Citrus Sinensis ID: 040620

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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----
Protein Sequence
MDVIHGENGAREHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISLQLQGSTILLLIADATFTTSFHFLSTWLQNDDQTLFGTADGIFYEAMITDFELIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACHL
Secondary Structure (PSIPRED)
cccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHccccccHHHHHHHcccccccccHHHHHHHHHHHHcccEEEcccccccccccccccccccHHHHccccccHHHHHHHHcccccHHccccccccccccccccccccccccHHHHHHHcHHHHHHHHHHHHHHccccccEEEEccccHHHHHHHHHHccccEEEEccccc
Secondary Structure Prediction (SSPRO)
cccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHccccccHHHHHHHccccccccHHHHHHHHHHHHcccEEEEEccccccccEEEEEcHHHHHHccccccccHHHHHHHHcccHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHccHHHHHHHHHHHHHcHHccccEEEEccccHHHHHHHHHHHccccEEEEEEEEc
Coil and Loop (DISEMBL)
mdvihgengareHFQAQAQVWSYTYNYMKSLSLKRAIQLRipdiinnsgqpmTLTQIIVALnvhpnktrCTQILVCLLAHsgffvqqkdgkneqeeesillpphldffSRISLQLQGSTILLLIADATFTTSFHFLSTwlqnddqtlfgtADGIFYEAMITDFELIASVLIEDCnevskglkplvdvggstGTMARAIAtafpdtkctvfachl
Flexible Loop (DISEMBL)
mdvihgengarehfqAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISLQLQGSTILLLIADATFTTSFHFLSTWLQNDDQTLFGTADGIFYEAMITDFELIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACHL
Low Complexity Region (SEG)
MDVIHGENGAREHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISLQLQGSTILLLIADATFTTSFHFLSTWLQNDDQTLFGTADGIFYEAMITDFELIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACHL
Disordered region (IsUnstruct)
*************FQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQ************ILLPPHLDFFSRISLQLQGSTILLLIADATFTTSFHFLSTWLQNDDQTLFGTADGIFYEAMITDFELIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC**
Disordered Region (DISOPRED)
***************AQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISLQLQGSTILLLIADATFTTSFHFLSTWLQNDDQTLFGTADGIFYEAMITDFELIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACHL
Disordered Region (DISEMBL)
MDVIHGENGAREHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ**********SILLPPHLDFFSRISLQLQGSTILLLIADATFTTSFHFLSTWLQNDDQTLFGTADGIFYEAMITDFELIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACHL
Disordered Region (DISPRO)
********GAREHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISLQLQGSTILLLIADATFTTSFHFLSTWLQNDDQTLFGTADGIFYEAMITDFELIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACHL
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDVIHGENGAREHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISLQLQGSTILLLIADATFTTSFHFLSTWLQNDDQTLFGTADGIFYEAMITDFELIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACHL
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	214	2.2.26 [Sep-21-2011]
B6VJS4	357	Trans-resveratrol di-O-me	no	no	0.967	0.579	0.413	1e-40
Q93WU2	357	Eugenol O-methyltransfera	N/A	no	0.901	0.540	0.377	7e-32
Q93WU3	356	Chavicol O-methyltransfer	N/A	no	0.887	0.533	0.379	2e-31
B0EXJ8	355	Tabersonine 16-O-methyltr	N/A	no	0.911	0.549	0.4	1e-29
O22308	352	Isoflavone-7-O-methyltran	N/A	no	0.915	0.556	0.354	5e-27
O24529	352	Isoflavone-7-O-methyltran	N/A	no	0.915	0.556	0.354	5e-27
Q84KK5	357	Isoflavone 7-O-methyltran	N/A	no	0.939	0.563	0.318	5e-27
O22309	352	Isoflavone-7-O-methyltran	N/A	no	0.915	0.556	0.354	1e-26
Q6VMW0	366	8-hydroxyquercetin 8-O-me	N/A	no	0.976	0.571	0.372	2e-26
O24305	360	6a-hydroxymaackiain methy	N/A	no	0.920	0.547	0.336	2e-25

>sp|B6VJS4|ROMT_VITVI Trans-resveratrol di-O-methyltransferase OS=Vitis vinifera GN=ROMT PE=1 SV=2

 Score =  166 bits (420), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 93/225 (41%), Positives = 131/225 (58%), Gaps = 18/225 (8%)

Query: 1   MDVIHGENGAREHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVA 60
           MD+ +G   A E   AQA VW++ +N++KS+SLK AIQL IPDII+N G+PMTL +++  
Sbjct: 1   MDLANGVISA-ELLHAQAHVWNHIFNFIKSMSLKCAIQLGIPDIIHNHGKPMTLPELVAK 59

Query: 61  LNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISLQLQGSTI 120
           L VHP +++C   L+ +L HSGF   Q+  + ++EE  +L           SL ++   +
Sbjct: 60  LPVHPKRSQCVYRLMRILVHSGFLAAQRVQQGKEEEGYVLTDASRLLLMDDSLSIR--PL 117

Query: 121 LLLIADATFTTSFHFLSTWLQNDDQTLFGTA---------------DGIFYEAMITDFEL 165
           +L + D   T  +H+LS W QNDD T F TA               +  F EAM +D  L
Sbjct: 118 VLAMLDPILTKPWHYLSAWFQNDDPTPFHTAYERSFWDYAGHEPQLNNSFNEAMASDARL 177

Query: 166 IASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
           + SVL+++   V  GL  LVDVGG TG +A+AIA AFP   CTV 
Sbjct: 178 LTSVLLKEGQGVFAGLNSLVDVGGGTGKVAKAIANAFPHLNCTVL 222

Catalyzes the biosynthesis of pterostilbene from resveratrol. Pterostilbene has both antifungal and pharmacological properties. Also has activity toward resveratrol monomethyl ether (RME).
Vitis vinifera (taxid: 29760)
EC: 2EC: .EC: 1EC: .EC: 1EC: .EC: 2EC: 4EC: 0

>sp|Q93WU2|EOMT1_OCIBA Eugenol O-methyltransferase OS=Ocimum basilicum GN=EOMT1 PE=1 SV=1

 Score =  137 bits (344), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 80/212 (37%), Positives = 117/212 (55%), Gaps = 19/212 (8%)

Query: 14  FQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQI 73
            QAQ  VW++ Y +  S+SLK AIQL IPDI++  G+PMTL+Q++ ++ ++  KT+C Q 
Sbjct: 16  LQAQVHVWNHMYAFANSMSLKCAIQLGIPDILHKHGRPMTLSQLLQSIPINKEKTQCFQR 75

Query: 74  LVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISLQLQGSTILLLIADATFTTSF 133
           L+  L +S FF+++ +  N QE    L P          L +  + ++ ++ D TFT  +
Sbjct: 76  LMRALVNSNFFIEENNSNN-QEVCYWLTPASCLLLKEAPLTV--TPLVQVVLDPTFTNPW 132

Query: 134 HFLSTWLQNDDQ-TLFGTADG---------------IFYEAMITDFELIASVLIEDCNEV 177
           H +S W  ++   T F  A+G                F EAM  D  LIA V  +D   V
Sbjct: 133 HHMSEWFTHEKHATQFEAANGCTFWEKLANEPSKGRFFDEAMSCDSRLIAHVFTKDYKHV 192

Query: 178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTV 209
            +G++ LVDVGG  GTMA+AI  A P  KCTV
Sbjct: 193 IEGIRTLVDVGGGNGTMAKAIVEAMPTIKCTV 224

Phenylpropene O-methyltransferase that catalyzes the methylation of the para-4-hydroxyl of eugenol to methyleugenol. Can also convert chavicol to methylchavicol but with less affinity.

Ocimum basilicum (taxid: 39350)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 1

EC: 4

EC: 6

>sp|Q93WU3|CVMT1_OCIBA Chavicol O-methyltransferase OS=Ocimum basilicum GN=CVOMT1 PE=1 SV=1

 Score =  135 bits (340), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 82/216 (37%), Positives = 121/216 (56%), Gaps = 26/216 (12%)

Query: 14  FQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQI 73
            QAQA VW++ Y +  S+SLK AIQL IPDI++    PMTL+Q++ A+ ++  K++  Q 
Sbjct: 16  LQAQAHVWNHMYAFANSMSLKCAIQLGIPDILHKHDHPMTLSQLLKAIPINKEKSQSFQR 75

Query: 74  LVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISLQ---LQGSTILLLIADATFT 130
           L+  L +S FF+++    N QE    L P      SR+ L+   L  + ++ ++ D TFT
Sbjct: 76  LMRALVNSNFFIEE--NSNNQEVCYWLTPA-----SRLLLKGAPLTVAPLVQVVLDPTFT 128

Query: 131 TSFHFLSTWLQNDDQ-TLFGTADG---------------IFYEAMITDFELIASVLIEDC 174
             +H++S W ++++  T F  A+G                F EAM  D  L+A VL +D 
Sbjct: 129 NPWHYMSEWFKHENHATQFEAANGCTFWEKLANKPSMGRFFDEAMSCDSRLVAHVLTKDY 188

Query: 175 NEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
             V  G++ LVDVGG  GTMA+AI  A P  KCTV 
Sbjct: 189 KHVIDGIRTLVDVGGGNGTMAKAIVEAVPTMKCTVL 224

Phenylpropene O-methyltransferase that catalyzes the methylation of the para-4-hydroxyl of chavicol to methylchavicol. Can also convert eugenol to methyleugenol but with less affinity.

Ocimum basilicum (taxid: 39350)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 1

EC: 4

EC: 6

>sp|B0EXJ8|HTOMT_CATRO Tabersonine 16-O-methyltransferase OS=Catharanthus roseus GN=16OMT PE=1 SV=1

 Score =  129 bits (325), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 88/220 (40%), Positives = 126/220 (57%), Gaps = 25/220 (11%)

Query: 12  EHFQ-AQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVAL--NVHPNKT 68
           E F+ AQAQ+WS + +++ S SLK A++L IPD I+N G+P+TL+++  AL   VHP+K 
Sbjct: 6   EEFRGAQAQIWSQSCSFITSASLKCAVKLGIPDTIDNHGKPITLSELTNALVPPVHPSKA 65

Query: 69  RCTQILVCLLAHSGFFVQQK-DGKNEQEEESILLPPHLDFFSRISLQLQGSTILLLIADA 127
                L+ +LA +GF  +++ DG  E E    L P       +  L L+G  I+L +AD 
Sbjct: 66  PFIYRLMRVLAKNGFCSEEQLDG--ETEPLYSLTPSSRILLKKEPLNLRG--IVLTMADP 121

Query: 128 TFTTSFHFLSTWLQNDD--QTLFGTADG---------------IFYEAMITDFELIASVL 170
               ++  LS W QN+D   T F TA G                F EAM +D +LI+ +L
Sbjct: 122 VQLKAWESLSDWYQNEDDSSTAFETAHGKNFWGYSSEHMEHAEFFNEAMASDSQLISKLL 181

Query: 171 IEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
           I +   + +GL  LVD+GG TGT+A+AIA  FP  KCTVF
Sbjct: 182 IGEYKFLFEGLASLVDIGGGTGTIAKAIAKNFPQLKCTVF 221

16-O-methyltransferase involved in the biosynthesis of vindoline. Highly specific for 16-hydroxytabersonine. No activity with tabersonine, 3-hydroxytyramine, 4-hydroxytyramine, 5-hydroxytryptamine (5HT), 2,3-dihydro-3-hydroxytabersonine, lochnericine, hoerhammericine, 16-hydroxy-2,3-dihydro-3-hydroxytabersonine, 16-hydroxylochnericine, 16-hydroxyhoerhammericine, quercetin, kaempferol and caffeic acid as substrates.

Catharanthus roseus (taxid: 4058)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 9

EC: 4

>sp|O22308|7OMT6_MEDSA Isoflavone-7-O-methyltransferase 6 OS=Medicago sativa PE=2 SV=1

 Score =  120 bits (302), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 78/220 (35%), Positives = 120/220 (54%), Gaps = 24/220 (10%)

Query: 8   NGAR--EHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHP 65
           NG +  E F+AQA ++ + Y ++ S+SLK A+++ IP+II N G+P++L+ ++  L V  
Sbjct: 6   NGRKPSEIFKAQALLYKHIYAFIDSMSLKWAVEMNIPNIIQNHGKPISLSNLVSILQVPS 65

Query: 66  NKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISLQLQGSTILLLIA 125
           +K    + L+  LAH+GFF         +EEES  L    +   R S  L  + ++  + 
Sbjct: 66  SKIGNVRRLMRYLAHNGFFEIIT-----KEEESYALTVASELLVRGS-DLCLAPMVECVL 119

Query: 126 DATFTTSFHFLSTWLQNDDQTLFGTADG---------------IFYEAMITDFELIASVL 170
           D T + S+H L  W+  +D TLFG   G                F +AM +D +LI ++ 
Sbjct: 120 DPTLSGSYHELKKWIYEEDLTLFGVTLGSGFWDFLDKNPEYNTSFNDAMASDSKLI-NLA 178

Query: 171 IEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
           + DC+ V  GL+ +VDVGG TGT A+ I   FP  KC VF
Sbjct: 179 LRDCDFVFDGLESIVDVGGGTGTTAKIICETFPKLKCIVF 218

Transfers a methyl group to 7-hydroxyls of the isoflavones daidzein, genistein and 6,7,4'-trihydroxyisoflavone. Can also methylate (+)6a-hydroxymaackiain with lower efficiency.

Medicago sativa (taxid: 3879)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 1

EC: 5

EC: 0

>sp|O24529|7OMT8_MEDSA Isoflavone-7-O-methyltransferase 8 OS=Medicago sativa PE=1 SV=1

 Score =  120 bits (302), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 78/220 (35%), Positives = 120/220 (54%), Gaps = 24/220 (10%)

Query: 8   NGAR--EHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHP 65
           NG +  E F+AQA ++ + Y ++ S+SLK A+++ IP+II N G+P++L+ ++  L V  
Sbjct: 6   NGRKPSEIFKAQALLYKHIYAFIDSMSLKWAVEMNIPNIIQNHGKPISLSNLVSILQVPS 65

Query: 66  NKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISLQLQGSTILLLIA 125
           +K    + L+  LAH+GFF         +EEES  L    +   R S  L  + ++  + 
Sbjct: 66  SKIGNVRRLMRYLAHNGFFEIIT-----KEEESYALTVASELLVRGS-DLCLAPMVECVL 119

Query: 126 DATFTTSFHFLSTWLQNDDQTLFGTADG---------------IFYEAMITDFELIASVL 170
           D T + S+H L  W+  +D TLFG   G                F +AM +D +LI ++ 
Sbjct: 120 DPTLSGSYHELKKWIYEEDLTLFGVTLGSGFWDFLDKNPEYNTSFNDAMASDSKLI-NLA 178

Query: 171 IEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
           + DC+ V  GL+ +VDVGG TGT A+ I   FP  KC VF
Sbjct: 179 LRDCDFVFDGLESIVDVGGGTGTTAKIICETFPKLKCIVF 218

Transfers a methyl group to 7-hydroxyls of the isoflavones daidzein, genistein and 6,7,4'-trihydroxyisoflavone. Can also methylate (+)6a-hydroxymaackiain with lower efficiency.

Medicago sativa (taxid: 3879)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 1

EC: 5

EC: 0

>sp|Q84KK5|D7OMT_GLYEC Isoflavone 7-O-methyltransferase OS=Glycyrrhiza echinata GN=D7OMT PE=1 SV=1

 Score =  120 bits (302), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 70/220 (31%), Positives = 123/220 (55%), Gaps = 19/220 (8%)

Query: 8   NGAR--EHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHP 65
           NG +  E FQ QA ++ + Y ++ S+ LK  ++L IP+II+N G+P+T+++++  L V  
Sbjct: 6   NGRKPSEIFQGQALLYRHIYAFIDSMCLKWIVELDIPNIIHNHGKPITVSELVSILKVPQ 65

Query: 66  NKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISLQLQGSTILLLIA 125
            K    Q ++  +AH+GFF + +  + ++E E+  L    +   + S +L  + ++  + 
Sbjct: 66  TKAGNVQRIMRYMAHNGFFERVRIQEEQEENEAYALTAASELLVKGS-ELCLAPMVECVL 124

Query: 126 DATFTTSFHFLSTWLQNDDQTLFGTADG---------------IFYEAMITDFELIASVL 170
           D T + S+H L  W+  +D TLFG + G                F +AM +D ++I ++ 
Sbjct: 125 DPTLSGSYHQLKKWIYEEDLTLFGVSLGSHFWEFLNENPEYNKSFNDAMASDSQMI-NLA 183

Query: 171 IEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
           + DCN   +G++ +VDVGG  GT A+ I   FP+ KC VF
Sbjct: 184 LRDCNSGFEGVESIVDVGGGIGTTAKIICDTFPNLKCIVF 223

7-O-methyltransferase involved in the biosynthesis of isoformononetin. Can use daidzein as substrate, but not medicarpin or 2,7,4'-trihydroxyisoflavanone.

Glycyrrhiza echinata (taxid: 46348)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 1

EC: 5

EC: 0

>sp|O22309|7OMT9_MEDSA Isoflavone-7-O-methyltransferase 9 OS=Medicago sativa PE=2 SV=1

 Score =  119 bits (299), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 78/220 (35%), Positives = 120/220 (54%), Gaps = 24/220 (10%)

Query: 8   NGAR--EHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHP 65
           NG +  E F+AQA ++ + Y ++ S+SLK A+ + IP+II+N G+P++L+ ++  L V  
Sbjct: 6   NGRKPSEIFKAQALLYKHIYAFIDSMSLKWAVGMNIPNIIHNHGKPISLSNLVSILQVPS 65

Query: 66  NKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISLQLQGSTILLLIA 125
           +K    + L+  LAH+GFF         +EEES  L    +   R S  L  + ++  + 
Sbjct: 66  SKIGNVRRLMRYLAHNGFFEIIT-----KEEESYALTVASELLVRGS-DLCLAPMVECVL 119

Query: 126 DATFTTSFHFLSTWLQNDDQTLFGTADG---------------IFYEAMITDFELIASVL 170
           D T + S+H L  W+  +D TLFG   G                F +AM +D +LI ++ 
Sbjct: 120 DPTLSGSYHELKKWIYEEDLTLFGVTLGSGFWDFLDKNPEYNTSFNDAMASDSKLI-NLA 178

Query: 171 IEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
           + DC+ V  GL+ +VDVGG TGT A+ I   FP  KC VF
Sbjct: 179 LRDCDFVFDGLESIVDVGGGTGTTAKIICETFPKLKCIVF 218

Transfers a methyl group to 7-hydroxyls of the isoflavones daidzein, genistein and 6,7,4'-trihydroxyisoflavone. Can also methylate (+)6a-hydroxymaackiain with lower efficiency.

Medicago sativa (taxid: 3879)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 1

EC: 5

EC: 0

>sp|Q6VMW0|Q8OMT_MENPI 8-hydroxyquercetin 8-O-methyltransferase OS=Mentha piperita GN=OMT2 PE=1 SV=1

 Score =  119 bits (297), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 86/231 (37%), Positives = 126/231 (54%), Gaps = 22/231 (9%)

Query: 1   MDVIHGENGAREHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVA 60
           M + +G +  +E  +AQA VW++ Y+Y+ S+SLK AIQL IPD I+  G P+TL+Q+  A
Sbjct: 1   MALPNGISSKQELLEAQAHVWNHIYSYINSMSLKCAIQLGIPDAIHKHGNPITLSQLADA 60

Query: 61  LNVHPNKTRCTQILVCLLAHSGFF------VQQKDGKNEQEEESILLPPHLDFFSRISLQ 114
           LN++  K+     L+ +L HSGFF      V+ +    E+EE++  L P      R S  
Sbjct: 61  LNINKAKSHGLFRLMRILVHSGFFDKVKVKVKVEGEDEEEEEDAYSLTPASRLLLR-SEP 119

Query: 115 LQGSTILLLIADATFTTSFHFLSTWLQNDDQTLFGTADG---------------IFYEAM 159
           L  +   L ++D  +T ++H LS W +ND    F T  G               +F EAM
Sbjct: 120 LSVAPFALAMSDPVYTETWHHLSEWFRNDAVAAFDTKYGMTFPEYAVADDRLNVLFNEAM 179

Query: 160 ITDFELIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
             D   + S+L  +C E+  GL+ +VDVGG TG  A+ IA AFP  +CTV 
Sbjct: 180 ACDAGFVNSILTTECREIFDGLESMVDVGGGTGATAKGIAAAFPGMECTVL 230

8-O-methyltransferase active on various hydroxylated flavonoid substrates, including 7,8,3'4'-tetrahydroxy-flavone, 7,8,4'-trihydroxy-flavone and 8-hydroxy-flavone 7-methyl ether.

