~~~~~g~~~v~~~~~Da~~~~~~~~fD~Vl~  324 (445)
T PRK14904        248 PQPGSTVLDLCAAPGGKSTFMAELMQNRGQITAVDRYPQKLEKIRSHASALGITIIETIEGDARSFSPEEQPDAILL  324 (445)
T ss_pred             CCCCCEEEEECCCCCHHHHHHHHHhCCCcEEEEEECCHHHHHHHHHHHHHhCCCeEEEEeCcccccccCCCCCEEEE
Confidence            34457999999999999999888754 4589999985 466655542      5789999999873343  398875

>PF00398 RrnaAD: Ribosomal RNA adenine dimethylase; InterPro: IPR001737 This family of proteins include rRNA adenine dimethylases (e

Probab=96.58  E-value=0.0047  Score=51.80  Aligned_cols=68  Identities=13%  Similarity=0.300  Sum_probs=51.5

Q ss_pred             HHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccC----CCCceEEecCcCC-CCCC
Q 039903          156 TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSS----YSGVKHIGGIMLE-RIPK  226 (233)
Q Consensus       156 ~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~----~~ri~~~~gD~f~-~~P~  226 (233)
                      +..+++.++ ..+...|+|||.|.|.++..|++..  -+.+++|..+ -++..++    .++++.+.+|+++ ..+.
T Consensus        19 ~~~Iv~~~~-~~~~~~VlEiGpG~G~lT~~L~~~~--~~v~~vE~d~~~~~~L~~~~~~~~~~~vi~~D~l~~~~~~   92 (262)
T PF00398_consen   19 ADKIVDALD-LSEGDTVLEIGPGPGALTRELLKRG--KRVIAVEIDPDLAKHLKERFASNPNVEVINGDFLKWDLYD   92 (262)
T ss_dssp             HHHHHHHHT-CGTTSEEEEESSTTSCCHHHHHHHS--SEEEEEESSHHHHHHHHHHCTTCSSEEEEES-TTTSCGGG
T ss_pred             HHHHHHhcC-CCCCCEEEEeCCCCccchhhHhccc--CcceeecCcHhHHHHHHHHhhhcccceeeecchhccccHH
Confidence            355666666 6778999999999999999999998  6688888753 4443333    4899999999998 5544

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 ....

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

Probab=96.57  E-value=0.002  Score=52.75  Aligned_cols=40  Identities=20%  Similarity=0.117  Sum_probs=34.4

Q ss_pred             cceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC
Q 039903          169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY  210 (233)
Q Consensus       169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~  210 (233)
                      ..+|||||||.|.++..+++..  .+++..|+. +.|+.|+.+
T Consensus        60 g~~vLDvGCGgG~Lse~mAr~G--a~VtgiD~se~~I~~Ak~h  100 (243)
T COG2227          60 GLRVLDVGCGGGILSEPLARLG--ASVTGIDASEKPIEVAKLH  100 (243)
T ss_pred             CCeEEEecCCccHhhHHHHHCC--CeeEEecCChHHHHHHHHh
Confidence            3789999999999999999986  789999985 478888754

>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=96.56  E-value=0.0048  Score=40.03  Aligned_cols=44  Identities=16%  Similarity=0.187  Sum_probs=39.2

Q ss_pred             CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903           32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH   83 (233)
Q Consensus        32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~   83 (233)
                      .+.|..|||+.+++    +...+.++|+.|...|+++..    ..+.|.++|
T Consensus        24 ~~~s~~ela~~~g~----s~~tv~r~l~~L~~~g~i~~~----~~~~~~l~~   67 (67)
T cd00092          24 LPLTRQEIADYLGL----TRETVSRTLKELEEEGLISRR----GRGKYRVNP   67 (67)
T ss_pred             CCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEec----CCCeEEeCC
Confidence            58999999999999    999999999999999999985    337787764

>TIGR01983 UbiG ubiquinone biosynthesis O-methyltransferase

Probab=96.56  E-value=0.0048  Score=50.04  Aligned_cols=63  Identities=16%  Similarity=0.019  Sum_probs=45.8

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC------CCceEEecCcCC-CC--CC-CCEEEe
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY------SGVKHIGGIMLE-RI--PK-GDAILI  232 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~------~ri~~~~gD~f~-~~--P~-~D~~~l  232 (233)
                      +..+|+|+|||+|.++..+++..+  +++..|+. ..++.+++.      .++++..+|+.+ +.  |. .|++++
T Consensus        45 ~~~~vLdlG~G~G~~~~~l~~~~~--~v~~iD~s~~~~~~a~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~D~i~~  118 (224)
T TIGR01983        45 FGLRVLDVGCGGGLLSEPLARLGA--NVTGIDASEENIEVAKLHAKKDPLLKIEYRCTSVEDLAEKGAKSFDVVTC  118 (224)
T ss_pred             CCCeEEEECCCCCHHHHHHHhcCC--eEEEEeCCHHHHHHHHHHHHHcCCCceEEEeCCHHHhhcCCCCCccEEEe
Confidence            357899999999999999988755  48899985 466655442      258888888765 22  23 388864

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.

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

Probab=96.55  E-value=0.004  Score=42.45  Aligned_cols=66  Identities=11%  Similarity=0.154  Sum_probs=51.2

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC---CCCceeccHhhhHhh
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD---DQRLYGLAHVAKYFV   89 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~---~~~~y~lt~~s~~l~   89 (233)
                      ++++|...|...   +..+..+|.+.+++    +...+.+.|+.|...|+++....-.   ....|++|+.|+...
T Consensus         1 vRl~Il~~L~~~---~~~~f~~L~~~l~l----t~g~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~~lT~~Gr~~~   69 (80)
T PF13601_consen    1 VRLAILALLYAN---EEATFSELKEELGL----TDGNLSKHLKKLEEAGYVEVEKEFEGRRPRTWYSLTDKGREAF   69 (80)
T ss_dssp             HHHHHHHHHHHH---SEEEHHHHHHHTT------HHHHHHHHHHHHHTTSEEEEEE-SSS--EEEEEE-HHHHHHH
T ss_pred             CHHHHHHHHhhc---CCCCHHHHHHHhCc----CHHHHHHHHHHHHHCCCEEEEEeccCCCCeEEEEECHHHHHHH
Confidence            578899999986   58999999999999    9999999999999999999764321   112589999987544

>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein

Probab=96.50  E-value=0.0072  Score=42.25  Aligned_cols=68  Identities=16%  Similarity=0.274  Sum_probs=53.2

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      .++.|+..|...   ++.|..+||+.+++    +...+.+.++-|+..|++++....+  ....|.+|+.+..+...
T Consensus        11 ~~~~il~~l~~~---~~~~~~~la~~~~~----s~~~i~~~l~~L~~~g~v~~~~~~~~~r~~~~~lT~~g~~~~~~   80 (101)
T smart00347       11 TQFLVLRILYEE---GPLSVSELAKRLGV----SPSTVTRVLDRLEKKGLIRRLPSPEDRRSVLVSLTEEGRELIEE   80 (101)
T ss_pred             HHHHHHHHHHHc---CCcCHHHHHHHHCC----CchhHHHHHHHHHHCCCeEecCCCCCCCeEEEEECHhHHHHHHH
Confidence            356788888876   47999999999999    9999999999999999999763210  12367888888766543

>PF05724 TPMT: Thiopurine S-methyltransferase (TPMT); InterPro: IPR008854 This family consists of thiopurine S-methyltransferase proteins from both eukaryotes and prokaryotes

Probab=96.49  E-value=0.0054  Score=50.03  Aligned_cols=55  Identities=18%  Similarity=0.202  Sum_probs=42.8

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhcc--C----------------CCCceEEecCcCC
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSS--S----------------YSGVKHIGGIMLE  222 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~--~----------------~~ri~~~~gD~f~  222 (233)
                      .....++++.|||.|.-+..|+++  ..+++++|+.+ +++.+.  .                .++|++..||||+
T Consensus        35 ~~~~~rvLvPgCG~g~D~~~La~~--G~~VvGvDls~~Ai~~~~~e~~~~~~~~~~~~~~~~~~~~i~~~~gDfF~  108 (218)
T PF05724_consen   35 LKPGGRVLVPGCGKGYDMLWLAEQ--GHDVVGVDLSPTAIEQAFEENNLEPTVTSVGGFKRYQAGRITIYCGDFFE  108 (218)
T ss_dssp             TSTSEEEEETTTTTSCHHHHHHHT--TEEEEEEES-HHHHHHHHHHCTTEEECTTCTTEEEETTSSEEEEES-TTT
T ss_pred             CCCCCeEEEeCCCChHHHHHHHHC--CCeEEEEecCHHHHHHHHHHhccCCCcccccceeeecCCceEEEEccccc
Confidence            355579999999999999999997  56899999965 666551  1                0478999999998

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.

>KOG1541 consensus Predicted protein carboxyl methylase [General function prediction only]

Probab=96.48  E-value=0.0023  Score=51.73  Aligned_cols=61  Identities=16%  Similarity=0.310  Sum_probs=44.1

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCCCCc--eEEecCcCC--CCCCC--CEEE
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSYSGV--KHIGGIMLE--RIPKG--DAIL  231 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~~ri--~~~~gD~f~--~~P~~--D~~~  231 (233)
                      ...-|||||||+|..+..+...  ....+.+|+ |+.++.|.+ ..+  .++-+|+=+  |+++|  |.++
T Consensus        50 ~~~~iLDIGCGsGLSg~vL~~~--Gh~wiGvDiSpsML~~a~~-~e~egdlil~DMG~GlpfrpGtFDg~I  117 (270)
T KOG1541|consen   50 KSGLILDIGCGSGLSGSVLSDS--GHQWIGVDISPSMLEQAVE-RELEGDLILCDMGEGLPFRPGTFDGVI  117 (270)
T ss_pred             CCcEEEEeccCCCcchheeccC--CceEEeecCCHHHHHHHHH-hhhhcCeeeeecCCCCCCCCCccceEE
Confidence            3789999999999888777664  567899998 678888875 223  356677777  44455  6554

>PRK11783 rlmL 23S rRNA m(2)G2445 methyltransferase; Provisional

Probab=96.46  E-value=0.004  Score=59.40  Aligned_cols=64  Identities=14%  Similarity=0.038  Sum_probs=49.9

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC--------CCceEEecCcCCC---CCCC-CEEEe
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY--------SGVKHIGGIMLER---IPKG-DAILI  232 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~--------~ri~~~~gD~f~~---~P~~-D~~~l  232 (233)
                      +.++|+|+|||+|.++..+++. ...+++.+|+. ..++.++++        ++++++.+|.++.   .+.. |+|++
T Consensus       538 ~g~rVLDlf~gtG~~sl~aa~~-Ga~~V~~vD~s~~al~~a~~N~~~ng~~~~~v~~i~~D~~~~l~~~~~~fDlIil  614 (702)
T PRK11783        538 KGKDFLNLFAYTGTASVHAALG-GAKSTTTVDMSNTYLEWAERNFALNGLSGRQHRLIQADCLAWLKEAREQFDLIFI  614 (702)
T ss_pred             CCCeEEEcCCCCCHHHHHHHHC-CCCEEEEEeCCHHHHHHHHHHHHHhCCCccceEEEEccHHHHHHHcCCCcCEEEE
Confidence            4579999999999999999986 34469999985 577777653        4899999999873   2333 98876

>TIGR00095 RNA methyltransferase, RsmD family

Probab=96.45  E-value=0.0028  Score=50.53  Aligned_cols=53  Identities=15%  Similarity=0.013  Sum_probs=42.9

Q ss_pred             cceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC-------CCceEEecCcCC
Q 039903          169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY-------SGVKHIGGIMLE  222 (233)
Q Consensus       169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~-------~ri~~~~gD~f~  222 (233)
                      ..+++|++||+|.++.+++.+... +++.+|.. .+++.++++       ++++++.+|.++
T Consensus        50 g~~vLDLfaGsG~lglea~srga~-~v~~vE~~~~a~~~~~~N~~~~~~~~~~~~~~~D~~~  110 (189)
T TIGR00095        50 GAHLLDVFAGSGLLGEEALSRGAK-VAFLEEDDRKANQTLKENLALLKSGEQAEVVRNSALR  110 (189)
T ss_pred             CCEEEEecCCCcHHHHHHHhCCCC-EEEEEeCCHHHHHHHHHHHHHhCCcccEEEEehhHHH
Confidence            478999999999999999999764 78888985 466555442       478999999976

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.

>PRK15128 23S rRNA m(5)C1962 methyltransferase; Provisional

Probab=96.44  E-value=0.0041  Score=55.28  Aligned_cols=65  Identities=12%  Similarity=0.049  Sum_probs=48.5

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC--------CCceEEecCcCCCC------CC-CCEE
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY--------SGVKHIGGIMLERI------PK-GDAI  230 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~--------~ri~~~~gD~f~~~------P~-~D~~  230 (233)
                      .+.++|+|+|||+|.++.+.+.. ...+++.+|+. ..++.++++        ++++++.+|.|+.+      .. .|+|
T Consensus       219 ~~g~rVLDlfsgtG~~~l~aa~~-ga~~V~~VD~s~~al~~a~~N~~~Ngl~~~~v~~i~~D~~~~l~~~~~~~~~fDlV  297 (396)
T PRK15128        219 VENKRVLNCFSYTGGFAVSALMG-GCSQVVSVDTSQEALDIARQNVELNKLDLSKAEFVRDDVFKLLRTYRDRGEKFDVI  297 (396)
T ss_pred             cCCCeEEEeccCCCHHHHHHHhC-CCCEEEEEECCHHHHHHHHHHHHHcCCCCCcEEEEEccHHHHHHHHHhcCCCCCEE
Confidence            44589999999999998876653 45589999985 467666553        37999999999732      11 3998


Q ss_pred             Ee
Q 039903          231 LI  232 (233)
Q Consensus       231 ~l  232 (233)
                      ++
T Consensus       298 il  299 (396)
T PRK15128        298 VM  299 (396)
T ss_pred             EE
Confidence            86

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=96.43  E-value=0.006  Score=36.73  Aligned_cols=41  Identities=15%  Similarity=0.121  Sum_probs=36.6

Q ss_pred             CCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceecc
Q 039903           33 KISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLA   82 (233)
Q Consensus        33 ~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt   82 (233)
                      +.|..|||+.+++    +...+.+.|+.|...|+++..     .+.|.++
T Consensus         8 ~~s~~~la~~l~~----s~~tv~~~l~~L~~~g~l~~~-----~~~~~i~   48 (48)
T smart00419        8 PLTRQEIAELLGL----TRETVSRTLKRLEKEGLISRE-----GGRIVIL   48 (48)
T ss_pred             ccCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEe-----CCEEEEC
Confidence            7899999999999    999999999999999999985     5677653

>COG4262 Predicted spermidine synthase with an N-terminal membrane domain [General function prediction only]

Probab=96.41  E-value=0.0084  Score=52.03  Aligned_cols=55  Identities=18%  Similarity=0.297  Sum_probs=46.5

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCC-CcEEEeec-hHHHhhccCC-------------CCceEEecCcCC
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLH-IKGVNFDL-SHVIQDSSSY-------------SGVKHIGGIMLE  222 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~-l~~~v~Dl-p~v~~~a~~~-------------~ri~~~~gD~f~  222 (233)
                      ++..+++-+|||.|..++++++ ||. -+++.+|+ |.+++.++++             +|++.+.-|.|+
T Consensus       288 ~~a~~vLvlGGGDGLAlRellk-yP~~~qI~lVdLDP~miela~~~~vlr~~N~~sf~dpRv~Vv~dDAf~  357 (508)
T COG4262         288 RGARSVLVLGGGDGLALRELLK-YPQVEQITLVDLDPRMIELASHATVLRALNQGSFSDPRVTVVNDDAFQ  357 (508)
T ss_pred             cccceEEEEcCCchHHHHHHHh-CCCcceEEEEecCHHHHHHhhhhhHhhhhccCCccCCeeEEEeccHHH
Confidence            4568999999999999999987 895 46888898 7799988742             799999999997

>PRK10857 DNA-binding transcriptional regulator IscR; Provisional

Probab=96.38  E-value=0.0082  Score=46.73  Aligned_cols=62  Identities=11%  Similarity=0.177  Sum_probs=47.0

Q ss_pred             HHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903           10 PAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH   83 (233)
Q Consensus        10 s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~   83 (233)
                      -.+|++.+.+.    ....+  ++.|.++||+++++    ++..+.++|+.|...|++.....  .+|.|.+..
T Consensus         8 ~yAl~~l~~lA----~~~~~--~~vs~~eIA~~~~i----p~~~l~kIl~~L~~aGLv~s~rG--~~GGy~Lar   69 (164)
T PRK10857          8 RYAVTAMLDVA----LNSEA--GPVPLADISERQGI----SLSYLEQLFSRLRKNGLVSSVRG--PGGGYLLGK   69 (164)
T ss_pred             HHHHHHHHHHH----hCCCC--CcCcHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEeCCC--CCCCeeccC
Confidence            34555555554    12212  58999999999999    99999999999999999997432  467788764

>PRK03902 manganese transport transcriptional regulator; Provisional

Probab=96.37  E-value=0.011  Score=44.69  Aligned_cols=50  Identities=14%  Similarity=0.080  Sum_probs=44.8

Q ss_pred             CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhh
Q 039903           32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFV   89 (233)
Q Consensus        32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~   89 (233)
                      ++.+..+||+.+++    ++..+.+.++.|...|++.+.    ....|.+|+.|..+.
T Consensus        21 ~~~~~~ela~~l~v----s~~svs~~l~~L~~~Gli~~~----~~~~i~LT~~G~~~a   70 (142)
T PRK03902         21 GYARVSDIAEALSV----HPSSVTKMVQKLDKDEYLIYE----KYRGLVLTPKGKKIG   70 (142)
T ss_pred             CCcCHHHHHHHhCC----ChhHHHHHHHHHHHCCCEEEe----cCceEEECHHHHHHH
Confidence            68899999999999    999999999999999999975    467899999997654

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

Probab=96.37  E-value=0.0056  Score=40.44  Aligned_cols=44  Identities=14%  Similarity=0.295  Sum_probs=37.6

Q ss_pred             hhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeec
Q 039903           21 VFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTS   71 (233)
Q Consensus        21 lfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~   71 (233)
                      |-++|.+.   +.+|..|||..+++    ++..++.+|+.|+..|.+++..
T Consensus         5 i~~~l~~~---~~~S~~eLa~~~~~----s~~~ve~mL~~l~~kG~I~~~~   48 (69)
T PF09012_consen    5 IRDYLRER---GRVSLAELAREFGI----SPEAVEAMLEQLIRKGYIRKVD   48 (69)
T ss_dssp             HHHHHHHS----SEEHHHHHHHTT------HHHHHHHHHHHHCCTSCEEEE
T ss_pred             HHHHHHHc---CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCcEEEec
Confidence            56778886   58999999999999    9999999999999999999874

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

>PRK11760 putative 23S rRNA C2498 ribose 2'-O-ribose methyltransferase; Provisional

Probab=96.34  E-value=0.013  Score=50.74  Aligned_cols=63  Identities=16%  Similarity=0.135  Sum_probs=50.5

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCCCCceEEecCcCCCCC-C-C-CEEE
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIP-K-G-DAIL  231 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~~ri~~~~gD~f~~~P-~-~-D~~~  231 (233)
                      ....++||||++.|.++..++++  +.+++.+|...........+||+++.+|-|...| . . |.++
T Consensus       210 ~~g~~vlDLGAsPGGWT~~L~~r--G~~V~AVD~g~l~~~L~~~~~V~h~~~d~fr~~p~~~~vDwvV  275 (357)
T PRK11760        210 APGMRAVDLGAAPGGWTYQLVRR--GMFVTAVDNGPMAQSLMDTGQVEHLRADGFKFRPPRKNVDWLV  275 (357)
T ss_pred             CCCCEEEEeCCCCcHHHHHHHHc--CCEEEEEechhcCHhhhCCCCEEEEeccCcccCCCCCCCCEEE
Confidence            45689999999999999999998  5589999976655555667999999999998555 2 2 6654

>PF01170 UPF0020: Putative RNA methylase family UPF0020; InterPro: IPR000241 This domain is probably a methylase

Probab=96.34  E-value=0.0093  Score=47.10  Aligned_cols=74  Identities=16%  Similarity=0.160  Sum_probs=52.0

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCc---------EEEeec-hHHHhhccCC-------CCceEEecC
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIK---------GVNFDL-SHVIQDSSSY-------SGVKHIGGI  219 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~---------~~v~Dl-p~v~~~a~~~-------~ri~~~~gD  219 (233)
                      ..++.... |++...++|-=||+|.++++.+...++..         ++..|. +..++.++.+       +.|.+...|
T Consensus        18 ~~ll~la~-~~~~~~vlDP~CGsGtiliEaa~~~~~~~~~~~~~~~~~~g~Di~~~~v~~a~~N~~~ag~~~~i~~~~~D   96 (179)
T PF01170_consen   18 AALLNLAG-WRPGDVVLDPFCGSGTILIEAALMGANIPPLNDINELKIIGSDIDPKAVRGARENLKAAGVEDYIDFIQWD   96 (179)
T ss_dssp             HHHHHHTT---TTS-EEETT-TTSHHHHHHHHHHTTTSTTTH-CH--EEEEESSHHHHHHHHHHHHHTT-CGGEEEEE--
T ss_pred             HHHHHHhC-CCCCCEEeecCCCCCHHHHHHHHHhhCcccccccccccEEecCCCHHHHHHHHHHHHhcccCCceEEEecc
Confidence            34445444 77778999999999999999888888877         889998 4577766653       568999999


Q ss_pred             cCC-CCCCC--CEEE
Q 039903          220 MLE-RIPKG--DAIL  231 (233)
Q Consensus       220 ~f~-~~P~~--D~~~  231 (233)
                      +++ +++.+  |.++
T Consensus        97 ~~~l~~~~~~~d~Iv  111 (179)
T PF01170_consen   97 ARELPLPDGSVDAIV  111 (179)
T ss_dssp             GGGGGGTTSBSCEEE
T ss_pred             hhhcccccCCCCEEE
Confidence            998 75543  8776

It is associated with the THUMP domain that also occurs with RNA modification domains [].; PDB: 3LDU_A 3LDG_A 3K0B_A 3V8V_B 3V97_A 3TLJ_A 3TM5_B 3TM4_A 3TMA_A.

>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=96.34  E-value=0.011  Score=50.48  Aligned_cols=66  Identities=12%  Similarity=0.113  Sum_probs=49.7

Q ss_pred             HHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-----CCceEEecCcCC
Q 039903          156 TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-----SGVKHIGGIMLE  222 (233)
Q Consensus       156 ~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-----~ri~~~~gD~f~  222 (233)
                      ..++++.+. -.....+||+==|.|.++.++++++|+.+.+.+|. |.+++.+++.     +|+.++.++|-+
T Consensus         9 l~Evl~~L~-~~~~g~~vD~T~G~GGHS~aiL~~~~~~~li~~DrD~~a~~~a~~~l~~~~~r~~~~~~~F~~   80 (310)
T PF01795_consen    9 LKEVLEALN-PKPGGIYVDCTFGGGGHSKAILEKLPNGRLIGIDRDPEALERAKERLKKFDDRFIFIHGNFSN   80 (310)
T ss_dssp             HHHHHHHHT---TT-EEEETT-TTSHHHHHHHHT-TT-EEEEEES-HHHHHHHHCCTCCCCTTEEEEES-GGG
T ss_pred             HHHHHHhhC-cCCCceEEeecCCcHHHHHHHHHhCCCCeEEEecCCHHHHHHHHHHHhhccceEEEEeccHHH
Confidence            456777766 56678999999999999999999999999999998 5688777653     799999999865

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.

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

Probab=96.33  E-value=0.0061  Score=55.93  Aligned_cols=64  Identities=13%  Similarity=0.112  Sum_probs=45.8

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeech--HHHhhccC-----CCCceEEecCcC---CCCCCC--CEEE
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS--HVIQDSSS-----YSGVKHIGGIML---ERIPKG--DAIL  231 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp--~v~~~a~~-----~~ri~~~~gD~f---~~~P~~--D~~~  231 (233)
                      +...+||||||.|.++..+++++|+..++++|.-  .+....+.     ..++.++.+|+-   .-+|.+  |.++
T Consensus       347 ~~p~~lEIG~G~G~~~~~~A~~~p~~~~iGiE~~~~~~~~~~~~~~~~~l~N~~~~~~~~~~~~~~~~~~sv~~i~  422 (506)
T PRK01544        347 KRKVFLEIGFGMGEHFINQAKMNPDALFIGVEVYLNGVANVLKLAGEQNITNFLLFPNNLDLILNDLPNNSLDGIY  422 (506)
T ss_pred             CCceEEEECCCchHHHHHHHHhCCCCCEEEEEeeHHHHHHHHHHHHHcCCCeEEEEcCCHHHHHHhcCcccccEEE
Confidence            3588999999999999999999999999999974  23322221     256777777763   245653  4443

>COG1959 Predicted transcriptional regulator [Transcription]

Probab=96.33  E-value=0.0087  Score=45.89  Aligned_cols=57  Identities=21%  Similarity=0.224  Sum_probs=46.1

Q ss_pred             hHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHh
Q 039903           22 FEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHV   84 (233)
Q Consensus        22 fd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~   84 (233)
                      .-.|+..+.+++.|+++||+..++    ++.+|.++|..|...|+++-.+.  .+|.|+|..-
T Consensus        14 L~~LA~~~~~~~~s~~~IA~~~~i----s~~~L~kil~~L~kaGlV~S~rG--~~GGy~Lar~   70 (150)
T COG1959          14 LLYLALLPGGGPVSSAEIAERQGI----SPSYLEKILSKLRKAGLVKSVRG--KGGGYRLARP   70 (150)
T ss_pred             HHHHHhCCCCCcccHHHHHHHhCc----CHHHHHHHHHHHHHcCCEEeecC--CCCCccCCCC
Confidence            344555443348899999999999    99999999999999999998753  4788988753

>PRK13256 thiopurine S-methyltransferase; Reviewed

Probab=96.32  E-value=0.02  Score=46.95  Aligned_cols=54  Identities=11%  Similarity=0.100  Sum_probs=43.7

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccC------------------CCCceEEecCcCC
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSS------------------YSGVKHIGGIMLE  222 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~------------------~~ri~~~~gD~f~  222 (233)
                      .+..+|++.|||.|..+.-|++.  ..+++.+|+.+ .++.+.+                  ..+|++..+|||+
T Consensus        42 ~~~~rvLvPgCGkg~D~~~LA~~--G~~V~GvDlS~~Ai~~~~~e~~~~~~~~~~~~~~~~~~~~i~~~~gD~f~  114 (226)
T PRK13256         42 NDSSVCLIPMCGCSIDMLFFLSK--GVKVIGIELSEKAVLSFFSQNTINYEVIHGNDYKLYKGDDIEIYVADIFN  114 (226)
T ss_pred             CCCCeEEEeCCCChHHHHHHHhC--CCcEEEEecCHHHHHHHHHHcCCCcceecccccceeccCceEEEEccCcC
Confidence            34579999999999999999997  66799999965 5655311                  1589999999998

>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR

Probab=96.32  E-value=0.0094  Score=44.81  Aligned_cols=46  Identities=11%  Similarity=0.213  Sum_probs=39.7

Q ss_pred             CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903           32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH   83 (233)
Q Consensus        32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~   83 (233)
                      ++.|.+|||+.+++    ++..++++|+.|...|+++....  .+|.|.++.
T Consensus        24 ~~~s~~~ia~~~~i----p~~~l~kil~~L~~~glv~s~~G--~~Ggy~l~~   69 (135)
T TIGR02010        24 GPVTLADISERQGI----SLSYLEQLFAKLRKAGLVKSVRG--PGGGYQLGR   69 (135)
T ss_pred             CcCcHHHHHHHHCc----CHHHHHHHHHHHHHCCceEEEeC--CCCCEeccC
Confidence            48999999999999    99999999999999999986432  456788765

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

>COG2519 GCD14 tRNA(1-methyladenosine) methyltransferase and related methyltransferases [Translation, ribosomal structure and biogenesis]

Probab=96.31  E-value=0.022  Score=47.07  Aligned_cols=84  Identities=14%  Similarity=0.166  Sum_probs=64.4

Q ss_pred             HHhcchhc----HHHHHHhcccccCcceEEEecCCccHHHHHHHH-HcCCCcEEEeec-hHHHhhccCC-------CCce
Q 039903          148 MLNHTSIV----TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIIS-NYLHIKGVNFDL-SHVIQDSSSY-------SGVK  214 (233)
Q Consensus       148 m~~~~~~~----~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~-~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~  214 (233)
                      |...++..    +..++.... .+...+|+|.|-|+|.++..|+. -.|.=+.+.+|. ++-.+.|+++       ++|+
T Consensus        71 ~~R~tQiIyPKD~~~I~~~~g-i~pg~rVlEAGtGSG~lt~~La~~vg~~G~v~tyE~r~d~~k~A~~Nl~~~~l~d~v~  149 (256)
T COG2519          71 MKRRTQIIYPKDAGYIVARLG-ISPGSRVLEAGTGSGALTAYLARAVGPEGHVTTYEIREDFAKTARENLSEFGLGDRVT  149 (256)
T ss_pred             CcCCCceecCCCHHHHHHHcC-CCCCCEEEEcccCchHHHHHHHHhhCCCceEEEEEecHHHHHHHHHHHHHhccccceE
Confidence            55555543    344555555 78889999999999999999997 578888999986 5677777664       6799


Q ss_pred             EEecCcCC-CCCCC-CEEEe
Q 039903          215 HIGGIMLE-RIPKG-DAILI  232 (233)
Q Consensus       215 ~~~gD~f~-~~P~~-D~~~l  232 (233)
                      +..+|..+ ..+.- |+++|
T Consensus       150 ~~~~Dv~~~~~~~~vDav~L  169 (256)
T COG2519         150 LKLGDVREGIDEEDVDAVFL  169 (256)
T ss_pred             EEeccccccccccccCEEEE
Confidence            99999998 44443 88876

>PRK14901 16S rRNA methyltransferase B; Provisional

Probab=96.30  E-value=0.0089  Score=53.84  Aligned_cols=71  Identities=11%  Similarity=-0.036  Sum_probs=52.0

Q ss_pred             HhcccccCcceEEEecCCccHHHHHHHHHcC-CCcEEEeec-hHHHhhccCC------CCceEEecCcCC-C----CCC-
Q 039903          161 DSSKGFEQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLE-R----IPK-  226 (233)
Q Consensus       161 ~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~-~----~P~-  226 (233)
                      ..++ .....+|+|+|||.|..+..+++..+ .-+++.+|. ++.++.++++      ++|+++.+|..+ +    .+. 
T Consensus       246 ~~l~-~~~g~~VLDl~ag~G~kt~~la~~~~~~g~v~a~D~~~~rl~~~~~n~~r~g~~~v~~~~~D~~~~~~~~~~~~~  324 (434)
T PRK14901        246 PLLD-PQPGEVILDACAAPGGKTTHIAELMGDQGEIWAVDRSASRLKKLQENAQRLGLKSIKILAADSRNLLELKPQWRG  324 (434)
T ss_pred             HHhC-CCCcCEEEEeCCCCchhHHHHHHHhCCCceEEEEcCCHHHHHHHHHHHHHcCCCeEEEEeCChhhcccccccccc
Confidence            3344 44568999999999999999999854 568999998 4466655442      569999999876 2    222 


Q ss_pred             -CCEEEe
Q 039903          227 -GDAILI  232 (233)
Q Consensus       227 -~D~~~l  232 (233)
                       .|.|++
T Consensus       325 ~fD~Vl~  331 (434)
T PRK14901        325 YFDRILL  331 (434)
T ss_pred             cCCEEEE
Confidence             398875

>KOG1270 consensus Methyltransferases [Coenzyme transport and metabolism]

Probab=96.29  E-value=0.0037  Score=51.78  Aligned_cols=60  Identities=17%  Similarity=0.123  Sum_probs=42.8

Q ss_pred             ceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC--------C----CceEEecCcCCCCCCCCEEE
Q 039903          170 KQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY--------S----GVKHIGGIMLERIPKGDAIL  231 (233)
Q Consensus       170 ~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~--------~----ri~~~~gD~f~~~P~~D~~~  231 (233)
                      .+|||||||.|.++..|++..  .+++..|.- ..++.|+++        .    |+++...|.-.-.+.-|+++
T Consensus        91 ~~ilDvGCGgGLLSepLArlg--a~V~GID~s~~~V~vA~~h~~~dP~~~~~~~y~l~~~~~~~E~~~~~fDaVv  163 (282)
T KOG1270|consen   91 MKILDVGCGGGLLSEPLARLG--AQVTGIDASDDMVEVANEHKKMDPVLEGAIAYRLEYEDTDVEGLTGKFDAVV  163 (282)
T ss_pred             ceEEEeccCccccchhhHhhC--CeeEeecccHHHHHHHHHhhhcCchhccccceeeehhhcchhhcccccceee
Confidence            679999999999999999985  668899984 577777663        2    46665555444333346554

>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR

Probab=96.27  E-value=0.014  Score=42.57  Aligned_cols=67  Identities=15%  Similarity=0.156  Sum_probs=53.9

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      +..|+..|...   ++.|..|||+.+++    +...+.++++-|...|++++.....  ..-.+.+|+.|..+...
T Consensus        30 q~~iL~~l~~~---~~~t~~ela~~~~~----~~~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT~~G~~~~~~   98 (118)
T TIGR02337        30 QWRILRILAEQ---GSMEFTQLANQACI----LRPSLTGILARLERDGLVTRLKASNDQRRVYISLTPKGQALYAS   98 (118)
T ss_pred             HHHHHHHHHHc---CCcCHHHHHHHhCC----CchhHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHHHH
Confidence            33477777776   58999999999999    9999999999999999999864321  12378999999887755

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.

>TIGR00563 rsmB ribosomal RNA small subunit methyltransferase RsmB

Probab=96.26  E-value=0.0081  Score=53.96  Aligned_cols=73  Identities=14%  Similarity=0.093  Sum_probs=51.5

Q ss_pred             HHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------C-CceEEecCcCCC-C--CC-
Q 039903          159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------S-GVKHIGGIMLER-I--PK-  226 (233)
Q Consensus       159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~-ri~~~~gD~f~~-~--P~-  226 (233)
                      ++..++ .....+|+|+|||.|..+..+++..|..+++.+|. ++.++.++++      + ++.++.+|..+. .  +. 
T Consensus       230 ~~~~L~-~~~g~~VLDlcag~G~kt~~la~~~~~~~v~a~D~~~~~l~~~~~n~~r~g~~~~v~~~~~d~~~~~~~~~~~  308 (426)
T TIGR00563       230 VATWLA-PQNEETILDACAAPGGKTTHILELAPQAQVVALDIHEHRLKRVYENLKRLGLTIKAETKDGDGRGPSQWAENE  308 (426)
T ss_pred             HHHHhC-CCCCCeEEEeCCCccHHHHHHHHHcCCCeEEEEeCCHHHHHHHHHHHHHcCCCeEEEEecccccccccccccc
Confidence            334444 45568999999999999999999988788999998 4566655542      2 344477887652 2  22 


Q ss_pred             -CCEEEe
Q 039903          227 -GDAILI  232 (233)
Q Consensus       227 -~D~~~l  232 (233)
                       .|.|++
T Consensus       309 ~fD~Vll  315 (426)
T TIGR00563       309 QFDRILL  315 (426)
T ss_pred             ccCEEEE
Confidence             388875

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.

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

Probab=96.25  E-value=0.0071  Score=52.99  Aligned_cols=51  Identities=14%  Similarity=0.121  Sum_probs=42.6

Q ss_pred             ceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCC
Q 039903          170 KQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLE  222 (233)
Q Consensus       170 ~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~  222 (233)
                      .+++|++||+|.++..+++...  +++.+|. ++.++.++++      ++++++.+|..+
T Consensus       199 ~~vlDl~~G~G~~sl~la~~~~--~v~~vE~~~~av~~a~~n~~~~~~~~v~~~~~d~~~  256 (353)
T TIGR02143       199 GDLLELYCGNGNFSLALAQNFR--RVLATEIAKPSVNAAQYNIAANNIDNVQIIRMSAEE  256 (353)
T ss_pred             CcEEEEeccccHHHHHHHHhCC--EEEEEECCHHHHHHHHHHHHHcCCCcEEEEEcCHHH
Confidence            4699999999999999998874  7999997 5577777653      579999999876

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.

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=96.20  E-value=0.013  Score=43.34  Aligned_cols=46  Identities=13%  Similarity=0.217  Sum_probs=39.7

Q ss_pred             ChhHHHH-hcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeecc
Q 039903           20 GVFEIIA-KAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSA   72 (233)
Q Consensus        20 glfd~L~-~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~   72 (233)
                      .++.+|- .+   +|.|+++||+.++.    +...++|-|+-|...|++.+...
T Consensus        31 ~v~~~LL~~~---~~~tvdelae~lnr----~rStv~rsl~~L~~~GlV~Rek~   77 (126)
T COG3355          31 EVYKALLEEN---GPLTVDELAEILNR----SRSTVYRSLQNLLEAGLVEREKV   77 (126)
T ss_pred             HHHHHHHhhc---CCcCHHHHHHHHCc----cHHHHHHHHHHHHHcCCeeeeee
Confidence            4566665 44   69999999999999    99999999999999999998643

>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=96.18  E-value=0.014  Score=40.53  Aligned_cols=69  Identities=22%  Similarity=0.185  Sum_probs=54.2

Q ss_pred             HHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHH----------HhcCCce-eeeccCCCCCceeccH
Q 039903           15 AASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRL----------LVTHRVL-RCTSAGDDQRLYGLAH   83 (233)
Q Consensus        15 ~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~----------L~~~gll-~~~~~~~~~~~y~lt~   83 (233)
                      .=++..|+..|....| .+.++.|||..+++    ++..+.--|+.          |+.+|++ ++.... +...|++|+
T Consensus         8 S~~R~~vl~~L~~~yp-~~~~~~eIar~v~~----~~snV~GaL~G~g~rY~~e~SLv~lGLV~~~~~~~-g~k~Y~lT~   81 (90)
T PF07381_consen    8 SKVRKKVLEYLCSIYP-EPAYPSEIARSVGS----DYSNVLGALRGDGKRYNKEDSLVGLGLVEEEEEKG-GFKYYRLTE   81 (90)
T ss_pred             HHHHHHHHHHHHHcCC-CcCCHHHHHHHHCC----CHHHHHHHHhcCCCCcCcchhHHHcCCeeEeeecC-CeeEEEeCh
Confidence            5567889999999833 58999999999999    99888777764          8999999 443222 356899999


Q ss_pred             hhhHhh
Q 039903           84 VAKYFV   89 (233)
Q Consensus        84 ~s~~l~   89 (233)
                      .+..++
T Consensus        82 ~G~~~~   87 (90)
T PF07381_consen   82 KGKRIA   87 (90)
T ss_pred             hhhhHH
Confidence            887654

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

>COG0030 KsgA Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]

Probab=96.16  E-value=0.022  Score=47.47  Aligned_cols=68  Identities=15%  Similarity=0.374  Sum_probs=50.1

Q ss_pred             HHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhcc----CCCCceEEecCcCC-CCCC
Q 039903          156 TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSS----SYSGVKHIGGIMLE-RIPK  226 (233)
Q Consensus       156 ~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~----~~~ri~~~~gD~f~-~~P~  226 (233)
                      ...+++..+ -.....|+.||.|.|.+...|+++...  ++.+++.. -++..+    ..++++.+.||+.+ .+|.
T Consensus        19 ~~kIv~~a~-~~~~d~VlEIGpG~GaLT~~Ll~~~~~--v~aiEiD~~l~~~L~~~~~~~~n~~vi~~DaLk~d~~~   92 (259)
T COG0030          19 IDKIVEAAN-ISPGDNVLEIGPGLGALTEPLLERAAR--VTAIEIDRRLAEVLKERFAPYDNLTVINGDALKFDFPS   92 (259)
T ss_pred             HHHHHHhcC-CCCCCeEEEECCCCCHHHHHHHhhcCe--EEEEEeCHHHHHHHHHhcccccceEEEeCchhcCcchh
Confidence            456666665 455789999999999999999999777  55555433 222222    24899999999998 7774

>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator)

Probab=96.15  E-value=0.012  Score=43.82  Aligned_cols=47  Identities=26%  Similarity=0.286  Sum_probs=39.5

Q ss_pred             CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHh
Q 039903           32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHV   84 (233)
Q Consensus        32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~   84 (233)
                      ++.|.++||+.+++    ++..++++|+.|...|++.....  ..+.|.++..
T Consensus        24 ~~~s~~eia~~~~i----~~~~v~~il~~L~~~gli~~~~g--~~ggy~l~~~   70 (132)
T TIGR00738        24 GPVSVKEIAERQGI----SRSYLEKILRTLRRAGLVESVRG--PGGGYRLARP   70 (132)
T ss_pred             CcCcHHHHHHHHCc----CHHHHHHHHHHHHHCCcEEeccC--CCCCccCCCC
Confidence            48999999999999    99999999999999999987421  3457877643

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.

>TIGR00478 tly hemolysin TlyA family protein

Probab=96.14  E-value=0.021  Score=46.92  Aligned_cols=55  Identities=15%  Similarity=0.134  Sum_probs=38.8

Q ss_pred             HHHHhcccc-cCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHh-hccCCCCce
Q 039903          158 RIIDSSKGF-EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQ-DSSSYSGVK  214 (233)
Q Consensus       158 ~~~~~~~~~-~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~-~a~~~~ri~  214 (233)
                      .+++.++ . .+..+++|||||+|.++..++++ +.-+++.+|... .+. ..+.++||.
T Consensus        65 ~~l~~~~-~~~~~~~vlDiG~gtG~~t~~l~~~-ga~~v~avD~~~~~l~~~l~~~~~v~  122 (228)
T TIGR00478        65 EALEEFN-IDVKNKIVLDVGSSTGGFTDCALQK-GAKEVYGVDVGYNQLAEKLRQDERVK  122 (228)
T ss_pred             HHHHhcC-CCCCCCEEEEcccCCCHHHHHHHHc-CCCEEEEEeCCHHHHHHHHhcCCCee
Confidence            4445544 2 24578999999999999999986 556799999865 443 345555644

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).

>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=96.13  E-value=0.014  Score=38.27  Aligned_cols=61  Identities=11%  Similarity=0.140  Sum_probs=48.0

Q ss_pred             hhHHHHhcCCCCCCCHHHHHHhCCCC-CCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhH
Q 039903           21 VFEIIAKAGPTAKISAVEIAAQMPSS-NPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKY   87 (233)
Q Consensus        21 lfd~L~~~~~~~~~t~~elA~~~~~~-~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~   87 (233)
                      |++.|.+.+  +|++..+|++.++.. ...+++.++|.|+.|-..|++.+.    ..+.+.+|+.+..
T Consensus         3 IL~~L~~~~--~P~g~~~l~~~L~~~g~~~se~avRrrLr~me~~Glt~~~----g~~G~~iT~~G~~   64 (66)
T PF08461_consen    3 ILRILAESD--KPLGRKQLAEELKLRGEELSEEAVRRRLRAMERDGLTRKV----GRQGRIITEKGLD   64 (66)
T ss_pred             HHHHHHHcC--CCCCHHHHHHHHHhcChhhhHHHHHHHHHHHHHCCCcccc----CCcccccCHHHHh
Confidence            567888875  799999999999762 122578999999999999988775    4566678887754

>PRK14903 16S rRNA methyltransferase B; Provisional

Probab=96.07  E-value=0.014  Score=52.58  Aligned_cols=67  Identities=19%  Similarity=0.060  Sum_probs=50.5

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHc-CCCcEEEeech-HHHhhccCC------CCceEEecCcCC-C-C-CC-CCEEEe
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNY-LHIKGVNFDLS-HVIQDSSSY------SGVKHIGGIMLE-R-I-PK-GDAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~-P~l~~~v~Dlp-~v~~~a~~~------~ri~~~~gD~f~-~-~-P~-~D~~~l  232 (233)
                      .....+|+|+|||.|..+..+++.. +.-+++.+|+. +.++.++++      ++|+++.+|..+ + . +. -|.|++
T Consensus       235 ~~~g~~VLD~cagpGgkt~~la~~~~~~g~V~a~Dis~~rl~~~~~n~~r~g~~~v~~~~~Da~~l~~~~~~~fD~Vl~  313 (431)
T PRK14903        235 LEPGLRVLDTCAAPGGKTTAIAELMKDQGKILAVDISREKIQLVEKHAKRLKLSSIEIKIADAERLTEYVQDTFDRILV  313 (431)
T ss_pred             CCCCCEEEEeCCCccHHHHHHHHHcCCCCEEEEEECCHHHHHHHHHHHHHcCCCeEEEEECchhhhhhhhhccCCEEEE
Confidence            4556799999999999999999886 56789999984 466655542      468899999875 2 2 22 388875

>TIGR00006 S-adenosyl-methyltransferase MraW

Probab=96.06  E-value=0.019  Score=49.15  Aligned_cols=66  Identities=12%  Similarity=0.122  Sum_probs=53.5

Q ss_pred             HHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-----CCceEEecCcCC
Q 039903          156 TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-----SGVKHIGGIMLE  222 (233)
Q Consensus       156 ~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-----~ri~~~~gD~f~  222 (233)
                      ..++++.+. -.....+||+=.|.|..+.+++++.|+.+++.+|. |.+++.+++.     +|++++.++|-+
T Consensus         9 l~Evl~~L~-~~~ggiyVD~TlG~GGHS~~iL~~l~~g~vigiD~D~~Al~~ak~~L~~~~~R~~~i~~nF~~   80 (305)
T TIGR00006         9 LDEVVEGLN-IKPDGIYIDCTLGFGGHSKAILEQLGTGRLIGIDRDPQAIAFAKERLSDFEGRVVLIHDNFAN   80 (305)
T ss_pred             HHHHHHhcC-cCCCCEEEEeCCCChHHHHHHHHhCCCCEEEEEcCCHHHHHHHHHHHhhcCCcEEEEeCCHHH
Confidence            356666665 45567999999999999999999998889999998 5577777552     589999999885

Genetics paper in 1972 links mra cluster to peptidoglycan biosynthesis in E. coli. Seems to be common in proteobacteria.wn.

>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR

Probab=96.05  E-value=0.016  Score=46.70  Aligned_cols=67  Identities=15%  Similarity=0.198  Sum_probs=51.8

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeecc-C--C-CCCceeccHhhhHhhcC
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSA-G--D-DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~-~--~-~~~~y~lt~~s~~l~~~   91 (233)
                      +..|+..|...   ++.|..|||+.+++    ++..+.+.|+.|...|++++... .  + ..-.|.+|+.+..+...
T Consensus         3 r~~IL~~L~~~---~~~t~~eLA~~lgi----s~~tV~~~L~~Le~~GlV~r~~~~~~~gRp~~~y~LT~~G~~~~~~   73 (203)
T TIGR02702         3 KEDILSYLLKQ---GQATAAALAEALAI----SPQAVRRHLKDLETEGLIEYEAVVQGMGRPQYHYQLSRQGREQFPQ   73 (203)
T ss_pred             HHHHHHHHHHc---CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCeEEeecccCCCCCceEEEECcchhhhccc
Confidence            34577788766   58999999999999    99999999999999999987521 1  0 12237888888766543

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.

>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]

Probab=95.99  E-value=0.021  Score=43.98  Aligned_cols=52  Identities=10%  Similarity=0.041  Sum_probs=47.4

Q ss_pred             CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhcC
Q 039903           32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~~   91 (233)
                      +++...+||+.+++    ++..+..+++-|...|+++..    ..+.+.+|+.|......
T Consensus        23 ~~~~~~diA~~L~V----sp~sVt~ml~rL~~~GlV~~~----~y~gi~LT~~G~~~a~~   74 (154)
T COG1321          23 GFARTKDIAERLKV----SPPSVTEMLKRLERLGLVEYE----PYGGVTLTEKGREKAKE   74 (154)
T ss_pred             CcccHHHHHHHhCC----CcHHHHHHHHHHHHCCCeEEe----cCCCeEEChhhHHHHHH
Confidence            69999999999999    999999999999999999997    68899999998866544

>PRK11050 manganese transport regulator MntR; Provisional

Probab=95.93  E-value=0.024  Score=43.54  Aligned_cols=59  Identities=17%  Similarity=0.229  Sum_probs=49.1

Q ss_pred             hhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhc
Q 039903           21 VFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVL   90 (233)
Q Consensus        21 lfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~   90 (233)
                      |..++...   ++.+..|||+.+++    +...+.++++.|...|++.+.    ....+.+|+.|..+..
T Consensus        42 I~~~l~~~---~~~t~~eLA~~l~i----s~stVsr~l~~Le~~GlI~r~----~~~~v~LT~~G~~l~~  100 (152)
T PRK11050         42 IADLIAEV---GEARQVDIAARLGV----SQPTVAKMLKRLARDGLVEMR----PYRGVFLTPEGEKLAQ  100 (152)
T ss_pred             HHHHHHhc---CCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEe----cCCceEECchHHHHHH
Confidence            44455553   58999999999999    999999999999999999986    4567889998887654

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

Probab=95.90  E-value=0.014  Score=37.69  Aligned_cols=45  Identities=16%  Similarity=0.149  Sum_probs=38.0

Q ss_pred             ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      .|.+.|....  +|.+..|||+.+++    +....+++|..|...|.+++.
T Consensus         4 ~Il~~i~~~~--~p~~T~eiA~~~gl----s~~~aR~yL~~Le~eG~V~~~   48 (62)
T PF04703_consen    4 KILEYIKEQN--GPLKTREIADALGL----SIYQARYYLEKLEKEGKVERS   48 (62)
T ss_dssp             CHHHHHHHHT--S-EEHHHHHHHHTS-----HHHHHHHHHHHHHCTSEEEE
T ss_pred             HHHHHHHHcC--CCCCHHHHHHHhCC----CHHHHHHHHHHHHHCCCEEEe
Confidence            5677777732  69999999999999    999999999999999999975

>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=95.89  E-value=0.025  Score=47.74  Aligned_cols=56  Identities=13%  Similarity=0.105  Sum_probs=46.0

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCC--CcEEEeech-HHHhhccCC------CC-ceEEecCcCC
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLH--IKGVNFDLS-HVIQDSSSY------SG-VKHIGGIMLE  222 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~--l~~~v~Dlp-~v~~~a~~~------~r-i~~~~gD~f~  222 (233)
                      ....+||||.||+|-+....++.+|.  .++.+.|.. ..++.+++.      .. ++|..+|.|+
T Consensus       134 g~pvrIlDIAaG~GRYvlDal~~~~~~~~~i~LrDys~~Nv~~g~~li~~~gL~~i~~f~~~dAfd  199 (311)
T PF12147_consen  134 GRPVRILDIAAGHGRYVLDALEKHPERPDSILLRDYSPINVEKGRALIAERGLEDIARFEQGDAFD  199 (311)
T ss_pred             CCceEEEEeccCCcHHHHHHHHhCCCCCceEEEEeCCHHHHHHHHHHHHHcCCccceEEEecCCCC
Confidence            35689999999999999999999998  778888974 466666542      44 5999999997

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.

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

Probab=95.87  E-value=0.0087  Score=52.60  Aligned_cols=51  Identities=14%  Similarity=0.119  Sum_probs=42.2

Q ss_pred             ceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCC
Q 039903          170 KQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLE  222 (233)
Q Consensus       170 ~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~  222 (233)
                      .+++|++||+|.++..+++...  +++.+|. ++.++.++++      ++++++.+|.++
T Consensus       208 ~~vLDl~~G~G~~sl~la~~~~--~v~~vE~~~~ai~~a~~N~~~~~~~~v~~~~~d~~~  265 (362)
T PRK05031        208 GDLLELYCGNGNFTLALARNFR--RVLATEISKPSVAAAQYNIAANGIDNVQIIRMSAEE  265 (362)
T ss_pred             CeEEEEeccccHHHHHHHhhCC--EEEEEECCHHHHHHHHHHHHHhCCCcEEEEECCHHH
Confidence            4799999999999999998864  6899997 4577766653      589999999876

>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=95.87  E-value=0.013  Score=49.86  Aligned_cols=39  Identities=13%  Similarity=0.236  Sum_probs=30.2

Q ss_pred             HHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEee
Q 039903          159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFD  199 (233)
Q Consensus       159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~D  199 (233)
                      +...++++++ ++|+|||||+|.++-.++++.|. .++++|
T Consensus       107 l~p~l~~L~g-k~VLDIGC~nGY~~frM~~~GA~-~ViGiD  145 (315)
T PF08003_consen  107 LLPHLPDLKG-KRVLDIGCNNGYYSFRMLGRGAK-SVIGID  145 (315)
T ss_pred             HHhhhCCcCC-CEEEEecCCCcHHHHHHhhcCCC-EEEEEC
Confidence            3344432544 79999999999999999999776 378888

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

>PLN02589 caffeoyl-CoA O-methyltransferase

Probab=95.81  E-value=0.0099  Score=49.41  Aligned_cols=67  Identities=13%  Similarity=0.100  Sum_probs=52.7

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcC-CCcEEEeech-HHHhhccCC-------CCceEEecCcCCCCC---------CC
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDLS-HVIQDSSSY-------SGVKHIGGIMLERIP---------KG  227 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dlp-~v~~~a~~~-------~ri~~~~gD~f~~~P---------~~  227 (233)
                      ..+.+++|+||.+.|.-+..+++..| +-+++-+|.. +..+.|+++       ++|+++.||..+.+|         ..
T Consensus        77 ~~~ak~iLEiGT~~GySal~la~al~~~g~v~tiE~~~~~~~~Ar~~~~~ag~~~~I~~~~G~a~e~L~~l~~~~~~~~~  156 (247)
T PLN02589         77 LINAKNTMEIGVYTGYSLLATALALPEDGKILAMDINRENYELGLPVIQKAGVAHKIDFREGPALPVLDQMIEDGKYHGT  156 (247)
T ss_pred             HhCCCEEEEEeChhhHHHHHHHhhCCCCCEEEEEeCCHHHHHHHHHHHHHCCCCCceEEEeccHHHHHHHHHhccccCCc
Confidence            45678999999999999999999865 7789999984 456666542       799999999887432         23


Q ss_pred             -CEEEe
Q 039903          228 -DAILI  232 (233)
Q Consensus       228 -D~~~l  232 (233)
                       |++++
T Consensus       157 fD~iFi  162 (247)
T PLN02589        157 FDFIFV  162 (247)
T ss_pred             ccEEEe
Confidence             88876

>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=95.75  E-value=0.024  Score=35.91  Aligned_cols=44  Identities=20%  Similarity=0.367  Sum_probs=40.5

Q ss_pred             ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      .|.+.|.+.   +..|+.|||+.+++    ++.-++|=|..|...|++.+.
T Consensus         4 ~Il~~l~~~---~~~s~~ela~~~~V----S~~TiRRDl~~L~~~g~i~r~   47 (57)
T PF08220_consen    4 QILELLKEK---GKVSVKELAEEFGV----SEMTIRRDLNKLEKQGLIKRT   47 (57)
T ss_pred             HHHHHHHHc---CCEEHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEE
Confidence            467888886   59999999999999    999999999999999999997

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

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

Probab=95.74  E-value=0.011  Score=48.21  Aligned_cols=67  Identities=10%  Similarity=0.268  Sum_probs=45.7

Q ss_pred             HHHHHHHHHhcchhcHHHHH----HhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccCC
Q 039903          141 NGVFNKAMLNHTSIVTNRII----DSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSSY  210 (233)
Q Consensus       141 ~~~f~~am~~~~~~~~~~~~----~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~~  210 (233)
                      .++|.+.....-....|..+    ...+ ...+++++|+|||+|....+|...--+  .+.+|+.+ .++.|.+.
T Consensus        95 Ae~Fd~~LVdkL~Y~vP~~l~emI~~~~-~g~F~~~lDLGCGTGL~G~~lR~~a~~--ltGvDiS~nMl~kA~eK  166 (287)
T COG4976          95 AERFDHILVDKLGYSVPELLAEMIGKAD-LGPFRRMLDLGCGTGLTGEALRDMADR--LTGVDISENMLAKAHEK  166 (287)
T ss_pred             HHHHHHHHHHHhcCccHHHHHHHHHhcc-CCccceeeecccCcCcccHhHHHHHhh--ccCCchhHHHHHHHHhc
Confidence            45677776665444444433    3333 334899999999999999888877444  67789875 67777653

>COG4742 Predicted transcriptional regulator [Transcription]

Probab=95.73  E-value=0.027  Score=46.87  Aligned_cols=67  Identities=10%  Similarity=0.163  Sum_probs=59.8

Q ss_pred             HHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhcC
Q 039903           12 AMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        12 ~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~~   91 (233)
                      .+...-|.+|+=.|.+    ||.|.+||-..+++    ++..+..=++-|...|++.+     +++.|++|++|..++..
T Consensus         9 if~SekRk~lLllL~e----gPkti~EI~~~l~v----s~~ai~pqiKkL~~~~LV~~-----~~~~Y~LS~~G~iiv~k   75 (260)
T COG4742           9 LFLSEKRKDLLLLLKE----GPKTIEEIKNELNV----SSSAILPQIKKLKDKGLVVQ-----EGDRYSLSSLGKIIVEK   75 (260)
T ss_pred             HHccHHHHHHHHHHHh----CCCCHHHHHHHhCC----CcHHHHHHHHHHhhCCCEEe-----cCCEEEecchHHHHHHH
Confidence            4455668889999998    79999999999999    99999999999999999999     48999999999988755

>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=95.71  E-value=0.041  Score=44.34  Aligned_cols=107  Identities=11%  Similarity=0.051  Sum_probs=55.2

Q ss_pred             hhhHHHHHHcCCcchhhhhCCccccccccCchHHHHHH----HHHHhcchhcHHHHHHhcccccCcceEEEecCCccHHH
Q 039903          108 PYEIYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFN----KAMLNHTSIVTNRIIDSSKGFEQIKQLVDVGGGLGVNV  183 (233)
Q Consensus       108 ~~~L~~~l~~g~~~~~~~~g~~~~~~~~~~~~~~~~f~----~am~~~~~~~~~~~~~~~~~~~~~~~vvDvGGG~G~~~  183 (233)
                      +..|.|.|-+..+       ..-++.+.++|+.-..++    +.+..|.......+++.+...++...|.|.|||.+.++
T Consensus        15 FR~lNE~LYT~~s-------~~A~~lf~~dP~~F~~YH~Gfr~Qv~~WP~nPvd~iI~~l~~~~~~~viaD~GCGdA~la   87 (219)
T PF05148_consen   15 FRWLNEQLYTTSS-------EEALKLFQEDPELFDIYHEGFRQQVKKWPVNPVDVIIEWLKKRPKSLVIADFGCGDAKLA   87 (219)
T ss_dssp             HHHHHHHHHHS-H-------HHHHHHHHH-HHHHHHHHHHHHHHHCTSSS-HHHHHHHHHCTS-TTS-EEEES-TT-HHH
T ss_pred             hHHHHHhHhcCCH-------HHHHHHHHhCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHHHhcCCCEEEEECCCchHHHH
Confidence            4455565554432       122344556777655444    44444444445566666552344579999999999999


Q ss_pred             HHHHHHcCCCcEEEeechHHHhhccCCCCceEEecCcCC-CCCCC--CEEEe
Q 039903          184 NIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLE-RIPKG--DAILI  232 (233)
Q Consensus       184 ~~l~~~~P~l~~~v~Dlp~v~~~a~~~~ri~~~~gD~f~-~~P~~--D~~~l  232 (233)
                      .++.+   ..++--|||-..      +++  .+++|+-+ |++.+  |++++
T Consensus        88 ~~~~~---~~~V~SfDLva~------n~~--Vtacdia~vPL~~~svDv~Vf  128 (219)
T PF05148_consen   88 KAVPN---KHKVHSFDLVAP------NPR--VTACDIANVPLEDESVDVAVF  128 (219)
T ss_dssp             HH--S------EEEEESS-S------STT--EEES-TTS-S--TT-EEEEEE
T ss_pred             Hhccc---CceEEEeeccCC------CCC--EEEecCccCcCCCCceeEEEE
Confidence            66542   356777887432      244  45799976 77764  88764

; GO: 0008168 methyltransferase activity; PDB: 2ZFU_B.

>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=95.70  E-value=0.016  Score=36.92  Aligned_cols=49  Identities=14%  Similarity=0.266  Sum_probs=39.8

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeec
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTS   71 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~   71 (233)
                      +..|+-.|...++ .+.|..|||+.+++    ++..+.++++.|...|++++..
T Consensus         7 q~~vL~~l~~~~~-~~~t~~~la~~l~~----~~~~vs~~v~~L~~~Glv~r~~   55 (62)
T PF12802_consen    7 QFRVLMALARHPG-EELTQSELAERLGI----SKSTVSRIVKRLEKKGLVERER   55 (62)
T ss_dssp             HHHHHHHHHHSTT-SGEEHHHHHHHHTS-----HHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHHCCC-CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEeC
Confidence            4556667777641 12899999999999    9999999999999999999874

...

>TIGR00446 nop2p NOL1/NOP2/sun family putative RNA methylase

Probab=95.67  E-value=0.025  Score=47.46  Aligned_cols=66  Identities=18%  Similarity=0.033  Sum_probs=48.4

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcC-CCcEEEeech-HHHhhccCC------CCceEEecCcCC-CC--CCCCEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDLS-HVIQDSSSY------SGVKHIGGIMLE-RI--PKGDAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dlp-~v~~~a~~~------~ri~~~~gD~f~-~~--P~~D~~~l  232 (233)
                      ....+|+|+|+|.|..+..+++... .-+++.+|+. ..++.++++      .+|+++.+|... +.  +..|.|++
T Consensus        70 ~~g~~VLDl~ag~G~kt~~la~~~~~~g~v~a~D~~~~~l~~~~~n~~~~g~~~v~~~~~D~~~~~~~~~~fD~Vl~  146 (264)
T TIGR00446        70 DPPERVLDMAAAPGGKTTQISALMKNEGAIVANEFSKSRTKVLIANINRCGVLNVAVTNFDGRVFGAAVPKFDAILL  146 (264)
T ss_pred             CCcCEEEEECCCchHHHHHHHHHcCCCCEEEEEcCCHHHHHHHHHHHHHcCCCcEEEecCCHHHhhhhccCCCEEEE
Confidence            4557899999999999999998875 3578999984 456555432      568888888654 22  23488875

>COG3432 Predicted transcriptional regulator [Transcription]

Probab=95.66  E-value=0.015  Score=40.72  Aligned_cols=64  Identities=16%  Similarity=0.267  Sum_probs=49.8

Q ss_pred             hhHHHH-hcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhcC
Q 039903           21 VFEIIA-KAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        21 lfd~L~-~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~~   91 (233)
                      +||+|. ..+  ++....-|+-.+++    +.+..+.+++.|+..|++.... ++....|.+|+.|..|...
T Consensus        20 i~dIL~~~~~--~~~~~Tri~y~aNl----ny~~~~~yi~~L~~~Gli~~~~-~~~~~~y~lT~KG~~fle~   84 (95)
T COG3432          20 IFDILKAISE--GGIGITRIIYGANL----NYKRAQKYIEMLVEKGLIIKQD-NGRRKVYELTEKGKRFLEK   84 (95)
T ss_pred             HHHHHHHhcC--CCCCceeeeeecCc----CHHHHHHHHHHHHhCCCEEecc-CCccceEEEChhHHHHHHH
Confidence            577777 222  68888899999999    9999999999999999766652 1112379999999988654

>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=95.64  E-value=0.02  Score=39.82  Aligned_cols=62  Identities=11%  Similarity=0.166  Sum_probs=47.9

Q ss_pred             hhHHHHhcCCCCCCCHHHHHHhC-CCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhc
Q 039903           21 VFEIIAKAGPTAKISAVEIAAQM-PSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVL   90 (233)
Q Consensus        21 lfd~L~~~~~~~~~t~~elA~~~-~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~   90 (233)
                      |...|..    |+....||.+.+ ++    ++..|.+=|+.|...|++++.....  ..-.|++|+.|..|..
T Consensus        10 IL~~l~~----g~~rf~el~~~l~~i----s~~~L~~~L~~L~~~GLv~r~~~~~~p~~v~Y~LT~~G~~l~~   74 (90)
T PF01638_consen   10 ILRALFQ----GPMRFSELQRRLPGI----SPKVLSQRLKELEEAGLVERRVYPEVPPRVEYSLTEKGKELLP   74 (90)
T ss_dssp             HHHHHTT----SSEEHHHHHHHSTTS-----HHHHHHHHHHHHHTTSEEEEEESSSSSEEEEEE-HHHHHHHH
T ss_pred             HHHHHHh----CCCcHHHHHHhcchh----HHHHHHHHHHHHHHcchhhcccccCCCCCCccCCCcCHHHHHH
Confidence            4455665    699999999999 89    9999999999999999999864321  1135999999988763

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.

>PHA00738 putative HTH transcription regulator

Probab=95.64  E-value=0.028  Score=40.19  Aligned_cols=61  Identities=16%  Similarity=0.139  Sum_probs=49.9

Q ss_pred             HHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHh
Q 039903           16 ASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHV   84 (233)
Q Consensus        16 a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~   84 (233)
                      -.++.|++.|...   ++.++.||++.+++    +...+.+-|+.|...|+++....+ ..-.|++++.
T Consensus        12 ptRr~IL~lL~~~---e~~~V~eLae~l~l----SQptVS~HLKvLreAGLV~srK~G-r~vyY~Ln~~   72 (108)
T PHA00738         12 ILRRKILELIAEN---YILSASLISHTLLL----SYTTVLRHLKILNEQGYIELYKEG-RTLYAKIREN   72 (108)
T ss_pred             HHHHHHHHHHHHc---CCccHHHHHHhhCC----CHHHHHHHHHHHHHCCceEEEEEC-CEEEEEECCC
Confidence            4678899999884   37999999999999    999999999999999999987432 3345666653

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

Probab=95.63  E-value=0.014  Score=45.82  Aligned_cols=57  Identities=14%  Similarity=0.032  Sum_probs=38.4

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCC---------CCceEEecCcCC
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSY---------SGVKHIGGIMLE  222 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~---------~ri~~~~gD~f~  222 (233)
                      ..+..+|+++|+|.|..++.+++.++..++++-|.+++++..+.+         .+|++.+.|+-+
T Consensus        43 ~~~~~~VLELGaG~Gl~gi~~a~~~~~~~Vv~TD~~~~l~~l~~Ni~~N~~~~~~~v~v~~L~Wg~  108 (173)
T PF10294_consen   43 LFRGKRVLELGAGTGLPGIAAAKLFGAARVVLTDYNEVLELLRRNIELNGSLLDGRVSVRPLDWGD  108 (173)
T ss_dssp             GTTTSEEEETT-TTSHHHHHHHHT-T-SEEEEEE-S-HHHHHHHHHHTT--------EEEE--TTS
T ss_pred             hcCCceEEEECCccchhHHHHHhccCCceEEEeccchhhHHHHHHHHhccccccccccCcEEEecC
Confidence            345589999999999999999998888889999999877655432         679999999876

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.

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=95.60  E-value=0.033  Score=33.96  Aligned_cols=44  Identities=23%  Similarity=0.342  Sum_probs=38.7

Q ss_pred             ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      .|++.|...   ++.+..+|++.+++    +...+.+.|+.|...|++.+.
T Consensus         4 ~il~~l~~~---~~~s~~~l~~~l~~----s~~tv~~~l~~L~~~g~i~~~   47 (53)
T smart00420        4 QILELLAQQ---GKVSVEELAELLGV----SEMTIRRDLNKLEEQGLLTRV   47 (53)
T ss_pred             HHHHHHHHc---CCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEe
Confidence            356667665   47999999999999    999999999999999999986

>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial

Probab=95.59  E-value=0.022  Score=42.37  Aligned_cols=46  Identities=28%  Similarity=0.274  Sum_probs=38.3

Q ss_pred             CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903           32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH   83 (233)
Q Consensus        32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~   83 (233)
                      ++.|..|||+++++    ++..+.++|+.|...|++.....  .++.|.+..
T Consensus        24 ~~~s~~eia~~l~i----s~~~v~~~l~~L~~~Gli~~~~g--~~ggy~l~~   69 (130)
T TIGR02944        24 QPYSAAEIAEQTGL----NAPTVSKILKQLSLAGIVTSKRG--VEGGYTLAR   69 (130)
T ss_pred             CCccHHHHHHHHCc----CHHHHHHHHHHHHHCCcEEecCC--CCCChhhcC
Confidence            58999999999999    99999999999999999986421  345676643

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.

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

Probab=95.58  E-value=0.031  Score=36.49  Aligned_cols=57  Identities=16%  Similarity=0.345  Sum_probs=45.4

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH   83 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~   83 (233)
                      +..|+..+..    ++.+..||++.+++    +...+.+.|+.|...|++...... ....|++|+
T Consensus         9 ~~~il~~l~~----~~~~~~ei~~~~~i----~~~~i~~~l~~L~~~g~i~~~~~~-~~~~~~~~~   65 (78)
T cd00090           9 RLRILRLLLE----GPLTVSELAERLGL----SQSTVSRHLKKLEEAGLVESRREG-RRVYYSLTD   65 (78)
T ss_pred             HHHHHHHHHH----CCcCHHHHHHHHCc----CHhHHHHHHHHHHHCCCeEEEEec-cEEEEEeCC
Confidence            4456677776    35999999999999    999999999999999999975322 236777775

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.

>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators

Probab=95.52  E-value=0.035  Score=40.27  Aligned_cols=63  Identities=22%  Similarity=0.361  Sum_probs=46.4

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCC-CCCChhhHHHHHHHHhcCCceeeeccCCCCCceecc
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSS-NPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLA   82 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~-~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt   82 (233)
                      +.-|++.|...+  ++.|+.||.+++.-. ++.+..-++|.|+.|+..|++.+...+++...|.++
T Consensus         3 R~~Il~~l~~~~--~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~~~~~~~~~y~~~   66 (116)
T cd07153           3 RLAILEVLLESD--GHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIELGDGKARYELN   66 (116)
T ss_pred             HHHHHHHHHhCC--CCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEEEeCCCceEEEeC
Confidence            456888888764  689999999998421 122888999999999999999987543222456543

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.

>COG4122 Predicted O-methyltransferase [General function prediction only]

Probab=95.48  E-value=0.02  Score=46.61  Aligned_cols=67  Identities=10%  Similarity=0.172  Sum_probs=54.0

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcC-CCcEEEeech-HHHhhccCC-------CCceEEe-cCcCCC---C-CCC-CEE
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDLS-HVIQDSSSY-------SGVKHIG-GIMLER---I-PKG-DAI  230 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dlp-~v~~~a~~~-------~ri~~~~-gD~f~~---~-P~~-D~~  230 (233)
                      .++.++++.||.+.|.-++.++..-| +-+.+-+|+. +-++.|+++       ++|+.+. ||..+.   . ... |++
T Consensus        57 ~~~~k~iLEiGT~~GySal~mA~~l~~~g~l~tiE~~~e~~~~A~~n~~~ag~~~~i~~~~~gdal~~l~~~~~~~fDli  136 (219)
T COG4122          57 LSGPKRILEIGTAIGYSALWMALALPDDGRLTTIERDEERAEIARENLAEAGVDDRIELLLGGDALDVLSRLLDGSFDLV  136 (219)
T ss_pred             hcCCceEEEeecccCHHHHHHHhhCCCCCeEEEEeCCHHHHHHHHHHHHHcCCcceEEEEecCcHHHHHHhccCCCccEE
Confidence            56889999999999999999999999 8888999985 567777764       6788888 588762   2 222 998


Q ss_pred             Ee
Q 039903          231 LI  232 (233)
Q Consensus       231 ~l  232 (233)
                      |+
T Consensus       137 FI  138 (219)
T COG4122         137 FI  138 (219)
T ss_pred             EE
Confidence            86

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

Probab=95.47  E-value=0.012  Score=46.31  Aligned_cols=60  Identities=20%  Similarity=0.188  Sum_probs=41.3

Q ss_pred             HHHHhccccc--CcceEEEecCCccHHHHHHHHHc-CCCcEEEeechHHHhhccCCCCceEEecCcC
Q 039903          158 RIIDSSKGFE--QIKQLVDVGGGLGVNVNIIISNY-LHIKGVNFDLSHVIQDSSSYSGVKHIGGIML  221 (233)
Q Consensus       158 ~~~~~~~~~~--~~~~vvDvGGG~G~~~~~l~~~~-P~l~~~v~Dlp~v~~~a~~~~ri~~~~gD~f  221 (233)
                      ++.+.++-++  +..++||+|++.|.++..++++. +..+++.+|+...-    ....+.++.+|++
T Consensus        11 ei~~~~~~~~~~~~~~vlDlG~aPGGws~~~~~~~~~~~~v~avDl~~~~----~~~~~~~i~~d~~   73 (181)
T PF01728_consen   11 EIDEKFKIFKPGKGFTVLDLGAAPGGWSQVLLQRGGPAGRVVAVDLGPMD----PLQNVSFIQGDIT   73 (181)
T ss_dssp             HHHHTTSSS-TTTTEEEEEET-TTSHHHHHHHTSTTTEEEEEEEESSSTG----S-TTEEBTTGGGE
T ss_pred             HHHHHCCCCCcccccEEEEcCCcccceeeeeeecccccceEEEEeccccc----cccceeeeecccc
Confidence            4555555233  45999999999999999999998 78889999987651    1134444455554

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 ....

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=95.46  E-value=0.054  Score=34.19  Aligned_cols=54  Identities=15%  Similarity=0.337  Sum_probs=42.4

Q ss_pred             hhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903           21 VFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH   83 (233)
Q Consensus        21 lfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~   83 (233)
                      |+..|..    ++.|..+|++.+++    +...+.+.|+.|...|++...... ....|.+|.
T Consensus         2 il~~l~~----~~~~~~~i~~~l~i----s~~~v~~~l~~L~~~g~i~~~~~~-~~~~~~~~~   55 (66)
T smart00418        2 ILKLLAE----GELCVCELAEILGL----SQSTVSHHLKKLREAGLVESRREG-KRVYYSLTD   55 (66)
T ss_pred             HHHHhhc----CCccHHHHHHHHCC----CHHHHHHHHHHHHHCCCeeeeecC-CEEEEEEch
Confidence            4555653    58999999999999    999999999999999999975321 235666665

>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein

Probab=95.35  E-value=0.031  Score=44.95  Aligned_cols=59  Identities=22%  Similarity=0.338  Sum_probs=48.5

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhh
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVA   85 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s   85 (233)
                      +..|...|...   ++.+..|||+.+++    ++..+.|.|+.|...|++++...  ....|.+|+.|
T Consensus       145 ~~~IL~~l~~~---g~~s~~eia~~l~i----s~stv~r~L~~Le~~GlI~r~~~--r~~~~~lT~~G  203 (203)
T TIGR01884       145 ELKVLEVLKAE---GEKSVKNIAKKLGK----SLSTISRHLRELEKKGLVEQKGR--KGKRYSLTKLG  203 (203)
T ss_pred             HHHHHHHHHHc---CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEEcC--CccEEEeCCCC
Confidence            45677888775   48899999999999    99999999999999999998631  24668887653

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.

>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=95.32  E-value=0.018  Score=36.47  Aligned_cols=48  Identities=15%  Similarity=0.306  Sum_probs=40.7

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeecc
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSA   72 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~   72 (233)
                      +..+...|.+.   ++.+..|||+.+++    +...+.++++-|...|++++...
T Consensus         5 q~~iL~~l~~~---~~~~~~~la~~~~~----~~~~~t~~i~~L~~~g~I~r~~~   52 (59)
T PF01047_consen    5 QFRILRILYEN---GGITQSELAEKLGI----SRSTVTRIIKRLEKKGLIERERD   52 (59)
T ss_dssp             HHHHHHHHHHH---SSEEHHHHHHHHTS-----HHHHHHHHHHHHHTTSEEEEEE
T ss_pred             HHHHHHHHHHc---CCCCHHHHHHHHCC----ChhHHHHHHHHHHHCCCEEeccC
Confidence            45566677777   48999999999999    99999999999999999998653

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 ....

>COG2345 Predicted transcriptional regulator [Transcription]

Probab=95.28  E-value=0.04  Score=44.70  Aligned_cols=64  Identities=19%  Similarity=0.283  Sum_probs=50.4

Q ss_pred             ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC----CCCceeccHhhhHhhc
Q 039903           20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD----DQRLYGLAHVAKYFVL   90 (233)
Q Consensus        20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~----~~~~y~lt~~s~~l~~   90 (233)
                      .|...|.+.   +|+|+.|||+++|+    ++..++|-|..|++.|+++.....+    ..-.|++|..+.....
T Consensus        15 ~il~lL~~~---g~~sa~elA~~Lgi----s~~avR~HL~~Le~~Glv~~~~~~~g~GRP~~~y~Lt~~g~~~f~   82 (218)
T COG2345          15 RILELLKKS---GPVSADELAEELGI----SPMAVRRHLDDLEAEGLVEVERQQGGRGRPAKLYRLTEKGREQFP   82 (218)
T ss_pred             HHHHHHhcc---CCccHHHHHHHhCC----CHHHHHHHHHHHHhCcceeeeeccCCCCCCceeeeecccchhhcc
Confidence            456667766   69999999999999    9999999999999999998653221    2347888887766443

>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional

Probab=95.22  E-value=0.031  Score=49.49  Aligned_cols=63  Identities=13%  Similarity=-0.050  Sum_probs=48.6

Q ss_pred             ceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCCCCC---CCCEEEe
Q 039903          170 KQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLERIP---KGDAILI  232 (233)
Q Consensus       170 ~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~~P---~~D~~~l  232 (233)
                      .+++|++||+|.+++.++.+.+..+++..|. |..++.++++      +.+++..+|..+-++   ..|++.+
T Consensus        59 ~~vLDl~aGsG~~~l~~a~~~~~~~V~a~Din~~Av~~a~~N~~~N~~~~~~v~~~Da~~~l~~~~~fD~V~l  131 (382)
T PRK04338         59 ESVLDALSASGIRGIRYALETGVEKVTLNDINPDAVELIKKNLELNGLENEKVFNKDANALLHEERKFDVVDI  131 (382)
T ss_pred             CEEEECCCcccHHHHHHHHHCCCCEEEEEeCCHHHHHHHHHHHHHhCCCceEEEhhhHHHHHhhcCCCCEEEE
Confidence            5899999999999999999888668999998 5577777653      456788888765222   2488765

>KOG3115 consensus Methyltransferase-like protein [General function prediction only]

Probab=95.16  E-value=0.0095  Score=47.62  Aligned_cols=33  Identities=12%  Similarity=0.255  Sum_probs=29.8

Q ss_pred             cceEEEecCCccHHHHHHHHHcCCCcEEEeech
Q 039903          169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS  201 (233)
Q Consensus       169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp  201 (233)
                      -..++|||||.|.+++.|...||+--..++++-
T Consensus        61 kvefaDIGCGyGGLlv~Lsp~fPdtLiLGmEIR   93 (249)
T KOG3115|consen   61 KVEFADIGCGYGGLLMKLAPKFPDTLILGMEIR   93 (249)
T ss_pred             cceEEeeccCccchhhhccccCccceeeeehhh
Confidence            367999999999999999999999888888864

>TIGR00122 birA_repr_reg BirA biotin operon repressor domain

Probab=95.15  E-value=0.037  Score=36.34  Aligned_cols=55  Identities=15%  Similarity=0.173  Sum_probs=44.2

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHh
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHV   84 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~   84 (233)
                      ++.|+..|.+    ++.+..+||+.+++    +...+.+-++.|...|+....    .+..|.+.+.
T Consensus         2 ~~~il~~L~~----~~~~~~eLa~~l~v----S~~tv~~~l~~L~~~g~~i~~----~~~g~~l~~~   56 (69)
T TIGR00122         2 PLRLLALLAD----NPFSGEKLGEALGM----SRTAVNKHIQTLREWGVDVLT----VGKGYRLPPP   56 (69)
T ss_pred             hHHHHHHHHc----CCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCeEEe----cCCceEecCc
Confidence            3567778887    58899999999999    999999999999999996654    3455666543

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.

>PF02475 Met_10: Met-10+ like-protein; InterPro: IPR003402 This entry represents the Trm5 family

Probab=95.10  E-value=0.037  Score=44.51  Aligned_cols=67  Identities=16%  Similarity=0.170  Sum_probs=47.2

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCCCCCC--CCEEEe
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLERIPK--GDAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~~P~--~D~~~l  232 (233)
                      .....+|+|.-||.|.|+..+++..+..++...|+ |.+++..+++       ++|..+.+|..+-.+.  +|-++|
T Consensus        99 v~~~e~VlD~faGIG~f~l~~ak~~~~~~V~A~d~Np~a~~~L~~Ni~lNkv~~~i~~~~~D~~~~~~~~~~drvim  175 (200)
T PF02475_consen   99 VKPGEVVLDMFAGIGPFSLPIAKHGKAKRVYAVDLNPDAVEYLKENIRLNKVENRIEVINGDAREFLPEGKFDRVIM  175 (200)
T ss_dssp             --TT-EEEETT-TTTTTHHHHHHHT-SSEEEEEES-HHHHHHHHHHHHHTT-TTTEEEEES-GGG---TT-EEEEEE
T ss_pred             CCcceEEEEccCCccHHHHHHhhhcCccEEEEecCCHHHHHHHHHHHHHcCCCCeEEEEcCCHHHhcCccccCEEEE
Confidence            35568999999999999999999888888999999 5666655442       7899999999874433  377765

Trm5 specifically methylates the N1 position of guanosine-37 in various tRNAs [, , ]. Another members of this family, tRNA wybutosine-synthesizing protein 2 (Tyw2) and its homologues, are S-adenosyl-L-methionine-dependent transferases that act as a component of the wybutosine biosynthesis pathway [, ]. tRNA wybutosine-synthesizing protein 2 was originally thought to be a methyltransferase [].; GO: 0016740 transferase activity; PDB: 3A27_A 2ZZN_B 2YX1_A 2ZZM_A 3AY0_B 3K6R_A 3A26_A 3A25_A.

>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element

Probab=95.08  E-value=0.047  Score=38.12  Aligned_cols=47  Identities=15%  Similarity=0.194  Sum_probs=41.6

Q ss_pred             HHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhc
Q 039903           36 AVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVL   90 (233)
Q Consensus        36 ~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~   90 (233)
                      ..+||+.+++    +...+.+.++.|...|++.+.    .+..|.+|+.+..+..
T Consensus         2 ~~ela~~l~i----s~stvs~~l~~L~~~glI~r~----~~~~~~lT~~g~~~~~   48 (96)
T smart00529        2 TSEIAERLNV----SPPTVTQMLKKLEKDGLVEYE----PYRGITLTEKGRRLAR   48 (96)
T ss_pred             HHHHHHHhCC----ChHHHHHHHHHHHHCCCEEEc----CCCceEechhHHHHHH
Confidence            4689999999    999999999999999999997    4568999998887753

iron dependent repressor

>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed

Probab=95.03  E-value=0.041  Score=42.29  Aligned_cols=46  Identities=20%  Similarity=0.151  Sum_probs=40.8

Q ss_pred             CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903           32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH   83 (233)
Q Consensus        32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~   83 (233)
                      ++.|..+||+..++    ++.+|+++|..|...|+++-.+.  .+|.|+++.
T Consensus        23 ~~~s~~eIA~~~~i----s~~~L~kIl~~L~~aGlv~S~rG--~~GGy~La~   68 (153)
T PRK11920         23 KLSRIPEIARAYGV----SELFLFKILQPLVEAGLVETVRG--RNGGVRLGR   68 (153)
T ss_pred             CcCcHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEeecC--CCCCeeecC
Confidence            47899999999999    99999999999999999998753  568898875

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

Probab=95.03  E-value=0.026  Score=35.19  Aligned_cols=43  Identities=26%  Similarity=0.362  Sum_probs=35.3

Q ss_pred             HHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHH
Q 039903            9 LPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLL   61 (233)
Q Consensus         9 ~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L   61 (233)
                      .-.+|.+|+++|-||.=.      ..|+.|||+.+|+    ++..+...||-.
T Consensus         5 Q~e~L~~A~~~GYfd~PR------~~tl~elA~~lgi----s~st~~~~LRra   47 (53)
T PF04967_consen    5 QREILKAAYELGYFDVPR------RITLEELAEELGI----SKSTVSEHLRRA   47 (53)
T ss_pred             HHHHHHHHHHcCCCCCCC------cCCHHHHHHHhCC----CHHHHHHHHHHH
Confidence            457899999999999754      5899999999999    887777666643

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

>PRK11512 DNA-binding transcriptional repressor MarR; Provisional

Probab=95.00  E-value=0.062  Score=40.65  Aligned_cols=65  Identities=22%  Similarity=0.139  Sum_probs=50.4

Q ss_pred             ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      .|+-.|...   ++.|..|||+.+++    ++..+.++++-|...|++++.....  ..-...+|+.|..+...
T Consensus        44 ~vL~~l~~~---~~~t~~eLa~~l~i----~~~tvsr~l~~Le~~GlI~R~~~~~DrR~~~l~LT~~G~~~~~~  110 (144)
T PRK11512         44 KVLCSIRCA---ACITPVELKKVLSV----DLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTSGAAICEQ  110 (144)
T ss_pred             HHHHHHHHc---CCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEeccCcccCCeeEeEEChhHHHHHHH
Confidence            345566554   58999999999999    9999999999999999999864421  12345778888876644

>PF08704 GCD14: tRNA methyltransferase complex GCD14 subunit; InterPro: IPR014816 GCD14 is a subunit of the tRNA methyltransferase complex and is required for 1-methyladenosine modification and maturation of initiator methionyl-tRNA []

Probab=94.97  E-value=0.085  Score=43.86  Aligned_cols=88  Identities=11%  Similarity=0.138  Sum_probs=55.5

Q ss_pred             HHHHHHhcchhc----HHHHHHhcccccCcceEEEecCCccHHHHHHHHH-cCCCcEEEeec-hHHHhhccCC-------
Q 039903          144 FNKAMLNHTSIV----TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISN-YLHIKGVNFDL-SHVIQDSSSY-------  210 (233)
Q Consensus       144 f~~am~~~~~~~----~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~-~P~l~~~v~Dl-p~v~~~a~~~-------  210 (233)
                      |...|...++..    +..++-.++ .....+|++.|-|+|.++..|++. .|+=++.-+|. ++-++.|+++       
T Consensus        13 ~~~~l~rrtQIiYpkD~~~I~~~l~-i~pG~~VlEaGtGSG~lt~~l~r~v~p~G~v~t~E~~~~~~~~A~~n~~~~gl~   91 (247)
T PF08704_consen   13 WTLSLPRRTQIIYPKDISYILMRLD-IRPGSRVLEAGTGSGSLTHALARAVGPTGHVYTYEFREDRAEKARKNFERHGLD   91 (247)
T ss_dssp             HHHTS-SSS----HHHHHHHHHHTT---TT-EEEEE--TTSHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHHHTTCC
T ss_pred             HHHhccCCcceeeCchHHHHHHHcC-CCCCCEEEEecCCcHHHHHHHHHHhCCCeEEEccccCHHHHHHHHHHHHHcCCC
Confidence            444444444432    344556666 778899999999999999999975 68888888887 4456666553       


Q ss_pred             CCceEEecCcCC-CCC----C-CCEEEe
Q 039903          211 SGVKHIGGIMLE-RIP----K-GDAILI  232 (233)
Q Consensus       211 ~ri~~~~gD~f~-~~P----~-~D~~~l  232 (233)
                      ++|++..+|.-+ .++    . .|+++|
T Consensus        92 ~~v~~~~~Dv~~~g~~~~~~~~~DavfL  119 (247)
T PF08704_consen   92 DNVTVHHRDVCEEGFDEELESDFDAVFL  119 (247)
T ss_dssp             TTEEEEES-GGCG--STT-TTSEEEEEE
T ss_pred             CCceeEecceecccccccccCcccEEEE
Confidence            689999999975 343    2 398886

; GO: 0016429 tRNA (adenine-N1-)-methyltransferase activity, 0030488 tRNA methylation; PDB: 2YVL_C 1YB2_A 2B25_B 1O54_A 2PWY_B 1I9G_A 3LGA_B 3LHD_C 3MB5_A.

>PRK03573 transcriptional regulator SlyA; Provisional

Probab=94.82  E-value=0.1  Score=39.34  Aligned_cols=65  Identities=14%  Similarity=0.147  Sum_probs=50.0

Q ss_pred             hhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           21 VFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        21 lfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      ++..|...+  ++.|..|||+.+++    +...+.++++-|...|++++...+.  ..-...+|+.|..+...
T Consensus        36 vL~~l~~~~--~~~t~~eLa~~l~~----~~~tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~~  102 (144)
T PRK03573         36 TLHNIHQLP--PEQSQIQLAKAIGI----EQPSLVRTLDQLEEKGLISRQTCASDRRAKRIKLTEKAEPLISE  102 (144)
T ss_pred             HHHHHHHcC--CCCCHHHHHHHhCC----ChhhHHHHHHHHHHCCCEeeecCCCCcCeeeeEEChHHHHHHHH
Confidence            445555433  36899999999999    9999999999999999999875421  12356788988877654

>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=94.80  E-value=0.081  Score=32.88  Aligned_cols=41  Identities=15%  Similarity=0.239  Sum_probs=34.2

Q ss_pred             hChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCC
Q 039903           19 LGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHR   65 (233)
Q Consensus        19 lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~g   65 (233)
                      ..|...|....  +++|..+||+.+++    +.+-+++-+..|...|
T Consensus         3 ~~il~~L~~~~--~~it~~eLa~~l~v----S~rTi~~~i~~L~~~~   43 (55)
T PF08279_consen    3 KQILKLLLESK--EPITAKELAEELGV----SRRTIRRDIKELREWG   43 (55)
T ss_dssp             HHHHHHHHHTT--TSBEHHHHHHHCTS-----HHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHcC--CCcCHHHHHHHhCC----CHHHHHHHHHHHHHCC
Confidence            34667775543  57999999999999    9999999999999999

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 ....

>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=94.76  E-value=0.035  Score=39.84  Aligned_cols=32  Identities=31%  Similarity=0.475  Sum_probs=24.9

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL  200 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl  200 (233)
                      .....+||||||+|.+.--|.+.  ..+|..+|.
T Consensus        57 ~~~~~FVDlGCGNGLLV~IL~~E--Gy~G~GiD~   88 (112)
T PF07757_consen   57 QKFQGFVDLGCGNGLLVYILNSE--GYPGWGIDA   88 (112)
T ss_pred             CCCCceEEccCCchHHHHHHHhC--CCCcccccc
Confidence            35678999999999987777665  555777774

; GO: 0008168 methyltransferase activity

>COG0293 FtsJ 23S rRNA methylase [Translation, ribosomal structure and biogenesis]

Probab=94.71  E-value=0.11  Score=41.91  Aligned_cols=63  Identities=19%  Similarity=0.137  Sum_probs=48.5

Q ss_pred             HHHHHHhcccccCcceEEEecCCccHHHHHHHHHcC-CCcEEEeechHHHhhccCCCCceEEecCcCC
Q 039903          156 TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDLSHVIQDSSSYSGVKHIGGIMLE  222 (233)
Q Consensus       156 ~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dlp~v~~~a~~~~ri~~~~gD~f~  222 (233)
                      ..++.+.+.-|++..+|+|+|.-.|.++..+++.-. ..+++.+|+-+.-.    .+.|.++.+||+.
T Consensus        33 L~el~~k~~i~~~~~~ViDLGAAPGgWsQva~~~~~~~~~ivavDi~p~~~----~~~V~~iq~d~~~   96 (205)
T COG0293          33 LLELNEKFKLFKPGMVVVDLGAAPGGWSQVAAKKLGAGGKIVAVDILPMKP----IPGVIFLQGDITD   96 (205)
T ss_pred             HHHHHHhcCeecCCCEEEEcCCCCCcHHHHHHHHhCCCCcEEEEECccccc----CCCceEEeeeccC
Confidence            345666665468889999999999999998887754 46689999765432    2458999999996

>COG0275 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]

Probab=94.71  E-value=0.092  Score=44.59  Aligned_cols=66  Identities=14%  Similarity=0.125  Sum_probs=54.3

Q ss_pred             HHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCc-EEEeec-hHHHhhccCC-----CCceEEecCcCC
Q 039903          156 TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIK-GVNFDL-SHVIQDSSSY-----SGVKHIGGIMLE  222 (233)
Q Consensus       156 ~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~-~~v~Dl-p~v~~~a~~~-----~ri~~~~gD~f~  222 (233)
                      ..++++.+. .......||+-=|.|.++.++++++|+.. .+.+|. |.+++.|++.     +|++++.++|-+
T Consensus        12 l~E~i~~L~-~~~~giyiD~TlG~GGHS~~iL~~l~~~~~li~~DrD~~Ai~~a~~~l~~~~~r~~~v~~~F~~   84 (314)
T COG0275          12 LNEVVELLA-PKPDGIYIDGTLGAGGHSRAILEKLPDLGRLIGIDRDPQAIAIAKERLKEFDGRVTLVHGNFAN   84 (314)
T ss_pred             HHHHHHhcc-cCCCcEEEEecCCCcHhHHHHHHhCCCCCeEEEEcCCHHHHHHHHHHhhccCCcEEEEeCcHHH
Confidence            345666665 55668999999999999999999999887 899998 5688888763     699999998764

>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function

Probab=94.70  E-value=0.12  Score=36.13  Aligned_cols=47  Identities=19%  Similarity=0.152  Sum_probs=41.9

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      ..+.|...|...   ||-...-||..+++    +...+...|+-|..+|++++.
T Consensus         8 l~~~IL~hl~~~---~~Dy~k~ia~~l~~----~~~~v~~~l~~Le~~GLler~   54 (92)
T PF10007_consen    8 LDLKILQHLKKA---GPDYAKSIARRLKI----PLEEVREALEKLEEMGLLERV   54 (92)
T ss_pred             hHHHHHHHHHHH---CCCcHHHHHHHHCC----CHHHHHHHHHHHHHCCCeEEe
Confidence            356678888887   47888999999999    999999999999999999997

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=94.53  E-value=0.069  Score=38.17  Aligned_cols=46  Identities=20%  Similarity=0.274  Sum_probs=41.8

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceee
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRC   69 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~   69 (233)
                      .+..|+..|...   ++.|..+||+.+|+    ++..+.+.++.|...|++.+
T Consensus         4 ~D~~il~~L~~~---~~~~~~~la~~l~~----s~~tv~~~l~~L~~~g~i~~   49 (108)
T smart00344        4 IDRKILEELQKD---ARISLAELAKKVGL----SPSTVHNRVKRLEEEGVIKG   49 (108)
T ss_pred             HHHHHHHHHHHh---CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCeec
Confidence            467788899886   58999999999999    99999999999999999985

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

>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family

Probab=94.52  E-value=0.1  Score=37.58  Aligned_cols=68  Identities=16%  Similarity=0.211  Sum_probs=50.3

Q ss_pred             hhChhHHHH--hcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCC--CCceeccHhhhHhhc
Q 039903           18 ELGVFEIIA--KAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDD--QRLYGLAHVAKYFVL   90 (233)
Q Consensus        18 ~lglfd~L~--~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~--~~~y~lt~~s~~l~~   90 (233)
                      +..++..|.  ... .++.|..+||..+++    +...+.++++.|...|++.+...+.+  .-.+.+|+.+..+..
T Consensus        27 q~~vL~~l~~~~~~-~~~~t~~eL~~~l~~----~~stvs~~i~~Le~kg~I~r~~~~~D~R~~~i~lT~~G~~~~~   98 (109)
T TIGR01889        27 ELLILYYLGKLENN-EGKLTLKEIIKEILI----KQSALVKIIKKLSKKGYLSKERSEDDERKVIISINKEQRSKIE   98 (109)
T ss_pred             HHHHHHHHHhhhcc-CCcCcHHHHHHHHCC----CHHHHHHHHHHHHHCCCEeccCCcccCCeEEEEECHHHHHHHH
Confidence            344566665  221 158999999999999    99999999999999999998654311  124568888876653

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.

>PRK15431 ferrous iron transport protein FeoC; Provisional

Probab=94.43  E-value=0.095  Score=35.29  Aligned_cols=43  Identities=16%  Similarity=0.262  Sum_probs=39.6

Q ss_pred             hhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           21 VFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        21 lfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      |=|+|...   |..++.|||..++.    ++..++-+|..++.+|-+++.
T Consensus         7 lRd~l~~~---gr~s~~~Ls~~~~~----p~~~VeaMLe~l~~kGkverv   49 (78)
T PRK15431          7 VRDLLALR---GRMEAAQISQTLNT----PQPMINAMLQQLESMGKAVRI   49 (78)
T ss_pred             HHHHHHHc---CcccHHHHHHHHCc----CHHHHHHHHHHHHHCCCeEee
Confidence            45778887   58999999999999    999999999999999999987

>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators

Probab=94.40  E-value=0.11  Score=33.06  Aligned_cols=40  Identities=18%  Similarity=0.104  Sum_probs=33.7

Q ss_pred             CCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceec
Q 039903           34 ISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGL   81 (233)
Q Consensus        34 ~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~l   81 (233)
                      .|..+||..+++    +...+.+.+..|...|+++..    .+..|.+
T Consensus        26 ~~~~~la~~~~i----s~~~v~~~l~~L~~~G~i~~~----~~~~~~l   65 (66)
T cd07377          26 PSERELAEELGV----SRTTVREALRELEAEGLVERR----PGRGTFV   65 (66)
T ss_pred             CCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEec----CCCeEEe
Confidence            359999999999    999999999999999999875    3445544

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

>KOG1661 consensus Protein-L-isoaspartate(D-aspartate) O-methyltransferase [Posttranslational modification, protein turnover, chaperones]

Probab=94.37  E-value=0.11  Score=41.90  Aligned_cols=66  Identities=15%  Similarity=0.113  Sum_probs=45.9

Q ss_pred             ccCcceEEEecCCccHHHHHHHHH--cCCCcEEEeec-hHHHhhccCC----------------CCceEEecCcCCCCCC
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISN--YLHIKGVNFDL-SHVIQDSSSY----------------SGVKHIGGIMLERIPK  226 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~--~P~l~~~v~Dl-p~v~~~a~~~----------------~ri~~~~gD~f~~~P~  226 (233)
                      +....++||||+|+|.++..++.-  -|....+.+|+ |++++.+.++                .++.++.||=.+-.|.
T Consensus        80 L~pG~s~LdvGsGSGYLt~~~~~mvg~~g~~~~GIEh~~eLVe~Sk~nl~k~i~~~e~~~~~~~~~l~ivvGDgr~g~~e  159 (237)
T KOG1661|consen   80 LQPGASFLDVGSGSGYLTACFARMVGATGGNVHGIEHIPELVEYSKKNLDKDITTSESSSKLKRGELSIVVGDGRKGYAE  159 (237)
T ss_pred             hccCcceeecCCCccHHHHHHHHHhcCCCccccchhhhHHHHHHHHHHHHhhccCchhhhhhccCceEEEeCCccccCCc
Confidence            456678999999999987766632  23332356664 7888877653                5789999999884443


Q ss_pred             -C--CEEE
Q 039903          227 -G--DAIL  231 (233)
Q Consensus       227 -~--D~~~  231 (233)
                       +  |.|.
T Consensus       160 ~a~YDaIh  167 (237)
T KOG1661|consen  160 QAPYDAIH  167 (237)
T ss_pred             cCCcceEE
Confidence             3  7765

>PRK11783 rlmL 23S rRNA m(2)G2445 methyltransferase; Provisional

Probab=94.36  E-value=0.13  Score=49.27  Aligned_cols=76  Identities=17%  Similarity=0.108  Sum_probs=53.5

Q ss_pred             HHHHHHhcccc-cCcceEEEecCCccHHHHHHHHH------------c------------------------------CC
Q 039903          156 TNRIIDSSKGF-EQIKQLVDVGGGLGVNVNIIISN------------Y------------------------------LH  192 (233)
Q Consensus       156 ~~~~~~~~~~~-~~~~~vvDvGGG~G~~~~~l~~~------------~------------------------------P~  192 (233)
                      +..++.... | ++...++|-.||+|.++++.+..            |                              +.
T Consensus       178 Aaa~l~~a~-w~~~~~~l~DP~CGSGTilIEAa~~~~~~~pg~~r~~f~f~~~~~~~~~~w~~~~~~a~~~~~~~~~~~~  256 (702)
T PRK11783        178 AAAILLRSG-WPQEGTPLLDPMCGSGTLLIEAAMMAADIAPGLHRERWGFSGWLGHDEALWQELLEEAQERARAGLAELP  256 (702)
T ss_pred             HHHHHHHcC-CCCCCCeEEccCCCccHHHHHHHHHHhcCCCCccccccccccCCCCCHHHHHHHHHHHHHHHhhcccccC
Confidence            344554434 7 45689999999999999887652            1                              12


Q ss_pred             CcEEEeec-hHHHhhccCC-------CCceEEecCcCC-CCCC----CCEEEe
Q 039903          193 IKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLE-RIPK----GDAILI  232 (233)
Q Consensus       193 l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~-~~P~----~D~~~l  232 (233)
                      .+++.+|+ |.+++.|+.+       ++|++..+|+++ +.|.    .|+++.
T Consensus       257 ~~i~G~Did~~av~~A~~N~~~~g~~~~i~~~~~D~~~~~~~~~~~~~d~Ivt  309 (702)
T PRK11783        257 SKFYGSDIDPRVIQAARKNARRAGVAELITFEVKDVADLKNPLPKGPTGLVIS  309 (702)
T ss_pred             ceEEEEECCHHHHHHHHHHHHHcCCCcceEEEeCChhhcccccccCCCCEEEE
Confidence            36889998 5688877764       579999999987 4432    377753

>KOG3010 consensus Methyltransferase [General function prediction only]

Probab=94.29  E-value=0.047  Score=44.84  Aligned_cols=43  Identities=21%  Similarity=0.225  Sum_probs=33.7

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCCCC
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSYSG  212 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~~r  212 (233)
                      ..+.++|||||+|..++.+++.|-+  ++..|.. ..++.+++.++
T Consensus        33 ~h~~a~DvG~G~Gqa~~~iae~~k~--VIatD~s~~mL~~a~k~~~   76 (261)
T KOG3010|consen   33 GHRLAWDVGTGNGQAARGIAEHYKE--VIATDVSEAMLKVAKKHPP   76 (261)
T ss_pred             CcceEEEeccCCCcchHHHHHhhhh--heeecCCHHHHHHhhcCCC
Confidence            3459999999999778888887665  7888985 47888887633

>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional

Probab=94.12  E-value=0.12  Score=41.99  Aligned_cols=55  Identities=22%  Similarity=0.213  Sum_probs=46.8

Q ss_pred             CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhcC
Q 039903           32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~~   91 (233)
                      ..+|..|||+.+++    +...+.|+|+.|...|++++.... .+..+.+|+.+..+...
T Consensus        20 ~~IS~~eLA~~L~i----S~~Tvsr~Lk~LEe~GlI~R~~~~-r~~~v~LTekG~~ll~~   74 (217)
T PRK14165         20 VKISSSEFANHTGT----SSKTAARILKQLEDEGYITRTIVP-RGQLITITEKGLDVLYN   74 (217)
T ss_pred             CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEEEcC-CceEEEECHHHHHHHHH
Confidence            46899999999999    999999999999999999986433 46789999999866533

>KOG2361 consensus Predicted methyltransferase [General function prediction only]

Probab=94.11  E-value=0.048  Score=44.78  Aligned_cols=64  Identities=20%  Similarity=0.247  Sum_probs=49.2

Q ss_pred             cceEEEecCCccHHHHHHHHHcCC--CcEEEeec-hHHHhhccCC-----CCceEEecCcCC-----CCCCC--CEEEe
Q 039903          169 IKQLVDVGGGLGVNVNIIISNYLH--IKGVNFDL-SHVIQDSSSY-----SGVKHIGGIMLE-----RIPKG--DAILI  232 (233)
Q Consensus       169 ~~~vvDvGGG~G~~~~~l~~~~P~--l~~~v~Dl-p~v~~~a~~~-----~ri~~~~gD~f~-----~~P~~--D~~~l  232 (233)
                      ..+++.||||.|...--+++.+|+  ++...+|. |.+++..+++     .|+.....|+-.     +.+++  |++.|
T Consensus        72 ~~~ilEvGCGvGNtvfPll~~~~n~~l~v~acDfsp~Ai~~vk~~~~~~e~~~~afv~Dlt~~~~~~~~~~~svD~it~  150 (264)
T KOG2361|consen   72 AETILEVGCGVGNTVFPLLKTSPNNRLKVYACDFSPRAIELVKKSSGYDESRVEAFVWDLTSPSLKEPPEEGSVDIITL  150 (264)
T ss_pred             hhhheeeccCCCcccchhhhcCCCCCeEEEEcCCChHHHHHHHhccccchhhhcccceeccchhccCCCCcCccceEEE
Confidence            348999999999999999999998  88899997 6688877664     467766777765     23334  77654

>KOG2730 consensus Methylase [General function prediction only]

Probab=94.09  E-value=0.032  Score=45.19  Aligned_cols=53  Identities=19%  Similarity=0.158  Sum_probs=44.8

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCC
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLE  222 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~  222 (233)
                      ....++|.=||-|...++++.++|.  ++.+|+ |.-|..|+.+       +||+|+.|||++
T Consensus        94 ~~~~iidaf~g~gGntiqfa~~~~~--VisIdiDPikIa~AkhNaeiYGI~~rItFI~GD~ld  154 (263)
T KOG2730|consen   94 NAEVIVDAFCGVGGNTIQFALQGPY--VIAIDIDPVKIACARHNAEVYGVPDRITFICGDFLD  154 (263)
T ss_pred             CcchhhhhhhcCCchHHHHHHhCCe--EEEEeccHHHHHHHhccceeecCCceeEEEechHHH
Confidence            5678999999999999999999998  566666 5567777765       799999999997

>COG4076 Predicted RNA methylase [General function prediction only]

Probab=94.07  E-value=0.12  Score=41.10  Aligned_cols=60  Identities=10%  Similarity=0.179  Sum_probs=47.3

Q ss_pred             ceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCC-CCCCCCEEE
Q 039903          170 KQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLE-RIPKGDAIL  231 (233)
Q Consensus       170 ~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~-~~P~~D~~~  231 (233)
                      .++.|+|.|+|.++.-.+++  .-|++.+++ |...+.|.++      .+++.+.||..+ .+-.||+++
T Consensus        34 d~~~DLGaGsGiLs~~Aa~~--A~rViAiE~dPk~a~~a~eN~~v~g~~n~evv~gDA~~y~fe~ADvvi  101 (252)
T COG4076          34 DTFADLGAGSGILSVVAAHA--AERVIAIEKDPKRARLAEENLHVPGDVNWEVVVGDARDYDFENADVVI  101 (252)
T ss_pred             hceeeccCCcchHHHHHHhh--hceEEEEecCcHHHHHhhhcCCCCCCcceEEEecccccccccccceeH
Confidence            57899999999998877776  556777776 5566667664      689999999999 785578874

>PF06080 DUF938: Protein of unknown function (DUF938); InterPro: IPR010342 This family consists of several hypothetical proteins from both prokaryotes and eukaryotes

Probab=94.04  E-value=0.065  Score=43.09  Aligned_cols=37  Identities=11%  Similarity=0.190  Sum_probs=30.2

Q ss_pred             ccCcc-eEEEecCCccHHHHHHHHHcCCCcEEEeechH
Q 039903          166 FEQIK-QLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH  202 (233)
Q Consensus       166 ~~~~~-~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~  202 (233)
                      +.... +||.||+|+|..+..+++++|+++.-==|.+.
T Consensus        22 l~~~~~~vLEiaSGtGqHa~~FA~~lP~l~WqPSD~~~   59 (204)
T PF06080_consen   22 LPDSGTRVLEIASGTGQHAVYFAQALPHLTWQPSDPDD   59 (204)
T ss_pred             hCccCceEEEEcCCccHHHHHHHHHCCCCEEcCCCCCh
Confidence            44445 49999999999999999999999875556544

The function of this family is unknown.

>COG2384 Predicted SAM-dependent methyltransferase [General function prediction only]

Probab=93.98  E-value=0.11  Score=42.17  Aligned_cols=64  Identities=14%  Similarity=0.131  Sum_probs=48.7

Q ss_pred             cceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhc----cCC---CCceEEecCcCCCCC-C-C-CEEEe
Q 039903          169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDS----SSY---SGVKHIGGIMLERIP-K-G-DAILI  232 (233)
Q Consensus       169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a----~~~---~ri~~~~gD~f~~~P-~-~-D~~~l  232 (233)
                      ...+.||||-|+.+.+.+++.+|..+++.-|. |.-++.|    +++   +||+..-||=|.++- . . |++++
T Consensus        17 ~~~iaDIGsDHAYLp~~Lv~~~~~~~~va~eV~~gpl~~a~~~v~~~~l~~~i~vr~~dgl~~l~~~d~~d~ivI   91 (226)
T COG2384          17 GARIADIGSDHAYLPIYLVKNNPASTAVAGEVVPGPLESAIRNVKKNNLSERIDVRLGDGLAVLELEDEIDVIVI   91 (226)
T ss_pred             CCceeeccCchhHhHHHHHhcCCcceEEEeecccCHHHHHHHHHHhcCCcceEEEeccCCccccCccCCcCEEEE
Confidence            34499999999999999999999999999997 3333333    332   899999999988543 3 2 66653

>PRK11014 transcriptional repressor NsrR; Provisional

Probab=93.97  E-value=0.13  Score=38.87  Aligned_cols=46  Identities=11%  Similarity=0.056  Sum_probs=39.2

Q ss_pred             CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903           32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH   83 (233)
Q Consensus        32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~   83 (233)
                      .+.+..+||+.+++    +...++++|+.|...|+++....  .+|.|.++.
T Consensus        24 ~~~s~~~ia~~~~i----s~~~vrk~l~~L~~~Glv~s~~G--~~GG~~l~~   69 (141)
T PRK11014         24 RMTSISEVTEVYGV----SRNHMVKIINQLSRAGYVTAVRG--KNGGIRLGK   69 (141)
T ss_pred             CccCHHHHHHHHCc----CHHHHHHHHHHHHhCCEEEEecC--CCCCeeecC
Confidence            47899999999999    99999999999999999998642  346787764

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=93.94  E-value=0.17  Score=31.58  Aligned_cols=34  Identities=24%  Similarity=0.273  Sum_probs=31.8

Q ss_pred             CC-CHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           33 KI-SAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        33 ~~-t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      .+ |..|||+.+++    +...+++.++.|...|+++..
T Consensus        19 ~l~s~~~la~~~~v----s~~tv~~~l~~L~~~g~i~~~   53 (60)
T smart00345       19 KLPSERELAAQLGV----SRTTVREALSRLEAEGLVQRR   53 (60)
T ss_pred             cCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEe
Confidence            45 89999999999    999999999999999999876

>KOG3191 consensus Predicted N6-DNA-methyltransferase [Translation, ribosomal structure and biogenesis]

Probab=93.79  E-value=0.14  Score=40.35  Aligned_cols=64  Identities=13%  Similarity=0.193  Sum_probs=46.5

Q ss_pred             cceEEEecCCccHHHHHHHHH-cCCCcEEEeec-hHHHhhccC----C-CCceEEecCcCCCCC-CC-CEEEe
Q 039903          169 IKQLVDVGGGLGVNVNIIISN-YLHIKGVNFDL-SHVIQDSSS----Y-SGVKHIGGIMLERIP-KG-DAILI  232 (233)
Q Consensus       169 ~~~vvDvGGG~G~~~~~l~~~-~P~l~~~v~Dl-p~v~~~a~~----~-~ri~~~~gD~f~~~P-~~-D~~~l  232 (233)
                      ..-.++||||+|..+..+++. -|......-|+ |++++...+    + -++..+..|++..+- .. |+.++
T Consensus        44 ~~i~lEIG~GSGvvstfL~~~i~~~~~~latDiNp~A~~~Tl~TA~~n~~~~~~V~tdl~~~l~~~~VDvLvf  116 (209)
T KOG3191|consen   44 PEICLEIGCGSGVVSTFLASVIGPQALYLATDINPEALEATLETARCNRVHIDVVRTDLLSGLRNESVDVLVF  116 (209)
T ss_pred             ceeEEEecCCcchHHHHHHHhcCCCceEEEecCCHHHHHHHHHHHHhcCCccceeehhHHhhhccCCccEEEE
Confidence            688999999999998888775 36777888898 555554332    2 457788889998433 33 87765

>PF07091 FmrO: Ribosomal RNA methyltransferase (FmrO); PDB: 3LCU_A 3LCV_B 3FRH_A 3FRI_A 3B89_A 3FZG_A

Probab=93.70  E-value=0.19  Score=41.59  Aligned_cols=88  Identities=15%  Similarity=0.155  Sum_probs=55.8

Q ss_pred             HHHHHhcchhc--HHHHHHhccc-c---cCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccC-----CCC
Q 039903          145 NKAMLNHTSIV--TNRIIDSSKG-F---EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSS-----YSG  212 (233)
Q Consensus       145 ~~am~~~~~~~--~~~~~~~~~~-~---~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~-----~~r  212 (233)
                      .++|..+.+..  .+.+-+.|+. |   ..+.+|+|||||--=++.-.....|+...+..|+.. .++....     ..+
T Consensus        76 r~lL~~HaST~ERl~~Ld~fY~~if~~~~~p~sVlDigCGlNPlalp~~~~~~~a~Y~a~DID~~~ve~l~~~l~~l~~~  155 (251)
T PF07091_consen   76 RRLLAGHASTRERLPNLDEFYDEIFGRIPPPDSVLDIGCGLNPLALPWMPEAPGATYIAYDIDSQLVEFLNAFLAVLGVP  155 (251)
T ss_dssp             HHHHHTSHHHHCCGGGHHHHHHHHCCCS---SEEEEET-TTCHHHHHTTTSSTT-EEEEEESBHHHHHHHHHHHHHTT-C
T ss_pred             HHHHhhccchhhhhhhHHHHHHHHHhcCCCCchhhhhhccCCceehhhcccCCCcEEEEEeCCHHHHHHHHHHHHhhCCC
Confidence            34666555431  2233333331 3   337899999999999999888999999999999975 4443332     267


Q ss_pred             ceEEecCcCCCCCC--CCEEEe
Q 039903          213 VKHIGGIMLERIPK--GDAILI  232 (233)
Q Consensus       213 i~~~~gD~f~~~P~--~D~~~l  232 (233)
                      .+....|.+...|.  +|+.+|
T Consensus       156 ~~~~v~Dl~~~~~~~~~DlaLl  177 (251)
T PF07091_consen  156 HDARVRDLLSDPPKEPADLALL  177 (251)
T ss_dssp             EEEEEE-TTTSHTTSEESEEEE
T ss_pred             cceeEeeeeccCCCCCcchhhH
Confidence            88888899997665  488765

>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=93.68  E-value=0.13  Score=33.44  Aligned_cols=48  Identities=23%  Similarity=0.275  Sum_probs=36.0

Q ss_pred             hhChhHHHHh----cCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           18 ELGVFEIIAK----AGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        18 ~lglfd~L~~----~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      +..|++.|.+    .|  -|-|+.|||+.+|++   ++..+.+.|+.|...|++++.
T Consensus         8 Q~~vL~~I~~~~~~~G--~~Pt~rEIa~~~g~~---S~~tv~~~L~~Le~kG~I~r~   59 (65)
T PF01726_consen    8 QKEVLEFIREYIEENG--YPPTVREIAEALGLK---STSTVQRHLKALERKGYIRRD   59 (65)
T ss_dssp             HHHHHHHHHHHHHHHS--S---HHHHHHHHTSS---SHHHHHHHHHHHHHTTSEEEG
T ss_pred             HHHHHHHHHHHHHHcC--CCCCHHHHHHHhCCC---ChHHHHHHHHHHHHCcCccCC
Confidence            4445555544    45  467999999999992   499999999999999999985

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.

>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional

Probab=93.67  E-value=0.12  Score=47.35  Aligned_cols=67  Identities=13%  Similarity=0.183  Sum_probs=55.4

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhcCC
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLNR   92 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~~~   92 (233)
                      .+..|...|...   ++.|..+||+.+++    ++..+.++++.|.+.|+++....  ....|.+|+.|+.++.+.
T Consensus         7 ~e~~vL~~L~~~---~~~s~~eLA~~l~l----~~~tVt~~i~~Le~kGlV~~~~~--~~~~i~LTeeG~~~~~~g   73 (489)
T PRK04172          7 NEKKVLKALKEL---KEATLEELAEKLGL----PPEAVMRAAEWLEEKGLVKVEER--VEEVYVLTEEGKKYAEEG   73 (489)
T ss_pred             HHHHHHHHHHhC---CCCCHHHHHHHhCc----CHHHHHHHHHHHHhCCCEEEEee--eEEEEEECHHHHHHHHhc
Confidence            455667777765   58999999999999    99999999999999999998632  246799999999877653

>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function

Probab=93.64  E-value=0.21  Score=36.78  Aligned_cols=53  Identities=17%  Similarity=0.235  Sum_probs=46.9

Q ss_pred             HHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           11 AAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        11 ~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      +-=+..+...|.+...++   |.+|..|++..+|+    +-..+.+.++.|++.|-|-..
T Consensus         7 ~eer~eLk~rIvElVRe~---GRiTi~ql~~~TGa----sR~Tvk~~lreLVa~G~l~~~   59 (127)
T PF06163_consen    7 PEEREELKARIVELVREH---GRITIKQLVAKTGA----SRNTVKRYLRELVARGDLYRH   59 (127)
T ss_pred             HHHHHHHHHHHHHHHHHc---CCccHHHHHHHHCC----CHHHHHHHHHHHHHcCCeEeC
Confidence            334556778899999998   69999999999999    999999999999999999985

>PF01739 CheR: CheR methyltransferase, SAM binding domain; InterPro: IPR022642 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=93.63  E-value=0.37  Score=38.62  Aligned_cols=66  Identities=17%  Similarity=0.220  Sum_probs=38.8

Q ss_pred             CcceEEEecCCccH--HHHH--HHHHc---C--CCcEEEeech-HHHhhccCC---------------------------
Q 039903          168 QIKQLVDVGGGLGV--NVNI--IISNY---L--HIKGVNFDLS-HVIQDSSSY---------------------------  210 (233)
Q Consensus       168 ~~~~vvDvGGG~G~--~~~~--l~~~~---P--~l~~~v~Dlp-~v~~~a~~~---------------------------  210 (233)
                      +.-+|...||++|.  ++++  +.+..   .  ++++..-|+. .+++.|++-                           
T Consensus        31 ~~lrIWSagCStGeE~YSlAmll~e~~~~~~~~~~~I~atDi~~~~L~~Ar~G~Y~~~~~~~~~~~~~~ryf~~~~~~~~  110 (196)
T PF01739_consen   31 RPLRIWSAGCSTGEEPYSLAMLLLELLPGALGWDFRILATDISPSALEKARAGIYPERSLRGLPPAYLRRYFTERDGGGY  110 (196)
T ss_dssp             S-EEEEETT-TTTHHHHHHHHHHHHHH-S-TT-SEEEEEEES-HHHHHHHHHTEEEGGGGTTS-HHHHHHHEEEE-CCCT
T ss_pred             CCeEEEECCCCCChhHHHHHHHHHHHhcccCCCceEEEEEECCHHHHHHHHhCCCCHHHHhhhHHHHHHHhccccCCCce
Confidence            56789999999996  4444  44422   2  3567778985 588877641                           


Q ss_pred             -------CCceEEecCcCC-CCCCC--CEEEeC
Q 039903          211 -------SGVKHIGGIMLE-RIPKG--DAILIK  233 (233)
Q Consensus       211 -------~ri~~~~gD~f~-~~P~~--D~~~lk  233 (233)
                             .+|+|..+|.++ +.|.+  |+|+.|
T Consensus       111 ~v~~~lr~~V~F~~~NL~~~~~~~~~fD~I~CR  143 (196)
T PF01739_consen  111 RVKPELRKMVRFRRHNLLDPDPPFGRFDLIFCR  143 (196)
T ss_dssp             TE-HHHHTTEEEEE--TT-S------EEEEEE-
T ss_pred             eEChHHcCceEEEecccCCCCcccCCccEEEec
Confidence                   589999999999 33333  999754

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 []. Flagellated bacteria swim towards favourable chemicals and away from deleterious ones. Sensing of chemoeffector gradients involves chemotaxis receptors, transmembrane (TM) proteins that detect stimuli through their periplasmic domains and transduce the signals via their cytoplasmic domains []. Signalling outputs from these receptors are influenced both by the binding of the chemoeffector ligand to their periplasmic domains and by methylation of specific glutamate residues on their cytoplasmic domains. Methylation is catalysed by CheR, an S-adenosylmethionine-dependent methyltransferase [], which reversibly methylates specific glutamate residues within a coiled coil region, to form gamma-glutamyl methyl ester residues [, ]. The structure of the Salmonella typhimurium chemotaxis receptor methyltransferase CheR, bound to S-adenosylhomocysteine, has been determined to a resolution of 2.0 A []. The structure reveals CheR to be a two-domain protein, with a smaller N-terminal helical domain linked via a single polypeptide connection to a larger C-terminal alpha/beta domain. The C-terminal domain has the characteristics of a nucleotide-binding fold, with an insertion of a small anti-parallel beta-sheet subdomain. The S-adenosylhomocysteine-binding site is formed mainly by the large domain, with contributions from residues within the N-terminal domain and the linker region []. CheR proteins are part of the chemotaxis signaling mechanism which methylates the chemotaxis receptor at specific glutamate residues. This entry refers to the C-terminal SAM-binding domain of the CherR-type MCP methyltransferases, which are found in bacteria, archaea and green plants. This entry is found in association with PF03705 from PFAM. ; PDB: 1AF7_A 1BC5_A.

>COG4189 Predicted transcriptional regulator [Transcription]

Probab=93.49  E-value=0.17  Score=41.34  Aligned_cols=57  Identities=11%  Similarity=0.268  Sum_probs=51.2

Q ss_pred             chHHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903            7 IVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus         7 ~~~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      +=.-++|...++..|.+.|+..   +|+.+.|||+++++    +..-+..-+..|...|+++-.
T Consensus        14 ~dv~kalaS~vRv~Il~lL~~k---~plNvneiAe~lgL----pqst~s~~ik~Le~aGlirT~   70 (308)
T COG4189          14 LDVLKALASKVRVAILQLLHRK---GPLNVNEIAEALGL----PQSTMSANIKVLEKAGLIRTE   70 (308)
T ss_pred             chHHHHHHHHHHHHHHHHHHHh---CCCCHHHHHHHhCC----chhhhhhhHHHHHhcCceeee
Confidence            3456799999999999999997   59999999999999    899999999999999999853

>PRK06266 transcription initiation factor E subunit alpha; Validated

Probab=93.42  E-value=0.25  Score=39.00  Aligned_cols=45  Identities=22%  Similarity=0.262  Sum_probs=40.7

Q ss_pred             hChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           19 LGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        19 lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      ..|+++|...   |++|.+|||..+|+    +...++++|..|...|++...
T Consensus        25 ~~Vl~~L~~~---g~~tdeeLA~~Lgi----~~~~VRk~L~~L~e~gLv~~~   69 (178)
T PRK06266         25 FEVLKALIKK---GEVTDEEIAEQTGI----KLNTVRKILYKLYDARLADYK   69 (178)
T ss_pred             hHHHHHHHHc---CCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCeEEe
Confidence            3489998886   59999999999999    999999999999999999953

>COG4190 Predicted transcriptional regulator [Transcription]

Probab=93.41  E-value=0.21  Score=37.00  Aligned_cols=55  Identities=20%  Similarity=0.184  Sum_probs=47.5

Q ss_pred             HHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903            9 LPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus         9 ~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      ....+.+=-.+.|...|++.   +|.|..|+|+..|-    +...+.|=|+.|...|++...
T Consensus        57 ~la~vLsp~nleLl~~Ia~~---~P~Si~ElAe~vgR----dv~nvhr~Ls~l~~~GlI~fe  111 (144)
T COG4190          57 DLARVLSPRNLELLELIAQE---EPASINELAELVGR----DVKNVHRTLSTLADLGLIFFE  111 (144)
T ss_pred             HHHHHhChhHHHHHHHHHhc---CcccHHHHHHHhCc----chHHHHHHHHHHHhcCeEEEe
Confidence            33444455577899999987   69999999999999    999999999999999999985

>PHA02943 hypothetical protein; Provisional

Probab=93.39  E-value=0.24  Score=37.67  Aligned_cols=55  Identities=15%  Similarity=0.201  Sum_probs=43.5

Q ss_pred             ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903           20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH   83 (233)
Q Consensus        20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~   83 (233)
                      .|.+.|..    |+.|..|||+++|+    +-..++-.|..|...|.+.+.+-+ ....|.+.+
T Consensus        15 eILE~Lk~----G~~TtseIAkaLGl----S~~qa~~~LyvLErEG~VkrV~~G-~~tyw~l~~   69 (165)
T PHA02943         15 KTLRLLAD----GCKTTSRIANKLGV----SHSMARNALYQLAKEGMVLKVEIG-RAAIWCLDE   69 (165)
T ss_pred             HHHHHHhc----CCccHHHHHHHHCC----CHHHHHHHHHHHHHcCceEEEeec-ceEEEEECh
Confidence            46677733    69999999999999    999999999999999999997432 233455554

>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=93.38  E-value=0.14  Score=32.72  Aligned_cols=35  Identities=11%  Similarity=0.265  Sum_probs=32.6

Q ss_pred             CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      ++++..+||+.+++    ++..+...++-|...|+++..
T Consensus        21 ~~v~~~~iA~~L~v----s~~tvt~ml~~L~~~GlV~~~   55 (60)
T PF01325_consen   21 GPVRTKDIAERLGV----SPPTVTEMLKRLAEKGLVEYE   55 (60)
T ss_dssp             SSBBHHHHHHHHTS-----HHHHHHHHHHHHHTTSEEEE
T ss_pred             CCccHHHHHHHHCC----ChHHHHHHHHHHHHCCCEEec
Confidence            69999999999999    999999999999999999985

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 ....

>PRK06474 hypothetical protein; Provisional

Probab=93.29  E-value=0.17  Score=39.91  Aligned_cols=71  Identities=10%  Similarity=0.250  Sum_probs=55.1

Q ss_pred             HHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhC-CCCCCCChhhHHHHHHHHhcCCceeeeccC----CCCCceeccHh
Q 039903           10 PAAMQAASELGVFEIIAKAGPTAKISAVEIAAQM-PSSNPNAAVMLDRILRLLVTHRVLRCTSAG----DDQRLYGLAHV   84 (233)
Q Consensus        10 s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~-~~~~~~~~~~l~rlL~~L~~~gll~~~~~~----~~~~~y~lt~~   84 (233)
                      ..+|.--.++.|++.|...+  .+.|+.||++.+ ++    +...++|.|+.|...|++++....    +....|++++.
T Consensus         5 ~~~La~p~R~~Il~~L~~~~--~~~ta~el~~~l~~i----s~aTvYrhL~~L~e~GLI~~~~~~~~~~~~ek~y~~~~~   78 (178)
T PRK06474          5 AEILMHPVRMKICQVLMRNK--EGLTPLELVKILKDV----PQATLYRHLQTMVDSGILHVVKEKKVRSVSEKYYAINEE   78 (178)
T ss_pred             HHhhCCHHHHHHHHHHHhCC--CCCCHHHHHHHhcCC----CHHHHHHHHHHHHHCCCEEEeecccccCceeEEEEeccc
Confidence            45677778999999998864  359999999999 67    888999999999999999986421    01235777765


Q ss_pred             hh
Q 039903           85 AK   86 (233)
Q Consensus        85 s~   86 (233)
                      +.
T Consensus        79 ~~   80 (178)
T PRK06474         79 DA   80 (178)
T ss_pred             ee
Confidence            43

>PRK05638 threonine synthase; Validated

Probab=93.08  E-value=0.19  Score=45.35  Aligned_cols=66  Identities=11%  Similarity=0.156  Sum_probs=53.0

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCC--CCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhc
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMP--SSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVL   90 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~--~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~   90 (233)
                      .++.|+..|.+    ++.+..||++.++  +    +...+++.|+.|...|+++.....+..-.|++|+.+..++.
T Consensus       372 ~r~~IL~~L~~----~~~~~~el~~~l~~~~----s~~~v~~hL~~Le~~GLV~~~~~~g~~~~Y~Lt~~g~~~l~  439 (442)
T PRK05638        372 TKLEILKILSE----REMYGYEIWKALGKPL----KYQAVYQHIKELEELGLIEEAYRKGRRVYYKLTEKGRRLLE  439 (442)
T ss_pred             hHHHHHHHHhh----CCccHHHHHHHHcccC----CcchHHHHHHHHHHCCCEEEeecCCCcEEEEECcHHHHHHH
Confidence            46778888987    5899999999998  7    88999999999999999986321112346999999887653

>PF14394 DUF4423: Domain of unknown function (DUF4423)

Probab=92.78  E-value=0.25  Score=38.67  Aligned_cols=47  Identities=13%  Similarity=0.044  Sum_probs=41.6

Q ss_pred             CCCHHHHHHhC--CCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhH
Q 039903           33 KISAVEIAAQM--PSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKY   87 (233)
Q Consensus        33 ~~t~~elA~~~--~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~   87 (233)
                      ..+..+||+++  ++    +..-++.-|+.|..+|+++++    ++|.|..|..+-.
T Consensus        39 ~~d~~~iak~l~p~i----s~~ev~~sL~~L~~~gli~k~----~~g~y~~t~~~l~   87 (171)
T PF14394_consen   39 APDPEWIAKRLRPKI----SAEEVRDSLEFLEKLGLIKKD----GDGKYVQTDKSLT   87 (171)
T ss_pred             CCCHHHHHHHhcCCC----CHHHHHHHHHHHHHCCCeEEC----CCCcEEEecceee
Confidence            34999999999  99    999999999999999999998    6789998876544

>TIGR00373 conserved hypothetical protein TIGR00373

Probab=92.63  E-value=0.21  Score=38.62  Aligned_cols=45  Identities=11%  Similarity=0.017  Sum_probs=39.7

Q ss_pred             hChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           19 LGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        19 lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      ..|+++|...   +.+|-+|||+.+|+    +...++++|..|...|++...
T Consensus        17 v~Vl~aL~~~---~~~tdEeLa~~Lgi----~~~~VRk~L~~L~e~~Lv~~~   61 (158)
T TIGR00373        17 GLVLFSLGIK---GEFTDEEISLELGI----KLNEVRKALYALYDAGLADYK   61 (158)
T ss_pred             HHHHHHHhcc---CCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCceee
Confidence            3478888765   58999999999999    999999999999999999653

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.

>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain

Probab=92.49  E-value=0.26  Score=34.63  Aligned_cols=44  Identities=14%  Similarity=0.204  Sum_probs=38.1

Q ss_pred             CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceecc
Q 039903           32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLA   82 (233)
Q Consensus        32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt   82 (233)
                      .++|-.|||+.+++    +...+.|.|+.|...|++.+..   +-+.|..|
T Consensus        46 ~~is~~eLa~~~g~----sr~tVsr~L~~Le~~GlI~r~~---~~~~~~~n   89 (95)
T TIGR01610        46 DRVTATVIAELTGL----SRTHVSDAIKSLARRRIIFRQG---MMGIVGVN   89 (95)
T ss_pred             CccCHHHHHHHHCc----CHHHHHHHHHHHHHCCCeeeec---CCceeecC
Confidence            48999999999999    9999999999999999999752   23677665

This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.

>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain

Probab=92.40  E-value=0.28  Score=44.63  Aligned_cols=69  Identities=12%  Similarity=0.132  Sum_probs=57.7

Q ss_pred             HHHhhChhHHHHhcCCCCC-CCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhcCC
Q 039903           15 AASELGVFEIIAKAGPTAK-ISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLNR   92 (233)
Q Consensus        15 ~a~~lglfd~L~~~~~~~~-~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~~~   92 (233)
                      ++.+..|...|...   ++ .+..+||+.+|+    +...+.+.+..|.+.|+++....  ....|.+|+.|+..+.+.
T Consensus         2 ~~~e~~iL~~l~~~---~~~~~~~~la~~~g~----~~~~v~~~~~~L~~kg~v~~~~~--~~~~~~LT~eG~~~l~~G   71 (492)
T PLN02853          2 AMAEEALLGALSNN---EEISDSGQFAASHGL----DHNEVVGVIKSLHGFRYVDAQDI--KRETWVLTEEGKKYAAEG   71 (492)
T ss_pred             chHHHHHHHHHHhc---CCCCCHHHHHHHcCC----CHHHHHHHHHHHHhCCCEEEEEE--EEEEEEECHHHHHHHHcC
Confidence            35677788888875   34 799999999999    99999999999999999986543  468999999999877654

>COG3963 Phospholipid N-methyltransferase [Lipid metabolism]

Probab=92.36  E-value=0.36  Score=37.60  Aligned_cols=67  Identities=18%  Similarity=0.272  Sum_probs=50.0

Q ss_pred             cHHHHHHhcccccCcceEEEecCCccHHHHHHHHH-cCCCcEEEeec-hHHHhh-ccCCCCceEEecCcCC
Q 039903          155 VTNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISN-YLHIKGVNFDL-SHVIQD-SSSYSGVKHIGGIMLE  222 (233)
Q Consensus       155 ~~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~-~P~l~~~v~Dl-p~v~~~-a~~~~ri~~~~gD~f~  222 (233)
                      .+..+....+ +++..-|+.+|-|+|.+..+++++ .+.-..+..+. |+-... -+..+.++++.||.|.
T Consensus        36 lA~~M~s~I~-pesglpVlElGPGTGV~TkaIL~~gv~~~~L~~iE~~~dF~~~L~~~~p~~~ii~gda~~  105 (194)
T COG3963          36 LARKMASVID-PESGLPVLELGPGTGVITKAILSRGVRPESLTAIEYSPDFVCHLNQLYPGVNIINGDAFD  105 (194)
T ss_pred             HHHHHHhccC-cccCCeeEEEcCCccHhHHHHHhcCCCccceEEEEeCHHHHHHHHHhCCCccccccchhh
Confidence            3556666777 888889999999999999998886 44455566654 554444 3446889999999986

>PRK10870 transcriptional repressor MprA; Provisional

Probab=92.32  E-value=0.3  Score=38.35  Aligned_cols=56  Identities=14%  Similarity=0.124  Sum_probs=46.3

Q ss_pred             CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      ++.|..|||+.+++    +...+.++++-|...|++++...+.  ..-...+|+.|..+...
T Consensus        70 ~~it~~eLa~~l~l----~~~tvsr~v~rLe~kGlV~R~~~~~DrR~~~v~LT~~G~~~~~~  127 (176)
T PRK10870         70 HSIQPSELSCALGS----SRTNATRIADELEKRGWIERRESDNDRRCLHLQLTEKGHEFLRE  127 (176)
T ss_pred             CCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHH
Confidence            57899999999999    9999999999999999999865431  11356789999887755

>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=92.27  E-value=0.15  Score=28.26  Aligned_cols=31  Identities=19%  Similarity=0.295  Sum_probs=25.7

Q ss_pred             CCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCce
Q 039903           33 KISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVL   67 (233)
Q Consensus        33 ~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll   67 (233)
                      |+|-.|||..+|+    ..+-+.|+|..|...|++
T Consensus         2 ~mtr~diA~~lG~----t~ETVSR~l~~l~~~glI   32 (32)
T PF00325_consen    2 PMTRQDIADYLGL----TRETVSRILKKLERQGLI   32 (32)
T ss_dssp             E--HHHHHHHHTS-----HHHHHHHHHHHHHTTSE
T ss_pred             CcCHHHHHHHhCC----cHHHHHHHHHHHHHcCCC
Confidence            5788999999999    999999999999988874

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 ....

>KOG3045 consensus Predicted RNA methylase involved in rRNA processing [RNA processing and modification]

Probab=92.07  E-value=0.55  Score=39.23  Aligned_cols=88  Identities=18%  Similarity=0.149  Sum_probs=50.9

Q ss_pred             ccccccCchHHHHHHHHHHh----cchhcHHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhh
Q 039903          131 YEYAGNDFRFNGVFNKAMLN----HTSIVTNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQD  206 (233)
Q Consensus       131 ~~~~~~~~~~~~~f~~am~~----~~~~~~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~  206 (233)
                      ++.+..||..-+.|++....    |-......+++.+..-++-..|-|+|||.+-++.   ..  .-++.-|||-.+   
T Consensus       139 ~~lfkedp~afdlYH~gfr~QV~kWP~nPld~ii~~ik~r~~~~vIaD~GCGEakiA~---~~--~~kV~SfDL~a~---  210 (325)
T KOG3045|consen  139 FDLFKEDPTAFDLYHAGFRSQVKKWPENPLDVIIRKIKRRPKNIVIADFGCGEAKIAS---SE--RHKVHSFDLVAV---  210 (325)
T ss_pred             HHHHhcCcHHHHHHHHHHHHHHHhCCCChHHHHHHHHHhCcCceEEEecccchhhhhh---cc--ccceeeeeeecC---
Confidence            34455677766666555443    3333344555555423456789999999998776   11  223566676432   


Q ss_pred             ccCCCCceEEecCcCC-CCCC--CCEEE
Q 039903          207 SSSYSGVKHIGGIMLE-RIPK--GDAIL  231 (233)
Q Consensus       207 a~~~~ri~~~~gD~f~-~~P~--~D~~~  231 (233)
                         ++  ..+++|+-+ |++.  .|+.+
T Consensus       211 ---~~--~V~~cDm~~vPl~d~svDvaV  233 (325)
T KOG3045|consen  211 ---NE--RVIACDMRNVPLEDESVDVAV  233 (325)
T ss_pred             ---CC--ceeeccccCCcCccCcccEEE
Confidence               13  345788887 6654  26654

>COG1352 CheR Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]

Probab=91.84  E-value=1.4  Score=37.04  Aligned_cols=66  Identities=12%  Similarity=0.143  Sum_probs=49.7

Q ss_pred             CcceEEEecCCccH----HHHHHHHHcC-----CCcEEEeech-HHHhhccCC---------------------------
Q 039903          168 QIKQLVDVGGGLGV----NVNIIISNYL-----HIKGVNFDLS-HVIQDSSSY---------------------------  210 (233)
Q Consensus       168 ~~~~vvDvGGG~G~----~~~~l~~~~P-----~l~~~v~Dlp-~v~~~a~~~---------------------------  210 (233)
                      +.-+|--.||++|.    +++.+.+.+|     .++++.-|+. .+++.|+.-                           
T Consensus        96 ~~irIWSaaCStGEEpYSiAm~l~e~~~~~~~~~~~I~AtDId~~~L~~A~~G~Y~~~~~~~~~~~~~~~ryF~~~~~~~  175 (268)
T COG1352          96 RPIRIWSAACSTGEEPYSLAMLLLEALGKLAGFRVKILATDIDLSVLEKARAGIYPSRELLRGLPPELLRRYFERGGDGS  175 (268)
T ss_pred             CceEEEecCcCCCccHHHHHHHHHHHhccccCCceEEEEEECCHHHHHHHhcCCCChhHhhccCCHHHHhhhEeecCCCc
Confidence            46789999999995    5666778887     4677888986 478777540                           


Q ss_pred             --------CCceEEecCcCCC--CCCC-CEEEeC
Q 039903          211 --------SGVKHIGGIMLER--IPKG-DAILIK  233 (233)
Q Consensus       211 --------~ri~~~~gD~f~~--~P~~-D~~~lk  233 (233)
                              ..|.|..+|.+++  .+.. |+|+-|
T Consensus       176 y~v~~~ir~~V~F~~~NLl~~~~~~~~fD~IfCR  209 (268)
T COG1352         176 YRVKEELRKMVRFRRHNLLDDSPFLGKFDLIFCR  209 (268)
T ss_pred             EEEChHHhcccEEeecCCCCCccccCCCCEEEEc
Confidence                    3699999999984  4444 999864

>COG1846 MarR Transcriptional regulators [Transcription]

Probab=91.67  E-value=0.46  Score=34.06  Aligned_cols=69  Identities=16%  Similarity=0.213  Sum_probs=52.3

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcCC
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLNR   92 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~~   92 (233)
                      .+..+...|...+   +.+..+||+.+++    +...+.++++-|...|++++.....  ..-.+.+|+.|..+....
T Consensus        23 ~q~~~L~~l~~~~---~~~~~~la~~l~i----~~~~vt~~l~~Le~~glv~r~~~~~DrR~~~l~lT~~G~~~~~~~   93 (126)
T COG1846          23 PQYQVLLALYEAG---GITVKELAERLGL----DRSTVTRLLKRLEDKGLIERLRDPEDRRAVLVRLTEKGRELLEQL   93 (126)
T ss_pred             HHHHHHHHHHHhC---CCcHHHHHHHHCC----CHHHHHHHHHHHHHCCCeeecCCccccceeeEEECccHHHHHHHh
Confidence            4455666777753   3443999999999    9999999999999999999875431  123678899888776554

>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=91.54  E-value=0.35  Score=36.52  Aligned_cols=36  Identities=14%  Similarity=0.131  Sum_probs=34.3

Q ss_pred             CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeec
Q 039903           32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTS   71 (233)
Q Consensus        32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~   71 (233)
                      |++|++|||.+.|+    +.+.+-.-|.++++.|-|.+..
T Consensus         5 Ga~T~eELA~~FGv----ttRkvaStLa~~ta~Grl~Rv~   40 (155)
T PF07789_consen    5 GAKTAEELAGKFGV----TTRKVASTLAMVTATGRLIRVN   40 (155)
T ss_pred             CcccHHHHHHHhCc----chhhhHHHHHHHHhcceeEEec
Confidence            79999999999999    9999999999999999999874

The region in question is approximately 150 amino acid residues long.

>PF02527 GidB: rRNA small subunit methyltransferase G; InterPro: IPR003682 This entry represents a rRNA small subunit methyltransferase G

Probab=91.46  E-value=0.23  Score=39.39  Aligned_cols=62  Identities=16%  Similarity=0.220  Sum_probs=42.5

Q ss_pred             eEEEecCCccHHHHHHHHHcCCCcEEEeech----HHHhhccC---CCCceEEecCcCC-CCCCC-CEEEe
Q 039903          171 QLVDVGGGLGVNVNIIISNYLHIKGVNFDLS----HVIQDSSS---YSGVKHIGGIMLE-RIPKG-DAILI  232 (233)
Q Consensus       171 ~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp----~v~~~a~~---~~ri~~~~gD~f~-~~P~~-D~~~l  232 (233)
                      +++|||.|.|.=++-++=.+|+++++++|--    ..++.+..   .++|+.+.+..-+ ..+.. |+++.
T Consensus        51 ~~lDiGSGaGfPGipLaI~~p~~~~~LvEs~~KK~~FL~~~~~~L~L~nv~v~~~R~E~~~~~~~fd~v~a  121 (184)
T PF02527_consen   51 KVLDIGSGAGFPGIPLAIARPDLQVTLVESVGKKVAFLKEVVRELGLSNVEVINGRAEEPEYRESFDVVTA  121 (184)
T ss_dssp             EEEEETSTTTTTHHHHHHH-TTSEEEEEESSHHHHHHHHHHHHHHT-SSEEEEES-HHHTTTTT-EEEEEE
T ss_pred             eEEecCCCCCChhHHHHHhCCCCcEEEEeCCchHHHHHHHHHHHhCCCCEEEEEeeecccccCCCccEEEe
Confidence            7999999999999999999999999999953    22333222   2678887777666 23332 77664

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.

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=91.42  E-value=0.38  Score=36.79  Aligned_cols=47  Identities=13%  Similarity=0.200  Sum_probs=42.9

Q ss_pred             HHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceee
Q 039903           16 ASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRC   69 (233)
Q Consensus        16 a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~   69 (233)
                      ..+..|.+.|..+   +..|..+||+++|+    ++..+.+=++-|...|++..
T Consensus         9 ~~D~~Il~~Lq~d---~R~s~~eiA~~lgl----S~~tV~~Ri~rL~~~GvI~~   55 (153)
T PRK11179          9 NLDRGILEALMEN---ARTPYAELAKQFGV----SPGTIHVRVEKMKQAGIITG   55 (153)
T ss_pred             HHHHHHHHHHHHc---CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCeee
Confidence            3577899999987   58999999999999    99999999999999999985

>COG0357 GidB Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]

Probab=91.40  E-value=0.2  Score=40.70  Aligned_cols=53  Identities=15%  Similarity=0.247  Sum_probs=38.7

Q ss_pred             cceEEEecCCccHHHHHHHHHcCCCcEEEeech----HHHhhccC---CCCceEEecCcC
Q 039903          169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS----HVIQDSSS---YSGVKHIGGIML  221 (233)
Q Consensus       169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp----~v~~~a~~---~~ri~~~~gD~f  221 (233)
                      ..+++|||.|.|.=++-++=.+|+++++++|--    .-++.+..   .++++++.+..=
T Consensus        68 ~~~~~DIGSGaGfPGipLAI~~p~~~vtLles~~Kk~~FL~~~~~eL~L~nv~i~~~RaE  127 (215)
T COG0357          68 AKRVLDIGSGAGFPGIPLAIAFPDLKVTLLESLGKKIAFLREVKKELGLENVEIVHGRAE  127 (215)
T ss_pred             CCEEEEeCCCCCCchhhHHHhccCCcEEEEccCchHHHHHHHHHHHhCCCCeEEehhhHh
Confidence            589999999999999999889999999999943    22333322   255666655443

>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=91.12  E-value=0.95  Score=30.51  Aligned_cols=53  Identities=8%  Similarity=-0.041  Sum_probs=42.8

Q ss_pred             CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhc
Q 039903           32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVL   90 (233)
Q Consensus        32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~   90 (233)
                      .|+...+||+.++.    ++--++..|..|..+|+++....  ..+.|..|..+-.+..
T Consensus        22 ~PVgSk~ia~~l~~----s~aTIRN~M~~Le~lGlve~~p~--~s~GriPT~~aYr~~~   74 (78)
T PF03444_consen   22 EPVGSKTIAEELGR----SPATIRNEMADLEELGLVESQPH--PSGGRIPTDKAYRALN   74 (78)
T ss_pred             CCcCHHHHHHHHCC----ChHHHHHHHHHHHHCCCccCCCC--CCCCCCcCHHHHHHHc
Confidence            59999999999999    99999999999999999985211  2466778877765443

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

>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins

Probab=91.03  E-value=0.31  Score=35.57  Aligned_cols=67  Identities=21%  Similarity=0.334  Sum_probs=49.1

Q ss_pred             HHHhhChhHHHHhcCCCCCCCHHHHHHhCCCC-CCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903           15 AASELGVFEIIAKAGPTAKISAVEIAAQMPSS-NPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH   83 (233)
Q Consensus        15 ~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~-~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~   83 (233)
                      +.-+.-|++.|.+.+  ++.|+.||-+.+.-. ++.+..-++|-|+.|...|++.+...+++...|....
T Consensus         7 T~~R~~Il~~l~~~~--~~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~~~~~~~~~Y~~~~   74 (120)
T PF01475_consen    7 TPQRLAILELLKESP--EHLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKIEFGDGESRYELST   74 (120)
T ss_dssp             HHHHHHHHHHHHHHS--SSEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEETTSEEEEEESS
T ss_pred             CHHHHHHHHHHHcCC--CCCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEEEcCCCcceEeecC
Confidence            445677899999976  699999999988531 1227778999999999999999975432334565544

These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....

>PF04182 B-block_TFIIIC: B-block binding subunit of TFIIIC; InterPro: IPR007309 Yeast transcription factor IIIC (TFIIIC) is a multisubunit protein complex that interacts with two control elements of class III promoters called the A and B blocks

Probab=90.96  E-value=0.36  Score=32.28  Aligned_cols=49  Identities=12%  Similarity=0.089  Sum_probs=42.7

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      .+..+++.|+.++. .+.+..||++.++.    |++.+...++.|...|++.+.
T Consensus         3 ~~~~~Le~I~rsR~-~Gi~q~~L~~~~~~----D~r~i~~~~k~L~~~gLI~k~   51 (75)
T PF04182_consen    3 IQYCLLERIARSRY-NGITQSDLSKLLGI----DPRSIFYRLKKLEKKGLIVKQ   51 (75)
T ss_pred             hHHHHHHHHHhcCC-CCEehhHHHHHhCC----CchHHHHHHHHHHHCCCEEEE
Confidence            45567788888653 47899999999999    999999999999999999985

This family represents the subunit within TFIIIC involved in B-block binding []. Although defined as a yeast protein, it is also found in a number of other organisms.

>PRK11169 leucine-responsive transcriptional regulator; Provisional

Probab=90.86  E-value=0.38  Score=37.30  Aligned_cols=48  Identities=15%  Similarity=0.185  Sum_probs=43.5

Q ss_pred             HHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceee
Q 039903           15 AASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRC   69 (233)
Q Consensus        15 ~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~   69 (233)
                      -..+..|..+|..+   +.+|..|||+++|+    ++..+.+=++-|...|+++.
T Consensus        13 D~~D~~IL~~Lq~d---~R~s~~eiA~~lgl----S~~tv~~Ri~rL~~~GvI~~   60 (164)
T PRK11169         13 DRIDRNILNELQKD---GRISNVELSKRVGL----SPTPCLERVRRLERQGFIQG   60 (164)
T ss_pred             HHHHHHHHHHhccC---CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCeEE
Confidence            34678899999987   59999999999999    99999999999999999985

>COG1522 Lrp Transcriptional regulators [Transcription]

Probab=90.80  E-value=0.46  Score=36.01  Aligned_cols=48  Identities=17%  Similarity=0.266  Sum_probs=43.3

Q ss_pred             HHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           16 ASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        16 a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      ..+..|.+.|...   ++.+..+||+++|+    ++..+.+-++-|...|++...
T Consensus         8 ~~D~~IL~~L~~d---~r~~~~eia~~lgl----S~~~v~~Ri~~L~~~GiI~~~   55 (154)
T COG1522           8 DIDRRILRLLQED---ARISNAELAERVGL----SPSTVLRRIKRLEEEGVIKGY   55 (154)
T ss_pred             HHHHHHHHHHHHh---CCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCceeeE
Confidence            3567788999987   58999999999999    999999999999999999875

>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional

Probab=90.69  E-value=0.62  Score=42.53  Aligned_cols=69  Identities=7%  Similarity=0.129  Sum_probs=57.1

Q ss_pred             HHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhcCC
Q 039903           16 ASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLNR   92 (233)
Q Consensus        16 a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~~~   92 (233)
                      ..+..|...|...+  +..+..+||+.+++    +...+.+.+..|.+.|+++....  ....|.+|+.|+..+.+.
T Consensus         6 ~~e~~iL~~l~~~~--~~~~~~~la~~~~~----~~~~v~~~~~~L~~kg~v~~~~~--~~~~~~LT~eG~~~~~~G   74 (494)
T PTZ00326          6 LEENTILSKLESEN--EIVNSLALAESLNI----DHQKVVGAIKSLESANYITTEMK--KSNTWTLTEEGEDYLKNG   74 (494)
T ss_pred             HHHHHHHHHHHhcC--CCCCHHHHHHHcCC----CHHHHHHHHHHHHhCCCEEEEEE--EEEEEEECHHHHHHHHcC
Confidence            45667788888722  47899999999999    99999999999999999986543  468999999999877654

>COG5459 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]

Probab=90.64  E-value=0.33  Score=42.23  Aligned_cols=68  Identities=19%  Similarity=0.272  Sum_probs=44.2

Q ss_pred             ccccCcceEEEecCCccHHHHHHHHHcCCCcE-EEeechH----HHhhccCC---CCceEEecCcCC---CCCCCCEEEe
Q 039903          164 KGFEQIKQLVDVGGGLGVNVNIIISNYLHIKG-VNFDLSH----VIQDSSSY---SGVKHIGGIMLE---RIPKGDAILI  232 (233)
Q Consensus       164 ~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~-~v~Dlp~----v~~~a~~~---~ri~~~~gD~f~---~~P~~D~~~l  232 (233)
                      ++|+ .++|+|||-|.|.-+.++-.-+|+++- ++++...    |+....++   .+-..-..|+-.   ++|.+|.|.+
T Consensus       110 ~dfa-pqsiLDvG~GPgtgl~A~n~i~Pdl~sa~ile~sp~lrkV~~tl~~nv~t~~td~r~s~vt~dRl~lp~ad~ytl  188 (484)
T COG5459         110 PDFA-PQSILDVGAGPGTGLWALNDIWPDLKSAVILEASPALRKVGDTLAENVSTEKTDWRASDVTEDRLSLPAADLYTL  188 (484)
T ss_pred             CCcC-cchhhccCCCCchhhhhhcccCCCchhhhhhccCHHHHHHHHHHHhhcccccCCCCCCccchhccCCCccceeeh
Confidence            3344 367999999999999999999999984 6666543    33322222   222333445543   6777888865

>COG1378 Predicted transcriptional regulators [Transcription]

Probab=90.54  E-value=0.72  Score=38.36  Aligned_cols=61  Identities=13%  Similarity=0.132  Sum_probs=48.2

Q ss_pred             hChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHh
Q 039903           19 LGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYF   88 (233)
Q Consensus        19 lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l   88 (233)
                      -.+.-+|-..   |+.|+.|||+.+|+    +...++.+|+.|...|+++....  ....|+.-+-...+
T Consensus        19 a~vY~aLl~~---g~~tA~eis~~sgv----P~~kvY~vl~sLe~kG~v~~~~g--~P~~y~av~p~~~i   79 (247)
T COG1378          19 AKVYLALLCL---GEATAKEISEASGV----PRPKVYDVLRSLEKKGLVEVIEG--RPKKYRAVPPEELI   79 (247)
T ss_pred             HHHHHHHHHh---CCccHHHHHHHcCC----CchhHHHHHHHHHHCCCEEeeCC--CCceEEeCCHHHHH
Confidence            3455555555   69999999999999    99999999999999999998632  56788776655443

>PRK13509 transcriptional repressor UlaR; Provisional

Probab=90.53  E-value=0.53  Score=39.21  Aligned_cols=47  Identities=11%  Similarity=0.126  Sum_probs=42.4

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      .+..|.+.|.+.   +..+..|||+.+++    ++.-++|-|+.|...|++.+.
T Consensus         6 R~~~Il~~l~~~---~~~~~~ela~~l~v----S~~TirRdL~~Le~~g~i~r~   52 (251)
T PRK13509          6 RHQILLELLAQL---GFVTVEKVIERLGI----SPATARRDINKLDESGKLKKV   52 (251)
T ss_pred             HHHHHHHHHHHc---CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEe
Confidence            345688889887   58999999999999    999999999999999999987

>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=90.46  E-value=0.33  Score=34.60  Aligned_cols=44  Identities=9%  Similarity=0.238  Sum_probs=34.3

Q ss_pred             ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      -|++.|...   |.++-+|||+.+++    +..-++++|..|...|++...
T Consensus        17 ~Il~~L~~~---~~l~de~la~~~~l----~~~~vRkiL~~L~~~~lv~~~   60 (105)
T PF02002_consen   17 RILDALLRK---GELTDEDLAKKLGL----KPKEVRKILYKLYEDGLVSYR   60 (105)
T ss_dssp             HHHHHHHHH-----B-HHHHHHTT-S-----HHHHHHHHHHHHHHSS-EEE
T ss_pred             HHHHHHHHc---CCcCHHHHHHHhCC----CHHHHHHHHHHHHHCCCeEEE
Confidence            378888866   58999999999999    999999999999999999764

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.

>PRK13777 transcriptional regulator Hpr; Provisional

Probab=90.30  E-value=0.86  Score=36.18  Aligned_cols=65  Identities=15%  Similarity=0.045  Sum_probs=50.9

Q ss_pred             ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      .+.-.|...   ++.|..+||+.+.+    +...+.++++-|...|++.+...++  ..-...+|+.|+.+...
T Consensus        49 ~iL~~L~~~---~~itq~eLa~~l~l----~~sTvtr~l~rLE~kGlI~R~~~~~DrR~~~I~LTekG~~l~~~  115 (185)
T PRK13777         49 HILWIAYHL---KGASISEIAKFGVM----HVSTAFNFSKKLEERGYLTFSKKEDDKRNTYIELTEKGEELLLE  115 (185)
T ss_pred             HHHHHHHhC---CCcCHHHHHHHHCC----CHhhHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHH
Confidence            456666665   48999999999999    9899999999999999999864321  22345789999887654

>PF04672 Methyltransf_19: S-adenosyl methyltransferase; InterPro: IPR006764 This is a family of uncharacterised proteins

Probab=90.16  E-value=0.85  Score=38.29  Aligned_cols=56  Identities=16%  Similarity=0.175  Sum_probs=32.9

Q ss_pred             CcceEEEecCCcc---HHHHHHHHHcCCCcEEEeech-HHHhhccC----CCC--ceEEecCcCCC
Q 039903          168 QIKQLVDVGGGLG---VNVNIIISNYLHIKGVNFDLS-HVIQDSSS----YSG--VKHIGGIMLER  223 (233)
Q Consensus       168 ~~~~vvDvGGG~G---~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~----~~r--i~~~~gD~f~~  223 (233)
                      ++..+||||+|.-   ..-....+..|+.+++=.|.. -|+.+++.    +++  ..++.+|+.++
T Consensus        68 GIrQFLDlGsGlPT~~nvHevAq~~~P~aRVVYVD~DPvv~ah~ralL~~~~~g~t~~v~aD~r~p  133 (267)
T PF04672_consen   68 GIRQFLDLGSGLPTAGNVHEVAQRVAPDARVVYVDNDPVVLAHARALLADNPRGRTAYVQADLRDP  133 (267)
T ss_dssp             ---EEEEET--S--SS-HHHHHHHH-TT-EEEEEESSHHHHHCCHHHHTT-TTSEEEEEE--TT-H
T ss_pred             CcceEEEcccCCCCCCCHhHHHHhhCCCceEEEECCCchHHHHHHhhhcCCCCccEEEEeCCCCCH
Confidence            7899999999975   333334556999999999984 57787765    245  89999999873

; PDB: 3GIW_A 3GO4_A 2QE6_A.

>COG1733 Predicted transcriptional regulators [Transcription]

Probab=90.11  E-value=1  Score=33.05  Aligned_cols=55  Identities=15%  Similarity=0.132  Sum_probs=45.8

Q ss_pred             CCCCHHHHHHhCC-CCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhc
Q 039903           32 AKISAVEIAAQMP-SSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVL   90 (233)
Q Consensus        32 ~~~t~~elA~~~~-~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~   90 (233)
                      |+.-..||-..++ +    ++.-|.+=|+.|...|++++..-+.  ..-.|++|+.+..|..
T Consensus        35 g~~RF~eL~r~i~~I----s~k~Ls~~Lk~Le~~Glv~R~~~~~~PprveY~LT~~G~~L~~   92 (120)
T COG1733          35 GPKRFNELRRSIGGI----SPKMLSRRLKELEEDGLVERVVYPEEPPRVEYRLTEKGRDLLP   92 (120)
T ss_pred             CCCcHHHHHHHcccc----CHHHHHHHHHHHHHCCCEEeeecCCCCceeEEEEhhhHHHHHH
Confidence            5899999999999 9    9999999999999999999864321  1347999999887763

>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]

Probab=90.08  E-value=0.43  Score=39.94  Aligned_cols=48  Identities=21%  Similarity=0.391  Sum_probs=43.8

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeec
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTS   71 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~   71 (233)
                      +..+.++|...|  |..+-+||.+++|+    +...+.|+|+-|..+|++++..
T Consensus       197 e~~il~~i~~~G--Gri~Q~eL~r~lgl----sktTvsR~L~~LEk~GlIe~~K  244 (258)
T COG2512         197 EKEILDLIRERG--GRITQAELRRALGL----SKTTVSRILRRLEKRGLIEKEK  244 (258)
T ss_pred             HHHHHHHHHHhC--CEEeHHHHHHhhCC----ChHHHHHHHHHHHhCCceEEEE
Confidence            456889999987  78999999999999    9999999999999999999864

>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=89.99  E-value=0.61  Score=36.74  Aligned_cols=56  Identities=16%  Similarity=0.213  Sum_probs=41.1

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCC---------CCceEEecCcCC
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSY---------SGVKHIGGIMLE  222 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~---------~ri~~~~gD~f~  222 (233)
                      ++...||-+|||-=.....+...+++++..=+|+|+|++.-++.         .++++++.|+.+
T Consensus        77 ~~~~qvV~LGaGlDTr~~Rl~~~~~~~~~~evD~p~v~~~K~~~l~~~~~~~~~~~~~v~~Dl~~  141 (183)
T PF04072_consen   77 PGARQVVNLGAGLDTRAYRLDNPAGGVRWFEVDLPEVIALKRRLLPESGARPPANYRYVPADLRD  141 (183)
T ss_dssp             TTESEEEEET-TT--HHHHHHHTTTTEEEEEEE-HHHHHHHHHHHHHTHHHHHEESSEEES-TTS
T ss_pred             CCCcEEEEcCCCCCchHHHhhccccceEEEEeCCHHHHHHHHHHHHhCcccCCcceeEEeccccc
Confidence            45669999999999999999998889999999999988754331         236789999986

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 ....

>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication

Probab=89.83  E-value=0.47  Score=36.96  Aligned_cols=43  Identities=14%  Similarity=0.209  Sum_probs=39.6

Q ss_pred             CCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHh
Q 039903           34 ISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHV   84 (233)
Q Consensus        34 ~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~   84 (233)
                      .|..+||+.+++    +..-+.|.+..|...+++.+.    ..+.|.++|.
T Consensus        76 ~t~~~ia~~l~i----S~~Tv~r~ik~L~e~~iI~k~----~~G~Y~iNP~  118 (165)
T PF05732_consen   76 ATQKEIAEKLGI----SKPTVSRAIKELEEKNIIKKI----RNGAYMINPN  118 (165)
T ss_pred             eeHHHHHHHhCC----CHHHHHHHHHHHHhCCcEEEc----cCCeEEECcH
Confidence            488999999999    999999999999999999997    5789999984

; GO: 0006260 DNA replication, 0006276 plasmid maintenance

>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed

Probab=89.77  E-value=0.53  Score=42.15  Aligned_cols=43  Identities=23%  Similarity=0.197  Sum_probs=38.1

Q ss_pred             CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceecc
Q 039903           32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLA   82 (233)
Q Consensus        32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt   82 (233)
                      .|.|.+||++.+++    +++.++++|+.|...|++.+.    +++.|.+.
T Consensus       309 ~~~t~~~La~~l~~----~~~~v~~iL~~L~~agLI~~~----~~g~~~l~  351 (412)
T PRK04214        309 KALDVDEIRRLEPM----GYDELGELLCELARIGLLRRG----ERGQWVLA  351 (412)
T ss_pred             CCCCHHHHHHHhCC----CHHHHHHHHHHHHhCCCeEec----CCCceEec
Confidence            58999999999999    999999999999999999975    45667554

>COG2521 Predicted archaeal methyltransferase [General function prediction only]

Probab=89.73  E-value=0.49  Score=38.95  Aligned_cols=64  Identities=20%  Similarity=0.165  Sum_probs=48.9

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcE-EEeechHHHhhccCC--------CCceEEecCcCC---CCCCC--CEEE
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKG-VNFDLSHVIQDSSSY--------SGVKHIGGIMLE---RIPKG--DAIL  231 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~-~v~Dlp~v~~~a~~~--------~ri~~~~gD~f~---~~P~~--D~~~  231 (233)
                      ++..+|+|..+|-|..+++.+++-. +++ ++---|.|++.|.-+        .+|+.+-||.++   .++..  |+++
T Consensus       133 ~~G~rVLDtC~GLGYtAi~a~~rGA-~~VitvEkdp~VLeLa~lNPwSr~l~~~~i~iilGD~~e~V~~~~D~sfDaIi  210 (287)
T COG2521         133 KRGERVLDTCTGLGYTAIEALERGA-IHVITVEKDPNVLELAKLNPWSRELFEIAIKIILGDAYEVVKDFDDESFDAII  210 (287)
T ss_pred             ccCCEeeeeccCccHHHHHHHHcCC-cEEEEEeeCCCeEEeeccCCCCccccccccEEecccHHHHHhcCCccccceEe
Confidence            5678999999999999999999854 244 343348899988765        478999999997   45542  7765

>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term

Probab=89.72  E-value=0.57  Score=34.19  Aligned_cols=36  Identities=8%  Similarity=0.096  Sum_probs=33.8

Q ss_pred             CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeec
Q 039903           32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTS   71 (233)
Q Consensus        32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~   71 (233)
                      .++|++|||+.+.+    +++.++.+|+-|...|.++...
T Consensus        18 ~~vtl~elA~~l~c----S~Rn~r~lLkkm~~~gWi~W~p   53 (115)
T PF12793_consen   18 VEVTLDELAELLFC----SRRNARTLLKKMQEEGWITWQP   53 (115)
T ss_pred             cceeHHHHHHHhCC----CHHHHHHHHHHHHHCCCeeeeC
Confidence            47899999999999    9999999999999999999863

>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A

Probab=89.70  E-value=0.57  Score=30.94  Aligned_cols=42  Identities=17%  Similarity=0.218  Sum_probs=37.1

Q ss_pred             CCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903           33 KISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH   83 (233)
Q Consensus        33 ~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~   83 (233)
                      +.|-++||..+|+    +...+.|+|+.|...|+++..     .+.+....
T Consensus        28 ~lt~~~iA~~~g~----sr~tv~r~l~~l~~~g~I~~~-----~~~i~I~d   69 (76)
T PF13545_consen   28 PLTQEEIADMLGV----SRETVSRILKRLKDEGIIEVK-----RGKIIILD   69 (76)
T ss_dssp             ESSHHHHHHHHTS----CHHHHHHHHHHHHHTTSEEEE-----TTEEEESS
T ss_pred             cCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEc-----CCEEEECC
Confidence            7899999999999    999999999999999999985     56665543

...

>KOG4589 consensus Cell division protein FtsJ [Cell cycle control, cell division, chromosome partitioning]

Probab=89.69  E-value=0.57  Score=37.23  Aligned_cols=44  Identities=16%  Similarity=0.195  Sum_probs=34.9

Q ss_pred             HhcccccCcceEEEecCCccHHHHHHHHHc-CCCcEEEeechHHH
Q 039903          161 DSSKGFEQIKQLVDVGGGLGVNVNIIISNY-LHIKGVNFDLSHVI  204 (233)
Q Consensus       161 ~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~-P~l~~~v~Dlp~v~  204 (233)
                      +.|.-++...+|+|||+-.|.++.-..++. |+-.+..+|+-++.
T Consensus        62 dKy~~l~p~~~VlD~G~APGsWsQVavqr~~p~g~v~gVDllh~~  106 (232)
T KOG4589|consen   62 DKYRFLRPEDTVLDCGAAPGSWSQVAVQRVNPNGMVLGVDLLHIE  106 (232)
T ss_pred             hhccccCCCCEEEEccCCCChHHHHHHHhhCCCceEEEEeeeecc
Confidence            344424667999999999999998888875 99888999986544

>PRK10611 chemotaxis methyltransferase CheR; Provisional

Probab=89.56  E-value=6.6  Score=33.42  Aligned_cols=64  Identities=16%  Similarity=0.073  Sum_probs=44.9

Q ss_pred             cceEEEecCCccH--HH--HHHHHHcC----CCcEEEeech-HHHhhccCC-----------------------------
Q 039903          169 IKQLVDVGGGLGV--NV--NIIISNYL----HIKGVNFDLS-HVIQDSSSY-----------------------------  210 (233)
Q Consensus       169 ~~~vvDvGGG~G~--~~--~~l~~~~P----~l~~~v~Dlp-~v~~~a~~~-----------------------------  210 (233)
                      .-+|...||++|.  ++  +.+.+..+    +++++.-|+. .+++.|++-                             
T Consensus       116 ~irIWSAgCStGEEpYSlAmll~e~~~~~~~~~~I~atDIs~~aL~~Ar~G~Y~~~~~r~~p~~~~~ryF~~~~~~~~~~  195 (287)
T PRK10611        116 EYRVWSAAASTGEEPYSIAMTLADTLGTAPGRWKVFASDIDTEVLEKARSGIYRQEELKTLSPQQLQRYFMRGTGPHEGL  195 (287)
T ss_pred             CEEEEEccccCCHHHHHHHHHHHHhhcccCCCcEEEEEECCHHHHHHHHhCCCCHHHHhcCCHHHHHHHcccccCCCCce
Confidence            3689999999996  44  44555443    4678888985 477766430                             


Q ss_pred             --------CCceEEecCcCC-CCC-C-C-CEEEe
Q 039903          211 --------SGVKHIGGIMLE-RIP-K-G-DAILI  232 (233)
Q Consensus       211 --------~ri~~~~gD~f~-~~P-~-~-D~~~l  232 (233)
                              .+|+|..+|.++ +.| . . |+|+.
T Consensus       196 ~~v~~~lr~~V~F~~~NL~~~~~~~~~~fD~I~c  229 (287)
T PRK10611        196 VRVRQELANYVDFQQLNLLAKQWAVPGPFDAIFC  229 (287)
T ss_pred             EEEChHHHccCEEEcccCCCCCCccCCCcceeeH
Confidence                    468999999998 555 2 3 99874

>TIGR00498 lexA SOS regulatory protein LexA

Probab=89.20  E-value=0.89  Score=36.26  Aligned_cols=49  Identities=20%  Similarity=0.185  Sum_probs=39.8

Q ss_pred             HHhhChhHHHHhc----CCCCCCCHHHHHHhCCCCCCCC-hhhHHHHHHHHhcCCceeee
Q 039903           16 ASELGVFEIIAKA----GPTAKISAVEIAAQMPSSNPNA-AVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        16 a~~lglfd~L~~~----~~~~~~t~~elA~~~~~~~~~~-~~~l~rlL~~L~~~gll~~~   70 (233)
                      ..+..|++.|.+.    +  -+.|..|||+.+++    + ...+.+.|+.|...|++++.
T Consensus         6 ~~q~~iL~~l~~~~~~~~--~~~~~~ela~~~~~----~s~~tv~~~l~~L~~~g~i~~~   59 (199)
T TIGR00498         6 ARQQEVLDLIRAHIESTG--YPPSIREIARAVGL----RSPSAAEEHLKALERKGYIERD   59 (199)
T ss_pred             HHHHHHHHHHHHHHHhcC--CCCcHHHHHHHhCC----CChHHHHHHHHHHHHCCCEecC
Confidence            3455666666642    2  36889999999999    8 89999999999999999985

LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.

>PF03602 Cons_hypoth95: Conserved hypothetical protein 95; InterPro: IPR004398 This entry contains Ribosomal RNA small subunit methyltransferase D as well as the putative rRNA methyltransferase YlbH

Probab=89.04  E-value=0.33  Score=38.41  Aligned_cols=64  Identities=16%  Similarity=0.108  Sum_probs=44.5

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC-------CCceEEecCcCCCC------CCC-CEEEe
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY-------SGVKHIGGIMLERI------PKG-DAILI  232 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~-------~ri~~~~gD~f~~~------P~~-D~~~l  232 (233)
                      ...++||+=+|+|.++.+.+.+.- -+++.+|.. .++...+++       ++++.+.+|.+..+      ... |+|++
T Consensus        42 ~g~~vLDLFaGSGalGlEALSRGA-~~v~fVE~~~~a~~~i~~N~~~l~~~~~~~v~~~d~~~~l~~~~~~~~~fDiIfl  120 (183)
T PF03602_consen   42 EGARVLDLFAGSGALGLEALSRGA-KSVVFVEKNRKAIKIIKKNLEKLGLEDKIRVIKGDAFKFLLKLAKKGEKFDIIFL  120 (183)
T ss_dssp             TT-EEEETT-TTSHHHHHHHHTT--SEEEEEES-HHHHHHHHHHHHHHT-GGGEEEEESSHHHHHHHHHHCTS-EEEEEE
T ss_pred             CCCeEEEcCCccCccHHHHHhcCC-CeEEEEECCHHHHHHHHHHHHHhCCCcceeeeccCHHHHHHhhcccCCCceEEEE
Confidence            347899999999999999998853 368888874 466655543       57899999987522      233 98886

They methylate the guanosine in position 966 of 16S rRNA in the assembled 30S particle [].; GO: 0008168 methyltransferase activity, 0031167 rRNA methylation; PDB: 3P9N_A 2ESR_B 2IFT_A 1WS6_A 2FPO_B 2FHP_A.

>PRK10411 DNA-binding transcriptional activator FucR; Provisional

Probab=88.97  E-value=0.87  Score=37.67  Aligned_cols=47  Identities=13%  Similarity=0.205  Sum_probs=41.8

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      .+..|.+.|.+.   +..+..|||+.+++    +++-++|-|..|...|.+.+.
T Consensus         5 R~~~Il~~l~~~---~~~~~~eLa~~l~V----S~~TiRRdL~~L~~~~~l~r~   51 (240)
T PRK10411          5 RQQAIVDLLLNH---TSLTTEALAEQLNV----SKETIRRDLNELQTQGKILRN   51 (240)
T ss_pred             HHHHHHHHHHHc---CCCcHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEe
Confidence            345688888886   59999999999999    999999999999999999876

>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=88.92  E-value=0.54  Score=33.28  Aligned_cols=51  Identities=18%  Similarity=0.195  Sum_probs=40.2

Q ss_pred             HHhhChhHHHHhc-CCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           16 ASELGVFEIIAKA-GPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        16 a~~lglfd~L~~~-~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      .++-.|++.|... ..+.++++.+|++++++    ++..++..|+.|+..|++=.+
T Consensus        47 ~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~----~~~~v~~al~~L~~eG~IYsT   98 (102)
T PF08784_consen   47 PLQDKVLNFIKQQPNSEEGVHVDEIAQQLGM----SENEVRKALDFLSNEGHIYST   98 (102)
T ss_dssp             HHHHHHHHHHHC----TTTEEHHHHHHHSTS-----HHHHHHHHHHHHHTTSEEES
T ss_pred             HHHHHHHHHHHhcCCCCCcccHHHHHHHhCc----CHHHHHHHHHHHHhCCeEecc
Confidence            3456788888872 22358999999999999    999999999999999988654

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.

>TIGR02147 Fsuc_second hypothetical protein, TIGR02147

Probab=88.78  E-value=0.87  Score=38.40  Aligned_cols=46  Identities=17%  Similarity=0.150  Sum_probs=40.0

Q ss_pred             CCCCHHHHHHhCC--CCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhh
Q 039903           32 AKISAVEIAAQMP--SSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVA   85 (233)
Q Consensus        32 ~~~t~~elA~~~~--~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s   85 (233)
                      +..+..+||+.++  +    +..-++.-|+.|..+|+++++    ++|.|..|..+
T Consensus       136 ~~~~~~~ia~~l~p~i----s~~ev~~sL~~L~~~glikk~----~~g~y~~t~~~  183 (271)
T TIGR02147       136 FADDPEELAKRCFPKI----SAEQVKESLDLLERLGLIKKN----EDGFYKQTDKA  183 (271)
T ss_pred             CCCCHHHHHHHhCCCC----CHHHHHHHHHHHHHCCCeeEC----CCCcEEeecce
Confidence            3447889999998  6    899999999999999999997    67889988764

This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.

>PF09243 Rsm22: Mitochondrial small ribosomal subunit Rsm22; InterPro: IPR015324 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=88.69  E-value=0.91  Score=38.31  Aligned_cols=49  Identities=16%  Similarity=0.243  Sum_probs=35.0

Q ss_pred             HHHhcccccCcceEEEecCCccHHHHHHHHHcCCCc-EEEeech-HHHhhcc
Q 039903          159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIK-GVNFDLS-HVIQDSS  208 (233)
Q Consensus       159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~-~~v~Dlp-~v~~~a~  208 (233)
                      +....++| .+.+|||+|+|.|.-+-+..+.+|+++ .+.+|.. ..++.++
T Consensus        25 l~~r~p~f-~P~~vLD~GsGpGta~wAa~~~~~~~~~~~~vd~s~~~~~l~~   75 (274)
T PF09243_consen   25 LRKRLPDF-RPRSVLDFGSGPGTALWAAREVWPSLKEYTCVDRSPEMLELAK   75 (274)
T ss_pred             HHHhCcCC-CCceEEEecCChHHHHHHHHHHhcCceeeeeecCCHHHHHHHH
Confidence            33333433 347999999999999999999999654 6788975 3555443

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

>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=88.42  E-value=1.5  Score=27.70  Aligned_cols=55  Identities=16%  Similarity=0.176  Sum_probs=43.6

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhc---CCceeeeccCCCCCceeccHhhh
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVT---HRVLRCTSAGDDQRLYGLAHVAK   86 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~---~gll~~~~~~~~~~~y~lt~~s~   86 (233)
                      ++.+|..+.+.     .+...-|+.+++    ++..+.+-++.|..   .-+|++.     ++.+.+|+.|+
T Consensus         3 ~l~~f~~v~~~-----gs~~~AA~~l~i----s~~~vs~~i~~LE~~lg~~Lf~r~-----~~~~~lT~~G~   60 (60)
T PF00126_consen    3 QLRYFLAVAET-----GSISAAAEELGI----SQSAVSRQIKQLEEELGVPLFERS-----GRGLRLTEAGE   60 (60)
T ss_dssp             HHHHHHHHHHH-----SSHHHHHHHCTS----SHHHHHHHHHHHHHHHTS-SEEEC-----SSSEEE-HHHH
T ss_pred             HHHHHHHHHHh-----CCHHHHHHHhhc----cchHHHHHHHHHHHHhCCeEEEEC-----CCCeeEChhhC
Confidence            46678888884     499999999999    99999999888766   6788884     56799998774

These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....

>PF03291 Pox_MCEL: mRNA capping enzyme; InterPro: IPR004971 This is a family of viral mRNA capping enzymes

Probab=88.33  E-value=1.1  Score=38.89  Aligned_cols=78  Identities=14%  Similarity=0.084  Sum_probs=45.9

Q ss_pred             HHHHHHHHHhcchhcHHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC---------
Q 039903          141 NGVFNKAMLNHTSIVTNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY---------  210 (233)
Q Consensus       141 ~~~f~~am~~~~~~~~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~---------  210 (233)
                      .+.|+.++...-   +...+.....-.+..+|||+|||.|.-+....++.+ -+.+.+|+. +.|+.|++.         
T Consensus        38 lR~fNNwvKs~L---I~~~~~~~~~~~~~~~VLDl~CGkGGDL~Kw~~~~i-~~~vg~Dis~~si~ea~~Ry~~~~~~~~  113 (331)
T PF03291_consen   38 LRNFNNWVKSVL---IQKYAKKVKQNRPGLTVLDLCCGKGGDLQKWQKAKI-KHYVGIDISEESIEEARERYKQLKKRNN  113 (331)
T ss_dssp             HHHHHHHHHHHH---HHHHCHCCCCTTTT-EEEEET-TTTTTHHHHHHTT--SEEEEEES-HHHHHHHHHHHHHHHTSTT
T ss_pred             HHHHhHHHHHHH---HHHHHHhhhccCCCCeEEEecCCCchhHHHHHhcCC-CEEEEEeCCHHHHHHHHHHHHHhccccc
Confidence            456777666422   222222211011568999999999999888887632 246889986 467766541         


Q ss_pred             ---C----CceEEecCcCC
Q 039903          211 ---S----GVKHIGGIMLE  222 (233)
Q Consensus       211 ---~----ri~~~~gD~f~  222 (233)
                         .    ...|+.+|-|.
T Consensus       114 ~~~~~~~f~a~f~~~D~f~  132 (331)
T PF03291_consen  114 SKQYRFDFIAEFIAADCFS  132 (331)
T ss_dssp             -HTSEECCEEEEEESTTCC
T ss_pred             cccccccchhheecccccc
Confidence               1    35678888885

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.

>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2

Probab=88.32  E-value=0.67  Score=29.79  Aligned_cols=44  Identities=16%  Similarity=0.274  Sum_probs=36.6

Q ss_pred             ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      .|++.|-..   |+.|+.+|++.+++    +.+.++.-|-.|...|++...
T Consensus        17 ~V~~~Ll~~---G~ltl~~i~~~t~l----~~~~Vk~~L~~LiQh~~v~y~   60 (62)
T PF08221_consen   17 KVGEVLLSR---GRLTLREIVRRTGL----SPKQVKKALVVLIQHNLVQYF   60 (62)
T ss_dssp             HHHHHHHHC----SEEHHHHHHHHT------HHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHc---CCcCHHHHHHHhCC----CHHHHHHHHHHHHHcCCeeee
Confidence            467777776   69999999999999    999999999999999999864

7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.

>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]

Probab=88.08  E-value=0.89  Score=36.77  Aligned_cols=44  Identities=25%  Similarity=0.363  Sum_probs=37.2

Q ss_pred             hhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           21 VFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        21 lfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      |.+.|...  +.+.|++|+|+++|+    +.--.+|-|.+|++.|+++..
T Consensus       163 i~~~~~~~--~~~~Taeela~~~gi----SRvTaRRYLeyl~~~~~l~a~  206 (224)
T COG4565         163 VREALKEP--DQELTAEELAQALGI----SRVTARRYLEYLVSNGILEAE  206 (224)
T ss_pred             HHHHHhCc--CCccCHHHHHHHhCc----cHHHHHHHHHHHHhcCeeeEE
Confidence            45566632  259999999999999    999999999999999999864

>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional

Probab=88.06  E-value=0.87  Score=37.95  Aligned_cols=47  Identities=13%  Similarity=0.195  Sum_probs=42.5

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      .+..|.+.|.+.   +.+++.|||+.+++    ++.-++|-|+.|...|++.+.
T Consensus         6 R~~~Il~~l~~~---~~~~~~ela~~l~v----S~~TiRRdL~~Le~~g~l~r~   52 (252)
T PRK10906          6 RHDAIIELVKQQ---GYVSTEELVEHFSV----SPQTIRRDLNDLAEQNKILRH   52 (252)
T ss_pred             HHHHHHHHHHHc---CCEeHHHHHHHhCC----CHHHHHHHHHHHHHCCCEEEe
Confidence            455688889886   58999999999999    999999999999999999987

>PF03141 Methyltransf_29: Putative S-adenosyl-L-methionine-dependent methyltransferase; InterPro: IPR004159 Members of this family of hypothetical plant proteins are putative methyltransferases

Probab=88.02  E-value=0.43  Score=43.34  Aligned_cols=24  Identities=21%  Similarity=0.327  Sum_probs=21.7

Q ss_pred             cCcceEEEecCCccHHHHHHHHHc
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNY  190 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~  190 (233)
                      ..+++++|||||.|.|+..|++++
T Consensus       116 g~iR~~LDvGcG~aSF~a~l~~r~  139 (506)
T PF03141_consen  116 GGIRTALDVGCGVASFGAYLLERN  139 (506)
T ss_pred             CceEEEEeccceeehhHHHHhhCC
Confidence            457999999999999999999984

; GO: 0008168 methyltransferase activity

>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=87.77  E-value=0.8  Score=29.36  Aligned_cols=35  Identities=17%  Similarity=0.241  Sum_probs=30.8

Q ss_pred             CCC-CHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           32 AKI-SAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        32 ~~~-t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      ..+ |..+||+.+++    +..-+++-|+.|...|+++..
T Consensus        22 ~~lps~~~la~~~~v----sr~tvr~al~~L~~~g~i~~~   57 (64)
T PF00392_consen   22 DRLPSERELAERYGV----SRTTVREALRRLEAEGLIERR   57 (64)
T ss_dssp             SBE--HHHHHHHHTS-----HHHHHHHHHHHHHTTSEEEE
T ss_pred             CEeCCHHHHHHHhcc----CCcHHHHHHHHHHHCCcEEEE
Confidence            467 89999999999    999999999999999999986

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 ....

>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional

Probab=87.71  E-value=0.96  Score=38.08  Aligned_cols=48  Identities=8%  Similarity=0.136  Sum_probs=43.5

Q ss_pred             HHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           16 ASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        16 a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      -....|.+.|...   +..++.|||+.+++    +++-++|=|..|...|++.+.
T Consensus        17 eR~~~Il~~L~~~---~~vtv~eLa~~l~V----S~~TIRRDL~~Le~~G~l~r~   64 (269)
T PRK09802         17 ERREQIIQRLRQQ---GSVQVNDLSALYGV----STVTIRNDLAFLEKQGIAVRA   64 (269)
T ss_pred             HHHHHHHHHHHHc---CCEeHHHHHHHHCC----CHHHHHHHHHHHHhCCCeEEE
Confidence            3556789999987   58999999999999    999999999999999999997

>COG5631 Predicted transcription regulator, contains HTH domain (MarR family) [Transcription]

Probab=87.51  E-value=1.3  Score=34.07  Aligned_cols=78  Identities=19%  Similarity=0.238  Sum_probs=56.8

Q ss_pred             cccchHHHHHHHHHhhCh-------hHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCC
Q 039903            4 AMSIVLPAAMQAASELGV-------FEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQ   76 (233)
Q Consensus         4 ~~~~~~s~~L~~a~~lgl-------fd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~   76 (233)
                      +++.|.-.|+.+|.+.++       .-++...+  .|+++.||+..++.+   +...+.--||-|...|+++....+ .+
T Consensus        64 Af~rW~vrCmAaag~~~ls~~e~l~lH~irhrd--R~K~laDic~~ln~e---Dth~itYslrKL~k~gLit~t~~g-ke  137 (199)
T COG5631          64 AFGRWQVRCMAAAGEFSLSGPENLLLHIIRHRD--RPKSLADICQMLNRE---DTHNITYSLRKLLKGGLITRTGSG-KE  137 (199)
T ss_pred             HHHHHHHHHHHHhcCCCCcchHHHHHHHHhhcC--chhhHHHHHHHhccc---cchhHHHHHHHHHhccceecCCCC-ce
Confidence            356677777777766542       23333333  599999999999994   566778889999999999987443 34


Q ss_pred             CceeccHhhhH
Q 039903           77 RLYGLAHVAKY   87 (233)
Q Consensus        77 ~~y~lt~~s~~   87 (233)
                      -+|..|+.+..
T Consensus       138 vTy~vTa~G~~  148 (199)
T COG5631         138 VTYEVTALGHR  148 (199)
T ss_pred             EEEEEecchHH
Confidence            68999988754

>PF09821 AAA_assoc_C: C-terminal AAA-associated domain; InterPro: IPR018632 Members of this family are found in various prokaryotic ABC transporters, predominantly involved in nitrate, sulphonate and bicarbonate translocation

Probab=87.49  E-value=0.95  Score=33.28  Aligned_cols=46  Identities=11%  Similarity=0.021  Sum_probs=41.9

Q ss_pred             HHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhcCC
Q 039903           38 EIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLNR   92 (233)
Q Consensus        38 elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~~~   92 (233)
                      +||+.+++    +-+-|--+++++..+|+++..     +|-..+|+.|+.++...
T Consensus         2 ~La~~l~~----eiDdL~p~~eAaelLgf~~~~-----~Gdi~LT~~G~~f~~a~   47 (120)
T PF09821_consen    2 QLADELHL----EIDDLLPIVEAAELLGFAEVE-----EGDIRLTPLGRRFAEAD   47 (120)
T ss_pred             chHHHhCC----cHHHHHHHHHHHHHcCCeeec-----CCcEEeccchHHHHHCC
Confidence            58999999    999999999999999999994     78899999999998664

>PF13730 HTH_36: Helix-turn-helix domain

Probab=87.32  E-value=0.75  Score=28.38  Aligned_cols=29  Identities=14%  Similarity=0.224  Sum_probs=27.5

Q ss_pred             CHHHHHHhCCCCCCCChhhHHHHHHHHhcCCce
Q 039903           35 SAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVL   67 (233)
Q Consensus        35 t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll   67 (233)
                      |.+.||+.+|+    +.+.+.+.++.|...|++
T Consensus        27 S~~~la~~~g~----s~~Tv~~~i~~L~~~G~I   55 (55)
T PF13730_consen   27 SQETLAKDLGV----SRRTVQRAIKELEEKGLI   55 (55)
T ss_pred             CHHHHHHHHCc----CHHHHHHHHHHHHHCcCC
Confidence            88999999999    999999999999999975

>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=87.21  E-value=0.99  Score=26.56  Aligned_cols=37  Identities=14%  Similarity=0.256  Sum_probs=26.8

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHH
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRL   60 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~   60 (233)
                      ++..|.+.|...   +..|..+||+.+|+    ++..+.+=++.
T Consensus         4 ~D~~Il~~Lq~d---~r~s~~~la~~lgl----S~~~v~~Ri~r   40 (42)
T PF13404_consen    4 LDRKILRLLQED---GRRSYAELAEELGL----SESTVRRRIRR   40 (42)
T ss_dssp             HHHHHHHHHHH----TTS-HHHHHHHHTS-----HHHHHHHHHH
T ss_pred             HHHHHHHHHHHc---CCccHHHHHHHHCc----CHHHHHHHHHH
Confidence            456788889887   58999999999999    88776554443

...

>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms

Probab=87.17  E-value=0.75  Score=27.40  Aligned_cols=23  Identities=30%  Similarity=0.297  Sum_probs=17.9

Q ss_pred             CCCHHHHHHhCCCCCCCChhhHHHHHH
Q 039903           33 KISAVEIAAQMPSSNPNAAVMLDRILR   59 (233)
Q Consensus        33 ~~t~~elA~~~~~~~~~~~~~l~rlL~   59 (233)
                      +.|..+||+.+|+    +..-++|+|+
T Consensus        21 G~si~~IA~~~gv----sr~TvyR~l~   43 (45)
T PF02796_consen   21 GMSIAEIAKQFGV----SRSTVYRYLN   43 (45)
T ss_dssp             T--HHHHHHHTTS-----HHHHHHHHC
T ss_pred             CCCHHHHHHHHCc----CHHHHHHHHh
Confidence            4999999999999    9999998874

Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....

>PF02384 N6_Mtase: N-6 DNA Methylase; InterPro: IPR003356 This domain is fpound in N-6 adenine-specific DNA methylase (2

Probab=87.05  E-value=1.4  Score=37.54  Aligned_cols=67  Identities=16%  Similarity=0.110  Sum_probs=44.3

Q ss_pred             ccCcceEEEecCCccHHHHHHHHH-------cCCCcEEEeechH-HHhhccCC--------CCceEEecCcCC-C-CC--
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISN-------YLHIKGVNFDLSH-VIQDSSSY--------SGVKHIGGIMLE-R-IP--  225 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~-------~P~l~~~v~Dlp~-v~~~a~~~--------~ri~~~~gD~f~-~-~P--  225 (233)
                      -....+|+|-.||+|.++.++.+.       .+..+..++|..+ ++..+..+        .......+|.|. + ..  
T Consensus        44 ~~~~~~VlDPacGsG~fL~~~~~~i~~~~~~~~~~~i~G~ei~~~~~~la~~nl~l~~~~~~~~~i~~~d~l~~~~~~~~  123 (311)
T PF02384_consen   44 PKKGDSVLDPACGSGGFLVAAMEYIKEKRNKIKEINIYGIEIDPEAVALAKLNLLLHGIDNSNINIIQGDSLENDKFIKN  123 (311)
T ss_dssp             T-TTEEEEETT-TTSHHHHHHHHHHHTCHHHHCCEEEEEEES-HHHHHHHHHHHHHTTHHCBGCEEEES-TTTSHSCTST
T ss_pred             ccccceeechhhhHHHHHHHHHHhhcccccccccceeEeecCcHHHHHHHHhhhhhhccccccccccccccccccccccc
Confidence            345578999999999999998874       5888899999854 55544321        334678899987 2 32  


Q ss_pred             C-CCEEEe
Q 039903          226 K-GDAILI  232 (233)
Q Consensus       226 ~-~D~~~l  232 (233)
                      . .|+++.
T Consensus       124 ~~~D~ii~  131 (311)
T PF02384_consen  124 QKFDVIIG  131 (311)
T ss_dssp             --EEEEEE
T ss_pred             cccccccC
Confidence            2 287764

1.1.72 from EC) from Type I and Type IC restriction systems. These enzymes are responsible for the methylation of specific DNA sequences in order to prevent the host from digesting its own genome via its restriction enzymes. These methylases have the same sequence specificity as their corresponding restriction enzymes. The type I restriction and modification system is composed of three polypeptides R, M and S. The M and S subunits together form a methyltransferase that methylates two adenine residues in complementary strands of a bipartite DNA recognition sequence. In the presence of the R subunit, the complex can also act as an endonuclease, binding to the same target sequence but cutting the DNA some distance from this site. Whether the DNA is cut or modified depends on the methylation state of the target sequence. When the target site is unmodified, the DNA is cut. When the target site is hemimethylated, the complex acts as a maintenance methyltransferase, modifying the DNA so that both strands become methylated.; GO: 0003677 DNA binding, 0008170 N-methyltransferase activity, 0006306 DNA methylation; PDB: 2F8L_A 2Y7C_C 2Y7H_C 2AR0_B 3KHK_A 3LKD_A 2OKC_B.

>TIGR00308 TRM1 tRNA(guanine-26,N2-N2) methyltransferase

Probab=86.90  E-value=0.95  Score=40.02  Aligned_cols=63  Identities=8%  Similarity=0.036  Sum_probs=46.8

Q ss_pred             ceEEEecCCccHHHHHHHHHcCCC-cEEEeec-hHHHhhccCC------CCceEEecCcCCCCC---C-CCEEEe
Q 039903          170 KQLVDVGGGLGVNVNIIISNYLHI-KGVNFDL-SHVIQDSSSY------SGVKHIGGIMLERIP---K-GDAILI  232 (233)
Q Consensus       170 ~~vvDvGGG~G~~~~~l~~~~P~l-~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~~P---~-~D~~~l  232 (233)
                      -+++|.-+|+|..+++.+++-++. +++..|+ |++++.++++      ..++++.+|.+.-+.   . .|+|.+
T Consensus        46 ~~vLD~faGsG~rgir~a~e~~ga~~Vv~nD~n~~Av~~i~~N~~~N~~~~~~v~~~Da~~~l~~~~~~fDvIdl  120 (374)
T TIGR00308        46 INIADALSASGIRAIRYAHEIEGVREVFANDINPKAVESIKNNVEYNSVENIEVPNEDAANVLRYRNRKFHVIDI  120 (374)
T ss_pred             CEEEECCCchhHHHHHHHhhCCCCCEEEEEeCCHHHHHHHHHHHHHhCCCcEEEEchhHHHHHHHhCCCCCEEEe
Confidence            479999999999999999987654 5788898 5677766553      357788888886222   2 387765

This enzyme is responsible for two methylations of a characteristic guanine of most tRNA molecules. The activity has been demonstrated for eukaryotic and archaeal proteins, which are active when expressed in E. coli, a species that lacks this enzyme. At least one Eubacterium, Aquifex aeolicus, has an ortholog, as do all completed archaeal genomes.

>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=86.81  E-value=0.2  Score=33.24  Aligned_cols=37  Identities=22%  Similarity=0.198  Sum_probs=31.9

Q ss_pred             CCCCHHHHHHhC---CCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           32 AKISAVEIAAQM---PSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        32 ~~~t~~elA~~~---~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      +.+++.++|+.+   +.  ....++++-++.+|.++|++++.
T Consensus        23 ~~i~l~~ia~~l~~~~~--k~~~RRlYDI~NVLealgli~K~   62 (71)
T PF02319_consen   23 KSISLNEIADKLISENV--KTQRRRLYDIINVLEALGLIEKQ   62 (71)
T ss_dssp             TEEEHHHHHHHCHHHCC--HHHCHHHHHHHHHHHHCTSEEEE
T ss_pred             CcccHHHHHHHHccccc--ccccchhhHHHHHHHHhCceeec
Confidence            689999999999   64  11578999999999999999996

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.

>PF14338 Mrr_N: Mrr N-terminal domain

Probab=86.78  E-value=4.6  Score=27.92  Aligned_cols=32  Identities=3%  Similarity=0.108  Sum_probs=27.4

Q ss_pred             HHHHHhcCCceeeeccCCCCCceeccHhhhHhhcCC
Q 039903           57 ILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLNR   92 (233)
Q Consensus        57 lL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~~~   92 (233)
                      -+..|...|+++++    ..|.|++|+.|+.++..+
T Consensus        60 a~~~L~~aGli~~~----~rG~~~iT~~G~~~l~~~   91 (92)
T PF14338_consen   60 ARSYLKKAGLIERP----KRGIWRITEKGRKALAEH   91 (92)
T ss_pred             HHHHHHHCCCccCC----CCCceEECHhHHHHHhhC
Confidence            36889999999997    689999999999877654

>PRK09462 fur ferric uptake regulator; Provisional

Probab=86.69  E-value=1.8  Score=32.84  Aligned_cols=66  Identities=11%  Similarity=0.222  Sum_probs=46.7

Q ss_pred             HHhhChhHHHHhcCCCCCCCHHHHHHhCCCC-CCCChhhHHHHHHHHhcCCceeeeccCCCCCceecc
Q 039903           16 ASELGVFEIIAKAGPTAKISAVEIAAQMPSS-NPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLA   82 (233)
Q Consensus        16 a~~lglfd~L~~~~~~~~~t~~elA~~~~~~-~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt   82 (233)
                      .-+.-|++.|.... .++.|+.||-+.+.-. ++.+..-++|.|+.|+..|++.+...+++..+|.++
T Consensus        17 ~qR~~Il~~l~~~~-~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~~~~~~~~~~~y~~~   83 (148)
T PRK09462         17 LPRLKILEVLQEPD-NHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHNFEGGKSVFELT   83 (148)
T ss_pred             HHHHHHHHHHHhCC-CCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEEEEEcCCCcEEEEeC
Confidence            34566899998631 1589999999888531 233788899999999999999986432123456543

>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]

Probab=86.66  E-value=1.3  Score=33.58  Aligned_cols=65  Identities=20%  Similarity=0.262  Sum_probs=49.0

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCC-CCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHh
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPS-SNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHV   84 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~-~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~   84 (233)
                      |+.|+++|.+++  ++.|+++|=.++.- .++++..-++|-|+.|...|++++...+++..+|.++..
T Consensus        23 R~~vl~~L~~~~--~~~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~~~~~~~~~y~~~~~   88 (145)
T COG0735          23 RLAVLELLLEAD--GHLSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRLEFEGGKTRYELNSE   88 (145)
T ss_pred             HHHHHHHHHhcC--CCCCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEEEeCCCEEEEecCCC
Confidence            567999999875  67999999888774 245588899999999999999998754322234655443

>TIGR02987 met_A_Alw26 type II restriction m6 adenine DNA methyltransferase, Alw26I/Eco31I/Esp3I family

Probab=86.48  E-value=0.69  Score=42.72  Aligned_cols=55  Identities=11%  Similarity=0.141  Sum_probs=39.3

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCC--------CcEEEeechH-HHhhccCC----C--CceEEecCcCC
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLH--------IKGVNFDLSH-VIQDSSSY----S--GVKHIGGIMLE  222 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~--------l~~~v~Dlp~-v~~~a~~~----~--ri~~~~gD~f~  222 (233)
                      ...+|+|.|||+|.++.+++++.+.        +....+|+.+ ++..++.+    .  .++...+|++.
T Consensus        31 ~~~~ilDP~cGsG~fl~~~~~~~~~~~~~~~~~~~i~g~DId~~a~~~a~~~l~~~~~~~~~i~~~d~l~  100 (524)
T TIGR02987        31 TKTKIIDPCCGDGRLIAALLKKNEEINYFKEVELNIYFADIDKTLLKRAKKLLGEFALLEINVINFNSLS  100 (524)
T ss_pred             cceEEEeCCCCccHHHHHHHHHHHhcCCcccceeeeeeechhHHHHHHHHHHHhhcCCCCceeeeccccc
Confidence            4568999999999999999988763        4568888854 55555432    2  45666666664

Members of this family are the m6-adenine DNA methyltransferase protein, or domain of a fusion protein that also carries m5 cytosine methyltransferase activity, of type II restriction systems of the Alw26I/Eco31I/Esp3I family. A methyltransferase of this family is alway accompanied by a type II restriction endonuclease from the Alw26I/Eco31I/Esp3I family (TIGR02986) and by an adenine-specific modification methyltransferase. Members of this family are unusual in that regions of similarity to homologs outside this family are circularly permuted.

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

Probab=86.43  E-value=0.65  Score=40.67  Aligned_cols=47  Identities=15%  Similarity=0.260  Sum_probs=35.0

Q ss_pred             eEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecC
Q 039903          171 QLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGI  219 (233)
Q Consensus       171 ~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD  219 (233)
                      .++|+=||.|.++..+++..-+  ++.+|. ++.++.|+.+      ++++|+.++
T Consensus       199 ~vlDlycG~G~fsl~la~~~~~--V~gvE~~~~av~~A~~Na~~N~i~n~~f~~~~  252 (352)
T PF05958_consen  199 DVLDLYCGVGTFSLPLAKKAKK--VIGVEIVEEAVEDARENAKLNGIDNVEFIRGD  252 (352)
T ss_dssp             EEEEES-TTTCCHHHHHCCSSE--EEEEES-HHHHHHHHHHHHHTT--SEEEEE--
T ss_pred             cEEEEeecCCHHHHHHHhhCCe--EEEeeCCHHHHHHHHHHHHHcCCCcceEEEee
Confidence            7999999999999999998754  777776 5677777653      688988654

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

>COG3413 Predicted DNA binding protein [General function prediction only]

Probab=86.19  E-value=0.68  Score=37.54  Aligned_cols=43  Identities=19%  Similarity=0.274  Sum_probs=34.2

Q ss_pred             hHHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHH
Q 039903            8 VLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRL   60 (233)
Q Consensus         8 ~~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~   60 (233)
                      ..-.+|+.|.++|-||.=.      ..++.|||+.+|+    ++..+...||-
T Consensus       159 rQ~~vL~~A~~~GYFd~PR------~~~l~dLA~~lGI----Skst~~ehLRr  201 (215)
T COG3413         159 RQLEVLRLAYKMGYFDYPR------RVSLKDLAKELGI----SKSTLSEHLRR  201 (215)
T ss_pred             HHHHHHHHHHHcCCCCCCc------cCCHHHHHHHhCC----CHHHHHHHHHH
Confidence            3557999999999999764      5899999999999    66655555543

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

Probab=86.19  E-value=0.74  Score=41.94  Aligned_cols=55  Identities=18%  Similarity=0.250  Sum_probs=42.7

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEec---CcCC
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGG---IMLE  222 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~g---D~f~  222 (233)
                      .+..+.++||-||+|.++.++++..-  +++.+++ |+.++.|+.+      .+.+|+.|   |.|.
T Consensus       381 l~~~k~llDv~CGTG~iglala~~~~--~ViGvEi~~~aV~dA~~nA~~NgisNa~Fi~gqaE~~~~  445 (534)
T KOG2187|consen  381 LPADKTLLDVCCGTGTIGLALARGVK--RVIGVEISPDAVEDAEKNAQINGISNATFIVGQAEDLFP  445 (534)
T ss_pred             CCCCcEEEEEeecCCceehhhhcccc--ceeeeecChhhcchhhhcchhcCccceeeeecchhhccc
Confidence            45558999999999999999998644  4666654 7888888764      67899988   5554

>PF09929 DUF2161: Uncharacterized conserved protein (DUF2161); InterPro: IPR018679 This family of various hypothetical prokaryotic proteins has no known function

Probab=85.92  E-value=1.8  Score=31.50  Aligned_cols=59  Identities=14%  Similarity=0.155  Sum_probs=43.0

Q ss_pred             HHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhH
Q 039903            9 LPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKY   87 (233)
Q Consensus         9 ~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~   87 (233)
                      .-+||++|      ..|.+.   ||.+..+|++.+++    +  ...+||+. --.|+|++.    +-|.|.||+.++.
T Consensus        58 RQ~Al~~A------~~L~~~---Gp~~~~~l~~~~~~----~--~A~~IL~~-N~YGWFeRv----~rGvY~LT~~G~~  116 (118)
T PF09929_consen   58 RQDALRCA------AALAEH---GPSRPADLRKATGV----P--KATSILRD-NHYGWFERV----ERGVYALTPAGRA  116 (118)
T ss_pred             HHHHHHHH------HHHHHc---CCCCHHHHHHhcCC----C--hHHHHHHh-Ccccceeee----ccceEecCcchhh
Confidence            34566655      467766   69999999999998    3  33344432 347999998    7999999998763

>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus

Probab=85.83  E-value=2.2  Score=28.32  Aligned_cols=44  Identities=14%  Similarity=0.104  Sum_probs=38.7

Q ss_pred             hChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           19 LGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        19 lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      ..|...++.    ++.|++||-+.+|+    +...+-..|.-|...|++.+.
T Consensus         8 ~~IL~~ls~----~c~TLeeL~ekTgi----~k~~LlV~LsrL~k~GiI~Rk   51 (72)
T PF05584_consen    8 QKILIILSK----RCCTLEELEEKTGI----SKNTLLVYLSRLAKRGIIERK   51 (72)
T ss_pred             HHHHHHHHh----ccCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCeeee
Confidence            345666776    59999999999999    999999999999999999984

>PRK11639 zinc uptake transcriptional repressor; Provisional

Probab=85.56  E-value=1.8  Score=33.73  Aligned_cols=53  Identities=15%  Similarity=0.227  Sum_probs=42.6

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCC-CCCChhhHHHHHHHHhcCCceeeec
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSS-NPNAAVMLDRILRLLVTHRVLRCTS   71 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~-~~~~~~~l~rlL~~L~~~gll~~~~   71 (233)
                      -++-|++.|...+  ++.|++||.+.+.-. ++.+..-++|.|+.|+..|++.+..
T Consensus        27 qR~~IL~~l~~~~--~hlSa~eI~~~L~~~~~~is~aTVYRtL~~L~e~Glv~~~~   80 (169)
T PRK11639         27 QRLEVLRLMSLQP--GAISAYDLLDLLREAEPQAKPPTVYRALDFLLEQGFVHKVE   80 (169)
T ss_pred             HHHHHHHHHHhcC--CCCCHHHHHHHHHhhCCCCCcchHHHHHHHHHHCCCEEEEe
Confidence            3556889988764  699999999998642 2337778999999999999999973

>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]

Probab=85.45  E-value=1.4  Score=36.83  Aligned_cols=53  Identities=17%  Similarity=0.164  Sum_probs=46.1

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceec
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGL   81 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~l   81 (233)
                      +..|.++|.+.   |.++++|||+.+++    ++.-++|=|+.|...|++.+.    -+|....
T Consensus         7 ~~~Il~~l~~~---g~v~v~eLa~~~~V----S~~TIRRDL~~Le~~g~l~R~----hGGa~~~   59 (253)
T COG1349           7 HQKILELLKEK---GKVSVEELAELFGV----SEMTIRRDLNELEEQGLLLRV----HGGAVLP   59 (253)
T ss_pred             HHHHHHHHHHc---CcEEHHHHHHHhCC----CHHHHHHhHHHHHHCCcEEEE----eCCEecC
Confidence            45688999997   59999999999999    999999999999999999997    4555543

>PRK10742 putative methyltransferase; Provisional

Probab=85.26  E-value=2.4  Score=35.21  Aligned_cols=73  Identities=14%  Similarity=0.180  Sum_probs=52.1

Q ss_pred             HHHHHhcccccCcc--eEEEecCCccHHHHHHHHHcCCCcEEEeechHHHh--------hcc------C--CCCceEEec
Q 039903          157 NRIIDSSKGFEQIK--QLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQ--------DSS------S--YSGVKHIGG  218 (233)
Q Consensus       157 ~~~~~~~~~~~~~~--~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~--------~a~------~--~~ri~~~~g  218 (233)
                      +.+++... .++..  +|+|+=+|.|..+..++.+  ..+++.+|...++.        .+.      .  ..||+.+.+
T Consensus        76 ~~l~kAvg-lk~g~~p~VLD~TAGlG~Da~~las~--G~~V~~vEr~p~vaalL~dgL~ra~~~~~~~~~~~~ri~l~~~  152 (250)
T PRK10742         76 EAVAKAVG-IKGDYLPDVVDATAGLGRDAFVLASV--GCRVRMLERNPVVAALLDDGLARGYADAEIGGWLQERLQLIHA  152 (250)
T ss_pred             cHHHHHhC-CCCCCCCEEEECCCCccHHHHHHHHc--CCEEEEEECCHHHHHHHHHHHHHhhhccccchhhhceEEEEeC
Confidence            45666665 55544  9999999999999999998  66699999864432        221      0  047999999


Q ss_pred             CcCC---CCCCC-CEEEe
Q 039903          219 IMLE---RIPKG-DAILI  232 (233)
Q Consensus       219 D~f~---~~P~~-D~~~l  232 (233)
                      |..+   ..+.. |+|+|
T Consensus       153 da~~~L~~~~~~fDVVYl  170 (250)
T PRK10742        153 SSLTALTDITPRPQVVYL  170 (250)
T ss_pred             cHHHHHhhCCCCCcEEEE
Confidence            9887   23443 99886

>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional

Probab=85.15  E-value=1.4  Score=36.79  Aligned_cols=47  Identities=19%  Similarity=0.240  Sum_probs=42.9

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      .+..|.+.|.+.   +.+++.|||+.+++    ++.-++|=|+.|...|++.+.
T Consensus         6 R~~~Il~~L~~~---~~v~v~eLa~~l~V----S~~TIRRDL~~Le~~g~l~r~   52 (256)
T PRK10434          6 RQAAILEYLQKQ---GKTSVEELAQYFDT----TGTTIRKDLVILEHAGTVIRT   52 (256)
T ss_pred             HHHHHHHHHHHc---CCEEHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEE
Confidence            455688999987   58999999999999    999999999999999999987

>PF01861 DUF43: Protein of unknown function DUF43; InterPro: IPR002723 This family of prokaryotic proteins have not been characterised

Probab=85.00  E-value=1.6  Score=35.98  Aligned_cols=70  Identities=11%  Similarity=0.181  Sum_probs=37.2

Q ss_pred             HHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccC----C-CCceEEecCcCCCCCC---C--
Q 039903          159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSS----Y-SGVKHIGGIMLERIPK---G--  227 (233)
Q Consensus       159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~----~-~ri~~~~gD~f~~~P~---~--  227 (233)
                      +.+..+ +.+ ++|+=|| -+=..|++++-.++..+++|+|+.+ .++..++    . -.|+.+.+|+.+++|.   +  
T Consensus        37 ~~~~gd-L~g-k~il~lG-DDDLtSlA~al~~~~~~I~VvDiDeRll~fI~~~a~~~gl~i~~~~~DlR~~LP~~~~~~f  113 (243)
T PF01861_consen   37 MAERGD-LEG-KRILFLG-DDDLTSLALALTGLPKRITVVDIDERLLDFINRVAEEEGLPIEAVHYDLRDPLPEELRGKF  113 (243)
T ss_dssp             HHHTT--STT--EEEEES--TT-HHHHHHHHT--SEEEEE-S-HHHHHHHHHHHHHHT--EEEE---TTS---TTTSS-B
T ss_pred             HHhcCc-ccC-CEEEEEc-CCcHHHHHHHhhCCCCeEEEEEcCHHHHHHHHHHHHHcCCceEEEEecccccCCHHHhcCC
Confidence            334433 443 7788888 4455677777778888999999975 5544332    1 2499999999999996   3  


Q ss_pred             CEEE
Q 039903          228 DAIL  231 (233)
Q Consensus       228 D~~~  231 (233)
                      |+++
T Consensus       114 D~f~  117 (243)
T PF01861_consen  114 DVFF  117 (243)
T ss_dssp             SEEE
T ss_pred             CEEE
Confidence            8876

All the members are 350-400 amino acids long.; PDB: 2QM3_A.

>KOG1975 consensus mRNA cap methyltransferase [RNA processing and modification]

Probab=84.86  E-value=1.6  Score=37.75  Aligned_cols=71  Identities=15%  Similarity=0.186  Sum_probs=50.6

Q ss_pred             HHHHHHHHHhcchhcHHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCC-cEEEeechH-HHhhccCC--------
Q 039903          141 NGVFNKAMLNHTSIVTNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHI-KGVNFDLSH-VIQDSSSY--------  210 (233)
Q Consensus       141 ~~~f~~am~~~~~~~~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l-~~~v~Dlp~-v~~~a~~~--------  210 (233)
                      .++||.+|.+       .++..|-  +....++|+|||-|.-++..-++  .+ ..+..|+.+ .|+++++.        
T Consensus        99 lRnfNNwIKs-------~LI~~y~--~~~~~~~~LgCGKGGDLlKw~kA--gI~~~igiDIAevSI~qa~~RYrdm~~r~  167 (389)
T KOG1975|consen   99 LRNFNNWIKS-------VLINLYT--KRGDDVLDLGCGKGGDLLKWDKA--GIGEYIGIDIAEVSINQARKRYRDMKNRF  167 (389)
T ss_pred             hhhhhHHHHH-------HHHHHHh--ccccccceeccCCcccHhHhhhh--cccceEeeehhhccHHHHHHHHHHHHhhh
Confidence            3567766653       4555543  66788999999999998887765  33 368899987 57878762        


Q ss_pred             C----CceEEecCcCC
Q 039903          211 S----GVKHIGGIMLE  222 (233)
Q Consensus       211 ~----ri~~~~gD~f~  222 (233)
                      +    .+.|+.+|=|.
T Consensus       168 ~~~~f~a~f~~~Dc~~  183 (389)
T KOG1975|consen  168 KKFIFTAVFIAADCFK  183 (389)
T ss_pred             hcccceeEEEEeccch
Confidence            2    36788888875

>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional

Probab=84.71  E-value=1.8  Score=37.26  Aligned_cols=57  Identities=12%  Similarity=0.125  Sum_probs=43.8

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHh
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHV   84 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~   84 (233)
                      ...|.+.|.+.   .+.+..+||+++++    +...+.+.++.|...|++-+..   .+..|.+.+.
T Consensus         6 ~~~il~~L~~~---~~~s~~~LA~~lgv----sr~tV~~~l~~L~~~G~~i~~~---~~~Gy~L~~~   62 (319)
T PRK11886          6 MLQLLSLLADG---DFHSGEQLGEELGI----SRAAIWKHIQTLEEWGLDIFSV---KGKGYRLAEP   62 (319)
T ss_pred             HHHHHHHHHcC---CCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCceEEe---cCCeEEecCc
Confidence            34567777764   47899999999999    9999999999999999944331   2346876543

>COG0116 Predicted N6-adenine-specific DNA methylase [DNA replication, recombination, and repair]

Probab=84.63  E-value=3.1  Score=36.79  Aligned_cols=75  Identities=13%  Similarity=0.109  Sum_probs=55.1

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCc---------------------------------------EEE
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIK---------------------------------------GVN  197 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~---------------------------------------~~v  197 (233)
                      ..++..- +|.....++|==||+|.++++.+...+++-                                       .+.
T Consensus       181 aAil~la-gw~~~~pl~DPmCGSGTi~IEAAl~~~niAPg~~R~~~f~~w~~~~~~lw~~~~~ea~~~a~~~~~~~~~~G  259 (381)
T COG0116         181 AAILLLA-GWKPDEPLLDPMCGSGTILIEAALIAANIAPGLNRRFGFEFWDWFDKDLWDKLREEAEERARRGKELPIIYG  259 (381)
T ss_pred             HHHHHHc-CCCCCCccccCCCCccHHHHHHHHhccccCCccccccchhhhhhccHHHHHHHHHHHHHHHhhcCccceEEE
Confidence            3444433 387778999999999999999888876422                                       568


Q ss_pred             eec-hHHHhhccCC-------CCceEEecCcCC-CCC-CC-CEEEe
Q 039903          198 FDL-SHVIQDSSSY-------SGVKHIGGIMLE-RIP-KG-DAILI  232 (233)
Q Consensus       198 ~Dl-p~v~~~a~~~-------~ri~~~~gD~f~-~~P-~~-D~~~l  232 (233)
                      .|+ |.+++.|+.+       +.|+|..+|+-. +-| .. |+++.
T Consensus       260 ~Did~r~i~~Ak~NA~~AGv~d~I~f~~~d~~~l~~~~~~~gvvI~  305 (381)
T COG0116         260 SDIDPRHIEGAKANARAAGVGDLIEFKQADATDLKEPLEEYGVVIS  305 (381)
T ss_pred             ecCCHHHHHHHHHHHHhcCCCceEEEEEcchhhCCCCCCcCCEEEe
Confidence            898 4588877765       789999999887 444 33 77653

>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C

Probab=84.63  E-value=0.96  Score=27.26  Aligned_cols=40  Identities=13%  Similarity=0.151  Sum_probs=23.6

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCC
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHR   65 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~g   65 (233)
                      .++.+...+.+     +.|..+||+.+|+    +..-+.+|++--...|
T Consensus         6 ~R~~ii~l~~~-----G~s~~~ia~~lgv----s~~Tv~~w~kr~~~~G   45 (50)
T PF13384_consen    6 RRAQIIRLLRE-----GWSIREIAKRLGV----SRSTVYRWIKRYREEG   45 (50)
T ss_dssp             ----HHHHHHH-----T--HHHHHHHHTS-----HHHHHHHHT------
T ss_pred             HHHHHHHHHHC-----CCCHHHHHHHHCc----CHHHHHHHHHHccccc
Confidence            34556666666     6899999999999    9999999997765555

>COG1497 Predicted transcriptional regulator [Transcription]

Probab=83.84  E-value=3.7  Score=33.84  Aligned_cols=49  Identities=12%  Similarity=0.232  Sum_probs=43.9

Q ss_pred             CCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhh
Q 039903           33 KISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFV   89 (233)
Q Consensus        33 ~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~   89 (233)
                      .....|||+++|+    .+..+..-++-|+.-|++++.    +-+.|..|..+...+
T Consensus        25 ~v~q~eIA~~lgi----T~QaVsehiK~Lv~eG~i~~~----gR~~Y~iTkkG~e~l   73 (260)
T COG1497          25 RVKQKEIAKKLGI----TLQAVSEHIKELVKEGLIEKE----GRGEYEITKKGAEWL   73 (260)
T ss_pred             CCCHHHHHHHcCC----CHHHHHHHHHHHHhccceeec----CCeeEEEehhHHHHH
Confidence            6788999999999    999999999999999999995    567999999987533

>TIGR01321 TrpR trp operon repressor, proteobacterial

Probab=83.44  E-value=1.8  Score=30.33  Aligned_cols=40  Identities=15%  Similarity=0.191  Sum_probs=33.8

Q ss_pred             HHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHh
Q 039903           15 AASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLV   62 (233)
Q Consensus        15 ~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~   62 (233)
                      .+.+.||+..|-.    ++.|-.|||+.+|+    +...+.|+=+.|.
T Consensus        41 l~~R~~i~~~Ll~----~~~tQrEIa~~lGi----S~atIsR~sn~lk   80 (94)
T TIGR01321        41 LGDRIRIVNELLN----GNMSQREIASKLGV----SIATITRGSNNLK   80 (94)
T ss_pred             HHHHHHHHHHHHh----CCCCHHHHHHHhCC----ChhhhhHHHhhcc
Confidence            4568899998877    58999999999999    8888888777665

This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.

>PF13518 HTH_28: Helix-turn-helix domain

Probab=83.41  E-value=2.2  Score=25.65  Aligned_cols=29  Identities=17%  Similarity=0.113  Sum_probs=26.4

Q ss_pred             CCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCc
Q 039903           34 ISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRV   66 (233)
Q Consensus        34 ~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gl   66 (233)
                      .|..++|+.+|+    +...+.+|++..-..|+
T Consensus        13 ~s~~~~a~~~gi----s~~tv~~w~~~y~~~G~   41 (52)
T PF13518_consen   13 ESVREIAREFGI----SRSTVYRWIKRYREGGI   41 (52)
T ss_pred             CCHHHHHHHHCC----CHhHHHHHHHHHHhcCH
Confidence            499999999999    99999999998888775

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

Probab=83.33  E-value=1.1  Score=40.52  Aligned_cols=65  Identities=14%  Similarity=0.147  Sum_probs=48.3

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCC--C-CC--C-CCEEEe
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLE--R-IP--K-GDAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~--~-~P--~-~D~~~l  232 (233)
                      ..+..+++|.=||.|.|+..++++  --+++..|+ |+.++.|+++      ++++|+.+|..+  + +.  . .|++++
T Consensus       291 ~~~~~~vlDlYCGvG~f~l~lA~~--~~~V~gvEi~~~aV~~A~~NA~~n~i~N~~f~~~~ae~~~~~~~~~~~~d~Vvv  368 (432)
T COG2265         291 LAGGERVLDLYCGVGTFGLPLAKR--VKKVHGVEISPEAVEAAQENAAANGIDNVEFIAGDAEEFTPAWWEGYKPDVVVV  368 (432)
T ss_pred             hcCCCEEEEeccCCChhhhhhccc--CCEEEEEecCHHHHHHHHHHHHHcCCCcEEEEeCCHHHHhhhccccCCCCEEEE
Confidence            345679999999999999999965  445777776 6677776653      679999999887  2 22  2 388775

>PF09681 Phage_rep_org_N: N-terminal phage replisome organiser (Phage_rep_org_N); InterPro: IPR010056 This entry is represented by the N-terminal domain of Bacteriophage A500, Gp45

Probab=83.29  E-value=2.7  Score=30.92  Aligned_cols=49  Identities=8%  Similarity=0.045  Sum_probs=42.9

Q ss_pred             CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHh
Q 039903           32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYF   88 (233)
Q Consensus        32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l   88 (233)
                      -|.|.++||..++-    +.+.++.-|.++...|+++..    +++.|.++.....-
T Consensus        52 ipy~~e~LA~~~~~----~~~~V~~AL~~f~k~glIe~~----ed~~i~i~~~~~~~  100 (121)
T PF09681_consen   52 IPYTAEMLALEFDR----PVDTVRLALAVFQKLGLIEID----EDGVIYIPNWEKHQ  100 (121)
T ss_pred             CCCcHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEe----cCCeEEeecHHHHh
Confidence            49999999999999    999999999999999999997    68888777655443

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. The proteins in this entry contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The low-complexity region is adjacent to this N-terminal domain.

>KOG0822 consensus Protein kinase inhibitor [Cell cycle control, cell division, chromosome partitioning]

Probab=82.98  E-value=5.2  Score=36.87  Aligned_cols=94  Identities=19%  Similarity=0.210  Sum_probs=56.6

Q ss_pred             cccccccCchHHHHHHHHHHhcchhcHHHHHHhccccc--CcceEEEecCCccHHHHHHHHH----cCCCcEEEeec-hH
Q 039903          130 FYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFE--QIKQLVDVGGGLGVNVNIIISN----YLHIKGVNFDL-SH  202 (233)
Q Consensus       130 ~~~~~~~~~~~~~~f~~am~~~~~~~~~~~~~~~~~~~--~~~~vvDvGGG~G~~~~~l~~~----~P~l~~~v~Dl-p~  202 (233)
                      .|+.+++||-.=..+.+|.-       ..+++..++-+  ....+.-+|||.|-+..+..++    +-+++..+++- |.
T Consensus       334 TYetFEkD~VKY~~Yq~Ai~-------~AL~Drvpd~~a~~~tVimvlGaGRGPLv~~~lkaa~~~~RkVklyavEKNPN  406 (649)
T KOG0822|consen  334 TYETFEKDPVKYDQYQQAIL-------KALLDRVPDESAKTTTVIMVLGAGRGPLVDASLKAAEETDRKVKLYAVEKNPN  406 (649)
T ss_pred             hhhhhhccchHHHHHHHHHH-------HHHHhhCcccccCceEEEEEecCCCccHHHHHHHHHHHhcCceEEEEEecCcc
Confidence            35666677755555555433       23444333222  2677888999999876655443    44566666664 55


Q ss_pred             HHhhccC------CCCceEEecCcCC-CCC-C-CCEE
Q 039903          203 VIQDSSS------YSGVKHIGGIMLE-RIP-K-GDAI  230 (233)
Q Consensus       203 v~~~a~~------~~ri~~~~gD~f~-~~P-~-~D~~  230 (233)
                      ++-....      ..||+.+.+||.+ .-| . +|++
T Consensus       407 AivtL~~~n~~~W~~~Vtii~~DMR~w~ap~eq~DI~  443 (649)
T KOG0822|consen  407 AIVTLQNRNFECWDNRVTIISSDMRKWNAPREQADII  443 (649)
T ss_pred             hhhhhhhhchhhhcCeeEEEeccccccCCchhhccch
Confidence            4433322      1789999999999 544 2 5765

>KOG1709 consensus Guanidinoacetate methyltransferase and related proteins [Amino acid transport and metabolism]

Probab=82.96  E-value=5.4  Score=32.59  Aligned_cols=61  Identities=15%  Similarity=0.166  Sum_probs=49.6

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCC-----CCceEEecCcC---CCCCC
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSY-----SGVKHIGGIML---ERIPK  226 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~-----~ri~~~~gD~f---~~~P~  226 (233)
                      +.+..+|+.||=|-|.....+-++.|..+.++---|+|.+.-+..     ++|....|-+=   ..+|.
T Consensus        99 ~tkggrvLnVGFGMgIidT~iQe~~p~~H~IiE~hp~V~krmr~~gw~ek~nViil~g~WeDvl~~L~d  167 (271)
T KOG1709|consen   99 STKGGRVLNVGFGMGIIDTFIQEAPPDEHWIIEAHPDVLKRMRDWGWREKENVIILEGRWEDVLNTLPD  167 (271)
T ss_pred             hhCCceEEEeccchHHHHHHHhhcCCcceEEEecCHHHHHHHHhcccccccceEEEecchHhhhccccc
Confidence            467799999999999999999999999999999999999887763     56766666433   34554

>PRK10046 dpiA two-component response regulator DpiA; Provisional

Probab=82.84  E-value=2.3  Score=34.29  Aligned_cols=45  Identities=13%  Similarity=0.236  Sum_probs=37.2

Q ss_pred             ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      .|.+.+.+.-  ++.|..|||+++++    ++.-+++-+..|+..|++...
T Consensus       166 ~Vl~~~~~g~--~g~s~~eIa~~l~i----S~~Tv~~~~~~~~~~~~~~~~  210 (225)
T PRK10046        166 AVRKLFKEPG--VQHTAETVAQALTI----SRTTARRYLEYCASRHLIIAE  210 (225)
T ss_pred             HHHHHHHcCC--CCcCHHHHHHHhCc----cHHHHHHHHHHHHhCCeEEEE
Confidence            3556665510  15899999999999    999999999999999999974

>KOG1562 consensus Spermidine synthase [Amino acid transport and metabolism]

Probab=82.80  E-value=0.81  Score=38.91  Aligned_cols=66  Identities=24%  Similarity=0.344  Sum_probs=49.7

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCc-EEEeechH-HHhhccCC----------CCceEEecCcCC---CCCCC--C
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIK-GVNFDLSH-VIQDSSSY----------SGVKHIGGIMLE---RIPKG--D  228 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~-~~v~Dlp~-v~~~a~~~----------~ri~~~~gD~f~---~~P~~--D  228 (233)
                      ..+++.++-||||.|.+.+..++. +.+. ..++|..+ |++..+++          +||..+.||=|.   -.+..  |
T Consensus       119 ~~npkkvlVVgggDggvlrevikH-~~ve~i~~~eiD~~Vie~sk~y~p~la~gy~~~~v~l~iGDG~~fl~~~~~~~~d  197 (337)
T KOG1562|consen  119 HPNPKKVLVVGGGDGGVLREVIKH-KSVENILLCEIDENVIESSKQYLPTLACGYEGKKVKLLIGDGFLFLEDLKENPFD  197 (337)
T ss_pred             CCCCCeEEEEecCCccceeeeecc-ccccceeeehhhHHHHHHHHHHhHHHhcccCCCceEEEeccHHHHHHHhccCCce
Confidence            356789999999999999999886 7765 56778765 66655542          799999999775   34443  8


Q ss_pred             EEEe
Q 039903          229 AILI  232 (233)
Q Consensus       229 ~~~l  232 (233)
                      +++.
T Consensus       198 Vii~  201 (337)
T KOG1562|consen  198 VIIT  201 (337)
T ss_pred             EEEE
Confidence            7764

>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family

Probab=81.92  E-value=3.2  Score=30.86  Aligned_cols=51  Identities=14%  Similarity=0.206  Sum_probs=38.5

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      .|+.|.+.|=..   ++.|+.||.+.++-..+.+..-+..+|+-|...|++++.
T Consensus         5 ~E~~VM~vlW~~---~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~KG~v~~~   55 (130)
T TIGR02698         5 AEWEVMRVVWTL---GETTSRDIIRILAEKKDWSDSTIKTLLGRLVDKGCLTTE   55 (130)
T ss_pred             HHHHHHHHHHcC---CCCCHHHHHHHHhhccCCcHHHHHHHHHHHHHCCceeee
Confidence            466677777665   589999977776311111888999999999999999975

This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.

>PRK11642 exoribonuclease R; Provisional

Probab=81.58  E-value=2.8  Score=40.99  Aligned_cols=58  Identities=22%  Similarity=0.244  Sum_probs=44.3

Q ss_pred             ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903           20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH   83 (233)
Q Consensus        20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~   83 (233)
                      .|.+.|...+  +|++..+|++++++.+..+...+.+.|+.|...|.+.+.    ..+.|.+..
T Consensus        23 ~Il~~l~~~~--~~~~~~~L~~~l~l~~~~~~~~l~~~L~~L~~~g~l~~~----~~~~~~~~~   80 (813)
T PRK11642         23 FILEHLTKRE--KPASREELAVELNIEGEEQLEALRRRLRAMERDGQLVFT----RRQCYALPE   80 (813)
T ss_pred             HHHHHHHhcC--CCCCHHHHHHHhCCCChHHHHHHHHHHHHHHHCCCEEEc----CCceEecCC
Confidence            4677776643  699999999999993222345699999999999999986    466776653

>PF13814 Replic_Relax: Replication-relaxation

Probab=81.39  E-value=3.9  Score=32.04  Aligned_cols=61  Identities=13%  Similarity=0.146  Sum_probs=48.0

Q ss_pred             HHHhcCCCCCCCHHHHHHhCCCCCCCChh---hHHHHHHHHhcCCceeeeccC------CCCCceeccHhhhHhhcC
Q 039903           24 IIAKAGPTAKISAVEIAAQMPSSNPNAAV---MLDRILRLLVTHRVLRCTSAG------DDQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        24 ~L~~~~~~~~~t~~elA~~~~~~~~~~~~---~l~rlL~~L~~~gll~~~~~~------~~~~~y~lt~~s~~l~~~   91 (233)
                      .|...   +.+|..||+.....    +..   .+++.|+-|...|++......      ...-.|.+|+.|..++.+
T Consensus         3 ~L~~~---r~lt~~Qi~~l~~~----~~~~~~~~~rrL~~L~~~glv~~~~~~~~~~~g~~~~vy~Lt~~G~~~l~~   72 (191)
T PF13814_consen    3 LLARH---RFLTTDQIARLLFP----SSKSERTARRRLKRLRELGLVDRFRRRVGARGGSQPYVYYLTPAGARLLAD   72 (191)
T ss_pred             hHHHh---cCcCHHHHHHHHcC----CCcchHHHHHHHHHHhhCCcEEeecccccccCCCcceEEEECHHHHHHHHh
Confidence            34554   48999999999998    554   899999999999999987431      134689999999877653

>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions []

Probab=81.07  E-value=2.4  Score=26.77  Aligned_cols=39  Identities=18%  Similarity=0.243  Sum_probs=32.8

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHh
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLV   62 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~   62 (233)
                      .++.|++.|-+.   +..|+.|||+.+++    +++-++.-+..|-
T Consensus         6 rq~~Ll~~L~~~---~~~~~~ela~~l~~----S~rti~~~i~~L~   44 (59)
T PF08280_consen    6 RQLKLLELLLKN---KWITLKELAKKLNI----SERTIKNDINELN   44 (59)
T ss_dssp             HHHHHHHHHHHH---TSBBHHHHHHHCTS-----HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcC---CCCcHHHHHHHHCC----CHHHHHHHHHHHH
Confidence            467788888875   58999999999999    9999988888776

; PDB: 2WTE_A 3SQN_A.

>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes

Probab=81.05  E-value=2.5  Score=26.98  Aligned_cols=30  Identities=23%  Similarity=0.388  Sum_probs=23.7

Q ss_pred             hHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHH
Q 039903           22 FEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRI   57 (233)
Q Consensus        22 fd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rl   57 (233)
                      |++-.+++  |.+++.|||+++|+    ++.-+++|
T Consensus        13 ~e~y~~~~--g~i~lkdIA~~Lgv----s~~tIr~W   42 (60)
T PF10668_consen   13 FEIYKESN--GKIKLKDIAEKLGV----SESTIRKW   42 (60)
T ss_pred             HHHHHHhC--CCccHHHHHHHHCC----CHHHHHHH
Confidence            44444444  79999999999999    88888776

Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].

>PF06969 HemN_C: HemN C-terminal domain; InterPro: IPR010723 Proteins containing this domain are all oxygen-independent coproporphyrinogen-III oxidases (HemN)

Probab=81.00  E-value=3.1  Score=26.65  Aligned_cols=46  Identities=13%  Similarity=0.086  Sum_probs=35.0

Q ss_pred             CCCCHHHHHHhCCCCCCCCh-hhHHHHHHHHhcCCceeeeccCCCCCceeccHhhh
Q 039903           32 AKISAVEIAAQMPSSNPNAA-VMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAK   86 (233)
Q Consensus        32 ~~~t~~elA~~~~~~~~~~~-~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~   86 (233)
                      .+++.+++.++.|.    +. ......++.+...|+++.+     ++++++|+.|.
T Consensus        19 ~Gi~~~~~~~~~g~----~~~~~~~~~l~~l~~~Gll~~~-----~~~l~lT~~G~   65 (66)
T PF06969_consen   19 EGIDLSEFEQRFGI----DFAEEFQKELEELQEDGLLEID-----GGRLRLTEKGR   65 (66)
T ss_dssp             SEEEHHHHHHHTT------THHH-HHHHHHHHHTTSEEE------SSEEEE-TTTG
T ss_pred             CCcCHHHHHHHHCc----CHHHHHHHHHHHHHHCCCEEEe-----CCEEEECcccC
Confidence            37899999999998    53 3447789999999999994     89999999775

This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX [], one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain suggest it may be a substrate binding domain.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin-containing compound biosynthetic process, 0055114 oxidation-reduction process, 0005737 cytoplasm; PDB: 1OLT_A.

>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional

Probab=80.93  E-value=1.4  Score=34.90  Aligned_cols=47  Identities=13%  Similarity=0.035  Sum_probs=42.4

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      .+..|.+.|...   +.+++.|||+.+++    ++.-++|=|+.|...|++.+.
T Consensus         8 R~~~Il~~l~~~---~~~~~~~La~~~~v----S~~TiRRDl~~L~~~g~~~r~   54 (185)
T PRK04424          8 RQKALQELIEEN---PFITDEELAEKFGV----SIQTIRLDRMELGIPELRERI   54 (185)
T ss_pred             HHHHHHHHHHHC---CCEEHHHHHHHHCc----CHHHHHHHHHHHhcchHHHHH
Confidence            445678888887   58999999999999    999999999999999999986

>KOG2651 consensus rRNA adenine N-6-methyltransferase [RNA processing and modification]

Probab=80.91  E-value=2.8  Score=36.98  Aligned_cols=46  Identities=26%  Similarity=0.397  Sum_probs=34.7

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHH
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVI  204 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~  204 (233)
                      +++..+-+|.++.++||||.|.|+++.-+.=.| ++++..+|-..+.
T Consensus       143 elvSsi~~f~gi~~vvD~GaG~G~LSr~lSl~y-~lsV~aIegsq~~  188 (476)
T KOG2651|consen  143 ELVSSISDFTGIDQVVDVGAGQGHLSRFLSLGY-GLSVKAIEGSQRL  188 (476)
T ss_pred             HHHHHHHhhcCCCeeEEcCCCchHHHHHHhhcc-CceEEEeccchHH
Confidence            445544448899999999999999988776654 6778888866543

>COG1092 Predicted SAM-dependent methyltransferases [General function prediction only]

Probab=80.64  E-value=1.7  Score=38.70  Aligned_cols=65  Identities=15%  Similarity=0.120  Sum_probs=51.0

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccCC--------CCceEEecCcCCCC----CCC---CEE
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSSY--------SGVKHIGGIMLERI----PKG---DAI  230 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~~--------~ri~~~~gD~f~~~----P~~---D~~  230 (233)
                      .+.++|||+=|=+|.++...+..- .-++|.+|+.. +++.|+++        ++++++.+|.|+-+    ..+   |+|
T Consensus       216 ~~GkrvLNlFsYTGgfSv~Aa~gG-A~~vt~VD~S~~al~~a~~N~~LNg~~~~~~~~i~~Dvf~~l~~~~~~g~~fDlI  294 (393)
T COG1092         216 AAGKRVLNLFSYTGGFSVHAALGG-ASEVTSVDLSKRALEWARENAELNGLDGDRHRFIVGDVFKWLRKAERRGEKFDLI  294 (393)
T ss_pred             ccCCeEEEecccCcHHHHHHHhcC-CCceEEEeccHHHHHHHHHHHHhcCCCccceeeehhhHHHHHHHHHhcCCcccEE
Confidence            347899999999999999988862 23789999975 78877764        67999999999732    323   888


Q ss_pred             Ee
Q 039903          231 LI  232 (233)
Q Consensus       231 ~l  232 (233)
                      +|
T Consensus       295 il  296 (393)
T COG1092         295 IL  296 (393)
T ss_pred             EE
Confidence            86

>COG1568 Predicted methyltransferases [General function prediction only]

Probab=80.63  E-value=7.6  Score=32.94  Aligned_cols=166  Identities=11%  Similarity=0.102  Sum_probs=94.4

Q ss_pred             CCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhcCCCCCCccchhcc----ccC---
Q 039903           34 ISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLNRDGVSLCPSRPW----LET---  106 (233)
Q Consensus        34 ~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~~~~~~~~~~~~~~----~~~---  106 (233)
                      -+.-.|+....+    +.+.+..+++.|...|++..+     ++...+|..|..|+..-   .+..--.+    +..   
T Consensus        35 ~d~wkIvd~s~~----plp~v~~i~~~l~~egiv~~~-----~g~v~~TekG~E~~e~~---gi~~~~~~~C~~CeGrgi  102 (354)
T COG1568          35 NDFWKIVDYSDL----PLPLVASILEILEDEGIVKIE-----EGGVELTEKGEELAEEL---GIKKKYDYTCECCEGRGI  102 (354)
T ss_pred             cchHhhhhhccC----CchHHHHHHHHHHhcCcEEEe-----cCcEeehhhhHHHHHHh---CCCccccccccCcCCccc
Confidence            388899999999    899999999999999999996     55599999999888642   12211111    110   


Q ss_pred             chhhHHHHHHcCCcchhhhhCCccccccccCchHHHHHHHHHHhcchhcHHHHHHhcc--cccCcceEEEecCCccHHHH
Q 039903          107 KPYEIYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSK--GFEQIKQLVDVGGGLGVNVN  184 (233)
Q Consensus       107 ~~~~L~~~l~~g~~~~~~~~g~~~~~~~~~~~~~~~~f~~am~~~~~~~~~~~~~~~~--~~~~~~~vvDvGGG~G~~~~  184 (233)
                      ......|.++            .|-++....|+-...++++-...-.. ...++=.+.  ++.+ +.++-|| -.-..++
T Consensus       103 ~l~~f~dll~------------kf~eiaK~RP~p~~~yDQgfvTpEtt-v~Rv~lm~~RGDL~g-K~I~vvG-DDDLtsi  167 (354)
T COG1568         103 SLQAFKDLLE------------KFREIAKDRPEPLHQYDQGFVTPETT-VSRVALMYSRGDLEG-KEIFVVG-DDDLTSI  167 (354)
T ss_pred             cchhHHHHHH------------HHHHHHhcCCCcchhcccccccccce-eeeeeeeccccCcCC-CeEEEEc-CchhhHH
Confidence            1111222211            11122222333222222211110000 000000111  1222 5677787 6666677


Q ss_pred             HHHHHcCCCcEEEeechH-HHhh----ccC--CCCceEEecCcCCCCCC
Q 039903          185 IIISNYLHIKGVNFDLSH-VIQD----SSS--YSGVKHIGGIMLERIPK  226 (233)
Q Consensus       185 ~l~~~~P~l~~~v~Dlp~-v~~~----a~~--~~ri~~~~gD~f~~~P~  226 (233)
                      +++-.+---++.|+|+.+ .+.-    |++  .++|+.+..|..+|+|+
T Consensus       168 a~aLt~mpk~iaVvDIDERli~fi~k~aee~g~~~ie~~~~Dlr~plpe  216 (354)
T COG1568         168 ALALTGMPKRIAVVDIDERLIKFIEKVAEELGYNNIEAFVFDLRNPLPE  216 (354)
T ss_pred             HHHhcCCCceEEEEechHHHHHHHHHHHHHhCccchhheeehhcccChH
Confidence            766655555789999876 3332    233  26799999999999996

>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4

Probab=80.47  E-value=1.7  Score=29.23  Aligned_cols=36  Identities=17%  Similarity=0.287  Sum_probs=25.0

Q ss_pred             hhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhc
Q 039903           21 VFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVT   63 (233)
Q Consensus        21 lfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~   63 (233)
                      |+..|+. |  .|+|.++||+++|.    +.+.+...|..+..
T Consensus        29 LLr~LA~-G--~PVt~~~LA~a~g~----~~e~v~~~L~~~p~   64 (77)
T PF12324_consen   29 LLRLLAK-G--QPVTVEQLAAALGW----PVEEVRAALAAMPD   64 (77)
T ss_dssp             HHHHHTT-T--S-B-HHHHHHHHT------HHHHHHHHHH-TT
T ss_pred             HHHHHHc-C--CCcCHHHHHHHHCC----CHHHHHHHHHhCCC
Confidence            6777887 4  69999999999999    88887777776653

99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.

>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional

Probab=80.07  E-value=3.2  Score=33.65  Aligned_cols=42  Identities=10%  Similarity=0.182  Sum_probs=37.0

Q ss_pred             CCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903           33 KISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH   83 (233)
Q Consensus        33 ~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~   83 (233)
                      |+|-++||..+|+    +...+.|+|+.|...|+++..     .+.+....
T Consensus       184 ~lt~~~iA~~lG~----sr~tvsR~l~~l~~~g~I~~~-----~~~i~i~d  225 (235)
T PRK11161        184 TMTRGDIGNYLGL----TVETISRLLGRFQKSGMLAVK-----GKYITIEN  225 (235)
T ss_pred             cccHHHHHHHhCC----cHHHHHHHHHHHHHCCCEEec-----CCEEEEcC
Confidence            6899999999999    999999999999999999985     56666654

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	233
1kyw_A	365	Crystal Structure Analysis Of Caffeic Acid5-Hydroxy		1e-58
3reo_A	368	Monolignol O-Methyltransferase (Momt) Length = 368		4e-54
3p9c_A	364	Crystal Structure Of Perennial Ryegrass Lpomt1 Boun		2e-45
1fp1_D	372	Crystal Structure Analysis Of Chalcone O-Methyltran		2e-34
1fpq_A	372	Crystal Structure Analysis Of Selenomethionine Subs		2e-26
1fp2_A	352	Crystal Structure Analysis Of Isoflavone O-Methyltr		9e-10
2qyo_A	357	Crystal Structure Of Isoflavone O-Methyltransferase		1e-07
1fpx_A	352	Crystal Structure Analysis Of Selenomethionine Subs		2e-07
1zga_A	357	Crystal Structure Of Isoflavanone 4'-o-methyltransf		3e-04
1zg3_A	358	Crystal Structure Of The Isoflavanone 4'-O-Methyltr		3e-04
1zgj_A	354	Crystal Structure Of Isoflavanone 4'-O-Methyltransf		3e-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 =  223 bits (567), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 118/242 (48%), Positives = 154/242 (63%), Gaps = 9/242 (3%)
Query: 1   MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRL 60
           MQ A + VLP  +++A EL + EIIAKAGP A+IS +EIA+Q+P++NP+A VMLDR+LRL
Sbjct: 24  MQLASASVLPMILKSALELDLLEIIAKAGPGAQISPIEIASQLPTTNPDAPVMLDRMLRL 83
Query: 61  LVTHRVLRCT----SAGDDQRLYGLAHVAKYFVLNRDGVS-----LCPSRPWLETKPYEI 111
           L  + +L C+      G  QRLYGLA VAKY V N DGVS     L      L    Y +
Sbjct: 84  LACYIILTCSVRTQQDGKVQRLYGLATVAKYLVKNEDGVSISALNLMNQDKVLMESWYHL 143
Query: 112 YDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIKQ 171
            DAVL+GGI FNK +G   +EY G D RFN VFNK M +H++I   +I+++  GFE +K 
Sbjct: 144 KDAVLDGGIPFNKAYGMTAFEYHGTDPRFNKVFNKGMSDHSTITMKKILETYTGFEGLKS 203
Query: 172 XXXXXXXXXXXXXIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAIL 231
                         I+S Y  IKG+NFDL HVI+D+ SY GV+H+GG M   IPK DA+ 
Sbjct: 204 LVDVGGGTGAVINTIVSKYPTIKGINFDLPHVIEDAPSYPGVEHVGGDMFVSIPKADAVF 263
Query: 232 IK 233
           +K
Sbjct: 264 MK 265

>pdb|3REO|A Chain A, Monolignol O-Methyltransferase (Momt) Length = 368

Iteration: 1
 Score =  207 bits (527), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 112/248 (45%), Positives = 150/248 (60%), Gaps = 20/248 (8%)
Query: 1   MQPAMSIVLPAAMQAASELGVFEIIAKA-GPTAKISAVEIAAQMPSSNPNAAVMLDRILR 59
           MQ A + VLP A++AA EL V EI+AK+  P+  IS  EIAAQ+P++NP A VMLDR+LR
Sbjct: 26  MQLASAAVLPMALKAAIELDVLEIMAKSVPPSGYISPAEIAAQLPTTNPEAPVMLDRVLR 85
Query: 60  LLVTHRV----LRCTSAGDDQRLYGLAHVAKYFVLNRDGVSLCPS----------RPWLE 105
           LL ++ V    LR   +G  +RLYGLA V K+   N DGVSL P            PW  
Sbjct: 86  LLASYSVVTYTLRELPSGKVERLYGLAPVCKFLTKNEDGVSLAPFLLLATDKVLLEPWFY 145
Query: 106 TKPYEIYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKG 165
            K     DA+LEGGI FNK +G   ++Y G D R N VFNK M ++++I   +I++   G
Sbjct: 146 LK-----DAILEGGIPFNKAYGMNIFDYHGTDHRINKVFNKGMSSNSTITMKKILEMYNG 200
Query: 166 FEQIKQXXXXXXXXXXXXXIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIP 225
           FE +               +I++ Y  I  +NFDL HVIQD+ ++SGV+H+GG M + +P
Sbjct: 201 FEGLTTIVDVGGGTGAVASMIVAKYPSINAINFDLPHVIQDAPAFSGVEHLGGDMFDGVP 260
Query: 226 KGDAILIK 233
           KGDAI IK
Sbjct: 261 KGDAIFIK 268

>pdb|3P9C|A Chain A, Crystal Structure Of Perennial Ryegrass Lpomt1 Bound To Sah Length = 364

Iteration: 1
 Score =  178 bits (452), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 102/244 (41%), Positives = 144/244 (59%), Gaps = 13/244 (5%)
Query: 1   MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSS-NPNAAVMLDRILR 59
           +Q A S VLP  ++ A ELG+ EI+  AG  + ++  E+AA++PS+ NP A  M+DRILR
Sbjct: 25  LQLASSSVLPMTLKNAIELGLLEILVAAGGKS-LTPTEVAAKLPSAANPEAPDMVDRILR 83
Query: 60  LLVTHRVLRC-TSAGDDQRL---YGLAHVAKYFVLNRDGVSLCP------SRPWLETKPY 109
           LL ++ V+ C    G D RL   YG A V K+   N DGVS+         +  +E+  Y
Sbjct: 84  LLASYNVVTCLVEEGKDGRLSRSYGAAPVCKFLTPNEDGVSMAALALMNQDKVLMESW-Y 142
Query: 110 EIYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQI 169
            + DAVL+GGI FNK +G   +EY G D RFN VFN+ M NH+ I+T ++++   GFE +
Sbjct: 143 YLKDAVLDGGIPFNKAYGMSAFEYHGTDPRFNRVFNEGMKNHSIIITKKLLELYHGFEGL 202
Query: 170 KQXXXXXXXXXXXXXIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDA 229
                           I ++Y  IKGVNFDL HVI ++  + GV H+GG M + +P GD 
Sbjct: 203 GTLVDVGGGVGATVAAIAAHYPTIKGVNFDLPHVISEAPQFPGVTHVGGDMFKEVPSGDT 262
Query: 230 ILIK 233
           IL+K
Sbjct: 263 ILMK 266

>pdb|1FP1|D Chain D, Crystal Structure Analysis Of Chalcone O-Methyltransferase Length = 372

Iteration: 1
 Score =  142 bits (357), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 90/246 (36%), Positives = 140/246 (56%), Gaps = 23/246 (9%)
Query: 6   SIVLPAAMQAASELGVFEIIAKAGPT-AKISAVEIAAQMPSSNPNAAV--MLDRILRLLV 62
           ++V PA + AA +L +FEIIAKA P  A +S  EIA+++P+S  ++ +   LDR+LRLL 
Sbjct: 34  NLVYPAVLNAAIDLNLFEIIAKATPPGAFMSPSEIASKLPASTQHSDLPNRLDRMLRLLA 93
Query: 63  THRVLRCTSA----GDDQRLYGLAHVAKYFVLNRD-------GVSLC-PS--RPWLETKP 108
           ++ VL  T+     G  +R+YGL+ V KY V +            LC P+  + W+  K 
Sbjct: 94  SYSVLTSTTRTIEDGGAERVYGLSMVGKYLVPDESRGYLASFTTFLCYPALLQVWMNFK- 152
Query: 109 YEIYDAVLEGGIS-FNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFE 167
               +AV++  I  F  VHG   YE+ G D + N +FNK+M++  +    R+++   GFE
Sbjct: 153 ----EAVVDEDIDLFKNVHGVTKYEFMGKDKKMNQIFNKSMVDVCATEMKRMLEIYTGFE 208
Query: 168 QIKQXXXXXXXXXXXXXIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKG 227
            I               +IIS Y  IKG+NFDL  VI+++   SG++H+GG M   +P+G
Sbjct: 209 GISTLVDVGGGSGRNLELIISKYPLIKGINFDLPQVIENAPPLSGIEHVGGDMFASVPQG 268
Query: 228 DAILIK 233
           DA+++K
Sbjct: 269 DAMILK 274

>pdb|1FPQ|A Chain A, Crystal Structure Analysis Of Selenomethionine Substituted Chalcone O- Methyltransferase Length = 372

Iteration: 1
 Score =  115 bits (289), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 83/245 (33%), Positives = 121/245 (49%), Gaps = 17/245 (6%)
Query: 4   AMSIVLPAAMQAASELGVFEIIAKAGPT-AKISAVEIAAQMPSSN-----PNAAVMLDRI 57
             ++V PA + AA +L +FEIIAKA P  A  S  EIA+++P+S      PN      R+
Sbjct: 32  TTNLVYPAVLNAAIDLNLFEIIAKATPPGAFXSPSEIASKLPASTQHSDLPNRLDRXLRL 91
Query: 58  L-RLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLNRD-------GVSLCPSRPWLETKPY 109
           L    V     R    G  +R+YGL+ V KY V +            LC   P L     
Sbjct: 92  LASYSVLTSTTRTIEDGGAERVYGLSXVGKYLVPDESRGYLASFTTFLC--YPALLQVWX 149
Query: 110 EIYDAVLEGGIS-FNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQ 168
              +AV++  I  F  VHG   YE+ G D + N +FNK+ ++  +    R ++   GFE 
Sbjct: 150 NFKEAVVDEDIDLFKNVHGVTKYEFXGKDKKXNQIFNKSXVDVCATEXKRXLEIYTGFEG 209
Query: 169 IKQXXXXXXXXXXXXXIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGD 228
           I               +IIS Y  IKG+NFDL  VI+++   SG++H+GG     +P+GD
Sbjct: 210 ISTLVDVGGGSGRNLELIISKYPLIKGINFDLPQVIENAPPLSGIEHVGGDXFASVPQGD 269
Query: 229 AILIK 233
           A ++K
Sbjct: 270 AXILK 274

>pdb|1FP2|A Chain A, Crystal Structure Analysis Of Isoflavone O-Methyltransferase Length = 352

Iteration: 1
 Score = 60.1 bits (144), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 49/227 (21%), Positives = 98/227 (43%), Gaps = 10/227 (4%)
Query: 12  AMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTS 71
           +++ A E+ +  II   G    +S +    Q+PSS       + R++R L  +      +
Sbjct: 32  SLKWAVEMNIPNIIQNHGKPISLSNLVSILQVPSSKIGN---VRRLMRYLAHNGFFEIIT 88
Query: 72  AGDDQRLYGLAHVAKYFVLNRD----GVSLCPSRPWLETKPYEIYDAVLEGGIS-FNKVH 126
              ++  Y L   ++  V   D     +  C   P L    +E+   + E  ++ F    
Sbjct: 89  K--EEESYALTVASELLVRGSDLCLAPMVECVLDPTLSGSYHELKKWIYEEDLTLFGVTL 146
Query: 127 GTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIKQXXXXXXXXXXXXXII 186
           G+GF+++   +  +N  FN AM + + ++   + D    F+ ++              II
Sbjct: 147 GSGFWDFLDKNPEYNTSFNDAMASDSKLINLALRDCDFVFDGLESIVDVGGGTGTTAKII 206
Query: 187 ISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAILIK 233
              +  +K + FD   V+++ S  + + ++GG M   IP  DA+L+K
Sbjct: 207 CETFPKLKCIVFDRPQVVENLSGSNNLTYVGGDMFTSIPNADAVLLK 253

>pdb|2QYO|A Chain A, Crystal Structure Of Isoflavone O-Methyltransferase Homolog In Complex With Biochanin A And Sah Length = 357

Iteration: 1
 Score = 53.1 bits (126), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 46/233 (19%), Positives = 101/233 (43%), Gaps = 17/233 (7%)
Query: 12  AMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTH---RVLR 68
           +++ + E+ +  II   G    +S +    Q+PS+  +    + R++R L  +    ++ 
Sbjct: 32  SLKWSIEMNIPNIIHNHGKPITLSNLVSILQIPSTKVDN---VQRLMRYLAHNGFFEIIT 88
Query: 69  CTSAGDDQRLYGLAHVAKYFVLNRDGVSLCPS-------RPWLETKPYEIYDAVLEGGIS 121
                +++  Y L   ++  V    G  LC +        P L T  + +   V E  ++
Sbjct: 89  NQELENEEEAYALTVASELLV---KGTELCLAPMVECVLDPTLSTSFHNLKKWVYEEDLT 145
Query: 122 FNKVH-GTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIKQXXXXXXXXX 180
              V+ G   +E+   +  +N ++N A+ + + ++   + D +  FE ++          
Sbjct: 146 LFAVNLGCDLWEFLNKNPEYNTLYNDALASDSKMINLAMKDCNLVFEGLESIVDVGGGNG 205
Query: 181 XXXXIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAILIK 233
               II   +  +  V FD   V+++    + + ++GG M   +PK DA+L+K
Sbjct: 206 TTGKIICETFPKLTCVVFDRPKVVENLCGSNNLTYVGGDMFISVPKADAVLLK 258

>pdb|1FPX|A Chain A, Crystal Structure Analysis Of Selenomethionine Substituted Isoflavone O-Methyltransferase Length = 352

Iteration: 1
 Score = 52.4 bits (124), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 48/228 (21%), Positives = 95/228 (41%), Gaps = 12/228 (5%)
Query: 12  AMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTS 71
           +++ A E  +  II   G    +S +    Q+PSS       + R+ R L  +      +
Sbjct: 32  SLKWAVEXNIPNIIQNHGKPISLSNLVSILQVPSSKIGN---VRRLXRYLAHNGFFEIIT 88
Query: 72  AGDDQRLYGLAHVAKYFVLNRDGVSLCPS-----RPWLETKPYEIYDAVLEGGIS-FNKV 125
              ++  Y L   ++  V   D + L P       P L    +E+   + E  ++ F   
Sbjct: 89  K--EEESYALTVASELLVRGSD-LCLAPXVECVLDPTLSGSYHELKKWIYEEDLTLFGVT 145
Query: 126 HGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIKQXXXXXXXXXXXXXI 185
            G+GF+++   +  +N  FN A  + + ++   + D    F+ ++              I
Sbjct: 146 LGSGFWDFLDKNPEYNTSFNDAXASDSKLINLALRDCDFVFDGLESIVDVGGGTGTTAKI 205
Query: 186 IISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAILIK 233
           I   +  +K + FD   V+++ S  + + ++GG     IP  DA+L+K
Sbjct: 206 ICETFPKLKCIVFDRPQVVENLSGSNNLTYVGGDXFTSIPNADAVLLK 253

>pdb|1ZGA|A Chain A, Crystal Structure Of Isoflavanone 4'-o-methyltransferase Complexed With (+)-6a-hydroxymaackiain Length = 357

Iteration: 1
 Score = 42.0 bits (97), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 49/238 (20%), Positives = 100/238 (42%), Gaps = 21/238 (8%)
Query: 12  AMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHR------ 65
           A+++A ELG+ + I   G    +S +  + ++   +P+   +L R LRLL TH       
Sbjct: 25  ALKSAMELGIADAIHNHGKPMTLSELASSLKL---HPSKVNILHRFLRLL-THNGFFAKT 80
Query: 66  -VLRCTSAGDDQRLYGLAHVAKYFVLNRDGV-------SLCPSRPWLETKPYEIYDAVLE 117
            V       +++  Y L   +K  +  +          +L PS   + +   + ++   E
Sbjct: 81  IVKGKEGDEEEEIAYSLTPPSKLLISGKPTCLSSIVKGALHPSSLDMWSSSKKWFNEDKE 140
Query: 118 GGISFNKVHGTGFYEYAGNDFRFN--GVFNKAMLNHTSIVTNRIIDSSKGFEQIKQXXXX 175
             + F    G  F+++   D   +   +F  AM + + +    + ++ + FE ++     
Sbjct: 141 QTL-FECATGESFWDFLNKDSESSTLSMFQDAMASDSRMFKLVLQENKRVFEGLESLVDV 199
Query: 176 XXXXXXXXXIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAILIK 233
                    +I   + H+K   FD   V+ + +    +  +GG M + IP  DA+L+K
Sbjct: 200 GGGTGGVTKLIHEIFPHLKCTVFDQPQVVGNLTGNENLNFVGGDMFKSIPSADAVLLK 257

>pdb|1ZG3|A Chain A, Crystal Structure Of The Isoflavanone 4'-O-Methyltransferase Complexed With Sah And 2,7,4'-Trihydroxyisoflavanone Length = 358

Iteration: 1
 Score = 42.0 bits (97), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 49/238 (20%), Positives = 100/238 (42%), Gaps = 21/238 (8%)
Query: 12  AMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHR------ 65
           A+++A ELG+ + I   G    +S +  + ++   +P+   +L R LRLL TH       
Sbjct: 26  ALKSAMELGIADAIHNHGKPMTLSELASSLKL---HPSKVNILHRFLRLL-THNGFFAKT 81
Query: 66  -VLRCTSAGDDQRLYGLAHVAKYFVLNRDGV-------SLCPSRPWLETKPYEIYDAVLE 117
            V       +++  Y L   +K  +  +          +L PS   + +   + ++   E
Sbjct: 82  IVKGKEGDEEEEIAYSLTPPSKLLISGKPTCLSSIVKGALHPSSLDMWSSSKKWFNEDKE 141
Query: 118 GGISFNKVHGTGFYEYAGNDFRFN--GVFNKAMLNHTSIVTNRIIDSSKGFEQIKQXXXX 175
             + F    G  F+++   D   +   +F  AM + + +    + ++ + FE ++     
Sbjct: 142 QTL-FECATGESFWDFLNKDSESSTLSMFQDAMASDSRMFKLVLQENKRVFEGLESLVDV 200
Query: 176 XXXXXXXXXIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAILIK 233
                    +I   + H+K   FD   V+ + +    +  +GG M + IP  DA+L+K
Sbjct: 201 GGGTGGVTKLIHEIFPHLKCTVFDQPQVVGNLTGNENLNFVGGDMFKSIPSADAVLLK 258

>pdb|1ZGJ|A Chain A, Crystal Structure Of Isoflavanone 4'-O-Methyltransferase Complexed With (+)-Pisatin Length = 354

Iteration: 1
 Score = 42.0 bits (97), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 49/238 (20%), Positives = 100/238 (42%), Gaps = 21/238 (8%)
Query: 12  AMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHR------ 65
           A+++A ELG+ + I   G    +S +  + ++   +P+   +L R LRLL TH       
Sbjct: 22  ALKSAMELGIADAIHNHGKPMTLSELASSLKL---HPSKVNILHRFLRLL-THNGFFAKT 77
Query: 66  -VLRCTSAGDDQRLYGLAHVAKYFVLNRDGV-------SLCPSRPWLETKPYEIYDAVLE 117
            V       +++  Y L   +K  +  +          +L PS   + +   + ++   E
Sbjct: 78  IVKGKEGDEEEEIAYSLTPPSKLLISGKPTCLSSIVKGALHPSSLDMWSSSKKWFNEDKE 137
Query: 118 GGISFNKVHGTGFYEYAGNDFRFN--GVFNKAMLNHTSIVTNRIIDSSKGFEQIKQXXXX 175
             + F    G  F+++   D   +   +F  AM + + +    + ++ + FE ++     
Sbjct: 138 QTL-FECATGESFWDFLNKDSESSTLSMFQDAMASDSRMFKLVLQENKRVFEGLESLVDV 196
Query: 176 XXXXXXXXXIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAILIK 233
                    +I   + H+K   FD   V+ + +    +  +GG M + IP  DA+L+K
Sbjct: 197 GGGTGGVTKLIHEIFPHLKCTVFDQPQVVGNLTGNENLNFVGGDMFKSIPSADAVLLK 254

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	233
3reo_A	368	(ISO)eugenol O-methyltransferase; directed evoluti	2e-72
1fp1_D	372	Isoliquiritigenin 2'-O-methyltransferase; protein-	1e-69
3p9c_A	364	Caffeic acid O-methyltransferase; S-adenosylmethio	6e-69
1fp2_A	352	Isoflavone O-methyltransferase; protein-product co	4e-65
1zg3_A	358	Isoflavanone 4'-O-methyltransferase; rossman fold,	2e-58
3i53_A	332	O-methyltransferase; CO-complex, rossmann-like fol	5e-57
3lst_A	348	CALO1 methyltransferase; calicheamicin, enediyne,	3e-56
1qzz_A	374	RDMB, aclacinomycin-10-hydroxylase; anthracycline,	5e-55
3gwz_A	369	MMCR; methyltransferase, mitomycin, S-adenosyl met	7e-55
1tw3_A	360	COMT, carminomycin 4-O-methyltransferase; anthracy	2e-54
2ip2_A	334	Probable phenazine-specific methyltransferase; pyo	6e-49
1x19_A	359	CRTF-related protein; methyltransferase, bacterioc	1e-38
2r3s_A	335	Uncharacterized protein; methyltransferase domain,	2e-36
3dp7_A	363	SAM-dependent methyltransferase; structural genomi	3e-33
3mcz_A	352	O-methyltransferase; adomet_mtases, S-adenosylmeth	3e-31

>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 =  224 bits (572), Expect = 2e-72
 Identities = 117/248 (47%), Positives = 160/248 (64%), Gaps = 20/248 (8%)

Query: 1   MQPAMSIVLPAAMQAASELGVFEIIAKAG-PTAKISAVEIAAQMPSSNPNAAVMLDRILR 59
           MQ A + VLP A++AA EL V EI+AK+  P+  IS  EIAAQ+P++NP A VMLDR+LR
Sbjct: 26  MQLASAAVLPMALKAAIELDVLEIMAKSVPPSGYISPAEIAAQLPTTNPEAPVMLDRVLR 85

Query: 60  LLVTHRVLRCT----SAGDDQRLYGLAHVAKYFVLNRDGVSLCPS----------RPWLE 105
           LL ++ V+  T     +G  +RLYGLA V K+   N DGVSL P            PW  
Sbjct: 86  LLASYSVVTYTLRELPSGKVERLYGLAPVCKFLTKNEDGVSLAPFLLLATDKVLLEPW-- 143

Query: 106 TKPYEIYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKG 165
              + + DA+LEGGI FNK +G   ++Y G D R N VFNK M ++++I   +I++   G
Sbjct: 144 ---FYLKDAILEGGIPFNKAYGMNIFDYHGTDHRINKVFNKGMSSNSTITMKKILEMYNG 200

Query: 166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIP 225
           FE +  +VDVGGG G   ++I++ Y  I  +NFDL HVIQD+ ++SGV+H+GG M + +P
Sbjct: 201 FEGLTTIVDVGGGTGAVASMIVAKYPSINAINFDLPHVIQDAPAFSGVEHLGGDMFDGVP 260

Query: 226 KGDAILIK 233
           KGDAI IK
Sbjct: 261 KGDAIFIK 268

>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 =  217 bits (553), Expect = 1e-69
 Identities = 97/246 (39%), Positives = 144/246 (58%), Gaps = 13/246 (5%)

Query: 1   MQPAMSIVLPAAMQAASELGVFEIIAKAG-PTAKISAVEIAAQMP--SSNPNAAVMLDRI 57
           M    ++V PA + AA +L +FEIIAKA  P A +S  EIA+++P  + + +    LDR+
Sbjct: 29  MVLTTNLVYPAVLNAAIDLNLFEIIAKATPPGAFMSPSEIASKLPASTQHSDLPNRLDRM 88

Query: 58  LRLLVTHRVLRCTSA----GDDQRLYGLAHVAKYFVLNRDGVSLCP-----SRPWLETKP 108
           LRLL ++ VL  T+     G  +R+YGL+ V KY V +     L         P L    
Sbjct: 89  LRLLASYSVLTSTTRTIEDGGAERVYGLSMVGKYLVPDESRGYLASFTTFLCYPALLQVW 148

Query: 109 YEIYDAVLEGGIS-FNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFE 167
               +AV++  I  F  VHG   YE+ G D + N +FNK+M++  +    R+++   GFE
Sbjct: 149 MNFKEAVVDEDIDLFKNVHGVTKYEFMGKDKKMNQIFNKSMVDVCATEMKRMLEIYTGFE 208

Query: 168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKG 227
            I  LVDVGGG G N+ +IIS Y  IKG+NFDL  VI+++   SG++H+GG M   +P+G
Sbjct: 209 GISTLVDVGGGSGRNLELIISKYPLIKGINFDLPQVIENAPPLSGIEHVGGDMFASVPQG 268

Query: 228 DAILIK 233
           DA+++K
Sbjct: 269 DAMILK 274

>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 =  215 bits (548), Expect = 6e-69
 Identities = 109/248 (43%), Positives = 149/248 (60%), Gaps = 21/248 (8%)

Query: 1   MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSS-NPNAAVMLDRILR 59
           +Q A S VLP  ++ A ELG+ EI+  AG  + ++  E+AA++PS+ NP A  M+DRILR
Sbjct: 25  LQLASSSVLPMTLKNAIELGLLEILVAAGGKS-LTPTEVAAKLPSAANPEAPDMVDRILR 83

Query: 60  LLVTHRVLRC----TSAGDDQRLYGLAHVAKYFVLNRDGVSLCP----------SRPWLE 105
           LL ++ V+ C       G   R YG A V K+   N DGVS+               W  
Sbjct: 84  LLASYNVVTCLVEEGKDGRLSRSYGAAPVCKFLTPNEDGVSMAALALMNQDKVLMESW-- 141

Query: 106 TKPYEIYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKG 165
              Y + DAVL+GGI FNK +G   +EY G D RFN VFN+ M NH+ I+T ++++   G
Sbjct: 142 ---YYLKDAVLDGGIPFNKAYGMSAFEYHGTDPRFNRVFNEGMKNHSIIITKKLLELYHG 198

Query: 166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIP 225
           FE +  LVDVGGG+G  V  I ++Y  IKGVNFDL HVI ++  + GV H+GG M + +P
Sbjct: 199 FEGLGTLVDVGGGVGATVAAIAAHYPTIKGVNFDLPHVISEAPQFPGVTHVGGDMFKEVP 258

Query: 226 KGDAILIK 233
            GD IL+K
Sbjct: 259 SGDTILMK 266

>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 =  204 bits (521), Expect = 4e-65
 Identities = 53/239 (22%), Positives = 106/239 (44%), Gaps = 12/239 (5%)

Query: 1   MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRL 60
            +   + +   +++ A E+ +  II   G    +S   + + +     +    + R++R 
Sbjct: 21  YKHIYAFIDSMSLKWAVEMNIPNIIQNHGKPISLS--NLVSILQV-PSSKIGNVRRLMRY 77

Query: 61  LVTHRVLRCTSAGDDQRLYGLAHVAKYFVLNRDGVSLCP-----SRPWLETKPYEIYDAV 115
           L  +          ++  Y L   ++  V   D   L P       P L    +E+   +
Sbjct: 78  LAHNGFFEII--TKEEESYALTVASELLVRGSDL-CLAPMVECVLDPTLSGSYHELKKWI 134

Query: 116 LEGGIS-FNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIKQLVD 174
            E  ++ F    G+GF+++   +  +N  FN AM + + ++   + D    F+ ++ +VD
Sbjct: 135 YEEDLTLFGVTLGSGFWDFLDKNPEYNTSFNDAMASDSKLINLALRDCDFVFDGLESIVD 194

Query: 175 VGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAILIK 233
           VGGG G    II   +  +K + FD   V+++ S  + + ++GG M   IP  DA+L+K
Sbjct: 195 VGGGTGTTAKIICETFPKLKCIVFDRPQVVENLSGSNNLTYVGGDMFTSIPNADAVLLK 253

>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 =  187 bits (476), Expect = 2e-58
 Identities = 56/248 (22%), Positives = 102/248 (41%), Gaps = 19/248 (7%)

Query: 1   MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRL 60
            +   + V   A+++A ELG+ + I   G     +  E+A+ +   +P+   +L R LRL
Sbjct: 15  YKHVYNFVSSMALKSAMELGIADAIHNHGKPM--TLSELASSLKL-HPSKVNILHRFLRL 71

Query: 61  LVTHRVLRCTSA------GDDQRLYGLAHVAKYFVLNRDGVSLCP-----SRPWLETKPY 109
           L  +     T         +++  Y L   +K  +  +    L         P       
Sbjct: 72  LTHNGFFAKTIVKGKEGDEEEEIAYSLTPPSKLLISGKPT-CLSSIVKGALHPSSLDMWS 130

Query: 110 EIYDAVLEGG--ISFNKVHGTGFYEYAGNDFRFN--GVFNKAMLNHTSIVTNRIIDSSKG 165
                  E      F    G  F+++   D   +   +F  AM + + +    + ++ + 
Sbjct: 131 SSKKWFNEDKEQTLFECATGESFWDFLNKDSESSTLSMFQDAMASDSRMFKLVLQENKRV 190

Query: 166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIP 225
           FE ++ LVDVGGG G    +I   + H+K   FD   V+ + +    +  +GG M + IP
Sbjct: 191 FEGLESLVDVGGGTGGVTKLIHEIFPHLKCTVFDQPQVVGNLTGNENLNFVGGDMFKSIP 250

Query: 226 KGDAILIK 233
             DA+L+K
Sbjct: 251 SADAVLLK 258

>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 =  183 bits (466), Expect = 5e-57
 Identities = 52/246 (21%), Positives = 100/246 (40%), Gaps = 26/246 (10%)

Query: 1   MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRL 60
           ++    +  P A++ A+ L V + IA AG     +A EIA+   +     A  LDR+LR 
Sbjct: 10  LRALADLATPMAVRVAATLRVADHIA-AGH---RTAAEIASAAGAH----ADSLDRLLRH 61

Query: 61  LVTHRVLRCTSAGDDQRLYGLAHVAKYFVLN-----RDGVSLCPSRPWLETKPYEIYDAV 115
           LV   +       D Q +YGL    +    +     R  + +  +    +    E+  ++
Sbjct: 62  LVAVGLFTR----DGQGVYGLTEFGEQLRDDHAAGKRKWLDMNSAVGRGDLGFVELAHSI 117

Query: 116 LEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIKQLVDV 175
             G  ++   +GT F+E  G+D   +  F+  M +H  +    I      +  +  +VDV
Sbjct: 118 RTGQPAYPVRYGTSFWEDLGSDPVLSASFDTLMSHHLELDYTGIAAKYD-WAALGHVVDV 176

Query: 176 GGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSY-------SGVKHIGGIMLERIPKG- 227
           GGG G  ++ +++ +  + G   DL      +             + + G   + +P G 
Sbjct: 177 GGGSGGLLSALLTAHEDLSGTVLDLQGPASAAHRRFLDTGLSGRAQVVVGSFFDPLPAGA 236

Query: 228 DAILIK 233
              ++ 
Sbjct: 237 GGYVLS 242

>3lst_A CALO1 methyltransferase; calicheamicin, enediyne, SAH, STRU genomics, PSI-2, protein structure initiative; HET: SAH; 2.40A {Micromonospora echinospora} Length = 348

 Score =  181 bits (462), Expect = 3e-56
 Identities = 49/248 (19%), Positives = 91/248 (36%), Gaps = 35/248 (14%)

Query: 1   MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRL 60
            + AM     AA++AA+ +GV + +   GP    +  E+AA   +     A  L R+LRL
Sbjct: 27  YEEAMGYTYAAALRAAAAVGVADHLV-DGP---RTPAELAAATGTD----ADALRRVLRL 78

Query: 61  LVTHRVLRCTSAGDDQRLYGLAHVAKYFVLNRDGVSLCPS----------RPWLETKPYE 110
           L    V+R          + L         +   V                       + 
Sbjct: 79  LAVRDVVRE-----SDGRFALTDKGAALR-SDSPVPARAGILMFTDTMFWTMS-----HR 127

Query: 111 IYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIK 170
           +  A+     +F  + G+    Y   D     ++ + M   ++     +  +   F    
Sbjct: 128 VASALGPERPAFADIFGSSLDAYFDGDAEVEALYYEGMETVSAAEHLILARA-GDFPATG 186

Query: 171 QLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVI----QDSSSYSG-VKHIGGIMLERIP 225
            + DVGGG G  +  ++  +  ++GV  D + V+     D+   +G  K + G  L  +P
Sbjct: 187 TVADVGGGRGGFLLTVLREHPGLQGVLLDRAEVVARHRLDAPDVAGRWKVVEGDFLREVP 246

Query: 226 KGDAILIK 233
             D  ++K
Sbjct: 247 HADVHVLK 254

>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 =  179 bits (456), Expect = 5e-55
 Identities = 41/246 (16%), Positives = 85/246 (34%), Gaps = 24/246 (9%)

Query: 1   MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRL 60
           ++   ++V P A++ A+ L + + +  AG     +   +A +  +        L R++R 
Sbjct: 21  LKNLGNLVTPMALRVAATLRLVDHLL-AGA---DTLAGLADRTDTH----PQALSRLVRH 72

Query: 61  LVTHRVLRCTSAGDDQRLYGLAHVAKYFVLNRDG-----VSLCPSRPWLETKPYEIYDAV 115
           L    VL         R      +               + L  +    +     + D V
Sbjct: 73  LTVVGVLEGGE--KQGRPLRPTRLGMLLADGHPAQQRAWLDLNGAVSHADLAFTGLLDVV 130

Query: 116 LEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIKQLVDV 175
             G  ++   +G  F+E    D      F+  M     +      D+   +  ++ ++DV
Sbjct: 131 RTGRPAYAGRYGRPFWEDLSADVALADSFDALMSCDEDLAYEAPADAYD-WSAVRHVLDV 189

Query: 176 GGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSY-------SGVKHIGGIMLERIPKG- 227
           GGG G  +  I     H++G   +L+   + +            V    G   + +P   
Sbjct: 190 GGGNGGMLAAIALRAPHLRGTLVELAGPAERARRRFADAGLADRVTVAEGDFFKPLPVTA 249

Query: 228 DAILIK 233
           D +L+ 
Sbjct: 250 DVVLLS 255

>3gwz_A MMCR; methyltransferase, mitomycin, S-adenosyl methionine, transferase; HET: MSE SAH; 1.91A {Streptomyces lavendulae} PDB: 3gxo_A* Length = 369

 Score =  178 bits (454), Expect = 7e-55
 Identities = 52/246 (21%), Positives = 94/246 (38%), Gaps = 26/246 (10%)

Query: 1   MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRL 60
                      A+  A ELGV E++ + GP    +A  +A    +        L R+LRL
Sbjct: 43  NDILQGAWKARAIHVAVELGVPELLQE-GP---RTATALAEATGAH----EQTLRRLLRL 94

Query: 61  LVTHRVLRCTSAGDDQRLYGLAHVAKYFVLNRDGVSLCP-----SRPWLETKPYEIYDAV 115
           L T  V           L+    ++   +       +       + PW      ++  +V
Sbjct: 95  LATVGVFDDL---GHDDLFAQNALSAVLL-PDPASPVATDARFQAAPWHWRAWEQLTHSV 150

Query: 116 LEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIKQLVDV 175
             G  SF+  +GT F++    D +   +FN+AM + +     ++  +   F      VD+
Sbjct: 151 RTGEASFDVANGTSFWQLTHEDPKARELFNRAMGSVSLTEAGQVAAAYD-FSGAATAVDI 209

Query: 176 GGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSY-------SGVKHIGGIMLERIPKG- 227
           GGG G  +  ++  +  ++G   +   V +++             + + G   E IP G 
Sbjct: 210 GGGRGSLMAAVLDAFPGLRGTLLERPPVAEEARELLTGRGLADRCEILPGDFFETIPDGA 269

Query: 228 DAILIK 233
           D  LIK
Sbjct: 270 DVYLIK 275

>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 =  177 bits (451), Expect = 2e-54
 Identities = 43/246 (17%), Positives = 89/246 (36%), Gaps = 26/246 (10%)

Query: 1   MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRL 60
           +    S+  P  ++ A+ L + + I  AG     +   +AA+  +        L R++R 
Sbjct: 24  LIRLGSLHTPMVVRTAATLRLVDHIL-AGA---RTVKALAARTDTR----PEALLRLIRH 75

Query: 61  LVTHRVLRCTSAGDDQRLYGLAHVAKYFVLNRDG-----VSLCPSRPWLETKPYEIYDAV 115
           LV   +L      D    +    V +    +          L  +    +     + DA+
Sbjct: 76  LVAIGLLEE----DAPGEFVPTEVGELLADDHPAAQRAWHDLTQAVARADISFTRLPDAI 131

Query: 116 LEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIKQLVDV 175
             G  ++  ++G  FYE           F+  +     +  +    +   +  ++ ++DV
Sbjct: 132 RTGRPTYESIYGKPFYEDLAGRPDLRASFDSLLACDQDVAFDAPAAAY-DWTNVRHVLDV 190

Query: 176 GGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSY-------SGVKHIGGIMLERIPKG- 227
           GGG G     I     H+     +++  +  + SY         V  + G   E +P+  
Sbjct: 191 GGGKGGFAAAIARRAPHVSATVLEMAGTVDTARSYLKDEGLSDRVDVVEGDFFEPLPRKA 250

Query: 228 DAILIK 233
           DAI++ 
Sbjct: 251 DAIILS 256

>2ip2_A Probable phenazine-specific methyltransferase; pyocyanin, phenazine-1-carboxy PHZM; 1.80A {Pseudomonas aeruginosa} Length = 334

 Score =  162 bits (412), Expect = 6e-49
 Identities = 52/248 (20%), Positives = 85/248 (34%), Gaps = 35/248 (14%)

Query: 1   MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRL 60
           +Q          +  A+ LG+ ++I   G     S   +AA + S     A  + R++RL
Sbjct: 13  IQVVTGEWKSRCVYVATRLGLADLIES-GI---DSDETLAAAVGSD----AERIHRLMRL 64

Query: 61  LVTHRVLRCTSAGDDQRLYGLAHVAKYFVLNRDGVSLCPSRPWLE--TKPY-----EIYD 113
           LV   + +     D +  Y     +               R  +    + +        +
Sbjct: 65  LVAFEIFQG----DTRDGYANTPTSHLLRDVEGSF-----RDMVLFYGEEFHAAWTPACE 115

Query: 114 AVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIKQLV 173
           A+L G   F    G  FY Y          F  AM   +++  + I      F   +  V
Sbjct: 116 ALLSGTPGFELAFGEDFYSYLKRCPDAGRRFLLAM-KASNLAFHEIPRL-LDFR-GRSFV 172

Query: 174 DVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSY-------SGVKHIGGIMLERIP- 225
           DVGGG G     I+      +GV  D    +  +            V  +GG ML+ +P 
Sbjct: 173 DVGGGSGELTKAILQAEPSARGVMLDREGSLGVARDNLSSLLAGERVSLVGGDMLQEVPS 232

Query: 226 KGDAILIK 233
            GD  L+ 
Sbjct: 233 NGDIYLLS 240

>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 =  135 bits (343), Expect = 1e-38
 Identities = 45/240 (18%), Positives = 88/240 (36%), Gaps = 33/240 (13%)

Query: 8   VLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVL 67
           +  + M+AA EL +F  +A+ GP        +AA   S        L+ +L  L   RV+
Sbjct: 43  IEFSCMKAAIELDLFSHMAE-GP---KDLATLAADTGSV----PPRLEMLLETLRQMRVI 94

Query: 68  RCTSAGDDQRLYGLAHVAKYFV------LNRDGVSLCPSRPWLETKPYEIYDAVLEGGIS 121
                  +   + L   A Y         N     +  +  +L    Y      + G  +
Sbjct: 95  NL-----EDGKWSLTEFADYMFSPTPKEPNLHQTPVAKAMAFLADDFYMGLSQAVRGQKN 149

Query: 122 FNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIKQLVDVGGGLGV 181
           F      G   Y       N  F +   ++       +++ +K  + +K+++DVGGG+G 
Sbjct: 150 FK-----GQVPYPPVTREDNLYFEEIHRSNAKFAIQLLLEEAK-LDGVKKMIDVGGGIGD 203

Query: 182 NVNIIISNYLHIKGVNFDLSHVIQDSSSYSG-------VKHIGGIML-ERIPKGDAILIK 233
               ++ ++  +     +L   I   +  +        ++ I   +  E  P+ DA+L  
Sbjct: 204 ISAAMLKHFPELDSTILNLPGAIDLVNENAAEKGVADRMRGIAVDIYKESYPEADAVLFC 263

>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 =  129 bits (327), Expect = 2e-36
 Identities = 37/247 (14%), Positives = 85/247 (34%), Gaps = 32/247 (12%)

Query: 1   MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRL 60
                +    AA++AA EL VF  I++   +++     +A +  +S       +  +   
Sbjct: 11  FNTVNAYQRSAAIKAAVELNVFTAISQGIESSQ----SLAQKCQTS----ERGMRMLCDY 62

Query: 61  LVTHRVLRCTSAGDDQRLYGLAHVAKYFVLNRDGVSLCP-----SRPWLETKPYEIYDAV 115
           LV    +   + G     Y L   +  F+  +    +         P +     ++  AV
Sbjct: 63  LVIIGFMTKQAEG-----YRLTSDSAMFLDRQSKFYVGDAIEFLLSPMITNGFNDLTAAV 117

Query: 116 LEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIKQLVDV 175
           L+GG + +               +F    +  M N   ++   + ++    E +K ++D+
Sbjct: 118 LKGGTAISSEGT--LSPEHPVWVQFAKAMSPMMANPAQLIAQLVNEN--KIEPLK-VLDI 172

Query: 176 GGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSG-------VKHIGGIMLER--IPK 226
               G+    +  +  + +    D + V++ +   +           I G   E      
Sbjct: 173 SASHGLFGIAVAQHNPNAEIFGVDWASVLEVAKENARIQGVASRYHTIAGSAFEVDYGND 232

Query: 227 GDAILIK 233
            D +L+ 
Sbjct: 233 YDLVLLP 239

>3dp7_A SAM-dependent methyltransferase; structural genomics, protein structure initiative, NEW YORK structural genomix research; 2.33A {Bacteroides vulgatus} Length = 363

 Score =  122 bits (307), Expect = 3e-33
 Identities = 39/253 (15%), Positives = 80/253 (31%), Gaps = 37/253 (14%)

Query: 1   MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRL 60
            + A   V+    +   + G+F++++        +  EI+ +   +   A      +L  
Sbjct: 20  QEIAFGPVVFQVSRLMLKFGIFQLLSGKREGY--TLQEISGRTGLT-RYA---AQVLLEA 73

Query: 61  LVTHRVLRCTSAGDDQRLYGLAHVAKYFVLNRDGVSLCPS-------RPWLETKPYEIYD 113
            +T   +      ++ R Y LA    +  LN     +          +       + + +
Sbjct: 74  SLTIGTILL----EEDR-YVLAKAGWFL-LNDKMARVNMEFNHDVNYQGL-----FHLEE 122

Query: 114 AVLEGGISFNKVHGTG--FYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIKQ 171
           A+L G     KV G     YE                 +  S  +             K+
Sbjct: 123 ALLNGRPEGLKVFGEWPTIYEGLSQLPEQVQKSWFGFDHFYSDQSFGKALEIVFSHHPKR 182

Query: 172 LVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSG-------VKHIGGIMLER- 223
           L+D+GG  G      +     ++    DL   ++     +        +   G  +L+R 
Sbjct: 183 LLDIGGNTGKWATQCVQYNKEVEVTIVDLPQQLEMMRKQTAGLSGSERIHGHGANLLDRD 242

Query: 224 --IPKG-DAILIK 233
              P G DA+ + 
Sbjct: 243 VPFPTGFDAVWMS 255

>3mcz_A O-methyltransferase; adomet_mtases, S-adenosylmethionine-dependent methyltransfer structural genomics, PSI-2; HET: MSE; 1.90A {Burkholderia thailandensis} Length = 352

 Score =  116 bits (292), Expect = 3e-31
 Identities = 29/250 (11%), Positives = 77/250 (30%), Gaps = 40/250 (16%)

Query: 1   MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRL 60
           ++ +      A +  A    +F++          +  E+AA               +L  
Sbjct: 29  VKLSDQYRQSAILHYAVADKLFDLTQTG-----RTPAEVAASFGMV----EGKAAILLHA 79

Query: 61  LVTHRVLRCTSAGDDQRLYGLAHVAKYFVLNRDGVSLCPSRPWLETKP------YEIYDA 114
           L    +L       +   +    + + ++       +    P +E +         + + 
Sbjct: 80  LAALGLLTK-----EGDAFRNTALTERYLTTTSADYI---GPIVEHQYLQWDNWPRLGEI 131

Query: 115 VLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIKQLVD 174
           +        K           +D R    FN AM+  +  + + + +    F + + ++D
Sbjct: 132 LRSE-----KPLAFQQESRFAHDTRARDAFNDAMVRLSQPMVDVVSELG-VFARARTVID 185

Query: 175 VGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSG-------VKHIGGIMLERIP-- 225
           + GG G  +  ++  +  + G  +DL      +            V+     +L+     
Sbjct: 186 LAGGHGTYLAQVLRRHPQLTGQIWDLPTTRDAARKTIHAHDLGGRVEFFEKNLLDARNFE 245

Query: 226 --KGDAILIK 233
               D +++ 
Sbjct: 246 GGAADVVMLN 255

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	233
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
3i53_A	332	O-methyltransferase; CO-complex, rossmann-like fol	100.0
3lst_A	348	CALO1 methyltransferase; calicheamicin, enediyne,	100.0
3gwz_A	369	MMCR; methyltransferase, mitomycin, S-adenosyl met	100.0
1zg3_A	358	Isoflavanone 4'-O-methyltransferase; rossman fold,	100.0
2ip2_A	334	Probable phenazine-specific methyltransferase; pyo	100.0
1fp1_D	372	Isoliquiritigenin 2'-O-methyltransferase; protein-	100.0
1fp2_A	352	Isoflavone O-methyltransferase; protein-product co	100.0
3dp7_A	363	SAM-dependent methyltransferase; structural genomi	100.0
1qzz_A	374	RDMB, aclacinomycin-10-hydroxylase; anthracycline,	100.0
1tw3_A	360	COMT, carminomycin 4-O-methyltransferase; anthracy	100.0
1x19_A	359	CRTF-related protein; methyltransferase, bacterioc	100.0
2r3s_A	335	Uncharacterized protein; methyltransferase domain,	100.0
3mcz_A	352	O-methyltransferase; adomet_mtases, S-adenosylmeth	100.0
2qm3_A	373	Predicted methyltransferase; putative methyltransf	99.45
1ve3_A	227	Hypothetical protein PH0226; dimer, riken structur	98.72
4gek_A	261	TRNA (CMO5U34)-methyltransferase; structural genom	98.7
3dtn_A	234	Putative methyltransferase MM_2633; structural gen	98.63
1yb2_A	275	Hypothetical protein TA0852; structural genomics,	98.58
3mb5_A	255	SAM-dependent methyltransferase; RNA methyltransfe	98.56
3vc1_A	312	Geranyl diphosphate 2-C-methyltransferase; rossman	98.56
3kr9_A	225	SAM-dependent methyltransferase; class I rossmann-	98.56
3e05_A	204	Precorrin-6Y C5,15-methyltransferase (decarboxyla;	98.55
3dlc_A	219	Putative S-adenosyl-L-methionine-dependent methylt	98.55
1yzh_A	214	TRNA (guanine-N(7)-)-methyltransferase; alpha-beta	98.54
3ege_A	261	Putative methyltransferase from antibiotic biosyn	98.51
3dh0_A	219	SAM dependent methyltransferase; cystal structure,	98.49
3mq2_A	218	16S rRNA methyltransferase; methyltranferase, ribo	98.48
1vl5_A	260	Unknown conserved protein BH2331; putative methylt	98.47
3lec_A	230	NADB-rossmann superfamily protein; PSI, MCSG, stru	98.46
3bus_A	273	REBM, methyltransferase; rebeccamycin synthesis; H	98.46
3f4k_A	257	Putative methyltransferase; structural genomics, P	98.46
1jsx_A	207	Glucose-inhibited division protein B; methyltransf	98.46
3ou2_A	218	SAM-dependent methyltransferase; O-methyltransfera	98.45
3ujc_A	266	Phosphoethanolamine N-methyltransferase; parasite;	98.44
2fca_A	213	TRNA (guanine-N(7)-)-methyltransferase; 2.10A {Bac	98.44
3g5l_A	253	Putative S-adenosylmethionine dependent methyltran	98.44
2o57_A	297	Putative sarcosine dimethylglycine methyltransfera	98.43
2qe6_A	274	Uncharacterized protein TFU_2867; putative methylt	98.43
2p35_A	259	Trans-aconitate 2-methyltransferase; SAM dependent	98.43
3gnl_A	244	Uncharacterized protein, DUF633, LMOF2365_1472; st	98.43
3mgg_A	276	Methyltransferase; NYSGXRC, PSI-II, protein struct	98.43
3kkz_A	267	Uncharacterized protein Q5LES9; putative methyltra	98.43
2pwy_A	258	TRNA (adenine-N(1)-)-methyltransferase; mtase, ado	98.4
1nv8_A	284	HEMK protein; class I adoMet-dependent methyltrans	98.4
1nkv_A	256	Hypothetical protein YJHP; structural genomics, PS	98.4
3uwp_A	438	Histone-lysine N-methyltransferase, H3 lysine-79;	98.4
3g07_A	292	7SK snRNA methylphosphate capping enzyme; structur	98.39
3jwg_A	219	HEN1, methyltransferase type 12; 1.90A {Clostridiu	98.39
3jwh_A	217	HEN1; methyltransferase; HET: SAH; 2.20A {Anabaena	98.39
2b3t_A	276	Protein methyltransferase HEMK; translation termin	98.39
3hm2_A	178	Precorrin-6Y C5,15-methyltransferase; alpha-beta-s	98.38
3g5t_A	299	Trans-aconitate 3-methyltransferase; structural ge	98.37
3gu3_A	284	Methyltransferase; alpha-beta protein, structural	98.36
4dzr_A	215	Protein-(glutamine-N5) methyltransferase, release	98.36
3pfg_A	263	N-methyltransferase; N,N-dimethyltransferase, SAM	98.36
3dxy_A	218	TRNA (guanine-N(7)-)-methyltransferase; rossmann f	98.36
4dcm_A	375	Ribosomal RNA large subunit methyltransferase G; 2	98.35
2yxd_A	183	Probable cobalt-precorrin-6Y C(15)-methyltransfer	98.35
3b3j_A	480	Histone-arginine methyltransferase CARM1; protein	98.35
3bkw_A	243	MLL3908 protein, S-adenosylmethionine dependent me	98.35
3ntv_A	232	MW1564 protein; rossmann fold, putative methyltran	98.35
4hg2_A	257	Methyltransferase type 11; structural genomics, PS	98.34
3q87_B	170	N6 adenine specific DNA methylase; SAM-methyltrans	98.32
1xxl_A	239	YCGJ protein; structural genomics, protein structu	98.31
3ckk_A	235	TRNA (guanine-N(7)-)-methyltransferase; mettl1, S-	98.31
3gjy_A	317	Spermidine synthase; APC62791, structural genomics	98.31
1xtp_A	254	LMAJ004091AAA; SGPP, structural genomics, PSI, pro	98.29
3dli_A	240	Methyltransferase; PSI-II, NYSGXRC, structural gen	98.29
1o54_A	277	SAM-dependent O-methyltransferase; TM0748, structu	98.29
3hem_A	302	Cyclopropane-fatty-acyl-phospholipid synthase 2; p	98.28
1i9g_A	280	Hypothetical protein RV2118C; mtase, adoMet, cryst	98.28
3ccf_A	279	Cyclopropane-fatty-acyl-phospholipid synthase; YP_	98.27
3cgg_A	195	SAM-dependent methyltransferase; NP_600671.1, meth	98.26
3njr_A	204	Precorrin-6Y methylase; methyltransferase, decarbo	98.26
3bxo_A	239	N,N-dimethyltransferase; desosamine, sugar, carboh	98.25
3q7e_A	349	Protein arginine N-methyltransferase 1; HET: SAH;	98.25
1pjz_A	203	Thiopurine S-methyltransferase; polymorphism, S-ad	98.25
3hnr_A	220	Probable methyltransferase BT9727_4108; structural	98.24
3bkx_A	275	SAM-dependent methyltransferase; YP_807781.1, cycl	98.23
3ocj_A	305	Putative exported protein; structural genomics, PS	98.23
3g2m_A	299	PCZA361.24; SAM-dependent methyltransferase, glyco	98.23
2h00_A	254	Methyltransferase 10 domain containing protein; st	98.22
2yqz_A	263	Hypothetical protein TTHA0223; RNA methyltransfera	98.21
2plw_A	201	Ribosomal RNA methyltransferase, putative; malaria	98.21
1jg1_A	235	PIMT;, protein-L-isoaspartate O-methyltransferase;	98.2
2vdv_E	246	TRNA (guanine-N(7)-)-methyltransferase; S-adenosyl	98.2
1wzn_A	252	SAM-dependent methyltransferase; structural genomi	98.2
2fyt_A	340	Protein arginine N-methyltransferase 3; structural	98.19
3adn_A	294	Spermidine synthase; aminopropyltransferase, polya	98.19
1dus_A	194	MJ0882; hypothetical protein, methanococcus jannas	98.19
3fzg_A	200	16S rRNA methylase; methyltransferase, plasmid, tr	98.19
3fpf_A	298	Mtnas, putative uncharacterized protein; thermonic	98.19
4fsd_A	383	Arsenic methyltransferase; rossmann fold; 1.75A {C	98.19
2xvm_A	199	Tellurite resistance protein TEHB; antibiotic resi	98.18
2ozv_A	260	Hypothetical protein ATU0636; structural genomics,	98.18
3duw_A	223	OMT, O-methyltransferase, putative; alternating of	98.18
1xdz_A	240	Methyltransferase GIDB; MCSG, protein structure in	98.17
2gpy_A	233	O-methyltransferase; structural genomics, PSI, pro	98.17
3l8d_A	242	Methyltransferase; structural genomics, PSI, nysgr	98.17
4htf_A	285	S-adenosylmethionine-dependent methyltransferase;	98.17
3tfw_A	248	Putative O-methyltransferase; PSI-biology, nysgrc,	98.17
3h2b_A	203	SAM-dependent methyltransferase; alpha-beta protei	98.16
2yxe_A	215	Protein-L-isoaspartate O-methyltransferase; rossma	98.16
2esr_A	177	Methyltransferase; structural genomics, hypothetic	98.16
3orh_A	236	Guanidinoacetate N-methyltransferase; structura ge	98.15
3tma_A	354	Methyltransferase; thump domain; 2.05A {Thermus th	98.15
2pxx_A	215	Uncharacterized protein MGC2408; structural genomi	98.15
1kpg_A	287	CFA synthase;, cyclopropane-fatty-acyl-phospholipi	98.15
2pjd_A	343	Ribosomal RNA small subunit methyltransferase C; g	98.14
3grz_A	205	L11 mtase, ribosomal protein L11 methyltransferase	98.13
1fbn_A	230	MJ fibrillarin homologue; MJ proteins, ribosomal R	98.13
2p7i_A	250	Hypothetical protein; putative methyltransferase,	98.12
3lpm_A	259	Putative methyltransferase; structural genomics, p	98.12
3tr6_A	225	O-methyltransferase; cellular processes; HET: SAH;	98.12
3eey_A	197	Putative rRNA methylase; rRNA methylation, S-adeno	98.11
3lbf_A	210	Protein-L-isoaspartate O-methyltransferase; modifi	98.11
3i9f_A	170	Putative type 11 methyltransferase; structural gen	98.11
2ipx_A	233	RRNA 2'-O-methyltransferase fibrillarin; FBL, stru	98.11
2fhp_A	187	Methylase, putative; alpha-beta-alpha sandwich, st	98.1
1zq9_A	285	Probable dimethyladenosine transferase; SGC, struc	98.09
3u81_A	221	Catechol O-methyltransferase; neurotransmitter deg	98.09
3d2l_A	243	SAM-dependent methyltransferase; ZP_00538691.1, st	98.09
3g89_A	249	Ribosomal RNA small subunit methyltransferase G; 1	98.08
2avd_A	229	Catechol-O-methyltransferase; structural genomics,	98.08
2bm8_A	236	Cephalosporin hydroxylase CMCI; cephamycin biosynt	98.08
2fk8_A	318	Methoxy mycolic acid synthase 4; S-adenosylmethion	98.08
1qam_A	244	ERMC' methyltransferase; rRNA methyltransferase ER	98.08
2y1w_A	348	Histone-arginine methyltransferase CARM1; histone	98.08
3p2e_A	225	16S rRNA methylase; methyltransferase, transferase	98.07
3m33_A	226	Uncharacterized protein; structural genomics, PSI-	98.07
3gru_A	295	Dimethyladenosine transferase; rossman fold, ribos	98.07
1m6y_A	301	S-adenosyl-methyltransferase MRAW; SAM-dependent m	98.07
1g6q_1	328	HnRNP arginine N-methyltransferase; SAM-binding do	98.07
1iy9_A	275	Spermidine synthase; rossmann fold, structural gen	98.06
1nt2_A	210	Fibrillarin-like PRE-rRNA processing protein; adeM	98.06
1p91_A	269	Ribosomal RNA large subunit methyltransferase A; R	98.05
1ej0_A	180	FTSJ; methyltransferase, adoMet, adenosyl methioni	98.05
3ofk_A	216	Nodulation protein S; NODS, N-methyltransferase, S	98.04
1ne2_A	200	Hypothetical protein TA1320; structural genomics,	98.04
3ggd_A	245	SAM-dependent methyltransferase; YP_325210.1, stru	98.04
2b25_A	336	Hypothetical protein; structural genomics, methyl	98.04
3mti_A	185	RRNA methylase; SAM-dependent, PSI, MCSG, structur	98.04
3sm3_A	235	SAM-dependent methyltransferases; NESG, structural	98.03
3c3p_A	210	Methyltransferase; NP_951602.1, structural genomic	98.03
2frn_A	278	Hypothetical protein PH0793; structural genomics,	98.02
2yvl_A	248	TRMI protein, hypothetical protein; tRNA, methyltr	98.02
1g8a_A	227	Fibrillarin-like PRE-rRNA processing protein; rRNA	98.02
3a27_A	272	TYW2, uncharacterized protein MJ1557; wybutosine m	98.01
3e23_A	211	Uncharacterized protein RPA2492; alpha-beta protei	98.01
3frh_A	253	16S rRNA methylase; methyltransferase domain, heli	98.0
3uzu_A	279	Ribosomal RNA small subunit methyltransferase A; s	98.0
3p9n_A	189	Possible methyltransferase (methylase); RV2966C, a	98.0
1l3i_A	192	Precorrin-6Y methyltransferase/putative decarboxyl	97.99
3lcc_A	235	Putative methyl chloride transferase; halide methy	97.99
3thr_A	293	Glycine N-methyltransferase; GNMT, folate, methylt	97.99
3cc8_A	230	Putative methyltransferase; structural genomics, j	97.98
1dl5_A	317	Protein-L-isoaspartate O-methyltransferase; isoasp	97.98
1y8c_A	246	S-adenosylmethionine-dependent methyltransferase;	97.98
3r0q_C	376	Probable protein arginine N-methyltransferase 4.2;	97.97
1zx0_A	236	Guanidinoacetate N-methyltransferase; structural g	97.97
2hnk_A	239	SAM-dependent O-methyltransferase; modified rossma	97.97
3r3h_A	242	O-methyltransferase, SAM-dependent; structural gen	97.96
1sui_A	247	Caffeoyl-COA O-methyltransferase; rossmann fold, p	97.96
4hc4_A	376	Protein arginine N-methyltransferase 6; HRMT1L6, S	97.96
3m70_A	286	Tellurite resistance protein TEHB homolog; structu	97.96
1xj5_A	334	Spermidine synthase 1; structural genomics, protei	97.96
3ftd_A	249	Dimethyladenosine transferase; KSGA, rossmann-like	97.96
3c3y_A	237	Pfomt, O-methyltransferase; plant secondary metabo	97.96
2gb4_A	252	Thiopurine S-methyltransferase; 18204406, thiopuri	97.96
3dr5_A	221	Putative O-methyltransferase; Q8NRD3, CGL1119, PF0	97.95
3gdh_A	241	Trimethylguanosine synthase homolog; M7G, CAP, dim	97.95
2o07_A	304	Spermidine synthase; structural genomics, structur	97.95
1vbf_A	231	231AA long hypothetical protein-L-isoaspartate O-	97.94
2h1r_A	299	Dimethyladenosine transferase, putative; SGC toron	97.94
3tm4_A	373	TRNA (guanine N2-)-methyltransferase TRM14; rossma	97.93
2nxc_A	254	L11 mtase, ribosomal protein L11 methyltransferase	97.93
2fpo_A	202	Methylase YHHF; structural genomics, putative meth	97.93
1o9g_A	250	RRNA methyltransferase; antibiotic resistance, Se-	97.93
3fut_A	271	Dimethyladenosine transferase; methyltransferase,	97.93
1inl_A	296	Spermidine synthase; beta-barrel, rossman fold, st	97.92
3evz_A	230	Methyltransferase; NYSGXRC, NEW YORK SGX research	97.92
2ex4_A	241	Adrenal gland protein AD-003; methyltransferase, s	97.91
3bwc_A	304	Spermidine synthase; SAM, SGPP, structura genomics	97.91
2pt6_A	321	Spermidine synthase; transferase, structural genom	97.9
3e8s_A	227	Putative SAM dependent methyltransferase; NP_74470	97.9
3htx_A	950	HEN1; HEN1, small RNA methyltransferase, protein-R	97.9
2kw5_A	202	SLR1183 protein; structural genomics, northeast st	97.89
1u2z_A	433	Histone-lysine N-methyltransferase, H3 lysine-79 s	97.88
2p8j_A	209	S-adenosylmethionine-dependent methyltransferase;	97.88
1ws6_A	171	Methyltransferase; structural genomics, riken stru	97.88
2ih2_A	421	Modification methylase TAQI; DNA, DNA methyltransf	97.88
1uir_A	314	Polyamine aminopropyltransferase; spermidien synth	97.87
1wy7_A	207	Hypothetical protein PH1948; seven-stranded beta s	97.86
3dou_A	191	Ribosomal RNA large subunit methyltransferase J; c	97.86
3tqs_A	255	Ribosomal RNA small subunit methyltransferase A; p	97.85
2cmg_A	262	Spermidine synthase; transferase, putrescine amino	97.85
2i7c_A	283	Spermidine synthase; transferase, structural genom	97.85
2b2c_A	314	Spermidine synthase; beta-alpha, transferase; 2.50	97.84
3k0b_A	393	Predicted N6-adenine-specific DNA methylase; methy	97.83
1r18_A	227	Protein-L-isoaspartate(D-aspartate)-O-methyltrans;	97.83
1mjf_A	281	Spermidine synthase; spermidine synthetase, struct	97.82
3ldu_A	385	Putative methylase; structural genomics, PSI-2, pr	97.81
1ri5_A	298	MRNA capping enzyme; methyltransferase, M7G, messe	97.81
2ift_A	201	Putative methylase HI0767; NESG, Y767_haein, struc	97.8
2pbf_A	227	Protein-L-isoaspartate O-methyltransferase beta-A	97.79
2zfu_A	215	Nucleomethylin, cerebral protein 1; nucleolar prot	97.78
3cbg_A	232	O-methyltransferase; cyanobacterium; HET: SAH FER	97.77
3ldg_A	384	Putative uncharacterized protein SMU.472; YPSC, me	97.76
1qyr_A	252	KSGA, high level kasugamycin resistance protein, S	97.76
1yub_A	245	Ermam, rRNA methyltransferase; MLS antibiotics; NM	97.74
1uwv_A	433	23S rRNA (uracil-5-)-methyltransferase RUMA; RNA m	97.73
2gs9_A	211	Hypothetical protein TT1324; methyl transferase, s	97.73
3bgv_A	313	MRNA CAP guanine-N7 methyltransferase; alternative	97.72
3b73_A	111	PHIH1 repressor-like protein; winged-helix-turn-he	97.72
1vlm_A	219	SAM-dependent methyltransferase; possible histamin	97.71
1i1n_A	226	Protein-L-isoaspartate O-methyltransferase; S-aden	97.69
2nyu_A	196	Putative ribosomal RNA methyltransferase 2; SAM, s	97.69
1af7_A	274	Chemotaxis receptor methyltransferase CHER; chemot	97.68
3lcv_B	281	Sisomicin-gentamicin resistance methylase SGM; ant	97.68
2avn_A	260	Ubiquinone/menaquinone biosynthesis methyltransfe	97.67
3k6r_A	278	Putative transferase PH0793; structural genomics,	97.64
2oxt_A	265	Nucleoside-2'-O-methyltransferase; flavivirus, vir	97.61
1ixk_A	315	Methyltransferase; open beta sheet; 1.90A {Pyrococ	97.61
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	97.61
3iv6_A	261	Putative Zn-dependent alcohol dehydrogenase; alpha	97.61
2wa2_A	276	Non-structural protein 5; transferase, S-adenosyl-	97.6
3o4f_A	294	Spermidine synthase; aminopropyltransferase, polya	97.59
2r6z_A	258	UPF0341 protein in RSP 3' region; alpha-beta prote	97.54
3ajd_A	274	Putative methyltransferase MJ0026; tRNA, M5C, ross	97.54
1y0u_A	96	Arsenical resistance operon repressor, putative; s	97.51
3sso_A	419	Methyltransferase; macrolide, natural product, ros	97.51
3dmg_A	381	Probable ribosomal RNA small subunit methyltransf;	97.5
2p41_A	305	Type II methyltransferase; vizier, viral enzymes i	97.43
4df3_A	233	Fibrillarin-like rRNA/TRNA 2'-O-methyltransferase;	97.4
2qfm_A	364	Spermine synthase; spermidine aminopropyltransfera	97.39
3id6_C	232	Fibrillarin-like rRNA/TRNA 2'-O-methyltransferase;	97.38
4gqb_A	637	Protein arginine N-methyltransferase 5; TIM barrel	97.34
2igt_A	332	SAM dependent methyltransferase; alpha-beta sandwi	97.34
2f8l_A	344	Hypothetical protein LMO1582; structural genomics,	97.34
2yx1_A	336	Hypothetical protein MJ0883; methyl transferase, t	97.33
2jjq_A	425	Uncharacterized RNA methyltransferase pyrab10780;	97.32
3bzb_A	281	Uncharacterized protein; RED ALGA, protein structu	97.31
3giw_A	277	Protein of unknown function DUF574; rossmann-fold	97.31
2i62_A	265	Nicotinamide N-methyltransferase; structural genom	97.29
2yxl_A	450	PH0851 protein, 450AA long hypothetical FMU protei	97.28
3mq0_A	275	Transcriptional repressor of the blcabc operon; he	97.28
4azs_A	569	Methyltransferase WBDD; kinase; HET: AMP SAM; 2.15	97.27
1wg8_A	285	Predicted S-adenosylmethionine-dependent methyltra	97.25
1xmk_A	79	Double-stranded RNA-specific adenosine deaminase;	97.24
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	97.22
2b78_A	385	Hypothetical protein SMU.776; structure genomics,	97.15
2oyr_A	258	UPF0341 protein YHIQ; alpha-beta protein, structur	97.09
1ub9_A	100	Hypothetical protein PH1061; helix-turn-helix moti	97.07
3v97_A	703	Ribosomal RNA large subunit methyltransferase L; Y	97.07
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	97.07
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	97.06
3ll7_A	410	Putative methyltransferase; methytransferase, stru	97.05
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	97.03
1sqg_A	429	SUN protein, FMU protein; rossmann-fold, mixed bet	97.02
2as0_A	396	Hypothetical protein PH1915; RNA methyltransferase	97.02
1mkm_A	249	ICLR transcriptional regulator; structural genomic	97.01
1wxx_A	382	TT1595, hypothetical protein TTHA1280; thermus the	96.99
2xrn_A	241	HTH-type transcriptional regulator TTGV; DNA-bindi	96.96
2vdw_A	302	Vaccinia virus capping enzyme D1 subunit; nucleoti	96.94
1r7j_A	95	Conserved hypothetical protein SSO10A; winged heli	96.92
3jth_A	98	Transcription activator HLYU; transcription factor	96.92
1u2w_A	122	CADC repressor, cadmium efflux system accessory pr	96.91
3f6o_A	118	Probable transcriptional regulator, ARSR family pr	96.9
2okc_A	445	Type I restriction enzyme stysji M protein; NP_813	96.89
3bt7_A	369	TRNA (uracil-5-)-methyltransferase; methyluridine,	96.88
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	96.87
4auk_A	375	Ribosomal RNA large subunit methyltransferase M; Y	96.86
1on2_A	142	Transcriptional regulator MNTR; helix-turn-helix,	96.85
3ua3_A	745	Protein arginine N-methyltransferase 5; TIM-barrel	96.83
3df8_A	111	Possible HXLR family transcriptional factor; APC89	96.81
4e2x_A	416	TCAB9; kijanose, tetronitrose, tetradeoxy sugar, s	96.79
3c0k_A	396	UPF0064 protein YCCW; PUA domain, adoMet dependent	96.79
2y75_A	129	HTH-type transcriptional regulator CYMR; DNA bindi	96.78
3r4k_A	260	Transcriptional regulator, ICLR family; DNA/RNA-bi	96.77
1tbx_A	99	ORF F-93, hypothetical 11.0 kDa protein; sulfolobu	96.77
2aot_A	292	HMT, histamine N-methyltransferase; classic methyl	96.72
3m6w_A	464	RRNA methylase; rRNA methyltransferase, 5-methylcy	96.72
2b9e_A	309	NOL1/NOP2/SUN domain family, member 5 isoform 2; m	96.71
2wte_A	244	CSA3; antiviral protein, viral resistance, winged	96.71
3v97_A	703	Ribosomal RNA large subunit methyltransferase L; Y	96.7
3tka_A	347	Ribosomal RNA small subunit methyltransferase H; H	96.7
3f6v_A	151	Possible transcriptional regulator, ARSR family pr	96.7
2g72_A	289	Phenylethanolamine N-methyltransferase; HET: SAM F	96.69
2a14_A	263	Indolethylamine N-methyltransferase; SGC,INMT, str	96.68
2jsc_A	118	Transcriptional regulator RV1994C/MT2050; cadmium,	96.67
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	96.66
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	96.65
2o0y_A	260	Transcriptional regulator; ICLR-family, structural	96.63
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	96.63
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	96.61
2hzt_A	107	Putative HTH-type transcriptional regulator YTCD;	96.6
2g7u_A	257	Transcriptional regulator; ICLR family, structural	96.59
4dmg_A	393	Putative uncharacterized protein TTHA1493; rRNA, m	96.58
3hp7_A	291	Hemolysin, putative; structural genomics, APC64019	96.55
3opn_A	232	Putative hemolysin; structural genomics, PSI-2, pr	96.55
3m4x_A	456	NOL1/NOP2/SUN family protein; mtase domain, PUA do	96.54
2kko_A	108	Possible transcriptional regulatory protein (possi	96.54
2k4m_A	153	TR8_protein, UPF0146 protein MTH_1000; alpha+beta,	96.54
2frx_A	479	Hypothetical protein YEBU; rossmann-type S-adenosy	96.51
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	96.5
1z7u_A	112	Hypothetical protein EF0647; winged-helix-turn-hel	96.46
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	96.46
4a5n_A	131	Uncharacterized HTH-type transcriptional regulato;	96.44
2pg4_A	95	Uncharacterized protein; structural genomics, join	96.43
3bja_A	139	Transcriptional regulator, MARR family, putative;	96.34
3t8r_A	143	Staphylococcus aureus CYMR; transcriptional regula	96.34
3fm5_A	150	Transcriptional regulator; MCSG, PF04017, PSI, MAR	96.31
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	96.31
2dul_A	378	N(2),N(2)-dimethylguanosine tRNA methyltransferas;	96.3
2nnn_A	140	Probable transcriptional regulator; structural gen	96.3
3lwf_A	159	LIN1550 protein, putative transcriptional regulato	96.29
2fsw_A	107	PG_0823 protein; alpha-beta structure, helix-turn-	96.28
1yyv_A	131	Putative transcriptional regulator; reductive meth	96.27
2f2e_A	146	PA1607; transcription factor, helix-TRUN-helix, AP	96.27
2ia2_A	265	Putative transcriptional regulator; SAD, PSI-2, st	96.27
2hr3_A	147	Probable transcriptional regulator; MCSG, structur	96.27
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	96.27
3g3z_A	145	NMB1585, transcriptional regulator, MARR family; t	96.24
2xyq_A	290	Putative 2'-O-methyl transferase; transferase-vira	96.22
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	96.21
2h09_A	155	Transcriptional regulator MNTR; transcription regu	96.21
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	96.19
2gxg_A	146	146AA long hypothetical transcriptional regulator;	96.19
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	96.14
2eth_A	154	Transcriptional regulator, putative, MAR family; M	96.13
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	96.12
3k0l_A	162	Repressor protein; helix-turn-helix, structural ge	96.1
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	96.08
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	96.08
2obp_A	96	Putative DNA-binding protein; structural genomics,	96.08
1sfx_A	109	Conserved hypothetical protein AF2008; structural	96.06
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	96.05
3bj6_A	152	Transcriptional regulator, MARR family; helix-turn	96.04
3axs_A	392	Probable N(2),N(2)-dimethylguanosine tRNA methylt	96.04
3cdh_A	155	Transcriptional regulator, MARR family; helix-turn	96.03
2fbi_A	142	Probable transcriptional regulator; MARR, APC5816,	96.02
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	96.02
1lj9_A	144	Transcriptional regulator SLYA; HTH DNA binding pr	96.0
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	95.97
2a61_A	145	Transcriptional regulator TM0710; APC4350, MCSG, m	95.96
2nyx_A	168	Probable transcriptional regulatory protein, RV14;	95.95
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	95.9
1bja_A	95	Transcription regulatory protein MOTA; activation	95.88
3u1d_A	151	Uncharacterized protein; GNTR-superfamily, structu	95.88
3kp7_A	151	Transcriptional regulator TCAR; multiple drug resi	95.85
1ylf_A	149	RRF2 family protein; structural genomics, transcri	95.85
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	95.84
2pex_A	153	Transcriptional regulator OHRR; transcription regu	95.82
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	95.79
3e6m_A	161	MARR family transcriptional regulator; APC88769, s	95.74
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	95.72
2bv6_A	142	MGRA, HTH-type transcriptional regulator MGRA; mul	95.71
1s3j_A	155	YUSO protein; structural genomics, MARR transcript	95.71
3s2w_A	159	Transcriptional regulator, MARR family; structural	95.68
3cjn_A	162	Transcriptional regulator, MARR family; silicibact	95.65
3r0a_A	123	Putative transcriptional regulator; structural gen	95.64
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	95.62
1z91_A	147	Organic hydroperoxide resistance transcriptional;	95.61
3p8z_A	267	Mtase, non-structural protein 5; methyltransferase	95.59
3hsr_A	140	HTH-type transcriptional regulator SARZ; helix-tur	95.57
3k69_A	162	Putative transcription regulator; putative transcr	95.57
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	95.56
3boq_A	160	Transcriptional regulator, MARR family; MARR famil	95.54
2zkz_A	99	Transcriptional repressor PAGR; protein-DNA, HTH m	95.53
3c6k_A	381	Spermine synthase; spermidine aminopropyltransfera	95.51
2frh_A	127	SARA, staphylococcal accessory regulator A; winged	95.48
3deu_A	166	Transcriptional regulator SLYA; MARR, WING-helix,	95.48
3f3x_A	144	Transcriptional regulator, MARR family, putative;	95.46
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	95.45
3jw4_A	148	Transcriptional regulator, MARR/EMRR family; DNA-b	95.45
1xd7_A	145	YWNA; structural genomics, protein structure initi	95.45
4aik_A	151	Transcriptional regulator SLYA; transcription, tra	95.43
3b5i_A	374	S-adenosyl-L-methionine:salicylic acid carboxyl me	95.37
3hrs_A	214	Metalloregulator SCAR; DTXR/MNTR family member, tr	95.37
2fe3_A	145	Peroxide operon regulator; oxidative stress regula	95.36
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	95.34
2o03_A	131	Probable zinc uptake regulation protein FURB; DNA-	95.13
2fxa_A	207	Protease production regulatory protein HPR; protea	95.09
2p4w_A	202	Transcriptional regulatory protein ARSR family; ar	95.04
2px2_A	269	Genome polyprotein [contains: capsid protein C (co	95.0
3u2r_A	168	Regulatory protein MARR; structural genomics, PSI-	94.99
1rjd_A	334	PPM1P, carboxy methyl transferase for protein phos	94.87
3nqo_A	189	MARR-family transcriptional regulator; structural	94.8
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	94.71
2lnb_A	80	Z-DNA-binding protein 1; structural genomics, nort	94.7
1ku9_A	152	Hypothetical protein MJ223; putative transcription	94.69
2ar0_A	541	M.ecoki, type I restriction enzyme ecoki M protein	94.67
1okr_A	123	MECI, methicillin resistance regulatory protein ME	94.65
1i4w_A	353	Mitochondrial replication protein MTF1; mitochondr	94.59
2vn2_A	128	DNAD, chromosome replication initiation protein; D	94.54
2k4b_A	99	Transcriptional regulator; DNA binding protein, wi	94.54
2fbk_A	181	Transcriptional regulator, MARR family; winged-hel	94.53
2qlz_A	232	Transcription factor PF0095; 2.50A {Pyrococcus fur	94.51
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	94.35
2efj_A	384	3,7-dimethylxanthine methyltransferase; SAM-depend	94.32
3khk_A	544	Type I restriction-modification system methylation	94.29
3mwm_A	139	ZUR, putative metal uptake regulation protein; FUR	94.25
2w25_A	150	Probable transcriptional regulatory protein; trans	94.25
4b8x_A	147	SCO5413, possible MARR-transcriptional regulator;	94.17
4esf_A	117	PADR-like transcriptional regulator; PADR family,	94.07
3cta_A	230	Riboflavin kinase; structural genomics, transferas	94.03
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	94.02
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	93.99
2esh_A	118	Conserved hypothetical protein TM0937; APC5794, st	93.96
2xig_A	150	Ferric uptake regulation protein; hpfur, transcrip	93.94
1p6r_A	82	Penicillinase repressor; transcription regulation,	93.9
3lkd_A	542	Type I restriction-modification system methyltrans	93.9
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	93.84
4fx0_A	148	Probable transcriptional repressor protein; helix-	93.77
1m6e_X	359	S-adenosyl-L-methionnine:salicylic acid carboxyl m	93.7
3s1s_A	878	Restriction endonuclease bpusi; PD--(D/E)XK cataly	93.7
3elk_A	117	Putative transcriptional regulator TA0346; structu	93.52
1uly_A	192	Hypothetical protein PH1932; helix-turn-helix, str	93.51
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	93.49
3f8b_A	116	Transcriptional regulator, PADR-like family; winge	93.47
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	93.33
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	93.32
3gcz_A	282	Polyprotein; flavivirus, RNA capping, methyltransf	93.3
1fx7_A	230	Iron-dependent repressor IDER; DTXR, iron-dependen	93.28
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	93.26
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	93.24
3hhh_A	116	Transcriptional regulator, PADR family; PF03551, s	93.22
2qy6_A	257	UPF0209 protein YFCK; structural genomics, unknown	93.11
2dk5_A	91	DNA-directed RNA polymerase III 39 kDa polypeptide	93.06
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	92.93
3l7w_A	108	Putative uncharacterized protein SMU.1704; PADR, t	92.92
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	92.81
2p8t_A	200	Hypothetical protein PH0730; pyrococcus horikoshii	92.76
2qq9_A	226	Diphtheria toxin repressor; regulator, DTXR, helix	92.73
2v79_A	135	DNA replication protein DNAD; primosome, DNA-bindi	92.72
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	92.65
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	92.61
1j5y_A	187	Transcriptional regulator, biotin repressor famil;	92.57
2xvc_A	59	ESCRT-III, SSO0910; cell cycle, cell division, cyt	92.34
3lkz_A	321	Non-structural protein 5; flavivirus, methyltransf	92.3
1xma_A	145	Predicted transcriptional regulator; southea colla	92.1
1mzb_A	136	Ferric uptake regulation protein; ferric uptake re	92.01
1sfu_A	75	34L protein; protein/Z-DNA complex, DNA binding pr	91.72
3i71_A	68	Ethanolamine utilization protein EUTK; helix-turn-	91.64
3evf_A	277	RNA-directed RNA polymerase NS5; NS5 methyltransfe	91.6
2zig_A	297	TTHA0409, putative modification methylase; methylt	91.38
2wk1_A	282	NOVP; transferase, O-methyltransferase, novobiocin	91.32
1yg2_A	179	Gene activator APHA; virulence factor, winged heli	91.23
2g9w_A	138	Conserved hypothetical protein; DNA-binding domain	90.97
1hsj_A	487	Fusion protein consisting of staphylococcus access	90.83
2hoe_A	380	N-acetylglucosamine kinase; TM1224, structural gen	90.78
2uyo_A	310	Hypothetical protein ML2640; putative methyltransf	90.38
1jhg_A	101	Trp operon repressor; complex (regulatory protein-	90.26
4g6q_A	182	Putative uncharacterized protein; structural genom	90.22
1v4r_A	102	Transcriptional repressor; helix-turn-helix, winge	90.21
1zkd_A	387	DUF185; NESG, RPR58, structural genomics, PSI, pro	90.18
4esb_A	115	Transcriptional regulator, PADR family; DNA bindin	90.15
1sd4_A	126	Penicillinase repressor; BLAI, MECI, methicillin,	89.65
3eyy_A	145	Putative iron uptake regulatory protein; NUR, nick	89.4
1z6r_A	406	MLC protein; transcriptional repressor, ROK family	89.26
4ets_A	162	Ferric uptake regulation protein; metal binding pr	89.16
1cf7_A	76	Protein (transcription factor E2F-4); E2F, winged-	88.98
2o0m_A	345	Transcriptional regulator, SORC family; structural	88.9
2w57_A	150	Ferric uptake regulation protein; gene regulation,	88.75
2p5k_A	64	Arginine repressor; DNA-binding domain, winged hel	88.51
1bia_A	321	BIRA bifunctional protein; transcription regulatio	87.88
2vxz_A	165	Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Py	87.8
2pjp_A	121	Selenocysteine-specific elongation factor; SELB, p	87.79
3eld_A	300	Methyltransferase; flavivirus, RNA capping, guanyl	87.41
3lmm_A	583	Uncharacterized protein; multi-domained alpha-beta	87.13
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	86.96
1z05_A	429	Transcriptional regulator, ROK family; structural	86.89
2w48_A	315	Sorbitol operon regulator; SORC, activator, repres	86.48
2qlz_A	232	Transcription factor PF0095; 2.50A {Pyrococcus fur	85.37
2yu3_A	95	DNA-directed RNA polymerase III 39 kDa polypeptide	85.31
2ld4_A	176	Anamorsin; methyltransferase-like fold, alpha/beta	85.12
3ri2_A	123	Transcriptional regulator, PADR-like family; PSI-b	84.91
3eyi_A	72	Z-DNA-binding protein 1; alternative splicing, DNA	84.41
3iht_A	174	S-adenosyl-L-methionine methyl transferase; YP_165	83.8
2py6_A	409	Methyltransferase FKBM; YP_546752.1, structural ge	83.67
2dql_A	115	PEX protein; circadian clock associated protein, c	83.13
3cvo_A	202	Methyltransferase-like protein of unknown functio;	82.7
3maj_A	382	DNA processing chain A; MCSG, PSI-2, structural ge	82.41
2co5_A	99	Viral protein F93; viral protein-winged helix comp	81.78
2b0l_A	102	GTP-sensing transcriptional pleiotropic repressor;	81.77
3eqx_A	373	FIC domain containing transcriptional regulator; F	81.68
2ek5_A	129	Predicted transcriptional regulators; helix-turn-h	81.53
3tqn_A	113	Transcriptional regulator, GNTR family; regulatory	81.42
1lva_A	258	Selenocysteine-specific elongation factor; winged-	80.39
3rkx_A	323	Biotin-[acetyl-COA-carboxylase] ligase; biotin pro	80.14

>4a6d_A Hydroxyindole O-methyltransferase; melatonin, circadian clock; HET: SAM; 2.40A {Homo sapiens} PDB: 4a6e_A*

Probab=100.00  E-value=3.3e-44  Score=311.37  Aligned_cols=223  Identities=19%  Similarity=0.293  Sum_probs=198.2

Q ss_pred             cccccchHHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceec
Q 039903            2 QPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGL   81 (233)
Q Consensus         2 ~~~~~~~~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~l   81 (233)
                      +++.||+.|++|++|++|||||+|.+.+  +|+|++|||+++++    +++.++||||+|+++|+|++...+ ..++|++
T Consensus        14 ~l~~Gf~~s~~L~aa~eLglfd~L~~~~--~p~t~~eLA~~~g~----~~~~l~rlLr~L~~~gll~~~~~~-~~~~y~~   86 (353)
T 4a6d_A           14 DYANGFMVSQVLFAACELGVFDLLAEAP--GPLDVAAVAAGVRA----SAHGTELLLDICVSLKLLKVETRG-GKAFYRN   86 (353)
T ss_dssp             HHHHHHHHHHHHHHHHHHTHHHHHHHSS--SCBCHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEEEET-TEEEEEE
T ss_pred             HHHHHHHHHHHHHHHHHcCHHHHHhcCC--CCCCHHHHHHhhCc----CHHHHHHHHHHHHHCCCEEEeccC-ccceeeC
Confidence            6789999999999999999999999865  69999999999999    999999999999999999875322 3568999


Q ss_pred             cHhhhHhh-cCCCCCCccchhccccC----chhhHHHHHHcCCcchhhhhC---CccccccccCchHHHHHHHHHHhcch
Q 039903           82 AHVAKYFV-LNRDGVSLCPSRPWLET----KPYEIYDAVLEGGISFNKVHG---TGFYEYAGNDFRFNGVFNKAMLNHTS  153 (233)
Q Consensus        82 t~~s~~l~-~~~~~~~~~~~~~~~~~----~~~~L~~~l~~g~~~~~~~~g---~~~~~~~~~~~~~~~~f~~am~~~~~  153 (233)
                      |+.++.|+ .+++ .++.+++.+...    .|.+|++++++|+++|...+|   .++|+++.++|+....|+++|...+.
T Consensus        87 t~~s~~~l~~~~~-~~~~~~~~~~~~~~~~~~~~L~~~vr~g~~~~~~~~g~~~~~~~~~~~~~~~~~~~f~~aM~~~~~  165 (353)
T 4a6d_A           87 TELSSDYLTTVSP-TSQCSMLKYMGRTSYRCWGHLADAVREGRNQYLETFGVPAEELFTAIYRSEGERLQFMQALQEVWS  165 (353)
T ss_dssp             CHHHHHHHSTTST-TCCHHHHHHHHHTHHHHHTTHHHHHHHTSCCHHHHHSCCCSSHHHHHTSSHHHHHHHHHHHHTTHH
T ss_pred             CHHHHHHhhcCCc-hHHHHHHHHhCHHHHHHHHHHHHHHhcCCChhHHhcCCChHHHHHHHhhCHHHHHHHHHHHHHHHH
Confidence            99998755 4444 578888776543    789999999999999999888   36789999999999999999999998


Q ss_pred             hcHHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCC------CCceEEecCcCC-CCCC
Q 039903          154 IVTNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSY------SGVKHIGGIMLE-RIPK  226 (233)
Q Consensus       154 ~~~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~------~ri~~~~gD~f~-~~P~  226 (233)
                      ...+.+++.++ |++..+|||||||+|.++.+++++||+++++++|+|+|++.+++.      +||++++||||+ +.|.
T Consensus       166 ~~~~~~~~~~~-~~~~~~v~DvGgG~G~~~~~l~~~~p~~~~~~~dlp~v~~~a~~~~~~~~~~rv~~~~gD~~~~~~~~  244 (353)
T 4a6d_A          166 VNGRSVLTAFD-LSVFPLMCDLGGGAGALAKECMSLYPGCKITVFDIPEVVWTAKQHFSFQEEEQIDFQEGDFFKDPLPE  244 (353)
T ss_dssp             HHHHHHHHSSC-GGGCSEEEEETCTTSHHHHHHHHHCSSCEEEEEECHHHHHHHHHHSCC--CCSEEEEESCTTTSCCCC
T ss_pred             HHHHHHHHhcC-cccCCeEEeeCCCCCHHHHHHHHhCCCceeEeccCHHHHHHHHHhhhhcccCceeeecCccccCCCCC
Confidence            88889999998 999999999999999999999999999999999999999988652      799999999998 5666


Q ss_pred             CCEEEeC
Q 039903          227 GDAILIK  233 (233)
Q Consensus       227 ~D~~~lk  233 (233)
                      +|+|+++
T Consensus       245 ~D~~~~~  251 (353)
T 4a6d_A          245 ADLYILA  251 (353)
T ss_dssp             CSEEEEE
T ss_pred             ceEEEee
Confidence            8999985

>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=1.8e-41  Score=295.32  Aligned_cols=232  Identities=46%  Similarity=0.781  Sum_probs=202.1

Q ss_pred             CcccccchHHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCC-CCCCChhhHHHHHHHHhcCCceeeeccCC--C--
Q 039903            1 MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPS-SNPNAAVMLDRILRLLVTHRVLRCTSAGD--D--   75 (233)
Q Consensus         1 ~~~~~~~~~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~-~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~--   75 (233)
                      +++++|++.+++|++|++|||||+|.+.| ++|+|++|||+++++ .+|.++..++||||+|++.|+|++...++  +  
T Consensus        25 ~~l~~~~~~~~~l~~a~~Lgifd~L~~~g-~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~  103 (364)
T 3p9c_A           25 LQLASSSVLPMTLKNAIELGLLEILVAAG-GKSLTPTEVAAKLPSAANPEAPDMVDRILRLLASYNVVTCLVEEGKDGRL  103 (364)
T ss_dssp             HHHTTTTHHHHHHHHHHHHTHHHHHHHTT-TCCBCHHHHHHTTTCTTCTTHHHHHHHHHHHHHHTTSEEEEEEECSSSCE
T ss_pred             HHHHHhHHHHHHHHHHHHCChHHHHhhcC-CCCCCHHHHHHhcCCCCCccchhhHHHHHHHHHhCCCEEEeccccCCCCc
Confidence            36889999999999999999999999853 148999999999995 22223349999999999999999862100  1  


Q ss_pred             CCceeccHhhhHhhcCCCCCCccchhccccC-----chhhHHHHHHcCCcchhhhhCCccccccccCchHHHHHHHHHHh
Q 039903           76 QRLYGLAHVAKYFVLNRDGVSLCPSRPWLET-----KPYEIYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLN  150 (233)
Q Consensus        76 ~~~y~lt~~s~~l~~~~~~~~~~~~~~~~~~-----~~~~L~~~l~~g~~~~~~~~g~~~~~~~~~~~~~~~~f~~am~~  150 (233)
                      +++|++|+.++.|+.+.++.++++++.+..+     .|.+|++++++|+++|+..+|.++|+|+.++|+..+.|+++|..
T Consensus       104 ~~~y~~t~~s~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~~r~g~~~~~~~~g~~~~~~~~~~~~~~~~f~~~m~~  183 (364)
T 3p9c_A          104 SRSYGAAPVCKFLTPNEDGVSMAALALMNQDKVLMESWYYLKDAVLDGGIPFNKAYGMSAFEYHGTDPRFNRVFNEGMKN  183 (364)
T ss_dssp             EEEEEECGGGGGSSCCTTSCCTHHHHHHHTSHHHHGGGGGHHHHHHHCSCHHHHHHSSCHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CCEEecCHHHHHHcCCCCCCCHHHHHHHhcCHHHHHHHhCHHHHHhhCCChHHHhcCCCHHHHHHhCHHHHHHHHHHHHH
Confidence            4789999999998876543578888765433     89999999999999999999999999999999999999999999


Q ss_pred             cchhcHHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCCCCceEEecCcCCCCCCCCEE
Q 039903          151 HTSIVTNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAI  230 (233)
Q Consensus       151 ~~~~~~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~~ri~~~~gD~f~~~P~~D~~  230 (233)
                      .+....+.+++.+++|++..+|||||||+|.++..+++++|+++++++|+|++++.+++.+||+++.+|||+++|.+|+|
T Consensus       184 ~~~~~~~~~~~~~~~~~~~~~vlDvG~G~G~~~~~l~~~~p~~~~~~~D~~~~~~~a~~~~~v~~~~~D~~~~~p~~D~v  263 (364)
T 3p9c_A          184 HSIIITKKLLELYHGFEGLGTLVDVGGGVGATVAAIAAHYPTIKGVNFDLPHVISEAPQFPGVTHVGGDMFKEVPSGDTI  263 (364)
T ss_dssp             HHHHHHHHHHHHCCTTTTCSEEEEETCTTSHHHHHHHHHCTTCEEEEEECHHHHTTCCCCTTEEEEECCTTTCCCCCSEE
T ss_pred             hhHHHHHHHHHhcccccCCCEEEEeCCCCCHHHHHHHHHCCCCeEEEecCHHHHHhhhhcCCeEEEeCCcCCCCCCCCEE
Confidence            88887788888887688889999999999999999999999999999999999999998899999999999999988999


Q ss_pred             EeC
Q 039903          231 LIK  233 (233)
Q Consensus       231 ~lk  233 (233)
                      +++
T Consensus       264 ~~~  266 (364)
T 3p9c_A          264 LMK  266 (364)
T ss_dssp             EEE
T ss_pred             Eeh
Confidence            874

>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=2.6e-41  Score=294.68  Aligned_cols=233  Identities=49%  Similarity=0.801  Sum_probs=202.4

Q ss_pred             CcccccchHHHHHHHHHhhChhHHHHhc-CCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC-C---
Q 039903            1 MQPAMSIVLPAAMQAASELGVFEIIAKA-GPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD-D---   75 (233)
Q Consensus         1 ~~~~~~~~~s~~L~~a~~lglfd~L~~~-~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~-~---   75 (233)
                      ++++.|++.+++|++|++|||||+|++. |+++|+|++|||++++..+|.+++.++||||+|++.|+|++...++ .   
T Consensus        26 ~~l~~~~~~~~~l~~a~~Lglfd~L~~~~gp~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~g~~  105 (368)
T 3reo_A           26 MQLASAAVLPMALKAAIELDVLEIMAKSVPPSGYISPAEIAAQLPTTNPEAPVMLDRVLRLLASYSVVTYTLRELPSGKV  105 (368)
T ss_dssp             HHHHTTTHHHHHHHHHHHTTHHHHHHHHCCTTCCBCHHHHHTTSSCCCTTHHHHHHHHHHHHHHTTSEEEEEEECTTSCE
T ss_pred             HHHHHHHHHHHHHHHHHHCCchhHHhhcCCCCCCcCHHHHHHhcCcCCCcchhhHHHHHHHHHhCCCeEEecccCCCCcc
Confidence            3678999999999999999999999986 5446899999999998322223459999999999999999852100 1   


Q ss_pred             CCceeccHhhhHhhcCCCCCCccchhccccC-----chhhHHHHHHcCCcchhhhhCCccccccccCchHHHHHHHHHHh
Q 039903           76 QRLYGLAHVAKYFVLNRDGVSLCPSRPWLET-----KPYEIYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLN  150 (233)
Q Consensus        76 ~~~y~lt~~s~~l~~~~~~~~~~~~~~~~~~-----~~~~L~~~l~~g~~~~~~~~g~~~~~~~~~~~~~~~~f~~am~~  150 (233)
                      +++|++|+.++.|+.+..+.++++++.+..+     .|.+|++++++|+++|+..+|.++|+|+.++|+..+.|+++|..
T Consensus       106 ~~~y~~t~~s~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~r~g~~~~~~~~g~~~~~~~~~~~~~~~~f~~~m~~  185 (368)
T 3reo_A          106 ERLYGLAPVCKFLTKNEDGVSLAPFLLLATDKVLLEPWFYLKDAILEGGIPFNKAYGMNIFDYHGTDHRINKVFNKGMSS  185 (368)
T ss_dssp             EEEEEECTTHHHHSCCTTSCCSHHHHHHHTCHHHHGGGGGHHHHHHHCSCHHHHHSSSCHHHHHTTCHHHHHHHHHHHHH
T ss_pred             cceeCcCHHHHHHhCCCCCCCHHHHHHHhcCHHHHhhhhchHHHHhcCCCHHHHHhCCCHHHHHhhCHHHHHHHHHHHHh
Confidence            3789999999999876543578888765433     89999999999999999999999999999999999999999999


Q ss_pred             cchhcHHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCCCCceEEecCcCCCCCCCCEE
Q 039903          151 HTSIVTNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAI  230 (233)
Q Consensus       151 ~~~~~~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~~ri~~~~gD~f~~~P~~D~~  230 (233)
                      .+....+.+++.+++|++..+|||||||+|.++..+++++|+++++++|+|++++.+++.+||+++.+|||+++|.+|+|
T Consensus       186 ~~~~~~~~~~~~~~~~~~~~~vlDvG~G~G~~~~~l~~~~p~~~~~~~D~~~~~~~a~~~~~v~~~~~d~~~~~p~~D~v  265 (368)
T 3reo_A          186 NSTITMKKILEMYNGFEGLTTIVDVGGGTGAVASMIVAKYPSINAINFDLPHVIQDAPAFSGVEHLGGDMFDGVPKGDAI  265 (368)
T ss_dssp             HHHHHHHHHHTTCCTTTTCSEEEEETCTTSHHHHHHHHHCTTCEEEEEECHHHHTTCCCCTTEEEEECCTTTCCCCCSEE
T ss_pred             hhhhHHHHHHHhcccccCCCEEEEeCCCcCHHHHHHHHhCCCCEEEEEehHHHHHhhhhcCCCEEEecCCCCCCCCCCEE
Confidence            88887788888887688889999999999999999999999999999999999999998899999999999999988999


Q ss_pred             EeC
Q 039903          231 LIK  233 (233)
Q Consensus       231 ~lk  233 (233)
                      +++
T Consensus       266 ~~~  268 (368)
T 3reo_A          266 FIK  268 (368)
T ss_dssp             EEE
T ss_pred             EEe
Confidence            874

>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=2.3e-39  Score=278.37  Aligned_cols=219  Identities=21%  Similarity=0.310  Sum_probs=197.8

Q ss_pred             CcccccchHHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCcee
Q 039903            1 MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYG   80 (233)
Q Consensus         1 ~~~~~~~~~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~   80 (233)
                      ++++.||+.+++|++|++|||||.|.+    ||+|++|||+++++    +++.++||||+|++.|+++++    ++++|+
T Consensus        10 ~~~~~g~~~~~~l~~a~~lglf~~l~~----g~~t~~elA~~~~~----~~~~l~rlLr~l~~~gl~~~~----~~~~y~   77 (332)
T 3i53_A           10 LRALADLATPMAVRVAATLRVADHIAA----GHRTAAEIASAAGA----HADSLDRLLRHLVAVGLFTRD----GQGVYG   77 (332)
T ss_dssp             HHHHTCCHHHHHHHHHHHHTHHHHHHT----TCCBHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEC----TTSBEE
T ss_pred             HHHHHhhHHHHHHHHHHHcChHHHHhc----CCCCHHHHHHHHCc----CHHHHHHHHHHHHhCCcEEec----CCCeEE
Confidence            367899999999999999999999986    69999999999999    999999999999999999997    579999


Q ss_pred             ccHhhhHhhcCCCCCCccchhcccc------CchhhHHHHHHcCCcchhhhhCCccccccccCchHHHHHHHHHHhcchh
Q 039903           81 LAHVAKYFVLNRDGVSLCPSRPWLE------TKPYEIYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSI  154 (233)
Q Consensus        81 lt~~s~~l~~~~~~~~~~~~~~~~~------~~~~~L~~~l~~g~~~~~~~~g~~~~~~~~~~~~~~~~f~~am~~~~~~  154 (233)
                      +|+.++.|..+++ .++..++.+..      ..|.+|++++++|+++|+..+|.++|+|+.++|+..+.|+++|...+..