Mentha piperita (taxid: 34256)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 8

EC: 8

>sp|O24305|M3OM1_PEA 6a-hydroxymaackiain methyltransferase 1 OS=Pisum sativum GN=HMM1 PE=1 SV=1

 Score =  115 bits (288), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 76/226 (33%), Positives = 117/226 (51%), Gaps = 29/226 (12%)

Query: 8   NGAREH--FQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHP 65
           NG+ E   + AQ  ++ + YN++ S++LK A++L I D I+N G+PMTL ++  +L +HP
Sbjct: 6   NGSEESELYHAQIHLYKHVYNFVSSMALKSAMELGIADAIHNHGKPMTLPELSSSLKLHP 65

Query: 66  NKTRCTQILVCLLAHSGFFVQQKDGKNEQEEES--ILLPPHLDFFSRISLQLQGSTILLL 123
           +K       + LL H+GFF +     NE EEE+  +L P      S++ +  + + +  L
Sbjct: 66  SKVNILYRFLRLLTHNGFFAKTTVKSNEGEEETAYVLTPS-----SKLLVSGKSTCLSSL 120

Query: 124 IADATFTTSFHFLST---WLQND-DQTLFGTADG---------------IFYEAMITDFE 164
           +  A   +S         W   D +QTLF  A G               +F +AM  D  
Sbjct: 121 VKGALHPSSLDMWGVSKKWFHEDKEQTLFECATGENYWDFLNKDSDSLSMFQDAMAADSR 180

Query: 165 LIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
           L   + I++   V +GL+ LVDV G TG +A+ I  AFP  KCTVF
Sbjct: 181 LF-KLAIQENKHVFEGLESLVDVAGGTGGVAKLIHEAFPHIKCTVF 225

Methyltransferase involved in the phytoalexin pisatin biosynthesis. Has both 3- and 4'-O-methyltransferase activities. Can use (+)-6a-hydroxymaackiain, 2,7,4'-trihydroxyisoflavanone and with much less activity (+)-medicarpin as substrates, but not (-)-6a-hydroxymaackiain, daidzein, formononetin or isoliquiritigenin. May be involved in formononetin biosynthesis.

Pisum sativum (taxid: 3888)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 4

EC: 6

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	214
225446487	357	PREDICTED: tabersonine 16-O-methyltransf	0.953	0.571	0.451	9e-44
359485253	351	PREDICTED: tabersonine 16-O-methyltransf	0.953	0.581	0.451	1e-43
225446491	357	PREDICTED: 8-hydroxyquercetin 8-O-methyl	0.915	0.549	0.452	4e-43
147826879	357	hypothetical protein VITISV_021917 [Viti	0.953	0.571	0.447	1e-42
147816431	357	hypothetical protein VITISV_020020 [Viti	0.915	0.549	0.447	1e-42
255568369	356	o-methyltransferase, putative [Ricinus c	0.934	0.561	0.430	6e-42
359485251	357	PREDICTED: tabersonine 16-O-methyltransf	0.962	0.577	0.434	3e-41
225446485	356	PREDICTED: tabersonine 16-O-methyltransf	0.920	0.553	0.447	5e-41
225454044	358	PREDICTED: tabersonine 16-O-methyltransf	0.971	0.581	0.453	2e-40
359485261	357	PREDICTED: tabersonine 16-O-methyltransf	0.967	0.579	0.426	2e-40

>gi|225446487|ref|XP_002278149.1| PREDICTED: tabersonine 16-O-methyltransferase isoform 1 [Vitis vinifera]

 Score =  182 bits (461), Expect = 9e-44,   Method: Compositional matrix adjust.
 Identities = 103/228 (45%), Positives = 139/228 (60%), Gaps = 24/228 (10%)

Query: 1   MDVIHGENGAREHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVA 60
           MDV  G+  A    QAQA VW++T N++ S++LK A++L IPD INN GQP+TL++++ A
Sbjct: 1   MDVGSGKR-ASLLLQAQAHVWNHTMNFVNSMALKCAVRLGIPDAINNHGQPITLSELVTA 59

Query: 61  LNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISLQLQ---G 117
           L+++P K  C   L+ +L HSGFF QQ+   NEQE+        L + SR  L+ +   G
Sbjct: 60  LSINPIKAPCLHRLMRVLVHSGFFAQQQADHNEQEQLY-----SLTYASRFLLKDEPTSG 114

Query: 118 STILLLIADATFTTSFHFLSTWLQNDDQTLFGTADG---------------IFYEAMITD 162
           + +LL+  D   T   HFLS W +N D T F TA G                F EAM +D
Sbjct: 115 APLLLVQVDPHLTNPCHFLSDWFRNSDPTPFVTAYGKPFWDYAAHEPKFNNFFNEAMASD 174

Query: 163 FELIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
            +LIASV++ +C EV +GL  L+DVGG TGTMA+ IA AFP  KCTVF
Sbjct: 175 SQLIASVVVGECKEVFRGLSSLIDVGGGTGTMAKVIAKAFPHLKCTVF 222

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359485253|ref|XP_003633246.1| PREDICTED: tabersonine 16-O-methyltransferase isoform 2 [Vitis vinifera]

 Score =  182 bits (461), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 103/228 (45%), Positives = 139/228 (60%), Gaps = 24/228 (10%)

Query: 1   MDVIHGENGAREHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVA 60
           MDV  G+  A    QAQA VW++T N++ S++LK A++L IPD INN GQP+TL++++ A
Sbjct: 1   MDVGSGKR-ASLLLQAQAHVWNHTMNFVNSMALKCAVRLGIPDAINNHGQPITLSELVTA 59

Query: 61  LNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISLQLQ---G 117
           L+++P K  C   L+ +L HSGFF QQ+   NEQE+        L + SR  L+ +   G
Sbjct: 60  LSINPIKAPCLHRLMRVLVHSGFFAQQQADHNEQEQLY-----SLTYASRFLLKDEPTSG 114

Query: 118 STILLLIADATFTTSFHFLSTWLQNDDQTLFGTADG---------------IFYEAMITD 162
           + +LL+  D   T   HFLS W +N D T F TA G                F EAM +D
Sbjct: 115 APLLLVQVDPHLTNPCHFLSDWFRNSDPTPFVTAYGKPFWDYAAHEPKFNNFFNEAMASD 174

Query: 163 FELIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
            +LIASV++ +C EV +GL  L+DVGG TGTMA+ IA AFP  KCTVF
Sbjct: 175 SQLIASVVVGECKEVFRGLSSLIDVGGGTGTMAKVIAKAFPHLKCTVF 222

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225446491|ref|XP_002278211.1| PREDICTED: 8-hydroxyquercetin 8-O-methyltransferase [Vitis vinifera]

 Score =  180 bits (456), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 99/219 (45%), Positives = 130/219 (59%), Gaps = 23/219 (10%)

Query: 10  AREHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTR 69
           + E   AQA VW++ +N++ S+SLK AIQL IPDII+N G+PMTL +++  L +HP K  
Sbjct: 9   SSELLHAQAHVWNHIFNFINSMSLKCAIQLGIPDIIHNHGKPMTLPELVAKLPIHPKKVW 68

Query: 70  CTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISLQ---LQGSTILLLIAD 126
           C   L+ +L  SGFF +QK  ++EQEE  +     L   SR+ L+   L     LL + D
Sbjct: 69  CVYRLMRILVQSGFFARQKVEESEQEEGYV-----LTHASRLLLEDDPLSVRPFLLAMLD 123

Query: 127 ATFTTSFHFLSTWLQNDDQTLFGTADG---------------IFYEAMITDFELIASVLI 171
              T  +H++S W QNDD T F TA G                F EAM +D  L+ SVLI
Sbjct: 124 PILTKPWHYVSAWFQNDDPTPFDTAHGRTFWDYGGHEPKINNFFNEAMASDARLVTSVLI 183

Query: 172 EDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
           +DC  V +GL  LVDVGG TGT+A+AIA AFP   CTVF
Sbjct: 184 KDCKGVFEGLNSLVDVGGGTGTVAKAIANAFPHLNCTVF 222

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147826879|emb|CAN73269.1| hypothetical protein VITISV_021917 [Vitis vinifera]

 Score =  178 bits (452), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 102/228 (44%), Positives = 138/228 (60%), Gaps = 24/228 (10%)

Query: 1   MDVIHGENGAREHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVA 60
           MDV  G+  A    QAQA VW++T N++ S++LK A++L IPD INN GQP+TL++++ A
Sbjct: 1   MDVGSGKR-ASLLLQAQAHVWNHTMNFVNSMALKCAVRLGIPDAINNHGQPITLSELVTA 59

Query: 61  LNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISLQLQ---G 117
           L+++P K  C   L+ +L  SGFF QQ+   NEQE+        L + SR  L+ +   G
Sbjct: 60  LSINPIKAPCLHRLMRVLVXSGFFAQQQADHNEQEQLY-----SLTYASRFLLKDEPTSG 114

Query: 118 STILLLIADATFTTSFHFLSTWLQNDDQTLFGTADG---------------IFYEAMITD 162
           + +LL+  D   T   HFLS W +N D T F TA G                F EAM +D
Sbjct: 115 APLLLVQVDPHLTNPCHFLSDWFRNSDPTPFVTAYGKPFWDYAAHEPKFNNFFNEAMASD 174

Query: 163 FELIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
            +LIASV++ +C EV +GL  L+DVGG TGTMA+ IA AFP  KCTVF
Sbjct: 175 SQLIASVVVGECKEVFRGLSSLIDVGGGTGTMAKVIAKAFPHLKCTVF 222

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147816431|emb|CAN61955.1| hypothetical protein VITISV_020020 [Vitis vinifera]

 Score =  178 bits (451), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 98/219 (44%), Positives = 129/219 (58%), Gaps = 23/219 (10%)

Query: 10  AREHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTR 69
           + E   AQA VW++ +N++ S+SLK AIQL IPDII+N G+PMTL +++  L +HP K  
Sbjct: 9   SSELLHAQAHVWNHIFNFINSMSLKCAIQLGIPDIIHNHGKPMTLPELVAKLPIHPKKVW 68

Query: 70  CTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISLQ---LQGSTILLLIAD 126
           C   L+ +L  SGFF +QK  ++EQEE  +     L   SR+ L+   L     LL + D
Sbjct: 69  CVYRLMRILVQSGFFARQKVEESEQEEGYV-----LTHASRLLLEDDPLSVRPFLLAMLD 123

Query: 127 ATFTTSFHFLSTWLQNDDQTLFGTADG---------------IFYEAMITDFELIASVLI 171
              T  +H++S W QNDD T F TA G                F EAM +D  L+ S LI
Sbjct: 124 PILTKPWHYVSAWFQNDDPTPFDTAHGXTFWDYGGHEPKJNNFFNEAMASDARLVTSXLI 183

Query: 172 EDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
           +DC  V +GL  LVDVGG TGT+A+AIA AFP   CTVF
Sbjct: 184 KDCKGVFEGLNSLVDVGGGTGTVAKAIANAFPHLNCTVF 222

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255568369|ref|XP_002525159.1| o-methyltransferase, putative [Ricinus communis] gi|223535618|gb|EEF37286.1| o-methyltransferase, putative [Ricinus communis]

 Score =  176 bits (446), Expect = 6e-42,   Method: Compositional matrix adjust.
 Identities = 96/223 (43%), Positives = 135/223 (60%), Gaps = 23/223 (10%)

Query: 6   GENGAREHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHP 65
           G++ A+E  QAQA +W++ +N++ S+SLK AIQL IPD I++ G+P++L+ +I AL +HP
Sbjct: 4   GKHDAQELLQAQAYIWNHIFNFINSMSLKTAIQLGIPDAIHSHGKPISLSLLIAALPIHP 63

Query: 66  NKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISLQ---LQGSTILL 122
            K RC   L+ +L HSGFF + K  +N++ E  +L        S++ L+      +  LL
Sbjct: 64  AKARCIPRLMRILIHSGFFAKAKLKENDEAEGYVLTKA-----SKLLLKDNPFSVTPFLL 118

Query: 123 LIADATFTTSFHFLSTWLQNDDQTLFGTADGI---------------FYEAMITDFELIA 167
            + D   T  +H+LSTW QNDD T F TA G+               F EAM +D  L+ 
Sbjct: 119 AMLDRILTEPWHYLSTWFQNDDATAFTTAHGMGFWEYAGNEPKLNNFFNEAMASDARLVM 178

Query: 168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
            VLI++   V +GLK LVDVGG TGTMA+AIA AFP   C VF
Sbjct: 179 RVLIDEYKGVFEGLKSLVDVGGGTGTMAKAIAKAFPRLDCIVF 221

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359485251|ref|XP_003633245.1| PREDICTED: tabersonine 16-O-methyltransferase-like isoform 2 [Vitis vinifera]

 Score =  174 bits (440), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 99/228 (43%), Positives = 129/228 (56%), Gaps = 22/228 (9%)

Query: 1   MDVIHGENGAREHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVA 60
           M+ +     A E  QAQ   W +T N++ S+ LK AIQL IPD+I++ GQPM L+Q+I A
Sbjct: 1   MECLGSRERATELLQAQVHTWKHTTNFVNSMVLKCAIQLGIPDVIHSHGQPMALSQLITA 60

Query: 61  LNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISLQ---LQG 117
           L++ P K  C   L+ +L HSGFF QQK   N +EEE       L F S+  L+   + G
Sbjct: 61  LSLEPTKAPCLYRLMRVLVHSGFFAQQKLLHNSEEEEGY----SLTFASQFLLKDEPVSG 116

Query: 118 STILLLIADATFTTSFHFLSTWLQNDDQTLFGTA---------------DGIFYEAMITD 162
              LLL  D   T  +HFL  W QN+D T F TA               + IF E M++D
Sbjct: 117 VPFLLLQLDPILTAPWHFLGDWFQNEDPTPFHTAHRKSFWDYAVHEPKLNDIFNETMVSD 176

Query: 163 FELIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
             LIA++++    EV +GL  LVDVGG TGTM +AIA AFP  KC VF
Sbjct: 177 SRLIANMIVRQYKEVFEGLASLVDVGGGTGTMVKAIAKAFPQLKCIVF 224

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225446485|ref|XP_002278106.1| PREDICTED: tabersonine 16-O-methyltransferase-like isoform 1 [Vitis vinifera]

 Score =  173 bits (438), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 98/219 (44%), Positives = 126/219 (57%), Gaps = 22/219 (10%)

Query: 10  AREHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTR 69
           A E  QAQ   W +T N++ S+ LK AIQL IPD+I++ GQPM L+Q+I AL++ P K  
Sbjct: 9   ATELLQAQVHTWKHTTNFVNSMVLKCAIQLGIPDVIHSHGQPMALSQLITALSLEPTKAP 68

Query: 70  CTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISLQ---LQGSTILLLIAD 126
           C   L+ +L HSGFF QQK   N +EEE       L F S+  L+   + G   LLL  D
Sbjct: 69  CLYRLMRVLVHSGFFAQQKLLHNSEEEEGY----SLTFASQFLLKDEPVSGVPFLLLQLD 124

Query: 127 ATFTTSFHFLSTWLQNDDQTLFGTA---------------DGIFYEAMITDFELIASVLI 171
              T  +HFL  W QN+D T F TA               + IF E M++D  LIA++++
Sbjct: 125 PILTAPWHFLGDWFQNEDPTPFHTAHRKSFWDYAVHEPKLNDIFNETMVSDSRLIANMIV 184

Query: 172 EDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
               EV +GL  LVDVGG TGTM +AIA AFP  KC VF
Sbjct: 185 RQYKEVFEGLASLVDVGGGTGTMVKAIAKAFPQLKCIVF 223

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225454044|ref|XP_002262833.1| PREDICTED: tabersonine 16-O-methyltransferase-like [Vitis vinifera]

 Score =  171 bits (433), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 102/225 (45%), Positives = 130/225 (57%), Gaps = 17/225 (7%)

Query: 1   MDVIHGENGAREHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVA 60
           MD+   E  A E  QAQAQV ++ +N+M S++LK AI L IPD+I++ GQPM L+Q++ A
Sbjct: 1   MDLGSAER-ADELLQAQAQVVNHVFNFMNSMALKCAIDLAIPDVIHSHGQPMLLSQLVTA 59

Query: 61  LNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISLQLQGSTI 120
           L+V P+K  C   L+ LL HSGFF QQ+   N ++EE   L     F  +    L G  +
Sbjct: 60  LSVQPSKAPCLHRLMRLLVHSGFFSQQQVIHNNEQEEGYSLTSASRFLLKDE-PLTGLPL 118

Query: 121 LLLIADATFTTSFHFLSTWLQNDDQTLFGTADG---------------IFYEAMITDFEL 165
            LL  +   T  +HFLS W +N D T F TA G               +F EAM +D  +
Sbjct: 119 SLLHLNPVLTAPWHFLSGWFRNGDPTPFYTAHGKPYWDYTAQEPDFNDLFNEAMASDSRI 178

Query: 166 IASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
           IASVLI  C E  KGL  LVDVG  TGTM +AIA AFP  KC VF
Sbjct: 179 IASVLITKCKEQFKGLFSLVDVGAGTGTMTKAIAKAFPHLKCIVF 223

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359485261|ref|XP_003633249.1| PREDICTED: tabersonine 16-O-methyltransferase-like [Vitis vinifera]

 Score =  171 bits (432), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 96/225 (42%), Positives = 131/225 (58%), Gaps = 18/225 (8%)

Query: 1   MDVIHGENGAREHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVA 60
           MD  +GE  A E   AQA VW++  N++KS+SLK AIQL IPDII+N G+PMTL +++  
Sbjct: 1   MDFANGEISA-ELLHAQAHVWNHILNFIKSVSLKCAIQLGIPDIIHNHGKPMTLPELVAK 59

Query: 61  LNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISLQLQGSTI 120
           L VHP +++C   L+ +L HSGF   Q+  + E+EE  +L           SL ++   +
Sbjct: 60  LPVHPKRSQCVYRLMRILVHSGFLAAQRVQQGEEEEGYVLTDASRLLLMDDSLSIR--PL 117

Query: 121 LLLIADATFTTSFHFLSTWLQNDDQTLFGTA---------------DGIFYEAMITDFEL 165
           LL + D   T  +H+LS W QNDD T F TA               +  F EAM +D  L
Sbjct: 118 LLAMLDPILTKPWHYLSAWFQNDDPTPFHTAHERPFWDYAGHEPQLNNFFNEAMASDARL 177

Query: 166 IASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
           + SVL+++   V +GL  LVDVGG TG +A+AIA AFP   CTV 
Sbjct: 178 VTSVLLKEGKGVFEGLNSLVDVGGGTGQVAKAIANAFPHLNCTVL 222