T Consensus        78 ~t~~s~~l~~~~~-~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~g~~~~~~~~~~~~~~~~f~~~m~~~~~~  156 (332)
T 3i53_A           78 LTEFGEQLRDDHA-AGKRKWLDMNSAVGRGDLGFVELAHSIRTGQPAYPVRYGTSFWEDLGSDPVLSASFDTLMSHHLEL  156 (332)
T ss_dssp             ECTTGGGGSTTCT-TCCHHHHCTTSHHHHHGGGGGGHHHHHHHSSCSHHHHHSSCHHHHHHHCHHHHHHHHHHHHHHHHH
T ss_pred             cCHhHHHHhcCCc-hhHHHHHHHcCCHhHHHHHHHHhHHHHhcCCCHHHHhhCCCHHHHHHhCHHHHHHHHHHHHHhHHh
Confidence            9999999977655 47777776543      3689999999999999999999899999999999999999999998877


Q ss_pred             cHHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCC-------CCceEEecCcCCCCCC-
Q 039903          155 VTNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSY-------SGVKHIGGIMLERIPK-  226 (233)
Q Consensus       155 ~~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~-------~ri~~~~gD~f~~~P~-  226 (233)
                      ..+.+++.++ |++..+|||||||+|.++..+++++|+++++++|+|++++.+++.       +||+++.+|+++++|. 
T Consensus       157 ~~~~~~~~~~-~~~~~~vlDvG~G~G~~~~~l~~~~p~~~~~~~D~~~~~~~a~~~~~~~~~~~~v~~~~~d~~~~~p~~  235 (332)
T 3i53_A          157 DYTGIAAKYD-WAALGHVVDVGGGSGGLLSALLTAHEDLSGTVLDLQGPASAAHRRFLDTGLSGRAQVVVGSFFDPLPAG  235 (332)
T ss_dssp             HHTTGGGSSC-CGGGSEEEEETCTTSHHHHHHHHHCTTCEEEEEECHHHHHHHHHHHHHTTCTTTEEEEECCTTSCCCCS
T ss_pred             hHHHHHHhCC-CCCCCEEEEeCCChhHHHHHHHHHCCCCeEEEecCHHHHHHHHHhhhhcCcCcCeEEecCCCCCCCCCC
Confidence            7777788887 888899999999999999999999999999999999999888752       7899999999998995 


Q ss_pred             CCEEEeC
Q 039903          227 GDAILIK  233 (233)
Q Consensus       227 ~D~~~lk  233 (233)
                      .|+|+++
T Consensus       236 ~D~v~~~  242 (332)
T 3i53_A          236 AGGYVLS  242 (332)
T ss_dssp             CSEEEEE
T ss_pred             CcEEEEe
Confidence            5999873

>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=3.5e-39  Score=279.14  Aligned_cols=217  Identities=21%  Similarity=0.296  Sum_probs=196.1

Q ss_pred             cccccchHHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceec
Q 039903            2 QPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGL   81 (233)
Q Consensus         2 ~~~~~~~~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~l   81 (233)
                      +++.|++.+++|++|++|||||.|.+    +|+|++|||+++++    +++.++||||+|++.|+|++.     +++|++
T Consensus        28 ~~~~~~~~~~~l~~a~~lglf~~l~~----g~~t~~elA~~~g~----~~~~l~rlLr~l~~~g~l~~~-----~~~y~~   94 (348)
T 3lst_A           28 EEAMGYTYAAALRAAAAVGVADHLVD----GPRTPAELAAATGT----DADALRRVLRLLAVRDVVRES-----DGRFAL   94 (348)
T ss_dssp             HHHTTHHHHHHHHHHHHHTGGGGGTT----SCBCHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEE-----TTEEEE
T ss_pred             HHHHHHHHHHHHHHHHHcCchhHhhC----CCCCHHHHHHHhCc----CHHHHHHHHHHHHhCCCEEec-----CCEEec
Confidence            57899999999999999999999986    69999999999999    999999999999999999993     789999


Q ss_pred             cHhhhHhhcCCCCCCccchhccccC-----chhhHHHHHHcCCcchhhhhCCccccccccCchHHHHHHHHHHhcchhcH
Q 039903           82 AHVAKYFVLNRDGVSLCPSRPWLET-----KPYEIYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVT  156 (233)
Q Consensus        82 t~~s~~l~~~~~~~~~~~~~~~~~~-----~~~~L~~~l~~g~~~~~~~~g~~~~~~~~~~~~~~~~f~~am~~~~~~~~  156 (233)
                      |+.|+.|.++++ .++.+++.+..+     .|.+|++++++|+++|+..+|.++|+|+.++|+..+.|+++|...+....
T Consensus        95 t~~s~~l~~~~~-~~~~~~~~~~~~~~~~~~~~~l~~~l~~g~~~~~~~~g~~~~~~~~~~~~~~~~f~~~m~~~~~~~~  173 (348)
T 3lst_A           95 TDKGAALRSDSP-VPARAGILMFTDTMFWTMSHRVASALGPERPAFADIFGSSLDAYFDGDAEVEALYYEGMETVSAAEH  173 (348)
T ss_dssp             CTTTGGGSTTSS-SCSHHHHHHHTSHHHHHHHHTHHHHTCTTCCCHHHHHSSCHHHHHTTCHHHHHHHHHHHHHHHHTTH
T ss_pred             CHHHHHHhcCCC-ccHHHHHHHhcCHHHHHHHHHHHHHHhcCCChhhHHhCCCHHHHHHhCHHHHHHHHHHHHHhhhhhH
Confidence            999999977665 478887765433     78999999999999999999999999999999999999999999998888


Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccC-----CCCceEEecCcCCCCCCCCEEE
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSS-----YSGVKHIGGIMLERIPKGDAIL  231 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~-----~~ri~~~~gD~f~~~P~~D~~~  231 (233)
                      +.+++.++ |++..+|||||||+|.++..+++++|+++++++|+|+++..++.     .+||+++.+|+++++|..|+|+
T Consensus       174 ~~~~~~~~-~~~~~~vLDvG~G~G~~~~~l~~~~p~~~~~~~D~~~~~~~~~~~~~~~~~~v~~~~~d~~~~~p~~D~v~  252 (348)
T 3lst_A          174 LILARAGD-FPATGTVADVGGGRGGFLLTVLREHPGLQGVLLDRAEVVARHRLDAPDVAGRWKVVEGDFLREVPHADVHV  252 (348)
T ss_dssp             HHHHHHSC-CCSSEEEEEETCTTSHHHHHHHHHCTTEEEEEEECHHHHTTCCCCCGGGTTSEEEEECCTTTCCCCCSEEE
T ss_pred             HHHHHhCC-ccCCceEEEECCccCHHHHHHHHHCCCCEEEEecCHHHhhcccccccCCCCCeEEEecCCCCCCCCCcEEE
Confidence            88999998 99999999999999999999999999999999999998873321     2689999999999899559998


Q ss_pred             eC
Q 039903          232 IK  233 (233)
Q Consensus       232 lk  233 (233)
                      ++
T Consensus       253 ~~  254 (348)
T 3lst_A          253 LK  254 (348)
T ss_dssp             EE
T ss_pred             Ee
Confidence            63

>3gwz_A MMCR; methyltransferase, mitomycin, S-adenosyl methionine, transferase; HET: MSE SAH; 1.91A {Streptomyces lavendulae} PDB: 3gxo_A*

Probab=100.00  E-value=5.4e-39  Score=280.10  Aligned_cols=218  Identities=21%  Similarity=0.325  Sum_probs=198.5

Q ss_pred             cccccchHHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCc-ee
Q 039903            2 QPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRL-YG   80 (233)
Q Consensus         2 ~~~~~~~~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~-y~   80 (233)
                      +++.|++.+++|++|++|||||.|.+    +|+|++|||+++++    +++.++||||+|++.|+|+++    ++++ |+
T Consensus        44 ~l~~~~~~~~~l~~a~~lglf~~l~~----g~~t~~eLA~~~g~----~~~~l~rlLr~L~~~g~l~~~----~~~~~y~  111 (369)
T 3gwz_A           44 DILQGAWKARAIHVAVELGVPELLQE----GPRTATALAEATGA----HEQTLRRLLRLLATVGVFDDL----GHDDLFA  111 (369)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTGGGGTT----SCEEHHHHHHHHTC----CHHHHHHHHHHHHHTTSSEEC----SSTTEEE
T ss_pred             HHHHHHHHHHHHHHHHHCChhhhhcC----CCCCHHHHHHHHCc----CHHHHHHHHHHHHhCCCEEEe----CCCceEe
Confidence            57889999999999999999999996    69999999999999    999999999999999999997    5788 99


Q ss_pred             ccHhhhHhhcCCCCCCccchhccccC-----chhhHHHHHHcCCcchhhhhCCccccccccCchHHHHHHHHHHhcchhc
Q 039903           81 LAHVAKYFVLNRDGVSLCPSRPWLET-----KPYEIYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIV  155 (233)
Q Consensus        81 lt~~s~~l~~~~~~~~~~~~~~~~~~-----~~~~L~~~l~~g~~~~~~~~g~~~~~~~~~~~~~~~~f~~am~~~~~~~  155 (233)
                      +|+.++.|.++.+ .++..++.+..+     .|.+|++++++|+++|...+|.++|+|+.++|+..+.|+++|...+...
T Consensus       112 ~t~~s~~L~~~~~-~~~~~~~~~~~~~~~~~~~~~l~~~l~~g~~~~~~~~g~~~~~~~~~~~~~~~~f~~~m~~~~~~~  190 (369)
T 3gwz_A          112 QNALSAVLLPDPA-SPVATDARFQAAPWHWRAWEQLTHSVRTGEASFDVANGTSFWQLTHEDPKARELFNRAMGSVSLTE  190 (369)
T ss_dssp             CCHHHHTTSCCTT-CHHHHHHHHHHSHHHHHHHHTHHHHHHHSSCSHHHHHSSCHHHHHHHCHHHHHHHHHHHHHHHHHH
T ss_pred             cCHHHHHHhcCCc-hhHHHHHHHcCCHHHHHHHHhHHHHHhCCCChhHhhcCCCHHHHHHhCHHHHHHHHHHHHHHHhhh
Confidence            9999999877665 467777765432     7899999999999999999998999999999999999999999998887


Q ss_pred             HHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccC-------CCCceEEecCcCCCCCC-C
Q 039903          156 TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSS-------YSGVKHIGGIMLERIPK-G  227 (233)
Q Consensus       156 ~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~-------~~ri~~~~gD~f~~~P~-~  227 (233)
                      .+.+++.++ +++..+|||||||+|.++..+++++|+++++++|+|++++.+++       .+||+++.+|+++++|. .
T Consensus       191 ~~~l~~~~~-~~~~~~vlDvG~G~G~~~~~l~~~~p~~~~~~~D~~~~~~~a~~~~~~~~l~~~v~~~~~d~~~~~p~~~  269 (369)
T 3gwz_A          191 AGQVAAAYD-FSGAATAVDIGGGRGSLMAAVLDAFPGLRGTLLERPPVAEEARELLTGRGLADRCEILPGDFFETIPDGA  269 (369)
T ss_dssp             HHHHHHHSC-CTTCSEEEEETCTTSHHHHHHHHHCTTCEEEEEECHHHHHHHHHHHHHTTCTTTEEEEECCTTTCCCSSC
T ss_pred             HHHHHHhCC-CccCcEEEEeCCCccHHHHHHHHHCCCCeEEEEcCHHHHHHHHHhhhhcCcCCceEEeccCCCCCCCCCc
Confidence            888999988 99999999999999999999999999999999999999988875       27899999999998996 5


Q ss_pred             CEEEeC
Q 039903          228 DAILIK  233 (233)
Q Consensus       228 D~~~lk  233 (233)
                      |+|+++
T Consensus       270 D~v~~~  275 (369)
T 3gwz_A          270 DVYLIK  275 (369)
T ss_dssp             SEEEEE
T ss_pred             eEEEhh
Confidence            999873

>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=6.6e-38  Score=272.03  Aligned_cols=227  Identities=25%  Similarity=0.404  Sum_probs=197.8

Q ss_pred             cccccchHHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeec----c-CCC-
Q 039903            2 QPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTS----A-GDD-   75 (233)
Q Consensus         2 ~~~~~~~~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~----~-~~~-   75 (233)
                      +++.+++.+++|++|++|||||.|+..+  +|.|++|||+++++ +|.+++.++||||+|++.|+|++..    . ++. 
T Consensus        16 ~~~~~~~~~~~l~~a~~lgif~~L~~~~--~~~t~~eLA~~~g~-~~~~~~~l~rlLr~L~~~gll~~~~~~~~~~~g~~   92 (358)
T 1zg3_A           16 KHVYNFVSSMALKSAMELGIADAIHNHG--KPMTLSELASSLKL-HPSKVNILHRFLRLLTHNGFFAKTIVKGKEGDEEE   92 (358)
T ss_dssp             HHHTTHHHHHHHHHHHHHTHHHHHHHHT--SCEEHHHHHHHTTC-CTTTHHHHHHHHHHHHHTTSEEEEEECCSSSSCCC
T ss_pred             HHHHHHHHHHHHHHHHHCChHhHHhhcC--CCcCHHHHHHhcCC-CCcchHHHHHHHHHHhhCCcEEEecccccccCCCC
Confidence            4677999999999999999999999853  48999999999999 3334889999999999999999851    0 000 


Q ss_pred             CCceeccHhhhHhhcCCCCCCccchhccccC-----chhhHHHHHHcC--CcchhhhhCCccccccccCchHHH--HHHH
Q 039903           76 QRLYGLAHVAKYFVLNRDGVSLCPSRPWLET-----KPYEIYDAVLEG--GISFNKVHGTGFYEYAGNDFRFNG--VFNK  146 (233)
Q Consensus        76 ~~~y~lt~~s~~l~~~~~~~~~~~~~~~~~~-----~~~~L~~~l~~g--~~~~~~~~g~~~~~~~~~~~~~~~--~f~~  146 (233)
                      +++|++|+.++.|+++++ .++++++.+..+     .|.+|++++++|  .++|+..+|.++|+|+.++|+..+  .|++
T Consensus        93 ~~~y~~t~~s~~l~~~~~-~~~~~~~~~~~~~~~~~~~~~L~~~l~~g~~~~~~~~~~g~~~~~~~~~~p~~~~~~~f~~  171 (358)
T 1zg3_A           93 EIAYSLTPPSKLLISGKP-TCLSSIVKGALHPSSLDMWSSSKKWFNEDKEQTLFECATGESFWDFLNKDSESSTLSMFQD  171 (358)
T ss_dssp             EEEEEECHHHHTTCTTST-TCCHHHHHHHTSHHHHGGGGGHHHHHHCSCCCCHHHHHHSSCHHHHHTSGGGHHHHHHHHH
T ss_pred             CCEEeCCHHHHHHhCCCC-ccHHHHHHHhcCcHHHHHHHHHHHHHhCCCCCChHHHHhCCCHHHHHhcChhhhhHHHHHH
Confidence            479999999998887765 478888776542     789999999998  788998899999999999999999  9999


Q ss_pred             HHHhcchhcHHHHHHhcc-cccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCCCCceEEecCcCCCCC
Q 039903          147 AMLNHTSIVTNRIIDSSK-GFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIP  225 (233)
Q Consensus       147 am~~~~~~~~~~~~~~~~-~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~~ri~~~~gD~f~~~P  225 (233)
                      +|...+.... .+++.++ +|++..+|||||||+|.++..+++++|+++++++|+|++++.+++.++|+++.+|+++++|
T Consensus       172 ~m~~~~~~~~-~~~~~~~~~~~~~~~vlDvG~G~G~~~~~l~~~~p~~~~~~~D~~~~~~~a~~~~~v~~~~~d~~~~~~  250 (358)
T 1zg3_A          172 AMASDSRMFK-LVLQENKRVFEGLESLVDVGGGTGGVTKLIHEIFPHLKCTVFDQPQVVGNLTGNENLNFVGGDMFKSIP  250 (358)
T ss_dssp             HHHHHHHTHH-HHHHHTHHHHHTCSEEEEETCTTSHHHHHHHHHCTTSEEEEEECHHHHSSCCCCSSEEEEECCTTTCCC
T ss_pred             HHhcccHHHH-HHHHhcchhccCCCEEEEECCCcCHHHHHHHHHCCCCeEEEeccHHHHhhcccCCCcEEEeCccCCCCC
Confidence            9999887766 7888883 3888899999999999999999999999999999999999999887789999999999888


Q ss_pred             CCCEEEeC
Q 039903          226 KGDAILIK  233 (233)
Q Consensus       226 ~~D~~~lk  233 (233)
                      .+|+|+++
T Consensus       251 ~~D~v~~~  258 (358)
T 1zg3_A          251 SADAVLLK  258 (358)
T ss_dssp             CCSEEEEE
T ss_pred             CceEEEEc
Confidence            78999873

>2ip2_A Probable phenazine-specific methyltransferase; pyocyanin, phenazine-1-carboxy PHZM; 1.80A {Pseudomonas aeruginosa}

Probab=100.00  E-value=7.3e-38  Score=269.01  Aligned_cols=215  Identities=23%  Similarity=0.301  Sum_probs=194.5

Q ss_pred             cccccchHHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceec
Q 039903            2 QPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGL   81 (233)
Q Consensus         2 ~~~~~~~~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~l   81 (233)
                      +++.|++.+++|+++++||||+.|.+    +|.|++|||+++++    +++.++||||+|++.|+|++.    +++.|++
T Consensus        14 ~~~~~~~~~~~l~~~~~lgi~~~l~~----~~~t~~ela~~~~~----~~~~l~r~Lr~L~~~g~l~~~----~~~~y~~   81 (334)
T 2ip2_A           14 QVVTGEWKSRCVYVATRLGLADLIES----GIDSDETLAAAVGS----DAERIHRLMRLLVAFEIFQGD----TRDGYAN   81 (334)
T ss_dssp             HHHHHHHHHHHHHHHHHTTHHHHHHT----TCCSHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEE----TTTEEEE
T ss_pred             HHHHHHHHHHHHHHHHHcCcHHHHhC----CCCCHHHHHHHhCc----CHHHHHHHHHHHHhCCceEec----CCCeEec
Confidence            56789999999999999999999986    69999999999999    999999999999999999997    5689999


Q ss_pred             cHhhhHhhcCCCCCCccchhccccC----chhhHHHHHHcCCcchhhhhCCccccccccCchHHHHHHHHHHhcchhcHH
Q 039903           82 AHVAKYFVLNRDGVSLCPSRPWLET----KPYEIYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTN  157 (233)
Q Consensus        82 t~~s~~l~~~~~~~~~~~~~~~~~~----~~~~L~~~l~~g~~~~~~~~g~~~~~~~~~~~~~~~~f~~am~~~~~~~~~  157 (233)
                      |+.++.|. +++ .++..++.+..+    .|.+|++++++++++|+..+|.++|+|+.++|+..+.|+++| ..+....+
T Consensus        82 t~~s~~l~-~~~-~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~g~~~~~~~~~~~~~~~~f~~~m-~~~~~~~~  158 (334)
T 2ip2_A           82 TPTSHLLR-DVE-GSFRDMVLFYGEEFHAAWTPACEALLSGTPGFELAFGEDFYSYLKRCPDAGRRFLLAM-KASNLAFH  158 (334)
T ss_dssp             CHHHHTTS-SST-TCSHHHHHHHTTHHHHHTTTHHHHHHHCCCHHHHHHSSCHHHHHHHCHHHHHHHHHHH-GGGHHHHH
T ss_pred             CHHHHHHh-CCC-ccHHHHHHHhcCchhhHHHHHHHHHhcCCChhhhhcCCCHHHHHhhChHHHHHHHHHH-HHHHHHHH
Confidence            99999888 654 478888766543    799999999999999998899999999999999999999999 88777778


Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCC-------CCceEEecCcCCCCCCC-CE
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSY-------SGVKHIGGIMLERIPKG-DA  229 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~-------~ri~~~~gD~f~~~P~~-D~  229 (233)
                      .+++.++ |++ .+|+|||||+|.++..+++++|+++++++|+|++++.+++.       +||+++.+|+++++|.. |+
T Consensus       159 ~~~~~~~-~~~-~~vlDvG~G~G~~~~~l~~~~p~~~~~~~D~~~~~~~a~~~~~~~~~~~~v~~~~~d~~~~~~~~~D~  236 (334)
T 2ip2_A          159 EIPRLLD-FRG-RSFVDVGGGSGELTKAILQAEPSARGVMLDREGSLGVARDNLSSLLAGERVSLVGGDMLQEVPSNGDI  236 (334)
T ss_dssp             HHHHHSC-CTT-CEEEEETCTTCHHHHHHHHHCTTCEEEEEECTTCTHHHHHHTHHHHHTTSEEEEESCTTTCCCSSCSE
T ss_pred             HHHHhCC-CCC-CEEEEeCCCchHHHHHHHHHCCCCEEEEeCcHHHHHHHHHHHhhcCCCCcEEEecCCCCCCCCCCCCE
Confidence            8888887 888 99999999999999999999999999999998888887652       68999999999988874 99


Q ss_pred             EEeC
Q 039903          230 ILIK  233 (233)
Q Consensus       230 ~~lk  233 (233)
                      |+++
T Consensus       237 v~~~  240 (334)
T 2ip2_A          237 YLLS  240 (334)
T ss_dssp             EEEE
T ss_pred             EEEc
Confidence            9863

>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=1.3e-37  Score=271.59  Aligned_cols=230  Identities=40%  Similarity=0.670  Sum_probs=186.8

Q ss_pred             cccccchHHHHHHHHHhhChhHHHHhcCCCCC---CCHHHHHHhCCCC--CCCChhhHHHHHHHHhcCCceeeecc--CC
Q 039903            2 QPAMSIVLPAAMQAASELGVFEIIAKAGPTAK---ISAVEIAAQMPSS--NPNAAVMLDRILRLLVTHRVLRCTSA--GD   74 (233)
Q Consensus         2 ~~~~~~~~s~~L~~a~~lglfd~L~~~~~~~~---~t~~elA~~~~~~--~~~~~~~l~rlL~~L~~~gll~~~~~--~~   74 (233)
                      +++.|++.+++|++|++|||||.|++.|  +|   +|++|||++++++  +|.+++.++||||+|++.|+|++...  ++
T Consensus        30 ~l~~~~~~~~~l~~a~~lgif~~L~~~g--~pg~~~t~~eLA~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~~~~~~~  107 (372)
T 1fp1_D           30 VLTTNLVYPAVLNAAIDLNLFEIIAKAT--PPGAFMSPSEIASKLPASTQHSDLPNRLDRMLRLLASYSVLTSTTRTIED  107 (372)
T ss_dssp             HHHHTTHHHHHHHHHHHTTHHHHHHTCS--STTCCBCHHHHHTTSCGGGCCTTHHHHHHHHHHHHHHTTSEEEEEEECTT
T ss_pred             HHHHHHHHHHHHHHHHHCChHHHHHhcC--CCCCCcCHHHHHHhcCCCCCCCcChHHHHHHHHHHhhCCceEecccccCC
Confidence            6788999999999999999999999852  15   9999999999982  44468899999999999999998510  00


Q ss_pred             C--CCceeccHhhhHhhcCCCCCCccchhccccC-----chhhHHHHHHcC-CcchhhhhCCccccccccCchHHHHHHH
Q 039903           75 D--QRLYGLAHVAKYFVLNRDGVSLCPSRPWLET-----KPYEIYDAVLEG-GISFNKVHGTGFYEYAGNDFRFNGVFNK  146 (233)
Q Consensus        75 ~--~~~y~lt~~s~~l~~~~~~~~~~~~~~~~~~-----~~~~L~~~l~~g-~~~~~~~~g~~~~~~~~~~~~~~~~f~~  146 (233)
                      +  .+.|++|+.++.|+.+++..++++++.+..+     .|.+|+++++++ +++|+..+|.++|+|+.++|+..+.|++
T Consensus       108 g~~~~~y~~t~~s~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~g~~~~~~~~~g~~~~~~~~~~~~~~~~f~~  187 (372)
T 1fp1_D          108 GGAERVYGLSMVGKYLVPDESRGYLASFTTFLCYPALLQVWMNFKEAVVDEDIDLFKNVHGVTKYEFMGKDKKMNQIFNK  187 (372)
T ss_dssp             SCEEEEEEECTTGGGGSTTCTTCCCTHHHHHHTCHHHHHHHTTHHHHHHSCC--------------CCSSCHHHHHHHHH
T ss_pred             CCcCCeEecCHHHHHHhCCCCCCCHHHHHHHhcCchHHHHHHHHHHHHHcCCCChhHHHhCCCHHHHHHhCHHHHHHHHH
Confidence            1  3699999999988877542368888776543     789999999999 8899998999999999999999999999


Q ss_pred             HHHhcchhcHHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCCCCceEEecCcCCCCCC
Q 039903          147 AMLNHTSIVTNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPK  226 (233)
Q Consensus       147 am~~~~~~~~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~~ri~~~~gD~f~~~P~  226 (233)
                      +|...+....+.+++.+++|++..+|||||||+|.++..+++++|+++++++|+|++++.+++.++|+++.+|+++++|.
T Consensus       188 ~m~~~~~~~~~~l~~~~~~~~~~~~vLDvG~G~G~~~~~l~~~~~~~~~~~~D~~~~~~~a~~~~~v~~~~~d~~~~~~~  267 (372)
T 1fp1_D          188 SMVDVCATEMKRMLEIYTGFEGISTLVDVGGGSGRNLELIISKYPLIKGINFDLPQVIENAPPLSGIEHVGGDMFASVPQ  267 (372)
T ss_dssp             HHHHHHHHHHHHHHHHCCTTTTCSEEEEETCTTSHHHHHHHHHCTTCEEEEEECHHHHTTCCCCTTEEEEECCTTTCCCC
T ss_pred             HHHhhhHHHHHHHHHHhhccCCCCEEEEeCCCCcHHHHHHHHHCCCCeEEEeChHHHHHhhhhcCCCEEEeCCcccCCCC
Confidence            99998887778888888658888999999999999999999999999999999999999998888999999999998887


Q ss_pred             CCEEEeC
Q 039903          227 GDAILIK  233 (233)
Q Consensus       227 ~D~~~lk  233 (233)
                      +|+|+++
T Consensus       268 ~D~v~~~  274 (372)
T 1fp1_D          268 GDAMILK  274 (372)
T ss_dssp             EEEEEEE
T ss_pred             CCEEEEe
Confidence            8999863

>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=1.6e-37  Score=269.04  Aligned_cols=225  Identities=23%  Similarity=0.421  Sum_probs=197.3

Q ss_pred             cccccchHHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceec
Q 039903            2 QPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGL   81 (233)
Q Consensus         2 ~~~~~~~~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~l   81 (233)
                      +++.+++.+++|+++++||||+.|...+  +|.|++|||+++++ +|.+++.++||||+|++.|+|++.. + +++.|++
T Consensus        22 ~~~~~~~~~~~l~~a~~lgif~~L~~~~--~~~t~~ela~~~~~-~~~~~~~l~rlLr~L~~~gll~~~~-~-~~~~y~~   96 (352)
T 1fp2_A           22 KHIYAFIDSMSLKWAVEMNIPNIIQNHG--KPISLSNLVSILQV-PSSKIGNVRRLMRYLAHNGFFEIIT-K-EEESYAL   96 (352)
T ss_dssp             HHHTTHHHHHHHHHHHHTTHHHHHHHHT--SCEEHHHHHHHHTC-CGGGHHHHHHHHHHHHHTTSEEEEE-S-SSEEEEE
T ss_pred             HHHHHHHHHHHHHHHHHCChhhhhhhcC--CCccHHHHHHHhCc-CCCChHHHHHHHHHHHhCCeEEEec-C-CCCeEeC
Confidence            4567999999999999999999999853  58999999999999 2223779999999999999999851 0 1589999


Q ss_pred             cHhhhHhhcCCCCCCccchhccccC-----chhhHHHHHH-cCCcchhhhhCCccccccccCchHHHHHHHHHHhcchhc
Q 039903           82 AHVAKYFVLNRDGVSLCPSRPWLET-----KPYEIYDAVL-EGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIV  155 (233)
Q Consensus        82 t~~s~~l~~~~~~~~~~~~~~~~~~-----~~~~L~~~l~-~g~~~~~~~~g~~~~~~~~~~~~~~~~f~~am~~~~~~~  155 (233)
                      |+.|+.|+.+++ .++++++.+..+     .|.+|+++++ +|+++|+..+|.++|+|+.++|+..+.|+++|...+...
T Consensus        97 t~~s~~L~~~~~-~~~~~~~~~~~~~~~~~~~~~L~~~l~~~g~~~~~~~~g~~~~~~~~~~~~~~~~f~~~m~~~~~~~  175 (352)
T 1fp2_A           97 TVASELLVRGSD-LCLAPMVECVLDPTLSGSYHELKKWIYEEDLTLFGVTLGSGFWDFLDKNPEYNTSFNDAMASDSKLI  175 (352)
T ss_dssp             CHHHHTTSTTSS-SCCHHHHHHHTCHHHHHGGGGHHHHHTCSSCCHHHHHHSSCHHHHHHHCHHHHHHHHHHHHHTHHHH
T ss_pred             CHHHHHHhCCCC-ccHHHHHHHhcCchHHHHHHHHHHHHHhcCCChHHHHcCCCHHHHHHhChHHHHHHHHHHHhcchhh
Confidence            999998887765 478888766432     7899999999 888999999999999999999999999999999988776


Q ss_pred             HHHHHHhcc-cccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCCCCceEEecCcCCCCCCCCEEEeC
Q 039903          156 TNRIIDSSK-GFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAILIK  233 (233)
Q Consensus       156 ~~~~~~~~~-~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~~ri~~~~gD~f~~~P~~D~~~lk  233 (233)
                      .+. ++.++ +|++..+|||||||+|.++..+++++|+++++++|+|++++.+++.++|+++.+|+++++|..|+|+++
T Consensus       176 ~~~-~~~~~~~~~~~~~vlDvG~G~G~~~~~l~~~~p~~~~~~~D~~~~~~~a~~~~~v~~~~~d~~~~~p~~D~v~~~  253 (352)
T 1fp2_A          176 NLA-LRDCDFVFDGLESIVDVGGGTGTTAKIICETFPKLKCIVFDRPQVVENLSGSNNLTYVGGDMFTSIPNADAVLLK  253 (352)
T ss_dssp             HHH-HHTCHHHHTTCSEEEEETCTTSHHHHHHHHHCTTCEEEEEECHHHHTTCCCBTTEEEEECCTTTCCCCCSEEEEE
T ss_pred             hhH-HHhcccccccCceEEEeCCCccHHHHHHHHHCCCCeEEEeeCHHHHhhcccCCCcEEEeccccCCCCCccEEEee
Confidence            666 77782 288889999999999999999999999999999999999999988778999999999988878999863

>3dp7_A SAM-dependent methyltransferase; structural genomics, protein structure initiative, NEW YORK structural genomix research; 2.33A {Bacteroides vulgatus}

Probab=100.00  E-value=8.5e-36  Score=259.38  Aligned_cols=214  Identities=16%  Similarity=0.194  Sum_probs=179.5

Q ss_pred             cccccchHHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceec
Q 039903            2 QPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGL   81 (233)
Q Consensus         2 ~~~~~~~~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~l   81 (233)
                      +++.|++.+++|+++++|||||.|++.+  +|+|++|||+++++    +++.++||||+|++.|+|++.     +++|++
T Consensus        21 ~l~~g~~~~~~l~~a~~lgifd~L~~~~--~~~t~~eLA~~~g~----~~~~l~rlLr~l~~~g~l~~~-----~~~y~~   89 (363)
T 3dp7_A           21 EIAFGPVVFQVSRLMLKFGIFQLLSGKR--EGYTLQEISGRTGL----TRYAAQVLLEASLTIGTILLE-----EDRYVL   89 (363)
T ss_dssp             HHHHHHHHHHHHHHHHHTTHHHHHHTCT--TCBCHHHHHHHHTC----CHHHHHHHHHHHHHHTSEEEE-----TTEEEE
T ss_pred             HHHhhHHHHHHHHHHHHhCHHHHHHhcC--CCCCHHHHHHHhCc----CHHHHHHHHHHHhhCCCeEec-----CCEEec
Confidence            5788999999999999999999999843  69999999999999    999999999999999999884     689999


Q ss_pred             cHhhhHhhcCCCCCCccchhcccc----CchhhHHHHHHcCCcchhhhhC--CccccccccCchHHH----HHHHHHHhc
Q 039903           82 AHVAKYFVLNRDGVSLCPSRPWLE----TKPYEIYDAVLEGGISFNKVHG--TGFYEYAGNDFRFNG----VFNKAMLNH  151 (233)
Q Consensus        82 t~~s~~l~~~~~~~~~~~~~~~~~----~~~~~L~~~l~~g~~~~~~~~g--~~~~~~~~~~~~~~~----~f~~am~~~  151 (233)
                      |+.|+.|+++++   ...++.+..    ..|.+|++++++|++++...+|  .++|+++.++|+..+    .|+++|...
T Consensus        90 t~~s~~L~~~~~---~~~~~~~~~~~~~~~~~~L~~~lr~g~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~  166 (363)
T 3dp7_A           90 AKAGWFLLNDKM---ARVNMEFNHDVNYQGLFHLEEALLNGRPEGLKVFGEWPTIYEGLSQLPEQVQKSWFGFDHFYSDQ  166 (363)
T ss_dssp             CHHHHHHHHCHH---HHHHHHHHHHTTHHHHTTHHHHHHHSSCGGGGGTCCCSSHHHHGGGSCHHHHHHHHHHHHHTTCC
T ss_pred             ccchHHhhCCCc---ccchheeecHHhhhhHHHHHHHHhcCCCccccccCchHhHHHHHhhCHHHHHHHHHHHHHHhhhh
Confidence            999998887653   222222221    1889999999999999888888  689999999999776    366666654


Q ss_pred             chhcHHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCC-------CCceEEecCcCCC-
Q 039903          152 TSIVTNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSY-------SGVKHIGGIMLER-  223 (233)
Q Consensus       152 ~~~~~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~-------~ri~~~~gD~f~~-  223 (233)
                      .   ...+++.+. ..+..+|||||||+|.++..+++++|+++++++|+|++++.+++.       +||+++.+|++++ 
T Consensus       167 ~---~~~~l~~~~-~~~~~~vlDvG~G~G~~~~~l~~~~p~~~~~~~D~~~~~~~a~~~~~~~~~~~~v~~~~~d~~~~~  242 (363)
T 3dp7_A          167 S---FGKALEIVF-SHHPKRLLDIGGNTGKWATQCVQYNKEVEVTIVDLPQQLEMMRKQTAGLSGSERIHGHGANLLDRD  242 (363)
T ss_dssp             C---CHHHHHHHG-GGCCSEEEEESCTTCHHHHHHHHHSTTCEEEEEECHHHHHHHHHHHTTCTTGGGEEEEECCCCSSS
T ss_pred             h---HHHHHHHhc-ccCCCEEEEeCCCcCHHHHHHHHhCCCCEEEEEeCHHHHHHHHHHHHhcCcccceEEEEccccccC
Confidence            3   234555544 467799999999999999999999999999999999999888753       5899999999984 


Q ss_pred             --CCC-CCEEEeC
Q 039903          224 --IPK-GDAILIK  233 (233)
Q Consensus       224 --~P~-~D~~~lk  233 (233)
                        +|. .|+|+++
T Consensus       243 ~~~p~~~D~v~~~  255 (363)
T 3dp7_A          243 VPFPTGFDAVWMS  255 (363)
T ss_dssp             CCCCCCCSEEEEE
T ss_pred             CCCCCCcCEEEEe
Confidence              675 4999873

>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=100.00  E-value=2e-35  Score=257.38  Aligned_cols=217  Identities=17%  Similarity=0.241  Sum_probs=194.9

Q ss_pred             cccccchHHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCC--ce
Q 039903            2 QPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQR--LY   79 (233)
Q Consensus         2 ~~~~~~~~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~--~y   79 (233)
                      +++.+++.+++|++++++|||+.|..    +|.|++|||+++++    +++.++||||+|++.|+|++.    +++  .|
T Consensus        22 ~~~~~~~~~~~l~~~~~l~i~~~l~~----~~~t~~eLA~~~g~----~~~~l~r~Lr~L~~~Gll~~~----~~~~~~y   89 (374)
T 1qzz_A           22 KNLGNLVTPMALRVAATLRLVDHLLA----GADTLAGLADRTDT----HPQALSRLVRHLTVVGVLEGG----EKQGRPL   89 (374)
T ss_dssp             HTTTCCHHHHHHHHHHHTTHHHHHHT----TCCSHHHHHHHHTC----CHHHHHHHHHHHHHTTSEECC----CC-CCCC
T ss_pred             HHHHhhHHHHHHHHHHHcChHHHHhC----CCCCHHHHHHHhCc----CHHHHHHHHHHHhhCCCEEEe----CCCCeEE
Confidence            57899999999999999999999965    69999999999999    999999999999999999986    456  99


Q ss_pred             eccHhhhHhhcCCCCCCccchhcccc------CchhhHHHHHHcCCcchhhhhCCccccccccCchHHHHHHHHHHhcch
Q 039903           80 GLAHVAKYFVLNRDGVSLCPSRPWLE------TKPYEIYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTS  153 (233)
Q Consensus        80 ~lt~~s~~l~~~~~~~~~~~~~~~~~------~~~~~L~~~l~~g~~~~~~~~g~~~~~~~~~~~~~~~~f~~am~~~~~  153 (233)
                      ++|+.+..|..+++ .++..++.+..      ..|.+|++++++|+++|+..+|.++|+++..+|+..+.|+++|.....
T Consensus        90 ~~t~~s~~l~~~~~-~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~~~~  168 (374)
T 1qzz_A           90 RPTRLGMLLADGHP-AQQRAWLDLNGAVSHADLAFTGLLDVVRTGRPAYAGRYGRPFWEDLSADVALADSFDALMSCDED  168 (374)
T ss_dssp             EECTTGGGGSTTCT-TCHHHHHCTTSHHHHHHGGGGGHHHHHHHSCCSHHHHHSSCHHHHHHHCHHHHHHHHHTCGGGST
T ss_pred             EEChHHHhhcCCCc-ccHHHHHHHcCChhhHHHHHHHHHHHHhcCCChhhhhhCCCHHHHHhhChHHHHHHHHHHHHhhH
Confidence            99999998887765 47777776553      468999999999999999999999999999999999999999998887


Q ss_pred             hcHHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCC-------CCceEEecCcCCCCCC
Q 039903          154 IVTNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSY-------SGVKHIGGIMLERIPK  226 (233)
Q Consensus       154 ~~~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~-------~ri~~~~gD~f~~~P~  226 (233)
                      ...+.+++.++ +++..+|||||||+|.++..+++++|+++++++|+|++++.+++.       +||+++.+|+++++|.
T Consensus       169 ~~~~~~~~~~~-~~~~~~vlDvG~G~G~~~~~l~~~~~~~~~~~~D~~~~~~~a~~~~~~~~~~~~v~~~~~d~~~~~~~  247 (374)
T 1qzz_A          169 LAYEAPADAYD-WSAVRHVLDVGGGNGGMLAAIALRAPHLRGTLVELAGPAERARRRFADAGLADRVTVAEGDFFKPLPV  247 (374)
T ss_dssp             TTTHHHHHTSC-CTTCCEEEEETCTTSHHHHHHHHHCTTCEEEEEECHHHHHHHHHHHHHTTCTTTEEEEECCTTSCCSC
T ss_pred             hHHHHHHHhCC-CCCCCEEEEECCCcCHHHHHHHHHCCCCEEEEEeCHHHHHHHHHHHHhcCCCCceEEEeCCCCCcCCC
Confidence            77788888888 888899999999999999999999999999999998899887652       4899999999998888


Q ss_pred             C-CEEEe
Q 039903          227 G-DAILI  232 (233)
Q Consensus       227 ~-D~~~l  232 (233)
                      . |+|++
T Consensus       248 ~~D~v~~  254 (374)
T 1qzz_A          248 TADVVLL  254 (374)
T ss_dssp             CEEEEEE
T ss_pred             CCCEEEE
Confidence            5 99986

>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=100.00  E-value=7.9e-35  Score=252.49  Aligned_cols=217  Identities=18%  Similarity=0.286  Sum_probs=195.4

Q ss_pred             cccccchHHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceec
Q 039903            2 QPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGL   81 (233)
Q Consensus         2 ~~~~~~~~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~l   81 (233)
                      +++.|++.+++|++++++|||+.|.+    +|.|++|||+++++    +++.+.|+|++|++.|+|++.    ++++|++
T Consensus        25 ~~~~~~~~~~~l~~~~~l~i~~~l~~----~~~t~~ela~~~~~----~~~~l~r~L~~L~~~g~~~~~----~~g~y~~   92 (360)
T 1tw3_A           25 IRLGSLHTPMVVRTAATLRLVDHILA----GARTVKALAARTDT----RPEALLRLIRHLVAIGLLEED----APGEFVP   92 (360)
T ss_dssp             HHHHCSHHHHHHHHHHHTTHHHHHHT----TCCBHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEE----ETTEEEE
T ss_pred             HHHHhHHHHHHHHHHHHhCHHHHHhC----CCCCHHHHHHHhCc----CHHHHHHHHHHHHHCCCEEec----CCCeEEe
Confidence            57789999999999999999999975    69999999999999    999999999999999999996    4789999


Q ss_pred             cHhhhHhhcCCCCCCccchhcccc------CchhhHHHHHHcCCcchhhhhCCccccccccCchHHHHHHHHHHhcchhc
Q 039903           82 AHVAKYFVLNRDGVSLCPSRPWLE------TKPYEIYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIV  155 (233)
Q Consensus        82 t~~s~~l~~~~~~~~~~~~~~~~~------~~~~~L~~~l~~g~~~~~~~~g~~~~~~~~~~~~~~~~f~~am~~~~~~~  155 (233)
                      |+.+..|..+++ .++..++.+..      ..|.+|.+++++|+++|+..+|.++|+++..+|+....|+.+|...+...
T Consensus        93 t~~s~~l~~~~~-~~~~~~~~~~~~~~~~~~~~~~l~~~l~~g~~~~~~~~g~~~~~~~~~~p~~~~~f~~~~~~~~~~~  171 (360)
T 1tw3_A           93 TEVGELLADDHP-AAQRAWHDLTQAVARADISFTRLPDAIRTGRPTYESIYGKPFYEDLAGRPDLRASFDSLLACDQDVA  171 (360)
T ss_dssp             CTTGGGGSTTST-TCHHHHTCTTSHHHHHGGGGGGHHHHHHHCCCCHHHHHSSCHHHHHHTCHHHHHHHHHHHTTTTTTT
T ss_pred             CHHHHHHhcCCc-hhHHHHHHHhcCchhHHHHHHHHHHHHHcCCCHHHHhcCCCHHHHHHhChHHHHHHHHHHHHHHHHh
Confidence            999998887765 47777765543      27899999999999999988999999999999999999999999888877


Q ss_pred             HHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCC-------CCceEEecCcCCCCCCC-
Q 039903          156 TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSY-------SGVKHIGGIMLERIPKG-  227 (233)
Q Consensus       156 ~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~-------~ri~~~~gD~f~~~P~~-  227 (233)
                      .+.+++.++ +++..+|||||||+|.++..+++++|+++++.+|+|++++.++++       +||+++.+|+++++|.. 
T Consensus       172 ~~~l~~~~~-~~~~~~vLDvG~G~G~~~~~l~~~~~~~~~~~~D~~~~~~~a~~~~~~~~~~~~v~~~~~d~~~~~~~~~  250 (360)
T 1tw3_A          172 FDAPAAAYD-WTNVRHVLDVGGGKGGFAAAIARRAPHVSATVLEMAGTVDTARSYLKDEGLSDRVDVVEGDFFEPLPRKA  250 (360)
T ss_dssp             THHHHHHSC-CTTCSEEEEETCTTSHHHHHHHHHCTTCEEEEEECTTHHHHHHHHHHHTTCTTTEEEEECCTTSCCSSCE
T ss_pred             HHHHHHhCC-CccCcEEEEeCCcCcHHHHHHHHhCCCCEEEEecCHHHHHHHHHHHHhcCCCCceEEEeCCCCCCCCCCc
Confidence            788889888 888899999999999999999999999999999998898887652       48999999999988885 


Q ss_pred             CEEEe
Q 039903          228 DAILI  232 (233)
Q Consensus       228 D~~~l  232 (233)
                      |+|++
T Consensus       251 D~v~~  255 (360)
T 1tw3_A          251 DAIIL  255 (360)
T ss_dssp             EEEEE
T ss_pred             cEEEE
Confidence            99886

>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=100.00  E-value=1.3e-33  Score=245.13  Aligned_cols=204  Identities=18%  Similarity=0.263  Sum_probs=177.9

Q ss_pred             ccchHHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHh
Q 039903            5 MSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHV   84 (233)
Q Consensus         5 ~~~~~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~   84 (233)
                      .|++.+++|+++++|||||.|.+    +|.|++|||+++++    +++.++||||+|++.|+|++.     ++.|++|+.
T Consensus        40 ~~~~~~~~l~~a~~lgif~~L~~----~~~t~~eLA~~~g~----~~~~l~rlLr~L~~~gll~~~-----~~~y~~t~~  106 (359)
T 1x19_A           40 KGLIEFSCMKAAIELDLFSHMAE----GPKDLATLAADTGS----VPPRLEMLLETLRQMRVINLE-----DGKWSLTEF  106 (359)
T ss_dssp             HHHHHHHHHHHHHHHTHHHHHTT----CCBCHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEE-----TTEEEECHH
T ss_pred             HHHHHHHHHHHHHHcCcHHHHcC----CCCCHHHHHHHhCc----ChHHHHHHHHHHHhCCCeEee-----CCeEecCHH
Confidence            38999999999999999999987    59999999999999    999999999999999999996     569999997


Q ss_pred             hh-HhhcCCCC--CCccchhccccC----chhhHHHHHHcCCcchhhhhCCccccccccCch---HHHHHHHHHHhcch-
Q 039903           85 AK-YFVLNRDG--VSLCPSRPWLET----KPYEIYDAVLEGGISFNKVHGTGFYEYAGNDFR---FNGVFNKAMLNHTS-  153 (233)
Q Consensus        85 s~-~l~~~~~~--~~~~~~~~~~~~----~~~~L~~~l~~g~~~~~~~~g~~~~~~~~~~~~---~~~~f~~am~~~~~-  153 (233)
                      +. .|.++++.  .++++++.+...    .|.+|+++++++.+          |+++.++|+   ..+.|.++|...+. 
T Consensus       107 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~g~~----------~~~~~~~p~~~~~~~~f~~~m~~~~~~  176 (359)
T 1x19_A          107 ADYMFSPTPKEPNLHQTPVAKAMAFLADDFYMGLSQAVRGQKN----------FKGQVPYPPVTREDNLYFEEIHRSNAK  176 (359)
T ss_dssp             HHHHSSSSCSBTTBCCHHHHHHHHHHHHHTGGGHHHHHTTSCC----------CCCSSCSSCCSHHHHHHHHHHHHTTCH
T ss_pred             HHHHhcCCCCCccccHHHHHHHHHHHHHHHHHHHHHHHhcCCC----------CcccccCchhhHHHHHHHHHHHHhccc
Confidence            55 55555430  367777765422    89999999998764          788888999   99999999999988 


Q ss_pred             hcHHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCC-------CCceEEecCcCC-CCC
Q 039903          154 IVTNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSY-------SGVKHIGGIMLE-RIP  225 (233)
Q Consensus       154 ~~~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~-------~ri~~~~gD~f~-~~P  225 (233)
                      ...+.+++.++ +++..+|||||||+|.++..+++++|+++++++|+|.+++.++++       +||+++.+|+++ ++|
T Consensus       177 ~~~~~l~~~~~-~~~~~~vLDvG~G~G~~~~~l~~~~p~~~~~~~D~~~~~~~a~~~~~~~~~~~~v~~~~~d~~~~~~~  255 (359)
T 1x19_A          177 FAIQLLLEEAK-LDGVKKMIDVGGGIGDISAAMLKHFPELDSTILNLPGAIDLVNENAAEKGVADRMRGIAVDIYKESYP  255 (359)
T ss_dssp             HHHHHHHHHCC-CTTCCEEEEESCTTCHHHHHHHHHCTTCEEEEEECGGGHHHHHHHHHHTTCTTTEEEEECCTTTSCCC
T ss_pred             hhHHHHHHhcC-CCCCCEEEEECCcccHHHHHHHHHCCCCeEEEEecHHHHHHHHHHHHhcCCCCCEEEEeCccccCCCC
Confidence            77788889888 888899999999999999999999999999999999899888642       579999999998 677


Q ss_pred             CCCEEEe
Q 039903          226 KGDAILI  232 (233)
Q Consensus       226 ~~D~~~l  232 (233)
                      .+|+|++
T Consensus       256 ~~D~v~~  262 (359)
T 1x19_A          256 EADAVLF  262 (359)
T ss_dssp             CCSEEEE
T ss_pred             CCCEEEE
Confidence            7799986

>2r3s_A Uncharacterized protein; methyltransferase domain, structural genomics, joint center structural genomics, JCSG, protein structure initiative; HET: MSE; 2.15A {Nostoc punctiforme}

Probab=100.00  E-value=2e-33  Score=241.07  Aligned_cols=210  Identities=17%  Similarity=0.162  Sum_probs=185.7

Q ss_pred             cccccchHHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceec
Q 039903            2 QPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGL   81 (233)
Q Consensus         2 ~~~~~~~~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~l   81 (233)
                      +++.|++.+++|+++++||||+.|.+    +|.|++|||+++++    +++.++||||+|++.|+|++.     +++|++
T Consensus        12 ~~~~~~~~~~~l~~~~~l~i~~~l~~----~~~t~~ela~~~~~----~~~~l~r~L~~L~~~g~l~~~-----~~~y~~   78 (335)
T 2r3s_A           12 NTVNAYQRSAAIKAAVELNVFTAISQ----GIESSQSLAQKCQT----SERGMRMLCDYLVIIGFMTKQ-----AEGYRL   78 (335)
T ss_dssp             HHHTTHHHHHHHHHHHHTTHHHHHTT----SEECHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEE-----TTEEEE
T ss_pred             HHHHHHHHHHHHHHHHHcChHHHHhc----CCCCHHHHHHHhCC----CchHHHHHHHHHHhcCCeEec-----CCEEec
Confidence            56789999999999999999999997    59999999999999    999999999999999999984     789999


Q ss_pred             cHhh-hHhhcCCCCCCccchhccccC-----chhhHHHHHHcCCcchhhhhCCccccccccCchHHHHHHHHHHhcchhc
Q 039903           82 AHVA-KYFVLNRDGVSLCPSRPWLET-----KPYEIYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIV  155 (233)
Q Consensus        82 t~~s-~~l~~~~~~~~~~~~~~~~~~-----~~~~L~~~l~~g~~~~~~~~g~~~~~~~~~~~~~~~~f~~am~~~~~~~  155 (233)
                      |+.+ ..|.++++ .++..++.+..+     .|.+|++++++++++|+     + |+++.++|+....|.+.|.......
T Consensus        79 t~~~~~~l~~~~~-~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~-----~-~~~~~~~~~~~~~~~~~~~~~~~~~  151 (335)
T 2r3s_A           79 TSDSAMFLDRQSK-FYVGDAIEFLLSPMITNGFNDLTAAVLKGGTAIS-----S-EGTLSPEHPVWVQFAKAMSPMMANP  151 (335)
T ss_dssp             CHHHHHHTCTTST-TCCGGGHHHHTCHHHHGGGTTHHHHHHHTSCCST-----T-TGGGSTTCTHHHHHHHHSGGGGHHH
T ss_pred             CHHHHHHhccCCc-HHHHHHHHHhcchhhHHHHHhHHHHHhcCCCCCC-----C-cccccCCHHHHHHHHHHHHHHHhhh
Confidence            9999 56766655 478888766532     78999999999988764     3 8888899999999999999988877


Q ss_pred             HHHHHHhcccc--cCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCC-------CCceEEecCcCC-CCC
Q 039903          156 TNRIIDSSKGF--EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSY-------SGVKHIGGIMLE-RIP  225 (233)
Q Consensus       156 ~~~~~~~~~~~--~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~-------~ri~~~~gD~f~-~~P  225 (233)
                      ...+++.++ +  ++..+|+|||||+|.++..+++++|+.+++++|++.+++.+++.       +||+++.+|+++ ++|
T Consensus       152 ~~~~~~~~~-~~~~~~~~vlDvG~G~G~~~~~l~~~~p~~~~~~~D~~~~~~~a~~~~~~~~~~~~v~~~~~d~~~~~~~  230 (335)
T 2r3s_A          152 AQLIAQLVN-ENKIEPLKVLDISASHGLFGIAVAQHNPNAEIFGVDWASVLEVAKENARIQGVASRYHTIAGSAFEVDYG  230 (335)
T ss_dssp             HHHHHHHHT-C--CCCSEEEEETCTTCHHHHHHHHHCTTCEEEEEECHHHHHHHHHHHHHHTCGGGEEEEESCTTTSCCC
T ss_pred             HHHHHHhcc-cccCCCCEEEEECCCcCHHHHHHHHHCCCCeEEEEecHHHHHHHHHHHHhcCCCcceEEEecccccCCCC
Confidence            778888887 7  78899999999999999999999999999999999888877653       579999999998 777


Q ss_pred             CC-CEEEe
Q 039903          226 KG-DAILI  232 (233)
Q Consensus       226 ~~-D~~~l  232 (233)
                      .+ |+|++
T Consensus       231 ~~~D~v~~  238 (335)
T 2r3s_A          231 NDYDLVLL  238 (335)
T ss_dssp             SCEEEEEE
T ss_pred             CCCcEEEE
Confidence            75 99986

>3mcz_A O-methyltransferase; adomet_mtases, S-adenosylmethionine-dependent methyltransfer structural genomics, PSI-2; HET: MSE; 1.90A {Burkholderia thailandensis}

Probab=100.00  E-value=7e-33  Score=239.57  Aligned_cols=209  Identities=13%  Similarity=0.154  Sum_probs=174.8

Q ss_pred             cccccchHHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceec
Q 039903            2 QPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGL   81 (233)
Q Consensus         2 ~~~~~~~~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~l   81 (233)
                      +++.|++.+++|++|++|||||.|..     |+|++|||+++++    +++.++||||+|++.|+|++.     ++.|++
T Consensus        30 ~~~~~~~~~~~l~~a~~lgif~~l~~-----~~t~~elA~~~~~----~~~~l~rlLr~L~~~gll~~~-----~~~y~~   95 (352)
T 3mcz_A           30 KLSDQYRQSAILHYAVADKLFDLTQT-----GRTPAEVAASFGM----VEGKAAILLHALAALGLLTKE-----GDAFRN   95 (352)
T ss_dssp             HHHHTHHHHHHHHHHHHTTHHHHTTS-----CBCHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEE-----TTEEEE
T ss_pred             HHHHHHHHHHHHHHHHHCChHHHhCC-----CCCHHHHHHHhCc----ChHHHHHHHHHHHHCCCeEec-----CCeeec
Confidence            57889999999999999999999964     8999999999999    999999999999999999996     578999


Q ss_pred             cHhhhHhh-cCCCCCCccchhcccc---CchhhHHHHHHcCCcc-hhhhhCCccccccccCchHHHHHHHHHHhcchhcH
Q 039903           82 AHVAKYFV-LNRDGVSLCPSRPWLE---TKPYEIYDAVLEGGIS-FNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVT  156 (233)
Q Consensus        82 t~~s~~l~-~~~~~~~~~~~~~~~~---~~~~~L~~~l~~g~~~-~~~~~g~~~~~~~~~~~~~~~~f~~am~~~~~~~~  156 (233)
                      |+.++.++ ++.+ .+++.++.+..   ..|.+|++++++|.+. |+..      .++..+|+..+.|+++|...... .
T Consensus        96 t~~s~~~l~~~~~-~~~~~~~~~~~~~~~~~~~l~~~l~~g~~~~f~~~------~~~~~~~~~~~~f~~~m~~~~~~-~  167 (352)
T 3mcz_A           96 TALTERYLTTTSA-DYIGPIVEHQYLQWDNWPRLGEILRSEKPLAFQQE------SRFAHDTRARDAFNDAMVRLSQP-M  167 (352)
T ss_dssp             CHHHHHHHSTTCT-TCCHHHHHHHHTTTTTGGGHHHHHTCSSCCTTSHH------HHTTTCHHHHHHHHHHHHHHHHH-H
T ss_pred             CHHHHhhccCCCh-hhHHHHHHHhHHHHHHHHHHHHHHhCCCCCCcccc------cccccCHHHHHHHHHHHHhhhhh-H
Confidence            99998655 4444 56777765432   2899999999998754 3322      12357899999999999984433 2


Q ss_pred             HHHHHhcccccC-cceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCC-------CCceEEecCcCCC---CC
Q 039903          157 NRIIDSSKGFEQ-IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSY-------SGVKHIGGIMLER---IP  225 (233)
Q Consensus       157 ~~~~~~~~~~~~-~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~-------~ri~~~~gD~f~~---~P  225 (233)
                      ..+++.++ +++ ..+|||||||+|.++..+++++|+++++++|+|++++.+++.       +||+++.+|+++.   .|
T Consensus       168 ~~~l~~~~-~~~~~~~vlDvG~G~G~~~~~l~~~~p~~~~~~~D~~~~~~~a~~~~~~~~~~~~v~~~~~d~~~~~~~~~  246 (352)
T 3mcz_A          168 VDVVSELG-VFARARTVIDLAGGHGTYLAQVLRRHPQLTGQIWDLPTTRDAARKTIHAHDLGGRVEFFEKNLLDARNFEG  246 (352)
T ss_dssp             HHHHHTCG-GGTTCCEEEEETCTTCHHHHHHHHHCTTCEEEEEECGGGHHHHHHHHHHTTCGGGEEEEECCTTCGGGGTT
T ss_pred             HHHHHhCC-CcCCCCEEEEeCCCcCHHHHHHHHhCCCCeEEEEECHHHHHHHHHHHHhcCCCCceEEEeCCcccCcccCC
Confidence            47888888 877 899999999999999999999999999999999988877652       5899999999994   56


Q ss_pred             CC-CEEEeC
Q 039903          226 KG-DAILIK  233 (233)
Q Consensus       226 ~~-D~~~lk  233 (233)
                      .+ |+|+++
T Consensus       247 ~~~D~v~~~  255 (352)
T 3mcz_A          247 GAADVVMLN  255 (352)
T ss_dssp             CCEEEEEEE
T ss_pred             CCccEEEEe
Confidence            64 999863

>2qm3_A Predicted methyltransferase; putative methyltransferase, structural genomics, pyrococcus PSI-2, protein structure initiative; HET: MSE; 2.05A {Pyrococcus furiosus dsm 3638}

Probab=99.45  E-value=6.6e-13  Score=115.42  Aligned_cols=178  Identities=10%  Similarity=0.005  Sum_probs=114.4

Q ss_pred             ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhcCCCCCCccc
Q 039903           20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLNRDGVSLCP   99 (233)
Q Consensus        20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~~~~~~~~~~   99 (233)
                      ++|..| .    +|.|+.|||..+++    +++.+++||+.|++.|+++..     ++ |++|+.+..++..........
T Consensus        47 ~ll~~L-~----~~~t~~eLa~~~g~----~~~~v~~~L~~l~~~gll~~~-----~~-~~lt~~~~~~l~~~~~~~~~~  111 (373)
T 2qm3_A           47 NVLSAV-L----ASDDIWRIVDLSEE----PLPLVVAILESLNELGYVTFE-----DG-VKLTEKGEELVAEYGIGKRYD  111 (373)
T ss_dssp             HHHHHH-H----HCSCHHHHHHHHTS----CHHHHHHHHHHHHHTTSEECS-----SS-SEECHHHHHHHHHHTCCCCCC
T ss_pred             HHHHHh-c----CCCCHHHHHHHhCC----ChHHHHHHHHHHhhCCcEEEC-----CC-EEECHHHHHHHHhcCcccccc
Confidence            789999 4    48999999999999    999999999999999999874     35 999998776543211111111


Q ss_pred             hh-cccc----------CchhhHHHHHHcCCcchhhhhCCccccccccCchHHHHHHHHHHhcchhcHHHHHHhcccccC
Q 039903          100 SR-PWLE----------TKPYEIYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQ  168 (233)
Q Consensus       100 ~~-~~~~----------~~~~~L~~~l~~g~~~~~~~~g~~~~~~~~~~~~~~~~f~~am~~~~~~~~~~~~~~~~~~~~  168 (233)
                      .+ ....          ..|..+.+.++....+      ...|+.....++.  .....+         ..... . ...
T Consensus       112 ~~~~~~~g~g~~~~~~~~~~~~l~~~~~~~~~~------~~~~~~~~~~~~~--~~~~~l---------~~~~~-~-~~~  172 (373)
T 2qm3_A          112 FTCPHCQGKTVDLQAFADLLEQFREIVKDRPEP------LHEFDQAYVTPET--TVARVI---------LMHTR-G-DLE  172 (373)
T ss_dssp             ------------CGGGHHHHHHHHHHHTTCCCC------CGGGTCCCBCHHH--HHHHHH---------HHHHT-T-CST
T ss_pred             ccchhhcCCCcchhhhHHHHHHHHHHHhcCCcc------chhcCCeecCHHH--HHHHHH---------HHhhc-C-CCC
Confidence            11 0001          0233444444432211      1111110011111  111111         00111 1 123


Q ss_pred             cceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCCCCCC----C-CEEEe
Q 039903          169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLERIPK----G-DAILI  232 (233)
Q Consensus       169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~~P~----~-D~~~l  232 (233)
                      ..+|+||| |+|.++..+++..|..+++.+|+ |.+++.++++      +||+++.+|+++++|.    . |+|++
T Consensus       173 ~~~VLDlG-G~G~~~~~la~~~~~~~v~~vDi~~~~l~~a~~~~~~~g~~~v~~~~~D~~~~l~~~~~~~fD~Vi~  247 (373)
T 2qm3_A          173 NKDIFVLG-DDDLTSIALMLSGLPKRIAVLDIDERLTKFIEKAANEIGYEDIEIFTFDLRKPLPDYALHKFDTFIT  247 (373)
T ss_dssp             TCEEEEES-CTTCHHHHHHHHTCCSEEEEECSCHHHHHHHHHHHHHHTCCCEEEECCCTTSCCCTTTSSCBSEEEE
T ss_pred             CCEEEEEC-CCCHHHHHHHHhCCCCEEEEEECCHHHHHHHHHHHHHcCCCCEEEEEChhhhhchhhccCCccEEEE
Confidence            57999999 99999999999999899999999 7788887763      4899999999986653    3 99986

>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=98.72  E-value=1.1e-08  Score=81.70  Aligned_cols=64  Identities=19%  Similarity=0.305  Sum_probs=53.3

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-----CCceEEecCcCC-CCCCC--CEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-----SGVKHIGGIMLE-RIPKG--DAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-----~ri~~~~gD~f~-~~P~~--D~~~l  232 (233)
                      +...+|+|||||+|.++..+++++|  +++.+|+ |++++.+++.     ++|+++.+|+.+ ++|.+  |+++.
T Consensus        37 ~~~~~vLDlG~G~G~~~~~l~~~~~--~v~~vD~s~~~~~~a~~~~~~~~~~~~~~~~d~~~~~~~~~~~D~v~~  109 (227)
T 1ve3_A           37 KKRGKVLDLACGVGGFSFLLEDYGF--EVVGVDISEDMIRKAREYAKSRESNVEFIVGDARKLSFEDKTFDYVIF  109 (227)
T ss_dssp             CSCCEEEEETCTTSHHHHHHHHTTC--EEEEEESCHHHHHHHHHHHHHTTCCCEEEECCTTSCCSCTTCEEEEEE
T ss_pred             CCCCeEEEEeccCCHHHHHHHHcCC--EEEEEECCHHHHHHHHHHHHhcCCCceEEECchhcCCCCCCcEEEEEE
Confidence            3467999999999999999999988  7999998 6677777653     789999999998 66653  98874

>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=98.70  E-value=5e-08  Score=80.56  Aligned_cols=66  Identities=20%  Similarity=0.245  Sum_probs=55.1

Q ss_pred             cCcceEEEecCCccHHHHHHHHHc--CCCcEEEeec-hHHHhhccCC-------CCceEEecCcCC-CCCCCCEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNY--LHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLE-RIPKGDAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~--P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~-~~P~~D~~~l  232 (233)
                      +...+|+|||||+|.++..+++++  |+++++.+|+ |..++.|++.       .+|+++.+|+.+ +++..|++++
T Consensus        69 ~~~~~vLDlGcGtG~~~~~la~~~~~~~~~v~gvD~s~~ml~~A~~~~~~~~~~~~v~~~~~D~~~~~~~~~d~v~~  145 (261)
T 4gek_A           69 QPGTQVYDLGCSLGAATLSVRRNIHHDNCKIIAIDNSPAMIERCRRHIDAYKAPTPVDVIEGDIRDIAIENASMVVL  145 (261)
T ss_dssp             CTTCEEEEETCTTTHHHHHHHHTCCSSSCEEEEEESCHHHHHHHHHHHHTSCCSSCEEEEESCTTTCCCCSEEEEEE
T ss_pred             CCCCEEEEEeCCCCHHHHHHHHhcCCCCCEEEEEECCHHHHHHHHHHHHhhccCceEEEeeccccccccccccccee
Confidence            556899999999999999999985  6789999998 5678877642       589999999998 7776788764

>3dtn_A Putative methyltransferase MM_2633; structural genomics, unknown function, PSI-2, protein structure initiative; 2.09A {Methanosarcina mazei}

Probab=98.63  E-value=1.3e-07  Score=75.88  Aligned_cols=75  Identities=13%  Similarity=0.183  Sum_probs=58.9

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC----CCceEEecCcCC-CCCCC-CEE
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY----SGVKHIGGIMLE-RIPKG-DAI  230 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~----~ri~~~~gD~f~-~~P~~-D~~  230 (233)
                      .++..+....+..+|||||||+|.++..+++++|..+++.+|+ |..++.+++.    .+|+++.+|+.+ +.+.. |++
T Consensus        34 ~~~~~~~~~~~~~~vLDiG~G~G~~~~~l~~~~~~~~v~~vD~s~~~~~~a~~~~~~~~~~~~~~~d~~~~~~~~~fD~v  113 (234)
T 3dtn_A           34 VSVSIASVDTENPDILDLGAGTGLLSAFLMEKYPEATFTLVDMSEKMLEIAKNRFRGNLKVKYIEADYSKYDFEEKYDMV  113 (234)
T ss_dssp             HHHHTCCCSCSSCEEEEETCTTSHHHHHHHHHCTTCEEEEEESCHHHHHHHHHHTCSCTTEEEEESCTTTCCCCSCEEEE
T ss_pred             HHHHHhhcCCCCCeEEEecCCCCHHHHHHHHhCCCCeEEEEECCHHHHHHHHHhhccCCCEEEEeCchhccCCCCCceEE
Confidence            3444433124558999999999999999999999999999999 6677776542    489999999998 55543 988


Q ss_pred             Ee
Q 039903          231 LI  232 (233)
Q Consensus       231 ~l  232 (233)
                      +.
T Consensus       114 ~~  115 (234)
T 3dtn_A          114 VS  115 (234)
T ss_dssp             EE
T ss_pred             EE
Confidence            75

>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=98.58  E-value=8.7e-08  Score=79.42  Aligned_cols=74  Identities=15%  Similarity=0.126  Sum_probs=57.5

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHH-cCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCCCCCCC-
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISN-YLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLERIPKG-  227 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~-~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~~P~~-  227 (233)
                      .++..++ .....+|+|+|||+|.++..+++. +|..+++.+|+ |..++.++++       ++++++.+|+.+++|.+ 
T Consensus       101 ~~~~~~~-~~~~~~VLD~G~G~G~~~~~la~~~~~~~~v~~vD~s~~~~~~a~~~~~~~~g~~~v~~~~~d~~~~~~~~~  179 (275)
T 1yb2_A          101 YIIMRCG-LRPGMDILEVGVGSGNMSSYILYALNGKGTLTVVERDEDNLKKAMDNLSEFYDIGNVRTSRSDIADFISDQM  179 (275)
T ss_dssp             -----CC-CCTTCEEEEECCTTSHHHHHHHHHHTTSSEEEEECSCHHHHHHHHHHHHTTSCCTTEEEECSCTTTCCCSCC
T ss_pred             HHHHHcC-CCCcCEEEEecCCCCHHHHHHHHHcCCCCEEEEEECCHHHHHHHHHHHHhcCCCCcEEEEECchhccCcCCC
Confidence            4555555 667789999999999999999998 79999999999 6677666532       58999999999977753 


Q ss_pred             -CEEEe
Q 039903          228 -DAILI  232 (233)
Q Consensus       228 -D~~~l  232 (233)
                       |+|++
T Consensus       180 fD~Vi~  185 (275)
T 1yb2_A          180 YDAVIA  185 (275)
T ss_dssp             EEEEEE
T ss_pred             ccEEEE
Confidence             98875

>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=98.56  E-value=4.4e-08  Score=79.92  Aligned_cols=75  Identities=13%  Similarity=0.110  Sum_probs=61.9

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHH-cCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCCCCCCC
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISN-YLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLERIPKG  227 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~-~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~~P~~  227 (233)
                      ..++..++ .....+|+|+|||+|.++..+++. .|..+++.+|+ |+.++.|+++       +||+++.+|+.+.+|..
T Consensus        83 ~~i~~~~~-~~~~~~vldiG~G~G~~~~~l~~~~~~~~~v~~~D~~~~~~~~a~~~~~~~~~~~~v~~~~~d~~~~~~~~  161 (255)
T 3mb5_A           83 ALIVAYAG-ISPGDFIVEAGVGSGALTLFLANIVGPEGRVVSYEIREDFAKLAWENIKWAGFDDRVTIKLKDIYEGIEEE  161 (255)
T ss_dssp             HHHHHHTT-CCTTCEEEEECCTTSHHHHHHHHHHCTTSEEEEECSCHHHHHHHHHHHHHHTCTTTEEEECSCGGGCCCCC
T ss_pred             HHHHHhhC-CCCCCEEEEecCCchHHHHHHHHHhCCCeEEEEEecCHHHHHHHHHHHHHcCCCCceEEEECchhhccCCC
Confidence            34555555 667789999999999999999999 89999999999 5677777653       56999999999987763


Q ss_pred             --CEEEe
Q 039903          228 --DAILI  232 (233)
Q Consensus       228 --D~~~l  232 (233)
                        |++++
T Consensus       162 ~~D~v~~  168 (255)
T 3mb5_A          162 NVDHVIL  168 (255)
T ss_dssp             SEEEEEE
T ss_pred             CcCEEEE
Confidence              98875

>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=98.56  E-value=2.4e-07  Score=78.05  Aligned_cols=84  Identities=18%  Similarity=0.122  Sum_probs=62.6

Q ss_pred             HHhcchhcHHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecC
Q 039903          148 MLNHTSIVTNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGI  219 (233)
Q Consensus       148 m~~~~~~~~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD  219 (233)
                      +..........+++.++......+|||||||.|.++..+++++ ..+++.+|+ |..++.++++       ++|+++.+|
T Consensus        97 ~~~~~~~~~~~l~~~l~~~~~~~~vLDiGcG~G~~~~~la~~~-~~~v~gvD~s~~~~~~a~~~~~~~~~~~~v~~~~~d  175 (312)
T 3vc1_A           97 LHRLESAQAEFLMDHLGQAGPDDTLVDAGCGRGGSMVMAHRRF-GSRVEGVTLSAAQADFGNRRARELRIDDHVRSRVCN  175 (312)
T ss_dssp             HHHHHHHHHHHHHTTSCCCCTTCEEEEESCTTSHHHHHHHHHH-CCEEEEEESCHHHHHHHHHHHHHTTCTTTEEEEECC
T ss_pred             hhhHHHHHHHHHHHHhccCCCCCEEEEecCCCCHHHHHHHHHc-CCEEEEEeCCHHHHHHHHHHHHHcCCCCceEEEECC
Confidence            3333333334555555435567899999999999999999986 678999998 5677777642       589999999


Q ss_pred             cCC-CCCCC--CEEEe
Q 039903          220 MLE-RIPKG--DAILI  232 (233)
Q Consensus       220 ~f~-~~P~~--D~~~l  232 (233)
                      +.+ ++|.+  |+|+.
T Consensus       176 ~~~~~~~~~~fD~V~~  191 (312)
T 3vc1_A          176 MLDTPFDKGAVTASWN  191 (312)
T ss_dssp             TTSCCCCTTCEEEEEE
T ss_pred             hhcCCCCCCCEeEEEE
Confidence            998 77753  99874

>3kr9_A SAM-dependent methyltransferase; class I rossmann-like methyltransferase fold; 2.00A {Streptococcus pneumoniae} PDB: 3ku1_A*

Probab=98.56  E-value=6.7e-08  Score=77.99  Aligned_cols=66  Identities=14%  Similarity=-0.003  Sum_probs=55.8

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC-------CCceEEecCcCCCCCC---CCEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY-------SGVKHIGGIMLERIPK---GDAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~-------~ri~~~~gD~f~~~P~---~D~~~l  232 (233)
                      ++..+|+|||||+|.+++.+++.+|..+++..|.. ..++.|+++       +||+++.+|.++++|.   .|++++
T Consensus        14 ~~g~~VlDIGtGsG~l~i~la~~~~~~~V~avDi~~~al~~A~~N~~~~gl~~~i~~~~~d~l~~l~~~~~~D~Ivi   90 (225)
T 3kr9_A           14 SQGAILLDVGSDHAYLPIELVERGQIKSAIAGEVVEGPYQSAVKNVEAHGLKEKIQVRLANGLAAFEETDQVSVITI   90 (225)
T ss_dssp             CTTEEEEEETCSTTHHHHHHHHTTSEEEEEEEESSHHHHHHHHHHHHHTTCTTTEEEEECSGGGGCCGGGCCCEEEE
T ss_pred             CCCCEEEEeCCCcHHHHHHHHHhCCCCEEEEEECCHHHHHHHHHHHHHcCCCceEEEEECchhhhcccCcCCCEEEE
Confidence            34579999999999999999999999999999984 577777653       5899999999998773   488764

>3e05_A Precorrin-6Y C5,15-methyltransferase (decarboxyla; porphyrin metabolism, S-adenosyl-methionine; 1.80A {Geobacter metallireducens} SCOP: c.66.1.0

Probab=98.55  E-value=2.3e-07  Score=73.15  Aligned_cols=74  Identities=9%  Similarity=0.062  Sum_probs=60.3

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCCCCC---CC
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLERIP---KG  227 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~~P---~~  227 (233)
                      .++..++ .....+|+|||||+|.++..+++.+|..+++.+|+ |+.++.++++      ++++++.+|+.+.++   ..
T Consensus        31 ~~l~~l~-~~~~~~vLDiG~G~G~~~~~la~~~~~~~v~~vD~s~~~~~~a~~~~~~~~~~~v~~~~~d~~~~~~~~~~~  109 (204)
T 3e05_A           31 VTLSKLR-LQDDLVMWDIGAGSASVSIEASNLMPNGRIFALERNPQYLGFIRDNLKKFVARNVTLVEAFAPEGLDDLPDP  109 (204)
T ss_dssp             HHHHHTT-CCTTCEEEEETCTTCHHHHHHHHHCTTSEEEEEECCHHHHHHHHHHHHHHTCTTEEEEECCTTTTCTTSCCC
T ss_pred             HHHHHcC-CCCCCEEEEECCCCCHHHHHHHHHCCCCEEEEEeCCHHHHHHHHHHHHHhCCCcEEEEeCChhhhhhcCCCC
Confidence            3455555 66778999999999999999999999999999998 6677777653      689999999987544   24


Q ss_pred             CEEEe
Q 039903          228 DAILI  232 (233)
Q Consensus       228 D~~~l  232 (233)
                      |++++
T Consensus       110 D~i~~  114 (204)
T 3e05_A          110 DRVFI  114 (204)
T ss_dssp             SEEEE
T ss_pred             CEEEE
Confidence            98875

>3dlc_A Putative S-adenosyl-L-methionine-dependent methyltransferase; structural genomics, joint center for structural genomics; HET: MSE SAM; 1.15A {Methanococcus maripaludis}

Probab=98.55  E-value=8.9e-08  Score=75.68  Aligned_cols=73  Identities=16%  Similarity=0.213  Sum_probs=57.8

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCC-CCCCC
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLE-RIPKG  227 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~-~~P~~  227 (233)
                      ..+++.++ .++. +|||||||+|.++..++++ |..+++.+|+ |..++.+++.       ++++++.+|+.+ ++|.+
T Consensus        34 ~~~~~~~~-~~~~-~vLdiG~G~G~~~~~l~~~-~~~~v~~~D~s~~~~~~a~~~~~~~~~~~~~~~~~~d~~~~~~~~~  110 (219)
T 3dlc_A           34 ENIINRFG-ITAG-TCIDIGSGPGALSIALAKQ-SDFSIRALDFSKHMNEIALKNIADANLNDRIQIVQGDVHNIPIEDN  110 (219)
T ss_dssp             HHHHHHHC-CCEE-EEEEETCTTSHHHHHHHHH-SEEEEEEEESCHHHHHHHHHHHHHTTCTTTEEEEECBTTBCSSCTT
T ss_pred             HHHHHhcC-CCCC-EEEEECCCCCHHHHHHHHc-CCCeEEEEECCHHHHHHHHHHHHhccccCceEEEEcCHHHCCCCcc
Confidence            33444444 3443 9999999999999999998 8899999998 6677776653       589999999998 77753


Q ss_pred             --CEEEe
Q 039903          228 --DAILI  232 (233)
Q Consensus       228 --D~~~l  232 (233)
                        |+|+.
T Consensus       111 ~~D~v~~  117 (219)
T 3dlc_A          111 YADLIVS  117 (219)
T ss_dssp             CEEEEEE
T ss_pred             cccEEEE
Confidence              98875

>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=98.54  E-value=1.9e-07  Score=74.22  Aligned_cols=65  Identities=18%  Similarity=0.218  Sum_probs=54.5

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCC-C--CCCC--CEEEe
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLE-R--IPKG--DAILI  232 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~-~--~P~~--D~~~l  232 (233)
                      ...+++|||||+|.++..+++++|+.+++.+|+ +..++.++++      ++|+++.+|+.+ +  +|.+  |++++
T Consensus        41 ~~~~vLDiGcG~G~~~~~la~~~p~~~v~gvD~s~~~l~~a~~~~~~~~~~~v~~~~~d~~~~~~~~~~~~~D~i~~  117 (214)
T 1yzh_A           41 DNPIHVEVGSGKGAFVSGMAKQNPDINYIGIDIQKSVLSYALDKVLEVGVPNIKLLWVDGSDLTDYFEDGEIDRLYL  117 (214)
T ss_dssp             CCCEEEEESCTTSHHHHHHHHHCTTSEEEEEESCHHHHHHHHHHHHHHCCSSEEEEECCSSCGGGTSCTTCCSEEEE
T ss_pred             CCCeEEEEccCcCHHHHHHHHHCCCCCEEEEEcCHHHHHHHHHHHHHcCCCCEEEEeCCHHHHHhhcCCCCCCEEEE
Confidence            457899999999999999999999999999998 5677776542      689999999987 4  5553  88874

>3ege_A Putative methyltransferase from antibiotic biosyn pathway; YP_324569.1, putative methyltransferase from antibiotic BIOS pathway; 2.40A {Anabaena variabilis atcc 29413}

Probab=98.51  E-value=4.1e-07  Score=74.58  Aligned_cols=73  Identities=16%  Similarity=0.203  Sum_probs=59.8

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCCCCceEEecCcCC-CCCCC--CEEEe
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSYSGVKHIGGIMLE-RIPKG--DAILI  232 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~~ri~~~~gD~f~-~~P~~--D~~~l  232 (233)
                      ..+++.++ .....+|||||||+|.++..+++  |..+++.+|+ |..++.++...+++++.+|+.+ ++|.+  |+|+.
T Consensus        24 ~~l~~~~~-~~~~~~vLDiGcG~G~~~~~l~~--~~~~v~gvD~s~~~~~~a~~~~~~~~~~~d~~~~~~~~~~fD~v~~  100 (261)
T 3ege_A           24 NAIINLLN-LPKGSVIADIGAGTGGYSVALAN--QGLFVYAVEPSIVMRQQAVVHPQVEWFTGYAENLALPDKSVDGVIS  100 (261)
T ss_dssp             HHHHHHHC-CCTTCEEEEETCTTSHHHHHHHT--TTCEEEEECSCHHHHHSSCCCTTEEEECCCTTSCCSCTTCBSEEEE
T ss_pred             HHHHHHhC-CCCCCEEEEEcCcccHHHHHHHh--CCCEEEEEeCCHHHHHHHHhccCCEEEECchhhCCCCCCCEeEEEE
Confidence            34555555 56778999999999999999998  7889999998 4578888777799999999988 77653  99875

>3dh0_A SAM dependent methyltransferase; cystal structure, PSI-2, NYSGXRC, structural genomics, protein structure initiative; HET: SAM; 2.72A {Aquifex aeolicus}

Probab=98.49  E-value=2.1e-07  Score=73.94  Aligned_cols=75  Identities=15%  Similarity=0.222  Sum_probs=61.7

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHc-CCCcEEEeec-hHHHhhccCC------CCceEEecCcCC-CCCCC
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNY-LHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLE-RIPKG  227 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~-~~P~~  227 (233)
                      ..+++.++ .....+|||||||+|.++..+++.. |..+++.+|. +..++.+++.      ++|+++.+|+.+ +++.+
T Consensus        27 ~~~~~~~~-~~~~~~vLDiG~G~G~~~~~l~~~~~~~~~v~~vD~s~~~~~~a~~~~~~~~~~~~~~~~~d~~~~~~~~~  105 (219)
T 3dh0_A           27 EKVLKEFG-LKEGMTVLDVGTGAGFYLPYLSKMVGEKGKVYAIDVQEEMVNYAWEKVNKLGLKNVEVLKSEENKIPLPDN  105 (219)
T ss_dssp             HHHHHHHT-CCTTCEEEESSCTTCTTHHHHHHHHTTTCEEEEEESCHHHHHHHHHHHHHHTCTTEEEEECBTTBCSSCSS
T ss_pred             HHHHHHhC-CCCCCEEEEEecCCCHHHHHHHHHhCCCcEEEEEECCHHHHHHHHHHHHHcCCCcEEEEecccccCCCCCC
Confidence            45666666 6777899999999999999999997 8899999998 5677777653      589999999988 67664


Q ss_pred             --CEEEe
Q 039903          228 --DAILI  232 (233)
Q Consensus       228 --D~~~l  232 (233)
                        |+|+.
T Consensus       106 ~fD~v~~  112 (219)
T 3dh0_A          106 TVDFIFM  112 (219)
T ss_dssp             CEEEEEE
T ss_pred             CeeEEEe
Confidence              99875

>3mq2_A 16S rRNA methyltransferase; methyltranferase, ribosomal, antibiotic resistance, aminoglycoside, S-adenosyl-L-methionine; HET: SAH; 1.69A {Streptomyces SP}

Probab=98.48  E-value=4.7e-07  Score=71.97  Aligned_cols=71  Identities=11%  Similarity=0.097  Sum_probs=54.1

Q ss_pred             HHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhh----ccC------CCCceEEecCcCC-CCCCC
Q 039903          160 IDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQD----SSS------YSGVKHIGGIMLE-RIPKG  227 (233)
Q Consensus       160 ~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~----a~~------~~ri~~~~gD~f~-~~P~~  227 (233)
                      +..++ .....+|||||||+|.++..+++++|..+++.+|+.+ .++.    +++      .++|+++.+|+.+ +++.+
T Consensus        20 ~~~l~-~~~~~~vLDiGcG~G~~~~~la~~~p~~~v~gvD~s~~~l~~~~~~a~~~~~~~~~~~v~~~~~d~~~l~~~~~   98 (218)
T 3mq2_A           20 FEQLR-SQYDDVVLDVGTGDGKHPYKVARQNPSRLVVALDADKSRMEKISAKAAAKPAKGGLPNLLYLWATAERLPPLSG   98 (218)
T ss_dssp             HHHHH-TTSSEEEEEESCTTCHHHHHHHHHCTTEEEEEEESCGGGGHHHHHHHTSCGGGTCCTTEEEEECCSTTCCSCCC
T ss_pred             HHHhh-ccCCCEEEEecCCCCHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHhhhhcCCCceEEEecchhhCCCCCC
Confidence            34444 4566899999999999999999999999999999854 3432    322      2589999999998 65543


Q ss_pred             -CEEE
Q 039903          228 -DAIL  231 (233)
Q Consensus       228 -D~~~  231 (233)
                       |.+.
T Consensus        99 ~d~v~  103 (218)
T 3mq2_A           99 VGELH  103 (218)
T ss_dssp             EEEEE
T ss_pred             CCEEE
Confidence             5554

>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=98.47  E-value=2.6e-07  Score=75.49  Aligned_cols=76  Identities=16%  Similarity=0.233  Sum_probs=59.7

Q ss_pred             hcHHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCC-CCC
Q 039903          154 IVTNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLE-RIP  225 (233)
Q Consensus       154 ~~~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~-~~P  225 (233)
                      .....+++.++ .....+|||||||+|.++..++++.+  +++.+|+ |..++.+++.      ++|+++.+|+.+ ++|
T Consensus        24 ~~~~~l~~~l~-~~~~~~vLDiGcG~G~~~~~l~~~~~--~v~gvD~s~~~l~~a~~~~~~~~~~~v~~~~~d~~~l~~~  100 (260)
T 1vl5_A           24 SDLAKLMQIAA-LKGNEEVLDVATGGGHVANAFAPFVK--KVVAFDLTEDILKVARAFIEGNGHQQVEYVQGDAEQMPFT  100 (260)
T ss_dssp             CCHHHHHHHHT-CCSCCEEEEETCTTCHHHHHHGGGSS--EEEEEESCHHHHHHHHHHHHHTTCCSEEEEECCC-CCCSC
T ss_pred             HHHHHHHHHhC-CCCCCEEEEEeCCCCHHHHHHHHhCC--EEEEEeCCHHHHHHHHHHHHhcCCCceEEEEecHHhCCCC
Confidence            33456666666 66778999999999999999999986  7999998 5677766542      679999999988 777


Q ss_pred             CC--CEEEe
Q 039903          226 KG--DAILI  232 (233)
Q Consensus       226 ~~--D~~~l  232 (233)
                      .+  |+|+.
T Consensus       101 ~~~fD~V~~  109 (260)
T 1vl5_A          101 DERFHIVTC  109 (260)
T ss_dssp             TTCEEEEEE
T ss_pred             CCCEEEEEE
Confidence            53  99874

>3lec_A NADB-rossmann superfamily protein; PSI, MCSG, structural genomics, midwest CENT structural genomics, protein structure initiative; 1.80A {Streptococcus agalactiae}

Probab=98.46  E-value=1.6e-07  Score=75.95  Aligned_cols=66  Identities=15%  Similarity=0.014  Sum_probs=55.3

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC-------CCceEEecCcCCCCCC---CCEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY-------SGVKHIGGIMLERIPK---GDAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~-------~ri~~~~gD~f~~~P~---~D~~~l  232 (233)
                      ++..+|+|||||+|.+++.+++..|..+++..|+. ..++.|+++       +||+++.+|.++.++.   .|++++
T Consensus        20 ~~g~~VlDIGtGsG~l~i~la~~~~~~~V~AvDi~~~al~~A~~N~~~~gl~~~I~~~~gD~l~~~~~~~~~D~Ivi   96 (230)
T 3lec_A           20 PKGARLLDVGSDHAYLPIFLLQMGYCDFAIAGEVVNGPYQSALKNVSEHGLTSKIDVRLANGLSAFEEADNIDTITI   96 (230)
T ss_dssp             CTTEEEEEETCSTTHHHHHHHHTTCEEEEEEEESSHHHHHHHHHHHHHTTCTTTEEEEECSGGGGCCGGGCCCEEEE
T ss_pred             CCCCEEEEECCchHHHHHHHHHhCCCCEEEEEECCHHHHHHHHHHHHHcCCCCcEEEEECchhhccccccccCEEEE
Confidence            44589999999999999999999999999999984 577777653       6899999999996553   498764

>3bus_A REBM, methyltransferase; rebeccamycin synthesis; HET: SAH; 2.65A {Lechevalieria aerocolonigenes}

Probab=98.46  E-value=4.8e-07  Score=74.30  Aligned_cols=74  Identities=12%  Similarity=0.223  Sum_probs=59.5

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCC-CCCCC
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLE-RIPKG  227 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~-~~P~~  227 (233)
                      ..+++.++ .....+|||||||.|.++..+++++ ..+++.+|+ +..++.+++.       ++|+++.+|+.+ ++|.+
T Consensus        51 ~~l~~~~~-~~~~~~vLDiGcG~G~~~~~l~~~~-~~~v~gvD~s~~~~~~a~~~~~~~~~~~~~~~~~~d~~~~~~~~~  128 (273)
T 3bus_A           51 DEMIALLD-VRSGDRVLDVGCGIGKPAVRLATAR-DVRVTGISISRPQVNQANARATAAGLANRVTFSYADAMDLPFEDA  128 (273)
T ss_dssp             HHHHHHSC-CCTTCEEEEESCTTSHHHHHHHHHS-CCEEEEEESCHHHHHHHHHHHHHTTCTTTEEEEECCTTSCCSCTT
T ss_pred             HHHHHhcC-CCCCCEEEEeCCCCCHHHHHHHHhc-CCEEEEEeCCHHHHHHHHHHHHhcCCCcceEEEECccccCCCCCC
Confidence            45666666 6677899999999999999999987 689999998 5566666542       589999999998 77753


Q ss_pred             --CEEEe
Q 039903          228 --DAILI  232 (233)
Q Consensus       228 --D~~~l  232 (233)
                        |+|+.
T Consensus       129 ~fD~v~~  135 (273)
T 3bus_A          129 SFDAVWA  135 (273)
T ss_dssp             CEEEEEE
T ss_pred             CccEEEE
Confidence              98874

>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=98.46  E-value=4.2e-07  Score=73.90  Aligned_cols=73  Identities=19%  Similarity=0.197  Sum_probs=57.2

Q ss_pred             HHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCC-CCCCC--
Q 039903          159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLE-RIPKG--  227 (233)
Q Consensus       159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~-~~P~~--  227 (233)
                      ++..+...+...+|||||||+|.++..+++++|. +++.+|+ |..++.+++.       +||+++.+|+.+ ++|.+  
T Consensus        37 ~l~~l~~~~~~~~vLDiG~G~G~~~~~l~~~~~~-~v~~vD~s~~~~~~a~~~~~~~~~~~~~~~~~~d~~~~~~~~~~f  115 (257)
T 3f4k_A           37 AVSFINELTDDAKIADIGCGTGGQTLFLADYVKG-QITGIDLFPDFIEIFNENAVKANCADRVKGITGSMDNLPFQNEEL  115 (257)
T ss_dssp             HHTTSCCCCTTCEEEEETCTTSHHHHHHHHHCCS-EEEEEESCHHHHHHHHHHHHHTTCTTTEEEEECCTTSCSSCTTCE
T ss_pred             HHHHHhcCCCCCeEEEeCCCCCHHHHHHHHhCCC-eEEEEECCHHHHHHHHHHHHHcCCCCceEEEECChhhCCCCCCCE
Confidence            4444433556679999999999999999999987 9999998 5577766542       579999999977 66653  


Q ss_pred             CEEEe
Q 039903          228 DAILI  232 (233)
Q Consensus       228 D~~~l  232 (233)
                      |+|+.
T Consensus       116 D~v~~  120 (257)
T 3f4k_A          116 DLIWS  120 (257)
T ss_dssp             EEEEE
T ss_pred             EEEEe
Confidence            99874

>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=98.46  E-value=1.4e-07  Score=74.26  Aligned_cols=64  Identities=13%  Similarity=0.081  Sum_probs=53.0

Q ss_pred             cceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCCCCCC-C-CEEEe
Q 039903          169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLERIPK-G-DAILI  232 (233)
Q Consensus       169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~~P~-~-D~~~l  232 (233)
                      ..+|+|||||+|.++..+++.+|..+++.+|. |..++.++++      ++|+++.+|+.+..|. . |+++.
T Consensus        66 ~~~vLDiG~G~G~~~~~l~~~~~~~~v~~vD~s~~~~~~a~~~~~~~~~~~v~~~~~d~~~~~~~~~~D~i~~  138 (207)
T 1jsx_A           66 GERFIDVGTGPGLPGIPLSIVRPEAHFTLLDSLGKRVRFLRQVQHELKLENIEPVQSRVEEFPSEPPFDGVIS  138 (207)
T ss_dssp             SSEEEEETCTTTTTHHHHHHHCTTSEEEEEESCHHHHHHHHHHHHHTTCSSEEEEECCTTTSCCCSCEEEEEC
T ss_pred             CCeEEEECCCCCHHHHHHHHHCCCCEEEEEeCCHHHHHHHHHHHHHcCCCCeEEEecchhhCCccCCcCEEEE
Confidence            57999999999999999999999999999998 5577766542      4599999999984444 3 98874

>3ou2_A SAM-dependent methyltransferase; O-methyltransferase, SAH; HET: SAH; 1.50A {Streptomyces luridus} PDB: 3ou6_A* 3ou7_A*

Probab=98.45  E-value=9.8e-07  Score=69.69  Aligned_cols=74  Identities=11%  Similarity=0.166  Sum_probs=57.5

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC--CCceEEecCcCCCCCCC--CEEE
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY--SGVKHIGGIMLERIPKG--DAIL  231 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~--~ri~~~~gD~f~~~P~~--D~~~  231 (233)
                      ..+++.+.......+|||||||+|.++..++++  ..+++.+|+ |..++.+++.  ++++++.+|+.+..|.+  |+++
T Consensus        35 ~~~~~~l~~~~~~~~vLdiG~G~G~~~~~l~~~--~~~v~~~D~s~~~~~~a~~~~~~~~~~~~~d~~~~~~~~~~D~v~  112 (218)
T 3ou2_A           35 PAALERLRAGNIRGDVLELASGTGYWTRHLSGL--ADRVTALDGSAEMIAEAGRHGLDNVEFRQQDLFDWTPDRQWDAVF  112 (218)
T ss_dssp             HHHHHHHTTTTSCSEEEEESCTTSHHHHHHHHH--SSEEEEEESCHHHHHHHGGGCCTTEEEEECCTTSCCCSSCEEEEE
T ss_pred             HHHHHHHhcCCCCCeEEEECCCCCHHHHHHHhc--CCeEEEEeCCHHHHHHHHhcCCCCeEEEecccccCCCCCceeEEE
Confidence            344554443455679999999999999999998  568999998 5677777653  68999999999865543  9887


Q ss_pred             e
Q 039903          232 I  232 (233)
Q Consensus       232 l  232 (233)
                      .
T Consensus       113 ~  113 (218)
T 3ou2_A          113 F  113 (218)
T ss_dssp             E
T ss_pred             E
Confidence            5

>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=98.44  E-value=4.3e-07  Score=74.02  Aligned_cols=74  Identities=19%  Similarity=0.378  Sum_probs=59.7

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC----CCceEEecCcCC-CCCCC--C
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY----SGVKHIGGIMLE-RIPKG--D  228 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~----~ri~~~~gD~f~-~~P~~--D  228 (233)
                      ..+++.++ .....+|||||||+|.++..+++++ ..+++.+|+ |..++.+++.    ++|+++.+|+.+ ++|.+  |
T Consensus        45 ~~~~~~~~-~~~~~~vLdiG~G~G~~~~~l~~~~-~~~v~~vD~s~~~~~~a~~~~~~~~~~~~~~~d~~~~~~~~~~fD  122 (266)
T 3ujc_A           45 KKILSDIE-LNENSKVLDIGSGLGGGCMYINEKY-GAHTHGIDICSNIVNMANERVSGNNKIIFEANDILTKEFPENNFD  122 (266)
T ss_dssp             HHHTTTCC-CCTTCEEEEETCTTSHHHHHHHHHH-CCEEEEEESCHHHHHHHHHTCCSCTTEEEEECCTTTCCCCTTCEE
T ss_pred             HHHHHhcC-CCCCCEEEEECCCCCHHHHHHHHHc-CCEEEEEeCCHHHHHHHHHHhhcCCCeEEEECccccCCCCCCcEE
Confidence            34455555 6667899999999999999999998 789999998 5577776653    689999999998 77653  9


Q ss_pred             EEEe
Q 039903          229 AILI  232 (233)
Q Consensus       229 ~~~l  232 (233)
                      +|+.
T Consensus       123 ~v~~  126 (266)
T 3ujc_A          123 LIYS  126 (266)
T ss_dssp             EEEE
T ss_pred             EEeH
Confidence            9875

>2fca_A TRNA (guanine-N(7)-)-methyltransferase; 2.10A {Bacillus subtilis} SCOP: c.66.1.53

Probab=98.44  E-value=3.2e-07  Score=73.20  Aligned_cols=65  Identities=17%  Similarity=0.177  Sum_probs=53.0

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccC------CCCceEEecCcCC-C--CCCC--CEEEe
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSS------YSGVKHIGGIMLE-R--IPKG--DAILI  232 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~------~~ri~~~~gD~f~-~--~P~~--D~~~l  232 (233)
                      ...+|||||||+|.++..+++.+|+.+++.+|+. ..++.|++      .++|+++.+|+.+ +  +|.+  |.+++
T Consensus        38 ~~~~vLDiGcG~G~~~~~la~~~p~~~v~giD~s~~~l~~a~~~~~~~~~~nv~~~~~d~~~l~~~~~~~~~d~v~~  114 (213)
T 2fca_A           38 DNPIHIEVGTGKGQFISGMAKQNPDINYIGIELFKSVIVTAVQKVKDSEAQNVKLLNIDADTLTDVFEPGEVKRVYL  114 (213)
T ss_dssp             CCCEEEEECCTTSHHHHHHHHHCTTSEEEEECSCHHHHHHHHHHHHHSCCSSEEEECCCGGGHHHHCCTTSCCEEEE
T ss_pred             CCceEEEEecCCCHHHHHHHHHCCCCCEEEEEechHHHHHHHHHHHHcCCCCEEEEeCCHHHHHhhcCcCCcCEEEE
Confidence            4578999999999999999999999999999984 57766654      2689999999987 3  5553  77653

>3g5l_A Putative S-adenosylmethionine dependent methyltransferase; structural genomics, PSI-2, protein structure initiative; 2.35A {Listeria monocytogenes str}

Probab=98.44  E-value=4.8e-07  Score=73.52  Aligned_cols=73  Identities=15%  Similarity=0.149  Sum_probs=57.7

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC---CCceEEecCcCC-CCCCC--CEE
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY---SGVKHIGGIMLE-RIPKG--DAI  230 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~---~ri~~~~gD~f~-~~P~~--D~~  230 (233)
                      .+.+.++ .....+|||||||+|.++..++++.+. +++.+|+ |..++.+++.   .+|+++.+|+.+ ++|.+  |+|
T Consensus        35 ~l~~~~~-~~~~~~vLD~GcG~G~~~~~l~~~~~~-~v~~vD~s~~~~~~a~~~~~~~~~~~~~~d~~~~~~~~~~fD~v  112 (253)
T 3g5l_A           35 ELKKMLP-DFNQKTVLDLGCGFGWHCIYAAEHGAK-KVLGIDLSERMLTEAKRKTTSPVVCYEQKAIEDIAIEPDAYNVV  112 (253)
T ss_dssp             HHHTTCC-CCTTCEEEEETCTTCHHHHHHHHTTCS-EEEEEESCHHHHHHHHHHCCCTTEEEEECCGGGCCCCTTCEEEE
T ss_pred             HHHHhhh-ccCCCEEEEECCCCCHHHHHHHHcCCC-EEEEEECCHHHHHHHHHhhccCCeEEEEcchhhCCCCCCCeEEE
Confidence            3444444 345689999999999999999999775 8999998 5677777653   689999999987 66653  998


Q ss_pred             Ee
Q 039903          231 LI  232 (233)
Q Consensus       231 ~l  232 (233)
                      +.
T Consensus       113 ~~  114 (253)
T 3g5l_A          113 LS  114 (253)
T ss_dssp             EE
T ss_pred             EE
Confidence            75

>2o57_A Putative sarcosine dimethylglycine methyltransferase; structural genomics, protein structure initiative, PSI-2; 1.95A {Galdieria sulphuraria} SCOP: c.66.1.18

Probab=98.43  E-value=4.9e-07  Score=75.30  Aligned_cols=74  Identities=14%  Similarity=0.238  Sum_probs=58.8

Q ss_pred             HHHHHhc----ccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCC-C
Q 039903          157 NRIIDSS----KGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLE-R  223 (233)
Q Consensus       157 ~~~~~~~----~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~-~  223 (233)
                      ..+++.+    . +....+|||||||.|.++..+++++ ..+++.+|+ |..++.+++.       ++|+++.+|+.+ +
T Consensus        68 ~~l~~~l~~~~~-~~~~~~vLDiGcG~G~~~~~l~~~~-~~~v~gvD~s~~~~~~a~~~~~~~~~~~~~~~~~~d~~~~~  145 (297)
T 2o57_A           68 EWLASELAMTGV-LQRQAKGLDLGAGYGGAARFLVRKF-GVSIDCLNIAPVQNKRNEEYNNQAGLADNITVKYGSFLEIP  145 (297)
T ss_dssp             HHHHHHHHHTTC-CCTTCEEEEETCTTSHHHHHHHHHH-CCEEEEEESCHHHHHHHHHHHHHHTCTTTEEEEECCTTSCS
T ss_pred             HHHHHHhhhccC-CCCCCEEEEeCCCCCHHHHHHHHHh-CCEEEEEeCCHHHHHHHHHHHHhcCCCcceEEEEcCcccCC
Confidence            4455555    4 6677899999999999999999987 458999998 4567766542       689999999998 7


Q ss_pred             CCCC--CEEEe
Q 039903          224 IPKG--DAILI  232 (233)
Q Consensus       224 ~P~~--D~~~l  232 (233)
                      +|.+  |+|+.
T Consensus       146 ~~~~~fD~v~~  156 (297)
T 2o57_A          146 CEDNSYDFIWS  156 (297)
T ss_dssp             SCTTCEEEEEE
T ss_pred             CCCCCEeEEEe
Confidence            7764  98875

>2qe6_A Uncharacterized protein TFU_2867; putative methyltransferase, structural genomics, joint cente structural genomics, JCSG; HET: NEP SAM; 1.95A {Thermobifida fusca}

Probab=98.43  E-value=6.3e-07  Score=74.38  Aligned_cols=56  Identities=18%  Similarity=0.236  Sum_probs=49.2

Q ss_pred             cCcceEEEecCCc---cHHHHHHHHHcCCCcEEEeec-hHHHhhccCC----CCceEEecCcCC
Q 039903          167 EQIKQLVDVGGGL---GVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY----SGVKHIGGIMLE  222 (233)
Q Consensus       167 ~~~~~vvDvGGG~---G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~----~ri~~~~gD~f~  222 (233)
                      .+..+|||||||+   |.++..+.+.+|+.+++.+|+ |.+++.+++.    ++++++.+|+++
T Consensus        76 ~~~~~vLDlGcG~pt~G~~~~~~~~~~p~~~v~~vD~sp~~l~~Ar~~~~~~~~v~~~~~D~~~  139 (274)
T 2qe6_A           76 AGISQFLDLGSGLPTVQNTHEVAQSVNPDARVVYVDIDPMVLTHGRALLAKDPNTAVFTADVRD  139 (274)
T ss_dssp             TCCCEEEEETCCSCCSSCHHHHHHHHCTTCEEEEEESSHHHHHHHHHHHTTCTTEEEEECCTTC
T ss_pred             cCCCEEEEECCCCCCCChHHHHHHHhCCCCEEEEEECChHHHHHHHHhcCCCCCeEEEEeeCCC
Confidence            3568999999999   999888888999999999999 7788887652    789999999986

>2p35_A Trans-aconitate 2-methyltransferase; SAM dependent methyltrans agrobacterium tumefaciens, structural genomics, PSI-2; HET: SAH; 1.95A {Agrobacterium tumefaciens str}

Probab=98.43  E-value=4.2e-07  Score=73.92  Aligned_cols=73  Identities=12%  Similarity=0.227  Sum_probs=59.7

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccC-CCCceEEecCcCC-CCCCC--CEEEe
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSS-YSGVKHIGGIMLE-RIPKG--DAILI  232 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~-~~ri~~~~gD~f~-~~P~~--D~~~l  232 (233)
                      .+++.++ .....+|||||||+|.++..+++++|..+++.+|+ |..++.+++ .++++++.+|+.+ + |.+  |+|+.
T Consensus        24 ~l~~~~~-~~~~~~vLdiG~G~G~~~~~l~~~~~~~~v~~~D~s~~~~~~a~~~~~~~~~~~~d~~~~~-~~~~fD~v~~  101 (259)
T 2p35_A           24 DLLAQVP-LERVLNGYDLGCGPGNSTELLTDRYGVNVITGIDSDDDMLEKAADRLPNTNFGKADLATWK-PAQKADLLYA  101 (259)
T ss_dssp             HHHTTCC-CSCCSSEEEETCTTTHHHHHHHHHHCTTSEEEEESCHHHHHHHHHHSTTSEEEECCTTTCC-CSSCEEEEEE
T ss_pred             HHHHhcC-CCCCCEEEEecCcCCHHHHHHHHhCCCCEEEEEECCHHHHHHHHHhCCCcEEEECChhhcC-ccCCcCEEEE
Confidence            4555555 56668999999999999999999999999999998 567777765 3789999999987 5 543  98875

>3gnl_A Uncharacterized protein, DUF633, LMOF2365_1472; structural genomics, PSI-2, protein structure initiative; 1.50A {Listeria monocytogenes str}

Probab=98.43  E-value=2.1e-07  Score=75.93  Aligned_cols=66  Identities=17%  Similarity=0.141  Sum_probs=55.2

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC-------CCceEEecCcCCCCCC---CCEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY-------SGVKHIGGIMLERIPK---GDAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~-------~ri~~~~gD~f~~~P~---~D~~~l  232 (233)
                      ++..+|+|||||+|.+++.+++..|..+++..|+. ..++.|+++       +||++..+|.++.++.   .|++++
T Consensus        20 ~~g~~VlDIGtGsG~l~i~la~~~~~~~V~avDi~~~al~~A~~N~~~~gl~~~I~v~~gD~l~~~~~~~~~D~Ivi   96 (244)
T 3gnl_A           20 TKNERIADIGSDHAYLPCFAVKNQTASFAIAGEVVDGPFQSAQKQVRSSGLTEQIDVRKGNGLAVIEKKDAIDTIVI   96 (244)
T ss_dssp             CSSEEEEEETCSTTHHHHHHHHTTSEEEEEEEESSHHHHHHHHHHHHHTTCTTTEEEEECSGGGGCCGGGCCCEEEE
T ss_pred             CCCCEEEEECCccHHHHHHHHHhCCCCEEEEEECCHHHHHHHHHHHHHcCCCceEEEEecchhhccCccccccEEEE
Confidence            44589999999999999999999999999999984 577777653       6899999999996553   488764

>3mgg_A Methyltransferase; NYSGXRC, PSI-II, protein structure initiative, structural genomics, NEW YORK SGX research center for structural genomics; 1.86A {Methanosarcina mazei}

Probab=98.43  E-value=4.2e-07  Score=74.85  Aligned_cols=67  Identities=15%  Similarity=0.338  Sum_probs=56.9

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCC-CCCCC--CEEEe
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLE-RIPKG--DAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~-~~P~~--D~~~l  232 (233)
                      +....+|||||||+|.++..+++++|..+++.+|+ |..++.+++.      ++++++.+|+.+ ++|.+  |+|+.
T Consensus        35 ~~~~~~vLDiG~G~G~~~~~l~~~~~~~~v~~vD~s~~~~~~a~~~~~~~~~~~~~~~~~d~~~~~~~~~~fD~v~~  111 (276)
T 3mgg_A           35 YPPGAKVLEAGCGIGAQTVILAKNNPDAEITSIDISPESLEKARENTEKNGIKNVKFLQANIFSLPFEDSSFDHIFV  111 (276)
T ss_dssp             CCTTCEEEETTCTTSHHHHHHHHHCTTSEEEEEESCHHHHHHHHHHHHHTTCCSEEEEECCGGGCCSCTTCEEEEEE
T ss_pred             CCCCCeEEEecCCCCHHHHHHHHhCCCCEEEEEECCHHHHHHHHHHHHHcCCCCcEEEEcccccCCCCCCCeeEEEE
Confidence            56678999999999999999999999999999998 5677766542      689999999998 66653  99875

>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=98.43  E-value=4.5e-07  Score=74.40  Aligned_cols=73  Identities=18%  Similarity=0.209  Sum_probs=57.6

Q ss_pred             HHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCC-CCCCC--
Q 039903          159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLE-RIPKG--  227 (233)
Q Consensus       159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~-~~P~~--  227 (233)
                      ++..++......+|||||||+|.++..+++. |..+++.+|+ |..++.+++.       ++|+++.+|+.+ ++|.+  
T Consensus        37 ~l~~l~~~~~~~~vLDiGcG~G~~~~~la~~-~~~~v~gvD~s~~~~~~a~~~~~~~~~~~~v~~~~~d~~~~~~~~~~f  115 (267)
T 3kkz_A           37 ALSFIDNLTEKSLIADIGCGTGGQTMVLAGH-VTGQVTGLDFLSGFIDIFNRNARQSGLQNRVTGIVGSMDDLPFRNEEL  115 (267)
T ss_dssp             HHTTCCCCCTTCEEEEETCTTCHHHHHHHTT-CSSEEEEEESCHHHHHHHHHHHHHTTCTTTEEEEECCTTSCCCCTTCE
T ss_pred             HHHhcccCCCCCEEEEeCCCCCHHHHHHHhc-cCCEEEEEeCCHHHHHHHHHHHHHcCCCcCcEEEEcChhhCCCCCCCE
Confidence            3333332456789999999999999999998 8899999998 5677766542       679999999987 66653  


Q ss_pred             CEEEe
Q 039903          228 DAILI  232 (233)
Q Consensus       228 D~~~l  232 (233)
                      |+|+.
T Consensus       116 D~i~~  120 (267)
T 3kkz_A          116 DLIWS  120 (267)
T ss_dssp             EEEEE
T ss_pred             EEEEE
Confidence            99875

>2pwy_A TRNA (adenine-N(1)-)-methyltransferase; mtase, adoMet, TRMI, tRNA-M1A58; HET: SAH; 1.70A {Thermus thermophilus}

Probab=98.40  E-value=2.4e-07  Score=75.39  Aligned_cols=74  Identities=11%  Similarity=0.157  Sum_probs=60.4

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHH-cCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCC-CCCCC
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISN-YLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLE-RIPKG  227 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~-~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~-~~P~~  227 (233)
                      .++..++ .....+|||+|||+|.++..+++. .|..+++.+|. |..++.++++       ++|+++.+|+.+ ++|.+
T Consensus        87 ~~~~~~~-~~~~~~vLdiG~G~G~~~~~l~~~~~~~~~v~~~D~~~~~~~~a~~~~~~~~g~~~v~~~~~d~~~~~~~~~  165 (258)
T 2pwy_A           87 AMVTLLD-LAPGMRVLEAGTGSGGLTLFLARAVGEKGLVESYEARPHHLAQAERNVRAFWQVENVRFHLGKLEEAELEEA  165 (258)
T ss_dssp             HHHHHTT-CCTTCEEEEECCTTSHHHHHHHHHHCTTSEEEEEESCHHHHHHHHHHHHHHCCCCCEEEEESCGGGCCCCTT
T ss_pred             HHHHHcC-CCCCCEEEEECCCcCHHHHHHHHHhCCCCEEEEEeCCHHHHHHHHHHHHHhcCCCCEEEEECchhhcCCCCC
Confidence            4556555 677789999999999999999999 78899999998 6677766542       689999999998 47753


Q ss_pred             --CEEEe
Q 039903          228 --DAILI  232 (233)
Q Consensus       228 --D~~~l  232 (233)
                        |++++
T Consensus       166 ~~D~v~~  172 (258)
T 2pwy_A          166 AYDGVAL  172 (258)
T ss_dssp             CEEEEEE
T ss_pred             CcCEEEE
Confidence              98875

>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=98.40  E-value=3.9e-07  Score=76.04  Aligned_cols=64  Identities=20%  Similarity=0.154  Sum_probs=53.8

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCCCCCC-C---CEEEe
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLERIPK-G---DAILI  232 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~~P~-~---D~~~l  232 (233)
                      ...+|+|||||+|.++..+++. |+.+++.+|+ +..++.|+++       +||+++.+|++++++. -   |+|+.
T Consensus       123 ~~~~vLDlG~GsG~~~~~la~~-~~~~v~~vDis~~al~~A~~n~~~~~l~~~v~~~~~D~~~~~~~~f~~~D~Ivs  198 (284)
T 1nv8_A          123 GIKTVADIGTGSGAIGVSVAKF-SDAIVFATDVSSKAVEIARKNAERHGVSDRFFVRKGEFLEPFKEKFASIEMILS  198 (284)
T ss_dssp             TCCEEEEESCTTSHHHHHHHHH-SSCEEEEEESCHHHHHHHHHHHHHTTCTTSEEEEESSTTGGGGGGTTTCCEEEE
T ss_pred             CCCEEEEEeCchhHHHHHHHHC-CCCEEEEEECCHHHHHHHHHHHHHcCCCCceEEEECcchhhcccccCCCCEEEE
Confidence            4568999999999999999999 9999999998 6688877653       4799999999986543 4   88864

>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=98.40  E-value=8e-07  Score=72.20  Aligned_cols=74  Identities=15%  Similarity=0.156  Sum_probs=57.8

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCC-CCCCC
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLE-RIPKG  227 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~-~~P~~  227 (233)
                      ..+++.++ .....+|||||||+|.++..+++++ ..+++.+|+ |..++.+++.       ++|+++.+|+.+ +.+..
T Consensus        26 ~~l~~~~~-~~~~~~VLDiGcG~G~~~~~la~~~-~~~v~gvD~s~~~l~~a~~~~~~~~~~~~v~~~~~d~~~~~~~~~  103 (256)
T 1nkv_A           26 ATLGRVLR-MKPGTRILDLGSGSGEMLCTWARDH-GITGTGIDMSSLFTAQAKRRAEELGVSERVHFIHNDAAGYVANEK  103 (256)
T ss_dssp             HHHHHHTC-CCTTCEEEEETCTTCHHHHHHHHHT-CCEEEEEESCHHHHHHHHHHHHHTTCTTTEEEEESCCTTCCCSSC
T ss_pred             HHHHHhcC-CCCCCEEEEECCCCCHHHHHHHHhc-CCeEEEEeCCHHHHHHHHHHHHhcCCCcceEEEECChHhCCcCCC
Confidence            34555555 6677899999999999999999988 678999998 5677766542       589999999988 44333


Q ss_pred             -CEEEe
Q 039903          228 -DAILI  232 (233)
Q Consensus       228 -D~~~l  232 (233)
                       |+|+.
T Consensus       104 fD~V~~  109 (256)
T 1nkv_A          104 CDVAAC  109 (256)
T ss_dssp             EEEEEE
T ss_pred             CCEEEE
Confidence             98874

>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=98.40  E-value=4.5e-07  Score=79.16  Aligned_cols=75  Identities=16%  Similarity=0.176  Sum_probs=58.5

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccC---------------CCCceEEecCc
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSS---------------YSGVKHIGGIM  220 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~---------------~~ri~~~~gD~  220 (233)
                      ..+++.+. .....+|+|||||+|..+..++..++.-+++.+|+. ..++.|++               .++|+++.||+
T Consensus       163 ~~il~~l~-l~~gd~VLDLGCGtG~l~l~lA~~~g~~kVvGIDiS~~~lelAr~n~e~frkr~~~~Gl~~~rVefi~GD~  241 (438)
T 3uwp_A          163 AQMIDEIK-MTDDDLFVDLGSGVGQVVLQVAAATNCKHHYGVEKADIPAKYAETMDREFRKWMKWYGKKHAEYTLERGDF  241 (438)
T ss_dssp             HHHHHHHC-CCTTCEEEEESCTTSHHHHHHHHHCCCSEEEEEECCHHHHHHHHHHHHHHHHHHHHHTBCCCEEEEEECCT
T ss_pred             HHHHHhcC-CCCCCEEEEeCCCCCHHHHHHHHHCCCCEEEEEeCCHHHHHHHHHHHHHHHHHHHHhCCCCCCeEEEECcc
Confidence            34555555 667789999999999999999999887789999995 45555432               26899999999


Q ss_pred             CC-CCC----CCCEEEe
Q 039903          221 LE-RIP----KGDAILI  232 (233)
Q Consensus       221 f~-~~P----~~D~~~l  232 (233)
                      ++ +++    .+|+|++
T Consensus       242 ~~lp~~d~~~~aDVVf~  258 (438)
T 3uwp_A          242 LSEEWRERIANTSVIFV  258 (438)
T ss_dssp             TSHHHHHHHHTCSEEEE
T ss_pred             cCCccccccCCccEEEE
Confidence            98 553    4699875

>3g07_A 7SK snRNA methylphosphate capping enzyme; structural genomics consortium (SGC), methyltransferase, phosphoprotein, S-adenosyl-L-methionine; HET: SAM; 2.65A {Homo sapiens}

Probab=98.39  E-value=7e-07  Score=74.60  Aligned_cols=43  Identities=19%  Similarity=0.274  Sum_probs=37.2

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccC
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSS  209 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~  209 (233)
                      ....+|||||||+|.++..+++++|..+++.+|+ +..++.|++
T Consensus        45 ~~~~~VLDiGCG~G~~~~~la~~~~~~~v~gvDis~~~i~~A~~   88 (292)
T 3g07_A           45 FRGRDVLDLGCNVGHLTLSIACKWGPSRMVGLDIDSRLIHSARQ   88 (292)
T ss_dssp             TTTSEEEEESCTTCHHHHHHHHHTCCSEEEEEESCHHHHHHHHH
T ss_pred             cCCCcEEEeCCCCCHHHHHHHHHcCCCEEEEECCCHHHHHHHHH
Confidence            3568999999999999999999999999999999 456766654

>3jwg_A HEN1, methyltransferase type 12; 1.90A {Clostridium thermocellum} PDB: 3jwi_A

Probab=98.39  E-value=4.5e-07  Score=72.09  Aligned_cols=66  Identities=14%  Similarity=0.194  Sum_probs=54.0

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-----------CCceEEecCcCC-CCCC--CCEEE
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-----------SGVKHIGGIMLE-RIPK--GDAIL  231 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-----------~ri~~~~gD~f~-~~P~--~D~~~  231 (233)
                      .+..+|||||||+|.++..+++++|..+++.+|+ |..++.+++.           ++|+++.+|+.. +.+.  .|+|+
T Consensus        28 ~~~~~vLDiGcG~G~~~~~l~~~~~~~~v~gvD~s~~~~~~a~~~~~~~~~~~~~~~~v~~~~~d~~~~~~~~~~fD~V~  107 (219)
T 3jwg_A           28 VNAKKVIDLGCGEGNLLSLLLKDKSFEQITGVDVSYSVLERAKDRLKIDRLPEMQRKRISLFQSSLVYRDKRFSGYDAAT  107 (219)
T ss_dssp             TTCCEEEEETCTTCHHHHHHHTSTTCCEEEEEESCHHHHHHHHHHHTGGGSCHHHHTTEEEEECCSSSCCGGGTTCSEEE
T ss_pred             cCCCEEEEecCCCCHHHHHHHhcCCCCEEEEEECCHHHHHHHHHHHHhhccccccCcceEEEeCcccccccccCCCCEEE
Confidence            4567999999999999999999999999999998 5677777642           289999999965 4433  39987


Q ss_pred             e
Q 039903          232 I  232 (233)
Q Consensus       232 l  232 (233)
                      .
T Consensus       108 ~  108 (219)
T 3jwg_A          108 V  108 (219)
T ss_dssp             E
T ss_pred             E
Confidence            4

>3jwh_A HEN1; methyltransferase; HET: SAH; 2.20A {Anabaena variabilis} PDB: 3jwj_A

Probab=98.39  E-value=5.4e-07  Score=71.57  Aligned_cols=73  Identities=15%  Similarity=0.238  Sum_probs=56.3

Q ss_pred             HHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-----------CCceEEecCcCC-CCC
Q 039903          159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-----------SGVKHIGGIMLE-RIP  225 (233)
Q Consensus       159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-----------~ri~~~~gD~f~-~~P  225 (233)
                      +++.++ ..+..+|||||||+|.++..+++++|..+++.+|+ |..++.+++.           ++|+++.+|+.. +.+
T Consensus        21 l~~~l~-~~~~~~vLDiGcG~G~~~~~l~~~~~~~~v~gvD~s~~~~~~a~~~~~~~~~~~~~~~~v~~~~~d~~~~~~~   99 (217)
T 3jwh_A           21 VVAALK-QSNARRVIDLGCGQGNLLKILLKDSFFEQITGVDVSYRSLEIAQERLDRLRLPRNQWERLQLIQGALTYQDKR   99 (217)
T ss_dssp             HHHHHH-HTTCCEEEEETCTTCHHHHHHHHCTTCSEEEEEESCHHHHHHHHHHHTTCCCCHHHHTTEEEEECCTTSCCGG
T ss_pred             HHHHHH-hcCCCEEEEeCCCCCHHHHHHHhhCCCCEEEEEECCHHHHHHHHHHHHHhcCCcccCcceEEEeCCccccccc
Confidence            333333 34567999999999999999999999999999998 5577766542           289999999865 444


Q ss_pred             C--CCEEEe
Q 039903          226 K--GDAILI  232 (233)
Q Consensus       226 ~--~D~~~l  232 (233)
                      .  .|+++.
T Consensus       100 ~~~fD~v~~  108 (217)
T 3jwh_A          100 FHGYDAATV  108 (217)
T ss_dssp             GCSCSEEEE
T ss_pred             CCCcCEEee
Confidence            3  399874

>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=98.39  E-value=6e-07  Score=74.29  Aligned_cols=66  Identities=14%  Similarity=0.163  Sum_probs=55.5

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCCCCCC-C-CEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLERIPK-G-DAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~~P~-~-D~~~l  232 (233)
                      ....+|+|||||+|.++..+++.+|+.+++.+|. |..++.++++      ++|+++.+|+++++|. . |+|+.
T Consensus       108 ~~~~~vLDlG~GsG~~~~~la~~~~~~~v~~vD~s~~~l~~a~~n~~~~~~~~v~~~~~d~~~~~~~~~fD~Iv~  182 (276)
T 2b3t_A          108 EQPCRILDLGTGTGAIALALASERPDCEIIAVDRMPDAVSLAQRNAQHLAIKNIHILQSDWFSALAGQQFAMIVS  182 (276)
T ss_dssp             SSCCEEEEETCTTSHHHHHHHHHCTTSEEEEECSSHHHHHHHHHHHHHHTCCSEEEECCSTTGGGTTCCEEEEEE
T ss_pred             cCCCEEEEecCCccHHHHHHHHhCCCCEEEEEECCHHHHHHHHHHHHHcCCCceEEEEcchhhhcccCCccEEEE
Confidence            3457899999999999999999999999999998 5677777653      5799999999997654 3 98875

>3hm2_A Precorrin-6Y C5,15-methyltransferase; alpha-beta-sandwich, structural genomics, PSI-2, protein structure initiative; 2.21A {Corynebacterium diphtheriae}

Probab=98.38  E-value=4e-07  Score=69.71  Aligned_cols=72  Identities=19%  Similarity=0.193  Sum_probs=56.6

Q ss_pred             HHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC-------CCceEEecCcCCCCCC----
Q 039903          159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY-------SGVKHIGGIMLERIPK----  226 (233)
Q Consensus       159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~-------~ri~~~~gD~f~~~P~----  226 (233)
                      +++.++ .....+|+|||||+|.++..+++++|..+++.+|+. ..++.++++       +++ ++.+|..+.+|.    
T Consensus        17 ~~~~~~-~~~~~~vldiG~G~G~~~~~l~~~~~~~~v~~vD~~~~~~~~a~~~~~~~~~~~~~-~~~~d~~~~~~~~~~~   94 (178)
T 3hm2_A           17 AISALA-PKPHETLWDIGGGSGSIAIEWLRSTPQTTAVCFEISEERRERILSNAINLGVSDRI-AVQQGAPRAFDDVPDN   94 (178)
T ss_dssp             HHHHHC-CCTTEEEEEESTTTTHHHHHHHTTSSSEEEEEECSCHHHHHHHHHHHHTTTCTTSE-EEECCTTGGGGGCCSC
T ss_pred             HHHHhc-ccCCCeEEEeCCCCCHHHHHHHHHCCCCeEEEEeCCHHHHHHHHHHHHHhCCCCCE-EEecchHhhhhccCCC
Confidence            444455 566689999999999999999999999999999984 577766542       378 888998875543    


Q ss_pred             CCEEEe
Q 039903          227 GDAILI  232 (233)
Q Consensus       227 ~D~~~l  232 (233)
                      .|++++
T Consensus        95 ~D~i~~  100 (178)
T 3hm2_A           95 PDVIFI  100 (178)
T ss_dssp             CSEEEE
T ss_pred             CCEEEE
Confidence            398875

>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=98.37  E-value=1.2e-06  Score=73.24  Aligned_cols=66  Identities=23%  Similarity=0.226  Sum_probs=55.2

Q ss_pred             cCcceEEEecCCccHHHHHHHHHc-CCCcEEEeec-hHHHhhccC--------CCCceEEecCcCC-CCCC------C--
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNY-LHIKGVNFDL-SHVIQDSSS--------YSGVKHIGGIMLE-RIPK------G--  227 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~v~~~a~~--------~~ri~~~~gD~f~-~~P~------~--  227 (233)
                      ....+|||||||+|.++..+++++ |..+++.+|+ |..++.+++        .++|+++.+|+.+ +++.      +  
T Consensus        35 ~~~~~vLDiGcG~G~~~~~la~~~~~~~~v~gvD~s~~~~~~a~~~~~~~~~~~~~v~~~~~d~~~~~~~~~~~~~~~~f  114 (299)
T 3g5t_A           35 GERKLLVDVGCGPGTATLQMAQELKPFEQIIGSDLSATMIKTAEVIKEGSPDTYKNVSFKISSSDDFKFLGADSVDKQKI  114 (299)
T ss_dssp             SCCSEEEEETCTTTHHHHHHHHHSSCCSEEEEEESCHHHHHHHHHHHHHCC-CCTTEEEEECCTTCCGGGCTTTTTSSCE
T ss_pred             CCCCEEEEECCCCCHHHHHHHHhCCCCCEEEEEeCCHHHHHHHHHHHHhccCCCCceEEEEcCHHhCCccccccccCCCe
Confidence            466899999999999999999997 8999999998 557777754        3689999999998 6554      3  


Q ss_pred             CEEEe
Q 039903          228 DAILI  232 (233)
Q Consensus       228 D~~~l  232 (233)
                      |+|+.
T Consensus       115 D~V~~  119 (299)
T 3g5t_A          115 DMITA  119 (299)
T ss_dssp             EEEEE
T ss_pred             eEEeH
Confidence            88874

>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=98.36  E-value=5.9e-07  Score=74.59  Aligned_cols=67  Identities=15%  Similarity=0.206  Sum_probs=55.4

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCC-CcEEEeec-hHHHhhccCC-----CCceEEecCcCC-CCCCC-CEEEe
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLH-IKGVNFDL-SHVIQDSSSY-----SGVKHIGGIMLE-RIPKG-DAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~-l~~~v~Dl-p~v~~~a~~~-----~ri~~~~gD~f~-~~P~~-D~~~l  232 (233)
                      ..+..+|||||||+|.++..+++.+|. .+++.+|+ |..++.+++.     .+|+++.+|+.+ +.+.. |+|+.
T Consensus        20 ~~~~~~vLDiGcG~G~~~~~l~~~~~~~~~v~gvD~s~~~~~~a~~~~~~~~~~v~~~~~d~~~~~~~~~fD~v~~   95 (284)
T 3gu3_A           20 ITKPVHIVDYGCGYGYLGLVLMPLLPEGSKYTGIDSGETLLAEARELFRLLPYDSEFLEGDATEIELNDKYDIAIC   95 (284)
T ss_dssp             CCSCCEEEEETCTTTHHHHHHTTTSCTTCEEEEEESCHHHHHHHHHHHHSSSSEEEEEESCTTTCCCSSCEEEEEE
T ss_pred             cCCCCeEEEecCCCCHHHHHHHHhCCCCCEEEEEECCHHHHHHHHHHHHhcCCceEEEEcchhhcCcCCCeeEEEE
Confidence            566789999999999999999999995 89999998 5567666542     389999999998 55554 98875

>4dzr_A Protein-(glutamine-N5) methyltransferase, release specific; structural genomics, PSI-biology; 2.55A {Alicyclobacillus acidocaldarius subsp}

Probab=98.36  E-value=1.2e-07  Score=74.63  Aligned_cols=75  Identities=19%  Similarity=0.126  Sum_probs=49.3

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-----CCceEEecCcCCCCCC-----
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-----SGVKHIGGIMLERIPK-----  226 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-----~ri~~~~gD~f~~~P~-----  226 (233)
                      .+++.+....+..+|+|||||+|.++..+++.+|+.+++.+|+ |..++.++++     .+++++.+|++++++.     
T Consensus        20 ~~~~~l~~~~~~~~vLDiG~G~G~~~~~l~~~~~~~~v~~vD~~~~~~~~a~~~~~~~~~~~~~~~~d~~~~~~~~~~~~   99 (215)
T 4dzr_A           20 EAIRFLKRMPSGTRVIDVGTGSGCIAVSIALACPGVSVTAVDLSMDALAVARRNAERFGAVVDWAAADGIEWLIERAERG   99 (215)
T ss_dssp             HHHHHHTTCCTTEEEEEEESSBCHHHHHHHHHCTTEEEEEEECC-------------------CCHHHHHHHHHHHHHTT
T ss_pred             HHHHHhhhcCCCCEEEEecCCHhHHHHHHHHhCCCCeEEEEECCHHHHHHHHHHHHHhCCceEEEEcchHhhhhhhhhcc
Confidence            3444443125678999999999999999999999999999999 5688877764     1789999999985552     


Q ss_pred             --CCEEEe
Q 039903          227 --GDAILI  232 (233)
Q Consensus       227 --~D~~~l  232 (233)
                        .|+++.
T Consensus       100 ~~fD~i~~  107 (215)
T 4dzr_A          100 RPWHAIVS  107 (215)
T ss_dssp             CCBSEEEE
T ss_pred             CcccEEEE
Confidence              398875

>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=98.36  E-value=9.4e-07  Score=72.27  Aligned_cols=64  Identities=14%  Similarity=0.229  Sum_probs=53.2

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccC-CCCceEEecCcCC-CCCCC-CEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSS-YSGVKHIGGIMLE-RIPKG-DAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~-~~ri~~~~gD~f~-~~P~~-D~~~l  232 (233)
                      ++..+|||||||+|.++..++++.+  +++.+|+ |..++.+++ ..+|+++.+|+.+ +.+.. |+|+.
T Consensus        49 ~~~~~vLDiGcG~G~~~~~l~~~~~--~v~gvD~s~~~~~~a~~~~~~~~~~~~d~~~~~~~~~fD~v~~  116 (263)
T 3pfg_A           49 PKAASLLDVACGTGMHLRHLADSFG--TVEGLELSADMLAIARRRNPDAVLHHGDMRDFSLGRRFSAVTC  116 (263)
T ss_dssp             TTCCEEEEETCTTSHHHHHHTTTSS--EEEEEESCHHHHHHHHHHCTTSEEEECCTTTCCCSCCEEEEEE
T ss_pred             CCCCcEEEeCCcCCHHHHHHHHcCC--eEEEEECCHHHHHHHHhhCCCCEEEECChHHCCccCCcCEEEE
Confidence            4568999999999999999999865  6899998 668887766 3689999999998 55544 99875

>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=98.36  E-value=5.1e-07  Score=72.41  Aligned_cols=65  Identities=12%  Similarity=0.204  Sum_probs=52.4

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCCC----CCCC--CEEEe
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLER----IPKG--DAILI  232 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~----~P~~--D~~~l  232 (233)
                      ...+|||||||+|.++..+++++|+.+++.+|. +..++.++++      ++|+++.+|..+.    +|.+  |.+++
T Consensus        34 ~~~~vLDiGcG~G~~~~~lA~~~p~~~v~giD~s~~~l~~a~~~~~~~~l~nv~~~~~Da~~~l~~~~~~~~~d~v~~  111 (218)
T 3dxy_A           34 EAPVTLEIGFGMGASLVAMAKDRPEQDFLGIEVHSPGVGACLASAHEEGLSNLRVMCHDAVEVLHKMIPDNSLRMVQL  111 (218)
T ss_dssp             CCCEEEEESCTTCHHHHHHHHHCTTSEEEEECSCHHHHHHHHHHHHHTTCSSEEEECSCHHHHHHHHSCTTCEEEEEE
T ss_pred             CCCeEEEEeeeChHHHHHHHHHCCCCeEEEEEecHHHHHHHHHHHHHhCCCcEEEEECCHHHHHHHHcCCCChheEEE
Confidence            457999999999999999999999999999998 4566665432      5799999998762    5654  77654

>4dcm_A Ribosomal RNA large subunit methyltransferase G; 23S rRNA (guanine1835-N2)-methyltransferase; HET: SAM; 2.30A {Escherichia coli}

Probab=98.35  E-value=8.1e-07  Score=77.05  Aligned_cols=74  Identities=18%  Similarity=0.118  Sum_probs=59.6

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC---------CCceEEecCcCCCCCCC
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY---------SGVKHIGGIMLERIPKG  227 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~---------~ri~~~~gD~f~~~P~~  227 (233)
                      .+++.++ .....+|+|+|||+|.++..+++++|..+++.+|. +..++.++++         .+++++.+|+++++|.+
T Consensus       213 ~ll~~l~-~~~~~~VLDlGcG~G~~s~~la~~~p~~~V~gvD~s~~al~~Ar~n~~~ngl~~~~~v~~~~~D~~~~~~~~  291 (375)
T 4dcm_A          213 FFMQHLP-ENLEGEIVDLGCGNGVIGLTLLDKNPQAKVVFVDESPMAVASSRLNVETNMPEALDRCEFMINNALSGVEPF  291 (375)
T ss_dssp             HHHHTCC-CSCCSEEEEETCTTCHHHHHHHHHCTTCEEEEEESCHHHHHHHHHHHHHHCGGGGGGEEEEECSTTTTCCTT
T ss_pred             HHHHhCc-ccCCCeEEEEeCcchHHHHHHHHHCCCCEEEEEECcHHHHHHHHHHHHHcCCCcCceEEEEechhhccCCCC
Confidence            3455555 33448999999999999999999999999999998 5577777653         25888999999987763


Q ss_pred             --CEEEe
Q 039903          228 --DAILI  232 (233)
Q Consensus       228 --D~~~l  232 (233)
                        |+|+.
T Consensus       292 ~fD~Ii~  298 (375)
T 4dcm_A          292 RFNAVLC  298 (375)
T ss_dssp             CEEEEEE
T ss_pred             CeeEEEE
Confidence              99875

>2yxd_A Probable cobalt-precorrin-6Y C(15)-methyltransfer [decarboxylating]; alpha and beta protein (A/B) class; HET: MES; 2.30A {Methanocaldococcus jannaschii}

Probab=98.35  E-value=4.8e-07  Score=69.35  Aligned_cols=72  Identities=19%  Similarity=0.124  Sum_probs=57.2

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCCCCCC--CC
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLERIPK--GD  228 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~~P~--~D  228 (233)
                      .+++.++ ..+..+|+|||||+|.++..+++  +..+++.+|. |..++.++++      ++++++.+|+.+++|.  .|
T Consensus        26 ~~~~~~~-~~~~~~vLdiG~G~G~~~~~l~~--~~~~v~~vD~~~~~~~~a~~~~~~~~~~~~~~~~~d~~~~~~~~~~D  102 (183)
T 2yxd_A           26 VSIGKLN-LNKDDVVVDVGCGSGGMTVEIAK--RCKFVYAIDYLDGAIEVTKQNLAKFNIKNCQIIKGRAEDVLDKLEFN  102 (183)
T ss_dssp             HHHHHHC-CCTTCEEEEESCCCSHHHHHHHT--TSSEEEEEECSHHHHHHHHHHHHHTTCCSEEEEESCHHHHGGGCCCS
T ss_pred             HHHHHcC-CCCCCEEEEeCCCCCHHHHHHHh--cCCeEEEEeCCHHHHHHHHHHHHHcCCCcEEEEECCccccccCCCCc
Confidence            3444444 55667999999999999999999  8889999998 5577776653      6899999999986664  39


Q ss_pred             EEEe
Q 039903          229 AILI  232 (233)
Q Consensus       229 ~~~l  232 (233)
                      +++.
T Consensus       103 ~i~~  106 (183)
T 2yxd_A          103 KAFI  106 (183)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            9875

>3b3j_A Histone-arginine methyltransferase CARM1; protein arginine methyltransferase 4, APO catalytic domain, regulator, mRNA processing; 2.55A {Rattus norvegicus}

Probab=98.35  E-value=1.9e-06  Score=77.09  Aligned_cols=74  Identities=22%  Similarity=0.202  Sum_probs=59.2

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCC-------CCceEEecCcCC-CCCCC-
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSY-------SGVKHIGGIMLE-RIPKG-  227 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~-------~ri~~~~gD~f~-~~P~~-  227 (233)
                      ..+++.+. ..+..+|+|||||+|.++..+++ .|..+++.+|+.+.++.|++.       ++|+++.+|+++ ++|.. 
T Consensus       148 ~~il~~l~-~~~~~~VLDiGcGtG~la~~la~-~~~~~V~gvD~s~~l~~A~~~~~~~gl~~~v~~~~~d~~~~~~~~~f  225 (480)
T 3b3j_A          148 RAILQNHT-DFKDKIVLDVGCGSGILSFFAAQ-AGARKIYAVEASTMAQHAEVLVKSNNLTDRIVVIPGKVEEVSLPEQV  225 (480)
T ss_dssp             HHHHHTGG-GTTTCEEEEESCSTTHHHHHHHH-TTCSEEEEEECHHHHHHHHHHHHHTTCTTTEEEEESCTTTCCCSSCE
T ss_pred             HHHHHhhh-hcCCCEEEEecCcccHHHHHHHH-cCCCEEEEEEcHHHHHHHHHHHHHcCCCCcEEEEECchhhCccCCCe
Confidence            45556555 45568999999999999998887 688899999998776666542       689999999998 77764 


Q ss_pred             CEEEe
Q 039903          228 DAILI  232 (233)
Q Consensus       228 D~~~l  232 (233)
                      |+|+.
T Consensus       226 D~Ivs  230 (480)
T 3b3j_A          226 DIIIS  230 (480)
T ss_dssp             EEEEC
T ss_pred             EEEEE
Confidence            99874

>3bkw_A MLL3908 protein, S-adenosylmethionine dependent methyltransferase; NP_104914.1; HET: MSE; 1.60A {Mesorhizobium loti}

Probab=98.35  E-value=1.3e-06  Score=70.21  Aligned_cols=73  Identities=14%  Similarity=0.129  Sum_probs=56.1

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC---CCceEEecCcCC-CCCCC--CEE
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY---SGVKHIGGIMLE-RIPKG--DAI  230 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~---~ri~~~~gD~f~-~~P~~--D~~  230 (233)
                      .+...++ .....+|||||||+|.++..++++.+ .+++.+|+ +..++.+++.   .+|+++.+|+.+ ++|.+  |++
T Consensus        34 ~l~~~~~-~~~~~~vLdiG~G~G~~~~~l~~~~~-~~v~~vD~s~~~~~~a~~~~~~~~~~~~~~d~~~~~~~~~~fD~v  111 (243)
T 3bkw_A           34 ALRAMLP-EVGGLRIVDLGCGFGWFCRWAHEHGA-SYVLGLDLSEKMLARARAAGPDTGITYERADLDKLHLPQDSFDLA  111 (243)
T ss_dssp             HHHHHSC-CCTTCEEEEETCTTCHHHHHHHHTTC-SEEEEEESCHHHHHHHHHTSCSSSEEEEECCGGGCCCCTTCEEEE
T ss_pred             HHHHhcc-ccCCCEEEEEcCcCCHHHHHHHHCCC-CeEEEEcCCHHHHHHHHHhcccCCceEEEcChhhccCCCCCceEE
Confidence            4555554 45568999999999999999998733 38999998 5677777653   479999999988 66553  988


Q ss_pred             Ee
Q 039903          231 LI  232 (233)
Q Consensus       231 ~l  232 (233)
                      +.
T Consensus       112 ~~  113 (243)
T 3bkw_A          112 YS  113 (243)
T ss_dssp             EE
T ss_pred             EE
Confidence            74

>3ntv_A MW1564 protein; rossmann fold, putative methyltransferase, transferase; HET: MSE; 1.55A {Staphylococcus aureus}

Probab=98.35  E-value=4e-07  Score=73.46  Aligned_cols=67  Identities=22%  Similarity=0.322  Sum_probs=55.9

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCCCCC---C-C-CEEEe
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLERIP---K-G-DAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~~P---~-~-D~~~l  232 (233)
                      ..+..+|||||||+|..+..+++.+|..+++.+|+ |+.++.|+++       ++|+++.+|+.+.+|   . . |++++
T Consensus        69 ~~~~~~vLDiG~G~G~~~~~la~~~~~~~v~~vD~~~~~~~~a~~~~~~~~~~~~v~~~~~d~~~~~~~~~~~~fD~V~~  148 (232)
T 3ntv_A           69 MNNVKNILEIGTAIGYSSMQFASISDDIHVTTIERNETMIQYAKQNLATYHFENQVRIIEGNALEQFENVNDKVYDMIFI  148 (232)
T ss_dssp             HHTCCEEEEECCSSSHHHHHHHTTCTTCEEEEEECCHHHHHHHHHHHHHTTCTTTEEEEESCGGGCHHHHTTSCEEEEEE
T ss_pred             hcCCCEEEEEeCchhHHHHHHHHhCCCCEEEEEECCHHHHHHHHHHHHHcCCCCcEEEEECCHHHHHHhhccCCccEEEE
Confidence            45668999999999999999999999999999998 5677777652       589999999998555   2 3 98875

>4hg2_A Methyltransferase type 11; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; HET: MES; 1.60A {Anaeromyxobacter dehalogenans}

Probab=98.34  E-value=7.6e-07  Score=73.24  Aligned_cols=63  Identities=14%  Similarity=0.103  Sum_probs=54.2

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCCCCceEEecCcCC-CCCCC--CEEEe
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSYSGVKHIGGIMLE-RIPKG--DAILI  232 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~~ri~~~~gD~f~-~~P~~--D~~~l  232 (233)
                      ...++||||||+|.++..|++++.  +++.+|.. ..++.|++.++|+++.+|+-+ ++|.+  |+|+.
T Consensus        39 ~~~~vLDvGcGtG~~~~~l~~~~~--~v~gvD~s~~ml~~a~~~~~v~~~~~~~e~~~~~~~sfD~v~~  105 (257)
T 4hg2_A           39 ARGDALDCGCGSGQASLGLAEFFE--RVHAVDPGEAQIRQALRHPRVTYAVAPAEDTGLPPASVDVAIA  105 (257)
T ss_dssp             CSSEEEEESCTTTTTHHHHHTTCS--EEEEEESCHHHHHTCCCCTTEEEEECCTTCCCCCSSCEEEEEE
T ss_pred             CCCCEEEEcCCCCHHHHHHHHhCC--EEEEEeCcHHhhhhhhhcCCceeehhhhhhhcccCCcccEEEE
Confidence            346899999999999999999874  68999984 588989888999999999988 78875  98874

>3q87_B N6 adenine specific DNA methylase; SAM-methyltransferase, methyltransferase, methylation, trans activator-transferase complex; HET: SAM; 2.00A {Encephalitozoon cuniculi}

Probab=98.32  E-value=1.2e-06  Score=67.19  Aligned_cols=59  Identities=20%  Similarity=0.322  Sum_probs=49.6

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCCCCceEEecCcCCCCCCC--CEEEe
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSYSGVKHIGGIMLERIPKG--DAILI  232 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~~ri~~~~gD~f~~~P~~--D~~~l  232 (233)
                      +..+|+|||||+|.++..++++.   +++.+|+. ..++.   .++++++.+|++++++.+  |+++.
T Consensus        23 ~~~~vLD~GcG~G~~~~~l~~~~---~v~gvD~s~~~~~~---~~~~~~~~~d~~~~~~~~~fD~i~~   84 (170)
T 3q87_B           23 EMKIVLDLGTSTGVITEQLRKRN---TVVSTDLNIRALES---HRGGNLVRADLLCSINQESVDVVVF   84 (170)
T ss_dssp             CSCEEEEETCTTCHHHHHHTTTS---EEEEEESCHHHHHT---CSSSCEEECSTTTTBCGGGCSEEEE
T ss_pred             CCCeEEEeccCccHHHHHHHhcC---cEEEEECCHHHHhc---ccCCeEEECChhhhcccCCCCEEEE
Confidence            34699999999999999999987   89999985 46665   578999999999977743  98875

>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=98.31  E-value=1.1e-06  Score=70.98  Aligned_cols=74  Identities=18%  Similarity=0.310  Sum_probs=58.8

Q ss_pred             HHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCC-CCCCC
Q 039903          156 TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLE-RIPKG  227 (233)
Q Consensus       156 ~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~-~~P~~  227 (233)
                      ...+++.++ .....+|||||||+|.++..+++..+  +++.+|+ |..++.+++.      ++|+++.+|+.+ ++|.+
T Consensus        10 ~~~~~~~~~-~~~~~~vLDiGcG~G~~~~~l~~~~~--~v~~vD~s~~~~~~a~~~~~~~~~~~v~~~~~d~~~~~~~~~   86 (239)
T 1xxl_A           10 LGLMIKTAE-CRAEHRVLDIGAGAGHTALAFSPYVQ--ECIGVDATKEMVEVASSFAQEKGVENVRFQQGTAESLPFPDD   86 (239)
T ss_dssp             HHHHHHHHT-CCTTCEEEEESCTTSHHHHHHGGGSS--EEEEEESCHHHHHHHHHHHHHHTCCSEEEEECBTTBCCSCTT
T ss_pred             cchHHHHhC-cCCCCEEEEEccCcCHHHHHHHHhCC--EEEEEECCHHHHHHHHHHHHHcCCCCeEEEecccccCCCCCC
Confidence            345666666 77789999999999999999999886  7899998 5577766542      689999999987 66653


Q ss_pred             --CEEEe
Q 039903          228 --DAILI  232 (233)
Q Consensus       228 --D~~~l  232 (233)
                        |+++.
T Consensus        87 ~fD~v~~   93 (239)
T 1xxl_A           87 SFDIITC   93 (239)
T ss_dssp             CEEEEEE
T ss_pred             cEEEEEE
Confidence              98874

>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=98.31  E-value=1.1e-06  Score=71.34  Aligned_cols=66  Identities=11%  Similarity=0.229  Sum_probs=52.0

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhcc------------CCCCceEEecCcCCC----CCCC--
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSS------------SYSGVKHIGGIMLER----IPKG--  227 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~------------~~~ri~~~~gD~f~~----~P~~--  227 (233)
                      .+..+|||||||+|.++..+++.+|+.+++.+|+. .+++.|+            ..++|+++.+|+.+.    +|.+  
T Consensus        45 ~~~~~vLDiGcG~G~~~~~la~~~p~~~v~GiDis~~~l~~A~~~~~~l~~~~~~~~~nv~~~~~d~~~~l~~~~~~~~~  124 (235)
T 3ckk_A           45 QAQVEFADIGCGYGGLLVELSPLFPDTLILGLEIRVKVSDYVQDRIRALRAAPAGGFQNIACLRSNAMKHLPNFFYKGQL  124 (235)
T ss_dssp             -CCEEEEEETCTTCHHHHHHGGGSTTSEEEEEESCHHHHHHHHHHHHHHHHSTTCCCTTEEEEECCTTTCHHHHCCTTCE
T ss_pred             CCCCeEEEEccCCcHHHHHHHHHCCCCeEEEEECCHHHHHHHHHHHHHHHHHHhcCCCeEEEEECcHHHhhhhhCCCcCe
Confidence            44578999999999999999999999999999984 4665442            136899999999863    4554  


Q ss_pred             CEEEe
Q 039903          228 DAILI  232 (233)
Q Consensus       228 D~~~l  232 (233)
                      |.+++
T Consensus       125 D~v~~  129 (235)
T 3ckk_A          125 TKMFF  129 (235)
T ss_dssp             EEEEE
T ss_pred             eEEEE
Confidence            77654

>3gjy_A Spermidine synthase; APC62791, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.47A {Corynebacterium glutamicum atcc 13032}

Probab=98.31  E-value=6.1e-07  Score=75.93  Aligned_cols=63  Identities=16%  Similarity=0.189  Sum_probs=53.6

Q ss_pred             ceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCC---CCCC-C-CEEEe
Q 039903          170 KQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLE---RIPK-G-DAILI  232 (233)
Q Consensus       170 ~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~---~~P~-~-D~~~l  232 (233)
                      .+|||||||.|.+++.+++.+|+.+++++|+ |.+++.++++      +||+++.+|.++   ..+. . |+|++
T Consensus        91 ~rVLdIG~G~G~la~~la~~~p~~~v~~VEidp~vi~~Ar~~~~~~~~~rv~v~~~Da~~~l~~~~~~~fDvIi~  165 (317)
T 3gjy_A           91 LRITHLGGGACTMARYFADVYPQSRNTVVELDAELARLSREWFDIPRAPRVKIRVDDARMVAESFTPASRDVIIR  165 (317)
T ss_dssp             CEEEEESCGGGHHHHHHHHHSTTCEEEEEESCHHHHHHHHHHSCCCCTTTEEEEESCHHHHHHTCCTTCEEEEEE
T ss_pred             CEEEEEECCcCHHHHHHHHHCCCcEEEEEECCHHHHHHHHHhccccCCCceEEEECcHHHHHhhccCCCCCEEEE
Confidence            4999999999999999999999999999999 5688887652      689999999886   3443 3 98875

>1xtp_A LMAJ004091AAA; SGPP, structural genomics, PSI, protein structure initiative dependent methyltransferase; HET: SAI; 1.94A {Leishmania major} SCOP: c.66.1.42

Probab=98.29  E-value=3.8e-07  Score=73.99  Aligned_cols=74  Identities=19%  Similarity=0.250  Sum_probs=57.9

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC----CCceEEecCcCC-CCCCC--C
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY----SGVKHIGGIMLE-RIPKG--D  228 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~----~ri~~~~gD~f~-~~P~~--D  228 (233)
                      ..+++.++ .....+|||||||+|.++..++++. ..+++.+|. |..++.+++.    ++++++.+|+.+ ++|.+  |
T Consensus        83 ~~~l~~l~-~~~~~~vLDiG~G~G~~~~~l~~~~-~~~v~~vD~s~~~~~~a~~~~~~~~~~~~~~~d~~~~~~~~~~fD  160 (254)
T 1xtp_A           83 RNFIASLP-GHGTSRALDCGAGIGRITKNLLTKL-YATTDLLEPVKHMLEEAKRELAGMPVGKFILASMETATLPPNTYD  160 (254)
T ss_dssp             HHHHHTST-TCCCSEEEEETCTTTHHHHHTHHHH-CSEEEEEESCHHHHHHHHHHTTTSSEEEEEESCGGGCCCCSSCEE
T ss_pred             HHHHHhhc-ccCCCEEEEECCCcCHHHHHHHHhh-cCEEEEEeCCHHHHHHHHHHhccCCceEEEEccHHHCCCCCCCeE
Confidence            34555555 5567899999999999999999987 557999998 5677776653    579999999988 66653  9


Q ss_pred             EEEe
Q 039903          229 AILI  232 (233)
Q Consensus       229 ~~~l  232 (233)
                      +|+.
T Consensus       161 ~v~~  164 (254)
T 1xtp_A          161 LIVI  164 (254)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            8875

>3dli_A Methyltransferase; PSI-II, NYSGXRC, structural genomics, protein structure initiative; 2.46A {Archaeoglobus fulgidus}

Probab=98.29  E-value=2.2e-06  Score=69.07  Aligned_cols=70  Identities=17%  Similarity=0.347  Sum_probs=54.0

Q ss_pred             HHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCCCCceEEecCcCC---CCCCC--CEEEe
Q 039903          159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSYSGVKHIGGIMLE---RIPKG--DAILI  232 (233)
Q Consensus       159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~~ri~~~~gD~f~---~~P~~--D~~~l  232 (233)
                      +...++.+++..+|||||||+|.++..++++  ..+++.+|+ +..++.+++.  ++++.+|+.+   ++|.+  |+|+.
T Consensus        32 ~~~~l~~~~~~~~vLDiGcG~G~~~~~l~~~--~~~v~gvD~s~~~~~~a~~~--~~~~~~d~~~~~~~~~~~~fD~i~~  107 (240)
T 3dli_A           32 LRRYIPYFKGCRRVLDIGCGRGEFLELCKEE--GIESIGVDINEDMIKFCEGK--FNVVKSDAIEYLKSLPDKYLDGVMI  107 (240)
T ss_dssp             HGGGGGGTTTCSCEEEETCTTTHHHHHHHHH--TCCEEEECSCHHHHHHHHTT--SEEECSCHHHHHHTSCTTCBSEEEE
T ss_pred             HHHHHhhhcCCCeEEEEeCCCCHHHHHHHhC--CCcEEEEECCHHHHHHHHhh--cceeeccHHHHhhhcCCCCeeEEEE
Confidence            3333332456689999999999999999998  456899998 5678877764  9999999887   66653  99874

>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=98.29  E-value=1.3e-06  Score=72.34  Aligned_cols=75  Identities=15%  Similarity=0.119  Sum_probs=61.1

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHH-cCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCCCCCC-
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISN-YLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLERIPK-  226 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~-~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~~P~-  226 (233)
                      ..++..++ .....+|||+|||+|.++..++++ .|..+++.+|. |..++.++++       ++++++.+|+.+.+|. 
T Consensus       102 ~~i~~~~~-~~~~~~VLDiG~G~G~~~~~la~~~~~~~~v~~vD~s~~~~~~a~~~~~~~~~~~~v~~~~~d~~~~~~~~  180 (277)
T 1o54_A          102 SFIAMMLD-VKEGDRIIDTGVGSGAMCAVLARAVGSSGKVFAYEKREEFAKLAESNLTKWGLIERVTIKVRDISEGFDEK  180 (277)
T ss_dssp             HHHHHHTT-CCTTCEEEEECCTTSHHHHHHHHHTTTTCEEEEECCCHHHHHHHHHHHHHTTCGGGEEEECCCGGGCCSCC
T ss_pred             HHHHHHhC-CCCCCEEEEECCcCCHHHHHHHHHhCCCcEEEEEECCHHHHHHHHHHHHHcCCCCCEEEEECCHHHcccCC
Confidence            34556555 667789999999999999999999 78999999998 6677777653       5899999999987765 


Q ss_pred             C-CEEEe
Q 039903          227 G-DAILI  232 (233)
Q Consensus       227 ~-D~~~l  232 (233)
                      . |++++
T Consensus       181 ~~D~V~~  187 (277)
T 1o54_A          181 DVDALFL  187 (277)
T ss_dssp             SEEEEEE
T ss_pred             ccCEEEE
Confidence            3 99875

>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=98.28  E-value=1.7e-06  Score=72.34  Aligned_cols=73  Identities=16%  Similarity=0.185  Sum_probs=58.2

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCCCCCCC-
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLERIPKG-  227 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~~P~~-  227 (233)
                      ..+++.++ .....+|||||||+|.++..+++++| .+++.+|+ |..++.+++.       ++|+++.+|+.+- +.. 
T Consensus        62 ~~~~~~~~-~~~~~~vLDiGcG~G~~~~~la~~~~-~~v~gvD~s~~~~~~a~~~~~~~~~~~~v~~~~~d~~~~-~~~f  138 (302)
T 3hem_A           62 KLALDKLN-LEPGMTLLDIGCGWGSTMRHAVAEYD-VNVIGLTLSENQYAHDKAMFDEVDSPRRKEVRIQGWEEF-DEPV  138 (302)
T ss_dssp             HHHHHTTC-CCTTCEEEEETCTTSHHHHHHHHHHC-CEEEEEECCHHHHHHHHHHHHHSCCSSCEEEEECCGGGC-CCCC
T ss_pred             HHHHHHcC-CCCcCEEEEeeccCcHHHHHHHHhCC-CEEEEEECCHHHHHHHHHHHHhcCCCCceEEEECCHHHc-CCCc
Confidence            34556665 67778999999999999999999988 89999998 5677777542       4899999999765 443 


Q ss_pred             CEEEe
Q 039903          228 DAILI  232 (233)
Q Consensus       228 D~~~l  232 (233)
                      |+|+.
T Consensus       139 D~v~~  143 (302)
T 3hem_A          139 DRIVS  143 (302)
T ss_dssp             SEEEE
T ss_pred             cEEEE
Confidence            88874

>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=98.28  E-value=1.4e-06  Score=71.95  Aligned_cols=75  Identities=8%  Similarity=0.179  Sum_probs=59.0

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHH-cCCCcEEEeec-hHHHhhccC---------CCCceEEecCcCC-CC
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISN-YLHIKGVNFDL-SHVIQDSSS---------YSGVKHIGGIMLE-RI  224 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~-~P~l~~~v~Dl-p~v~~~a~~---------~~ri~~~~gD~f~-~~  224 (233)
                      ..++..++ .....+|+|||||+|.++..++++ .|..+++.+|+ |+.++.+++         .++|+++.+|+.+ ++
T Consensus        89 ~~i~~~~~-~~~~~~vLdiG~G~G~~~~~l~~~~~~~~~v~~vD~~~~~~~~a~~~~~~~~g~~~~~v~~~~~d~~~~~~  167 (280)
T 1i9g_A           89 AQIVHEGD-IFPGARVLEAGAGSGALTLSLLRAVGPAGQVISYEQRADHAEHARRNVSGCYGQPPDNWRLVVSDLADSEL  167 (280)
T ss_dssp             HHHHHHTT-CCTTCEEEEECCTTSHHHHHHHHHHCTTSEEEEECSCHHHHHHHHHHHHHHHTSCCTTEEEECSCGGGCCC
T ss_pred             HHHHHHcC-CCCCCEEEEEcccccHHHHHHHHHhCCCCEEEEEeCCHHHHHHHHHHHHHhcCCCCCcEEEEECchHhcCC
Confidence            34555555 667789999999999999999996 58899999998 667766653         2589999999998 55


Q ss_pred             CC-C-CEEEe
Q 039903          225 PK-G-DAILI  232 (233)
Q Consensus       225 P~-~-D~~~l  232 (233)
                      +. . |++++
T Consensus       168 ~~~~~D~v~~  177 (280)
T 1i9g_A          168 PDGSVDRAVL  177 (280)
T ss_dssp             CTTCEEEEEE
T ss_pred             CCCceeEEEE
Confidence            54 3 98875

>3ccf_A Cyclopropane-fatty-acyl-phospholipid synthase; YP_321342.1, putative methyltransferase; 1.90A {Anabaena variabilis atcc 29413}

Probab=98.27  E-value=1.3e-06  Score=72.16  Aligned_cols=74  Identities=15%  Similarity=0.143  Sum_probs=59.2

Q ss_pred             HHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-CCceEEecCcCC-CCCCC-CEEE
Q 039903          156 TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-SGVKHIGGIMLE-RIPKG-DAIL  231 (233)
Q Consensus       156 ~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-~ri~~~~gD~f~-~~P~~-D~~~  231 (233)
                      ...+++.++ .....+|||||||+|.++..+++  |..+++.+|+ |..++.+++. ++++++.+|+.+ +++.. |+|+
T Consensus        46 ~~~l~~~l~-~~~~~~vLDiGcG~G~~~~~l~~--~~~~v~gvD~s~~~~~~a~~~~~~~~~~~~d~~~~~~~~~fD~v~  122 (279)
T 3ccf_A           46 GEDLLQLLN-PQPGEFILDLGCGTGQLTEKIAQ--SGAEVLGTDNAATMIEKARQNYPHLHFDVADARNFRVDKPLDAVF  122 (279)
T ss_dssp             CCHHHHHHC-CCTTCEEEEETCTTSHHHHHHHH--TTCEEEEEESCHHHHHHHHHHCTTSCEEECCTTTCCCSSCEEEEE
T ss_pred             HHHHHHHhC-CCCCCEEEEecCCCCHHHHHHHh--CCCeEEEEECCHHHHHHHHhhCCCCEEEECChhhCCcCCCcCEEE
Confidence            445666665 56678999999999999999998  8889999998 5677777653 789999999988 55544 9887


Q ss_pred             e
Q 039903          232 I  232 (233)
Q Consensus       232 l  232 (233)
                      .
T Consensus       123 ~  123 (279)
T 3ccf_A          123 S  123 (279)
T ss_dssp             E
T ss_pred             E
Confidence            4

>3cgg_A SAM-dependent methyltransferase; NP_600671.1, methyltransferase domain, structural genomics; HET: NHE CIT; 2.00A {Corynebacterium glutamicum atcc 13032}

Probab=98.26  E-value=1.8e-06  Score=66.63  Aligned_cols=71  Identities=20%  Similarity=0.241  Sum_probs=56.1

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-CCceEEecCcCC-CCCC-C-CEEEe
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-SGVKHIGGIMLE-RIPK-G-DAILI  232 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-~ri~~~~gD~f~-~~P~-~-D~~~l  232 (233)
                      .++..+  .+...+|+|||||.|.++..+++.  ..+++.+|. |..++.+++. ++++++.+|+.+ ++|. . |+++.
T Consensus        38 ~~l~~~--~~~~~~vLdiG~G~G~~~~~l~~~--~~~v~~~D~~~~~~~~a~~~~~~~~~~~~d~~~~~~~~~~~D~i~~  113 (195)
T 3cgg_A           38 RLIDAM--APRGAKILDAGCGQGRIGGYLSKQ--GHDVLGTDLDPILIDYAKQDFPEARWVVGDLSVDQISETDFDLIVS  113 (195)
T ss_dssp             HHHHHH--SCTTCEEEEETCTTTHHHHHHHHT--TCEEEEEESCHHHHHHHHHHCTTSEEEECCTTTSCCCCCCEEEEEE
T ss_pred             HHHHHh--ccCCCeEEEECCCCCHHHHHHHHC--CCcEEEEcCCHHHHHHHHHhCCCCcEEEcccccCCCCCCceeEEEE
Confidence            344544  356689999999999999999987  568999998 5677777654 689999999998 6664 3 98875

>3njr_A Precorrin-6Y methylase; methyltransferase, decarboxylase, transferase; HET: SAH PG4; 2.70A {Rhodobacter capsulatus}

Probab=98.26  E-value=2.5e-06  Score=67.47  Aligned_cols=71  Identities=15%  Similarity=0.201  Sum_probs=55.8

Q ss_pred             HHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------C-CceEEecCcCCCCC---CC
Q 039903          159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------S-GVKHIGGIMLERIP---KG  227 (233)
Q Consensus       159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~-ri~~~~gD~f~~~P---~~  227 (233)
                      ++..++ .....+|+|||||+|.++..++++  ..+++.+|+ |+.++.|+++      + +|+++.+|+.+.++   ..
T Consensus        47 ~l~~l~-~~~~~~vLDlGcG~G~~~~~la~~--~~~v~~vD~s~~~~~~a~~~~~~~g~~~~v~~~~~d~~~~~~~~~~~  123 (204)
T 3njr_A           47 TLAALA-PRRGELLWDIGGGSGSVSVEWCLA--GGRAITIEPRADRIENIQKNIDTYGLSPRMRAVQGTAPAALADLPLP  123 (204)
T ss_dssp             HHHHHC-CCTTCEEEEETCTTCHHHHHHHHT--TCEEEEEESCHHHHHHHHHHHHHTTCTTTEEEEESCTTGGGTTSCCC
T ss_pred             HHHhcC-CCCCCEEEEecCCCCHHHHHHHHc--CCEEEEEeCCHHHHHHHHHHHHHcCCCCCEEEEeCchhhhcccCCCC
Confidence            344455 566689999999999999999998  788999998 5677776642      4 89999999998433   34


Q ss_pred             CEEEe
Q 039903          228 DAILI  232 (233)
Q Consensus       228 D~~~l  232 (233)
                      |++++
T Consensus       124 D~v~~  128 (204)
T 3njr_A          124 EAVFI  128 (204)
T ss_dssp             SEEEE
T ss_pred             CEEEE
Confidence            98875

>3bxo_A N,N-dimethyltransferase; desosamine, sugar, carbohydrate, antibiotic, SAM, adoMet; HET: SAM UPP; 2.00A {Streptomyces venezuelae}

Probab=98.25  E-value=2.9e-06  Score=67.94  Aligned_cols=63  Identities=16%  Similarity=0.322  Sum_probs=53.0

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-CCceEEecCcCC-CCCCC-CEEE
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-SGVKHIGGIMLE-RIPKG-DAIL  231 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-~ri~~~~gD~f~-~~P~~-D~~~  231 (233)
                      .+..+|||||||+|.++..++++++  +++.+|+ |..++.+++. ++++++.+|+.+ +.+.. |+++
T Consensus        39 ~~~~~vLdiG~G~G~~~~~l~~~~~--~v~~~D~s~~~~~~a~~~~~~~~~~~~d~~~~~~~~~~D~v~  105 (239)
T 3bxo_A           39 PEASSLLDVACGTGTHLEHFTKEFG--DTAGLELSEDMLTHARKRLPDATLHQGDMRDFRLGRKFSAVV  105 (239)
T ss_dssp             TTCCEEEEETCTTSHHHHHHHHHHS--EEEEEESCHHHHHHHHHHCTTCEEEECCTTTCCCSSCEEEEE
T ss_pred             CCCCeEEEecccCCHHHHHHHHhCC--cEEEEeCCHHHHHHHHHhCCCCEEEECCHHHcccCCCCcEEE
Confidence            4568999999999999999999987  7899998 6688877654 789999999998 55444 9887

>3q7e_A Protein arginine N-methyltransferase 1; HET: SAH; 2.20A {Rattus norvegicus} PDB: 1orh_A* 1ori_A* 1or8_A*

Probab=98.25  E-value=1.5e-06  Score=74.51  Aligned_cols=65  Identities=23%  Similarity=0.241  Sum_probs=54.0

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCC-------CCceEEecCcCC-CCCC-C-CEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSY-------SGVKHIGGIMLE-RIPK-G-DAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~-------~ri~~~~gD~f~-~~P~-~-D~~~l  232 (233)
                      .+..+|||||||+|.++..++++ +..+++.+|..+.++.|++.       ++|+++.+|+.+ ++|. . |+|+.
T Consensus        65 ~~~~~VLDvGcG~G~~~~~la~~-g~~~v~gvD~s~~l~~a~~~~~~~~~~~~v~~~~~d~~~~~~~~~~fD~Iis  139 (349)
T 3q7e_A           65 FKDKVVLDVGSGTGILCMFAAKA-GARKVIGIECSSISDYAVKIVKANKLDHVVTIIKGKVEEVELPVEKVDIIIS  139 (349)
T ss_dssp             HTTCEEEEESCTTSHHHHHHHHT-TCSEEEEEECSTHHHHHHHHHHHTTCTTTEEEEESCTTTCCCSSSCEEEEEE
T ss_pred             CCCCEEEEEeccchHHHHHHHHC-CCCEEEEECcHHHHHHHHHHHHHcCCCCcEEEEECcHHHccCCCCceEEEEE
Confidence            44589999999999999999997 77799999998777766542       579999999998 7885 3 99874

>1pjz_A Thiopurine S-methyltransferase; polymorphism, S-adenosylmethionine, drug metabolism; NMR {Pseudomonas syringae PV} SCOP: c.66.1.36

Probab=98.25  E-value=1.1e-06  Score=69.53  Aligned_cols=68  Identities=12%  Similarity=0.058  Sum_probs=52.7

Q ss_pred             HhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccC------------------CCCceEEecCcC
Q 039903          161 DSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSS------------------YSGVKHIGGIML  221 (233)
Q Consensus       161 ~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~------------------~~ri~~~~gD~f  221 (233)
                      ..+. .....+|+|||||+|.++..++++  ..+++.+|+. ..++.|++                  ..+|+++.+|++
T Consensus        16 ~~l~-~~~~~~vLD~GCG~G~~~~~la~~--g~~V~gvD~S~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~v~~~~~d~~   92 (203)
T 1pjz_A           16 SSLN-VVPGARVLVPLCGKSQDMSWLSGQ--GYHVVGAELSEAAVERYFTERGEQPHITSQGDFKVYAAPGIEIWCGDFF   92 (203)
T ss_dssp             HHHC-CCTTCEEEETTTCCSHHHHHHHHH--CCEEEEEEECHHHHHHHHHHHCSCSEEEEETTEEEEECSSSEEEEECCS
T ss_pred             Hhcc-cCCCCEEEEeCCCCcHhHHHHHHC--CCeEEEEeCCHHHHHHHHHHccCCcccccccccccccCCccEEEECccc
Confidence            3343 556689999999999999999997  5689999985 57776643                  258999999999


Q ss_pred             C-CCC--CC-CEEE
Q 039903          222 E-RIP--KG-DAIL  231 (233)
Q Consensus       222 ~-~~P--~~-D~~~  231 (233)
                      + +.+  .. |+++
T Consensus        93 ~l~~~~~~~fD~v~  106 (203)
T 1pjz_A           93 ALTARDIGHCAAFY  106 (203)
T ss_dssp             SSTHHHHHSEEEEE
T ss_pred             cCCcccCCCEEEEE
Confidence            8 544  23 8886

>3hnr_A Probable methyltransferase BT9727_4108; structural genomics, PSI-2, protein structure initiative; 2.80A {Bacillus thuringiensis serovarkonkukian}

Probab=98.24  E-value=2e-06  Score=68.25  Aligned_cols=72  Identities=14%  Similarity=0.188  Sum_probs=56.7

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC--CCceEEecCcCC-CCCCC-CEEEe
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY--SGVKHIGGIMLE-RIPKG-DAILI  232 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~--~ri~~~~gD~f~-~~P~~-D~~~l  232 (233)
                      .+++.+. .....+|||||||+|.++..++++  ..+++.+|. |..++.+++.  ++++++.+|+.+ +.+.. |+++.
T Consensus        36 ~~l~~~~-~~~~~~vLDiGcG~G~~~~~l~~~--~~~v~~vD~s~~~~~~a~~~~~~~~~~~~~d~~~~~~~~~fD~v~~  112 (220)
T 3hnr_A           36 DILEDVV-NKSFGNVLEFGVGTGNLTNKLLLA--GRTVYGIEPSREMRMIAKEKLPKEFSITEGDFLSFEVPTSIDTIVS  112 (220)
T ss_dssp             HHHHHHH-HTCCSEEEEECCTTSHHHHHHHHT--TCEEEEECSCHHHHHHHHHHSCTTCCEESCCSSSCCCCSCCSEEEE
T ss_pred             HHHHHhh-ccCCCeEEEeCCCCCHHHHHHHhC--CCeEEEEeCCHHHHHHHHHhCCCceEEEeCChhhcCCCCCeEEEEE
Confidence            4455544 456689999999999999999997  568999998 5577777653  489999999998 66643 99875

>3bkx_A SAM-dependent methyltransferase; YP_807781.1, cyclopropane-fatty-acyl-phospholipid synthase-L protein, methyltransferase domain; 1.85A {Lactobacillus casei}

Probab=98.23  E-value=1.7e-06  Score=71.08  Aligned_cols=74  Identities=9%  Similarity=0.173  Sum_probs=57.2

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHc-CCCcEEEeechH-------HHhhccCC-------CCceEEecC-cC
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNY-LHIKGVNFDLSH-------VIQDSSSY-------SGVKHIGGI-ML  221 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~-P~l~~~v~Dlp~-------v~~~a~~~-------~ri~~~~gD-~f  221 (233)
                      .+++.++ .....+|||||||+|.++..+++++ |+.+++.+|+.+       .++.+++.       ++|+++.+| ++
T Consensus        34 ~l~~~~~-~~~~~~vLDiGcG~G~~~~~l~~~~g~~~~v~gvD~s~~~~~~~~~~~~a~~~~~~~~~~~~v~~~~~d~~~  112 (275)
T 3bkx_A           34 AIAEAWQ-VKPGEKILEIGCGQGDLSAVLADQVGSSGHVTGIDIASPDYGAPLTLGQAWNHLLAGPLGDRLTVHFNTNLS  112 (275)
T ss_dssp             HHHHHHT-CCTTCEEEEESCTTSHHHHHHHHHHCTTCEEEEECSSCTTCCSSSCHHHHHHHHHTSTTGGGEEEECSCCTT
T ss_pred             HHHHHcC-CCCCCEEEEeCCCCCHHHHHHHHHhCCCCEEEEEECCccccccHHHHHHHHHHHHhcCCCCceEEEECChhh
Confidence            4556665 6677899999999999999999997 889999999854       56666542       589999998 65


Q ss_pred             C---CCCCC--CEEEe
Q 039903          222 E---RIPKG--DAILI  232 (233)
Q Consensus       222 ~---~~P~~--D~~~l  232 (233)
                      .   ++|.+  |+|+.
T Consensus       113 ~~~~~~~~~~fD~v~~  128 (275)
T 3bkx_A          113 DDLGPIADQHFDRVVL  128 (275)
T ss_dssp             TCCGGGTTCCCSEEEE
T ss_pred             hccCCCCCCCEEEEEE
Confidence            4   34443  99874

>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=98.23  E-value=4.7e-07  Score=75.98  Aligned_cols=67  Identities=10%  Similarity=0.058  Sum_probs=55.6

Q ss_pred             ccCcceEEEecCCccHHHHHHH-HHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCC-CCCCC-CEEEe
Q 039903          166 FEQIKQLVDVGGGLGVNVNIII-SNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLE-RIPKG-DAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~-~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~-~~P~~-D~~~l  232 (233)
                      .....+|+|||||+|.++..++ ..+|+.+++.+|+ |..++.++++       +||+++.+|+.+ +++.. |+|+.
T Consensus       116 l~~~~~vLDiGcG~G~~~~~la~~~~~~~~v~gvD~s~~~~~~a~~~~~~~~~~~~v~~~~~d~~~~~~~~~fD~v~~  193 (305)
T 3ocj_A          116 LRPGCVVASVPCGWMSELLALDYSACPGVQLVGIDYDPEALDGATRLAAGHALAGQITLHRQDAWKLDTREGYDLLTS  193 (305)
T ss_dssp             CCTTCEEEETTCTTCHHHHTSCCTTCTTCEEEEEESCHHHHHHHHHHHTTSTTGGGEEEEECCGGGCCCCSCEEEEEC
T ss_pred             CCCCCEEEEecCCCCHHHHHHHHhcCCCCeEEEEECCHHHHHHHHHHHHhcCCCCceEEEECchhcCCccCCeEEEEE
Confidence            4667899999999999999996 6799999999999 6677777642       469999999998 66644 98875

>3g2m_A PCZA361.24; SAM-dependent methyltransferase, glycopeptide antibiotics biosynthesis, structural genomics; 2.00A {Amycolatopsis orientalis} PDB: 3g2o_A* 3g2p_A* 3g2q_A*

Probab=98.23  E-value=1.5e-06  Score=72.64  Aligned_cols=73  Identities=11%  Similarity=0.166  Sum_probs=56.1

Q ss_pred             HHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC---------CCceEEecCcCC-CC
Q 039903          156 TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY---------SGVKHIGGIMLE-RI  224 (233)
Q Consensus       156 ~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~---------~ri~~~~gD~f~-~~  224 (233)
                      ...+++.++  ....+|||||||+|.++..++++  ..+++.+|+ |..++.+++.         ++|+++.+|+.+ +.
T Consensus        72 ~~~~~~~~~--~~~~~vLDlGcG~G~~~~~l~~~--~~~v~gvD~s~~~~~~a~~~~~~~~~~~~~~v~~~~~d~~~~~~  147 (299)
T 3g2m_A           72 AREFATRTG--PVSGPVLELAAGMGRLTFPFLDL--GWEVTALELSTSVLAAFRKRLAEAPADVRDRCTLVQGDMSAFAL  147 (299)
T ss_dssp             HHHHHHHHC--CCCSCEEEETCTTTTTHHHHHTT--TCCEEEEESCHHHHHHHHHHHHTSCHHHHTTEEEEECBTTBCCC
T ss_pred             HHHHHHhhC--CCCCcEEEEeccCCHHHHHHHHc--CCeEEEEECCHHHHHHHHHHHhhcccccccceEEEeCchhcCCc
Confidence            445555554  23349999999999999999998  568999998 5677777652         579999999998 66


Q ss_pred             CCC-CEEEe
Q 039903          225 PKG-DAILI  232 (233)
Q Consensus       225 P~~-D~~~l  232 (233)
                      +.. |+|++
T Consensus       148 ~~~fD~v~~  156 (299)
T 3g2m_A          148 DKRFGTVVI  156 (299)
T ss_dssp             SCCEEEEEE
T ss_pred             CCCcCEEEE
Confidence            554 97764

>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=98.22  E-value=1.6e-06  Score=70.66  Aligned_cols=65  Identities=8%  Similarity=0.054  Sum_probs=52.6

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCc----CCCCC----CC-CEE
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIM----LERIP----KG-DAI  230 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~----f~~~P----~~-D~~  230 (233)
                      +..+|+|||||+|.++..+++++|+.+++.+|+ |..++.|+++       +||+++.+|.    +++++    .. |++
T Consensus        65 ~~~~vLDlG~G~G~~~~~la~~~~~~~v~gvD~s~~~~~~a~~~~~~~~~~~~v~~~~~d~~~~~~~~~~~~~~~~fD~i  144 (254)
T 2h00_A           65 TLRRGIDIGTGASCIYPLLGATLNGWYFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVPQKTLLMDALKEESEIIYDFC  144 (254)
T ss_dssp             CCCEEEEESCTTTTHHHHHHHHHHCCEEEEEESCHHHHHHHHHHHHHTTCTTTEEEEECCTTCSSTTTSTTCCSCCBSEE
T ss_pred             CCCEEEEeCCChhHHHHHHHHhCCCCeEEEEECCHHHHHHHHHHHHHcCCCccEEEEEcchhhhhhhhhhcccCCcccEE
Confidence            457999999999999999999999999999998 5677777652       4799999994    44555    23 888


Q ss_pred             Ee
Q 039903          231 LI  232 (233)
Q Consensus       231 ~l  232 (233)
                      +.
T Consensus       145 ~~  146 (254)
T 2h00_A          145 MC  146 (254)
T ss_dssp             EE
T ss_pred             EE
Confidence            75

>2yqz_A Hypothetical protein TTHA0223; RNA methyltransferase, SAM, structural genomics, NPPSFA; HET: SAM; 1.80A {Thermus thermophilus} PDB: 2yr0_A

Probab=98.21  E-value=3.6e-06  Score=68.38  Aligned_cols=65  Identities=11%  Similarity=0.174  Sum_probs=52.4

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccC-----CCCceEEecCcCC-CCCCC--CEEEe
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSS-----YSGVKHIGGIMLE-RIPKG--DAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~-----~~ri~~~~gD~f~-~~P~~--D~~~l  232 (233)
                      .....+|+|||||+|.++..++++  ..+++.+|. |..++.+++     .++++++.+|+.+ ++|.+  |+++.
T Consensus        37 ~~~~~~vLDiG~G~G~~~~~l~~~--~~~v~~vD~s~~~~~~a~~~~~~~~~~~~~~~~d~~~~~~~~~~fD~v~~  110 (263)
T 2yqz_A           37 KGEEPVFLELGVGTGRIALPLIAR--GYRYIALDADAAMLEVFRQKIAGVDRKVQVVQADARAIPLPDESVHGVIV  110 (263)
T ss_dssp             SSSCCEEEEETCTTSTTHHHHHTT--TCEEEEEESCHHHHHHHHHHTTTSCTTEEEEESCTTSCCSCTTCEEEEEE
T ss_pred             CCCCCEEEEeCCcCCHHHHHHHHC--CCEEEEEECCHHHHHHHHHHhhccCCceEEEEcccccCCCCCCCeeEEEE
Confidence            566789999999999999999987  568999998 456666654     2689999999987 66653  98875

>2plw_A Ribosomal RNA methyltransferase, putative; malaria, SAM, structural genomics, structural genomics consortium, SGC; HET: SAM; 1.70A {Plasmodium falciparum}

Probab=98.21  E-value=3.6e-06  Score=65.79  Aligned_cols=61  Identities=16%  Similarity=0.126  Sum_probs=48.7

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcC--CCcEEEeechHHHhhccCCCCceEEecCcCC
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYL--HIKGVNFDLSHVIQDSSSYSGVKHIGGIMLE  222 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P--~l~~~v~Dlp~v~~~a~~~~ri~~~~gD~f~  222 (233)
                      .+.+.+..+....+|+|||||+|.++..+++++|  ..+++.+|+.+..    ..++++++.+|+.+
T Consensus        12 ~~~~~~~~~~~~~~vLDlGcG~G~~~~~l~~~~~~~~~~v~gvD~s~~~----~~~~v~~~~~d~~~   74 (201)
T 2plw_A           12 ELDNKYLFLKKNKIILDIGCYPGSWCQVILERTKNYKNKIIGIDKKIMD----PIPNVYFIQGEIGK   74 (201)
T ss_dssp             HHHHHHCCCCTTEEEEEESCTTCHHHHHHHHHTTTSCEEEEEEESSCCC----CCTTCEEEECCTTT
T ss_pred             HHHHHcCCCCCCCEEEEeCCCCCHHHHHHHHHcCCCCceEEEEeCCccC----CCCCceEEEccccc
Confidence            3445554235668999999999999999999998  6899999987631    23689999999987

>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=98.20  E-value=2.2e-06  Score=69.03  Aligned_cols=74  Identities=16%  Similarity=0.242  Sum_probs=58.5

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCCCCCC-C-
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLERIPK-G-  227 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~~P~-~-  227 (233)
                      ..+++.++ .....+|||||||+|.++..+++..| .+++.+|+ |..++.++++      ++|+++.+|+..++|. + 
T Consensus        81 ~~~~~~l~-~~~~~~vLdiG~G~G~~~~~la~~~~-~~v~~vD~~~~~~~~a~~~~~~~~~~~v~~~~~d~~~~~~~~~~  158 (235)
T 1jg1_A           81 AIMLEIAN-LKPGMNILEVGTGSGWNAALISEIVK-TDVYTIERIPELVEFAKRNLERAGVKNVHVILGDGSKGFPPKAP  158 (235)
T ss_dssp             HHHHHHHT-CCTTCCEEEECCTTSHHHHHHHHHHC-SCEEEEESCHHHHHHHHHHHHHTTCCSEEEEESCGGGCCGGGCC
T ss_pred             HHHHHhcC-CCCCCEEEEEeCCcCHHHHHHHHHhC-CEEEEEeCCHHHHHHHHHHHHHcCCCCcEEEECCcccCCCCCCC
Confidence            34555555 66678999999999999999999998 89999996 5677776652      5799999999666664 2 


Q ss_pred             -CEEEe
Q 039903          228 -DAILI  232 (233)
Q Consensus       228 -D~~~l  232 (233)
                       |+|++
T Consensus       159 fD~Ii~  164 (235)
T 1jg1_A          159 YDVIIV  164 (235)
T ss_dssp             EEEEEE
T ss_pred             ccEEEE
Confidence             88875

>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=98.20  E-value=4e-06  Score=68.10  Aligned_cols=57  Identities=11%  Similarity=0.200  Sum_probs=47.5

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhcc--------------CCCCceEEecCcCCC
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSS--------------SYSGVKHIGGIMLER  223 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~--------------~~~ri~~~~gD~f~~  223 (233)
                      ++..+|||||||+|.++..+++.+|+.+++.+|+ +.+++.++              ..++|+++.+|.++.
T Consensus        48 ~~~~~vLDiGcG~G~~~~~la~~~~~~~v~gvD~s~~~l~~a~~~~~~~~~~~~~~~~~~nv~~~~~D~~~~  119 (246)
T 2vdv_E           48 TKKVTIADIGCGFGGLMIDLSPAFPEDLILGMEIRVQVTNYVEDRIIALRNNTASKHGFQNINVLRGNAMKF  119 (246)
T ss_dssp             SCCEEEEEETCTTSHHHHHHHHHSTTSEEEEEESCHHHHHHHHHHHHHHHHTC-CCSTTTTEEEEECCTTSC
T ss_pred             CCCCEEEEEcCCCCHHHHHHHHhCCCCCEEEEEcCHHHHHHHHHHHHHHhhccccccCCCcEEEEeccHHHH
Confidence            4567999999999999999999999999999997 45665543              226899999999873

>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=98.20  E-value=6.9e-06  Score=66.48  Aligned_cols=64  Identities=17%  Similarity=0.352  Sum_probs=51.8

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-----CCceEEecCcCC-CCCCC-CEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-----SGVKHIGGIMLE-RIPKG-DAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-----~ri~~~~gD~f~-~~P~~-D~~~l  232 (233)
                      .+..+|||||||+|.++..++++  ..+++.+|+ |..++.+++.     .+|+++.+|+.+ +.+.. |++++
T Consensus        40 ~~~~~vLDlGcG~G~~~~~l~~~--~~~v~gvD~s~~~l~~a~~~~~~~~~~v~~~~~d~~~~~~~~~fD~v~~  111 (252)
T 1wzn_A           40 REVRRVLDLACGTGIPTLELAER--GYEVVGLDLHEEMLRVARRKAKERNLKIEFLQGDVLEIAFKNEFDAVTM  111 (252)
T ss_dssp             SCCCEEEEETCTTCHHHHHHHHT--TCEEEEEESCHHHHHHHHHHHHHTTCCCEEEESCGGGCCCCSCEEEEEE
T ss_pred             cCCCEEEEeCCCCCHHHHHHHHC--CCeEEEEECCHHHHHHHHHHHHhcCCceEEEECChhhcccCCCccEEEE
Confidence            45679999999999999999987  568999998 5677776542     479999999998 55554 98874

>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=98.19  E-value=3.4e-06  Score=72.06  Aligned_cols=72  Identities=22%  Similarity=0.286  Sum_probs=56.4

Q ss_pred             HHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCC-------CCceEEecCcCC-CCCC-C-C
Q 039903          159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSY-------SGVKHIGGIMLE-RIPK-G-D  228 (233)
Q Consensus       159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~-------~ri~~~~gD~f~-~~P~-~-D  228 (233)
                      +.+... ..+..+|+|||||+|.++..++++ +..+++.+|..+.++.+++.       ++|+++.+|+.+ ++|. . |
T Consensus        56 i~~~~~-~~~~~~VLDiGcGtG~ls~~la~~-g~~~v~gvD~s~~~~~a~~~~~~~~~~~~i~~~~~d~~~~~~~~~~~D  133 (340)
T 2fyt_A           56 IYQNPH-IFKDKVVLDVGCGTGILSMFAAKA-GAKKVLGVDQSEILYQAMDIIRLNKLEDTITLIKGKIEEVHLPVEKVD  133 (340)
T ss_dssp             HHHCGG-GTTTCEEEEETCTTSHHHHHHHHT-TCSEEEEEESSTHHHHHHHHHHHTTCTTTEEEEESCTTTSCCSCSCEE
T ss_pred             HHhhhh-hcCCCEEEEeeccCcHHHHHHHHc-CCCEEEEEChHHHHHHHHHHHHHcCCCCcEEEEEeeHHHhcCCCCcEE
Confidence            334334 455689999999999999999987 55689999997777766542       689999999998 7774 3 9


Q ss_pred             EEEe
Q 039903          229 AILI  232 (233)
Q Consensus       229 ~~~l  232 (233)
                      +++.
T Consensus       134 ~Ivs  137 (340)
T 2fyt_A          134 VIIS  137 (340)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            9873

>1dus_A MJ0882; hypothetical protein, methanococcus jannaschii, structural genomics, BSGC structure funded by NIH; 1.80A {Methanocaldococcus jannaschii} SCOP: c.66.1.4

Probab=98.19  E-value=3.5e-06  Score=64.93  Aligned_cols=73  Identities=12%  Similarity=0.241  Sum_probs=57.0

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------C--CceEEecCcCCCCCC-
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------S--GVKHIGGIMLERIPK-  226 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~--ri~~~~gD~f~~~P~-  226 (233)
                      ..+++.+. .....+|+|||||+|.++..+++.  ..+++.+|+ |..++.++++      +  |++++.+|+.+..+. 
T Consensus        42 ~~l~~~~~-~~~~~~vLdiG~G~G~~~~~~~~~--~~~v~~~D~~~~~~~~a~~~~~~~~~~~~~~~~~~~d~~~~~~~~  118 (194)
T 1dus_A           42 KILVENVV-VDKDDDILDLGCGYGVIGIALADE--VKSTTMADINRRAIKLAKENIKLNNLDNYDIRVVHSDLYENVKDR  118 (194)
T ss_dssp             HHHHHHCC-CCTTCEEEEETCTTSHHHHHHGGG--SSEEEEEESCHHHHHHHHHHHHHTTCTTSCEEEEECSTTTTCTTS
T ss_pred             HHHHHHcc-cCCCCeEEEeCCCCCHHHHHHHHc--CCeEEEEECCHHHHHHHHHHHHHcCCCccceEEEECchhcccccC
Confidence            34555555 566789999999999999999998  778999998 5677766542      3  599999999986655 


Q ss_pred             C-CEEEe
Q 039903          227 G-DAILI  232 (233)
Q Consensus       227 ~-D~~~l  232 (233)
                      . |+++.
T Consensus       119 ~~D~v~~  125 (194)
T 1dus_A          119 KYNKIIT  125 (194)
T ss_dssp             CEEEEEE
T ss_pred             CceEEEE
Confidence            3 98875

>3fzg_A 16S rRNA methylase; methyltransferase, plasmid, transferase; HET: SAM; 2.00A {Escherichia coli}

Probab=98.19  E-value=8.8e-07  Score=69.45  Aligned_cols=64  Identities=16%  Similarity=0.125  Sum_probs=51.1

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC-------CCceEEecCcCCCCCC-C-CEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY-------SGVKHIGGIMLERIPK-G-DAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~-------~ri~~~~gD~f~~~P~-~-D~~~l  232 (233)
                      ....+|+|+|||.|-++..++...|+.+.+..|.. ..++.++++       .++++  .|..+..|. . |++++
T Consensus        48 ~~~~~VLDlGCG~GplAl~l~~~~p~a~~~A~Di~~~~leiar~~~~~~g~~~~v~~--~d~~~~~~~~~~DvVLa  121 (200)
T 3fzg_A           48 KHVSSILDFGCGFNPLALYQWNENEKIIYHAYDIDRAEIAFLSSIIGKLKTTIKYRF--LNKESDVYKGTYDVVFL  121 (200)
T ss_dssp             CCCSEEEEETCTTHHHHHHHHCSSCCCEEEEECSCHHHHHHHHHHHHHSCCSSEEEE--ECCHHHHTTSEEEEEEE
T ss_pred             CCCCeEEEecCCCCHHHHHHHhcCCCCEEEEEeCCHHHHHHHHHHHHhcCCCccEEE--ecccccCCCCCcChhhH
Confidence            45789999999999999999999999999999995 477777653       25655  788774444 3 99874

>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=98.19  E-value=2.3e-06  Score=71.62  Aligned_cols=66  Identities=21%  Similarity=0.266  Sum_probs=54.6

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCCCCCC--CCEEEe
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLERIPK--GDAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~~P~--~D~~~l  232 (233)
                      .+...+|+|||||+|.++..++.+.|+.+++.+|+ |+.++.|+++      ++|+++.+|..+ +|.  .|++++
T Consensus       120 l~~g~rVLDIGcG~G~~ta~~lA~~~ga~V~gIDis~~~l~~Ar~~~~~~gl~~v~~v~gDa~~-l~d~~FDvV~~  194 (298)
T 3fpf_A          120 FRRGERAVFIGGGPLPLTGILLSHVYGMRVNVVEIEPDIAELSRKVIEGLGVDGVNVITGDETV-IDGLEFDVLMV  194 (298)
T ss_dssp             CCTTCEEEEECCCSSCHHHHHHHHTTCCEEEEEESSHHHHHHHHHHHHHHTCCSEEEEESCGGG-GGGCCCSEEEE
T ss_pred             CCCcCEEEEECCCccHHHHHHHHHccCCEEEEEECCHHHHHHHHHHHHhcCCCCeEEEECchhh-CCCCCcCEEEE
Confidence            67789999999999988877777789999999998 6688887753      799999999987 233  399875

>4fsd_A Arsenic methyltransferase; rossmann fold; 1.75A {Cyanidioschyzon SP} PDB: 4fr0_A* 4fs8_A 3p7e_A 3qnh_A 3qhu_A

Probab=98.19  E-value=3.1e-06  Score=73.46  Aligned_cols=66  Identities=21%  Similarity=0.387  Sum_probs=55.0

Q ss_pred             cCcceEEEecCCccHHHHHHHHHc-CCCcEEEeec-hHHHhhccCC--------------CCceEEecCcCC-------C
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNY-LHIKGVNFDL-SHVIQDSSSY--------------SGVKHIGGIMLE-------R  223 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~v~~~a~~~--------------~ri~~~~gD~f~-------~  223 (233)
                      ....+|||||||+|.++..+++.+ |..+++.+|+ |..++.++++              ++|+++.+|+.+       +
T Consensus        82 ~~~~~VLDlGcG~G~~~~~la~~~~~~~~v~gvD~s~~~l~~a~~~~~~~~~~~~g~~~~~~v~~~~~d~~~l~~~~~~~  161 (383)
T 4fsd_A           82 LEGATVLDLGCGTGRDVYLASKLVGEHGKVIGVDMLDNQLEVARKYVEYHAEKFFGSPSRSNVRFLKGFIENLATAEPEG  161 (383)
T ss_dssp             GTTCEEEEESCTTSHHHHHHHHHHTTTCEEEEEECCHHHHHHHHHTHHHHHHHHHSSTTCCCEEEEESCTTCGGGCBSCC
T ss_pred             CCCCEEEEecCccCHHHHHHHHHhCCCCEEEEEECCHHHHHHHHHHHHHhhhhcccccCCCceEEEEccHHHhhhcccCC
Confidence            345799999999999999999997 8999999998 5677777653              689999999987       5


Q ss_pred             CCCC--CEEEe
Q 039903          224 IPKG--DAILI  232 (233)
Q Consensus       224 ~P~~--D~~~l  232 (233)
                      +|.+  |+|+.
T Consensus       162 ~~~~~fD~V~~  172 (383)
T 4fsd_A          162 VPDSSVDIVIS  172 (383)
T ss_dssp             CCTTCEEEEEE
T ss_pred             CCCCCEEEEEE
Confidence            6653  98874

>2xvm_A Tellurite resistance protein TEHB; antibiotic resistance, transferase; HET: SAH; 1.48A {Escherichia coli} PDB: 2xva_A* 4dq0_A* 2i6g_A*

Probab=98.18  E-value=3.8e-06  Score=65.26  Aligned_cols=73  Identities=16%  Similarity=0.180  Sum_probs=56.5

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCC-CCCCC-
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLE-RIPKG-  227 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~-~~P~~-  227 (233)
                      +.+++.++ ..+..+|+|||||+|.++..++++  ..+++.+|. |..++.+++.      ++++++.+|+.+ +++.. 
T Consensus        22 ~~l~~~~~-~~~~~~vLdiG~G~G~~~~~l~~~--~~~v~~vD~s~~~~~~a~~~~~~~~~~~~~~~~~d~~~~~~~~~~   98 (199)
T 2xvm_A           22 SEVLEAVK-VVKPGKTLDLGCGNGRNSLYLAAN--GYDVDAWDKNAMSIANVERIKSIENLDNLHTRVVDLNNLTFDRQY   98 (199)
T ss_dssp             HHHHHHTT-TSCSCEEEEETCTTSHHHHHHHHT--TCEEEEEESCHHHHHHHHHHHHHHTCTTEEEEECCGGGCCCCCCE
T ss_pred             HHHHHHhh-ccCCCeEEEEcCCCCHHHHHHHHC--CCeEEEEECCHHHHHHHHHHHHhCCCCCcEEEEcchhhCCCCCCc
Confidence            34555555 555679999999999999999987  568999998 5677776542      479999999998 55444 


Q ss_pred             CEEEe
Q 039903          228 DAILI  232 (233)
Q Consensus       228 D~~~l  232 (233)
                      |+++.
T Consensus        99 D~v~~  103 (199)
T 2xvm_A           99 DFILS  103 (199)
T ss_dssp             EEEEE
T ss_pred             eEEEE
Confidence            88874

>2ozv_A Hypothetical protein ATU0636; structural genomics, predicted transferase, predicted O-methyltransferase, PFAM PF05175; HET: MSE; 1.70A {Agrobacterium tumefaciens str}

Probab=98.18  E-value=2.7e-06  Score=69.91  Aligned_cols=67  Identities=9%  Similarity=0.196  Sum_probs=54.2

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC----------CCceEEecCcCCC--------CCC
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY----------SGVKHIGGIMLER--------IPK  226 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~----------~ri~~~~gD~f~~--------~P~  226 (233)
                      .....+|||+|||+|.++..+++++|..+++.+|+ |..++.++++          +||+++.+|+.+.        ++.
T Consensus        34 ~~~~~~VLDlG~G~G~~~l~la~~~~~~~v~gvDi~~~~~~~a~~n~~~~~~~~l~~~v~~~~~D~~~~~~~~~~~~~~~  113 (260)
T 2ozv_A           34 DDRACRIADLGAGAGAAGMAVAARLEKAEVTLYERSQEMAEFARRSLELPDNAAFSARIEVLEADVTLRAKARVEAGLPD  113 (260)
T ss_dssp             CCSCEEEEECCSSSSHHHHHHHHHCTTEEEEEEESSHHHHHHHHHHTTSGGGTTTGGGEEEEECCTTCCHHHHHHTTCCT
T ss_pred             ccCCCEEEEeCChHhHHHHHHHHhCCCCeEEEEECCHHHHHHHHHHHHhhhhCCCcceEEEEeCCHHHHhhhhhhhccCC
Confidence            45567999999999999999999999999999998 5566665432          3699999999874        344


Q ss_pred             -C-CEEEe
Q 039903          227 -G-DAILI  232 (233)
Q Consensus       227 -~-D~~~l  232 (233)
                       . |+|+.
T Consensus       114 ~~fD~Vv~  121 (260)
T 2ozv_A          114 EHFHHVIM  121 (260)
T ss_dssp             TCEEEEEE
T ss_pred             CCcCEEEE
Confidence             3 98875

>3duw_A OMT, O-methyltransferase, putative; alternating of alpha and beta with complex SAH; HET: SAH; 1.20A {Bacillus cereus} PDB: 3dul_A*

Probab=98.18  E-value=7.3e-07  Score=71.13  Aligned_cols=67  Identities=15%  Similarity=0.180  Sum_probs=54.3

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcC-CCcEEEeec-hHHHhhccCC-------CCceEEecCcCCCCC-------C-CC
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLERIP-------K-GD  228 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~~P-------~-~D  228 (233)
                      ..+..+|||||||+|..+..+++++| +.+++.+|+ |+.++.++++       ++|+++.+|+.+.+|       . -|
T Consensus        56 ~~~~~~vLdiG~G~G~~~~~la~~~~~~~~v~~vD~~~~~~~~a~~~~~~~~~~~~v~~~~~d~~~~~~~~~~~~~~~fD  135 (223)
T 3duw_A           56 IQGARNILEIGTLGGYSTIWLARGLSSGGRVVTLEASEKHADIARSNIERANLNDRVEVRTGLALDSLQQIENEKYEPFD  135 (223)
T ss_dssp             HHTCSEEEEECCTTSHHHHHHHTTCCSSCEEEEEESCHHHHHHHHHHHHHTTCTTTEEEEESCHHHHHHHHHHTTCCCCS
T ss_pred             hhCCCEEEEecCCccHHHHHHHHhCCCCCEEEEEECCHHHHHHHHHHHHHcCCCCcEEEEEcCHHHHHHHHHhcCCCCcC
Confidence            45668999999999999999999999 889999998 6677766542       579999999986322       2 38


Q ss_pred             EEEe
Q 039903          229 AILI  232 (233)
Q Consensus       229 ~~~l  232 (233)
                      ++++
T Consensus       136 ~v~~  139 (223)
T 3duw_A          136 FIFI  139 (223)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            8875

>1xdz_A Methyltransferase GIDB; MCSG, protein structure initiative, structural genomics, methyltransferase fold, PSI; 1.60A {Bacillus subtilis} SCOP: c.66.1.20

Probab=98.17  E-value=1.4e-06  Score=70.47  Aligned_cols=67  Identities=18%  Similarity=0.183  Sum_probs=53.9

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCC-CCC----CC-CEEEe
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLE-RIP----KG-DAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~-~~P----~~-D~~~l  232 (233)
                      +++..+|+|||||+|.++..+++.+|+.+++.+|. +..++.++++      ++|+++.+|+.+ +.+    .. |+|+.
T Consensus        68 ~~~~~~vLDiG~G~G~~~~~la~~~~~~~v~~vD~s~~~~~~a~~~~~~~~~~~v~~~~~d~~~~~~~~~~~~~fD~V~~  147 (240)
T 1xdz_A           68 FNQVNTICDVGAGAGFPSLPIKICFPHLHVTIVDSLNKRITFLEKLSEALQLENTTFCHDRAETFGQRKDVRESYDIVTA  147 (240)
T ss_dssp             GGGCCEEEEECSSSCTTHHHHHHHCTTCEEEEEESCHHHHHHHHHHHHHHTCSSEEEEESCHHHHTTCTTTTTCEEEEEE
T ss_pred             cCCCCEEEEecCCCCHHHHHHHHhCCCCEEEEEeCCHHHHHHHHHHHHHcCCCCEEEEeccHHHhcccccccCCccEEEE
Confidence            35668999999999999999999999999999998 4567666542      579999999977 442    23 88874

>2gpy_A O-methyltransferase; structural genomics, PSI, protein structure initiative, NEW research center for structural genomics, nysgxrc; HET: MSE; 1.90A {Bacillus halodurans}

Probab=98.17  E-value=4.4e-06  Score=67.07  Aligned_cols=67  Identities=12%  Similarity=0.163  Sum_probs=54.5

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCCCCC-----CC-CEEE
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLERIP-----KG-DAIL  231 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~~P-----~~-D~~~  231 (233)
                      ..+..+|||||||+|..+..+++.+|..+++.+|. |..++.++++       ++|+++.+|+.+.+|     .. |+|+
T Consensus        52 ~~~~~~vLdiG~G~G~~~~~la~~~~~~~v~~vD~~~~~~~~a~~~~~~~~~~~~v~~~~~d~~~~~~~~~~~~~fD~I~  131 (233)
T 2gpy_A           52 MAAPARILEIGTAIGYSAIRMAQALPEATIVSIERDERRYEEAHKHVKALGLESRIELLFGDALQLGEKLELYPLFDVLF  131 (233)
T ss_dssp             HHCCSEEEEECCTTSHHHHHHHHHCTTCEEEEECCCHHHHHHHHHHHHHTTCTTTEEEECSCGGGSHHHHTTSCCEEEEE
T ss_pred             ccCCCEEEEecCCCcHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHcCCCCcEEEEECCHHHHHHhcccCCCccEEE
Confidence            34567999999999999999999999999999998 5677776653       579999999987322     33 8887


Q ss_pred             e
Q 039903          232 I  232 (233)
Q Consensus       232 l  232 (233)
                      +
T Consensus       132 ~  132 (233)
T 2gpy_A          132 I  132 (233)
T ss_dssp             E
T ss_pred             E
Confidence            4

>3l8d_A Methyltransferase; structural genomics, PSI, nysgrc, protein structure initiative, NEW YORK SGX research center for STRU genomics; 1.70A {Bacillus thuringiensis}

Probab=98.17  E-value=7.7e-06  Score=65.64  Aligned_cols=64  Identities=22%  Similarity=0.326  Sum_probs=53.4

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC---CCceEEecCcCC-CCCCC--CEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY---SGVKHIGGIMLE-RIPKG--DAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~---~ri~~~~gD~f~-~~P~~--D~~~l  232 (233)
                      +...+|||||||+|.++..++++  ..+++.+|+ |..++.+++.   .+++++.+|+.+ ++|.+  |+++.
T Consensus        52 ~~~~~vLDiG~G~G~~~~~l~~~--~~~v~~vD~s~~~~~~a~~~~~~~~~~~~~~d~~~~~~~~~~fD~v~~  122 (242)
T 3l8d_A           52 KKEAEVLDVGCGDGYGTYKLSRT--GYKAVGVDISEVMIQKGKERGEGPDLSFIKGDLSSLPFENEQFEAIMA  122 (242)
T ss_dssp             CTTCEEEEETCTTSHHHHHHHHT--TCEEEEEESCHHHHHHHHTTTCBTTEEEEECBTTBCSSCTTCEEEEEE
T ss_pred             CCCCeEEEEcCCCCHHHHHHHHc--CCeEEEEECCHHHHHHHHhhcccCCceEEEcchhcCCCCCCCccEEEE
Confidence            45679999999999999999998  568999998 5677777664   789999999998 77653  98874

>4htf_A S-adenosylmethionine-dependent methyltransferase; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; HET: MSE SAM; 1.60A {Escherichia coli}

Probab=98.17  E-value=2.5e-06  Score=70.59  Aligned_cols=71  Identities=20%  Similarity=0.273  Sum_probs=54.7

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCC-C-CCCC
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLE-R-IPKG  227 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~-~-~P~~  227 (233)
                      .++..++  .+..+|||||||+|.++..++++  ..+++.+|+ |..++.+++.       ++|+++.+|+.+ + ++.+
T Consensus        60 ~~l~~~~--~~~~~vLDiGcG~G~~~~~l~~~--~~~v~gvD~s~~~~~~a~~~~~~~~~~~~v~~~~~d~~~~~~~~~~  135 (285)
T 4htf_A           60 RVLAEMG--PQKLRVLDAGGGEGQTAIKMAER--GHQVILCDLSAQMIDRAKQAAEAKGVSDNMQFIHCAAQDVASHLET  135 (285)
T ss_dssp             HHHHHTC--SSCCEEEEETCTTCHHHHHHHHT--TCEEEEEESCHHHHHHHHHHHHC-CCGGGEEEEESCGGGTGGGCSS
T ss_pred             HHHHhcC--CCCCEEEEeCCcchHHHHHHHHC--CCEEEEEECCHHHHHHHHHHHHhcCCCcceEEEEcCHHHhhhhcCC
Confidence            3444444  23579999999999999999998  668999998 5677777652       689999999998 3 4543


Q ss_pred             --CEEEe
Q 039903          228 --DAILI  232 (233)
Q Consensus       228 --D~~~l  232 (233)
                        |+|+.
T Consensus       136 ~fD~v~~  142 (285)
T 4htf_A          136 PVDLILF  142 (285)
T ss_dssp             CEEEEEE
T ss_pred             CceEEEE
Confidence              98875

>3tfw_A Putative O-methyltransferase; PSI-biology, nysgrc, structural genomics, NEW YORK structura genomics research consortium; 1.88A {Klebsiella pneumoniae subsp}

Probab=98.17  E-value=9.9e-07  Score=71.94  Aligned_cols=67  Identities=18%  Similarity=0.187  Sum_probs=54.7

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcC-CCcEEEeec-hHHHhhccCC-------CCceEEecCcCCC---CCC---CCEE
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLER---IPK---GDAI  230 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~---~P~---~D~~  230 (233)
                      ..+..+|||||||+|..+..+++.+| +.+++.+|+ |+.++.|+++       ++|+++.+|+.+.   ++.   .|++
T Consensus        61 ~~~~~~VLdiG~G~G~~~~~la~~~~~~~~v~~vD~s~~~~~~a~~~~~~~g~~~~v~~~~~d~~~~l~~~~~~~~fD~V  140 (248)
T 3tfw_A           61 LTQAKRILEIGTLGGYSTIWMARELPADGQLLTLEADAHHAQVARENLQLAGVDQRVTLREGPALQSLESLGECPAFDLI  140 (248)
T ss_dssp             HHTCSEEEEECCTTSHHHHHHHTTSCTTCEEEEEECCHHHHHHHHHHHHHTTCTTTEEEEESCHHHHHHTCCSCCCCSEE
T ss_pred             hcCCCEEEEecCCchHHHHHHHHhCCCCCEEEEEECCHHHHHHHHHHHHHcCCCCcEEEEEcCHHHHHHhcCCCCCeEEE
Confidence            45668999999999999999999998 899999999 6677776652       5899999998762   322   3998


Q ss_pred             Ee
Q 039903          231 LI  232 (233)
Q Consensus       231 ~l  232 (233)
                      ++
T Consensus       141 ~~  142 (248)
T 3tfw_A          141 FI  142 (248)
T ss_dssp             EE
T ss_pred             EE
Confidence            75

>3h2b_A SAM-dependent methyltransferase; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; HET: SAH; 2.00A {Corynebacterium glutamicum atcc 13032}

Probab=98.16  E-value=1.8e-06  Score=67.60  Aligned_cols=62  Identities=15%  Similarity=0.154  Sum_probs=52.1

Q ss_pred             cceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccC-CCCceEEecCcCC-CCCCC--CEEEe
Q 039903          169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSS-YSGVKHIGGIMLE-RIPKG--DAILI  232 (233)
Q Consensus       169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~-~~ri~~~~gD~f~-~~P~~--D~~~l  232 (233)
                      ..+|||||||+|.++..++++  ..+++.+|+ +..++.+++ .++++++.+|+.+ ++|.+  |+++.
T Consensus        42 ~~~vLDiGcG~G~~~~~l~~~--~~~v~gvD~s~~~~~~a~~~~~~~~~~~~d~~~~~~~~~~fD~v~~  108 (203)
T 3h2b_A           42 DGVILDVGSGTGRWTGHLASL--GHQIEGLEPATRLVELARQTHPSVTFHHGTITDLSDSPKRWAGLLA  108 (203)
T ss_dssp             CSCEEEETCTTCHHHHHHHHT--TCCEEEECCCHHHHHHHHHHCTTSEEECCCGGGGGGSCCCEEEEEE
T ss_pred             CCeEEEecCCCCHHHHHHHhc--CCeEEEEeCCHHHHHHHHHhCCCCeEEeCcccccccCCCCeEEEEe
Confidence            578999999999999999998  558999998 567777766 4789999999998 66653  98875

>2yxe_A Protein-L-isoaspartate O-methyltransferase; rossman-type fold, alpha/beta/alpha sandwich structure, STRU genomics, NPPSFA; 2.00A {Methanocaldococcus jannaschii}

Probab=98.16  E-value=4.1e-06  Score=66.26  Aligned_cols=74  Identities=12%  Similarity=0.075  Sum_probs=57.6

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHc-CCCcEEEeec-hHHHhhccCC------CCceEEecCcCCCCC-C-C
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNY-LHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLERIP-K-G  227 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~~P-~-~  227 (233)
                      .+++.+. .....+|+|||||+|.++..+++.. |+.+++.+|. |..++.+++.      ++++++.+|+..++| . .
T Consensus        68 ~~~~~~~-~~~~~~vLdiG~G~G~~~~~l~~~~~~~~~v~~vD~~~~~~~~a~~~~~~~~~~~v~~~~~d~~~~~~~~~~  146 (215)
T 2yxe_A           68 MMCELLD-LKPGMKVLEIGTGCGYHAAVTAEIVGEDGLVVSIERIPELAEKAERTLRKLGYDNVIVIVGDGTLGYEPLAP  146 (215)
T ss_dssp             HHHHHTT-CCTTCEEEEECCTTSHHHHHHHHHHCTTSEEEEEESCHHHHHHHHHHHHHHTCTTEEEEESCGGGCCGGGCC
T ss_pred             HHHHhhC-CCCCCEEEEECCCccHHHHHHHHHhCCCCEEEEEeCCHHHHHHHHHHHHHcCCCCeEEEECCcccCCCCCCC
Confidence            3444444 5566899999999999999999998 7789999998 5577766542      579999999977665 2 2


Q ss_pred             -CEEEe
Q 039903          228 -DAILI  232 (233)
Q Consensus       228 -D~~~l  232 (233)
                       |+++.
T Consensus       147 fD~v~~  152 (215)
T 2yxe_A          147 YDRIYT  152 (215)
T ss_dssp             EEEEEE
T ss_pred             eeEEEE
Confidence             88875

>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=98.16  E-value=1.2e-06  Score=67.19  Aligned_cols=74  Identities=9%  Similarity=-0.015  Sum_probs=54.9

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCCC---CCC
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLER---IPK  226 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~---~P~  226 (233)
                      .+++.+....+..+|+|||||+|.++..++++ +..+++.+|+ +..++.++++       ++++++.+|+.+.   .+.
T Consensus        21 ~~~~~l~~~~~~~~vLDlGcG~G~~~~~l~~~-~~~~v~~vD~~~~~~~~a~~~~~~~~~~~~~~~~~~d~~~~~~~~~~   99 (177)
T 2esr_A           21 AIFNMIGPYFNGGRVLDLFAGSGGLAIEAVSR-GMSAAVLVEKNRKAQAIIQDNIIMTKAENRFTLLKMEAERAIDCLTG   99 (177)
T ss_dssp             HHHHHHCSCCCSCEEEEETCTTCHHHHHHHHT-TCCEEEEECCCHHHHHHHHHHHHTTTCGGGEEEECSCHHHHHHHBCS
T ss_pred             HHHHHHHhhcCCCeEEEeCCCCCHHHHHHHHc-CCCEEEEEECCHHHHHHHHHHHHHcCCCCceEEEECcHHHhHHhhcC
Confidence            34444332345579999999999999999987 7789999999 5677776542       4799999999873   223


Q ss_pred             C-CEEEe
Q 039903          227 G-DAILI  232 (233)
Q Consensus       227 ~-D~~~l  232 (233)
                      . |++++
T Consensus       100 ~fD~i~~  106 (177)
T 2esr_A          100 RFDLVFL  106 (177)
T ss_dssp             CEEEEEE
T ss_pred             CCCEEEE
Confidence            3 88875

>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=98.15  E-value=7.9e-07  Score=72.02  Aligned_cols=64  Identities=19%  Similarity=0.344  Sum_probs=50.1

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-----CCceEEecCcCC---CCCCC--CEEE
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-----SGVKHIGGIMLE---RIPKG--DAIL  231 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-----~ri~~~~gD~f~---~~P~~--D~~~  231 (233)
                      ....+|||||||.|..+..+++..|. +.+++|+ |.+++.|++.     .+++++.+|...   ++|.+  |.++
T Consensus        59 ~~G~rVLdiG~G~G~~~~~~~~~~~~-~v~~id~~~~~~~~a~~~~~~~~~~~~~~~~~a~~~~~~~~~~~FD~i~  133 (236)
T 3orh_A           59 SKGGRVLEVGFGMAIAASKVQEAPID-EHWIIECNDGVFQRLRDWAPRQTHKVIPLKGLWEDVAPTLPDGHFDGIL  133 (236)
T ss_dssp             TTCEEEEEECCTTSHHHHHHTTSCEE-EEEEEECCHHHHHHHHHHGGGCSSEEEEEESCHHHHGGGSCTTCEEEEE
T ss_pred             cCCCeEEEECCCccHHHHHHHHhCCc-EEEEEeCCHHHHHHHHHHHhhCCCceEEEeehHHhhcccccccCCceEE
Confidence            44579999999999999999998885 7889998 6688887652     568888888754   45653  7665

>3tma_A Methyltransferase; thump domain; 2.05A {Thermus thermophilus}

Probab=98.15  E-value=3.7e-06  Score=72.08  Aligned_cols=75  Identities=13%  Similarity=-0.034  Sum_probs=60.4

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHc-CCCcEEEeec-hHHHhhccCC------CCceEEecCcCC-CCCC-
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNY-LHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLE-RIPK-  226 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~-~~P~-  226 (233)
                      ..++.... +....+++|+|||+|.+++.++... |+.+++.+|+ |.+++.|+++      ++|+++.+|+.+ +.|. 
T Consensus       193 ~~l~~~~~-~~~~~~vLD~gcGsG~~~ie~a~~~~~~~~v~g~Di~~~~i~~a~~n~~~~g~~~i~~~~~D~~~~~~~~~  271 (354)
T 3tma_A          193 QALLRLAD-ARPGMRVLDPFTGSGTIALEAASTLGPTSPVYAGDLDEKRLGLAREAALASGLSWIRFLRADARHLPRFFP  271 (354)
T ss_dssp             HHHHHHTT-CCTTCCEEESSCTTSHHHHHHHHHHCTTSCEEEEESCHHHHHHHHHHHHHTTCTTCEEEECCGGGGGGTCC
T ss_pred             HHHHHHhC-CCCCCEEEeCCCCcCHHHHHHHHhhCCCceEEEEECCHHHHHHHHHHHHHcCCCceEEEeCChhhCccccC
Confidence            34445445 7777899999999999999999998 9999999998 5678777653      489999999998 5443 


Q ss_pred             C-CEEEe
Q 039903          227 G-DAILI  232 (233)
Q Consensus       227 ~-D~~~l  232 (233)
                      . |+++.
T Consensus       272 ~~D~Ii~  278 (354)
T 3tma_A          272 EVDRILA  278 (354)
T ss_dssp             CCSEEEE
T ss_pred             CCCEEEE
Confidence            3 88875

>2pxx_A Uncharacterized protein MGC2408; structural genomics consortium, SGC, methyltransferase, LOC84291, transferase; HET: SAH; 1.30A {Homo sapiens}

Probab=98.15  E-value=3e-06  Score=66.59  Aligned_cols=65  Identities=12%  Similarity=0.116  Sum_probs=53.3

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC----CCceEEecCcCC-CCCCC--CEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY----SGVKHIGGIMLE-RIPKG--DAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~----~ri~~~~gD~f~-~~P~~--D~~~l  232 (233)
                      ....+|+|||||+|.++..++++.+. +++.+|+ |..++.+++.    ++|+++.+|+.+ ++|.+  |+|+.
T Consensus        41 ~~~~~vLdiGcG~G~~~~~l~~~~~~-~v~~~D~s~~~~~~a~~~~~~~~~i~~~~~d~~~~~~~~~~fD~v~~  113 (215)
T 2pxx_A           41 RPEDRILVLGCGNSALSYELFLGGFP-NVTSVDYSSVVVAAMQACYAHVPQLRWETMDVRKLDFPSASFDVVLE  113 (215)
T ss_dssp             CTTCCEEEETCTTCSHHHHHHHTTCC-CEEEEESCHHHHHHHHHHTTTCTTCEEEECCTTSCCSCSSCEEEEEE
T ss_pred             CCCCeEEEECCCCcHHHHHHHHcCCC-cEEEEeCCHHHHHHHHHhcccCCCcEEEEcchhcCCCCCCcccEEEE
Confidence            45579999999999999999998776 8999998 5577766542    689999999998 67653  99874

>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=98.15  E-value=4.8e-06  Score=68.88  Aligned_cols=73  Identities=15%  Similarity=0.161  Sum_probs=56.3

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCCCCCC-C
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLERIPK-G  227 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~~P~-~  227 (233)
                      ..+++.++ .....+|||||||.|.++..++++++. +++.+|+ |+.++.+++.       ++|+++.+|+.+ +|. .
T Consensus        54 ~~~~~~~~-~~~~~~vLDiGcG~G~~~~~l~~~~~~-~v~gvd~s~~~~~~a~~~~~~~~~~~~~~~~~~d~~~-~~~~f  130 (287)
T 1kpg_A           54 DLALGKLG-LQPGMTLLDVGCGWGATMMRAVEKYDV-NVVGLTLSKNQANHVQQLVANSENLRSKRVLLAGWEQ-FDEPV  130 (287)
T ss_dssp             HHHHTTTT-CCTTCEEEEETCTTSHHHHHHHHHHCC-EEEEEESCHHHHHHHHHHHHTCCCCSCEEEEESCGGG-CCCCC
T ss_pred             HHHHHHcC-CCCcCEEEEECCcccHHHHHHHHHcCC-EEEEEECCHHHHHHHHHHHHhcCCCCCeEEEECChhh-CCCCe
Confidence            34555555 666789999999999999999988765 9999998 5577666542       589999999964 444 3


Q ss_pred             CEEEe
Q 039903          228 DAILI  232 (233)
Q Consensus       228 D~~~l  232 (233)
                      |+|+.
T Consensus       131 D~v~~  135 (287)
T 1kpg_A          131 DRIVS  135 (287)
T ss_dssp             SEEEE
T ss_pred             eEEEE
Confidence            98874

>2pjd_A Ribosomal RNA small subunit methyltransferase C; gene duplication, RNA modification, SAM binding; 2.10A {Escherichia coli}

Probab=98.14  E-value=3e-06  Score=72.41  Aligned_cols=75  Identities=16%  Similarity=0.180  Sum_probs=57.8

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC-----CCceEEecCcCCCCCCC-CE
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY-----SGVKHIGGIMLERIPKG-DA  229 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~-----~ri~~~~gD~f~~~P~~-D~  229 (233)
                      ..+++.++ .....+|+|||||+|.++..+++++|+.+++.+|.. ..++.++++     .+++++.+|+++..+.. |+
T Consensus       186 ~~ll~~l~-~~~~~~VLDlGcG~G~~~~~la~~~~~~~v~~vD~s~~~l~~a~~~~~~~~~~~~~~~~d~~~~~~~~fD~  264 (343)
T 2pjd_A          186 QLLLSTLT-PHTKGKVLDVGCGAGVLSVAFARHSPKIRLTLCDVSAPAVEASRATLAANGVEGEVFASNVFSEVKGRFDM  264 (343)
T ss_dssp             HHHHHHSC-TTCCSBCCBTTCTTSHHHHHHHHHCTTCBCEEEESBHHHHHHHHHHHHHTTCCCEEEECSTTTTCCSCEEE
T ss_pred             HHHHHhcC-cCCCCeEEEecCccCHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHhCCCCEEEEccccccccCCeeE
Confidence            34555554 334568999999999999999999999999999994 567776653     34788999999854444 98


Q ss_pred             EEe
Q 039903          230 ILI  232 (233)
Q Consensus       230 ~~l  232 (233)
                      |+.
T Consensus       265 Iv~  267 (343)
T 2pjd_A          265 IIS  267 (343)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            875

>3grz_A L11 mtase, ribosomal protein L11 methyltransferase; methylase, SAM-binding domain, PSI-2, nysgxrc; 2.00A {Lactobacillus delbrueckii subsp}

Probab=98.13  E-value=4.8e-06  Score=65.39  Aligned_cols=65  Identities=14%  Similarity=0.115  Sum_probs=52.2

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCCCCCCC-CEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLERIPKG-DAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~~P~~-D~~~l  232 (233)
                      ....+|||||||+|.++..+++ +|..+++.+|+ |..++.++++      ++|+++.+|+++..+.. |+++.
T Consensus        59 ~~~~~vLDiG~G~G~~~~~l~~-~~~~~v~~vD~s~~~~~~a~~~~~~~~~~~v~~~~~d~~~~~~~~fD~i~~  131 (205)
T 3grz_A           59 VKPLTVADVGTGSGILAIAAHK-LGAKSVLATDISDESMTAAEENAALNGIYDIALQKTSLLADVDGKFDLIVA  131 (205)
T ss_dssp             SSCCEEEEETCTTSHHHHHHHH-TTCSEEEEEESCHHHHHHHHHHHHHTTCCCCEEEESSTTTTCCSCEEEEEE
T ss_pred             cCCCEEEEECCCCCHHHHHHHH-CCCCEEEEEECCHHHHHHHHHHHHHcCCCceEEEeccccccCCCCceEEEE
Confidence            4567999999999999999776 67789999998 5677777652      34999999998855554 98874

>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=98.13  E-value=3.8e-06  Score=67.45  Aligned_cols=66  Identities=11%  Similarity=0.112  Sum_probs=51.8

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhc----cCCCCceEEecCcCCC-----CCCC-CEEE
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDS----SSYSGVKHIGGIMLER-----IPKG-DAIL  231 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a----~~~~ri~~~~gD~f~~-----~P~~-D~~~  231 (233)
                      ..+..+|+|||||+|.++..+++.+|..+++.+|.. ..++.+    +..++|+++.+|+.++     ++.. |+++
T Consensus        72 ~~~~~~VLDlGcG~G~~~~~la~~~~~~~v~gvD~s~~~~~~a~~~~~~~~~v~~~~~d~~~~~~~~~~~~~~D~v~  148 (230)
T 1fbn_A           72 IKRDSKILYLGASAGTTPSHVADIADKGIVYAIEYAPRIMRELLDACAERENIIPILGDANKPQEYANIVEKVDVIY  148 (230)
T ss_dssp             CCTTCEEEEESCCSSHHHHHHHHHTTTSEEEEEESCHHHHHHHHHHTTTCTTEEEEECCTTCGGGGTTTSCCEEEEE
T ss_pred             CCCCCEEEEEcccCCHHHHHHHHHcCCcEEEEEECCHHHHHHHHHHhhcCCCeEEEECCCCCcccccccCccEEEEE
Confidence            556689999999999999999999998899999984 456544    3347899999999862     2223 8875

>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=98.12  E-value=3.6e-06  Score=67.58  Aligned_cols=64  Identities=13%  Similarity=0.137  Sum_probs=51.2

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC--CCceEEecCcCCCCCCC--CEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY--SGVKHIGGIMLERIPKG--DAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~--~ri~~~~gD~f~~~P~~--D~~~l  232 (233)
                      ....+|||||||+|.++..++++++  +++.+|+ +..++.+++.  .+|+++.+|+.+..|.+  |+|++
T Consensus        41 ~~~~~vLDiGcG~G~~~~~l~~~~~--~v~gvD~s~~~~~~a~~~~~~~v~~~~~d~~~~~~~~~fD~v~~  109 (250)
T 2p7i_A           41 FRPGNLLELGSFKGDFTSRLQEHFN--DITCVEASEEAISHAQGRLKDGITYIHSRFEDAQLPRRYDNIVL  109 (250)
T ss_dssp             CCSSCEEEESCTTSHHHHHHTTTCS--CEEEEESCHHHHHHHHHHSCSCEEEEESCGGGCCCSSCEEEEEE
T ss_pred             cCCCcEEEECCCCCHHHHHHHHhCC--cEEEEeCCHHHHHHHHHhhhCCeEEEEccHHHcCcCCcccEEEE
Confidence            3457899999999999999999887  5888998 4577777653  28999999998854443  98875

>3lpm_A Putative methyltransferase; structural genomics, protein structure initiative, NEW YORK structural genomix research consortium, nysgxrc; 2.40A {Listeria monocytogenes}

Probab=98.12  E-value=3.4e-06  Score=69.07  Aligned_cols=66  Identities=15%  Similarity=0.206  Sum_probs=54.0

Q ss_pred             cc-CcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCCC---CCC-C-CEEE
Q 039903          166 FE-QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLER---IPK-G-DAIL  231 (233)
Q Consensus       166 ~~-~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~---~P~-~-D~~~  231 (233)
                      .+ +..+|+|||||+|.++..++++.+. +++.+|+ |..++.|+++       +||+++.+|+.+.   +|. . |+|+
T Consensus        46 ~~~~~~~vLDlG~G~G~~~~~la~~~~~-~v~gvDi~~~~~~~a~~n~~~~~~~~~v~~~~~D~~~~~~~~~~~~fD~Ii  124 (259)
T 3lpm_A           46 LPIRKGKIIDLCSGNGIIPLLLSTRTKA-KIVGVEIQERLADMAKRSVAYNQLEDQIEIIEYDLKKITDLIPKERADIVT  124 (259)
T ss_dssp             CCSSCCEEEETTCTTTHHHHHHHTTCCC-EEEEECCSHHHHHHHHHHHHHTTCTTTEEEECSCGGGGGGTSCTTCEEEEE
T ss_pred             CCCCCCEEEEcCCchhHHHHHHHHhcCC-cEEEEECCHHHHHHHHHHHHHCCCcccEEEEECcHHHhhhhhccCCccEEE
Confidence            55 6789999999999999999999876 8999998 5577777653       5899999999982   444 3 9887


Q ss_pred             e
Q 039903          232 I  232 (233)
Q Consensus       232 l  232 (233)
                      .
T Consensus       125 ~  125 (259)
T 3lpm_A          125 C  125 (259)
T ss_dssp             E
T ss_pred             E
Confidence            5

>3tr6_A O-methyltransferase; cellular processes; HET: SAH; 2.70A {Coxiella burnetii} SCOP: c.66.1.0

Probab=98.12  E-value=2.5e-06  Score=67.98  Aligned_cols=67  Identities=15%  Similarity=0.101  Sum_probs=53.5

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcC-CCcEEEeec-hHHHhhccCC-------CCceEEecCcCCCCC--------CC-
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLERIP--------KG-  227 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~~P--------~~-  227 (233)
                      ..+..+|||||||+|..+..+++++| +.+++.+|. |+.++.++++       ++|+++.+|..+.+|        .. 
T Consensus        62 ~~~~~~vLdiG~G~G~~~~~la~~~~~~~~v~~vD~~~~~~~~a~~~~~~~~~~~~v~~~~~d~~~~~~~~~~~~~~~~f  141 (225)
T 3tr6_A           62 LMQAKKVIDIGTFTGYSAIAMGLALPKDGTLITCDVDEKSTALAKEYWEKAGLSDKIGLRLSPAKDTLAELIHAGQAWQY  141 (225)
T ss_dssp             HHTCSEEEEECCTTSHHHHHHHTTCCTTCEEEEEESCHHHHHHHHHHHHHTTCTTTEEEEESCHHHHHHHHHTTTCTTCE
T ss_pred             hhCCCEEEEeCCcchHHHHHHHHhCCCCCEEEEEeCCHHHHHHHHHHHHHCCCCCceEEEeCCHHHHHHHhhhccCCCCc
Confidence            34567999999999999999999998 899999998 5577766542       579999999976322        33 


Q ss_pred             CEEEe
Q 039903          228 DAILI  232 (233)
Q Consensus       228 D~~~l  232 (233)
                      |++++
T Consensus       142 D~v~~  146 (225)
T 3tr6_A          142 DLIYI  146 (225)
T ss_dssp             EEEEE
T ss_pred             cEEEE
Confidence            88875

>3eey_A Putative rRNA methylase; rRNA methylation, S-adenosyl-methionine, structural genomics structure initiative, PSI; HET: SAM; 2.20A {Clostridium thermocellum atcc 27405}

Probab=98.11  E-value=3.8e-06  Score=65.50  Aligned_cols=67  Identities=16%  Similarity=0.182  Sum_probs=53.4

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHc-CCCcEEEeec-hHHHhhccCC-------CCceEEecCcCC-C-CCC-C-CEEEe
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNY-LHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLE-R-IPK-G-DAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~-~-~P~-~-D~~~l  232 (233)
                      .+...+|+|+|||+|.++..+++++ |..+++.+|+ |..++.++++       ++++++.+|+.+ + .+. . |++++
T Consensus        20 ~~~~~~vLDlGcG~G~~~~~l~~~~~~~~~v~~vD~s~~~~~~a~~~~~~~~~~~~v~~~~~d~~~~~~~~~~~fD~v~~   99 (197)
T 3eey_A           20 VKEGDTVVDATCGNGNDTAFLASLVGENGRVFGFDIQDKAIANTTKKLTDLNLIDRVTLIKDGHQNMDKYIDCPVKAVMF   99 (197)
T ss_dssp             CCTTCEEEESCCTTSHHHHHHHHHHCTTCEEEEECSCHHHHHHHHHHHHHTTCGGGEEEECSCGGGGGGTCCSCEEEEEE
T ss_pred             CCCCCEEEEcCCCCCHHHHHHHHHhCCCCEEEEEECCHHHHHHHHHHHHHcCCCCCeEEEECCHHHHhhhccCCceEEEE
Confidence            4556799999999999999999986 7789999998 5577777653       589999999876 2 333 3 88874

>3lbf_A Protein-L-isoaspartate O-methyltransferase; modified rossman-type fold, S-adenosyl-L- methionine; HET: SAH; 1.80A {Escherichia coli}

Probab=98.11  E-value=5.8e-06  Score=65.11  Aligned_cols=71  Identities=13%  Similarity=0.160  Sum_probs=55.7

Q ss_pred             HHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCCCCCC--C-C
Q 039903          159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLERIPK--G-D  228 (233)
Q Consensus       159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~~P~--~-D  228 (233)
                      +++.++ ..+..+|+|||||+|.++..+++.  ..+++.+|. |..++.++++      ++++++.+|+++..+.  . |
T Consensus        69 ~~~~l~-~~~~~~vLdiG~G~G~~~~~la~~--~~~v~~vD~~~~~~~~a~~~~~~~~~~~v~~~~~d~~~~~~~~~~~D  145 (210)
T 3lbf_A           69 MTELLE-LTPQSRVLEIGTGSGYQTAILAHL--VQHVCSVERIKGLQWQARRRLKNLDLHNVSTRHGDGWQGWQARAPFD  145 (210)
T ss_dssp             HHHHTT-CCTTCEEEEECCTTSHHHHHHHHH--SSEEEEEESCHHHHHHHHHHHHHTTCCSEEEEESCGGGCCGGGCCEE
T ss_pred             HHHhcC-CCCCCEEEEEcCCCCHHHHHHHHh--CCEEEEEecCHHHHHHHHHHHHHcCCCceEEEECCcccCCccCCCcc
Confidence            444555 567789999999999999999998  678999998 5677766542      5799999999985442  2 9


Q ss_pred             EEEe
Q 039903          229 AILI  232 (233)
Q Consensus       229 ~~~l  232 (233)
                      ++++
T Consensus       146 ~i~~  149 (210)
T 3lbf_A          146 AIIV  149 (210)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            8875

>3i9f_A Putative type 11 methyltransferase; structural genomics, PSI-2, protein structure initiative; 2.50A {Sulfolobus solfataricus}

Probab=98.11  E-value=1.5e-06  Score=66.13  Aligned_cols=69  Identities=19%  Similarity=0.256  Sum_probs=54.9

Q ss_pred             HHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccC-CCCceEEecCcCCCCCCC--CEEEe
Q 039903          159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSS-YSGVKHIGGIMLERIPKG--DAILI  232 (233)
Q Consensus       159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~-~~ri~~~~gD~f~~~P~~--D~~~l  232 (233)
                      +++.++ ..+..+|||||||+|.++..+++++.  +++.+|+ +..++.+++ .++|+++.+|  .++|.+  |+++.
T Consensus         9 ~~~~~~-~~~~~~vLDiG~G~G~~~~~l~~~~~--~v~~vD~s~~~~~~a~~~~~~v~~~~~d--~~~~~~~~D~v~~   81 (170)
T 3i9f_A            9 YLPNIF-EGKKGVIVDYGCGNGFYCKYLLEFAT--KLYCIDINVIALKEVKEKFDSVITLSDP--KEIPDNSVDFILF   81 (170)
T ss_dssp             THHHHH-SSCCEEEEEETCTTCTTHHHHHTTEE--EEEEECSCHHHHHHHHHHCTTSEEESSG--GGSCTTCEEEEEE
T ss_pred             HHHhcC-cCCCCeEEEECCCCCHHHHHHHhhcC--eEEEEeCCHHHHHHHHHhCCCcEEEeCC--CCCCCCceEEEEE
Confidence            444555 66778999999999999999999984  8999998 567777765 4899999999  555553  98874

>2ipx_A RRNA 2'-O-methyltransferase fibrillarin; FBL, structural genomics, structural genomics consortium, SGC; HET: MTA; 1.82A {Homo sapiens}

Probab=98.11  E-value=2.9e-06  Score=68.26  Aligned_cols=67  Identities=12%  Similarity=0.056  Sum_probs=53.5

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHc-CCCcEEEeechH-----HHhhccCCCCceEEecCcCCC--CC--C-C-CEEEe
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNY-LHIKGVNFDLSH-----VIQDSSSYSGVKHIGGIMLER--IP--K-G-DAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~-P~l~~~v~Dlp~-----v~~~a~~~~ri~~~~gD~f~~--~P--~-~-D~~~l  232 (233)
                      .....+|+|||||+|.++..+++++ |..+++.+|+.+     .++.++.+++++++.+|+.++  +|  . . |+++.
T Consensus        75 ~~~~~~vLDlG~G~G~~~~~la~~~g~~~~v~gvD~s~~~i~~~~~~a~~~~~v~~~~~d~~~~~~~~~~~~~~D~V~~  153 (233)
T 2ipx_A           75 IKPGAKVLYLGAASGTTVSHVSDIVGPDGLVYAVEFSHRSGRDLINLAKKRTNIIPVIEDARHPHKYRMLIAMVDVIFA  153 (233)
T ss_dssp             CCTTCEEEEECCTTSHHHHHHHHHHCTTCEEEEECCCHHHHHHHHHHHHHCTTEEEECSCTTCGGGGGGGCCCEEEEEE
T ss_pred             CCCCCEEEEEcccCCHHHHHHHHHhCCCcEEEEEECCHHHHHHHHHHhhccCCeEEEEcccCChhhhcccCCcEEEEEE
Confidence            5566899999999999999999997 788999999853     355555558999999999873  33  2 3 88875

>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=98.10  E-value=2e-06  Score=66.31  Aligned_cols=66  Identities=11%  Similarity=-0.051  Sum_probs=51.8

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCCCC------CCC-CEE
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLERI------PKG-DAI  230 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~~------P~~-D~~  230 (233)
                      .....+|+|+|||+|.++..+++ .+..+++.+|+ |..++.++++       ++++++.+|+.+..      +.. |++
T Consensus        42 ~~~~~~vLD~GcG~G~~~~~~~~-~~~~~v~~vD~~~~~~~~a~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~fD~i  120 (187)
T 2fhp_A           42 YFDGGMALDLYSGSGGLAIEAVS-RGMDKSICIEKNFAALKVIKENIAITKEPEKFEVRKMDANRALEQFYEEKLQFDLV  120 (187)
T ss_dssp             CCSSCEEEETTCTTCHHHHHHHH-TTCSEEEEEESCHHHHHHHHHHHHHHTCGGGEEEEESCHHHHHHHHHHTTCCEEEE
T ss_pred             hcCCCCEEEeCCccCHHHHHHHH-cCCCEEEEEECCHHHHHHHHHHHHHhCCCcceEEEECcHHHHHHHHHhcCCCCCEE
Confidence            34557999999999999999888 56788999998 5677777653       57999999998732      233 888


Q ss_pred             Ee
Q 039903          231 LI  232 (233)
Q Consensus       231 ~l  232 (233)
                      ++
T Consensus       121 ~~  122 (187)
T 2fhp_A          121 LL  122 (187)
T ss_dssp             EE
T ss_pred             EE
Confidence            75

>1zq9_A Probable dimethyladenosine transferase; SGC, structural genomics, structural genomics consortium; HET: SAM; 1.90A {Homo sapiens} SCOP: c.66.1.24

Probab=98.09  E-value=5.2e-06  Score=69.21  Aligned_cols=73  Identities=22%  Similarity=0.319  Sum_probs=56.6

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCC-CCCCC
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLE-RIPKG  227 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~-~~P~~  227 (233)
                      ..+++.++ .....+|+|||||+|.++..++++..  +++.+|+ +..++.+++.       ++++++.+|+.+ ++|..
T Consensus        18 ~~i~~~~~-~~~~~~VLDiG~G~G~lt~~L~~~~~--~v~~vD~~~~~~~~a~~~~~~~~~~~~v~~~~~D~~~~~~~~f   94 (285)
T 1zq9_A           18 NSIIDKAA-LRPTDVVLEVGPGTGNMTVKLLEKAK--KVVACELDPRLVAELHKRVQGTPVASKLQVLVGDVLKTDLPFF   94 (285)
T ss_dssp             HHHHHHTC-CCTTCEEEEECCTTSTTHHHHHHHSS--EEEEEESCHHHHHHHHHHHTTSTTGGGEEEEESCTTTSCCCCC
T ss_pred             HHHHHhcC-CCCCCEEEEEcCcccHHHHHHHhhCC--EEEEEECCHHHHHHHHHHHHhcCCCCceEEEEcceecccchhh
Confidence            34556665 66678999999999999999999854  7899998 4566655432       579999999998 77766


Q ss_pred             CEEEe
Q 039903          228 DAILI  232 (233)
Q Consensus       228 D~~~l  232 (233)
                      |+++.
T Consensus        95 D~vv~   99 (285)
T 1zq9_A           95 DTCVA   99 (285)
T ss_dssp             SEEEE
T ss_pred             cEEEE
Confidence            87763

>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=98.09  E-value=2.1e-06  Score=68.48  Aligned_cols=67  Identities=7%  Similarity=0.113  Sum_probs=53.5

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcC-CCcEEEeec-hHHHhhccCC-------CCceEEecCcCC---CCC-----C-C
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLE---RIP-----K-G  227 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~---~~P-----~-~  227 (233)
                      ..+..+|||||||+|..+..++++.| +.+++.+|+ |+.++.|+++       +||+++.+|+.+   .++     . -
T Consensus        56 ~~~~~~vLdiG~G~G~~~~~la~~~~~~~~v~~vD~~~~~~~~a~~~~~~~~~~~~v~~~~~d~~~~l~~~~~~~~~~~f  135 (221)
T 3u81_A           56 EYSPSLVLELGAYCGYSAVRMARLLQPGARLLTMEINPDCAAITQQMLNFAGLQDKVTILNGASQDLIPQLKKKYDVDTL  135 (221)
T ss_dssp             HHCCSEEEEECCTTSHHHHHHHTTSCTTCEEEEEESCHHHHHHHHHHHHHHTCGGGEEEEESCHHHHGGGTTTTSCCCCC
T ss_pred             hcCCCEEEEECCCCCHHHHHHHHhCCCCCEEEEEeCChHHHHHHHHHHHHcCCCCceEEEECCHHHHHHHHHHhcCCCce
Confidence            34568999999999999999999875 889999998 5677777653       579999999865   233     2 3


Q ss_pred             CEEEe
Q 039903          228 DAILI  232 (233)
Q Consensus       228 D~~~l  232 (233)
                      |++++
T Consensus       136 D~V~~  140 (221)
T 3u81_A          136 DMVFL  140 (221)
T ss_dssp             SEEEE
T ss_pred             EEEEE
Confidence            99875

>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=98.09  E-value=5.3e-06  Score=66.61  Aligned_cols=63  Identities=25%  Similarity=0.345  Sum_probs=51.4

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-----CCceEEecCcCC-CCCCC-CEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-----SGVKHIGGIMLE-RIPKG-DAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-----~ri~~~~gD~f~-~~P~~-D~~~l  232 (233)
                      +...+|||||||+|.++..++++   .+++.+|+ |..++.+++.     .+++++.+|+.+ +.|.. |++++
T Consensus        32 ~~~~~vLdiG~G~G~~~~~l~~~---~~v~~vD~s~~~~~~a~~~~~~~~~~~~~~~~d~~~~~~~~~fD~v~~  102 (243)
T 3d2l_A           32 EPGKRIADIGCGTGTATLLLADH---YEVTGVDLSEEMLEIAQEKAMETNRHVDFWVQDMRELELPEPVDAITI  102 (243)
T ss_dssp             CTTCEEEEESCTTCHHHHHHTTT---SEEEEEESCHHHHHHHHHHHHHTTCCCEEEECCGGGCCCSSCEEEEEE
T ss_pred             CCCCeEEEecCCCCHHHHHHhhC---CeEEEEECCHHHHHHHHHhhhhcCCceEEEEcChhhcCCCCCcCEEEE
Confidence            34489999999999999999987   78999998 5677777653     579999999988 56654 98874

>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=98.08  E-value=2.8e-06  Score=69.45  Aligned_cols=66  Identities=12%  Similarity=0.051  Sum_probs=53.1

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCC-CCC----CC-CEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLE-RIP----KG-DAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~-~~P----~~-D~~~l  232 (233)
                      ....+|+|||||+|..+..++..+|+.+++.+|. +..++.++++      .+|+++.+|+.+ +..    .. |+++.
T Consensus        79 ~~~~~vLDiG~G~G~~~i~la~~~~~~~v~~vD~s~~~~~~a~~~~~~~~l~~v~~~~~d~~~~~~~~~~~~~fD~I~s  157 (249)
T 3g89_A           79 QGPLRVLDLGTGAGFPGLPLKIVRPELELVLVDATRKKVAFVERAIEVLGLKGARALWGRAEVLAREAGHREAYARAVA  157 (249)
T ss_dssp             CSSCEEEEETCTTTTTHHHHHHHCTTCEEEEEESCHHHHHHHHHHHHHHTCSSEEEEECCHHHHTTSTTTTTCEEEEEE
T ss_pred             CCCCEEEEEcCCCCHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHhCCCceEEEECcHHHhhcccccCCCceEEEE
Confidence            4568999999999999999999999999999997 4566666542      569999999887 321    23 88874

>2avd_A Catechol-O-methyltransferase; structural genomics, structural genomics consortium, SGC; HET: SAM; 1.70A {Homo sapiens} SCOP: c.66.1.1

Probab=98.08  E-value=1.3e-06  Score=69.94  Aligned_cols=67  Identities=13%  Similarity=0.076  Sum_probs=53.6

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcC-CCcEEEeec-hHHHhhccCC-------CCceEEecCcCCC---CC-----CC-
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLER---IP-----KG-  227 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~---~P-----~~-  227 (233)
                      ..+..+|+|||||+|..+..+++..| ..+++.+|. |..++.++++       ++|+++.+|+++.   ++     .. 
T Consensus        67 ~~~~~~vLdiG~G~G~~~~~la~~~~~~~~v~~vD~~~~~~~~a~~~~~~~g~~~~i~~~~~d~~~~~~~~~~~~~~~~~  146 (229)
T 2avd_A           67 LIQAKKALDLGTFTGYSALALALALPADGRVVTCEVDAQPPELGRPLWRQAEAEHKIDLRLKPALETLDELLAAGEAGTF  146 (229)
T ss_dssp             HTTCCEEEEECCTTSHHHHHHHTTSCTTCEEEEEESCSHHHHHHHHHHHHTTCTTTEEEEESCHHHHHHHHHHTTCTTCE
T ss_pred             hcCCCEEEEEcCCccHHHHHHHHhCCCCCEEEEEECCHHHHHHHHHHHHHCCCCCeEEEEEcCHHHHHHHHHhcCCCCCc
Confidence            45568999999999999999999988 789999998 6677766542       6899999998763   21     33 


Q ss_pred             CEEEe
Q 039903          228 DAILI  232 (233)
Q Consensus       228 D~~~l  232 (233)
                      |++++
T Consensus       147 D~v~~  151 (229)
T 2avd_A          147 DVAVV  151 (229)
T ss_dssp             EEEEE
T ss_pred             cEEEE
Confidence            88875

>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=98.08  E-value=6.9e-06  Score=66.49  Aligned_cols=65  Identities=14%  Similarity=0.086  Sum_probs=52.4

Q ss_pred             CcceEEEecCCccHHHHHHHHH----cCCCcEEEeec-hHHHhhccC-CCCceEEecCcCCC--CC---C--CCEEEe
Q 039903          168 QIKQLVDVGGGLGVNVNIIISN----YLHIKGVNFDL-SHVIQDSSS-YSGVKHIGGIMLER--IP---K--GDAILI  232 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~----~P~l~~~v~Dl-p~v~~~a~~-~~ri~~~~gD~f~~--~P---~--~D~~~l  232 (233)
                      +..+|||||||+|..+..+++.    +|+.+++.+|+ |+.++.|+. .++|+++.+|..+.  +|   .  -|++++
T Consensus        81 ~~~~VLDiG~GtG~~t~~la~~~~~~~~~~~V~gvD~s~~~l~~a~~~~~~v~~~~gD~~~~~~l~~~~~~~fD~I~~  158 (236)
T 2bm8_A           81 RPRTIVELGVYNGGSLAWFRDLTKIMGIDCQVIGIDRDLSRCQIPASDMENITLHQGDCSDLTTFEHLREMAHPLIFI  158 (236)
T ss_dssp             CCSEEEEECCTTSHHHHHHHHHHHHTTCCCEEEEEESCCTTCCCCGGGCTTEEEEECCSSCSGGGGGGSSSCSSEEEE
T ss_pred             CCCEEEEEeCCCCHHHHHHHHhhhhcCCCCEEEEEeCChHHHHHHhccCCceEEEECcchhHHHHHhhccCCCCEEEE
Confidence            3479999999999999999998    79999999998 556776654 37899999999873  22   2  288874

>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=98.08  E-value=7.6e-06  Score=68.80  Aligned_cols=73  Identities=12%  Similarity=0.197  Sum_probs=56.6

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCCCCCC-C
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLERIPK-G  227 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~~P~-~  227 (233)
                      ..+++.++ .....+|||||||.|.++..+++++ ..+++.+|+ |..++.+++.       ++|+++.+|+.+ +|. .
T Consensus        80 ~~~~~~~~-~~~~~~vLDiGcG~G~~~~~la~~~-~~~v~gvD~s~~~~~~a~~~~~~~~~~~~v~~~~~d~~~-~~~~f  156 (318)
T 2fk8_A           80 DLNLDKLD-LKPGMTLLDIGCGWGTTMRRAVERF-DVNVIGLTLSKNQHARCEQVLASIDTNRSRQVLLQGWED-FAEPV  156 (318)
T ss_dssp             HHHHTTSC-CCTTCEEEEESCTTSHHHHHHHHHH-CCEEEEEESCHHHHHHHHHHHHTSCCSSCEEEEESCGGG-CCCCC
T ss_pred             HHHHHhcC-CCCcCEEEEEcccchHHHHHHHHHC-CCEEEEEECCHHHHHHHHHHHHhcCCCCceEEEECChHH-CCCCc
Confidence            34555555 6667899999999999999999987 569999998 5677766542       579999999865 344 3


Q ss_pred             CEEEe
Q 039903          228 DAILI  232 (233)
Q Consensus       228 D~~~l  232 (233)
                      |+|+.
T Consensus       157 D~v~~  161 (318)
T 2fk8_A          157 DRIVS  161 (318)
T ss_dssp             SEEEE
T ss_pred             CEEEE
Confidence            98874

>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=98.08  E-value=6.8e-06  Score=66.91  Aligned_cols=67  Identities=10%  Similarity=0.300  Sum_probs=53.1

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccC----CCCceEEecCcCC-CCCC
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSS----YSGVKHIGGIMLE-RIPK  226 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~----~~ri~~~~gD~f~-~~P~  226 (233)
                      ..+++.++ .....+|+|||||+|.++..++++.  .+++.+|+ +..++.+++    .++++++.+|+.+ ++|.
T Consensus        20 ~~i~~~~~-~~~~~~VLDiG~G~G~lt~~l~~~~--~~v~~vD~~~~~~~~a~~~~~~~~~v~~~~~D~~~~~~~~   92 (244)
T 1qam_A           20 DKIMTNIR-LNEHDNIFEIGSGKGHFTLELVQRC--NFVTAIEIDHKLCKTTENKLVDHDNFQVLNKDILQFKFPK   92 (244)
T ss_dssp             HHHHTTCC-CCTTCEEEEECCTTSHHHHHHHHHS--SEEEEECSCHHHHHHHHHHTTTCCSEEEECCCGGGCCCCS
T ss_pred             HHHHHhCC-CCCCCEEEEEeCCchHHHHHHHHcC--CeEEEEECCHHHHHHHHHhhccCCCeEEEEChHHhCCccc
Confidence            44555555 5666899999999999999999986  67999998 456666654    2689999999998 6764

>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=98.08  E-value=6.8e-06  Score=70.39  Aligned_cols=73  Identities=22%  Similarity=0.212  Sum_probs=56.6

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCC-------CCceEEecCcCC-CCCCC-C
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSY-------SGVKHIGGIMLE-RIPKG-D  228 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~-------~ri~~~~gD~f~-~~P~~-D  228 (233)
                      .+++.+. ..+..+|||||||+|.++..++++ +..+++.+|..+.++.+++.       ++|+++.+|+.+ +.|.. |
T Consensus        41 ~i~~~l~-~~~~~~VLDiGcGtG~ls~~la~~-g~~~V~~vD~s~~~~~a~~~~~~~~l~~~v~~~~~d~~~~~~~~~~D  118 (348)
T 2y1w_A           41 AILQNHT-DFKDKIVLDVGCGSGILSFFAAQA-GARKIYAVEASTMAQHAEVLVKSNNLTDRIVVIPGKVEEVSLPEQVD  118 (348)
T ss_dssp             HHHHTGG-GTTTCEEEEETCTTSHHHHHHHHT-TCSEEEEEECSTHHHHHHHHHHHTTCTTTEEEEESCTTTCCCSSCEE
T ss_pred             HHHhccc-cCCcCEEEEcCCCccHHHHHHHhC-CCCEEEEECCHHHHHHHHHHHHHcCCCCcEEEEEcchhhCCCCCcee
Confidence            4455554 445689999999999999998885 66789999997766655431       689999999998 66654 9


Q ss_pred             EEEe
Q 039903          229 AILI  232 (233)
Q Consensus       229 ~~~l  232 (233)
                      +|+.
T Consensus       119 ~Ivs  122 (348)
T 2y1w_A          119 IIIS  122 (348)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            8874

>3p2e_A 16S rRNA methylase; methyltransferase, transferase, NPMA; HET: SAH; 1.68A {Escherichia coli} PDB: 3p2i_A 3p2k_A* 3pb3_A* 3mte_A*

Probab=98.07  E-value=6.3e-06  Score=66.27  Aligned_cols=56  Identities=18%  Similarity=0.090  Sum_probs=46.0

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHH-hhc---cCC------CCceEEecCcCC
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVI-QDS---SSY------SGVKHIGGIMLE  222 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~-~~a---~~~------~ri~~~~gD~f~  222 (233)
                      ....+|||||||+|.++..+++++|..+++.+|+. +.+ +.|   ++.      ++|+++.+|..+
T Consensus        23 ~~~~~vLDiGCG~G~~~~~la~~~~~~~v~GvD~s~~~ml~~A~~A~~~~~~~~~~~v~~~~~d~~~   89 (225)
T 3p2e_A           23 QFDRVHIDLGTGDGRNIYKLAINDQNTFYIGIDPVKENLFDISKKIIKKPSKGGLSNVVFVIAAAES   89 (225)
T ss_dssp             TCSEEEEEETCTTSHHHHHHHHTCTTEEEEEECSCCGGGHHHHHHHTSCGGGTCCSSEEEECCBTTB
T ss_pred             CCCCEEEEEeccCcHHHHHHHHhCCCCEEEEEeCCHHHHHHHHHHHHHHHHHcCCCCeEEEEcCHHH
Confidence            45579999999999999999999999999999996 543 433   442      579999999876

>3m33_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, MCSG, midwest center for structural genomics; 2.19A {Deinococcus radiodurans}

Probab=98.07  E-value=5.1e-06  Score=66.48  Aligned_cols=64  Identities=8%  Similarity=0.057  Sum_probs=52.1

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccC-CCCceEEecCcCC--CCC-CC--CEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSS-YSGVKHIGGIMLE--RIP-KG--DAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~-~~ri~~~~gD~f~--~~P-~~--D~~~l  232 (233)
                      ....+|||||||+|.++..++++  ..+++.+|+ |..++.+++ .++++++.+|+.+  +++ .+  |+|+.
T Consensus        47 ~~~~~vLDiGcG~G~~~~~l~~~--~~~v~~vD~s~~~~~~a~~~~~~~~~~~~d~~~~~~~~~~~~fD~v~~  117 (226)
T 3m33_A           47 TPQTRVLEAGCGHGPDAARFGPQ--AARWAAYDFSPELLKLARANAPHADVYEWNGKGELPAGLGAPFGLIVS  117 (226)
T ss_dssp             CTTCEEEEESCTTSHHHHHHGGG--SSEEEEEESCHHHHHHHHHHCTTSEEEECCSCSSCCTTCCCCEEEEEE
T ss_pred             CCCCeEEEeCCCCCHHHHHHHHc--CCEEEEEECCHHHHHHHHHhCCCceEEEcchhhccCCcCCCCEEEEEe
Confidence            45579999999999999999998  568999998 567877765 3789999999987  444 32  88874

>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=98.07  E-value=8.2e-06  Score=68.40  Aligned_cols=72  Identities=17%  Similarity=0.301  Sum_probs=56.5

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccC----CCCceEEecCcCC-CCCC--CC
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSS----YSGVKHIGGIMLE-RIPK--GD  228 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~----~~ri~~~~gD~f~-~~P~--~D  228 (233)
                      ..+++..+ .....+|+|||||+|.++..++++  ..+++.+|+. ..++.+++    .++++++.+|+.+ ++|.  .|
T Consensus        40 ~~Iv~~l~-~~~~~~VLEIG~G~G~lT~~La~~--~~~V~aVEid~~li~~a~~~~~~~~~v~vi~gD~l~~~~~~~~fD  116 (295)
T 3gru_A           40 NKAVESAN-LTKDDVVLEIGLGKGILTEELAKN--AKKVYVIEIDKSLEPYANKLKELYNNIEIIWGDALKVDLNKLDFN  116 (295)
T ss_dssp             HHHHHHTT-CCTTCEEEEECCTTSHHHHHHHHH--SSEEEEEESCGGGHHHHHHHHHHCSSEEEEESCTTTSCGGGSCCS
T ss_pred             HHHHHhcC-CCCcCEEEEECCCchHHHHHHHhc--CCEEEEEECCHHHHHHHHHHhccCCCeEEEECchhhCCcccCCcc
Confidence            34555555 566689999999999999999998  4678999984 46666654    3799999999998 7776  38


Q ss_pred             EEE
Q 039903          229 AIL  231 (233)
Q Consensus       229 ~~~  231 (233)
                      +++
T Consensus       117 ~Iv  119 (295)
T 3gru_A          117 KVV  119 (295)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            776

>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=98.07  E-value=5.4e-06  Score=69.69  Aligned_cols=66  Identities=20%  Similarity=0.178  Sum_probs=53.9

Q ss_pred             HHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-----CCceEEecCcCC
Q 039903          156 TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-----SGVKHIGGIMLE  222 (233)
Q Consensus       156 ~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-----~ri~~~~gD~f~  222 (233)
                      ...+++.+. .....++||+|||+|.++..+++++|+.+++.+|. |..++.|+++     +|++++.+||.+
T Consensus        15 l~e~l~~L~-~~~g~~vLD~g~G~G~~s~~la~~~~~~~VigvD~d~~al~~A~~~~~~~g~~v~~v~~d~~~   86 (301)
T 1m6y_A           15 VREVIEFLK-PEDEKIILDCTVGEGGHSRAILEHCPGCRIIGIDVDSEVLRIAEEKLKEFSDRVSLFKVSYRE   86 (301)
T ss_dssp             HHHHHHHHC-CCTTCEEEETTCTTSHHHHHHHHHCTTCEEEEEESCHHHHHHHHHHTGGGTTTEEEEECCGGG
T ss_pred             HHHHHHhcC-CCCCCEEEEEeCCcCHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHhcCCcEEEEECCHHH
Confidence            345556555 55668999999999999999999999999999998 5577776542     689999999865

>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=98.07  E-value=5.4e-06  Score=70.42  Aligned_cols=66  Identities=20%  Similarity=0.297  Sum_probs=53.0

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCC-------CCceEEecCcCC-CCCC-C-CEEEe
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSY-------SGVKHIGGIMLE-RIPK-G-DAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~-------~ri~~~~gD~f~-~~P~-~-D~~~l  232 (233)
                      ..+..+|+|||||+|.++..++++ +..+++.+|..+.++.+++.       ++|+++.+|+.+ ++|. . |+++.
T Consensus        36 ~~~~~~VLDiGcGtG~ls~~la~~-g~~~v~~vD~s~~~~~a~~~~~~~~~~~~i~~~~~d~~~~~~~~~~~D~Ivs  111 (328)
T 1g6q_1           36 LFKDKIVLDVGCGTGILSMFAAKH-GAKHVIGVDMSSIIEMAKELVELNGFSDKITLLRGKLEDVHLPFPKVDIIIS  111 (328)
T ss_dssp             HHTTCEEEEETCTTSHHHHHHHHT-CCSEEEEEESSTHHHHHHHHHHHTTCTTTEEEEESCTTTSCCSSSCEEEEEE
T ss_pred             hcCCCEEEEecCccHHHHHHHHHC-CCCEEEEEChHHHHHHHHHHHHHcCCCCCEEEEECchhhccCCCCcccEEEE
Confidence            344579999999999999998886 66689999998777666542       689999999998 6774 3 98874

>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=98.06  E-value=3.5e-06  Score=69.93  Aligned_cols=66  Identities=23%  Similarity=0.220  Sum_probs=53.3

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccC----------CCCceEEecCcCCCC---CCC-CEEE
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSS----------YSGVKHIGGIMLERI---PKG-DAIL  231 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~----------~~ri~~~~gD~f~~~---P~~-D~~~  231 (233)
                      .+..+|+|||||+|..++.+++.+|..+++++|+ |.+++.+++          .+|++++.+|.++.+   +.. |+|+
T Consensus        74 ~~~~~VLdiG~G~G~~~~~l~~~~~~~~v~~vEid~~~v~~ar~~~~~~~~~~~~~rv~v~~~D~~~~l~~~~~~fD~Ii  153 (275)
T 1iy9_A           74 PNPEHVLVVGGGDGGVIREILKHPSVKKATLVDIDGKVIEYSKKFLPSIAGKLDDPRVDVQVDDGFMHIAKSENQYDVIM  153 (275)
T ss_dssp             SSCCEEEEESCTTCHHHHHHTTCTTCSEEEEEESCHHHHHHHHHHCHHHHTTTTSTTEEEEESCSHHHHHTCCSCEEEEE
T ss_pred             CCCCEEEEECCchHHHHHHHHhCCCCceEEEEECCHHHHHHHHHHhHhhccccCCCceEEEECcHHHHHhhCCCCeeEEE
Confidence            3568999999999999999999878889999998 567777653          268999999988732   233 9887


Q ss_pred             e
Q 039903          232 I  232 (233)
Q Consensus       232 l  232 (233)
                      +
T Consensus       154 ~  154 (275)
T 1iy9_A          154 V  154 (275)
T ss_dssp             E
T ss_pred             E
Confidence            5

>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=98.06  E-value=9.2e-06  Score=64.57  Aligned_cols=67  Identities=10%  Similarity=0.002  Sum_probs=51.9

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-----HHhhccCCCCceEEecCcCCC-----CCCC-CEEEe
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-----VIQDSSSYSGVKHIGGIMLER-----IPKG-DAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-----v~~~a~~~~ri~~~~gD~f~~-----~P~~-D~~~l  232 (233)
                      .++..+|||||||+|.++..+++..|.-+++.+|+.+     .++.++...+|.++.+|..++     ++.. |+++.
T Consensus        55 ~~~g~~VLDlGcGtG~~~~~la~~~~~~~V~gvD~s~~~l~~~~~~a~~~~~v~~~~~d~~~~~~~~~~~~~fD~V~~  132 (210)
T 1nt2_A           55 LRGDERVLYLGAASGTTVSHLADIVDEGIIYAVEYSAKPFEKLLELVRERNNIIPLLFDASKPWKYSGIVEKVDLIYQ  132 (210)
T ss_dssp             CCSSCEEEEETCTTSHHHHHHHHHTTTSEEEEECCCHHHHHHHHHHHHHCSSEEEECSCTTCGGGTTTTCCCEEEEEE
T ss_pred             CCCCCEEEEECCcCCHHHHHHHHHcCCCEEEEEECCHHHHHHHHHHHhcCCCeEEEEcCCCCchhhcccccceeEEEE
Confidence            4566799999999999999999999877899999864     344455456899999998763     2333 88874

>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=98.05  E-value=4.9e-06  Score=68.15  Aligned_cols=66  Identities=17%  Similarity=0.242  Sum_probs=54.8

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-CCceEEecCcCC-CCCCC--CEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-SGVKHIGGIMLE-RIPKG--DAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-~ri~~~~gD~f~-~~P~~--D~~~l  232 (233)
                      ....+|+|||||.|.++..+++++|..+++.+|. +..++.+++. +++.++.+|+.+ +++.+  |+++.
T Consensus        84 ~~~~~vLdiG~G~G~~~~~l~~~~~~~~v~~vD~s~~~~~~a~~~~~~~~~~~~d~~~~~~~~~~fD~v~~  154 (269)
T 1p91_A           84 DKATAVLDIGCGEGYYTHAFADALPEITTFGLDVSKVAIKAAAKRYPQVTFCVASSHRLPFSDTSMDAIIR  154 (269)
T ss_dssp             TTCCEEEEETCTTSTTHHHHHHTCTTSEEEEEESCHHHHHHHHHHCTTSEEEECCTTSCSBCTTCEEEEEE
T ss_pred             CCCCEEEEECCCCCHHHHHHHHhCCCCeEEEEeCCHHHHHHHHHhCCCcEEEEcchhhCCCCCCceeEEEE
Confidence            4557999999999999999999999999999998 4577777653 789999999987 66653  88863

>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=98.05  E-value=8.9e-06  Score=61.51  Aligned_cols=71  Identities=18%  Similarity=0.214  Sum_probs=54.4

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHc-CCCcEEEeechHHHhhccCCCCceEEecCcCC-C--------CCC-
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNY-LHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLE-R--------IPK-  226 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~-P~l~~~v~Dlp~v~~~a~~~~ri~~~~gD~f~-~--------~P~-  226 (233)
                      .+++.+.......+|+|||||+|.++..+++.+ |+.+++.+|+.+.+    ..++++++.+|+.+ +        +|. 
T Consensus        12 ~~~~~~~~~~~~~~vLd~G~G~G~~~~~l~~~~~~~~~v~~~D~~~~~----~~~~~~~~~~d~~~~~~~~~~~~~~~~~   87 (180)
T 1ej0_A           12 EIQQSDKLFKPGMTVVDLGAAPGGWSQYVVTQIGGKGRIIACDLLPMD----PIVGVDFLQGDFRDELVMKALLERVGDS   87 (180)
T ss_dssp             HHHHHHCCCCTTCEEEEESCTTCHHHHHHHHHHCTTCEEEEEESSCCC----CCTTEEEEESCTTSHHHHHHHHHHHTTC
T ss_pred             HHHHHhCCCCCCCeEEEeCCCCCHHHHHHHHHhCCCCeEEEEECcccc----ccCcEEEEEcccccchhhhhhhccCCCC
Confidence            344444323456799999999999999999995 78999999997722    22789999999998 4        664 


Q ss_pred             C-CEEEe
Q 039903          227 G-DAILI  232 (233)
Q Consensus       227 ~-D~~~l  232 (233)
                      . |+++.
T Consensus        88 ~~D~i~~   94 (180)
T 1ej0_A           88 KVQVVMS   94 (180)
T ss_dssp             CEEEEEE
T ss_pred             ceeEEEE
Confidence            3 88875

>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=98.04  E-value=6.8e-06  Score=64.93  Aligned_cols=65  Identities=12%  Similarity=0.168  Sum_probs=51.9

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccC----CCCceEEecCcCCCCCC-C-CEEEe
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSS----YSGVKHIGGIMLERIPK-G-DAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~----~~ri~~~~gD~f~~~P~-~-D~~~l  232 (233)
                      .....+|||||||+|.++..++++.  .+++.+|+ +..++.+++    .++|+++.+|+.+..|. . |+++.
T Consensus        49 ~~~~~~vLDiGcG~G~~~~~l~~~~--~~v~~vD~s~~~~~~a~~~~~~~~~~~~~~~d~~~~~~~~~fD~v~~  120 (216)
T 3ofk_A           49 SGAVSNGLEIGCAAGAFTEKLAPHC--KRLTVIDVMPRAIGRACQRTKRWSHISWAATDILQFSTAELFDLIVV  120 (216)
T ss_dssp             TSSEEEEEEECCTTSHHHHHHGGGE--EEEEEEESCHHHHHHHHHHTTTCSSEEEEECCTTTCCCSCCEEEEEE
T ss_pred             cCCCCcEEEEcCCCCHHHHHHHHcC--CEEEEEECCHHHHHHHHHhcccCCCeEEEEcchhhCCCCCCccEEEE
Confidence            4566899999999999999999986  37899998 557776654    26899999999983354 3 98875

>1ne2_A Hypothetical protein TA1320; structural genomics, conserved hypothetical protein, PSI, protein structure initiative; 1.75A {Thermoplasma acidophilum} SCOP: c.66.1.32

Probab=98.04  E-value=6.2e-06  Score=64.57  Aligned_cols=64  Identities=19%  Similarity=0.194  Sum_probs=52.0

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-CCceEEecCcCCCCCCC-CEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-SGVKHIGGIMLERIPKG-DAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-~ri~~~~gD~f~~~P~~-D~~~l  232 (233)
                      ....+|+|+|||+|.++..+++. +..+++.+|+ |..++.++++ .+++++.+|+++ +|.. |++++
T Consensus        50 ~~~~~vlD~gcG~G~~~~~l~~~-~~~~v~~vD~~~~~~~~a~~~~~~~~~~~~d~~~-~~~~~D~v~~  116 (200)
T 1ne2_A           50 IGGRSVIDAGTGNGILACGSYLL-GAESVTAFDIDPDAIETAKRNCGGVNFMVADVSE-ISGKYDTWIM  116 (200)
T ss_dssp             SBTSEEEEETCTTCHHHHHHHHT-TBSEEEEEESCHHHHHHHHHHCTTSEEEECCGGG-CCCCEEEEEE
T ss_pred             CCCCEEEEEeCCccHHHHHHHHc-CCCEEEEEECCHHHHHHHHHhcCCCEEEECcHHH-CCCCeeEEEE
Confidence            45579999999999999999987 6567999998 6688877664 489999999987 4443 88875

>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=98.04  E-value=6e-06  Score=66.63  Aligned_cols=55  Identities=13%  Similarity=0.151  Sum_probs=46.6

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC---CCceEEecCcCC
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY---SGVKHIGGIMLE  222 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~---~ri~~~~gD~f~  222 (233)
                      .....+|||||||+|.++..+++..+  +++.+|. |..++.+++.   .+|+++.+|+.+
T Consensus        54 ~~~~~~vLD~GcG~G~~~~~la~~~~--~v~gvD~s~~~~~~a~~~~~~~~~~~~~~d~~~  112 (245)
T 3ggd_A           54 FNPELPLIDFACGNGTQTKFLSQFFP--RVIGLDVSKSALEIAAKENTAANISYRLLDGLV  112 (245)
T ss_dssp             SCTTSCEEEETCTTSHHHHHHHHHSS--CEEEEESCHHHHHHHHHHSCCTTEEEEECCTTC
T ss_pred             cCCCCeEEEEcCCCCHHHHHHHHhCC--CEEEEECCHHHHHHHHHhCcccCceEEECcccc
Confidence            34557899999999999999999998  7899998 4577776542   589999999998

>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=98.04  E-value=9.9e-06  Score=68.84  Aligned_cols=75  Identities=15%  Similarity=0.147  Sum_probs=56.5

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHH-cCCCcEEEeec-hHHHhhccCC-----------------CCceEEe
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISN-YLHIKGVNFDL-SHVIQDSSSY-----------------SGVKHIG  217 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~-~P~l~~~v~Dl-p~v~~~a~~~-----------------~ri~~~~  217 (233)
                      ..++..++ .....+|||||||+|.++..+++. .|+.+++.+|+ |..++.|+++                 ++|+++.
T Consensus        95 ~~~l~~l~-~~~g~~VLDiG~G~G~~~~~la~~~g~~~~v~~vD~~~~~~~~a~~~~~~~~~~~~ln~~~~~~~~v~~~~  173 (336)
T 2b25_A           95 NMILSMMD-INPGDTVLEAGSGSGGMSLFLSKAVGSQGRVISFEVRKDHHDLAKKNYKHWRDSWKLSHVEEWPDNVDFIH  173 (336)
T ss_dssp             HHHHHHHT-CCTTCEEEEECCTTSHHHHHHHHHHCTTCEEEEEESSHHHHHHHHHHHHHHHHHHTTTCSSCCCCCEEEEE
T ss_pred             HHHHHhcC-CCCCCEEEEeCCCcCHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHHHHHhhcccccccccccCCceEEEE
Confidence            34555555 666789999999999999999998 58899999998 5566666541                 5899999


Q ss_pred             cCcCCC---CCCC--CEEEe
Q 039903          218 GIMLER---IPKG--DAILI  232 (233)
Q Consensus       218 gD~f~~---~P~~--D~~~l  232 (233)
                      +|+.+.   ++.+  |+|++
T Consensus       174 ~d~~~~~~~~~~~~fD~V~~  193 (336)
T 2b25_A          174 KDISGATEDIKSLTFDAVAL  193 (336)
T ss_dssp             SCTTCCC-------EEEEEE
T ss_pred             CChHHcccccCCCCeeEEEE
Confidence            999873   4442  98875

>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=98.04  E-value=6.2e-06  Score=63.63  Aligned_cols=65  Identities=15%  Similarity=0.149  Sum_probs=50.5

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCC--CCCC-C-CEEEe
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLE--RIPK-G-DAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~--~~P~-~-D~~~l  232 (233)
                      .+...+|+|||||+|.++..++++  ..+++.+|+ |..++.|+++      ++|+++.+|+..  +.+. . |++++
T Consensus        20 ~~~~~~vLDiGcG~G~~~~~la~~--~~~v~~vD~s~~~l~~a~~~~~~~~~~~v~~~~~~~~~l~~~~~~~fD~v~~   95 (185)
T 3mti_A           20 LDDESIVVDATMGNGNDTAFLAGL--SKKVYAFDVQEQALGKTSQRLSDLGIENTELILDGHENLDHYVREPIRAAIF   95 (185)
T ss_dssp             CCTTCEEEESCCTTSHHHHHHHTT--SSEEEEEESCHHHHHHHHHHHHHHTCCCEEEEESCGGGGGGTCCSCEEEEEE
T ss_pred             CCCCCEEEEEcCCCCHHHHHHHHh--CCEEEEEECCHHHHHHHHHHHHHcCCCcEEEEeCcHHHHHhhccCCcCEEEE
Confidence            456689999999999999999998  788999998 5577777653      689999977654  2333 3 88764

>3sm3_A SAM-dependent methyltransferases; NESG, structural genomics, PSI-biology, protein structure in northeast structural genomics; 2.20A {Methanosarcina mazei}

Probab=98.03  E-value=8.4e-06  Score=64.92  Aligned_cols=64  Identities=14%  Similarity=0.145  Sum_probs=51.6

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-----------CCceEEecCcCC-CCCCC--CEEE
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-----------SGVKHIGGIMLE-RIPKG--DAIL  231 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-----------~ri~~~~gD~f~-~~P~~--D~~~  231 (233)
                      +...+|||||||+|.++..++++  ..+++.+|+ |..++.+++.           ++++++.+|+.+ ++|..  |+++
T Consensus        29 ~~~~~vLdiG~G~G~~~~~l~~~--~~~v~~vD~s~~~~~~a~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~D~v~  106 (235)
T 3sm3_A           29 QEDDEILDIGCGSGKISLELASK--GYSVTGIDINSEAIRLAETAARSPGLNQKTGGKAEFKVENASSLSFHDSSFDFAV  106 (235)
T ss_dssp             CTTCEEEEETCTTSHHHHHHHHT--TCEEEEEESCHHHHHHHHHHTTCCSCCSSSSCEEEEEECCTTSCCSCTTCEEEEE
T ss_pred             CCCCeEEEECCCCCHHHHHHHhC--CCeEEEEECCHHHHHHHHHHHHhcCCccccCcceEEEEecccccCCCCCceeEEE
Confidence            45689999999999999999998  668999998 5577666541           268999999998 66653  9887


Q ss_pred             e
Q 039903          232 I  232 (233)
Q Consensus       232 l  232 (233)
                      +
T Consensus       107 ~  107 (235)
T 3sm3_A          107 M  107 (235)
T ss_dssp             E
T ss_pred             E
Confidence            5

>3c3p_A Methyltransferase; NP_951602.1, structural genomics, joint for structural genomics, JCSG, protein structure initiative transferase; 1.90A {Geobacter sulfurreducens pca}

Probab=98.03  E-value=3.9e-06  Score=66.28  Aligned_cols=66  Identities=18%  Similarity=0.147  Sum_probs=52.8

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcC-CCcEEEeec-hHHHhhccCC-------CCceEEecCcCCCCC--C-CCEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLERIP--K-GDAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~~P--~-~D~~~l  232 (233)
                      .+..+|||||||+|..+..+++..| +.+++.+|+ |..++.++++       ++|+++.+|..+.+|  . -|++++
T Consensus        55 ~~~~~vLdiG~G~G~~~~~la~~~~~~~~v~~vD~~~~~~~~a~~~~~~~~~~~~v~~~~~d~~~~~~~~~~fD~v~~  132 (210)
T 3c3p_A           55 KQPQLVVVPGDGLGCASWWFARAISISSRVVMIDPDRDNVEHARRMLHDNGLIDRVELQVGDPLGIAAGQRDIDILFM  132 (210)
T ss_dssp             HCCSEEEEESCGGGHHHHHHHTTSCTTCEEEEEESCHHHHHHHHHHHHHHSGGGGEEEEESCHHHHHTTCCSEEEEEE
T ss_pred             hCCCEEEEEcCCccHHHHHHHHhCCCCCEEEEEECCHHHHHHHHHHHHHCCCCceEEEEEecHHHHhccCCCCCEEEE
Confidence            4567999999999999999999998 889999998 5677777642       579999999986323  2 377764

>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=98.02  E-value=5.4e-06  Score=68.76  Aligned_cols=65  Identities=14%  Similarity=-0.033  Sum_probs=53.0

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCCCCCC-C-CEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLERIPK-G-DAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~~P~-~-D~~~l  232 (233)
                      +...+|+|+|||+|.++..++++.+. +++.+|+ |..++.++++       ++++++.+|+++..+. . |++++
T Consensus       124 ~~~~~VLDlgcG~G~~~~~la~~~~~-~V~~vD~s~~~~~~a~~n~~~n~~~~~v~~~~~D~~~~~~~~~fD~Vi~  198 (278)
T 2frn_A          124 KPDELVVDMFAGIGHLSLPIAVYGKA-KVIAIEKDPYTFKFLVENIHLNKVEDRMSAYNMDNRDFPGENIADRILM  198 (278)
T ss_dssp             CTTCEEEETTCTTTTTHHHHHHHTCC-EEEEECCCHHHHHHHHHHHHHTTCTTTEEEECSCTTTCCCCSCEEEEEE
T ss_pred             CCCCEEEEecccCCHHHHHHHHhCCC-EEEEEECCHHHHHHHHHHHHHcCCCceEEEEECCHHHhcccCCccEEEE
Confidence            44689999999999999999999887 8999998 5677776642       4699999999984433 3 88875

>2yvl_A TRMI protein, hypothetical protein; tRNA, methyltransferase, S-adenosylmethionine, structural GE NPPSFA; HET: SAM; 2.20A {Aquifex aeolicus}

Probab=98.02  E-value=1.5e-05  Score=64.28  Aligned_cols=72  Identities=14%  Similarity=0.180  Sum_probs=56.7

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCCCC-CC-C
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLERI-PK-G  227 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~~-P~-~  227 (233)
                      .++..++ .....+|+|+|||+|.++..++++  ..+++.+|. |+.++.++++       ++++++.+|+.+.. +. .
T Consensus        82 ~~~~~~~-~~~~~~vldiG~G~G~~~~~l~~~--~~~v~~vD~~~~~~~~a~~~~~~~~~~~~~~~~~~d~~~~~~~~~~  158 (248)
T 2yvl_A           82 YIALKLN-LNKEKRVLEFGTGSGALLAVLSEV--AGEVWTFEAVEEFYKTAQKNLKKFNLGKNVKFFNVDFKDAEVPEGI  158 (248)
T ss_dssp             HHHHHTT-CCTTCEEEEECCTTSHHHHHHHHH--SSEEEEECSCHHHHHHHHHHHHHTTCCTTEEEECSCTTTSCCCTTC
T ss_pred             HHHHhcC-CCCCCEEEEeCCCccHHHHHHHHh--CCEEEEEecCHHHHHHHHHHHHHcCCCCcEEEEEcChhhcccCCCc
Confidence            4445554 566789999999999999999998  778999997 5577766542       68999999999865 54 3


Q ss_pred             -CEEEe
Q 039903          228 -DAILI  232 (233)
Q Consensus       228 -D~~~l  232 (233)
                       |++++
T Consensus       159 ~D~v~~  164 (248)
T 2yvl_A          159 FHAAFV  164 (248)
T ss_dssp             BSEEEE
T ss_pred             ccEEEE
Confidence             99875

>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=98.02  E-value=1.3e-05  Score=63.91  Aligned_cols=67  Identities=15%  Similarity=0.097  Sum_probs=51.5

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHc-CCCcEEEeechH-HHh----hccCCCCceEEecCcCCC-----CCCC-CEEEe
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNY-LHIKGVNFDLSH-VIQ----DSSSYSGVKHIGGIMLER-----IPKG-DAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~-P~l~~~v~Dlp~-v~~----~a~~~~ri~~~~gD~f~~-----~P~~-D~~~l  232 (233)
                      .....+|+|+|||+|.++..++++. |..+++.+|..+ .++    .++..++|+++.+|+.+.     ++.. |++++
T Consensus        71 ~~~~~~vLDlG~G~G~~~~~la~~~~~~~~v~~vD~s~~~~~~~~~~~~~~~~v~~~~~d~~~~~~~~~~~~~~D~v~~  149 (227)
T 1g8a_A           71 IKPGKSVLYLGIASGTTASHVSDIVGWEGKIFGIEFSPRVLRELVPIVEERRNIVPILGDATKPEEYRALVPKVDVIFE  149 (227)
T ss_dssp             CCTTCEEEEETTTSTTHHHHHHHHHCTTSEEEEEESCHHHHHHHHHHHSSCTTEEEEECCTTCGGGGTTTCCCEEEEEE
T ss_pred             CCCCCEEEEEeccCCHHHHHHHHHhCCCeEEEEEECCHHHHHHHHHHHhccCCCEEEEccCCCcchhhcccCCceEEEE
Confidence            4566799999999999999999985 678899999854 333    334447899999999872     2333 88874

>3a27_A TYW2, uncharacterized protein MJ1557; wybutosine modification, transferase; HET: SAM; 2.00A {Methanocaldococcus jannaschii}

Probab=98.01  E-value=6e-06  Score=68.31  Aligned_cols=67  Identities=10%  Similarity=-0.003  Sum_probs=55.2

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCCC-CCCC-CEEEe
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLER-IPKG-DAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~-~P~~-D~~~l  232 (233)
                      +.+..+|+|+|||+|.++..++++.+..+++.+|+ |..++.++++      ++++++.+|+++. .+.. |++++
T Consensus       117 ~~~~~~VLDlgcG~G~~s~~la~~~~~~~V~~vD~s~~av~~a~~n~~~n~l~~~~~~~~d~~~~~~~~~~D~Vi~  192 (272)
T 3a27_A          117 SNENEVVVDMFAGIGYFTIPLAKYSKPKLVYAIEKNPTAYHYLCENIKLNKLNNVIPILADNRDVELKDVADRVIM  192 (272)
T ss_dssp             CCTTCEEEETTCTTTTTHHHHHHHTCCSEEEEEECCHHHHHHHHHHHHHTTCSSEEEEESCGGGCCCTTCEEEEEE
T ss_pred             cCCCCEEEEecCcCCHHHHHHHHhCCCCEEEEEeCCHHHHHHHHHHHHHcCCCCEEEEECChHHcCccCCceEEEE
Confidence            45668999999999999999999999889999998 6688777653      5789999999985 2223 88876

>3e23_A Uncharacterized protein RPA2492; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; HET: SAM; 1.60A {Rhodopseudomonas palustris}

Probab=98.01  E-value=8.8e-06  Score=64.11  Aligned_cols=64  Identities=13%  Similarity=0.163  Sum_probs=51.9

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCCCCceEEecCcCC-CCCC-C-CEEEe
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSYSGVKHIGGIMLE-RIPK-G-DAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~~ri~~~~gD~f~-~~P~-~-D~~~l  232 (233)
                      +....+|||||||+|.++..++++  ..+++.+|+ |..++.+++.-+++++.+|+.+ + +. . |+|+.
T Consensus        41 ~~~~~~vLDiGcG~G~~~~~l~~~--~~~v~~vD~s~~~~~~a~~~~~~~~~~~d~~~~~-~~~~fD~v~~  108 (211)
T 3e23_A           41 LPAGAKILELGCGAGYQAEAMLAA--GFDVDATDGSPELAAEASRRLGRPVRTMLFHQLD-AIDAYDAVWA  108 (211)
T ss_dssp             SCTTCEEEESSCTTSHHHHHHHHT--TCEEEEEESCHHHHHHHHHHHTSCCEECCGGGCC-CCSCEEEEEE
T ss_pred             cCCCCcEEEECCCCCHHHHHHHHc--CCeEEEECCCHHHHHHHHHhcCCceEEeeeccCC-CCCcEEEEEe
Confidence            455679999999999999999987  568999998 5677777765578889999987 5 44 3 98875

>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=98.00  E-value=8.4e-06  Score=66.16  Aligned_cols=63  Identities=16%  Similarity=0.056  Sum_probs=51.4

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC-----CCceEEecCcCC-CCCC-CCEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY-----SGVKHIGGIMLE-RIPK-GDAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~-----~ri~~~~gD~f~-~~P~-~D~~~l  232 (233)
                      ....+|+|||||.|-++..+.   |..+.+.+|+. ..++.++++     .+.++..+|+.. +.|. +|++++
T Consensus       104 ~~p~~VLDlGCG~gpLal~~~---~~~~y~a~DId~~~i~~ar~~~~~~g~~~~~~v~D~~~~~~~~~~DvvLl  174 (253)
T 3frh_A          104 ETPRRVLDIACGLNPLALYER---GIASVWGCDIHQGLGDVITPFAREKDWDFTFALQDVLCAPPAEAGDLALI  174 (253)
T ss_dssp             CCCSEEEEETCTTTHHHHHHT---TCSEEEEEESBHHHHHHHHHHHHHTTCEEEEEECCTTTSCCCCBCSEEEE
T ss_pred             CCCCeEEEecCCccHHHHHhc---cCCeEEEEeCCHHHHHHHHHHHHhcCCCceEEEeecccCCCCCCcchHHH
Confidence            457899999999999999888   99999999995 467666553     678899999998 5555 499954

>3uzu_A Ribosomal RNA small subunit methyltransferase A; ssgcid, seattle structural genomics center for infectio disease; 1.75A {Burkholderia pseudomallei}

Probab=98.00  E-value=3.9e-06  Score=69.83  Aligned_cols=68  Identities=18%  Similarity=0.217  Sum_probs=53.7

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcCC--CcEEEeech-HHHhhccCC--CCceEEecCcCC-CCCC
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLH--IKGVNFDLS-HVIQDSSSY--SGVKHIGGIMLE-RIPK  226 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~--l~~~v~Dlp-~v~~~a~~~--~ri~~~~gD~f~-~~P~  226 (233)
                      .+++.++ .....+|+|||||+|.++..++++.+.  .+++.+|+. +.++.++++  ++++++.+|+++ ++|.
T Consensus        33 ~iv~~~~-~~~~~~VLEIG~G~G~lt~~La~~~~~~~~~V~avDid~~~l~~a~~~~~~~v~~i~~D~~~~~~~~  106 (279)
T 3uzu_A           33 AIVAAIR-PERGERMVEIGPGLGALTGPVIARLATPGSPLHAVELDRDLIGRLEQRFGELLELHAGDALTFDFGS  106 (279)
T ss_dssp             HHHHHHC-CCTTCEEEEECCTTSTTHHHHHHHHCBTTBCEEEEECCHHHHHHHHHHHGGGEEEEESCGGGCCGGG
T ss_pred             HHHHhcC-CCCcCEEEEEccccHHHHHHHHHhCCCcCCeEEEEECCHHHHHHHHHhcCCCcEEEECChhcCChhH
Confidence            4555555 566789999999999999999998765  668999984 567766653  789999999998 6554

>3p9n_A Possible methyltransferase (methylase); RV2966C, adoMet binding, RNA methylase, RSMD, SAM-fold, RNA methyltransferase; 1.90A {Mycobacterium tuberculosis}

Probab=98.00  E-value=8.3e-06  Score=63.29  Aligned_cols=64  Identities=14%  Similarity=-0.011  Sum_probs=50.8

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCCC---CCC--CCEEEe
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLER---IPK--GDAILI  232 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~---~P~--~D~~~l  232 (233)
                      +..+|+|+|||+|.++..++++ +..+++.+|+ |+.++.++++      ++++++.+|+.+.   ++.  .|++++
T Consensus        44 ~~~~vLDlgcG~G~~~~~~~~~-~~~~v~~vD~~~~~~~~a~~~~~~~~~~~v~~~~~d~~~~~~~~~~~~fD~i~~  119 (189)
T 3p9n_A           44 TGLAVLDLYAGSGALGLEALSR-GAASVLFVESDQRSAAVIARNIEALGLSGATLRRGAVAAVVAAGTTSPVDLVLA  119 (189)
T ss_dssp             TTCEEEEETCTTCHHHHHHHHT-TCSEEEEEECCHHHHHHHHHHHHHHTCSCEEEEESCHHHHHHHCCSSCCSEEEE
T ss_pred             CCCEEEEeCCCcCHHHHHHHHC-CCCeEEEEECCHHHHHHHHHHHHHcCCCceEEEEccHHHHHhhccCCCccEEEE
Confidence            4578999999999999988774 6678999998 5677777653      5899999999872   333  399875

>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=97.99  E-value=6.1e-06  Score=63.45  Aligned_cols=71  Identities=20%  Similarity=0.144  Sum_probs=55.3

Q ss_pred             HHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCCCCCC---C
Q 039903          159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLERIPK---G  227 (233)
Q Consensus       159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~~P~---~  227 (233)
                      +++.++ .....+|+|+|||+|.++..+++..  .+++.+|. |..++.++++       ++++++.+|+.+++|.   .
T Consensus        25 ~~~~~~-~~~~~~vldiG~G~G~~~~~l~~~~--~~v~~~D~~~~~~~~a~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~  101 (192)
T 1l3i_A           25 IMCLAE-PGKNDVAVDVGCGTGGVTLELAGRV--RRVYAIDRNPEAISTTEMNLQRHGLGDNVTLMEGDAPEALCKIPDI  101 (192)
T ss_dssp             HHHHHC-CCTTCEEEEESCTTSHHHHHHHTTS--SEEEEEESCHHHHHHHHHHHHHTTCCTTEEEEESCHHHHHTTSCCE
T ss_pred             HHHhcC-CCCCCEEEEECCCCCHHHHHHHHhc--CEEEEEECCHHHHHHHHHHHHHcCCCcceEEEecCHHHhcccCCCC
Confidence            344444 5666899999999999999999987  78999998 5677766542       5899999999875543   3


Q ss_pred             CEEEe
Q 039903          228 DAILI  232 (233)
Q Consensus       228 D~~~l  232 (233)
                      |+++.
T Consensus       102 D~v~~  106 (192)
T 1l3i_A          102 DIAVV  106 (192)
T ss_dssp             EEEEE
T ss_pred             CEEEE
Confidence            88875

>3lcc_A Putative methyl chloride transferase; halide methyltransferase; HET: SAH; 1.80A {Arabidopsis thaliana}

Probab=97.99  E-value=5.8e-06  Score=66.33  Aligned_cols=61  Identities=16%  Similarity=0.124  Sum_probs=49.1

Q ss_pred             ceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCCCCCC-C-CEEEe
Q 039903          170 KQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLERIPK-G-DAILI  232 (233)
Q Consensus       170 ~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~~P~-~-D~~~l  232 (233)
                      .+|||||||+|.++..+++  +..+++.+|+ |..++.+++.       ++|+++.+|+.+..|. . |+|+.
T Consensus        68 ~~vLDiGcG~G~~~~~l~~--~~~~v~gvD~s~~~~~~a~~~~~~~~~~~~v~~~~~d~~~~~~~~~fD~v~~  138 (235)
T 3lcc_A           68 GRALVPGCGGGHDVVAMAS--PERFVVGLDISESALAKANETYGSSPKAEYFSFVKEDVFTWRPTELFDLIFD  138 (235)
T ss_dssp             EEEEEETCTTCHHHHHHCB--TTEEEEEECSCHHHHHHHHHHHTTSGGGGGEEEECCCTTTCCCSSCEEEEEE
T ss_pred             CCEEEeCCCCCHHHHHHHh--CCCeEEEEECCHHHHHHHHHHhhccCCCcceEEEECchhcCCCCCCeeEEEE
Confidence            5999999999999999976  6778999998 5577766542       4699999999984454 3 98874

>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=97.99  E-value=5e-06  Score=68.91  Aligned_cols=71  Identities=13%  Similarity=0.196  Sum_probs=53.9

Q ss_pred             HHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccC----------CCCceEEecCcCC-C---
Q 039903          159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSS----------YSGVKHIGGIMLE-R---  223 (233)
Q Consensus       159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~----------~~ri~~~~gD~f~-~---  223 (233)
                      +.+.++ ..+..+|||||||+|.++..++++.+  +++.+|+ |..++.+++          ..++.+..+|+.+ +   
T Consensus        49 l~~~l~-~~~~~~vLDiGcG~G~~~~~l~~~~~--~v~gvD~s~~~l~~a~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~  125 (293)
T 3thr_A           49 LLGLLR-QHGCHRVLDVACGTGVDSIMLVEEGF--SVTSVDASDKMLKYALKERWNRRKEPAFDKWVIEEANWLTLDKDV  125 (293)
T ss_dssp             HHHHHH-HTTCCEEEETTCTTSHHHHHHHHTTC--EEEEEESCHHHHHHHHHHHHHTTTSHHHHTCEEEECCGGGHHHHS
T ss_pred             HHHHhc-ccCCCEEEEecCCCCHHHHHHHHCCC--eEEEEECCHHHHHHHHHhhhhcccccccceeeEeecChhhCcccc
Confidence            334443 34568999999999999999999854  8999998 457776643          1578999999988 5   


Q ss_pred             CCCC--CEEEe
Q 039903          224 IPKG--DAILI  232 (233)
Q Consensus       224 ~P~~--D~~~l  232 (233)
                      ++.+  |+|+.
T Consensus       126 ~~~~~fD~V~~  136 (293)
T 3thr_A          126 PAGDGFDAVIC  136 (293)
T ss_dssp             CCTTCEEEEEE
T ss_pred             ccCCCeEEEEE
Confidence            5653  99875

>3cc8_A Putative methyltransferase; structural genomics, joint center for structural genomics, JCSG, protein structure initiative, PS transferase; 1.64A {Bacillus cereus}

Probab=97.98  E-value=1.9e-05  Score=62.51  Aligned_cols=73  Identities=14%  Similarity=0.172  Sum_probs=54.5

Q ss_pred             cHHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCCCCceEEecCcCC---CCCCC--C
Q 039903          155 VTNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSYSGVKHIGGIMLE---RIPKG--D  228 (233)
Q Consensus       155 ~~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~~ri~~~~gD~f~---~~P~~--D  228 (233)
                      ....+++.++  .+..+|+|||||+|.++..+++. + .+++.+|. +..++.+++. ..+++.+|+.+   ++|.+  |
T Consensus        21 ~~~~l~~~~~--~~~~~vLdiG~G~G~~~~~l~~~-~-~~~~~~D~~~~~~~~~~~~-~~~~~~~d~~~~~~~~~~~~fD   95 (230)
T 3cc8_A           21 VNPNLLKHIK--KEWKEVLDIGCSSGALGAAIKEN-G-TRVSGIEAFPEAAEQAKEK-LDHVVLGDIETMDMPYEEEQFD   95 (230)
T ss_dssp             CCHHHHTTCC--TTCSEEEEETCTTSHHHHHHHTT-T-CEEEEEESSHHHHHHHHTT-SSEEEESCTTTCCCCSCTTCEE
T ss_pred             HHHHHHHHhc--cCCCcEEEeCCCCCHHHHHHHhc-C-CeEEEEeCCHHHHHHHHHh-CCcEEEcchhhcCCCCCCCccC
Confidence            3345556544  45689999999999999999998 5 88999998 5577777653 24788999875   34443  8


Q ss_pred             EEEe
Q 039903          229 AILI  232 (233)
Q Consensus       229 ~~~l  232 (233)
                      +++.
T Consensus        96 ~v~~   99 (230)
T 3cc8_A           96 CVIF   99 (230)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            8874

>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=97.98  E-value=1.4e-05  Score=67.53  Aligned_cols=74  Identities=15%  Similarity=0.232  Sum_probs=57.2

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcC-CCcEEEeec-hHHHhhccCC------CCceEEecCcCCCCC-CC-
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLERIP-KG-  227 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~~P-~~-  227 (233)
                      .+++.+. .....+|+|||||.|.++..+++..+ +.+++.+|+ |+.++.++++      ++|+++.+|+.+..| .+ 
T Consensus        66 ~l~~~l~-~~~~~~VLDiGcG~G~~~~~la~~~~~~~~v~gvD~s~~~~~~a~~~~~~~g~~~v~~~~~d~~~~~~~~~~  144 (317)
T 1dl5_A           66 LFMEWVG-LDKGMRVLEIGGGTGYNAAVMSRVVGEKGLVVSVEYSRKICEIAKRNVERLGIENVIFVCGDGYYGVPEFSP  144 (317)
T ss_dssp             HHHHHTT-CCTTCEEEEECCTTSHHHHHHHHHHCTTCEEEEEESCHHHHHHHHHHHHHTTCCSEEEEESCGGGCCGGGCC
T ss_pred             HHHHhcC-CCCcCEEEEecCCchHHHHHHHHhcCCCCEEEEEECCHHHHHHHHHHHHHcCCCCeEEEECChhhccccCCC
Confidence            3445454 56668999999999999999999988 488999998 5577766542      569999999988443 22 


Q ss_pred             -CEEEe
Q 039903          228 -DAILI  232 (233)
Q Consensus       228 -D~~~l  232 (233)
                       |+|+.
T Consensus       145 fD~Iv~  150 (317)
T 1dl5_A          145 YDVIFV  150 (317)
T ss_dssp             EEEEEE
T ss_pred             eEEEEE
Confidence             88875

>1y8c_A S-adenosylmethionine-dependent methyltransferase; structural genomics, protein structure initiative, PSI; 2.50A {Clostridium acetobutylicum} SCOP: c.66.1.43

Probab=97.98  E-value=1.1e-05  Score=64.72  Aligned_cols=63  Identities=13%  Similarity=0.142  Sum_probs=51.3

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-----CCceEEecCcCC-CCCCC-CEEEe
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-----SGVKHIGGIMLE-RIPKG-DAILI  232 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-----~ri~~~~gD~f~-~~P~~-D~~~l  232 (233)
                      +..+|||||||+|.++..++++  ..+++.+|. |..++.+++.     .+++++.+|+.+ ++|.. |+++.
T Consensus        37 ~~~~vLdiG~G~G~~~~~l~~~--~~~~~~~D~s~~~~~~a~~~~~~~~~~~~~~~~d~~~~~~~~~fD~v~~  107 (246)
T 1y8c_A           37 VFDDYLDLACGTGNLTENLCPK--FKNTWAVDLSQEMLSEAENKFRSQGLKPRLACQDISNLNINRKFDLITC  107 (246)
T ss_dssp             CTTEEEEETCTTSTTHHHHGGG--SSEEEEECSCHHHHHHHHHHHHHTTCCCEEECCCGGGCCCSCCEEEEEE
T ss_pred             CCCeEEEeCCCCCHHHHHHHHC--CCcEEEEECCHHHHHHHHHHHhhcCCCeEEEecccccCCccCCceEEEE
Confidence            4579999999999999999998  457999998 5677777653     289999999988 66644 99875

>3r0q_C Probable protein arginine N-methyltransferase 4.2; arginine methyltransferase, methylation; HET: SAH; 2.61A {Arabidopsis thaliana}

Probab=97.97  E-value=1e-05  Score=70.01  Aligned_cols=66  Identities=20%  Similarity=0.225  Sum_probs=53.2

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCC-------CCceEEecCcCC-CCCCC-CEEEe
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSY-------SGVKHIGGIMLE-RIPKG-DAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~-------~ri~~~~gD~f~-~~P~~-D~~~l  232 (233)
                      ..+..+|||||||+|.++..++++. ..+++.+|..+.++.+++.       ++|+++.+|+.+ ++|.. |+|+.
T Consensus        61 ~~~~~~VLDlGcGtG~ls~~la~~g-~~~V~gvD~s~~~~~a~~~~~~~~~~~~v~~~~~d~~~~~~~~~~D~Iv~  135 (376)
T 3r0q_C           61 HFEGKTVLDVGTGSGILAIWSAQAG-ARKVYAVEATKMADHARALVKANNLDHIVEVIEGSVEDISLPEKVDVIIS  135 (376)
T ss_dssp             TTTTCEEEEESCTTTHHHHHHHHTT-CSEEEEEESSTTHHHHHHHHHHTTCTTTEEEEESCGGGCCCSSCEEEEEE
T ss_pred             cCCCCEEEEeccCcCHHHHHHHhcC-CCEEEEEccHHHHHHHHHHHHHcCCCCeEEEEECchhhcCcCCcceEEEE
Confidence            4556899999999999999999973 3489999998777666542       679999999988 67654 99874

>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=97.97  E-value=3.6e-06  Score=67.80  Aligned_cols=65  Identities=18%  Similarity=0.337  Sum_probs=50.1

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC-----CCceEEecCcCC---CCCCC--CEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY-----SGVKHIGGIMLE---RIPKG--DAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~-----~ri~~~~gD~f~---~~P~~--D~~~l  232 (233)
                      ....+|||||||+|.++..+++..+. +++.+|+. ..++.|++.     .+++++.+|+.+   ++|.+  |+|+.
T Consensus        59 ~~~~~vLDiGcGtG~~~~~l~~~~~~-~v~gvD~s~~~l~~a~~~~~~~~~~v~~~~~d~~~~~~~~~~~~fD~V~~  134 (236)
T 1zx0_A           59 SKGGRVLEVGFGMAIAASKVQEAPID-EHWIIECNDGVFQRLRDWAPRQTHKVIPLKGLWEDVAPTLPDGHFDGILY  134 (236)
T ss_dssp             TTCEEEEEECCTTSHHHHHHHTSCEE-EEEEEECCHHHHHHHHHHGGGCSSEEEEEESCHHHHGGGSCTTCEEEEEE
T ss_pred             CCCCeEEEEeccCCHHHHHHHhcCCC-eEEEEcCCHHHHHHHHHHHHhcCCCeEEEecCHHHhhcccCCCceEEEEE
Confidence            44578999999999999999765443 88999984 577766542     579999999876   46653  98875

>2hnk_A SAM-dependent O-methyltransferase; modified rossman fold; HET: SAH; 2.30A {Leptospira interrogans}

Probab=97.97  E-value=8.2e-06  Score=65.83  Aligned_cols=57  Identities=18%  Similarity=0.137  Sum_probs=47.9

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcC-CCcEEEeec-hHHHhhccCC-------CCceEEecCcCC
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLE  222 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~  222 (233)
                      ..+..+|||||||+|..+..+++.+| ..+++.+|. |..++.++++       ++|+++.+|+.+
T Consensus        58 ~~~~~~VLdiG~G~G~~~~~la~~~~~~~~v~~vD~~~~~~~~a~~~~~~~g~~~~v~~~~~d~~~  123 (239)
T 2hnk_A           58 ISGAKRIIEIGTFTGYSSLCFASALPEDGKILCCDVSEEWTNVARKYWKENGLENKIFLKLGSALE  123 (239)
T ss_dssp             HHTCSEEEEECCTTCHHHHHHHHHSCTTCEEEEEESCHHHHHHHHHHHHHTTCGGGEEEEESCHHH
T ss_pred             hhCcCEEEEEeCCCCHHHHHHHHhCCCCCEEEEEECCHHHHHHHHHHHHHcCCCCCEEEEECCHHH
Confidence            45568999999999999999999998 789999998 5677766543       469999999876

>3r3h_A O-methyltransferase, SAM-dependent; structural genomics, PSI-biology, NEW YORK structural genomi research consortium, nysgrc; 2.65A {Legionella pneumophila subsp}

Probab=97.96  E-value=2.2e-06  Score=69.75  Aligned_cols=67  Identities=16%  Similarity=0.220  Sum_probs=53.0

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcC-CCcEEEeec-hHHHhhccCC-------CCceEEecCcCCCCC--------CC-
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLERIP--------KG-  227 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~~P--------~~-  227 (233)
                      ..+..+|||||||+|..+..+++..| +.+++.+|+ |+.++.|+++       ++|+++.+|..+.+|        .. 
T Consensus        58 ~~~~~~VLDiG~G~G~~t~~la~~~~~~~~v~~iD~~~~~~~~a~~~~~~~g~~~~i~~~~gda~~~l~~~~~~~~~~~f  137 (242)
T 3r3h_A           58 LTRAKKVLELGTFTGYSALAMSLALPDDGQVITCDINEGWTKHAHPYWREAKQEHKIKLRLGPALDTLHSLLNEGGEHQF  137 (242)
T ss_dssp             HHTCSEEEEEESCCSHHHHHHHHTSCTTCEEEEEECCCSSCCCSHHHHHHTTCTTTEEEEESCHHHHHHHHHHHHCSSCE
T ss_pred             hcCcCEEEEeeCCcCHHHHHHHHhCCCCCEEEEEECCHHHHHHHHHHHHHcCCCCcEEEEEcCHHHHHHHHhhccCCCCE
Confidence            34568999999999999999999987 889999998 4566666542       589999999987322        33 


Q ss_pred             CEEEe
Q 039903          228 DAILI  232 (233)
Q Consensus       228 D~~~l  232 (233)
                      |++++
T Consensus       138 D~V~~  142 (242)
T 3r3h_A          138 DFIFI  142 (242)
T ss_dssp             EEEEE
T ss_pred             eEEEE
Confidence            88875

>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=97.96  E-value=4.2e-06  Score=68.26  Aligned_cols=67  Identities=13%  Similarity=0.096  Sum_probs=53.7

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcC-CCcEEEeec-hHHHhhccCC-------CCceEEecCcCCC---C------CCC
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLER---I------PKG  227 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~---~------P~~  227 (233)
                      ..+..+|||||||+|..+..+++..| +.+++.+|+ |+.++.|+++       ++|+++.+|..+.   +      +..
T Consensus        77 ~~~~~~VLeiG~G~G~~~~~la~~~~~~~~v~~iD~s~~~~~~a~~~~~~~g~~~~i~~~~gda~~~l~~l~~~~~~~~~  156 (247)
T 1sui_A           77 LINAKNTMEIGVYTGYSLLATALAIPEDGKILAMDINKENYELGLPVIKKAGVDHKIDFREGPALPVLDEMIKDEKNHGS  156 (247)
T ss_dssp             HTTCCEEEEECCGGGHHHHHHHHHSCTTCEEEEEESCCHHHHHHHHHHHHTTCGGGEEEEESCHHHHHHHHHHSGGGTTC
T ss_pred             hhCcCEEEEeCCCcCHHHHHHHHhCCCCCEEEEEECCHHHHHHHHHHHHHcCCCCCeEEEECCHHHHHHHHHhccCCCCC
Confidence            34568999999999999999999998 789999998 5677766542       5899999998762   2      233


Q ss_pred             -CEEEe
Q 039903          228 -DAILI  232 (233)
Q Consensus       228 -D~~~l  232 (233)
                       |++++
T Consensus       157 fD~V~~  162 (247)
T 1sui_A          157 YDFIFV  162 (247)
T ss_dssp             BSEEEE
T ss_pred             EEEEEE
Confidence             99875

>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=97.96  E-value=8.4e-06  Score=70.57  Aligned_cols=62  Identities=23%  Similarity=0.283  Sum_probs=49.7

Q ss_pred             cceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccC----C---CCceEEecCcCC-CCCCC-CEEE
Q 039903          169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSS----Y---SGVKHIGGIMLE-RIPKG-DAIL  231 (233)
Q Consensus       169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~----~---~ri~~~~gD~f~-~~P~~-D~~~  231 (233)
                      .++|||||||+|.++...+++. .-+++.+|..+.++.|++    +   ++|+++.+|+.+ ++|.. |+++
T Consensus        84 ~k~VLDvG~GtGiLs~~Aa~aG-A~~V~ave~s~~~~~a~~~~~~n~~~~~i~~i~~~~~~~~lpe~~Dviv  154 (376)
T 4hc4_A           84 GKTVLDVGAGTGILSIFCAQAG-ARRVYAVEASAIWQQAREVVRFNGLEDRVHVLPGPVETVELPEQVDAIV  154 (376)
T ss_dssp             TCEEEEETCTTSHHHHHHHHTT-CSEEEEEECSTTHHHHHHHHHHTTCTTTEEEEESCTTTCCCSSCEEEEE
T ss_pred             CCEEEEeCCCccHHHHHHHHhC-CCEEEEEeChHHHHHHHHHHHHcCCCceEEEEeeeeeeecCCccccEEE
Confidence            3789999999999988777653 347899998776666654    2   789999999998 78874 9885

>3m70_A Tellurite resistance protein TEHB homolog; structural genomics, PSI-2, protein ST initiative; 1.95A {Haemophilus influenzae}

Probab=97.96  E-value=1.3e-05  Score=66.21  Aligned_cols=73  Identities=16%  Similarity=0.136  Sum_probs=56.4

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-----CCceEEecCcCC-CCCCC-C
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-----SGVKHIGGIMLE-RIPKG-D  228 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-----~ri~~~~gD~f~-~~P~~-D  228 (233)
                      ..+++.++ .....+|||||||+|.++..++++  ..+++.+|. |..++.+++.     .+++++.+|+.+ +.+.. |
T Consensus       110 ~~~~~~~~-~~~~~~vLD~GcG~G~~~~~l~~~--g~~v~~vD~s~~~~~~a~~~~~~~~~~~~~~~~d~~~~~~~~~fD  186 (286)
T 3m70_A          110 GDVVDAAK-IISPCKVLDLGCGQGRNSLYLSLL--GYDVTSWDHNENSIAFLNETKEKENLNISTALYDINAANIQENYD  186 (286)
T ss_dssp             HHHHHHHH-HSCSCEEEEESCTTCHHHHHHHHT--TCEEEEEESCHHHHHHHHHHHHHTTCCEEEEECCGGGCCCCSCEE
T ss_pred             HHHHHHhh-ccCCCcEEEECCCCCHHHHHHHHC--CCeEEEEECCHHHHHHHHHHHHHcCCceEEEEeccccccccCCcc
Confidence            45555555 446689999999999999999998  568999998 4577766542     289999999998 44444 9


Q ss_pred             EEEe
Q 039903          229 AILI  232 (233)
Q Consensus       229 ~~~l  232 (233)
                      +|+.
T Consensus       187 ~i~~  190 (286)
T 3m70_A          187 FIVS  190 (286)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            9875

>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=97.96  E-value=5.4e-06  Score=70.73  Aligned_cols=66  Identities=17%  Similarity=0.179  Sum_probs=53.8

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccC----------CCCceEEecCcCC---CCCC-C-CEE
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSS----------YSGVKHIGGIMLE---RIPK-G-DAI  230 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~----------~~ri~~~~gD~f~---~~P~-~-D~~  230 (233)
                      .+..+|||||||+|..++.+++..|..+++.+|+ |.+++.|++          .+||+++.+|.++   ..+. . |+|
T Consensus       119 ~~~~~VLdIG~G~G~~a~~la~~~~~~~V~~VDis~~~l~~Ar~~~~~~~~gl~~~rv~~~~~D~~~~l~~~~~~~fDlI  198 (334)
T 1xj5_A          119 PNPKKVLVIGGGDGGVLREVARHASIEQIDMCEIDKMVVDVSKQFFPDVAIGYEDPRVNLVIGDGVAFLKNAAEGSYDAV  198 (334)
T ss_dssp             SCCCEEEEETCSSSHHHHHHTTCTTCCEEEEEESCHHHHHHHHHHCHHHHGGGGSTTEEEEESCHHHHHHTSCTTCEEEE
T ss_pred             CCCCEEEEECCCccHHHHHHHHcCCCCEEEEEECCHHHHHHHHHHHHhhccccCCCcEEEEECCHHHHHHhccCCCccEE
Confidence            4568999999999999999999888899999998 567776653          2689999999876   2343 3 988


Q ss_pred             Ee
Q 039903          231 LI  232 (233)
Q Consensus       231 ~l  232 (233)
                      ++
T Consensus       199 i~  200 (334)
T 1xj5_A          199 IV  200 (334)
T ss_dssp             EE
T ss_pred             EE
Confidence            75

>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=97.96  E-value=1e-05  Score=66.12  Aligned_cols=68  Identities=18%  Similarity=0.268  Sum_probs=53.9

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC--CCceEEecCcCC-CCCC
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY--SGVKHIGGIMLE-RIPK  226 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~--~ri~~~~gD~f~-~~P~  226 (233)
                      ..+++..+ .....+|+|||||+|.++..++++ +..+++.+|+. ..++.++++  ++++++.+|+.+ ++|.
T Consensus        21 ~~iv~~~~-~~~~~~VLDiG~G~G~lt~~L~~~-~~~~v~avEid~~~~~~~~~~~~~~v~~i~~D~~~~~~~~   92 (249)
T 3ftd_A           21 KKIAEELN-IEEGNTVVEVGGGTGNLTKVLLQH-PLKKLYVIELDREMVENLKSIGDERLEVINEDASKFPFCS   92 (249)
T ss_dssp             HHHHHHTT-CCTTCEEEEEESCHHHHHHHHTTS-CCSEEEEECCCHHHHHHHTTSCCTTEEEECSCTTTCCGGG
T ss_pred             HHHHHhcC-CCCcCEEEEEcCchHHHHHHHHHc-CCCeEEEEECCHHHHHHHHhccCCCeEEEEcchhhCChhH
Confidence            34556555 566689999999999999999987 56789999985 466666653  679999999998 6664

>3c3y_A Pfomt, O-methyltransferase; plant secondary metabolism; HET: SAH; 1.37A {Mesembryanthemum crystallinum}

Probab=97.96  E-value=9.4e-06  Score=65.66  Aligned_cols=67  Identities=12%  Similarity=0.105  Sum_probs=53.8

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcC-CCcEEEeec-hHHHhhccCC-------CCceEEecCcCCC---C------CCC
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLER---I------PKG  227 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~---~------P~~  227 (233)
                      ..+..+|||||||+|..+..++++.| +.+++.+|+ |+.++.++++       +||+++.+|.++.   +      +..
T Consensus        68 ~~~~~~VLeiG~G~G~~~~~la~~~~~~~~v~~iD~~~~~~~~a~~~~~~~g~~~~i~~~~gda~~~l~~l~~~~~~~~~  147 (237)
T 3c3y_A           68 LVNAKKTIEVGVFTGYSLLLTALSIPDDGKITAIDFDREAYEIGLPFIRKAGVEHKINFIESDAMLALDNLLQGQESEGS  147 (237)
T ss_dssp             HTTCCEEEEECCTTSHHHHHHHHHSCTTCEEEEEESCHHHHHHHHHHHHHTTCGGGEEEEESCHHHHHHHHHHSTTCTTC
T ss_pred             hhCCCEEEEeCCCCCHHHHHHHHhCCCCCEEEEEECCHHHHHHHHHHHHHcCCCCcEEEEEcCHHHHHHHHHhccCCCCC
Confidence            34568999999999999999999988 789999998 5677766542       5899999999862   2      233


Q ss_pred             -CEEEe
Q 039903          228 -DAILI  232 (233)
Q Consensus       228 -D~~~l  232 (233)
                       |++++
T Consensus       148 fD~I~~  153 (237)
T 3c3y_A          148 YDFGFV  153 (237)
T ss_dssp             EEEEEE
T ss_pred             cCEEEE
Confidence             88875

>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=97.96  E-value=7.6e-06  Score=66.99  Aligned_cols=64  Identities=9%  Similarity=-0.003  Sum_probs=50.1

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccC-----------------------CCCceEEecCcCC
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSS-----------------------YSGVKHIGGIMLE  222 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~-----------------------~~ri~~~~gD~f~  222 (233)
                      ....+|||||||+|..+..|+++  ..+++.+|+. ..++.|++                       ..+|+++.+|+++
T Consensus        67 ~~~~~vLD~GCG~G~~~~~La~~--G~~V~gvD~S~~~i~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~D~~~  144 (252)
T 2gb4_A           67 QSGLRVFFPLCGKAIEMKWFADR--GHTVVGVEISEIGIREFFAEQNLSYTEEPLAEIAGAKVFKSSSGSISLYCCSIFD  144 (252)
T ss_dssp             CCSCEEEETTCTTCTHHHHHHHT--TCEEEEECSCHHHHHHHHHHTTCCEEEEECTTSTTCEEEEETTSSEEEEESCTTT
T ss_pred             CCCCeEEEeCCCCcHHHHHHHHC--CCeEEEEECCHHHHHHHHHhcccccccccccccccccccccCCCceEEEECcccc
Confidence            34579999999999999999987  5689999985 56766532                       1579999999998


Q ss_pred             -CCC--CC-CEEEe
Q 039903          223 -RIP--KG-DAILI  232 (233)
Q Consensus       223 -~~P--~~-D~~~l  232 (233)
                       +.+  .. |+|+.
T Consensus       145 l~~~~~~~FD~V~~  158 (252)
T 2gb4_A          145 LPRANIGKFDRIWD  158 (252)
T ss_dssp             GGGGCCCCEEEEEE
T ss_pred             CCcccCCCEEEEEE
Confidence             543  23 98874

>3dr5_A Putative O-methyltransferase; Q8NRD3, CGL1119, PF01596, CGR117, NESG, structural genomics, PSI-2, protein structure initiative; 2.25A {Corynebacterium glutamicum}

Probab=97.95  E-value=7.3e-06  Score=65.73  Aligned_cols=63  Identities=11%  Similarity=0.099  Sum_probs=50.7

Q ss_pred             ceEEEecCCccHHHHHHHHHcC-CCcEEEeec-hHHHhhccCC--------CCceEEecCcCCC---CCC-C-CEEEe
Q 039903          170 KQLVDVGGGLGVNVNIIISNYL-HIKGVNFDL-SHVIQDSSSY--------SGVKHIGGIMLER---IPK-G-DAILI  232 (233)
Q Consensus       170 ~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~v~~~a~~~--------~ri~~~~gD~f~~---~P~-~-D~~~l  232 (233)
                      .+|+|||||+|..+..++++.| +.+++.+|+ |+.++.|+++        +||+++.+|..+.   ++. . |++++
T Consensus        58 ~~vLdiG~G~G~~~~~la~~~~~~~~v~~vD~~~~~~~~a~~~~~~~g~~~~~i~~~~gda~~~l~~~~~~~fD~V~~  135 (221)
T 3dr5_A           58 TGAIAITPAAGLVGLYILNGLADNTTLTCIDPESEHQRQAKALFREAGYSPSRVRFLLSRPLDVMSRLANDSYQLVFG  135 (221)
T ss_dssp             CEEEEESTTHHHHHHHHHHHSCTTSEEEEECSCHHHHHHHHHHHHHTTCCGGGEEEECSCHHHHGGGSCTTCEEEEEE
T ss_pred             CCEEEEcCCchHHHHHHHHhCCCCCEEEEEECCHHHHHHHHHHHHHcCCCcCcEEEEEcCHHHHHHHhcCCCcCeEEE
Confidence            3999999999999999999986 889999998 4566666542        4899999998872   323 3 99876

>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=97.95  E-value=6.6e-06  Score=66.25  Aligned_cols=63  Identities=17%  Similarity=0.193  Sum_probs=50.9

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCCCCCC--CCEEEe
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLERIPK--GDAILI  232 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~~P~--~D~~~l  232 (233)
                      ...+|+|||||+|.++..+++..  .+++.+|+ |..++.++++       ++|+++.+|+.+..+.  .|+|++
T Consensus        78 ~~~~vLD~gcG~G~~~~~la~~~--~~v~~vD~s~~~~~~a~~~~~~~~~~~~~~~~~~d~~~~~~~~~~D~v~~  150 (241)
T 3gdh_A           78 KCDVVVDAFCGVGGNTIQFALTG--MRVIAIDIDPVKIALARNNAEVYGIADKIEFICGDFLLLASFLKADVVFL  150 (241)
T ss_dssp             CCSEEEETTCTTSHHHHHHHHTT--CEEEEEESCHHHHHHHHHHHHHTTCGGGEEEEESCHHHHGGGCCCSEEEE
T ss_pred             CCCEEEECccccCHHHHHHHHcC--CEEEEEECCHHHHHHHHHHHHHcCCCcCeEEEECChHHhcccCCCCEEEE
Confidence            45799999999999999999974  78999998 5577776643       4899999999983343  398875

>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=97.95  E-value=6.7e-06  Score=69.23  Aligned_cols=66  Identities=21%  Similarity=0.204  Sum_probs=53.4

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccC----------CCCceEEecCcCCC--CCC-C-CEEE
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSS----------YSGVKHIGGIMLER--IPK-G-DAIL  231 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~----------~~ri~~~~gD~f~~--~P~-~-D~~~  231 (233)
                      .+..+|||||||+|.++..++++.|..+++.+|+ |.+++.+++          .+||+++.+|.++.  .+. . |+|+
T Consensus        94 ~~~~~VLdiG~G~G~~~~~l~~~~~~~~v~~vDid~~~i~~ar~~~~~~~~~~~~~rv~v~~~Da~~~l~~~~~~fD~Ii  173 (304)
T 2o07_A           94 PNPRKVLIIGGGDGGVLREVVKHPSVESVVQCEIDEDVIQVSKKFLPGMAIGYSSSKLTLHVGDGFEFMKQNQDAFDVII  173 (304)
T ss_dssp             SSCCEEEEEECTTSHHHHHHTTCTTCCEEEEEESCHHHHHHHHHHCHHHHGGGGCTTEEEEESCHHHHHHTCSSCEEEEE
T ss_pred             CCCCEEEEECCCchHHHHHHHHcCCCCEEEEEECCHHHHHHHHHHhHHhhcccCCCcEEEEECcHHHHHhhCCCCceEEE
Confidence            4568999999999999999999888899999998 567776653          36899999998762  222 3 8887


Q ss_pred             e
Q 039903          232 I  232 (233)
Q Consensus       232 l  232 (233)
                      +
T Consensus       174 ~  174 (304)
T 2o07_A          174 T  174 (304)
T ss_dssp             E
T ss_pred             E
Confidence            4

>1vbf_A 231AA long hypothetical protein-L-isoaspartate O- methyltransferase; trimeric coiled coil assembly; 2.80A {Sulfolobus tokodaii} SCOP: c.66.1.7

Probab=97.94  E-value=1.9e-05  Score=62.99  Aligned_cols=72  Identities=17%  Similarity=0.266  Sum_probs=55.5

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC----CCceEEecCcCCCCCC--C-CE
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY----SGVKHIGGIMLERIPK--G-DA  229 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~----~ri~~~~gD~f~~~P~--~-D~  229 (233)
                      .+++.+. .....+|+|||||+|.++..+++..  .+++.+|. |..++.+++.    .+++++.+|+.+..|.  . |+
T Consensus        61 ~~~~~~~-~~~~~~vLdiG~G~G~~~~~l~~~~--~~v~~vD~~~~~~~~a~~~~~~~~~v~~~~~d~~~~~~~~~~fD~  137 (231)
T 1vbf_A           61 FMLDELD-LHKGQKVLEIGTGIGYYTALIAEIV--DKVVSVEINEKMYNYASKLLSYYNNIKLILGDGTLGYEEEKPYDR  137 (231)
T ss_dssp             HHHHHTT-CCTTCEEEEECCTTSHHHHHHHHHS--SEEEEEESCHHHHHHHHHHHTTCSSEEEEESCGGGCCGGGCCEEE
T ss_pred             HHHHhcC-CCCCCEEEEEcCCCCHHHHHHHHHc--CEEEEEeCCHHHHHHHHHHHhhcCCeEEEECCcccccccCCCccE
Confidence            4445554 5666899999999999999999986  68999998 5577766653    3899999999885442  2 88


Q ss_pred             EEe
Q 039903          230 ILI  232 (233)
Q Consensus       230 ~~l  232 (233)
                      ++.
T Consensus       138 v~~  140 (231)
T 1vbf_A          138 VVV  140 (231)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            875

>2h1r_A Dimethyladenosine transferase, putative; SGC toronto dimethyladenosine transferase, structural genomics, structural genomics consortium; 1.89A {Plasmodium falciparum}

Probab=97.94  E-value=7.7e-06  Score=68.65  Aligned_cols=73  Identities=21%  Similarity=0.342  Sum_probs=52.0

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccC------CCCceEEecCcCC-CCCCCC
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSS------YSGVKHIGGIMLE-RIPKGD  228 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~------~~ri~~~~gD~f~-~~P~~D  228 (233)
                      ..+++.++ .....+|+|||||+|.++..++++  ..+++.+|+ +..++.+++      .++++++.+|+.+ +.+..|
T Consensus        32 ~~i~~~~~-~~~~~~VLDiG~G~G~lt~~La~~--~~~v~~vDi~~~~~~~a~~~~~~~~~~~v~~~~~D~~~~~~~~~D  108 (299)
T 2h1r_A           32 DKIIYAAK-IKSSDIVLEIGCGTGNLTVKLLPL--AKKVITIDIDSRMISEVKKRCLYEGYNNLEVYEGDAIKTVFPKFD  108 (299)
T ss_dssp             HHHHHHHC-CCTTCEEEEECCTTSTTHHHHTTT--SSEEEEECSCHHHHHHHHHHHHHTTCCCEEC----CCSSCCCCCS
T ss_pred             HHHHHhcC-CCCcCEEEEEcCcCcHHHHHHHhc--CCEEEEEECCHHHHHHHHHHHHHcCCCceEEEECchhhCCcccCC
Confidence            34555555 566689999999999999999987  457999998 456666553      2689999999998 565558


Q ss_pred             EEEe
Q 039903          229 AILI  232 (233)
Q Consensus       229 ~~~l  232 (233)
                      +++.
T Consensus       109 ~Vv~  112 (299)
T 2h1r_A          109 VCTA  112 (299)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            8764

>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=97.93  E-value=8e-06  Score=70.63  Aligned_cols=67  Identities=10%  Similarity=-0.022  Sum_probs=55.8

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCC-CCCC-C-CEEEe
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLE-RIPK-G-DAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~-~~P~-~-D~~~l  232 (233)
                      +.+..+|+|+|||+|.+++.+++..+..+++.+|+ |.+++.|+++       ++|+++.+|+.+ +.|. . |+++.
T Consensus       215 ~~~~~~vLD~gCGsG~~~i~~a~~~~~~~v~g~Dis~~~l~~A~~n~~~~gl~~~i~~~~~D~~~~~~~~~~fD~Ii~  292 (373)
T 3tm4_A          215 ELDGGSVLDPMCGSGTILIELALRRYSGEIIGIEKYRKHLIGAEMNALAAGVLDKIKFIQGDATQLSQYVDSVDFAIS  292 (373)
T ss_dssp             TCCSCCEEETTCTTCHHHHHHHHTTCCSCEEEEESCHHHHHHHHHHHHHTTCGGGCEEEECCGGGGGGTCSCEEEEEE
T ss_pred             cCCCCEEEEccCcCcHHHHHHHHhCCCCeEEEEeCCHHHHHHHHHHHHHcCCCCceEEEECChhhCCcccCCcCEEEE
Confidence            46668999999999999999999988778999998 5577777653       589999999998 6654 3 88875

>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=97.93  E-value=4.9e-06  Score=68.10  Aligned_cols=64  Identities=17%  Similarity=0.224  Sum_probs=50.6

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC----C-CceEEecCcCCCCCC--CCEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY----S-GVKHIGGIMLERIPK--GDAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~----~-ri~~~~gD~f~~~P~--~D~~~l  232 (233)
                      .+..+|+|||||+|.++..+++..+  +++.+|+ |..++.++++    . .++++.+|+.+.+|.  .|+++.
T Consensus       119 ~~~~~VLDiGcG~G~l~~~la~~g~--~v~gvDi~~~~v~~a~~n~~~~~~~v~~~~~d~~~~~~~~~fD~Vv~  190 (254)
T 2nxc_A          119 RPGDKVLDLGTGSGVLAIAAEKLGG--KALGVDIDPMVLPQAEANAKRNGVRPRFLEGSLEAALPFGPFDLLVA  190 (254)
T ss_dssp             CTTCEEEEETCTTSHHHHHHHHTTC--EEEEEESCGGGHHHHHHHHHHTTCCCEEEESCHHHHGGGCCEEEEEE
T ss_pred             CCCCEEEEecCCCcHHHHHHHHhCC--eEEEEECCHHHHHHHHHHHHHcCCcEEEEECChhhcCcCCCCCEEEE
Confidence            4568999999999999999999776  8999998 5677776653    1 289999999886654  288874

>2fpo_A Methylase YHHF; structural genomics, putative methyltransferase, PSI, protei structure initiative; HET: MSE; 2.05A {Escherichia coli} SCOP: c.66.1.46

Probab=97.93  E-value=8.6e-06  Score=64.17  Aligned_cols=64  Identities=13%  Similarity=0.093  Sum_probs=49.7

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCC--CCCC-C-CEEEe
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLE--RIPK-G-DAILI  232 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~--~~P~-~-D~~~l  232 (233)
                      ...+|+|+|||+|.++..++++.. .+++.+|+ |..++.++++      ++|+++.+|+.+  +.+. . |++++
T Consensus        54 ~~~~vLDlgcG~G~~~~~l~~~~~-~~V~~vD~s~~~l~~a~~~~~~~~~~~v~~~~~D~~~~~~~~~~~fD~V~~  128 (202)
T 2fpo_A           54 VDAQCLDCFAGSGALGLEALSRYA-AGATLIEMDRAVSQQLIKNLATLKAGNARVVNSNAMSFLAQKGTPHNIVFV  128 (202)
T ss_dssp             TTCEEEETTCTTCHHHHHHHHTTC-SEEEEECSCHHHHHHHHHHHHHTTCCSEEEECSCHHHHHSSCCCCEEEEEE
T ss_pred             CCCeEEEeCCCcCHHHHHHHhcCC-CEEEEEECCHHHHHHHHHHHHHcCCCcEEEEECCHHHHHhhcCCCCCEEEE
Confidence            347899999999999999888754 37999998 4577777653      589999999987  3333 3 88875

>1o9g_A RRNA methyltransferase; antibiotic resistance, Se-MAD; 1.5A {Streptomyces viridochromogenes} SCOP: c.66.1.29 PDB: 1o9h_A

Probab=97.93  E-value=1.1e-05  Score=65.57  Aligned_cols=42  Identities=12%  Similarity=-0.016  Sum_probs=36.6

Q ss_pred             CcceEEEecCCccHHHHHHHHH--cCCCcEEEeec-hHHHhhccC
Q 039903          168 QIKQLVDVGGGLGVNVNIIISN--YLHIKGVNFDL-SHVIQDSSS  209 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~--~P~l~~~v~Dl-p~v~~~a~~  209 (233)
                      ...+|+|+|||+|.++..+++.  +|..+++.+|+ |..++.|+.
T Consensus        51 ~~~~vLD~gcGsG~~~~~la~~~~~~~~~v~gvDis~~~l~~A~~   95 (250)
T 1o9g_A           51 GPVTLWDPCCGSGYLLTVLGLLHRRSLRQVIASDVDPAPLELAAK   95 (250)
T ss_dssp             SCEEEEETTCTTSHHHHHHHHHTGGGEEEEEEEESCHHHHHHHHH
T ss_pred             CCCeEEECCCCCCHHHHHHHHHhccCCCeEEEEECCHHHHHHHHH
Confidence            4579999999999999999998  88889999999 567777764

>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=97.93  E-value=1.4e-05  Score=66.09  Aligned_cols=65  Identities=14%  Similarity=0.103  Sum_probs=50.4

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC---CCceEEecCcCC-CCCC
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY---SGVKHIGGIMLE-RIPK  226 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~---~ri~~~~gD~f~-~~P~  226 (233)
                      .+++..+ .... +|+|||||+|.++..++++.  .+++.+|+. +.++.+++.   ++++++.+|+++ ++|.
T Consensus        38 ~Iv~~~~-~~~~-~VLEIG~G~G~lt~~L~~~~--~~V~avEid~~~~~~l~~~~~~~~v~vi~~D~l~~~~~~  107 (271)
T 3fut_A           38 RIVEAAR-PFTG-PVFEVGPGLGALTRALLEAG--AEVTAIEKDLRLRPVLEETLSGLPVRLVFQDALLYPWEE  107 (271)
T ss_dssp             HHHHHHC-CCCS-CEEEECCTTSHHHHHHHHTT--CCEEEEESCGGGHHHHHHHTTTSSEEEEESCGGGSCGGG
T ss_pred             HHHHhcC-CCCC-eEEEEeCchHHHHHHHHHcC--CEEEEEECCHHHHHHHHHhcCCCCEEEEECChhhCChhh
Confidence            4555555 5555 99999999999999999985  578999984 466665542   689999999998 6653

>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=97.92  E-value=8.2e-06  Score=68.37  Aligned_cols=65  Identities=18%  Similarity=0.218  Sum_probs=52.3

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccC----------CCCceEEecCcCCCC--C-CC-CEEEe
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSS----------YSGVKHIGGIMLERI--P-KG-DAILI  232 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~----------~~ri~~~~gD~f~~~--P-~~-D~~~l  232 (233)
                      +..+|+|||||+|..+..+++..|..+++++|+ |.+++.+++          .+||+++.+|.++.+  + .. |+|++
T Consensus        90 ~~~~VLdiG~G~G~~~~~l~~~~~~~~v~~vDid~~~~~~a~~~~~~~~~~~~~~~v~~~~~D~~~~l~~~~~~fD~Ii~  169 (296)
T 1inl_A           90 NPKKVLIIGGGDGGTLREVLKHDSVEKAILCEVDGLVIEAARKYLKQTSCGFDDPRAEIVIANGAEYVRKFKNEFDVIII  169 (296)
T ss_dssp             SCCEEEEEECTTCHHHHHHTTSTTCSEEEEEESCHHHHHHHHHHCHHHHGGGGCTTEEEEESCHHHHGGGCSSCEEEEEE
T ss_pred             CCCEEEEEcCCcCHHHHHHHhcCCCCEEEEEECCHHHHHHHHHHhHhhccccCCCceEEEECcHHHHHhhCCCCceEEEE
Confidence            457999999999999999999888899999998 567776643          268999999987632  2 33 98874

>3evz_A Methyltransferase; NYSGXRC, NEW YORK SGX research CE structural genomics, protein structure initiative, pyrococc furiosus, PSI-2; 2.20A {Pyrococcus furiosus}

Probab=97.92  E-value=2e-05  Score=62.93  Aligned_cols=66  Identities=12%  Similarity=0.193  Sum_probs=53.2

Q ss_pred             ccCcceEEEecCC-ccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-----CCceEEecCc--CCCCCCC--CEEEe
Q 039903          166 FEQIKQLVDVGGG-LGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-----SGVKHIGGIM--LERIPKG--DAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG-~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-----~ri~~~~gD~--f~~~P~~--D~~~l  232 (233)
                      .++..+|+||||| +|.++..+++.. ..+++.+|+ |..++.++++     .+++++.+|+  +.++|.+  |+++.
T Consensus        53 ~~~~~~vLDlG~G~~G~~~~~la~~~-~~~v~~vD~s~~~~~~a~~~~~~~~~~v~~~~~d~~~~~~~~~~~fD~I~~  129 (230)
T 3evz_A           53 LRGGEVALEIGTGHTAMMALMAEKFF-NCKVTATEVDEEFFEYARRNIERNNSNVRLVKSNGGIIKGVVEGTFDVIFS  129 (230)
T ss_dssp             CCSSCEEEEECCTTTCHHHHHHHHHH-CCEEEEEECCHHHHHHHHHHHHHTTCCCEEEECSSCSSTTTCCSCEEEEEE
T ss_pred             cCCCCEEEEcCCCHHHHHHHHHHHhc-CCEEEEEECCHHHHHHHHHHHHHhCCCcEEEeCCchhhhhcccCceeEEEE
Confidence            4566899999999 999999999987 788999998 5677777653     3799999996  4566643  98874

>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=97.91  E-value=7.2e-06  Score=66.09  Aligned_cols=64  Identities=14%  Similarity=0.157  Sum_probs=51.3

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCC-CCCCC--CEEEe
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLE-RIPKG--DAILI  232 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~-~~P~~--D~~~l  232 (233)
                      ...+|||||||+|.++..++++. ..+++.+|+ |..++.+++.      .+++++.+|+.+ +.+.+  |+|++
T Consensus        79 ~~~~vLDiGcG~G~~~~~l~~~~-~~~v~~vD~s~~~~~~a~~~~~~~~~~~~~~~~~d~~~~~~~~~~fD~v~~  152 (241)
T 2ex4_A           79 GTSCALDCGAGIGRITKRLLLPL-FREVDMVDITEDFLVQAKTYLGEEGKRVRNYFCCGLQDFTPEPDSYDVIWI  152 (241)
T ss_dssp             CCSEEEEETCTTTHHHHHTTTTT-CSEEEEEESCHHHHHHHHHHTGGGGGGEEEEEECCGGGCCCCSSCEEEEEE
T ss_pred             CCCEEEEECCCCCHHHHHHHHhc-CCEEEEEeCCHHHHHHHHHHhhhcCCceEEEEEcChhhcCCCCCCEEEEEE
Confidence            46899999999999999999987 568999998 5677766542      368999999887 55553  98875

>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=97.91  E-value=6.2e-06  Score=69.36  Aligned_cols=66  Identities=18%  Similarity=0.199  Sum_probs=53.3

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccC----------CCCceEEecCcCC-CC--CC-C-CEE
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSS----------YSGVKHIGGIMLE-RI--PK-G-DAI  230 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~----------~~ri~~~~gD~f~-~~--P~-~-D~~  230 (233)
                      ++..+|+|||||.|.++..+++..|..+++++|+ |.+++.+++          .+|++++.+|.++ ..  +. . |+|
T Consensus        94 ~~~~~VLdiG~G~G~~~~~l~~~~~~~~v~~vDid~~~i~~a~~~~~~~~~~~~~~~v~~~~~D~~~~~~~~~~~~fDvI  173 (304)
T 3bwc_A           94 PKPERVLIIGGGDGGVLREVLRHGTVEHCDLVDIDGEVMEQSKQHFPQISRSLADPRATVRVGDGLAFVRQTPDNTYDVV  173 (304)
T ss_dssp             SSCCEEEEEECTTSHHHHHHHTCTTCCEEEEEESCHHHHHHHHHHCHHHHGGGGCTTEEEEESCHHHHHHSSCTTCEEEE
T ss_pred             CCCCeEEEEcCCCCHHHHHHHhCCCCCEEEEEECCHHHHHHHHHHhHHhhcccCCCcEEEEECcHHHHHHhccCCceeEE
Confidence            4568999999999999999999878889999999 557776653          2689999999987 21  33 3 988


Q ss_pred             Ee
Q 039903          231 LI  232 (233)
Q Consensus       231 ~l  232 (233)
                      +.
T Consensus       174 i~  175 (304)
T 3bwc_A          174 II  175 (304)
T ss_dssp             EE
T ss_pred             EE
Confidence            74

>2pt6_A Spermidine synthase; transferase, structural genomics consor SGC,dcadoMet complex; HET: S4M 1PG; 2.00A {Plasmodium falciparum} PDB: 2pss_A* 2pt9_A*

Probab=97.90  E-value=6.7e-06  Score=69.74  Aligned_cols=66  Identities=18%  Similarity=0.111  Sum_probs=53.0

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccC----------CCCceEEecCcCCCC---CCC-CEEE
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSS----------YSGVKHIGGIMLERI---PKG-DAIL  231 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~----------~~ri~~~~gD~f~~~---P~~-D~~~  231 (233)
                      .+..+|+|||||+|..++.+++..|..+++.+|+ |.+++.+++          .+|++++.+|.++.+   +.. |+|+
T Consensus       115 ~~~~~VLdiG~G~G~~~~~l~~~~~~~~v~~vDis~~~l~~ar~~~~~~~~~~~~~~v~~~~~D~~~~l~~~~~~fDvIi  194 (321)
T 2pt6_A          115 KEPKNVLVVGGGDGGIIRELCKYKSVENIDICEIDETVIEVSKIYFKNISCGYEDKRVNVFIEDASKFLENVTNTYDVII  194 (321)
T ss_dssp             SSCCEEEEEECTTCHHHHHHTTCTTCCEEEEEESCHHHHHHHHHHCTTTSGGGGSTTEEEEESCHHHHHHHCCSCEEEEE
T ss_pred             CCCCEEEEEcCCccHHHHHHHHcCCCCEEEEEECCHHHHHHHHHHHHhhccccCCCcEEEEEccHHHHHhhcCCCceEEE
Confidence            3458999999999999999999878899999998 567776653          258999999988732   333 8887


Q ss_pred             e
Q 039903          232 I  232 (233)
Q Consensus       232 l  232 (233)
                      .
T Consensus       195 ~  195 (321)
T 2pt6_A          195 V  195 (321)
T ss_dssp             E
T ss_pred             E
Confidence            4

>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=97.90  E-value=1.2e-05  Score=63.53  Aligned_cols=72  Identities=15%  Similarity=0.094  Sum_probs=55.0

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCCCCceEEecCcCCC-----CCCC--CE
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSYSGVKHIGGIMLER-----IPKG--DA  229 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~~ri~~~~gD~f~~-----~P~~--D~  229 (233)
                      .+++.+. .....+|||||||+|.++..+++.  ..+++.+|+ |..++.+++..+++++.+|+.+.     .+..  |+
T Consensus        43 ~~~~~~~-~~~~~~vLdiG~G~G~~~~~l~~~--~~~v~~vD~s~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~fD~  119 (227)
T 3e8s_A           43 AILLAIL-GRQPERVLDLGCGEGWLLRALADR--GIEAVGVDGDRTLVDAARAAGAGEVHLASYAQLAEAKVPVGKDYDL  119 (227)
T ss_dssp             HHHHHHH-HTCCSEEEEETCTTCHHHHHHHTT--TCEEEEEESCHHHHHHHHHTCSSCEEECCHHHHHTTCSCCCCCEEE
T ss_pred             HHHHHhh-cCCCCEEEEeCCCCCHHHHHHHHC--CCEEEEEcCCHHHHHHHHHhcccccchhhHHhhcccccccCCCccE
Confidence            3445544 345589999999999999999998  568999998 56888888778889999888752     2222  88


Q ss_pred             EEe
Q 039903          230 ILI  232 (233)
Q Consensus       230 ~~l  232 (233)
                      |+.