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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	214
UNIPROTKB|Q84KK5	357	D7OMT "Isoflavone 7-O-methyltr	0.939	0.563	0.318	8.4e-26
UNIPROTKB|B0EXJ8	355	16OMT "Tabersonine 16-O-methyl	0.897	0.540	0.369	1.1e-23
UNIPROTKB|Q8GSN1	348	Q8GSN1 "Myricetin O-methyltran	0.873	0.537	0.334	1e-22
UNIPROTKB|Q6VMW0	366	OMT2 "8-hydroxyquercetin 8-O-m	0.827	0.483	0.363	3.4e-22
UNIPROTKB|Q84KK6	367	HI4'OMT "Isoflavone 4'-O-methy	0.710	0.414	0.304	2.3e-15
UNIPROTKB|A8QW53	374	OMT3 "5-pentadecatrienyl resor	0.415	0.237	0.337	2e-14
UNIPROTKB|Q84KK4	365	HI4'OMT "Isoflavone 4'-O-methy	0.738	0.432	0.302	4.8e-14
TAIR|locus:2132806	382	AT4G35160 [Arabidopsis thalian	0.355	0.198	0.325	8.4e-08
TAIR|locus:2132801	325	AT4G35150 [Arabidopsis thalian	0.355	0.233	0.337	1.2e-07

UNIPROTKB|Q84KK5 D7OMT "Isoflavone 7-O-methyltransferase" [Glycyrrhiza echinata (taxid:46348)]

 Score = 292 (107.8 bits), Expect = 8.4e-26, P = 8.4e-26
 Identities = 70/220 (31%), Positives = 123/220 (55%)

Query:     8 NGAR--EHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHP 65
             NG +  E FQ QA ++ + Y ++ S+ LK  ++L IP+II+N G+P+T+++++  L V  
Sbjct:     6 NGRKPSEIFQGQALLYRHIYAFIDSMCLKWIVELDIPNIIHNHGKPITVSELVSILKVPQ 65

Query:    66 NKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISLQLQGSTILLLIA 125
              K    Q ++  +AH+GFF + +  + ++E E+  L    +   + S +L  + ++  + 
Sbjct:    66 TKAGNVQRIMRYMAHNGFFERVRIQEEQEENEAYALTAASELLVKGS-ELCLAPMVECVL 124

Query:   126 DATFTTSFHFLSTWLQNDDQTLFGTADGI---------------FYEAMITDFELIASVL 170
             D T + S+H L  W+  +D TLFG + G                F +AM +D ++I ++ 
Sbjct:   125 DPTLSGSYHQLKKWIYEEDLTLFGVSLGSHFWEFLNENPEYNKSFNDAMASDSQMI-NLA 183

Query:   171 IEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
             + DCN   +G++ +VDVGG  GT A+ I   FP+ KC VF
Sbjct:   184 LRDCNSGFEGVESIVDVGGGIGTTAKIICDTFPNLKCIVF 223

GO:0009717 "isoflavonoid biosynthetic process" evidence=IDA

GO:0033800 "isoflavone 7-O-methyltransferase activity" evidence=IDA

UNIPROTKB|B0EXJ8 16OMT "Tabersonine 16-O-methyltransferase" [Catharanthus roseus (taxid:4058)]

 Score = 272 (100.8 bits), Expect = 1.1e-23, P = 1.1e-23
 Identities = 79/214 (36%), Positives = 114/214 (53%)

Query:    16 AQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVAL--NVHPNKTRCTQI 73
             AQAQ+WS + +++ S SLK A++L IPD I+N G+P+TL+++  AL   VHP+K      
Sbjct:    11 AQAQIWSQSCSFITSASLKCAVKLGIPDTIDNHGKPITLSELTNALVPPVHPSKAPFIYR 70

Query:    74 LVCLLAHSGFFVQQK-DGKNEQEEESILLPPHLDFFSRISLQLQGSTILLLIADATFTTS 132
             L+ +LA +GF  +++ DG  E E    L P       +  L L+G  +L +         
Sbjct:    71 LMRVLAKNGFCSEEQLDG--ETEPLYSLTPSSRILLKKEPLNLRG-IVLTMADPVQLKAW 127

Query:   133 FHFLSTWLQNDDQ-TLFGTADG---------------IFYEAMITDFELIASVLIEDCNE 176
                   +   DD  T F TA G                F EAM +D +LI+ +LI +   
Sbjct:   128 ESLSDWYQNEDDSSTAFETAHGKNFWGYSSEHMEHAEFFNEAMASDSQLISKLLIGEYKF 187

Query:   177 VSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
             + +GL  LVD+GG TGT+A+AIA  FP  KCTVF
Sbjct:   188 LFEGLASLVDIGGGTGTIAKAIAKNFPQLKCTVF 221

GO:0005737 "cytoplasm" evidence=IDA

GO:0009821 "alkaloid biosynthetic process" evidence=IDA

GO:0030766 "11-O-demethyl-17-O-deacetylvindoline O-methyltransferase activity" evidence=IDA

GO:0032259 "methylation" evidence=IDA

GO:0042803 "protein homodimerization activity" evidence=IDA

UNIPROTKB|Q8GSN1 Q8GSN1 "Myricetin O-methyltransferase" [Catharanthus roseus (taxid:4058)]

 Score = 263 (97.6 bits), Expect = 1.0e-22, P = 1.0e-22
 Identities = 70/209 (33%), Positives = 113/209 (54%)

Query:    16 AQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILV 75
             AQA  ++  +++    SLK A+QL IPD I++ G+PM L+ +  +L ++P+K      L+
Sbjct:    11 AQAHFFTQVFSFTSMSSLKCAVQLGIPDAIHSHGKPMALSDLTNSLPINPSKAPYIYRLM 70

Query:    76 CLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISLQLQGSTILLLIADATFTTSFHF 135
              +L  +G+F       +E+E+    L P      +    L   +++L +       +++ 
Sbjct:    71 RILVAAGYF-------SEEEKNVYSLTPFTRLLLKND-PLNSISMVLGVNQIAELKAWNA 122

Query:   136 LSTWLQNDDQTLFGTADGI-FYE-------------AMITDFELIASVLIEDCNEVSKGL 181
             +S W QN+D T F TA G  F++              M  D  L++ +LI + N + +GL
Sbjct:   123 MSEWFQNEDLTAFETAHGKNFWDFGAEDKYGKNFDGVMAADSILVSKMLIPEFNYLFEGL 182

Query:   182 KPLVDVGGSTGTMARAIATAFPDTKCTVF 210
               LVDVGG TGT+A+AIA +FPD KCTVF
Sbjct:   183 DSLVDVGGGTGTIAKAIAKSFPDLKCTVF 211

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

UNIPROTKB|Q6VMW0 OMT2 "8-hydroxyquercetin 8-O-methyltransferase" [Mentha x piperita (taxid:34256)]

 Score = 258 (95.9 bits), Expect = 3.4e-22, P = 3.4e-22
 Identities = 68/187 (36%), Positives = 103/187 (55%)

Query:     1 MDVIHGENGAREHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVA 60
             M + +G +  +E  +AQA VW++ Y+Y+ S+SLK AIQL IPD I+  G P+TL+Q+  A
Sbjct:     1 MALPNGISSKQELLEAQAHVWNHIYSYINSMSLKCAIQLGIPDAIHKHGNPITLSQLADA 60

Query:    61 LNVHPNKTRCTQILVCLLAHSGFFVQQK-----DGKNEQEEESIL-LPPHLDFFSRISLQ 114
             LN++  K+     L+ +L HSGFF + K     +G++E+EEE    L P      R S  
Sbjct:    61 LNINKAKSHGLFRLMRILVHSGFFDKVKVKVKVEGEDEEEEEDAYSLTPASRLLLR-SEP 119

Query:   115 LQGSTILLLIADATFTTSFHFLSTWLQNDDQTLFGTADGI-FYEAMITDFELIASVLIED 173
             L  +   L ++D  +T ++H LS W +ND    F T  G+ F E  + D  L  +VL  +
Sbjct:   120 LSVAPFALAMSDPVYTETWHHLSEWFRNDAVAAFDTKYGMTFPEYAVADDRL--NVLFNE 177

Query:   174 CNEVSKG 180
                   G
Sbjct:   178 AMACDAG 184

GO:0009812 "flavonoid metabolic process" evidence=IDA

GO:0030761 "8-hydroxyquercitin 8-O-methyltransferase activity" evidence=IDA

GO:0032259 "methylation" evidence=IDA

UNIPROTKB|Q84KK6 HI4'OMT "Isoflavone 4'-O-methyltransferase" [Glycyrrhiza echinata (taxid:46348)]

 Score = 198 (74.8 bits), Expect = 2.3e-15, P = 2.3e-15
 Identities = 52/171 (30%), Positives = 93/171 (54%)

Query:     8 NGAREH--FQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHP 65
             NG+ E   + AQ  ++ + YN++ S++LK A++L I D+I+N G+P+TL ++  AL +HP
Sbjct:     6 NGSEEIELYHAQIHLYKHVYNFVSSMALKSAMELGIADVIHNHGKPITLPELASALKLHP 65

Query:    66 NKTRCTQILVCLLAHSGFFVQQ-------KDGKNEQEEESILLPPHLDFFSRISLQLQGS 118
             +K       + LL H+GFF +        KDG+ E+E    L PP     S++ ++ + +
Sbjct:    66 SKVGILYRFLRLLTHNGFFAKTTVPSQNGKDGEEEEETAYALTPP-----SKLLVKGKPT 120

Query:   119 TILLLIADATFTTSFHFLST---WLQNDDQ-TLFGTADG-IFYEAMITDFE 164
              +  ++  A   +S     +   W + D + TLF +A G  F++ +  D E
Sbjct:   121 CLASIVRGALHPSSLDMWRSSEKWFKEDKELTLFESATGESFWDFLNKDSE 171

GO:0009701 "isoflavonoid phytoalexin biosynthetic process" evidence=IDA

GO:0030746 "isoflavone 4'-O-methyltransferase activity" evidence=IDA

UNIPROTKB|A8QW53 OMT3 "5-pentadecatrienyl resorcinol O-methyltransferase" [Sorghum bicolor (taxid:4558)]

 Score = 127 (49.8 bits), Expect = 2.0e-14, Sum P(2) = 2.0e-14
 Identities = 30/89 (33%), Positives = 47/89 (52%)

Query:    10 AREHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTR 69
             +RE  QA  ++W+ TY++MKS++L  A+ L I D I+  G   TL+QI+  + V P K  
Sbjct:     8 SRELLQAHVELWNQTYSFMKSVALAVALDLHIADAIHRRGGAATLSQILGEIGVRPCKLP 67

Query:    70 CTQILVCLLAHSGFFVQQKDGKNEQEEES 98
                 ++ +L  SG F   +        ES
Sbjct:    68 GLHRIMRVLTVSGTFTIVQPSAETMSSES 96

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

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

GO:0032259 "methylation" evidence=IDA

UNIPROTKB|Q84KK4 HI4'OMT "Isoflavone 4'-O-methyltransferase" [Lotus japonicus (taxid:34305)]

 Score = 186 (70.5 bits), Expect = 4.8e-14, P = 4.8e-14
 Identities = 53/175 (30%), Positives = 93/175 (53%)

Query:     1 MDVIHGENGAR--EHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQII 58
             MD     NG+   E  QAQ  ++ + YN++ S++LK A++L I D+I++ G+P+TL ++ 
Sbjct:     1 MD-FSSSNGSEDTELSQAQIHLYKHVYNFVSSMALKSAMELGIADVIHSHGKPITLPELA 59

Query:    59 VALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNE-QEEESI--LLPPHLDFFSRISLQL 115
              ALN+ P+K       + LL H+GFF +    + E  EEE+   L PP     S++ ++ 
Sbjct:    60 TALNLRPSKIGVLHRFLRLLTHNGFFAKTTVSRGEGAEEETAYGLTPP-----SKLLVKS 114

Query:   116 QGSTILLLIADATFTTSFHFLST---WL--QNDDQTLFGTADG-IFYEAMITDFE 164
               + +  ++  A   +S     +   W    N++ TLF +A G  F+E +  + E
Sbjct:   115 NSTCLAPIVKGALHPSSLDMWRSSKKWFLEDNEELTLFESATGESFWEFLNKETE 169

GO:0009701 "isoflavonoid phytoalexin biosynthetic process" evidence=IDA

GO:0030746 "isoflavone 4'-O-methyltransferase activity" evidence=IDA

TAIR|locus:2132806 AT4G35160 [Arabidopsis thaliana (taxid:3702)]

 Score = 113 (44.8 bits), Expect = 8.4e-08, Sum P(2) = 8.4e-08
 Identities = 27/83 (32%), Positives = 43/83 (51%)

Query:    12 EHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINN--SGQPMTLTQIIVALNVHPNKTR 69
             E  +A   +W Y + +    + K AI L+IP+ I N  S QP+TL ++  A++  P+  R
Sbjct:    25 EEAKASLDIWKYVFGFADIAAAKCAIDLKIPEAIENHPSSQPVTLAELSSAVSASPSHLR 84

Query:    70 CTQILVCLLAHSGFF--VQQKDG 90
                 ++  L H G F  +  KDG
Sbjct:    85 R---IMRFLVHQGIFKEIPTKDG 104

GO:0005634 "nucleus" evidence=ISM

GO:0008168 "methyltransferase activity" evidence=IEA

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

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0005829 "cytosol" evidence=TAS

TAIR|locus:2132801 AT4G35150 [Arabidopsis thaliana (taxid:3702)]

 Score = 114 (45.2 bits), Expect = 1.2e-07, Sum P(2) = 1.2e-07
 Identities = 28/83 (33%), Positives = 44/83 (53%)

Query:    12 EHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINN--SGQPMTLTQIIVALNVHPNKTR 69
             E  +A   +W Y + +    + K AI L+IP+ I N  S QP+TL+++  A++  P+  R
Sbjct:    11 EEAKASLDIWRYVFGFADIAAAKCAIDLKIPEAIENHPSSQPVTLSELSSAVSASPSHLR 70

Query:    70 CTQILVCLLAHSGFF--VQQKDG 90
                 ++  L H G F  V  KDG
Sbjct:    71 R---IMRFLVHQGLFKEVPTKDG 90

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	LOW CONFIDENCE prediction!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	214
pfam00891	239	pfam00891, Methyltransf_2, O-methyltransferase	2e-10
pfam08100	50	pfam08100, Dimerisation, Dimerisation domain	3e-07

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

 Score = 58.4 bits (142), Expect = 2e-10
 Identities = 33/104 (31%), Positives = 45/104 (43%), Gaps = 15/104 (14%)

Query: 121 LLLIADATFTTSFHFLSTWLQNDDQTLFGTADGI-FYEAMITDFEL-------------I 166
           LL+ AD T   S+  L   ++ +    F  A G+ F+E +  D E              +
Sbjct: 29  LLMYADPTLLESWAHLKDAVR-EGGPPFERAFGMPFFEYLGADPEFNRVFNRAMAAHSRL 87

Query: 167 ASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
               I +      GL  LVDVGG TG +A AI  A+P  K  VF
Sbjct: 88  VMKKILETAFDFSGLSSLVDVGGGTGALAAAIVRAYPHIKGIVF 131

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

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

 Score = 45.3 bits (108), Expect = 3e-07
 Identities = 19/50 (38%), Positives = 29/50 (58%), Gaps = 1/50 (2%)