T Consensus       120 v~~  122 (227)
T 3e8s_A          120 ICA  122 (227)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            764

>3htx_A HEN1; HEN1, small RNA methyltransferase, protein-RNA complex; HET: SAH; 3.10A {Arabidopsis thaliana}

Probab=97.90  E-value=1.7e-05  Score=74.62  Aligned_cols=66  Identities=17%  Similarity=0.176  Sum_probs=53.9

Q ss_pred             cCcceEEEecCCccHHHHHHHHHc-CCCcEEEeec-hHHHhhccC------------CCCceEEecCcCC-CCCC-C-CE
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNY-LHIKGVNFDL-SHVIQDSSS------------YSGVKHIGGIMLE-RIPK-G-DA  229 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~v~~~a~~------------~~ri~~~~gD~f~-~~P~-~-D~  229 (233)
                      .+..+|||||||+|.++..+++.. |..+++.+|+ +..++.|++            .++|+++.+|+.+ +.+. . |+
T Consensus       720 ~~g~rVLDVGCGTG~lai~LAr~g~p~a~VtGVDIS~emLe~AReRLa~~lnAkr~gl~nVefiqGDa~dLp~~d~sFDl  799 (950)
T 3htx_A          720 SSASTLVDFGCGSGSLLDSLLDYPTSLQTIIGVDISPKGLARAAKMLHVKLNKEACNVKSATLYDGSILEFDSRLHDVDI  799 (950)
T ss_dssp             SCCSEEEEETCSSSHHHHHHTSSCCCCCEEEEEESCHHHHHHHHHHHHHHTTTTCSSCSEEEEEESCTTSCCTTSCSCCE
T ss_pred             cCCCEEEEECCCCCHHHHHHHHhCCCCCeEEEEECCHHHHHHHHHHhhhccchhhcCCCceEEEECchHhCCcccCCeeE
Confidence            456899999999999999999998 5679999998 457777644            2579999999998 5554 3 99


Q ss_pred             EEe
Q 039903          230 ILI  232 (233)
Q Consensus       230 ~~l  232 (233)
                      |+.
T Consensus       800 VV~  802 (950)
T 3htx_A          800 GTC  802 (950)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            874

>2kw5_A SLR1183 protein; structural genomics, northeast structural genomics consortium (NESG), PSI-2, protein structure initiative, unknown function; NMR {Synechocystis} PDB: 3mer_A

Probab=97.89  E-value=1.5e-05  Score=62.20  Aligned_cols=60  Identities=13%  Similarity=0.173  Sum_probs=49.3

Q ss_pred             eEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-----CCceEEecCcCC-CCCCC--CEEEe
Q 039903          171 QLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-----SGVKHIGGIMLE-RIPKG--DAILI  232 (233)
Q Consensus       171 ~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-----~ri~~~~gD~f~-~~P~~--D~~~l  232 (233)
                      +|+|||||+|.++..+++.  ..+++.+|. +..++.+++.     .+++++.+|+.+ ++|.+  |+++.
T Consensus        32 ~vLdiGcG~G~~~~~l~~~--~~~v~~vD~s~~~~~~a~~~~~~~~~~~~~~~~d~~~~~~~~~~fD~v~~  100 (202)
T 2kw5_A           32 KILCLAEGEGRNACFLASL--GYEVTAVDQSSVGLAKAKQLAQEKGVKITTVQSNLADFDIVADAWEGIVS  100 (202)
T ss_dssp             EEEECCCSCTHHHHHHHTT--TCEEEEECSSHHHHHHHHHHHHHHTCCEEEECCBTTTBSCCTTTCSEEEE
T ss_pred             CEEEECCCCCHhHHHHHhC--CCeEEEEECCHHHHHHHHHHHHhcCCceEEEEcChhhcCCCcCCccEEEE
Confidence            9999999999999999987  568999998 4577776653     389999999998 66643  98874

>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=97.88  E-value=3.6e-05  Score=67.77  Aligned_cols=74  Identities=14%  Similarity=0.221  Sum_probs=54.4

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhc-------cC--------CCCceEEecCcC
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDS-------SS--------YSGVKHIGGIML  221 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a-------~~--------~~ri~~~~gD~f  221 (233)
                      .+++.+. .....+|||||||+|.++..+++.+|..+++.+|+.. .++.|       ++        .++|+++.+|-+
T Consensus       233 ~ml~~l~-l~~g~~VLDLGCGsG~la~~LA~~~g~~~V~GVDis~~~l~~A~~Ml~~ar~~~~~~Gl~~~nV~~i~gD~~  311 (433)
T 1u2z_A          233 DVYQQCQ-LKKGDTFMDLGSGVGNCVVQAALECGCALSFGCEIMDDASDLTILQYEELKKRCKLYGMRLNNVEFSLKKSF  311 (433)
T ss_dssp             HHHHHTT-CCTTCEEEEESCTTSHHHHHHHHHHCCSEEEEEECCHHHHHHHHHHHHHHHHHHHHTTBCCCCEEEEESSCS
T ss_pred             HHHHhcC-CCCCCEEEEeCCCcCHHHHHHHHHCCCCEEEEEeCCHHHHHHHHHhHHHHHHHHHHcCCCCCceEEEEcCcc
Confidence            3445554 5667899999999999999999999988999999854 55555       32        258999987544


Q ss_pred             -CC--C----CCCCEEEe
Q 039903          222 -ER--I----PKGDAILI  232 (233)
Q Consensus       222 -~~--~----P~~D~~~l  232 (233)
                       .+  +    ...|+|++
T Consensus       312 ~~~~~~~~~~~~FDvIvv  329 (433)
T 1u2z_A          312 VDNNRVAELIPQCDVILV  329 (433)
T ss_dssp             TTCHHHHHHGGGCSEEEE
T ss_pred             ccccccccccCCCCEEEE
Confidence             32  2    22499875

>2p8j_A S-adenosylmethionine-dependent methyltransferase; NP_349143.1; HET: PGE GOL; 2.00A {Clostridium acetobutylicum}

Probab=97.88  E-value=1.7e-05  Score=62.15  Aligned_cols=66  Identities=11%  Similarity=0.105  Sum_probs=50.4

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-----CCceEEecCcCC-CCCCC--CEEEe
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-----SGVKHIGGIMLE-RIPKG--DAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-----~ri~~~~gD~f~-~~P~~--D~~~l  232 (233)
                      .....+|+|||||+|.++..++.+ +..+++.+|. +..++.+++.     .+++++.+|+.+ ++|.+  |+++.
T Consensus        21 ~~~~~~vLDiGcG~G~~~~~~~~~-~~~~v~~vD~s~~~~~~a~~~~~~~~~~~~~~~~d~~~~~~~~~~fD~v~~   95 (209)
T 2p8j_A           21 SNLDKTVLDCGAGGDLPPLSIFVE-DGYKTYGIEISDLQLKKAENFSRENNFKLNISKGDIRKLPFKDESMSFVYS   95 (209)
T ss_dssp             SSSCSEEEEESCCSSSCTHHHHHH-TTCEEEEEECCHHHHHHHHHHHHHHTCCCCEEECCTTSCCSCTTCEEEEEE
T ss_pred             cCCCCEEEEECCCCCHHHHHHHHh-CCCEEEEEECCHHHHHHHHHHHHhcCCceEEEECchhhCCCCCCceeEEEE
Confidence            345579999999999985555543 6779999998 4577766542     689999999998 67653  98874

>1ws6_A Methyltransferase; structural genomics, riken structural genomics/proteomics initiative, RSGI; 2.50A {Thermus thermophilus} SCOP: c.66.1.46

Probab=97.88  E-value=4.7e-06  Score=63.12  Aligned_cols=63  Identities=11%  Similarity=0.047  Sum_probs=50.4

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC----C-CceEEecCcCCCCC-------CCCEEEe
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY----S-GVKHIGGIMLERIP-------KGDAILI  232 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~----~-ri~~~~gD~f~~~P-------~~D~~~l  232 (233)
                      ...+|+|+|||+|.++..++++.++  ++.+|+ |..++.++++    . +++++.+|+.+..|       ..|+++.
T Consensus        41 ~~~~vLD~GcG~G~~~~~l~~~~~~--v~~vD~~~~~~~~a~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~D~i~~  116 (171)
T 1ws6_A           41 RRGRFLDPFAGSGAVGLEAASEGWE--AVLVEKDPEAVRLLKENVRRTGLGARVVALPVEVFLPEAKAQGERFTVAFM  116 (171)
T ss_dssp             TCCEEEEETCSSCHHHHHHHHTTCE--EEEECCCHHHHHHHHHHHHHHTCCCEEECSCHHHHHHHHHHTTCCEEEEEE
T ss_pred             CCCeEEEeCCCcCHHHHHHHHCCCe--EEEEeCCHHHHHHHHHHHHHcCCceEEEeccHHHHHHhhhccCCceEEEEE
Confidence            5578999999999999999999877  999998 5677777653    2 89999999987322       2388764

>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=97.88  E-value=2.9e-05  Score=67.67  Aligned_cols=71  Identities=11%  Similarity=0.045  Sum_probs=54.9

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHc-CCCcEEEeech-HHHhhccCCCCceEEecCcCCCCCC-C-CEEEe
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNY-LHIKGVNFDLS-HVIQDSSSYSGVKHIGGIMLERIPK-G-DAILI  232 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~-P~l~~~v~Dlp-~v~~~a~~~~ri~~~~gD~f~~~P~-~-D~~~l  232 (233)
                      .+++.+. ..+..+|+|+|||+|.++..+++++ +..+++.+|+. ..++.|   ++++++.+|+++..+. . |+|+.
T Consensus        30 ~~~~~~~-~~~~~~vLD~gcGtG~~~~~~~~~~~~~~~i~gvDi~~~~~~~a---~~~~~~~~D~~~~~~~~~fD~Ii~  104 (421)
T 2ih2_A           30 FMVSLAE-APRGGRVLEPACAHGPFLRAFREAHGTAYRFVGVEIDPKALDLP---PWAEGILADFLLWEPGEAFDLILG  104 (421)
T ss_dssp             HHHHHCC-CCTTCEEEEETCTTCHHHHHHHHHHCSCSEEEEEESCTTTCCCC---TTEEEEESCGGGCCCSSCEEEEEE
T ss_pred             HHHHhhc-cCCCCEEEECCCCChHHHHHHHHHhCCCCeEEEEECCHHHHHhC---CCCcEEeCChhhcCccCCCCEEEE
Confidence            3444444 3345699999999999999999988 78899999985 466555   6899999999985443 3 98875

>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=97.87  E-value=8.4e-06  Score=68.89  Aligned_cols=66  Identities=17%  Similarity=0.211  Sum_probs=52.8

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccC-----------CCCceEEecCcCCC--C-CCC-CEE
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSS-----------YSGVKHIGGIMLER--I-PKG-DAI  230 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~-----------~~ri~~~~gD~f~~--~-P~~-D~~  230 (233)
                      .+..+|+|||||+|..+..+++..|..+++++|+ |.+++.+++           .+||+++.+|.++.  . +.. |+|
T Consensus        76 ~~~~~VLdiG~G~G~~~~~l~~~~~~~~v~~vDid~~~i~~ar~~~~~~~~~~~~~~~v~~~~~D~~~~l~~~~~~fD~I  155 (314)
T 1uir_A           76 PEPKRVLIVGGGEGATLREVLKHPTVEKAVMVDIDGELVEVAKRHMPEWHQGAFDDPRAVLVIDDARAYLERTEERYDVV  155 (314)
T ss_dssp             SCCCEEEEEECTTSHHHHHHTTSTTCCEEEEEESCHHHHHHHHHHCHHHHTTGGGCTTEEEEESCHHHHHHHCCCCEEEE
T ss_pred             CCCCeEEEEcCCcCHHHHHHHhcCCCCEEEEEECCHHHHHHHHHHhHhhccccccCCceEEEEchHHHHHHhcCCCccEE
Confidence            4558999999999999999999888889999998 457776543           26899999999873  2 233 888


Q ss_pred             Ee
Q 039903          231 LI  232 (233)
Q Consensus       231 ~l  232 (233)
                      ++
T Consensus       156 i~  157 (314)
T 1uir_A          156 II  157 (314)
T ss_dssp             EE
T ss_pred             EE
Confidence            74

>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=97.86  E-value=2.6e-05  Score=61.15  Aligned_cols=64  Identities=16%  Similarity=0.101  Sum_probs=50.2

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC----C-CceEEecCcCCCCCC-CCEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY----S-GVKHIGGIMLERIPK-GDAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~----~-ri~~~~gD~f~~~P~-~D~~~l  232 (233)
                      ....+|+|+|||+|.++..+++..+ -+++.+|+ |..++.++++    . +++++.+|+.+ +|. .|++++
T Consensus        48 ~~~~~vlD~g~G~G~~~~~l~~~~~-~~v~~vD~~~~~~~~a~~~~~~~~~~~~~~~~d~~~-~~~~~D~v~~  118 (207)
T 1wy7_A           48 IEGKVVADLGAGTGVLSYGALLLGA-KEVICVEVDKEAVDVLIENLGEFKGKFKVFIGDVSE-FNSRVDIVIM  118 (207)
T ss_dssp             STTCEEEEETCTTCHHHHHHHHTTC-SEEEEEESCHHHHHHHHHHTGGGTTSEEEEESCGGG-CCCCCSEEEE
T ss_pred             CCcCEEEEeeCCCCHHHHHHHHcCC-CEEEEEECCHHHHHHHHHHHHHcCCCEEEEECchHH-cCCCCCEEEE
Confidence            3457999999999999999998743 37999998 5677776653    2 79999999987 343 488875

>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=97.86  E-value=2.7e-05  Score=60.89  Aligned_cols=59  Identities=17%  Similarity=0.275  Sum_probs=47.1

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCCCCceEEecCcCC
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLE  222 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~~ri~~~~gD~f~  222 (233)
                      ++.+.+.-+++..+|||+|||+|.++..++++  ..+++.+|+.+.    ...++|+++.+|+.+
T Consensus        15 ei~~~~~~~~~g~~VLDlG~G~G~~s~~la~~--~~~V~gvD~~~~----~~~~~v~~~~~D~~~   73 (191)
T 3dou_A           15 FLLDRYRVVRKGDAVIEIGSSPGGWTQVLNSL--ARKIISIDLQEM----EEIAGVRFIRCDIFK   73 (191)
T ss_dssp             HHHHHHCCSCTTCEEEEESCTTCHHHHHHTTT--CSEEEEEESSCC----CCCTTCEEEECCTTS
T ss_pred             HHHHHcCCCCCCCEEEEEeecCCHHHHHHHHc--CCcEEEEecccc----ccCCCeEEEEccccC
Confidence            45555553466789999999999999999998  778999998653    223689999999987

>3tqs_A Ribosomal RNA small subunit methyltransferase A; protein synthesis; 1.98A {Coxiella burnetii} SCOP: c.66.1.0

Probab=97.85  E-value=1.1e-05  Score=66.11  Aligned_cols=66  Identities=11%  Similarity=0.208  Sum_probs=51.9

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccC----CCCceEEecCcCC-CCC
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSS----YSGVKHIGGIMLE-RIP  225 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~----~~ri~~~~gD~f~-~~P  225 (233)
                      ..+++..+ .....+|+|||||+|.++..++++.  .+++.+|+. +.++.+++    .++++++.+|+++ +++
T Consensus        19 ~~iv~~~~-~~~~~~VLEIG~G~G~lt~~La~~~--~~V~avEid~~~~~~~~~~~~~~~~v~~i~~D~~~~~~~   90 (255)
T 3tqs_A           19 QKIVSAIH-PQKTDTLVEIGPGRGALTDYLLTEC--DNLALVEIDRDLVAFLQKKYNQQKNITIYQNDALQFDFS   90 (255)
T ss_dssp             HHHHHHHC-CCTTCEEEEECCTTTTTHHHHTTTS--SEEEEEECCHHHHHHHHHHHTTCTTEEEEESCTTTCCGG
T ss_pred             HHHHHhcC-CCCcCEEEEEcccccHHHHHHHHhC--CEEEEEECCHHHHHHHHHHHhhCCCcEEEEcchHhCCHH
Confidence            34555555 5667899999999999999999985  578999984 56666654    3789999999998 554

>2cmg_A Spermidine synthase; transferase, putrescine aminopropyltransferase, spermidine biosynthesis, polyamine biosynthesis, SPEE; 2.0A {Helicobacter pylori} PDB: 2cmh_A

Probab=97.85  E-value=2.3e-05  Score=64.51  Aligned_cols=63  Identities=14%  Similarity=0.091  Sum_probs=52.0

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC----------CCceEEecCcCCCCCCC-CEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY----------SGVKHIGGIMLERIPKG-DAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~----------~ri~~~~gD~f~~~P~~-D~~~l  232 (233)
                      .+..+|+|||||+|..+.++++. + .+++.+|+ |.+++.|+++          +|++++.+|.++-. .. |+|++
T Consensus        71 ~~~~~VL~iG~G~G~~~~~ll~~-~-~~v~~veid~~~i~~ar~~~~~~~~~~~~~rv~~~~~D~~~~~-~~fD~Ii~  145 (262)
T 2cmg_A           71 KELKEVLIVDGFDLELAHQLFKY-D-THIDFVQADEKILDSFISFFPHFHEVKNNKNFTHAKQLLDLDI-KKYDLIFC  145 (262)
T ss_dssp             SCCCEEEEESSCCHHHHHHHTTS-S-CEEEEECSCHHHHGGGTTTSTTHHHHHTCTTEEEESSGGGSCC-CCEEEEEE
T ss_pred             CCCCEEEEEeCCcCHHHHHHHhC-C-CEEEEEECCHHHHHHHHHHHHhhccccCCCeEEEEechHHHHH-hhCCEEEE
Confidence            45589999999999999999998 8 89999998 5688887653          58999999998744 33 88875

>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=97.85  E-value=9.4e-06  Score=67.55  Aligned_cols=66  Identities=18%  Similarity=0.113  Sum_probs=53.4

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccC----------CCCceEEecCcCCC---CCCC-CEEE
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSS----------YSGVKHIGGIMLER---IPKG-DAIL  231 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~----------~~ri~~~~gD~f~~---~P~~-D~~~  231 (233)
                      .+..+|+|||||.|..+..+++..|..+++++|+ |.+++.+++          .+|++++.+|..+.   .+.. |+|+
T Consensus        77 ~~~~~VLdiG~G~G~~~~~l~~~~~~~~v~~vDid~~~i~~a~~~~~~~~~~~~~~~v~~~~~D~~~~l~~~~~~fD~Ii  156 (283)
T 2i7c_A           77 KEPKNVLVVGGGDGGIIRELCKYKSVENIDICEIDETVIEVSKIYFKNISCGYEDKRVNVFIEDASKFLENVTNTYDVII  156 (283)
T ss_dssp             SSCCEEEEEECTTSHHHHHHTTCTTCCEEEEEESCHHHHHHHHHHCTTTSGGGGSTTEEEEESCHHHHHHHCCSCEEEEE
T ss_pred             CCCCeEEEEeCCcCHHHHHHHHcCCCCEEEEEECCHHHHHHHHHHhHHhccccCCCcEEEEECChHHHHHhCCCCceEEE
Confidence            4568999999999999999999888899999998 567776653          26899999999862   2333 8887


Q ss_pred             e
Q 039903          232 I  232 (233)
Q Consensus       232 l  232 (233)
                      +
T Consensus       157 ~  157 (283)
T 2i7c_A          157 V  157 (283)
T ss_dssp             E
T ss_pred             E
Confidence            5

>2b2c_A Spermidine synthase; beta-alpha, transferase; 2.50A {Caenorhabditis elegans} SCOP: c.66.1.17

Probab=97.84  E-value=9.4e-06  Score=68.64  Aligned_cols=66  Identities=20%  Similarity=0.204  Sum_probs=53.1

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccC----------CCCceEEecCcCCCC--CC-C-CEEE
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSS----------YSGVKHIGGIMLERI--PK-G-DAIL  231 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~----------~~ri~~~~gD~f~~~--P~-~-D~~~  231 (233)
                      .+..+|+|||||+|..++.+++..|..+++.+|+ |.+++.|++          .+||+++.+|.++.+  +. . |+|+
T Consensus       107 ~~~~~VLdIG~G~G~~~~~l~~~~~~~~v~~vDid~~~i~~Ar~~~~~~~~~~~~~rv~~~~~D~~~~l~~~~~~fD~Ii  186 (314)
T 2b2c_A          107 PDPKRVLIIGGGDGGILREVLKHESVEKVTMCEIDEMVIDVAKKFLPGMSCGFSHPKLDLFCGDGFEFLKNHKNEFDVII  186 (314)
T ss_dssp             SSCCEEEEESCTTSHHHHHHTTCTTCCEEEEECSCHHHHHHHHHHCTTTSGGGGCTTEEEECSCHHHHHHHCTTCEEEEE
T ss_pred             CCCCEEEEEcCCcCHHHHHHHHcCCCCEEEEEECCHHHHHHHHHHHHHhccccCCCCEEEEEChHHHHHHhcCCCceEEE
Confidence            4558999999999999999999888899999998 567776653          268999999998732  22 3 8887


Q ss_pred             e
Q 039903          232 I  232 (233)
Q Consensus       232 l  232 (233)
                      +
T Consensus       187 ~  187 (314)
T 2b2c_A          187 T  187 (314)
T ss_dssp             E
T ss_pred             E
Confidence            4

>3k0b_A Predicted N6-adenine-specific DNA methylase; methylase,PF01170, putative RNA methylase, PSI,MCSG, structu genomics; 1.50A {Listeria monocytogenes str}

Probab=97.83  E-value=3.5e-05  Score=67.15  Aligned_cols=75  Identities=7%  Similarity=-0.002  Sum_probs=57.9

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCC--------------------------------------CcEEEe
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLH--------------------------------------IKGVNF  198 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~--------------------------------------l~~~v~  198 (233)
                      ..++.... |.+...++|.+||+|.++++.+....+                                      .+++.+
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 877889999999999999988876554                                      569999


Q ss_pred             ec-hHHHhhccCC-------CCceEEecCcCC-CCCCC-CEEEe
Q 039903          199 DL-SHVIQDSSSY-------SGVKHIGGIMLE-RIPKG-DAILI  232 (233)
Q Consensus       199 Dl-p~v~~~a~~~-------~ri~~~~gD~f~-~~P~~-D~~~l  232 (233)
                      |+ |.+++.|+.+       ++|+++.+|+++ +.|.. |+|+.
T Consensus       270 Did~~al~~Ar~Na~~~gl~~~I~~~~~D~~~~~~~~~fD~Iv~  313 (393)
T 3k0b_A          270 DIDARLIEIAKQNAVEAGLGDLITFRQLQVADFQTEDEYGVVVA  313 (393)
T ss_dssp             ESCHHHHHHHHHHHHHTTCTTCSEEEECCGGGCCCCCCSCEEEE
T ss_pred             ECCHHHHHHHHHHHHHcCCCCceEEEECChHhCCCCCCCCEEEE
Confidence            98 5578777653       579999999998 44443 98875

>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=97.83  E-value=2.3e-05  Score=62.64  Aligned_cols=67  Identities=16%  Similarity=0.234  Sum_probs=53.0

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcC------CCcEEEeec-hHHHhhccC-----------CCCceEEecCcCCCCCC-
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYL------HIKGVNFDL-SHVIQDSSS-----------YSGVKHIGGIMLERIPK-  226 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P------~l~~~v~Dl-p~v~~~a~~-----------~~ri~~~~gD~f~~~P~-  226 (233)
                      .....+|+|||||+|.++..+++..+      ..+++.+|+ |+.++.+++           .++|+++.+|..+++|. 
T Consensus        82 ~~~~~~VLdiG~G~G~~~~~la~~~~~~~~~~~~~v~~vD~~~~~~~~a~~~~~~~~~~~~~~~~v~~~~~d~~~~~~~~  161 (227)
T 1r18_A           82 LKPGARILDVGSGSGYLTACFYRYIKAKGVDADTRIVGIEHQAELVRRSKANLNTDDRSMLDSGQLLIVEGDGRKGYPPN  161 (227)
T ss_dssp             CCTTCEEEEESCTTSHHHHHHHHHHHHSCCCTTCEEEEEESCHHHHHHHHHHHHHHHHHHHHHTSEEEEESCGGGCCGGG
T ss_pred             CCCCCEEEEECCCccHHHHHHHHhcccccCCccCEEEEEEcCHHHHHHHHHHHHhcCccccCCCceEEEECCcccCCCcC
Confidence            44557999999999999999999766      368999997 456666654           25899999999987665 


Q ss_pred             C--CEEEe
Q 039903          227 G--DAILI  232 (233)
Q Consensus       227 ~--D~~~l  232 (233)
                      +  |+|+.
T Consensus       162 ~~fD~I~~  169 (227)
T 1r18_A          162 APYNAIHV  169 (227)
T ss_dssp             CSEEEEEE
T ss_pred             CCccEEEE
Confidence            3  88864

>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=97.82  E-value=1.4e-05  Score=66.42  Aligned_cols=65  Identities=25%  Similarity=0.279  Sum_probs=51.4

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhcc----------------CCCCceEEecCcCCCC--CCC
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSS----------------SYSGVKHIGGIMLERI--PKG  227 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~----------------~~~ri~~~~gD~f~~~--P~~  227 (233)
                      .+..+|+|||||+|.++..+++. |..+++++|+ |.+++.++                ..+||+++.+|.++.+  +..
T Consensus        74 ~~~~~VLdiG~G~G~~~~~l~~~-~~~~v~~vDid~~~i~~ar~~~~~~~~l~~~~~~~~~~~v~~~~~D~~~~l~~~~~  152 (281)
T 1mjf_A           74 PKPKRVLVIGGGDGGTVREVLQH-DVDEVIMVEIDEDVIMVSKDLIKIDNGLLEAMLNGKHEKAKLTIGDGFEFIKNNRG  152 (281)
T ss_dssp             SCCCEEEEEECTTSHHHHHHTTS-CCSEEEEEESCHHHHHHHHHHTCTTTTHHHHHHTTCCSSEEEEESCHHHHHHHCCC
T ss_pred             CCCCeEEEEcCCcCHHHHHHHhC-CCCEEEEEECCHHHHHHHHHHHhhccccccccccCCCCcEEEEECchHHHhcccCC
Confidence            34579999999999999999998 8889999998 56776654                2368999999987522  333


Q ss_pred             -CEEEe
Q 039903          228 -DAILI  232 (233)
Q Consensus       228 -D~~~l  232 (233)
                       |+|++
T Consensus       153 fD~Ii~  158 (281)
T 1mjf_A          153 FDVIIA  158 (281)
T ss_dssp             EEEEEE
T ss_pred             eeEEEE
Confidence             88874

>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=97.81  E-value=2.8e-05  Score=67.53  Aligned_cols=75  Identities=15%  Similarity=0.088  Sum_probs=57.7

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCC--------------------------------------CcEEEe
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLH--------------------------------------IKGVNF  198 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~--------------------------------------l~~~v~  198 (233)
                      ..++.... |.+..+++|++||+|.++++.+..-.+                                      .+++.+
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            34445445 777789999999999999998876432                                      679999


Q ss_pred             ec-hHHHhhccCC-------CCceEEecCcCC-CCCCC-CEEEe
Q 039903          199 DL-SHVIQDSSSY-------SGVKHIGGIMLE-RIPKG-DAILI  232 (233)
Q Consensus       199 Dl-p~v~~~a~~~-------~ri~~~~gD~f~-~~P~~-D~~~l  232 (233)
                      |+ |.+++.|+.+       ++|+++.+|+++ +.|.. |+++.
T Consensus       264 Did~~ai~~Ar~Na~~~gl~~~i~~~~~D~~~l~~~~~~D~Iv~  307 (385)
T 3ldu_A          264 DIDEESIDIARENAEIAGVDEYIEFNVGDATQFKSEDEFGFIIT  307 (385)
T ss_dssp             ESCHHHHHHHHHHHHHHTCGGGEEEEECCGGGCCCSCBSCEEEE
T ss_pred             ECCHHHHHHHHHHHHHcCCCCceEEEECChhhcCcCCCCcEEEE
Confidence            98 5688887764       479999999998 44443 98875

>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=97.81  E-value=2.3e-05  Score=64.79  Aligned_cols=65  Identities=15%  Similarity=0.027  Sum_probs=51.4

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCC-CC-CCC--CEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLE-RI-PKG--DAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~-~~-P~~--D~~~l  232 (233)
                      ....+|||||||+|.++..+++. +..+++.+|+ |..++.+++.       ++|+++.+|+.+ ++ +.+  |+|+.
T Consensus        63 ~~~~~vLDiGcG~G~~~~~l~~~-~~~~v~gvD~s~~~~~~a~~~~~~~~~~~~v~~~~~d~~~~~~~~~~~fD~v~~  139 (298)
T 1ri5_A           63 KRGDSVLDLGCGKGGDLLKYERA-GIGEYYGVDIAEVSINDARVRARNMKRRFKVFFRAQDSYGRHMDLGKEFDVISS  139 (298)
T ss_dssp             CTTCEEEEETCTTTTTHHHHHHH-TCSEEEEEESCHHHHHHHHHHHHTSCCSSEEEEEESCTTTSCCCCSSCEEEEEE
T ss_pred             CCCCeEEEECCCCCHHHHHHHHC-CCCEEEEEECCHHHHHHHHHHHHhcCCCccEEEEECCccccccCCCCCcCEEEE
Confidence            55689999999999999998775 6668999998 5577766542       469999999998 66 343  98874

>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=97.80  E-value=1.2e-05  Score=63.22  Aligned_cols=64  Identities=16%  Similarity=0.073  Sum_probs=48.9

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC--------CCceEEecCcCCCCC-----C-CCEEEe
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY--------SGVKHIGGIMLERIP-----K-GDAILI  232 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~--------~ri~~~~gD~f~~~P-----~-~D~~~l  232 (233)
                      +..+|||+|||+|.++..++++.+ .+++.+|+. ..++.++++        ++|+++.+|+++..+     . .|++++
T Consensus        53 ~~~~vLDlGcGtG~~~~~~~~~~~-~~v~gvD~s~~~l~~a~~~~~~~~~~~~~v~~~~~d~~~~~~~~~~~~~fD~I~~  131 (201)
T 2ift_A           53 HQSECLDGFAGSGSLGFEALSRQA-KKVTFLELDKTVANQLKKNLQTLKCSSEQAEVINQSSLDFLKQPQNQPHFDVVFL  131 (201)
T ss_dssp             TTCEEEETTCTTCHHHHHHHHTTC-SEEEEECSCHHHHHHHHHHHHHTTCCTTTEEEECSCHHHHTTSCCSSCCEEEEEE
T ss_pred             CCCeEEEcCCccCHHHHHHHHccC-CEEEEEECCHHHHHHHHHHHHHhCCCccceEEEECCHHHHHHhhccCCCCCEEEE
Confidence            347899999999999999887754 579999984 577777652        589999999987322     2 477765

>2pbf_A Protein-L-isoaspartate O-methyltransferase beta-A methyltransferase; protein repair, isoaspartyl formation, P. falciparum; HET: SAH; 2.00A {Plasmodium falciparum}

Probab=97.79  E-value=4e-05  Score=61.01  Aligned_cols=67  Identities=16%  Similarity=0.123  Sum_probs=52.6

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHc-----CCCcEEEeec-hHHHhhccCC-----------CCceEEecCcCCCC----
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNY-----LHIKGVNFDL-SHVIQDSSSY-----------SGVKHIGGIMLERI----  224 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~-----P~l~~~v~Dl-p~v~~~a~~~-----------~ri~~~~gD~f~~~----  224 (233)
                      .....+|+|||||+|.++..+++..     |+.+++.+|. |+.++.++++           ++|+++.+|+.+..    
T Consensus        78 ~~~~~~VLdiG~G~G~~~~~la~~~~~~~~~~~~v~~vD~~~~~~~~a~~~~~~~~~~~~~~~~v~~~~~d~~~~~~~~~  157 (227)
T 2pbf_A           78 LKPGSRAIDVGSGSGYLTVCMAIKMNVLENKNSYVIGLERVKDLVNFSLENIKRDKPELLKIDNFKIIHKNIYQVNEEEK  157 (227)
T ss_dssp             SCTTCEEEEESCTTSHHHHHHHHHTTTTTCTTCEEEEEESCHHHHHHHHHHHHHHCGGGGSSTTEEEEECCGGGCCHHHH
T ss_pred             CCCCCEEEEECCCCCHHHHHHHHHhcccCCCCCEEEEEeCCHHHHHHHHHHHHHcCccccccCCEEEEECChHhcccccC
Confidence            4556899999999999999999986     6789999998 4566666542           48999999998844    


Q ss_pred             C-C--CCEEEe
Q 039903          225 P-K--GDAILI  232 (233)
Q Consensus       225 P-~--~D~~~l  232 (233)
                      + .  .|+|+.
T Consensus       158 ~~~~~fD~I~~  168 (227)
T 2pbf_A          158 KELGLFDAIHV  168 (227)
T ss_dssp             HHHCCEEEEEE
T ss_pred             ccCCCcCEEEE
Confidence            2 2  288864

>2zfu_A Nucleomethylin, cerebral protein 1; nucleolar protein, SAM-binding protein, protein structure, N phosphoprotein, nuclear protein; HET: SAH; 2.00A {Homo sapiens}

Probab=97.78  E-value=5e-05  Score=59.88  Aligned_cols=62  Identities=18%  Similarity=0.088  Sum_probs=46.5

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCCCCceEEecCcCC-CCCCC--CEEEe
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLE-RIPKG--DAILI  232 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~~ri~~~~gD~f~-~~P~~--D~~~l  232 (233)
                      .+++.+.......+|+|||||+|.++..++     .+++.+|+.+.        +++++.+|+.+ ++|.+  |+++.
T Consensus        57 ~~~~~l~~~~~~~~vLDiG~G~G~~~~~l~-----~~v~~~D~s~~--------~~~~~~~d~~~~~~~~~~fD~v~~  121 (215)
T 2zfu_A           57 RIARDLRQRPASLVVADFGCGDCRLASSIR-----NPVHCFDLASL--------DPRVTVCDMAQVPLEDESVDVAVF  121 (215)
T ss_dssp             HHHHHHHTSCTTSCEEEETCTTCHHHHHCC-----SCEEEEESSCS--------STTEEESCTTSCSCCTTCEEEEEE
T ss_pred             HHHHHHhccCCCCeEEEECCcCCHHHHHhh-----ccEEEEeCCCC--------CceEEEeccccCCCCCCCEeEEEE
Confidence            344544324456899999999999998883     67899998654        67889999988 66653  88874

>3cbg_A O-methyltransferase; cyanobacterium; HET: SAH FER 4FE; 2.00A {Synechocystis SP}

Probab=97.77  E-value=9.8e-06  Score=65.26  Aligned_cols=66  Identities=17%  Similarity=0.153  Sum_probs=52.1

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcC-CCcEEEeec-hHHHhhccCC-------CCceEEecCcCCC---CC-----CC-C
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLER---IP-----KG-D  228 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~---~P-----~~-D  228 (233)
                      .+..+|||||||+|..+..+++..| +.+++.+|. |+.++.|+++       ++|+++.+|..+.   +|     .. |
T Consensus        71 ~~~~~vLdiG~G~G~~~~~la~~~~~~~~v~~iD~~~~~~~~a~~~~~~~g~~~~i~~~~~d~~~~l~~l~~~~~~~~fD  150 (232)
T 3cbg_A           71 TGAKQVLEIGVFRGYSALAMALQLPPDGQIIACDQDPNATAIAKKYWQKAGVAEKISLRLGPALATLEQLTQGKPLPEFD  150 (232)
T ss_dssp             HTCCEEEEECCTTSHHHHHHHTTSCTTCEEEEEESCHHHHHHHHHHHHHHTCGGGEEEEESCHHHHHHHHHTSSSCCCEE
T ss_pred             cCCCEEEEecCCCCHHHHHHHHhCCCCCEEEEEECCHHHHHHHHHHHHHcCCCCcEEEEEcCHHHHHHHHHhcCCCCCcC
Confidence            4557999999999999999999988 789999998 5577766542       5799999998652   21     33 8


Q ss_pred             EEEe
Q 039903          229 AILI  232 (233)
Q Consensus       229 ~~~l  232 (233)
                      ++++
T Consensus       151 ~V~~  154 (232)
T 3cbg_A          151 LIFI  154 (232)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            8875

>3ldg_A Putative uncharacterized protein SMU.472; YPSC, methyltransferase, transferase; HET: SAH; 1.96A {Streptococcus mutans}

Probab=97.76  E-value=5.3e-05  Score=65.81  Aligned_cols=76  Identities=17%  Similarity=0.094  Sum_probs=58.3

Q ss_pred             HHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCC--------------------------------------CcEEE
Q 039903          156 TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLH--------------------------------------IKGVN  197 (233)
Q Consensus       156 ~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~--------------------------------------l~~~v  197 (233)
                      +..++.... |.....++|.+||+|.++++.+....+                                      .+++.
T Consensus       183 Aaall~l~~-~~~~~~llDp~CGSGt~lIEAa~~a~~iapg~~R~f~f~~w~~~~~~~w~~~~~~a~~~~~~~~~~~v~G  261 (384)
T 3ldg_A          183 AAAIILLSN-WFPDKPFVDPTCGSGTFCIEAAMIGMNIAPGFNRDFAFEEWPWVDEALVTRVRNEADEQADYDIQLDISG  261 (384)
T ss_dssp             HHHHHHHTT-CCTTSCEEETTCTTSHHHHHHHHHHTTCCTTTTCCCGGGGCTTSCHHHHHHHHHHHHHHCCTTCCCCEEE
T ss_pred             HHHHHHHhC-CCCCCeEEEeCCcCCHHHHHHHHHhcCcCCCccccchhhhhccCCHHHHHHHHHHHHHhhhccCCceEEE
Confidence            344555545 888889999999999999998876554                                      56999


Q ss_pred             eec-hHHHhhccCC-------CCceEEecCcCC-CCCCC-CEEEe
Q 039903          198 FDL-SHVIQDSSSY-------SGVKHIGGIMLE-RIPKG-DAILI  232 (233)
Q Consensus       198 ~Dl-p~v~~~a~~~-------~ri~~~~gD~f~-~~P~~-D~~~l  232 (233)
                      +|. |.+++.|+.+       ++|+++.+|+++ +.|.. |+++.
T Consensus       262 vDid~~al~~Ar~Na~~~gl~~~I~~~~~D~~~l~~~~~fD~Iv~  306 (384)
T 3ldg_A          262 FDFDGRMVEIARKNAREVGLEDVVKLKQMRLQDFKTNKINGVLIS  306 (384)
T ss_dssp             EESCHHHHHHHHHHHHHTTCTTTEEEEECCGGGCCCCCCSCEEEE
T ss_pred             EECCHHHHHHHHHHHHHcCCCCceEEEECChHHCCccCCcCEEEE
Confidence            998 4578777653       579999999998 44443 98875

>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=97.76  E-value=2.2e-05  Score=64.32  Aligned_cols=66  Identities=9%  Similarity=0.068  Sum_probs=50.0

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC----CCceEEecCcCC-CCC
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY----SGVKHIGGIMLE-RIP  225 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~----~ri~~~~gD~f~-~~P  225 (233)
                      ..+++.++ .....+|+|||||+|.++. + ++.++.+++.+|+ |+.++.+++.    ++++++.+|+.+ ++|
T Consensus        11 ~~iv~~~~-~~~~~~VLEIG~G~G~lt~-l-~~~~~~~v~avEid~~~~~~a~~~~~~~~~v~~i~~D~~~~~~~   82 (252)
T 1qyr_A           11 DSIVSAIN-PQKGQAMVEIGPGLAALTE-P-VGERLDQLTVIELDRDLAARLQTHPFLGPKLTIYQQDAMTFNFG   82 (252)
T ss_dssp             HHHHHHHC-CCTTCCEEEECCTTTTTHH-H-HHTTCSCEEEECCCHHHHHHHHTCTTTGGGEEEECSCGGGCCHH
T ss_pred             HHHHHhcC-CCCcCEEEEECCCCcHHHH-h-hhCCCCeEEEEECCHHHHHHHHHHhccCCceEEEECchhhCCHH
Confidence            44555555 5666789999999999999 5 4555555999998 4577777653    589999999998 554

>1yub_A Ermam, rRNA methyltransferase; MLS antibiotics; NMR {Streptococcus pneumoniae} SCOP: c.66.1.24

Probab=97.74  E-value=1.6e-05  Score=64.64  Aligned_cols=67  Identities=22%  Similarity=0.326  Sum_probs=53.8

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC----CCceEEecCcCC-CCCC
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY----SGVKHIGGIMLE-RIPK  226 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~----~ri~~~~gD~f~-~~P~  226 (233)
                      ..+++.++ .....+|+|||||+|.++..++++.  .+++.+|+ ++.++.++++    ++++++.+|+.+ ++|.
T Consensus        19 ~~i~~~~~-~~~~~~VLDiG~G~G~~~~~l~~~~--~~v~~id~~~~~~~~a~~~~~~~~~v~~~~~D~~~~~~~~   91 (245)
T 1yub_A           19 NQIIKQLN-LKETDTVYEIGTGKGHLTTKLAKIS--KQVTSIELDSHLFNLSSEKLKLNTRVTLIHQDILQFQFPN   91 (245)
T ss_dssp             HHHHHHCC-CCSSEEEEECSCCCSSCSHHHHHHS--SEEEESSSSCSSSSSSSCTTTTCSEEEECCSCCTTTTCCC
T ss_pred             HHHHHhcC-CCCCCEEEEEeCCCCHHHHHHHHhC--CeEEEEECCHHHHHHHHHHhccCCceEEEECChhhcCccc
Confidence            45566665 6667899999999999999999985  78999998 4577777653    589999999998 6663

>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=97.73  E-value=4.4e-05  Score=67.29  Aligned_cols=71  Identities=13%  Similarity=0.159  Sum_probs=54.5

Q ss_pred             HHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCCCCC-----C
Q 039903          159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLERIP-----K  226 (233)
Q Consensus       159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~~P-----~  226 (233)
                      +++.++ ..+..+|+|+|||+|.++..++++  ..+++.+|. ++.++.|+++      ++++|+.+|+++.++     .
T Consensus       278 ~~~~l~-~~~~~~VLDlgcG~G~~~~~la~~--~~~V~gvD~s~~al~~A~~n~~~~~~~~v~f~~~d~~~~l~~~~~~~  354 (433)
T 1uwv_A          278 ALEWLD-VQPEDRVLDLFCGMGNFTLPLATQ--AASVVGVEGVPALVEKGQQNARLNGLQNVTFYHENLEEDVTKQPWAK  354 (433)
T ss_dssp             HHHHHT-CCTTCEEEEESCTTTTTHHHHHTT--SSEEEEEESCHHHHHHHHHHHHHTTCCSEEEEECCTTSCCSSSGGGT
T ss_pred             HHHhhc-CCCCCEEEECCCCCCHHHHHHHhh--CCEEEEEeCCHHHHHHHHHHHHHcCCCceEEEECCHHHHhhhhhhhc
Confidence            334444 455679999999999999999988  678999998 5677777653      589999999998432     2


Q ss_pred             --CCEEEe
Q 039903          227 --GDAILI  232 (233)
Q Consensus       227 --~D~~~l  232 (233)
                        .|++++
T Consensus       355 ~~fD~Vv~  362 (433)
T 1uwv_A          355 NGFDKVLL  362 (433)
T ss_dssp             TCCSEEEE
T ss_pred             CCCCEEEE
Confidence              398875

>2gs9_A Hypothetical protein TT1324; methyl transferase, structural genomics, NPPSFA, national PR protein structural and functional analyses; HET: SAH; 2.60A {Thermus thermophilus}

Probab=97.73  E-value=3.5e-05  Score=60.53  Aligned_cols=60  Identities=15%  Similarity=0.231  Sum_probs=48.7

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCC-cEEEeec-hHHHhhccCC-CCceEEecCcCC-CCCCC--CEEEe
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHI-KGVNFDL-SHVIQDSSSY-SGVKHIGGIMLE-RIPKG--DAILI  232 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l-~~~v~Dl-p~v~~~a~~~-~ri~~~~gD~f~-~~P~~--D~~~l  232 (233)
                      ...+|+|||||+|.++..+     .. +++.+|. |..++.+++. ++++++.+|+.+ ++|.+  |++++
T Consensus        36 ~~~~vLdiG~G~G~~~~~l-----~~~~v~~vD~s~~~~~~a~~~~~~~~~~~~d~~~~~~~~~~fD~v~~  101 (211)
T 2gs9_A           36 PGESLLEVGAGTGYWLRRL-----PYPQKVGVEPSEAMLAVGRRRAPEATWVRAWGEALPFPGESFDVVLL  101 (211)
T ss_dssp             CCSEEEEETCTTCHHHHHC-----CCSEEEEECCCHHHHHHHHHHCTTSEEECCCTTSCCSCSSCEEEEEE
T ss_pred             CCCeEEEECCCCCHhHHhC-----CCCeEEEEeCCHHHHHHHHHhCCCcEEEEcccccCCCCCCcEEEEEE
Confidence            5679999999999999888     44 8999998 4577777654 789999999988 66653  98875

>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=97.72  E-value=0.00012  Score=61.32  Aligned_cols=87  Identities=14%  Similarity=0.053  Sum_probs=58.6

Q ss_pred             HHHHHHHHhcchhcHHHHHHhccc-ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC---------
Q 039903          142 GVFNKAMLNHTSIVTNRIIDSSKG-FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY---------  210 (233)
Q Consensus       142 ~~f~~am~~~~~~~~~~~~~~~~~-~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~---------  210 (233)
                      +.|+..+...-   ...+++.+.. .....+|+|||||+|.++..+++ .+..+++.+|+. ..++.+++.         
T Consensus        10 r~~~~~~k~~l---~~~~~~~l~~~~~~~~~VLDlGcG~G~~~~~l~~-~~~~~v~gvD~s~~~l~~a~~~~~~~~~~~~   85 (313)
T 3bgv_A           10 RNFNNWMKSVL---IGEFLEKVRQKKKRDITVLDLGCGKGGDLLKWKK-GRINKLVCTDIADVSVKQCQQRYEDMKNRRD   85 (313)
T ss_dssp             HHHHHHHHHHH---HHHHHHHHHHTC--CCEEEEETCTTTTTHHHHHH-TTCSEEEEEESCHHHHHHHHHHHHHHHSSSC
T ss_pred             hhccHHHHHHH---HHHHHHHhhhccCCCCEEEEECCCCcHHHHHHHh-cCCCEEEEEeCCHHHHHHHHHHHHHhhhccc
Confidence            45666655422   2334443331 23568999999999999999988 467789999984 566666542         


Q ss_pred             ----CCceEEecCcCC-C----CC--C-C-CEEEe
Q 039903          211 ----SGVKHIGGIMLE-R----IP--K-G-DAILI  232 (233)
Q Consensus       211 ----~ri~~~~gD~f~-~----~P--~-~-D~~~l  232 (233)
                          .+++++.+|+.+ +    ++  . . |+|+.
T Consensus        86 ~~~~~~~~~~~~D~~~~~~~~~~~~~~~~fD~V~~  120 (313)
T 3bgv_A           86 SEYIFSAEFITADSSKELLIDKFRDPQMCFDICSC  120 (313)
T ss_dssp             C-CCCEEEEEECCTTTSCSTTTCSSTTCCEEEEEE
T ss_pred             ccccceEEEEEecccccchhhhcccCCCCEEEEEE
Confidence                379999999987 4    43  2 3 88874

>3b73_A PHIH1 repressor-like protein; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 2.12A {Haloarcula marismortui atcc 43049}

Probab=97.72  E-value=6.4e-05  Score=53.63  Aligned_cols=64  Identities=17%  Similarity=0.224  Sum_probs=56.5

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhC--CCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhcC
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQM--PSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~--~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~~   91 (233)
                      .+..|++.|...   |+.|+.+||+.+  ++    +...+.+-|+.|...|+++..    ..+.|++|+.+..++..
T Consensus        14 ~d~~IL~~L~~~---g~~s~~eLA~~l~~gi----S~~aVs~rL~~Le~~GLV~~~----~rg~Y~LT~~G~~~l~~   79 (111)
T 3b73_A           14 WDDRILEIIHEE---GNGSPKELEDRDEIRI----SKSSVSRRLKKLADHDLLQPL----ANGVYVITEEGEAYLNG   79 (111)
T ss_dssp             HHHHHHHHHHHH---SCBCHHHHHTSTTCCS----CHHHHHHHHHHHHHTTSEEEC----STTCEEECHHHHHHHTT
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHhcCC----CHHHHHHHHHHHHHCCCEEec----CCceEEECchHHHHHHH
Confidence            356788999876   599999999999  99    999999999999999999986    45699999999987765

>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=97.71  E-value=5.8e-05  Score=59.84  Aligned_cols=57  Identities=16%  Similarity=0.173  Sum_probs=47.0

Q ss_pred             cceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCCCCceEEecCcCC-CCCCC--CEEEe
Q 039903          169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSYSGVKHIGGIMLE-RIPKG--DAILI  232 (233)
Q Consensus       169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~~ri~~~~gD~f~-~~P~~--D~~~l  232 (233)
                      ..+|+|||||+|.++..++++      +.+|. +..++.+++. +++++.+|+.+ +++.+  |+++.
T Consensus        48 ~~~vLDiG~G~G~~~~~l~~~------~~vD~s~~~~~~a~~~-~~~~~~~d~~~~~~~~~~fD~v~~  108 (219)
T 1vlm_A           48 EGRGVEIGVGTGRFAVPLKIK------IGVEPSERMAEIARKR-GVFVLKGTAENLPLKDESFDFALM  108 (219)
T ss_dssp             SSCEEEETCTTSTTHHHHTCC------EEEESCHHHHHHHHHT-TCEEEECBTTBCCSCTTCEEEEEE
T ss_pred             CCcEEEeCCCCCHHHHHHHHH------hccCCCHHHHHHHHhc-CCEEEEcccccCCCCCCCeeEEEE
Confidence            679999999999999998775      88998 5677777765 89999999987 66653  98875

>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=97.69  E-value=6.9e-05  Score=59.58  Aligned_cols=67  Identities=21%  Similarity=0.215  Sum_probs=52.0

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHc-CCCcEEEeec-hHHHhhccC-----------CCCceEEecCcCCCCC-C-C-CE
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNY-LHIKGVNFDL-SHVIQDSSS-----------YSGVKHIGGIMLERIP-K-G-DA  229 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~v~~~a~~-----------~~ri~~~~gD~f~~~P-~-~-D~  229 (233)
                      .....+|+|||||+|.++..+++.. |..+++.+|+ |..++.+++           .++|+++.+|+.+..+ . . |+
T Consensus        75 ~~~~~~vLDiG~G~G~~~~~la~~~~~~~~v~~vD~s~~~~~~a~~~~~~~~~~~~~~~~v~~~~~d~~~~~~~~~~fD~  154 (226)
T 1i1n_A           75 LHEGAKALDVGSGSGILTACFARMVGCTGKVIGIDHIKELVDDSVNNVRKDDPTLLSSGRVQLVVGDGRMGYAEEAPYDA  154 (226)
T ss_dssp             SCTTCEEEEETCTTSHHHHHHHHHHCTTCEEEEEESCHHHHHHHHHHHHHHCTHHHHTSSEEEEESCGGGCCGGGCCEEE
T ss_pred             CCCCCEEEEEcCCcCHHHHHHHHHhCCCcEEEEEeCCHHHHHHHHHHHHhhcccccCCCcEEEEECCcccCcccCCCcCE
Confidence            3456799999999999999999985 7789999998 556666653           2489999999987433 2 2 88


Q ss_pred             EEe
Q 039903          230 ILI  232 (233)
Q Consensus       230 ~~l  232 (233)
                      ++.
T Consensus       155 i~~  157 (226)
T 1i1n_A          155 IHV  157 (226)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            864

>2nyu_A Putative ribosomal RNA methyltransferase 2; SAM, structural genomics, structural genomics consortium, SGC; HET: SAM; 1.76A {Homo sapiens}

Probab=97.69  E-value=9.3e-05  Score=57.28  Aligned_cols=60  Identities=12%  Similarity=0.173  Sum_probs=47.0

Q ss_pred             HHHhcccccCcceEEEecCCccHHHHHHHHHcCC---------CcEEEeechHHHhhccCCCCceEE-ecCcCC
Q 039903          159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLH---------IKGVNFDLSHVIQDSSSYSGVKHI-GGIMLE  222 (233)
Q Consensus       159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~---------l~~~v~Dlp~v~~~a~~~~ri~~~-~gD~f~  222 (233)
                      +.+.+..+....+|||||||+|.++..+++++|.         .+++.+|+.+..    ..++++++ .+|+.+
T Consensus        13 l~~~~~~~~~~~~vLDlGcG~G~~~~~la~~~~~~~~~~~~~~~~v~~vD~s~~~----~~~~~~~~~~~d~~~   82 (196)
T 2nyu_A           13 VNERHQILRPGLRVLDCGAAPGAWSQVAVQKVNAAGTDPSSPVGFVLGVDLLHIF----PLEGATFLCPADVTD   82 (196)
T ss_dssp             HHHHHCCCCTTCEEEEETCCSCHHHHHHHHHTTTTCCCTTSCCCEEEEECSSCCC----CCTTCEEECSCCTTS
T ss_pred             HHHhcCCCCCCCEEEEeCCCCCHHHHHHHHHhccccccccCCCceEEEEechhcc----cCCCCeEEEeccCCC
Confidence            3344442455689999999999999999999875         789999987631    23678999 999876

>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=97.68  E-value=6.5e-05  Score=62.24  Aligned_cols=64  Identities=17%  Similarity=0.099  Sum_probs=49.4

Q ss_pred             cceEEEecCCccH----HHHHHHHHcC----CCcEEEeech-HHHhhccCC-----------------------------
Q 039903          169 IKQLVDVGGGLGV----NVNIIISNYL----HIKGVNFDLS-HVIQDSSSY-----------------------------  210 (233)
Q Consensus       169 ~~~vvDvGGG~G~----~~~~l~~~~P----~l~~~v~Dlp-~v~~~a~~~-----------------------------  210 (233)
                      ..+|+|+|||+|.    +++.+++..|    +.+++..|+. .+++.|++.                             
T Consensus       106 ~~rIld~GCgTGee~ysiAi~L~e~~~~~~~~~~I~atDis~~~L~~Ar~~~y~~~~~~~~~~~~~~~~f~~~~~~~~~~  185 (274)
T 1af7_A          106 EYRVWSAAASTGEEPYSIAITLADALGMAPGRWKVFASDIDTEVLEKARSGIYRLSELKTLSPQQLQRYFMRGTGPHEGL  185 (274)
T ss_dssp             CEEEEESCCTTTHHHHHHHHHHHHHHCSCTTSEEEEEEESCHHHHHHHHHTEEEGGGGTTSCHHHHHHHEEECCTTSCSE
T ss_pred             CcEEEEeeccCChhHHHHHHHHHHhcccCCCCeEEEEEECCHHHHHHHHhcCCchhhhhcCCHHHHHHHhhccccCCCCc
Confidence            4689999999998    5666777766    4689999994 577776531                             


Q ss_pred             --------CCceEEecCcCC-CCC-C-C-CEEEe
Q 039903          211 --------SGVKHIGGIMLE-RIP-K-G-DAILI  232 (233)
Q Consensus       211 --------~ri~~~~gD~f~-~~P-~-~-D~~~l  232 (233)
                              ++|+|..+|+++ ++| . . |+|+.
T Consensus       186 ~~v~~~lr~~V~F~~~dl~~~~~~~~~~fDlI~c  219 (274)
T 1af7_A          186 VRVRQELANYVEFSSVNLLEKQYNVPGPFDAIFC  219 (274)
T ss_dssp             EEECHHHHTTEEEEECCTTCSSCCCCCCEEEEEE
T ss_pred             eeechhhcccCeEEecccCCCCCCcCCCeeEEEE
Confidence                    269999999999 576 2 3 99875

>3lcv_B Sisomicin-gentamicin resistance methylase SGM; antibiotic resistance, methyltransferase, transferase; HET: SAM; 2.00A {Micromonospora zionensis} PDB: 3lcu_A*

Probab=97.68  E-value=1.4e-05  Score=65.54  Aligned_cols=66  Identities=14%  Similarity=0.040  Sum_probs=54.6

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccCC-----CCceEEecCcCCCCCC--CCEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSSY-----SGVKHIGGIMLERIPK--GDAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~~-----~ri~~~~gD~f~~~P~--~D~~~l  232 (233)
                      ....+|+|||||.|-++..+...+|..+.+.+|+.+ .++.++++     .+.++...|+..+.|.  +|++++
T Consensus       131 ~~p~~VLDLGCG~GpLAl~~~~~~p~a~y~a~DId~~~le~a~~~l~~~g~~~~~~v~D~~~~~p~~~~DvaL~  204 (281)
T 3lcv_B          131 PRPNTLRDLACGLNPLAAPWMGLPAETVYIASDIDARLVGFVDEALTRLNVPHRTNVADLLEDRLDEPADVTLL  204 (281)
T ss_dssp             CCCSEEEETTCTTGGGCCTTTTCCTTCEEEEEESBHHHHHHHHHHHHHTTCCEEEEECCTTTSCCCSCCSEEEE
T ss_pred             CCCceeeeeccCccHHHHHHHhhCCCCEEEEEeCCHHHHHHHHHHHHhcCCCceEEEeeecccCCCCCcchHHH
Confidence            346899999999999999999999999999999964 67666553     5688999999995554  499964

>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=97.67  E-value=5.8e-05  Score=61.52  Aligned_cols=63  Identities=17%  Similarity=0.256  Sum_probs=49.0

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCCCCceEEecCcCC-CCCCC--CEEEe
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSYSGVKHIGGIMLE-RIPKG--DAILI  232 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~~ri~~~~gD~f~-~~P~~--D~~~l  232 (233)
                      ...+|||||||+|.++..++++  ..+++.+|. |..++.+++...-.++.+|+.+ ++|.+  |+++.
T Consensus        54 ~~~~vLDiGcG~G~~~~~l~~~--~~~v~gvD~s~~~l~~a~~~~~~~~~~~d~~~~~~~~~~fD~v~~  120 (260)
T 2avn_A           54 NPCRVLDLGGGTGKWSLFLQER--GFEVVLVDPSKEMLEVAREKGVKNVVEAKAEDLPFPSGAFEAVLA  120 (260)
T ss_dssp             SCCEEEEETCTTCHHHHHHHTT--TCEEEEEESCHHHHHHHHHHTCSCEEECCTTSCCSCTTCEEEEEE
T ss_pred             CCCeEEEeCCCcCHHHHHHHHc--CCeEEEEeCCHHHHHHHHhhcCCCEEECcHHHCCCCCCCEEEEEE
Confidence            5679999999999999999987  568999998 5577777653212388999987 66653  88874

>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=97.64  E-value=4.8e-05  Score=63.13  Aligned_cols=66  Identities=14%  Similarity=-0.007  Sum_probs=52.9

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCCCCCC--CCEEEe
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLERIPK--GDAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~~P~--~D~~~l  232 (233)
                      ++...+|+|+|||+|.+++.++++ ...+++.+|+ |.+++.++++       ++|+++.+|.++-.+.  +|.|+|
T Consensus       123 ~~~g~~VlD~~aG~G~~~i~~a~~-g~~~V~avD~np~a~~~~~~N~~~N~v~~~v~~~~~D~~~~~~~~~~D~Vi~  198 (278)
T 3k6r_A          123 AKPDELVVDMFAGIGHLSLPIAVY-GKAKVIAIEKDPYTFKFLVENIHLNKVEDRMSAYNMDNRDFPGENIADRILM  198 (278)
T ss_dssp             CCTTCEEEETTCTTTTTTHHHHHH-TCCEEEEECCCHHHHHHHHHHHHHTTCTTTEEEECSCTTTCCCCSCEEEEEE
T ss_pred             cCCCCEEEEecCcCcHHHHHHHHh-cCCeEEEEECCHHHHHHHHHHHHHcCCCCcEEEEeCcHHHhccccCCCEEEE
Confidence            455689999999999999999886 5678999998 5677776653       7899999999984444  488776

>2oxt_A Nucleoside-2'-O-methyltransferase; flavivirus, viral enzyme, RNA capping, S-adenosyl-L-methionine, viral protein; HET: SAM; 2.90A {Meaban virus}

Probab=97.61  E-value=9e-05  Score=61.06  Aligned_cols=63  Identities=14%  Similarity=0.066  Sum_probs=47.5

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCC--C------CceEE--ecCcCC-CCCC-CCEEEe
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSY--S------GVKHI--GGIMLE-RIPK-GDAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~--~------ri~~~--~gD~f~-~~P~-~D~~~l  232 (233)
                      +....+|||||||+|.++..++++   -+++.+|+.+.+..+++.  .      +|.++  .+|+++ + +. .|+++.
T Consensus        72 ~~~g~~VLDlGcGtG~~s~~la~~---~~V~gvD~s~m~~~a~~~~~~~~~~~~~v~~~~~~~D~~~l~-~~~fD~V~s  146 (265)
T 2oxt_A           72 VELTGRVVDLGCGRGGWSYYAASR---PHVMDVRAYTLGVGGHEVPRITESYGWNIVKFKSRVDIHTLP-VERTDVIMC  146 (265)
T ss_dssp             CCCCEEEEEESCTTSHHHHHHHTS---TTEEEEEEECCCCSSCCCCCCCCBTTGGGEEEECSCCTTTSC-CCCCSEEEE
T ss_pred             CCCCCEEEEeCcCCCHHHHHHHHc---CcEEEEECchhhhhhhhhhhhhhccCCCeEEEecccCHhHCC-CCCCcEEEE
Confidence            456689999999999999999987   679999986653333221  2      68999  999987 3 33 398874

>1ixk_A Methyltransferase; open beta sheet; 1.90A {Pyrococcus horikoshii} SCOP: c.66.1.38

Probab=97.61  E-value=7.6e-05  Score=62.95  Aligned_cols=71  Identities=13%  Similarity=0.076  Sum_probs=54.5

Q ss_pred             HhcccccCcceEEEecCCccHHHHHHHHHcC-CCcEEEeech-HHHhhccCC------CCceEEecCcCC-C-CCCC-CE
Q 039903          161 DSSKGFEQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDLS-HVIQDSSSY------SGVKHIGGIMLE-R-IPKG-DA  229 (233)
Q Consensus       161 ~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dlp-~v~~~a~~~------~ri~~~~gD~f~-~-~P~~-D~  229 (233)
                      ..++ .....+|+|+|||.|..+..+++..+ ..+++.+|+. ..++.++++      ++|+++.+|+.+ + .+.. |+
T Consensus       112 ~~l~-~~~g~~VLDlg~G~G~~t~~la~~~~~~~~v~avD~s~~~l~~a~~~~~~~g~~~v~~~~~D~~~~~~~~~~fD~  190 (315)
T 1ixk_A          112 VALD-PKPGEIVADMAAAPGGKTSYLAQLMRNDGVIYAFDVDENRLRETRLNLSRLGVLNVILFHSSSLHIGELNVEFDK  190 (315)
T ss_dssp             HHHC-CCTTCEEEECCSSCSHHHHHHHHHTTTCSEEEEECSCHHHHHHHHHHHHHHTCCSEEEESSCGGGGGGGCCCEEE
T ss_pred             HHhC-CCCCCEEEEeCCCCCHHHHHHHHHhCCCCEEEEEcCCHHHHHHHHHHHHHhCCCeEEEEECChhhcccccccCCE
Confidence            3344 56668999999999999999999975 5889999984 466666543      579999999987 3 2333 88


Q ss_pred             EEe
Q 039903          230 ILI  232 (233)
Q Consensus       230 ~~l  232 (233)
                      |++
T Consensus       191 Il~  193 (315)
T 1ixk_A          191 ILL  193 (315)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            875

>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A

Probab=97.61  E-value=4.6e-05  Score=49.26  Aligned_cols=56  Identities=9%  Similarity=0.287  Sum_probs=47.9

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceecc
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLA   82 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt   82 (233)
                      .+..|.+.|...+  .++|..|||+.+++    +...+.+++..|...|++...    ..+.|+++
T Consensus        11 ~~~~IL~~L~~~~--~~~s~~eLA~~lgl----sr~tv~~~l~~L~~~G~I~~~----~~G~y~lg   66 (67)
T 2heo_A           11 LEQKILQVLSDDG--GPVAIFQLVKKCQV----PKKTLNQVLYRLKKEDRVSSP----SPKYWSIG   66 (67)
T ss_dssp             HHHHHHHHHHHHC--SCEEHHHHHHHHCS----CHHHHHHHHHHHHHTTSEEEE----ETTEEEEC
T ss_pred             HHHHHHHHHHHcC--CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCcEecC----CCceEeeC
Confidence            3567899998764  48999999999999    999999999999999999875    46788764

>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=97.61  E-value=7e-05  Score=61.62  Aligned_cols=51  Identities=12%  Similarity=0.075  Sum_probs=40.1

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY  210 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~  210 (233)
                      ..+++.++ .....+|||||||+|.++..++++  ..+++.+|+. ..++.++++
T Consensus        35 ~~il~~l~-l~~g~~VLDlGcGtG~~a~~La~~--g~~V~gvD~S~~ml~~Ar~~   86 (261)
T 3iv6_A           35 ENDIFLEN-IVPGSTVAVIGASTRFLIEKALER--GASVTVFDFSQRMCDDLAEA   86 (261)
T ss_dssp             HHHHHTTT-CCTTCEEEEECTTCHHHHHHHHHT--TCEEEEEESCHHHHHHHHHH
T ss_pred             HHHHHhcC-CCCcCEEEEEeCcchHHHHHHHhc--CCEEEEEECCHHHHHHHHHH
Confidence            44555555 666789999999999999999987  4579999984 577777653

>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=97.60  E-value=8.3e-05  Score=61.65  Aligned_cols=63  Identities=16%  Similarity=0.084  Sum_probs=47.6

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCC--C------CceEE--ecCcCC-CCCC-CCEEEe
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSY--S------GVKHI--GGIMLE-RIPK-GDAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~--~------ri~~~--~gD~f~-~~P~-~D~~~l  232 (233)
                      +....+|||||||+|.++..++++   -+++.+|+.+.+..+++.  .      +|+++  .+|+.+ + +. .|+++.
T Consensus        80 ~~~g~~VLDlGcGtG~~s~~la~~---~~V~gVD~s~m~~~a~~~~~~~~~~~~~v~~~~~~~D~~~l~-~~~fD~Vvs  154 (276)
T 2wa2_A           80 VELKGTVVDLGCGRGSWSYYAASQ---PNVREVKAYTLGTSGHEKPRLVETFGWNLITFKSKVDVTKME-PFQADTVLC  154 (276)
T ss_dssp             CCCCEEEEEESCTTCHHHHHHHTS---TTEEEEEEECCCCTTSCCCCCCCCTTGGGEEEECSCCGGGCC-CCCCSEEEE
T ss_pred             CCCCCEEEEeccCCCHHHHHHHHc---CCEEEEECchhhhhhhhchhhhhhcCCCeEEEeccCcHhhCC-CCCcCEEEE
Confidence            456689999999999999999987   579999987653333221  2      78999  999987 3 33 398874

>3o4f_A Spermidine synthase; aminopropyltransferase, polyamine synthase, rossmann fold, P biosynthesis, spermidine biosynthesis, transferase; 2.90A {Escherichia coli}

Probab=97.59  E-value=0.0001  Score=61.56  Aligned_cols=66  Identities=14%  Similarity=0.114  Sum_probs=54.0

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccC-----------CCCceEEecCcCCCC--CC-C-CEE
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSS-----------YSGVKHIGGIMLERI--PK-G-DAI  230 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~-----------~~ri~~~~gD~f~~~--P~-~-D~~  230 (233)
                      +++++|+=||||.|..++++++..|.-+++++|+ |.|++.+++           .+|++.+.+|-++-+  .. . |+|
T Consensus        82 p~pk~VLIiGgGdG~~~revlk~~~v~~v~~VEID~~Vv~~a~~~lp~~~~~~~~dpRv~v~~~Dg~~~l~~~~~~yDvI  161 (294)
T 3o4f_A           82 GHAKHVLIIGGGDGAMLREVTRHKNVESITMVEIDAGVVSFCRQYLPNHNAGSYDDPRFKLVIDDGVNFVNQTSQTFDVI  161 (294)
T ss_dssp             SCCCEEEEESCTTSHHHHHHHTCTTCCEEEEEESCHHHHHHHHHHCHHHHTTGGGCTTEEEEESCTTTTTSCSSCCEEEE
T ss_pred             CCCCeEEEECCCchHHHHHHHHcCCcceEEEEcCCHHHHHHHHhcCccccccccCCCcEEEEechHHHHHhhccccCCEE
Confidence            5678999999999999999999777788999998 568887654           279999999999832  22 3 888


Q ss_pred             Ee
Q 039903          231 LI  232 (233)
Q Consensus       231 ~l  232 (233)
                      ++
T Consensus       162 i~  163 (294)
T 3o4f_A          162 IS  163 (294)
T ss_dssp             EE
T ss_pred             EE
Confidence            75

>2r6z_A UPF0341 protein in RSP 3' region; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 1.80A {Neisseria gonorrhoeae}

Probab=97.54  E-value=6.4e-05  Score=61.69  Aligned_cols=65  Identities=15%  Similarity=0.162  Sum_probs=49.9

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech--------HHHhhccCC-------CCceEEecCcCCC---CC--
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS--------HVIQDSSSY-------SGVKHIGGIMLER---IP--  225 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp--------~v~~~a~~~-------~ri~~~~gD~f~~---~P--  225 (233)
                      .....+|+|+|||+|.++..+++.  ..+++.+|+.        +.++.++.+       +||+++.+|..+-   +|  
T Consensus        81 ~~~~~~VLDlgcG~G~~a~~lA~~--g~~V~~vD~s~~~~~ll~~~l~~a~~n~~~~~~~~ri~~~~~d~~~~l~~~~~~  158 (258)
T 2r6z_A           81 HTAHPTVWDATAGLGRDSFVLASL--GLTVTAFEQHPAVACLLSDGIRRALLNPETQDTAARINLHFGNAAEQMPALVKT  158 (258)
T ss_dssp             GGGCCCEEETTCTTCHHHHHHHHT--TCCEEEEECCHHHHHHHHHHHHHHHHSHHHHHHHTTEEEEESCHHHHHHHHHHH
T ss_pred             cCCcCeEEEeeCccCHHHHHHHHh--CCEEEEEECChhhhHHHHHHHHHHHhHHHhhCCccCeEEEECCHHHHHHhhhcc
Confidence            444578999999999999999996  4689999984        455555543       5799999999872   43  


Q ss_pred             -C-CCEEEe
Q 039903          226 -K-GDAILI  232 (233)
Q Consensus       226 -~-~D~~~l  232 (233)
                       . .|+|++
T Consensus       159 ~~~fD~V~~  167 (258)
T 2r6z_A          159 QGKPDIVYL  167 (258)
T ss_dssp             HCCCSEEEE
T ss_pred             CCCccEEEE
Confidence             3 398876

>3ajd_A Putative methyltransferase MJ0026; tRNA, M5C, rossmann fold, structural genomics, riken structu genomics/proteomics initiative; 1.27A {Methanocaldococcus jannaschii} PDB: 3a4t_A

Probab=97.54  E-value=6e-05  Score=62.21  Aligned_cols=67  Identities=15%  Similarity=0.023  Sum_probs=52.6

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCC-CcEEEeech-HHHhhccCC------CCceEEecCcCC-CC-----CCC-CEE
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLH-IKGVNFDLS-HVIQDSSSY------SGVKHIGGIMLE-RI-----PKG-DAI  230 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~-l~~~v~Dlp-~v~~~a~~~------~ri~~~~gD~f~-~~-----P~~-D~~  230 (233)
                      .....+|+|+|||+|..+..+++..++ .+++.+|+. ..++.++++      ++|+++.+|+.+ +.     +.. |+|
T Consensus        81 ~~~g~~VLDlgaG~G~~t~~la~~~~~~~~v~avD~~~~~l~~~~~~~~~~g~~~v~~~~~D~~~~~~~~~~~~~~fD~V  160 (274)
T 3ajd_A           81 PREDDFILDMCAAPGGKTTHLAQLMKNKGTIVAVEISKTRTKALKSNINRMGVLNTIIINADMRKYKDYLLKNEIFFDKI  160 (274)
T ss_dssp             CCTTCEEEETTCTTCHHHHHHHHHTTTCSEEEEEESCHHHHHHHHHHHHHTTCCSEEEEESCHHHHHHHHHHTTCCEEEE
T ss_pred             CCCcCEEEEeCCCccHHHHHHHHHcCCCCEEEEECCCHHHHHHHHHHHHHhCCCcEEEEeCChHhcchhhhhccccCCEE
Confidence            455679999999999999999999887 889999985 456665542      589999999987 32     333 888


Q ss_pred             Ee
Q 039903          231 LI  232 (233)
Q Consensus       231 ~l  232 (233)
                      ++
T Consensus       161 l~  162 (274)
T 3ajd_A          161 LL  162 (274)
T ss_dssp             EE
T ss_pred             EE
Confidence            74

>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=97.51  E-value=9.7e-05  Score=51.02  Aligned_cols=61  Identities=15%  Similarity=0.175  Sum_probs=52.3

Q ss_pred             HHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhh
Q 039903           12 AMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAK   86 (233)
Q Consensus        12 ~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~   86 (233)
                      ++..-.++.|++.| .    ++.|..|||+.+++    +...+.+.|+.|...|++.+.    . +.|++|+.+.
T Consensus        27 ~l~~~~r~~Il~~L-~----~~~~~~eLa~~l~i----s~~tv~~~L~~L~~~Glv~~~----~-g~y~l~~~g~   87 (96)
T 1y0u_A           27 AVTNPVRRKILRML-D----KGRSEEEIMQTLSL----SKKQLDYHLKVLEAGFCIERV----G-ERWVVTDAGK   87 (96)
T ss_dssp             HHSCHHHHHHHHHH-H----TTCCHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEE----T-TEEEECTTTC
T ss_pred             HhCCHHHHHHHHHH-c----CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEE----C-CEEEECCCch
Confidence            44444577899999 5    58999999999999    999999999999999999987    5 6899998654

>3sso_A Methyltransferase; macrolide, natural product, rossman fold; HET: SAH; 1.90A {Micromonospora griseorubida} PDB: 3ssn_A* 3ssm_A*

Probab=97.51  E-value=9.2e-05  Score=64.40  Aligned_cols=63  Identities=13%  Similarity=0.133  Sum_probs=48.1

Q ss_pred             CcceEEEecCC------ccHHHHHHHHH-cCCCcEEEeechHHHhhccCCCCceEEecCcCC-CCC------C-C-CEEE
Q 039903          168 QIKQLVDVGGG------LGVNVNIIISN-YLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLE-RIP------K-G-DAIL  231 (233)
Q Consensus       168 ~~~~vvDvGGG------~G~~~~~l~~~-~P~l~~~v~Dlp~v~~~a~~~~ri~~~~gD~f~-~~P------~-~-D~~~  231 (233)
                      +..+|||||||      +|..+..++++ +|+.+++.+|+.+...  ...++|+++.+|+.+ +++      . . |+|+
T Consensus       216 ~~~rVLDIGCG~~~~~~TGG~Sl~la~~~fP~a~V~GVDiSp~m~--~~~~rI~fv~GDa~dlpf~~~l~~~d~sFDlVi  293 (419)
T 3sso_A          216 QQVRVLEIGVGGYKHPEWGGGSLRMWKSFFPRGQIYGLDIMDKSH--VDELRIRTIQGDQNDAEFLDRIARRYGPFDIVI  293 (419)
T ss_dssp             SCCEEEEECCSCTTCSSCCCHHHHHHHHHCTTCEEEEEESSCCGG--GCBTTEEEEECCTTCHHHHHHHHHHHCCEEEEE
T ss_pred             CCCEEEEEecCCCcCCCCCHHHHHHHHHhCCCCEEEEEECCHHHh--hcCCCcEEEEecccccchhhhhhcccCCccEEE
Confidence            35799999999      67777777766 5999999999965432  234799999999988 555      2 2 8886


Q ss_pred             e
Q 039903          232 I  232 (233)
Q Consensus       232 l  232 (233)
                      .
T Consensus       294 s  294 (419)
T 3sso_A          294 D  294 (419)
T ss_dssp             E
T ss_pred             E
Confidence            3

>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=97.50  E-value=0.00011  Score=63.61  Aligned_cols=63  Identities=14%  Similarity=0.094  Sum_probs=50.4

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-----CCceEEecCcCCC-CC-CC-CEEEe
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-----SGVKHIGGIMLER-IP-KG-DAILI  232 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-----~ri~~~~gD~f~~-~P-~~-D~~~l  232 (233)
                      ...+|+|+|||+|.++..++++  ..+++.+|. +..++.++++     .+++++.+|+++. .+ .. |+|+.
T Consensus       233 ~~~~VLDlGcG~G~~~~~la~~--g~~V~gvDis~~al~~A~~n~~~~~~~v~~~~~D~~~~~~~~~~fD~Ii~  304 (381)
T 3dmg_A          233 RGRQVLDLGAGYGALTLPLARM--GAEVVGVEDDLASVLSLQKGLEANALKAQALHSDVDEALTEEARFDIIVT  304 (381)
T ss_dssp             TTCEEEEETCTTSTTHHHHHHT--TCEEEEEESBHHHHHHHHHHHHHTTCCCEEEECSTTTTSCTTCCEEEEEE
T ss_pred             CCCEEEEEeeeCCHHHHHHHHc--CCEEEEEECCHHHHHHHHHHHHHcCCCeEEEEcchhhccccCCCeEEEEE
Confidence            4479999999999999999998  568999998 5577777653     3599999999984 44 23 99875

>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=97.43  E-value=0.00014  Score=61.09  Aligned_cols=64  Identities=16%  Similarity=0.053  Sum_probs=46.7

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-----hHHHhhcc--CC--CCceEEec-CcCC-CCCCCCEEEe
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-----SHVIQDSS--SY--SGVKHIGG-IMLE-RIPKGDAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-----p~v~~~a~--~~--~ri~~~~g-D~f~-~~P~~D~~~l  232 (233)
                      ++...+|||||||+|.++..++++   -+++.+|+     +..++...  ..  ++|+++.+ |+++ +....|+|+.
T Consensus        80 ~~~g~~VLDlGcG~G~~s~~la~~---~~V~gvD~~~~~~~~~~~~~~~~~~~~~~v~~~~~~D~~~l~~~~fD~V~s  154 (305)
T 2p41_A           80 VTPEGKVVDLGCGRGGWSYYCGGL---KNVREVKGLTKGGPGHEEPIPMSTYGWNLVRLQSGVDVFFIPPERCDTLLC  154 (305)
T ss_dssp             SCCCEEEEEETCTTSHHHHHHHTS---TTEEEEEEECCCSTTSCCCCCCCSTTGGGEEEECSCCTTTSCCCCCSEEEE
T ss_pred             CCCCCEEEEEcCCCCHHHHHHHhc---CCEEEEeccccCchhHHHHHHhhhcCCCCeEEEeccccccCCcCCCCEEEE
Confidence            455689999999999999999987   37888998     43333222  12  57999999 9987 3223498874

>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=97.40  E-value=0.00044  Score=55.81  Aligned_cols=57  Identities=11%  Similarity=0.040  Sum_probs=47.0

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHc-CCCcEEEeec-hHHHhhcc----CCCCceEEecCcCC
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNY-LHIKGVNFDL-SHVIQDSS----SYSGVKHIGGIMLE  222 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~v~~~a~----~~~ri~~~~gD~f~  222 (233)
                      .+...+|+|+|||+|.++..+++.- |+=+++.+|. |+.++.++    +..+|..+.+|...
T Consensus        75 ikpG~~VldlG~G~G~~~~~la~~VG~~G~V~avD~s~~~~~~l~~~a~~~~ni~~V~~d~~~  137 (233)
T 4df3_A           75 VKEGDRILYLGIASGTTASHMSDIIGPRGRIYGVEFAPRVMRDLLTVVRDRRNIFPILGDARF  137 (233)
T ss_dssp             CCTTCEEEEETCTTSHHHHHHHHHHCTTCEEEEEECCHHHHHHHHHHSTTCTTEEEEESCTTC
T ss_pred             CCCCCEEEEecCcCCHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhHhhcCeeEEEEeccC
Confidence            6778999999999999999999984 8989999998 45665543    34689999888876

>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=97.38  E-value=0.00071  Score=54.58  Aligned_cols=67  Identities=10%  Similarity=0.080  Sum_probs=51.3

Q ss_pred             ccCcceEEEecCCccHHHHHHHHH-cCCCcEEEeechH-H----HhhccCCCCceEEecCcCCCC-----CC-CCEEEe
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISN-YLHIKGVNFDLSH-V----IQDSSSYSGVKHIGGIMLERI-----PK-GDAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~-~P~l~~~v~Dlp~-v----~~~a~~~~ri~~~~gD~f~~~-----P~-~D~~~l  232 (233)
                      ++...+|+|+|||+|.++..+++. .|+-+++.+|+.+ .    ++.+++..+|.++.+|..++.     +. .|+++.
T Consensus        74 l~~g~~VLDlG~GtG~~t~~la~~v~~~G~V~avD~s~~~l~~l~~~a~~r~nv~~i~~Da~~~~~~~~~~~~~D~I~~  152 (232)
T 3id6_C           74 IRKGTKVLYLGAASGTTISHVSDIIELNGKAYGVEFSPRVVRELLLVAQRRPNIFPLLADARFPQSYKSVVENVDVLYV  152 (232)
T ss_dssp             CCTTCEEEEETCTTSHHHHHHHHHHTTTSEEEEEECCHHHHHHHHHHHHHCTTEEEEECCTTCGGGTTTTCCCEEEEEE
T ss_pred             CCCCCEEEEEeecCCHHHHHHHHHhCCCCEEEEEECcHHHHHHHHHHhhhcCCeEEEEcccccchhhhccccceEEEEe
Confidence            566789999999999999999987 4688899999854 3    344544578999999987631     22 388864

>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=97.34  E-value=0.00035  Score=64.24  Aligned_cols=95  Identities=21%  Similarity=0.185  Sum_probs=63.3

Q ss_pred             cccccccCchHHHHHHHHHHhcchhcHHHHHHhccc---ccCcceEEEecCCccHHHHHHHHH----cCCCcEEEeechH
Q 039903          130 FYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKG---FEQIKQLVDVGGGLGVNVNIIISN----YLHIKGVNFDLSH  202 (233)
Q Consensus       130 ~~~~~~~~~~~~~~f~~am~~~~~~~~~~~~~~~~~---~~~~~~vvDvGGG~G~~~~~l~~~----~P~l~~~v~Dlp~  202 (233)
                      .||.+++||-.-..|.+|+..       .+....+.   -.+...|+|||+|+|-++...+++    .-++++..++-.+
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            366777888777777777653       22222110   234578999999999874333332    2334677788766


Q ss_pred             HHhhccCC-------CCceEEecCcCC-CCCCC-CEEE
Q 039903          203 VIQDSSSY-------SGVKHIGGIMLE-RIPKG-DAIL  231 (233)
Q Consensus       203 v~~~a~~~-------~ri~~~~gD~f~-~~P~~-D~~~  231 (233)
                      .+..+++.       ++|+++.||+.+ .+|+. |+++
T Consensus       396 ~A~~a~~~v~~N~~~dkVtVI~gd~eev~LPEKVDIIV  433 (637)
T 4gqb_A          396 NAVVTLENWQFEEWGSQVTVVSSDMREWVAPEKADIIV  433 (637)
T ss_dssp             HHHHHHHHHHHHTTGGGEEEEESCTTTCCCSSCEEEEE
T ss_pred             HHHHHHHHHHhccCCCeEEEEeCcceeccCCcccCEEE
Confidence            55555441       799999999999 89984 9885

>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=97.34  E-value=9.1e-05  Score=63.03  Aligned_cols=63  Identities=16%  Similarity=0.092  Sum_probs=49.8

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------C-CceEEecCcCCCC------CC-CCEEE
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------S-GVKHIGGIMLERI------PK-GDAIL  231 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~-ri~~~~gD~f~~~------P~-~D~~~  231 (233)
                      +..+|||+|||+|.++..+++...  +++.+|+ +..++.++++       + +++++.+|+++..      .. .|+|+
T Consensus       153 ~~~~VLDlgcGtG~~sl~la~~ga--~V~~VD~s~~al~~a~~n~~~~gl~~~~v~~i~~D~~~~l~~~~~~~~~fD~Ii  230 (332)
T 2igt_A          153 RPLKVLNLFGYTGVASLVAAAAGA--EVTHVDASKKAIGWAKENQVLAGLEQAPIRWICEDAMKFIQREERRGSTYDIIL  230 (332)
T ss_dssp             SCCEEEEETCTTCHHHHHHHHTTC--EEEEECSCHHHHHHHHHHHHHHTCTTSCEEEECSCHHHHHHHHHHHTCCBSEEE
T ss_pred             CCCcEEEcccccCHHHHHHHHcCC--EEEEEECCHHHHHHHHHHHHHcCCCccceEEEECcHHHHHHHHHhcCCCceEEE
Confidence            446899999999999999999754  8999998 5577777653       2 5999999999732      22 39987


Q ss_pred             e
Q 039903          232 I  232 (233)
Q Consensus       232 l  232 (233)
                      +
T Consensus       231 ~  231 (332)
T 2igt_A          231 T  231 (332)
T ss_dssp             E
T ss_pred             E
Confidence            6

>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=97.34  E-value=0.00017  Score=61.43  Aligned_cols=66  Identities=11%  Similarity=0.093  Sum_probs=52.5

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCC-----CcEEEeec-hHHHhhccCC-----CCceEEecCcCCCCCC-C-CEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLH-----IKGVNFDL-SHVIQDSSSY-----SGVKHIGGIMLERIPK-G-DAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~-----l~~~v~Dl-p~v~~~a~~~-----~ri~~~~gD~f~~~P~-~-D~~~l  232 (233)
                      ....+|+|+|||+|.++..+++..|.     .+++.+|+ |..++.|+.+     .+++++.+|.+++.+. . |+|+.
T Consensus       129 ~~~~~VlDp~cGsG~~l~~~~~~~~~~~~~~~~v~GiDi~~~~~~~a~~n~~~~g~~~~i~~~D~l~~~~~~~fD~Ii~  207 (344)
T 2f8l_A          129 KKNVSILDPACGTANLLTTVINQLELKGDVDVHASGVDVDDLLISLALVGADLQRQKMTLLHQDGLANLLVDPVDVVIS  207 (344)
T ss_dssp             CSEEEEEETTCTTSHHHHHHHHHHHTTSSCEEEEEEEESCHHHHHHHHHHHHHHTCCCEEEESCTTSCCCCCCEEEEEE
T ss_pred             CCCCEEEeCCCCccHHHHHHHHHHHHhcCCCceEEEEECCHHHHHHHHHHHHhCCCCceEEECCCCCccccCCccEEEE
Confidence            34579999999999999999998875     68899998 5577766653     3689999999986553 3 88763

>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=97.33  E-value=0.00019  Score=61.09  Aligned_cols=63  Identities=19%  Similarity=0.113  Sum_probs=50.6

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCCCCCCCCEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLERIPKGDAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~~P~~D~~~l  232 (233)
                      .+..+|+|+|||+|.++.. ++  ...+++.+|+ |..++.++++       ++++++.+|.++.....|++++
T Consensus       194 ~~~~~VLDlg~G~G~~~l~-a~--~~~~V~~vD~s~~ai~~a~~n~~~n~l~~~v~~~~~D~~~~~~~fD~Vi~  264 (336)
T 2yx1_A          194 SLNDVVVDMFAGVGPFSIA-CK--NAKKIYAIDINPHAIELLKKNIKLNKLEHKIIPILSDVREVDVKGNRVIM  264 (336)
T ss_dssp             CTTCEEEETTCTTSHHHHH-TT--TSSEEEEEESCHHHHHHHHHHHHHTTCTTTEEEEESCGGGCCCCEEEEEE
T ss_pred             CCCCEEEEccCccCHHHHh-cc--CCCEEEEEECCHHHHHHHHHHHHHcCCCCcEEEEECChHHhcCCCcEEEE
Confidence            4567999999999999999 77  5778999998 6677777653       5899999999985423488876

>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=97.32  E-value=0.00036  Score=61.29  Aligned_cols=63  Identities=14%  Similarity=0.107  Sum_probs=50.5

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCCCCCC-CCEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLERIPK-GDAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~~P~-~D~~~l  232 (233)
                      .+..+|+|+|||+|.++..+++.  ..+++.+|. |+.++.|+++      + ++++.+|+++..+. .|++++
T Consensus       289 ~~~~~VLDlgcG~G~~sl~la~~--~~~V~gvD~s~~ai~~A~~n~~~ngl~-v~~~~~d~~~~~~~~fD~Vv~  359 (425)
T 2jjq_A          289 VEGEKILDMYSGVGTFGIYLAKR--GFNVKGFDSNEFAIEMARRNVEINNVD-AEFEVASDREVSVKGFDTVIV  359 (425)
T ss_dssp             CCSSEEEEETCTTTHHHHHHHHT--TCEEEEEESCHHHHHHHHHHHHHHTCC-EEEEECCTTTCCCTTCSEEEE
T ss_pred             CCCCEEEEeeccchHHHHHHHHc--CCEEEEEECCHHHHHHHHHHHHHcCCc-EEEEECChHHcCccCCCEEEE
Confidence            44578999999999999999987  457999998 4677777653      4 99999999985554 488875

>3bzb_A Uncharacterized protein; RED ALGA, protein structure initiat center for eukaryotic structural genomics, CESG, structural genomics; 2.79A {Cyanidioschyzon merolae}

Probab=97.31  E-value=0.00046  Score=57.06  Aligned_cols=65  Identities=14%  Similarity=0.110  Sum_probs=45.9

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec--hHHHhhccCC----------------CCceEEecCcCC---CC-
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL--SHVIQDSSSY----------------SGVKHIGGIMLE---RI-  224 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl--p~v~~~a~~~----------------~ri~~~~gD~f~---~~-  224 (233)
                      ....+|+|||||+|.++..+++. ...+++.+|+  |.+++.++++                ++|+++..|+-+   .+ 
T Consensus        78 ~~~~~vLDlG~G~G~~~~~~a~~-~~~~v~~~D~s~~~~~~~a~~n~~~N~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~  156 (281)
T 3bzb_A           78 IAGKTVCELGAGAGLVSIVAFLA-GADQVVATDYPDPEILNSLESNIREHTANSCSSETVKRASPKVVPYRWGDSPDSLQ  156 (281)
T ss_dssp             TTTCEEEETTCTTSHHHHHHHHT-TCSEEEEEECSCHHHHHHHHHHHHTTCC----------CCCEEEECCTTSCTHHHH
T ss_pred             cCCCeEEEecccccHHHHHHHHc-CCCEEEEEeCCCHHHHHHHHHHHHHhhhhhcccccCCCCCeEEEEecCCCccHHHH
Confidence            44579999999999999988886 3458999999  4676655431                378888666543   22 


Q ss_pred             ---C-C-CCEEEe
Q 039903          225 ---P-K-GDAILI  232 (233)
Q Consensus       225 ---P-~-~D~~~l  232 (233)
                         + . .|+|++
T Consensus       157 ~~~~~~~fD~Ii~  169 (281)
T 3bzb_A          157 RCTGLQRFQVVLL  169 (281)
T ss_dssp             HHHSCSSBSEEEE
T ss_pred             hhccCCCCCEEEE
Confidence               2 2 388874

>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=97.31  E-value=0.00037  Score=57.64  Aligned_cols=56  Identities=25%  Similarity=0.281  Sum_probs=44.4

Q ss_pred             cCcceEEEecCCc--cHHHHHH-HHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCC
Q 039903          167 EQIKQLVDVGGGL--GVNVNII-ISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLE  222 (233)
Q Consensus       167 ~~~~~vvDvGGG~--G~~~~~l-~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~  222 (233)
                      .++.++||||||.  +.+..++ .+.+|+.+++.+|. |.+++.|++.      .+++++.+|+.+
T Consensus        77 ~g~~q~LDLGcG~pT~~~~~~la~~~~P~arVv~VD~sp~mLa~Ar~~l~~~~~~~~~~v~aD~~~  142 (277)
T 3giw_A           77 AGIRQFLDIGTGIPTSPNLHEIAQSVAPESRVVYVDNDPIVLTLSQGLLASTPEGRTAYVEADMLD  142 (277)
T ss_dssp             SCCCEEEEESCCSCCSSCHHHHHHHHCTTCEEEEEECCHHHHHTTHHHHCCCSSSEEEEEECCTTC
T ss_pred             cCCCEEEEeCCCCCcccHHHHHHHHHCCCCEEEEEeCChHHHHHHHHHhccCCCCcEEEEEecccC
Confidence            4678999999997  3344444 45689999999998 7799888752      379999999987

>2i62_A Nicotinamide N-methyltransferase; structural genomics, structural genomics consortium, SGC; HET: SAH; 1.80A {Mus musculus} PDB: 2iip_A* 3rod_A*

Probab=97.29  E-value=8e-05  Score=60.37  Aligned_cols=42  Identities=12%  Similarity=0.150  Sum_probs=33.8

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccC
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSS  209 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~  209 (233)
                      .+..+|||||||+|.++..+++..+ .+++.+|+. ..++.+++
T Consensus        55 ~~~~~vLDlGcG~G~~~~~l~~~~~-~~v~gvD~s~~~l~~a~~   97 (265)
T 2i62_A           55 VKGELLIDIGSGPTIYQLLSACESF-TEIIVSDYTDQNLWELQK   97 (265)
T ss_dssp             CCEEEEEEESCTTCCGGGTTGGGTE-EEEEEEESCHHHHHHHHH
T ss_pred             cCCCEEEEECCCccHHHHHHhhccc-CeEEEecCCHHHHHHHHH
Confidence            4457999999999999999988876 679999984 56666643

>2yxl_A PH0851 protein, 450AA long hypothetical FMU protein; FMU-homolog, methyltransferase, structural genomics, NPPSFA; HET: SFG; 2.55A {Pyrococcus horikoshii}

Probab=97.28  E-value=0.00038  Score=61.59  Aligned_cols=71  Identities=15%  Similarity=0.084  Sum_probs=54.8

Q ss_pred             HhcccccCcceEEEecCCccHHHHHHHHHcCC-CcEEEeech-HHHhhccCC------CCceEEecCcCC-C--CC-CC-
Q 039903          161 DSSKGFEQIKQLVDVGGGLGVNVNIIISNYLH-IKGVNFDLS-HVIQDSSSY------SGVKHIGGIMLE-R--IP-KG-  227 (233)
Q Consensus       161 ~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~-l~~~v~Dlp-~v~~~a~~~------~ri~~~~gD~f~-~--~P-~~-  227 (233)
                      ..++ .....+|+|+|||.|..+..+++..++ .+++.+|+. ..++.++++      ++|+++.+|+.+ +  ++ .. 
T Consensus       253 ~~l~-~~~g~~VLDlgaG~G~~t~~la~~~~~~~~v~a~D~s~~~l~~~~~~~~~~g~~~v~~~~~D~~~~~~~~~~~~f  331 (450)
T 2yxl_A          253 IVLD-PKPGETVVDLAAAPGGKTTHLAELMKNKGKIYAFDVDKMRMKRLKDFVKRMGIKIVKPLVKDARKAPEIIGEEVA  331 (450)
T ss_dssp             HHHC-CCTTCEEEESSCTTCHHHHHHHHHTTTCSEEEEECSCHHHHHHHHHHHHHTTCCSEEEECSCTTCCSSSSCSSCE
T ss_pred             HhcC-CCCcCEEEEeCCCccHHHHHHHHHcCCCCEEEEEcCCHHHHHHHHHHHHHcCCCcEEEEEcChhhcchhhccCCC
Confidence            3344 556679999999999999999999887 889999985 456555432      579999999987 3  55 33 


Q ss_pred             CEEEe
Q 039903          228 DAILI  232 (233)
Q Consensus       228 D~~~l  232 (233)
                      |+|++
T Consensus       332 D~Vl~  336 (450)
T 2yxl_A          332 DKVLL  336 (450)
T ss_dssp             EEEEE
T ss_pred             CEEEE
Confidence            98875

>3mq0_A Transcriptional repressor of the blcabc operon; helix-turn-helix, GAF fold, transcription repressor; 1.79A {Agrobacterium tumefaciens}

Probab=97.28  E-value=0.00018  Score=59.50  Aligned_cols=61  Identities=8%  Similarity=0.181  Sum_probs=50.3

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHh
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYF   88 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l   88 (233)
                      =+.|++.|...+  ++.|+.|||+.+|+    +...+.|+|+.|+..|+++++    ++++|++++....|
T Consensus        32 al~IL~~l~~~~--~~ltl~eia~~lgl----~ksTv~RlL~tL~~~G~v~~~----~~~~Y~LG~~~~~l   92 (275)
T 3mq0_A           32 AVRILDLVAGSP--RDLTAAELTRFLDL----PKSSAHGLLAVMTELDLLARS----ADGTLRIGPHSLRW   92 (275)
T ss_dssp             HHHHHHHHHHCS--SCEEHHHHHHHHTC----C--CHHHHHHHHHHTTSEEEC----TTSEEEECTHHHHH
T ss_pred             HHHHHHHHhhCC--CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEC----CCCcEEehHHHHHH
Confidence            356899998865  58999999999999    999999999999999999997    56789999864433

>4azs_A Methyltransferase WBDD; kinase; HET: AMP SAM; 2.15A {Escherichia coli} PDB: 4azt_A* 4azv_A* 4azw_A*

Probab=97.27  E-value=0.00017  Score=65.80  Aligned_cols=63  Identities=16%  Similarity=0.148  Sum_probs=48.3

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC------CCceEEecCcCC---CCCC-C-CEEE
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY------SGVKHIGGIMLE---RIPK-G-DAIL  231 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~------~ri~~~~gD~f~---~~P~-~-D~~~  231 (233)
                      .+..+|||||||.|.++..+++.  ..+++++|+. ..|+.|+.+      -.|+|..+|.-+   +.+. . |+|+
T Consensus        65 ~~~~~vLDvGCG~G~~~~~la~~--ga~V~giD~~~~~i~~a~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~fD~v~  139 (569)
T 4azs_A           65 GRPLNVLDLGCAQGFFSLSLASK--GATIVGIDFQQENINVCRALAEENPDFAAEFRVGRIEEVIAALEEGEFDLAI  139 (569)
T ss_dssp             TSCCEEEEETCTTSHHHHHHHHT--TCEEEEEESCHHHHHHHHHHHHTSTTSEEEEEECCHHHHHHHCCTTSCSEEE
T ss_pred             CCCCeEEEECCCCcHHHHHHHhC--CCEEEEECCCHHHHHHHHHHHHhcCCCceEEEECCHHHHhhhccCCCccEEE
Confidence            34568999999999999999997  6679999985 577766542      258999998764   3443 2 9886

>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=97.25  E-value=0.00051  Score=56.81  Aligned_cols=64  Identities=13%  Similarity=0.111  Sum_probs=52.8

Q ss_pred             HHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC--CCceEEecCcCC
Q 039903          156 TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY--SGVKHIGGIMLE  222 (233)
Q Consensus       156 ~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~--~ri~~~~gD~f~  222 (233)
                      ...+++.+. .+....+||++||.|.++.+|+++  +.+++.+|. |.+++.+++.  +|++++.+||-+
T Consensus        11 l~e~le~L~-~~~gg~~VD~T~G~GGHS~~il~~--~g~VigiD~Dp~Ai~~A~~L~~~rv~lv~~~f~~   77 (285)
T 1wg8_A           11 YQEALDLLA-VRPGGVYVDATLGGAGHARGILER--GGRVIGLDQDPEAVARAKGLHLPGLTVVQGNFRH   77 (285)
T ss_dssp             HHHHHHHHT-CCTTCEEEETTCTTSHHHHHHHHT--TCEEEEEESCHHHHHHHHHTCCTTEEEEESCGGG
T ss_pred             HHHHHHhhC-CCCCCEEEEeCCCCcHHHHHHHHC--CCEEEEEeCCHHHHHHHHhhccCCEEEEECCcch
Confidence            466777776 677789999999999999999998  778999998 4577665432  699999999975

>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=97.24  E-value=0.00038  Score=46.38  Aligned_cols=62  Identities=8%  Similarity=0.100  Sum_probs=52.1

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChh-hHHHHHHHHhcCCceeeeccCCCCCceeccHhhhH
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAV-MLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKY   87 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~-~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~   87 (233)
                      .+-.|.+.|...   ||.|+.+||+.+++    +.. .+++.|..|...|++++...+ .. .|.+|+.+..
T Consensus        12 ~~~~IL~~Lk~~---g~~ta~eiA~~Lgi----t~~~aVr~hL~~Le~eGlV~~~~~g-RP-~w~LT~~g~~   74 (79)
T 1xmk_A           12 IKEKICDYLFNV---SDSSALNLAKNIGL----TKARDINAVLIDMERQGDVYRQGTT-PP-IWHLTDKKRE   74 (79)
T ss_dssp             HHHHHHHHHHHT---CCEEHHHHHHHHCG----GGHHHHHHHHHHHHHTTSEEEECSS-SC-EEEECHHHHT
T ss_pred             HHHHHHHHHHHc---CCcCHHHHHHHcCC----CcHHHHHHHHHHHHHCCCEEecCCC-CC-CeEeCHhHHh
Confidence            456788999998   59999999999999    998 999999999999999865221 23 8999988764

>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=97.22  E-value=0.00057  Score=45.80  Aligned_cols=70  Identities=13%  Similarity=0.243  Sum_probs=51.9

Q ss_pred             HHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhh
Q 039903           14 QAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFV   89 (233)
Q Consensus        14 ~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~   89 (233)
                      ..-.+..|.+.|.+.++..++|+.|||+++|+    +...+++.|.-|...|+++....  ..+.|...+....+.
T Consensus         8 ~~~~~~~IL~~L~~~~pg~~~t~~eLA~~Lgv----sr~tV~~~L~~Le~~G~I~~~g~--~~~~W~i~~~~~~~~   77 (81)
T 1qbj_A            8 YQDQEQRILKFLEELGEGKATTAHDLSGKLGT----PKKEINRVLYSLAKKGKLQKEAG--TPPLWKIAVSTQAWN   77 (81)
T ss_dssp             HHHHHHHHHHHHHHHCTTCCBCHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEESS--SSCEEEEC-------
T ss_pred             chHHHHHHHHHHHHcCCCCCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEecCC--CCCeeEEeCcHHhcc
Confidence            33456778899998754447999999999999    99999999999999999987532  357888887665443

>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=97.15  E-value=0.00016  Score=62.69  Aligned_cols=65  Identities=11%  Similarity=-0.052  Sum_probs=50.3

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------C--CceEEecCcCCCCC------C-CCEE
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------S--GVKHIGGIMLERIP------K-GDAI  230 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~--ri~~~~gD~f~~~P------~-~D~~  230 (233)
                      .+..+|+|+|||+|.++..++++. .-+++.+|+ |..++.|+++      +  +++++.+|.++.+|      . .|+|
T Consensus       211 ~~~~~VLDl~cGtG~~sl~la~~g-a~~V~~vD~s~~al~~A~~N~~~n~~~~~~v~~~~~D~~~~l~~~~~~~~~fD~I  289 (385)
T 2b78_A          211 AAGKTVLNLFSYTAAFSVAAAMGG-AMATTSVDLAKRSRALSLAHFEANHLDMANHQLVVMDVFDYFKYARRHHLTYDII  289 (385)
T ss_dssp             TBTCEEEEETCTTTHHHHHHHHTT-BSEEEEEESCTTHHHHHHHHHHHTTCCCTTEEEEESCHHHHHHHHHHTTCCEEEE
T ss_pred             cCCCeEEEEeeccCHHHHHHHHCC-CCEEEEEECCHHHHHHHHHHHHHcCCCccceEEEECCHHHHHHHHHHhCCCccEE
Confidence            455799999999999999999863 337999998 5577777653      3  89999999987332      1 3888


Q ss_pred             Ee
Q 039903          231 LI  232 (233)
Q Consensus       231 ~l  232 (233)
                      ++
T Consensus       290 i~  291 (385)
T 2b78_A          290 II  291 (385)
T ss_dssp             EE
T ss_pred             EE
Confidence            75

>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=97.09  E-value=0.00056  Score=56.06  Aligned_cols=73  Identities=14%  Similarity=0.195  Sum_probs=52.6

Q ss_pred             HHHHHhcccccCc--ceEEEecCCccHHHHHHHHHcCCCcEEEeechHH--------HhhccC-------C-CCceEEec
Q 039903          157 NRIIDSSKGFEQI--KQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHV--------IQDSSS-------Y-SGVKHIGG  218 (233)
Q Consensus       157 ~~~~~~~~~~~~~--~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v--------~~~a~~-------~-~ri~~~~g  218 (233)
                      ..+.+.+. .++.  .+|+|+|||.|..+..++++  ..+++.+|..+.        ++.++.       . +||+++.+
T Consensus        76 e~l~~al~-l~~g~~~~VLDl~~G~G~dal~lA~~--g~~V~~vE~~~~~~~l~~~~l~~a~~~~~~~~~l~~~i~~~~~  152 (258)
T 2oyr_A           76 EAVAKAVG-IKGDYLPDVVDATAGLGRDAFVLASV--GCRVRMLERNPVVAALLDDGLARGYADAEIGGWLQERLQLIHA  152 (258)
T ss_dssp             SHHHHHTT-CBTTBCCCEEETTCTTCHHHHHHHHH--TCCEEEEECCHHHHHHHHHHHHHHHHCTTTHHHHHHHEEEEES
T ss_pred             HHHHHHhc-ccCCCCCEEEEcCCcCCHHHHHHHHc--CCEEEEEECCHHHHHHHHHHHHHHHhhHhhhhhhhcCEEEEEC
Confidence            34555554 5555  79999999999999999998  457999998653        333321       1 47999999


Q ss_pred             CcCCC---CCCC-CEEEe
Q 039903          219 IMLER---IPKG-DAILI  232 (233)
Q Consensus       219 D~f~~---~P~~-D~~~l  232 (233)
                      |.++-   ++.. |+|++
T Consensus       153 D~~~~L~~~~~~fDvV~l  170 (258)
T 2oyr_A          153 SSLTALTDITPRPQVVYL  170 (258)
T ss_dssp             CHHHHSTTCSSCCSEEEE
T ss_pred             CHHHHHHhCcccCCEEEE
Confidence            98862   3433 99886

>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=97.07  E-value=0.00068  Score=46.59  Aligned_cols=72  Identities=11%  Similarity=0.141  Sum_probs=57.8

Q ss_pred             HHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeecc--CCCCCceeccHhhhHh
Q 039903           11 AAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSA--GDDQRLYGLAHVAKYF   88 (233)
Q Consensus        11 ~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~--~~~~~~y~lt~~s~~l   88 (233)
                      .++..-.++.|+..|...   ++.|..|||+.+++    ++..+.+.|+.|...|++++...  ++....|.+|+.+...
T Consensus        11 ~~l~~~~~~~iL~~L~~~---~~~~~~ela~~l~i----s~~tvs~~l~~L~~~gli~~~~~~~~~r~~~~~lt~~g~~~   83 (100)
T 1ub9_A           11 HILGNPVRLGIMIFLLPR---RKAPFSQIQKVLDL----TPGNLDSHIRVLERNGLVKTYKVIADRPRTVVEITDFGMEE   83 (100)
T ss_dssp             HHHHSHHHHHHHHHHHHH---SEEEHHHHHHHTTC----CHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECHHHHHH
T ss_pred             cccCChHHHHHHHHHHhc---CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEEecCCCcceEEEEECHHHHHH
Confidence            466777889999999765   58999999999999    99999999999999999996431  1123468899988644


Q ss_pred             h
Q 039903           89 V   89 (233)
Q Consensus        89 ~   89 (233)
                      .
T Consensus        84 ~   84 (100)
T 1ub9_A           84 A   84 (100)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=97.07  E-value=0.00085  Score=62.65  Aligned_cols=75  Identities=16%  Similarity=0.023  Sum_probs=56.4

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHH------------------------------------------cCCCc
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISN------------------------------------------YLHIK  194 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~------------------------------------------~P~l~  194 (233)
                      ..++.... |.....++|.+||+|.++++.+..                                          .|+.+
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            34555444 777789999999999999887764                                          34578


Q ss_pred             EEEeec-hHHHhhccCC-------CCceEEecCcCC-CCC----CCCEEEe
Q 039903          195 GVNFDL-SHVIQDSSSY-------SGVKHIGGIMLE-RIP----KGDAILI  232 (233)
Q Consensus       195 ~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~-~~P----~~D~~~l  232 (233)
                      ++..|+ |.+++.|+.+       ++|++..+|+++ ..|    ..|+++.
T Consensus       259 i~G~Did~~av~~A~~N~~~agv~~~i~~~~~D~~~~~~~~~~~~~d~Iv~  309 (703)
T 3v97_A          259 FYGSDSDARVIQRARTNARLAGIGELITFEVKDVAQLTNPLPKGPYGTVLS  309 (703)
T ss_dssp             EEEEESCHHHHHHHHHHHHHTTCGGGEEEEECCGGGCCCSCTTCCCCEEEE
T ss_pred             EEEEECCHHHHHHHHHHHHHcCCCCceEEEECChhhCccccccCCCCEEEe
Confidence            999998 5688877764       469999999997 334    2388764

>2oqg_A Possible transcriptional regulator, ARSR family P; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 1.54A {Rhodococcus SP}

Probab=97.07  E-value=0.00059  Score=48.24  Aligned_cols=66  Identities=14%  Similarity=0.231  Sum_probs=51.6

Q ss_pred             HHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhH
Q 039903           13 MQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKY   87 (233)
Q Consensus        13 L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~   87 (233)
                      +..-.++.|+..|..    ++.|..|||+.+++    ++..+.+.|+.|...|+++....+ ....|.+|+.+..
T Consensus        18 l~~~~r~~IL~~L~~----~~~~~~ela~~l~i----s~~tv~~~l~~L~~~gli~~~~~g-r~~~y~l~~~~~~   83 (114)
T 2oqg_A           18 LSDETRWEILTELGR----ADQSASSLATRLPV----SRQAIAKHLNALQACGLVESVKVG-REIRYRALGAELN   83 (114)
T ss_dssp             TTCHHHHHHHHHHHH----SCBCHHHHHHHSSS----CHHHHHHHHHHHHHTTSEEEEEET-TEEEEEECSHHHH
T ss_pred             hCChHHHHHHHHHHc----CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCeeEEecC-CEEEEEechHHHH
Confidence            333457789999944    58999999999999    999999999999999999875311 2234888876653

>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=97.06  E-value=0.00069  Score=47.09  Aligned_cols=65  Identities=15%  Similarity=0.189  Sum_probs=52.2

Q ss_pred             HHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHh
Q 039903           11 AAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHV   84 (233)
Q Consensus        11 ~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~   84 (233)
                      .+|..-.++.|+..|..    ++.|+.|||+.+++    ++..+.+.|+.|...|+++....+ ....|++|+.
T Consensus        18 ~~l~~~~r~~Il~~L~~----~~~~~~ela~~l~i----s~~tvs~~L~~L~~~Glv~~~~~g-~~~~y~l~~~   82 (102)
T 3pqk_A           18 KTLSHPVRLMLVCTLVE----GEFSVGELEQQIGI----GQPTLSQQLGVLRESGIVETRRNI-KQIFYRLTEA   82 (102)
T ss_dssp             HHHCSHHHHHHHHHHHT----CCBCHHHHHHHHTC----CTTHHHHHHHHHHHTTSEEEECSS-SCCEEEECSS
T ss_pred             HHcCCHHHHHHHHHHHh----CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCeEEEEeC-CEEEEEECcH
Confidence            34555567889999976    68999999999999    999999999999999999876322 3456777763

>3ll7_A Putative methyltransferase; methytransferase, structural genomics, MCSG, PSI-2, protein initiative; HET: MSE; 1.80A {Porphyromonas gingivalis}

Probab=97.05  E-value=0.00033  Score=61.20  Aligned_cols=65  Identities=22%  Similarity=0.403  Sum_probs=49.9

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC--------CCceEEecCcCCCCC-----CCCEEE
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY--------SGVKHIGGIMLERIP-----KGDAIL  231 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~--------~ri~~~~gD~f~~~P-----~~D~~~  231 (233)
                      ++...+|+|+|||+|..+..+++.  ..+++.+|+. ..++.|+.+        ++|+++.+|+++.++     ..|+|+
T Consensus        91 l~~g~~VLDLgcG~G~~al~LA~~--g~~V~~VD~s~~~l~~Ar~N~~~~~~gl~~i~~i~~Da~~~L~~~~~~~fDvV~  168 (410)
T 3ll7_A           91 IREGTKVVDLTGGLGIDFIALMSK--ASQGIYIERNDETAVAARHNIPLLLNEGKDVNILTGDFKEYLPLIKTFHPDYIY  168 (410)
T ss_dssp             SCTTCEEEESSCSSSHHHHHHHTT--CSEEEEEESCHHHHHHHHHHHHHHSCTTCEEEEEESCGGGSHHHHHHHCCSEEE
T ss_pred             cCCCCEEEEeCCCchHHHHHHHhc--CCEEEEEECCHHHHHHHHHhHHHhccCCCcEEEEECcHHHhhhhccCCCceEEE
Confidence            333589999999999999999887  4589999984 566666542        479999999997422     239988


Q ss_pred             e
Q 039903          232 I  232 (233)
Q Consensus       232 l  232 (233)
                      +
T Consensus       169 l  169 (410)
T 3ll7_A          169 V  169 (410)
T ss_dssp             E
T ss_pred             E
Confidence            6

>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=97.03  E-value=0.00064  Score=45.09  Aligned_cols=63  Identities=14%  Similarity=0.277  Sum_probs=50.8

Q ss_pred             HHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903           15 AASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH   83 (233)
Q Consensus        15 ~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~   83 (233)
                      .-.+..|++.|...+++.++|+.|||+++++    +...+.+.|.-|...|++.....  ..+.|..++
T Consensus        13 ~~~~~~IL~~L~~~~~~~~~t~~eLA~~Lgv----s~~tV~~~L~~L~~~G~I~~~g~--~~~~W~i~~   75 (77)
T 1qgp_A           13 QDQEQRILKFLEELGEGKATTAHDLSGKLGT----PKKEINRVLYSLAKKGKLQKEAG--TPPLWKIAV   75 (77)
T ss_dssp             HHHHHHHHHHHHHHCSSSCEEHHHHHHHHCC----CHHHHHHHHHHHHHHTSEEEECS--SSCEEEECC
T ss_pred             HHHHHHHHHHHHHcCCCCCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEecCC--CCCceEecC
Confidence            3446778899999843348999999999999    99999999999999999988632  346776654

>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=97.02  E-value=0.00092  Score=58.69  Aligned_cols=67  Identities=13%  Similarity=0.069  Sum_probs=52.6

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC-----CCceEEecCcCC-C--CCC-C-CEEEe
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY-----SGVKHIGGIMLE-R--IPK-G-DAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~-----~ri~~~~gD~f~-~--~P~-~-D~~~l  232 (233)
                      .....+|+|+|||.|..+..+++..|+.+++.+|.. ..++.++++     -+++++.+|+.+ +  ++. . |+|++
T Consensus       244 ~~~g~~VLDlgaG~G~~t~~la~~~~~~~v~a~D~~~~~l~~~~~~~~~~g~~~~~~~~D~~~~~~~~~~~~fD~Vl~  321 (429)
T 1sqg_A          244 PQNGEHILDLCAAPGGKTTHILEVAPEAQVVAVDIDEQRLSRVYDNLKRLGMKATVKQGDGRYPSQWCGEQQFDRILL  321 (429)
T ss_dssp             CCTTCEEEEESCTTCHHHHHHHHHCTTCEEEEEESSTTTHHHHHHHHHHTTCCCEEEECCTTCTHHHHTTCCEEEEEE
T ss_pred             CCCcCeEEEECCCchHHHHHHHHHcCCCEEEEECCCHHHHHHHHHHHHHcCCCeEEEeCchhhchhhcccCCCCEEEE
Confidence            455679999999999999999999999899999984 456555442     358999999987 2  443 3 98875

>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=97.02  E-value=0.00026  Score=61.53  Aligned_cols=64  Identities=16%  Similarity=0.103  Sum_probs=50.7

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCCCC------CCC-CEEEe
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLERI------PKG-DAILI  232 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~~------P~~-D~~~l  232 (233)
                      +..+|+|+|||+|.++..+++. +..+++.+|+ |..++.++++       ++++++.+|+++..      +.. |++++
T Consensus       217 ~~~~VLDl~~G~G~~~~~la~~-g~~~v~~vD~s~~~l~~a~~n~~~n~~~~~v~~~~~d~~~~~~~~~~~~~~fD~Vi~  295 (396)
T 2as0_A          217 PGDRVLDVFTYTGGFAIHAAIA-GADEVIGIDKSPRAIETAKENAKLNGVEDRMKFIVGSAFEEMEKLQKKGEKFDIVVL  295 (396)
T ss_dssp             TTCEEEETTCTTTHHHHHHHHT-TCSEEEEEESCHHHHHHHHHHHHHTTCGGGEEEEESCHHHHHHHHHHTTCCEEEEEE
T ss_pred             CCCeEEEecCCCCHHHHHHHHC-CCCEEEEEeCCHHHHHHHHHHHHHcCCCccceEEECCHHHHHHHHHhhCCCCCEEEE
Confidence            5689999999999999999986 4558999998 5677777653       28999999998732      223 88876

>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=97.01  E-value=0.00098  Score=54.17  Aligned_cols=61  Identities=13%  Similarity=0.162  Sum_probs=51.1

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHh
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYF   88 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l   88 (233)
                      -+.|++.|...+  ++.|+.|||+.+++    +...+.|+|+.|...|++++.    ..+.|++++....|
T Consensus        10 ~l~iL~~l~~~~--~~~~~~ela~~~gl----~~stv~r~l~~L~~~G~v~~~----~~~~Y~lg~~~~~l   70 (249)
T 1mkm_A           10 AFEILDFIVKNP--GDVSVSEIAEKFNM----SVSNAYKYMVVLEEKGFVLRK----KDKRYVPGYKLIEY   70 (249)
T ss_dssp             HHHHHHHHHHCS--SCBCHHHHHHHTTC----CHHHHHHHHHHHHHTTSEEEC----TTSCEEECTHHHHH
T ss_pred             HHHHHHHHHhCC--CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCcEEEC----CCCcEEECHHHHHH
Confidence            356788887753  47999999999999    999999999999999999986    46889998854433

>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=96.99  E-value=0.00026  Score=61.27  Aligned_cols=63  Identities=11%  Similarity=0.106  Sum_probs=50.5

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCCCC------CCC-CEEEe
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLERI------PKG-DAILI  232 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~~------P~~-D~~~l  232 (233)
                      +..+|+|+|||+|.++..+++.  ..+++.+|+ |..++.++++      ++++++.+|+++..      +.. |++++
T Consensus       209 ~~~~VLDlg~G~G~~~~~la~~--~~~v~~vD~s~~~~~~a~~n~~~n~~~~~~~~~~d~~~~~~~~~~~~~~fD~Ii~  285 (382)
T 1wxx_A          209 RGERALDVFSYAGGFALHLALG--FREVVAVDSSAEALRRAEENARLNGLGNVRVLEANAFDLLRRLEKEGERFDLVVL  285 (382)
T ss_dssp             CEEEEEEETCTTTHHHHHHHHH--EEEEEEEESCHHHHHHHHHHHHHTTCTTEEEEESCHHHHHHHHHHTTCCEEEEEE
T ss_pred             CCCeEEEeeeccCHHHHHHHHh--CCEEEEEECCHHHHHHHHHHHHHcCCCCceEEECCHHHHHHHHHhcCCCeeEEEE
Confidence            5679999999999999999998  567899998 5677777653      45999999998732      223 88876

>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=96.96  E-value=0.00065  Score=55.00  Aligned_cols=62  Identities=11%  Similarity=0.140  Sum_probs=51.2

Q ss_pred             hChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhh
Q 039903           19 LGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFV   89 (233)
Q Consensus        19 lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~   89 (233)
                      +.|++.|...+  ++.|+.|||+.+|+    +...+.|+|+.|...|+++++.   +.++|++++....|.
T Consensus         9 l~iL~~l~~~~--~~~s~~ela~~~gl----~~stv~r~l~~L~~~G~v~~~~---~~~~Y~lg~~~~~lg   70 (241)
T 2xrn_A            9 ASIMRALGSHP--HGLSLAAIAQLVGL----PRSTVQRIINALEEEFLVEALG---PAGGFRLGPALGQLI   70 (241)
T ss_dssp             HHHHHHHHTCT--TCEEHHHHHHHTTS----CHHHHHHHHHHHHTTTSEEECG---GGCEEEECSHHHHHH
T ss_pred             HHHHHHHHhCC--CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEeC---CCCeEEECHHHHHHH
Confidence            45778887653  47999999999999    9999999999999999999862   247899988655543

>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=96.94  E-value=0.00076  Score=56.47  Aligned_cols=52  Identities=13%  Similarity=0.097  Sum_probs=38.5

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC-----C-------CceEEecCc
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY-----S-------GVKHIGGIM  220 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~-----~-------ri~~~~gD~  220 (233)
                      ...+|||||||+|..+..+++. ...+++.+|+. ..++.|++.     .       +++++..|+
T Consensus        48 ~~~~VLDlGCG~G~~l~~~~~~-~~~~v~GiD~S~~~l~~A~~~~~~~~~~~~~~~~~~~f~~~d~  112 (302)
T 2vdw_A           48 NKRKVLAIDFGNGADLEKYFYG-EIALLVATDPDADAIARGNERYNKLNSGIKTKYYKFDYIQETI  112 (302)
T ss_dssp             SCCEEEETTCTTTTTHHHHHHT-TCSEEEEEESCHHHHHHHHHHHHHHCC----CCCEEEEEECCT
T ss_pred             CCCeEEEEecCCcHhHHHHHhc-CCCeEEEEECCHHHHHHHHHHHHhccccccccccccchhhhhc
Confidence            3578999999999877776664 34579999985 578877653     1       256777777

>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=96.92  E-value=0.0014  Score=45.22  Aligned_cols=49  Identities=12%  Similarity=0.207  Sum_probs=45.0

Q ss_pred             CCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhcC
Q 039903           34 ISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        34 ~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~~   91 (233)
                      .+..+||..+++    +++.+++.++.|...|++++.     .+.|.+|+.|..+...
T Consensus        21 ~~~t~La~~~~l----s~~~~~~~l~~L~~~GLI~~~-----~~~~~LT~kG~~~l~~   69 (95)
T 1r7j_A           21 SPKTRIMYGANL----SYALTGRYIKMLMDLEIIRQE-----GKQYMLTKKGEELLED   69 (95)
T ss_dssp             BCHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEE-----TTEEEECHHHHHHHHH
T ss_pred             CCHHHHHHHhCc----CHHHHHHHHHHHHHCCCeEEE-----CCeeEEChhHHHHHHH
Confidence            899999999999    999999999999999999996     5569999999987644

>3jth_A Transcription activator HLYU; transcription factor, RTXA, DNA-binding, transcription regulation; 2.00A {Vibrio vulnificus}

Probab=96.92  E-value=0.00054  Score=47.25  Aligned_cols=65  Identities=17%  Similarity=0.249  Sum_probs=51.9

Q ss_pred             HHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhh
Q 039903           12 AMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVA   85 (233)
Q Consensus        12 ~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s   85 (233)
                      +|..-.++.|+..|.+    ++.|+.|||+.+++    +...+.+.|+.|...|++++...+ ....|++++..
T Consensus        19 ~l~~~~r~~Il~~L~~----~~~~~~ela~~l~i----s~~tvs~~L~~L~~~Glv~~~~~g-~~~~y~l~~~~   83 (98)
T 3jth_A           19 AMANERRLQILCMLHN----QELSVGELCAKLQL----SQSALSQHLAWLRRDGLVTTRKEA-QTVYYTLKSEE   83 (98)
T ss_dssp             HHCSHHHHHHHHHTTT----SCEEHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEECCT-TCCEEEECCHH
T ss_pred             HcCCHHHHHHHHHHhc----CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCeEEEEeC-CEEEEEECHHH
Confidence            4444567788888887    59999999999999    999999999999999999976322 23457777643

>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=96.91  E-value=0.00086  Score=48.38  Aligned_cols=68  Identities=16%  Similarity=0.217  Sum_probs=52.7

Q ss_pred             HHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhh
Q 039903           10 PAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVA   85 (233)
Q Consensus        10 s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s   85 (233)
                      ..+|..-.++.|+..|...   ++.|+.|||+.+++    ++..+.+.|+.|...|++.....+ ....|++++.+
T Consensus        36 ~~al~~~~rl~IL~~L~~~---~~~s~~eLa~~l~i----s~stvs~~L~~L~~~Glv~~~~~g-r~~~y~l~~~~  103 (122)
T 1u2w_A           36 LKAIADENRAKITYALCQD---EELCVCDIANILGV----TIANASHHLRTLYKQGVVNFRKEG-KLALYSLGDEH  103 (122)
T ss_dssp             HHHHHSHHHHHHHHHHHHS---SCEEHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEC-----CCEEEESCHH
T ss_pred             HHHhCCHHHHHHHHHHHHC---CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCeEEEEEC-CEEEEEECHHH
Confidence            3445555688899999865   58999999999999    999999999999999999875321 23368877654

>3f6o_A Probable transcriptional regulator, ARSR family protein; transcriptional regulator,RHA00566,MCSG, structural genomics, PSI-2; 1.90A {Rhodococcus SP}

Probab=96.90  E-value=0.00091  Score=47.91  Aligned_cols=68  Identities=13%  Similarity=0.158  Sum_probs=55.8

Q ss_pred             HHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhh
Q 039903           10 PAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAK   86 (233)
Q Consensus        10 s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~   86 (233)
                      ..+|.--.++.|+..|..    ++.++.|||+.+++    +...+.+.|+.|...|++.....+ ....|++++.+.
T Consensus        12 ~~al~~~~R~~Il~~L~~----~~~~~~eLa~~l~i----s~~tvs~hL~~L~~~GlV~~~~~g-r~~~y~l~~~~~   79 (118)
T 3f6o_A           12 FQALADPTRRAVLGRLSR----GPATVSELAKPFDM----ALPSFMKHIHFLEDSGWIRTHKQG-RVRTCAIEKEPF   79 (118)
T ss_dssp             HHHHTSHHHHHHHHHHHT----CCEEHHHHHTTCCS----CHHHHHHHHHHHHHTTSEEEEEET-TEEEEEECSHHH
T ss_pred             HHHhCCHHHHHHHHHHHh----CCCCHHHHHHHhCc----CHHHHHHHHHHHHHCCCeEEEecC-CEEEEEECHHHH
Confidence            455666678999999986    69999999999999    999999999999999999876321 335688887554

>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=96.89  E-value=0.001  Score=58.69  Aligned_cols=73  Identities=16%  Similarity=0.034  Sum_probs=52.6

Q ss_pred             HHHhcccccCcceEEEecCCccHHHHHHHHHc-------------CCCcEEEeec-hHHHhhccCC------C--CceEE
Q 039903          159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNY-------------LHIKGVNFDL-SHVIQDSSSY------S--GVKHI  216 (233)
Q Consensus       159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~-------------P~l~~~v~Dl-p~v~~~a~~~------~--ri~~~  216 (233)
                      +++... .....+|+|.|||+|.++..+++..             +..++.++|+ |.+++.|+.+      .  +++++
T Consensus       163 mv~~l~-~~~~~~VlDpacGsG~fl~~~~~~l~~~~~~~~~~~~~~~~~i~G~Ei~~~~~~lA~~nl~l~g~~~~~~~i~  241 (445)
T 2okc_A          163 MVDCIN-PQMGETVCDPACGTGGFLLTAYDYMKGQSASKEKRDFLRDKALHGVDNTPLVVTLASMNLYLHGIGTDRSPIV  241 (445)
T ss_dssp             HHHHHC-CCTTCCEEETTCTTCHHHHHHHHHHHTCC-CCHHHHHHHHTTEEEEESCHHHHHHHHHHHHHTTCCSSCCSEE
T ss_pred             HHHHhC-CCCCCEEeccCCCcchHHHHHHHHHHHhcCCHHHHHhhcCeEEEEEeCCHHHHHHHHHHHHHhCCCcCCCCEe
Confidence            344433 3445689999999999999988764             5678999998 5577766542      2  78899


Q ss_pred             ecCcCCC-CCCC-CEEEe
Q 039903          217 GGIMLER-IPKG-DAILI  232 (233)
Q Consensus       217 ~gD~f~~-~P~~-D~~~l  232 (233)
                      .+|++.. .+.. |+|+.
T Consensus       242 ~gD~l~~~~~~~fD~Iv~  259 (445)
T 2okc_A          242 CEDSLEKEPSTLVDVILA  259 (445)
T ss_dssp             ECCTTTSCCSSCEEEEEE
T ss_pred             eCCCCCCcccCCcCEEEE
Confidence            9999983 3333 88764

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

Probab=96.88  E-value=0.00062  Score=58.60  Aligned_cols=51  Identities=14%  Similarity=0.109  Sum_probs=42.1

Q ss_pred             ceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCC
Q 039903          170 KQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLE  222 (233)
Q Consensus       170 ~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~  222 (233)
                      .+|+|+|||+|.++..+++..  -+++.+|. |+.++.|+++      ++++++.+|.++
T Consensus       215 ~~vLDl~cG~G~~~l~la~~~--~~V~gvd~~~~ai~~a~~n~~~ng~~~v~~~~~d~~~  272 (369)
T 3bt7_A          215 GDLLELYCGNGNFSLALARNF--DRVLATEIAKPSVAAAQYNIAANHIDNVQIIRMAAEE  272 (369)
T ss_dssp             SEEEEESCTTSHHHHHHGGGS--SEEEEECCCHHHHHHHHHHHHHTTCCSEEEECCCSHH
T ss_pred             CEEEEccCCCCHHHHHHHhcC--CEEEEEECCHHHHHHHHHHHHHcCCCceEEEECCHHH
Confidence            679999999999999998854  47899998 5577777653      589999999876

>3cuo_A Uncharacterized HTH-type transcriptional regulato; DNA-binding transcriptional regulator, structural genomics, MCSG; 2.00A {Escherichia coli K12}

Probab=96.87  E-value=0.00076  Score=46.28  Aligned_cols=66  Identities=17%  Similarity=0.191  Sum_probs=52.6

Q ss_pred             HHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhh
Q 039903           12 AMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVA   85 (233)
Q Consensus        12 ~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s   85 (233)
                      ++..-.++.|+..|...   ++.|..|||+.+++    +...+.+.|+.|...|++.+...+ ....|++|+.+
T Consensus        20 ~l~~~~~~~il~~l~~~---~~~s~~ela~~l~i----s~~tvs~~l~~L~~~glv~~~~~~-r~~~y~l~~~~   85 (99)
T 3cuo_A           20 AMSHPKRLLILCMLSGS---PGTSAGELTRITGL----SASATSQHLARMRDEGLIDSQRDA-QRILYSIKNEA   85 (99)
T ss_dssp             HHCSHHHHHHHHHHTTC---CSEEHHHHHHHHCC----CHHHHHHHHHHHHHTTSEEEEECS-SCEEEEECCHH
T ss_pred             HhCChHHHHHHHHHHhC---CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEEecC-CEEEEEEChHH
Confidence            44445677888888774   48999999999999    999999999999999999986421 23457787755

>4auk_A Ribosomal RNA large subunit methyltransferase M; YGDE; HET: TLA PGE; 1.90A {Escherichia coli} PDB: 4atn_A* 4b17_A*

Probab=96.86  E-value=0.0015  Score=56.03  Aligned_cols=64  Identities=13%  Similarity=0.044  Sum_probs=50.7

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCCCCceEEecCcCCCCCC-C--CEEE
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPK-G--DAIL  231 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~~ri~~~~gD~f~~~P~-~--D~~~  231 (233)
                      +....++||+|++.|.++..++++  ..+++.+|.-+.-......++|+++.+|.|+..|. +  |+++
T Consensus       209 l~~G~~vlDLGAaPGGWT~~l~~r--g~~V~aVD~~~l~~~l~~~~~V~~~~~d~~~~~~~~~~~D~vv  275 (375)
T 4auk_A          209 LANGMWAVDLGACPGGWTYQLVKR--NMWVYSVDNGPMAQSLMDTGQVTWLREDGFKFRPTRSNISWMV  275 (375)
T ss_dssp             SCTTCEEEEETCTTCHHHHHHHHT--TCEEEEECSSCCCHHHHTTTCEEEECSCTTTCCCCSSCEEEEE
T ss_pred             CCCCCEEEEeCcCCCHHHHHHHHC--CCEEEEEEhhhcChhhccCCCeEEEeCccccccCCCCCcCEEE
Confidence            356689999999999999999988  67899999755444445568999999999994443 3  7664

>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=96.85  E-value=0.0019  Score=47.42  Aligned_cols=51  Identities=14%  Similarity=0.070  Sum_probs=46.1

Q ss_pred             CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhc
Q 039903           32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVL   90 (233)
Q Consensus        32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~   90 (233)
                      ++.|..+||+.+++    ++..+.++++.|...|++.+.    ....|.+|+.+..+..
T Consensus        21 ~~~~~~ela~~l~v----s~~tvs~~l~~Le~~Glv~r~----~~~~~~LT~~g~~~~~   71 (142)
T 1on2_A           21 GYARVSDIAEALAV----HPSSVTKMVQKLDKDEYLIYE----KYRGLVLTSKGKKIGK   71 (142)
T ss_dssp             SSCCHHHHHHHHTS----CHHHHHHHHHHHHHTTSEEEE----TTTEEEECHHHHHHHH
T ss_pred             CCCCHHHHHHHhCC----CHHHHHHHHHHHHHCCCEEEe----eCceEEEchhHHHHHH
Confidence            58999999999999    999999999999999999987    4678999999887654

>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=96.83  E-value=0.0015  Score=60.37  Aligned_cols=95  Identities=19%  Similarity=0.113  Sum_probs=59.4

Q ss_pred             cccccccCchHHHHHHHHHHhcchhcHHHHHHhcccccCcceEEEecCCccHHHHHHHH----Hc---------CCCcEE
Q 039903          130 FYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIIS----NY---------LHIKGV  196 (233)
Q Consensus       130 ~~~~~~~~~~~~~~f~~am~~~~~~~~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~----~~---------P~l~~~  196 (233)
                      .||.+.+|+-+-+.|.+|+...       +....++-.+.+.|+|||||+|-++...++    +.         ...++.
T Consensus       378 tYe~fekD~vRy~~Y~~AI~~a-------l~d~~~~~~~~~VVldVGaGtGpLs~~al~A~~~a~~~~~~~~~~~~~kVy  450 (745)
T 3ua3_A          378 VYNTFEQDQIKYDVYGEAVVGA-------LKDLGADGRKTVVIYLLGGGRGPIGTKILKSEREYNNTFRQGQESLKVKLY  450 (745)
T ss_dssp             HHHHHHHCHHHHHHHHHHHHHH-------HHHHHTTCCSEEEEEEESCTTCHHHHHHHHHHHHHHHHHSTTSCCCEEEEE
T ss_pred             HHHHHcCChhhHHHHHHHHHHH-------HHHhhcccCCCcEEEEECCCCCHHHHHHHHHHHHhCccccccccccccEEE
Confidence            3666667777777777766542       111111012457899999999999643222    22         345788


Q ss_pred             EeechH-HHhhccC------CCCceEEecCcCC-CC------CC-CCEEE
Q 039903          197 NFDLSH-VIQDSSS------YSGVKHIGGIMLE-RI------PK-GDAIL  231 (233)
Q Consensus       197 v~Dlp~-v~~~a~~------~~ri~~~~gD~f~-~~------P~-~D~~~  231 (233)
                      .+|-.. ++...+.      .++|+++.||+-+ ++      |+ .|+++
T Consensus       451 AVEknp~A~~~l~~~~~Ng~~d~VtVI~gd~eev~lp~~~~~~ekVDIIV  500 (745)
T 3ua3_A          451 IVEKNPNAIVTLKYMNVRTWKRRVTIIESDMRSLPGIAKDRGFEQPDIIV  500 (745)
T ss_dssp             EEECCHHHHHHHHHHHHHTTTTCSEEEESCGGGHHHHHHHTTCCCCSEEE
T ss_pred             EEeCChHHHHHHHHHHhcCCCCeEEEEeCchhhcccccccCCCCcccEEE
Confidence            888754 2222111      1789999999998 67      55 59885

>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=96.81  E-value=0.0017  Score=46.08  Aligned_cols=69  Identities=10%  Similarity=0.169  Sum_probs=55.2

Q ss_pred             HHHHHHhhChhHHHHhcCCCCCCC--HHHHHHhC-CCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHh
Q 039903           12 AMQAASELGVFEIIAKAGPTAKIS--AVEIAAQM-PSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYF   88 (233)
Q Consensus        12 ~L~~a~~lglfd~L~~~~~~~~~t--~~elA~~~-~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l   88 (233)
                      +|.--.++.|+..|..    |+.+  ..||++.+ ++    ++..+.+.|+.|...|++++...  ....|++|+.|+.+
T Consensus        23 ~l~~~wrl~IL~~L~~----g~~~~~~~eL~~~l~gi----s~~~ls~~L~~Le~~GlV~r~~~--r~~~y~LT~~G~~l   92 (111)
T 3df8_A           23 LLGKKYTMLIISVLGN----GSTRQNFNDIRSSIPGI----SSTILSRRIKDLIDSGLVERRSG--QITTYALTEKGMNV   92 (111)
T ss_dssp             HHHSTTHHHHHHHHTS----SSSCBCHHHHHHTSTTC----CHHHHHHHHHHHHHTTSEEEEES--SSEEEEECHHHHHH
T ss_pred             HHcCccHHHHHHHHhc----CCCCCCHHHHHHHccCC----CHHHHHHHHHHHHHCCCEEEeec--CcEEEEECccHHHH
Confidence            3333345667777774    5777  99999999 99    99999999999999999998632  25689999999877


Q ss_pred             hc
Q 039903           89 VL   90 (233)
Q Consensus        89 ~~   90 (233)
                      ..
T Consensus        93 ~~   94 (111)
T 3df8_A           93 RN   94 (111)
T ss_dssp             HH
T ss_pred             HH
Confidence            63

>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=96.79  E-value=0.0011  Score=57.68  Aligned_cols=52  Identities=13%  Similarity=0.196  Sum_probs=41.3

Q ss_pred             HHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC
Q 039903          156 TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY  210 (233)
Q Consensus       156 ~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~  210 (233)
                      ...+++.+. .....+|||||||+|.++..++++.  .+++.+|.. ..++.+++.
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            345666665 6667899999999999999999874  489999985 577777764

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

Probab=96.79  E-value=0.00049  Score=59.75  Aligned_cols=65  Identities=9%  Similarity=0.023  Sum_probs=50.5

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------C-CceEEecCcCCCCC------C-CCEE
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------S-GVKHIGGIMLERIP------K-GDAI  230 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~-ri~~~~gD~f~~~P------~-~D~~  230 (233)
                      .+..+|+|+|||+|.++..+++.. ..+++.+|+ |..++.++++       + +++++.+|+++..+      . .|++
T Consensus       219 ~~~~~VLDl~cG~G~~sl~la~~g-~~~V~~vD~s~~al~~a~~n~~~ngl~~~~v~~~~~D~~~~~~~~~~~~~~fD~I  297 (396)
T 3c0k_A          219 VENKRVLNCFSYTGGFAVSALMGG-CSQVVSVDTSQEALDIARQNVELNKLDLSKAEFVRDDVFKLLRTYRDRGEKFDVI  297 (396)
T ss_dssp             CTTCEEEEESCTTCSHHHHHHHTT-CSEEEEEESCHHHHHHHHHHHHHTTCCGGGEEEEESCHHHHHHHHHHTTCCEEEE
T ss_pred             hCCCeEEEeeccCCHHHHHHHHCC-CCEEEEEECCHHHHHHHHHHHHHcCCCccceEEEECCHHHHHHHHHhcCCCCCEE
Confidence            455799999999999999999874 457999998 5577776542       2 78999999987322      2 3888


Q ss_pred             Ee
Q 039903          231 LI  232 (233)
Q Consensus       231 ~l  232 (233)
                      ++
T Consensus       298 i~  299 (396)
T 3c0k_A          298 VM  299 (396)
T ss_dssp             EE
T ss_pred             EE
Confidence            75

>2y75_A HTH-type transcriptional regulator CYMR; DNA binding protein; 2.00A {Bacillus subtilis}

Probab=96.78  E-value=0.0018  Score=47.00  Aligned_cols=57  Identities=16%  Similarity=0.127  Sum_probs=42.3

Q ss_pred             hhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903           21 VFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH   83 (233)
Q Consensus        21 lfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~   83 (233)
                      +...|.....+++.|..|||+.+++    ++..++++|+.|...|+++....  .++.|.++.
T Consensus        14 iL~~la~~~~~~~~s~~ela~~~~i----~~~~v~~il~~L~~~Glv~~~~g--~~ggy~L~~   70 (129)
T 2y75_A           14 IMIELAKKHGEGPTSLKSIAQTNNL----SEHYLEQLVSPLRNAGLVKSIRG--AYGGYVLGS   70 (129)
T ss_dssp             HHHHHHHTTTSCCBCHHHHHHHTTS----CHHHHHHHHHHHHHTTSEEEC------CCEEESS
T ss_pred             HHHHHHhCCCCCcCCHHHHHHHHCc----CHHHHHHHHHHHHHCCceEecCC--CCCceEeCC
Confidence            3444554321258999999999999    99999999999999999987531  246787764

>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=96.77  E-value=0.00034  Score=57.34  Aligned_cols=61  Identities=11%  Similarity=0.131  Sum_probs=49.4

Q ss_pred             hChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHh
Q 039903           19 LGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYF   88 (233)
Q Consensus        19 lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l   88 (233)
                      +.|++.|...+  ++.|+.|||+++|+    +...+.|+|+.|+..|+++++.   +.++|++++.-..|
T Consensus         9 l~IL~~l~~~~--~~lsl~eia~~lgl----~ksT~~RlL~tL~~~G~v~~~~---~~~~Y~lG~~~~~l   69 (260)
T 3r4k_A            9 LTLLTYFNHGR--LEIGLSDLTRLSGM----NKATVYRLMSELQEAGFVEQVE---GARSYRLGPQVLRL   69 (260)
T ss_dssp             HHHHTTCBTTB--SEEEHHHHHHHHCS----CHHHHHHHHHHHHHTTSEEECS---SSSEEEECTTHHHH
T ss_pred             HHHHHHHhhCC--CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEcC---CCCcEEcCHHHHHH
Confidence            34666666533  58999999999999    9999999999999999999972   23899998765443

>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=96.77  E-value=0.0018  Score=44.65  Aligned_cols=66  Identities=14%  Similarity=0.250  Sum_probs=52.9

Q ss_pred             hhChhHHHHhcCCCCCCCHHHH----HHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhcC
Q 039903           18 ELGVFEIIAKAGPTAKISAVEI----AAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~el----A~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~~   91 (233)
                      ++.|+..|...   ++.|..||    |+.+++    +...+.++++.|...|++++.... ....|.+|+.|..+...
T Consensus        10 q~~iL~~l~~~---~~~~~~el~~~la~~l~i----s~~tvs~~l~~Le~~gli~r~~~~-r~~~~~LT~~G~~~~~~   79 (99)
T 1tbx_A           10 EAIVLAYLYDN---EGIATYDLYKKVNAEFPM----STATFYDAKKFLIQEGFVKERQER-GEKRLYLTEKGKLFAIS   79 (99)
T ss_dssp             HHHHHHHHTTC---TTCBHHHHHHHHHTTSCC----CHHHHHHHHHHHHHTTSEEEEEET-TEEEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHHc---CCcCHHHHHHHHHHHcCC----CHHHHHHHHHHHHHCCCEEEEecC-CceEEEECHHHHHHHHH
Confidence            44566677665   58999999    999999    999999999999999999985432 24568899999877643

>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=96.72  E-value=0.0017  Score=53.69  Aligned_cols=41  Identities=17%  Similarity=0.169  Sum_probs=30.3

Q ss_pred             CcceEEEecCCccHHHH----HHHHHcCCCcE--EEeech-HHHhhcc
Q 039903          168 QIKQLVDVGGGLGVNVN----IIISNYLHIKG--VNFDLS-HVIQDSS  208 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~----~l~~~~P~l~~--~v~Dlp-~v~~~a~  208 (233)
                      ...+|||||||+|.++.    .++.++|+.++  +++|.. +.++.++
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            34689999999997554    45667798865  999974 4666554

>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=96.72  E-value=0.00096  Score=59.23  Aligned_cols=66  Identities=5%  Similarity=-0.043  Sum_probs=51.6

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCC-CcEEEeech-HHHhhccCC------CCceEEecCcCC-C--CCCC-CEEEe
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLH-IKGVNFDLS-HVIQDSSSY------SGVKHIGGIMLE-R--IPKG-DAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~-l~~~v~Dlp-~v~~~a~~~------~ri~~~~gD~f~-~--~P~~-D~~~l  232 (233)
                      .....+|+|+|||.|..+..+++..++ .+++.+|+. ..++.++++      . |+++.+|..+ +  .+.. |+|++
T Consensus        99 ~~~g~~VLDlgaGpG~kt~~LA~~~~~~g~V~AvDis~~~l~~a~~n~~r~G~~-v~~~~~Da~~l~~~~~~~FD~Il~  176 (464)
T 3m6w_A           99 PKPGERVLDLAAAPGGKTTHLAARMGGKGLLLANEVDGKRVRGLLENVERWGAP-LAVTQAPPRALAEAFGTYFHRVLL  176 (464)
T ss_dssp             CCTTCEEEESSCTTCHHHHHHHHHTTTCSEEEEECSCHHHHHHHHHHHHHHCCC-CEEECSCHHHHHHHHCSCEEEEEE
T ss_pred             cCCCCEEEEEcCCcCHHHHHHHHhCCCCCEEEEEECCHHHHHHHHHHHHHcCCe-EEEEECCHHHhhhhccccCCEEEE
Confidence            456689999999999999999999875 789999984 466666543      4 9999999876 2  3443 88874

>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=96.71  E-value=0.0029  Score=53.16  Aligned_cols=67  Identities=16%  Similarity=0.120  Sum_probs=51.2

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHc-CCCcEEEeech-HHHhhccCC------CCceEEecCcCCCC---C---CCCEEE
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNY-LHIKGVNFDLS-HVIQDSSSY------SGVKHIGGIMLERI---P---KGDAIL  231 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~-P~l~~~v~Dlp-~v~~~a~~~------~ri~~~~gD~f~~~---P---~~D~~~  231 (233)
                      .....+|+|+|+|.|..+..+++.. +.-+++.+|+. ..++.++++      ++|+++.+|+.+..   +   ..|.|+
T Consensus       100 ~~~g~~VLDlcaG~G~kt~~la~~~~~~g~V~a~D~~~~~l~~~~~n~~r~g~~~v~~~~~D~~~~~~~~~~~~~fD~Vl  179 (309)
T 2b9e_A          100 PPPGSHVIDACAAPGNKTSHLAALLKNQGKIFAFDLDAKRLASMATLLARAGVSCCELAEEDFLAVSPSDPRYHEVHYIL  179 (309)
T ss_dssp             CCTTCEEEESSCTTCHHHHHHHHHHTTCSEEEEEESCHHHHHHHHHHHHHTTCCSEEEEECCGGGSCTTCGGGTTEEEEE
T ss_pred             CCCCCEEEEeCCChhHHHHHHHHHhCCCCEEEEEeCCHHHHHHHHHHHHHcCCCeEEEEeCChHhcCccccccCCCCEEE
Confidence            4556799999999999999999985 56889999984 456655542      57999999998721   1   138887


Q ss_pred             e
Q 039903          232 I  232 (233)
Q Consensus       232 l  232 (233)
                      +
T Consensus       180 ~  180 (309)
T 2b9e_A          180 L  180 (309)
T ss_dssp             E
T ss_pred             E
Confidence            5

>2wte_A CSA3; antiviral protein, viral resistance, winged helix-turn-helix prnai nucleotide-binding domain; HET: MSE; 1.80A {Sulfolobus solfataricus}

Probab=96.71  E-value=0.002  Score=52.25  Aligned_cols=65  Identities=12%  Similarity=0.150  Sum_probs=55.2

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhcC
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~~   91 (233)
                      .++.|+..|...   ++.|..|||+.+++    +...+.|+|+.|...|++++..   ....|.+|+.+..+...
T Consensus       153 ~~~~IL~~L~~~---~~~s~~eLA~~lgl----sksTv~r~L~~Le~~GlV~r~~---r~~~~~LT~~G~~l~~~  217 (244)
T 2wte_A          153 EEMKLLNVLYET---KGTGITELAKMLDK----SEKTLINKIAELKKFGILTQKG---KDRKVELNELGLNVIKL  217 (244)
T ss_dssp             HHHHHHHHHHHH---TCBCHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEET---TTTEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEeC---CccEEEECHHHHHHHHH
Confidence            455677887766   58999999999999    9999999999999999999863   45789999999887543

>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=96.70  E-value=0.0011  Score=61.93  Aligned_cols=64  Identities=14%  Similarity=0.044  Sum_probs=49.4

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC--------CCceEEecCcCCCCC---CC-CEEEe
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY--------SGVKHIGGIMLERIP---KG-DAILI  232 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~--------~ri~~~~gD~f~~~P---~~-D~~~l  232 (233)
                      +..+|||+|||+|.++..+++... -+++.+|+. ..++.++++        ++++++.+|.++.++   .. |+|++
T Consensus       539 ~g~~VLDlg~GtG~~sl~aa~~ga-~~V~aVD~s~~al~~a~~N~~~ngl~~~~v~~i~~D~~~~l~~~~~~fD~Ii~  615 (703)
T 3v97_A          539 KGKDFLNLFSYTGSATVHAGLGGA-RSTTTVDMSRTYLEWAERNLRLNGLTGRAHRLIQADCLAWLREANEQFDLIFI  615 (703)
T ss_dssp             TTCEEEEESCTTCHHHHHHHHTTC-SEEEEEESCHHHHHHHHHHHHHTTCCSTTEEEEESCHHHHHHHCCCCEEEEEE
T ss_pred             CCCcEEEeeechhHHHHHHHHCCC-CEEEEEeCCHHHHHHHHHHHHHcCCCccceEEEecCHHHHHHhcCCCccEEEE
Confidence            347899999999999999998533 469999985 577777653        389999999998322   22 88876

>3tka_A Ribosomal RNA small subunit methyltransferase H; HET: SAM CTN PG4; 2.25A {Escherichia coli}

Probab=96.70  E-value=0.004  Score=52.75  Aligned_cols=66  Identities=14%  Similarity=0.117  Sum_probs=54.8

Q ss_pred             HHHHHHhcccccCcceEEEecCCccHHHHHHHHHc-CCCcEEEeech-HHHhhccCC--CCceEEecCcCC
Q 039903          156 TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNY-LHIKGVNFDLS-HVIQDSSSY--SGVKHIGGIMLE  222 (233)
Q Consensus       156 ~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~-P~l~~~v~Dlp-~v~~~a~~~--~ri~~~~gD~f~  222 (233)
                      ..++++.+. ......+||+.+|.|..+.+|+++. |+.+++.+|.. .+++.++..  +|++++.++|-+
T Consensus        46 l~Evl~~L~-i~pggiyVD~TlG~GGHS~~iL~~lg~~GrVig~D~Dp~Al~~A~rL~~~Rv~lv~~nF~~  115 (347)
T 3tka_A           46 LDEAVNGLN-IRPDGIYIDGTFGRGGHSRLILSQLGEEGRLLAIDRDPQAIAVAKTIDDPRFSIIHGPFSA  115 (347)
T ss_dssp             THHHHHHTC-CCTTCEEEESCCTTSHHHHHHHTTCCTTCEEEEEESCHHHHHHHTTCCCTTEEEEESCGGG
T ss_pred             HHHHHHhhC-CCCCCEEEEeCcCCCHHHHHHHHhCCCCCEEEEEECCHHHHHHHHhhcCCcEEEEeCCHHH
Confidence            467777776 5667899999999999999999984 88999999984 577777532  799999999875

>3f6v_A Possible transcriptional regulator, ARSR family protein; probable transcriptional repressor ARSR family, structural genomics, PSI-2; 1.48A {Rhodococcus SP}

Probab=96.70  E-value=0.0015  Score=49.10  Aligned_cols=70  Identities=14%  Similarity=0.239  Sum_probs=57.7

Q ss_pred             HHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhH
Q 039903            9 LPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKY   87 (233)
Q Consensus         9 ~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~   87 (233)
                      ...+|.--.++.|+..|..    ++.|+.|||+.+++    +...+.+.|+.|...|+++....+ ....|++|+.+..
T Consensus        51 ~l~aL~~p~R~~IL~~L~~----~~~t~~eLa~~lgl----s~stvs~hL~~L~~aGlV~~~~~G-r~~~y~lt~~~~~  120 (151)
T 3f6v_A           51 QLEVAAEPTRRRLVQLLTS----GEQTVNNLAAHFPA----SRSAISQHLRVLTEAGLVTPRKDG-RFRYYRLDPQGLA  120 (151)
T ss_dssp             HHHHHTSHHHHHHHHHGGG----CCEEHHHHHTTSSS----CHHHHHHHHHHHHHTTSEEEEEET-TEEEEEECHHHHH
T ss_pred             HHHHhCCHHHHHHHHHHHh----CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEEecC-CEEEEEEChHHHH
Confidence            3566777778999999985    69999999999999    999999999999999999976321 2346888887654

>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=96.69  E-value=0.00061  Score=56.25  Aligned_cols=41  Identities=17%  Similarity=0.113  Sum_probs=29.5

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccC
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSS  209 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~  209 (233)
                      ...+|||||||+|.++ .++.+.+..+++.+|+. ..++.+++
T Consensus        71 ~~~~vLDiGcG~G~~~-~l~~~~~~~~v~gvD~s~~~l~~a~~  112 (289)
T 2g72_A           71 SGRTLIDIGSGPTVYQ-LLSACSHFEDITMTDFLEVNRQELGR  112 (289)
T ss_dssp             CCSEEEEETCTTCCGG-GTTGGGGCSEEEEECSCHHHHHHHHH
T ss_pred             CCCeEEEECCCcChHH-HHhhccCCCeEEEeCCCHHHHHHHHH
Confidence            4579999999999944 44444456689999984 56665543

>2a14_A Indolethylamine N-methyltransferase; SGC,INMT, structural genomics, structural genomics consortium; HET: SAH; 1.70A {Homo sapiens} SCOP: c.66.1.15

Probab=96.68  E-value=0.00032  Score=57.32  Aligned_cols=41  Identities=15%  Similarity=0.145  Sum_probs=29.0

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhcc
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSS  208 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~  208 (233)
                      .+..+|||||||+|.++..++...- -+++.+|+. ..++.++
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            3457899999999988776554422 268999985 4666544

>1xn7_A Hypothetical protein YHGG; alpha+beta, GFT structural genomics, protein structure initiative, PSI, NESG; NMR {Escherichia coli} SCOP: a.4.5.62

Probab=96.66  E-value=0.0024  Score=42.38  Aligned_cols=44  Identities=16%  Similarity=0.249  Sum_probs=40.4

Q ss_pred             ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      .|.+.|.+.   |.+++.|||+.+++    ++.-++|.|+.|...|++.+.
T Consensus         6 ~Il~~L~~~---g~vsv~eLa~~l~V----S~~TIRrdL~~Le~~G~l~R~   49 (78)
T 1xn7_A            6 QVRDLLALR---GRMEAAQISQTLNT----PQPMINAMLQQLESMGKAVRI   49 (78)
T ss_dssp             HHHHHHHHS---CSBCHHHHHHHTTC----CHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHc---CCCcHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEe
Confidence            367788887   69999999999999    999999999999999999986

>2k02_A Ferrous iron transport protein C; FEOC, iron-sulfur, metal-binding, metal binding protein; NMR {Klebsiella pneumoniae subsp}

Probab=96.65  E-value=0.0022  Score=43.41  Aligned_cols=45  Identities=16%  Similarity=0.276  Sum_probs=40.9

Q ss_pred             ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeec
Q 039903           20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTS   71 (233)
Q Consensus        20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~   71 (233)
                      .|.+.|.+.   |.+++.|||+.+++    ++.-++|.|+.|...|++.+..
T Consensus         6 ~Il~~L~~~---g~vsv~eLA~~l~V----S~~TIRrDL~~Le~~G~l~R~~   50 (87)
T 2k02_A            6 EVRDMLALQ---GRMEAKQLSARLQT----PQPLIDAMLERMEAMGKVVRIS   50 (87)
T ss_dssp             HHHHHHHHS---CSEEHHHHHHHTTC----CHHHHHHHHHHHHTTCCSEEEE
T ss_pred             HHHHHHHHc---CCCcHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEEe
Confidence            367788887   69999999999999    9999999999999999999973

>2o0y_A Transcriptional regulator; ICLR-family, structural genomics, protein structure initiative, midwest center for structural genomics, MCSG; 2.00A {Rhodococcus SP}

Probab=96.63  E-value=0.00097  Score=54.58  Aligned_cols=60  Identities=15%  Similarity=0.205  Sum_probs=48.2

Q ss_pred             hChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHh
Q 039903           19 LGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYF   88 (233)
Q Consensus        19 lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l   88 (233)
                      +.|++.|...+  ++.|+.|||+.+|+    +...+.|+|+.|+..|+++++    .++.|++++....|
T Consensus        26 l~iL~~l~~~~--~~~~~~eia~~~gl----~kstv~r~l~tL~~~G~v~~~----~~~~Y~lg~~~~~l   85 (260)
T 2o0y_A           26 IDLLELFDAAH--PTRSLKELVEGTKL----PKTTVVRLVATMCARSVLTSR----ADGSYSLGPEMLRW   85 (260)
T ss_dssp             HHHHTTCBTTB--SSBCHHHHHHHHCC----CHHHHHHHHHHHHHTTSEEEC----TTSCEEECHHHHHH
T ss_pred             HHHHHHHhhCC--CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEC----CCCeEEecHHHHHH
Confidence            34566665432  58999999999999    999999999999999999996    34489998765433

>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=96.63  E-value=0.0014  Score=45.92  Aligned_cols=66  Identities=17%  Similarity=0.340  Sum_probs=51.5

Q ss_pred             HHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhh
Q 039903           11 AAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVA   85 (233)
Q Consensus        11 ~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s   85 (233)
                      .+|..-.++.|+..|..    ++.|+.|||+.+++    ++..+.+.|+.|...|++.....+ ....|++++..
T Consensus        21 ~~l~~~~r~~IL~~L~~----~~~~~~ela~~l~i----s~stvs~~L~~L~~~Glv~~~~~g-r~~~y~l~~~~   86 (106)
T 1r1u_A           21 KALGDYNRIRIMELLSV----SEASVGHISHQLNL----SQSNVSHQLKLLKSVHLVKAKRQG-QSMIYSLDDIH   86 (106)
T ss_dssp             HHTCSHHHHHHHHHHHH----CCBCHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEEEET-TEEEEEESSHH
T ss_pred             HHhCCHHHHHHHHHHHh----CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCeEEEEeC-CEEEEEEChHH
Confidence            34444567889999985    58999999999999    999999999999999999976321 12357776543

>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2}

Probab=96.61  E-value=0.0022  Score=42.41  Aligned_cols=45  Identities=20%  Similarity=0.214  Sum_probs=39.9

Q ss_pred             ChhHHHHhc-----CCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           20 GVFEIIAKA-----GPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        20 glfd~L~~~-----~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      .|++.|.+.     |  +|.|+.|||+.+|+    ++..+++-|..|...|++.+.
T Consensus         8 ~IL~~I~~~i~~~~g--~~psv~EIa~~lgv----S~~TVrr~L~~Le~kG~I~R~   57 (77)
T 2jt1_A            8 KIISIVQERQNMDDG--APVKTRDIADAAGL----SIYQVRLYLEQLHDVGVLEKV   57 (77)
T ss_dssp             HHHHHHHHHHHHHTT--SCEEHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHhhccC--CCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCcEEec
Confidence            366666665     5  69999999999999    999999999999999999987

>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=96.60  E-value=0.0026  Score=44.68  Aligned_cols=64  Identities=17%  Similarity=0.192  Sum_probs=50.1

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhC-CCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhh
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQM-PSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFV   89 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~-~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~   89 (233)
                      ++.|...|..    ++.+..|||+.+ ++    ++..+.+.|+.|...|++++.....  ..-.|.+|+.+..+.
T Consensus        16 ~~~IL~~L~~----~~~~~~eLa~~l~~i----s~~tls~~L~~Le~~GlI~r~~~~~d~r~~~y~LT~~G~~l~   82 (107)
T 2hzt_A           16 KXVILXHLTH----GKKRTSELKRLMPNI----TQKMLTQQLRELEADGVINRIVYNQVPPKVEYELSEYGRSLE   82 (107)
T ss_dssp             HHHHHHHHTT----CCBCHHHHHHHCTTS----CHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECTTGGGGH
T ss_pred             HHHHHHHHHh----CCCCHHHHHHHhcCC----CHHHHHHHHHHHHHCCCEEEeecCCCCCeEEEEECccHHHHH
Confidence            3446666653    689999999999 99    9999999999999999999864321  123689998876654

>2g7u_A Transcriptional regulator; ICLR family, structural genomics, PSI, protein structure initiative, midwest center for struc genomics; 2.30A {Rhodococcus SP}

Probab=96.59  E-value=0.0013  Score=53.79  Aligned_cols=62  Identities=13%  Similarity=0.068  Sum_probs=51.4

Q ss_pred             hChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhcC
Q 039903           19 LGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        19 lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~~   91 (233)
                      +.|++.|...+  ++.|+.|||+.+++    +...+.|+|+.|+..|+++++     ++.|++++....|...
T Consensus        17 l~iL~~l~~~~--~~~~~~eia~~~gl----~~stv~r~l~~L~~~G~v~~~-----~~~Y~Lg~~~~~l~~~   78 (257)
T 2g7u_A           17 FAVLLAFDAQR--PNPTLAELATEAGL----SRPAVRRILLTLQKLGYVAGS-----GGRWSLTPRVLSIGQH   78 (257)
T ss_dssp             HHHHHTCSSSC--SSCBHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEE-----TTEEEECGGGHHHHTT
T ss_pred             HHHHHHHHhCC--CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEeC-----CCEEEEcHHHHHHHHH
Confidence            45666666533  58999999999999    999999999999999999995     5899999877666543

>4dmg_A Putative uncharacterized protein TTHA1493; rRNA, methyltransferase, S-adenosyl-methionine, 23S ribosoma transferase; HET: SAM; 1.70A {Thermus thermophilus}

Probab=96.58  E-value=0.0019  Score=56.16  Aligned_cols=62  Identities=13%  Similarity=-0.006  Sum_probs=46.8

Q ss_pred             cceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC-----CCceEEecCcCCCC---CC-CCEEEe
Q 039903          169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY-----SGVKHIGGIMLERI---PK-GDAILI  232 (233)
Q Consensus       169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~-----~ri~~~~gD~f~~~---P~-~D~~~l  232 (233)
                      ..+|||+|||+|.++..+++....  ++.+|+. ..++.++++     -..++..+|.++.+   +. .|+|++
T Consensus       215 g~~VLDlg~GtG~~sl~~a~~ga~--V~avDis~~al~~a~~n~~~ng~~~~~~~~D~~~~l~~~~~~fD~Ii~  286 (393)
T 4dmg_A          215 GERVLDVYSYVGGFALRAARKGAY--ALAVDKDLEALGVLDQAALRLGLRVDIRHGEALPTLRGLEGPFHHVLL  286 (393)
T ss_dssp             TCEEEEESCTTTHHHHHHHHTTCE--EEEEESCHHHHHHHHHHHHHHTCCCEEEESCHHHHHHTCCCCEEEEEE
T ss_pred             CCeEEEcccchhHHHHHHHHcCCe--EEEEECCHHHHHHHHHHHHHhCCCCcEEEccHHHHHHHhcCCCCEEEE
Confidence            689999999999999999997544  9999984 577777653     12356799998732   33 388875

>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=96.55  E-value=0.003  Score=52.58  Aligned_cols=57  Identities=11%  Similarity=0.122  Sum_probs=40.3

Q ss_pred             HHHHhccccc-CcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhh-ccCCCCceEE
Q 039903          158 RIIDSSKGFE-QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQD-SSSYSGVKHI  216 (233)
Q Consensus       158 ~~~~~~~~~~-~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~-a~~~~ri~~~  216 (233)
                      .+++.+. .. ...+++|||||+|.++..++++ +.-+++.+|.. ..++. .+..+|+..+
T Consensus        75 ~~l~~~~-~~~~g~~vLDiGcGTG~~t~~L~~~-ga~~V~aVDvs~~mL~~a~r~~~rv~~~  134 (291)
T 3hp7_A           75 KALAVFN-LSVEDMITIDIGASTGGFTDVMLQN-GAKLVYAVDVGTNQLVWKLRQDDRVRSM  134 (291)
T ss_dssp             HHHHHTT-CCCTTCEEEEETCTTSHHHHHHHHT-TCSEEEEECSSSSCSCHHHHTCTTEEEE
T ss_pred             HHHHhcC-CCccccEEEecCCCccHHHHHHHhC-CCCEEEEEECCHHHHHHHHHhCccccee
Confidence            4455554 33 3479999999999999988886 66689999984 45655 3444565544

>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=96.55  E-value=0.0034  Score=50.43  Aligned_cols=49  Identities=12%  Similarity=0.146  Sum_probs=35.6

Q ss_pred             HHHHhcccc-cCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhcc
Q 039903          158 RIIDSSKGF-EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSS  208 (233)
Q Consensus       158 ~~~~~~~~~-~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~  208 (233)
                      .+++.++ . ....++||||||+|.++..++++ ...+++.+|+. ..++.+.
T Consensus        27 ~~L~~~~-~~~~g~~VLDiGcGtG~~t~~la~~-g~~~V~gvDis~~ml~~a~   77 (232)
T 3opn_A           27 KALKEFH-LEINGKTCLDIGSSTGGFTDVMLQN-GAKLVYALDVGTNQLAWKI   77 (232)
T ss_dssp             HHHHHTT-CCCTTCEEEEETCTTSHHHHHHHHT-TCSEEEEECSSCCCCCHHH
T ss_pred             HHHHHcC-CCCCCCEEEEEccCCCHHHHHHHhc-CCCEEEEEcCCHHHHHHHH
Confidence            3444444 3 23469999999999999999987 33489999984 4655544

>3m4x_A NOL1/NOP2/SUN family protein; mtase domain, PUA domain, RRM motif, transferase; 2.28A {Enterococcus faecium}

Probab=96.54  E-value=0.0013  Score=58.24  Aligned_cols=71  Identities=11%  Similarity=-0.014  Sum_probs=53.3

Q ss_pred             HhcccccCcceEEEecCCccHHHHHHHHHcCC-CcEEEeech-HHHhhccCC------CCceEEecCcCC-C--CCCC-C
Q 039903          161 DSSKGFEQIKQLVDVGGGLGVNVNIIISNYLH-IKGVNFDLS-HVIQDSSSY------SGVKHIGGIMLE-R--IPKG-D  228 (233)
Q Consensus       161 ~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~-l~~~v~Dlp-~v~~~a~~~------~ri~~~~gD~f~-~--~P~~-D  228 (233)
                      ..++ .....+|+|+|||.|..+..+++..++ -+++.+|+. ..++.++++      .+|.++.+|..+ .  .+.. |
T Consensus        99 ~~L~-~~~g~~VLDlcaGpGgkt~~lA~~~~~~g~V~AvDis~~rl~~~~~n~~r~g~~nv~v~~~Da~~l~~~~~~~FD  177 (456)
T 3m4x_A           99 TAAA-AKPGEKVLDLCAAPGGKSTQLAAQMKGKGLLVTNEIFPKRAKILSENIERWGVSNAIVTNHAPAELVPHFSGFFD  177 (456)
T ss_dssp             HHHC-CCTTCEEEESSCTTCHHHHHHHHHHTTCSEEEEECSSHHHHHHHHHHHHHHTCSSEEEECCCHHHHHHHHTTCEE
T ss_pred             HHcC-CCCCCEEEEECCCcCHHHHHHHHHcCCCCEEEEEeCCHHHHHHHHHHHHHcCCCceEEEeCCHHHhhhhccccCC
Confidence            3344 455689999999999999999998764 689999984 466655542      579999999876 2  3443 8


Q ss_pred             EEEe
Q 039903          229 AILI  232 (233)
Q Consensus       229 ~~~l  232 (233)
                      +|++
T Consensus       178 ~Il~  181 (456)
T 3m4x_A          178 RIVV  181 (456)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            8875

>2kko_A Possible transcriptional regulatory protein (possibly ARSR-family); NESG, DNA-binding, transcription regulation, WHTH, homodimer; NMR {Mycobacterium bovis} PDB: 3gw2_A

Probab=96.54  E-value=0.00066  Score=47.91  Aligned_cols=61  Identities=15%  Similarity=0.244  Sum_probs=48.3

Q ss_pred             HHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhh
Q 039903           16 ASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVA   85 (233)
Q Consensus        16 a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s   85 (233)
                      -.++.|+..|..    ++.|..|||+.+++    ++..+.+.|+.|...|+++....+ ....|++++.+
T Consensus        25 ~~r~~IL~~L~~----~~~s~~eLa~~lgi----s~stvs~~L~~L~~~GlV~~~~~g-r~~~y~l~~~~   85 (108)
T 2kko_A           25 GRRLQILDLLAQ----GERAVEAIATATGM----NLTTASANLQALKSGGLVEARREG-TRQYYRIAGED   85 (108)
T ss_dssp             STTHHHHHHHTT----CCEEHHHHHHHHTC----CHHHHHHHHHHHHHHTSEEEEEET-TEEEEEESCHH
T ss_pred             HHHHHHHHHHHc----CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCeEEEEeC-CEEEEEEChHH
Confidence            345678888875    58999999999999    999999999999999999876321 22357777643

>2k4m_A TR8_protein, UPF0146 protein MTH_1000; alpha+beta, rossman fold, structural genomics, PSI-2; NMR {Methanothermobacterthermautotrophicus str}

Probab=96.54  E-value=0.0026  Score=47.35  Aligned_cols=55  Identities=15%  Similarity=0.039  Sum_probs=42.0

Q ss_pred             ccCcceEEEecCCccH-HHHHHHHHcCCCcEEEeec-hHHHhhccCCCCceEEecCcCCCCCC----CCEE
Q 039903          166 FEQIKQLVDVGGGLGV-NVNIIISNYLHIKGVNFDL-SHVIQDSSSYSGVKHIGGIMLERIPK----GDAI  230 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~-~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~~ri~~~~gD~f~~~P~----~D~~  230 (233)
                      +....++||||||.|. .+..|+++ -+..++..|+ |..++         ++..|+|++.+.    +|+|
T Consensus        33 ~~~~~rVlEVG~G~g~~vA~~La~~-~g~~V~atDInp~Av~---------~v~dDiF~P~~~~Y~~~DLI   93 (153)
T 2k4m_A           33 SGPGTRVVEVGAGRFLYVSDYIRKH-SKVDLVLTDIKPSHGG---------IVRDDITSPRMEIYRGAALI   93 (153)
T ss_dssp             SCSSSEEEEETCTTCCHHHHHHHHH-SCCEEEEECSSCSSTT---------EECCCSSSCCHHHHTTEEEE
T ss_pred             CCCCCcEEEEccCCChHHHHHHHHh-CCCeEEEEECCccccc---------eEEccCCCCcccccCCcCEE
Confidence            4455799999999995 78877763 5677999997 44554         889999997762    3877

>2frx_A Hypothetical protein YEBU; rossmann-type S-adenosylmethionine-dependent methyltransfera domain; 2.90A {Escherichia coli}

Probab=96.51  E-value=0.0042  Score=55.36  Aligned_cols=65  Identities=18%  Similarity=0.104  Sum_probs=51.3

Q ss_pred             CcceEEEecCCccHHHHHHHHHcC-CCcEEEeech-HHHhhccCC------CCceEEecCcCC-C--CCCC-CEEEe
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDLS-HVIQDSSSY------SGVKHIGGIMLE-R--IPKG-DAILI  232 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dlp-~v~~~a~~~------~ri~~~~gD~f~-~--~P~~-D~~~l  232 (233)
                      ...+|+|+|||.|..+..+++..+ .-+++.+|+. ..++.++++      ++|+++.+|..+ +  .+.. |+|++
T Consensus       117 ~g~~VLDl~aGpG~kt~~lA~~~~~~g~V~avDis~~~l~~~~~n~~r~g~~nv~~~~~D~~~~~~~~~~~fD~Il~  193 (479)
T 2frx_A          117 APQRVMDVAAAPGSKTTQISARMNNEGAILANEFSASRVKVLHANISRCGISNVALTHFDGRVFGAAVPEMFDAILL  193 (479)
T ss_dssp             CCSEEEESSCTTSHHHHHHHHHTTTCSEEEEECSSHHHHHHHHHHHHHHTCCSEEEECCCSTTHHHHSTTCEEEEEE
T ss_pred             CCCEEEEeCCCCCHHHHHHHHhCCCCCEEEEEECCHHHHHHHHHHHHHcCCCcEEEEeCCHHHhhhhccccCCEEEE
Confidence            567999999999999999999875 5789999985 456655542      579999999987 3  3443 98875

>2fu4_A Ferric uptake regulation protein; DNA binding domain, helix-turn-helix, DNA binding protein; 1.80A {Escherichia coli}

Probab=96.50  E-value=0.0015  Score=43.48  Aligned_cols=59  Identities=12%  Similarity=0.270  Sum_probs=45.1

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhC-----CCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceec
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQM-----PSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGL   81 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~-----~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~l   81 (233)
                      +..|++.|...+ +++.|+.||++.+     ++    +..-++|.|+.|+..|++.+...+++..+|.+
T Consensus        19 r~~IL~~l~~~~-~~~~s~~el~~~l~~~~~~i----s~~TVyR~L~~L~~~Glv~~~~~~~~~~~y~~   82 (83)
T 2fu4_A           19 RLKILEVLQEPD-NHHVSAEDLYKRLIDMGEEI----GLATVYRVLNQFDDAGIVTRHNFEGGKSVFEL   82 (83)
T ss_dssp             HHHHHHHHTSGG-GSSBCHHHHHHHHHHTTCCC----CHHHHHHHHHHHHHHTSEEEEECGGGCEEEEE
T ss_pred             HHHHHHHHHhCC-CCCCCHHHHHHHHHHhCCCC----CHhhHHHHHHHHHHCCCeEEEeeCCCceEeec
Confidence            456888887641 0389999999999     88    99999999999999999998743212334543

>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=96.46  E-value=0.0031  Score=44.63  Aligned_cols=63  Identities=11%  Similarity=0.080  Sum_probs=50.5

Q ss_pred             ChhHHHHhcCCCCCCCHHHHHHhC-CCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhc
Q 039903           20 GVFEIIAKAGPTAKISAVEIAAQM-PSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVL   90 (233)
Q Consensus        20 glfd~L~~~~~~~~~t~~elA~~~-~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~   90 (233)
                      .|...|..    ++.+..|||+.+ ++    ++..+.+.|+.|...|++++.....  ..-.|.+|+.|..+..
T Consensus        26 ~IL~~L~~----~~~~~~eLa~~l~~i----s~~tvs~~L~~Le~~GlI~r~~~~~d~r~~~~~LT~~G~~~~~   91 (112)
T 1z7u_A           26 SLMDELFQ----GTKRNGELMRALDGI----TQRVLTDRLREMEKDGLVHRESFNELPPRVEYTLTPEGYALYD   91 (112)
T ss_dssp             HHHHHHHH----SCBCHHHHHHHSTTC----CHHHHHHHHHHHHHHTSEEEEEECCSSCEEEEEECHHHHHHHH
T ss_pred             HHHHHHHh----CCCCHHHHHHHhccC----CHHHHHHHHHHHHHCCCEEEeecCCCCCeEEEEECHhHHHHHH
Confidence            46666765    589999999999 99    9999999999999999999864321  1135899999887653

>2htj_A P fimbrial regulatory protein KS71A; winged helix-turn-helix, PAP PILI, transcription activator; NMR {Escherichia coli} SCOP: a.4.5.73

Probab=96.46  E-value=0.0038  Score=41.45  Aligned_cols=45  Identities=16%  Similarity=0.163  Sum_probs=40.0

Q ss_pred             hChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           19 LGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        19 lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      ..|++.|...   ++.|..|||+.+++    +...+.+.|+.|...|++.+.
T Consensus         3 ~~Il~~L~~~---~~~s~~eLa~~lgv----s~~tv~r~L~~L~~~GlI~~~   47 (81)
T 2htj_A            3 NEILEFLNRH---NGGKTAEIAEALAV----TDYQARYYLLLLEKAGMVQRS   47 (81)
T ss_dssp             HHHHHHHHHS---CCCCHHHHHHHHTS----CHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHHc---CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEe
Confidence            4577888775   58999999999999    999999999999999999954

>4a5n_A Uncharacterized HTH-type transcriptional regulato; activator, DNA binding, MARR-like; 1.81A {Bacillus subtilis} PDB: 4a5m_A

Probab=96.44  E-value=0.0035  Score=45.90  Aligned_cols=63  Identities=16%  Similarity=0.088  Sum_probs=50.6

Q ss_pred             ChhHHHHhcCCCCCCCHHHHHHhC-CCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhc
Q 039903           20 GVFEIIAKAGPTAKISAVEIAAQM-PSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVL   90 (233)
Q Consensus        20 glfd~L~~~~~~~~~t~~elA~~~-~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~   90 (233)
                      -|...|..    |+.+..||++.+ ++    ++..|.+.|+.|...|++++.....  ..-.|++|+.|+.|..
T Consensus        30 ~IL~~L~~----g~~rf~eL~~~l~gI----s~~~Ls~~L~~Le~~GLV~R~~~~~d~r~v~y~LT~~G~~l~~   95 (131)
T 4a5n_A           30 ILFYHMID----GKKRFNEFRRICPSI----TQRMLTLQLRELEADGIVHREVYHQVPPKVEYSLTEFGRTLEP   95 (131)
T ss_dssp             HHHHHHTT----SCBCHHHHHHHCTTS----CHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECTTGGGGHH
T ss_pred             HHHHHHhc----CCcCHHHHHHHhccc----CHHHHHHHHHHHHHCCCEEEEecCCCCCeEEEEECHhHHHHHH
Confidence            35555553    699999999999 99    9999999999999999999874321  1247999999987764

>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=96.43  E-value=0.0037  Score=42.71  Aligned_cols=66  Identities=12%  Similarity=0.071  Sum_probs=50.3

Q ss_pred             hChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhh-HHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhc
Q 039903           19 LGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVM-LDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVL   90 (233)
Q Consensus        19 lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~-l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~   90 (233)
                      +.++..|...+  .+.|..|||+.+++    +... +.++++.|...|++..+..+...-.+.+|+.|..+..
T Consensus        18 l~~L~~l~~~~--~~~t~~eLa~~l~i----s~~t~vs~~l~~Le~~Glv~~~~~drR~~~~~LT~~G~~~~~   84 (95)
T 2pg4_A           18 LPTLLEFEKKG--YEPSLAEIVKASGV----SEKTFFMGLKDRLIRAGLVKEETLSYRVKTLKLTEKGRRLAE   84 (95)
T ss_dssp             HHHHHHHHHTT--CCCCHHHHHHHHCC----CHHHHHTTHHHHHHHTTSEEEEEEETTEEEEEECHHHHHHHH
T ss_pred             HHHHHHHHhcC--CCCCHHHHHHHHCC----CchHHHHHHHHHHHHCCCeecCCCCCCeEEEEECHhHHHHHH
Confidence            34555666652  27999999999999    9999 9999999999999995422212345789999987664

>3bja_A Transcriptional regulator, MARR family, putative; NP_978771.1, putative MARR-like transcription regulator, MAR structural genomics; 2.38A {Bacillus cereus}

Probab=96.34  E-value=0.0059  Score=44.14  Aligned_cols=67  Identities=13%  Similarity=0.220  Sum_probs=52.4

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      ++.|+..|...   ++.|..+||+.+++    +...+.++++.|...|++++.....  ..-.+.+|+.|..+...
T Consensus        35 ~~~iL~~l~~~---~~~~~~ela~~l~~----~~~tvs~~l~~L~~~gli~r~~~~~d~r~~~~~lT~~G~~~~~~  103 (139)
T 3bja_A           35 QFGVIQVLAKS---GKVSMSKLIENMGC----VPSNMTTMIQRMKRDGYVMTEKNPNDQRETLVYLTKKGEETKKQ  103 (139)
T ss_dssp             HHHHHHHHHHS---CSEEHHHHHHHCSS----CCTTHHHHHHHHHHTTSEEEEECSSCTTCEEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHHc---CCcCHHHHHHHHCC----ChhHHHHHHHHHHHCCCeeeccCCCCCceeEEEECHHHHHHHHH
Confidence            44577777775   58999999999999    9999999999999999999853221  12237889988876643

>3t8r_A Staphylococcus aureus CYMR; transcriptional regulator protein, dimer, sulfenic acid, UNK function; 1.70A {Staphylococcus aureus} PDB: 3t8t_A

Probab=96.34  E-value=0.0039  Score=46.26  Aligned_cols=46  Identities=20%  Similarity=0.222  Sum_probs=39.6

Q ss_pred             CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903           32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH   83 (233)
Q Consensus        32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~   83 (233)
                      ++.|..+||+.+++    ++..++++|..|...|+++..+.  .+|.|.++.
T Consensus        27 ~~~s~~~IA~~~~i----~~~~l~kil~~L~~aGlv~s~rG--~~GGy~Lar   72 (143)
T 3t8r_A           27 GCISLKSIAEENNL----SDLYLEQLVGPLRNAGLIRSVRG--AKGGYQLRV   72 (143)
T ss_dssp             CCEEHHHHHHHTTC----CHHHHHHHHHHHHHTTSEEECSS--SSSEEEESS
T ss_pred             CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCEEEecCC--CCCCeeecC
Confidence            48999999999999    99999999999999999986532  356788764

>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=96.31  E-value=0.0043  Score=45.79  Aligned_cols=68  Identities=10%  Similarity=0.097  Sum_probs=49.9

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      +..++..|...+  +++|..|||+.+++    ++..+.++++.|...|++++.....  ..-.+.+|+.|..+...
T Consensus        41 q~~vL~~l~~~~--~~~t~~eLa~~l~i----~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~~  110 (150)
T 3fm5_A           41 SYSVLVLACEQA--EGVNQRGVAATMGL----DPSQIVGLVDELEERGLVVRTLDPSDRRNKLIAATEEGRRLRDD  110 (150)
T ss_dssp             HHHHHHHHHHST--TCCCSHHHHHHHTC----CHHHHHHHHHHHHTTTSEEC-----------CEECHHHHHHHHH
T ss_pred             HHHHHHHHHhCC--CCcCHHHHHHHHCC----CHhHHHHHHHHHHHCCCEEeeCCccccchheeeECHHHHHHHHH
Confidence            445667776554  47899999999999    9999999999999999999853211  11237889988877644

>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=96.31  E-value=0.0063  Score=44.02  Aligned_cols=67  Identities=21%  Similarity=0.142  Sum_probs=52.5

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      ++.++..|...   ++.|..+||+.+++    +...+.++++.|...|++++.....  ..-.+.+|+.|..+...
T Consensus        36 ~~~iL~~l~~~---~~~~~~~la~~l~~----~~~tvs~~l~~L~~~gli~r~~~~~d~R~~~~~lT~~G~~~~~~  104 (138)
T 1jgs_A           36 QFKVLCSIRCA---ACITPVELKKVLSV----DLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTGGAAICEQ  104 (138)
T ss_dssp             HHHHHHHHHHH---SSBCHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEEECTTCSSCEEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHhc---CCCCHHHHHHHHCC----ChHHHHHHHHHHHHCCCEEecCCcccCceeEeEEChhHHHHHHH
Confidence            44567777765   48999999999999    9999999999999999999864321  11247899998877644

>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=96.30  E-value=0.0049  Score=53.23  Aligned_cols=65  Identities=8%  Similarity=-0.166  Sum_probs=49.8

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC---------------------CCceEEecCcCCC--
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY---------------------SGVKHIGGIMLER--  223 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~---------------------~ri~~~~gD~f~~--  223 (233)
                      ...+|+|+|||+|.+++.++++.|..+++..|+ |+.++.++++                     ++|+++.+|..+.  
T Consensus        47 ~~~~VLDl~aGtG~~~l~~a~~~~~~~V~avDi~~~av~~a~~N~~~n~~~~~~~~~~~~~~~gl~~i~v~~~Da~~~~~  126 (378)
T 2dul_A           47 NPKIVLDALSATGIRGIRFALETPAEEVWLNDISEDAYELMKRNVMLNFDGELRESKGRAILKGEKTIVINHDDANRLMA  126 (378)
T ss_dssp             CCSEEEESSCTTSHHHHHHHHHSSCSEEEEEESCHHHHHHHHHHHHHHCCSCCEECSSEEEEESSSEEEEEESCHHHHHH
T ss_pred             CCCEEEECCCchhHHHHHHHHhCCCCeEEEEECCHHHHHHHHHHHHHhcccccccccccccccCCCceEEEcCcHHHHHH
Confidence            347899999999999999999999889999998 4566655432                     2388999998762  


Q ss_pred             -CCC-CCEEEe
Q 039903          224 -IPK-GDAILI  232 (233)
Q Consensus       224 -~P~-~D~~~l  232 (233)
                       .+. .|+|++
T Consensus       127 ~~~~~fD~I~l  137 (378)
T 2dul_A          127 ERHRYFHFIDL  137 (378)
T ss_dssp             HSTTCEEEEEE
T ss_pred             hccCCCCEEEe
Confidence             233 388765

>2nnn_A Probable transcriptional regulator; structural genomics, PSI-2, protein structure initiative, M center for structural genomics, MCSG; 2.40A {Pseudomonas aeruginosa}

Probab=96.30  E-value=0.0065  Score=43.95  Aligned_cols=67  Identities=7%  Similarity=0.110  Sum_probs=52.8

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      ++.|+..|...   ++.|..+||+.+++    +...+.++++.|...|++++.....  ..-.+.+|+.|..+...
T Consensus        40 ~~~iL~~l~~~---~~~t~~ela~~l~~----~~~tvs~~l~~L~~~glv~r~~~~~d~R~~~~~lT~~G~~~~~~  108 (140)
T 2nnn_A           40 QWAALVRLGET---GPCPQNQLGRLTAM----DAATIKGVVERLDKRGLIQRSADPDDGRRLLVSLSPAGRAELEA  108 (140)
T ss_dssp             HHHHHHHHHHH---SSBCHHHHHHHTTC----CHHHHHHHHHHHHHTTCEEEEEETTEEEEEEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHHc---CCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEeeCCCCCCCeeeeEECHhHHHHHHH
Confidence            45577888776   48999999999999    9999999999999999999853210  11247889988876643

>3lwf_A LIN1550 protein, putative transcriptional regulator; structural genomics, JOI for structural genomics, JCSG; HET: SO4; 2.06A {Listeria innocua}

Probab=96.29  E-value=0.0049  Score=46.65  Aligned_cols=46  Identities=17%  Similarity=0.187  Sum_probs=40.0

Q ss_pred             CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903           32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH   83 (233)
Q Consensus        32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~   83 (233)
                      ++.|.++||+.+++    ++..++++|..|...|+++..+.  .+|.|.++.
T Consensus        43 ~~~s~~eIA~~~~i----~~~~l~kil~~L~~aGlv~s~rG--~~GGy~Lar   88 (159)
T 3lwf_A           43 GPISLRSIAQDKNL----SEHYLEQLIGPLRNAGIVKSIRG--AHGGYVLNG   88 (159)
T ss_dssp             CCBCHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEECS--TTCEEEECS
T ss_pred             CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCeEEEecC--CCCceEecC
Confidence            58999999999999    99999999999999999997642  356787764

>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=96.28  E-value=0.0049  Score=43.18  Aligned_cols=62  Identities=16%  Similarity=0.196  Sum_probs=49.2

Q ss_pred             ChhHHHHhcCCCCCCCHHHHHHhCC-CCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhh
Q 039903           20 GVFEIIAKAGPTAKISAVEIAAQMP-SSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFV   89 (233)
Q Consensus        20 glfd~L~~~~~~~~~t~~elA~~~~-~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~   89 (233)
                      .|...|..    ++.+..||++.++ +    ++..+.+.|+.|...|++++...+.  ..-.|.+|+.|+.+.
T Consensus        29 ~IL~~L~~----~~~~~~eL~~~l~gi----s~~~ls~~L~~Le~~GlV~r~~~~~d~r~~~y~LT~~G~~l~   93 (107)
T 2fsw_A           29 LIIFQINR----RIIRYGELKRAIPGI----SEKMLIDELKFLCGKGLIKKKQYPEVPPRVEYSLTPLGEKVL   93 (107)
T ss_dssp             HHHHHHTT----SCEEHHHHHHHSTTC----CHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECHHHHTTH
T ss_pred             HHHHHHHh----CCcCHHHHHHHcccC----CHHHHHHHHHHHHHCCCEEEeecCCCCCeeEEEECccHHHHH
Confidence            35666653    6899999999995 9    9999999999999999999864321  113699999987655

>1yyv_A Putative transcriptional regulator; reductive methylation, D lysine, structural genomics, PSI; HET: MLY; 2.35A {Salmonella typhimurium} SCOP: a.4.5.69

Probab=96.27  E-value=0.0036  Score=45.72  Aligned_cols=66  Identities=14%  Similarity=0.084  Sum_probs=52.3

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhC-CCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhc
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQM-PSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVL   90 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~-~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~   90 (233)
                      .++.|...|..    ++.+..||++.+ ++    ++..+.+.|+.|...|++++.....  ..-.|++|+.|..+..
T Consensus        36 w~l~IL~~L~~----g~~~~~eLa~~l~gi----s~~tls~~L~~Le~~GlV~r~~~~~d~r~~~y~LT~~G~~l~~  104 (131)
T 1yyv_A           36 WGVLILVALRD----GTHRFSDLRRXMGGV----SEXMLAQSLQALEQDGFLNRVSYPVVPPHVEYSLTPLGEQVSD  104 (131)
T ss_dssp             HHHHHHHHGGG----CCEEHHHHHHHSTTC----CHHHHHHHHHHHHHHTCEEEEEECSSSCEEEEEECHHHHHHHH
T ss_pred             cHHHHHHHHHc----CCCCHHHHHHHhccC----CHHHHHHHHHHHHHCCcEEEEecCCCCCeEEEEECccHHHHHH
Confidence            34556667764    689999999999 79    9999999999999999999864321  1237999999987663

>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=96.27  E-value=0.0055  Score=45.57  Aligned_cols=63  Identities=19%  Similarity=0.179  Sum_probs=49.8

Q ss_pred             hChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC-CCCceeccHhhhHhh
Q 039903           19 LGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD-DQRLYGLAHVAKYFV   89 (233)
Q Consensus        19 lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~-~~~~y~lt~~s~~l~   89 (233)
                      +.|...|..    |+.+..||++.+++    +...+.+.|+.|...|++++..... ..-.|.+|+.|..+.
T Consensus        27 l~IL~~L~~----g~~~~~eLa~~lgi----s~~tls~~L~~Le~~GlI~r~~~~~d~~~~y~LT~~G~~l~   90 (146)
T 2f2e_A           27 MLIVRDAFE----GLTRFGEFQKSLGL----AKNILAARLRNLVEHGVMVAVPAESGSHQEYRLTDKGRALF   90 (146)
T ss_dssp             HHHHHHHHT----TCCSHHHHHHHHCC----CHHHHHHHHHHHHHTTSEEEEECSSSSCEEEEECHHHHTTH
T ss_pred             HHHHHHHHh----CCCCHHHHHHHhCC----CHHHHHHHHHHHHHCCCEEEEecCCCCeEEEEECchHHHHH
Confidence            335555654    68999999999999    9999999999999999999864310 124799999887654

>2ia2_A Putative transcriptional regulator; SAD, PSI-2, structural genomics, structure initiative, midwest center for structural genomic transcription; 2.10A {Rhodococcus SP}

Probab=96.27  E-value=0.0012  Score=54.13  Aligned_cols=57  Identities=14%  Similarity=0.114  Sum_probs=47.8

Q ss_pred             hChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhh
Q 039903           19 LGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAK   86 (233)
Q Consensus        19 lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~   86 (233)
                      +.|++.|...+  ++.|+.|||+.+|+    +...+.|+|+.|+..|+++++     ++.|++++...
T Consensus        24 l~iL~~l~~~~--~~~~~~eia~~~gl----~~stv~r~l~tL~~~G~v~~~-----~~~Y~Lg~~~~   80 (265)
T 2ia2_A           24 LAVIRCFDHRN--QRRTLSDVARATDL----TRATARRFLLTLVELGYVATD-----GSAFWLTPRVL   80 (265)
T ss_dssp             HHHHHTCCSSC--SSEEHHHHHHHHTC----CHHHHHHHHHHHHHHTSEEES-----SSEEEECGGGG
T ss_pred             HHHHHHHHhCC--CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEec-----CCEEEEcHHHH
Confidence            45666666433  58999999999999    999999999999999999995     58999987543

>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=96.27  E-value=0.0098  Score=43.47  Aligned_cols=68  Identities=18%  Similarity=0.181  Sum_probs=53.0

Q ss_pred             HhhChhHHHHh-cCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccC--CCCCceeccHhhhHhhcC
Q 039903           17 SELGVFEIIAK-AGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAG--DDQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        17 ~~lglfd~L~~-~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~--~~~~~y~lt~~s~~l~~~   91 (233)
                      .++.|+..|.. .   ++.|..+||+.+++    +...+.++++.|...|++++....  ...-.+.+|+.|..+...
T Consensus        36 ~~~~iL~~l~~~~---~~~~~~~la~~l~i----~~~~vs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~~~~  106 (147)
T 2hr3_A           36 SQLVVLGAIDRLG---GDVTPSELAAAERM----RSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYG  106 (147)
T ss_dssp             HHHHHHHHHHHTT---SCBCHHHHHHHTTC----CHHHHHHHHHHHHHTTSEEEEC------CCEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHHHcC---CCCCHHHHHHHhCC----ChhhHHHHHHHHHHCCCEeeCCCCCCCCceeeEECHHHHHHHHH
Confidence            45667788876 5   58999999999999    999999999999999999986321  112347889988876644

>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=96.27  E-value=0.0032  Score=45.37  Aligned_cols=62  Identities=16%  Similarity=0.308  Sum_probs=49.3

Q ss_pred             HHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhh
Q 039903           15 AASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVA   85 (233)
Q Consensus        15 ~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s   85 (233)
                      .-.++.|+..|.+    ++.++.|||+.+++    +...+.+.|+.|...|++.....+ ..-.|++++..
T Consensus        45 ~~~rl~IL~~L~~----~~~s~~ela~~lgi----s~stvs~~L~~Le~~Glv~~~~~g-r~~~y~l~~~~  106 (122)
T 1r1t_A           45 DPNRLRLLSLLAR----SELCVGDLAQAIGV----SESAVSHQLRSLRNLRLVSYRKQG-RHVYYQLQDHH  106 (122)
T ss_dssp             CHHHHHHHHHHTT----CCBCHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEEEET-TEEEEEESSHH
T ss_pred             CHHHHHHHHHHHc----CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCeEEEEeC-CEEEEEEChHH
Confidence            3357789999976    58999999999999    999999999999999999875321 22356776543

>3g3z_A NMB1585, transcriptional regulator, MARR family; transcription factor, structur genomics, oxford protein production facility; 2.10A {Neisseria meningitidis serogroup B}

Probab=96.24  E-value=0.0065  Score=44.45  Aligned_cols=67  Identities=12%  Similarity=0.194  Sum_probs=53.3

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      +..|+..|...   ++.|..|||+.+++    +...+.++++.|...|++++.....  ..-.+.+|+.|..+...
T Consensus        33 q~~iL~~l~~~---~~~t~~eLa~~l~~----~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~~  101 (145)
T 3g3z_A           33 LFAVLYTLATE---GSRTQKHIGEKWSL----PKQTVSGVCKTLAGQGLIEWQEGEQDRRKRLLSLTETGKAYAAP  101 (145)
T ss_dssp             HHHHHHHHHHH---CSBCHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEECCCSSCGGGSCEEECHHHHHHHHH
T ss_pred             HHHHHHHHHHC---CCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEeeccCCCCCceeeeeEChhHHHHHHH
Confidence            45577778776   48999999999999    9999999999999999999853321  12357899998877644

>2xyq_A Putative 2'-O-methyl transferase; transferase-viral protein complex, rossman fold; HET: SAH; 2.00A {Sars coronavirus} PDB: 2xyv_A* 2xyr_A*

Probab=96.22  E-value=0.0063  Score=50.61  Aligned_cols=59  Identities=17%  Similarity=0.169  Sum_probs=44.5

Q ss_pred             ccCcceEEEecCC------ccHHHHHHHHHcC-CCcEEEeechHHHhhccCCCCceE-EecCcCC-CCCCC-CEEEe
Q 039903          166 FEQIKQLVDVGGG------LGVNVNIIISNYL-HIKGVNFDLSHVIQDSSSYSGVKH-IGGIMLE-RIPKG-DAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG------~G~~~~~l~~~~P-~l~~~v~Dlp~v~~~a~~~~ri~~-~~gD~f~-~~P~~-D~~~l  232 (233)
                      .+...+|||+|||      .|.  ..+++..| ..+++.+|+.+.      .++|++ +.+|+.+ +++.. |+|+.
T Consensus        61 l~~g~~VLDLGcGsg~~~GpGs--~~~a~~~~~~~~V~gvDis~~------v~~v~~~i~gD~~~~~~~~~fD~Vvs  129 (290)
T 2xyq_A           61 VPYNMRVIHFGAGSDKGVAPGT--AVLRQWLPTGTLLVDSDLNDF------VSDADSTLIGDCATVHTANKWDLIIS  129 (290)
T ss_dssp             CCTTCEEEEESCCCTTSBCHHH--HHHHHHSCTTCEEEEEESSCC------BCSSSEEEESCGGGCCCSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCCCcHH--HHHHHHcCCCCEEEEEECCCC------CCCCEEEEECccccCCccCcccEEEE
Confidence            5666799999994      477  45567777 689999998655      257999 9999998 45443 88863

>2x4h_A Hypothetical protein SSO2273; transcription; 2.30A {Sulfolobus solfataricus}

Probab=96.21  E-value=0.007  Score=44.13  Aligned_cols=49  Identities=8%  Similarity=-0.014  Sum_probs=44.6

Q ss_pred             CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhh
Q 039903           32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFV   89 (233)
Q Consensus        32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~   89 (233)
                      ++.|..+||+.+++    +...+.+.++.|...|++++.    . ..|.+|+.+..+.
T Consensus        30 ~~~s~~ela~~l~i----s~~tv~~~l~~Le~~Gli~r~----~-~~~~Lt~~g~~~~   78 (139)
T 2x4h_A           30 EGAKINRIAKDLKI----APSSVFEEVSHLEEKGLVKKK----E-DGVWITNNGTRSI   78 (139)
T ss_dssp             SCBCHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEE----T-TEEEECHHHHHHH
T ss_pred             CCcCHHHHHHHhCC----ChHHHHHHHHHHHHCCCEEec----C-CeEEEChhHHHHH
Confidence            58999999999999    999999999999999999986    3 7799999887765

>2h09_A Transcriptional regulator MNTR; transcription regulator, diphtheria toxin, manganese transport, structural genomics, NPPSFA; 2.10A {Escherichia coli}

Probab=96.21  E-value=0.01  Score=44.22  Aligned_cols=56  Identities=16%  Similarity=0.199  Sum_probs=48.2

Q ss_pred             HHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhc
Q 039903           24 IIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVL   90 (233)
Q Consensus        24 ~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~   90 (233)
                      .|...   ++.|..+||+.+++    +...+.+.++.|...|++++.    .+..+.+|+.+..+..
T Consensus        48 ~l~~~---~~~~~~~la~~l~v----s~~tvs~~l~~Le~~Glv~r~----~~~~~~lT~~g~~~~~  103 (155)
T 2h09_A           48 LIREV---GEARQVDMAARLGV----SQPTVAKMLKRLATMGLIEMI----PWRGVFLTAEGEKLAQ  103 (155)
T ss_dssp             HHHHH---SCCCHHHHHHHHTS----CHHHHHHHHHHHHHTTCEEEE----TTTEEEECHHHHHHHH
T ss_pred             HHHhC---CCcCHHHHHHHhCc----CHHHHHHHHHHHHHCCCEEEe----cCCceEEChhHHHHHH
Confidence            56554   58999999999999    999999999999999999986    4667889999887653

>2rdp_A Putative transcriptional regulator MARR; PFAM PF01047, winged-helix binding motif, structural genomics, PSI-2; 2.30A {Geobacillus stearothermophilus}

Probab=96.19  E-value=0.0069  Score=44.50  Aligned_cols=67  Identities=6%  Similarity=0.070  Sum_probs=52.4

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      ++.|+..|...   ++.|..+||+.+++    +...+.++++.|...|++++.....  ..-.+.+|+.|..+...
T Consensus        44 ~~~iL~~l~~~---~~~t~~ela~~l~~----~~~tvs~~l~~Le~~Glv~r~~~~~d~R~~~~~lT~~G~~~~~~  112 (150)
T 2rdp_A           44 QFVALQWLLEE---GDLTVGELSNKMYL----ACSTTTDLVDRMERNGLVARVRDEHDRRVVRIRLLEKGERIIEE  112 (150)
T ss_dssp             HHHHHHHHHHH---CSBCHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEEECCC---CEEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHHc---CCCCHHHHHHHHCC----CchhHHHHHHHHHHCCCeeecCCCCCcceeEeEECHhHHHHHHH
Confidence            44567777776   58999999999999    9999999999999999999864221  12347889988876643

>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=96.19  E-value=0.0099  Score=43.34  Aligned_cols=66  Identities=6%  Similarity=-0.015  Sum_probs=51.5

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      ++.|+..|. .   ++.|..+||+.+++    +...+.++++.|...|++++.....  ..-.+.+|+.|..+...
T Consensus        39 ~~~iL~~l~-~---~~~~~~ela~~l~~----s~~tvs~~l~~Le~~glv~r~~~~~d~r~~~~~lT~~G~~~~~~  106 (146)
T 2gxg_A           39 DFLVLRATS-D---GPKTMAYLANRYFV----TQSAITASVDKLEEMGLVVRVRDREDRRKILIEITEKGLETFNK  106 (146)
T ss_dssp             HHHHHHHHT-T---SCBCHHHHHHHTTC----CHHHHHHHHHHHHHTTSEEEEECSSCTTCEEEEECHHHHHHHHH
T ss_pred             HHHHHHHHh-c---CCcCHHHHHHHhCC----CchhHHHHHHHHHHCCCEEeecCCCCCceEEEEECHHHHHHHHH
Confidence            445667776 4   69999999999999    9999999999999999999864321  12247889988876643

>3nrv_A Putative transcriptional regulator (MARR/EMRR FAM; PSI-2, protein structure initiati structural genomics; HET: MSE; 2.00A {Acinetobacter SP}

Probab=96.14  E-value=0.0064  Score=44.61  Aligned_cols=67  Identities=10%  Similarity=0.173  Sum_probs=51.3

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccC--CCCCceeccHhhhHhhcC
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAG--DDQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~--~~~~~y~lt~~s~~l~~~   91 (233)
                      ++.++..|...   ++.|..|||+.+++    ++..+.++++.|...|++++....  .....+.+|+.|..+...
T Consensus        42 ~~~iL~~l~~~---~~~t~~ela~~l~~----~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~~~lT~~G~~~~~~  110 (148)
T 3nrv_A           42 EWRIISVLSSA---SDCSVQKISDILGL----DKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQELYEV  110 (148)
T ss_dssp             HHHHHHHHHHS---SSBCHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEC---------CCBEECHHHHHHHHH
T ss_pred             HHHHHHHHHcC---CCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEeecCCCCcceeEeEECHhHHHHHHH
Confidence            45577777776   58999999999999    999999999999999999986321  123467889988876644

>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=96.13  E-value=0.012  Score=43.65  Aligned_cols=68  Identities=15%  Similarity=0.037  Sum_probs=53.8

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      .++.|+..|...   ++.|..+||+.+++    +...+.++++.|...|++++.....  ..-.+.+|+.+..+...
T Consensus        45 ~~~~iL~~l~~~---~~~t~~ela~~l~i----s~~tvs~~l~~Le~~Gli~r~~~~~d~R~~~~~lT~~G~~~~~~  114 (154)
T 2eth_A           45 TELYAFLYVALF---GPKKMKEIAEFLST----TKSNVTNVVDSLEKRGLVVREMDPVDRRTYRVVLTEKGKEIFGE  114 (154)
T ss_dssp             HHHHHHHHHHHH---CCBCHHHHHHHTTS----CHHHHHHHHHHHHHTTSEEEEECTTTSSCEEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEeeCCCCCcceeEEEECHHHHHHHHH
Confidence            455678888776   48999999999999    9999999999999999999864221  12347889888876643

>3bpv_A Transcriptional regulator; MARR, DNA binding, transcription factor, winged helix motif, DNA-binding; 1.40A {Methanobacterium thermoautotrophicum} PDB: 3bpx_A*

Probab=96.12  E-value=0.006  Score=44.07  Aligned_cols=67  Identities=12%  Similarity=0.125  Sum_probs=51.7

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      ++.|+..|...   ++.|..|||+.+++    +...+.++++.|...|++++.....  ..-.+.+|+.+..+...
T Consensus        31 ~~~iL~~l~~~---~~~~~~ela~~l~~----s~~tvs~~l~~L~~~glv~~~~~~~d~R~~~~~lT~~G~~~~~~   99 (138)
T 3bpv_A           31 QVACLLRIHRE---PGIKQDELATFFHV----DKGTIARTLRRLEESGFIEREQDPENRRRYILEVTRRGEEIIPL   99 (138)
T ss_dssp             HHHHHHHHHHS---TTCBHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHTHHH
T ss_pred             HHHHHHHHHHc---CCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEeecCCCCceeEEeeECHhHHHHHHH
Confidence            44567777775   58999999999999    9999999999999999999853210  11237788888776543

>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=96.10  E-value=0.011  Score=44.29  Aligned_cols=67  Identities=10%  Similarity=0.110  Sum_probs=53.6

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      +..|+..|...   ++.|..|||+.+++    +...+.++++.|...|++++.....  ..-.+.+|+.|..+...
T Consensus        48 q~~iL~~l~~~---~~~t~~eLa~~l~~----~~~tvs~~l~~Le~~Glv~r~~~~~DrR~~~l~LT~~G~~~~~~  116 (162)
T 3k0l_A           48 QFTALSVLAAK---PNLSNAKLAERSFI----KPQSANKILQDLLANGWIEKAPDPTHGRRILVTVTPSGLDKLNQ  116 (162)
T ss_dssp             HHHHHHHHHHC---TTCCHHHHHHHHTS----CGGGHHHHHHHHHHTTSEEEEECCSSSCCEEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHHC---CCCCHHHHHHHHCC----CHHHHHHHHHHHHHCcCeEecCCCCcCCeeEeEECHhHHHHHHH
Confidence            34577778776   58999999999999    9999999999999999999864321  12357899998877644

>3bdd_A Regulatory protein MARR; putative multiple antibiotic-resistance repressor, structura genomics, joint center for structural genomics, JCSG; 2.20A {Streptococcus suis}

Probab=96.08  E-value=0.0098  Score=43.09  Aligned_cols=67  Identities=13%  Similarity=0.164  Sum_probs=54.5

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccC--CCCCceeccHhhhHhh-cC
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAG--DDQRLYGLAHVAKYFV-LN   91 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~--~~~~~y~lt~~s~~l~-~~   91 (233)
                      ++.|+..|...   ++.|..+||+.+++    +...+.+.++.|...|++++....  .....|.+|+.+..+. ..
T Consensus        33 ~~~iL~~l~~~---~~~~~~ela~~l~i----s~~~vs~~l~~L~~~gli~~~~~~~d~r~~~~~lT~~G~~~~~~~  102 (142)
T 3bdd_A           33 RYSILQTLLKD---APLHQLALQERLQI----DRAAVTRHLKLLEESGYIIRKRNPDNQREVLVWPTEQAREALITN  102 (142)
T ss_dssp             HHHHHHHHHHH---CSBCHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEEECSSSTTCEEEEECHHHHHHHTTS
T ss_pred             HHHHHHHHHhC---CCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHHH
Confidence            44577788776   48999999999999    999999999999999999986432  1233588999999887 54

>3oop_A LIN2960 protein; protein structure initiative, PSI-2, structural genomics, MI center for structural genomics, MCSG, unknown function; 1.78A {Listeria innocua}

Probab=96.08  E-value=0.0061  Score=44.50  Aligned_cols=67  Identities=19%  Similarity=0.209  Sum_probs=52.7

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      +..|+..|...   ++.|..|||+.+++    ++..+.++++.|...|++++.....  ..-.+.+|+.|..+...
T Consensus        39 ~~~iL~~l~~~---~~~t~~eLa~~l~~----~~~~vs~~l~~L~~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~~  107 (143)
T 3oop_A           39 QWSVLEGIEAN---EPISQKEIALWTKK----DTPTVNRIVDVLLRKELIVREISTEDRRISLLSLTDKGRKETTE  107 (143)
T ss_dssp             HHHHHHHHHHH---SSEEHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEEC----CCSCEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHHc---CCcCHHHHHHHHCC----CHhhHHHHHHHHHHCCCeeccCCCccCceeeeeECHHHHHHHHH
Confidence            44577777776   58999999999999    9999999999999999999864321  22357889988877644

>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=96.08  E-value=0.01  Score=40.86  Aligned_cols=55  Identities=16%  Similarity=0.147  Sum_probs=46.5

Q ss_pred             CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhc
Q 039903           32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVL   90 (233)
Q Consensus        32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~   90 (233)
                      ++.+..+||+.+++    +...|.|+|.-|...|+++....++.-+...+|+.++.++.
T Consensus        35 ~~~s~~eLa~~l~l----~~stLsR~l~rLe~~GLV~r~~~~D~R~~v~LT~~G~~~l~   89 (96)
T 2obp_A           35 TPWSLPKIAKRAQL----PMSVLRRVLTQLQAAGLADVSVEADGRGHASLTQEGAALAA   89 (96)
T ss_dssp             CCCBHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEEECTTSCEEEEECHHHHHHHH
T ss_pred             CCcCHHHHHHHhCC----chhhHHHHHHHHHHCCCEEeecCCCCceeEEECHHHHHHHH
Confidence            57899999999999    99999999999999999998654333455788999987653

>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=96.06  E-value=0.0055  Score=42.30  Aligned_cols=48  Identities=17%  Similarity=0.344  Sum_probs=41.9

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeec
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTS   71 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~   71 (233)
                      .+..|+..|...   ++.|..|||+.+++    +...+.+.|+.|...|++.+..
T Consensus        21 ~~~~il~~l~~~---~~~s~~ela~~l~i----s~~tv~~~l~~L~~~glv~~~~   68 (109)
T 1sfx_A           21 SDVRIYSLLLER---GGMRVSEIARELDL----SARFVRDRLKVLLKRGFVRREI   68 (109)
T ss_dssp             HHHHHHHHHHHH---CCBCHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEEe
Confidence            345578888765   58999999999999    9999999999999999999863

>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=96.05  E-value=0.0067  Score=44.26  Aligned_cols=68  Identities=15%  Similarity=0.188  Sum_probs=48.1

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      .+..|+..|...   ++.|..|||+.+++    ++..+.++++.|...|++++.....  ..-.+.+|+.|+.+...
T Consensus        38 ~~~~vL~~l~~~---~~~t~~eLa~~l~~----~~~tvs~~l~~L~~~Glv~r~~~~~DrR~~~~~LT~~G~~~~~~  107 (142)
T 3ech_A           38 PDVHVLKLIDEQ---RGLNLQDLGRQMCR----DKALITRKIRELEGRNLVRRERNPSDQRSFQLFLTDEGLAIHLH  107 (142)
T ss_dssp             HHHHHHHHHHHT---TTCCHHHHHHHHC-------CHHHHHHHHHHHTTSEEC----------CCEECHHHHHHHHH
T ss_pred             HHHHHHHHHHhC---CCcCHHHHHHHhCC----CHHHHHHHHHHHHHCCCEeeccCCCCCCeeeeEECHHHHHHHHH
Confidence            345577778776   58999999999999    9999999999999999999864321  11247888888876644

>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=96.04  E-value=0.0072  Score=44.49  Aligned_cols=67  Identities=12%  Similarity=0.168  Sum_probs=52.5

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccC--CCCCceeccHhhhHhhcC
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAG--DDQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~--~~~~~y~lt~~s~~l~~~   91 (233)
                      +..|+..|...   ++.|..+||+.+++    +...+.++++.|...|++++....  ...-.+.+|+.|..+...
T Consensus        42 ~~~iL~~l~~~---~~~t~~ela~~l~~----~~~~vs~~l~~Le~~Glv~r~~~~~d~R~~~~~lT~~G~~~~~~  110 (152)
T 3bj6_A           42 QRAILEGLSLT---PGATAPQLGAALQM----KRQYISRILQEVQRAGLIERRTNPEHARSHRYWLTPRGEAIITA  110 (152)
T ss_dssp             HHHHHHHHHHS---TTEEHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEECCSSSTTSCEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHhC---CCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCeeecCCcccccceeeEEChhhHHHHHH
Confidence            44577777775   48999999999999    999999999999999999986321  112257888888776543

>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=96.04  E-value=0.0044  Score=53.79  Aligned_cols=65  Identities=14%  Similarity=-0.016  Sum_probs=50.7

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCC-CcEEEeec-hHHHhhccCC-------CC-ceEEecCcCCC----CCCC-CEEEe
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLH-IKGVNFDL-SHVIQDSSSY-------SG-VKHIGGIMLER----IPKG-DAILI  232 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~-l~~~v~Dl-p~v~~~a~~~-------~r-i~~~~gD~f~~----~P~~-D~~~l  232 (233)
                      ...+|+|+++|+|.+++.++++.++ -+++..|+ |..++.++++       ++ ++++.+|.++-    .+.. |+|++
T Consensus        52 ~g~~VLDlfaGtG~~sl~aa~~~~ga~~V~avDi~~~av~~~~~N~~~Ngl~~~~v~v~~~Da~~~l~~~~~~~fD~V~l  131 (392)
T 3axs_A           52 RPVKVADPLSASGIRAIRFLLETSCVEKAYANDISSKAIEIMKENFKLNNIPEDRYEIHGMEANFFLRKEWGFGFDYVDL  131 (392)
T ss_dssp             SCEEEEESSCTTSHHHHHHHHHCSCEEEEEEECSCHHHHHHHHHHHHHTTCCGGGEEEECSCHHHHHHSCCSSCEEEEEE
T ss_pred             CCCEEEECCCcccHHHHHHHHhCCCCCEEEEEECCHHHHHHHHHHHHHhCCCCceEEEEeCCHHHHHHHhhCCCCcEEEE
Confidence            4578999999999999999998765 56899998 5677777653       35 99999998762    2333 88876

>3cdh_A Transcriptional regulator, MARR family; helix-turn-hleix, structura genomics, PSI-2, protein structure initiative; 2.69A {Silicibacter pomeroyi dss-3}

Probab=96.03  E-value=0.0095  Score=44.08  Aligned_cols=67  Identities=9%  Similarity=0.088  Sum_probs=51.3

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccC--CCCCceeccHhhhHhhcC
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAG--DDQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~--~~~~~y~lt~~s~~l~~~   91 (233)
                      ++.|+..|...   ++.|..+||+.+++    +...+.++++.|...|++++....  ...-.+.+|+.|..+...
T Consensus        45 ~~~iL~~l~~~---~~~t~~ela~~l~i----~~~tvs~~l~~Le~~Glv~r~~~~~d~R~~~~~lT~~G~~~~~~  113 (155)
T 3cdh_A           45 EWRVLACLVDN---DAMMITRLAKLSLM----EQSRMTRIVDQMDARGLVTRVADAKDKRRVRVRLTDDGRALAES  113 (155)
T ss_dssp             HHHHHHHHSSC---SCBCHHHHHHHTTC----CHHHHHHHHHHHHHTTSEEECC------CCCEEECHHHHHHHHH
T ss_pred             HHHHHHHHHHC---CCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEeccCCCcCCeeEeEECHHHHHHHHH
Confidence            34466667665   58999999999999    999999999999999999975321  012357899998876644

>2fbi_A Probable transcriptional regulator; MARR, APC5816, structural genomic protein structure initiative; 2.10A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=96.02  E-value=0.0068  Score=43.97  Aligned_cols=67  Identities=13%  Similarity=0.162  Sum_probs=52.5

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      +..|+..|...   ++.|..+||+.+++    +...+.++++.|...|++++.....  ..-.+.+|+.+..+...
T Consensus        38 ~~~iL~~l~~~---~~~t~~ela~~l~~----s~~~vs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~~~~  106 (142)
T 2fbi_A           38 QWRVIRILRQQ---GEMESYQLANQACI----LRPSMTGVLARLERDGIVRRWKAPKDQRRVYVNLTEKGQQCFVS  106 (142)
T ss_dssp             HHHHHHHHHHH---CSEEHHHHHHHTTC----CHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHHc---CCCCHHHHHHHHCC----CHhHHHHHHHHHHHCCCEEeecCCCCCCeeEEEECHHHHHHHHH
Confidence            45577778776   48999999999999    9999999999999999999863211  11237889888876643

>2fa5_A Transcriptional regulator MARR/EMRR family; multiple antibiotics resistance repressor, XCC structural genomics, X-RAY diffraction; 1.80A {Xanthomonas campestris}

Probab=96.02  E-value=0.0084  Score=44.67  Aligned_cols=67  Identities=19%  Similarity=0.254  Sum_probs=50.7

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccC--CCCCceeccHhhhHhhcC
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAG--DDQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~--~~~~~y~lt~~s~~l~~~   91 (233)
                      ++.|+..|...   ++.|..|||+.+++    +...+.++++.|...|++++....  .....+.+|+.|..+...
T Consensus        51 ~~~iL~~l~~~---~~~t~~ela~~l~i----s~~tvs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~~~~  119 (162)
T 2fa5_A           51 EWRVITILALY---PGSSASEVSDRTAM----DKVAVSRAVARLLERGFIRRETHGDDRRRSMLALSPAGRQVYET  119 (162)
T ss_dssp             HHHHHHHHHHS---TTCCHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEC---------CCCEECHHHHHHHHH
T ss_pred             HHHHHHHHHhC---CCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEeeecCCCCCCeeEEEECHHHHHHHHH
Confidence            34567777765   58999999999999    999999999999999999985321  112457889888876643

>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=96.00  E-value=0.0087  Score=43.60  Aligned_cols=66  Identities=9%  Similarity=-0.009  Sum_probs=51.9

Q ss_pred             hChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           19 LGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        19 lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      ..++..|...   ++.|..+||+.+++    +...+.++++.|...|++.+.....  ..-.+.+|+.+..+...
T Consensus        32 ~~iL~~l~~~---~~~t~~~la~~l~~----s~~~vs~~l~~Le~~gli~r~~~~~d~R~~~~~lT~~G~~~~~~   99 (144)
T 1lj9_A           32 YLYLVRVCEN---PGIIQEKIAELIKV----DRTTAARAIKRLEEQGFIYRQEDASNKKIKRIYATEKGKNVYPI   99 (144)
T ss_dssp             HHHHHHHHHS---TTEEHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEEECSSCTTCEEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHC---cCcCHHHHHHHHCC----CHhHHHHHHHHHHHCCCEEeecCCCCCceeeeEEChhHHHHHHH
Confidence            3467777775   48999999999999    9999999999999999999864321  12247889988876643

>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=95.97  E-value=0.0042  Score=42.51  Aligned_cols=53  Identities=11%  Similarity=0.191  Sum_probs=42.7

Q ss_pred             CCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhc
Q 039903           33 KISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVL   90 (233)
Q Consensus        33 ~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~   90 (233)
                      +.|..|||+.+++    +...+.++++.|...|++... .+.....+.+|+.|..+..
T Consensus        30 ~~t~~eLa~~l~i----~~~tvs~~l~~Le~~Glv~~~-~d~R~~~v~LT~~G~~~~~   82 (95)
T 2qvo_A           30 DVYIQYIASKVNS----PHSYVWLIIKKFEEAKMVECE-LEGRTKIIRLTDKGQKIAQ   82 (95)
T ss_dssp             CEEHHHHHHHSSS----CHHHHHHHHHHHHHTTSEEEE-EETTEEEEEECHHHHHHHH
T ss_pred             CcCHHHHHHHHCc----CHHHHHHHHHHHHHCcCccCC-CCCCeEEEEEChhHHHHHH
Confidence            3899999999999    999999999999999999433 1111235899999987754

>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=95.96  E-value=0.007  Score=44.12  Aligned_cols=67  Identities=9%  Similarity=0.083  Sum_probs=52.6

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      ++.|+..|...   ++.|..+||+.+++    +...+.++++.|...|++++.....  ..-.+.+|+.+..+...
T Consensus        35 ~~~iL~~l~~~---~~~~~~~la~~l~~----s~~tvs~~l~~L~~~glv~r~~~~~d~r~~~~~lT~~G~~~~~~  103 (145)
T 2a61_A           35 QFDILQKIYFE---GPKRPGELSVLLGV----AKSTVTGLVKRLEADGYLTRTPDPADRRAYFLVITRKGEEVIEK  103 (145)
T ss_dssp             HHHHHHHHHHH---CCBCHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHHc---CCCCHHHHHHHHCC----CchhHHHHHHHHHHCCCeeecCCCCCCceEEEEECHHHHHHHHH
Confidence            45577777765   58999999999999    9999999999999999999863210  11257889988876643

>2nyx_A Probable transcriptional regulatory protein, RV14; alpha/beta, structural genomics, PSI-2; 2.30A {Mycobacterium tuberculosis}

Probab=95.95  E-value=0.0081  Score=45.32  Aligned_cols=67  Identities=13%  Similarity=0.172  Sum_probs=52.8

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      ++.|+..|...   ++.|..|||+.+++    +...+.++++.|...|++++.....  ..-.+.+|+.+..+...
T Consensus        47 ~~~iL~~L~~~---~~~t~~eLa~~l~i----s~~tvs~~l~~Le~~GlV~r~~~~~DrR~~~~~LT~~G~~~~~~  115 (168)
T 2nyx_A           47 QFRTLVILSNH---GPINLATLATLLGV----QPSATGRMVDRLVGAELIDRLPHPTSRRELLAALTKRGRDVVRQ  115 (168)
T ss_dssp             HHHHHHHHHHH---CSEEHHHHHHHHTS----CHHHHHHHHHHHHHTTSEEEEECSSCSSCEEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHHc---CCCCHHHHHHHhCC----CHHHHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHHHHHHHHH
Confidence            44577777776   58999999999999    9999999999999999999854321  12247899998876644

>2fbh_A Transcriptional regulator PA3341; MARR, transcription regulator, APC5857, structural genomics, protein structure initiative; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=95.90  E-value=0.01  Score=43.16  Aligned_cols=65  Identities=15%  Similarity=0.142  Sum_probs=49.9

Q ss_pred             hChhHHH-HhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhc
Q 039903           19 LGVFEII-AKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVL   90 (233)
Q Consensus        19 lglfd~L-~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~   90 (233)
                      ..|+..| ...   ++.|..+||+.+++    +...+.++++.|...|++++.....  ..-.+.+|+.+..+..
T Consensus        40 ~~iL~~l~~~~---~~~t~~~la~~l~~----s~~~vs~~l~~L~~~glv~r~~~~~d~R~~~~~lT~~G~~~~~  107 (146)
T 2fbh_A           40 WLVLLHLARHR---DSPTQRELAQSVGV----EGPTLARLLDGLESQGLVRRLAVAEDRRAKHIVLTPKADVLIA  107 (146)
T ss_dssp             HHHHHHHHHCS---SCCBHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEECCBTTBCSCEEEECTTHHHHHH
T ss_pred             HHHHHHHHHcC---CCCCHHHHHHHhCC----ChhhHHHHHHHHHHCCCeeecCCCcccCeeeeEECHhHHHHHH
Confidence            3466677 443   58999999999999    9999999999999999999863210  1224778888776653

>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=95.88  E-value=0.018  Score=39.51  Aligned_cols=62  Identities=15%  Similarity=0.183  Sum_probs=51.3

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHH-hCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhcC
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAA-QMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~-~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~~   91 (233)
                      +..|+-.|...   ++.|..+||+ .+++    +...+.|=++.|...|+++.+    +++ +.+|+.|+.+...
T Consensus        18 QfsiL~~L~~~---~~~t~~~Lae~~l~~----drstvsrnl~~L~r~GlVe~~----~~D-l~LT~~G~~~l~~   80 (95)
T 1bja_A           18 TATILITIAKK---DFITAAEVREVHPDL----GNAVVNSNIGVLIKKGLVEKS----GDG-LIITGEAQDIISN   80 (95)
T ss_dssp             HHHHHHHHHHS---TTBCHHHHHHTCTTS----CHHHHHHHHHHHHTTTSEEEE----TTE-EEECHHHHHHHHH
T ss_pred             HHHHHHHHHHC---CCCCHHHHHHHHhcc----cHHHHHHHHHHHHHCCCeecC----CCC-eeeCHhHHHHHHH
Confidence            34456667776   4899999999 9999    999999999999999999943    344 9999999987654

>3u1d_A Uncharacterized protein; GNTR-superfamily, structural genomics, PSI-biology, midwest for structural genomics, MCSG; 1.80A {Halomicrobium mukohataei}

Probab=95.88  E-value=0.016  Score=43.25  Aligned_cols=88  Identities=13%  Similarity=0.135  Sum_probs=64.6

Q ss_pred             HHhhChhHHHHhcCCCCCCCHHHHHHhCC-CCCCCChhhHHHHHHHHhcCCceeeeccCC-------CCCceeccHhhhH
Q 039903           16 ASELGVFEIIAKAGPTAKISAVEIAAQMP-SSNPNAAVMLDRILRLLVTHRVLRCTSAGD-------DQRLYGLAHVAKY   87 (233)
Q Consensus        16 a~~lglfd~L~~~~~~~~~t~~elA~~~~-~~~~~~~~~l~rlL~~L~~~gll~~~~~~~-------~~~~y~lt~~s~~   87 (233)
                      -.++.|+..|...+ .+..|+.||++.++ +    +...++|-|+.|+..|++++...++       ....|++|+.++.
T Consensus        29 ~tR~~IL~~Ll~~p-~~~~ta~eL~~~l~~l----S~aTVyrhL~~L~eaGLV~~~~~~~~~~~rGrP~k~Y~LT~~Gr~  103 (151)
T 3u1d_A           29 ETRLDVLHQILAQP-DGVLSVEELLYRNPDE----TEANLRYHVDELVDRGIVEKIPVPRAKSVDDPPTTFYAVTGEGIA  103 (151)
T ss_dssp             HHHHHHHHHHHHST-TSCBCHHHHHHHCTTS----CHHHHHHHHHHHHHTTSEEEEECCCCTTSSSCCCEEEEECHHHHH
T ss_pred             hHHHHHHHHHHcCC-CCCCCHHHHHHhcCCC----CHHHHHHHHHHHHHCCCeEEeecCcCcccCCCCceEEEECHHHHH
Confidence            34677888887753 24689999999999 8    9999999999999999999653221       1128999999997


Q ss_pred             hhcCCCCCCccchhccccCchhhHHHHH
Q 039903           88 FVLNRDGVSLCPSRPWLETKPYEIYDAV  115 (233)
Q Consensus        88 l~~~~~~~~~~~~~~~~~~~~~~L~~~l  115 (233)
                      ++...+  .+...     ..|..|.+.+
T Consensus       104 ~l~~y~--~la~~-----~alr~l~~~v  124 (151)
T 3u1d_A          104 LLRAVS--MYEEA-----AVWRSVYEQM  124 (151)
T ss_dssp             HHHHTT--CSTHH-----HHTHHHHHHS
T ss_pred             HHHHhH--HHhHH-----HHHHHHHHHh
Confidence            665432  33321     1677777776

>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=95.85  E-value=0.0085  Score=44.18  Aligned_cols=66  Identities=9%  Similarity=0.243  Sum_probs=49.6

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee----ccCCCCCceeccHhhhHhhcC
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT----SAGDDQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~----~~~~~~~~y~lt~~s~~l~~~   91 (233)
                      +..++..| ..   ++.|..|||+.+++    +...+.++++.|...|++++.    ..+...-.+.+|+.|..+...
T Consensus        40 q~~iL~~l-~~---~~~t~~eLa~~l~~----~~~~vs~~l~~Le~~Glv~r~~~~~~~D~R~~~~~lT~~G~~~~~~  109 (151)
T 3kp7_A           40 QSHVLNML-SI---EALTVGQITEKQGV----NKAAVSRRVKKLLNAELVKLEKPDSNTDQRLKIIKLSNKGKKYIKE  109 (151)
T ss_dssp             HHHHHHHH-HH---SCBCHHHHHHHHCS----CSSHHHHHHHHHHHTTSEEC-----------CCBEECHHHHHHHHH
T ss_pred             HHHHHHHH-Hc---CCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEeeCCCCCCCCCeeEEEECHhHHHHHHH
Confidence            34477778 54   59999999999999    999999999999999999972    111122356788888877644

>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=95.85  E-value=0.0079  Score=44.84  Aligned_cols=60  Identities=15%  Similarity=0.124  Sum_probs=44.9

Q ss_pred             HHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903           10 PAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH   83 (233)
Q Consensus        10 s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~   83 (233)
                      ..+|++.+.|...    . +  ++.|..+||+.+++    ++..++++|..|...|+++..+   +.|.|.++.
T Consensus        14 ~yAl~~L~~La~~----~-~--~~~~~~~iA~~~~i----~~~~l~kil~~L~~~Glv~s~r---G~GGy~L~~   73 (149)
T 1ylf_A           14 SIAVHILSILKNN----P-S--SLCTSDYMAESVNT----NPVVIRKIMSYLKQAGFVYVNR---GPGGAGLLK   73 (149)
T ss_dssp             HHHHHHHHHHHHS----C-G--GGCCHHHHHHHHTS----CHHHHHHHHHHHHHTTSEEEC------CCEEESS
T ss_pred             HHHHHHHHHHHhC----C-C--CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCcEEEcc---CCCceEeCC
Confidence            3456665555321    1 1  58999999999999    9999999999999999998753   267787765

>2qww_A Transcriptional regulator, MARR family; YP_013417.1, multiple antibiotic-resistance repressor (MARR) structural genomics; HET: MSE; 2.07A {Listeria monocytogenes str}

Probab=95.84  E-value=0.011  Score=43.72  Aligned_cols=67  Identities=9%  Similarity=0.095  Sum_probs=52.3

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceee--eccCC--CCCceeccHhhhHhhcC
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRC--TSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~--~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      ++.|+..|...   ++.|..+||+.+++    +...+.++++.|...|++++  .....  ..-.+.+|+.|..+...
T Consensus        43 ~~~iL~~l~~~---~~~t~~eLa~~l~~----~~~tvs~~l~~Le~~Glv~r~~~~~~~d~R~~~~~LT~~G~~~~~~  113 (154)
T 2qww_A           43 QLAMINVIYST---PGISVADLTKRLII----TGSSAAANVDGLISLGLVVKLNKTIPNDSMDLTLKLSKKGEDLSKR  113 (154)
T ss_dssp             HHHHHHHHHHS---TTEEHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEESCC--CTTCTTCEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHHC---CCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEecCcCCCCCCceeEeEECHHHHHHHHH
Confidence            44567777776   48999999999999    99999999999999999998  43211  12358899999877644

>2pex_A Transcriptional regulator OHRR; transcription regulator; 1.90A {Xanthomonas campestris} PDB: 2pfb_A

Probab=95.82  E-value=0.01  Score=43.81  Aligned_cols=67  Identities=16%  Similarity=0.187  Sum_probs=52.3

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      ++.|+..|...   ++.|..+||+.+++    +...+.++++.|...|++++.....  ..-.+.+|+.+..+...
T Consensus        49 ~~~iL~~l~~~---~~~t~~ela~~l~~----s~~tvs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~~~~  117 (153)
T 2pex_A           49 QYLVMLVLWET---DERSVSEIGERLYL----DSATLTPLLKRLQAAGLVTRTRAASDERQVIIALTETGRALRSK  117 (153)
T ss_dssp             HHHHHHHHHHS---CSEEHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEEC-------CEEEECHHHHHGGGG
T ss_pred             HHHHHHHHHhC---CCcCHHHHHHHhCC----CcccHHHHHHHHHHCCCEeecCCcccCCeeEeeECHHHHHHHHH
Confidence            44567777765   58999999999999    9999999999999999999863210  12257889999887654

>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19

Probab=95.79  E-value=0.0073  Score=40.31  Aligned_cols=59  Identities=8%  Similarity=0.034  Sum_probs=46.5

Q ss_pred             HHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHh
Q 039903           16 ASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHV   84 (233)
Q Consensus        16 a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~   84 (233)
                      .....|.+.|...    +.|+.|||+++|+    +...+++.|..|...|++.....  ..=.|+++..
T Consensus        17 ~~~~~IL~lL~~~----g~sa~eLAk~Lgi----Sk~aVr~~L~~Le~eG~I~~~~~--~PP~W~~~~~   75 (82)
T 1oyi_A           17 EIVCEAIKTIGIE----GATAAQLTRQLNM----EKREVNKALYDLQRSAMVYSSDD--IPPRWFMTTE   75 (82)
T ss_dssp             HHHHHHHHHHSSS----TEEHHHHHHHSSS----CHHHHHHHHHHHHHHTSSEECSS--SSCEEESCC-
T ss_pred             HHHHHHHHHHHHc----CCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEeCCC--CCCcceeccC
Confidence            3455678888864    4999999999999    99999999999999999998521  2345666654

>3e6m_A MARR family transcriptional regulator; APC88769, silicibacter pomeroyi DSS, structural genomics, PSI-2, protein structure initiative; 2.20A {Silicibacter pomeroyi}

Probab=95.74  E-value=0.01  Score=44.29  Aligned_cols=67  Identities=12%  Similarity=0.101  Sum_probs=52.6

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      ++.|+..|...   ++.|..|||+.+++    +...+.++++.|...|++++.....  ..-.+.+|+.|..+...
T Consensus        55 q~~vL~~l~~~---~~~t~~eLa~~l~~----~~~~vs~~l~~Le~~Glv~r~~~~~DrR~~~~~LT~~G~~~~~~  123 (161)
T 3e6m_A           55 KLRLLSSLSAY---GELTVGQLATLGVM----EQSTTSRTVDQLVDEGLAARSISDADQRKRTVVLTRKGKKKLAE  123 (161)
T ss_dssp             HHHHHHHHHHH---SEEEHHHHHHHTTC----CHHHHHHHHHHHHHTTSEEECC---CCCSCEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHhC---CCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEeeCCcccCCeeEeeECHHHHHHHHH
Confidence            34477777776   48999999999999    9999999999999999999864321  12357889998877644

>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=95.72  E-value=0.013  Score=42.48  Aligned_cols=69  Identities=12%  Similarity=0.140  Sum_probs=53.3

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      +..++..|...|. ++.|..|||+.+++    ++..+.++++.|...|++++.....  ..-.+.+|+.|..+...
T Consensus        33 ~~~vL~~l~~~~~-~~~t~~ela~~l~~----~~~tvs~~l~~Le~~Gli~r~~~~~D~R~~~~~LT~~G~~~~~~  103 (139)
T 3eco_A           33 QGHTLGYLYAHQQ-DGLTQNDIAKALQR----TGPTVSNLLRNLERKKLIYRYVDAQDTRRKNIGLTTSGIKLVEA  103 (139)
T ss_dssp             HHHHHHHHHHSTT-TCEEHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEEECCC--CCEEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHhcCC-CCcCHHHHHHHhCC----CcccHHHHHHHHHHCCCEeecCCCCCCCeeeeEECHHHHHHHHH
Confidence            4456777777521 38999999999999    9999999999999999999864321  12356889988877644

>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=95.71  E-value=0.011  Score=42.99  Aligned_cols=67  Identities=6%  Similarity=0.128  Sum_probs=52.7

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      ++.|+..|...   ++.|..+||+.+++    +...+.++++.|...|++++.....  ..-.+.+|+.+..+...
T Consensus        39 ~~~iL~~l~~~---~~~~~~ela~~l~~----~~~tvs~~l~~L~~~gli~r~~~~~d~R~~~~~lT~~G~~~~~~  107 (142)
T 2bv6_A           39 QFLVLTILWDE---SPVNVKKVVTELAL----DTGTVSPLLKRMEQVDLIKRERSEVDQREVFIHLTDKSETIRPE  107 (142)
T ss_dssp             HHHHHHHHHHS---SEEEHHHHHHHTTC----CTTTHHHHHHHHHHTTSEEEEECSSSTTCEEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHHc---CCcCHHHHHHHHCC----ChhhHHHHHHHHHHCCCEEeecCCCCcceEEEEEChHHHHHHHH
Confidence            44577777765   48999999999999    9999999999999999999864321  12257889988876644

>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=95.71  E-value=0.0072  Score=44.67  Aligned_cols=67  Identities=15%  Similarity=0.097  Sum_probs=52.1

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      ++.|+..|...   ++.|..+||+.+++    +...+.++++.|...|++++.....  ..-.+.+|+.+..+...
T Consensus        39 ~~~iL~~l~~~---~~~t~~ela~~l~~----s~~tvs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~~~~  107 (155)
T 1s3j_A           39 QLFVLASLKKH---GSLKVSEIAERMEV----KPSAVTLMADRLEQKNLIARTHNTKDRRVIDLSLTDEGDIKFEE  107 (155)
T ss_dssp             HHHHHHHHHHH---SEEEHHHHHHHHTS----CHHHHHHHHHHHHHTTSEEEEECSSCTTSEEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHHc---CCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEeecCCCCCCceEEEEECHHHHHHHHH
Confidence            34467777765   48999999999999    9999999999999999999864211  11257889888776643

>3s2w_A Transcriptional regulator, MARR family; structural genomics, PSI-biology, protein structure initiati midwest center for structural genomics; 2.45A {Methanosarcina mazei}

Probab=95.68  E-value=0.011  Score=43.98  Aligned_cols=66  Identities=9%  Similarity=0.008  Sum_probs=51.9

Q ss_pred             hChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           19 LGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        19 lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      ..++..|...   ++.|..|||+.+++    ++..+.++++.|...|++++.....  ..-.+.+|+.|..+...
T Consensus        53 ~~vL~~l~~~---~~~t~~eLa~~l~~----~~~tvs~~l~~Le~~Glv~r~~~~~DrR~~~l~LT~~G~~~~~~  120 (159)
T 3s2w_A           53 FPFLMRLYRE---DGINQESLSDYLKI----DKGTTARAIQKLVDEGYVFRQRDEKDRRSYRVFLTEKGKKLEPD  120 (159)
T ss_dssp             HHHHHHHHHS---CSEEHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEEECC---CCEEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHC---CCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEecCCCCCCeeEEEECHHHHHHHHH
Confidence            3466667665   58999999999999    9999999999999999999864321  12357889988877644

>3cjn_A Transcriptional regulator, MARR family; silicibacter pomeroy structural genomics, PSI-2, protein structure initiative; 1.95A {Silicibacter pomeroyi dss-3}

Probab=95.65  E-value=0.01  Score=44.28  Aligned_cols=67  Identities=10%  Similarity=0.067  Sum_probs=52.4

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccC--CCCCceeccHhhhHhhcC
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAG--DDQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~--~~~~~y~lt~~s~~l~~~   91 (233)
                      ++.|+..|...   ++.|..+||+.+++    +...+.++++.|...|++++....  ...-.+.+|+.+..+...
T Consensus        54 ~~~iL~~l~~~---~~~t~~ela~~l~i----s~~tvs~~l~~Le~~Gli~r~~~~~d~R~~~~~lT~~G~~~~~~  122 (162)
T 3cjn_A           54 KMRALAILSAK---DGLPIGTLGIFAVV----EQSTLSRALDGLQADGLVRREVDSDDQRSSRVYLTPAGRAVYDR  122 (162)
T ss_dssp             HHHHHHHHHHS---CSEEHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEEEC--CCSSEEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHHC---CCCCHHHHHHHHCC----ChhHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHH
Confidence            44577777775   58999999999999    999999999999999999986321  112347888888876643

>3r0a_A Putative transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; 2.31A {Methanosarcina mazei}

Probab=95.64  E-value=0.0078  Score=43.34  Aligned_cols=47  Identities=13%  Similarity=0.256  Sum_probs=41.7

Q ss_pred             hhChhHHHHhcCCCCC-CCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           18 ELGVFEIIAKAGPTAK-ISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~-~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      +..|+..|...+  +| +|..|||+.+++    +...+.|.|+.|...|++.+.
T Consensus        28 e~~il~~L~~~~--~~~~t~~eLa~~l~~----s~sTV~r~L~~L~~~GlV~r~   75 (123)
T 3r0a_A           28 DLNVMKSFLNEP--DRWIDTDALSKSLKL----DVSTVQRSVKKLHEKEILQRS   75 (123)
T ss_dssp             HHHHHHHHHHST--TCCEEHHHHHHHHTS----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHCC--CCCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEee
Confidence            556888888764  46 899999999999    999999999999999999985

>2lkp_A Transcriptional regulator, ARSR family; symmetric homodimer, NI(II) binding protein, DNA binding Pro transcription regulator; NMR {Mycobacterium tuberculosis}

Probab=95.62  E-value=0.0085  Score=42.58  Aligned_cols=51  Identities=14%  Similarity=0.226  Sum_probs=44.6

Q ss_pred             HHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           12 AMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        12 ~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      ++..-.++.|+..|.+    ++.|..+||+.+++    ++..+.+.|+.|...|++...
T Consensus        28 ~l~~~~~~~il~~L~~----~~~s~~ela~~l~i----s~stvsr~l~~Le~~Glv~~~   78 (119)
T 2lkp_A           28 ALATPSRLMILTQLRN----GPLPVTDLAEAIGM----EQSAVSHQLRVLRNLGLVVGD   78 (119)
T ss_dssp             HHCCHHHHHHHHHHHH----CCCCHHHHHHHHSS----CHHHHHHHHHHHHHHCSEEEE
T ss_pred             HhCCHHHHHHHHHHHH----CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEE
Confidence            3444467889999987    48999999999999    999999999999999999875

>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=95.61  E-value=0.0095  Score=43.54  Aligned_cols=67  Identities=7%  Similarity=0.110  Sum_probs=52.8

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      ++.|+..|...   ++.|..+||+.+++    +...+.++++.|...|++++.....  ..-.+.+|+.|..+...
T Consensus        42 ~~~iL~~l~~~---~~~~~~~la~~l~~----~~~tvs~~l~~L~~~glv~r~~~~~d~R~~~~~LT~~G~~~~~~  110 (147)
T 1z91_A           42 QYLALLLLWEH---ETLTVKKMGEQLYL----DSGTLTPMLKRMEQQGLITRKRSEEDERSVLISLTEDGALLKEK  110 (147)
T ss_dssp             HHHHHHHHHHH---SEEEHHHHHHTTTC----CHHHHHHHHHHHHHHTSEECCBCSSCTTSBEEEECHHHHSGGGG
T ss_pred             HHHHHHHHHHC---CCCCHHHHHHHHCC----CcCcHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHHHH
Confidence            44567777765   48999999999999    9999999999999999999854311  12347889998877654

>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=95.59  E-value=0.023  Score=45.72  Aligned_cols=74  Identities=16%  Similarity=0.153  Sum_probs=51.5

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhh----ccCC--CCceEEec-CcCCCCCC-CC
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQD----SSSY--SGVKHIGG-IMLERIPK-GD  228 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~----a~~~--~ri~~~~g-D~f~~~P~-~D  228 (233)
                      .++.+.+. +....++||+||+.|.++.-.+....--++..+|+-..-..    .+..  .-|+|+.+ |+|.--|. .|
T Consensus        68 ~ei~ek~~-l~~g~~VvDLGaapGGWSq~~a~~~g~~~V~avdvG~~ghe~P~~~~s~gwn~v~fk~gvDv~~~~~~~~D  146 (267)
T 3p8z_A           68 QWFVERNM-VIPEGRVIDLGCGRGGWSYYCAGLKKVTEVRGYTKGGPGHEEPVPMSTYGWNIVKLMSGKDVFYLPPEKCD  146 (267)
T ss_dssp             HHHHHTTS-SCCCEEEEEESCTTSHHHHHHHTSTTEEEEEEECCCSTTSCCCCCCCCTTTTSEEEECSCCGGGCCCCCCS
T ss_pred             HHHHHhcC-CCCCCEEEEcCCCCCcHHHHHHHhcCCCEEEEEecCCCCccCcchhhhcCcCceEEEeccceeecCCcccc
Confidence            34555553 66668999999999999998887766667889997532211    1111  67999999 98862223 48


Q ss_pred             EEE
Q 039903          229 AIL  231 (233)
Q Consensus       229 ~~~  231 (233)
                      +++
T Consensus       147 tll  149 (267)
T 3p8z_A          147 TLL  149 (267)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            776

>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=95.57  E-value=0.0062  Score=44.44  Aligned_cols=65  Identities=14%  Similarity=0.078  Sum_probs=49.5

Q ss_pred             ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      .|...|...   ++.|..|||+.+++    ++..+.++++.|...|++++.....  ..-.+.+|+.|+.+...
T Consensus        40 ~vL~~l~~~---~~~t~~eLa~~l~~----~~~tvs~~l~~L~~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~~  106 (140)
T 3hsr_A           40 IVLMAIEND---EKLNIKKLGERVFL----DSGTLTPLLKKLEKKDYVVRTREEKDERNLQISLTEQGKAIKSP  106 (140)
T ss_dssp             HHHHHSCTT---CEEEHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEEC-------CEEEECHHHHHTHHH
T ss_pred             HHHHHHHHc---CCcCHHHHHHHHCC----ChhhHHHHHHHHHHCCCeEecCCCCCcceeeeeEChHHHHHHHH
Confidence            355555544   58999999999999    9999999999999999999864321  12367889988876644

>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=95.57  E-value=0.012  Score=44.49  Aligned_cols=46  Identities=28%  Similarity=0.366  Sum_probs=40.0

Q ss_pred             CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903           32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH   83 (233)
Q Consensus        32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~   83 (233)
                      ++.|.++||+.+++    ++..++++|..|...|+++..+.  .+|.|++..
T Consensus        27 ~~~s~~~IA~~~~i----s~~~l~kil~~L~~aGlv~s~rG--~~GGy~Lar   72 (162)
T 3k69_A           27 SKVASRELAQSLHL----NPVMIRNILSVLHKHGYLTGTVG--KNGGYQLDL   72 (162)
T ss_dssp             SCBCHHHHHHHHTS----CGGGTHHHHHHHHHTTSSEEECS--TTCEEECCS
T ss_pred             CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEeecC--CCCCeEecC
Confidence            58999999999999    99999999999999999987532  456798875

>3tgn_A ADC operon repressor ADCR; helix-turn-helix, transcriptional regulator, transcription; 2.00A {Streptococcus pneumoniae}

Probab=95.56  E-value=0.015  Score=42.43  Aligned_cols=67  Identities=12%  Similarity=0.288  Sum_probs=49.2

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccC--CCCCceeccHhhhHhhcC
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAG--DDQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~--~~~~~y~lt~~s~~l~~~   91 (233)
                      .+..|+..|...    +.|..|||+.+++    +...+.++++.|...|++++....  ...-.+.+|+.+..+...
T Consensus        39 ~~~~iL~~l~~~----~~t~~eLa~~l~~----s~~tvs~~l~~L~~~Glv~r~~~~~d~R~~~~~lT~~g~~~~~~  107 (146)
T 3tgn_A           39 TQEHILMLLSEE----SLTNSELARRLNV----SQAAVTKAIKSLVKEGMLETSKDSKDARVIFYQLTDLARPIAEE  107 (146)
T ss_dssp             HHHHHHHHHTTC----CCCHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEC----------CCEECGGGHHHHHH
T ss_pred             HHHHHHHHHHhC----CCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCeEeccCCCCCceeEEEECHhHHHHHHH
Confidence            355567777763    4999999999999    999999999999999999985421  122467888888766543

>3boq_A Transcriptional regulator, MARR family; MARR famil structural genomics, PSI-2, protein structure initiative; 2.39A {Silicibacter pomeroyi dss-3}

Probab=95.54  E-value=0.011  Score=43.85  Aligned_cols=68  Identities=7%  Similarity=0.072  Sum_probs=50.4

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      ++.|+..|...+  ++.|..+||+.+++    +...+.++++.|...|++++.....  ..-.+.+|+.|..+...
T Consensus        49 ~~~iL~~L~~~~--~~~~~~ela~~l~i----~~~tvs~~l~~Le~~Gli~r~~~~~d~R~~~~~lT~~G~~~~~~  118 (160)
T 3boq_A           49 KFDAMAQLARNP--DGLSMGKLSGALKV----TNGNVSGLVNRLIKDGMVVKAMSADDRRSFSAKLTDAGLTTFKQ  118 (160)
T ss_dssp             HHHHHHHHHHCT--TCEEHHHHHHHCSS----CCSCHHHHHHHHHHHTSEEEC--------CEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHHcC--CCCCHHHHHHHHCC----ChhhHHHHHHHHHHCCCEEeecCCCCCCeEEEEEChhHHHHHHH
Confidence            445777784322  58999999999999    9999999999999999999853210  11237889988876643

>2zkz_A Transcriptional repressor PAGR; protein-DNA, HTH motif, dimer, DN binding, transcription regulation; 2.00A {Bacillus anthracis}

Probab=95.53  E-value=0.0078  Score=41.54  Aligned_cols=67  Identities=13%  Similarity=0.168  Sum_probs=51.3

Q ss_pred             HHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhh
Q 039903           10 PAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVA   85 (233)
Q Consensus        10 s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s   85 (233)
                      ..+|..-.++.|+..|...   ++.++.|||+.+|+    ++..+.+.|+.|... ++.....+ ..-.|++++..
T Consensus        21 ~~aL~~~~Rl~IL~~l~~~---~~~~~~ela~~l~i----s~stvs~hL~~L~~~-lv~~~~~g-r~~~y~l~~~~   87 (99)
T 2zkz_A           21 LKTMAHPMRLKIVNELYKH---KALNVTQIIQILKL----PQSTVSQHLCKMRGK-VLKRNRQG-LEIYYSINNPK   87 (99)
T ss_dssp             HHHHCSHHHHHHHHHHHHH---SCEEHHHHHHHHTC----CHHHHHHHHHHHBTT-TBEEEEET-TEEEEECCCHH
T ss_pred             HHHhCCHHHHHHHHHHHHC---CCcCHHHHHHHHCc----CHHHHHHHHHHHHHH-hhhheEeC-cEEEEEEChHH
Confidence            3455555788899666554   58999999999999    999999999999999 99865321 23467777654

>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=95.51  E-value=0.014  Score=50.17  Aligned_cols=54  Identities=17%  Similarity=0.143  Sum_probs=44.1

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC--------------CCceEEecCcCC
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY--------------SGVKHIGGIMLE  222 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~--------------~ri~~~~gD~f~  222 (233)
                      ..++|+=||||.|..++++++ +|.-+++++|+ |.|++.++++              +|++.+.+|.++
T Consensus       205 ~pkrVLIIGgGdG~~~revlk-h~~~~V~~VEIDp~VVe~ar~yfp~~~~~~~d~pr~~rv~vii~Da~~  273 (381)
T 3c6k_A          205 TGKDVLILGGGDGGILCEIVK-LKPKMVTMVEIDQMVIDGCKKYMRKTCGDVLDNLKGDCYQVLIEDCIP  273 (381)
T ss_dssp             TTCEEEEEECTTCHHHHHHHT-TCCSEEEEEESCHHHHHHHHHHCCC----CCSSSEETTEEEEESCHHH
T ss_pred             CCCeEEEECCCcHHHHHHHHh-cCCceeEEEccCHHHHHHHHhhchhhhhhhhccccccceeeehHHHHH
Confidence            357899999999999999997 56678999998 5688877641              578999999875

>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=95.48  E-value=0.011  Score=42.46  Aligned_cols=68  Identities=7%  Similarity=0.077  Sum_probs=51.3

Q ss_pred             hChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccC--CCCCceeccHhhhHhhcC
Q 039903           19 LGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAG--DDQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        19 lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~--~~~~~y~lt~~s~~l~~~   91 (233)
                      ..+...|...+ +++.|..|||+.+++    +...+.++++.|...|++++....  ...-.+.+|+.|..+...
T Consensus        40 ~~vL~~l~~~~-~~~~t~~eLa~~l~~----~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~i~LT~~G~~~~~~  109 (127)
T 2frh_A           40 FAVLTYISENK-EKEYYLKDIINHLNY----KQPQVVKAVKILSQEDYFDKKRNEHDERTVLILVNAQQRKKIES  109 (127)
T ss_dssp             HHHHHHHHHTC-CSEEEHHHHHHHSSS----HHHHHHHHHHHHHHTTSSCCBCCSSSSCCCEEECCSHHHHHHHH
T ss_pred             HHHHHHHHhcc-CCCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHH
Confidence            34666666641 147999999999999    999999999999999999985332  123356889988876643

>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=95.48  E-value=0.014  Score=44.06  Aligned_cols=68  Identities=13%  Similarity=0.124  Sum_probs=51.3

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      ++.|+..|...+  ++.|..|||+.+++    +...+.++++.|...|++++.....  ..-.+.+|+.|+.+...
T Consensus        55 q~~vL~~L~~~~--~~~t~~eLa~~l~i----~~~tvs~~l~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~~  124 (166)
T 3deu_A           55 HWVTLHNIHQLP--PDQSQIQLAKAIGI----EQPSLVRTLDQLEDKGLISRQTCASDRRAKRIKLTEKAEPLIAE  124 (166)
T ss_dssp             HHHHHHHHHHSC--SSEEHHHHHHHHTS----CHHHHHHHHHHHHHTTSEEEC--------CEEEECGGGHHHHHH
T ss_pred             HHHHHHHHHHcC--CCCCHHHHHHHHCC----CHhhHHHHHHHHHHCCCEEeeCCCCCCCeeEEEECHHHHHHHHH
Confidence            445677777632  57999999999999    9999999999999999999864321  12357888888877644

>3f3x_A Transcriptional regulator, MARR family, putative; DNA binding protein, DNA-binding, transcription regulation; 1.90A {Sulfolobus solfataricus}

Probab=95.46  E-value=0.011  Score=43.14  Aligned_cols=65  Identities=11%  Similarity=0.207  Sum_probs=52.1

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCC---ceeccHhhhHhhcC
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQR---LYGLAHVAKYFVLN   91 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~---~y~lt~~s~~l~~~   91 (233)
                      +..|+..|...|   + |..+||+.+++    ++..+.++++.|...|++++...+ .+.   .+.+|+.|..+...
T Consensus        39 ~~~iL~~l~~~~---~-~~~~la~~l~~----~~~tvs~~l~~Le~~Glv~r~~~~-~D~R~~~~~LT~~G~~~~~~  106 (144)
T 3f3x_A           39 DFSILKATSEEP---R-SMVYLANRYFV----TQSAITAAVDKLEAKGLVRRIRDS-KDRRIVIVEITPKGRQVLLE  106 (144)
T ss_dssp             HHHHHHHHHHSC---E-EHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEEEET-TEEEEEEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHHCC---C-CHHHHHHHHCC----ChhHHHHHHHHHHHCCCEEeccCC-CCCceEEEEECHHHHHHHHH
Confidence            456777787763   5 99999999999    999999999999999999986432 111   58899999877644

>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=95.45  E-value=0.016  Score=41.91  Aligned_cols=68  Identities=9%  Similarity=0.210  Sum_probs=50.9

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhc
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVL   90 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~   90 (233)
                      +..++..|...+. ++.|..+||+.+++    +...+.++++.|...|++++.....  ..-.+.+|+.+..+..
T Consensus        36 ~~~iL~~l~~~~~-~~~~~~ela~~l~~----~~~tvs~~l~~Le~~Gli~r~~~~~d~R~~~i~lT~~G~~~~~  105 (141)
T 3bro_A           36 QMTIIDYLSRNKN-KEVLQRDLESEFSI----KSSTATVLLQRMEIKKLLYRKVSGKDSRQKCLKLTKKANKLET  105 (141)
T ss_dssp             HHHHHHHHHHTTT-SCCBHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEEECSSCTTSEEEEECHHHHTTHH
T ss_pred             HHHHHHHHHHCCC-CCcCHHHHHHHHCC----CcchHHHHHHHHHHCCCEEeeCCCcCCCeeeeEECHHHHHHHH
Confidence            3446677777530 27999999999999    9999999999999999999864321  1125678888876553

>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=95.45  E-value=0.016  Score=42.51  Aligned_cols=69  Identities=10%  Similarity=0.034  Sum_probs=45.0

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      +..++..|...+. ++.|..|||+.+++    ++..+.++++.|...|++++.....  ..-.+.+|+.|+.+...
T Consensus        43 q~~vL~~l~~~~~-~~~t~~eLa~~l~~----~~~~vs~~l~~L~~~Glv~r~~~~~DrR~~~~~LT~~G~~~~~~  113 (148)
T 3jw4_A           43 QGRMIGYIYENQE-SGIIQKDLAQFFGR----RGASITSMLQGLEKKGYIERRIPENNARQKNIYVLPKGAALVEE  113 (148)
T ss_dssp             HHHHHHHHHHHTT-TCCCHHHHHHC----------CHHHHHHHHHHTTSBCCC--------CCCCBCHHHHHHHHH
T ss_pred             HHHHHHHHHhCCC-CCCCHHHHHHHHCC----ChhHHHHHHHHHHHCCCEEeeCCCCCchhheeeECHHHHHHHHH
Confidence            3456667766521 48999999999999    9999999999999999999864321  12357788888877644

>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=95.45  E-value=0.014  Score=43.32  Aligned_cols=60  Identities=20%  Similarity=0.221  Sum_probs=45.3

Q ss_pred             hHHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903            8 VLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH   83 (233)
Q Consensus         8 ~~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~   83 (233)
                      ....+|++.+.|      +..+  ++ |.++||+.+++    ++..++++|..|...|+++..+   ++|.|.++.
T Consensus         7 ~~~yAl~~L~~L------a~~~--~~-s~~~IA~~~~i----~~~~l~kIl~~L~~aGlv~s~r---G~GGy~Lar   66 (145)
T 1xd7_A            7 RLAVAIHILSLI------SMDE--KT-SSEIIADSVNT----NPVVVRRMISLLKKADILTSRA---GVPGASLKK   66 (145)
T ss_dssp             HHHHHHHHHHHH------HTCS--CC-CHHHHHHHHTS----CHHHHHHHHHHHHHTTSEECCS---SSSSCEESS
T ss_pred             HHHHHHHHHHHH------HhCC--CC-CHHHHHHHHCc----CHHHHHHHHHHHHHCCceEeec---CCCCceecC
Confidence            344555555544      3332  35 99999999999    9999999999999999998764   256687764

>4aik_A Transcriptional regulator SLYA; transcription, transcription factor; 1.85A {Yersinia pseudotuberculosis} PDB: 4aih_A 4aij_A 3qpt_A* 3q5f_A*

Probab=95.43  E-value=0.028  Score=41.72  Aligned_cols=66  Identities=12%  Similarity=0.110  Sum_probs=50.4

Q ss_pred             ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      .+.-.|...+  ++.+..|||+.+++    +...+.++++-|...|++++...+.  ..-...+|+.|..+...
T Consensus        35 ~vL~~L~~~~--~~~~~~eLa~~l~~----~~~tvs~~v~~Le~~GlV~R~~~~~DrR~~~l~LT~~G~~~~~~  102 (151)
T 4aik_A           35 VTLYNINRLP--PEQSQIQLAKAIGI----EQPSLVRTLDQLEEKGLITRHTSANDRRAKRIKLTEQSSPIIEQ  102 (151)
T ss_dssp             HHHHHHHHSC--TTSCHHHHHHHHTS----CHHHHHHHHHHHHHTTSEEEEECSSCTTCEEEEECGGGHHHHHH
T ss_pred             HHHHHHHHcC--CCCcHHHHHHHHCc----CHHHHHHHHHHHHhCCCeEeecCCCCCcchhhhcCHHHHHHHHH
Confidence            3555666544  46788999999999    9999999999999999999865431  11247789988877644

>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=95.37  E-value=0.041  Score=47.33  Aligned_cols=63  Identities=22%  Similarity=0.170  Sum_probs=44.0

Q ss_pred             cceEEEecCCccHHHHHH--------HHHc-------CCCcEEEeechHH--------HhhccC----------C---C-
Q 039903          169 IKQLVDVGGGLGVNVNII--------ISNY-------LHIKGVNFDLSHV--------IQDSSS----------Y---S-  211 (233)
Q Consensus       169 ~~~vvDvGGG~G~~~~~l--------~~~~-------P~l~~~v~Dlp~v--------~~~a~~----------~---~-  211 (233)
                      .-+|+|+|||+|..+..+        .+++       |.+++..-|||..        ++....          .   + 
T Consensus        53 ~~~IaDlGCssG~Nt~~~v~~ii~~i~~~~~~~~~~~pe~~v~~nDLp~NDFn~lF~~L~~~~~~~~~~~~~~~~~~~~~  132 (374)
T 3b5i_A           53 PFTAVDLGCSSGANTVHIIDFIVKHISKRFDAAGIDPPEFTAFFSDLPSNDFNTLFQLLPPLVSNTCMEECLAADGNRSY  132 (374)
T ss_dssp             CEEEEEETCCSSHHHHHHHHHHHHHHHHHHHHTTCCCCCEEEEEEECTTSCHHHHHHHSCCBCCCC--CCC---CCCBCS
T ss_pred             ceEEEecCCCCChhHHHHHHHHHHHHHHHHhhcCCCCCceeEEecCCCccchHHHHhhhhhhhhhcchhhhccccCCCce
Confidence            578999999999877665        4455       8899999999852        122111          0   1 


Q ss_pred             CceEEecCcCC-CCCCC--CEEE
Q 039903          212 GVKHIGGIMLE-RIPKG--DAIL  231 (233)
Q Consensus       212 ri~~~~gD~f~-~~P~~--D~~~  231 (233)
                      =+.-++|.|+. .+|..  |+++
T Consensus       133 f~~gvpgSFy~rlfP~~S~d~v~  155 (374)
T 3b5i_A          133 FVAGVPGSFYRRLFPARTIDFFH  155 (374)
T ss_dssp             EEEEEESCTTSCCSCTTCEEEEE
T ss_pred             EEEecChhhhcccCCCcceEEEE
Confidence            15667899998 78875  7764

>3hrs_A Metalloregulator SCAR; DTXR/MNTR family member, transcription; 2.70A {Streptococcus gordonii} PDB: 3hrt_A 3hru_A

Probab=95.37  E-value=0.016  Score=45.81  Aligned_cols=52  Identities=21%  Similarity=0.268  Sum_probs=46.9

Q ss_pred             CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhcC
Q 039903           32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~~   91 (233)
                      ++.+..+||+.+++    ++..+.+.++-|...|++++.    ....+.+|+.|+.+...
T Consensus        19 ~~~~~~~lA~~l~v----s~~tvs~~l~~Le~~GlV~r~----~~~~i~LT~~G~~~~~~   70 (214)
T 3hrs_A           19 NKITNKEIAQLMQV----SPPAVTEMMKKLLAEELLIKD----KKAGYLLTDLGLKLVSD   70 (214)
T ss_dssp             SCCCHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEE----TTTEEEECHHHHHHHHH
T ss_pred             CCcCHHHHHHHHCC----ChhHHHHHHHHHHHCCCEEEe----cCCCeEECHHHHHHHHH
Confidence            68999999999999    999999999999999999997    56789999999876543

>2fe3_A Peroxide operon regulator; oxidative stress regulator, DNA binding protein; 1.75A {Bacillus subtilis} PDB: 3f8n_A 2rgv_A*

Probab=95.36  E-value=0.026  Score=41.74  Aligned_cols=59  Identities=14%  Similarity=0.216  Sum_probs=46.9

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhC-----CCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceecc
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQM-----PSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLA   82 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~-----~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt   82 (233)
                      +.-|++.|...+  ++.|++||.+.+     ++    +..-++|.|+.|+..|++.+...+++..+|.++
T Consensus        24 R~~Il~~L~~~~--~~~sa~ei~~~l~~~~~~i----s~aTVYR~L~~L~e~Glv~~~~~~~~~~~Y~~~   87 (145)
T 2fe3_A           24 RHAILEYLVNSM--AHPTADDIYKALEGKFPNM----SVATVYNNLRVFRESGLVKELTYGDASSRFDFV   87 (145)
T ss_dssp             HHHHHHHHHHCS--SCCCHHHHHHHHGGGCTTC----CHHHHHHHHHHHHHTTSEEEECCTTSCCEEEEC
T ss_pred             HHHHHHHHHhCC--CCCCHHHHHHHHHHhCCCC----ChhhHHHHHHHHHHCCCEEEEeeCCCceEEECC
Confidence            455899998754  689999999999     56    899999999999999999987543223457653

>4hbl_A Transcriptional regulator, MARR family; HTH, transcription factor, DNA binding; 2.50A {Staphylococcus epidermidis}

Probab=95.34  E-value=0.0096  Score=43.88  Aligned_cols=66  Identities=11%  Similarity=0.035  Sum_probs=50.2

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhc
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVL   90 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~   90 (233)
                      +..|...|...   ++.|..|||+.+++    ++..+.++++.|...|++++.....  ..-.+.+|+.|..+..
T Consensus        43 q~~iL~~l~~~---~~~~~~eLa~~l~~----~~~~vs~~l~~L~~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~  110 (149)
T 4hbl_A           43 QYLVMLTLWEE---NPQTLNSIGRHLDL----SSNTLTPMLKRLEQSGWVKRERQQSDKRQLIITLTDNGQQQQE  110 (149)
T ss_dssp             HHHHHHHHHHS---SSEEHHHHHHHHTC----CHHHHHHHHHHHHHHTSEEC---------CEEEECSHHHHHHH
T ss_pred             HHHHHHHHHHC---CCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEeeCCCCCCcceeeeeECHHHHHHHH
Confidence            44567777765   58999999999999    9999999999999999999864321  1235788888887654

>2o03_A Probable zinc uptake regulation protein FURB; DNA-binding, helix-turn-helix, zinc binding, GE regulation; 2.70A {Mycobacterium tuberculosis}

Probab=95.13  E-value=0.029  Score=40.76  Aligned_cols=61  Identities=10%  Similarity=0.151  Sum_probs=48.6

Q ss_pred             HHHhhChhHHHHhcCCCCCCCHHHHHHhC-----CCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceec
Q 039903           15 AASELGVFEIIAKAGPTAKISAVEIAAQM-----PSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGL   81 (233)
Q Consensus        15 ~a~~lglfd~L~~~~~~~~~t~~elA~~~-----~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~l   81 (233)
                      +.-+.-|++.|...+  ++.|++||.+.+     ++    +..-++|.|+.|+..|++.+...+++..+|..
T Consensus        10 T~qR~~Il~~l~~~~--~~~sa~ei~~~l~~~~~~i----s~~TVYR~L~~L~e~Glv~~~~~~~~~~~y~~   75 (131)
T 2o03_A           10 TRQRAAISTLLETLD--DFRSAQELHDELRRRGENI----GLTTVYRTLQSMASSGLVDTLHTDTGESVYRR   75 (131)
T ss_dssp             HHHHHHHHHHHHHCC--SCEEHHHHHHHHHHTTCCC----CHHHHHHHHHHHHTTTSEEEEECTTSCEEEEE
T ss_pred             CHHHHHHHHHHHhCC--CCCCHHHHHHHHHHhCCCC----CHhhHHHHHHHHHHCCCEEEEEeCCCceEEEe
Confidence            445677899998754  689999999998     67    99999999999999999998754323345654

>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=95.09  E-value=0.021  Score=44.89  Aligned_cols=66  Identities=14%  Similarity=-0.019  Sum_probs=51.7

Q ss_pred             hChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           19 LGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        19 lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      ..|+..|...   ++.|..|||+.+++    +...+.++++.|...|++++.....  ..-.+.+|+.|..+...
T Consensus        51 ~~iL~~L~~~---~~~t~~eLa~~l~i----~~stvs~~l~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~~  118 (207)
T 2fxa_A           51 HHILWIAYQL---NGASISEIAKFGVM----HVSTAFNFSKKLEERGYLRFSKRLNDKRNTYVQLTEEGTEVFWS  118 (207)
T ss_dssp             HHHHHHHHHH---TSEEHHHHHHHTTC----CHHHHHHHHHHHHHHTSEEEECC------CEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHC---CCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEecCCCCCceEEEEECHHHHHHHHH
Confidence            3466777766   48999999999999    9999999999999999999864311  11267899999876643

>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=95.04  E-value=0.026  Score=44.31  Aligned_cols=69  Identities=9%  Similarity=0.140  Sum_probs=55.3

Q ss_pred             HHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccC----CCCCceeccHhh
Q 039903           10 PAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAG----DDQRLYGLAHVA   85 (233)
Q Consensus        10 s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~----~~~~~y~lt~~s   85 (233)
                      ..+|..-.++.|+..|..    +|.+..|||+.+++    +...+.+.|+.|...|++......    +..-.|++|+.+
T Consensus         9 lkaL~~~~rl~IL~~L~~----~~~s~~eLa~~l~i----s~stvs~hLk~Le~~GLV~~~~~~~~~g~~~~~Y~Lt~~~   80 (202)
T 2p4w_A            9 LDVLGNETRRRILFLLTK----RPYFVSELSRELGV----GQKAVLEHLRILEEAGLIESRVEKIPRGRPRKYYMIKKGL   80 (202)
T ss_dssp             HHHHHSHHHHHHHHHHHH----SCEEHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEEECCBTTBCCCEEEEECTTE
T ss_pred             HHHhCCHHHHHHHHHHHh----CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCceEEEeeccCCCCceEEEEEChHH
Confidence            456666778899999976    69999999999999    999999999999999999986431    123467777655


Q ss_pred             h
Q 039903           86 K   86 (233)
Q Consensus        86 ~   86 (233)
                      .
T Consensus        81 ~   81 (202)
T 2p4w_A           81 R   81 (202)
T ss_dssp             E
T ss_pred             H
Confidence            4

>2px2_A Genome polyprotein [contains: capsid protein C (core protein); envelope protein M...; methyltransferase, SAH; HET: SAH; 2.00A {Murray valley encephalitis virus} PDB: 2px4_A* 2px5_A* 2pxa_A* 2pxc_A* 2px8_A* 2oy0_A*

Probab=95.00  E-value=0.018  Score=46.89  Aligned_cols=72  Identities=17%  Similarity=0.158  Sum_probs=43.4

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHH--cCCCcEEE--eechHHHhhccCCCCc---eEEec-CcCCCCCC-CC
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISN--YLHIKGVN--FDLSHVIQDSSSYSGV---KHIGG-IMLERIPK-GD  228 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~--~P~l~~~v--~Dlp~v~~~a~~~~ri---~~~~g-D~f~~~P~-~D  228 (233)
                      ++-+.+- ++...+|||+||+.|.++.-.+++  -..+++.+  .|+ +..........+   .++.| ||++.-|. .|
T Consensus        64 EIdeK~l-ikpg~~VVDLGaAPGGWSQvAa~~~~vg~V~G~vig~D~-~~~P~~~~~~Gv~~i~~~~G~Df~~~~~~~~D  141 (269)
T 2px2_A           64 WLVERRF-VQPIGKVVDLGCGRGGWSYYAATMKNVQEVRGYTKGGPG-HEEPMLMQSYGWNIVTMKSGVDVFYKPSEISD  141 (269)
T ss_dssp             HHHHTTS-CCCCEEEEEETCTTSHHHHHHTTSTTEEEEEEECCCSTT-SCCCCCCCSTTGGGEEEECSCCGGGSCCCCCS
T ss_pred             HHHHcCC-CCCCCEEEEcCCCCCHHHHHHhhhcCCCCceeEEEcccc-ccCCCcccCCCceEEEeeccCCccCCCCCCCC
Confidence            3444442 677899999999999999999886  32224433  343 111111111454   55557 99984443 48


Q ss_pred             EEE
Q 039903          229 AIL  231 (233)
Q Consensus       229 ~~~  231 (233)
                      +++
T Consensus       142 vVL  144 (269)
T 2px2_A          142 TLL  144 (269)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            886

>3u2r_A Regulatory protein MARR; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, helix-turn-helix; 2.20A {Planctomyces limnophilus}

Probab=94.99  E-value=0.02  Score=43.07  Aligned_cols=68  Identities=15%  Similarity=0.248  Sum_probs=49.8

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCC---ceeccHhhhHhhcC
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQR---LYGLAHVAKYFVLN   91 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~---~y~lt~~s~~l~~~   91 (233)
                      ++.|+..|...+. ++.|..+||+.+++    +...+.++++.|...|++++.... .+.   .+.+|+.|..+...
T Consensus        48 q~~vL~~l~~~~~-~~~t~~eLa~~l~~----~~~tvs~~l~~Le~~Glv~r~~~~-~DrR~~~l~LT~~G~~~~~~  118 (168)
T 3u2r_A           48 QYNTLRLLRSVHP-EGMATLQIADRLIS----RAPDITRLIDRLDDRGLVLRTRKP-ENRRVVEVALTDAGLKLLKD  118 (168)
T ss_dssp             HHHHHHHHHHHTT-SCEEHHHHHHHC-------CTHHHHHHHHHHHTTSEEEEEET-TEEEEEEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHhcCC-CCcCHHHHHHHHCC----ChhhHHHHHHHHHHCCCEeecCCC-CCCCeeEeEECHHHHHHHHH
Confidence            4456667776421 48999999999999    999999999999999999986432 122   57889998877654

>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=94.87  E-value=0.039  Score=46.72  Aligned_cols=56  Identities=16%  Similarity=0.232  Sum_probs=47.4

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccC---------------------------CCCceEEecC
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSS---------------------------YSGVKHIGGI  219 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~---------------------------~~ri~~~~gD  219 (233)
                      .+...||.+|||.....-.+...+|++++.=+|+|+|++.-++                           .+++.++++|
T Consensus        96 ~~~~qVV~LGaGlDTr~~RL~~~~~~~~~~EvD~P~vi~~K~~~l~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~v~~D  175 (334)
T 1rjd_A           96 NEKVQVVNLGCGSDLRMLPLLQMFPHLAYVDIDYNESVELKNSILRESEILRISLGLSKEDTAKSPFLIDQGRYKLAACD  175 (334)
T ss_dssp             CSSEEEEEETCTTCCTHHHHHHHCTTEEEEEEECHHHHHHHHHHHHHSHHHHHHHTCCSSCCCCTTEEEECSSEEEEECC
T ss_pred             CCCcEEEEeCCCCccHHHHhcCcCCCCEEEECCCHHHHHHHHHHhhhccchhhhcccccccccccccccCCCceEEEecC
Confidence            4568999999999999999999899999999999998763221                           1689999999


Q ss_pred             cCC
Q 039903          220 MLE  222 (233)
Q Consensus       220 ~f~  222 (233)
                      +.+
T Consensus       176 L~d  178 (334)
T 1rjd_A          176 LND  178 (334)
T ss_dssp             TTC
T ss_pred             CCC
Confidence            987

>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=94.80  E-value=0.037  Score=42.57  Aligned_cols=70  Identities=10%  Similarity=0.089  Sum_probs=54.2

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      .+..|+..|...+ .++.|..+||+.+++    +...+.++++.|...|++++.....  ..-.+.+|+.|..+...
T Consensus        42 ~q~~vL~~L~~~~-~~~~t~~eLa~~l~i----s~~tvs~~l~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~~  113 (189)
T 3nqo_A           42 RQYMTILSILHLP-EEETTLNNIARKMGT----SKQNINRLVANLEKNGYVDVIPSPHDKRAINVKVTDLGKKVMVT  113 (189)
T ss_dssp             HHHHHHHHHHHSC-GGGCCHHHHHHHHTS----CHHHHHHHHHHHHHTTSEEEEECSSCSSCEEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHHhcc-CCCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHHHHHHHHH
Confidence            3556777777521 158999999999999    9999999999999999999864321  12457899999877654

>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=94.71  E-value=0.03  Score=39.08  Aligned_cols=47  Identities=21%  Similarity=0.309  Sum_probs=40.1

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      ++.|+..+...|  .+.|..+||+.+|+    +...+++.|+.|...|+++..
T Consensus        20 ~l~Il~~l~~~g--~~~s~~eLa~~lgv----s~~tV~~~L~~L~~~GlV~~~   66 (110)
T 1q1h_A           20 VIDVLRILLDKG--TEMTDEEIANQLNI----KVNDVRKKLNLLEEQGFVSYR   66 (110)
T ss_dssp             THHHHHHHHHHC--SCBCHHHHHHTTTS----CHHHHHHHHHHHHHHTSCEEE
T ss_pred             HHHHHHHHHHcC--CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEE
Confidence            456777775543  37899999999999    999999999999999999875

>2lnb_A Z-DNA-binding protein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, immune system; NMR {Homo sapiens}

Probab=94.70  E-value=0.034  Score=36.25  Aligned_cols=56  Identities=13%  Similarity=0.257  Sum_probs=48.2

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceecc
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLA   82 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt   82 (233)
                      .+-.|++.|.++|  .|++..|||+++|+    +..-+...|..|-.-|.+..+    .--.|+++
T Consensus        20 ~eekVLe~LkeaG--~PlkageIae~~Gv----dKKeVdKaik~LKkEgkI~SP----kRCyw~~~   75 (80)
T 2lnb_A           20 LEQRILQVLTEAG--SPVKLAQLVKECQA----PKRELNQVLYRMKKELKVSLT----SPATWCLG   75 (80)
T ss_dssp             HHHHHHHHHHHHT--SCEEHHHHHHHHTS----CHHHHHHHHHHHHHTTSEEEE----ETTEEEES
T ss_pred             HHHHHHHHHHHcC--CCCCHHHHHHHHCC----CHHHHHHHHHHHHHcCCccCC----CCceeeCC
Confidence            3557899999987  79999999999999    999999999999999999886    35566554

>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=94.69  E-value=0.034  Score=40.42  Aligned_cols=57  Identities=14%  Similarity=0.139  Sum_probs=42.9

Q ss_pred             hhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903           21 VFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH   83 (233)
Q Consensus        21 lfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~   83 (233)
                      ++..|....  ++.|..|||+.+++    +...+.++++.|...|++++....++...|.++.
T Consensus        31 il~~L~~~~--~~~t~~ela~~l~~----~~stvs~~l~~L~~~G~v~r~~~~~d~r~~~~~~   87 (152)
T 1ku9_A           31 VYAILYLSD--KPLTISDIMEELKI----SKGNVSMSLKKLEELGFVRKVWIKGERKNYYEAV   87 (152)
T ss_dssp             HHHHHHHCS--SCEEHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEECCTTCSSCEEEEC
T ss_pred             HHHHHHHcC--CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEEecCCCceEEEeec
Confidence            466664222  58999999999999    9999999999999999999863221234555554

>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=94.67  E-value=0.02  Score=51.73  Aligned_cols=73  Identities=15%  Similarity=-0.028  Sum_probs=49.7

Q ss_pred             HHHhcccccCcceEEEecCCccHHHHHHHHHcC------------------CCcEEEeech-HHHhhccCC------CC-
Q 039903          159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYL------------------HIKGVNFDLS-HVIQDSSSY------SG-  212 (233)
Q Consensus       159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P------------------~l~~~v~Dlp-~v~~~a~~~------~r-  212 (233)
                      +++... -....+|+|.+||+|.++..+.+...                  ..++..+|+. ..++.|+.+      +. 
T Consensus       161 mv~~l~-p~~~~~VlDPaCGSG~fLi~a~~~l~~~~~~~~~~~~~~~~~~~~~~i~GiEid~~~~~lA~~nl~l~gi~~~  239 (541)
T 2ar0_A          161 IIHLLK-PQPREVVQDPAAGTAGFLIEADRYVKSQTNDLDDLDGDTQDFQIHRAFIGLELVPGTRRLALMNCLLHDIEGN  239 (541)
T ss_dssp             HHHHHC-CCTTCCEEETTCTTTHHHHHHHHHHHTTTTTTTTSCHHHHHHHHHTSEEEEESCHHHHHHHHHHHHTTTCCCB
T ss_pred             HHHHhc-cCCCCeEecCCcccchHHHHHHHHHHHhhcccccCCHHHHhhhhcceEEEEcCCHHHHHHHHHHHHHhCCCcc
Confidence            344433 33456899999999999988877532                  2468999984 566666532      32 


Q ss_pred             ----ceEEecCcCC-C-CC--CCCEEEe
Q 039903          213 ----VKHIGGIMLE-R-IP--KGDAILI  232 (233)
Q Consensus       213 ----i~~~~gD~f~-~-~P--~~D~~~l  232 (233)
                          +.+..+|.+. + .+  ..|+|+.
T Consensus       240 ~~~~~~I~~gDtL~~~~~~~~~fD~Vv~  267 (541)
T 2ar0_A          240 LDHGGAIRLGNTLGSDGENLPKAHIVAT  267 (541)
T ss_dssp             GGGTBSEEESCTTSHHHHTSCCEEEEEE
T ss_pred             ccccCCeEeCCCcccccccccCCeEEEE
Confidence                7889999997 2 22  2388874

>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=94.65  E-value=0.013  Score=41.76  Aligned_cols=65  Identities=15%  Similarity=0.112  Sum_probs=48.7

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCC----CCCCCChhhHHHHHHHHhcCCceeeeccCCCCCc-eeccHhhhHhhc
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMP----SSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRL-YGLAHVAKYFVL   90 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~----~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~-y~lt~~s~~l~~   90 (233)
                      +..|...|...   ++.|..|||+.++    +    +...+.++|+-|...|++++...+ .... +.+|+.+..+..
T Consensus        12 ~~~vL~~l~~~---~~~t~~ela~~l~~~~~~----s~~tv~~~l~~L~~~Glv~r~~~~-rr~~~~~lT~~g~~~~~   81 (123)
T 1okr_A           12 EWEVMNIIWMK---KYASANNIIEEIQMQKDW----SPKTIRTLITRLYKKGFIDRKKDN-KIFQYYSLVEESDIKYK   81 (123)
T ss_dssp             HHHHHHHHHHH---SSEEHHHHHHHHHHHCCC----CHHHHHHHHHHHHHHTSEEEEEET-TEEEEEESSCHHHHHHH
T ss_pred             HHHHHHHHHhC---CCcCHHHHHHHHhccCCC----cHhhHHHHHHHHHHCCCeEEEecC-CeEEEEEecCHHHHHHH
Confidence            44566677665   5899999999999    6    799999999999999999986421 1112 357777776553

>1i4w_A Mitochondrial replication protein MTF1; mitochondrial transcription factor, transcription initiation; 2.60A {Saccharomyces cerevisiae} SCOP: c.66.1.24

Probab=94.59  E-value=0.089  Score=44.88  Aligned_cols=54  Identities=11%  Similarity=0.096  Sum_probs=41.3

Q ss_pred             cceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhcc---CCCCceEEecCcCC
Q 039903          169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSS---SYSGVKHIGGIMLE  222 (233)
Q Consensus       169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~---~~~ri~~~~gD~f~  222 (233)
                      ..+||+||.|.|.++..|+++...-+.+++++.. -++..+   ..++++.+.+|+++
T Consensus        59 ~~~VlEIGPG~G~LT~~Ll~~~~~~~vvavE~D~~l~~~L~~~~~~~~l~ii~~D~l~  116 (353)
T 1i4w_A           59 ELKVLDLYPGVGIQSAIFYNKYCPRQYSLLEKRSSLYKFLNAKFEGSPLQILKRDPYD  116 (353)
T ss_dssp             TCEEEEESCTTCHHHHHHHHHHCCSEEEEECCCHHHHHHHHHHTTTSSCEEECSCTTC
T ss_pred             CCEEEEECCCCCHHHHHHHhhCCCCEEEEEecCHHHHHHHHHhccCCCEEEEECCccc
Confidence            4789999999999999999975445688887653 222221   34799999999975

>2vn2_A DNAD, chromosome replication initiation protein; DNA replication, primosome; 2.3A {Geobacillus kaustophilus HTA426}

Probab=94.54  E-value=0.056  Score=39.05  Aligned_cols=51  Identities=20%  Similarity=0.234  Sum_probs=38.0

Q ss_pred             CCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCC----CceeccHhhhH
Q 039903           33 KISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQ----RLYGLAHVAKY   87 (233)
Q Consensus        33 ~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~----~~y~lt~~s~~   87 (233)
                      ..|..+||+.+++    ++..+.+.++.|...|++++....+++    +.|.++|+-..
T Consensus        51 ~ps~~~LA~~l~~----s~~~V~~~l~~Le~kGlI~~~~~~~~~g~~~~~Ydl~pl~~k  105 (128)
T 2vn2_A           51 FPTPAELAERMTV----SAAECMEMVRRLLQKGMIAIEEHTDEQGIRNEKYTLEPLWEK  105 (128)
T ss_dssp             SCCHHHHHHTSSS----CHHHHHHHHHHHHHTTSSEECC----------CEECHHHHHH
T ss_pred             CCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEEeEECCCCcEEEEEehHHHHHH
Confidence            3799999999999    999999999999999999985321111    35666665443

>2k4b_A Transcriptional regulator; DNA binding protein, winged helix; NMR {Lactococcus lactis subsp}

Probab=94.54  E-value=0.023  Score=39.33  Aligned_cols=51  Identities=25%  Similarity=0.271  Sum_probs=41.3

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeec
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTS   71 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~   71 (233)
                      +..|...|.+.   ++.|..||++.++..++.+...+.++|+-|+..|++++..
T Consensus        37 e~~VL~~L~~~---~~~t~~eL~~~l~~~~~~s~sTVt~~L~rLe~KGlV~R~~   87 (99)
T 2k4b_A           37 ELIVMRVIWSL---GEARVDEIYAQIPQELEWSLATVKTLLGRLVKKEMLSTEK   87 (99)
T ss_dssp             CSHHHHHHHHH---SCEEHHHHHHTCCGGGCCCHHHHHHHHHHHHHTTSCEEEE
T ss_pred             HHHHHHHHHhC---CCCCHHHHHHHHhcccCCCHhhHHHHHHHHHHCCCEEEEe
Confidence            45578888775   5899999999998521225789999999999999999863

>2fbk_A Transcriptional regulator, MARR family; winged-helix-turn-helix; 2.30A {Deinococcus radiodurans} SCOP: a.4.5.28

Probab=94.53  E-value=0.022  Score=43.39  Aligned_cols=70  Identities=9%  Similarity=0.117  Sum_probs=51.3

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      ++.|+..|...++.++.|..+||+.+++    +...+.++++.|...|++++.....  ..-.+.+|+.|..+...
T Consensus        71 ~~~iL~~L~~~~~~~~~t~~eLa~~l~i----s~~tvs~~l~~Le~~GlV~r~~~~~DrR~~~~~LT~~G~~~~~~  142 (181)
T 2fbk_A           71 GWDLLLTLYRSAPPEGLRPTELSALAAI----SGPSTSNRIVRLLEKGLIERREDERDRRSASIRLTPQGRALVTH  142 (181)
T ss_dssp             HHHHHHHHHHHCCSSCBCHHHHHHHCSC----CSGGGSSHHHHHHHHTSEECCC-------CCBEECHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCCCCHHHHHHHHCC----CHHHHHHHHHHHHHCcCEEecCCCCCCCeeEEEECHHHHHHHHH
Confidence            4457777777641013999999999999    9999999999999999999853210  12257889888876643

>2qlz_A Transcription factor PF0095; 2.50A {Pyrococcus furiosus} PDB: 2quf_A

Probab=94.51  E-value=0.012  Score=47.39  Aligned_cols=70  Identities=7%  Similarity=0.149  Sum_probs=54.4

Q ss_pred             HHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCC-----CCceeccH
Q 039903            9 LPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDD-----QRLYGLAH   83 (233)
Q Consensus         9 ~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~-----~~~y~lt~   83 (233)
                      ...+|..-.++.|+..|..    +|.|..|||+.+++    +...+.+.|+.|...|++......+.     .-.|++|+
T Consensus         5 ilkaL~~~~R~~IL~~L~~----g~~s~~ELa~~lgl----S~stVs~hL~~Le~aGLV~~~~~~gr~~GRp~~~Y~Lt~   76 (232)
T 2qlz_A            5 LFYILGNKVRRDLLSHLTC----MECYFSLLSSKVSV----SSTAVAKHLKIMEREGVLQSYEKEERFIGPTKKYYKISI   76 (232)
T ss_dssp             HHHHHTSHHHHHHHHHHTT----TTTCSSSSCTTCCC----CHHHHHHHHHHHHHTTSEEEEEECC-----CEEEEEECC
T ss_pred             HHHHhCCHHHHHHHHHHHh----CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEeeecCCCCCCccEEEEEcc
Confidence            3456666778889999986    69999999999999    99999999999999999998221111     22477777


Q ss_pred             hhh
Q 039903           84 VAK   86 (233)
Q Consensus        84 ~s~   86 (233)
                      .+.
T Consensus        77 ~~~   79 (232)
T 2qlz_A           77 AKS   79 (232)
T ss_dssp             CEE
T ss_pred             chh
Confidence            554

>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=94.35  E-value=0.045  Score=40.20  Aligned_cols=47  Identities=15%  Similarity=0.278  Sum_probs=41.9

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      .+..|.+.|...   ++.|..|||+++|+    ++..+.+.++.|...|++.+.
T Consensus         6 ~d~~il~~L~~~---~~~s~~ela~~lg~----s~~tv~~~l~~L~~~G~i~~~   52 (144)
T 2cfx_A            6 IDLNIIEELKKD---SRLSMRELGRKIKL----SPPSVTERVRQLESFGIIKQY   52 (144)
T ss_dssp             HHHHHHHHHHHC---SCCCHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCeEEE
Confidence            355688888876   58999999999999    999999999999999999864

>2efj_A 3,7-dimethylxanthine methyltransferase; SAM-dependant methyltransferase, SAH, theobromine; HET: SAH 37T; 2.00A {Coffea canephora} PDB: 2eg5_A*

Probab=94.32  E-value=0.083  Score=45.59  Aligned_cols=63  Identities=14%  Similarity=0.147  Sum_probs=43.8

Q ss_pred             cceEEEecCCccHHHHHHHHH-----------------cCCCcEEEeech-----------HHH-hh-----ccCCCC--
Q 039903          169 IKQLVDVGGGLGVNVNIIISN-----------------YLHIKGVNFDLS-----------HVI-QD-----SSSYSG--  212 (233)
Q Consensus       169 ~~~vvDvGGG~G~~~~~l~~~-----------------~P~l~~~v~Dlp-----------~v~-~~-----a~~~~r--  212 (233)
                      .-+|+|+||++|..+..++..                 .|.+++..-|||           +.. +.     ....+.  
T Consensus        53 ~~~IaDlGCssG~NT~~~v~~ii~~i~~~~~~~~~~~~~pe~~v~~nDLp~NDFN~lF~~L~~~~~~~~~~~g~~~~~~f  132 (384)
T 2efj_A           53 CFKVGDLGCASGPNTFSTVRDIVQSIDKVGQEKKNELERPTIQIFLNDLFQNDFNSVFKLLPSFYRNLEKENGRKIGSCL  132 (384)
T ss_dssp             EEEEEEETCCSSHHHHHHHHHHHHHHTCC----------CEEEEEEECCTTSCHHHHHHHHHHHHHHHHHHTCCCTTSEE
T ss_pred             ceEEEecCCCCCchHHHHHHHHHHHHHHHhhhcccCCCCCceEEEecCCCccchHHHHhhhhhhHhhhhhhccCCCCceE
Confidence            678999999999988777666                 578888999999           211 11     111111  


Q ss_pred             ceEEecCcCC-CCCCC--CEEE
Q 039903          213 VKHIGGIMLE-RIPKG--DAIL  231 (233)
Q Consensus       213 i~~~~gD~f~-~~P~~--D~~~  231 (233)
                      +.-++|.|+. -+|..  |+++
T Consensus       133 ~~gvpgSFy~rlfp~~S~d~v~  154 (384)
T 2efj_A          133 IGAMPGSFYSRLFPEESMHFLH  154 (384)
T ss_dssp             EEECCSCTTSCCSCTTCEEEEE
T ss_pred             EEecchhhhhccCCCCceEEEE
Confidence            5567899998 78875  7764

>3khk_A Type I restriction-modification system methylation subunit; structural genomics, PSI-2, protein structure initiative; 2.55A {Methanosarcina mazei}

Probab=94.29  E-value=0.023  Score=51.33  Aligned_cols=63  Identities=10%  Similarity=-0.066  Sum_probs=45.0

Q ss_pred             ceEEEecCCccHHHHHHHHHcC---------------CCcEEEeech-HHHhhccCC-------CCceEEecCcCC-C-C
Q 039903          170 KQLVDVGGGLGVNVNIIISNYL---------------HIKGVNFDLS-HVIQDSSSY-------SGVKHIGGIMLE-R-I  224 (233)
Q Consensus       170 ~~vvDvGGG~G~~~~~l~~~~P---------------~l~~~v~Dlp-~v~~~a~~~-------~ri~~~~gD~f~-~-~  224 (233)
                      .+|+|.+||+|.++.++.+..+               +.++..+|+. .++..|+.+       .+|.+..+|.+. + .
T Consensus       246 ~~VlDPaCGSG~fLi~a~~~l~~~~~~~~~~~~~~~~~~~i~G~Eid~~~~~lA~~Nl~l~gi~~~i~i~~gDtL~~~~~  325 (544)
T 3khk_A          246 GRVYDPAMGSGGFFVSSDKFIEKHANVKHYNASEQKKQISVYGQESNPTTWKLAAMNMVIRGIDFNFGKKNADSFLDDQH  325 (544)
T ss_dssp             EEEEESSCTTCHHHHHHHHHHHHHHHHHTSCHHHHGGGEEEEECCCCHHHHHHHHHHHHHTTCCCBCCSSSCCTTTSCSC
T ss_pred             CeEeCcccCcCcHHHHHHHHHHHhccccccchHHHhhhceEEEEeCCHHHHHHHHHHHHHhCCCcccceeccchhcCccc
Confidence            4999999999999988765432               5678999984 566666542       345558899987 3 3


Q ss_pred             CC-C-CEEEe
Q 039903          225 PK-G-DAILI  232 (233)
Q Consensus       225 P~-~-D~~~l  232 (233)
                      +. . |+|+.
T Consensus       326 ~~~~fD~Iv~  335 (544)
T 3khk_A          326 PDLRADFVMT  335 (544)
T ss_dssp             TTCCEEEEEE
T ss_pred             ccccccEEEE
Confidence            33 2 88874

>3mwm_A ZUR, putative metal uptake regulation protein; FUR, regulatory metal, graded transcription regulation, transcription; 2.40A {Streptomyces coelicolor}

Probab=94.25  E-value=0.052  Score=39.84  Aligned_cols=66  Identities=12%  Similarity=0.127  Sum_probs=49.1

Q ss_pred             HHHhhChhHHHHhcCCCCCCCHHHHHHhCCCC-CCCChhhHHHHHHHHhcCCceeeeccCCCCCceecc
Q 039903           15 AASELGVFEIIAKAGPTAKISAVEIAAQMPSS-NPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLA   82 (233)
Q Consensus        15 ~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~-~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt   82 (233)
                      +.-+.-|++.|...+  ++.|++||.+.+.-. +..+..-++|.|+.|+..|++++...+++..+|.+.
T Consensus        13 T~qR~~Il~~L~~~~--~h~sa~eI~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~~~~~g~~~Y~~~   79 (139)
T 3mwm_A           13 TRQRAAVSAALQEVE--EFRSAQELHDMLKHKGDAVGLTTVYRTLQSLADAGEVDVLRTAEGESVYRRC   79 (139)
T ss_dssp             HHHHHHHHHHHTTCS--SCEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTSSEEEECTTSCEEEECC
T ss_pred             CHHHHHHHHHHHhCC--CCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHHHCCCEEEEEcCCCceEEEEC
Confidence            345677899998764  689999999988311 122889999999999999999987543234567654

>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=94.25  E-value=0.048  Score=40.32  Aligned_cols=47  Identities=13%  Similarity=0.118  Sum_probs=41.9

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      .+..|...|...   ++.|..|||+++|+    ++..+.+.++.|...|++.+.
T Consensus         8 ~~~~iL~~L~~~---~~~s~~ela~~lg~----s~~tv~~~l~~L~~~G~i~~~   54 (150)
T 2w25_A            8 IDRILVRELAAD---GRATLSELATRAGL----SVSAVQSRVRRLESRGVVQGY   54 (150)
T ss_dssp             HHHHHHHHHHHC---TTCCHHHHHHHHTS----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEE
Confidence            456788888876   58999999999999    999999999999999999864

>4b8x_A SCO5413, possible MARR-transcriptional regulator; winged helix motif; HET: CME; 1.25A {Streptomyces coelicolor}

Probab=94.17  E-value=0.031  Score=41.20  Aligned_cols=56  Identities=9%  Similarity=0.107  Sum_probs=45.4

Q ss_pred             CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      ++.|..+||+.+++    +...+.++++-|...|++++.....  ..-...+|+.|+.+...
T Consensus        50 ~~~t~~eLa~~l~~----~~~tvs~~v~~Le~~Glv~r~~~~~DrR~~~l~LT~~G~~~~~~  107 (147)
T 4b8x_A           50 GELPMSKIGERLMV----HPTSVTNTVDRLVRSGLVAKRPNPNDGRGTLATITDKGREVVEA  107 (147)
T ss_dssp             GEEEHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEEECC----CEEEEECHHHHHHHHH
T ss_pred             CCcCHHHHHHHHCC----CHHHHHHHHHHHHhCCCEEEeecCCcCceeEEEECHHHHHHHHH
Confidence            57999999999999    9999999999999999999875421  11247789998877643

>4esf_A PADR-like transcriptional regulator; PADR family, DNA binding protein, HTH fold; 2.20A {Bacillus cereus}

Probab=94.07  E-value=0.15  Score=36.24  Aligned_cols=74  Identities=16%  Similarity=0.207  Sum_probs=58.3

Q ss_pred             HHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhC------CCCCCCChhhHHHHHHHHhcCCceeeeccC---C-CCCce
Q 039903           10 PAAMQAASELGVFEIIAKAGPTAKISAVEIAAQM------PSSNPNAAVMLDRILRLLVTHRVLRCTSAG---D-DQRLY   79 (233)
Q Consensus        10 s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~------~~~~~~~~~~l~rlL~~L~~~gll~~~~~~---~-~~~~y   79 (233)
                      ++.++-.+++=|.-.|..    +|.+--||++.+      ++    ++..++..|+-|...|+++.....   + ....|
T Consensus         5 ~~l~~g~l~~~IL~lL~~----~p~~Gyei~~~l~~~g~~~i----s~gtlY~~L~rLe~~GlI~~~~~~~~~g~~rk~Y   76 (117)
T 4esf_A            5 TEMLKGSLEGCVLEIISR----RETYGYEITRHLNDLGFTEV----VEGTVYTILVRLEKKKLVNIEKKPSDMGPPRKFY   76 (117)
T ss_dssp             HHHHHHHHHHHHHHHHHH----SCBCHHHHHHHHHHHTCTTC----CHHHHHHHHHHHHHTTCEEEEEEC-----CEEEE
T ss_pred             HHHHHChHHHHHHHHHHc----CCCCHHHHHHHHHHcCCCCC----CccHHHHHHHHHHHCCCEEEEeecCCCCCCceEE
Confidence            456666677778888887    699999999997      67    999999999999999999976321   0 12369


Q ss_pred             eccHhhhHhhcC
Q 039903           80 GLAHVAKYFVLN   91 (233)
Q Consensus        80 ~lt~~s~~l~~~   91 (233)
                      ++|+.|+..+..
T Consensus        77 ~LT~~G~~~l~~   88 (117)
T 4esf_A           77 SLNEAGRQELEL   88 (117)
T ss_dssp             EECHHHHHHHHH
T ss_pred             EECHHHHHHHHH
Confidence            999999876644

>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=94.03  E-value=0.044  Score=43.65  Aligned_cols=69  Identities=12%  Similarity=0.105  Sum_probs=52.6

Q ss_pred             hhChhHHHHhcCC---CCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhcC
Q 039903           18 ELGVFEIIAKAGP---TAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        18 ~lglfd~L~~~~~---~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~~   91 (233)
                      ++.+|..|...+.   .++.|..++|+++++    ++..+.+.++.|...|+|++.... ....+.+|+.|+.+...
T Consensus         9 ~l~~l~~l~~~~~l~~~~~~s~s~aA~~L~i----sq~avSr~I~~LE~~~L~~R~~~~-R~~~v~LT~~G~~l~~~   80 (230)
T 3cta_A            9 YYRAIKKIKEAAEASNRAYLTSSKLADMLGI----SQQSASRIIIDLEKNGYITRTVTK-RGQILNITEKGLDVLYT   80 (230)
T ss_dssp             HHHHHHHHHHHTTTSSEEECCHHHHHHHHTS----CHHHHHHHHHHHHHTTSEEEEEET-TEEEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHHhcccccCCCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEEEcC-CeEEEEECHHHHHHHHH
Confidence            4455666654320   136889999999999    999999999999999999985211 15678999999887644

>2p5v_A Transcriptional regulator, LRP/ASNC family; NMB0573, structu genomics; 1.99A {Neisseria meningitidis} PDB: 2p6s_A 2p6t_A

Probab=94.02  E-value=0.056  Score=40.54  Aligned_cols=47  Identities=13%  Similarity=0.315  Sum_probs=42.0

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      .+..|.+.|...   ++.|..|||+++|+    ++..+.+.++.|...|++.+.
T Consensus        11 ~~~~il~~L~~~---~~~s~~ela~~lg~----s~~tv~~~l~~L~~~G~i~~~   57 (162)
T 2p5v_A           11 TDIKILQVLQEN---GRLTNVELSERVAL----SPSPCLRRLKQLEDAGIVRQY   57 (162)
T ss_dssp             HHHHHHHHHHHC---TTCCHHHHHHHHTS----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEeee
Confidence            456788888886   58999999999999    999999999999999999874

>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=93.99  E-value=0.041  Score=40.62  Aligned_cols=47  Identities=23%  Similarity=0.271  Sum_probs=41.9

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      .++.|...|...   ++.|..|||+.+|+    ++..+.+.++.|...|++.+.
T Consensus         4 ~~~~il~~L~~~---~~~~~~ela~~lg~----s~~tv~~~l~~L~~~G~i~~~   50 (150)
T 2pn6_A            4 IDLRILKILQYN---AKYSLDEIAREIRI----PKATLSYRIKKLEKDGVIKGY   50 (150)
T ss_dssp             HHHHHHHHHTTC---TTSCHHHHHHHHTS----CHHHHHHHHHHHHHTTSSCCC
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCcEEEE
Confidence            456788888875   58999999999999    999999999999999999873

>2esh_A Conserved hypothetical protein TM0937; APC5794, structural genomics, PSI, protein structure initiative; 2.30A {Thermotoga maritima} SCOP: a.4.5.61

Probab=93.96  E-value=0.12  Score=36.66  Aligned_cols=72  Identities=13%  Similarity=0.126  Sum_probs=55.9

Q ss_pred             HHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCC--------CCCCCCh-hhHHHHHHHHhcCCceeeeccC--C-CCCce
Q 039903           12 AMQAASELGVFEIIAKAGPTAKISAVEIAAQMP--------SSNPNAA-VMLDRILRLLVTHRVLRCTSAG--D-DQRLY   79 (233)
Q Consensus        12 ~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~--------~~~~~~~-~~l~rlL~~L~~~gll~~~~~~--~-~~~~y   79 (233)
                      .+....++-|...|..    +|.+..||++.++        +    ++ ..+.+.|+-|...|+++.....  + ..-.|
T Consensus         9 ~~~~~~~~~IL~~L~~----~~~~gyel~~~l~~~g~~~~~i----s~~~tly~~L~~Le~~GlI~~~~~~~~~~~r~~Y   80 (118)
T 2esh_A            9 FRGWWLASTILLLVAE----KPSHGYELAERLAEFGIEIPGI----GHMGNIYRVLADLEESGFLSTEWDTTVSPPRKIY   80 (118)
T ss_dssp             HHHHHHHHHHHHHHHH----SCBCHHHHHHHHHTTCCSSTTC----CCCCCHHHHHHHHHHTTSEEEEEECSSSSCEEEE
T ss_pred             cccchHHHHHHHHHHc----CCCCHHHHHHHHHHhCCcccCC----CCcchHHHHHHHHHHCCCeEEEeecCCCCCceEE
Confidence            3455567778888877    5899999999983        6    88 9999999999999999876421  1 12368


Q ss_pred             eccHhhhHhhcC
Q 039903           80 GLAHVAKYFVLN   91 (233)
Q Consensus        80 ~lt~~s~~l~~~   91 (233)
                      ++|+.|..+...
T Consensus        81 ~LT~~G~~~l~~   92 (118)
T 2esh_A           81 RITPQGKLYLRE   92 (118)
T ss_dssp             EECHHHHHHHHH
T ss_pred             EEChHHHHHHHH
Confidence            999999876644

>2xig_A Ferric uptake regulation protein; hpfur, transcription, homeostasis; HET: CIT; 1.85A {Helicobacter pylori}

Probab=93.94  E-value=0.072  Score=39.60  Aligned_cols=60  Identities=18%  Similarity=0.331  Sum_probs=47.2

Q ss_pred             HHhhChhHHHHhcCCCCCCCHHHHHHhC-----CCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceec
Q 039903           16 ASELGVFEIIAKAGPTAKISAVEIAAQM-----PSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGL   81 (233)
Q Consensus        16 a~~lglfd~L~~~~~~~~~t~~elA~~~-----~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~l   81 (233)
                      .-+.-|++.|...+  ++.|++||.+.+     ++    +..-++|.|+.|+..|++.+...+++..+|..
T Consensus        27 ~qR~~IL~~l~~~~--~~~sa~ei~~~l~~~~~~i----s~aTVYR~L~~L~e~Glv~~~~~~~~~~~Y~~   91 (150)
T 2xig_A           27 KQREEVVSVLYRSG--THLSPEEITHSIRQKDKNT----SISSVYRILNFLEKENFISVLETSKSGRRYEI   91 (150)
T ss_dssp             HHHHHHHHHHHHCS--SCBCHHHHHHHHHHHSTTC----CHHHHHHHHHHHHHTTSEEEEEETTTEEEEEE
T ss_pred             HHHHHHHHHHHhCC--CCCCHHHHHHHHHHhCCCC----CHhhHHHHHHHHHHCCcEEEEEeCCCceEEEe
Confidence            34556999998764  689999999998     56    89999999999999999998754322345654

>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=93.90  E-value=0.024  Score=37.36  Aligned_cols=52  Identities=19%  Similarity=0.311  Sum_probs=41.2

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeec
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTS   71 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~   71 (233)
                      .+..|.+.|...   ++.|..||++.++..++.+...+.++|+.|...|++++..
T Consensus        10 ~e~~vL~~L~~~---~~~t~~ei~~~l~~~~~~s~~Tv~~~l~rL~~kGlv~r~~   61 (82)
T 1p6r_A           10 AELEVMKVIWKH---SSINTNEVIKELSKTSTWSPKTIQTMLLRLIKKGALNHHK   61 (82)
T ss_dssp             HHHHHHHHHHTS---SSEEHHHHHHHHHHHSCCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHHcC---CCCCHHHHHHHHhhcCCccHHHHHHHHHHHHHCCCeEEEe
Confidence            456677888764   5899999999997311117889999999999999999864

>3lkd_A Type I restriction-modification system methyltransferase subunit; Q5M500_STRT2, STU0711, NESG, SUR80, structural genomics, PSI-2; 2.25A {Streptococcus thermophilus}

Probab=93.90  E-value=0.045  Score=49.47  Aligned_cols=65  Identities=15%  Similarity=-0.003  Sum_probs=49.2

Q ss_pred             CcceEEEecCCccHHHHHHHHHc---CCCcEEEeech-HHHhhccCC--------CCceEEecCcCC-CCC---C--CCE
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNY---LHIKGVNFDLS-HVIQDSSSY--------SGVKHIGGIMLE-RIP---K--GDA  229 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~---P~l~~~v~Dlp-~v~~~a~~~--------~ri~~~~gD~f~-~~P---~--~D~  229 (233)
                      ...+|+|.+||+|.++.++.+..   +..++.++|+. .++..|+.+        +++.+..+|.+. .+|   .  .|+
T Consensus       221 ~~~~VlDPaCGSG~fLi~a~~~l~~~~~~~i~G~Eid~~~~~lA~~Nl~l~gi~~~~~~I~~gDtL~~d~p~~~~~~fD~  300 (542)
T 3lkd_A          221 QGFTLYDATMGSGSLLLNAKRYSRQPQTVVYFGQELNTSTYNLARMNMILHGVPIENQFLHNADTLDEDWPTQEPTNFDG  300 (542)
T ss_dssp             TTCEEEETTCTTSTTGGGHHHHCSCTTTCEEEEEESCHHHHHHHHHHHHHTTCCGGGEEEEESCTTTSCSCCSSCCCBSE
T ss_pred             CCCEEeecccchhHHHHHHHHHHHhccCceEEEEECcHHHHHHHHHHHHHcCCCcCccceEecceecccccccccccccE
Confidence            45699999999999999998874   46778999985 466666542        467899999997 333   2  388


Q ss_pred             EEe
Q 039903          230 ILI  232 (233)
Q Consensus       230 ~~l  232 (233)
                      |+.
T Consensus       301 Iva  303 (542)
T 3lkd_A          301 VLM  303 (542)
T ss_dssp             EEE
T ss_pred             EEe
Confidence            874

>2dbb_A Putative HTH-type transcriptional regulator PH006; ASNC family, helix-turn-helix (HTH) domain, structural genom NPPSFA; 2.00A {Pyrococcus horikoshii}

Probab=93.84  E-value=0.064  Score=39.62  Aligned_cols=47  Identities=13%  Similarity=0.260  Sum_probs=42.1

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      .+..|.+.|...   ++.|..|||+++|+    ++..+.+.++.|...|++.+.
T Consensus        10 ~d~~il~~L~~~---~~~s~~ela~~lg~----s~~tv~~~l~~L~~~G~i~~~   56 (151)
T 2dbb_A           10 VDMQLVKILSEN---SRLTYRELADILNT----TRQRIARRIDKLKKLGIIRKF   56 (151)
T ss_dssp             HHHHHHHHHHHC---TTCCHHHHHHHTTS----CHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEE
Confidence            456788888886   58999999999999    999999999999999999864

>4fx0_A Probable transcriptional repressor protein; helix-turn-helix, DNA binding, transcription regulator; 2.70A {Mycobacterium tuberculosis} PDB: 4fx4_A*

Probab=93.77  E-value=0.053  Score=40.04  Aligned_cols=67  Identities=15%  Similarity=0.231  Sum_probs=42.5

Q ss_pred             hhHHHHhcC--CCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC-CCCceeccHhhhHhhcC
Q 039903           21 VFEIIAKAG--PTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD-DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        21 lfd~L~~~~--~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~-~~~~y~lt~~s~~l~~~   91 (233)
                      +...|...+  ..+++|..|||+.+++    ++..+.++++.|...|+++....++ ..-...+|+.|+.+...
T Consensus        38 vL~~l~~~~~~~~~~~t~~eLa~~l~~----~~~tvsr~v~~Le~~glVr~~~~~DrR~~~v~LT~~G~~~~~~  107 (148)
T 4fx0_A           38 TLAVISLSEGSAGIDLTMSELAARIGV----ERTTLTRNLEVMRRDGLVRVMAGADARCKRIELTAKGRAALQK  107 (148)
T ss_dssp             HHHHHHC---------CHHHHHHHHTC----CHHHHHHHHHHHHHTTSBC-----------CCBCHHHHHHHHH
T ss_pred             HHHHHHHhcCCCCCCcCHHHHHHHHCC----ChhhHHHHHHHHHHCCCEEeeCCCCCCeeEEEECHHHHHHHHH
Confidence            445555432  1246899999999999    9999999999999999996542211 11256788888876644

>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=93.70  E-value=0.073  Score=45.50  Aligned_cols=65  Identities=17%  Similarity=0.164  Sum_probs=42.3

Q ss_pred             cCcceEEEecCCccHHHHH--------HHHH--------cCCCcEEEeechHH----H-hhccC---CCC---ceEEecC
Q 039903          167 EQIKQLVDVGGGLGVNVNI--------IISN--------YLHIKGVNFDLSHV----I-QDSSS---YSG---VKHIGGI  219 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~--------l~~~--------~P~l~~~v~Dlp~v----~-~~a~~---~~r---i~~~~gD  219 (233)
                      ++.-+|+|+||++|..+..        +.++        .|.+++..-|||..    + .....   ..+   +.-++|.
T Consensus        50 ~~~~~IaDlGCs~G~Nt~~~v~~ii~~i~~~~~~~~~~~~pe~~v~~nDLp~NDFntlF~~L~~~~~~~~~~f~~gvpgS  129 (359)
T 1m6e_X           50 TTRLAIADLGCSSGPNALFAVTELIKTVEELRKKMGRENSPEYQIFLNDLPGNDFNAIFRSLPIENDVDGVCFINGVPGS  129 (359)
T ss_dssp             SSEECCEEESCCSSTTTTTGGGTTHHHHHHHHHSSSCSSCCEEEEEEEECTTSCHHHHHTTTTTSCSCTTCEEEEEEESC
T ss_pred             CCceEEEecCCCCCcchHHHHHHHHHHHHHHHHhcCCCCCCceEEEecCCCchHHHHHHHhcchhcccCCCEEEEecchh
Confidence            4567899999999975543        3332        57788888899942    2 11111   012   5667899


Q ss_pred             cCC-CCCCC--CEEE
Q 039903          220 MLE-RIPKG--DAIL  231 (233)
Q Consensus       220 ~f~-~~P~~--D~~~  231 (233)
                      |+. .+|..  |+++
T Consensus       130 Fy~rlfp~~S~d~v~  144 (359)
T 1m6e_X          130 FYGRLFPRNTLHFIH  144 (359)
T ss_dssp             SSSCCSCTTCBSCEE
T ss_pred             hhhccCCCCceEEEE
Confidence            998 78875  7664

>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=93.70  E-value=0.088  Score=49.65  Aligned_cols=67  Identities=7%  Similarity=0.000  Sum_probs=46.5

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcC---CCcEEEeech-HHHhhc--cC--------C--CCceEEecCcCCC--CCC-
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYL---HIKGVNFDLS-HVIQDS--SS--------Y--SGVKHIGGIMLER--IPK-  226 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P---~l~~~v~Dlp-~v~~~a--~~--------~--~ri~~~~gD~f~~--~P~-  226 (233)
                      +....+|+|.|||+|.++.+++++.+   ..++..+|+. .+++.|  +.        +  +.+.+...|++.+  .+. 
T Consensus       319 l~~g~rVLDPaCGSG~FLIaaA~~l~ei~~~~IyGvEIDp~Al~LAK~RlNL~lN~LlhGi~~~~I~~dD~L~~~~~~~~  398 (878)
T 3s1s_A          319 LTEDEVISDPAAGSGNLLATVSAGFNNVMPRQIWANDIETLFLELLSIRLGLLFPQLVSSNNAPTITGEDVCSLNPEDFA  398 (878)
T ss_dssp             CCTTCEEEETTCTTSHHHHHHHHTSTTCCGGGEEEECSCGGGHHHHHHHHHTTSTTTCBTTBCCEEECCCGGGCCGGGGT
T ss_pred             CCCCCEEEECCCCccHHHHHHHHHhcccCCCeEEEEECCHHHHHHHHHHHHHHHhhhhcCCCcceEEecchhcccccccC
Confidence            34567999999999999999999887   3578999984 466655  21        1  2345666777762  222 


Q ss_pred             -CCEEEe
Q 039903          227 -GDAILI  232 (233)
Q Consensus       227 -~D~~~l  232 (233)
                       .|+|+.
T Consensus       399 kFDVVIg  405 (878)
T 3s1s_A          399 NVSVVVM  405 (878)
T ss_dssp             TEEEEEE
T ss_pred             CCCEEEE
Confidence             288764

>3elk_A Putative transcriptional regulator TA0346; structural genomics, PSI-2, prote structure initiative; 1.70A {Thermoplasma acidophilum}

Probab=93.52  E-value=0.057  Score=38.43  Aligned_cols=76  Identities=12%  Similarity=0.174  Sum_probs=59.2

Q ss_pred             hHHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCC------CCCCCChhhHHHHHHHHhcCCceeeecc-C--C-CCC
Q 039903            8 VLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMP------SSNPNAAVMLDRILRLLVTHRVLRCTSA-G--D-DQR   77 (233)
Q Consensus         8 ~~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~------~~~~~~~~~l~rlL~~L~~~gll~~~~~-~--~-~~~   77 (233)
                      +.++.+.-..++-|...|..    +|.+--||++.++      +    ++..+++.|+-|...|+++.... .  + ...
T Consensus         6 ~~~~l~~g~l~~~IL~lL~~----~p~~gyel~~~l~~~~~~~i----~~gtly~~L~~Le~~GlI~~~~~~~~~~~~rk   77 (117)
T 3elk_A            6 TRERILHGLITLYILKELVK----RPMHGYELQKSMFETTGQAL----PQGSIYILLKTMKERGFVISESSVNEKGQQLT   77 (117)
T ss_dssp             -CCHHHHHHHHHHHHHHHHH----SCEEHHHHHHHHHHHHSCCC----CTTHHHHHHHHHHHHTSEEEEEEEC-CCCEEE
T ss_pred             HHHHHHhhHHHHHHHHHHHc----CCCCHHHHHHHHHHHhCCCC----CcchHHHHHHHHHHCCCEEEEeeecCCCCCce
Confidence            34566677778888889987    6899999999887      7    88999999999999999997532 1  0 123


Q ss_pred             ceeccHhhhHhhcC
Q 039903           78 LYGLAHVAKYFVLN   91 (233)
Q Consensus        78 ~y~lt~~s~~l~~~   91 (233)
                      .|++|+.|+..+..
T Consensus        78 ~Y~lT~~G~~~l~~   91 (117)
T 3elk_A           78 VYHITDAGKKFLCD   91 (117)
T ss_dssp             EEEECHHHHHHHHH
T ss_pred             EEEECHHHHHHHHH
Confidence            79999999976644

>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=93.51  E-value=0.078  Score=41.18  Aligned_cols=54  Identities=4%  Similarity=0.143  Sum_probs=47.1

Q ss_pred             HHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903            9 LPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus         9 ~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      ...++....+..|...|.+    ++.|..|||+.+|+    ++..+.+.++.|...|++...
T Consensus        13 ~~k~l~d~~~~~IL~~L~~----~~~s~~eLA~~lgl----S~stv~~~l~~Le~~GlI~~~   66 (192)
T 1uly_A           13 VIKVMLEDTRRKILKLLRN----KEMTISQLSEILGK----TPQTIYHHIEKLKEAGLVEVK   66 (192)
T ss_dssp             HHHHHHSHHHHHHHHHHTT----CCBCHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHhCCHHHHHHHHHHHc----CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEE
Confidence            3455566678889999984    58999999999999    999999999999999999875

>2ia0_A Putative HTH-type transcriptional regulator PF086; ASNC, PSI, structural genomics, southeast collaboratory for structural genomics; 2.37A {Pyrococcus furiosus}

Probab=93.49  E-value=0.078  Score=40.30  Aligned_cols=47  Identities=13%  Similarity=0.262  Sum_probs=42.0

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      .+..|.+.|...   ++.|..|||+++|+    ++..+.+.++.|...|++.+.
T Consensus        18 ~d~~IL~~L~~~---~~~s~~eLA~~lgl----S~~tv~~~l~~L~~~G~I~~~   64 (171)
T 2ia0_A           18 LDRNILRLLKKD---ARLTISELSEQLKK----PESTIHFRIKKLQERGVIERY   64 (171)
T ss_dssp             HHHHHHHHHHHC---TTCCHHHHHHHHTS----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEee
Confidence            456788889886   58999999999999    999999999999999999863

>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=93.47  E-value=0.17  Score=35.85  Aligned_cols=75  Identities=11%  Similarity=0.146  Sum_probs=58.4

Q ss_pred             HHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhC--------CCCCCCChhhHHHHHHHHhcCCceeeecc---CC-CC
Q 039903            9 LPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQM--------PSSNPNAAVMLDRILRLLVTHRVLRCTSA---GD-DQ   76 (233)
Q Consensus         9 ~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~--------~~~~~~~~~~l~rlL~~L~~~gll~~~~~---~~-~~   76 (233)
                      .++.++-..++=|...|.+    +|.+--||++.+        ++    ++..+++.|+-|...|+++....   ++ ..
T Consensus         5 ~~~~~~g~l~~~IL~~L~~----~~~~Gyei~~~l~~~~~~~~~i----~~gtly~~L~rLe~~GlI~~~~~~~~~~~~r   76 (116)
T 3f8b_A            5 PKEMLRAQTNVILLNVLKQ----GDNYVYGIIKQVKEASNGEMEL----NEATLYTIFKRLEKDGIISSYWGDESQGGRR   76 (116)
T ss_dssp             CHHHHHHHHHHHHHHHHHH----CCBCHHHHHHHHHHHTTTCCCC----CHHHHHHHHHHHHHTTSEEEEEEC----CCE
T ss_pred             HHHHHhchHHHHHHHHHHh----CCCCHHHHHHHHHHHhCCCCCC----CcchHHHHHHHHHHCCCEEEEeeccCCCCCc
Confidence            4566677778888888887    689999999887        57    99999999999999999997531   11 12


Q ss_pred             CceeccHhhhHhhcC
Q 039903           77 RLYGLAHVAKYFVLN   91 (233)
Q Consensus        77 ~~y~lt~~s~~l~~~   91 (233)
                      ..|++|+.|+..+..
T Consensus        77 k~Y~LT~~G~~~l~~   91 (116)
T 3f8b_A           77 KYYRLTEIGHENMRL   91 (116)
T ss_dssp             EEEEECHHHHHHHHH
T ss_pred             eEEEECHHHHHHHHH
Confidence            369999999876644

>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=93.33  E-value=0.055  Score=40.05  Aligned_cols=47  Identities=17%  Similarity=0.174  Sum_probs=41.9

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      .+..|.+.|...   ++.|..|||+++|+    ++..+.+.++.|...|++.+.
T Consensus         8 ~~~~il~~L~~~---~~~s~~ela~~lg~----s~~tv~~~l~~L~~~G~i~~~   54 (151)
T 2cyy_A            8 IDKKIIKILQND---GKAPLREISKITGL----AESTIHERIRKLRESGVIKKF   54 (151)
T ss_dssp             HHHHHHHHHHHC---TTCCHHHHHHHHCS----CHHHHHHHHHHHHHHTSSCCC
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCeEEE
Confidence            456788888876   58999999999999    999999999999999999864

>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=93.32  E-value=0.065  Score=39.66  Aligned_cols=47  Identities=13%  Similarity=0.205  Sum_probs=41.9

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      .+..|.+.|.+.   ++.|..|||+++|+    ++..+.+.++.|...|++...
T Consensus         9 ~d~~il~~L~~~---~~~s~~ela~~lg~----s~~tv~~~l~~L~~~G~i~~~   55 (152)
T 2cg4_A            9 LDRGILEALMGN---ARTAYAELAKQFGV----SPETIHVRVEKMKQAGIITGA   55 (152)
T ss_dssp             HHHHHHHHHHHC---TTSCHHHHHHHHTS----CHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHCc----CHHHHHHHHHHHHHcCCcceE
Confidence            355688888886   58999999999999    999999999999999999874

>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=93.30  E-value=0.063  Score=44.17  Aligned_cols=43  Identities=21%  Similarity=0.117  Sum_probs=33.2

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS  201 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp  201 (233)
                      ++.+.+. +....+|||+|||.|.++...+++.|-.+++.+|+-
T Consensus        81 ei~eK~~-Lk~~~~VLDLGaAPGGWsQvAa~~~gv~sV~GvdvG  123 (282)
T 3gcz_A           81 WMEERGY-VKPTGIVVDLGCGRGGWSYYAASLKNVKKVMAFTLG  123 (282)
T ss_dssp             HHHHTTS-CCCCEEEEEETCTTCHHHHHHHTSTTEEEEEEECCC
T ss_pred             HHHHhcC-CCCCCEEEEeCCCCCHHHHHHHHhcCCCeeeeEEec
Confidence            4445553 666789999999999999999987776666667763

>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=93.28  E-value=0.081  Score=42.13  Aligned_cols=48  Identities=13%  Similarity=0.232  Sum_probs=42.7

Q ss_pred             CHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhc
Q 039903           35 SAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVL   90 (233)
Q Consensus        35 t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~   90 (233)
                      +..+||+.+++    +...+.++++-|...|++++.    .+..+.+|+.+..+..
T Consensus        26 ~~~~La~~l~v----s~~tvs~~l~~Le~~GlV~r~----~~~~v~LT~~G~~~~~   73 (230)
T 1fx7_A           26 LRARIAERLDQ----SGPTVSQTVSRMERDGLLRVA----GDRHLELTEKGRALAI   73 (230)
T ss_dssp             CHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEC----TTSCEEECHHHHHHHH
T ss_pred             cHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEe----CCccEEECHHHHHHHH
Confidence            44999999999    999999999999999999997    4578999999987654

>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=93.24  E-value=0.075  Score=36.36  Aligned_cols=35  Identities=17%  Similarity=0.220  Sum_probs=33.6

Q ss_pred             CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      ++.|..|||+.+++    +...+.|.|+.|...|++++.
T Consensus        35 ~~~t~~ela~~l~i----s~~tv~~~l~~L~~~g~v~~~   69 (109)
T 2d1h_A           35 KPITSEELADIFKL----SKTTVENSLKKLIELGLVVRT   69 (109)
T ss_dssp             SCEEHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCeEee
Confidence            58999999999999    999999999999999999986

>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=93.22  E-value=0.16  Score=35.96  Aligned_cols=75  Identities=15%  Similarity=0.114  Sum_probs=58.3

Q ss_pred             HHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhC------CCCCCCChhhHHHHHHHHhcCCceeeeccCC----CCCc
Q 039903            9 LPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQM------PSSNPNAAVMLDRILRLLVTHRVLRCTSAGD----DQRL   78 (233)
Q Consensus         9 ~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~------~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~----~~~~   78 (233)
                      .++.++-..++=|...|.+    +|.+--||++.+      ++    ++..++..|+-|...|+++......    ....
T Consensus         6 ~~~l~~g~l~~~IL~lL~~----~p~~Gyei~~~l~~~g~~~i----s~gtlY~~L~rLe~~GlI~~~~~~~~~g~~rk~   77 (116)
T 3hhh_A            6 QTELLKGILEGLVLAIIQR----KETYGYEITKILNDQGFTEI----VEGTVYTILLRLEKNQWVIAEKKPSEKGPMRKF   77 (116)
T ss_dssp             HHHHHTTHHHHHHHHHHHH----SCBCHHHHHHHHHTTSCSSC----CHHHHHHHHHHHHHTTSEEEEEEECC--CEEEE
T ss_pred             HHHHHhhhHHHHHHHHHhc----CCCCHHHHHHHHHHcCCCCC----CccHHHHHHHHHHHCCCEEEEeeecCCCCCceE
Confidence            3566666677778888887    689999999997      57    9999999999999999998753210    1236


Q ss_pred             eeccHhhhHhhcC
Q 039903           79 YGLAHVAKYFVLN   91 (233)
Q Consensus        79 y~lt~~s~~l~~~   91 (233)
                      |++|+.|+..+..
T Consensus        78 Y~lT~~G~~~l~~   90 (116)
T 3hhh_A           78 YRLTSSGEAELAD   90 (116)
T ss_dssp             EEECHHHHHHHHH
T ss_pred             EEECHHHHHHHHH
Confidence            9999999876644

>2qy6_A UPF0209 protein YFCK; structural genomics, unknown function, PSI-2, protein struct initiative; 2.00A {Escherichia coli}

Probab=93.11  E-value=0.038  Score=45.05  Aligned_cols=33  Identities=15%  Similarity=0.246  Sum_probs=26.9

Q ss_pred             CcceEEEecCCccHHHHHHHHH-------cCC-----CcEEEeec
Q 039903          168 QIKQLVDVGGGLGVNVNIIISN-------YLH-----IKGVNFDL  200 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~-------~P~-----l~~~v~Dl  200 (233)
                      +..+|++||.|+|..+..+++.       +|+     ++++.+|.
T Consensus        60 ~~~~ILEiGfGtG~n~l~~~~~~~~~~~~~p~~~~~~l~~isiE~  104 (257)
T 2qy6_A           60 PLFVVAESGFGTGLNFLTLWQAFDQFREAHPQAQLQRLHFISFEK  104 (257)
T ss_dssp             SEEEEEESCCTTSHHHHHHHHHHHHHHHHCTTSSCCEEEEEEEES
T ss_pred             CCCEEEEECCChHHHHHHHHHHHHhhhhhCCCCCcceeEEEEEEC
Confidence            4579999999999988887665       684     68888886

>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=93.06  E-value=0.094  Score=35.60  Aligned_cols=48  Identities=21%  Similarity=0.345  Sum_probs=40.8

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      ++.|+..|.+.+. .+++..|||+++++    +..-+.++|+.|...|++.+.
T Consensus        22 q~~Vl~~I~~~g~-~gi~qkeLa~~~~l----~~~tvt~iLk~LE~kglIkr~   69 (91)
T 2dk5_A           22 EKLVYQIIEDAGN-KGIWSRDVRYKSNL----PLTEINKILKNLESKKLIKAV   69 (91)
T ss_dssp             HHHHHHHHHHHCT-TCEEHHHHHHHTTC----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHcCC-CCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEe
Confidence            4557788887421 37999999999999    999999999999999999954

>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=92.93  E-value=0.069  Score=38.83  Aligned_cols=46  Identities=17%  Similarity=0.270  Sum_probs=40.5

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      +..|...|...   ++.|..|||+.+|+    ++..+.+.++.|...|++.+.
T Consensus         6 ~~~il~~L~~~---~~~~~~ela~~lg~----s~~tv~~~l~~L~~~G~i~~~   51 (141)
T 1i1g_A            6 DKIILEILEKD---ARTPFTEIAKKLGI----SETAVRKRVKALEEKGIIEGY   51 (141)
T ss_dssp             HHHHHHHHHHC---TTCCHHHHHHHHTS----CHHHHHHHHHHHHHHTSSCCC
T ss_pred             HHHHHHHHHHc---CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEecc
Confidence            45677888775   58999999999999    999999999999999999863

>3l7w_A Putative uncharacterized protein SMU.1704; PADR, transcriptional factor, transcription; HET: MSE; 2.20A {Streptococcus mutans} SCOP: a.4.5.0

Probab=92.92  E-value=0.058  Score=37.72  Aligned_cols=70  Identities=16%  Similarity=0.175  Sum_probs=51.5

Q ss_pred             HHHHhhChhHHHHhcCCCCCCCHHHHHHh----CCCCCCCChhhHHHHHHHHhcCCceeeeccC--C-CCCceeccHhhh
Q 039903           14 QAASELGVFEIIAKAGPTAKISAVEIAAQ----MPSSNPNAAVMLDRILRLLVTHRVLRCTSAG--D-DQRLYGLAHVAK   86 (233)
Q Consensus        14 ~~a~~lglfd~L~~~~~~~~~t~~elA~~----~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~--~-~~~~y~lt~~s~   86 (233)
                      .-..++-|...|..    +|.+-.+|++.    +++    ++..+.++|+-|...|+++.....  + ....|++|+.|+
T Consensus         7 ~g~l~~~IL~~L~~----~~~~gyel~~~l~~~~~i----~~~tly~~L~~Le~~GlI~~~~~~~~~r~r~~y~LT~~G~   78 (108)
T 3l7w_A            7 ALLIEYLILAIVSK----HDSYGYDISQTIKLIASI----KESTLYPILKKLEKAGYLSTYTQEHQGRRRKYYHLTDSGE   78 (108)
T ss_dssp             HHHHHHHHHHHHHH----SCEEHHHHHHHHTTTCCC----CHHHHHHHHHHHHHTTSEEEEEEEETTEEEEEEEECHHHH
T ss_pred             HHHHHHHHHHHHHc----CCCcHHHHHHHHHHHhCC----CcChHHHHHHHHHHCCCeEEEeecCCCCcceEEEECHHHH
Confidence            34455666777776    57887777777    578    999999999999999999976321  0 012599999998


Q ss_pred             HhhcC
Q 039903           87 YFVLN   91 (233)
Q Consensus        87 ~l~~~   91 (233)
                      .....
T Consensus        79 ~~l~~   83 (108)
T 3l7w_A           79 KHLVY   83 (108)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            76643

>3i4p_A Transcriptional regulator, ASNC family; PSI, structural genom protein structure initiative, midwest center for structural genomics; 2.30A {Agrobacterium tumefaciens str}

Probab=92.81  E-value=0.083  Score=39.66  Aligned_cols=47  Identities=11%  Similarity=0.203  Sum_probs=42.0

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      .+..|.+.|.+.   +++|..+||+++|+    ++..+.+-++.|...|++...
T Consensus         4 ~d~~il~~L~~~---~~~s~~~la~~lg~----s~~tv~~rl~~L~~~g~i~~~   50 (162)
T 3i4p_A            4 LDRKILRILQED---STLAVADLAKKVGL----STTPCWRRIQKMEEDGVIRRR   50 (162)
T ss_dssp             HHHHHHHHHTTC---SCSCHHHHHHHHTC----CHHHHHHHHHHHHHTTSSCCC
T ss_pred             HHHHHHHHHHHC---CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCeeec
Confidence            456788889886   59999999999999    999999999999999999863

>2p8t_A Hypothetical protein PH0730; pyrococcus horikoshii OT3, STR genomics, PSI, protein structure initiative; 1.80A {Pyrococcus horikoshii} SCOP: a.4.5.72 d.74.4.2

Probab=92.76  E-value=0.12  Score=40.37  Aligned_cols=49  Identities=16%  Similarity=0.148  Sum_probs=43.2

Q ss_pred             CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhh
Q 039903           32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFV   89 (233)
Q Consensus        32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~   89 (233)
                      +|++..+||+.+++    ++..++..++.|...|+++..    . +...+|+.|+.++
T Consensus        29 ~~V~~~~LA~~Lgv----S~~SV~~~lkkL~e~GLV~~~----~-~Gv~LTe~G~~~A   77 (200)
T 2p8t_A           29 EPLGRKQISERLEL----GEGSVRTLLRKLSHLDIIRSK----Q-RGHFLTLKGKEIR   77 (200)
T ss_dssp             SCBCHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEC-------CEEECHHHHHHH
T ss_pred             CCccHHHHHHHhCC----CHHHHHHHHHHHHHCCCEEEe----C-CCeEECHHHHHHH
Confidence            48999999999999    999999999999999999996    4 7889999997554

>2qq9_A Diphtheria toxin repressor; regulator, DTXR, helix-turn-helix, metal ION, ACT DNA-binding, ferrous iron, transcription; 1.71A {Corynebacterium diphtheriae} PDB: 2tdx_A 1ddn_A 1g3t_A 1g3s_A 1g3w_A 2qqa_A 2qqb_A 2dtr_A 1bi0_A 1bi2_A 1bi3_A 1dpr_A 1bi1_A 1fwz_A 1g3y_A 1c0w_A* 3glx_A 1p92_A 1xcv_A 1f5t_A ...

Probab=92.73  E-value=0.17  Score=40.20  Aligned_cols=51  Identities=6%  Similarity=0.110  Sum_probs=44.0

Q ss_pred             CCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhcC
Q 039903           33 KISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        33 ~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~~   91 (233)
                      +.+..+||+.+++    ++..+.++++-|...|++++.    .+..+.+|+.|+.+...
T Consensus        24 ~~~~~~la~~l~v----s~~tvs~~l~~Le~~GlV~r~----~~~~v~LT~~G~~~~~~   74 (226)
T 2qq9_A           24 TPLRARIAERLEQ----SGPTVSQTVARMERDGLVVVA----SDRSLQMTPTGRTLATA   74 (226)
T ss_dssp             CCBHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEC----TTSBEEECHHHHHHHHH
T ss_pred             CccHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEe----CCCCeEECHHHHHHHHH
Confidence            3456999999999    999999999999999999996    46779999999876543

>2v79_A DNA replication protein DNAD; primosome, DNA-binding protein; HET: DNA; 2.00A {Bacillus subtilis}

Probab=92.72  E-value=0.14  Score=37.38  Aligned_cols=52  Identities=13%  Similarity=0.142  Sum_probs=40.6

Q ss_pred             CCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCC----CceeccHhhhHh
Q 039903           33 KISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQ----RLYGLAHVAKYF   88 (233)
Q Consensus        33 ~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~----~~y~lt~~s~~l   88 (233)
                      ..|.++||+.+++    ++..+.++++.|...|+++.....+++    ..|.++|+-..|
T Consensus        51 ~ps~~~LA~~~~~----s~~~v~~~L~~L~~KGlI~i~~~~d~~g~~~~~ydL~pL~ekL  106 (135)
T 2v79_A           51 FPTPNQLQEGMSI----SVEECTNRLRMFIQKGFLFIEECEDQNGIKFEKYSLQPLWGKL  106 (135)
T ss_dssp             SCCHHHHHTTSSS----CHHHHHHHHHHHHHHTSCEEEEEECTTCCEEEEEECHHHHHHH
T ss_pred             CCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEEeEecCCCceEEEeeHHHHHHHH
Confidence            5799999999999    999999999999999999984221112    467777755443

>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=92.65  E-value=0.12  Score=40.13  Aligned_cols=41  Identities=22%  Similarity=0.061  Sum_probs=35.5

Q ss_pred             HHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           24 IIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        24 ~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      .+.+.|  .|.|..|||+.+|+    +...+.+.|+.|...|++.+.
T Consensus        17 ~~~~~g--~~~s~~eia~~lgl----~~~tv~~~l~~Le~~G~i~~~   57 (196)
T 3k2z_A           17 FIEKNG--YPPSVREIARRFRI----TPRGALLHLIALEKKGYIERK   57 (196)
T ss_dssp             HHHHHS--SCCCHHHHHHHHTS----CHHHHHHHHHHHHHTTSEECC
T ss_pred             HHHHhC--CCCCHHHHHHHcCC----CcHHHHHHHHHHHHCCCEEec
Confidence            344444  48999999999999    888999999999999999985

>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=92.61  E-value=0.13  Score=41.69  Aligned_cols=68  Identities=10%  Similarity=0.072  Sum_probs=51.9

Q ss_pred             hChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           19 LGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        19 lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      ..|...|...+. ++.|..|||+.+++    ++..+.++++-|...|++++.....  ..-...+|+.|..+...