Query: 31 LSLKRAIQLRIPDIINNSGQPMTLTQIIVALN-VHPNKTRCTQILVCLLA 79
          + LK AI+L IPDII   G+P++ +++   L  V+P        L+ LLA
Sbjct: 1  MVLKCAIELGIPDIIAKHGKPLSPSELASKLPTVNPEAPVMLDRLLRLLA 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	214
TIGR02716	306	C20_methyl_CrtF C-20 methyltransferase BchU. Membe	99.91
KOG3178	342	consensus Hydroxyindole-O-methyltransferase and re	99.89
PF00891	241	Methyltransf_2: O-methyltransferase; InterPro: IPR	99.75
PF08100	51	Dimerisation: Dimerisation domain; InterPro: IPR01	98.92
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	97.83
PRK14103	255	trans-aconitate 2-methyltransferase; Provisional	97.67
COG4106	257	Tam Trans-aconitate methyltransferase [General fun	97.54
PRK08287	187	cobalt-precorrin-6Y C(15)-methyltransferase; Valid	97.53
TIGR02469	124	CbiT precorrin-6Y C5,15-methyltransferase (decarbo	97.5
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	97.41
PRK01683	258	trans-aconitate 2-methyltransferase; Provisional	97.39
COG2813	300	RsmC 16S RNA G1207 methylase RsmC [Translation, ri	97.33
PRK15001	378	SAM-dependent 23S ribosomal RNA mG1835 methyltrans	97.27
COG1414	246	IclR Transcriptional regulator [Transcription]	97.25
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	97.17
PRK06922	677	hypothetical protein; Provisional	97.16
PRK11569	274	transcriptional repressor IclR; Provisional	97.16
PRK00107	187	gidB 16S rRNA methyltransferase GidB; Reviewed	97.13
PRK10163	271	DNA-binding transcriptional repressor AllR; Provis	97.12
PF05175	170	MTS: Methyltransferase small domain; InterPro: IPR	97.07
PRK15090	257	DNA-binding transcriptional regulator KdgR; Provis	97.05
TIGR02752	231	MenG_heptapren 2-heptaprenyl-1,4-naphthoquinone me	97.04
TIGR02431	248	pcaR_pcaU beta-ketoadipate pathway transcriptional	97.03
TIGR00138	181	gidB 16S rRNA methyltransferase GidB. GidB (glucos	97.03
COG2230	283	Cfa Cyclopropane fatty acid synthase and related m	97.02
PRK14121	390	tRNA (guanine-N(7)-)-methyltransferase; Provisiona	96.97
PRK07402	196	precorrin-6B methylase; Provisional	96.96
TIGR03587	204	Pse_Me-ase pseudaminic acid biosynthesis-associate	96.92
PRK00121	202	trmB tRNA (guanine-N(7)-)-methyltransferase; Revie	96.9
PRK09834	263	DNA-binding transcriptional activator MhpR; Provis	96.89
PRK09489	342	rsmC 16S ribosomal RNA m2G1207 methyltransferase;	96.88
TIGR02072	240	BioC biotin biosynthesis protein BioC. This enzyme	96.87
TIGR00740	239	methyltransferase, putative. A simple BLAST search	96.85
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	96.75
PRK15451	247	tRNA cmo(5)U34 methyltransferase; Provisional	96.72
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	96.72
PRK11207	197	tellurite resistance protein TehB; Provisional	96.71
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	96.66
PRK15068	322	tRNA mo(5)U34 methyltransferase; Provisional	96.64
PF02353	273	CMAS: Mycolic acid cyclopropane synthetase; InterP	96.63
PRK00274	272	ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1	96.61
TIGR03533	284	L3_gln_methyl protein-(glutamine-N5) methyltransfe	96.6
PRK04457	262	spermidine synthase; Provisional	96.56
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	96.56
COG2890	280	HemK Methylase of polypeptide chain release factor	96.55
PF13489	161	Methyltransf_23: Methyltransferase domain; PDB: 3J	96.54
TIGR03534	251	RF_mod_PrmC protein-(glutamine-N5) methyltransfera	96.54
PRK06202	232	hypothetical protein; Provisional	96.52
TIGR00477	195	tehB tellurite resistance protein TehB. Part of a	96.52
PRK00216	239	ubiE ubiquinone/menaquinone biosynthesis methyltra	96.52
PRK11805	307	N5-glutamine S-adenosyl-L-methionine-dependent met	96.51
PRK09328	275	N5-glutamine S-adenosyl-L-methionine-dependent met	96.51
PRK14966	423	unknown domain/N5-glutamine S-adenosyl-L-methionin	96.49
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	96.49
TIGR00536	284	hemK_fam HemK family putative methylases. The gene	96.48
COG2242	187	CobL Precorrin-6B methylase 2 [Coenzyme metabolism	96.44
TIGR03704	251	PrmC_rel_meth putative protein-(glutamine-N5) meth	96.43
PLN02244	340	tocopherol O-methyltransferase	96.42
PRK10258	251	biotin biosynthesis protein BioC; Provisional	96.42
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	96.39
TIGR00452	314	methyltransferase, putative. Known examples to dat	96.35
TIGR02021	219	BchM-ChlM magnesium protoporphyrin O-methyltransfe	96.33
PRK05785	226	hypothetical protein; Provisional	96.33
PF02082	83	Rrf2: Transcriptional regulator; InterPro: IPR0009	96.31
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	96.3
PTZ00098	263	phosphoethanolamine N-methyltransferase; Provision	96.3
COG2226	238	UbiE Methylase involved in ubiquinone/menaquinone	96.28
COG4123	248	Predicted O-methyltransferase [General function pr	96.28
PRK01544	506	bifunctional N5-glutamine S-adenosyl-L-methionine-	96.22
TIGR00438	188	rrmJ cell division protein FtsJ.	96.21
PF13679	141	Methyltransf_32: Methyltransferase domain	96.19
TIGR01934	223	MenG_MenH_UbiE ubiquinone/menaquinone biosynthesis	96.18
PRK10857	164	DNA-binding transcriptional regulator IscR; Provis	96.18
PRK10141	117	DNA-binding transcriptional repressor ArsR; Provis	96.13
PRK11705	383	cyclopropane fatty acyl phospholipid synthase; Pro	96.12
PRK07580	230	Mg-protoporphyrin IX methyl transferase; Validated	96.09
PF09012	69	FeoC: FeoC like transcriptional regulator; InterPr	96.09
PLN02336	475	phosphoethanolamine N-methyltransferase	96.07
PRK11188	209	rrmJ 23S rRNA methyltransferase J; Provisional	96.02
COG0220	227	Predicted S-adenosylmethionine-dependent methyltra	95.99
PRK11088	272	rrmA 23S rRNA methyltransferase A; Provisional	95.98
TIGR00755	253	ksgA dimethyladenosine transferase. Alternate name	95.97
PLN02233	261	ubiquinone biosynthesis methyltransferase	95.97
TIGR02337	118	HpaR homoprotocatechuate degradation operon regula	95.92
TIGR00080	215	pimt protein-L-isoaspartate(D-aspartate) O-methylt	95.91
PRK14896	258	ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1	95.89
PRK13944	205	protein-L-isoaspartate O-methyltransferase; Provis	95.88
KOG2899	288	consensus Predicted methyltransferase [General fun	95.87
PF04703	62	FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.	95.87
smart00347	101	HTH_MARR helix_turn_helix multiple antibiotic resi	95.87
PRK11036	255	putative S-adenosyl-L-methionine-dependent methylt	95.82
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	95.8
PRK04266	226	fibrillarin; Provisional	95.79
PRK12335	287	tellurite resistance protein TehB; Provisional	95.76
TIGR03438	301	probable methyltransferase. This model represents	95.72
PLN03075	296	nicotianamine synthase; Provisional	95.71
TIGR02010	135	IscR iron-sulfur cluster assembly transcription fa	95.68
PRK00517	250	prmA ribosomal protein L11 methyltransferase; Revi	95.66
PRK00377	198	cbiT cobalt-precorrin-6Y C(15)-methyltransferase;	95.65
PF08003	315	Methyltransf_9: Protein of unknown function (DUF16	95.6
PRK13942	212	protein-L-isoaspartate O-methyltransferase; Provis	95.59
PLN02490	340	MPBQ/MSBQ methyltransferase	95.55
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	95.53
COG2345	218	Predicted transcriptional regulator [Transcription	95.51
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	95.47
PRK03902	142	manganese transport transcriptional regulator; Pro	95.46
COG3355	126	Predicted transcriptional regulator [Transcription	95.44
PF01209	233	Ubie_methyltran: ubiE/COQ5 methyltransferase famil	95.41
PHA03411	279	putative methyltransferase; Provisional	95.4
TIGR00738	132	rrf2_super rrf2 family protein (putative transcrip	95.33
COG2227	243	UbiG 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-	95.32
TIGR00122	69	birA_repr_reg BirA biotin operon repressor domain.	95.28
PLN02396	322	hexaprenyldihydroxybenzoate methyltransferase	95.26
smart00138	264	MeTrc Methyltransferase, chemotaxis proteins. Meth	95.22
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	95.2
PLN02672	1082	methionine S-methyltransferase	95.17
TIGR02702	203	SufR_cyano iron-sulfur cluster biosynthesis transc	95.09
COG1321	154	TroR Mn-dependent transcriptional regulator [Trans	95.08
PRK06266	178	transcription initiation factor E subunit alpha; V	95.07
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	95.06
PF06325	295	PrmA: Ribosomal protein L11 methyltransferase (Prm	95.05
PLN02336	475	phosphoethanolamine N-methyltransferase	95.04
TIGR00406	288	prmA ribosomal protein L11 methyltransferase. Ribo	95.0
PLN02366	308	spermidine synthase	94.99
PF03848	192	TehB: Tellurite resistance protein TehB; InterPro:	94.98
PF14947	77	HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_	94.93
PRK00811	283	spermidine synthase; Provisional	94.92
PRK01544	506	bifunctional N5-glutamine S-adenosyl-L-methionine-	94.89
PF07757	112	AdoMet_MTase: Predicted AdoMet-dependent methyltra	94.88
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	94.85
PRK03573	144	transcriptional regulator SlyA; Provisional	94.85
PRK11727	321	23S rRNA mA1618 methyltransferase; Provisional	94.84
PRK14967	223	putative methyltransferase; Provisional	94.83
TIGR01884	203	cas_HTH CRISPR locus-related DNA-binding protein.	94.82
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	94.82
PRK11050	152	manganese transport regulator MntR; Provisional	94.8
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	94.79
PLN02585	315	magnesium protoporphyrin IX methyltransferase	94.78
PRK10901	427	16S rRNA methyltransferase B; Provisional	94.76
KOG3115	249	consensus Methyltransferase-like protein [General	94.73
PRK11873	272	arsM arsenite S-adenosylmethyltransferase; Reviewe	94.66
COG2264	300	PrmA Ribosomal protein L11 methylase [Translation,	94.64
TIGR02944	130	suf_reg_Xantho FeS assembly SUF system regulator,	94.63
PHA00738	108	putative HTH transcription regulator	94.61
COG1959	150	Predicted transcriptional regulator [Transcription	94.58
TIGR00478	228	tly hemolysin TlyA family protein. Hemolysins are	94.57
PF08461	66	HTH_12: Ribonuclease R winged-helix domain; InterP	94.56
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	94.52
PHA03412	241	putative methyltransferase; Provisional	94.46
KOG1270	282	consensus Methyltransferases [Coenzyme transport a	94.4
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	94.39
TIGR03840	213	TMPT_Se_Te thiopurine S-methyltransferase, Se/Te d	94.35
KOG2904	328	consensus Predicted methyltransferase [General fun	94.28
PF13601	80	HTH_34: Winged helix DNA-binding domain; PDB: 1UB9	94.27
TIGR00373	158	conserved hypothetical protein TIGR00373. This fam	94.26
PRK14902	444	16S rRNA methyltransferase B; Provisional	94.26
PF05148	219	Methyltransf_8: Hypothetical methyltransferase; In	94.22
PTZ00338	294	dimethyladenosine transferase-like protein; Provis	94.19
PRK11512	144	DNA-binding transcriptional repressor MarR; Provis	94.14
PF06163	127	DUF977: Bacterial protein of unknown function (DUF	94.07
cd07377	66	WHTH_GntR Winged helix-turn-helix (WHTH) DNA-bindi	94.04
PRK05134	233	bifunctional 3-demethylubiquinone-9 3-methyltransf	94.02
PRK13168	443	rumA 23S rRNA m(5)U1939 methyltransferase; Reviewe	94.02
COG4190	144	Predicted transcriptional regulator [Transcription	93.95
PRK13943	322	protein-L-isoaspartate O-methyltransferase; Provis	93.93
PRK11014	141	transcriptional repressor NsrR; Provisional	93.93
cd00090	78	HTH_ARSR Arsenical Resistance Operon Repressor and	93.9
PF10294	173	Methyltransf_16: Putative methyltransferase; Inter	93.81
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	93.81
PRK01581	374	speE spermidine synthase; Validated	93.76
PRK00312	212	pcm protein-L-isoaspartate O-methyltransferase; Re	93.7
COG4742	260	Predicted transcriptional regulator [Transcription	93.65
PRK04148	134	hypothetical protein; Provisional	93.58
PRK11920	153	rirA iron-responsive transcriptional regulator; Re	93.55
TIGR00563	426	rsmB ribosomal RNA small subunit methyltransferase	93.46
KOG1540	296	consensus Ubiquinone biosynthesis methyltransferas	93.46
PRK13255	218	thiopurine S-methyltransferase; Reviewed	93.44
TIGR01889	109	Staph_reg_Sar staphylococcal accessory regulator f	93.4
cd07153	116	Fur_like Ferric uptake regulator(Fur) and related	93.36
PRK06474	178	hypothetical protein; Provisional	93.34
TIGR00417	270	speE spermidine synthase. the SpeE subunit of sper	93.23
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	93.19
TIGR01983	224	UbiG ubiquinone biosynthesis O-methyltransferase.	93.0
PRK15431	78	ferrous iron transport protein FeoC; Provisional	92.98
PRK03522	315	rumB 23S rRNA methyluridine methyltransferase; Rev	92.89
smart00529	96	HTH_DTXR Helix-turn-helix diphteria tox regulatory	92.54
PF02002	105	TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024	92.52
PF01638	90	HxlR: HxlR-like helix-turn-helix; InterPro: IPR002	92.31
COG4189	308	Predicted transcriptional regulator [Transcription	92.17
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	92.16
PF07381	90	DUF1495: Winged helix DNA-binding domain (DUF1495)	92.03
TIGR02085	374	meth_trns_rumB 23S rRNA (uracil-5-)-methyltransfer	92.02
PRK11169	164	leucine-responsive transcriptional regulator; Prov	91.92
KOG1271	227	consensus Methyltransferases [General function pre	91.91
PF02319	71	E2F_TDP: E2F/DP family winged-helix DNA-binding do	91.85
PF07789	155	DUF1627: Protein of unknown function (DUF1627); In	91.85
PRK03612	521	spermidine synthase; Provisional	91.82
PRK10909	199	rsmD 16S rRNA m(2)G966-methyltransferase; Provisio	91.76
PF02527	184	GidB: rRNA small subunit methyltransferase G; Inte	91.73
COG4565	224	CitB Response regulator of citrate/malate metaboli	91.54
PRK10870	176	transcriptional repressor MprA; Provisional	91.53
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	91.5
PF08221	62	HTH_9: RNA polymerase III subunit RPC82 helix-turn	91.31
PF14394	171	DUF4423: Domain of unknown function (DUF4423)	91.17
PRK04214	412	rbn ribonuclease BN/unknown domain fusion protein;	91.14
COG1522	154	Lrp Transcriptional regulators [Transcription]	91.1
COG0357	215	GidB Predicted S-adenosylmethionine-dependent meth	91.08
PLN02781	234	Probable caffeoyl-CoA O-methyltransferase	91.03
TIGR00479	431	rumA 23S rRNA (uracil-5-)-methyltransferase RumA.	90.95
PF00398	262	RrnaAD: Ribosomal RNA adenine dimethylase; InterPr	90.94
PF09243	274	Rsm22: Mitochondrial small ribosomal subunit Rsm22	90.86
TIGR00095	189	RNA methyltransferase, RsmD family. This model rep	90.78
PF13545	76	HTH_Crp_2: Crp-like helix-turn-helix domain; PDB:	90.17
PF08784	102	RPA_C: Replication protein A C terminal; InterPro:	90.04
PF08123	205	DOT1: Histone methylation protein DOT1 ; InterPro:	89.92
COG1378	247	Predicted transcriptional regulators [Transcriptio	89.86
PF01135	209	PCMT: Protein-L-isoaspartate(D-aspartate) O-methyl	89.83
PTZ00146	293	fibrillarin; Provisional	89.79
TIGR01177	329	conserved hypothetical protein TIGR01177. This fam	89.74
PRK14903	431	16S rRNA methyltransferase B; Provisional	89.72
PRK13509	251	transcriptional repressor UlaR; Provisional	89.72
KOG1499	346	consensus Protein arginine N-methyltransferase PRM	89.62
COG4976	287	Predicted methyltransferase (contains TPR repeat)	89.58
PRK04172	489	pheS phenylalanyl-tRNA synthetase subunit alpha; P	89.42
PRK14165	217	winged helix-turn-helix domain-containing protein/	89.29
PLN02823	336	spermine synthase	89.25
PRK00215	205	LexA repressor; Validated	89.2
PF13730	55	HTH_36: Helix-turn-helix domain	89.2
PF04182	75	B-block_TFIIIC: B-block binding subunit of TFIIIC;	89.14
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	89.1
KOG1541	270	consensus Predicted protein carboxyl methylase [Ge	89.06
PRK14901	434	16S rRNA methyltransferase B; Provisional	89.04
PRK00536	262	speE spermidine synthase; Provisional	89.01
TIGR00498	199	lexA SOS regulatory protein LexA. LexA acts as a h	88.96
PF03444	78	HrcA_DNA-bdg: Winged helix-turn-helix transcriptio	88.91
TIGR02787	251	codY_Gpos GTP-sensing transcriptional pleiotropic	88.87
TIGR02143	353	trmA_only tRNA (uracil-5-)-methyltransferase. This	88.79
PF00392	64	GntR: Bacterial regulatory proteins, gntR family;	88.65
COG1497	260	Predicted transcriptional regulator [Transcription	88.49
TIGR00446	264	nop2p NOL1/NOP2/sun family putative RNA methylase.	88.43
COG0030	259	KsgA Dimethyladenosine transferase (rRNA methylati	88.39
COG1846	126	MarR Transcriptional regulators [Transcription]	88.38
COG0421	282	SpeE Spermidine synthase [Amino acid transport and	88.14
PRK10906	252	DNA-binding transcriptional repressor GlpR; Provis	88.08
KOG3010	261	consensus Methyltransferase [General function pred	87.99
PHA02943	165	hypothetical protein; Provisional	87.8
KOG3420	185	consensus Predicted RNA methylase [Translation, ri	87.74
PRK14904	445	16S rRNA methyltransferase B; Provisional	87.6
PRK09802	269	DNA-binding transcriptional regulator AgaR; Provis	87.58
PRK11886	319	bifunctional biotin--[acetyl-CoA-carboxylase] synt	87.4
COG1349	253	GlpR Transcriptional regulators of sugar metabolis	87.35
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	87.29
PRK10046	225	dpiA two-component response regulator DpiA; Provis	87.11
PF01596	205	Methyltransf_3: O-methyltransferase; InterPro: IPR	87.06
PF10007	92	DUF2250: Uncharacterized protein conserved in arch	86.96
PF05732	165	RepL: Firmicute plasmid replication protein (RepL)	86.8
PRK13777	185	transcriptional regulator Hpr; Provisional	86.77
COG3432	95	Predicted transcriptional regulator [Transcription	86.71
PRK10434	256	srlR DNA-bindng transcriptional repressor SrlR; Pr	86.65
COG2512	258	Predicted membrane-associated trancriptional regul	86.59
PRK10411	240	DNA-binding transcriptional activator FucR; Provis	86.45
PRK05031	362	tRNA (uracil-5-)-methyltransferase; Validated	86.45
COG1510	177	Predicted transcriptional regulators [Transcriptio	86.4
COG2518	209	Pcm Protein-L-isoaspartate carboxylmethyltransfera	86.17
COG1733	120	Predicted transcriptional regulators [Transcriptio	85.96
KOG3045	325	consensus Predicted RNA methylase involved in rRNA	85.91
PF12793	115	SgrR_N: Sugar transport-related sRNA regulator N-t	85.74
PF05401	201	NodS: Nodulation protein S (NodS); InterPro: IPR00	85.56
PRK11639	169	zinc uptake transcriptional repressor; Provisional	85.21
PF13518	52	HTH_28: Helix-turn-helix domain	85.2
smart00531	147	TFIIE Transcription initiation factor IIE.	84.9
COG2263	198	Predicted RNA methylase [Translation, ribosomal st	84.88
TIGR02147	271	Fsuc_second hypothetical protein, TIGR02147. This	84.63
PF03141	506	Methyltransf_29: Putative S-adenosyl-L-methionine-	84.57
PRK12423	202	LexA repressor; Provisional	83.69
PF13384	50	HTH_23: Homeodomain-like domain; PDB: 2X48_C.	83.14
PF01564	246	Spermine_synth: Spermine/spermidine synthase; Inte	83.12
COG3413	215	Predicted DNA binding protein [General function pr	83.08
PF00165	42	HTH_AraC: Bacterial regulatory helix-turn-helix pr	82.91
PLN02853	492	Probable phenylalanyl-tRNA synthetase alpha chain	82.47
PF05584	72	Sulfolobus_pRN: Sulfolobus plasmid regulatory prot	82.27
COG1675	176	TFA1 Transcription initiation factor IIE, alpha su	82.24
PLN02476	278	O-methyltransferase	81.8
KOG2361	264	consensus Predicted methyltransferase [General fun	81.72
PRK05638	442	threonine synthase; Validated	81.65
TIGR03879	73	near_KaiC_dom probable regulatory domain. This mod	81.37
PF03428	177	RP-C: Replication protein C N-terminal domain; Int	81.29
COG1654	79	BirA Biotin operon repressor [Transcription]	81.06
PRK10736	374	hypothetical protein; Provisional	80.99
PRK15128	396	23S rRNA m(5)C1962 methyltransferase; Provisional	80.91
PTZ00326	494	phenylalanyl-tRNA synthetase alpha chain; Provisio	80.85
PRK11760	357	putative 23S rRNA C2498 ribose 2'-O-ribose methylt	80.76
PRK11753	211	DNA-binding transcriptional dual regulator Crp; Pr	80.68
COG4122	219	Predicted O-methyltransferase [General function pr	80.51
TIGR01321	94	TrpR trp operon repressor, proteobacterial. This m	80.45
PRK09954	362	putative kinase; Provisional	80.4
PRK04424	185	fatty acid biosynthesis transcriptional regulator;	80.36
PF01475	120	FUR: Ferric uptake regulator family; InterPro: IPR	80.29
PF08280	59	HTH_Mga: M protein trans-acting positive regulator	80.04

>TIGR02716 C20_methyl_CrtF C-20 methyltransferase BchU

Probab=99.91  E-value=2.5e-24  Score=185.74  Aligned_cols=165  Identities=18%  Similarity=0.286  Sum_probs=127.3

Q ss_pred             hHHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcc
Q 040620           28 MKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDF  107 (214)
Q Consensus        28 ~~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~  107 (214)
                      +...+|++|+++||||+|++  +|.|++|||+++|+++   +.++||||+|+++|+++++        +++|++|+.   
T Consensus         2 ~~~~~l~aa~~Lglfd~L~~--gp~t~~eLA~~~~~~~---~~~~~lL~~L~~lgll~~~--------~~~y~~t~~---   65 (306)
T TIGR02716         2 IEFSCMKAAIELDLFSHMAE--GPKDLATLAADTGSVP---PRLEMLLETLRQMRVINLE--------DGKWSLTEF---   65 (306)
T ss_pred             chHHHHHHHHHcCcHHHHhc--CCCCHHHHHHHcCCCh---HHHHHHHHHHHhCCCeEec--------CCcEecchh---
Confidence            46789999999999999987  8999999999999999   9999999999999999987        489999999   


Q ss_pred             cccccc-c--cc----hHHHHHHhhccchhhhhHhHHHhhcCCCCChhhHH---------HHHHHHHhhhh-hhhhHHHH
Q 040620          108 FSRISL-Q--LQ----GSTILLLIADATFTTSFHFLSTWLQNDDQTLFGTA---------DGIFYEAMITD-FELIASVL  170 (214)
Q Consensus       108 ~s~~l~-~--~~----~~~~~~~~~~~~~~~~~~~l~~~lr~~~~~~f~~~---------~g~f~~am~~~-~~~~~~~~  170 (214)
                       ++.++ +  +.    +..+...+.. .....|.++.+++|++.  +|...         ...|...|... .....+.+
T Consensus        66 -~~~~l~~~~~~~~~~~~~~~~~~~~-~~~~~~~~l~~~~r~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  141 (306)
T TIGR02716        66 -ADYMFSPTPKEPNLHQTPVAKAMAF-LADDFYMGLSQAVRGQK--NFKGQVPYPPVTREDNLYFEEIHRSNAKFAIQLL  141 (306)
T ss_pred             -HHhhccCCccchhhhcCchHHHHHH-HHHHHHHhHHHHhcCCc--ccccccCCCCCCHHHHHhHHHHHHhcchhHHHHH
Confidence             88776 2  21    1123322211 23356899999998532  23211         11455555433 33445556


Q ss_pred             HhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCCC
Q 040620          171 IEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACHL  214 (214)
Q Consensus       171 l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~  214 (214)
                      ++..+  +++..+|||||||+|.+++.+++++|+++++++|+|+
T Consensus       142 ~~~~~--~~~~~~vlDiG~G~G~~~~~~~~~~p~~~~~~~D~~~  183 (306)
T TIGR02716       142 LEEAK--LDGVKKMIDVGGGIGDISAAMLKHFPELDSTILNLPG  183 (306)
T ss_pred             HHHcC--CCCCCEEEEeCCchhHHHHHHHHHCCCCEEEEEecHH
Confidence            77766  7788999999999999999999999999999999873

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.