T Consensus       161 ~~vL~~L~~~~~-~~~t~~eLa~~l~i----~~~tvt~~v~rLe~~GlV~R~~~~~DrR~~~i~LT~~G~~~~~~  230 (250)
T 1p4x_A          161 FTILAIITSQNK-NIVLLKDLIETIHH----KYPQTVRALNNLKKQGYLIKERSTEDERKILIHMDDAQQDHAEQ  230 (250)
T ss_dssp             HHHHHHHHTTTT-CCEEHHHHHHHSSS----CHHHHHHHHHHHHHHTSSEEEECSSSTTCEEEECCHHHHHHHHH
T ss_pred             HHHHHHHHhCCC-CCcCHHHHHHHHCC----ChhhHHHHHHHHHHCCCEEeeCCCCCCCeEEEEECHHHHHHHHH
Confidence            346666766531 25999999999999    9999999999999999999875431  12256789988876643

>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=92.57  E-value=0.15  Score=39.26  Aligned_cols=58  Identities=16%  Similarity=0.218  Sum_probs=47.0

Q ss_pred             HHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCc-eeeeccCCCCCceeccH
Q 039903           15 AASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRV-LRCTSAGDDQRLYGLAH   83 (233)
Q Consensus        15 ~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gl-l~~~~~~~~~~~y~lt~   83 (233)
                      .-....|.+.|.+.+  +++|..|||+++++    +.+.++|=++.|...|+ +...     .+.|.+++
T Consensus        20 ~~R~~~Il~~L~~~~--~~~s~~eLa~~l~v----S~~Ti~rdi~~L~~~G~~I~~~-----~~Gy~l~~   78 (187)
T 1j5y_A           20 QERLKSIVRILERSK--EPVSGAQLAEELSV----SRQVIVQDIAYLRSLGYNIVAT-----PRGYVLAG   78 (187)
T ss_dssp             HHHHHHHHHHHHHCS--SCBCHHHHHHHHTS----CHHHHHHHHHHHHHHTCCCEEE-----TTEEECCT
T ss_pred             HHHHHHHHHHHHHcC--CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCeEEEE-----CCEEEECC
Confidence            345667899998653  47999999999999    99999999999999999 7653     35576664

>2xvc_A ESCRT-III, SSO0910; cell cycle, cell division, cytokinesis, winged-helix; 2.15A {Sulfolobus solfataricus}

Probab=92.34  E-value=0.12  Score=31.52  Aligned_cols=46  Identities=11%  Similarity=0.171  Sum_probs=41.4

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceee
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRC   69 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~   69 (233)
                      +-.|.+.|..+|  |=+.++.+|++.|+    +.+.+..+|+-|...|++.-
T Consensus        12 e~~lL~yIr~sG--GildI~~~a~kygV----~kdeV~~~LrrLe~KGLI~l   57 (59)
T 2xvc_A           12 ERELLDYIVNNG--GFLDIEHFSKVYGV----EKQEVVKLLEALKNKGLIAV   57 (59)
T ss_dssp             HHHHHHHHHHTT--SEEEHHHHHHHHCC----CHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHcC--CEEeHHHHHHHhCC----CHHHHHHHHHHHHHCCCeec
Confidence            445788999987  78899999999999    99999999999999999875

>3lkz_A Non-structural protein 5; flavivirus, methyltransferase, inhibitor, P nucleotide-binding, RNA replication, viral protein; HET: SFG; 2.00A {West nile virus}

Probab=92.30  E-value=0.18  Score=41.79  Aligned_cols=73  Identities=16%  Similarity=0.209  Sum_probs=48.1

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhh----ccCC--CCceEEec-CcCCCCCC-CCE
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQD----SSSY--SGVKHIGG-IMLERIPK-GDA  229 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~----a~~~--~ri~~~~g-D~f~~~P~-~D~  229 (233)
                      .+.+.+. +.....+||+||+.|.++.-.+....--++..+|+-..-..    .+..  .-|.++.+ |++.--|. .|+
T Consensus        85 ei~~~~~-l~~~~~VlDLGaapGGwsq~~~~~~gv~~V~avdvG~~~he~P~~~~ql~w~lV~~~~~~Dv~~l~~~~~D~  163 (321)
T 3lkz_A           85 WLVERRF-LEPVGKVIDLGCGRGGWCYYMATQKRVQEVRGYTKGGPGHEEPQLVQSYGWNIVTMKSGVDVFYRPSECCDT  163 (321)
T ss_dssp             HHHHTTS-CCCCEEEEEETCTTCHHHHHHTTCTTEEEEEEECCCSTTSCCCCCCCBTTGGGEEEECSCCTTSSCCCCCSE
T ss_pred             HHHHhcC-CCCCCEEEEeCCCCCcHHHHHHhhcCCCEEEEEEcCCCCccCcchhhhcCCcceEEEeccCHhhCCCCCCCE
Confidence            3444444 66667999999999999997777766557888997533111    0111  34888988 97762222 577


Q ss_pred             EE
Q 039903          230 IL  231 (233)
Q Consensus       230 ~~  231 (233)
                      ++
T Consensus       164 iv  165 (321)
T 3lkz_A          164 LL  165 (321)
T ss_dssp             EE
T ss_pred             EE
Confidence            65

>1xma_A Predicted transcriptional regulator; southea collaboratory for structural genomics, secsg, protein struc initiative, PSI; 2.30A {Clostridium thermocellum} SCOP: a.4.5.61

Probab=92.10  E-value=0.12  Score=38.22  Aligned_cols=70  Identities=7%  Similarity=0.097  Sum_probs=53.4

Q ss_pred             HHHHhhChhHHHHhcCCCCCCCHHHHHHhC--------CCCCCCChhhHHHHHHHHhcCCceeeeccC---C-CCCceec
Q 039903           14 QAASELGVFEIIAKAGPTAKISAVEIAAQM--------PSSNPNAAVMLDRILRLLVTHRVLRCTSAG---D-DQRLYGL   81 (233)
Q Consensus        14 ~~a~~lglfd~L~~~~~~~~~t~~elA~~~--------~~~~~~~~~~l~rlL~~L~~~gll~~~~~~---~-~~~~y~l   81 (233)
                      ..-.++-|...|..    +|.+..||++.+        ++    ++..+.+.|+-|...|+++.....   + ..-.|++
T Consensus        39 ~g~~~~~IL~~L~~----~~~~gyeI~~~l~~~~~~~~~i----s~gtLy~~L~rLE~~GlI~~~~~~~~~~~~rk~Y~L  110 (145)
T 1xma_A           39 RGYVDTIILSLLIE----GDSYGYEISKNIRIKTDELYVI----KETTLYSAFARLEKNGYIKSYYGEETQGKRRTYYRI  110 (145)
T ss_dssp             GGTHHHHHHHHHHH----CCEEHHHHHHHHHHHHTTSCCC----CHHHHHHHHHHHHHTTSEEEEEEEEC--CEEEEEEE
T ss_pred             cCcHHHHHHHHHHh----CCCCHHHHHHHHHHhhCCccCc----ChhHHHHHHHHHHHCCCEEEEEeccCCCCCeEEEEE
Confidence            33456667777876    589999998887        57    999999999999999999875321   0 1246999


Q ss_pred             cHhhhHhhcC
Q 039903           82 AHVAKYFVLN   91 (233)
Q Consensus        82 t~~s~~l~~~   91 (233)
                      |+.|+.++..
T Consensus       111 T~~G~~~l~~  120 (145)
T 1xma_A          111 TPEGIKYYKQ  120 (145)
T ss_dssp             CHHHHHHHHH
T ss_pred             CHHHHHHHHH
Confidence            9999876643

>1mzb_A Ferric uptake regulation protein; ferric uptake regulator, iron, DTXR, gene regulation; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.42

Probab=92.01  E-value=0.15  Score=37.16  Aligned_cols=60  Identities=10%  Similarity=0.222  Sum_probs=45.8

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhC-----CCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceec
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQM-----PSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGL   81 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~-----~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~l   81 (233)
                      -+.-|++.|...+ +++.|++||.+.+     ++    +..-++|-|+.|+..|++.+...+++..+|.+
T Consensus        19 qR~~Il~~L~~~~-~~~~sa~ei~~~l~~~~~~i----s~aTVYR~L~~L~e~Glv~~~~~~~~~~~Y~~   83 (136)
T 1mzb_A           19 PRVKILQMLDSAE-QRHMSAEDVYKALMEAGEDV----GLATVYRVLTQFEAAGLVVRHNFDGGHAVFEL   83 (136)
T ss_dssp             HHHHHHHHHHCC--CCSBCHHHHHHHHHHTTCCC----CHHHHHHHHHHHHHHTSEEEECSSSSSCEEEE
T ss_pred             HHHHHHHHHHhCC-CCCCCHHHHHHHHHhhCCCC----CHHHHHHHHHHHHHCCcEEEEEeCCCceEEEe
Confidence            3456888887641 1489999999998     56    89999999999999999998754223346765

>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=91.72  E-value=0.3  Score=31.74  Aligned_cols=35  Identities=9%  Similarity=0.163  Sum_probs=32.7

Q ss_pred             CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      +..|+.+||+++|+    +...+.|.|-.|...|.|...
T Consensus        28 ~~~Ta~~IAkkLg~----sK~~vNr~LY~L~kkG~V~~~   62 (75)
T 1sfu_A           28 DYTTAISLSNRLKI----NKKKINQQLYKLQKEDTVKMV   62 (75)
T ss_dssp             CEECHHHHHHHTTC----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             cchHHHHHHHHHCC----CHHHHHHHHHHHHHCCCEecC
Confidence            45999999999999    999999999999999999886

>3i71_A Ethanolamine utilization protein EUTK; helix-turn-helix, unknown function; HET: FLC; 2.10A {Escherichia coli}

Probab=91.64  E-value=0.43  Score=29.14  Aligned_cols=50  Identities=20%  Similarity=0.200  Sum_probs=42.4

Q ss_pred             HHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903           23 EIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH   83 (233)
Q Consensus        23 d~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~   83 (233)
                      ..|..-+  .++|+.|+|+..+.    +.+..+.-|+.|.+.|-+.+.     ..+|++.|
T Consensus        10 all~s~~--QGMTaGEVAA~f~w----~Le~ar~aLeqLf~~G~LRKR-----sSRYrlkp   59 (68)
T 3i71_A           10 ALLTSVR--QGMTAGEVAAHFGW----PLEKARNALEQLFSAGTLRKR-----SSRYRLKP   59 (68)
T ss_dssp             HHHHHCT--TCBCHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEE-----CCEEEECC
T ss_pred             HHHHHHh--ccccHHHHHHHhCC----cHHHHHHHHHHHHhcchhhhh-----ccccccCc
Confidence            3444433  58999999999999    999999999999999999996     78898876

>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=91.60  E-value=0.15  Score=41.82  Aligned_cols=35  Identities=17%  Similarity=0.118  Sum_probs=27.1

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL  200 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl  200 (233)
                      ++...+|||+|||.|.++..++++.+--+++.+|+
T Consensus        72 l~~~~~VLDLGaAPGGWSQvAa~~~~~~~v~g~dV  106 (277)
T 3evf_A           72 VKLEGRVIDLGCGRGGWCYYAAAQKEVSGVKGFTL  106 (277)
T ss_dssp             SCCCEEEEEETCTTCHHHHHHHTSTTEEEEEEECC
T ss_pred             CCCCCEEEEecCCCCHHHHHHHHhcCCCcceeEEE
Confidence            56667999999999999999888766545444444

>2zig_A TTHA0409, putative modification methylase; methyltransferase, S- adenosylmethionine, structural genomics, NPPSFA; 2.10A {Thermus thermophilus} PDB: 2zie_A* 2zif_A

Probab=91.38  E-value=0.23  Score=41.06  Aligned_cols=40  Identities=13%  Similarity=0.054  Sum_probs=32.2

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccC
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSS  209 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~  209 (233)
                      ....|+|++||+|..+.++++.  +.+++.+|+. ..++.|++
T Consensus       235 ~~~~vlD~f~GsGt~~~~a~~~--g~~~~g~e~~~~~~~~a~~  275 (297)
T 2zig_A          235 VGDVVLDPFAGTGTTLIAAARW--GRRALGVELVPRYAQLAKE  275 (297)
T ss_dssp             TTCEEEETTCTTTHHHHHHHHT--TCEEEEEESCHHHHHHHHH
T ss_pred             CCCEEEECCCCCCHHHHHHHHc--CCeEEEEeCCHHHHHHHHH
Confidence            4578999999999999998876  4689999995 46666654

>2wk1_A NOVP; transferase, O-methyltransferase, novobiocin, TYLF superfamily; HET: SAH; 1.40A {Streptomyces caeruleus}

Probab=91.32  E-value=0.15  Score=42.01  Aligned_cols=66  Identities=12%  Similarity=0.086  Sum_probs=46.0

Q ss_pred             cCcceEEEecCCccHHHHHHHHHc-----CCCcEEEeec----hH-----------------------HHhhccC-----
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNY-----LHIKGVNFDL----SH-----------------------VIQDSSS-----  209 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~-----P~l~~~v~Dl----p~-----------------------v~~~a~~-----  209 (233)
                      ...+.||.||...|..++.+++..     |+-+++.+|.    |+                       .++.+++     
T Consensus       105 ~~pg~IlEiGv~~G~Sai~ma~~l~~~g~~~~kI~~~DtfeG~pe~~~~~~~~d~~~~~~~~~~~~~~~~~~ar~n~~~~  184 (282)
T 2wk1_A          105 NVPGDLVETGVWRGGACILMRGILRAHDVRDRTVWVADSFQGIPDVGEDGYAGDRKMALHRRNSVLAVSEEEVRRNFRNY  184 (282)
T ss_dssp             TCCCEEEEECCTTSHHHHHHHHHHHHTTCCSCCEEEEECSSCSCCCCTTSCHHHHHHCGGGGHHHHCCCHHHHHHHHHHT
T ss_pred             CCCCcEEEeecCchHHHHHHHHHhHhcCCCCCEEEEEECCCCCCcccccccccccccccccccccchhHHHHHHHHHHHc
Confidence            346899999999999888877654     5788999983    21                       1122222     


Q ss_pred             ---CCCceEEecCcCCCCCC---C--CEEEe
Q 039903          210 ---YSGVKHIGGIMLERIPK---G--DAILI  232 (233)
Q Consensus       210 ---~~ri~~~~gD~f~~~P~---~--D~~~l  232 (233)
                         .++|+++.||+.+.+|.   +  |++++
T Consensus       185 gl~~~~I~li~Gda~etL~~~~~~~~d~vfI  215 (282)
T 2wk1_A          185 DLLDEQVRFLPGWFKDTLPTAPIDTLAVLRM  215 (282)
T ss_dssp             TCCSTTEEEEESCHHHHSTTCCCCCEEEEEE
T ss_pred             CCCcCceEEEEeCHHHHHhhCCCCCEEEEEE
Confidence               17899999999885543   2  66664

>1yg2_A Gene activator APHA; virulence factor, winged helix, transcripti factor, transcription; 2.20A {Vibrio cholerae} SCOP: a.4.5.61

Probab=91.23  E-value=0.31  Score=37.08  Aligned_cols=65  Identities=9%  Similarity=0.269  Sum_probs=49.5

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhC--------CCCCCCChhhHHHHHHHHhcCCceeeeccCC----CCCceeccHh
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQM--------PSSNPNAAVMLDRILRLLVTHRVLRCTSAGD----DQRLYGLAHV   84 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~--------~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~----~~~~y~lt~~   84 (233)
                      +++-|...|..    +|.+.-||++.+        ++    ++..+++.|+-|...|+++......    ....|++|+.
T Consensus         3 l~~~iL~lL~~----~~~~gyel~~~l~~~~~~~~~~----s~~~ly~~L~~Le~~GlI~~~~~~~~~~~~r~~Y~lT~~   74 (179)
T 1yg2_A            3 LPHVILTVLST----RDATGYDITKEFSASIGYFWKA----SHQQVYRELNKMGEQGLVTCVLEPQEGKPDRKVYSITQA   74 (179)
T ss_dssp             HHHHHHHHHHH----CCBCHHHHHHHHTTGGGGTCCC----CHHHHHHHHHHHHHTTSEEECCC---------CEEECHH
T ss_pred             hHHHHHHHHhc----CCCCHHHHHHHHHHHhCCccCC----CcCcHHHHHHHHHHCCCeEEEeecCCCCCCceEEEeChH
Confidence            35557777876    599999999998        56    8999999999999999999653210    1246999999


Q ss_pred             hhHhh
Q 039903           85 AKYFV   89 (233)
Q Consensus        85 s~~l~   89 (233)
                      |+...
T Consensus        75 G~~~l   79 (179)
T 1yg2_A           75 GRSAL   79 (179)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            97533

>2g9w_A Conserved hypothetical protein; DNA-binding domain, bacterial transcription repressor, DNA B protein; 1.80A {Mycobacterium tuberculosis} SCOP: a.4.5.39

Probab=90.97  E-value=0.17  Score=36.72  Aligned_cols=53  Identities=9%  Similarity=0.078  Sum_probs=41.6

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeec
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTS   71 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~   71 (233)
                      .+..|...|....  ++.|..||++.++..++.+...+.++|+-|...|++++..
T Consensus        10 ~e~~vL~~L~~~~--~~~t~~el~~~l~~~~~~~~~Tvt~~l~rLe~kGlv~r~~   62 (138)
T 2g9w_A           10 LERAVMDHLWSRT--EPQTVRQVHEALSARRDLAYTTVMAVLQRLAKKNLVLQIR   62 (138)
T ss_dssp             HHHHHHHHHHTCS--SCEEHHHHHHHHTTTCCCCHHHHHHHHHHHHHTTSEEEEC
T ss_pred             HHHHHHHHHHhcC--CCCCHHHHHHHHhccCCCCHHHHHHHHHHHHHCCCEEEEe
Confidence            4566777887631  5899999999998211118999999999999999999864

>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=90.83  E-value=0.18  Score=44.28  Aligned_cols=67  Identities=16%  Similarity=0.139  Sum_probs=51.1

Q ss_pred             hChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhc
Q 039903           19 LGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVL   90 (233)
Q Consensus        19 lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~   90 (233)
                      ..|+..|.+.+ ++++|..|||+.+++    +...+.|+++-|...|++++.+...  ..-...+|+.++.+..
T Consensus       407 ~~vl~~l~~~~-~~~~~~~~l~~~~~~----~~~~~t~~~~~le~~g~v~r~~~~~D~R~~~i~lT~~g~~~~~  475 (487)
T 1hsj_A          407 IYILNHILRSE-SNEISSKEIAKCSEF----KPYYLTKALQKLKDLKLLSKKRSLQDERTVIVYVTDTQKANIQ  475 (487)
T ss_dssp             HHHHHHHHTCS-CSEEEHHHHHHSSCC----CHHHHHHHHHHHHTTTTSCCEECCSSSSCCEEECCSSHHHHHH
T ss_pred             HHHHHHHHhCC-CCCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEeecCCCCCCCeEEEEECHHHHHHHH
Confidence            34666676641 147999999999999    9999999999999999999875431  2235678888877653

>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=90.78  E-value=0.14  Score=43.84  Aligned_cols=72  Identities=13%  Similarity=0.255  Sum_probs=50.2

Q ss_pred             hHHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC-----CCCceecc
Q 039903            8 VLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD-----DQRLYGLA   82 (233)
Q Consensus         8 ~~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~-----~~~~y~lt   82 (233)
                      ..+++++...+..|++.|. .   +++|..|||+.+++    +...+.++++-|...|++.+.....     ....|+++
T Consensus        12 ~~~~~~~~~~~~~il~~l~-~---~~~sr~~la~~~gl----s~~tv~~~v~~L~~~gli~~~~~~~~~~GR~~~~l~~~   83 (380)
T 2hoe_A           12 HMPKSVRAENISRILKRIM-K---SPVSRVELAEELGL----TKTTVGEIAKIFLEKGIVVEEKDSPKGVGRPTKSLKIS   83 (380)
T ss_dssp             ----------CCCSHHHHH-H---SCBCHHHHHHHHTC----CHHHHHHHHHHHHHHTSEEEEECCC----CCCEEEEEC
T ss_pred             cCchhHHHHHHHHHHHHHH-c---CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEeecCCCCCCCCCceEEEEc
Confidence            4566777778888999999 7   69999999999999    9999999999999999999863210     12346777


Q ss_pred             HhhhH
Q 039903           83 HVAKY   87 (233)
Q Consensus        83 ~~s~~   87 (233)
                      +...+
T Consensus        84 ~~~~~   88 (380)
T 2hoe_A           84 PNCAY   88 (380)
T ss_dssp             GGGCE
T ss_pred             cCCCe
Confidence            76543

>2uyo_A Hypothetical protein ML2640; putative methyltransferase, transferas; 1.7A {Mycobacterium leprae} SCOP: c.66.1.57 PDB: 2ckd_A 2uyq_A*

Probab=90.38  E-value=0.36  Score=40.26  Aligned_cols=54  Identities=15%  Similarity=0.157  Sum_probs=42.4

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcC-CCcEEEeechHHHhhccC---------CCCceEEecCcCC
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDLSHVIQDSSS---------YSGVKHIGGIMLE  222 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dlp~v~~~a~~---------~~ri~~~~gD~f~  222 (233)
                      .++..||++|||-=.....+.  +| ++++.-+|.|+|++..++         .++..++++|+.+
T Consensus       101 ~g~~QvV~LGaGlDTra~Rl~--~~~~~~v~evD~P~vi~~k~~lL~~~~~~~~~~~~~v~~Dl~d  164 (310)
T 2uyo_A          101 DGIRQFVILASGLDSRAYRLD--WPTGTTVYEIDQPKVLAYKSTTLAEHGVTPTADRREVPIDLRQ  164 (310)
T ss_dssp             TTCCEEEEETCTTCCHHHHSC--CCTTCEEEEEECHHHHHHHHHHHHHTTCCCSSEEEEEECCTTS
T ss_pred             hCCCeEEEeCCCCCchhhhcc--CCCCcEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEecchHh
Confidence            456789999999888866665  35 488999999999875432         3678999999986

>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=90.26  E-value=0.31  Score=33.66  Aligned_cols=41  Identities=12%  Similarity=0.216  Sum_probs=35.0

Q ss_pred             HHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhc
Q 039903           15 AASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVT   63 (233)
Q Consensus        15 ~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~   63 (233)
                      .+.++||+..|..    |+.|-.|||+.+|+    +...+.|+=|.|-.
T Consensus        44 l~~R~~l~~~L~~----ge~TQREIA~~lGi----S~stISRi~r~L~~   84 (101)
T 1jhg_A           44 LGTRVRIIEELLR----GEMSQRELKNELGA----GIATITRGSNSLKA   84 (101)
T ss_dssp             HHHHHHHHHHHHH----CCSCHHHHHHHHCC----CHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHc----CCcCHHHHHHHHCC----ChhhhhHHHHHHHH
Confidence            3567899999988    68999999999999    99999998777654

>4g6q_A Putative uncharacterized protein; structural genomics, PSI-biology, protein structure initiati midwest center for structural genomics, MCSG; 2.08A {Kribbella flavida}

Probab=90.22  E-value=0.11  Score=39.99  Aligned_cols=70  Identities=21%  Similarity=0.268  Sum_probs=53.0

Q ss_pred             HHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCC-CCCCCChhhHHHHHHHHhcCCceeeeccCC----CCCceeccHh
Q 039903           10 PAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMP-SSNPNAAVMLDRILRLLVTHRVLRCTSAGD----DQRLYGLAHV   84 (233)
Q Consensus        10 s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~-~~~~~~~~~l~rlL~~L~~~gll~~~~~~~----~~~~y~lt~~   84 (233)
                      ..+|.-=+++.|+..|.+    ++.|+.|||+.++ +    +...+.+.|+.|...|+++......    ....|++++.
T Consensus        17 ~~~La~P~Rl~il~~L~~----~~~~~~~l~~~l~~~----~~~~~s~Hl~~L~~aglv~~~~e~~~~g~~er~y~~~~~   88 (182)
T 4g6q_A           17 VDLLHHPLRWRITQLLIG----RSLTTRELAELLPDV----ATTTLYRQVGILVKAGVLMVTAEHQVRGAVERTYTLNTQ   88 (182)
T ss_dssp             HHHTTSHHHHHHHHHTTT----SCEEHHHHHHHCTTB----CHHHHHHHHHHHHHHTSEEEEEEEEETTEEEEEEEECTT
T ss_pred             HHHhCCHHHHHHHHHHHh----CCCCHHHHHHHhcCC----CHHHHHHHHHHHHHCCCeEEEEeecccCcceeEEEeccc
Confidence            445555679999999986    6999999999996 8    8889999999999999998543210    1235777665


Q ss_pred             hhH
Q 039903           85 AKY   87 (233)
Q Consensus        85 s~~   87 (233)
                      +..
T Consensus        89 ~~~   91 (182)
T 4g6q_A           89 AGD   91 (182)
T ss_dssp             TTT
T ss_pred             ccc
Confidence            543

>1v4r_A Transcriptional repressor; helix-turn-helix, winged-helix, gene regulation; NMR {Streptomyces} SCOP: a.4.5.6

Probab=90.21  E-value=0.15  Score=34.94  Aligned_cols=54  Identities=22%  Similarity=0.225  Sum_probs=41.8

Q ss_pred             HHHHHHHHhhChhH-HHHhcCCCCCC-CHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           10 PAAMQAASELGVFE-IIAKAGPTAKI-SAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        10 s~~L~~a~~lglfd-~L~~~~~~~~~-t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      +..++..++..|.+ .+.. |  ..+ |..+||+.+++    +...+++-|+.|...|+++..
T Consensus        13 ~~~l~~~i~~~I~~~~l~~-g--~~lps~~eLa~~~~v----Sr~tvr~al~~L~~~Gli~~~   68 (102)
T 1v4r_A           13 YADVATHFRTLIKSGELAP-G--DTLPSVADIRAQFGV----AAKTVSRALAVLKSEGLVSSR   68 (102)
T ss_dssp             HHHHHHHHHHHTTTTSCCT-T--SBCCCHHHHHHHSSS----CTTHHHHHTTTTTTSSCCEEE
T ss_pred             HHHHHHHHHHHHHhCCCCC-c--CCCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEe
Confidence            44555556666665 3333 2  355 99999999999    999999999999999999986

>1zkd_A DUF185; NESG, RPR58, structural genomics, PSI, protein structure INI northeast structural genomics consortium, unknown function; 2.10A {Rhodopseudomonas palustris} SCOP: c.66.1.52

Probab=90.18  E-value=0.89  Score=39.14  Aligned_cols=63  Identities=13%  Similarity=0.229  Sum_probs=40.8

Q ss_pred             chHHHHHHHHHHhcchhcHHHHHHhcccccCcceEEEecCCccHHHHHHHHH-------cCCCcEEEeechHHHh
Q 039903          138 FRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISN-------YLHIKGVNFDLSHVIQ  205 (233)
Q Consensus       138 ~~~~~~f~~am~~~~~~~~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~-------~P~l~~~v~Dlp~v~~  205 (233)
                      |+....|-+.++.+-..    +..... .+..-+||++|.|+|.++.-+++.       +..++..++|....+.
T Consensus        55 peis~~FGe~la~~~~~----~w~~~g-~p~~~~ivElGaG~GtLa~diL~~l~~~p~~~~~~~y~iVE~Sp~Lr  124 (387)
T 1zkd_A           55 PEISQMFGELLGLWSAS----VWKAAD-EPQTLRLIEIGPGRGTMMADALRALRVLPILYQSLSVHLVEINPVLR  124 (387)
T ss_dssp             HHHCHHHHHHHHHHHHH----HHHHTT-CCSSEEEEEECCTTSHHHHHHHHHHTTSHHHHTTEEEEEECCCHHHH
T ss_pred             CchHHHHHHHHHHHHHH----HHHHcC-CCCCcEEEEECCCcchHHHHHHHHHHhCCccccccEEEEEecCHHHH
Confidence            66666677665543211    112222 344567999999999998887764       2356789999876554

>4esb_A Transcriptional regulator, PADR family; DNA binding protein, HTH fold; 2.50A {Bacillus cereus}

Probab=90.15  E-value=0.3  Score=34.48  Aligned_cols=67  Identities=10%  Similarity=0.164  Sum_probs=50.3

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCC------CCCCCChhhHHHHHHHHhcCCceeeeccC---C-CCCceeccHhhh
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMP------SSNPNAAVMLDRILRLLVTHRVLRCTSAG---D-DQRLYGLAHVAK   86 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~------~~~~~~~~~l~rlL~~L~~~gll~~~~~~---~-~~~~y~lt~~s~   86 (233)
                      +++-|...|..    +|.+--||++.+.      +    ++..+++.|+-|...|+++.....   + ....|++|+.|+
T Consensus        10 l~~~IL~~L~~----~~~~Gyei~~~l~~~~~~~i----s~gtlY~~L~rLe~~GlI~~~~~~~~~g~~rk~Y~LT~~G~   81 (115)
T 4esb_A           10 LEGCILYIISQ----EEVYGYELSTKLNKHGFTFV----SEGSIYPLLLRMQKEKLIEGTLKASSLGPKRKYYHITDKGL   81 (115)
T ss_dssp             HHHHHHHHHHH----SCEEHHHHHHHHHHTTCTTC----CHHHHHHHHHHHHHTTSEEEEEEECTTSCEEEEEEECHHHH
T ss_pred             HHHHHHHHHHc----CCCCHHHHHHHHHHcCCCCC----CcChHHHHHHHHHHCCCeEEEeeecCCCCCcEEEEECHHHH
Confidence            34445666776    5899999998885      7    999999999999999999875321   0 113599999998


Q ss_pred             HhhcC
Q 039903           87 YFVLN   91 (233)
Q Consensus        87 ~l~~~   91 (233)
                      .....
T Consensus        82 ~~l~~   86 (115)
T 4esb_A           82 EQLEE   86 (115)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            76644

>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=89.65  E-value=0.18  Score=35.69  Aligned_cols=52  Identities=17%  Similarity=0.261  Sum_probs=41.6

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeec
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTS   71 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~   71 (233)
                      .+..|...|...   ++.|..|||+.++...+.++..+.++|+-|...|++++..
T Consensus        11 ~q~~vL~~L~~~---~~~t~~el~~~l~~~~~~~~~Tvt~~l~rLe~kGlv~R~~   62 (126)
T 1sd4_A           11 AEWDVMNIIWDK---KSVSANEIVVEIQKYKEVSDKTIRTLITRLYKKEIIKRYK   62 (126)
T ss_dssp             HHHHHHHHHHHS---SSEEHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHHhc---CCCCHHHHHHHHhhcCCCChhhHHHHHHHHHHCCceEEEe
Confidence            455677778776   5899999999997311127889999999999999999864

>3eyy_A Putative iron uptake regulatory protein; NUR, nickel-uptake regulator, D-domain, dimerization domain, DB-domain, DNA-binding domain; 2.40A {Streptomyces coelicolor}

Probab=89.40  E-value=0.24  Score=36.46  Aligned_cols=62  Identities=16%  Similarity=0.185  Sum_probs=45.5

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCC-CCCChhhHHHHHHHHhcCCceeeeccCCCCCceec
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSS-NPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGL   81 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~-~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~l   81 (233)
                      -+.-|++.|...   ++.|++||.+.+.-. +..+..-++|-|+.|+..|++.+...+++..+|.+
T Consensus        20 qR~~Il~~l~~~---~h~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Glv~~i~~~~~~~~Y~~   82 (145)
T 3eyy_A           20 QRQLVLEAVDTL---EHATPDDILGEVRKTASGINISTVYRTLELLEELGLVSHAHLGHGAPTYHL   82 (145)
T ss_dssp             HHHHHHHHHHHH---SSBCHHHHHHHHHTTCTTCCHHHHHHHHHHHHHHTSEEEEECGGGCEEEEE
T ss_pred             HHHHHHHHHHhc---CCCCHHHHHHHHHhhCCCCCHhHHHHHHHHHHHCCcEEEEEeCCCceEEEe
Confidence            456688888876   388999999887321 12288899999999999999998753222345654

>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=89.26  E-value=0.33  Score=41.81  Aligned_cols=51  Identities=10%  Similarity=0.275  Sum_probs=44.9

Q ss_pred             HHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           13 MQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        13 L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      ++..-+..|++.|...   +++|..|||+.+++    +...+.++++-|...|++.+.
T Consensus        13 ~r~~n~~~il~~l~~~---~~~sr~~la~~~~l----s~~tv~~~v~~L~~~g~i~~~   63 (406)
T 1z6r_A           13 IKQTNAGAVYRLIDQL---GPVSRIDLSRLAQL----APASITKIVHEMLEAHLVQEL   63 (406)
T ss_dssp             HHHHHHHHHHHHHHSS---CSCCHHHHHHHTTC----CHHHHHHHHHHHHHHTSEEEC
T ss_pred             HHHhHHHHHHHHHHHc---CCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCcEEee
Confidence            4555556689999887   59999999999999    999999999999999999985

>4ets_A Ferric uptake regulation protein; metal binding protein, transcription factor; 2.10A {Campylobacter jejuni subsp}

Probab=89.16  E-value=0.44  Score=35.76  Aligned_cols=63  Identities=14%  Similarity=0.187  Sum_probs=44.6

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCC---CCCChhhHHHHHHHHhcCCceeeeccCCCCCceecc
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSS---NPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLA   82 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~---~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt   82 (233)
                      +.-|++.|...+  ++.|++||.+.+.-.   +..+..-++|-|+.|+..|++.+...+++..+|...
T Consensus        35 R~~IL~~L~~~~--~h~sA~eI~~~l~~~~~~~~is~aTVYRtL~~L~e~Glv~~i~~~~~~~~Y~~~  100 (162)
T 4ets_A           35 REVLLKTLYHSD--THYTPESLYMEIKQAEPDLNVGIATVYRTLNLLEEAEMVTSISFGSAGKKYELA  100 (162)
T ss_dssp             HHHHHHHHHSCC--SCBCHHHHHHHHHHHCGGGCCCHHHHHHHHHHHHHTTSEEECC-----CCEEEC
T ss_pred             HHHHHHHHHhCC--CCCCHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHCCCEEEEEeCCCceEEEeC
Confidence            455899998864  699999998876321   122788999999999999999987432223457654

>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=88.98  E-value=0.29  Score=32.00  Aligned_cols=46  Identities=9%  Similarity=0.062  Sum_probs=37.4

Q ss_pred             hhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           21 VFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        21 lfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      +.+.+...+ ++.+++.++|+.+++.   ..++++.++.+|.++|++++.
T Consensus        19 Fi~l~~~~~-~~~i~l~~aa~~L~v~---~kRRiYDI~NVLe~igli~K~   64 (76)
T 1cf7_A           19 FVSLLQEAK-DGVLDLKLAADTLAVR---QKRRIYDITNVLEGIGLIEKK   64 (76)
T ss_dssp             HHHHHHHSS-TTEEEHHHHHHHTTTC---CTHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHhCC-CCcCcHHHHHHHhCCc---cceehhhHHHHHhHhcceeec
Confidence            445555532 3688999999999983   578999999999999999997

>2o0m_A Transcriptional regulator, SORC family; structural genomics, protein structure initiative, midwest center for structural genomics, MCSG; 1.60A {Enterococcus faecalis} SCOP: c.124.1.8

Probab=88.90  E-value=0.078  Score=44.97  Aligned_cols=61  Identities=10%  Similarity=0.028  Sum_probs=0.0

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhc
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVL   90 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~   90 (233)
                      +..|...|...   +++|..|||+.+++    ++..++|.|+.|...|++++.     .....+|+.|+.+..
T Consensus        22 ~~~iL~~l~~~---~~~t~~eLa~~l~v----s~~Tv~r~l~~Le~~Glv~~~-----~~gi~LT~~G~~~~~   82 (345)
T 2o0m_A           22 RFQILRNIYWM---QPIGRRSLSETMGI----TERVLRTETDVLKQLNLIEPS-----KSGMTLTERGLEVYQ   82 (345)
T ss_dssp             -------------------------------------------------------------------------
T ss_pred             HHHHHHHHHHc---CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEE-----ecceEEcHHHHHHHH
Confidence            44677777776   58999999999999    999999999999999999853     233567777765543

>2w57_A Ferric uptake regulation protein; gene regulation, transcription regulation, transport, iron, repressor, DNA-binding, transcription; 2.60A {Vibrio cholerae}

Probab=88.75  E-value=0.23  Score=36.82  Aligned_cols=60  Identities=15%  Similarity=0.266  Sum_probs=44.9

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhC-----CCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceec
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQM-----PSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGL   81 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~-----~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~l   81 (233)
                      -+.-|++.|...+ +++.|++||.+.+     ++    +..-++|.|+.|+..|++.+...+++..+|.+
T Consensus        18 qR~~Il~~L~~~~-~~h~sa~ei~~~l~~~~~~i----s~aTVYR~L~~L~e~Glv~~~~~~~~~~~Y~~   82 (150)
T 2w57_A           18 PRLKILEVLQQPE-CQHISAEELYKKLIDLGEEI----GLATVYRVLNQFDDAGIVTRHHFEGGKSVFEL   82 (150)
T ss_dssp             HHHHHHHHHTSGG-GSSEEHHHHHHHHHHTTCCC----CHHHHHHHHHHHHHTTSEEEEECGGGCEEEEE
T ss_pred             HHHHHHHHHHhCC-CCCCCHHHHHHHHHHhCCCC----CHHHHHHHHHHHHHCCcEEEEEeCCCceEEEe
Confidence            3455888887641 0389999999998     56    89999999999999999998743212345654

>2p5k_A Arginine repressor; DNA-binding domain, winged helix-turn-helix (WHTH), DNA binding protein; 1.00A {Bacillus subtilis} SCOP: a.4.5.3 PDB: 2p5l_C*

Probab=88.51  E-value=0.5  Score=29.01  Aligned_cols=39  Identities=13%  Similarity=0.172  Sum_probs=30.4

Q ss_pred             hhHHHHhcCCCCCCCHHHHHHhC-----CCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           21 VFEIIAKAGPTAKISAVEIAAQM-----PSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        21 lfd~L~~~~~~~~~t~~elA~~~-----~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      |...+...   ++.|++||++.+     ++    +..-++|-|+   .+|++ +.
T Consensus        10 i~~ll~~~---~~~t~~el~~~l~~~~~~v----s~~Tv~R~L~---~lg~v-~~   53 (64)
T 2p5k_A           10 IREIITSN---EIETQDELVDMLKQDGYKV----TQATVSRDIK---ELHLV-KV   53 (64)
T ss_dssp             HHHHHHHS---CCCSHHHHHHHHHHTTCCC----CHHHHHHHHH---HHTCE-EE
T ss_pred             HHHHHHcC---CCCCHHHHHHHHHHhCCCc----CHHHHHHHHH---HcCCE-EE
Confidence            33445544   589999999999     99    9999999998   55777 44

>1bia_A BIRA bifunctional protein; transcription regulation; 2.30A {Escherichia coli} SCOP: a.4.5.1 b.34.1.1 d.104.1.2 PDB: 1bib_A* 1hxd_A* 2ewn_A*

Probab=87.88  E-value=0.47  Score=39.70  Aligned_cols=56  Identities=14%  Similarity=0.185  Sum_probs=45.2

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH   83 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~   83 (233)
                      +..|.+.|.+.   +..|.+|||+.+++    ++..++|-++.|...|+..+..   .+..|++.+
T Consensus         7 ~~~Il~~L~~~---~~~s~~eLa~~l~v----S~~ti~r~l~~L~~~G~~i~~~---~g~GY~l~~   62 (321)
T 1bia_A            7 PLKLIALLANG---EFHSGEQLGETLGM----SRAAINKHIQTLRDWGVDVFTV---PGKGYSLPE   62 (321)
T ss_dssp             HHHHHHHHTTS---SCBCHHHHHHHHTS----CHHHHHHHHHHHHHTTCCCEEE---TTTEEECSS
T ss_pred             HHHHHHHHHcC---CCcCHHHHHHHHCC----CHHHHHHHHHHHHhCCCcEEEe---cCCCcEEee
Confidence            45577888664   58999999999999    9999999999999999986542   344687754

>2vxz_A Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Pyrobaculum spherical virus}

Probab=87.80  E-value=0.55  Score=34.64  Aligned_cols=47  Identities=6%  Similarity=0.027  Sum_probs=41.5

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeecc
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSA   72 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~   72 (233)
                      +-.|.++|. .   ||.|..+||+++|+    +....+-.|..|.-.|++.+...
T Consensus        13 k~~ILE~Lk-~---G~~~t~~Iak~LGl----Shg~aq~~Ly~LeREG~V~~Vk~   59 (165)
T 2vxz_A           13 LRDILALLA-D---GCKTTSLIQQRLGL----SHGRAKALIYVLEKEGRVTRVAF   59 (165)
T ss_dssp             HHHHHHHHT-T---CCEEHHHHHHHHTC----CHHHHHHHHHHHHHTTSCEEEEE
T ss_pred             HHHHHHHHH-h---CCccHHHHHHHhCC----cHHHHHHHHHHHHhcCceEEEEE
Confidence            345788888 3   79999999999999    99999999999999999998754

>2pjp_A Selenocysteine-specific elongation factor; SELB, protein-RNA complex, elongation factor, winged- helix, bulge, translation/RNA complex; 2.30A {Escherichia coli}

Probab=87.79  E-value=0.57  Score=33.21  Aligned_cols=43  Identities=9%  Similarity=0.062  Sum_probs=37.5

Q ss_pred             CCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903           33 KISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH   83 (233)
Q Consensus        33 ~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~   83 (233)
                      |.++.|||+.+++    ++..+..+|+.|+..|.+.+.    ..+.|-++.
T Consensus        20 p~~~~~la~~~~~----~~~~~~~~l~~l~~~G~l~~i----~~~~~~~~~   62 (121)
T 2pjp_A           20 PWWVRDLAKETGT----DEQAMRLTLRQAAQQGIITAI----VKDRYYRND   62 (121)
T ss_dssp             CEEHHHHHHHTTC----CHHHHHHHHHHHHHTTSEEEE----ETTEEEEHH
T ss_pred             CCCHHHHHHHhCC----CHHHHHHHHHHHHHCCCEEEe----cCCceECHH
Confidence            6799999999999    999999999999999999887    467665544

>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=87.41  E-value=0.35  Score=40.06  Aligned_cols=36  Identities=14%  Similarity=0.158  Sum_probs=29.8

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS  201 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp  201 (233)
                      +.+..++||+||+.|.++.-++++.+-..++.+|+.
T Consensus        79 ~~~g~~vlDLGaaPGgWsqva~~~~gv~sV~Gvdlg  114 (300)
T 3eld_A           79 LRITGRVLDLGCGRGGWSYYAAAQKEVMSVKGYTLG  114 (300)
T ss_dssp             CCCCEEEEEETCTTCHHHHHHHTSTTEEEEEEECCC
T ss_pred             CCCCCEEEEcCCCCCHHHHHHHHhcCCceeeeEEec
Confidence            567799999999999999999987766566667763

>3lmm_A Uncharacterized protein; multi-domained alpha-beta protein, structural genomics, PSI- 2, protein structure initiative; 3.00A {Corynebacterium diphtheriae}

Probab=87.13  E-value=0.6  Score=42.47  Aligned_cols=62  Identities=10%  Similarity=0.053  Sum_probs=52.3

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhc-----CCceeeeccCCCCCceeccHhhhHhhcC
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVT-----HRVLRCTSAGDDQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~-----~gll~~~~~~~~~~~y~lt~~s~~l~~~   91 (233)
                      ++-|++.|...   +.+|..+||+.+++    ++..+++.|+.|+.     .|+++..     ++.|.+++.....+..
T Consensus       432 ~~~iL~~l~~~---~~it~~~la~~l~~----s~~~~~~~L~~L~~~~~~~~glie~~-----g~~y~L~~~~~~~~~~  498 (583)
T 3lmm_A          432 IAIVLYLLFQR---PFITIDVVARGLQS----GKEAARNALEAARQTTVAGAPLIIAH-----DGVWLLGNACREILRK  498 (583)
T ss_dssp             HHHHHHHHHHS---SSBCHHHHHHHHTS----CHHHHHHHHHHHHTCEETTEESEEEE-----TTEEEECHHHHHHHTS
T ss_pred             HHHHHHHHHHC---CCcCHHHHHHHhCc----CHHHHHHHHHHHHhhhccccceEEEe-----CCEEEECHHHHHHhcc
Confidence            34578888887   48999999999999    99999999999999     8999996     5889999976655533

>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=86.96  E-value=0.68  Score=37.33  Aligned_cols=67  Identities=10%  Similarity=0.131  Sum_probs=50.3

Q ss_pred             ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCC--ceeccHhhhHhhcC
Q 039903           20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQR--LYGLAHVAKYFVLN   91 (233)
Q Consensus        20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~--~y~lt~~s~~l~~~   91 (233)
                      .+...|.+.+ .++.|..|||+.+++    +...+.++++-|...|++.+...+.+..  ...+|+.|+.+...
T Consensus        38 ~vL~~L~~~~-~~~~~~~el~~~l~~----~~~t~t~~l~rLe~~G~i~R~~~~~DrR~~~i~LT~~G~~~~~~  106 (250)
T 1p4x_A           38 ILLTYLFHQQ-ENTLPFKKIVSDLCY----KQSDLVQHIKVLVKHSYISKVRSKIDERNTYISISEEQREKIAE  106 (250)
T ss_dssp             HHHHHHHSCS-CSEEEHHHHHHHSSS----CGGGTHHHHHHHHHTTSCEEEECSSSTTSEEEECCHHHHHHHHH
T ss_pred             HHHHHHHhcC-CCCcCHHHHHHHHCC----CHhhHHHHHHHHHHCCCEEecCCCCCCCeEEEEECHHHHHHHHH
Confidence            3555665531 137899999999999    9999999999999999999876532122  45689988776533

>1z05_A Transcriptional regulator, ROK family; structural genomics, protein structure initiative, midwest center for structural genomics; 2.00A {Vibrio cholerae o1 biovar eltor} SCOP: a.4.5.63 c.55.1.10 c.55.1.10

Probab=86.89  E-value=0.64  Score=40.35  Aligned_cols=51  Identities=18%  Similarity=0.337  Sum_probs=45.4

Q ss_pred             HHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           13 MQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        13 L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      ++..-+..|++.|...   +++|..|||+.+++    +...+.++++-|...|++.+.
T Consensus        36 ~r~~n~~~il~~l~~~---~~~sr~ela~~~gl----s~~tv~~~v~~L~~~gli~~~   86 (429)
T 1z05_A           36 IKQINAGRVYKLIDQK---GPISRIDLSKESEL----APASITKITRELIDAHLIHET   86 (429)
T ss_dssp             HHHHHHHHHHHHHHHH---CSBCHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHHHHHc---CCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEec
Confidence            4555566789999887   59999999999999    999999999999999999986

>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding, transcription, transcription regulator, transcription regulation; 3.20A {Klebsiella pneumoniae}

Probab=86.48  E-value=0.9  Score=37.73  Aligned_cols=35  Identities=11%  Similarity=0.221  Sum_probs=33.2

Q ss_pred             CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCcee-ee
Q 039903           32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLR-CT   70 (233)
Q Consensus        32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~-~~   70 (233)
                      +++|..|||+++++    ++..++|.|..|...|+++ +.
T Consensus        20 ~~~~~~ela~~l~v----S~~tIrRdL~~l~~~G~v~iri   55 (315)
T 2w48_A           20 QDMTQAQIARELGI----YRTTISRLLKRGREQGIVTIAI   55 (315)
T ss_dssp             SCCCHHHHHHHTTC----CHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCcEEEEe
Confidence            58999999999999    9999999999999999998 65

>2qlz_A Transcription factor PF0095; 2.50A {Pyrococcus furiosus} PDB: 2quf_A

Probab=85.37  E-value=0.69  Score=36.92  Aligned_cols=51  Identities=4%  Similarity=0.090  Sum_probs=42.8

Q ss_pred             hhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903           21 VFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH   83 (233)
Q Consensus        21 lfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~   83 (233)
                      |.-.|..    ++.|.++||..+++    +++-+...|+-|...|++++.    .+++..+.+
T Consensus       170 l~~~l~~----~~~t~~~la~~~~l----~~~~V~~~l~~L~~~~~v~~~----~~~~~~~~~  220 (232)
T 2qlz_A          170 LHYLLLN----GRATVEELSDRLNL----KEREVREKISEMARFVPVKII----NDNTVVLDE  220 (232)
T ss_dssp             HHHHHHS----SEEEHHHHHHHHTC----CHHHHHHHHHHHTTTSCEEEE----TTTEEEECH
T ss_pred             HHHHHhc----CCCCHHHHHHHhCc----CHHHHHHHHHHHHhcCCeEEe----cCCeEEecH
Confidence            4444554    69999999999999    999999999999999999876    577776654

>2yu3_A DNA-directed RNA polymerase III 39 kDa polypeptide F variant; winged helix domain, RNA polymerase III C39 subunit, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=85.31  E-value=0.52  Score=32.14  Aligned_cols=49  Identities=20%  Similarity=0.339  Sum_probs=43.0

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      -|.-|+..|.+.|. .+++..||..++++    +..-+.++|+.|...+++...
T Consensus        38 ~E~lVy~~I~~aGn-~GIw~kdL~~~tnL----~~~~vtkiLK~LE~k~lIK~V   86 (95)
T 2yu3_A           38 QEKLVYQIIEDAGN-KGIWSRDVRYKSNL----PLTEINKILKNLESKKLIKAV   86 (95)
T ss_dssp             HHHHHHHHHHHHTT-SCEEHHHHHHHHTC----CHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHHHHhCC-CCCCHHHHHHHhCC----CHHHHHHHHHHHHhCCCEEEe
Confidence            45568888988652 47999999999999    999999999999999999986

>2ld4_A Anamorsin; methyltransferase-like fold, alpha/beta fold, iron-sulfur PR biogenesis, apoptosis; NMR {Homo sapiens} PDB: 2yui_A

Probab=85.12  E-value=0.31  Score=36.36  Aligned_cols=51  Identities=8%  Similarity=-0.046  Sum_probs=34.9

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC--CCceEEecCcCC-CC---CCC--CEEEe
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY--SGVKHIGGIMLE-RI---PKG--DAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~--~ri~~~~gD~f~-~~---P~~--D~~~l  232 (233)
                      .....+++|||||.                +.+|. +..++.+++.  .+++++.+|+.+ +.   |..  |+++.
T Consensus        10 ~~~g~~vL~~~~g~----------------v~vD~s~~ml~~a~~~~~~~~~~~~~d~~~~~~~~~~~~~fD~V~~   69 (176)
T 2ld4_A           10 ISAGQFVAVVWDKS----------------SPVEALKGLVDKLQALTGNEGRVSVENIKQLLQSAHKESSFDIILS   69 (176)
T ss_dssp             CCTTSEEEEEECTT----------------SCHHHHHHHHHHHHHHTTTTSEEEEEEGGGGGGGCCCSSCEEEEEE
T ss_pred             CCCCCEEEEecCCc----------------eeeeCCHHHHHHHHHhcccCcEEEEechhcCccccCCCCCEeEEEE
Confidence            56678999999996                22665 3466666542  368888888876 44   443  88764

>3eyi_A Z-DNA-binding protein 1; alternative splicing, DNA-binding, polymorphism, DNA binding protein/Z-DNA complex, DNA binding protein/DNA complex; 1.45A {Homo sapiens} PDB: 2l4m_A

Probab=84.41  E-value=1.3  Score=28.04  Aligned_cols=46  Identities=15%  Similarity=0.226  Sum_probs=39.9

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhh-HHHHHHHHhcCCceeee
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVM-LDRILRLLVTHRVLRCT   70 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~-l~rlL~~L~~~gll~~~   70 (233)
                      +-.|.+.|..+   ||.++-.||+++|+    .... +.+-|-.|...|+|..+
T Consensus        12 ee~I~~fL~~~---Gp~~AL~IAK~LGl----ktAK~VNp~LY~m~~~~lL~~D   58 (72)
T 3eyi_A           12 EEDIYRFLKDN---GPQRALVIAQALGM----RTAKDVNRDLYRMKSRHLLDMD   58 (72)
T ss_dssp             HHHHHHHHHHH---CSEEHHHHHHHTTC----CSGGGTHHHHHHHHHTTSEEEC
T ss_pred             HHHHHHHHHHc---CCchHHHHHHHhCc----chhhhcCHHHHHHHHccCcCCC
Confidence            45688999998   59999999999999    5555 99999999999999765

>3iht_A S-adenosyl-L-methionine methyl transferase; YP_165822.1, STR genomics, joint center for structural genomics, JCSG; HET: MSE SAM; 1.80A {Ruegeria pomeroyi dss-3}

Probab=83.80  E-value=1.8  Score=32.43  Aligned_cols=81  Identities=14%  Similarity=0.127  Sum_probs=51.1

Q ss_pred             HHHHHHHHHhcchhcHHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCCCCceEEecCc
Q 039903          141 NGVFNKAMLNHTSIVTNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIM  220 (233)
Q Consensus       141 ~~~f~~am~~~~~~~~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~~ri~~~~gD~  220 (233)
                      .+.|.+-|.+..... ...+....  .-..-|+|+|=|+|-.=-.+.+.+|+-++.|||+.-.+.-...-+.=.++-||+
T Consensus        16 LDsfirRltaQR~~L-~~a~~~v~--~~~GpVlElGLGNGRTydHLRe~~P~R~I~vfDR~~~~hp~~~P~~e~~ilGdi   92 (174)
T 3iht_A           16 LDLFIDRMVSQRACL-EHAIAQTA--GLSGPVYELGLGNGRTYHHLRQHVQGREIYVFERAVASHPDSTPPEAQLILGDI   92 (174)
T ss_dssp             HHHHHHHHHHHHHHH-HHHHHHTT--TCCSCEEEECCTTCHHHHHHHHHCCSSCEEEEESSCCCCGGGCCCGGGEEESCH
T ss_pred             HHHHHHHHHHHHHHH-HHHHHHhc--CCCCceEEecCCCChhHHHHHHhCCCCcEEEEEeeeccCCCCCCchHheecccH
Confidence            345666665433222 22223322  223679999999999999999999999999999854332222223445667776


Q ss_pred             CCCC
Q 039903          221 LERI  224 (233)
Q Consensus       221 f~~~  224 (233)
                      .+.+
T Consensus        93 ~~tL   96 (174)
T 3iht_A           93 RETL   96 (174)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            6543

>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=83.67  E-value=1.2  Score=38.49  Aligned_cols=39  Identities=15%  Similarity=0.176  Sum_probs=31.1

Q ss_pred             cCcceEEEecCCccHHHHHHH-HHcCC-CcEEEeec-hHHHh
Q 039903          167 EQIKQLVDVGGGLGVNVNIII-SNYLH-IKGVNFDL-SHVIQ  205 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~-~~~P~-l~~~v~Dl-p~v~~  205 (233)
                      ++..+++|||++.|.++..++ +..|. .+++.|+- |...+
T Consensus       225 ~~~~~viDvGAn~G~~s~~~a~~~~~~~~~V~afEP~p~~~~  266 (409)
T 2py6_A          225 SDSEKMVDCGASIGESLAGLIGVTKGKFERVWMIEPDRINLQ  266 (409)
T ss_dssp             CSSCEEEEETCTTSHHHHHHHHHHTSCCSEEEEECCCHHHHH
T ss_pred             CCCCEEEECCCCcCHHHHHHHHHhcCCCCEEEEEcCCHHHHH
Confidence            456899999999999999988 66776 78999984 44443

>2dql_A PEX protein; circadian clock associated protein, circadian clock protein; 1.70A {Anabaena SP}

Probab=83.13  E-value=2.3  Score=29.73  Aligned_cols=63  Identities=11%  Similarity=0.186  Sum_probs=46.3

Q ss_pred             hhHHHHhcCCCCCCCHHHHHHhC-------CCCCCCChhhHHHHHHHHhcCCceeeeccC----C-CCCceeccHhhhHh
Q 039903           21 VFEIIAKAGPTAKISAVEIAAQM-------PSSNPNAAVMLDRILRLLVTHRVLRCTSAG----D-DQRLYGLAHVAKYF   88 (233)
Q Consensus        21 lfd~L~~~~~~~~~t~~elA~~~-------~~~~~~~~~~l~rlL~~L~~~gll~~~~~~----~-~~~~y~lt~~s~~l   88 (233)
                      |...|.+    +|.+--||.+.+       ++    ++..++..|+-|...|+++.....    + ....|++|+.|+..
T Consensus        27 IL~lL~~----~~~~Gyei~~~l~~~~~~~~i----s~gtLY~~L~rLe~~GlI~~~~~~~~~~~~~rk~Y~LT~~G~~~   98 (115)
T 2dql_A           27 ILYVLLQ----GESYGTELIQQLETEHPTYRL----SDTVLYSAIKFLEDNRAITGYWKKLEGRGRPRRMYQVSPEWQHQ   98 (115)
T ss_dssp             HHHHHTT----SCBCHHHHHHHHHHHCTTEEC----CHHHHHHHHHHHHHTTSEEEEEECCTTCSSCEEEEEECGGGHHH
T ss_pred             HHHHHHh----CCCCHHHHHHHHHHHcCCCCC----CcchHHHHHHHHHHCCCEEEEeeecCCCCCCcEEEEECHHHHHH
Confidence            4555665    588888877766       46    899999999999999999875321    0 11359999999876


Q ss_pred             hcC
Q 039903           89 VLN   91 (233)
Q Consensus        89 ~~~   91 (233)
                      ...
T Consensus        99 l~~  101 (115)
T 2dql_A           99 AED  101 (115)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            543

>3cvo_A Methyltransferase-like protein of unknown functio; rossman fold, structural genomics, joint center for structur genomics, JCSG; HET: MSE PG4; 1.80A {Silicibacter pomeroyi dss-3}

Probab=82.70  E-value=3.2  Score=32.26  Aligned_cols=53  Identities=8%  Similarity=0.033  Sum_probs=35.5

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccC---------CCCceEEecCcC
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSS---------YSGVKHIGGIML  221 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~---------~~ri~~~~gD~f  221 (233)
                      ..+.++|++||+|  ..+.-+++ .|+-+++-+|.. +-.+.+++         .++|+++.||..
T Consensus        28 l~~a~~VLEiGtG--ySTl~lA~-~~~g~VvtvE~d~~~~~~ar~~l~~~g~~~~~~I~~~~gda~   90 (202)
T 3cvo_A           28 YEEAEVILEYGSG--GSTVVAAE-LPGKHVTSVESDRAWARMMKAWLAANPPAEGTEVNIVWTDIG   90 (202)
T ss_dssp             HHHCSEEEEESCS--HHHHHHHT-STTCEEEEEESCHHHHHHHHHHHHHSCCCTTCEEEEEECCCS
T ss_pred             hhCCCEEEEECch--HHHHHHHH-cCCCEEEEEeCCHHHHHHHHHHHHHcCCCCCCceEEEEeCch
Confidence            4566899999984  44444444 567888888864 34444432         357999999954

>3maj_A DNA processing chain A; MCSG, PSI-2, structural genomics, protein structure initiati midwest center for structural genomics; HET: DNA; 2.05A {Rhodopseudomonas palustris}

Probab=82.41  E-value=0.63  Score=39.96  Aligned_cols=52  Identities=12%  Similarity=0.130  Sum_probs=44.3

Q ss_pred             hChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceecc
Q 039903           19 LGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLA   82 (233)
Q Consensus        19 lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt   82 (233)
                      ..|++.|..    +|.++++|+.++++    +...+...|-.|.-.|++...    .+++|+++
T Consensus       331 ~~vl~~l~~----~~~~~D~l~~~~gl----~~~~v~~~L~~LEl~G~v~~~----~Gg~~~~~  382 (382)
T 3maj_A          331 TRILALLGP----SPVGIDDLIRLSGI----SPAVVRTILLELELAGRLERH----GGSLVSLS  382 (382)
T ss_dssp             HHHHHHCCS----SCEEHHHHHHHHCC----CHHHHHHHHHHHHHTTCCEEC----TTSEEEC-
T ss_pred             HHHHHhhCC----CCCCHHHHHHHHCc----CHHHHHHHHHHHHhCCcEEeC----CCceEecC
Confidence            347777764    58999999999999    999999999999999999987    67888764

>2co5_A Viral protein F93; viral protein-winged helix complex, winged helix, DNA-bindin WHTH, disulfide bond, STIV; 2.2A {Sulfolobus turreted icosahedral virus} SCOP: a.4.5.48

Probab=81.78  E-value=2.6  Score=28.77  Aligned_cols=53  Identities=17%  Similarity=0.140  Sum_probs=40.2

Q ss_pred             CCCHHHHHHhCC--CCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhc
Q 039903           33 KISAVEIAAQMP--SSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVL   90 (233)
Q Consensus        33 ~~t~~elA~~~~--~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~   90 (233)
                      .....+|.+..+  +    ++..++.+|+-|...|+++... +.....|++|+.|+..+.
T Consensus        28 ~~i~~ei~~~~~~~i----s~GtlYp~L~rLe~~GlI~~~~-~~~rk~Y~iT~~Gr~~l~   82 (99)
T 2co5_A           28 KRLRSEILKRFDIDI----SDGVLYPLIDSLIDDKILREEE-APDGKVLFLTEKGMKEFE   82 (99)
T ss_dssp             GGHHHHHHHHHCCBC----CHHHHHHHHHHHHHTTSEEEEC-CTTSCEEEECHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCC----CCCcHHHHHHHHHHCCCEEEee-CCCcEEEEECHHHHHHHH
Confidence            444567777654  5    8999999999999999999863 113457999999986543

>2b0l_A GTP-sensing transcriptional pleiotropic repressor; CODY, DNA-binding, nucleotide-binding, transcript regulation, winged HTH motif.; 2.90A {Bacillus subtilis} SCOP: a.4.5.66

Probab=81.77  E-value=1.1  Score=30.77  Aligned_cols=34  Identities=21%  Similarity=0.237  Sum_probs=31.9

Q ss_pred             CC-CHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           33 KI-SAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        33 ~~-t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      .+ |..+||+.+++    +...+++-|+.|...|+++..
T Consensus        42 ~lps~~eLa~~lgV----Sr~tVr~al~~L~~~GlI~~~   76 (102)
T 2b0l_A           42 GLLVASKIADRVGI----TRSVIVNALRKLESAGVIESR   76 (102)
T ss_dssp             EEECHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             cCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEE
Confidence            45 99999999999    999999999999999999986

>3eqx_A FIC domain containing transcriptional regulator; FIC family protein, structural genomics, joint center for ST genomics, JCSG; HET: MSE PGE; 1.60A {Shewanella oneidensis}

Probab=81.68  E-value=2.5  Score=36.14  Aligned_cols=65  Identities=11%  Similarity=0.142  Sum_probs=50.3

Q ss_pred             hhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhcCCC
Q 039903           21 VFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLNRD   93 (233)
Q Consensus        21 lfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~~~~   93 (233)
                      +.+.|.+.|   -.|..++++.+++    +..-.+|.|+.|+..|+|++...+ .+..|..++.-..|..+..
T Consensus       302 ll~~l~~~p---~~t~~~~~~~~~~----S~~TA~r~L~~L~e~GiL~~~~~g-R~~~y~~~~~l~il~~~~~  366 (373)
T 3eqx_A          302 LVQVIFEQP---YCRIQNLVESGLA----KRQTASVYLKQLCDIGVLEEVQSG-KEKLFVHPKFVTLMTKDSN  366 (373)
T ss_dssp             HHHHHHHCS---EEEHHHHHHTSSS----CHHHHHHHHHHHHHTTSCEEC--C-CSCEEECHHHHHHHHSSCC
T ss_pred             HHHHHHHCC---CccHHHHHHHhCc----CHHHHHHHHHHHHHCCcEEEeCCC-CceEeehHHHHHHHhccCc
Confidence            566666642   5789999999999    999999999999999999987432 4567877777777776653

>2ek5_A Predicted transcriptional regulators; helix-turn-helix, interwined alpha helices; 2.20A {Corynebacterium glutamicum atcc 13032} PDB: 2du9_A

Probab=81.53  E-value=2.7  Score=30.08  Aligned_cols=34  Identities=26%  Similarity=0.205  Sum_probs=31.8

Q ss_pred             CC-CHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           33 KI-SAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        33 ~~-t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      .+ |..+||+.+|+    +...+++-++.|...|+++..
T Consensus        27 ~LPse~~La~~~gv----Sr~tVr~Al~~L~~~Gli~~~   61 (129)
T 2ek5_A           27 RVPSTNELAAFHRI----NPATARNGLTLLVEAGILYKK   61 (129)
T ss_dssp             CBCCHHHHHHHTTC----CHHHHHHHHHHHHTTTSEEEE
T ss_pred             cCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCcEEEe
Confidence            55 88999999999    999999999999999999986

>3tqn_A Transcriptional regulator, GNTR family; regulatory functions; 2.80A {Coxiella burnetii}

Probab=81.42  E-value=1.9  Score=30.01  Aligned_cols=34  Identities=15%  Similarity=0.230  Sum_probs=31.7

Q ss_pred             CC-CHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           33 KI-SAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        33 ~~-t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      .+ |..+||+.+|+    +..-+++-++.|...|+++..
T Consensus        32 ~lPs~~~La~~~~v----Sr~tvr~al~~L~~~Gli~~~   66 (113)
T 3tqn_A           32 MIPSIRKISTEYQI----NPLTVSKAYQSLLDDNVIEKR   66 (113)
T ss_dssp             EECCHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             cCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEe
Confidence            44 88999999999    999999999999999999986

>1lva_A Selenocysteine-specific elongation factor; winged-helix, translation; 2.12A {Moorella thermoacetica} SCOP: a.4.5.35 a.4.5.35 a.4.5.35 a.4.5.35 PDB: 2uwm_A 2ply_A 1wsu_A

Probab=80.39  E-value=3.7  Score=33.00  Aligned_cols=59  Identities=17%  Similarity=0.085  Sum_probs=45.9

Q ss_pred             HHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903           16 ASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH   83 (233)
Q Consensus        16 a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~   83 (233)
                      .....|.+.+...|- .|-++.||++.+++    ++..++.+|+.|+..|.+.+.    .++.|-++.
T Consensus       141 ~~~~~i~~~~~~~g~-~pp~~~dl~~~l~~----~~~~~~~~l~~l~~~g~lv~l----~~~~~~~~~  199 (258)
T 1lva_A          141 KLLKDLEDKYRVSRW-QPPSFKEVAGSFNL----DPSELEELLHYLVREGVLVKI----NDEFYWHRQ  199 (258)
T ss_dssp             HHHHHHHHHHHHHTT-SCCBHHHHHHHTTC----CHHHHHHHHHHHHHTTSEEES----SSSBEEEHH
T ss_pred             HHHHHHHHHHHHCCC-CCCCHHHHHhHhCC----CHHHHHHHHHHHHHCCCEEEe----cCCeEEcHH
Confidence            344456667765432 26689999999999    999999999999999999987    567775544

>3rkx_A Biotin-[acetyl-COA-carboxylase] ligase; biotin protein ligase, 3 domains, enzyme DNA binding, biotin coupling domains; 2.10A {Staphylococcus aureus} PDB: 3rir_A* 3rkw_A 3rky_A* 3v7c_A* 3v7s_A* 3v8j_A 3v7r_A 3v8k_A* 3v8l_A* 4dq2_A*

Probab=80.14  E-value=1.8  Score=36.25  Aligned_cols=57  Identities=14%  Similarity=0.132  Sum_probs=45.3

Q ss_pred             hhChhHHHHhc-CCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903           18 ELGVFEIIAKA-GPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH   83 (233)
Q Consensus        18 ~lglfd~L~~~-~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~   83 (233)
                      +..|.+.|.++ +  .+.|.++||+.+++    +...+.+-++.|...|+..+..   .+..|++.+
T Consensus         5 ~~~iL~~L~~~~g--~~~Sg~eLa~~lgv----Sr~aV~k~i~~L~~~G~~i~~~---~~~GY~L~~   62 (323)
T 3rkx_A            5 SQDVLQLLYKNKP--NYISGQSIAESLNI----SRTAVKKVIDQLKLEGCKIDSV---NHKGHLLQQ   62 (323)
T ss_dssp             HHHHHHHHHHHTT--SCBCHHHHHHHHTS----CHHHHHHHHHHHHHTTCEEEEE---TTTEEEEEE
T ss_pred             HHHHHHHHHhCCC--CccCHHHHHHHHCC----CHHHHHHHHHHHHhcCCeEEEe---CCCeEEEec
Confidence            34577888543 2  48999999999999    9999999999999999965532   356788765

---

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	233
d1kyza1	107	a.4.5.29 (A:13-119) Caffeic acid/5-hydroxyferulic	2e-30
d1fp1d2	244	c.66.1.12 (D:129-372) Chalcone O-methyltransferase	7e-30
d1fp1d1	110	a.4.5.29 (D:19-128) Chalcone O-methyltransferase {	2e-29
d1fp2a2	244	c.66.1.12 (A:109-352) Isoflavone O-methyltransfera	4e-28
d1kyza2	243	c.66.1.12 (A:120-362) Caffeic acid/5-hydroxyferuli	1e-27
d1qzza2	256	c.66.1.12 (A:102-357) Aclacinomycin-10-hydroxylase	3e-17
d1tw3a2	253	c.66.1.12 (A:99-351) Carminomycin 4-O-methyltransf	7e-16
d1fp2a1	101	a.4.5.29 (A:8-108) Isoflavone O-methyltransferase	5e-15
d1qzza1	92	a.4.5.29 (A:10-101) Aclacinomycin-10-hydroxylase R	3e-08
d1tw3a1	85	a.4.5.29 (A:14-98) Carminomycin 4-O-methyltransfer	4e-08

>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 =  106 bits (267), Expect = 2e-30
 Identities = 53/95 (55%), Positives = 69/95 (72%), Gaps = 4/95 (4%)

Query: 1   MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRL 60
           MQ A + VLP  +++A EL + EIIAKAGP A+IS +EIA+Q+P++NP+A VMLDR+LRL
Sbjct: 12  MQLASASVLPMILKSALELDLLEIIAKAGPGAQISPIEIASQLPTTNPDAPVMLDRMLRL 71

Query: 61  LVTHRVLRCT----SAGDDQRLYGLAHVAKYFVLN 91
           L  + +L C+      G  QRLYGLA VAKY V N
Sbjct: 72  LACYIILTCSVRTQQDGKVQRLYGLATVAKYLVKN 106

>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 =  109 bits (273), Expect = 7e-30
 Identities = 56/135 (41%), Positives = 83/135 (61%), Gaps = 1/135 (0%)

Query: 100 SRPWLETKPYEIYDAVLEGGIS-FNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNR 158
             P L        +AV++  I  F  VHG   YE+ G D + N +FNK+M++  +    R
Sbjct: 12  CYPALLQVWMNFKEAVVDEDIDLFKNVHGVTKYEFMGKDKKMNQIFNKSMVDVCATEMKR 71

Query: 159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGG 218
           +++   GFE I  LVDVGGG G N+ +IIS Y  IKG+NFDL  VI+++   SG++H+GG
Sbjct: 72  MLEIYTGFEGISTLVDVGGGSGRNLELIISKYPLIKGINFDLPQVIENAPPLSGIEHVGG 131

Query: 219 IMLERIPKGDAILIK 233
            M   +P+GDA+++K
Sbjct: 132 DMFASVPQGDAMILK 146

>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 =  104 bits (260), Expect = 2e-29
 Identities = 40/100 (40%), Positives = 59/100 (59%), Gaps = 7/100 (7%)

Query: 1   MQPAMSIVLPAAMQAASELGVFEIIAKAG-PTAKISAVEIAAQMP--SSNPNAAVMLDRI 57
           M    ++V PA + AA +L +FEIIAKA  P A +S  EIA+++P  + + +    LDR+
Sbjct: 11  MVLTTNLVYPAVLNAAIDLNLFEIIAKATPPGAFMSPSEIASKLPASTQHSDLPNRLDRM 70

Query: 58  LRLLVTHRVLRCT----SAGDDQRLYGLAHVAKYFVLNRD 93
           LRLL ++ VL  T      G  +R+YGL+ V KY V +  
Sbjct: 71  LRLLASYSVLTSTTRTIEDGGAERVYGLSMVGKYLVPDES 110

>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 =  104 bits (261), Expect = 4e-28
 Identities = 40/145 (27%), Positives = 73/145 (50%), Gaps = 6/145 (4%)

Query: 95  VSLCP-----SRPWLETKPYEIYDAVLEGGIS-FNKVHGTGFYEYAGNDFRFNGVFNKAM 148
           + L P       P L    +E+   + E  ++ F    G+GF+++   +  +N  FN AM
Sbjct: 1   LCLAPMVECVLDPTLSGSYHELKKWIYEEDLTLFGVTLGSGFWDFLDKNPEYNTSFNDAM 60

Query: 149 LNHTSIVTNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSS 208
            + + ++   + D    F+ ++ +VDVGGG G    II   +  +K + FD   V+++ S
Sbjct: 61  ASDSKLINLALRDCDFVFDGLESIVDVGGGTGTTAKIICETFPKLKCIVFDRPQVVENLS 120

Query: 209 SYSGVKHIGGIMLERIPKGDAILIK 233
             + + ++GG M   IP  DA+L+K
Sbjct: 121 GSNNLTYVGGDMFTSIPNADAVLLK 145

>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 =  103 bits (258), Expect = 1e-27
 Identities = 73/151 (48%), Positives = 95/151 (62%), Gaps = 15/151 (9%)

Query: 93  DGVSLCP----------SRPWLETKPYEIYDAVLEGGISFNKVHGTGFYEYAGNDFRFNG 142
           DGVS+               W     Y + DAVL+GGI FNK +G   +EY G D RFN 
Sbjct: 1   DGVSISALNLMNQDKVLMESW-----YHLKDAVLDGGIPFNKAYGMTAFEYHGTDPRFNK 55

Query: 143 VFNKAMLNHTSIVTNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH 202
           VFNK M +H++I   +I+++  GFE +K LVDVGGG G  +N I+S Y  IKG+NFDL H
Sbjct: 56  VFNKGMSDHSTITMKKILETYTGFEGLKSLVDVGGGTGAVINTIVSKYPTIKGINFDLPH 115

Query: 203 VIQDSSSYSGVKHIGGIMLERIPKGDAILIK 233
           VI+D+ SY GV+H+GG M   IPK DA+ +K
Sbjct: 116 VIEDAPSYPGVEHVGGDMFVSIPKADAVFMK 146

>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 = 75.8 bits (185), Expect = 3e-17
 Identities = 20/94 (21%), Positives = 38/94 (40%), Gaps = 1/94 (1%)

Query: 113 DAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIKQL 172
           D V  G  ++   +G  F+E    D      F+  M     +      D+   +  ++ +
Sbjct: 27  DVVRTGRPAYAGRYGRPFWEDLSADVALADSFDALMSCDEDLAYEAPADAYD-WSAVRHV 85

Query: 173 VDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQD 206
           +DVGGG G  +  I     H++G   +L+   + 
Sbjct: 86  LDVGGGNGGMLAAIALRAPHLRGTLVELAGPAER 119

>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 = 72.4 bits (176), Expect = 7e-16
 Identities = 16/95 (16%), Positives = 36/95 (37%), Gaps = 1/95 (1%)

Query: 109 YEIYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQ 168
             + DA+  G  ++  ++G  FYE           F+  +     +  +    +   +  
Sbjct: 22  TRLPDAIRTGRPTYESIYGKPFYEDLAGRPDLRASFDSLLACDQDVAFDAPAAAYD-WTN 80

Query: 169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHV 203
           ++ ++DVGGG G     I     H+     +++  
Sbjct: 81  VRHVLDVGGGKGGFAAAIARRAPHVSATVLEMAGT 115

>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 = 66.5 bits (162), Expect = 5e-15
 Identities = 13/90 (14%), Positives = 33/90 (36%), Gaps = 5/90 (5%)

Query: 4   AMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVT 63
             + +   +++ A E+ +  II   G     S   + + +   +      + R++R L  
Sbjct: 17  IYAFIDSMSLKWAVEMNIPNIIQNHGKPI--SLSNLVSILQVPSSK-IGNVRRLMRYLAH 73

Query: 64  HRVLRCTSAGDDQRLYGLAHVAKYFVLNRD 93
           +      +   ++  Y L   ++  V   D
Sbjct: 74  NGFFEIIT--KEEESYALTVASELLVRGSD 101

>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 = 47.4 bits (113), Expect = 3e-08
 Identities = 16/94 (17%), Positives = 34/94 (36%), Gaps = 13/94 (13%)

Query: 1  MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRL 60
          ++   ++V P A++ A+ L + + +  AG     +   +A +  +     +    R++R 
Sbjct: 12 LKNLGNLVTPMALRVAATLRLVDHLL-AGA---DTLAGLADRTDTHPQALS----RLVRH 63

Query: 61 LVTHRVLRCTSAGDDQRLYGLAHVAKYFVLNRDG 94
          L    VL         R      +        DG
Sbjct: 64 LTVVGVL--EGGEKQGRPLRPTRLGMLLA---DG 92

>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 = 4e-08
 Identities = 15/85 (17%), Positives = 31/85 (36%), Gaps = 12/85 (14%)

Query: 5  MSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTH 64
           S+  P  ++ A+ L + + I         +   +AA+  +        L R++R LV  
Sbjct: 10 GSLHTPMVVRTAATLRLVDHILA----GARTVKALAARTDTR----PEALLRLIRHLVAI 61

Query: 65 RVLRCTSAGDDQRLYGLAHVAKYFV 89
           +L   + G     +    V +   
Sbjct: 62 GLLEEDAPG----EFVPTEVGELLA 82

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	233
d1kyza2	243	Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltra	99.97
d1fp1d2	244	Chalcone O-methyltransferase {Alfalfa (Medicago sa	99.97
d1fp2a2	244	Isoflavone O-methyltransferase {Alfalfa (Medicago	99.96
d1qzza2	256	Aclacinomycin-10-hydroxylase RdmB {Streptomyces pu	99.95
d1tw3a2	253	Carminomycin 4-O-methyltransferase {Streptomyces p	99.93
d1fp2a1	101	Isoflavone O-methyltransferase {Alfalfa (Medicago	99.77
d1tw3a1	85	Carminomycin 4-O-methyltransferase {Streptomyces p	99.75
d1kyza1	107	Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltra	99.71
d1qzza1	92	Aclacinomycin-10-hydroxylase RdmB {Streptomyces pu	99.7
d1fp1d1	110	Chalcone O-methyltransferase {Alfalfa (Medicago sa	99.63
d2o57a1	282	Putative sarcosine dimethylglycine methyltransfera	98.88
d1nkva_	245	Hypothetical Protein YjhP {Escherichia coli [TaxId	98.71
d2b3ta1	274	N5-glutamine methyltransferase, HemK {Escherichia	98.68
d1vl5a_	231	Hypothetical protein BH2331 {Bacillus halodurans [	98.64
d1p91a_	268	rRNA methyltransferase RlmA {Escherichia coli [Tax	98.6
d1xxla_	234	Hypothetical protein YcgJ {Bacillus subtilis [TaxI	98.58
d1im8a_	225	Hypothetical protein HI0319 (YecO) {Haemophilus in	98.55
d1dusa_	194	Hypothetical protein MJ0882 {Archaeon Methanococcu	98.53
d1wzna1	251	Hypothetical methyltransferase PH1305 {Archaeon Py	98.5
d1l3ia_	186	Precorrin-6Y methyltransferase (CbiT) {Archaeon Me	98.46
d2gh1a1	281	Methyltransferase BC2162 {Bacillus cereus [TaxId:	98.39
d2ex4a1	222	Adrenal gland protein AD-003 (C9orf32) {Human (Hom	98.34
d2fcaa1	204	tRNA (guanine-N(7)-)-methyltransferase TrmB {Bacil	98.34
d1xtpa_	254	Hypothetical protein Lmaj004091aaa (LmjF30.0810) {	98.31
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	98.3
d1i9ga_	264	Probable methyltransferase Rv2118c {Mycobacterium	98.3
d1yzha1	204	tRNA (guanine-N(7)-)-methyltransferase TrmB {Strep	98.29
d1yb2a1	250	Hypothetical protein Ta0852 {Thermoplasma acidophi	98.28
d2i6ga1	198	Putative methyltransferase TehB {Salmonella typhim	98.26
d2p7ia1	225	Hypothetical protein ECA1738 {Erwinia carotovora [	98.25
d1ve3a1	226	Hypothetical protein PH0226 {Archaeon Pyrococcus h	98.25
d1nw3a_	328	Catalytic, N-terminal domain of histone methyltran	98.23
d1y8ca_	246	Putative methyltransferase CAC2371 {Clostridium ac	98.2
d1dl5a1	213	Protein-L-isoaspartyl O-methyltransferase {Thermot	98.17
d1m6ya2	192	TM0872, methyltransferase domain {Thermotoga marit	98.15
d1zx0a1	229	Guanidinoacetate methyltransferase {Human (Homo sa	98.13
d1ne2a_	197	Hypothetical protein Ta1320 {Archaeon Thermoplasma	98.1
d2avna1	246	Hypothetical methyltransferase TM1389 {Thermotoga	98.09
d2nxca1	254	PrmA-like protein TTHA0656 (TT0836) {Thermus therm	98.08
d1ri5a_	252	mRNA cap (Guanine N-7) methyltransferase {Fungus (	98.06
d1vlma_	208	Possible histamine N-methyltransferase TM1293 {The	98.02
d1pjza_	201	Thiopurine S-methyltransferase {Pseudomonas syring	98.02
d2fyta1	311	Protein arginine N-methyltransferase 3, PRMT3 {Hum	97.99
d1nv8a_	271	N5-glutamine methyltransferase, HemK {Thermotoga m	97.98
d1g6q1_	328	Arginine methyltransferase, HMT1 {Baker's yeast (S	97.96
d1oria_	316	Protein arginine N-methyltransferase 1, PRMT1 {Rat	97.95
d1o54a_	266	Hypothetical protein TM0748 {Thermotoga maritima [	97.95
d1i1na_	224	Protein-L-isoaspartyl O-methyltransferase {Human (	97.92
d2esra1	152	Putative methyltransferase SPy1538 {Streptococcus	97.91
d2fk8a1	280	Methoxy mycolic acid synthase 4, Mma4 {Mycobacteri	97.88
d1kpga_	285	CmaA1 {Mycobacterium tuberculosis [TaxId: 1773]}	97.88
d1nt2a_	209	Fibrillarin homologue {Archaeon Archaeoglobus fulg	97.88
d1vbfa_	224	Protein-L-isoaspartyl O-methyltransferase {Sulfolo	97.85
d2bzga1	229	Thiopurine S-methyltransferase {Human (Homo sapien	97.84
d1wy7a1	201	Hypothetical protein PH1948 {Archaeon Pyrococcus h	97.83
d1kpia_	291	CmaA2 {Mycobacterium tuberculosis [TaxId: 1773]}	97.82
d1g8sa_	230	Fibrillarin homologue {Archaeon Methanococcus jann	97.82
d2frna1	260	Hypothetical protein PH0793 {Pyrococcus horikoshii	97.79
d2b25a1	324	Hypothetical protein FLJ20628 {Human (Homo sapiens	97.78
d1jg1a_	215	Protein-L-isoaspartyl O-methyltransferase {Archaeo	97.76
d2h00a1	250	Methyltransferase 10 domain containing protein MET	97.75
d1r18a_	223	Protein-L-isoaspartyl O-methyltransferase {Fruit f	97.64
d1xvaa_	292	Glycine N-methyltransferase {Rat (Rattus norvegicu	97.63
d1uira_	312	Spermidine synthase {Thermus thermophilus [TaxId:	97.56
d1u2za_	406	Catalytic, N-terminal domain of histone methyltran	97.52
d1qama_	235	rRNA adenine dimethylase {Bacillus subtilis, Ermc'	97.39
d2o07a1	285	Spermidine synthase {Human (Homo sapiens) [TaxId:	97.38
d1iy9a_	274	Spermidine synthase {Bacillus subtilis [TaxId: 142	97.38
d1inla_	295	Spermidine synthase {Thermotoga maritima [TaxId: 2	97.36
d1ub9a_	100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	97.2
d1xj5a_	290	Spermidine synthase {Thale cress (Arabidopsis thal	97.19
d2fpoa1	183	Methylase YhhF {Escherichia coli [TaxId: 562]}	97.17
d1mjfa_	276	Putative spermidine synthetase PF0127 (SpeE) {Arch	97.17
d2b2ca1	312	Spermidine synthase {Caenorhabditis elegans [TaxId	97.17
d1yuba_	245	rRNA adenine dimethylase {Streptococcus pneumoniae	97.09
d1wg8a2	182	TM0872, methyltransferase domain {Thermus thermoph	96.86
d1jqea_	280	Histamine methyltransferase {Human (Homo sapiens)	96.83
d1r7ja_	90	Sso10a (SSO10449) {Archaeon Sulfolobus solfataricu	96.8
d1r1ta_	98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	96.78
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	96.72
d1r1ua_	94	Metal-sensing transcriptional repressor CzrA {Stap	96.7
d1ws6a1	171	Methyltransferase TTHA0928 {Thermus thermophilus [	96.7
d1u2wa1	108	Cadmium efflux system accessory protein CadC {Stap	96.69
d1lvaa3	64	C-terminal fragment of elongation factor SelB {Moo	96.68
d2cl5a1	214	Catechol O-methyltransferase, COMT {Rat (Rattus no	96.66
d2as0a2	324	Hypothetical protein PH1915, middle and C-terminal	96.66
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	96.65
d2avda1	219	COMT domain-containing protein 1, COMTD1 {Human (H	96.57
d1g8aa_	227	Fibrillarin homologue {Archaeon Pyrococcus horikos	96.53
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	96.48
d3ctaa1	85	Ta1064 (RFK), N-terminal domain {Thermoplasma acid	96.44
d2hoea1	62	N-acetylglucosamine kinase {Thermotoga maritima [T	96.35
d2hr3a1	145	Probable transcriptional regulator PA3067 {Pseudom	96.31
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	96.25
d1z6ra1	70	Mlc protein N-terminal domain {Escherichia coli [T	96.2
d2etha1	140	Putative transcriptional regulator TM0816 {Thermot	96.17
d2ih2a1	223	DNA methylase TaqI, N-terminal domain {Thermus aqu	96.1
d1susa1	227	Caffeoyl-CoA O-methyltransferase {Alfalfa (Medicag	96.06
d1zq9a1	278	Probable dimethyladenosine transferase {Human (Hom	96.03
d2bv6a1	136	Transcriptional regulator MgrA {Staphylococcus aur	96.03
d2fhpa1	182	Putative methylase EF2452 {Enterococcus faecalis [	96.0
d1xd7a_	127	Hypothetical protein ywnA {Bacillus subtilis [TaxI	95.97
d2f8la1	328	Hypothetical protein Lmo1582 {Listeria monocytogen	95.95
d1s3ja_	143	Putative transcriptional regulator YusO {Bacillus	95.92
d2igta1	309	Putative methyltransferase Atu0340 {Agrobacterium	95.9
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	95.85
d2p4wa1	194	Transcriptional regulatory protein PF1790 {Pyrococ	95.8
d1qyra_	252	High level kasugamycin resistance protein KsgA {Es	95.78
d1wxxa2	318	Hypothetical protein TTHA1280, middle and C-termin	95.77
d2a14a1	257	Indolethylamine N-methyltransferase, INMT {Human (	95.74
d1ylfa1	138	Hypothetical protein BC1842 {Bacillus cereus [TaxI	95.66
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	95.65
d1ulya_	190	Hypothetical protein PH1932 {Pyrococcus horikoshii	95.65
d1lnwa_	141	MexR repressor {Pseudomonas aeruginosa [TaxId: 287	95.6
d1jgsa_	138	Multiple antibiotic resistance repressor, MarR {Es	95.55
d1uwva2	358	rRNA (Uracil-5-)-methyltransferase RumA, catalytic	95.5
d2hzta1	95	Putative transcriptional regulator YtcD {Bacillus	95.49
d2a61a1	139	Transcriptional regulator TM0710 {Thermotoga marit	95.43
d2fbha1	137	Transcriptional regulator PA3341 {Pseudomonas aeru	95.17
d1z91a1	137	Organic hydroperoxide resistance transcriptional r	95.17
d1lj9a_	144	Transcriptional regulator SlyA {Enterococcus faeca	95.09
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	95.03
d1dpua_	69	C-terminal domain of RPA32 {Human (Homo sapiens) [	95.01
d1j75a_	57	Dlm-1 {Mouse (Mus musculus) [TaxId: 10090]}	95.0
d2obpa1	81	Putative DNA-binding protein ReutB4095 {Ralstonia	94.99
d3deua1	140	Transcriptional regulator SlyA {Salmonella typhimu	94.96
d1jsxa_	207	Glucose-inhibited division protein B (GidB) {Esche	94.96
d1ej0a_	180	RNA methyltransferase FtsJ {Escherichia coli [TaxI	94.89
d2fbia1	136	Probable transcriptional regulator PA4135 {Pseudom	94.89
d1z7ua1	108	Hypothetical protein EF0647 {Enterococcus faecalis	94.86
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	94.76
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	94.75
d2fswa1	102	Hypothetical protein PG0823 {Porphyromonas gingiva	94.71
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	94.7
d2b78a2	317	Hypothetical protein SMu776, middle and C-terminal	94.67
d2g72a1	263	Phenylethanolamine N-methyltransferase, PNMTase {H	94.64
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	94.61
d2ev0a1	61	Manganese transport regulator MntR {Bacillus subti	94.6
d1yyva1	114	Putative transcriptional regulator YtfH {Salmonell	94.5
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	94.35
d2fbka1	172	Transcriptional regulator DR1159 {Deinococcus radi	94.26
d2frha1	115	Pleiotropic regulator of virulence genes, SarA {St	94.2
d2f2ea1	142	Hypothetical protein PA1607 {Pseudomonas aeruginos	94.07
d1p4xa2	125	Staphylococcal accessory regulator A homolog, SarS	93.95
d1p4xa1	125	Staphylococcal accessory regulator A homolog, SarS	93.92
d1xdza_	239	Glucose-inhibited division protein B (GidB) {Bacil	93.84
d2fxaa1	162	Protease production regulatory protein Hpr {Bacill	93.83
d1hsja1	115	Staphylococcal accessory regulator A homolog, SarR	93.77
d2p41a1	257	An RNA cap (nucleoside-2'-O-)-methyltransferase do	93.49
d2gxba1	59	Z-alpha domain of dsRNA-specific adenosine deamina	93.45
d1i4wa_	322	Transcription factor sc-mtTFB {Baker's yeast (Sacc	93.04
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	92.96
d2ifta1	183	Putative methylase HI0767 {Haemophilus influenzae	92.4
d1xmka1	73	Z-alpha domain of dsRNA-specific adenosine deamina	92.11
d1q1ha_	88	Transcription factor E/IIe-alpha, N-terminal domai	91.31
d2p8ta1	69	Hypothetical protein PH0730 {Pyrococcus horikoshii	90.06
d1af7a2	193	Chemotaxis receptor methyltransferase CheR, C-term	89.94
d1cf7a_	67	Cell cycle transcription factor E2F-4 {Human (Homo	89.65
d1bl0a1	54	MarA {Escherichia coli [TaxId: 562]}	89.57
d1zyba1	73	Probable transcription regulator BT4300, C-termina	88.94
d2gaua1	81	Transcriptional regulator PG0396, C-terminal domai	88.62
d1stza1	87	Heat-inducible transcription repressor HrcA, N-ter	88.01
d3bwga1	78	Transcriptional regulator YydK {Bacillus subtilis	87.62
d1ft9a1	80	CO-sensing protein CooA, C-terminal domain {Rhodos	87.55
d2zcwa1	82	Transcriptional regulator TTHA1359, C-terminal dom	87.52
d2okca1	425	Type I restriction enzyme StySJI M protein {Bacter	87.29
d1i5za1	69	Catabolite gene activator protein (CAP), C-termina	86.44
d2g9wa1	122	Hypothetical protein Rv1846c {Mycobacterium tuberc	86.33
d1d5ya1	54	Rob transcription factor, N-terminal domain {Esche	85.93
d2bm8a1	232	Cephalosporin hydroxylase CmcI {Streptomyces clavu	85.92
d1sfua_	70	34L {Yaba-like disease virus, YLDV [TaxId: 132475]	85.9
d1hw1a1	74	Fatty acid responsive transcription factor FadR, N	85.8
d2hs5a1	69	Putative transcriptional regulator RHA1_ro03477 {R	85.43
d1okra_	120	Methicillin resistance regulatory protein MecI {St	85.32
d1xn7a_	78	Hypothetical protein YhgG {Escherichia coli [TaxId	85.29
d3e5ua1	80	Chlorophenol reduction protein CprK {Desulfitobact	84.1
d2oyra1	250	Hypothetical protein YhiQ {Shigella flexneri [TaxI	83.85
d2dk5a1	78	DNA-directed RNA polymerase III subunit RPC6, RPO3	83.71
d1mzba_	134	Ferric uptake regulation protein, FUR {Pseudomonas	83.03
d1xmaa_	103	Predicted transcriptional regulator {Clostridium t	81.68
d1ixca1	89	LysR-type regulatory protein CbnR {Ralstonia eutro	80.17

>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=99.97  E-value=1.6e-31  Score=218.46  Aligned_cols=139  Identities=50%  Similarity=0.861  Sum_probs=129.8

Q ss_pred             CCccchhccccC-----chhhHHHHHHcCCcchhhhhCCccccccccCchHHHHHHHHHHhcchhcHHHHHHhcccccCc
Q 039903           95 VSLCPSRPWLET-----KPYEIYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQI  169 (233)
Q Consensus        95 ~~~~~~~~~~~~-----~~~~L~~~l~~g~~~~~~~~g~~~~~~~~~~~~~~~~f~~am~~~~~~~~~~~~~~~~~~~~~  169 (233)
                      .|+++++.+.++     .|.+|++++|+|+++|+..+|.++|+|+.++|+..+.|+++|...+....+.+++.++.+++.
T Consensus         3 ~s~~~~~~~~~~~~~~~~W~~L~~avrtG~~~f~~~~G~~~~~~~~~~p~~~~~F~~aM~~~~~~~~~~~~~~~~~~~~~   82 (243)
T d1kyza2           3 VSISALNLMNQDKVLMESWYHLKDAVLDGGIPFNKAYGMTAFEYHGTDPRFNKVFNKGMSDHSTITMKKILETYTGFEGL   82 (243)
T ss_dssp             CCTHHHHHHHTSHHHHGGGGGHHHHHHHCSCHHHHHHSSCHHHHGGGCHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSC
T ss_pred             CcHHHHHHHhcCHHHHHHHHHHHHHHhhCCCHHHhhcCCCHHHHHHhCHHHHHHHHHHHhHhhhhHHHHHHHhcccccCC
Confidence            478888877665     899999999999999999999999999999999999999999999988888999998834778


Q ss_pred             ceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCCCCceEEecCcCCCCCCCCEEEeC
Q 039903          170 KQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAILIK  233 (233)
Q Consensus       170 ~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~~ri~~~~gD~f~~~P~~D~~~lk  233 (233)
                      ++|||||||+|.++++++++||+++++++|+|++++.+...+|++++++|||+++|.+|+|+++
T Consensus        83 ~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~~~~~~r~~~~~~d~~~~~P~ad~~~l~  146 (243)
T d1kyza2          83 KSLVDVGGGTGAVINTIVSKYPTIKGINFDLPHVIEDAPSYPGVEHVGGDMFVSIPKADAVFMK  146 (243)
T ss_dssp             SEEEEETCTTSHHHHHHHHHCTTSEEEEEECTTTTTTCCCCTTEEEEECCTTTCCCCCSCEECS
T ss_pred             cEEEEecCCCcHHHHHHHHHCCCCeEEEcccHHhhhhcccCCceEEecccccccCCCcceEEEE
Confidence            9999999999999999999999999999999999999998899999999999999999999885

>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=99.97  E-value=1.3e-31  Score=218.73  Aligned_cols=138  Identities=40%  Similarity=0.710  Sum_probs=117.1

Q ss_pred             CccchhccccC-----chhhHHHHHHcCC-cchhhhhCCccccccccCchHHHHHHHHHHhcchhcHHHHHHhcccccCc
Q 039903           96 SLCPSRPWLET-----KPYEIYDAVLEGG-ISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQI  169 (233)
Q Consensus        96 ~~~~~~~~~~~-----~~~~L~~~l~~g~-~~~~~~~g~~~~~~~~~~~~~~~~f~~am~~~~~~~~~~~~~~~~~~~~~  169 (233)
                      |+++++.+..+     .|.+|++++++|+ ++|+.++|.++|||+.+||+..+.|+++|...+...++.+++.++.|++.
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            68888887765     7999999999876 67999999999999999999999999999999998889999999878999


Q ss_pred             ceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCCCCceEEecCcCCCCCCCCEEEeC
Q 039903          170 KQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAILIK  233 (233)
Q Consensus       170 ~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~~ri~~~~gD~f~~~P~~D~~~lk  233 (233)
                      .+|||||||+|.++++++++||+++++++|+|+|++.+...+||++++||||+++|.+|+|+|+
T Consensus        83 ~~vlDiGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~~~~~~ri~~~~gd~~~~~p~~D~~~l~  146 (244)
T d1fp1d2          83 STLVDVGGGSGRNLELIISKYPLIKGINFDLPQVIENAPPLSGIEHVGGDMFASVPQGDAMILK  146 (244)
T ss_dssp             SEEEEETCTTSHHHHHHHHHCTTCEEEEEECHHHHTTCCCCTTEEEEECCTTTCCCCEEEEEEE
T ss_pred             cEEEEecCCCcHHHHHHHHHCCCCeEEEecchhhhhccCCCCCeEEecCCcccccccceEEEEe
Confidence            9999999999999999999999999999999999999888899999999999999999999985

>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=99.96  E-value=4.2e-30  Score=209.80  Aligned_cols=138  Identities=28%  Similarity=0.513  Sum_probs=122.2

Q ss_pred             CccchhccccC-----chhhHHHHHHcCC-cchhhhhCCccccccccCchHHHHHHHHHHhcchhcHHHHHHhcccccCc
Q 039903           96 SLCPSRPWLET-----KPYEIYDAVLEGG-ISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQI  169 (233)
Q Consensus        96 ~~~~~~~~~~~-----~~~~L~~~l~~g~-~~~~~~~g~~~~~~~~~~~~~~~~f~~am~~~~~~~~~~~~~~~~~~~~~  169 (233)
                      |+.+++.+..+     .|..|+++++++. ++|+.++|.++|+|+.+||+..+.|+++|...+......+.+...+|++.
T Consensus         2 s~ap~~~~~~~p~~~~~w~~l~~~~~~~~~~~f~~a~G~~~~e~l~~~pe~~~~F~~aM~~~s~~~~~~~~~~~~~~~~~   81 (244)
T d1fp2a2           2 CLAPMVECVLDPTLSGSYHELKKWIYEEDLTLFGVTLGSGFWDFLDKNPEYNTSFNDAMASDSKLINLALRDCDFVFDGL   81 (244)
T ss_dssp             CCHHHHHHHTCHHHHHGGGGHHHHHTCSSCCHHHHHHSSCHHHHHHHCHHHHHHHHHHHHHTHHHHHHHHHTCHHHHTTC
T ss_pred             ChHHHHHHHhCHHHHHHHHHHHHHHhcCCCCHHHHhhCCCHHHHHHhCHHHHHHHHHHhhhhhhhhhhhHhhhcccccCc
Confidence            45566666554     7999999999885 68999999999999999999999999999998887666665432238999


Q ss_pred             ceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccCCCCceEEecCcCCCCCCCCEEEeC
Q 039903          170 KQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSSYSGVKHIGGIMLERIPKGDAILIK  233 (233)
Q Consensus       170 ~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~~~ri~~~~gD~f~~~P~~D~~~lk  233 (233)
                      .+|||||||+|.++++++++||+++++++|+|+|++.+...+||++++||||+++|.+|+|+++
T Consensus        82 ~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~vi~~~~~~~rv~~~~gD~f~~~p~aD~~~l~  145 (244)
T d1fp2a2          82 ESIVDVGGGTGTTAKIICETFPKLKCIVFDRPQVVENLSGSNNLTYVGGDMFTSIPNADAVLLK  145 (244)
T ss_dssp             SEEEEETCTTSHHHHHHHHHCTTCEEEEEECHHHHTTCCCBTTEEEEECCTTTCCCCCSEEEEE
T ss_pred             eEEEEecCCccHHHHHHHHhCCCCeEEEecCHHHHHhCcccCceEEEecCcccCCCCCcEEEEE
Confidence            9999999999999999999999999999999999999988899999999999999988999985

>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=99.95  E-value=3.8e-28  Score=199.69  Aligned_cols=138  Identities=18%  Similarity=0.265  Sum_probs=126.0

Q ss_pred             CCccchhccccC------chhhHHHHHHcCCcchhhhhCCccccccccCchHHHHHHHHHHhcchhcHHHHHHhcccccC
Q 039903           95 VSLCPSRPWLET------KPYEIYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQ  168 (233)
Q Consensus        95 ~~~~~~~~~~~~------~~~~L~~~l~~g~~~~~~~~g~~~~~~~~~~~~~~~~f~~am~~~~~~~~~~~~~~~~~~~~  168 (233)
                      .++++|+.+...      +|.+|.+++|+|+++|+..+|.++|+|+.++|+..+.|+++|...+...++.+++.++ |++
T Consensus         3 ~~~~~~~~l~~~~~~~~~~~~~L~~~~rtG~~~~~~~~G~~~~e~~~~~p~~~~~f~~~m~~~~~~~~~~~~~~~d-~~~   81 (256)
T d1qzza2           3 AQQRAWLDLNGAVSHADLAFTGLLDVVRTGRPAYAGRYGRPFWEDLSADVALADSFDALMSCDEDLAYEAPADAYD-WSA   81 (256)
T ss_dssp             TCHHHHHCTTSHHHHHHGGGGGHHHHHHHSCCSHHHHHSSCHHHHHHHCHHHHHHHHHTCGGGSTTTTHHHHHTSC-CTT
T ss_pred             HHHHHHHhhcCchhhhHhhHHHHHHHHHhCCchhhhhhCCCHHHHHHhCHHHHHHHHHHHHhhHHHHHHHHHhcCC-Ccc
Confidence            367777766532      7999999999999999999999999999999999999999999999988999999999 999


Q ss_pred             cceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccC-------CCCceEEecCcCCCCCCC-CEEEeC
Q 039903          169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSS-------YSGVKHIGGIMLERIPKG-DAILIK  233 (233)
Q Consensus       169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~-------~~ri~~~~gD~f~~~P~~-D~~~lk  233 (233)
                      .++|||||||+|.++.+++++||+++++++|+|++++.+++       .+||+++.+|+|+++|.+ |+|+++
T Consensus        82 ~~~vlDvG~G~G~~~~~l~~~~P~~~~~~~Dlp~~~~~a~~~~~~~~~~~ri~~~~~d~~~~~p~~~D~v~~~  154 (256)
T d1qzza2          82 VRHVLDVGGGNGGMLAAIALRAPHLRGTLVELAGPAERARRRFADAGLADRVTVAEGDFFKPLPVTADVVLLS  154 (256)
T ss_dssp             CCEEEEETCTTSHHHHHHHHHCTTCEEEEEECHHHHHHHHHHHHHTTCTTTEEEEECCTTSCCSCCEEEEEEE
T ss_pred             CCEEEEECCCCCHHHHHHHHhhcCcEEEEecChHHHHHHHHHHhhcCCcceeeeeeeeccccccccchhhhcc
Confidence            99999999999999999999999999999999999887764       279999999999999875 999874

>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=99.93  E-value=2e-26  Score=188.94  Aligned_cols=126  Identities=20%  Similarity=0.395  Sum_probs=118.1

Q ss_pred             chhhHHHHHHcCCcchhhhhCCccccccccCchHHHHHHHHHHhcchhcHHHHHHhcccccCcceEEEecCCccHHHHHH
Q 039903          107 KPYEIYDAVLEGGISFNKVHGTGFYEYAGNDFRFNGVFNKAMLNHTSIVTNRIIDSSKGFEQIKQLVDVGGGLGVNVNII  186 (233)
Q Consensus       107 ~~~~L~~~l~~g~~~~~~~~g~~~~~~~~~~~~~~~~f~~am~~~~~~~~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l  186 (233)
                      +|.+|++++|+|+++|+..+|.++|+|+.++|+..+.|+.+|...+...++.+++.++ |++.++|||||||+|.++..+
T Consensus        20 ~~~~L~~~vr~G~~~~~~~~G~~~~~~~~~~~~~~~~f~~~m~~~~~~~~~~~~~~~d-~~~~~~VLDvGcG~G~~~~~l   98 (253)
T d1tw3a2          20 SFTRLPDAIRTGRPTYESIYGKPFYEDLAGRPDLRASFDSLLACDQDVAFDAPAAAYD-WTNVRHVLDVGGGKGGFAAAI   98 (253)
T ss_dssp             GGGGHHHHHHHCCCCHHHHHSSCHHHHHHTCHHHHHHHHHHHTTTTTTTTHHHHHHSC-CTTCSEEEEETCTTSHHHHHH
T ss_pred             cHHHHHHHHHhCCchhhhccCCCHHHHHhhCHHHHHHHHHHHHHhHHHHHHHHHhhcC-CccCCEEEEeCCCCCHHHHHH
Confidence            8999999999999999999999999999999999999999999999888899999999 999999999999999999999


Q ss_pred             HHHcCCCcEEEeechHHHhhccCC-------CCceEEecCcCCCCCCC-CEEEeC
Q 039903          187 ISNYLHIKGVNFDLSHVIQDSSSY-------SGVKHIGGIMLERIPKG-DAILIK  233 (233)
Q Consensus       187 ~~~~P~l~~~v~Dlp~v~~~a~~~-------~ri~~~~gD~f~~~P~~-D~~~lk  233 (233)
                      ++++|+++++++|+|++++.+++.       +||+++.+|+|+++|.. |+|+++
T Consensus        99 a~~~p~~~~~~~D~~~~~~~a~~~~~~~~~~~rv~~~~~D~~~~~~~~~D~v~~~  153 (253)
T d1tw3a2          99 ARRAPHVSATVLEMAGTVDTARSYLKDEGLSDRVDVVEGDFFEPLPRKADAIILS  153 (253)
T ss_dssp             HHHCTTCEEEEEECTTHHHHHHHHHHHTTCTTTEEEEECCTTSCCSSCEEEEEEE
T ss_pred             HHhcceeEEEEccCHHHHHHHHHHHHHhhcccchhhccccchhhcccchhheeec
Confidence            999999999999999988877652       79999999999988875 999873

>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=99.77  E-value=1e-19  Score=127.46  Aligned_cols=86  Identities=15%  Similarity=0.265  Sum_probs=74.5

Q ss_pred             cccccchHHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceec
Q 039903            2 QPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGL   81 (233)
Q Consensus         2 ~~~~~~~~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~l   81 (233)
                      ++++||+.|++|++|++|||||+|++.+  +|+|++|||+++++ ++.+.+.+.|+||+|++.|+|.+...  ++++|++
T Consensus        15 ~~~~gf~~s~aL~~aveLgi~d~l~~~~--~p~t~~eLa~~~~~-~~~~~~~L~RlLR~L~~~gi~~~~~~--~~~~Y~l   89 (101)
T d1fp2a1          15 KHIYAFIDSMSLKWAVEMNIPNIIQNHG--KPISLSNLVSILQV-PSSKIGNVRRLMRYLAHNGFFEIITK--EEESYAL   89 (101)
T ss_dssp             HHHTTHHHHHHHHHHHHTTHHHHHHHHT--SCEEHHHHHHHHTC-CGGGHHHHHHHHHHHHHTTSEEEEES--SSEEEEE
T ss_pred             HHHHhHHHHHHHHHHHHcCcHHHHHHcC--CCCCHHHHHHHcCC-CCccchHHHHHHHHHHhCCceeeecC--CCCeEec
Confidence            5789999999999999999999998875  79999999999998 22245679999999999999987532  4579999


Q ss_pred             cHhhhHhhcCC
Q 039903           82 AHVAKYFVLNR   92 (233)
Q Consensus        82 t~~s~~l~~~~   92 (233)
                      ||.|+.|++++
T Consensus        90 t~~s~~Lv~~~  100 (101)
T d1fp2a1          90 TVASELLVRGS  100 (101)
T ss_dssp             CHHHHTTSTTS
T ss_pred             CHHHHHhhcCC
Confidence            99999888764

>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=99.75  E-value=4.5e-19  Score=120.58  Aligned_cols=78  Identities=18%  Similarity=0.195  Sum_probs=73.2

Q ss_pred             ccccchHHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceecc
Q 039903            3 PAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLA   82 (233)
Q Consensus         3 ~~~~~~~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt   82 (233)
                      .+.+++.+++|++|++|||||+|.+    ||+|++|||+++|+    +++.+.|+||+|+++|+|+++    +++.|++|
T Consensus         8 ~l~~~~~~~aL~~av~L~ifd~l~~----gp~s~~eLA~~~g~----~~~~l~rlLr~l~a~gl~~e~----~~~~y~lt   75 (85)
T d1tw3a1           8 RLGSLHTPMVVRTAATLRLVDHILA----GARTVKALAARTDT----RPEALLRLIRHLVAIGLLEED----APGEFVPT   75 (85)
T ss_dssp             HHHCSHHHHHHHHHHHTTHHHHHHT----TCCBHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEE----ETTEEEEC
T ss_pred             HHHchHHHHHHHHHHHcCcHHHhcc----CCCCHHHHHHHhCc----ChhHHHHHHHHHHHCCCeEec----CCCeEecC
Confidence            4578999999999999999999986    79999999999999    999999999999999999997    68999999


Q ss_pred             HhhhHhhcCC
Q 039903           83 HVAKYFVLNR   92 (233)
Q Consensus        83 ~~s~~l~~~~   92 (233)
                      +.|+.|.++|
T Consensus        76 ~~s~~L~~Dh   85 (85)
T d1tw3a1          76 EVGELLADDH   85 (85)
T ss_dssp             TTGGGGSTTS
T ss_pred             HHHHHhhcCC
Confidence            9999998774

>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=99.71  E-value=1e-17  Score=117.57  Aligned_cols=91  Identities=56%  Similarity=0.856  Sum_probs=77.1

Q ss_pred             CcccccchHHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCC----
Q 039903            1 MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQ----   76 (233)
Q Consensus         1 ~~~~~~~~~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~----   76 (233)
                      |+++++++.+++|++|++|||||+|+..|+.+++|..|||.++...+|..+..++|+||.|++.|+|.+.....++    
T Consensus        12 ~~L~~~~v~pmaLk~AieLgI~DiI~~~G~~~~ls~~eia~~l~~~~p~~~~~L~RilR~Las~~vf~~~~~~~~dg~~~   91 (107)
T d1kyza1          12 MQLASASVLPMILKSALELDLLEIIAKAGPGAQISPIEIASQLPTTNPDAPVMLDRMLRLLACYIILTCSVRTQQDGKVQ   91 (107)
T ss_dssp             HHHHTTTHHHHHHHHHHHTTHHHHHHTTCTTCCBCHHHHHHTSSCCCTTHHHHHHHHHHHHHHTTSEEEEEEECTTSCEE
T ss_pred             HHHHHhhHHHHHHHHHHHcCCHHHHHHcCCCCCCCHHHHHHhcCCCCCcchHHHHHHHHHHHhcCceEEeeecCCCCCee
Confidence            4788999999999999999999999998755688999999999986564577899999999999999864322122    


Q ss_pred             CceeccHhhhHhhcC
Q 039903           77 RLYGLAHVAKYFVLN   91 (233)
Q Consensus        77 ~~y~lt~~s~~l~~~   91 (233)
                      .+|.+||.|++|+++
T Consensus        92 ~~Y~LTpvsk~Lv~d  106 (107)
T d1kyza1          92 RLYGLATVAKYLVKN  106 (107)
T ss_dssp             EEEEECHHHHHHSCC
T ss_pred             eEEecchhHHhhcCC
Confidence            379999999999876

>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=9.3e-18  Score=115.42  Aligned_cols=80  Identities=16%  Similarity=0.207  Sum_probs=71.5

Q ss_pred             CcccccchHHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCcee
Q 039903            1 MQPAMSIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYG   80 (233)
Q Consensus         1 ~~~~~~~~~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~   80 (233)
                      |+++.+++.+++|++|++|||||+|.+    ||+|++|||+++++    +++.+.|+||+|+++|+|++.++  +.+.|+
T Consensus        12 l~~~~~~~~~~~L~~aveL~ifd~L~~----gp~t~~eLA~~~g~----~~~~l~rLlr~L~a~gll~~~~d--~~~~~~   81 (92)
T d1qzza1          12 LKNLGNLVTPMALRVAATLRLVDHLLA----GADTLAGLADRTDT----HPQALSRLVRHLTVVGVLEGGEK--QGRPLR   81 (92)
T ss_dssp             HHTTTCCHHHHHHHHHHHTTHHHHHHT----TCCSHHHHHHHHTC----CHHHHHHHHHHHHHTTSEECCCC---CCCCE
T ss_pred             HHHHHchHHHHHHHHHHHcCchHHHhC----CCCCHHHHHHHHCc----CchHHHHHHHHHHHCCCeeeecC--CCceec
Confidence            367899999999999999999999987    79999999999999    99999999999999999999732  234688


Q ss_pred             ccHhhhHhhc
Q 039903           81 LAHVAKYFVL   90 (233)
Q Consensus        81 lt~~s~~l~~   90 (233)
                      +|+.|..|.+
T Consensus        82 ~t~~g~lL~d   91 (92)
T d1qzza1          82 PTRLGMLLAD   91 (92)
T ss_dssp             ECTTGGGGST
T ss_pred             ccHHHHhccC
Confidence            8999998875

>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=99.63  E-value=2.2e-16  Score=110.96  Aligned_cols=92  Identities=42%  Similarity=0.645  Sum_probs=74.3

Q ss_pred             CcccccchHHHHHHHHHhhChhHHHHhcC-CCCCCCHHHHHHhCCC--CCCCChhhHHHHHHHHhcCCceeeeccCCCC-
Q 039903            1 MQPAMSIVLPAAMQAASELGVFEIIAKAG-PTAKISAVEIAAQMPS--SNPNAAVMLDRILRLLVTHRVLRCTSAGDDQ-   76 (233)
Q Consensus         1 ~~~~~~~~~s~~L~~a~~lglfd~L~~~~-~~~~~t~~elA~~~~~--~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~-   76 (233)
                      |+++.++..+++|++|++|||||+|+..| +.+++|++|||.++.+  .+|..+..|.|+||.|++.|+|.+...++++ 
T Consensus        11 ~~L~~~~v~pMaLk~AieLgI~diI~~~G~~~~~ls~~ela~~lp~~~~~p~~~~~L~RiLRlLas~~vf~~~~~~~~~g   90 (110)
T d1fp1d1          11 MVLTTNLVYPAVLNAAIDLNLFEIIAKATPPGAFMSPSEIASKLPASTQHSDLPNRLDRMLRLLASYSVLTSTTRTIEDG   90 (110)
T ss_dssp             HHHHHTTHHHHHHHHHHHTTHHHHHHTCSSTTCCBCHHHHHTTSCGGGCCTTHHHHHHHHHHHHHHTTSEEEEEEECTTS
T ss_pred             HHHHHhhHHHHHHHHHHHcCCHHHHHHcCCCCCCCCHHHHHHhCCCCCCCccHHHHHHHHHHHHHHcCccccccccCCCC
Confidence            46889999999999999999999999876 3456899999999885  1232355799999999999999754322122 


Q ss_pred             ---CceeccHhhhHhhcCC
Q 039903           77 ---RLYGLAHVAKYFVLNR   92 (233)
Q Consensus        77 ---~~y~lt~~s~~l~~~~   92 (233)
                         ..|.+||.|++|++++
T Consensus        91 ~~e~~Y~Ltpvsk~Lv~de  109 (110)
T d1fp1d1          91 GAERVYGLSMVGKYLVPDE  109 (110)
T ss_dssp             CEEEEEEECTTGGGGSTTC
T ss_pred             CeeeEEecchhhHhhcCCC
Confidence               2699999999999875

>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=98.88  E-value=1.7e-09  Score=88.10  Aligned_cols=87  Identities=14%  Similarity=0.244  Sum_probs=65.7

Q ss_pred             HHHHHHhcchhcHHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceE
Q 039903          144 FNKAMLNHTSIVTNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKH  215 (233)
Q Consensus       144 f~~am~~~~~~~~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~  215 (233)
                      +..++.......+..+....+ +++..+|||||||+|.++..+++++ +.+++.+|+ |..++.|++.       ++|++
T Consensus        44 ~~~a~~~~~~~~~~~l~~~~~-l~~~~~vLDiGcG~G~~~~~la~~~-~~~v~gvD~s~~~i~~a~~~~~~~gl~~~v~~  121 (282)
T d2o57a1          44 IREASLRTDEWLASELAMTGV-LQRQAKGLDLGAGYGGAARFLVRKF-GVSIDCLNIAPVQNKRNEEYNNQAGLADNITV  121 (282)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTC-CCTTCEEEEETCTTSHHHHHHHHHH-CCEEEEEESCHHHHHHHHHHHHHHTCTTTEEE
T ss_pred             HHHHHHHHHHHHHHHHHHhcC-CCCCCEEEEeCCCCcHHHhhhhccC-CcEEEEEeccchhhhhhhcccccccccccccc
Confidence            444444444444455555555 7888999999999999999999876 578999998 5567766642       69999


Q ss_pred             EecCcCC-CCCCC--CEEEe
Q 039903          216 IGGIMLE-RIPKG--DAILI  232 (233)
Q Consensus       216 ~~gD~f~-~~P~~--D~~~l  232 (233)
                      +.+|+.+ ++|.+  |+|+.
T Consensus       122 ~~~d~~~l~~~~~sfD~V~~  141 (282)
T d2o57a1         122 KYGSFLEIPCEDNSYDFIWS  141 (282)
T ss_dssp             EECCTTSCSSCTTCEEEEEE
T ss_pred             cccccccccccccccchhhc
Confidence            9999998 88865  99864

>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=98.71  E-value=1.7e-08  Score=80.27  Aligned_cols=74  Identities=15%  Similarity=0.166  Sum_probs=58.9

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCCCCCCC-
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLERIPKG-  227 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~~P~~-  227 (233)
                      ..+.+.+. +....+|||||||+|.++..++++++ .+++.+|+ |..++.|++.       +||+++.+|+.+..|.+ 
T Consensus        23 ~~l~~~~~-l~pg~~VLDiGCG~G~~~~~la~~~~-~~v~GvD~s~~~~~~ar~~~~~~gl~~~v~~~~~d~~~~~~~~~  100 (245)
T d1nkva_          23 ATLGRVLR-MKPGTRILDLGSGSGEMLCTWARDHG-ITGTGIDMSSLFTAQAKRRAEELGVSERVHFIHNDAAGYVANEK  100 (245)
T ss_dssp             HHHHHHTC-CCTTCEEEEETCTTCHHHHHHHHHTC-CEEEEEESCHHHHHHHHHHHHHTTCTTTEEEEESCCTTCCCSSC
T ss_pred             HHHHHHcC-CCCCCEEEEEcCCCCHHHHHHHHhcC-CEEEEEecccchhhHHHHHHHHhhccccchhhhhHHhhccccCc
Confidence            34566666 77789999999999999999998876 78999999 4567666542       68999999999865553 


Q ss_pred             -CEEEe
Q 039903          228 -DAILI  232 (233)
Q Consensus       228 -D~~~l  232 (233)
                       |+++.
T Consensus       101 fD~v~~  106 (245)
T d1nkva_         101 CDVAAC  106 (245)
T ss_dssp             EEEEEE
T ss_pred             eeEEEE
Confidence             88863

>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=98.68  E-value=1.6e-08  Score=82.08  Aligned_cols=65  Identities=14%  Similarity=0.174  Sum_probs=57.0

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCCCCCC-C-CEEE
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLERIPK-G-DAIL  231 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~~P~-~-D~~~  231 (233)
                      ++..+++|+|||+|..++.+++.+|+.+++..|. +.+++.|+++      +||+++.+|+|+++|. . |+|+
T Consensus       107 ~~~~~vlDlGtGSG~I~i~la~~~p~~~v~avDis~~Al~~A~~Na~~~~~~~v~~~~~d~~~~~~~~~fDlIv  180 (274)
T d2b3ta1         107 EQPCRILDLGTGTGAIALALASERPDCEIIAVDRMPDAVSLAQRNAQHLAIKNIHILQSDWFSALAGQQFAMIV  180 (274)
T ss_dssp             SSCCEEEEETCTTSHHHHHHHHHCTTSEEEEECSSHHHHHHHHHHHHHHTCCSEEEECCSTTGGGTTCCEEEEE
T ss_pred             ccccceeeeehhhhHHHHHHHhhCCcceeeeccchhHHHhHHHHHHHHhCcccceeeecccccccCCCceeEEE
Confidence            4456799999999999999999999999999998 5688888764      6899999999998876 3 8886

>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=98.64  E-value=2.5e-08  Score=78.21  Aligned_cols=73  Identities=16%  Similarity=0.236  Sum_probs=58.0

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccC------CCCceEEecCcCC-CCCCC-
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSS------YSGVKHIGGIMLE-RIPKG-  227 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~------~~ri~~~~gD~f~-~~P~~-  227 (233)
                      ..+++..+ .++..+|||||||+|.++..++++.+  +++.+|+ ++.++.|++      .++|+++.+|+.+ ++|.+ 
T Consensus         5 ~~ll~~~~-l~~~~rVLDiGcG~G~~~~~l~~~~~--~v~gvD~s~~~i~~A~~~~~~~~~~~i~~~~~d~~~l~~~~~~   81 (231)
T d1vl5a_           5 AKLMQIAA-LKGNEEVLDVATGGGHVANAFAPFVK--KVVAFDLTEDILKVARAFIEGNGHQQVEYVQGDAEQMPFTDER   81 (231)
T ss_dssp             HHHHHHHT-CCSCCEEEEETCTTCHHHHHHGGGSS--EEEEEESCHHHHHHHHHHHHHTTCCSEEEEECCC-CCCSCTTC
T ss_pred             HHHHHhcC-CCCcCEEEEecccCcHHHHHHHHhCC--EEEEEECCHHHHhhhhhcccccccccccccccccccccccccc
Confidence            35566666 78889999999999999999999875  5788998 457776653      3789999999998 78764 


Q ss_pred             -CEEEe
Q 039903          228 -DAILI  232 (233)
Q Consensus       228 -D~~~l  232 (233)
                       |+|+.
T Consensus        82 fD~v~~   87 (231)
T d1vl5a_          82 FHIVTC   87 (231)
T ss_dssp             EEEEEE
T ss_pred             cccccc
Confidence             98874

>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=98.60  E-value=3.1e-08  Score=80.05  Aligned_cols=65  Identities=18%  Similarity=0.307  Sum_probs=56.7

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccC-CCCceEEecCcCC-CCCCC--CEEE
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSS-YSGVKHIGGIMLE-RIPKG--DAIL  231 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~-~~ri~~~~gD~f~-~~P~~--D~~~  231 (233)
                      .+..+|||||||+|.++..+++.+|+.+++.+|+ +..++.|++ .++++++.+|..+ +++.+  |+++
T Consensus        83 ~~~~~iLDiGcG~G~~~~~l~~~~~~~~~~giD~s~~~~~~a~~~~~~~~~~~~d~~~l~~~~~sfD~v~  152 (268)
T d1p91a_          83 DKATAVLDIGCGEGYYTHAFADALPEITTFGLDVSKVAIKAAAKRYPQVTFCVASSHRLPFSDTSMDAII  152 (268)
T ss_dssp             TTCCEEEEETCTTSTTHHHHHHTCTTSEEEEEESCHHHHHHHHHHCTTSEEEECCTTSCSBCTTCEEEEE
T ss_pred             CCCCEEEEeCCCCcHHHHHHHHHCCCCEEEEecchHhhhhhhhcccccccceeeehhhccCCCCCEEEEe
Confidence            4568999999999999999999999999999998 557777765 4899999999998 78764  8876

>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=98.58  E-value=3.6e-08  Score=77.75  Aligned_cols=72  Identities=18%  Similarity=0.329  Sum_probs=59.3

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC------CCceEEecCcCC-CCCCC--
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY------SGVKHIGGIMLE-RIPKG--  227 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~------~ri~~~~gD~f~-~~P~~--  227 (233)
                      -+++..+ ++...+|||||||+|.++..++++.+  +++.+|+. ..++.|++.      +++.++.+|..+ ++|.+  
T Consensus         7 ~l~~~~~-~~~~~rILDiGcGtG~~~~~la~~~~--~v~gvD~S~~~l~~A~~~~~~~~~~~~~~~~~d~~~~~~~~~~f   83 (234)
T d1xxla_           7 LMIKTAE-CRAEHRVLDIGAGAGHTALAFSPYVQ--ECIGVDATKEMVEVASSFAQEKGVENVRFQQGTAESLPFPDDSF   83 (234)
T ss_dssp             HHHHHHT-CCTTCEEEEESCTTSHHHHHHGGGSS--EEEEEESCHHHHHHHHHHHHHHTCCSEEEEECBTTBCCSCTTCE
T ss_pred             HHHHHhC-CCCCCEEEEeCCcCcHHHHHHHHhCC--eEEEEeCChhhhhhhhhhhccccccccccccccccccccccccc
Confidence            3556777 88899999999999999999999875  58999985 467766542      689999999988 77765  


Q ss_pred             CEEEe
Q 039903          228 DAILI  232 (233)
Q Consensus       228 D~~~l  232 (233)
                      |+|+.
T Consensus        84 D~v~~   88 (234)
T d1xxla_          84 DIITC   88 (234)
T ss_dssp             EEEEE
T ss_pred             ceeee
Confidence            98874

>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=98.55  E-value=1.1e-07  Score=74.45  Aligned_cols=66  Identities=12%  Similarity=0.142  Sum_probs=53.1

Q ss_pred             cCcceEEEecCCccHHHHHHHHH--cCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCC-CCCCCCEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISN--YLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLE-RIPKGDAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~--~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~-~~P~~D~~~l  232 (233)
                      +...+|||||||+|..+..+++.  +|+.+++++|+ |+.++.|++.       .++++..+|+.+ +.+..|++++
T Consensus        38 ~~~~~vLDlGCGtG~~~~~l~~~~~~~~~~v~giD~S~~ml~~A~~~~~~~~~~~~~~~~~~d~~~~~~~~~d~i~~  114 (225)
T d1im8a_          38 TADSNVYDLGCSRGAATLSARRNINQPNVKIIGIDNSQPMVERCRQHIAAYHSEIPVEILCNDIRHVEIKNASMVIL  114 (225)
T ss_dssp             CTTCEEEEESCTTCHHHHHHHHTCCCSSCEEEEECSCHHHHHHHHHHHHTSCCSSCEEEECSCTTTCCCCSEEEEEE
T ss_pred             CCCCEEEEeccchhhHHHHHHHhhcCCCCceEEeCCCHHHHHHHHHHhHhhcccchhhhccchhhccccccceeeEE
Confidence            45579999999999999999986  58999999999 6688888642       578888889887 5555576653

>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=98.53  E-value=8.4e-08  Score=73.62  Aligned_cols=71  Identities=13%  Similarity=0.247  Sum_probs=56.2

Q ss_pred             HHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccC--------CCCceEEecCcCCCCCCC--
Q 039903          159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSS--------YSGVKHIGGIMLERIPKG--  227 (233)
Q Consensus       159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~--------~~ri~~~~gD~f~~~P~~--  227 (233)
                      +++.++ -.+..+|+|||||+|.++..+++.+|+  ++++|+ |.+++.+++        ..+++++.+|++++++..  
T Consensus        44 Li~~l~-~~~~~~VLDiGcG~G~~~~~la~~~~~--v~~iD~s~~~i~~a~~n~~~~~l~~~~i~~~~~d~~~~~~~~~f  120 (194)
T d1dusa_          44 LVENVV-VDKDDDILDLGCGYGVIGIALADEVKS--TTMADINRRAIKLAKENIKLNNLDNYDIRVVHSDLYENVKDRKY  120 (194)
T ss_dssp             HHHHCC-CCTTCEEEEETCTTSHHHHHHGGGSSE--EEEEESCHHHHHHHHHHHHHTTCTTSCEEEEECSTTTTCTTSCE
T ss_pred             HHHhCC-cCCCCeEEEEeecCChhHHHHHhhccc--cceeeeccccchhHHHHHHHhCCccceEEEEEcchhhhhccCCc
Confidence            455555 566789999999999999999999885  677787 567777754        257999999999976653  


Q ss_pred             CEEEe
Q 039903          228 DAILI  232 (233)
Q Consensus       228 D~~~l  232 (233)
                      |++++
T Consensus       121 D~Ii~  125 (194)
T d1dusa_         121 NKIIT  125 (194)
T ss_dssp             EEEEE
T ss_pred             eEEEE
Confidence            98875

>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=98.50  E-value=2.1e-07  Score=73.61  Aligned_cols=72  Identities=17%  Similarity=0.316  Sum_probs=56.5

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC-----CCceEEecCcCC-CCCCC-CE
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY-----SGVKHIGGIMLE-RIPKG-DA  229 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~-----~ri~~~~gD~f~-~~P~~-D~  229 (233)
                      .+++.+. .++.++|||||||+|.++..++++..  +++++|+. ..++.|++.     .+|+++.+|+.+ ++|.- |+
T Consensus        32 ~~~~~~~-~~~~~~iLDiGcGtG~~~~~l~~~~~--~v~gvD~s~~mi~~a~~~~~~~~~~i~~~~~d~~~l~~~~~fD~  108 (251)
T d1wzna1          32 EIFKEDA-KREVRRVLDLACGTGIPTLELAERGY--EVVGLDLHEEMLRVARRKAKERNLKIEFLQGDVLEIAFKNEFDA  108 (251)
T ss_dssp             HHHHHTC-SSCCCEEEEETCTTCHHHHHHHHTTC--EEEEEESCHHHHHHHHHHHHHTTCCCEEEESCGGGCCCCSCEEE
T ss_pred             HHHHHhc-CCCCCEEEEeCCCCCccchhhcccce--EEEEEeeccccccccccccccccccchheehhhhhcccccccch
Confidence            3444444 56678999999999999999999754  68999985 588877653     589999999988 77764 88


Q ss_pred             EEe
Q 039903          230 ILI  232 (233)
Q Consensus       230 ~~l  232 (233)
                      ++.
T Consensus       109 I~~  111 (251)
T d1wzna1         109 VTM  111 (251)
T ss_dssp             EEE
T ss_pred             Hhh
Confidence            763

>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=98.46  E-value=7.3e-08  Score=73.52  Aligned_cols=71  Identities=18%  Similarity=0.119  Sum_probs=55.3

Q ss_pred             HHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCC-CCC--CC
Q 039903          159 IIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLE-RIP--KG  227 (233)
Q Consensus       159 ~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~-~~P--~~  227 (233)
                      ++..+. ..+..+|+|||||+|.+++++++..+  +++.+|+ |+.++.|+++       +||+++.+|+.+ ..+  ..
T Consensus        25 il~~l~-~~~g~~VLDiGcGsG~~s~~lA~~~~--~V~avD~~~~~l~~a~~n~~~~gl~~~v~~~~gda~~~~~~~~~~  101 (186)
T d1l3ia_          25 IMCLAE-PGKNDVAVDVGCGTGGVTLELAGRVR--RVYAIDRNPEAISTTEMNLQRHGLGDNVTLMEGDAPEALCKIPDI  101 (186)
T ss_dssp             HHHHHC-CCTTCEEEEESCTTSHHHHHHHTTSS--EEEEEESCHHHHHHHHHHHHHTTCCTTEEEEESCHHHHHTTSCCE
T ss_pred             HHHhcC-CCCCCEEEEEECCeEcccccccccce--EEEEecCCHHHHHHHHHHHHHcCCCcceEEEECchhhcccccCCc
Confidence            445555 66778999999999999999998765  6889998 5688877653       699999999887 333  34


Q ss_pred             CEEEe
Q 039903          228 DAILI  232 (233)
Q Consensus       228 D~~~l  232 (233)
                      |++++
T Consensus       102 D~v~~  106 (186)
T d1l3ia_         102 DIAVV  106 (186)
T ss_dssp             EEEEE
T ss_pred             CEEEE
Confidence            88764

>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=98.39  E-value=2.2e-07  Score=75.45  Aligned_cols=67  Identities=15%  Similarity=0.206  Sum_probs=55.6

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCC-CcEEEeec-hHHHhhccCC-----CCceEEecCcCC-CCCCC-CEEEe
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLH-IKGVNFDL-SHVIQDSSSY-----SGVKHIGGIMLE-RIPKG-DAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~-l~~~v~Dl-p~v~~~a~~~-----~ri~~~~gD~f~-~~P~~-D~~~l  232 (233)
                      +++..+|||||||+|.++..+++.+|. .+++++|+ +..++.|+++     .+++|+.+|+.+ +++.. |+|+.
T Consensus        25 ~~~~~~ILDiGcG~G~~~~~la~~~~~~~~v~giD~s~~~l~~a~~~~~~~~~~~~f~~~d~~~~~~~~~fD~v~~  100 (281)
T d2gh1a1          25 ITKPVHIVDYGCGYGYLGLVLMPLLPEGSKYTGIDSGETLLAEARELFRLLPYDSEFLEGDATEIELNDKYDIAIC  100 (281)
T ss_dssp             CCSCCEEEEETCTTTHHHHHHTTTSCTTCEEEEEECCHHHHHHHHHHHHSSSSEEEEEESCTTTCCCSSCEEEEEE
T ss_pred             cCCcCEEEEecCcCCHHHHHHHHhCCCCCEEEEEecchhHhhhhhcccccccccccccccccccccccCCceEEEE
Confidence            677899999999999999999999885 78999998 4577777653     369999999988 66655 98874

>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=98.34  E-value=1.4e-07  Score=73.69  Aligned_cols=65  Identities=14%  Similarity=0.180  Sum_probs=52.4

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCC-CCCCC--CEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLE-RIPKG--DAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~-~~P~~--D~~~l  232 (233)
                      .+..+|||||||+|.++..++++++. +++++|+ +..++.|++.      ++++|+.+|+.+ +++..  |+|+.
T Consensus        59 ~~~~~vLDiGcG~G~~~~~l~~~~~~-~v~~vD~s~~~l~~ak~~~~~~~~~~~~f~~~d~~~~~~~~~~fD~I~~  133 (222)
T d2ex4a1          59 TGTSCALDCGAGIGRITKRLLLPLFR-EVDMVDITEDFLVQAKTYLGEEGKRVRNYFCCGLQDFTPEPDSYDVIWI  133 (222)
T ss_dssp             CCCSEEEEETCTTTHHHHHTTTTTCS-EEEEEESCHHHHHHHHHHTGGGGGGEEEEEECCGGGCCCCSSCEEEEEE
T ss_pred             CCCCEEEEeccCCCHhhHHHHHhcCC-EEEEeecCHHHhhcccccccccccccccccccccccccccccccccccc
Confidence            45689999999999999999887774 7899998 5688877652      578999999988 65553  88875

>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=98.34  E-value=2.8e-07  Score=71.43  Aligned_cols=64  Identities=17%  Similarity=0.181  Sum_probs=50.6

Q ss_pred             cceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccC------CCCceEEecCcCC---CCCCC--CEEEe
Q 039903          169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSS------YSGVKHIGGIMLE---RIPKG--DAILI  232 (233)
Q Consensus       169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~------~~ri~~~~gD~f~---~~P~~--D~~~l  232 (233)
                      -..+||||||+|.++..+++++|+..++.+|+ +..+..+..      .++|.++.+|+..   -+|.+  |.+++
T Consensus        30 ~PlvLeIGcG~G~~~~~lA~~~p~~~~iGiD~~~~~i~~a~~~~~~~~l~Nv~~~~~Da~~l~~~~~~~~~d~v~i  105 (204)
T d2fcaa1          30 NPIHIEVGTGKGQFISGMAKQNPDINYIGIELFKSVIVTAVQKVKDSEAQNVKLLNIDADTLTDVFEPGEVKRVYL  105 (204)
T ss_dssp             CCEEEEECCTTSHHHHHHHHHCTTSEEEEECSCHHHHHHHHHHHHHSCCSSEEEECCCGGGHHHHCCTTSCCEEEE
T ss_pred             CceEEEEEecCcHHHHHHHHhCCCCcEEEeecchHHHHHHHHHHHHHhccCchhcccchhhhhcccCchhhhcccc
Confidence            35799999999999999999999999999997 555555432      2789999999875   26653  66553

>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=98.31  E-value=3.8e-07  Score=72.94  Aligned_cols=73  Identities=19%  Similarity=0.262  Sum_probs=57.1

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC----CCceEEecCcCC-CCCCC--CE
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY----SGVKHIGGIMLE-RIPKG--DA  229 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~----~ri~~~~gD~f~-~~P~~--D~  229 (233)
                      .+++.++ ..+..++||||||+|.++..|++++++ +++.+|. ++.++.|++.    ++++++.+|+.+ +++.+  |+
T Consensus        84 ~fl~~l~-~~~~~~vLD~GcG~G~~t~~ll~~~~~-~v~~vD~s~~~l~~a~~~~~~~~~~~~~~~d~~~~~~~~~~fD~  161 (254)
T d1xtpa_          84 NFIASLP-GHGTSRALDCGAGIGRITKNLLTKLYA-TTDLLEPVKHMLEEAKRELAGMPVGKFILASMETATLPPNTYDL  161 (254)
T ss_dssp             HHHHTST-TCCCSEEEEETCTTTHHHHHTHHHHCS-EEEEEESCHHHHHHHHHHTTTSSEEEEEESCGGGCCCCSSCEEE
T ss_pred             HHHhhCC-CCCCCeEEEecccCChhhHHHHhhcCc-eEEEEcCCHHHHHhhhccccccccceeEEccccccccCCCccce
Confidence            4555555 567789999999999999999988776 7888997 4577877642    568999999987 55543  99


Q ss_pred             EEe
Q 039903          230 ILI  232 (233)
Q Consensus       230 ~~l  232 (233)
                      |++
T Consensus       162 I~~  164 (254)
T d1xtpa_         162 IVI  164 (254)
T ss_dssp             EEE
T ss_pred             EEe
Confidence            875

>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=98.30  E-value=5.9e-07  Score=58.14  Aligned_cols=60  Identities=13%  Similarity=0.164  Sum_probs=52.2

Q ss_pred             hChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHh
Q 039903           19 LGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYF   88 (233)
Q Consensus        19 lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l   88 (233)
                      +.|.+.+...+  .|.|+.|||+++++    +...+.|+|..|+..|+++++    ++++|.+++..-.|
T Consensus         8 l~IL~~~a~~~--~~~s~~eia~~~~~----~~st~~rll~tL~~~g~l~~~----~~g~y~lG~~l~~l   67 (75)
T d1mkma1           8 FEILDFIVKNP--GDVSVSEIAEKFNM----SVSNAYKYMVVLEEKGFVLRK----KDKRYVPGYKLIEY   67 (75)
T ss_dssp             HHHHHHHHHCS--SCBCHHHHHHHTTC----CHHHHHHHHHHHHHTTSEEEC----TTSCEEECTHHHHH
T ss_pred             HHHHHHHHhCC--CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEC----CCCCEeecHHHHHH
Confidence            45788888875  68999999999999    999999999999999999997    57899998755433

>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=98.30  E-value=7.2e-07  Score=71.64  Aligned_cols=88  Identities=9%  Similarity=0.223  Sum_probs=69.7

Q ss_pred             HHHHHHhcchhc----HHHHHHhcccccCcceEEEecCCccHHHHHHHHH-cCCCcEEEeec-hHHHhhccCC-------
Q 039903          144 FNKAMLNHTSIV----TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISN-YLHIKGVNFDL-SHVIQDSSSY-------  210 (233)
Q Consensus       144 f~~am~~~~~~~----~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~-~P~l~~~v~Dl-p~v~~~a~~~-------  210 (233)
                      |...|...++..    +..++..++ .+...+|||+|||+|.++..|++. .|+-+++.+|. ++.++.|+++       
T Consensus        69 ~~~~~~r~tqiiypkD~s~Ii~~l~-i~PG~~VLE~G~GsG~lt~~La~~vgp~G~V~~~d~~~~~~~~Ar~n~~~~~~~  147 (264)
T d1i9ga_          69 YVMSMPRGPQVIYPKDAAQIVHEGD-IFPGARVLEAGAGSGALTLSLLRAVGPAGQVISYEQRADHAEHARRNVSGCYGQ  147 (264)
T ss_dssp             HHTTSCSCSCCCCHHHHHHHHHHTT-CCTTCEEEEECCTTSHHHHHHHHHHCTTSEEEEECSCHHHHHHHHHHHHHHHTS
T ss_pred             HHhhccCCccccchHHHHHHHHHhC-CCCCCEEEecCcCCcHHHHHHHHhhCCCcEEEEecCCHHHHHHHHHhhhhhccC
Confidence            445666655543    445666666 788899999999999999999998 79999999997 5677777652       


Q ss_pred             --CCceEEecCcCC-CCCCC--CEEEe
Q 039903          211 --SGVKHIGGIMLE-RIPKG--DAILI  232 (233)
Q Consensus       211 --~ri~~~~gD~f~-~~P~~--D~~~l  232 (233)
                        ++++++.+|+.+ ++|.+  |++++
T Consensus       148 ~~~nv~~~~~d~~~~~~~~~~fDaV~l  174 (264)
T d1i9ga_         148 PPDNWRLVVSDLADSELPDGSVDRAVL  174 (264)
T ss_dssp             CCTTEEEECSCGGGCCCCTTCEEEEEE
T ss_pred             CCceEEEEecccccccccCCCcceEEE
Confidence              789999999998 78874  98876

>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=98.29  E-value=6.6e-07  Score=69.20  Aligned_cols=64  Identities=19%  Similarity=0.213  Sum_probs=50.2

Q ss_pred             cceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccC------CCCceEEecCcCC---CCCCC--CEEEe
Q 039903          169 IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSS------YSGVKHIGGIMLE---RIPKG--DAILI  232 (233)
Q Consensus       169 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~------~~ri~~~~gD~f~---~~P~~--D~~~l  232 (233)
                      ...+||||||.|.++..+++.+|+..++.+|+ +..+..+.+      .++|.++.+|..+   -+|..  |.+++
T Consensus        32 ~plvLdIGcG~G~~~~~lA~~~p~~~~iGid~~~~~v~~a~~~~~~~~l~Ni~~~~~da~~l~~~~~~~~~~~i~i  107 (204)
T d1yzha1          32 NPIHVEVGSGKGAFVSGMAKQNPDINYIGIDIQKSVLSYALDKVLEVGVPNIKLLWVDGSDLTDYFEDGEIDRLYL  107 (204)
T ss_dssp             CCEEEEESCTTSHHHHHHHHHCTTSEEEEEESCHHHHHHHHHHHHHHCCSSEEEEECCSSCGGGTSCTTCCSEEEE
T ss_pred             CCeEEEEeccCCHHHHHHHHHCCCCceEEEeccHHHHHHHHHhhhhhccccceeeecCHHHHhhhccCCceehhcc
Confidence            35799999999999999999999999999997 445555533      2789999999765   35653  66543

>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=98.28  E-value=6.7e-07  Score=71.31  Aligned_cols=88  Identities=16%  Similarity=0.195  Sum_probs=60.4

Q ss_pred             HHHHHHhcchhc----HHHHHHhcccccCcceEEEecCCccHHHHHHHHH-cCCCcEEEeech-HHHhhccCC-------
Q 039903          144 FNKAMLNHTSIV----TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISN-YLHIKGVNFDLS-HVIQDSSSY-------  210 (233)
Q Consensus       144 f~~am~~~~~~~----~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~-~P~l~~~v~Dlp-~v~~~a~~~-------  210 (233)
                      |...|...++..    +..++..++ .....+|+|+|||+|.++..+++. .|+-+++.+|.. +.++.|+++       
T Consensus        58 ~~~~~~r~~qiiypkD~~~Ii~~l~-i~pG~rVLEiG~GsG~lt~~la~~v~~~g~V~~vD~~e~~~~~A~~n~~~~~~~  136 (250)
T d1yb2a1          58 FGRVIRRNTQIISEIDASYIIMRCG-LRPGMDILEVGVGSGNMSSYILYALNGKGTLTVVERDEDNLKKAMDNLSEFYDI  136 (250)
T ss_dssp             HHHHC------------------CC-CCTTCEEEEECCTTSHHHHHHHHHHTTSSEEEEECSCHHHHHHHHHHHHTTSCC
T ss_pred             HHhhCCCCCcccCHHHHHHHHHHcC-CCCcCEEEEeeeeCcHHHHHHHHHhCCCcEEEEEECCHHHHHHHHHHHHHhcCC
Confidence            555566555443    334555555 677799999999999999999987 688999999984 467766642       


Q ss_pred             CCceEEecCcCCCCCCC--CEEEe
Q 039903          211 SGVKHIGGIMLERIPKG--DAILI  232 (233)
Q Consensus       211 ~ri~~~~gD~f~~~P~~--D~~~l  232 (233)
                      ++|++..+|+.+.+|..  |++++
T Consensus       137 ~nv~~~~~Di~~~~~~~~fD~V~l  160 (250)
T d1yb2a1         137 GNVRTSRSDIADFISDQMYDAVIA  160 (250)
T ss_dssp             TTEEEECSCTTTCCCSCCEEEEEE
T ss_pred             CceEEEEeeeecccccceeeeeee
Confidence            68999999999877763  98875

>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=98.26  E-value=1e-06  Score=67.38  Aligned_cols=72  Identities=15%  Similarity=0.132  Sum_probs=54.3

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccC------CCCceEEecCcCC-CCCCC-C
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSS------YSGVKHIGGIMLE-RIPKG-D  228 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~------~~ri~~~~gD~f~-~~P~~-D  228 (233)
                      .++.... +-+..+|||||||+|..+..++++.+  +++.+|+. ..++.+++      .++|++..+|+.+ +.+.. |
T Consensus        21 ~~~~~~~-~~~~grvLDiGcG~G~~~~~la~~g~--~v~gvD~s~~~l~~a~~~~~~~~~~~~~~~~~d~~~~~~~~~fD   97 (198)
T d2i6ga1          21 DVLAAAK-VVAPGRTLDLGCGNGRNSLYLAANGY--DVTAWDKNPASMANLERIKAAEGLDNLQTDLVDLNTLTFDGEYD   97 (198)
T ss_dssp             HHHHHHT-TSCSCEEEEETCTTSHHHHHHHHTTC--EEEEEESCHHHHHHHHHHHHHTTCTTEEEEECCTTTCCCCCCEE
T ss_pred             HHHHHcc-cCCCCcEEEECCCCCHHHHHHHHHhh--hhccccCcHHHHHHHHHHhhhccccchhhhheeccccccccccc
Confidence            3444444 55567999999999999999999854  68999985 46776543      2679999999998 44444 8


Q ss_pred             EEEe
Q 039903          229 AILI  232 (233)
Q Consensus       229 ~~~l  232 (233)
                      +|+.
T Consensus        98 ~I~~  101 (198)
T d2i6ga1          98 FILS  101 (198)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            8864

>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=98.25  E-value=6.4e-07  Score=70.03  Aligned_cols=65  Identities=15%  Similarity=0.271  Sum_probs=52.2

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccC--CCCceEEecCcCC-CCCCC-CEEEe
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSS--YSGVKHIGGIMLE-RIPKG-DAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~--~~ri~~~~gD~f~-~~P~~-D~~~l  232 (233)
                      +.+..+|||||||+|.++..++++..  +++.+|+ |+.++.|++  .++++++.+|+-+ +.+.. |++++
T Consensus        18 ~~~~~~VLDiGcG~G~~~~~l~~~g~--~v~giD~s~~~i~~a~~~~~~~~~~~~~~~~~~~~~~~fD~I~~   87 (225)
T d2p7ia1          18 FFRPGNLLELGSFKGDFTSRLQEHFN--DITCVEASEEAISHAQGRLKDGITYIHSRFEDAQLPRRYDNIVL   87 (225)
T ss_dssp             GCCSSCEEEESCTTSHHHHHHTTTCS--CEEEEESCHHHHHHHHHHSCSCEEEEESCGGGCCCSSCEEEEEE
T ss_pred             hCCCCcEEEEeCCCcHHHHHHHHcCC--eEEEEeCcHHHhhhhhcccccccccccccccccccccccccccc
Confidence            55567899999999999999998865  5899998 557887765  3689999999887 44544 98875

>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=98.25  E-value=1.3e-06  Score=67.54  Aligned_cols=64  Identities=19%  Similarity=0.313  Sum_probs=51.6

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-----CCceEEecCcCC-CCCCC--CEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-----SGVKHIGGIMLE-RIPKG--DAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-----~ri~~~~gD~f~-~~P~~--D~~~l  232 (233)
                      ++-.+|||||||+|.++..+++.  ..+++.+|+ ++.++.|++.     .++.++.+|+.+ ++|..  |+|+.
T Consensus        36 ~~~~~ILDiGcG~G~~~~~la~~--~~~v~giD~S~~~i~~ak~~~~~~~~~~~~~~~d~~~l~~~~~~fD~I~~  108 (226)
T d1ve3a1          36 KKRGKVLDLACGVGGFSFLLEDY--GFEVVGVDISEDMIRKAREYAKSRESNVEFIVGDARKLSFEDKTFDYVIF  108 (226)
T ss_dssp             CSCCEEEEETCTTSHHHHHHHHT--TCEEEEEESCHHHHHHHHHHHHHTTCCCEEEECCTTSCCSCTTCEEEEEE
T ss_pred             CCCCEEEEECCCcchhhhhHhhh--hcccccccccccchhhhhhhhccccccccccccccccccccCcCceEEEE
Confidence            44578999999999999999985  567999998 4678777642     578999999998 77764  98874

>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=98.23  E-value=7.1e-07  Score=73.97  Aligned_cols=75  Identities=16%  Similarity=0.176  Sum_probs=59.2

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccC---------------CCCceEEecCc
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSS---------------YSGVKHIGGIM  220 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~---------------~~ri~~~~gD~  220 (233)
                      ..+++.+. .+...+|+|||||.|.++..+++.+|..+++++|+. ..++.|+.               ..+|+++.|||
T Consensus       141 ~~~~~~~~-l~~~~~vlD~GcG~G~~~~~~a~~~~~~~~~Gid~s~~~~~~a~~~~~~~~~~~~~~g~~~~~i~~~~gd~  219 (328)
T d1nw3a_         141 AQMIDEIK-MTDDDLFVDLGSGVGQVVLQVAAATNCKHHYGVEKADIPAKYAETMDREFRKWMKWYGKKHAEYTLERGDF  219 (328)
T ss_dssp             HHHHHHSC-CCTTCEEEEETCTTSHHHHHHHHHCCCSEEEEEECSHHHHHHHHHHHHHHHHHHHHHTCCCCCEEEEECCT
T ss_pred             HHHHHHcC-CCCCCEEEEcCCCCCHHHHHHHHHhCCCeEEEEeCCHHHHHHHHHHHHHHHHHhhhccccCCceEEEECcc
Confidence            45666666 777889999999999999999999999999999985 45555532               25799999999


Q ss_pred             CC-CCC----CCCEEEe
Q 039903          221 LE-RIP----KGDAILI  232 (233)
Q Consensus       221 f~-~~P----~~D~~~l  232 (233)
                      .+ ++.    .+|++++
T Consensus       220 ~~~~~~~~~~~advi~~  236 (328)
T d1nw3a_         220 LSEEWRERIANTSVIFV  236 (328)
T ss_dssp             TSHHHHHHHHHCSEEEE
T ss_pred             cccccccccCcceEEEE
Confidence            87 443    3578764

>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=98.20  E-value=4.4e-07  Score=71.76  Aligned_cols=62  Identities=15%  Similarity=0.189  Sum_probs=50.4

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC-----CCceEEecCcCC-CCCCC-CEEE
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY-----SGVKHIGGIMLE-RIPKG-DAIL  231 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~-----~ri~~~~gD~f~-~~P~~-D~~~  231 (233)
                      ..++|||||||+|.++..+++++.  +++.+|+. ..++.|++.     .+|+++.+|+.+ +++.. |+|+
T Consensus        37 ~~~~vLDiGCG~G~~~~~l~~~g~--~v~GvD~S~~ml~~A~~~~~~~~~~v~~~~~d~~~~~~~~~fD~i~  106 (246)
T d1y8ca_          37 VFDDYLDLACGTGNLTENLCPKFK--NTWAVDLSQEMLSEAENKFRSQGLKPRLACQDISNLNINRKFDLIT  106 (246)
T ss_dssp             CTTEEEEETCTTSTTHHHHGGGSS--EEEEECSCHHHHHHHHHHHHHTTCCCEEECCCGGGCCCSCCEEEEE
T ss_pred             CCCeEEEEeCcCCHHHHHHHHhCC--ccEeeccchhhhhhccccccccCccceeeccchhhhcccccccccc
Confidence            357899999999999999999865  68999985 567777642     579999999988 55554 9876

>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=98.17  E-value=1.8e-06  Score=67.08  Aligned_cols=74  Identities=15%  Similarity=0.260  Sum_probs=59.0

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHc-CCCcEEEeec-hHHHhhccCC------CCceEEecCcCCCCCC-C-
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNY-LHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLERIPK-G-  227 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~~P~-~-  227 (233)
                      .+++.++ .+...+|+|||||+|.++..+++.. |+-+++.+|. |+.++.|+.+      .++.++.+|..+..|. + 
T Consensus        66 ~~l~~l~-l~~g~~VLdiG~GtG~~s~~la~~~~~~g~V~~id~~~~~~~~a~~~~~~~~~~n~~~~~~d~~~~~~~~~~  144 (213)
T d1dl5a1          66 LFMEWVG-LDKGMRVLEIGGGTGYNAAVMSRVVGEKGLVVSVEYSRKICEIAKRNVERLGIENVIFVCGDGYYGVPEFSP  144 (213)
T ss_dssp             HHHHHTT-CCTTCEEEEECCTTSHHHHHHHHHHCTTCEEEEEESCHHHHHHHHHHHHHTTCCSEEEEESCGGGCCGGGCC
T ss_pred             HHHHhhh-ccccceEEEecCccchhHHHHHHHhCCCCcEEEeecchhhHHHhhhhHhhhcccccccccCchHHccccccc
Confidence            4556666 7888999999999999999999876 6788999997 5677777652      7899999999884443 3 


Q ss_pred             -CEEEe
Q 039903          228 -DAILI  232 (233)
Q Consensus       228 -D~~~l  232 (233)
                       |+|++
T Consensus       145 fD~I~~  150 (213)
T d1dl5a1         145 YDVIFV  150 (213)
T ss_dssp             EEEEEE
T ss_pred             hhhhhh
Confidence             98875

>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=98.15  E-value=1.6e-06  Score=66.31  Aligned_cols=66  Identities=20%  Similarity=0.179  Sum_probs=55.5

Q ss_pred             HHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccC-----CCCceEEecCcCC
Q 039903          156 TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSS-----YSGVKHIGGIMLE  222 (233)
Q Consensus       156 ~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~-----~~ri~~~~gD~f~  222 (233)
                      ..++++.+. -....+++|++||+|.++.++++++|+.+++.+|+ |++++.+++     .+|++++.++|-+
T Consensus        12 l~evi~~l~-~~~~~~~lD~t~G~Gghs~~il~~~~~~~vi~~D~d~~~l~~a~~~l~~~~~r~~~~~~~f~~   83 (192)
T d1m6ya2          12 VREVIEFLK-PEDEKIILDCTVGEGGHSRAILEHCPGCRIIGIDVDSEVLRIAEEKLKEFSDRVSLFKVSYRE   83 (192)
T ss_dssp             HHHHHHHHC-CCTTCEEEETTCTTSHHHHHHHHHCTTCEEEEEESCHHHHHHHHHHTGGGTTTEEEEECCGGG
T ss_pred             HHHHHHhhC-CCCCCEEEEecCCCcHHHHHHHhcCCCCeEEEeechHHHHHHHHHhhccccccccchhHHHhh
Confidence            456667665 45668999999999999999999999999999998 568887765     2799999999865

>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=98.13  E-value=5.5e-07  Score=70.76  Aligned_cols=64  Identities=19%  Similarity=0.344  Sum_probs=48.2

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-----CCceEEecCcCC---CCCCC--CEEE
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-----SGVKHIGGIMLE---RIPKG--DAIL  231 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-----~ri~~~~gD~f~---~~P~~--D~~~  231 (233)
                      ....+|||||||+|..+..++++.|. +++++|+ |.+++.|++.     .++..+.+|+..   ++|.+  |.++
T Consensus        52 ~~g~~VLdIGcG~G~~a~~~a~~~~~-~v~~id~s~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fD~i~  126 (229)
T d1zx0a1          52 SKGGRVLEVGFGMAIAASKVQEAPID-EHWIIECNDGVFQRLRDWAPRQTHKVIPLKGLWEDVAPTLPDGHFDGIL  126 (229)
T ss_dssp             TTCEEEEEECCTTSHHHHHHHTSCEE-EEEEEECCHHHHHHHHHHGGGCSSEEEEEESCHHHHGGGSCTTCEEEEE
T ss_pred             cCCCeEEEeeccchHHHHHHHHcCCC-eEEEeCCCHHHHHHHHHHhhhccccccccccccccccccccccccccee
Confidence            34578999999999999999987664 7899998 5688877652     567777777653   56654  7665

>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=98.10  E-value=1.6e-06  Score=66.50  Aligned_cols=64  Identities=19%  Similarity=0.233  Sum_probs=50.9

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-CCceEEecCcCCCCCC-CCEEEe
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-SGVKHIGGIMLERIPK-GDAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-~ri~~~~gD~f~~~P~-~D~~~l  232 (233)
                      +++ ++|+|+|||+|.+++.++...+. +++.+|. |.+++.++++ .+++++.+|+.+ +|. .|+|++
T Consensus        47 l~G-k~VLDlGcGtG~l~i~a~~~ga~-~V~~vDid~~a~~~ar~N~~~~~~~~~D~~~-l~~~fD~Vi~  113 (197)
T d1ne2a_          47 IGG-RSVIDAGTGNGILACGSYLLGAE-SVTAFDIDPDAIETAKRNCGGVNFMVADVSE-ISGKYDTWIM  113 (197)
T ss_dssp             SBT-SEEEEETCTTCHHHHHHHHTTBS-EEEEEESCHHHHHHHHHHCTTSEEEECCGGG-CCCCEEEEEE
T ss_pred             CCC-CEEEEeCCCCcHHHHHHHHcCCC-cccccccCHHHHHHHHHccccccEEEEehhh-cCCcceEEEe
Confidence            544 89999999999999888876554 7899998 5678888775 789999999876 344 388875

>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=98.09  E-value=2e-06  Score=67.23  Aligned_cols=63  Identities=17%  Similarity=0.267  Sum_probs=50.4

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCCCCceEEecCcCC-CCCCC--CEEE
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSYSGVKHIGGIMLE-RIPKG--DAIL  231 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~~ri~~~~gD~f~-~~P~~--D~~~  231 (233)
                      ++..+|||||||+|.++..++++  ..+++++|. +..++.|++.....++.+|+.+ ++|.+  |+|+
T Consensus        41 ~~~~~vLDiGcG~G~~~~~l~~~--~~~v~giD~s~~~l~~a~~~~~~~~~~~~~~~l~~~~~~fD~ii  107 (246)
T d2avna1          41 KNPCRVLDLGGGTGKWSLFLQER--GFEVVLVDPSKEMLEVAREKGVKNVVEAKAEDLPFPSGAFEAVL  107 (246)
T ss_dssp             CSCCEEEEETCTTCHHHHHHHTT--TCEEEEEESCHHHHHHHHHHTCSCEEECCTTSCCSCTTCEEEEE
T ss_pred             CCCCEEEEECCCCchhccccccc--ceEEEEeeccccccccccccccccccccccccccccccccccee
Confidence            55678999999999999999886  568999998 5688888775444567888887 77764  9876

>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=98.08  E-value=8.1e-07  Score=71.00  Aligned_cols=85  Identities=16%  Similarity=0.255  Sum_probs=57.3

Q ss_pred             HHHHHHHhcchhcHHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-----CCceEE
Q 039903          143 VFNKAMLNHTSIVTNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-----SGVKHI  216 (233)
Q Consensus       143 ~f~~am~~~~~~~~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-----~ri~~~  216 (233)
                      .|-..-+.+++.....+.+ +.  ....+|+|||||+|.+++++++.  ..+++.+|+ |..++.|+++     -+++++
T Consensus        98 aFGTG~H~TT~l~l~~l~~-~~--~~g~~VLDiGcGsG~l~i~aa~~--g~~V~gvDis~~av~~A~~na~~n~~~~~~~  172 (254)
T d2nxca1          98 AFGTGHHETTRLALKALAR-HL--RPGDKVLDLGTGSGVLAIAAEKL--GGKALGVDIDPMVLPQAEANAKRNGVRPRFL  172 (254)
T ss_dssp             ----CCSHHHHHHHHHHHH-HC--CTTCEEEEETCTTSHHHHHHHHT--TCEEEEEESCGGGHHHHHHHHHHTTCCCEEE
T ss_pred             ccCccccchhhHHHHHHHh-hc--CccCEEEEcccchhHHHHHHHhc--CCEEEEEECChHHHHHHHHHHHHcCCceeEE
Confidence            4655555555554444332 22  45589999999999999988875  457999998 5578777653     367888


Q ss_pred             ecCcCCCCCCC--CEEEe
Q 039903          217 GGIMLERIPKG--DAILI  232 (233)
Q Consensus       217 ~gD~f~~~P~~--D~~~l  232 (233)
                      .+|+.+.+|.+  |+++.
T Consensus       173 ~~d~~~~~~~~~fD~V~a  190 (254)
T d2nxca1         173 EGSLEAALPFGPFDLLVA  190 (254)
T ss_dssp             ESCHHHHGGGCCEEEEEE
T ss_pred             eccccccccccccchhhh
Confidence            99988766643  88763

>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=98.06  E-value=3.4e-06  Score=66.91  Aligned_cols=72  Identities=15%  Similarity=0.064  Sum_probs=53.2

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC-------CCceEEecCcCC-CCC-C-
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY-------SGVKHIGGIMLE-RIP-K-  226 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~-------~ri~~~~gD~f~-~~P-~-  226 (233)
                      .+++.+.  ++..+|||||||+|..+..+++..+ -+++.+|+. +.++.|++.       .++.+..+|.+. +++ . 
T Consensus        16 ~lI~~~~--~~~~~VLDlGCG~G~~~~~~~~~~~-~~v~GiD~S~~~l~~A~~r~~~~~~~~~v~f~~~D~~~~~~~~~~   92 (252)
T d1ri5a_          16 CLIRLYT--KRGDSVLDLGCGKGGDLLKYERAGI-GEYYGVDIAEVSINDARVRARNMKRRFKVFFRAQDSYGRHMDLGK   92 (252)
T ss_dssp             HHHHHHC--CTTCEEEEETCTTTTTHHHHHHHTC-SEEEEEESCHHHHHHHHHHHHTSCCSSEEEEEESCTTTSCCCCSS
T ss_pred             HHHHHhC--CCcCEEEEecccCcHHHHHHHHcCC-CeEEEecCCHHHHHHHHHHHHhcCCCcceEEEEcchhhhcccccc
Confidence            3455543  5568999999999999999988744 368999985 477777531       479999999987 443 3 


Q ss_pred             C-CEEEe
Q 039903          227 G-DAILI  232 (233)
Q Consensus       227 ~-D~~~l  232 (233)
                      . |+|+.
T Consensus        93 ~fD~V~~   99 (252)
T d1ri5a_          93 EFDVISS   99 (252)
T ss_dssp             CEEEEEE
T ss_pred             cceEEEE
Confidence            2 98864

>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=98.02  E-value=5.4e-06  Score=63.46  Aligned_cols=58  Identities=16%  Similarity=0.165  Sum_probs=46.0

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCCCCceEEecCcCC-CCCCC--CEEEe
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSYSGVKHIGGIMLE-RIPKG--DAILI  232 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~~ri~~~~gD~f~-~~P~~--D~~~l  232 (233)
                      ...+|||||||+|.++..+.      +.+.+|+ |..++.+++ .+++++.+|+.+ ++|..  |+|+.
T Consensus        36 ~~~~vLDiGcG~G~~~~~~~------~~~giD~s~~~~~~a~~-~~~~~~~~d~~~l~~~~~~fD~I~~   97 (208)
T d1vlma_          36 PEGRGVEIGVGTGRFAVPLK------IKIGVEPSERMAEIARK-RGVFVLKGTAENLPLKDESFDFALM   97 (208)
T ss_dssp             CSSCEEEETCTTSTTHHHHT------CCEEEESCHHHHHHHHH-TTCEEEECBTTBCCSCTTCEEEEEE
T ss_pred             CCCeEEEECCCCcccccccc------eEEEEeCChhhcccccc-ccccccccccccccccccccccccc
Confidence            34589999999999988874      3478898 567887776 479999999988 77754  98875

>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=98.02  E-value=4.8e-06  Score=62.66  Aligned_cols=68  Identities=12%  Similarity=0.048  Sum_probs=51.5

Q ss_pred             HhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC------------------CCceEEecCcC
Q 039903          161 DSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY------------------SGVKHIGGIML  221 (233)
Q Consensus       161 ~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~------------------~ri~~~~gD~f  221 (233)
                      ..+. .++..+|||||||+|..+..|+++  ..+++++|+. ..++.|++.                  ..+++..+|++
T Consensus        14 ~~l~-~~~~~rvLd~GCG~G~~a~~la~~--G~~V~gvD~S~~~i~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~   90 (201)
T d1pjza_          14 SSLN-VVPGARVLVPLCGKSQDMSWLSGQ--GYHVVGAELSEAAVERYFTERGEQPHITSQGDFKVYAAPGIEIWCGDFF   90 (201)
T ss_dssp             HHHC-CCTTCEEEETTTCCSHHHHHHHHH--CCEEEEEEECHHHHHHHHHHHCSCSEEEEETTEEEEECSSSEEEEECCS
T ss_pred             HHcC-CCCCCEEEEecCcCCHHHHHHHHc--CCceEeecccHHHHHHHHHHhccccchhhhhhhhhccccccceeccccc
Confidence            3344 667789999999999999999997  6789999985 477776541                  45788999998


Q ss_pred             CCCC--C-C-CEEE
Q 039903          222 ERIP--K-G-DAIL  231 (233)
Q Consensus       222 ~~~P--~-~-D~~~  231 (233)
                      +..|  . . |+++
T Consensus        91 ~l~~~~~~~~D~i~  104 (201)
T d1pjza_          91 ALTARDIGHCAAFY  104 (201)
T ss_dssp             SSTHHHHHSEEEEE
T ss_pred             ccccccccceeEEE
Confidence            8333  2 2 7664

>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=97.99  E-value=8e-06  Score=66.77  Aligned_cols=65  Identities=23%  Similarity=0.285  Sum_probs=50.3

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccC-------CCCceEEecCcCC-CCCC-C-CEEE
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSS-------YSGVKHIGGIMLE-RIPK-G-DAIL  231 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~-------~~ri~~~~gD~f~-~~P~-~-D~~~  231 (233)
                      ..+.++|||||||+|.++..++++.+ -+++.+|..+....+.+       .++|+++.+|..+ +.|. . |+++
T Consensus        33 ~~~~~~VLDiGcG~G~lsl~aa~~Ga-~~V~aid~s~~~~~a~~~~~~~~~~~~i~~~~~~~~~l~~~~~~~D~Iv  107 (311)
T d2fyta1          33 IFKDKVVLDVGCGTGILSMFAAKAGA-KKVLGVDQSEILYQAMDIIRLNKLEDTITLIKGKIEEVHLPVEKVDVII  107 (311)
T ss_dssp             GTTTCEEEEETCTTSHHHHHHHHTTC-SEEEEEESSTHHHHHHHHHHHTTCTTTEEEEESCTTTSCCSCSCEEEEE
T ss_pred             cCCcCEEEEECCCCCHHHHHHHHcCC-CEEEEEeCHHHHHHHHHHHHHhCCCccceEEEeeHHHhcCccccceEEE
Confidence            34458899999999999999998765 47999998765443322       2789999999998 6765 3 8876

>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=97.98  E-value=4.1e-06  Score=67.34  Aligned_cols=64  Identities=20%  Similarity=0.225  Sum_probs=52.7

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCCCCCC--C--CEEE
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLERIPK--G--DAIL  231 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~~P~--~--D~~~  231 (233)
                      .+..+++|+|||+|..+..++ ++|+.+++..|. |++++.|+++       +++.++.+|++++.+.  +  |+++
T Consensus       109 ~~~~~vld~g~GsG~i~~~la-~~~~~~v~a~Dis~~Al~~A~~Na~~~~~~~~~~i~~~~~~~~~~~~~~~fDlIV  184 (271)
T d1nv8a_         109 YGIKTVADIGTGSGAIGVSVA-KFSDAIVFATDVSSKAVEIARKNAERHGVSDRFFVRKGEFLEPFKEKFASIEMIL  184 (271)
T ss_dssp             HTCCEEEEESCTTSHHHHHHH-HHSSCEEEEEESCHHHHHHHHHHHHHTTCTTSEEEEESSTTGGGGGGTTTCCEEE
T ss_pred             ccccEEEEeeeeeehhhhhhh-hcccceeeechhhhhHHHHHHHHHHHcCCCceeEEeecccccccccccCcccEEE
Confidence            345689999999999999987 579999999998 5688877763       6899999999997653  2  8876

>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=97.96  E-value=4.8e-06  Score=68.71  Aligned_cols=63  Identities=21%  Similarity=0.308  Sum_probs=49.8

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccC-------CCCceEEecCcCC-CCCC--CCEEE
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSS-------YSGVKHIGGIMLE-RIPK--GDAIL  231 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~-------~~ri~~~~gD~f~-~~P~--~D~~~  231 (233)
                      +.++|||||||+|.++..++++.. -+++.+|..+.+..+++       .++|+++.+|+.+ ++|.  .|+++
T Consensus        38 ~~~~VLDlGcGtG~ls~~aa~~Ga-~~V~avd~s~~~~~a~~~~~~~~~~~~i~~i~~~~~~l~~~~~~~D~i~  110 (328)
T d1g6q1_          38 KDKIVLDVGCGTGILSMFAAKHGA-KHVIGVDMSSIIEMAKELVELNGFSDKITLLRGKLEDVHLPFPKVDIII  110 (328)
T ss_dssp             TTCEEEEETCTTSHHHHHHHHTCC-SEEEEEESSTHHHHHHHHHHHTTCTTTEEEEESCTTTSCCSSSCEEEEE
T ss_pred             CcCEEEEeCCCCCHHHHHHHHhCC-CEEEEEeCCHHHHHHHHHHHHhCccccceEEEeehhhccCcccceeEEE
Confidence            347899999999999988877644 47899999876655543       2789999999998 7775  38875

>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=97.95  E-value=4.5e-06  Score=68.55  Aligned_cols=63  Identities=24%  Similarity=0.272  Sum_probs=49.0

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHhhccC-------CCCceEEecCcCC-CCCC--CCEEE
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQDSSS-------YSGVKHIGGIMLE-RIPK--GDAIL  231 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~a~~-------~~ri~~~~gD~f~-~~P~--~D~~~  231 (233)
                      +.++|||||||+|.++..++++.+. +++.+|..+....+++       .++|+++.+|+.+ +.|.  .|+++
T Consensus        33 ~~~~VLDiGcG~G~ls~~aa~~Ga~-~V~avd~s~~~~~a~~~~~~n~~~~~v~~~~~~~~~~~~~~~~~D~iv  105 (316)
T d1oria_          33 KDKVVLDVGSGTGILCMFAAKAGAR-KVIGIECSSISDYAVKIVKANKLDHVVTIIKGKVEEVELPVEKVDIII  105 (316)
T ss_dssp             TTCEEEEETCTTSHHHHHHHHTTCS-EEEEEECSTTHHHHHHHHHHTTCTTTEEEEESCTTTCCCSSSCEEEEE
T ss_pred             CcCEEEEEecCCcHHHHHHHHhCCC-EEEEEcCcHHHhhhhhHHHHhCCccccceEeccHHHcccccceeEEEe
Confidence            3478999999999999988887554 7899998765544432       2789999999998 7775  38875

>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=97.95  E-value=7.4e-06  Score=65.68  Aligned_cols=94  Identities=16%  Similarity=0.094  Sum_probs=69.2

Q ss_pred             CchHHHHHHHHHHhcchhc----HHHHHHhcccccCcceEEEecCCccHHHHHHHHHc-CCCcEEEeec-hHHHhhccCC
Q 039903          137 DFRFNGVFNKAMLNHTSIV----TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNY-LHIKGVNFDL-SHVIQDSSSY  210 (233)
Q Consensus       137 ~~~~~~~f~~am~~~~~~~----~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~-P~l~~~v~Dl-p~v~~~a~~~  210 (233)
                      .|.... |...|...++..    +..++..++ .....+|+|+|||+|.++..+++.. |+-+++.+|. |+.++.|+++
T Consensus        70 ~p~~~d-~~~~~~r~~qiiypkd~~~Ii~~l~-i~pG~~VLDiG~GsG~lt~~lA~~~~~~G~V~~vD~~~~~~~~A~~~  147 (266)
T d1o54a_          70 IPSLID-EIMNMKRRTQIVYPKDSSFIAMMLD-VKEGDRIIDTGVGSGAMCAVLARAVGSSGKVFAYEKREEFAKLAESN  147 (266)
T ss_dssp             CCCHHH-HHHTCCC-CCCCCHHHHHHHHHHTT-CCTTCEEEEECCTTSHHHHHHHHHTTTTCEEEEECCCHHHHHHHHHH
T ss_pred             CCCHHH-HHhhccCCccccchHHHHHHHHhhC-CCCCCEEEECCCCCCHHHHHHHHHhCCCcEEEEEeCCHHHHHHHHHH
Confidence            454444 445665555433    345666666 7888999999999999999999884 8999999997 5678777653


Q ss_pred             -------CCceEEecCcCCCCCCC--CEEEe
Q 039903          211 -------SGVKHIGGIMLERIPKG--DAILI  232 (233)
Q Consensus       211 -------~ri~~~~gD~f~~~P~~--D~~~l  232 (233)
                             +++.+..+|+...++..  |.+++
T Consensus       148 ~~~~g~~~~v~~~~~d~~~~~~~~~~D~V~~  178 (266)
T d1o54a_         148 LTKWGLIERVTIKVRDISEGFDEKDVDALFL  178 (266)
T ss_dssp             HHHTTCGGGEEEECCCGGGCCSCCSEEEEEE
T ss_pred             HHHhccccCcEEEeccccccccccceeeeEe
Confidence                   68899899987766653  77764

>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=97.92  E-value=1.1e-05  Score=63.09  Aligned_cols=75  Identities=19%  Similarity=0.166  Sum_probs=56.9

Q ss_pred             HHHHhcc-cccCcceEEEecCCccHHHHHHHHH-cCCCcEEEeec-hHHHhhccCC-----------CCceEEecCcCCC
Q 039903          158 RIIDSSK-GFEQIKQLVDVGGGLGVNVNIIISN-YLHIKGVNFDL-SHVIQDSSSY-----------SGVKHIGGIMLER  223 (233)
Q Consensus       158 ~~~~~~~-~~~~~~~vvDvGGG~G~~~~~l~~~-~P~l~~~v~Dl-p~v~~~a~~~-----------~ri~~~~gD~f~~  223 (233)
                      .+++.+. +.+...+|||||||+|..+..+++. .|.-+++.+|+ ++.++.|+++           ++++++.+|.++.