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

Probab=99.89  E-value=1.1e-22  Score=174.91  Aligned_cols=188  Identities=22%  Similarity=0.282  Sum_probs=160.9

Q ss_pred             hhhhHHHHHHHHHHHHhHHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHcC--CCCCCcccHHHHHHHHHhCCceeeecC
Q 040620           12 EHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALN--VHPNKTRCTQILVCLLAHSGFFVQQKD   89 (214)
Q Consensus        12 ~~~~~~~~l~~~~~g~~~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g--~~~~~~~~l~rlLr~L~~~g~l~~~~~   89 (214)
                      +..++..+++++++++..+++|++|+||||||+|+++ ++  +.|||..+.  ..|+.+..+.|+||.|++.+++++...
T Consensus         2 ~e~~~~l~~~~l~~~~~~~~~lk~A~eL~v~d~l~~~-~~--p~~ia~~l~~~~~~~~p~ll~r~lr~L~s~~i~k~~~~   78 (342)
T KOG3178|consen    2 EENEASLRAMRLANGFALPMVLKAACELGVFDILANA-GS--PSEIASLLPTPKNPEAPVLLDRILRLLVSYSILKCRLV   78 (342)
T ss_pred             chhHHHHHHHHHHhhhhhHHHHHHHHHcChHHHHHhC-CC--HHHHHHhccCCCCCCChhHHHHHHHHHHHhhhceeeee
Confidence            4567788999999999999999999999999999986 33  788888776  333344899999999999999998862


Q ss_pred             CCCCCccceeeCCCCCcccccccc----ccchHHHHHHhhccchhhhhHhHHHhhcCCCCChhhHHHH------------
Q 040620           90 GKNEQEEESILLPPHLDFFSRISL----QLQGSTILLLIADATFTTSFHFLSTWLQNDDQTLFGTADG------------  153 (214)
Q Consensus        90 ~~~~~~~~~y~~t~~~~~~s~~l~----~~~~~~~~~~~~~~~~~~~~~~l~~~lr~~~~~~f~~~~g------------  153 (214)
                      .   . + .|++++.    ++.++    ..++.+++........++.|.++.++++.++ .+|..++|            
T Consensus        79 ~---~-~-~Y~~~~~----~~~~l~~~~~~S~a~~~~~~~~~v~~~~w~~l~dai~eg~-~~~~~~~G~~l~~~~~~~~~  148 (342)
T KOG3178|consen   79 G---G-E-VYSATPV----CKYFLKDSGGGSLAPLVLLNTSKVIMNTWQFLKDAILEGG-DAFATAHGMMLGGYGGADER  148 (342)
T ss_pred             c---c-e-eeeccch----hhhheecCCCCchhHHHHHhcccchhhhHHHHHHHHHhcc-cCCccccchhhhhhcccccc
Confidence            0   1 2 8999999    99987    2678888888888889999999999999876 35555554            


Q ss_pred             ---HHHHHhhhhhhhhHHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          154 ---IFYEAMITDFELIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       154 ---~f~~am~~~~~~~~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                         .|+++|...++...+.+++.+. +|++..++||||||.|..+..++.+||+++++.||+|
T Consensus       149 ~~~~~~~sm~~l~~~~~~~il~~~~-Gf~~v~~avDvGgGiG~v~k~ll~~fp~ik~infdlp  210 (342)
T KOG3178|consen  149 FSKDFNGSMSFLSTLVMKKILEVYT-GFKGVNVAVDVGGGIGRVLKNLLSKYPHIKGINFDLP  210 (342)
T ss_pred             cHHHHHHHHHHHHHHHHHhhhhhhc-ccccCceEEEcCCcHhHHHHHHHHhCCCCceeecCHH
Confidence               7899998888888888889887 5899999999999999999999999999999999998

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

Probab=99.75  E-value=2.5e-18  Score=143.50  Aligned_cols=112  Identities=29%  Similarity=0.416  Sum_probs=93.8

Q ss_pred             cceeeCCCCCcccccccc-c---cchHHHHHHhhccchhhhhHhHHHhhcCCCCChhhHHHH---------------HHH
Q 040620           96 EESILLPPHLDFFSRISL-Q---LQGSTILLLIADATFTTSFHFLSTWLQNDDQTLFGTADG---------------IFY  156 (214)
Q Consensus        96 ~~~y~~t~~~~~~s~~l~-~---~~~~~~~~~~~~~~~~~~~~~l~~~lr~~~~~~f~~~~g---------------~f~  156 (214)
                      +++|++|+.    |+.|+ +   .++..++.++.....+..|.+|.+++++|+ ++|...+|               .|+
T Consensus         3 ~~~y~~t~~----s~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~v~~g~-~~~~~~~g~~~~~~~~~~~~~~~~f~   77 (241)
T PF00891_consen    3 GDRYSLTPL----SELLLSDHSSPSMRGFVLFMISPELYPAWFRLTEAVRTGK-PPFEKAFGTPFFEYLEEDPELAKRFN   77 (241)
T ss_dssp             TEEEEE-HH----HHGGSTTTTTTHHHHHHHHHTCHHHHHGGGGHHHHHHHSS--HHHHHHSS-HHHHHHCSHHHHHHHH
T ss_pred             CCEEeChHH----HHHHhCCCCcCcHHHHHHHhcCHHHHHHHHHHHhhhccCC-CHHHHhcCCcHHHhhhhChHHHHHHH
Confidence            689999999    99988 3   357777777677788999999999999987 66666544               789


Q ss_pred             HHhhhhhhhhH-HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCCC
Q 040620          157 EAMITDFELIA-SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACHL  214 (214)
Q Consensus       157 ~am~~~~~~~~-~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~  214 (214)
                      ++|...+.... ..++..++  +++.++|||||||+|.++.+++++||+++++++|+|+
T Consensus        78 ~~m~~~~~~~~~~~~~~~~d--~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~  134 (241)
T PF00891_consen   78 AAMAEYSRLNAFDILLEAFD--FSGFKTVVDVGGGSGHFAIALARAYPNLRATVFDLPE  134 (241)
T ss_dssp             HHHHHHHHHHHHHHHHHHST--TTTSSEEEEET-TTSHHHHHHHHHSTTSEEEEEE-HH
T ss_pred             HHHHhhhhcchhhhhhcccc--ccCccEEEeccCcchHHHHHHHHHCCCCcceeeccHh
Confidence            99998888776 77888888  8888999999999999999999999999999999984

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=98.92  E-value=4.7e-10  Score=71.35  Aligned_cols=49  Identities=37%  Similarity=0.640  Sum_probs=42.3

Q ss_pred             HHHHHHHhcCcchhhhcCC-CCCCHHHHHHHcC-CCCCCcccHHHHHHHHH
Q 040620           31 LSLKRAIQLRIPDIINNSG-QPMTLTQIIVALN-VHPNKTRCTQILVCLLA   79 (214)
Q Consensus        31 ~~L~~a~~lglfd~L~~~~-~p~t~~eLA~~~g-~~~~~~~~l~rlLr~L~   79 (214)
                      .+|++|+||||||+|+.+| +|+|..||+.++. .+|.+...|+|+||+|+
T Consensus         1 MaLk~aveLgI~dii~~~g~~~ls~~eia~~l~~~~p~~~~~L~RimR~L~   51 (51)
T PF08100_consen    1 MALKCAVELGIPDIIHNAGGGPLSLSEIAARLPTSNPSAPPMLDRIMRLLV   51 (51)
T ss_dssp             HHHHHHHHTTHHHHHHHHTTS-BEHHHHHHTSTCT-TTHHHHHHHHHHHHH
T ss_pred             CcHHHHHHcCcHHHHHHcCCCCCCHHHHHHHcCCCCcchHHHHHHHHHHhC
Confidence            4799999999999999986 7999999999999 77756679999999986

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 ....

>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=97.83  E-value=6.2e-06  Score=52.52  Aligned_cols=47  Identities=30%  Similarity=0.485  Sum_probs=41.5

Q ss_pred             cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      +.|+++|...++++|+.|||+++|++.   ..++|+|..|+..|++.+++
T Consensus         6 l~iL~~l~~~~~~~t~~eia~~~gl~~---stv~r~L~tL~~~g~v~~dp   52 (52)
T PF09339_consen    6 LRILEALAESGGPLTLSEIARALGLPK---STVHRLLQTLVEEGYVERDP   52 (52)
T ss_dssp             HHHHHCHHCTBSCEEHHHHHHHHTS-H---HHHHHHHHHHHHTTSEEECS
T ss_pred             HHHHHHHHcCCCCCCHHHHHHHHCcCH---HHHHHHHHHHHHCcCeecCc
Confidence            457888888878899999999999999   99999999999999999873

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.

>PRK14103 trans-aconitate 2-methyltransferase; Provisional

Probab=97.67  E-value=0.00011  Score=61.72  Aligned_cols=43  Identities=19%  Similarity=0.382  Sum_probs=37.3

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+++.++  .....+|||||||+|.++..+++++|+.+++++|+
T Consensus        19 ~~ll~~l~--~~~~~~vLDlGcG~G~~~~~l~~~~p~~~v~gvD~   61 (255)
T PRK14103         19 YDLLARVG--AERARRVVDLGCGPGNLTRYLARRWPGAVIEALDS   61 (255)
T ss_pred             HHHHHhCC--CCCCCEEEEEcCCCCHHHHHHHHHCCCCEEEEEEC
Confidence            45666665  55678999999999999999999999999999997

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

Probab=97.54  E-value=0.00012  Score=59.99  Aligned_cols=44  Identities=23%  Similarity=0.326  Sum_probs=39.2

Q ss_pred             HHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          167 ASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       167 ~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +-.++..++  ......|+|+|||+|.....|++++|...++++|-
T Consensus        19 a~dLla~Vp--~~~~~~v~DLGCGpGnsTelL~~RwP~A~i~GiDs   62 (257)
T COG4106          19 ARDLLARVP--LERPRRVVDLGCGPGNSTELLARRWPDAVITGIDS   62 (257)
T ss_pred             HHHHHhhCC--ccccceeeecCCCCCHHHHHHHHhCCCCeEeeccC
Confidence            355777787  77889999999999999999999999999999984

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

Probab=97.53  E-value=0.00017  Score=57.77  Aligned_cols=35  Identities=31%  Similarity=0.466  Sum_probs=32.3

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+..+|||||||+|.+++.+++++|+.+++.+|.
T Consensus        29 ~~~~~~vLDiG~G~G~~~~~la~~~~~~~v~~vD~   63 (187)
T PRK08287         29 LHRAKHLIDVGAGTGSVSIEAALQFPSLQVTAIER   63 (187)
T ss_pred             CCCCCEEEEECCcCCHHHHHHHHHCCCCEEEEEEC
Confidence            45678999999999999999999999999999997

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

Probab=97.50  E-value=0.00029  Score=51.67  Aligned_cols=41  Identities=15%  Similarity=0.246  Sum_probs=34.1

Q ss_pred             HHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          170 LIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       170 ~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +++.++  .....+++|+|||.|.++..+++++|+.+++.+|.
T Consensus        11 ~~~~~~--~~~~~~vldlG~G~G~~~~~l~~~~~~~~v~~vD~   51 (124)
T TIGR02469        11 TLSKLR--LRPGDVLWDIGAGSGSITIEAARLVPNGRVYAIER   51 (124)
T ss_pred             HHHHcC--CCCCCEEEEeCCCCCHHHHHHHHHCCCceEEEEcC
Confidence            344444  34456999999999999999999999999999996

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.

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=97.41  E-value=0.00014  Score=51.17  Aligned_cols=57  Identities=18%  Similarity=0.255  Sum_probs=48.5

Q ss_pred             cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      +.|++.|...++++|+.|||+.+|+++   ..++|.|+.|...|++...+.      ++.|.+++.
T Consensus         8 ~~Il~~l~~~~~~~t~~~ia~~l~i~~---~tv~r~l~~L~~~g~l~~~~~------~~~y~l~~~   64 (91)
T smart00346        8 LAVLRALAEEPGGLTLAELAERLGLSK---STAHRLLNTLQELGYVEQDGQ------NGRYRLGPK   64 (91)
T ss_pred             HHHHHHHHhCCCCcCHHHHHHHhCCCH---HHHHHHHHHHHHCCCeeecCC------CCceeecHH
Confidence            456777876546899999999999999   999999999999999998742      567888776

>PRK01683 trans-aconitate 2-methyltransferase; Provisional

Probab=97.39  E-value=0.00032  Score=58.86  Aligned_cols=44  Identities=18%  Similarity=0.299  Sum_probs=37.8

Q ss_pred             HHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          167 ASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       167 ~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...++..++  ..+..+|+|||||.|.++..+++++|+.+++.+|.
T Consensus        20 ~~~ll~~~~--~~~~~~vLDiGcG~G~~~~~la~~~~~~~v~gvD~   63 (258)
T PRK01683         20 ARDLLARVP--LENPRYVVDLGCGPGNSTELLVERWPAARITGIDS   63 (258)
T ss_pred             HHHHHhhCC--CcCCCEEEEEcccCCHHHHHHHHHCCCCEEEEEEC
Confidence            345666665  56678999999999999999999999999999997

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

Probab=97.33  E-value=0.00038  Score=59.81  Aligned_cols=43  Identities=21%  Similarity=0.296  Sum_probs=36.1

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .-+++.++  .....+|+|+|||.|.+++.+++.+|+.+++.+|.
T Consensus       148 ~lLl~~l~--~~~~~~vlDlGCG~Gvlg~~la~~~p~~~vtmvDv  190 (300)
T COG2813         148 RLLLETLP--PDLGGKVLDLGCGYGVLGLVLAKKSPQAKLTLVDV  190 (300)
T ss_pred             HHHHHhCC--ccCCCcEEEeCCCccHHHHHHHHhCCCCeEEEEec
Confidence            44667777  33344999999999999999999999999999885

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

Probab=97.27  E-value=0.00046  Score=61.55  Aligned_cols=42  Identities=14%  Similarity=0.237  Sum_probs=34.7

Q ss_pred             HHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          170 LIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       170 ~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                      +++.++  .....+|+|+|||+|..++.+++++|+.+++.+|..
T Consensus       220 lL~~lp--~~~~~~VLDLGCGtGvi~i~la~~~P~~~V~~vD~S  261 (378)
T PRK15001        220 FMQHLP--ENLEGEIVDLGCGNGVIGLTLLDKNPQAKVVFVDES  261 (378)
T ss_pred             HHHhCC--cccCCeEEEEeccccHHHHHHHHhCCCCEEEEEECC
Confidence            455555  222369999999999999999999999999999974

>COG1414 IclR Transcriptional regulator [Transcription]

Probab=97.25  E-value=0.00022  Score=60.00  Aligned_cols=57  Identities=19%  Similarity=0.320  Sum_probs=49.9

Q ss_pred             cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      +.|+++|...+.++++.|||+++|+++   ..++|+|..|+..|++.+++.      +++|.+++.
T Consensus         7 l~iL~~l~~~~~~l~l~ela~~~glpk---sT~~RlL~tL~~~G~v~~d~~------~g~Y~Lg~~   63 (246)
T COG1414           7 LAILDLLAEGPGGLSLAELAERLGLPK---STVHRLLQTLVELGYVEQDPE------DGRYRLGPR   63 (246)
T ss_pred             HHHHHHHHhCCCCCCHHHHHHHhCcCH---HHHHHHHHHHHHCCCEEEcCC------CCcEeehHH
Confidence            457888887545577999999999999   999999999999999999974      578999988

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

Probab=97.17  E-value=0.00053  Score=46.15  Aligned_cols=60  Identities=18%  Similarity=0.219  Sum_probs=48.4

Q ss_pred             HhcCcchhhhcCCC-CCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           37 IQLRIPDIINNSGQ-PMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        37 ~~lglfd~L~~~~~-p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      .+-.|+..|..+|+ ++|+.|||+.+|++.   ..++|.|..|...|+++..+..     +..|.++..
T Consensus         7 ~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~---~~v~r~L~~L~~~G~V~~~~~~-----~~~W~i~~~   67 (68)
T smart00550        7 LEEKILEFLENSGDETSTALQLAKNLGLPK---KEVNRVLYSLEKKGKVCKQGGT-----PPLWKLTDK   67 (68)
T ss_pred             HHHHHHHHHHHCCCCCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEecCCC-----CCceEeecC
Confidence            44567788888744 399999999999999   9999999999999999986520     367777653

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

>PRK06922 hypothetical protein; Provisional

Probab=97.16  E-value=0.0008  Score=63.55  Aligned_cols=36  Identities=22%  Similarity=0.208  Sum_probs=32.8

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                      +.+..+|||||||+|.++..+++.+|+.+++++|+.
T Consensus       416 ~~~g~rVLDIGCGTG~ls~~LA~~~P~~kVtGIDIS  451 (677)
T PRK06922        416 YIKGDTIVDVGAGGGVMLDMIEEETEDKRIYGIDIS  451 (677)
T ss_pred             hcCCCEEEEeCCCCCHHHHHHHHhCCCCEEEEEECC
Confidence            345689999999999999999999999999999985

>PRK11569 transcriptional repressor IclR; Provisional

Probab=97.16  E-value=0.00035  Score=59.56  Aligned_cols=57  Identities=19%  Similarity=0.283  Sum_probs=49.9

Q ss_pred             cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      +.|+++|.+.+.|+|+.|||+++|+++   ..++|+|..|+..||+.+++.      .++|++.+.
T Consensus        31 l~IL~~l~~~~~~~~lseia~~lglpk---sTv~RlL~tL~~~G~l~~~~~------~~~Y~lG~~   87 (274)
T PRK11569         31 LKLLEWIAESNGSVALTELAQQAGLPN---STTHRLLTTMQQQGFVRQVGE------LGHWAIGAH   87 (274)
T ss_pred             HHHHHHHHhCCCCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEcCC------CCeEecCHH
Confidence            457777776557899999999999999   999999999999999998753      689999877

>PRK00107 gidB 16S rRNA methyltransferase GidB; Reviewed

Probab=97.13  E-value=0.00063  Score=54.89  Aligned_cols=32  Identities=28%  Similarity=0.378  Sum_probs=30.4

Q ss_pred             CCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          181 LKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       181 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+|+|||||+|..+..+++++|+.+++.+|.
T Consensus        46 g~~VLDiGcGtG~~al~la~~~~~~~V~giD~   77 (187)
T PRK00107         46 GERVLDVGSGAGFPGIPLAIARPELKVTLVDS   77 (187)
T ss_pred             CCeEEEEcCCCCHHHHHHHHHCCCCeEEEEeC
Confidence            68999999999999999999999999999986

>PRK10163 DNA-binding transcriptional repressor AllR; Provisional

Probab=97.12  E-value=0.00043  Score=58.92  Aligned_cols=57  Identities=18%  Similarity=0.193  Sum_probs=50.2

Q ss_pred             cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      +.|++.|..+++++|+.|||+++|+++   ..+.|+|..|+..|++.+++.      .++|.+++.
T Consensus        28 l~IL~~~~~~~~~~tl~eIa~~lglpk---Stv~RlL~tL~~~G~l~~~~~------~~~Y~lG~~   84 (271)
T PRK10163         28 IAILQYLEKSGGSSSVSDISLNLDLPL---STTFRLLKVLQAADFVYQDSQ------LGWWHIGLG   84 (271)
T ss_pred             HHHHHHHHhCCCCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEcCC------CCeEEecHH
Confidence            567788877657899999999999999   999999999999999998753      688999887

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

Probab=97.07  E-value=0.00059  Score=53.93  Aligned_cols=33  Identities=27%  Similarity=0.369  Sum_probs=30.7

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+++|+|||+|..++.+++++|+.+++..|.
T Consensus        31 ~~~~vLDlG~G~G~i~~~la~~~~~~~v~~vDi   63 (170)
T PF05175_consen   31 KGGRVLDLGCGSGVISLALAKRGPDAKVTAVDI   63 (170)
T ss_dssp             TTCEEEEETSTTSHHHHHHHHTSTCEEEEEEES
T ss_pred             cCCeEEEecCChHHHHHHHHHhCCCCEEEEEcC
Confidence            467999999999999999999999999998886

; 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 ....