T Consensus        65 ~~le~L~~~l~~g~~VLdiG~GsGy~ta~la~l~~~~g~V~~ie~~~~l~~~a~~~l~~~~~~~~~~~~~~~~~gD~~~~  144 (224)
T d1i1na_          65 YALELLFDQLHEGAKALDVGSGSGILTACFARMVGCTGKVIGIDHIKELVDDSVNNVRKDDPTLLSSGRVQLVVGDGRMG  144 (224)
T ss_dssp             HHHHHTTTTSCTTCEEEEETCTTSHHHHHHHHHHCTTCEEEEEESCHHHHHHHHHHHHHHCTHHHHTSSEEEEESCGGGC
T ss_pred             HHHHHHhhccCCCCeEEEecCCCCHHHHHHHHHhCCCceEEEEcCCHHHHHHHHHhccccCcccccccceEEEEeecccc
Confidence            4455542 2567789999999999999888885 67889999997 5577766542           6899999999984


Q ss_pred             CCC-C--CEEEe
Q 039903          224 IPK-G--DAILI  232 (233)
Q Consensus       224 ~P~-~--D~~~l  232 (233)
                      .|. +  |+|++
T Consensus       145 ~~~~~~fD~I~~  156 (224)
T d1i1na_         145 YAEEAPYDAIHV  156 (224)
T ss_dssp             CGGGCCEEEEEE
T ss_pred             cchhhhhhhhhh
Confidence            443 4  88875

>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=97.91  E-value=3.7e-06  Score=61.74  Aligned_cols=64  Identities=9%  Similarity=-0.043  Sum_probs=50.7

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCC--CCCC--CCEEEe
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLE--RIPK--GDAILI  232 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~--~~P~--~D~~~l  232 (233)
                      +..+|||+|||+|.++.+.+.+... +++.+|. |.+++.++++       ++++++.+|.++  +.+.  .|++++
T Consensus        14 ~g~~vlDl~~GtG~~~iea~~rga~-~v~~ve~~~~a~~~~~~n~~~~~~~~~~~ii~~D~~~~l~~~~~~fDiIf~   89 (152)
T d2esra1          14 NGGRVLDLFAGSGGLAIEAVSRGMS-AAVLVEKNRKAQAIIQDNIIMTKAENRFTLLKMEAERAIDCLTGRFDLVFL   89 (152)
T ss_dssp             CSCEEEEETCTTCHHHHHHHHTTCC-EEEEECCCHHHHHHHHHHHHTTTCGGGEEEECSCHHHHHHHBCSCEEEEEE
T ss_pred             CCCeEEEcCCccCHHHHHHHHhCcc-eeeeehhchhhhhhhhhhhhhcccccchhhhcccccccccccccccceeEe
Confidence            3578999999999999999988775 8999998 5576665542       789999999887  3333  398876

>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=97.88  E-value=1.4e-05  Score=64.58  Aligned_cols=72  Identities=14%  Similarity=0.201  Sum_probs=53.7

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccC-------CCCceEEecCcCCCCCCC-
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSS-------YSGVKHIGGIMLERIPKG-  227 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~-------~~ri~~~~gD~f~~~P~~-  227 (233)
                      ..+++.+. .+...+|||||||.|.++..++++++ .+++.+|+.+ .++.|++       ..++.+...|+.+ +|.. 
T Consensus        42 ~~~~~~l~-l~~g~~VLDiGCG~G~~a~~~a~~~g-~~v~gi~ls~~q~~~a~~~~~~~~l~~~~~~~~~d~~~-~~~~f  118 (280)
T d2fk8a1          42 DLNLDKLD-LKPGMTLLDIGCGWGTTMRRAVERFD-VNVIGLTLSKNQHARCEQVLASIDTNRSRQVLLQGWED-FAEPV  118 (280)
T ss_dssp             HHHHTTSC-CCTTCEEEEESCTTSHHHHHHHHHHC-CEEEEEESCHHHHHHHHHHHHTSCCSSCEEEEESCGGG-CCCCC
T ss_pred             HHHHHHcC-CCCCCEEEEecCCchHHHHHHHHhCc-eeEEEecchHHHHHHHHHHHHhhccccchhhhhhhhhh-hccch
Confidence            45777777 88889999999999999999998886 5999999854 5555443       2578877777654 3333 


Q ss_pred             CEEE
Q 039903          228 DAIL  231 (233)
Q Consensus       228 D~~~  231 (233)
                      |.++
T Consensus       119 D~i~  122 (280)
T d2fk8a1         119 DRIV  122 (280)
T ss_dssp             SEEE
T ss_pred             hhhh
Confidence            7665

>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=97.88  E-value=1.3e-05  Score=64.76  Aligned_cols=72  Identities=17%  Similarity=0.202  Sum_probs=54.4

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccC-------CCCceEEecCcCCCCCC-C
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSS-------YSGVKHIGGIMLERIPK-G  227 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~-------~~ri~~~~gD~f~~~P~-~  227 (233)
                      ..+++.+. .+...+|||||||.|..++.++++++ ++++++++.. -++.|++       .++|++..+|+.+ +|. -
T Consensus        52 ~~~~~~l~-l~~G~~VLDiGCG~G~~a~~~a~~~g-~~v~git~s~~Q~~~a~~~~~~~g~~~~v~~~~~d~~~-~~~~f  128 (285)
T d1kpga_          52 DLALGKLG-LQPGMTLLDVGCGWGATMMRAVEKYD-VNVVGLTLSKNQANHVQQLVANSENLRSKRVLLAGWEQ-FDEPV  128 (285)
T ss_dssp             HHHHTTTT-CCTTCEEEEETCTTSHHHHHHHHHHC-CEEEEEESCHHHHHHHHHHHHTCCCCSCEEEEESCGGG-CCCCC
T ss_pred             HHHHHHcC-CCCCCEEEEecCcchHHHHHHHhcCC-cceEEEeccHHHHHHHHHHHHhhhhhhhhHHHHhhhhc-ccccc
Confidence            45667776 78889999999999999999999995 7999999853 4444332       2799999999865 233 2


Q ss_pred             CEEE
Q 039903          228 DAIL  231 (233)
Q Consensus       228 D~~~  231 (233)
                      |.++
T Consensus       129 D~i~  132 (285)
T d1kpga_         129 DRIV  132 (285)
T ss_dssp             SEEE
T ss_pred             ccee
Confidence            6543

>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=97.88  E-value=1e-05  Score=62.45  Aligned_cols=59  Identities=7%  Similarity=-0.052  Sum_probs=50.5

Q ss_pred             cccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccC----CCCceEEecCcCC
Q 039903          163 SKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSS----YSGVKHIGGIMLE  222 (233)
Q Consensus       163 ~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~----~~ri~~~~gD~f~  222 (233)
                      ++ ++...+|||||||+|..+..+++..|+-+++.+|+ |..++.+++    .+++.++.+|...
T Consensus        52 l~-lkpg~~VLDlGcG~G~~~~~la~~v~~g~V~gvDis~~~i~~a~~~a~~~~ni~~i~~d~~~  115 (209)
T d1nt2a_          52 LK-LRGDERVLYLGAASGTTVSHLADIVDEGIIYAVEYSAKPFEKLLELVRERNNIIPLLFDASK  115 (209)
T ss_dssp             CC-CCSSCEEEEETCTTSHHHHHHHHHTTTSEEEEECCCHHHHHHHHHHHHHCSSEEEECSCTTC
T ss_pred             CC-CCCCCEEEEeCCcCCHHHHHHHHhccCCeEEEEeCCHHHHHHHHHHhhccCCceEEEeeccC
Confidence            44 67789999999999999999999999999999998 567776654    3789999998876

>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=97.85  E-value=1.4e-05  Score=62.46  Aligned_cols=72  Identities=18%  Similarity=0.305  Sum_probs=55.8

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccC----CCCceEEecCcCCCCCC-C--CE
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSS----YSGVKHIGGIMLERIPK-G--DA  229 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~----~~ri~~~~gD~f~~~P~-~--D~  229 (233)
                      .+++.++ .+...+|||||||+|.++..|++..  -+++.+|. ++.++.|++    .++|+++.+|.+...|. +  |+
T Consensus        61 ~ml~~L~-l~~g~~VLdIG~GsGy~ta~La~l~--~~V~aiE~~~~~~~~A~~~~~~~~nv~~~~~d~~~g~~~~~pfD~  137 (224)
T d1vbfa_          61 FMLDELD-LHKGQKVLEIGTGIGYYTALIAEIV--DKVVSVEINEKMYNYASKLLSYYNNIKLILGDGTLGYEEEKPYDR  137 (224)
T ss_dssp             HHHHHTT-CCTTCEEEEECCTTSHHHHHHHHHS--SEEEEEESCHHHHHHHHHHHTTCSSEEEEESCGGGCCGGGCCEEE
T ss_pred             HHHHHhh-hcccceEEEecCCCCHHHHHHHHHh--cccccccccHHHHHHHHHHHhcccccccccCchhhcchhhhhHHH
Confidence            3566666 7888999999999999998888875  35777786 556666654    37899999999986665 4  98


Q ss_pred             EEe
Q 039903          230 ILI  232 (233)
Q Consensus       230 ~~l  232 (233)
                      |++
T Consensus       138 Iiv  140 (224)
T d1vbfa_         138 VVV  140 (224)
T ss_dssp             EEE
T ss_pred             HHh
Confidence            875

>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=97.84  E-value=1.2e-05  Score=62.77  Aligned_cols=64  Identities=16%  Similarity=0.065  Sum_probs=49.2

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccC-----------------------CCCceEEecCcC
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSS-----------------------YSGVKHIGGIML  221 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~-----------------------~~ri~~~~gD~f  221 (233)
                      .....+|||+|||.|..+..|+++  ..+++.+|+. ..|+.+++                       .++|++..+|++
T Consensus        43 ~~~~~rvLd~GCG~G~~a~~LA~~--G~~V~gvD~S~~ai~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~d~~  120 (229)
T d2bzga1          43 GKSGLRVFFPLCGKAVEMKWFADR--GHSVVGVEISELGIQEFFTEQNLSYSEEPITEIPGTKVFKSSSGNISLYCCSIF  120 (229)
T ss_dssp             TCCSCEEEETTCTTCTHHHHHHHT--TCEEEEECSCHHHHHHHHHHTTCCEEEEECTTSTTCEEEEETTSSEEEEESCGG
T ss_pred             CCCCCEEEEeCCCCcHHHHHHHhC--CCcEEEEeCCHHHHHHHHHHhhccccccchhcccccceeeecCCcEEEEEcchh
Confidence            456679999999999999999986  6689999985 46765432                       158999999999


Q ss_pred             C--CCCCC--CEEE
Q 039903          222 E--RIPKG--DAIL  231 (233)
Q Consensus       222 ~--~~P~~--D~~~  231 (233)
                      +  +.+.+  |+++
T Consensus       121 ~l~~~~~~~fd~i~  134 (229)
T d2bzga1         121 DLPRTNIGKFDMIW  134 (229)
T ss_dssp             GGGGSCCCCEEEEE
T ss_pred             hccccccCceeEEE
Confidence            8  33333  7765

>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=97.83  E-value=1.5e-05  Score=61.19  Aligned_cols=65  Identities=17%  Similarity=0.134  Sum_probs=49.0

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC-----CCceEEecCcCCCCCCCCEEEe
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY-----SGVKHIGGIMLERIPKGDAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~-----~ri~~~~gD~f~~~P~~D~~~l  232 (233)
                      +++ .+|||+|||+|.++++++.+.+ .+++.+|.. ..++.++++     .+++++.+|..+.-..-|+|++
T Consensus        45 l~g-~~vLDlg~GtG~l~i~a~~~g~-~~v~~vdi~~~~~~~a~~N~~~~~~~~~~~~~d~~~~~~~fD~Vi~  115 (201)
T d1wy7a1          45 IEG-KVVADLGAGTGVLSYGALLLGA-KEVICVEVDKEAVDVLIENLGEFKGKFKVFIGDVSEFNSRVDIVIM  115 (201)
T ss_dssp             STT-CEEEEETCTTCHHHHHHHHTTC-SEEEEEESCHHHHHHHHHHTGGGTTSEEEEESCGGGCCCCCSEEEE
T ss_pred             CCC-CEEEECcCcchHHHHHHHHcCC-CEEEEEcCcHHHHHHHHHHHHHcCCCceEEECchhhhCCcCcEEEE
Confidence            444 7899999999999999887644 589999985 577766653     5788899998763222488875

>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=97.82  E-value=2.1e-05  Score=63.81  Aligned_cols=73  Identities=18%  Similarity=0.153  Sum_probs=53.7

Q ss_pred             HHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccC-------CCCceEEecCcCCCCCCCC
Q 039903          157 NRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSS-------YSGVKHIGGIMLERIPKGD  228 (233)
Q Consensus       157 ~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~-------~~ri~~~~gD~f~~~P~~D  228 (233)
                      ..+++.+. .+...+|||||||.|.+++.++++++ .+++.+++.+ -++.+++       .+++++...|+-.+-.+-|
T Consensus        51 ~~~~~~l~-l~~G~~VLDiGCG~G~~~~~~a~~~g-~~v~git~s~~q~~~a~~~~~~~~l~~~v~~~~~d~~~~~~~fD  128 (291)
T d1kpia_          51 KLALDKLN-LEPGMTLLDIGCGWGSTMRHAVAEYD-VNVIGLTLSENQYAHDKAMFDEVDSPRRKEVRIQGWEEFDEPVD  128 (291)
T ss_dssp             HHHHHTTC-CCTTCEEEEETCTTSHHHHHHHHHHC-CEEEEEESCHHHHHHHHHHHHHSCCSSCEEEEECCGGGCCCCCS
T ss_pred             HHHHHhcC-CCCCCEEEEecCcchHHHHHHHHhcC-cceeeccchHHHHHHHHHHHHhhccchhhhhhhhcccccccccc
Confidence            45667777 88889999999999999999999997 5999999864 4443332       2688888888743211237


Q ss_pred             EEE
Q 039903          229 AIL  231 (233)
Q Consensus       229 ~~~  231 (233)
                      .|+
T Consensus       129 ~i~  131 (291)
T d1kpia_         129 RIV  131 (291)
T ss_dssp             EEE
T ss_pred             eEe
Confidence            664

>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=97.82  E-value=8e-06  Score=64.08  Aligned_cols=58  Identities=7%  Similarity=0.041  Sum_probs=48.9

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhcc----CCCCceEEecCcCCC
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSS----SYSGVKHIGGIMLER  223 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~----~~~ri~~~~gD~f~~  223 (233)
                      .+...+|||||||+|..+..+++..|+-+++.+|+ |..++.+.    ..+++..+.+|...+
T Consensus        72 ikpG~~VLDlGcGsG~~~~~la~~~~~g~V~aVDiS~~~i~~a~~~a~~~~ni~~i~~d~~~~  134 (230)
T d1g8sa_          72 IKRDSKILYLGASAGTTPSHVADIADKGIVYAIEYAPRIMRELLDACAERENIIPILGDANKP  134 (230)
T ss_dssp             CCTTCEEEEESCCSSHHHHHHHHHTTTSEEEEEESCHHHHHHHHHHTTTCTTEEEEECCTTCG
T ss_pred             CCCCCEEEEeCEEcCHHHHHHHHhCCCCEEEEEeCcHHHHHHHHHHHhhhcccceEEEeeccC
Confidence            67779999999999999999999999999999998 55666554    347888888888873

>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=97.79  E-value=1.2e-05  Score=64.23  Aligned_cols=66  Identities=14%  Similarity=-0.007  Sum_probs=53.2

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCCCCCC--CCEEEe
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLERIPK--GDAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~~P~--~D~~~l  232 (233)
                      .+...+|||+|||.|.+++.++++ +..+++.+|+ |..++.++++       ++|+++.+|.++-.+.  +|.|+|
T Consensus       105 ~~~g~~VlD~~aG~G~~~l~~a~~-~~~~V~avd~n~~a~~~~~~N~~~n~l~~~v~~~~~D~~~~~~~~~~D~Ii~  180 (260)
T d2frna1         105 AKPDELVVDMFAGIGHLSLPIAVY-GKAKVIAIEKDPYTFKFLVENIHLNKVEDRMSAYNMDNRDFPGENIADRILM  180 (260)
T ss_dssp             CCTTCEEEETTCTTTTTHHHHHHH-TCCEEEEECCCHHHHHHHHHHHHHTTCTTTEEEECSCTTTCCCCSCEEEEEE
T ss_pred             cCCccEEEECcceEcHHHHHHHHh-CCcEEEEecCCHHHHHHHHHHHHHhCCCceEEEEEcchHHhccCCCCCEEEE
Confidence            456789999999999999999986 5678999998 5677766653       6899999999984444  487775

>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=97.78  E-value=2.6e-05  Score=64.09  Aligned_cols=94  Identities=15%  Similarity=0.141  Sum_probs=66.8

Q ss_pred             CchHHHHHHHHHHhcchhc----HHHHHHhcccccCcceEEEecCCccHHHHHHHHH-cCCCcEEEeec-hHHHhhccCC
Q 039903          137 DFRFNGVFNKAMLNHTSIV----TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISN-YLHIKGVNFDL-SHVIQDSSSY  210 (233)
Q Consensus       137 ~~~~~~~f~~am~~~~~~~----~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~-~P~l~~~v~Dl-p~v~~~a~~~  210 (233)
                      .|-... |...|...++..    +..++..++ .....+|+|+|||+|.++..|++. .|+-+++.+|+ ++.++.|+++
T Consensus        65 ~Pt~~d-~~~~~~r~tqiiypkD~~~Il~~l~-i~pG~rVLE~GtGsG~lt~~LAr~vg~~G~V~t~E~~~~~~~~A~~n  142 (324)
T d2b25a1          65 RPALED-YVVLMKRGTAITFPKDINMILSMMD-INPGDTVLEAGSGSGGMSLFLSKAVGSQGRVISFEVRKDHHDLAKKN  142 (324)
T ss_dssp             CCCHHH-HHHHSCCSSCCCCHHHHHHHHHHHT-CCTTCEEEEECCTTSHHHHHHHHHHCTTCEEEEEESSHHHHHHHHHH
T ss_pred             CCCHHH-HhhccCCCCcccccccHHHHHHHhC-CCCCCEEEEecccccHHHHHHHHHhCCCcEEEEecCCHHHHHHHHHH
Confidence            444333 555666655543    455677777 788899999999999999999987 68999999998 4566665531


Q ss_pred             -----------------CCceEEecCcCC---CCCCC--CEEEe
Q 039903          211 -----------------SGVKHIGGIMLE---RIPKG--DAILI  232 (233)
Q Consensus       211 -----------------~ri~~~~gD~f~---~~P~~--D~~~l  232 (233)
                                       ++|.++.+|+-+   .++..  |.++|
T Consensus       143 ~~~~~~~~~~~~~~~~~~nv~~~~~di~~~~~~~~~~~fD~V~L  186 (324)
T d2b25a1         143 YKHWRDSWKLSHVEEWPDNVDFIHKDISGATEDIKSLTFDAVAL  186 (324)
T ss_dssp             HHHHHHHHTTTCSSCCCCCEEEEESCTTCCC-------EEEEEE
T ss_pred             HHHhhhhhhhhhhhccccceeEEecchhhcccccCCCCcceEee
Confidence                             689999999865   24443  88875

>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=97.76  E-value=2.4e-05  Score=60.64  Aligned_cols=73  Identities=16%  Similarity=0.259  Sum_probs=56.1

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCCCCCC-C--
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLERIPK-G--  227 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~~P~-~--  227 (233)
                      .+++.++ .++..+|+|||+|+|..+..+++-. +-+++.+|. ++.++.|+++      ++|.++.||.++..|. +  
T Consensus        69 ~ml~~L~-l~~g~~VLeIGsGsGY~taila~l~-g~~V~~ie~~~~l~~~a~~~l~~~g~~nv~~~~gd~~~g~~~~~pf  146 (215)
T d1jg1a_          69 IMLEIAN-LKPGMNILEVGTGSGWNAALISEIV-KTDVYTIERIPELVEFAKRNLERAGVKNVHVILGDGSKGFPPKAPY  146 (215)
T ss_dssp             HHHHHHT-CCTTCCEEEECCTTSHHHHHHHHHH-CSCEEEEESCHHHHHHHHHHHHHTTCCSEEEEESCGGGCCGGGCCE
T ss_pred             HHHHhhc-cCccceEEEecCCCChhHHHHHHhh-CceeEEEeccHHHHHHHHHHHHHcCCceeEEEECccccCCcccCcc
Confidence            4556666 7888999999999999998888764 345777776 5567766652      8999999999986664 4  


Q ss_pred             CEEEe
Q 039903          228 DAILI  232 (233)
Q Consensus       228 D~~~l  232 (233)
                      |.|++
T Consensus       147 D~Iiv  151 (215)
T d1jg1a_         147 DVIIV  151 (215)
T ss_dssp             EEEEE
T ss_pred             eeEEe
Confidence            98875

>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=97.75  E-value=1.8e-05  Score=62.83  Aligned_cols=55  Identities=7%  Similarity=0.030  Sum_probs=46.0

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcC
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIML  221 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f  221 (233)
                      +...+++|||+|+|..+..|++++|+++++..|+ |++++.|+++       +|+.++..+..
T Consensus        60 ~~~~~~LDiGtGsg~I~~~l~~~~~~~~~~~~Di~~~al~~A~~N~~~n~l~~~~~~~~~~~~  122 (250)
T d2h00a1          60 STLRRGIDIGTGASCIYPLLGATLNGWYFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVPQK  122 (250)
T ss_dssp             CCCCEEEEESCTTTTHHHHHHHHHHCCEEEEEESCHHHHHHHHHHHHHTTCTTTEEEEECCTT
T ss_pred             cccceEEEeCCCchHHHHHHHHhCCCccccceecCHHHHHHHHHHHHHhCCCcceeeeeeccH
Confidence            4457899999999999999999999999999998 5688888763       78888765443

>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=97.64  E-value=6.3e-05  Score=58.51  Aligned_cols=75  Identities=15%  Similarity=0.201  Sum_probs=55.7

Q ss_pred             HHHHhcc-cccCcceEEEecCCccHHHHHHHHH------cCCCcEEEeec-hHHHhhccCC-----------CCceEEec
Q 039903          158 RIIDSSK-GFEQIKQLVDVGGGLGVNVNIIISN------YLHIKGVNFDL-SHVIQDSSSY-----------SGVKHIGG  218 (233)
Q Consensus       158 ~~~~~~~-~~~~~~~vvDvGGG~G~~~~~l~~~------~P~l~~~v~Dl-p~v~~~a~~~-----------~ri~~~~g  218 (233)
                      .+++.+. +.++..+|||||||+|.++..+++.      ++..+++.+|. ++.++.|+++           .+|.++.+
T Consensus        69 ~~l~~L~~~l~~g~~VLeIGtGsGY~ta~la~l~g~~g~~~~~~V~~iE~~~~l~~~a~~~l~~~~~~~~~~~nv~~~~~  148 (223)
T d1r18a_          69 FALEYLRDHLKPGARILDVGSGSGYLTACFYRYIKAKGVDADTRIVGIEHQAELVRRSKANLNTDDRSMLDSGQLLIVEG  148 (223)
T ss_dssp             HHHHHTTTTCCTTCEEEEESCTTSHHHHHHHHHHHHSCCCTTCEEEEEESCHHHHHHHHHHHHHHHHHHHHHTSEEEEES
T ss_pred             HHHHHHhhccCCCCeEEEecCCCCHHHHHHHHHhhhccCCcccEEEEEecCHHHHHHHHHhhhhcchhhcCccEEEEEec
Confidence            4555552 2677789999999999998777765      46678888887 5566666542           68999999


Q ss_pred             CcCCCCCC-C--CEEEe
Q 039903          219 IMLERIPK-G--DAILI  232 (233)
Q Consensus       219 D~f~~~P~-~--D~~~l  232 (233)
                      |..+..|. +  |.|++
T Consensus       149 d~~~~~~~~~~fD~Iiv  165 (223)
T d1r18a_         149 DGRKGYPPNAPYNAIHV  165 (223)
T ss_dssp             CGGGCCGGGCSEEEEEE
T ss_pred             ccccccccccceeeEEE
Confidence            99985543 4  98875

>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=97.63  E-value=5.9e-05  Score=60.74  Aligned_cols=64  Identities=19%  Similarity=0.283  Sum_probs=46.2

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC----------CCceEEecCcCC---CCCC--C-C
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY----------SGVKHIGGIMLE---RIPK--G-D  228 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~----------~ri~~~~gD~f~---~~P~--~-D  228 (233)
                      ..+.++|||||||+|.++..|+++  ..+++.+|+. +.++.|++.          .+..+...|+..   .+|.  . |
T Consensus        54 ~~~~~~vLD~GcG~G~~~~~la~~--g~~v~gvD~S~~ml~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fd  131 (292)
T d1xvaa_          54 QHGCHRVLDVACGTGVDSIMLVEE--GFSVTSVDASDKMLKYALKERWNRRKEPAFDKWVIEEANWLTLDKDVPAGDGFD  131 (292)
T ss_dssp             HTTCCEEEESSCTTSHHHHHHHHT--TCEEEEEESCHHHHHHHHHHHHHTTTSHHHHTCEEEECCGGGHHHHSCCTTCEE
T ss_pred             hcCCCEEEEecCCCcHHHHHHHHc--CCeeeeccCchHHHHHHHHHHHhcccccccceeeeeeccccccccccCCCCCce
Confidence            355679999999999999999987  5789999985 577776542          245566677764   2342  3 6


Q ss_pred             EEE
Q 039903          229 AIL  231 (233)
Q Consensus       229 ~~~  231 (233)
                      +++
T Consensus       132 ~v~  134 (292)
T d1xvaa_         132 AVI  134 (292)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            665

>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=97.56  E-value=2.2e-05  Score=64.30  Aligned_cols=66  Identities=18%  Similarity=0.253  Sum_probs=54.4

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccC-----------CCCceEEecCcCC---CCCCC-CEE
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSS-----------YSGVKHIGGIMLE---RIPKG-DAI  230 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~-----------~~ri~~~~gD~f~---~~P~~-D~~  230 (233)
                      ++.++||.||||.|..+.++++..|..+++++|+ |.|++.+++           .+|++++.+|.++   ..+.. |+|
T Consensus        76 ~~pk~VLiiG~G~G~~~~~ll~~~~~~~v~~VEiD~~Vi~~a~~~f~~~~~~~~~d~rv~i~~~Da~~~l~~~~~~yDvI  155 (312)
T d1uira_          76 PEPKRVLIVGGGEGATLREVLKHPTVEKAVMVDIDGELVEVAKRHMPEWHQGAFDDPRAVLVIDDARAYLERTEERYDVV  155 (312)
T ss_dssp             SCCCEEEEEECTTSHHHHHHTTSTTCCEEEEEESCHHHHHHHHHHCHHHHTTGGGCTTEEEEESCHHHHHHHCCCCEEEE
T ss_pred             CCcceEEEeCCCchHHHHHHHhcCCcceEEEecCCHHHHHHHHhcCcccccCccCCCceEEEEchHHHHhhhcCCcccEE
Confidence            5678999999999999999999888889999998 568877654           2799999999997   33444 888


Q ss_pred             Ee
Q 039903          231 LI  232 (233)
Q Consensus       231 ~l  232 (233)
                      ++
T Consensus       156 i~  157 (312)
T d1uira_         156 II  157 (312)
T ss_dssp             EE
T ss_pred             EE
Confidence            74

>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=97.52  E-value=5.6e-05  Score=63.88  Aligned_cols=53  Identities=9%  Similarity=0.115  Sum_probs=43.5

Q ss_pred             HHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccC
Q 039903          156 TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSS  209 (233)
Q Consensus       156 ~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~  209 (233)
                      +..+++.++ .....++||||||.|..+..+++.+|..+++++|+. ..++.|++
T Consensus       205 i~~Il~~l~-Lkpgd~fLDLGCG~G~~vl~aA~~~g~~~v~GIDiS~~~i~~Ak~  258 (406)
T d1u2za_         205 LSDVYQQCQ-LKKGDTFMDLGSGVGNCVVQAALECGCALSFGCEIMDDASDLTIL  258 (406)
T ss_dssp             HHHHHHHTT-CCTTCEEEEESCTTSHHHHHHHHHHCCSEEEEEECCHHHHHHHHH
T ss_pred             HHHHHHHhC-CCCCCEEEeCCCCCcHHHHHHHHHcCCCeEEEEeCCHHHHHHHHH
Confidence            345666666 777789999999999999999999998899999985 46666653

>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=97.39  E-value=9.7e-05  Score=57.86  Aligned_cols=69  Identities=12%  Similarity=0.317  Sum_probs=53.2

Q ss_pred             HHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhcc----CCCCceEEecCcCC-CCCCC
Q 039903          156 TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSS----SYSGVKHIGGIMLE-RIPKG  227 (233)
Q Consensus       156 ~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~----~~~ri~~~~gD~f~-~~P~~  227 (233)
                      +..+++..+ .+...+|++||+|.|.+...|+++..  +++.+|+.. .++..+    ..++++++.+|+++ ++|..
T Consensus        10 ~~~iv~~~~-~~~~d~VlEIGpG~G~LT~~Ll~~~~--~v~avE~D~~l~~~l~~~~~~~~n~~i~~~D~l~~~~~~~   84 (235)
T d1qama_          10 IDKIMTNIR-LNEHDNIFEIGSGKGHFTLELVQRCN--FVTAIEIDHKLCKTTENKLVDHDNFQVLNKDILQFKFPKN   84 (235)
T ss_dssp             HHHHHTTCC-CCTTCEEEEECCTTSHHHHHHHHHSS--EEEEECSCHHHHHHHHHHTTTCCSEEEECCCGGGCCCCSS
T ss_pred             HHHHHHhcC-CCCCCeEEEECCCchHHHHHHHhCcC--ceEEEeeccchHHHHHHHhhcccchhhhhhhhhhcccccc
Confidence            455666666 77889999999999999999999854  577777743 444443    24899999999999 77764

>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=97.38  E-value=6e-05  Score=60.78  Aligned_cols=66  Identities=21%  Similarity=0.222  Sum_probs=54.6

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccC----------CCCceEEecCcCC---CCCCC-CEEE
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSS----------YSGVKHIGGIMLE---RIPKG-DAIL  231 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~----------~~ri~~~~gD~f~---~~P~~-D~~~  231 (233)
                      +..++++-||||.|..+.++++..|..+++++|+ |.|++.+++          .+|++.+.+|.++   ..+.. |+|+
T Consensus        77 ~~pk~vLiiGgG~G~~~~~~l~~~~~~~v~~vEiD~~Vv~~a~~~~~~~~~~~~d~rv~i~~~Da~~~l~~~~~~yDvIi  156 (285)
T d2o07a1          77 PNPRKVLIIGGGDGGVLREVVKHPSVESVVQCEIDEDVIQVSKKFLPGMAIGYSSSKLTLHVGDGFEFMKQNQDAFDVII  156 (285)
T ss_dssp             SSCCEEEEEECTTSHHHHHHTTCTTCCEEEEEESCHHHHHHHHHHCHHHHGGGGCTTEEEEESCHHHHHHTCSSCEEEEE
T ss_pred             cCcCeEEEeCCCchHHHHHHHHcCCcceeeeccCCHHHHHHHHhhchhhccccCCCCceEEEccHHHHHhcCCCCCCEEE
Confidence            5678999999999999999998778889999998 568888865          2799999999886   33444 8887


Q ss_pred             e
Q 039903          232 I  232 (233)
Q Consensus       232 l  232 (233)
                      +
T Consensus       157 ~  157 (285)
T d2o07a1         157 T  157 (285)
T ss_dssp             E
T ss_pred             E
Confidence            4

>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=97.38  E-value=6.4e-05  Score=60.30  Aligned_cols=66  Identities=21%  Similarity=0.183  Sum_probs=53.7

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccC----------CCCceEEecCcCC--CC-CCC-CEEE
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSS----------YSGVKHIGGIMLE--RI-PKG-DAIL  231 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~----------~~ri~~~~gD~f~--~~-P~~-D~~~  231 (233)
                      .+.++|+-||||.|..+.++++..|..+++++|+ |.|++.+++          .+|++++.+|.++  .. +.. |+|+
T Consensus        74 ~~p~~vLiiGgG~G~~~~~~l~~~~~~~i~~VEID~~Vi~~a~~~~~~~~~~~~d~r~~i~~~D~~~~l~~~~~~yDvIi  153 (274)
T d1iy9a_          74 PNPEHVLVVGGGDGGVIREILKHPSVKKATLVDIDGKVIEYSKKFLPSIAGKLDDPRVDVQVDDGFMHIAKSENQYDVIM  153 (274)
T ss_dssp             SSCCEEEEESCTTCHHHHHHTTCTTCSEEEEEESCHHHHHHHHHHCHHHHTTTTSTTEEEEESCSHHHHHTCCSCEEEEE
T ss_pred             CCcceEEecCCCCcHHHHHHHhcCCcceEEEecCCHHHHHHHHHhChhhcccccCCCeEEEechHHHHHhhcCCCCCEEE
Confidence            5678999999999999999998777788999998 568887754          2799999999887  33 333 8887


Q ss_pred             e
Q 039903          232 I  232 (233)
Q Consensus       232 l  232 (233)
                      +
T Consensus       154 ~  154 (274)
T d1iy9a_         154 V  154 (274)
T ss_dssp             E
T ss_pred             E
Confidence            4

>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=97.36  E-value=6.3e-05  Score=60.91  Aligned_cols=66  Identities=20%  Similarity=0.293  Sum_probs=54.0

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC----------CCceEEecCcCC---CCCCC-CEEE
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY----------SGVKHIGGIMLE---RIPKG-DAIL  231 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~----------~ri~~~~gD~f~---~~P~~-D~~~  231 (233)
                      +++++|+-||||.|..+.++++..|..+++++|+ |.|++.++++          +|++.+.+|.++   ..+.. |+|+
T Consensus        88 ~~pk~VLiiGgG~G~~~r~~l~~~~~~~i~~VEIDp~Vi~~a~~~~~~~~~~~~d~rv~v~~~Da~~~l~~~~~~yDvIi  167 (295)
T d1inla_          88 PNPKKVLIIGGGDGGTLREVLKHDSVEKAILCEVDGLVIEAARKYLKQTSCGFDDPRAEIVIANGAEYVRKFKNEFDVII  167 (295)
T ss_dssp             SSCCEEEEEECTTCHHHHHHTTSTTCSEEEEEESCHHHHHHHHHHCHHHHGGGGCTTEEEEESCHHHHGGGCSSCEEEEE
T ss_pred             CCCceEEEecCCchHHHHHHHhcCCCceEEEecCCHHHHHHHHHHHHhhcccccCCCcEEEhhhHHHHHhcCCCCCCEEE
Confidence            5678999999999999999999777788999998 5688877652          799999999987   23334 8887


Q ss_pred             e
Q 039903          232 I  232 (233)
Q Consensus       232 l  232 (233)
                      +
T Consensus       168 ~  168 (295)
T d1inla_         168 I  168 (295)
T ss_dssp             E
T ss_pred             E
Confidence            5

>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=97.20  E-value=0.00014  Score=49.00  Aligned_cols=71  Identities=11%  Similarity=0.126  Sum_probs=57.2

Q ss_pred             HHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhh
Q 039903           12 AMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFV   89 (233)
Q Consensus        12 ~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~   89 (233)
                      .+..-.++.|...|...   ++.|..|||+.+++    ++..+.+.|+.|...|++++.....  ..-.|++|+.|+...
T Consensus        12 ~l~~p~r~~IL~~L~~~---~~~~~~eLa~~l~i----s~~~vs~~l~~L~~~glV~~~~~~~d~r~~~~~LT~~G~~~~   84 (100)
T d1ub9a_          12 ILGNPVRLGIMIFLLPR---RKAPFSQIQKVLDL----TPGNLDSHIRVLERNGLVKTYKVIADRPRTVVEITDFGMEEA   84 (100)
T ss_dssp             HHHSHHHHHHHHHHHHH---SEEEHHHHHHHTTC----CHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECHHHHHHH
T ss_pred             hcCCHHHHHHHHHhccC---CCeeHHHHHHHHhh----ccccccHHHHHHhhhceeEEEEcCcCCccccccCCHHHHHHH
Confidence            44455688999999876   58999999999999    9999999999999999998754321  112599999987654

>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=97.19  E-value=0.00014  Score=58.73  Aligned_cols=66  Identities=17%  Similarity=0.179  Sum_probs=54.1

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccC----------CCCceEEecCcCC---CCCC-C-CEE
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSS----------YSGVKHIGGIMLE---RIPK-G-DAI  230 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~----------~~ri~~~~gD~f~---~~P~-~-D~~  230 (233)
                      +++++|+=||||.|..+.++++..|-.+++++|+ |+|++.+++          .+|++.+.+|-++   ..+. . |+|
T Consensus        79 ~~pk~VLiiGgG~G~~~r~~l~~~~~~~i~~VEiD~~Vi~~~~~~f~~~~~~~~~~r~~i~~~Da~~~l~~~~~~~yDvI  158 (290)
T d1xj5a_          79 PNPKKVLVIGGGDGGVLREVARHASIEQIDMCEIDKMVVDVSKQFFPDVAIGYEDPRVNLVIGDGVAFLKNAAEGSYDAV  158 (290)
T ss_dssp             SCCCEEEEETCSSSHHHHHHTTCTTCCEEEEEESCHHHHHHHHHHCHHHHGGGGSTTEEEEESCHHHHHHTSCTTCEEEE
T ss_pred             CCCcceEEecCCchHHHHHHHhcccceeeEEecCCHHHHHHHHHhchhhhccccCCCcEEEEccHHHHHhhccccCccEE
Confidence            5678999999999999999999777678999998 568887765          2899999999876   3454 3 888


Q ss_pred             Ee
Q 039903          231 LI  232 (233)
Q Consensus       231 ~l  232 (233)
                      ++
T Consensus       159 i~  160 (290)
T d1xj5a_         159 IV  160 (290)
T ss_dssp             EE
T ss_pred             EE
Confidence            75

>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=97.17  E-value=0.00015  Score=54.36  Aligned_cols=62  Identities=13%  Similarity=0.135  Sum_probs=48.7

Q ss_pred             ceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC------CCceEEecCcCC--CCC-CC-CEEEe
Q 039903          170 KQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY------SGVKHIGGIMLE--RIP-KG-DAILI  232 (233)
Q Consensus       170 ~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~------~ri~~~~gD~f~--~~P-~~-D~~~l  232 (233)
                      .++||++||+|.++.+.+.+... +++.+|.. .+++.++++      .+++++.+|.++  ... .. |+|++
T Consensus        45 ~~vLDlfaGsG~~giealsrGa~-~v~~VE~~~~a~~~~k~N~~~~~~~~~~ii~~d~~~~l~~~~~~fDlIf~  117 (183)
T d2fpoa1          45 AQCLDCFAGSGALGLEALSRYAA-GATLIEMDRAVSQQLIKNLATLKAGNARVVNSNAMSFLAQKGTPHNIVFV  117 (183)
T ss_dssp             CEEEETTCTTCHHHHHHHHTTCS-EEEEECSCHHHHHHHHHHHHHTTCCSEEEECSCHHHHHSSCCCCEEEEEE
T ss_pred             hhhhhhhccccceeeeEEecCcc-eeEEEEEeechhhHHHHHHhhccccceeeeeecccccccccccccCEEEE
Confidence            68999999999999999998765 78999985 577666543      678999999887  222 23 99886

>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=97.17  E-value=0.00018  Score=57.60  Aligned_cols=65  Identities=23%  Similarity=0.228  Sum_probs=51.3

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccC----------------CCCceEEecCcCCC--CCCC
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSS----------------YSGVKHIGGIMLER--IPKG  227 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~----------------~~ri~~~~gD~f~~--~P~~  227 (233)
                      .+.++|+-||||.|..+.++++ +|..+++++|+ |.|++.+++                .+|++++.+|.++-  ....
T Consensus        71 ~~p~~vLiiG~G~G~~~~~~l~-~~~~~v~~VEiD~~Vi~~a~~~f~~~~~~~~~~~~~~d~rv~i~~~Da~~~l~~~~~  149 (276)
T d1mjfa_          71 PKPKRVLVIGGGDGGTVREVLQ-HDVDEVIMVEIDEDVIMVSKDLIKIDNGLLEAMLNGKHEKAKLTIGDGFEFIKNNRG  149 (276)
T ss_dssp             SCCCEEEEEECTTSHHHHHHTT-SCCSEEEEEESCHHHHHHHHHHTCTTTTHHHHHHTTCCSSEEEEESCHHHHHHHCCC
T ss_pred             CCCceEEEecCCchHHHHHHHH-hCCceEEEecCCHHHHHHHHHhhhhccchhhhhhccCCCCceEEEChHHHHHhccCC
Confidence            5678999999999999999986 67778999998 568887753                37999999998862  2233


Q ss_pred             -CEEEe
Q 039903          228 -DAILI  232 (233)
Q Consensus       228 -D~~~l  232 (233)
                       |+|++
T Consensus       150 yDvIi~  155 (276)
T d1mjfa_         150 FDVIIA  155 (276)
T ss_dssp             EEEEEE
T ss_pred             CCEEEE
Confidence             88764

>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=97.17  E-value=0.00011  Score=59.87  Aligned_cols=66  Identities=18%  Similarity=0.224  Sum_probs=53.1

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC----------CCceEEecCcCC---CCCCC-CEEE
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY----------SGVKHIGGIMLE---RIPKG-DAIL  231 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~----------~ri~~~~gD~f~---~~P~~-D~~~  231 (233)
                      +++++++-||||.|..+.++++..|-.+++++|+ |.|++.++++          +|++++.+|.++   .-+.. |+|+
T Consensus       105 ~~pk~VLIiGgG~G~~~rellk~~~v~~v~~VEID~~Vv~~a~~~~~~~~~~~~dprv~i~i~Da~~~l~~~~~~yDvII  184 (312)
T d2b2ca1         105 PDPKRVLIIGGGDGGILREVLKHESVEKVTMCEIDEMVIDVAKKFLPGMSCGFSHPKLDLFCGDGFEFLKNHKNEFDVII  184 (312)
T ss_dssp             SSCCEEEEESCTTSHHHHHHTTCTTCCEEEEECSCHHHHHHHHHHCTTTSGGGGCTTEEEECSCHHHHHHHCTTCEEEEE
T ss_pred             CCCCeEEEeCCCchHHHHHHHHcCCcceEEEEcccHHHHHHHHhhchhhccccCCCCeEEEEchHHHHHHhCCCCCCEEE
Confidence            5678999999999999999998767678999998 5688877652          799999999887   22333 8887


Q ss_pred             e
Q 039903          232 I  232 (233)
Q Consensus       232 l  232 (233)
                      +
T Consensus       185 ~  185 (312)
T d2b2ca1         185 T  185 (312)
T ss_dssp             E
T ss_pred             E
Confidence            4

>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=97.09  E-value=0.0002  Score=56.31  Aligned_cols=69  Identities=19%  Similarity=0.271  Sum_probs=54.0

Q ss_pred             HHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccC----CCCceEEecCcCC-CCCCC
Q 039903          156 TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSS----YSGVKHIGGIMLE-RIPKG  227 (233)
Q Consensus       156 ~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~----~~ri~~~~gD~f~-~~P~~  227 (233)
                      +..+++..+ .+...+|++||+|.|.++..|+++..  +++.+|+.. .++.+++    .++++++.+|+++ ++|..
T Consensus        18 i~kIv~~~~-~~~~d~VLEIGpG~G~LT~~L~~~~~--~v~aIE~D~~l~~~l~~~~~~~~n~~ii~~D~l~~~~~~~   92 (245)
T d1yuba_          18 LNQIIKQLN-LKETDTVYEIGTGKGHLTTKLAKISK--QVTSIELDSHLFNLSSEKLKLNTRVTLIHQDILQFQFPNK   92 (245)
T ss_dssp             HHHHHHHCC-CCSSEEEEECSCCCSSCSHHHHHHSS--EEEESSSSCSSSSSSSCTTTTCSEEEECCSCCTTTTCCCS
T ss_pred             HHHHHHhcC-CCCCCeEEEECCCccHHHHHHHhhcC--ceeEeeecccchhhhhhhhhhccchhhhhhhhhccccccc
Confidence            456777766 77889999999999999999999844  688888754 4444443    2689999999998 77763

>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=96.86  E-value=0.001  Score=49.74  Aligned_cols=64  Identities=13%  Similarity=0.097  Sum_probs=51.2

Q ss_pred             HHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccC--CCCceEEecCcCC
Q 039903          156 TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSS--YSGVKHIGGIMLE  222 (233)
Q Consensus       156 ~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~--~~ri~~~~gD~f~  222 (233)
                      ..++++.+. -....++||+..|.|.++.++++++  .+++.+|+ |+++..++.  .+|+.++.++|-+
T Consensus         7 l~Evl~~l~-~~~g~~~vD~T~G~GGhs~~iL~~~--~~viaiD~D~~ai~~a~~~~~~~~~~~~~~f~~   73 (182)
T d1wg8a2           7 YQEALDLLA-VRPGGVYVDATLGGAGHARGILERG--GRVIGLDQDPEAVARAKGLHLPGLTVVQGNFRH   73 (182)
T ss_dssp             HHHHHHHHT-CCTTCEEEETTCTTSHHHHHHHHTT--CEEEEEESCHHHHHHHHHTCCTTEEEEESCGGG
T ss_pred             HHHHHHhcC-CCCCCEEEEeCCCCcHHHHHHhccc--CcEEEEhhhhhHHHHHhhccccceeEeehHHHH
Confidence            456677665 4667899999999999999999975  57899998 567777765  3789998888765

>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=96.83  E-value=0.00046  Score=54.81  Aligned_cols=43  Identities=21%  Similarity=0.263  Sum_probs=30.1

Q ss_pred             cCcceEEEecCCccHHHHHHHH----HcCCCc--EEEeech-HHHhhccC
Q 039903          167 EQIKQLVDVGGGLGVNVNIIIS----NYLHIK--GVNFDLS-HVIQDSSS  209 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~----~~P~l~--~~v~Dlp-~v~~~a~~  209 (233)
                      ++..+|||||||+|.++..|++    ++|...  .+++|.. ..++.+++
T Consensus        39 ~~~~~VLDiGcG~G~~~~~ll~~l~~~~~~~~~~~~~vD~s~~~l~~a~~   88 (280)
T d1jqea_          39 KSEIKILSIGGGAGEIDLQILSKVQAQYPGVCINNEVVEPSAEQIAKYKE   88 (280)
T ss_dssp             CSEEEEEEETCTTSHHHHHHHHHHHHHSTTCEEEEEEECCCHHHHHHHHH
T ss_pred             CCCCeEEEEcCCCCHHHHHHHHHhhhhccCCceEEEEEeCcHHHHHHHHH
Confidence            3345799999999998766654    566654  5888974 46666543

>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=96.80  E-value=0.0012  Score=43.35  Aligned_cols=60  Identities=12%  Similarity=0.205  Sum_probs=49.5

Q ss_pred             hhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhcC
Q 039903           21 VFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        21 lfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~~   91 (233)
                      ++|+|....  ++.+...|...+++    +.+.+...|+.|+..|++++.     ++.|.+|+.|..|+..
T Consensus         8 i~DIL~~~~--~g~~kT~i~~~aNL----s~~~~~kyl~~L~~~GLI~~~-----~~~Y~iT~kG~~~L~~   67 (90)
T d1r7ja_           8 IQAILEACK--SGSPKTRIMYGANL----SYALTGRYIKMLMDLEIIRQE-----GKQYMLTKKGEELLED   67 (90)
T ss_dssp             HHHHHHHHT--TCBCHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEE-----TTEEEECHHHHHHHHH
T ss_pred             HHHHHHHHh--CCCCccHHHHHcCC----CHHHHHHHHHHHHHCCCeeec-----CCEEEECccHHHHHHH
Confidence            345554432  24578999999999    999999999999999999985     7899999999987754

>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=96.78  E-value=0.00042  Score=46.54  Aligned_cols=65  Identities=17%  Similarity=0.315  Sum_probs=53.4

Q ss_pred             HHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903           10 PAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH   83 (233)
Q Consensus        10 s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~   83 (233)
                      +++|.--.++.|+..|..    ++.++.|||+.+++    +...+..-|+.|...|++.....+ ..-.|++++
T Consensus        17 ~kaL~~p~Rl~Il~~L~~----~~~~v~ela~~l~i----s~stvS~HL~~L~~aglV~~~r~G-~~~~Y~l~~   81 (98)
T d1r1ta_          17 FAVLADPNRLRLLSLLAR----SELCVGDLAQAIGV----SESAVSHQLRSLRNLRLVSYRKQG-RHVYYQLQD   81 (98)
T ss_dssp             HHHHCCHHHHHHHHHHTT----CCBCHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEEEET-TEEEEEESS
T ss_pred             HHHhCCHHHHHHHHHHHc----CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCceEEEEEC-CEEEEEECh
Confidence            456666779999999976    69999999999999    999999999999999999876432 234577664

>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=96.72  E-value=0.00095  Score=40.88  Aligned_cols=56  Identities=14%  Similarity=0.177  Sum_probs=45.0

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceecc
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLA   82 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt   82 (233)
                      .++.|...|.+.   +..|.+|||+.+++    +...+.+-++.|...|+..+..   .+..|+++
T Consensus         6 ~~~~iL~~L~~~---~~~s~~eLa~~l~v----S~~ti~r~i~~L~~~G~~I~~~---~g~GY~L~   61 (63)
T d1biaa1           6 VPLKLIALLANG---EFHSGEQLGETLGM----SRAAINKHIQTLRDWGVDVFTV---PGKGYSLP   61 (63)
T ss_dssp             HHHHHHHHHTTS---SCBCHHHHHHHHTS----CHHHHHHHHHHHHHTTCCCEEE---TTTEEECS
T ss_pred             HHHHHHHHHHHC---CcCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCcEEEe---CCCeEEeC
Confidence            356788888774   58999999999999    9999999999999999844332   34468775

>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=96.70  E-value=0.00056  Score=45.51  Aligned_cols=65  Identities=17%  Similarity=0.314  Sum_probs=53.8

Q ss_pred             HHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903           10 PAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH   83 (233)
Q Consensus        10 s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~   83 (233)
                      +.+|.--.++.|+..|..    ++.++.|||+.+++    +...+.+-|+.|...|++.....+ ..-.|+++.
T Consensus        12 fkaL~d~~Rl~Il~~L~~----~~~~v~el~~~l~~----s~~~vS~HL~~L~~~glv~~~r~G-~~~~Y~l~~   76 (94)
T d1r1ua_          12 FKALGDYNRIRIMELLSV----SEASVGHISHQLNL----SQSNVSHQLKLLKSVHLVKAKRQG-QSMIYSLDD   76 (94)
T ss_dssp             HHHTCSHHHHHHHHHHHH----CCBCHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEEEET-TEEEEEESS
T ss_pred             HHHhCCHHHHHHHHHHHc----CCccHHHHHHHHCC----CHHHHHHHHHHHHHCCceEEEEEC-CEEEEEECc
Confidence            456666789999999998    69999999999999    999999999999999999986421 223477764

>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=96.70  E-value=0.00023  Score=52.79  Aligned_cols=65  Identities=9%  Similarity=-0.009  Sum_probs=46.3

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCCC---CC-C-CCEEEe
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLER---IP-K-GDAILI  232 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~---~P-~-~D~~~l  232 (233)
                      .....+|+|+|||+|.++++.+++.  .+++.+|. |.+++.++++       ++|....+|.|.+   .+ . .|+|++
T Consensus        39 ~~~g~~vLDl~~G~G~~~i~a~~~g--a~vv~vD~~~~a~~~~~~N~~~~~~~~~v~~~~~d~~~~~~~~~~~~fD~If~  116 (171)
T d1ws6a1          39 YPRRGRFLDPFAGSGAVGLEAASEG--WEAVLVEKDPEAVRLLKENVRRTGLGARVVALPVEVFLPEAKAQGERFTVAFM  116 (171)
T ss_dssp             CTTCCEEEEETCSSCHHHHHHHHTT--CEEEEECCCHHHHHHHHHHHHHHTCCCEEECSCHHHHHHHHHHTTCCEEEEEE
T ss_pred             ccCCCeEEEeccccchhhhhhhhcc--chhhhcccCHHHHhhhhHHHHhhccccceeeeehhcccccccccCCccceeEE
Confidence            4566799999999999999988874  46888998 4577766653       5666666666531   12 2 388875

>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=96.69  E-value=0.00075  Score=46.06  Aligned_cols=67  Identities=16%  Similarity=0.247  Sum_probs=54.4

Q ss_pred             HHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903            9 LPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH   83 (233)
Q Consensus         9 ~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~   83 (233)
                      .+.+|.--.++.|+..|...   ++.++.|||+.+++    +...+..-|+.|...|++.....+ ..-.|++++
T Consensus        24 ~~kaLadp~Rl~Il~~L~~~---~~~~v~ela~~l~~----s~s~vS~HL~~L~~aGlv~~~r~G-~~~~Y~l~~   90 (108)
T d1u2wa1          24 ILKAIADENRAKITYALCQD---EELCVCDIANILGV----TIANASHHLRTLYKQGVVNFRKEG-KLALYSLGD   90 (108)
T ss_dssp             HHHHHHSHHHHHHHHHHHHS---SCEEHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEC-----CCEEEESC
T ss_pred             HHHHhCCHHHHHHHHHHHhC---CCccHHHHHHHHcc----ChhHHHHHHHHHHHCCeeEEEEEC-CEEEEEECH
Confidence            35678888899999999765   58999999999999    999999999999999999986422 234677664

>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=96.68  E-value=0.002  Score=39.49  Aligned_cols=53  Identities=19%  Similarity=0.135  Sum_probs=44.2

Q ss_pred             hChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCcee
Q 039903           19 LGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYG   80 (233)
Q Consensus        19 lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~   80 (233)
                      -.|-+++.+.|- .|-++.|||+.+|+    ++..++.+|+.|+..|.+.+.    .++.|-
T Consensus        10 ~~I~~~~~~~g~-~PP~vrdl~~~l~~----~e~~~~~lL~~l~~~G~lvkI----~~d~yf   62 (64)
T d1lvaa3          10 KDLEDKYRVSRW-QPPSFKEVAGSFNL----DPSELEELLHYLVREGVLVKI----NDEFYW   62 (64)
T ss_dssp             HHHHHHHHHHTT-SCCBHHHHHHHTTC----CHHHHHHHHHHHHHTTSEEES----SSSBEE
T ss_pred             HHHHHHHHHcCC-CCCcHHHHHHHhCC----CHHHHHHHHHHHHHCCCEEEe----cccccc
Confidence            345666666543 48899999999999    999999999999999999998    567664

>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=96.66  E-value=0.00037  Score=53.58  Aligned_cols=59  Identities=8%  Similarity=0.069  Sum_probs=48.3

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcC-CCcEEEeech-HHHhhccCC-------CCceEEecCcCCCC
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDLS-HVIQDSSSY-------SGVKHIGGIMLERI  224 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dlp-~v~~~a~~~-------~ri~~~~gD~f~~~  224 (233)
                      ..++++||+||+|.|..+..++++.| +-+++.+|.. +.++.|+.+       ++|+++.||..+-+
T Consensus        54 ~~kpk~ILEiGt~~G~Sti~la~al~~~g~v~sid~~~~~~~~a~~~~~~~gl~~~i~l~~Gd~~e~l  121 (214)
T d2cl5a1          54 EYSPSLVLELGAYCGYSAVRMARLLQPGARLLTMEMNPDYAAITQQMLNFAGLQDKVTILNGASQDLI  121 (214)
T ss_dssp             HHCCSEEEEECCTTSHHHHHHHTTCCTTCEEEEEESCHHHHHHHHHHHHHHTCGGGEEEEESCHHHHG
T ss_pred             hhCCCEEEEEccCchhHHHHHHHhCCCccEEEEEeccHHHHHHHHHHHHHcCCCccceeeeccccccc
Confidence            35678999999999999999999876 5899999984 466666542       78999999998643

>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=96.66  E-value=0.00042  Score=56.62  Aligned_cols=65  Identities=15%  Similarity=0.119  Sum_probs=50.9

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC-------CCceEEecCcCCC---CC---CC-CEEE
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLER---IP---KG-DAIL  231 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~---~P---~~-D~~~  231 (233)
                      ++..+|||+|||+|.+++.++++.. .+++.+|+ +..++.++++       ++++++.+|.|+.   ++   .. |+|+
T Consensus       144 ~~g~~VLDl~~g~G~~si~~a~~ga-~~V~~vD~s~~al~~a~~N~~~ngl~~~~~~~~~d~~~~~~~~~~~~~~fD~Vi  222 (324)
T d2as0a2         144 QPGDRVLDVFTYTGGFAIHAAIAGA-DEVIGIDKSPRAIETAKENAKLNGVEDRMKFIVGSAFEEMEKLQKKGEKFDIVV  222 (324)
T ss_dssp             CTTCEEEETTCTTTHHHHHHHHTTC-SEEEEEESCHHHHHHHHHHHHHTTCGGGEEEEESCHHHHHHHHHHTTCCEEEEE
T ss_pred             CCCCeeecccCcccchhhhhhhcCC-cEEEeecCCHHHHHHHHHHHHHcCCCccceeeechhhhhhHHHHhccCCCCchh
Confidence            4568999999999999999998754 38999998 5577777653       6899999999862   22   12 8887


Q ss_pred             e
Q 039903          232 I  232 (233)
Q Consensus       232 l  232 (233)
                      +
T Consensus       223 ~  223 (324)
T d2as0a2         223 L  223 (324)
T ss_dssp             E
T ss_pred             c
Confidence            5

>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=96.65  E-value=0.0012  Score=41.31  Aligned_cols=46  Identities=20%  Similarity=0.346  Sum_probs=41.9

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      +..|+..|...   +++|..|||+.+|+    +...+.++++.|...|++.+.
T Consensus         8 ~~~Il~~l~~~---g~~sr~eLa~~~gl----S~~Tv~~~l~~L~~~Glv~e~   53 (71)
T d1z05a1           8 AGRVYKLIDQK---GPISRIDLSKESEL----APASITKITRELIDAHLIHET   53 (71)
T ss_dssp             HHHHHHHHHHH---CSBCHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHc---CCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEe
Confidence            44688889887   59999999999999    999999999999999999875

>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=96.57  E-value=0.00059  Score=52.61  Aligned_cols=57  Identities=14%  Similarity=0.045  Sum_probs=47.7

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcC-CCcEEEeech-HHHhhccCC-------CCceEEecCcCC
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDLS-HVIQDSSSY-------SGVKHIGGIMLE  222 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dlp-~v~~~a~~~-------~ri~~~~gD~f~  222 (233)
                      ..+.++||+||++.|.-+..++++-| +-+++.+|.. +..+.|+++       ++|+++.||..+
T Consensus        57 ~~~~k~vLEiGt~~GyStl~~a~al~~~g~i~tie~~~~~~~~A~~~~~~ag~~~~i~~~~Gda~e  122 (219)
T d2avda1          57 LIQAKKALDLGTFTGYSALALALALPADGRVVTCEVDAQPPELGRPLWRQAEAEHKIDLRLKPALE  122 (219)
T ss_dssp             HTTCCEEEEECCTTSHHHHHHHTTSCTTCEEEEEESCSHHHHHHHHHHHHTTCTTTEEEEESCHHH
T ss_pred             ccCCCeEEEEechhhHHHHHHHHhCCCCceEEEEeechhHHHHHHHHHHhcCccceEEEEEeehhh
Confidence            45789999999999999999999987 6889999974 566666542       789999999876

>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=96.53  E-value=0.0018  Score=50.11  Aligned_cols=57  Identities=14%  Similarity=0.112  Sum_probs=45.6

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHc-CCCcEEEeech-HHHhhccC----CCCceEEecCcCC
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNY-LHIKGVNFDLS-HVIQDSSS----YSGVKHIGGIMLE  222 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~-P~l~~~v~Dlp-~v~~~a~~----~~ri~~~~gD~f~  222 (233)
                      .+...+|+|+|||+|.++..+++.. |+-+++.+|+. ..++.++.    ...+..+.+|.-.
T Consensus        71 i~pG~~VLDlGaGsG~~t~~la~~VG~~G~V~aVD~s~~~l~~a~~~a~~~~~~~~i~~d~~~  133 (227)
T d1g8aa_          71 IKPGKSVLYLGIASGTTASHVSDIVGWEGKIFGIEFSPRVLRELVPIVEERRNIVPILGDATK  133 (227)
T ss_dssp             CCTTCEEEEETTTSTTHHHHHHHHHCTTSEEEEEESCHHHHHHHHHHHSSCTTEEEEECCTTC
T ss_pred             cCCCCEEEEeccCCCHHHHHHHHHhCCCCEEEEEeCcHHHHHHHHHHHHhcCCceEEEEECCC
Confidence            6777999999999999999999985 88899999984 46665543    3667777777654

>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=96.48  E-value=0.0019  Score=39.66  Aligned_cols=60  Identities=15%  Similarity=0.228  Sum_probs=47.7

Q ss_pred             HHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCc-eeeeccCCCCCceeccH
Q 039903           13 MQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRV-LRCTSAGDDQRLYGLAH   83 (233)
Q Consensus        13 L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gl-l~~~~~~~~~~~y~lt~   83 (233)
                      ++.--...|.+.|.+..  +++|..|||+.+++    +.+-++|=+..|...|+ +...     .+.|.+.+
T Consensus         4 ~k~eR~~~Il~~L~~~~--~~vs~~~La~~l~V----S~~TI~rdi~~L~~~G~~I~~~-----~gGY~L~~   64 (65)
T d1j5ya1           4 VRQERLKSIVRILERSK--EPVSGAQLAEELSV----SRQVIVQDIAYLRSLGYNIVAT-----PRGYVLAG   64 (65)
T ss_dssp             HHHHHHHHHHHHHHHCS--SCBCHHHHHHHHTS----CHHHHHHHHHHHHHHTCCCEEE-----TTEEECCT
T ss_pred             hHHHHHHHHHHHHHHcC--CCCcHHHHHHHHCC----CHHHHHHHHHHHHHCCCeEEEe-----CCCEEeCC
Confidence            34445567888887753  58999999999999    99999999999999997 4443     45788754

>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=96.44  E-value=0.00094  Score=43.48  Aligned_cols=54  Identities=11%  Similarity=0.119  Sum_probs=45.5

Q ss_pred             CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhc
Q 039903           32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVL   90 (233)
Q Consensus        32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~   90 (233)
                      +++|..|||+.+++    ++..+.++|+-|...|++++..+ +..-.+.+|+.|..+..
T Consensus        20 ~~lt~~eLa~~l~i----~~~~vs~~l~~Le~~GlV~r~~D-~R~~~i~LT~~G~~~l~   73 (85)
T d3ctaa1          20 AYLTSSKLADMLGI----SQQSASRIIIDLEKNGYITRTVT-KRGQILNITEKGLDVLY   73 (85)
T ss_dssp             EECCHHHHHHHHTS----CHHHHHHHHHHHHHTTSEEEEEE-TTEEEEEECHHHHHHHH
T ss_pred             CCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCeeeecc-cccccceECHHHHHHHH
Confidence            58999999999999    99999999999999999998642 23345788999886653

>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=96.35  E-value=0.0016  Score=39.66  Aligned_cols=43  Identities=16%  Similarity=0.318  Sum_probs=39.7

Q ss_pred             ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      .|+..|.+    +|+|-.|||+.+|+    +...+.++++-|...|++.+.
T Consensus         3 ~Il~~i~~----~pisr~eLa~~~gl----s~~TVs~~v~~L~~~GlV~e~   45 (62)
T d2hoea1           3 RILKRIMK----SPVSRVELAEELGL----TKTTVGEIAKIFLEKGIVVEE   45 (62)
T ss_dssp             CSHHHHHH----SCBCHHHHHHHHTC----CHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHH----CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEC
Confidence            47788876    69999999999999    999999999999999999985

>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=96.31  E-value=0.0047  Score=43.86  Aligned_cols=69  Identities=19%  Similarity=0.202  Sum_probs=53.2

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccC--CCCCceeccHhhhHhhcC
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAG--DDQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~--~~~~~y~lt~~s~~l~~~   91 (233)
                      .+..+...|...+  |++|..+||+.+++    +...+.++++-|...|++++....  ...-.+.+|+.|+.+...
T Consensus        35 ~q~~vL~~L~~~~--g~~t~~~La~~~~~----~~~~vs~~i~~L~~~glv~r~~~~~DrR~~~i~LT~~G~~~~~~  105 (145)
T d2hr3a1          35 SQLVVLGAIDRLG--GDVTPSELAAAERM----RSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYG  105 (145)
T ss_dssp             HHHHHHHHHHHTT--SCBCHHHHHHHTTC----CHHHHHHHHHHHHHTTSEEEEC------CCEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHHHcC--CCCCHHHHHHHHCC----CHHHHHHHHHHHHHcCCeEeeeCccchhHHHhccCHHHHHHHHH
Confidence            3455666776554  68999999999999    999999999999999999976431  122368899999877644

>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=96.25  E-value=0.0025  Score=43.33  Aligned_cols=44  Identities=16%  Similarity=0.339  Sum_probs=39.4

Q ss_pred             ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      .|+..|...   |+.|..|||+.+++    +...+.++|+-|...|++++.
T Consensus        24 ~v~~~L~~~---g~~t~~eia~~~~i----~~~~v~~~l~~L~~~GlV~r~   67 (109)
T d1sfxa_          24 RIYSLLLER---GGMRVSEIARELDL----SARFVRDRLKVLLKRGFVRRE   67 (109)
T ss_dssp             HHHHHHHHH---CCBCHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHhc---CCCCHHHHHHHhCC----CcchHHHHHHHHHhCCCEEEE
Confidence            366777776   59999999999999    999999999999999999875

>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=96.20  E-value=0.0037  Score=38.92  Aligned_cols=46  Identities=11%  Similarity=0.266  Sum_probs=41.6

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      +..|+..|...   +++|..|||+.+|+    +...+.++++-|...|++.+.
T Consensus         7 ~~~Il~~i~~~---g~~sr~eLa~~~gL----S~~Tvs~iv~~L~~~glv~e~   52 (70)
T d1z6ra1           7 AGAVYRLIDQL---GPVSRIDLSRLAQL----APASITKIVHEMLEAHLVQEL   52 (70)
T ss_dssp             HHHHHHHHHSS---CSCCHHHHHHHTTC----CHHHHHHHHHHHHHHTSEEEC
T ss_pred             HHHHHHHHHHc---CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEee
Confidence            34588888887   69999999999999    999999999999999999874

>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=96.17  E-value=0.0047  Score=43.55  Aligned_cols=67  Identities=15%  Similarity=0.030  Sum_probs=54.2

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      +.-++..|...   ++.|..+||+.+++    +...+.++++.|...|++++...+.  ..-...+|+.|..+...
T Consensus        34 q~~iL~~l~~~---~~~t~~~La~~l~i----~~~~vs~~v~~L~~~gli~r~~~~~D~R~~~l~lT~~G~~~~~~  102 (140)
T d2etha1          34 ELYAFLYVALF---GPKKMKEIAEFLST----TKSNVTNVVDSLEKRGLVVREMDPVDRRTYRVVLTEKGKEIFGE  102 (140)
T ss_dssp             HHHHHHHHHHH---CCBCHHHHHHHTTS----CHHHHHHHHHHHHHTTSEEEEECTTTSSCEEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHHc---CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCeeeeecccccchhhhhcCHHHHHHHHH
Confidence            44577778887   48999999999999    9999999999999999999875431  11367889998877644

>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=96.10  E-value=0.0073  Score=45.51  Aligned_cols=70  Identities=11%  Similarity=0.021  Sum_probs=48.2

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcCC-CcEEEeechHHH-hhccCCCCceEEecCcCCCCCC-C-CEEE
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLH-IKGVNFDLSHVI-QDSSSYSGVKHIGGIMLERIPK-G-DAIL  231 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~-l~~~v~Dlp~v~-~~a~~~~ri~~~~gD~f~~~P~-~-D~~~  231 (233)
                      -+++.+. ..+..+|+|.|||+|.++.++.++++. .+...+|+.+.. ..+   .+...+.+|++...+. . |+++
T Consensus        10 ~m~~l~~-~~~~~~IlDp~~G~G~fl~~~~~~~~~~~~i~g~ei~~~~~~~~---~~~~~~~~~~~~~~~~~~fd~ii   83 (223)
T d2ih2a1          10 FMVSLAE-APRGGRVLEPACAHGPFLRAFREAHGTAYRFVGVEIDPKALDLP---PWAEGILADFLLWEPGEAFDLIL   83 (223)
T ss_dssp             HHHHHCC-CCTTCEEEEETCTTCHHHHHHHHHHCSCSEEEEEESCTTTCCCC---TTEEEEESCGGGCCCSSCEEEEE
T ss_pred             HHHHhcC-CCCcCEEEECCCchHHHHHHHHHhccccceEEeeecCHHHHhhc---ccceeeeeehhccccccccceec
Confidence            3445444 455689999999999999999988876 458888985532 222   3456678888874332 2 6665

>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=96.06  E-value=0.0015  Score=50.54  Aligned_cols=67  Identities=13%  Similarity=0.100  Sum_probs=53.1

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcC-CCcEEEeec-hHHHhhccCC-------CCceEEecCcCCCCC---------CC
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDL-SHVIQDSSSY-------SGVKHIGGIMLERIP---------KG  227 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dl-p~v~~~a~~~-------~ri~~~~gD~f~~~P---------~~  227 (233)
                      ..++++||+||.+.|.-+..++++.| +-+++.+|. |+.++.|+++       ++|+++.||..+.+|         ..
T Consensus        57 ~~~~k~iLEiGT~~GyStl~la~al~~~g~v~tie~~~~~~~~A~~~~~~~g~~~~i~~~~g~a~~~L~~l~~~~~~~~~  136 (227)
T d1susa1          57 LINAKNTMEIGVYTGYSLLATALAIPEDGKILAMDINKENYELGLPVIKKAGVDHKIDFREGPALPVLDEMIKDEKNHGS  136 (227)
T ss_dssp             HHTCCEEEEECCGGGHHHHHHHHHSCTTCEEEEEESCCHHHHHHHHHHHHTTCGGGEEEEESCHHHHHHHHHHCGGGTTC
T ss_pred             hcCCCcEEEecchhhhhHHHHHhhCCCCcEEEEEeccchhHHHHHHHHHHhccccceeeeehHHHHHHHHHHhccccCCc
Confidence            46789999999999999999999988 578888997 4566666542       789999999986332         12


Q ss_pred             -CEEEe
Q 039903          228 -DAILI  232 (233)
Q Consensus       228 -D~~~l  232 (233)
                       |++++
T Consensus       137 fD~iFi  142 (227)
T d1susa1         137 YDFIFV  142 (227)
T ss_dssp             BSEEEE
T ss_pred             eeEEEe
Confidence             88876

>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=96.03  E-value=0.004  Score=49.49  Aligned_cols=70  Identities=23%  Similarity=0.319  Sum_probs=50.5

Q ss_pred             HHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhcc----C---CCCceEEecCcCC-CCCC
Q 039903          156 TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSS----S---YSGVKHIGGIMLE-RIPK  226 (233)
Q Consensus       156 ~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~----~---~~ri~~~~gD~f~-~~P~  226 (233)
                      +..+++... .....+|++||.|.|.+...|+++.+  +.+.++... -++..+    .   .++++++.+|+++ .+|.
T Consensus        10 ~~kIv~~~~-~~~~d~VlEIGPG~G~LT~~Ll~~~~--~v~aiE~D~~l~~~L~~~~~~~~~~~~~~~i~~D~l~~~~~~   86 (278)
T d1zq9a1          10 INSIIDKAA-LRPTDVVLEVGPGTGNMTVKLLEKAK--KVVACELDPRLVAELHKRVQGTPVASKLQVLVGDVLKTDLPF   86 (278)
T ss_dssp             HHHHHHHTC-CCTTCEEEEECCTTSTTHHHHHHHSS--EEEEEESCHHHHHHHHHHHTTSTTGGGEEEEESCTTTSCCCC
T ss_pred             HHHHHHHhC-CCCCCEEEEECCCchHHHHHHHhcCC--cEEEEEEccchhHHHHHHHhhhccccchhhhHHHHhhhhhhh
Confidence            345666655 66678999999999999999999865  566676643 233222    1   1689999999998 6665


Q ss_pred             CC
Q 039903          227 GD  228 (233)
Q Consensus       227 ~D  228 (233)
                      .+
T Consensus        87 ~~   88 (278)
T d1zq9a1          87 FD   88 (278)
T ss_dssp             CS
T ss_pred             hh
Confidence            43

>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=96.03  E-value=0.0041  Score=43.74  Aligned_cols=65  Identities=6%  Similarity=0.113  Sum_probs=51.9

Q ss_pred             ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      .+...|...   ++.|..|||+.+++    +...+.++++-|+..|++++...+.  ..-...+|+.|..+...
T Consensus        38 ~vL~~i~~~---~~~t~~~la~~l~~----~~~~~s~~l~~L~~~Gli~r~~~~~D~R~~~l~lT~~G~~~~~~  104 (136)
T d2bv6a1          38 LVLTILWDE---SPVNVKKVVTELAL----DTGTVSPLLKRMEQVDLIKRERSEVDQREVFIHLTDKSETIRPE  104 (136)
T ss_dssp             HHHHHHHHS---SEEEHHHHHHHTTC----CTTTHHHHHHHHHHTTSEEEEECSSSTTCEEEEECHHHHHHHHH
T ss_pred             HHHHHHHcC---CCCCHHHHHHHHCC----CHhHHHHHHHHHHHCCCEEEeecCCcccchhhccCHHHHHHHHH
Confidence            456667666   48999999999999    9999999999999999999865431  12256889999877644

>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=96.00  E-value=0.003  Score=46.95  Aligned_cols=64  Identities=11%  Similarity=0.016  Sum_probs=48.7

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC-------CCceEEecCcCCCC------CCC-CEEEe
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY-------SGVKHIGGIMLERI------PKG-DAILI  232 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~-------~ri~~~~gD~f~~~------P~~-D~~~l  232 (233)
                      ...+|||+.||+|.++.+.+.+... +++.+|.. .+++.++++       ++++++.+|.++-+      ... |+|++
T Consensus        41 ~~~~vLDlfaGsG~~g~ea~srGa~-~v~~ve~~~~a~~~~~~N~~~~~~~~~~~i~~~D~~~~l~~~~~~~~~fDlIfl  119 (182)
T d2fhpa1          41 DGGMALDLYSGSGGLAIEAVSRGMD-KSICIEKNFAALKVIKENIAITKEPEKFEVRKMDANRALEQFYEEKLQFDLVLL  119 (182)
T ss_dssp             SSCEEEETTCTTCHHHHHHHHTTCS-EEEEEESCHHHHHHHHHHHHHHTCGGGEEEEESCHHHHHHHHHHTTCCEEEEEE
T ss_pred             CCCEEEEcccccccccceeeecchh-HHHHHHHHHHHHHHHHHHhhhhhcccccccccccchhhhhhhcccCCCcceEEe
Confidence            4588999999999999999998654 68888985 466666543       58999999987621      112 88876

>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=95.97  E-value=0.0051  Score=42.84  Aligned_cols=52  Identities=21%  Similarity=0.291  Sum_probs=41.3

Q ss_pred             hHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903           22 FEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH   83 (233)
Q Consensus        22 fd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~   83 (233)
                      .-.|+..   ++.|.++||+.+++    ++..++++|+.|...|+++-.+.  .+|.| ++.
T Consensus        10 L~~la~~---~~~ss~~IA~~~~~----~~~~v~kIl~~L~~aglV~s~rG--~~GGy-Lar   61 (127)
T d1xd7a_          10 LSLISMD---EKTSSEIIADSVNT----NPVVVRRMISLLKKADILTSRAG--VPGAS-LKK   61 (127)
T ss_dssp             HHHHHTC---SCCCHHHHHHHHTS----CHHHHHHHHHHHHHTTSEECCSS--SSSCE-ESS
T ss_pred             HHHHhcC---CCCCHHHHHHHhCc----CHHHHHHHHHHHHHhCcccccCC--CCCcc-ccC
Confidence            4455554   48999999999999    99999999999999999997643  34445 543

>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=95.95  E-value=0.0063  Score=49.15  Aligned_cols=66  Identities=11%  Similarity=0.105  Sum_probs=49.5

Q ss_pred             cCcceEEEecCCccHHHHHHHHH-----cCCCcEEEeech-HHHhhccCC-----CCceEEecCcCCCCCC--CCEEEe
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISN-----YLHIKGVNFDLS-HVIQDSSSY-----SGVKHIGGIMLERIPK--GDAILI  232 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~-----~P~l~~~v~Dlp-~v~~~a~~~-----~ri~~~~gD~f~~~P~--~D~~~l  232 (233)
                      ....+|+|.+||+|.++.++.++     .++.+...+|+. ..+..|+.+     ..+.+..+|.+...|.  .|+|+.
T Consensus       116 ~~~~~vlDp~~GsG~~l~~~~~~l~~~~~~~~~~~g~di~~~~~~~a~~~~~~~~~~~~~~~~d~~~~~~~~~fD~vi~  194 (328)
T d2f8la1         116 KKNVSILDPACGTANLLTTVINQLELKGDVDVHASGVDVDDLLISLALVGADLQRQKMTLLHQDGLANLLVDPVDVVIS  194 (328)
T ss_dssp             CSEEEEEETTCTTSHHHHHHHHHHHTTSSCEEEEEEEESCHHHHHHHHHHHHHHTCCCEEEESCTTSCCCCCCEEEEEE
T ss_pred             CCCCEEEeCCCCcchhHHHHHHHHHhccCccceEEEecccHHHHHHHHHHHHHhhhhhhhhcccccccccccccccccc
Confidence            45678999999999999998764     355678899984 466666542     6788888999886554  388863

>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=95.92  E-value=0.0039  Score=44.20  Aligned_cols=66  Identities=17%  Similarity=0.148  Sum_probs=52.9

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCC---ceeccHhhhHhhcC
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQR---LYGLAHVAKYFVLN   91 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~---~y~lt~~s~~l~~~   91 (233)
                      +..++..|...   ++.|..+||+.+++    +...+.++++-|...|++++.... ++.   .+.+|+.|..+...
T Consensus        37 q~~iL~~l~~~---~~~t~~~la~~~~i----~~~~vs~~l~~L~~~glv~r~~~~-~D~R~~~v~lT~~G~~~~~~  105 (143)
T d1s3ja_          37 QLFVLASLKKH---GSLKVSEIAERMEV----KPSAVTLMADRLEQKNLIARTHNT-KDRRVIDLSLTDEGDIKFEE  105 (143)
T ss_dssp             HHHHHHHHHHH---SEEEHHHHHHHHTS----CHHHHHHHHHHHHHTTSEEEEECS-SCTTSEEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHHC---CCCCHHHHHHHHCc----CHHHHHHHHHHHHHhhhheeeeec-CCCCceEEEECHHHHHHHHH
Confidence            33466667766   48999999999999    999999999999999999976543 222   47899999877654

>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=95.90  E-value=0.0026  Score=51.42  Aligned_cols=65  Identities=17%  Similarity=0.122  Sum_probs=50.9

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC--------CCceEEecCcCCCC------CC-CCE
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY--------SGVKHIGGIMLERI------PK-GDA  229 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~--------~ri~~~~gD~f~~~------P~-~D~  229 (233)
                      ..+..+|||+.||+|.++..+++.  ..+++.+|.. ..++.|+++        .+++++.+|.|+-+      .. -|+
T Consensus       130 ~~~~~rVLdlf~~tG~~sl~aa~~--GA~V~~VD~s~~al~~a~~N~~ln~~~~~~~~~i~~D~~~~l~~~~~~~~~fD~  207 (309)
T d2igta1         130 ADRPLKVLNLFGYTGVASLVAAAA--GAEVTHVDASKKAIGWAKENQVLAGLEQAPIRWICEDAMKFIQREERRGSTYDI  207 (309)
T ss_dssp             SSSCCEEEEETCTTCHHHHHHHHT--TCEEEEECSCHHHHHHHHHHHHHHTCTTSCEEEECSCHHHHHHHHHHHTCCBSE
T ss_pred             ccCCCeEEEecCCCcHHHHHHHhC--CCeEEEEeChHHHHHHHHHhhhhhcccCCcEEEEeCCHHHhHHHHhhcCCCCCE
Confidence            556789999999999999999876  3479999985 577777653        47999999998732      12 288


Q ss_pred             EEe
Q 039903          230 ILI  232 (233)
Q Consensus       230 ~~l  232 (233)
                      |++
T Consensus       208 Iil  210 (309)
T d2igta1         208 ILT  210 (309)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            886

>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=95.85  E-value=0.0063  Score=42.53  Aligned_cols=69  Identities=9%  Similarity=0.200  Sum_probs=52.9

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      ++.++..|...+ ++++|..|||+.+++    +...+.++++.|...|++++.....  ..-.+.+|+.|..+...
T Consensus        31 q~~vL~~l~~~~-~~~it~~ela~~~~~----~~~~vs~~l~~L~~~g~v~r~~~~~D~R~~~i~lT~~G~~~~~~  101 (135)
T d3broa1          31 QMTIIDYLSRNK-NKEVLQRDLESEFSI----KSSTATVLLQRMEIKKLLYRKVSGKDSRQKCLKLTKKANKLETI  101 (135)
T ss_dssp             HHHHHHHHHHTT-TSCCBHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEEECSSCTTSEEEEECHHHHTTHHH
T ss_pred             HHHHHHHHHHcC-CCCCCHHHHHHHHCc----CHhHHHHHHHHHHHHHHHHHHhhhhhhhhhhhcccHHHHHHHHH
Confidence            445666677653 157999999999999    9999999999999999998765421  22368899988766544

>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=95.80  E-value=0.0034  Score=47.13  Aligned_cols=69  Identities=9%  Similarity=0.153  Sum_probs=54.4

Q ss_pred             HHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccC---C-CCCceeccHhhh
Q 039903           11 AAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAG---D-DQRLYGLAHVAK   86 (233)
Q Consensus        11 ~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~---~-~~~~y~lt~~s~   86 (233)
                      .+|..=.++.|++.|..    +|.|+.|||+.+++    ++..+.+.|+.|...|+++.....   | ....|++|..+.
T Consensus        10 ~~l~~~~R~~Il~~L~~----~~~~~~ela~~l~~----s~~~v~~HL~~L~~~Glv~~~~~~~~~G~~~~~y~l~~~~~   81 (194)
T d2p4wa1          10 DVLGNETRRRILFLLTK----RPYFVSELSRELGV----GQKAVLEHLRILEEAGLIESRVEKIPRGRPRKYYMIKKGLR   81 (194)
T ss_dssp             HHHHSHHHHHHHHHHHH----SCEEHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEEECCBTTBCCCEEEEECTTEE
T ss_pred             HHhCCHHHHHHHHHHHh----CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCeEEEEeecCCCCceEEEEecccce
Confidence            45555568889999987    69999999999999    999999999999999999864321   0 123688887654


Q ss_pred             H
Q 039903           87 Y   87 (233)
Q Consensus        87 ~   87 (233)
                      .
T Consensus        82 ~   82 (194)
T d2p4wa1          82 L   82 (194)
T ss_dssp             E
T ss_pred             e
Confidence            4

>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=95.78  E-value=0.0035  Score=49.13  Aligned_cols=64  Identities=9%  Similarity=0.097  Sum_probs=48.6

Q ss_pred             HHHHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccC----CCCceEEecCcCC
Q 039903          156 TNRIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSS----YSGVKHIGGIMLE  222 (233)
Q Consensus       156 ~~~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~----~~ri~~~~gD~f~  222 (233)
                      +..+++... ......|+.||+|.|.+...|+++..  +.+.+|+.. .++..++    .++++++.+|+++
T Consensus        10 ~~~Iv~~~~-~~~~d~vlEIGpG~G~LT~~Ll~~~~--~v~aiEiD~~l~~~L~~~~~~~~~~~ii~~D~l~   78 (252)
T d1qyra_          10 IDSIVSAIN-PQKGQAMVEIGPGLAALTEPVGERLD--QLTVIELDRDLAARLQTHPFLGPKLTIYQQDAMT   78 (252)
T ss_dssp             HHHHHHHHC-CCTTCCEEEECCTTTTTHHHHHTTCS--CEEEECCCHHHHHHHHTCTTTGGGEEEECSCGGG
T ss_pred             HHHHHHhcC-CCCCCEEEEECCCchHHHHHHHccCC--ceEEEEeccchhHHHHHHhhhccchhHHhhhhhh
Confidence            345666665 67778999999999999999999854  577777754 4444433    2789999999997

>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=95.77  E-value=0.0022  Score=52.05  Aligned_cols=63  Identities=13%  Similarity=0.096  Sum_probs=48.7

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC------CCceEEecCcCCC---CC---C-CCEEEe
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY------SGVKHIGGIMLER---IP---K-GDAILI  232 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~------~ri~~~~gD~f~~---~P---~-~D~~~l  232 (233)
                      +.++|+|++||+|.+++++++.  ..+++.+|.. ..++.++++      ++++++.+|.|+.   ++   . -|+|++
T Consensus       145 ~g~rVLDl~~gtG~~s~~~a~g--~~~V~~vD~s~~al~~a~~n~~~ngl~~~~~i~~d~~~~~~~~~~~~~~fD~Vi~  221 (318)
T d1wxxa2         145 RGERALDVFSYAGGFALHLALG--FREVVAVDSSAEALRRAEENARLNGLGNVRVLEANAFDLLRRLEKEGERFDLVVL  221 (318)
T ss_dssp             CEEEEEEETCTTTHHHHHHHHH--EEEEEEEESCHHHHHHHHHHHHHTTCTTEEEEESCHHHHHHHHHHTTCCEEEEEE
T ss_pred             CCCeeeccCCCCcHHHHHHHhc--CCcEEeecchHHHHHHHHHHHHHcCCCCcceeeccHHHHhhhhHhhhcCCCEEEE
Confidence            4589999999999999998865  3468999984 577777653      6899999999862   22   1 288875

>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=95.74  E-value=0.0012  Score=51.29  Aligned_cols=42  Identities=14%  Similarity=0.143  Sum_probs=31.5

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccC
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSS  209 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~  209 (233)
                      .+..+|||||||+|.++..+++... -+++.+|+. ..++.|++
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            4568999999999998876665533 368999985 47776653

>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=95.66  E-value=0.0037  Score=44.24  Aligned_cols=44  Identities=14%  Similarity=0.166  Sum_probs=37.4

Q ss_pred             CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceecc
Q 039903           32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLA   82 (233)
Q Consensus        32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt   82 (233)
                      .+.|..+||+.+++    ++..++++|+.|...|+++-.+   +.|.|.+.
T Consensus        22 ~~vss~~IA~~~~i----~~~~l~kil~~L~~aGlv~S~r---G~GG~~L~   65 (138)
T d1ylfa1          22 SLCTSDYMAESVNT----NPVVIRKIMSYLKQAGFVYVNR---GPGGAGLL   65 (138)
T ss_dssp             GGCCHHHHHHHHTS----CHHHHHHHHHHHHHTTSEEEC------CCEEES
T ss_pred             CcCcHHHHHHHHCc----CHHHHHHHHHHHHHCCCeEeec---CCCCceec
Confidence            48999999999999    9999999999999999998765   34667665

>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=95.65  E-value=0.0035  Score=42.43  Aligned_cols=47  Identities=15%  Similarity=0.200  Sum_probs=40.1

Q ss_pred             hChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeec
Q 039903           19 LGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTS   71 (233)
Q Consensus        19 lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~   71 (233)
                      ..|+..|...+  +|.|..|||+.+++    +...+.++++-|...|++.+..
T Consensus        24 ~~iL~~L~~~~--~~~t~~eLa~~~~i----~~~tvs~~l~~L~~~GlV~r~~   70 (109)
T d2d1ha1          24 VAVLLKMVEIE--KPITSEELADIFKL----SKTTVENSLKKLIELGLVVRTK   70 (109)
T ss_dssp             HHHHHHHHHHC--SCEEHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHcC--CCCCHHHHHHHHCc----cHhHHHHHHHHHHHCCCEEEee
Confidence            34666665544  68999999999999    9999999999999999999763

>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=95.65  E-value=0.0049  Score=45.91  Aligned_cols=57  Identities=4%  Similarity=0.112  Sum_probs=49.9

Q ss_pred             cchHHHHHHHHHhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903            6 SIVLPAAMQAASELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus         6 ~~~~s~~L~~a~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      ..-...+|..-.++.|++.|..    +|.|+.|||+.+|+    ++..+.+.|+.|...|+++..
T Consensus         9 d~~~~~~l~~p~R~~Il~~L~~----~~~s~~ela~~lg~----s~~~v~~hl~~L~~~glv~~~   65 (190)
T d1ulya_           9 DPEVIKVMLEDTRRKILKLLRN----KEMTISQLSEILGK----TPQTIYHHIEKLKEAGLVEVK   65 (190)
T ss_dssp             CHHHHHHHHSHHHHHHHHHHTT----CCBCHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHhCCHHHHHHHHHHHh----CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCeEEE
Confidence            3445667777889999999976    69999999999999    999999999999999999754

>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=95.60  E-value=0.011  Score=41.70  Aligned_cols=66  Identities=14%  Similarity=0.150  Sum_probs=50.8

Q ss_pred             hChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           19 LGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        19 lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      .-+...|...   ++.|..+||+.+++    +...+.|+++.|+..|++++....+  ..-.+.+|+.|..+...
T Consensus        39 ~~vL~~l~~~---~~~t~~~la~~l~~----~~~~vsr~l~~L~~~G~v~r~~~~~D~R~~~l~lT~~G~~~~~~  106 (141)
T d1lnwa_          39 VHVLKLIDEQ---RGLNLQDLGRQMCR----DKALITRKIRELEGRNLVRRERNPSDQRSFQLFLTDEGLAIHQH  106 (141)
T ss_dssp             HHHHHHHHSS---TTCBHHHHHHHTTC----CHHHHHHHHHHHHHTTSEEEEECSSSSSSEEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHC---CCCCHHHHHHHHCc----cHhHHHHHHHHHHHhhceeeeccCCCCcchhhccCHHHHHHHHH
Confidence            3355566655   47899999999999    9999999999999999999875432  12346788888766544

>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=95.55  E-value=0.011  Score=41.47  Aligned_cols=66  Identities=21%  Similarity=0.135  Sum_probs=52.4

Q ss_pred             hChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           19 LGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        19 lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      ..+...|...   ++.|..|||+.+++    +...+.+++..|...|++++.....  ..-.+++|+.|..+...
T Consensus        37 ~~vL~~l~~~---~~~t~~ela~~~~i----~~~~vs~~v~~L~~~glv~r~~~~~D~R~~~i~lT~~G~~~~~~  104 (138)
T d1jgsa_          37 FKVLCSIRCA---ACITPVELKKVLSV----DLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTGGAAICEQ  104 (138)
T ss_dssp             HHHHHHHHHH---SSBCHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEEECTTCSSCEEEEECHHHHHHHHH
T ss_pred             HHHHHhHHhC---cCCCHHHHHHHHCC----CHhHHHHHHHHHhhCCCEEEeeccCCCCeeEEEECHHHHHHHHH
Confidence            3455666666   48999999999999    9999999999999999999764421  12378899999887644

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

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

Probab=95.50  E-value=0.011  Score=48.22  Aligned_cols=65  Identities=14%  Similarity=0.215  Sum_probs=49.9

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeec-hHHHhhccCC------CCceEEecCcCCCCC------CC-CEEE
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDL-SHVIQDSSSY------SGVKHIGGIMLERIP------KG-DAIL  231 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dl-p~v~~~a~~~------~ri~~~~gD~f~~~P------~~-D~~~  231 (233)
                      ..+..+|+|+-||.|.++..|+++.  -+++.+|. ++.++.|+.+      .+++|+.+|..+.++      .. |+++
T Consensus       210 ~~~~~~vlDLycG~G~fsl~La~~~--~~V~gvE~~~~ai~~A~~na~~n~i~n~~~~~~~~~~~~~~~~~~~~~~d~vi  287 (358)
T d1uwva2         210 VQPEDRVLDLFCGMGNFTLPLATQA--ASVVGVEGVPALVEKGQQNARLNGLQNVTFYHENLEEDVTKQPWAKNGFDKVL  287 (358)
T ss_dssp             CCTTCEEEEESCTTTTTHHHHHTTS--SEEEEEESCHHHHHHHHHHHHHTTCCSEEEEECCTTSCCSSSGGGTTCCSEEE
T ss_pred             cCCCceEEEecccccccchhccccc--cEEEeccCcHHHHHHHHHhHHhcccccceeeecchhhhhhhhhhhhccCceEE
Confidence            4566899999999999999999865  35788887 5677777653      789999999887332      12 8887


Q ss_pred             e
Q 039903          232 I  232 (233)
Q Consensus       232 l  232 (233)
                      +
T Consensus       288 l  288 (358)
T d1uwva2         288 L  288 (358)
T ss_dssp             E
T ss_pred             e
Confidence            5

>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=95.49  E-value=0.012  Score=38.72  Aligned_cols=61  Identities=18%  Similarity=0.184  Sum_probs=47.8

Q ss_pred             hhHHHHhcCCCCCCCHHHHHHhC-CCCCCCChhhHHHHHHHHhcCCceeeeccCCC--CCceeccHhhhHhh
Q 039903           21 VFEIIAKAGPTAKISAVEIAAQM-PSSNPNAAVMLDRILRLLVTHRVLRCTSAGDD--QRLYGLAHVAKYFV   89 (233)
Q Consensus        21 lfd~L~~~~~~~~~t~~elA~~~-~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~--~~~y~lt~~s~~l~   89 (233)
                      |...|..    |+....||.+.+ |+    ++.-|.+=|+.|...|++++...+..  .-.|++|+.|..|.
T Consensus        16 Il~~L~~----g~~rF~el~~~l~gi----s~~~Ls~rLk~Le~~glv~r~~~~~~p~~veY~LT~~G~~L~   79 (95)
T d2hzta1          16 ILCHLTH----GKKRTSELKRLMPNI----TQKMLTQQLRELEADGVINRIVYNQVPPKVEYELSEYGRSLE   79 (95)
T ss_dssp             HHHHHTT----CCBCHHHHHHHCTTS----CHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECTTGGGGH
T ss_pred             HHHHHHc----CCCCHHHHHHHhhcC----ChhHHHHHHHHHHHhHHHhheeccccccchhhhhhhhHHHHH
Confidence            4444544    689999999998 89    99999999999999999998643210  12399999998776

>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=95.43  E-value=0.0081  Score=42.24  Aligned_cols=65  Identities=9%  Similarity=0.067  Sum_probs=51.9

Q ss_pred             ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      -+...|...   ++.|..+||+.+++    +...+.++++-|...|++++.....  ..-.+.+|+.|..+...
T Consensus        34 ~iL~~i~~~---~~~t~~~la~~l~i----~~~tvs~~l~~L~~~gli~r~~~~~D~R~~~i~LT~~G~~~~~~  100 (139)
T d2a61a1          34 DILQKIYFE---GPKRPGELSVLLGV----AKSTVTGLVKRLEADGYLTRTPDPADRRAYFLVITRKGEEVIEK  100 (139)
T ss_dssp             HHHHHHHHH---CCBCHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHHH
T ss_pred             HHHHHHHHc---CCCCHHHHHHHhCC----CcccchHHHHHHHhcCeeeeeeccCCCCeEEEEECHHHHHHHHH
Confidence            355566665   48999999999999    9999999999999999999764321  12467899999887654

>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=95.17  E-value=0.016  Score=40.49  Aligned_cols=65  Identities=17%  Similarity=0.199  Sum_probs=49.5

Q ss_pred             hhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           21 VFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        21 lfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      +.-.|...+  ++.|..+||+.+++    +...+.++++-|+..|++++.....  ..-...+|+.|+.+...
T Consensus        33 iL~~l~~~~--~~~t~~~la~~~~~----~~~~vs~~v~~L~~~gli~r~~~~~D~R~~~i~lT~~G~~~~~~   99 (137)
T d2fbha1          33 VLLHLARHR--DSPTQRELAQSVGV----EGPTLARLLDGLESQGLVRRLAVAEDRRAKHIVLTPKADVLIAD   99 (137)
T ss_dssp             HHHHHHHCS--SCCBHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEECCBTTBCSCEEEECTTHHHHHHH
T ss_pred             HHHHHHHcC--CCCcHHHHHHHHCC----CHHHHHHHHHHHHHcCCccccCCCCCCCchhhhcCHHHHHHHHH
Confidence            344555443  46899999999999    9999999999999999999874321  11257888888877644

>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=95.17  E-value=0.0078  Score=42.23  Aligned_cols=65  Identities=8%  Similarity=0.124  Sum_probs=51.5

Q ss_pred             hhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcCC
Q 039903           21 VFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLNR   92 (233)
Q Consensus        21 lfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~~   92 (233)
                      +...|...   ++.|..+||+.+++    +...+.|+++.|+..|++++.....  ..-...+|+.|..+....
T Consensus        38 vL~~l~~~---~~~t~~~La~~~~i----~~~~vsr~i~~L~~~glv~r~~~~~D~R~~~i~lT~~G~~~~~~~  104 (137)
T d1z91a1          38 ALLLLWEH---ETLTVKKMGEQLYL----DSGTLTPMLKRMEQQGLITRKRSEEDERSVLISLTEDGALLKEKA  104 (137)
T ss_dssp             HHHHHHHH---SEEEHHHHHHTTTC----CHHHHHHHHHHHHHHTSEECCBCSSCTTSBEEEECHHHHSGGGGT
T ss_pred             HHHHHHcC---CCCCHHHHHHHHCc----CHHHHHHHHHHHhhccceEEeecCCCCCeEEEEECHHHHHHHHHH
Confidence            45566665   48999999999999    9999999999999999999865431  123478899998776553

>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=95.09  E-value=0.013  Score=41.43  Aligned_cols=63  Identities=10%  Similarity=0.025  Sum_probs=50.2

Q ss_pred             hhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCC---ceeccHhhhHhhcC
Q 039903           21 VFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQR---LYGLAHVAKYFVLN   91 (233)
Q Consensus        21 lfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~---~y~lt~~s~~l~~~   91 (233)
                      +...|...   ++.|..+||+.+++    +...+.++++-|...|++++...+ .+.   ...+|+.|..+...
T Consensus        34 iL~~i~~~---~~~t~~~la~~l~i----~~~tvs~~l~~L~~~glI~r~~~~-~D~R~~~l~LT~~G~~~~~~   99 (144)
T d1lj9a_          34 YLVRVCEN---PGIIQEKIAELIKV----DRTTAARAIKRLEEQGFIYRQEDA-SNKKIKRIYATEKGKNVYPI   99 (144)
T ss_dssp             HHHHHHHS---TTEEHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEEECS-SCTTCEEEEECHHHHHHHHH
T ss_pred             HHHHHHhC---CCCCHHHHHHHHCc----cHhhHHHHHHHHHhhhcccccCCC-CCCCccccccCHHHHHHHHH
Confidence            44456665   47999999999999    999999999999999999987543 222   67788888876644

>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=95.03  E-value=0.014  Score=41.43  Aligned_cols=47  Identities=13%  Similarity=0.142  Sum_probs=40.2

Q ss_pred             ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeecc
Q 039903           20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSA   72 (233)
Q Consensus        20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~   72 (233)
                      .|+-.|..++  +|+|..|||+.+++    +...+.+.++.|...|++.+...
T Consensus        30 ~i~~~L~~~~--~plt~~ela~~l~v----sk~~vs~~l~~L~~~GlV~r~~~   76 (151)
T d1ku9a_          30 AVYAILYLSD--KPLTISDIMEELKI----SKGNVSMSLKKLEELGFVRKVWI   76 (151)
T ss_dssp             HHHHHHHHCS--SCEEHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEECC
T ss_pred             HHHHHHHhCC--CCcCHHHHHHHhCC----CcchHHHHHHHHHHCCCEEEEEc
Confidence            4566666554  68999999999999    99999999999999999987643

>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=95.01  E-value=0.024  Score=34.92  Aligned_cols=60  Identities=10%  Similarity=0.179  Sum_probs=48.9

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhC-CCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQM-PSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH   83 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~-~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~   83 (233)
                      .+..||+.|...+.+.+++..||++++ ++    +...++..++.|...|++=-+.   +++.|+-|.
T Consensus         7 ~q~~V~~~i~s~~~~eGi~~~el~~~l~~~----~~~~i~~aid~L~~eG~IYsTi---DddHfkstd   67 (69)
T d1dpua_           7 AQNQVLNLIKACPRPEGLNFQDLKNQLKHM----SVSSIKQAVDFLSNEGHIYSTV---DDDHFKSTD   67 (69)
T ss_dssp             HHHHHHHHHHHCCCTTTEEHHHHHHHSTTS----CHHHHHHHHHHHHHTTSEEECS---STTEEEESS
T ss_pred             HHHHHHHHHHhCCCccCcCHHHHHHHccCC----CHHHHHHHHHHHHhCCceeccc---ccchhcccC
Confidence            455678888876545689999999998 79    9999999999999999987653   478887653

>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=95.00  E-value=0.012  Score=33.77  Aligned_cols=54  Identities=9%  Similarity=0.265  Sum_probs=46.1

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceec
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGL   81 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~l   81 (233)
                      |-.|.+.|.+.|  +|....+|++++++    +...+.++|..|-..+=+...    +..+|++
T Consensus         3 EQkILQVL~dag--spvk~~ql~k~cqV----pkk~lNqVL~rlkke~kVsl~----~patW~l   56 (57)
T d1j75a_           3 EQKILQVLSDDG--GPVKIGQLVKKCQV----PKKTLNQVLYRLKKEDRVSSP----EPATWSI   56 (57)
T ss_dssp             HHHHHHHHHHHC--SCEEHHHHHHHHCS----CHHHHHHHHHHHHHTTSEEEE----ETTEEEE
T ss_pred             HHHHHHHHHhcC--CchHHHHHHHHHCC----CHHHHHHHHHHHHhccccccC----CCccccC
Confidence            557888999987  79999999999999    999999999999888877776    5666654

>d2obpa1 a.4.5.71 (A:12-92) Putative DNA-binding protein ReutB4095 {Ralstonia eutropha [TaxId: 106590]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ReutB4095-like
domain: Putative DNA-binding protein ReutB4095
species: Ralstonia eutropha [TaxId: 106590]

Probab=94.99  E-value=0.026  Score=35.04  Aligned_cols=55  Identities=16%  Similarity=0.147  Sum_probs=47.5

Q ss_pred             CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhc
Q 039903           32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVL   90 (233)
Q Consensus        32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~   90 (233)
                      ++-|++-|+++.++    +-..|+|.|-.|.+.|+.+-.-.+++.+.=++|+.++.|+.
T Consensus        23 ~~WSLaklsKra~~----PMS~LRR~LTqL~~aGl~~t~~~edG~G~A~Lt~~G~~lca   77 (81)
T d2obpa1          23 TPWSLPKIAKRAQL----PMSVLRRVLTQLQAAGLADVSVEADGRGHASLTQEGAALAA   77 (81)
T ss_dssp             CCCBHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEEECTTSCEEEEECHHHHHHHH
T ss_pred             CCccHHHHHhhcCC----cHHHHHHHHHHHhhcCceeeeeccCCcceeeccHHHHHHHH
Confidence            68999999999999    99999999999999999986554445678899999987753

>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=94.96  E-value=0.012  Score=41.20  Aligned_cols=65  Identities=14%  Similarity=0.148  Sum_probs=48.7

Q ss_pred             hhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           21 VFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        21 lfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      +.-.|...+  ++.|..+||+.+++    +...+.++++.|...|++++...+.  ..-.+.+|+.|..+...
T Consensus        36 ~L~~l~~~~--~~~t~~~la~~l~i----~~~~vs~~l~~L~~~glI~~~~~~~D~R~~~l~lT~~G~~~~~~  102 (140)
T d3deua1          36 TLHNIHQLP--PDQSQIQLAKAIGI----EQPSLVRTLDQLEDKGLISRQTCASDRRAKRIKLTEKAEPLIAE  102 (140)
T ss_dssp             HHHHHHHSC--SSEEHHHHHHHHTS----CHHHHHHHHHHHHHTTSEEEC--------CEEEECGGGHHHHHH
T ss_pred             HHHHHHHcC--CCccHHHHHHHHCC----CHhHHHHHHHHHHhCCCEEecccCCCCCceeeEECHHHHHHHHH
Confidence            455565533  46999999999999    9999999999999999999764321  11368899988877644

>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=94.96  E-value=0.029  Score=42.36  Aligned_cols=66  Identities=14%  Similarity=0.115  Sum_probs=47.2

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeechH----HHhhcc-C--CCCceEEecCcCCCCCC--CCEEEeC
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH----VIQDSS-S--YSGVKHIGGIMLERIPK--GDAILIK  233 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~----v~~~a~-~--~~ri~~~~gD~f~~~P~--~D~~~lk  233 (233)
                      ...+++|||.|.|.=++-++-.+|+++++++|.-.    .++.+. +  .++|+.+.+..-+-.+.  .|+++-|
T Consensus        65 ~~~~ilDiGsGaG~PGi~laI~~p~~~~~Lves~~KK~~FL~~~~~~L~L~nv~v~~~R~E~~~~~~~fD~V~sR  139 (207)
T d1jsxa_          65 QGERFIDVGTGPGLPGIPLSIVRPEAHFTLLDSLGKRVRFLRQVQHELKLENIEPVQSRVEEFPSEPPFDGVISR  139 (207)
T ss_dssp             CSSEEEEETCTTTTTHHHHHHHCTTSEEEEEESCHHHHHHHHHHHHHTTCSSEEEEECCTTTSCCCSCEEEEECS
T ss_pred             cCCceeeeeccCCceeeehhhhcccceEEEEecchHHHHHHHHHHHHcCCcceeeeccchhhhccccccceehhh
Confidence            34689999999999888888899999999999642    233222 1  26788887777663232  3877643

>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=94.89  E-value=0.04  Score=40.54  Aligned_cols=61  Identities=21%  Similarity=0.251  Sum_probs=46.0

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcC-CCcEEEeechHHHhhccCCCCceEEecCcCC
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYL-HIKGVNFDLSHVIQDSSSYSGVKHIGGIMLE  222 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P-~l~~~v~Dlp~v~~~a~~~~ri~~~~gD~f~  222 (233)
                      ++-+.|+-+++..+|||+|++.|.++..+.++.+ .-+++.+|+-..    ...+.+.++.+|+.+
T Consensus        12 EI~~k~~l~k~~~~vlDLg~aPGgw~q~~~~~~~~~~~v~~vDl~~~----~~i~~~~~~~~d~~~   73 (180)
T d1ej0a_          12 EIQQSDKLFKPGMTVVDLGAAPGGWSQYVVTQIGGKGRIIACDLLPM----DPIVGVDFLQGDFRD   73 (180)
T ss_dssp             HHHHHHCCCCTTCEEEEESCTTCHHHHHHHHHHCTTCEEEEEESSCC----CCCTTEEEEESCTTS
T ss_pred             HHHHHhCccCCCCeEEEEeccCCcceEEEEeeccccceEEEeecccc----cccCCceEeeccccc
Confidence            4555665357778999999999999999888654 467888897542    234678888888875

>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=94.89  E-value=0.016  Score=40.43  Aligned_cols=66  Identities=14%  Similarity=0.156  Sum_probs=52.3

Q ss_pred             hChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           19 LGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        19 lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      ..+...|...   ++.|..+||+.+++    +...+.++++-|...|++++.....  ..-.+.+|+.|..+...
T Consensus        33 ~~vL~~l~~~---~~~t~~~la~~~~i----~~~~vs~~i~~L~~~gli~r~~~~~D~R~~~l~lT~~G~~~~~~  100 (136)
T d2fbia1          33 WRVIRILRQQ---GEMESYQLANQACI----LRPSMTGVLARLERDGIVRRWKAPKDQRRVYVNLTEKGQQCFVS  100 (136)
T ss_dssp             HHHHHHHHHH---CSEEHHHHHHHTTC----CHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHc---CCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEeecCccCchhhhccCHHHHHHHHH
Confidence            3456677776   58999999999999    9999999999999999999765421  11357889988877654

>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=94.86  E-value=0.024  Score=38.24  Aligned_cols=62  Identities=11%  Similarity=0.079  Sum_probs=49.0

Q ss_pred             hhHHHHhcCCCCCCCHHHHHHhC-CCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhc
Q 039903           21 VFEIIAKAGPTAKISAVEIAAQM-PSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVL   90 (233)
Q Consensus        21 lfd~L~~~~~~~~~t~~elA~~~-~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~   90 (233)
                      |...|..    |+....||.+.+ ++    ++.-|.+=|+.|...|++++...+.  ..-.|++|+.|..|..
T Consensus        24 Il~~L~~----g~~RF~el~~~l~gI----S~~~Ls~rLk~L~~~glv~R~~~~~~p~~veY~LT~~G~~L~p   88 (108)
T d1z7ua1          24 LMDELFQ----GTKRNGELMRALDGI----TQRVLTDRLREMEKDGLVHRESFNELPPRVEYTLTPEGYALYD   88 (108)
T ss_dssp             HHHHHHH----SCBCHHHHHHHSTTC----CHHHHHHHHHHHHHHTSEEEEEECCSSCEEEEEECHHHHHHHH
T ss_pred             HHHHHHc----CCCCHHHHHHHCcCC----ChhHHHHHHHHHHHCCcceeeccCCCcceehhhhchhHHHHHH
Confidence            5555655    689999999998 79    9999999999999999999864211  0123999999998763

>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=94.76  E-value=0.021  Score=34.53  Aligned_cols=46  Identities=15%  Similarity=0.298  Sum_probs=41.6

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceee
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRC   69 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~   69 (233)
                      .+..|.++|..+   +..|..+||+.+|+    ++..+.+=++-|...|++..
T Consensus         6 ~D~~IL~~L~~n---~r~s~~~iA~~lgi----s~~tv~~Ri~~L~~~giI~~   51 (63)
T d2cfxa1           6 IDLNIIEELKKD---SRLSMRELGRKIKL----SPPSVTERVRQLESFGIIKQ   51 (63)
T ss_dssp             HHHHHHHHHHHC---SCCCHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCeee
Confidence            456788899987   58999999999999    99999999999999999975

>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=94.75  E-value=0.032  Score=33.67  Aligned_cols=35  Identities=11%  Similarity=0.179  Sum_probs=33.4

Q ss_pred             CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      ++.+..+||+.+++    ++..+.+.++-|...|+++..
T Consensus        22 ~~v~~~~iA~~L~v----s~~SVt~mvkrL~~~Glv~~~   56 (63)
T d2isya1          22 VTPLRARIAERLDQ----SGPTVSQTVSRMERDGLLRVA   56 (63)
T ss_dssp             CCCCHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEC
T ss_pred             CCCcHHHHHHHhCC----CchhHHHHHHHHHHCCCEEEc
Confidence            68999999999999    999999999999999999985

>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=94.71  E-value=0.019  Score=38.30  Aligned_cols=61  Identities=15%  Similarity=0.174  Sum_probs=47.9

Q ss_pred             hhHHHHhcCCCCCCCHHHHHHhC-CCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhh
Q 039903           21 VFEIIAKAGPTAKISAVEIAAQM-PSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFV   89 (233)
Q Consensus        21 lfd~L~~~~~~~~~t~~elA~~~-~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~   89 (233)
                      |...|..    |+....||.+.+ ++    ++..|.+=|+-|...|++++...++  ..-.|++|+.|..|.
T Consensus        25 Il~~L~~----g~~rF~el~~~l~gI----s~~~Ls~rLkeL~~~glv~r~~~~~~p~~veY~LT~~G~~L~   88 (102)
T d2fswa1          25 IIFQINR----RIIRYGELKRAIPGI----SEKMLIDELKFLCGKGLIKKKQYPEVPPRVEYSLTPLGEKVL   88 (102)
T ss_dssp             HHHHHTT----SCEEHHHHHHHSTTC----CHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECHHHHTTH
T ss_pred             HHHHHcc----CCCCHHHHHhhCccc----chhHHHHHHHHHHHCCceeecccCCCCCeehhhhhHhHHHHH
Confidence            4444554    689999999998 89    9999999999999999999864321  012499999998765

>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=94.70  E-value=0.019  Score=34.29  Aligned_cols=47  Identities=17%  Similarity=0.174  Sum_probs=42.0

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      ++..|.+.|.++   +..|..|||+++++    ++..+.+=++-|...|++...
T Consensus         4 ~D~~Il~~L~~n---~r~s~~eiA~~l~l----s~~~v~~Ri~~L~~~giI~~~   50 (60)
T d2cyya1           4 IDKKIIKILQND---GKAPLREISKITGL----AESTIHERIRKLRESGVIKKF   50 (60)
T ss_dssp             HHHHHHHHHHHC---TTCCHHHHHHHHCS----CHHHHHHHHHHHHHHTSSCCC
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCeEeE
Confidence            567788999997   58999999999999    999999999999999998753

>d2b78a2 c.66.1.51 (A:69-385) Hypothetical protein SMu776, middle and C-terminal domains {Streptococcus mutans [TaxId: 1309]}

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 SMu776, middle and C-terminal domains
species: Streptococcus mutans [TaxId: 1309]

Probab=94.67  E-value=0.011  Score=47.71  Aligned_cols=66  Identities=11%  Similarity=-0.047  Sum_probs=49.1

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhccCC--------CCceEEecCcCCCC------CCC-CE
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSSSY--------SGVKHIGGIMLERI------PKG-DA  229 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~~~--------~ri~~~~gD~f~~~------P~~-D~  229 (233)
                      +...++|||+.||+|.+++..+.. -.-+++.+|+. ..++.++++        .+++++.+|.|+.+      ... |+
T Consensus       142 ~~~g~~VLdlf~~~G~~sl~aa~~-ga~~V~~vD~s~~a~~~a~~N~~~n~l~~~~~~~i~~d~~~~l~~~~~~~~~fD~  220 (317)
T d2b78a2         142 SAAGKTVLNLFSYTAAFSVAAAMG-GAMATTSVDLAKRSRALSLAHFEANHLDMANHQLVVMDVFDYFKYARRHHLTYDI  220 (317)
T ss_dssp             TTBTCEEEEETCTTTHHHHHHHHT-TBSEEEEEESCTTHHHHHHHHHHHTTCCCTTEEEEESCHHHHHHHHHHTTCCEEE
T ss_pred             hhCCCceeecCCCCcHHHHHHHhC-CCceEEEecCCHHHHHHHHHHHHHhcccCcceEEEEccHHHHHHHHHhhcCCCCE
Confidence            456689999999999999887764 33468888984 467766542        57999999998732      222 88


Q ss_pred             EEe
Q 039903          230 ILI  232 (233)
Q Consensus       230 ~~l  232 (233)
                      |++
T Consensus       221 Ii~  223 (317)
T d2b78a2         221 III  223 (317)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            875

>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=94.64  E-value=0.0068  Score=47.48  Aligned_cols=41  Identities=17%  Similarity=0.114  Sum_probs=30.2

Q ss_pred             cCcceEEEecCCccHHHHHHHHHcCCCcEEEeech-HHHhhcc
Q 039903          167 EQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS-HVIQDSS  208 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp-~v~~~a~  208 (233)
                      .+..+++|||||+|.+....+.++.. +++..|.. ..++.++
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            45689999999999887655555544 79999984 4666554

>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=94.61  E-value=0.013  Score=35.06  Aligned_cols=46  Identities=17%  Similarity=0.283  Sum_probs=41.0

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceee
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRC   69 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~   69 (233)
                      .+..|...|..+   +.+|..+||+++|+    ++..+.+=++.|...|++..
T Consensus         4 ~D~kIl~~L~~n---~r~s~~~lA~~~gl----s~~~v~~Ri~~L~~~giI~~   49 (60)
T d1i1ga1           4 RDKIILEILEKD---ARTPFTEIAKKLGI----SETAVRKRVKALEEKGIIEG   49 (60)
T ss_dssp             HHHHHHHHHHHC---TTCCHHHHHHHHTS----CHHHHHHHHHHHHHHTSSCC
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCeEe
Confidence            356688888887   58999999999999    99999999999999999975

>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=94.60  E-value=0.024  Score=34.03  Aligned_cols=43  Identities=12%  Similarity=0.223  Sum_probs=36.2

Q ss_pred             hhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           21 VFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        21 lfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      |+....+.   ++.+..+||+.+|+    ++..+...++-|...|+++..
T Consensus        12 I~~l~~~~---~~v~~~~iA~~L~v----s~~SVs~mikrL~~~GlV~~~   54 (61)
T d2ev0a1          12 IYMLIEEK---GYARVSDIAEALAV----HPSSVTKMVQKLDKDEYLIYE   54 (61)
T ss_dssp             HHHHHHHH---SSCCHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEC-
T ss_pred             HHHHHhcC---CCccHHHHHHHhCC----CchhHHHHHHHHHHCCCEEEc
Confidence            34444444   58999999999999    999999999999999999974

>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=94.50  E-value=0.019  Score=39.10  Aligned_cols=62  Identities=15%  Similarity=0.123  Sum_probs=49.0

Q ss_pred             hhHHHHhcCCCCCCCHHHHHHhC-CCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhc
Q 039903           21 VFEIIAKAGPTAKISAVEIAAQM-PSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVL   90 (233)
Q Consensus        21 lfd~L~~~~~~~~~t~~elA~~~-~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~   90 (233)
                      |.-.|..    |+....||.+.+ ++    +++.|.+=|+-|...|++++...+.  ..-.|++|+.|..|..
T Consensus        29 Il~~L~~----g~~RF~el~~~l~gi----s~~~Ls~rL~~Le~~glv~R~~~~~~p~~veY~LT~~G~~L~~   93 (114)
T d1yyva1          29 ILVALRD----GTHRFSDLRRKMGGV----SEKMLAQSLQALEQDGFLNRVSYPVVPPHVEYSLTPLGEQVSD   93 (114)
T ss_dssp             HHHHGGG----CCEEHHHHHHHSTTC----CHHHHHHHHHHHHHHTCEEEEEECSSSCEEEEEECHHHHHHHH
T ss_pred             HHHHHhc----CCCCHHHHHHHcccc----chhHHHHHHHHHHHHHHHhhcccCCCCchhHhHhhHhHHHHHH
Confidence            4445554    689999999999 79    9999999999999999999874321  1124999999998873

>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=94.35  E-value=0.02  Score=34.59  Aligned_cols=46  Identities=13%  Similarity=0.205  Sum_probs=41.5

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceee
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRC   69 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~   69 (233)
                      ++..|...|..+   +..|..|||+++|+    ++..+.+=++-|...|++..
T Consensus         6 ~D~~IL~~L~~~---~r~s~~eiA~~l~l----s~~~v~~Ri~rL~~~GiI~~   51 (63)
T d2cg4a1           6 LDRGILEALMGN---ARTAYAELAKQFGV----SPETIHVRVEKMKQAGIITG   51 (63)
T ss_dssp             HHHHHHHHHHHC---TTSCHHHHHHHHTS----CHHHHHHHHHHHHHHTSEEE
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCeEe
Confidence            456788899987   58999999999999    99999999999999999985

>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=94.26  E-value=0.014  Score=42.59  Aligned_cols=67  Identities=9%  Similarity=0.129  Sum_probs=49.5

Q ss_pred             hhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           21 VFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        21 lfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      |.-.|...+++.++|..|||+.+++    +...+.++++-|...|++++.....  ..-..++|+.|..+...
T Consensus        67 vL~~L~~~~~~~~lt~~eLa~~l~i----~~~tvsr~l~~Le~~GlV~r~~~~~DrR~~~i~LT~~G~~l~~~  135 (172)
T d2fbka1          67 LLLTLYRSAPPEGLRPTELSALAAI----SGPSTSNRIVRLLEKGLIERREDERDRRSASIRLTPQGRALVTH  135 (172)
T ss_dssp             HHHHHHHHCCSSCBCHHHHHHHCSC----CSGGGSSHHHHHHHHTSEECCC-------CCBEECHHHHHHHHH
T ss_pred             HHHHHHhhCCCCCcCHHHHHHHHCc----CHhHHHHHHHHHHhCCCeeeeccccchhhHHhhcCHHHHHHHHH
Confidence            4455555543346899999999999    9999999999999999999874321  12356788988877644

>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=94.20  E-value=0.023  Score=38.61  Aligned_cols=64  Identities=8%  Similarity=0.066  Sum_probs=49.2

Q ss_pred             hhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhh
Q 039903           21 VFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFV   89 (233)
Q Consensus        21 lfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~   89 (233)
                      +...|...+ ++++|..+||+.+++    +...+.++++.|...|++.+.....  ..-.+.+|+.|+.+.
T Consensus        38 vL~~l~~~~-~~~~t~~~la~~l~~----~~~tvs~~i~~Le~~gli~r~~~~~D~R~~~i~LT~~G~~~~  103 (115)
T d2frha1          38 VLTYISENK-EKEYYLKDIINHLNY----KQPQVVKAVKILSQEDYFDKKRNEHDERTVLILVNAQQRKKI  103 (115)
T ss_dssp             HHHHHHHTC-CSEEEHHHHHHHSSS----HHHHHHHHHHHHHHTTSSCCBCCSSSSCCCEEECCSHHHHHH
T ss_pred             HHHHHHcCC-CCCCCHHHHHHHHCC----CHhHHHHHHHHHHhhhhheeeecccCCceEEEEECHHHHHHH
Confidence            344454432 257899999999999    9999999999999999999875432  224578899887654

>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=94.07  E-value=0.036  Score=39.18  Aligned_cols=54  Identities=22%  Similarity=0.231  Sum_probs=44.7

Q ss_pred             CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC-CCCceeccHhhhHhh
Q 039903           32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD-DQRLYGLAHVAKYFV   89 (233)
Q Consensus        32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~-~~~~y~lt~~s~~l~   89 (233)
                      |+....||.+.+++    ++..|.+=|+.|...|++++...+. ..-.|++|+.|..|.
T Consensus        32 G~~rf~el~~~lgi----s~~vLs~rL~~L~~~gLv~r~~~~~p~r~~Y~LT~~G~~L~   86 (142)
T d2f2ea1          32 GLTRFGEFQKSLGL----AKNILAARLRNLVEHGVMVAVPAESGSHQEYRLTDKGRALF   86 (142)
T ss_dssp             TCCSHHHHHHHHCC----CHHHHHHHHHHHHHTTSEEEEECSSSSCEEEEECHHHHTTH
T ss_pred             CCCCHHHHHHHhhc----cHHHHHHHHHHHHHhcceeeecCCCCCeeEEecCcCcchHH
Confidence            69999999999999    9999999999999999998742211 223599999988765

>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=93.95  E-value=0.036  Score=38.24  Aligned_cols=66  Identities=11%  Similarity=0.064  Sum_probs=50.0

Q ss_pred             ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhc
Q 039903           20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVL   90 (233)
Q Consensus        20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~   90 (233)
                      -+...|...+ +++.|..+||+.+++    +...+.++++-|...|++++.....  ..-...+|+.|+.+..
T Consensus        37 ~vL~~l~~~~-~~~~~~~~ia~~l~~----~~~~vs~~v~~L~~~glV~r~~~~~D~R~v~i~LT~~G~~~~~  104 (125)
T d1p4xa2          37 TILAIITSQN-KNIVLLKDLIETIHH----KYPQTVRALNNLKKQGYLIKERSTEDERKILIHMDDAQQDHAE  104 (125)
T ss_dssp             HHHHHHHTTT-TCCEEHHHHHHHSSS----CHHHHHHHHHHHHHHTSSEEEECSSSTTCEEEECCHHHHHHHH
T ss_pred             HHHHHHHHcc-CCCccHHHHHHHHCC----CcchHHHHHHHHHhccCEeeeecCCCCCeEEEEECHHHHHHHH
Confidence            3555664432 147899999999999    9999999999999999999875532  2235678888876653

>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=93.92  E-value=0.033  Score=38.35  Aligned_cols=66  Identities=8%  Similarity=0.074  Sum_probs=50.1

Q ss_pred             ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhc
Q 039903           20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVL   90 (233)
Q Consensus        20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~   90 (233)
                      -|+..|...+ ++++|..|||+.+++    +...+.++++.|...|++++.....  ..-...+|+.|+....
T Consensus        38 ~iL~~l~~~~-~~~~t~~eia~~~~~----~~~~vs~~l~~L~~~g~v~r~~~~~D~R~~~i~lT~~G~~~~~  105 (125)
T d1p4xa1          38 ILLTYLFHQQ-ENTLPFKKIVSDLCY----KQSDLVQHIKVLVKHSYISKVRSKIDERNTYISISEEQREKIA  105 (125)
T ss_dssp             HHHHHHHSCS-CSEEEHHHHHHHSSS----CGGGTHHHHHHHHHTTSCEEEECSSSTTSEEEECCHHHHHHHH
T ss_pred             HHHHHHHHhc-cCCcCHHHHHHHhCC----CcchHHHHHHHHHHCCCceeecccCCCCeEEEEECHHHHHHHH
Confidence            3555565532 257999999999999    9999999999999999999875431  1235678888876553

>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=93.84  E-value=0.02  Score=44.21  Aligned_cols=36  Identities=28%  Similarity=0.391  Sum_probs=31.9

Q ss_pred             ccCcceEEEecCCccHHHHHHHHHcCCCcEEEeech
Q 039903          166 FEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLS  201 (233)
Q Consensus       166 ~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp  201 (233)
                      ++...+++|||.|.|.=++-++=.+|+++++++|--
T Consensus        68 ~~~~~~ilDiGSGaGfPGi~laI~~p~~~v~Lves~  103 (239)
T d1xdza_          68 FNQVNTICDVGAGAGFPSLPIKICFPHLHVTIVDSL  103 (239)
T ss_dssp             GGGCCEEEEECSSSCTTHHHHHHHCTTCEEEEEESC
T ss_pred             ccCCCeEEeecCCCchHHHHHHHhCCCccceeecch
Confidence            456689999999999988888888999999999954

>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=93.83  E-value=0.031  Score=40.43  Aligned_cols=64  Identities=14%  Similarity=-0.002  Sum_probs=50.4

Q ss_pred             hhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhcC
Q 039903           21 VFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        21 lfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~~   91 (233)
                      +...|...   ++.|..+||+.+++    +...+.++++-|...|++++.....  ..-...+|+.|..+...
T Consensus        46 vL~~l~~~---~~~t~~~la~~~~l----~~~tvs~~i~rL~~~gli~r~~~~~D~R~~~l~lT~~G~~~~~~  111 (162)
T d2fxaa1          46 ILWIAYQL---NGASISEIAKFGVM----HVSTAFNFSKKLEERGYLRFSKRLNDKRNTYVQLTEEGTEVFWS  111 (162)
T ss_dssp             HHHHHHHH---TSEEHHHHHHHTTC----CHHHHHHHHHHHHHHTSEEEECC------CEEEECHHHHHHHHH
T ss_pred             HHhhhccC---CCcCHHHHHHHHcC----CchhhHHHHHHHHHCCCceeecccccCeeeeeccCHhHHHHHHH
Confidence            56667665   48999999999999    9999999999999999999864321  22367889999876643

>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=93.77  E-value=0.028  Score=38.19  Aligned_cols=65  Identities=17%  Similarity=0.150  Sum_probs=49.0

Q ss_pred             hhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCC--CCCceeccHhhhHhhc
Q 039903           21 VFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGD--DQRLYGLAHVAKYFVL   90 (233)
Q Consensus        21 lfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~--~~~~y~lt~~s~~l~~   90 (233)
                      +...|...+ +++.|..|||+.+++    +...+.++++.|...|++.+...+.  ..-...+|+.|..+..
T Consensus        37 vL~~l~~~~-~~~~t~~ela~~l~~----~~~~vs~~i~~Le~~gli~r~~~~~D~R~~~i~LT~~G~~~~~  103 (115)
T d1hsja1          37 ILNHILRSE-SNEISSKEIAKCSEF----KPYYLTKALQKLKDLKLLSKKRSLQDERTVIVYVTDTQKANIQ  103 (115)
T ss_dssp             HHHHHHTCS-CSEEEHHHHHHSSCC----CHHHHHHHHHHHHTTTTSCCEECCSSSSCCEEECCSSHHHHHH
T ss_pred             HHHHHHccC-CCCcCHHHHHHHHCC----ChhhHHHHHHHHHHcCCeEEEeecCCCceEEEEECHHHHHHHH
Confidence            445555321 158999999999999    9999999999999999999875531  2235678888876553

>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=93.49  E-value=0.059  Score=41.65  Aligned_cols=73  Identities=18%  Similarity=0.084  Sum_probs=43.6

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcCCCcEEEeechHHH---hh-ccCC--CCceEEecCcCCCCCC--CCE
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVI---QD-SSSY--SGVKHIGGIMLERIPK--GDA  229 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~---~~-a~~~--~ri~~~~gD~f~~~P~--~D~  229 (233)
                      .+.+.+- +....++||+|||.|.++..+++..+..++..+|+-.-.   .. ...+  +-+++..++-+...|.  +|+
T Consensus        57 ~~~~~~~-~~~~~~vvDlG~~pGgws~~~a~~~~v~~V~g~~iG~d~~e~P~~~~~~~~ni~~~~~~~dv~~l~~~~~D~  135 (257)
T d2p41a1          57 WFVERNL-VTPEGKVVDLGCGRGGWSYYCGGLKNVREVKGLTKGGPGHEEPIPMSTYGWNLVRLQSGVDVFFIPPERCDT  135 (257)
T ss_dssp             HHHHTTS-SCCCEEEEEETCTTSHHHHHHHTSTTEEEEEEECCCSTTSCCCCCCCSTTGGGEEEECSCCTTTSCCCCCSE
T ss_pred             HHHHhcC-ccCCCeEEEecCCCChHHHHHHhhcCCCceeEEEecCccccCCccccccccccccchhhhhHHhcCCCcCCE
Confidence            3444443 566678999999999999999988766665555542111   01 1111  3356666654443333  477


Q ss_pred             EE
Q 039903          230 IL  231 (233)
Q Consensus       230 ~~  231 (233)
                      ++
T Consensus       136 vl  137 (257)
T d2p41a1         136 LL  137 (257)
T ss_dssp             EE
T ss_pred             EE
Confidence            65

>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=93.45  E-value=0.057  Score=31.62  Aligned_cols=45  Identities=13%  Similarity=0.280  Sum_probs=37.4

Q ss_pred             hHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           22 FEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        22 fd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      ...|.+.|+....|+.+||.++++    +.+.+.|+|-.|...|.+.+.
T Consensus         5 l~~l~~lg~~~~~tA~~LA~kl~v----pKk~iNr~LYsL~~kgkl~k~   49 (59)
T d2gxba1           5 LKFLEELGEGKATTAHDLSGKLGT----PKKEINRVLYSLAKKGKLQKE   49 (59)
T ss_dssp             HHHHHHHCTTCCBCHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHhcCCccchhHHHHHHHhCC----cHHHHHHHHHHHHHccchhhc
Confidence            334444343368899999999999    999999999999999999985

>d1i4wa_ c.66.1.24 (A:) Transcription factor sc-mtTFB {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: rRNA adenine dimethylase-like
domain: Transcription factor sc-mtTFB
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.04  E-value=0.13  Score=41.22  Aligned_cols=55  Identities=11%  Similarity=0.082  Sum_probs=40.8

Q ss_pred             CcceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhc---cCCCCceEEecCcCC
Q 039903          168 QIKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDS---SSYSGVKHIGGIMLE  222 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a---~~~~ri~~~~gD~f~  222 (233)
                      ...+||+||.|.|.++.+|+++.---+.+++|... -++.-   ...+|++++.+|++.
T Consensus        43 ~~~~VlEIGPG~G~LT~~Ll~~~~~~~v~~iE~D~~~~~~L~~~~~~~~~~ii~~D~l~  101 (322)
T d1i4wa_          43 EELKVLDLYPGVGIQSAIFYNKYCPRQYSLLEKRSSLYKFLNAKFEGSPLQILKRDPYD  101 (322)
T ss_dssp             TTCEEEEESCTTCHHHHHHHHHHCCSEEEEECCCHHHHHHHHHHTTTSSCEEECSCTTC
T ss_pred             CCCeEEEECCCCCHHHHHHHhcCCCCEEEEEECCHHHHHHHHHhccCCCcEEEeCchhh
Confidence            35689999999999999999874224788888653 22222   224789999999985

>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=92.96  E-value=0.11  Score=31.94  Aligned_cols=41  Identities=20%  Similarity=0.271  Sum_probs=34.6

Q ss_pred             HHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           25 IAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        25 L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      +.+.|  -|-|+.|||+.+|+.   ++..+.+.|+.|...|++++.
T Consensus        18 ~~~~G--~~Ps~rei~~~~g~~---S~stv~~~l~~Le~kG~I~r~   58 (71)
T d1jhfa1          18 ISQTG--MPPTRAEIAQRLGFR---SPNAAEEHLKALARKGVIEIV   58 (71)
T ss_dssp             HHHHS--SCCCHHHHHHHTTCS---SHHHHHHHHHHHHHTTSEEEC
T ss_pred             HHHhC--CCCCHHHHHHHcCCC---CHHHHHHHHHHHHHCcCeecC
Confidence            33345  588999999999982   577899999999999999995

>d2ifta1 c.66.1.46 (A:11-193) Putative methylase HI0767 {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: YhhF-like
domain: Putative methylase HI0767
species: Haemophilus influenzae [TaxId: 727]

Probab=92.40  E-value=0.064  Score=39.34  Aligned_cols=62  Identities=18%  Similarity=0.160  Sum_probs=43.7

Q ss_pred             ceEEEecCCccHHHHHHHHHcCCCcEEEeechH-HHhhccCC--------CCceEEecCcCC--CCC--C--CCEEEe
Q 039903          170 KQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSH-VIQDSSSY--------SGVKHIGGIMLE--RIP--K--GDAILI  232 (233)
Q Consensus       170 ~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~-v~~~a~~~--------~ri~~~~gD~f~--~~P--~--~D~~~l  232 (233)
                      .++||+-+|+|.++.+.+.+-.+ +++.+|... +++..+++        ....++..|.++  ..+  .  .|+|++
T Consensus        45 ~~vLDlFaGsG~~glEalSRGA~-~v~fVE~~~~a~~~ik~Ni~~l~~~~~~~~~~~~d~~~~l~~~~~~~~fDlIFl  121 (183)
T d2ifta1          45 SECLDGFAGSGSLGFEALSRQAK-KVTFLELDKTVANQLKKNLQTLKCSSEQAEVINQSSLDFLKQPQNQPHFDVVFL  121 (183)
T ss_dssp             CEEEETTCTTCHHHHHHHHTTCS-EEEEECSCHHHHHHHHHHHHHTTCCTTTEEEECSCHHHHTTSCCSSCCEEEEEE
T ss_pred             ceEeecccCccceeeeeeeecce-eeEEeecccchhhhHhhHHhhhcccccccccccccccccccccccCCcccEEEe
Confidence            58999999999999999998755 788889753 55444432        356667776554  111  2  399886

>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=92.11  E-value=0.1  Score=32.21  Aligned_cols=60  Identities=8%  Similarity=0.097  Sum_probs=48.1

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCCh-hhHHHHHHHHhcCCceeeeccCCCCCceeccHhh
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAA-VMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVA   85 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~-~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s   85 (233)
                      .+..|.+.|...   |+.++-+||+.+|+    +. .-+.+.|-.|...|.+.+...  ..-.|.++.-.
T Consensus         6 ~eekI~~~L~~~---g~~~Al~iak~lGl----~kakeVN~~LY~L~k~g~v~k~~~--tPP~W~L~~~~   66 (73)
T d1xmka1           6 IKEKICDYLFNV---SDSSALNLAKNIGL----TKARDINAVLIDMERQGDVYRQGT--TPPIWHLTDKK   66 (73)
T ss_dssp             HHHHHHHHHHHT---CCEEHHHHHHHHCG----GGHHHHHHHHHHHHHTTSEEEECS--SSCEEEECHHH
T ss_pred             HHHHHHHHHHHc---CCchHHHHHHHhCC----CcHHHHhHHHHHHHHCCCeecCCC--CCCceeeecch
Confidence            456789999987   58999999999999    77 459999999999999998621  23368877644

>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=91.31  E-value=0.092  Score=33.65  Aligned_cols=46  Identities=22%  Similarity=0.309  Sum_probs=39.5

Q ss_pred             ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeec
Q 039903           20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTS   71 (233)
Q Consensus        20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~   71 (233)
                      .|++.|.+.+  +.+|=++||+++|+    ...-++++|..|...|++...+
T Consensus        22 ~v~~~L~~~~--~evtDe~iA~~tgi----~in~VRk~Ly~L~~~~L~~y~R   67 (88)
T d1q1ha_          22 DVLRILLDKG--TEMTDEEIANQLNI----KVNDVRKKLNLLEEQGFVSYRK   67 (88)
T ss_dssp             HHHHHHHHHC--SCBCHHHHHHTTTS----CHHHHHHHHHHHHHHTSCEEEE
T ss_pred             HHHHHHHhcc--CcCCHHHHHHHhCC----cHHHHHHHHHHHHhCCceEEEE
Confidence            4788776543  47999999999999    9999999999999999997553

>d2p8ta1 a.4.5.72 (A:14-82) Hypothetical protein PH0730 {Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PH0730 N-terminal domain-like
domain: Hypothetical protein PH0730
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=90.06  E-value=0.2  Score=30.48  Aligned_cols=50  Identities=18%  Similarity=0.130  Sum_probs=42.9

Q ss_pred             CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhhHhhc
Q 039903           32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAKYFVL   90 (233)
Q Consensus        32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~~l~~   90 (233)
                      .|+.-..||+.+++    .++.++-.++.|-..|+++..     ...-.+|+.|..++.
T Consensus        16 qPiGRr~La~~L~l----~Er~vRte~~~Lk~~gLI~~~-----~~Gm~lTe~G~~~l~   65 (69)
T d2p8ta1          16 EPLGRKQISERLEL----GEGSVRTLLRKLSHLDIIRSK-----QRGHFLTLKGKEIRD   65 (69)
T ss_dssp             SCBCHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEC-------CEEECHHHHHHHH
T ss_pred             CCccHHHHHHHcCC----cHHHHHHHHHHHHHCCCeeee-----CCCCEECHhHHHHHH
Confidence            48999999999999    999999999999999999986     344569998887653

>d1af7a2 c.66.1.8 (A:92-284) Chemotaxis receptor methyltransferase CheR, C-terminal domain {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: Chemotaxis receptor methyltransferase CheR, C-terminal domain
domain: Chemotaxis receptor methyltransferase CheR, C-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=89.94  E-value=0.41  Score=35.00  Aligned_cols=42  Identities=10%  Similarity=0.048  Sum_probs=28.0

Q ss_pred             cCcceEEEecCCccH----HHHHHHHHc----CCCcEEEeech-HHHhhcc
Q 039903          167 EQIKQLVDVGGGLGV----NVNIIISNY----LHIKGVNFDLS-HVIQDSS  208 (233)
Q Consensus       167 ~~~~~vvDvGGG~G~----~~~~l~~~~----P~l~~~v~Dlp-~v~~~a~  208 (233)
                      .+.-+|.++|||+|.    +++.+.+..    ++++++..|+. .+++.|+
T Consensus        23 ~~~lrIwsaGCstGeE~YSlA~~l~e~~~~~~~~~~I~atDi~~~~l~~A~   73 (193)
T d1af7a2          23 HGEYRVWSAAASTGEEPYSIAITLADALGMAPGRWKVFASDIDTEVLEKAR   73 (193)
T ss_dssp             CSCEEEEESCCTTTHHHHHHHHHHHHHHCSCTTSEEEEEEESCHHHHHHHH
T ss_pred             CCCeEEEEeCCCCchhHHHHHHHHHHhhhhcCCceEEEeecCChHHhhHhh
Confidence            345689999999997    344455442    23567888985 4777664

>d1cf7a_ a.4.5.17 (A:) Cell cycle transcription factor E2F-4 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Cell cycle transcription factor e2f-dp
domain: Cell cycle transcription factor E2F-4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.65  E-value=0.16  Score=30.74  Aligned_cols=46  Identities=9%  Similarity=0.052  Sum_probs=37.6

Q ss_pred             ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCC-hhhHHHHHHHHhcCCceeee
Q 039903           20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNA-AVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~-~~~l~rlL~~L~~~gll~~~   70 (233)
                      +....+.+++ ++..++.+.|+.+++    . .++++.+..+|.++|++++.
T Consensus        13 kFl~l~~~~~-~~~~~L~~aa~~L~v----~~kRRiYDI~NVLe~igli~K~   59 (67)
T d1cf7a_          13 KFVSLLQEAK-DGVLDLKLAADTLAV----RQKRRIYDITNVLEGIGLIEKK   59 (67)
T ss_dssp             HHHHHHHHSS-TTEEEHHHHHHHTTT----CCTHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHhhCC-CCeeeHHHHHHHhcC----cchhhHHHHHHHHhhhhhhhcc
Confidence            3444555543 367899999999998    6 69999999999999999997

>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=89.57  E-value=0.2  Score=28.58  Aligned_cols=42  Identities=12%  Similarity=0.168  Sum_probs=33.8

Q ss_pred             hhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCce
Q 039903           21 VFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVL   67 (233)
Q Consensus        21 lfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll   67 (233)
                      +.+.|.+.- ..++|+++||+.+++    +++.+.|+.+....+.+.
T Consensus         8 v~~yI~~~~-~~~~tl~~lA~~~~~----s~~~l~r~Fk~~~g~tp~   49 (54)
T d1bl0a1           8 ILDWIEDNL-ESPLSLEKVSERSGY----SKWHLQRMFKKETGHSLG   49 (54)
T ss_dssp             HHHHHHTTT-TSCCCCHHHHHHSSS----CHHHHHHHHHHHHSSCHH
T ss_pred             HHHHHHhcc-CCCCCHHHHHHHHCc----CHHHHHHHHHHHHCcCHH
Confidence            556677653 259999999999999    999999999887766543

>d1zyba1 a.4.5.4 (A:148-220) Probable transcription regulator BT4300, C-terminal domain {Bacteroides thetaiotaomicron [TaxId: 818]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Probable transcription regulator BT4300, C-terminal domain
species: Bacteroides thetaiotaomicron [TaxId: 818]

Probab=88.94  E-value=0.18  Score=31.01  Aligned_cols=42  Identities=10%  Similarity=0.180  Sum_probs=36.6

Q ss_pred             CCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccH
Q 039903           33 KISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAH   83 (233)
Q Consensus        33 ~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~   83 (233)
                      +.|-+|||..+|+    +...+.|.|..|...|+++..     .+.+....
T Consensus        27 ~lt~~elA~~lg~----sr~tvsr~l~~l~~~g~I~~~-----~~~i~I~d   68 (73)
T d1zyba1          27 KVKMDDLARCLDD----TRLNISKTLNELQDNGLIELH-----RKEILIPD   68 (73)
T ss_dssp             ECCHHHHHHHHTS----CHHHHHHHHHHHHHTTSCEEE-----TTEEEESC
T ss_pred             ecCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEec-----CCEEEEcc
Confidence            5799999999999    999999999999999999974     56665543

>d2gaua1 a.4.5.4 (A:152-232) Transcriptional regulator PG0396, C-terminal domain {Porphyromonas gingivalis [TaxId: 837]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Transcriptional regulator PG0396, C-terminal domain
species: Porphyromonas gingivalis [TaxId: 837]

Probab=88.62  E-value=0.4  Score=29.68  Aligned_cols=41  Identities=20%  Similarity=0.155  Sum_probs=36.1

Q ss_pred             CCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceecc
Q 039903           33 KISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLA   82 (233)
Q Consensus        33 ~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt   82 (233)
                      |.|-.|||..+|+    +...+.|.|..|...|+++..     .+.+...
T Consensus        29 ~lt~~eLA~~~G~----sretvsr~L~~l~~~glI~~~-----~~~i~I~   69 (81)
T d2gaua1          29 YLSREELATLSNM----TVSNAIRTLSTFVSERMLALD-----GKRIKII   69 (81)
T ss_dssp             CCCHHHHHHHTTS----CHHHHHHHHHHHHHTTSEEEE-----TTEEEES
T ss_pred             cCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEec-----CCEEEEc
Confidence            7899999999999    999999999999999999985     4555443

>d1stza1 a.4.5.51 (A:14-100) Heat-inducible transcription repressor HrcA, 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: Heat-inducible transcription repressor HrcA, N-terminal domain
domain: Heat-inducible transcription repressor HrcA, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=88.01  E-value=0.81  Score=28.99  Aligned_cols=50  Identities=4%  Similarity=-0.098  Sum_probs=38.0

Q ss_pred             CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceeccHhhh
Q 039903           32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLAHVAK   86 (233)
Q Consensus        32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt~~s~   86 (233)
                      .|.+..+|++..++  +.++.-++..|..|...|++++...  ..| .-.|..+-
T Consensus        22 ~Pv~s~~i~~~~~l--~~S~aTIRn~m~~LE~~G~l~~~h~--s~G-riPT~~g~   71 (87)
T d1stza1          22 KPVSSQRVLEVSNI--EFSSATIRNDMKKLEYLGYIYQPHT--SAG-RIPTDKGL   71 (87)
T ss_dssp             SCBCHHHHHHHSCC--CSCHHHHHHHHHHHHHTTSEECCSS--CSC-BEECHHHH
T ss_pred             CccCHHHHHHHhCC--CCCHHHHHHHHHHHHHCCcccCCCC--CCC-CcccHHHH
Confidence            69999999999665  1168899999999999999998643  233 33555553

>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=87.62  E-value=0.46  Score=29.34  Aligned_cols=36  Identities=17%  Similarity=0.176  Sum_probs=33.0

Q ss_pred             CCC-CHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeec
Q 039903           32 AKI-SAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTS   71 (233)
Q Consensus        32 ~~~-t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~   71 (233)
                      ..+ |..+||+.+++    +..-+++-++.|+..|++....
T Consensus        20 ~~LPse~~La~~~~v----Sr~tvr~Al~~L~~~Gli~~~~   56 (78)
T d3bwga1          20 DKLPVLETLMAQFEV----SKSTITKSLELLEQKGAIFQVR   56 (78)
T ss_dssp             CBCCCHHHHHHHTTC----CHHHHHHHHHHHHHTTSEEEET
T ss_pred             CCCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCcEEEEc
Confidence            466 78999999999    9999999999999999999873

>d1ft9a1 a.4.5.4 (A:134-213) CO-sensing protein CooA, C-terminal domain {Rhodospirillum rubrum [TaxId: 1085]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: CO-sensing protein CooA, C-terminal domain
species: Rhodospirillum rubrum [TaxId: 1085]

Probab=87.55  E-value=0.39  Score=29.76  Aligned_cols=42  Identities=17%  Similarity=0.205  Sum_probs=36.4

Q ss_pred             CCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceecc
Q 039903           33 KISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLA   82 (233)
Q Consensus        33 ~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt   82 (233)
                      |.|-+|||.-+|+    +...+.|.|+.|...|+++..    ..+.+...
T Consensus        30 ~~t~~eiA~~lG~----sretvsr~l~~l~~~g~I~~~----~~~~i~I~   71 (80)
T d1ft9a1          30 DFTVEEIANLIGS----SRQTTSTALNSLIKEGYISRQ----GRGHYTIP   71 (80)
T ss_dssp             CCCHHHHHHHHCS----CHHHHHHHHHHHHHTTSSEEC----STTCEECS
T ss_pred             CCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEC----CCCeEEEC
Confidence            7899999999999    999999999999999999974    34555544

>d2okca1 c.66.1.45 (A:9-433) Type I restriction enzyme StySJI M protein {Bacteroides thetaiotaomicron [TaxId: 818]}

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: Type I restriction enzyme StySJI M protein
species: Bacteroides thetaiotaomicron [TaxId: 818]

Probab=87.29  E-value=0.37  Score=39.78  Aligned_cols=74  Identities=18%  Similarity=0.066  Sum_probs=49.1

Q ss_pred             HHHHhcccccCcceEEEecCCccHHHHHHHHHcCC-------------CcEEEeechH-HHhhccC--------CCCceE
Q 039903          158 RIIDSSKGFEQIKQLVDVGGGLGVNVNIIISNYLH-------------IKGVNFDLSH-VIQDSSS--------YSGVKH  215 (233)
Q Consensus       158 ~~~~~~~~~~~~~~vvDvGGG~G~~~~~l~~~~P~-------------l~~~v~Dlp~-v~~~a~~--------~~ri~~  215 (233)
                      -+++.++ -....+|+|-.||+|.++.++.++...             .....+|... ....|+.        .+.+..
T Consensus       153 ~mv~ll~-~~~~~~IlDPacGsG~fL~~a~~~~~~~~~~~~~~~~~~~~~l~g~E~~~~~~~la~~n~~l~g~~~~~~~i  231 (425)
T d2okca1         153 AMVDCIN-PQMGETVCDPACGTGGFLLTAYDYMKGQSASKEKRDFLRDKALHGVDNTPLVVTLASMNLYLHGIGTDRSPI  231 (425)
T ss_dssp             HHHHHHC-CCTTCCEEETTCTTCHHHHHHHHHHHTCC-CCHHHHHHHHTTEEEEESCHHHHHHHHHHHHHTTCCSSCCSE
T ss_pred             hhheecc-CcccceeeccccccCccHHHHHHHHHhhccchhhhhhhhhhhhhhhhccHHHHHHHHhhhhhcCCcccccee
Confidence            3444443 344579999999999999888775432             3467788743 4444432        145778


Q ss_pred             EecCcCCCCCC--CCEEEe
Q 039903          216 IGGIMLERIPK--GDAILI  232 (233)
Q Consensus       216 ~~gD~f~~~P~--~D~~~l  232 (233)
                      ..+|++...+.  .|+|+.
T Consensus       232 ~~~d~l~~~~~~~fD~Ii~  250 (425)
T d2okca1         232 VCEDSLEKEPSTLVDVILA  250 (425)
T ss_dssp             EECCTTTSCCSSCEEEEEE
T ss_pred             ecCchhhhhcccccceEEe
Confidence            88999985554  388864

>d1i5za1 a.4.5.4 (A:138-206) Catabolite gene activator protein (CAP), C-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Catabolite gene activator protein (CAP), C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=86.44  E-value=0.32  Score=29.30  Aligned_cols=34  Identities=24%  Similarity=0.384  Sum_probs=32.4

Q ss_pred             CCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           33 KISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        33 ~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      |+|-+|||.-+|+    +...+.|+|+-|...|+++..
T Consensus        29 ~lt~~~lA~~~G~----sRetvsr~L~~l~~~glI~~~   62 (69)
T d1i5za1          29 KITRQEIGQIVGC----SRETVGRILKMLEDQNLISAH   62 (69)
T ss_dssp             ECCHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEc
Confidence            6899999999999    999999999999999999985

>d2g9wa1 a.4.5.39 (A:3-124) Hypothetical protein Rv1846c {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Penicillinase repressor
domain: Hypothetical protein Rv1846c
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=86.33  E-value=0.39  Score=32.49  Aligned_cols=53  Identities=9%  Similarity=0.078  Sum_probs=43.3

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeec
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTS   71 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~   71 (233)
                      .|+.|.+.|=+.|  +|.|+.||.+.+.-..+....-+..+|+-|+..|+|+...
T Consensus         8 ~E~~IM~~lW~~g--~~~t~~eI~~~l~~~~~~~~sTV~T~L~rL~~Kg~l~~~~   60 (122)
T d2g9wa1           8 LERAVMDHLWSRT--EPQTVRQVHEALSARRDLAYTTVMAVLQRLAKKNLVLQIR   60 (122)
T ss_dssp             HHHHHHHHHHTCS--SCEEHHHHHHHHTTTCCCCHHHHHHHHHHHHHTTSEEEEC
T ss_pred             HHHHHHHHHHcCC--CCccHHHHHHHHhccCCCcHHHHHHHHHHHHHCCCEEEee
Confidence            5667888887764  5889999999987544447779999999999999999863

>d1d5ya1 a.4.1.8 (A:3-56) Rob transcription factor, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: AraC type transcriptional activator
domain: Rob transcription factor, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=85.93  E-value=0.49  Score=26.85  Aligned_cols=42  Identities=14%  Similarity=0.168  Sum_probs=33.4

Q ss_pred             ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCc
Q 039903           20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRV   66 (233)
Q Consensus        20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gl   66 (233)
                      .+.+.|.+.- +.++|+++||+.+++    ++..+.|+.+.....-+
T Consensus         7 ~i~~yi~~~~-~~~itl~~lA~~~~~----S~~~l~r~Fk~~~g~tp   48 (54)
T d1d5ya1           7 DLLIWLEGHL-DQPLSLDNVAAKAGY----SKWHLQRMFKDVTGHAI   48 (54)
T ss_dssp             HHHHHHHTTS-SSSCCCHHHHTTTSS----CHHHHHHHHHHHHSSCH
T ss_pred             HHHHHHHHcc-CCCCCHHHHHHHHCc----CHHHHHHHHHHHHCcCH
Confidence            4667777752 359999999999999    99999999887665443

>d2bm8a1 c.66.1.50 (A:2-233) Cephalosporin hydroxylase CmcI {Streptomyces clavuligerus [TaxId: 1901]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: CmcI-like
domain: Cephalosporin hydroxylase CmcI
species: Streptomyces clavuligerus [TaxId: 1901]

Probab=85.92  E-value=0.54  Score=35.58  Aligned_cols=55  Identities=13%  Similarity=0.070  Sum_probs=38.9

Q ss_pred             CcceEEEecCCccHHHHHHHH----HcCCCcEEEeechH-HHhhc-cCCCCceEEecCcCC
Q 039903          168 QIKQLVDVGGGLGVNVNIIIS----NYLHIKGVNFDLSH-VIQDS-SSYSGVKHIGGIMLE  222 (233)
Q Consensus       168 ~~~~vvDvGGG~G~~~~~l~~----~~P~l~~~v~Dlp~-v~~~a-~~~~ri~~~~gD~f~  222 (233)
                      ++++||.||.+.|.-+.-+++    ..++.+++.+|+.. ..... ...+||+++.||..+
T Consensus        80 KPk~ILEIGv~~GgS~~~~a~~l~~~~~~~kI~giDId~~~~~~~~~~~~~I~~i~gDs~~  140 (232)
T d2bm8a1          80 RPRTIVELGVYNGGSLAWFRDLTKIMGIDCQVIGIDRDLSRCQIPASDMENITLHQGDCSD  140 (232)
T ss_dssp             CCSEEEEECCTTSHHHHHHHHHHHHTTCCCEEEEEESCCTTCCCCGGGCTTEEEEECCSSC
T ss_pred             CCCEEEEECCCCchHHHHHHHHHHhcCCCceEEecCcChhhhhhhhccccceeeeeccccc
Confidence            468999999999976544432    34788899999743 32222 224899999999765

>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=85.90  E-value=0.88  Score=27.46  Aligned_cols=36  Identities=8%  Similarity=0.163  Sum_probs=33.5

Q ss_pred             CCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           31 TAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        31 ~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      +...|+.+||+++|+    +.+-+.|.|-.|...|.+.+.
T Consensus        22 ~~~~tA~~LAk~Lg~----~Kk~VNr~LY~L~~~G~v~~~   57 (70)
T d1sfua_          22 NDYTTAISLSNRLKI----NKKKINQQLYKLQKEDTVKMV   57 (70)
T ss_dssp             TCEECHHHHHHHTTC----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCchHHHHHHHhCC----CHHHHHHHHHHHHHCCCeecC
Confidence            368899999999999    999999999999999999986

>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=85.80  E-value=0.38  Score=29.54  Aligned_cols=36  Identities=14%  Similarity=0.181  Sum_probs=33.0

Q ss_pred             CCC-CHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeec
Q 039903           32 AKI-SAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTS   71 (233)
Q Consensus        32 ~~~-t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~   71 (233)
                      ..+ |..+||+.+++    +..-+++-++.|+..|++....
T Consensus        25 ~~LPs~~eLa~~~~v----Sr~tvr~Al~~L~~~G~i~~~~   61 (74)
T d1hw1a1          25 TILPAERELSELIGV----TRTTLREVLQRLARDGWLTIQH   61 (74)
T ss_dssp             SBCCCHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEET
T ss_pred             CCCccHHHHHHHHCC----CHHHHHHHHHHHHHCCcEEEEe
Confidence            466 78999999999    9999999999999999999873

>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=85.43  E-value=0.37  Score=29.08  Aligned_cols=36  Identities=17%  Similarity=0.330  Sum_probs=33.0

Q ss_pred             CCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeec
Q 039903           32 AKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTS   71 (233)
Q Consensus        32 ~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~   71 (233)
                      ..++..+||+.+++    +..-+++-++.|...|+++...
T Consensus        24 ~~l~~~~La~~~~v----Sr~tvr~Al~~L~~~Gli~~~~   59 (69)
T d2hs5a1          24 ARLSEPDICAALDV----SRNTVREAFQILIEDRLVAHEL   59 (69)
T ss_dssp             CEECHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEEET
T ss_pred             CccCHHHHHHHHCC----CHHHHHHHHHHHHHCCcEEEEc
Confidence            46688999999999    9999999999999999999873

>d1okra_ a.4.5.39 (A:) Methicillin resistance regulatory protein MecI {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Penicillinase repressor
domain: Methicillin resistance regulatory protein MecI
species: Staphylococcus aureus [TaxId: 1280]

Probab=85.32  E-value=0.2  Score=33.85  Aligned_cols=52  Identities=15%  Similarity=0.143  Sum_probs=41.1

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeec
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTS   71 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~   71 (233)
                      .|+.|...|=+.   +|.|+.||.+.+....+.+..-+..+|+-|...|++++..
T Consensus         8 ~E~~VM~~lW~~---~~~t~~ei~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~r~~   59 (120)
T d1okra_           8 AEWEVMNIIWMK---KYASANNIIEEIQMQKDWSPKTIRTLITRLYKKGFIDRKK   59 (120)
T ss_dssp             HHHHHHHHHHHH---SSEEHHHHHHHHHHHCCCCHHHHHHHHHHHHHHTSEEEEE
T ss_pred             HHHHHHHHHHcC---CCCCHHHHHHHHhcccCccHHhHHHHHHHHHHCCCeEEEe
Confidence            567788888887   5899999888773211118889999999999999999864

>d1xn7a_ a.4.5.62 (A:) Hypothetical protein YhgG {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Hypothetical protein YhgG
domain: Hypothetical protein YhgG
species: Escherichia coli [TaxId: 562]

Probab=85.29  E-value=0.69  Score=28.18  Aligned_cols=45  Identities=16%  Similarity=0.245  Sum_probs=40.1

Q ss_pred             ChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeec
Q 039903           20 GVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTS   71 (233)
Q Consensus        20 glfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~   71 (233)
                      .|=|.|+-+   |.....+|+..+..    +...+..+|+-|+++|=+++.+
T Consensus         6 qvRD~iAL~---G~~da~qlS~qL~~----P~Plv~AMLerL~aMGK~erie   50 (78)
T d1xn7a_           6 QVRDLLALR---GRMEAAQISQTLNT----PQPMINAMLQQLESMGKAVRIQ   50 (78)
T ss_dssp             HHHHHHHHS---CSBCHHHHHHHTTC----CHHHHHHHHHHHHHHTSEEEEC
T ss_pred             HHHHHHHHc---CcccHHHHHHHHcC----ChHHHHHHHHHHHHhhcceecc
Confidence            355778887   58999999999999    9999999999999999999874

>d3e5ua1 a.4.5.4 (A:148-227) Chlorophenol reduction protein CprK {Desulfitobacterium hafniense [TaxId: 49338]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Chlorophenol reduction protein CprK
species: Desulfitobacterium hafniense [TaxId: 49338]

Probab=84.10  E-value=0.53  Score=29.07  Aligned_cols=41  Identities=17%  Similarity=0.130  Sum_probs=33.7

Q ss_pred             CCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeeeccCCCCCceecc
Q 039903           33 KISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGLA   82 (233)
Q Consensus        33 ~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~lt   82 (233)
                      |+|-.|||..+|+    +...+.|+|..|...|+++..     .+.+...
T Consensus        30 ~lt~~elA~~~g~----sretvsr~l~~l~~~glI~~~-----~~~i~I~   70 (80)
T d3e5ua1          30 PLSQKSIGEITGV----HHVTVSRVLASLKRENILDKK-----KNKIIVY   70 (80)
T ss_dssp             CCCHHHHHHHHTC----CHHHHHHHHHHHHHTTSEEC---------CEES
T ss_pred             CCCHHHHHHHHCC----CHHHHHHHHHHHHHCCcEEec-----CCEEEEc
Confidence            7899999999999    999999999999999999874     4555443

>d2oyra1 c.66.1.55 (A:1-250) Hypothetical protein YhiQ {Shigella flexneri [TaxId: 623]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: YhiQ-like
domain: Hypothetical protein YhiQ
species: Shigella flexneri [TaxId: 623]

Probab=83.85  E-value=0.56  Score=35.94  Aligned_cols=72  Identities=14%  Similarity=0.199  Sum_probs=50.1

Q ss_pred             HHHHhcccccC--cceEEEecCCccHHHHHHHHHcCCCcEEEeechHHHh--------hccCC--------CCceEEecC
Q 039903          158 RIIDSSKGFEQ--IKQLVDVGGGLGVNVNIIISNYLHIKGVNFDLSHVIQ--------DSSSY--------SGVKHIGGI  219 (233)
Q Consensus       158 ~~~~~~~~~~~--~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~--------~a~~~--------~ri~~~~gD  219 (233)
                      .++++.. ++.  ..+|+|.-+|.|..+..++...  .+++.++...++.        .+...        .|++++.+|
T Consensus        77 ~l~kA~g-l~~~~~~~VlD~TaGlG~Da~vlA~~G--~~V~~iEr~p~l~~ll~d~l~r~~~~~~~~~~~~~ri~li~~D  153 (250)
T d2oyra1          77 AVAKAVG-IKGDYLPDVVDATAGLGRDAFVLASVG--CRVRMLERNPVVAALLDDGLARGYADAEIGGWLQERLQLIHAS  153 (250)
T ss_dssp             HHHHHTT-CBTTBCCCEEETTCTTCHHHHHHHHHT--CCEEEEECCHHHHHHHHHHHHHHHHCTTTHHHHHHHEEEEESC
T ss_pred             HHHHHhc-CCCCCCCEEEECCCcccHHHHHHHhCC--CEEEEEccCHHHHHHHHHHHHHHHhCchhHHHHhhhheeecCc
Confidence            4555554 443  3589999999999999999884  6799999865432        22111        489999999


Q ss_pred             cCC---CCCC-CCEEEe
Q 039903          220 MLE---RIPK-GDAILI  232 (233)
Q Consensus       220 ~f~---~~P~-~D~~~l  232 (233)
                      ..+   .... .|+|+|
T Consensus       154 s~~~L~~~~~~~DvIYl  170 (250)
T d2oyra1         154 SLTALTDITPRPQVVYL  170 (250)
T ss_dssp             HHHHSTTCSSCCSEEEE
T ss_pred             HHHHHhccCCCCCEEEE
Confidence            766   2222 399876

>d2dk5a1 a.4.5.85 (A:8-85) DNA-directed RNA polymerase III subunit RPC6, RPO3F {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: RPO3F domain-like
domain: DNA-directed RNA polymerase III subunit RPC6, RPO3F
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.71  E-value=0.83  Score=28.32  Aligned_cols=45  Identities=20%  Similarity=0.389  Sum_probs=40.8

Q ss_pred             hhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhcCCceeee
Q 039903           21 VFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVTHRVLRCT   70 (233)
Q Consensus        21 lfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~~gll~~~   70 (233)
                      |++++..+|. .++...+|-.++++    +...+.+.|+.|.+.+++...
T Consensus        18 VY~~I~~ag~-~GIW~~dir~ktnL----~~~~l~K~LK~Lesk~lIK~V   62 (78)
T d2dk5a1          18 VYQIIEDAGN-KGIWSRDVRYKSNL----PLTEINKILKNLESKKLIKAV   62 (78)
T ss_dssp             HHHHHHHHCT-TCEEHHHHHHHTTC----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHccc-cceeHHHHHHHcCC----CHHHHHHHHHHHHhcCCceee
Confidence            7788888764 48999999999999    999999999999999999986

>d1mzba_ a.4.5.42 (A:) Ferric uptake regulation protein, FUR {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: FUR-like
domain: Ferric uptake regulation protein, FUR
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=83.03  E-value=0.62  Score=31.84  Aligned_cols=64  Identities=9%  Similarity=0.201  Sum_probs=44.4

Q ss_pred             HhhChhHHHHhcCCCCCCCHHHHHHhCCCC-CCCChhhHHHHHHHHhcCCceeeeccCCCCCceec
Q 039903           17 SELGVFEIIAKAGPTAKISAVEIAAQMPSS-NPNAAVMLDRILRLLVTHRVLRCTSAGDDQRLYGL   81 (233)
Q Consensus        17 ~~lglfd~L~~~~~~~~~t~~elA~~~~~~-~~~~~~~l~rlL~~L~~~gll~~~~~~~~~~~y~l   81 (233)
                      -+.-|++.|...+ ..+.|+.||-+.+.-. +..+..-++|.|+.|+..|++.+...+++..+|..
T Consensus        17 qR~~Il~~L~~~~-~~h~sa~ei~~~l~~~~~~i~~aTVYR~L~~l~e~gli~~~~~~~~~~~y~~   81 (134)
T d1mzba_          17 PRVKILQMLDSAE-QRHMSAEDVYKALMEAGEDVGLATVYRVLTQFEAAGLVVRHNFDGGHAVFEL   81 (134)
T ss_dssp             HHHHHHHHHHCC--CCSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSEEEECSSSSSCEEEE
T ss_pred             HHHHHHHHHHhCC-CCCCCHHHHHHHHHHhCCCccHHHHHHHHHHHHhccEEEEEeecCCceEEEe
Confidence            3556889997642 1389999998887531 12277789999999999999998754323334443

>d1xmaa_ a.4.5.61 (A:) Predicted transcriptional regulator {Clostridium thermocellum [TaxId: 1515]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PadR-like
domain: Predicted transcriptional regulator
species: Clostridium thermocellum [TaxId: 1515]

Probab=81.68  E-value=0.69  Score=30.20  Aligned_cols=66  Identities=9%  Similarity=0.117  Sum_probs=44.0

Q ss_pred             hhHHHHhcCCCCCCCHHHHHHhCCCC----CCCChhhHHHHHHHHhcCCceeeeccCCCC----CceeccHhhhHhhc
Q 039903           21 VFEIIAKAGPTAKISAVEIAAQMPSS----NPNAAVMLDRILRLLVTHRVLRCTSAGDDQ----RLYGLAHVAKYFVL   90 (233)
Q Consensus        21 lfd~L~~~~~~~~~t~~elA~~~~~~----~~~~~~~l~rlL~~L~~~gll~~~~~~~~~----~~y~lt~~s~~l~~   90 (233)
                      |...|.+    +|.+--||.+.+...    -+.++..++..|+-|...|+++......++    ..|++|+.|+..+.
T Consensus        12 IL~lL~~----~~~~GYei~~~l~~~~~~~~~is~gslY~~L~rLe~~GlI~~~~~~~~~g~~rk~Y~iT~~G~~~l~   85 (103)
T d1xmaa_          12 ILSLLIE----GDSYGYEISKNIRIKTDELYVIKETTLYSAFARLEKNGYIKSYYGEETQGKRRTYYRITPEGIKYYK   85 (103)
T ss_dssp             HHHHHHH----CCEEHHHHHHHHHHHHTTSCCCCHHHHHHHHHHHHHTTSEEEEEEEEC--CEEEEEEECHHHHHHHH
T ss_pred             HHHHHhh----CCccHHHHHHHHHHHcCCeecCCCCchHHHHHHHHHCCCeEEEeeccCCCCCceEEEECHHHHHHHH
Confidence            4445665    478888888765310    011889999999999999999843211012    24999999986543

>d1ixca1 a.4.5.37 (A:1-89) LysR-type regulatory protein CbnR {Ralstonia eutropha [TaxId: 106590]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: LysR-like transcriptional regulators
domain: LysR-type regulatory protein CbnR
species: Ralstonia eutropha [TaxId: 106590]

Probab=80.17  E-value=0.86  Score=28.80  Aligned_cols=60  Identities=18%  Similarity=0.201  Sum_probs=46.1

Q ss_pred             hhChhHHHHhcCCCCCCCHHHHHHhCCCCCCCChhhHHHHHHHHhc---CCceeeeccCCCCCceeccHhhhHhhcC
Q 039903           18 ELGVFEIIAKAGPTAKISAVEIAAQMPSSNPNAAVMLDRILRLLVT---HRVLRCTSAGDDQRLYGLAHVAKYFVLN   91 (233)
Q Consensus        18 ~lglfd~L~~~~~~~~~t~~elA~~~~~~~~~~~~~l~rlL~~L~~---~gll~~~~~~~~~~~y~lt~~s~~l~~~   91 (233)
                      +|.+|-.+.+.     -++..-|+.+++    ++..+.+-++.|..   .-+|.+.     ...+.+|+.+..|...
T Consensus         5 ~L~~f~~v~e~-----gs~~~AA~~L~i----sq~avs~~i~~LE~~lg~~Lf~R~-----~~~~~lT~~G~~l~~~   67 (89)
T d1ixca1           5 QLKYFIAVAEA-----GNMAAAAKRLHV----SQPPITRQMQALEADLGVVLLERS-----HRGIELTAAGHAFLED   67 (89)
T ss_dssp             HHHHHHHHHHH-----SSHHHHHHHHTC----CHHHHHHHHHHHHHHHTSCCBC----------CCBCHHHHHHHHH
T ss_pred             HHHHHHHHHHh-----CCHHHHHHHhCC----ChHHHHHHHHHHHhcCCceeeEec-----CCccCccHhHHHHHHH
Confidence            56788888885     489999999999    99999888877765   7889884     6779999999988754