>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional

Probab=97.05  E-value=0.00051  Score=57.89  Aligned_cols=56  Identities=11%  Similarity=0.195  Sum_probs=49.1

Q ss_pred             cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      +.|++.|... +++|+.|||+++|+++   ..++|+|+.|+..|++.+++.      .++|.+.+.
T Consensus        17 l~IL~~l~~~-~~l~l~eia~~lgl~k---stv~Rll~tL~~~G~l~~~~~------~~~Y~lG~~   72 (257)
T PRK15090         17 FGILQALGEE-REIGITELSQRVMMSK---STVYRFLQTMKTLGYVAQEGE------SEKYSLTLK   72 (257)
T ss_pred             HHHHHHhhcC-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEcCC------CCcEEecHH
Confidence            4566777765 6899999999999999   999999999999999998753      589999988

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

Probab=97.04  E-value=0.0012  Score=54.38  Aligned_cols=43  Identities=19%  Similarity=0.169  Sum_probs=34.7

Q ss_pred             HHHhhcccccCCCCcEEeecCCchHHHHHHHHHC-CCCeEEEecCC
Q 040620          169 VLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAF-PDTKCTVFACH  213 (214)
Q Consensus       169 ~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dlp  213 (214)
                      .++..++  .....+|||||||+|.++..+++.+ |+.+++++|+-
T Consensus        36 ~~l~~l~--~~~~~~vLDiGcG~G~~~~~la~~~~~~~~v~gvD~s   79 (231)
T TIGR02752        36 DTMKRMN--VQAGTSALDVCCGTADWSIALAEAVGPEGHVIGLDFS   79 (231)
T ss_pred             HHHHhcC--CCCCCEEEEeCCCcCHHHHHHHHHhCCCCEEEEEECC
Confidence            3445444  5556899999999999999999986 67899999973

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.

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

Probab=97.03  E-value=0.00051  Score=57.56  Aligned_cols=55  Identities=16%  Similarity=0.282  Sum_probs=49.0

Q ss_pred             cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      +.|++.|...+.|+|+.|||+++|+++   ..++|+|..|+..|++.++        +++|.+.+.
T Consensus        12 l~IL~~l~~~~~~~~l~eia~~lglpk---sT~~RlL~tL~~~G~l~~~--------~~~Y~lG~~   66 (248)
T TIGR02431        12 LAVIEAFGAERPRLTLTDVAEATGLTR---AAARRFLLTLVELGYVTSD--------GRLFWLTPR   66 (248)
T ss_pred             HHHHHHHhcCCCCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEeC--------CCEEEecHH
Confidence            567788876558899999999999999   9999999999999999875        478999988

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.

>TIGR00138 gidB 16S rRNA methyltransferase GidB

Probab=97.03  E-value=0.00067  Score=54.38  Aligned_cols=33  Identities=27%  Similarity=0.419  Sum_probs=30.5

Q ss_pred             CCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          181 LKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       181 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                      ..+|+|||||+|..+..++..+|+.+++.+|.-
T Consensus        43 ~~~vLDiGcGtG~~s~~la~~~~~~~V~~iD~s   75 (181)
T TIGR00138        43 GKKVIDIGSGAGFPGIPLAIARPELKLTLLESN   75 (181)
T ss_pred             CCeEEEecCCCCccHHHHHHHCCCCeEEEEeCc
Confidence            679999999999999999999999999999863

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.

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

Probab=97.02  E-value=0.0016  Score=55.71  Aligned_cols=43  Identities=19%  Similarity=0.214  Sum_probs=37.5

Q ss_pred             HHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          167 ASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       167 ~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+.+++.+.  +.+..+|||||||-|.+++-.+++| +.+++.+++
T Consensus        61 ~~~~~~kl~--L~~G~~lLDiGCGWG~l~~~aA~~y-~v~V~GvTl  103 (283)
T COG2230          61 LDLILEKLG--LKPGMTLLDIGCGWGGLAIYAAEEY-GVTVVGVTL  103 (283)
T ss_pred             HHHHHHhcC--CCCCCEEEEeCCChhHHHHHHHHHc-CCEEEEeeC
Confidence            355667666  8889999999999999999999999 999998876

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

Probab=96.97  E-value=0.0013  Score=58.86  Aligned_cols=33  Identities=18%  Similarity=0.130  Sum_probs=30.7

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ....+||||||+|.++..+++++|+..++++|+
T Consensus       122 ~~p~vLEIGcGsG~~ll~lA~~~P~~~~iGIEI  154 (390)
T PRK14121        122 QEKILIEIGFGSGRHLLYQAKNNPNKLFIGIEI  154 (390)
T ss_pred             CCCeEEEEcCcccHHHHHHHHhCCCCCEEEEEC
Confidence            456999999999999999999999999999986

>PRK07402 precorrin-6B methylase; Provisional

Probab=96.96  E-value=0.0017  Score=52.34  Aligned_cols=41  Identities=22%  Similarity=0.272  Sum_probs=34.1

Q ss_pred             HHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          170 LIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       170 ~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ++..++  .....+|+|+|||+|.++..+++..|..+++.+|+
T Consensus        32 l~~~l~--~~~~~~VLDiG~G~G~~~~~la~~~~~~~V~~vD~   72 (196)
T PRK07402         32 LISQLR--LEPDSVLWDIGAGTGTIPVEAGLLCPKGRVIAIER   72 (196)
T ss_pred             HHHhcC--CCCCCEEEEeCCCCCHHHHHHHHHCCCCEEEEEeC
Confidence            344444  44567999999999999999999999999999997

>TIGR03587 Pse_Me-ase pseudaminic acid biosynthesis-associated methylase

Probab=96.92  E-value=0.0013  Score=53.72  Aligned_cols=34  Identities=12%  Similarity=0.213  Sum_probs=30.9

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+..+|||||||+|..+..+++..|..+++.+|+
T Consensus        42 ~~~~~VLDiGCG~G~~~~~L~~~~~~~~v~giDi   75 (204)
T TIGR03587        42 PKIASILELGANIGMNLAALKRLLPFKHIYGVEI   75 (204)
T ss_pred             CCCCcEEEEecCCCHHHHHHHHhCCCCeEEEEEC
Confidence            3567999999999999999999999999999986

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

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

Probab=96.90  E-value=0.0011  Score=53.88  Aligned_cols=33  Identities=18%  Similarity=0.217  Sum_probs=30.6

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +..+|+|||||+|.++..+++.+|+.+++.+|.
T Consensus        40 ~~~~VLDiGcGtG~~~~~la~~~p~~~v~gVD~   72 (202)
T PRK00121         40 DAPIHLEIGFGKGEFLVEMAKANPDINFIGIEV   72 (202)
T ss_pred             CCCeEEEEccCCCHHHHHHHHHCCCccEEEEEe
Confidence            467999999999999999999999999999986

>PRK09834 DNA-binding transcriptional activator MhpR; Provisional

Probab=96.89  E-value=0.00085  Score=56.79  Aligned_cols=57  Identities=16%  Similarity=0.205  Sum_probs=49.5

Q ss_pred             cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      +.|++.|...++++|..|||+++|+++   ..+.|+|+.|...|++.+++.      +++|.+++.
T Consensus        14 l~iL~~l~~~~~~ls~~eia~~lgl~k---stv~RlL~tL~~~g~v~~~~~------~~~Y~Lg~~   70 (263)
T PRK09834         14 LMVLRALNRLDGGATVGLLAELTGLHR---TTVRRLLETLQEEGYVRRSAS------DDSFRLTLK   70 (263)
T ss_pred             HHHHHHHHhcCCCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEecC------CCcEEEcHH
Confidence            456777776546799999999999999   999999999999999998863      578999887

>PRK09489 rsmC 16S ribosomal RNA m2G1207 methyltransferase; Provisional

Probab=96.88  E-value=0.0018  Score=57.01  Aligned_cols=33  Identities=21%  Similarity=0.351  Sum_probs=30.2

Q ss_pred             CCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          181 LKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       181 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                      ..+|+|+|||.|.+++.+++++|+.+++..|.-
T Consensus       197 ~g~VLDlGCG~G~ls~~la~~~p~~~v~~vDis  229 (342)
T PRK09489        197 KGKVLDVGCGAGVLSAVLARHSPKIRLTLSDVS  229 (342)
T ss_pred             CCeEEEeccCcCHHHHHHHHhCCCCEEEEEECC
Confidence            458999999999999999999999999999863

>TIGR02072 BioC biotin biosynthesis protein BioC

Probab=96.87  E-value=0.0026  Score=51.95  Aligned_cols=34  Identities=24%  Similarity=0.440  Sum_probs=30.6

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                      ...+|||||||.|.++..+++..|+.++++.|..
T Consensus        34 ~~~~vLDlG~G~G~~~~~l~~~~~~~~~~~~D~~   67 (240)
T TIGR02072        34 IPASVLDIGCGTGYLTRALLKRFPQAEFIALDIS   67 (240)
T ss_pred             CCCeEEEECCCccHHHHHHHHhCCCCcEEEEeCh
Confidence            3478999999999999999999999999998863

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.

>TIGR00740 methyltransferase, putative

Probab=96.85  E-value=0.0014  Score=54.36  Aligned_cols=33  Identities=18%  Similarity=0.162  Sum_probs=29.8

Q ss_pred             CCCcEEeecCCchHHHHHHHHH--CCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATA--FPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~--~P~l~~~v~Dl  212 (214)
                      +..+|||||||+|..+..++++  +|+.+++++|+
T Consensus        53 ~~~~iLDlGcG~G~~~~~l~~~~~~p~~~v~gvD~   87 (239)
T TIGR00740        53 PDSNVYDLGCSRGAATLSARRNINQPNVKIIGIDN   87 (239)
T ss_pred             CCCEEEEecCCCCHHHHHHHHhcCCCCCeEEEEeC
Confidence            4578999999999999999997  48999999997

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.

>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=96.75  E-value=0.00073  Score=44.26  Aligned_cols=54  Identities=19%  Similarity=0.351  Sum_probs=44.6

Q ss_pred             HHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           31 LSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        31 ~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      .+|.--.++.|+..|... +|+|+.|||+.+|+++   ..+.+-|+.|...|++....
T Consensus         5 ~aL~~p~R~~Il~~L~~~-~~~t~~ela~~l~~~~---~t~s~hL~~L~~aGli~~~~   58 (61)
T PF12840_consen    5 KALSDPTRLRILRLLASN-GPMTVSELAEELGISQ---STVSYHLKKLEEAGLIEVER   58 (61)
T ss_dssp             HHHTSHHHHHHHHHHHHC-STBEHHHHHHHHTS-H---HHHHHHHHHHHHTTSEEEEE
T ss_pred             HHhCCHHHHHHHHHHhcC-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCeEEec
Confidence            344445667788888444 8999999999999999   99999999999999999875

...

>PRK15451 tRNA cmo(5)U34 methyltransferase; Provisional

Probab=96.72  E-value=0.0018  Score=54.27  Aligned_cols=33  Identities=15%  Similarity=0.159  Sum_probs=29.7

Q ss_pred             CCCcEEeecCCchHHHHHHHH--HCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIAT--AFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~--~~P~l~~~v~Dl  212 (214)
                      +..+|+|||||+|..+..+++  .+|+.+++.+|.
T Consensus        56 ~~~~vLDlGcGtG~~~~~l~~~~~~~~~~v~gvD~   90 (247)
T PRK15451         56 PGTQVYDLGCSLGAATLSVRRNIHHDNCKIIAIDN   90 (247)
T ss_pred             CCCEEEEEcccCCHHHHHHHHhcCCCCCeEEEEeC
Confidence            457899999999999999998  479999999996

>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=0.0011  Score=41.22  Aligned_cols=44  Identities=14%  Similarity=0.215  Sum_probs=37.4

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCcee
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFV   85 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~   85 (214)
                      +..|+..|.++ +++|..|||+++|++.   ..+++.++-|...|+++
T Consensus         5 ~~~Il~~l~~~-~~~t~~ela~~~~is~---~tv~~~l~~L~~~g~I~   48 (48)
T PF13412_consen    5 QRKILNYLREN-PRITQKELAEKLGISR---STVNRYLKKLEEKGLIE   48 (48)
T ss_dssp             HHHHHHHHHHC-TTS-HHHHHHHHTS-H---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHc-CCCCHHHHHHHhCCCH---HHHHHHHHHHHHCcCcC
Confidence            45677888887 7799999999999999   99999999999999874

...

>PRK11207 tellurite resistance protein TehB; Provisional

Probab=96.71  E-value=0.0028  Score=51.29  Aligned_cols=41  Identities=17%  Similarity=0.178  Sum_probs=33.0

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +.+++.++  .....+|||+|||.|..+..++++  ..+++.+|+
T Consensus        20 ~~l~~~l~--~~~~~~vLDiGcG~G~~a~~La~~--g~~V~gvD~   60 (197)
T PRK11207         20 SEVLEAVK--VVKPGKTLDLGCGNGRNSLYLAAN--GFDVTAWDK   60 (197)
T ss_pred             HHHHHhcc--cCCCCcEEEECCCCCHHHHHHHHC--CCEEEEEeC
Confidence            45556555  445689999999999999999986  568999987

>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=96.66  E-value=0.0083  Score=39.36  Aligned_cols=44  Identities=16%  Similarity=0.206  Sum_probs=39.6

Q ss_pred             CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCC
Q 040620           50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPP  103 (214)
Q Consensus        50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~  103 (214)
                      .++|..+||+.+|+++   ..+.+.++.|...|++....       .+.|.++|
T Consensus        24 ~~~s~~ela~~~g~s~---~tv~r~l~~L~~~g~i~~~~-------~~~~~l~~   67 (67)
T cd00092          24 LPLTRQEIADYLGLTR---ETVSRTLKELEEEGLISRRG-------RGKYRVNP   67 (67)
T ss_pred             CCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEecC-------CCeEEeCC
Confidence            7899999999999999   99999999999999999875       37787764

>PRK15068 tRNA mo(5)U34 methyltransferase; Provisional

Probab=96.64  E-value=0.0028  Score=55.37  Aligned_cols=32  Identities=16%  Similarity=0.059  Sum_probs=28.2

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..++|+|||||+|.++..+++..|. +++++|.
T Consensus       122 ~g~~VLDIGCG~G~~~~~la~~g~~-~V~GiD~  153 (322)
T PRK15068        122 KGRTVLDVGCGNGYHMWRMLGAGAK-LVVGIDP  153 (322)
T ss_pred             CCCEEEEeccCCcHHHHHHHHcCCC-EEEEEcC
Confidence            4589999999999999999999877 4888884

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

Probab=96.63  E-value=0.0031  Score=53.86  Aligned_cols=42  Identities=21%  Similarity=0.219  Sum_probs=30.7

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+++..+  ..+..+|||||||-|.+++.++++| +.+++++.+
T Consensus        52 ~~~~~~~~--l~~G~~vLDiGcGwG~~~~~~a~~~-g~~v~gitl   93 (273)
T PF02353_consen   52 DLLCEKLG--LKPGDRVLDIGCGWGGLAIYAAERY-GCHVTGITL   93 (273)
T ss_dssp             HHHHTTTT----TT-EEEEES-TTSHHHHHHHHHH---EEEEEES
T ss_pred             HHHHHHhC--CCCCCEEEEeCCCccHHHHHHHHHc-CcEEEEEEC
Confidence            45666665  7778899999999999999999999 889888765

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 ....

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

Probab=96.61  E-value=0.0038  Score=53.14  Aligned_cols=41  Identities=10%  Similarity=0.262  Sum_probs=32.6

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+++.++  .....+|+|||||+|.++..++++.+  +++.+|.
T Consensus        32 ~~i~~~l~--~~~~~~VLEiG~G~G~lt~~L~~~~~--~v~avE~   72 (272)
T PRK00274         32 DKIVDAAG--PQPGDNVLEIGPGLGALTEPLLERAA--KVTAVEI   72 (272)
T ss_pred             HHHHHhcC--CCCcCeEEEeCCCccHHHHHHHHhCC--cEEEEEC
Confidence            44555554  45567999999999999999999987  7777775

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

Probab=96.60  E-value=0.0027  Score=54.48  Aligned_cols=33  Identities=27%  Similarity=0.436  Sum_probs=30.6

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +..+|+|+|||+|.+++.+++++|+.+++.+|+
T Consensus       121 ~~~~vLDlG~GsG~i~~~la~~~~~~~v~avDi  153 (284)
T TIGR03533       121 PVKRILDLCTGSGCIAIACAYAFPEAEVDAVDI  153 (284)
T ss_pred             CCCEEEEEeCchhHHHHHHHHHCCCCEEEEEEC
Confidence            356899999999999999999999999999997

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.

>PRK04457 spermidine synthase; Provisional

Probab=96.56  E-value=0.003  Score=53.58  Aligned_cols=33  Identities=27%  Similarity=0.422  Sum_probs=31.1

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +.++|+|||||.|.++..+++.+|+.+++++|+
T Consensus        66 ~~~~vL~IG~G~G~l~~~l~~~~p~~~v~~VEi   98 (262)
T PRK04457         66 RPQHILQIGLGGGSLAKFIYTYLPDTRQTAVEI   98 (262)
T ss_pred             CCCEEEEECCCHhHHHHHHHHhCCCCeEEEEEC
Confidence            467999999999999999999999999999998

>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=96.56  E-value=0.00053  Score=45.86  Aligned_cols=47  Identities=13%  Similarity=0.165  Sum_probs=39.9

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      +..++..|-.+ +++|+++||+.+|++.   ..+++.|+.|...|++....
T Consensus        10 E~~vy~~Ll~~-~~~t~~eIa~~l~i~~---~~v~~~L~~L~~~GlV~~~~   56 (68)
T PF01978_consen   10 EAKVYLALLKN-GPATAEEIAEELGISR---STVYRALKSLEEKGLVEREE   56 (68)
T ss_dssp             HHHHHHHHHHH-CHEEHHHHHHHHTSSH---HHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEEc
Confidence            34455555444 8999999999999999   99999999999999999885

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.

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

Probab=96.55  E-value=0.0025  Score=54.65  Aligned_cols=30  Identities=27%  Similarity=0.469  Sum_probs=29.0

Q ss_pred             cEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          183 PLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       183 ~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +|+|||+|+|..+++++++.|+++++..|+
T Consensus       113 ~ilDlGTGSG~iai~la~~~~~~~V~a~Di  142 (280)
T COG2890         113 RILDLGTGSGAIAIALAKEGPDAEVIAVDI  142 (280)
T ss_pred             cEEEecCChHHHHHHHHhhCcCCeEEEEEC
Confidence            799999999999999999999999999986

>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=96.54  E-value=0.0044  Score=47.38  Aligned_cols=33  Identities=30%  Similarity=0.271  Sum_probs=27.5

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .....+|||||||.|.++..+.+..+  +++++|.
T Consensus        20 ~~~~~~vLDiGcG~G~~~~~l~~~~~--~~~g~D~   52 (161)
T PF13489_consen   20 LKPGKRVLDIGCGTGSFLRALAKRGF--EVTGVDI   52 (161)
T ss_dssp             TTTTSEEEEESSTTSHHHHHHHHTTS--EEEEEES
T ss_pred             cCCCCEEEEEcCCCCHHHHHHHHhCC--EEEEEEC
Confidence            34678999999999999999977644  8888885

...

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

Probab=96.54  E-value=0.0031  Score=52.25  Aligned_cols=33  Identities=30%  Similarity=0.507  Sum_probs=30.3

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+|+|+|||+|.++..+++.+|+.+++++|.
T Consensus        87 ~~~~ilDig~G~G~~~~~l~~~~~~~~v~~iD~  119 (251)
T TIGR03534        87 GPLRVLDLGTGSGAIALALAKERPDARVTAVDI  119 (251)
T ss_pred             CCCeEEEEeCcHhHHHHHHHHHCCCCEEEEEEC
Confidence            346899999999999999999999999999986

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.

>PRK06202 hypothetical protein; Provisional

Probab=96.52  E-value=0.0079  Score=49.66  Aligned_cols=34  Identities=21%  Similarity=0.154  Sum_probs=28.7

Q ss_pred             CCCCcEEeecCCchHHHHHHHHH----CCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATA----FPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~----~P~l~~~v~Dl  212 (214)
                      .+..+|+|||||+|.++..|++.    .|+.+++++|+
T Consensus        59 ~~~~~iLDlGcG~G~~~~~L~~~~~~~g~~~~v~gvD~   96 (232)
T PRK06202         59 DRPLTLLDIGCGGGDLAIDLARWARRDGLRLEVTAIDP   96 (232)
T ss_pred             CCCcEEEEeccCCCHHHHHHHHHHHhCCCCcEEEEEcC
Confidence            45679999999999999988864    46789999997

>TIGR00477 tehB tellurite resistance protein TehB

Probab=96.52  E-value=0.0042  Score=50.14  Aligned_cols=41  Identities=12%  Similarity=0.148  Sum_probs=31.9

Q ss_pred             HHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          169 VLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       169 ~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                      .+++.++  .....+|+|||||.|..+..++++  ..+++.+|+-
T Consensus        21 ~l~~~~~--~~~~~~vLDiGcG~G~~a~~la~~--g~~V~~iD~s   61 (195)
T TIGR00477        21 AVREAVK--TVAPCKTLDLGCGQGRNSLYLSLA--GYDVRAWDHN   61 (195)
T ss_pred             HHHHHhc--cCCCCcEEEeCCCCCHHHHHHHHC--CCeEEEEECC
Confidence            3445444  334679999999999999999985  5789999873

Part of a tellurite-reducing operon tehA and tehB

>PRK00216 ubiE ubiquinone/menaquinone biosynthesis methyltransferase; Reviewed

Probab=96.52  E-value=0.0057  Score=50.05  Aligned_cols=42  Identities=19%  Similarity=0.162  Sum_probs=33.9

Q ss_pred             HHhhcccccCCCCcEEeecCCchHHHHHHHHHCC-CCeEEEecCC
Q 040620          170 LIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFP-DTKCTVFACH  213 (214)
Q Consensus       170 ~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dlp  213 (214)
                      ++..+.  ..+..+|+|||||.|.++..+++..| +.+++++|+.
T Consensus        43 ~~~~~~--~~~~~~vldiG~G~G~~~~~l~~~~~~~~~v~~~D~s   85 (239)
T PRK00216         43 TIKWLG--VRPGDKVLDLACGTGDLAIALAKAVGKTGEVVGLDFS   85 (239)
T ss_pred             HHHHhC--CCCCCeEEEeCCCCCHHHHHHHHHcCCCCeEEEEeCC
Confidence            344443  33457999999999999999999998 7899999973

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

Probab=96.51  E-value=0.0029  Score=54.93  Aligned_cols=31  Identities=29%  Similarity=0.451  Sum_probs=29.7

Q ss_pred             CcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          182 KPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       182 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+|+|+|||+|.+++.+++.+|+.+++.+|+
T Consensus       135 ~~VLDlG~GsG~iai~la~~~p~~~V~avDi  165 (307)
T PRK11805        135 TRILDLCTGSGCIAIACAYAFPDAEVDAVDI  165 (307)
T ss_pred             CEEEEEechhhHHHHHHHHHCCCCEEEEEeC
Confidence            6899999999999999999999999999997

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

Probab=96.51  E-value=0.0057  Score=51.58  Aligned_cols=34  Identities=29%  Similarity=0.436  Sum_probs=31.1

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+..+|+|+|||+|..+..+++..|+.+++..|.
T Consensus       107 ~~~~~vLDiG~GsG~~~~~la~~~~~~~v~~iDi  140 (275)
T PRK09328        107 KEPLRVLDLGTGSGAIALALAKERPDAEVTAVDI  140 (275)
T ss_pred             cCCCEEEEEcCcHHHHHHHHHHHCCCCEEEEEEC
Confidence            3467899999999999999999999999999986

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

Probab=96.49  E-value=0.0045  Score=55.84  Aligned_cols=33  Identities=21%  Similarity=0.238  Sum_probs=30.5

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +..+++|+|||+|.+++.+++++|+.+++.+|+
T Consensus       251 ~~~rVLDLGcGSG~IaiaLA~~~p~a~VtAVDi  283 (423)
T PRK14966        251 ENGRVWDLGTGSGAVAVTVALERPDAFVRASDI  283 (423)
T ss_pred             CCCEEEEEeChhhHHHHHHHHhCCCCEEEEEEC
Confidence            446899999999999999999999999999997

>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=96.49  E-value=0.0013  Score=40.74  Aligned_cols=44  Identities=18%  Similarity=0.366  Sum_probs=38.1

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceee
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQ   86 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~   86 (214)
                      ++.|...|.+  +|.++.|||+.+|+++   ..+.+-|+.|...|++..
T Consensus         4 R~~Il~~L~~--~~~~~~el~~~l~~s~---~~vs~hL~~L~~~glV~~   47 (47)
T PF01022_consen    4 RLRILKLLSE--GPLTVSELAEELGLSQ---STVSHHLKKLREAGLVEK   47 (47)
T ss_dssp             HHHHHHHHTT--SSEEHHHHHHHHTS-H---HHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHh--CCCchhhHHHhccccc---hHHHHHHHHHHHCcCeeC
Confidence            3456777887  8999999999999999   999999999999999863

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 ....

>TIGR00536 hemK_fam HemK family putative methylases

Probab=96.48  E-value=0.0055  Score=52.45  Aligned_cols=31  Identities=26%  Similarity=0.502  Sum_probs=29.6

Q ss_pred             CcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          182 KPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       182 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+|+|+|||+|.+++.+++.+|+.+++.+|+
T Consensus       116 ~~vLDlG~GsG~i~l~la~~~~~~~v~avDi  146 (284)
T TIGR00536       116 LHILDLGTGSGCIALALAYEFPNAEVIAVDI  146 (284)
T ss_pred             CEEEEEeccHhHHHHHHHHHCCCCEEEEEEC
Confidence            6899999999999999999999999999986

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.

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

Probab=96.44  E-value=0.0056  Score=49.20  Aligned_cols=35  Identities=23%  Similarity=0.280  Sum_probs=32.2

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+...++|||||+|..++..+...|+.+++-+|.
T Consensus        32 ~~~g~~l~DIGaGtGsi~iE~a~~~p~~~v~AIe~   66 (187)
T COG2242          32 PRPGDRLWDIGAGTGSITIEWALAGPSGRVIAIER   66 (187)
T ss_pred             CCCCCEEEEeCCCccHHHHHHHHhCCCceEEEEec
Confidence            55678999999999999999999999999998885

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

Probab=96.43  E-value=0.0073  Score=50.86  Aligned_cols=32  Identities=19%  Similarity=0.213  Sum_probs=29.7

Q ss_pred             CCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          181 LKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       181 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+++|+|||+|.++..+++..|..+++.+|+
T Consensus        87 ~~~vLDlg~GsG~i~l~la~~~~~~~v~~vDi  118 (251)
T TIGR03704        87 TLVVVDLCCGSGAVGAALAAALDGIELHAADI  118 (251)
T ss_pred             CCEEEEecCchHHHHHHHHHhCCCCEEEEEEC
Confidence            45899999999999999999999999999986

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.

>PLN02244 tocopherol O-methyltransferase

Probab=96.42  E-value=0.0072  Score=53.12  Aligned_cols=33  Identities=27%  Similarity=0.372  Sum_probs=29.4

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ....+|||||||.|.++..+++++ +.+++++|+
T Consensus       117 ~~~~~VLDiGCG~G~~~~~La~~~-g~~v~gvD~  149 (340)
T PLN02244        117 KRPKRIVDVGCGIGGSSRYLARKY-GANVKGITL  149 (340)
T ss_pred             CCCCeEEEecCCCCHHHHHHHHhc-CCEEEEEEC
Confidence            456799999999999999999988 778999886

>PRK10258 biotin biosynthesis protein BioC; Provisional

Probab=96.42  E-value=0.0088  Score=49.90  Aligned_cols=43  Identities=19%  Similarity=0.255  Sum_probs=32.4

Q ss_pred             hHHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          166 IASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       166 ~~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+..+++.++  .....+|||+|||+|.++..+.+.  ..+++.+|+
T Consensus        30 ~a~~l~~~l~--~~~~~~vLDiGcG~G~~~~~l~~~--~~~v~~~D~   72 (251)
T PRK10258         30 SADALLAMLP--QRKFTHVLDAGCGPGWMSRYWRER--GSQVTALDL   72 (251)
T ss_pred             HHHHHHHhcC--ccCCCeEEEeeCCCCHHHHHHHHc--CCeEEEEEC
Confidence            4455566555  335679999999999999988764  567888886

>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=96.39  E-value=0.0019  Score=42.75  Aligned_cols=58  Identities=17%  Similarity=0.337  Sum_probs=39.7

Q ss_pred             hhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           43 DIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        43 d~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      ..|...+++++..+||+.+++++   ..+.+.++.|...|++.+....+|.- ...|.+|+.
T Consensus        10 ~~l~~~~~~~t~~~l~~~~~~~~---~~vs~~i~~L~~~glv~~~~~~~d~R-~~~~~LT~~   67 (68)
T PF13463_consen   10 RALAHSDGPMTQSDLAERLGISK---STVSRIIKKLEEKGLVEKERDPHDKR-SKRYRLTPA   67 (68)
T ss_dssp             HHHT--TS-BEHHHHHHHTT--H---HHHHHHHHHHHHTTSEEEEEESSCTT-SEEEEE-HH
T ss_pred             HHHHccCCCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEecCCCCcCC-eeEEEeCCC
Confidence            34442238999999999999999   99999999999999998765422222 245777753

>TIGR00452 methyltransferase, putative

Probab=96.35  E-value=0.0073  Score=52.63  Aligned_cols=33  Identities=12%  Similarity=0.031  Sum_probs=28.1

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...++|+|||||+|.++..+++..++ +++++|.
T Consensus       120 ~~g~~VLDvGCG~G~~~~~~~~~g~~-~v~GiDp  152 (314)
T TIGR00452       120 LKGRTILDVGCGSGYHMWRMLGHGAK-SLVGIDP  152 (314)
T ss_pred             CCCCEEEEeccCCcHHHHHHHHcCCC-EEEEEcC
Confidence            44689999999999999999998775 6888884

Known examples to date are restricted to the proteobacteria.

>TIGR02021 BchM-ChlM magnesium protoporphyrin O-methyltransferase

Probab=96.33  E-value=0.014  Score=47.76  Aligned_cols=31  Identities=19%  Similarity=0.235  Sum_probs=26.7

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +..+++|||||.|.++..+++.  +.+++++|.
T Consensus        55 ~~~~vLDiGcG~G~~~~~la~~--~~~v~gvD~   85 (219)
T TIGR02021        55 KGKRVLDAGCGTGLLSIELAKR--GAIVKAVDI   85 (219)
T ss_pred             CCCEEEEEeCCCCHHHHHHHHC--CCEEEEEEC
Confidence            4689999999999999999886  457888886

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.

>PRK05785 hypothetical protein; Provisional

Probab=96.33  E-value=0.0059  Score=50.56  Aligned_cols=31  Identities=16%  Similarity=0.291  Sum_probs=28.0

Q ss_pred             CCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          181 LKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       181 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+|||||||+|.++..+++++ +.+++++|.
T Consensus        52 ~~~VLDlGcGtG~~~~~l~~~~-~~~v~gvD~   82 (226)
T PRK05785         52 PKKVLDVAAGKGELSYHFKKVF-KYYVVALDY   82 (226)
T ss_pred             CCeEEEEcCCCCHHHHHHHHhc-CCEEEEECC
Confidence            5799999999999999999988 678999886

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

Probab=96.31  E-value=0.0047  Score=42.99  Aligned_cols=47  Identities=15%  Similarity=0.292  Sum_probs=38.2

Q ss_pred             CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      +++|.++||+++++++   ..+++++..|...|++.....    . .+.|.++..
T Consensus        24 ~~~s~~eiA~~~~i~~---~~l~kil~~L~~~Gli~s~~G----~-~GGy~L~~~   70 (83)
T PF02082_consen   24 KPVSSKEIAERLGISP---SYLRKILQKLKKAGLIESSRG----R-GGGYRLARP   70 (83)
T ss_dssp             C-BEHHHHHHHHTS-H---HHHHHHHHHHHHTTSEEEETS----T-TSEEEESS-
T ss_pred             CCCCHHHHHHHHCcCH---HHHHHHHHHHhhCCeeEecCC----C-CCceeecCC
Confidence            5699999999999999   999999999999999986642    1 477888776

(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.

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=96.30  E-value=0.007  Score=36.98  Aligned_cols=36  Identities=17%  Similarity=0.230  Sum_probs=33.3

Q ss_pred             CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      -|+|..+||+.+++++   ..+.+.|+.|...|++....
T Consensus         7 ~~~s~~~la~~l~~s~---~tv~~~l~~L~~~g~l~~~~   42 (48)
T smart00419        7 LPLTRQEIAELLGLTR---ETVSRTLKRLEKEGLISREG   42 (48)
T ss_pred             eccCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEEeC
Confidence            4789999999999999   99999999999999998763

>PTZ00098 phosphoethanolamine N-methyltransferase; Provisional

Probab=96.30  E-value=0.0076  Score=51.04  Aligned_cols=44  Identities=11%  Similarity=0.222  Sum_probs=35.1

Q ss_pred             HHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          167 ASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       167 ~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                      ...+++.++  ..+..+|||||||.|..+..+++.+ ..+++.+|+-
T Consensus        41 ~~~~l~~l~--l~~~~~VLDiGcG~G~~a~~la~~~-~~~v~giD~s   84 (263)
T PTZ00098         41 TTKILSDIE--LNENSKVLDIGSGLGGGCKYINEKY-GAHVHGVDIC   84 (263)
T ss_pred             HHHHHHhCC--CCCCCEEEEEcCCCChhhHHHHhhc-CCEEEEEECC
Confidence            355666665  6677899999999999999998875 6789988863

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

Probab=96.28  E-value=0.0055  Score=51.30  Aligned_cols=33  Identities=21%  Similarity=0.196  Sum_probs=31.1

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+|||||||+|-++..+++..++.++++.|.
T Consensus        51 ~g~~vLDva~GTGd~a~~~~k~~g~g~v~~~D~   83 (238)
T COG2226          51 PGDKVLDVACGTGDMALLLAKSVGTGEVVGLDI   83 (238)
T ss_pred             CCCEEEEecCCccHHHHHHHHhcCCceEEEEEC
Confidence            478999999999999999999999999999996

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

Probab=96.28  E-value=0.0043  Score=52.18  Aligned_cols=43  Identities=14%  Similarity=0.196  Sum_probs=35.4

Q ss_pred             HHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          170 LIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       170 ~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                      ++..|. ..+..++|+|+|+|.|..++.++++.|+.+++.+|+-
T Consensus        35 LL~~~~-~~~~~~~IlDlGaG~G~l~L~la~r~~~a~I~~VEiq   77 (248)
T COG4123          35 LLAAFA-PVPKKGRILDLGAGNGALGLLLAQRTEKAKIVGVEIQ   77 (248)
T ss_pred             HHHhhc-ccccCCeEEEecCCcCHHHHHHhccCCCCcEEEEEeC
Confidence            455543 1344889999999999999999999999999998874

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

Probab=96.22  E-value=0.0051  Score=56.98  Aligned_cols=32  Identities=13%  Similarity=0.370  Sum_probs=30.1

Q ss_pred             CCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          181 LKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       181 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+|+|||||+|.+++.+++.+|+.+++.+|+
T Consensus       139 ~~~VLDlG~GsG~iai~la~~~p~~~v~avDi  170 (506)
T PRK01544        139 FLNILELGTGSGCIAISLLCELPNANVIATDI  170 (506)
T ss_pred             CCEEEEccCchhHHHHHHHHHCCCCeEEEEEC
Confidence            46899999999999999999999999999997

>TIGR00438 rrmJ cell division protein FtsJ

Probab=96.21  E-value=0.01  Score=47.44  Aligned_cols=35  Identities=11%  Similarity=0.183  Sum_probs=30.0

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHC-CCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAF-PDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl  212 (214)
                      ..+..+|||+|||+|.++..+++++ +..+++.+|+
T Consensus        30 i~~g~~VLDiG~GtG~~~~~l~~~~~~~~~v~~vDi   65 (188)
T TIGR00438        30 IKPGDTVLDLGAAPGGWSQVAVEQVGGKGRVIAVDL   65 (188)
T ss_pred             cCCCCEEEEecCCCCHHHHHHHHHhCCCceEEEEec
Confidence            3567899999999999999999887 6678888886

>PF13679 Methyltransf_32: Methyltransferase domain

Probab=96.19  E-value=0.0064  Score=46.52  Aligned_cols=35  Identities=31%  Similarity=0.529  Sum_probs=30.0

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHH----CCCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATA----FPDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~----~P~l~~~v~Dl  212 (214)
                      ..+..+|||+|||.|+++..|+..    .|+++++.+|.
T Consensus        23 ~~~~~~vvD~GsG~GyLs~~La~~l~~~~~~~~v~~iD~   61 (141)
T PF13679_consen   23 SKRCITVVDLGSGKGYLSRALAHLLCNSSPNLRVLGIDC   61 (141)
T ss_pred             cCCCCEEEEeCCChhHHHHHHHHHHHhcCCCCeEEEEEC
Confidence            356789999999999999999992    38889999885

>TIGR01934 MenG_MenH_UbiE ubiquinone/menaquinone biosynthesis methyltransferases

Probab=96.18  E-value=0.0097  Score=48.13  Aligned_cols=34  Identities=29%  Similarity=0.308  Sum_probs=30.6

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCC-CeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPD-TKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dl  212 (214)
                      .+..+|+|+|||.|..+..+++.+|+ .+++++|.
T Consensus        38 ~~~~~vldiG~G~G~~~~~~~~~~~~~~~~~~iD~   72 (223)
T TIGR01934        38 FKGQKVLDVACGTGDLAIELAKSAPDRGKVTGVDF   72 (223)
T ss_pred             CCCCeEEEeCCCCChhHHHHHHhcCCCceEEEEEC
Confidence            35689999999999999999999998 78999886

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

>PRK10857 DNA-binding transcriptional regulator IscR; Provisional

Probab=96.18  E-value=0.011  Score=46.66  Aligned_cols=47  Identities=17%  Similarity=0.221  Sum_probs=40.8

Q ss_pred             CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      +|+|+++||+++++++   +.|.++|..|...|++.....    . .+.|.+..-
T Consensus        24 ~~vs~~eIA~~~~ip~---~~l~kIl~~L~~aGLv~s~rG----~-~GGy~Lar~   70 (164)
T PRK10857         24 GPVPLADISERQGISL---SYLEQLFSRLRKNGLVSSVRG----P-GGGYLLGKD   70 (164)
T ss_pred             CcCcHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEeCCC----C-CCCeeccCC
Confidence            6899999999999999   999999999999999997531    1 567888776

>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional

Probab=96.13  E-value=0.0059  Score=45.57  Aligned_cols=56  Identities=20%  Similarity=0.236  Sum_probs=48.5

Q ss_pred             HHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           29 KSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        29 ~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      .+.+|.--.++.|+..|.+. +++++.|||+.+++++   ..+.+-|+.|...|++....
T Consensus         9 ~fkaLadptRl~IL~~L~~~-~~~~v~ela~~l~lsq---stvS~HL~~L~~AGLV~~~r   64 (117)
T PRK10141          9 LFKILSDETRLGIVLLLRES-GELCVCDLCTALDQSQ---PKISRHLALLRESGLLLDRK   64 (117)
T ss_pred             HHHHhCCHHHHHHHHHHHHc-CCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCceEEEE
Confidence            45566667778888888754 7899999999999999   99999999999999998776

>PRK11705 cyclopropane fatty acyl phospholipid synthase; Provisional

Probab=96.12  E-value=0.013  Score=52.33  Aligned_cols=40  Identities=18%  Similarity=0.194  Sum_probs=31.8

Q ss_pred             HHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          170 LIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       170 ~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +++.++  ..+..+|||||||.|.++..+++.+ +.+++.+|+
T Consensus       159 l~~~l~--l~~g~rVLDIGcG~G~~a~~la~~~-g~~V~giDl  198 (383)
T PRK11705        159 ICRKLQ--LKPGMRVLDIGCGWGGLARYAAEHY-GVSVVGVTI  198 (383)
T ss_pred             HHHHhC--CCCCCEEEEeCCCccHHHHHHHHHC-CCEEEEEeC
Confidence            344444  4566799999999999999999876 678998886

>PRK07580 Mg-protoporphyrin IX methyl transferase; Validated

Probab=96.09  E-value=0.017  Score=47.14  Aligned_cols=32  Identities=16%  Similarity=0.130  Sum_probs=26.7

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+..+|||||||+|.++..+++..+  ++++.|+
T Consensus        62 ~~~~~vLDvGcG~G~~~~~l~~~~~--~v~~~D~   93 (230)
T PRK07580         62 LTGLRILDAGCGVGSLSIPLARRGA--KVVASDI   93 (230)
T ss_pred             CCCCEEEEEeCCCCHHHHHHHHcCC--EEEEEEC
Confidence            4467999999999999999998754  4787775

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

Probab=96.09  E-value=0.0029  Score=42.54  Aligned_cols=44  Identities=14%  Similarity=0.366  Sum_probs=37.2

Q ss_pred             cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      |-+.|.+. +.+|..|||.+++++|   ..+..+|+.|+..|.+.+..
T Consensus         5 i~~~l~~~-~~~S~~eLa~~~~~s~---~~ve~mL~~l~~kG~I~~~~   48 (69)
T PF09012_consen    5 IRDYLRER-GRVSLAELAREFGISP---EAVEAMLEQLIRKGYIRKVD   48 (69)
T ss_dssp             HHHHHHHS--SEEHHHHHHHTT--H---HHHHHHHHHHHCCTSCEEEE
T ss_pred             HHHHHHHc-CCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCcEEEec
Confidence            45677776 8999999999999999   99999999999999999875

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

>PLN02336 phosphoethanolamine N-methyltransferase

Probab=96.07  E-value=0.01  Score=54.25  Aligned_cols=43  Identities=19%  Similarity=0.220  Sum_probs=34.1

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                      ..+++.++  ..+..+|||||||+|..+..+++.+ +.+++.+|+-
T Consensus       256 e~l~~~~~--~~~~~~vLDiGcG~G~~~~~la~~~-~~~v~gvDiS  298 (475)
T PLN02336        256 KEFVDKLD--LKPGQKVLDVGCGIGGGDFYMAENF-DVHVVGIDLS  298 (475)
T ss_pred             HHHHHhcC--CCCCCEEEEEeccCCHHHHHHHHhc-CCEEEEEECC
Confidence            34555554  4556799999999999999999876 7799999973

>PRK11188 rrmJ 23S rRNA methyltransferase J; Provisional

Probab=96.02  E-value=0.0095  Score=48.77  Aligned_cols=34  Identities=18%  Similarity=0.219  Sum_probs=28.9

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHC-CCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAF-PDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl  212 (214)
                      .+..+|||||||+|.++..++++. |.-+++.+|+
T Consensus        50 ~~~~~VLDlG~GtG~~t~~l~~~~~~~~~V~aVDi   84 (209)
T PRK11188         50 KPGMTVVDLGAAPGGWSQYAVTQIGDKGRVIACDI   84 (209)
T ss_pred             CCCCEEEEEcccCCHHHHHHHHHcCCCceEEEEec
Confidence            456799999999999999999987 4568888886

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

Probab=95.99  E-value=0.0075  Score=50.17  Aligned_cols=31  Identities=13%  Similarity=0.212  Sum_probs=29.1

Q ss_pred             CcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          182 KPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       182 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+|+||||.|.+...+|+++|+..++++++
T Consensus        50 pi~lEIGfG~G~~l~~~A~~nP~~nfiGiEi   80 (227)
T COG0220          50 PIVLEIGFGMGEFLVEMAKKNPEKNFLGIEI   80 (227)
T ss_pred             cEEEEECCCCCHHHHHHHHHCCCCCEEEEEE
Confidence            5899999999999999999999999998875

>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional

Probab=95.98  E-value=0.009  Score=50.70  Aligned_cols=33  Identities=24%  Similarity=0.396  Sum_probs=28.2

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCC---eEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDT---KCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l---~~~v~Dl  212 (214)
                      ...+|||||||+|.++..+++.+|..   +++++|+
T Consensus        85 ~~~~vLDiGcG~G~~~~~l~~~~~~~~~~~v~giD~  120 (272)
T PRK11088         85 KATALLDIGCGEGYYTHALADALPEITTMQLFGLDI  120 (272)
T ss_pred             CCCeEEEECCcCCHHHHHHHHhcccccCCeEEEECC
Confidence            34689999999999999999998864   5788886

>TIGR00755 ksgA dimethyladenosine transferase

Probab=95.97  E-value=0.014  Score=49.10  Aligned_cols=41  Identities=12%  Similarity=0.233  Sum_probs=32.3

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+++..+  ..+..+|+|||||.|.++..++++.+.  ++.+|.
T Consensus        19 ~~i~~~~~--~~~~~~VLEiG~G~G~lt~~L~~~~~~--v~~iE~   59 (253)
T TIGR00755        19 QKIVEAAN--VLEGDVVLEIGPGLGALTEPLLKRAKK--VTAIEI   59 (253)
T ss_pred             HHHHHhcC--CCCcCEEEEeCCCCCHHHHHHHHhCCc--EEEEEC
Confidence            45556555  556789999999999999999999875  666654

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

>PLN02233 ubiquinone biosynthesis methyltransferase

Probab=95.97  E-value=0.01  Score=50.20  Aligned_cols=34  Identities=18%  Similarity=0.178  Sum_probs=29.6

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHC-CCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAF-PDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl  212 (214)
                      .+..+|+|||||+|.++..+++++ |+.+++.+|.
T Consensus        72 ~~~~~VLDlGcGtG~~~~~la~~~~~~~~V~gvD~  106 (261)
T PLN02233         72 KMGDRVLDLCCGSGDLAFLLSEKVGSDGKVMGLDF  106 (261)
T ss_pred             CCCCEEEEECCcCCHHHHHHHHHhCCCCEEEEEEC
Confidence            446799999999999999999885 6789999986

>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR

Probab=95.92  E-value=0.015  Score=42.98  Aligned_cols=67  Identities=19%  Similarity=0.264  Sum_probs=51.3

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      +..|+..|..+ +++|..+||+.+++++   ..+.+.++-|...|++......+|.- .-.+.+|+.    ++.+.
T Consensus        30 q~~iL~~l~~~-~~~t~~ela~~~~~~~---~tvs~~l~~Le~~GlI~r~~~~~D~R-~~~v~LT~~----G~~~~   96 (118)
T TIGR02337        30 QWRILRILAEQ-GSMEFTQLANQACILR---PSLTGILARLERDGLVTRLKASNDQR-RVYISLTPK----GQALY   96 (118)
T ss_pred             HHHHHHHHHHc-CCcCHHHHHHHhCCCc---hhHHHHHHHHHHCCCEEeccCCCCCC-eeEEEECHh----HHHHH
Confidence            34466777766 7899999999999999   89999999999999999865211111 235888888    66654

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.

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

Probab=95.91  E-value=0.017  Score=47.23  Aligned_cols=42  Identities=17%  Similarity=0.164  Sum_probs=32.0

Q ss_pred             HHHhhcccccCCCCcEEeecCCchHHHHHHHHHCC-CCeEEEecC
Q 040620          169 VLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFP-DTKCTVFAC  212 (214)
Q Consensus       169 ~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl  212 (214)
                      .+++.++  .....+|+|||||+|.++..+++..+ +.+++.+|+
T Consensus        68 ~~~~~l~--~~~~~~VLDiG~GsG~~a~~la~~~~~~g~V~~vD~  110 (215)
T TIGR00080        68 MMTELLE--LKPGMKVLEIGTGSGYQAAVLAEIVGRDGLVVSIER  110 (215)
T ss_pred             HHHHHhC--CCCcCEEEEECCCccHHHHHHHHHhCCCCEEEEEeC
Confidence            3444444  45678999999999999999999875 456777774

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

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

Probab=95.89  E-value=0.017  Score=48.68  Aligned_cols=42  Identities=14%  Similarity=0.317  Sum_probs=32.5

Q ss_pred             HHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          167 ASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       167 ~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+++..+  ..+..+|+|||||.|.++..++++.  .+++++|+
T Consensus        18 ~~~iv~~~~--~~~~~~VLEIG~G~G~lt~~L~~~~--~~v~~vEi   59 (258)
T PRK14896         18 VDRIVEYAE--DTDGDPVLEIGPGKGALTDELAKRA--KKVYAIEL   59 (258)
T ss_pred             HHHHHHhcC--CCCcCeEEEEeCccCHHHHHHHHhC--CEEEEEEC
Confidence            345555554  5567899999999999999999984  46777775

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

Probab=95.88  E-value=0.022  Score=46.34  Aligned_cols=35  Identities=20%  Similarity=0.209  Sum_probs=28.7

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCC-CCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFP-DTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl  212 (214)
                      ..+..+|+|||||+|..+..+++..+ ..+++.+|.
T Consensus        70 ~~~~~~VLDiG~GsG~~~~~la~~~~~~g~V~~iD~  105 (205)
T PRK13944         70 PRPGMKILEVGTGSGYQAAVCAEAIERRGKVYTVEI  105 (205)
T ss_pred             CCCCCEEEEECcCccHHHHHHHHhcCCCCEEEEEeC
Confidence            34557999999999999999998875 557888875

>KOG2899 consensus Predicted methyltransferase [General function prediction only]

Probab=95.87  E-value=0.01  Score=49.75  Aligned_cols=46  Identities=15%  Similarity=0.129  Sum_probs=38.3

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                      ...++.++..+-..+.+|||||++|.+++.|++.|-...++++|+-
T Consensus        46 D~rLk~L~~~~f~~~~~LDIGCNsG~lt~~iak~F~~r~iLGvDID   91 (288)
T KOG2899|consen   46 DPRLKVLEKDWFEPKQALDIGCNSGFLTLSIAKDFGPRRILGVDID   91 (288)
T ss_pred             ChhhhhccccccCcceeEeccCCcchhHHHHHHhhccceeeEeecc
Confidence            4456666544556889999999999999999999999999999873

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

Probab=95.87  E-value=0.0056  Score=40.45  Aligned_cols=46  Identities=17%  Similarity=0.218  Sum_probs=37.1

Q ss_pred             CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      .|.+.|....+|++..|||+.+|++.   ..++++|..|...|.+...+
T Consensus         4 ~Il~~i~~~~~p~~T~eiA~~~gls~---~~aR~yL~~Le~eG~V~~~~   49 (62)
T PF04703_consen    4 KILEYIKEQNGPLKTREIADALGLSI---YQARYYLEKLEKEGKVERSP   49 (62)
T ss_dssp             CHHHHHHHHTS-EEHHHHHHHHTS-H---HHHHHHHHHHHHCTSEEEES
T ss_pred             HHHHHHHHcCCCCCHHHHHHHhCCCH---HHHHHHHHHHHHCCCEEEec
Confidence            34555665228999999999999998   99999999999999998765

>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein

Probab=95.87  E-value=0.0086  Score=42.15  Aligned_cols=62  Identities=15%  Similarity=0.283  Sum_probs=47.1

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      ++.|+..|... +++|..+||+.+++++   ..+.+.++.|...|++.......+.. ...|.+|+.
T Consensus        12 ~~~il~~l~~~-~~~~~~~la~~~~~s~---~~i~~~l~~L~~~g~v~~~~~~~~~r-~~~~~lT~~   73 (101)
T smart00347       12 QFLVLRILYEE-GPLSVSELAKRLGVSP---STVTRVLDRLEKKGLIRRLPSPEDRR-SVLVSLTEE   73 (101)
T ss_pred             HHHHHHHHHHc-CCcCHHHHHHHHCCCc---hhHHHHHHHHHHCCCeEecCCCCCCC-eEEEEECHh
Confidence            34566677665 6799999999999999   99999999999999998765211111 235777777

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

Probab=95.82  E-value=0.016  Score=48.56  Aligned_cols=31  Identities=19%  Similarity=0.270  Sum_probs=27.1

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+|+|||||.|.++..+++.  ..+++++|+
T Consensus        44 ~~~~vLDiGcG~G~~a~~la~~--g~~v~~vD~   74 (255)
T PRK11036         44 RPLRVLDAGGGEGQTAIKLAEL--GHQVILCDL   74 (255)
T ss_pred             CCCEEEEeCCCchHHHHHHHHc--CCEEEEEEC
Confidence            4579999999999999999987  567888886

>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=95.80  E-value=0.014  Score=37.77  Aligned_cols=44  Identities=9%  Similarity=0.207  Sum_probs=40.1

Q ss_pred             cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      |.++|... +.+|+++||+.+++++   .-++|-|..|...|++...-
T Consensus         5 Il~~l~~~-~~~s~~ela~~~~VS~---~TiRRDl~~L~~~g~i~r~~   48 (57)
T PF08220_consen    5 ILELLKEK-GKVSVKELAEEFGVSE---MTIRRDLNKLEKQGLIKRTH   48 (57)
T ss_pred             HHHHHHHc-CCEEHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEEc
Confidence            56777776 8999999999999999   99999999999999998875

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

>PRK04266 fibrillarin; Provisional

Probab=95.79  E-value=0.02  Score=47.48  Aligned_cols=35  Identities=11%  Similarity=0.152  Sum_probs=30.6

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+..+|+|+|||+|.++..+++..|.-+++.+|+
T Consensus        70 i~~g~~VlD~G~G~G~~~~~la~~v~~g~V~avD~  104 (226)
T PRK04266         70 IKKGSKVLYLGAASGTTVSHVSDIVEEGVVYAVEF  104 (226)
T ss_pred             CCCCCEEEEEccCCCHHHHHHHHhcCCCeEEEEEC
Confidence            55678999999999999999999998667888886

>PRK12335 tellurite resistance protein TehB; Provisional

Probab=95.76  E-value=0.016  Score=49.67  Aligned_cols=31  Identities=16%  Similarity=0.113  Sum_probs=27.1

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+|||||||+|..+..+++.  ..+++.+|.
T Consensus       120 ~~~~vLDlGcG~G~~~~~la~~--g~~V~avD~  150 (287)
T PRK12335        120 KPGKALDLGCGQGRNSLYLALL--GFDVTAVDI  150 (287)
T ss_pred             CCCCEEEeCCCCCHHHHHHHHC--CCEEEEEEC
Confidence            4569999999999999999885  578999886

>TIGR03438 probable methyltransferase

Probab=95.72  E-value=0.016  Score=49.97  Aligned_cols=34  Identities=15%  Similarity=0.211  Sum_probs=30.1

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCC-CCeEEEecCC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFP-DTKCTVFACH  213 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dlp  213 (214)
                      ...+|||+|||+|..+..|+++.+ ..+++.+|+-
T Consensus        63 ~~~~iLELGcGtG~~t~~Ll~~l~~~~~~~~iDiS   97 (301)
T TIGR03438        63 AGCELVELGSGSSRKTRLLLDALRQPARYVPIDIS   97 (301)
T ss_pred             CCCeEEecCCCcchhHHHHHHhhccCCeEEEEECC
Confidence            457899999999999999999988 6889999974

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

>PLN03075 nicotianamine synthase; Provisional

Probab=95.71  E-value=0.018  Score=49.75  Aligned_cols=33  Identities=18%  Similarity=0.074  Sum_probs=27.6

Q ss_pred             CCCcEEeecCCch--HHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTG--TMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G--~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +.++|+|||||+|  +....+++.+|+.+++++|.
T Consensus       123 ~p~~VldIGcGpgpltaiilaa~~~p~~~~~giD~  157 (296)
T PLN03075        123 VPTKVAFVGSGPLPLTSIVLAKHHLPTTSFHNFDI  157 (296)
T ss_pred             CCCEEEEECCCCcHHHHHHHHHhcCCCCEEEEEeC
Confidence            6799999999998  44555557899999999996

>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR

Probab=95.68  E-value=0.024  Score=43.09  Aligned_cols=47  Identities=17%  Similarity=0.186  Sum_probs=40.2

Q ss_pred             CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      +++|+++||+++++++   ..++++|+.|...|++.....    . .|.|.++.-
T Consensus        24 ~~~s~~~ia~~~~ip~---~~l~kil~~L~~~glv~s~~G----~-~Ggy~l~~~   70 (135)
T TIGR02010        24 GPVTLADISERQGISL---SYLEQLFAKLRKAGLVKSVRG----P-GGGYQLGRP   70 (135)
T ss_pred             CcCcHHHHHHHHCcCH---HHHHHHHHHHHHCCceEEEeC----C-CCCEeccCC
Confidence            6899999999999999   999999999999999986431    1 466887776

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

>PRK00517 prmA ribosomal protein L11 methyltransferase; Reviewed

Probab=95.66  E-value=0.014  Score=48.98  Aligned_cols=32  Identities=28%  Similarity=0.247  Sum_probs=26.3

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+|+|||||+|.+++.+++..+. +++.+|+
T Consensus       119 ~~~~VLDiGcGsG~l~i~~~~~g~~-~v~giDi  150 (250)
T PRK00517        119 PGKTVLDVGCGSGILAIAAAKLGAK-KVLAVDI  150 (250)
T ss_pred             CCCEEEEeCCcHHHHHHHHHHcCCC-eEEEEEC
Confidence            5689999999999999987776543 6888886

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

Probab=95.65  E-value=0.021  Score=46.04  Aligned_cols=35  Identities=14%  Similarity=0.155  Sum_probs=30.1

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHC-CCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAF-PDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl  212 (214)
                      .....+++|+|||+|.++..+++.. |..+++.+|+
T Consensus        38 ~~~~~~vlDlG~GtG~~s~~~a~~~~~~~~v~avD~   73 (198)
T PRK00377         38 LRKGDMILDIGCGTGSVTVEASLLVGETGKVYAVDK   73 (198)
T ss_pred             CCCcCEEEEeCCcCCHHHHHHHHHhCCCCEEEEEEC
Confidence            4566899999999999999998874 6778999986

>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=95.60  E-value=0.017  Score=49.91  Aligned_cols=32  Identities=13%  Similarity=0.079  Sum_probs=26.2

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEec
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFA  211 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~D  211 (214)
                      ...++|+|||||+|.++..++++-|.. ++++|
T Consensus       114 L~gk~VLDIGC~nGY~~frM~~~GA~~-ViGiD  145 (315)
T PF08003_consen  114 LKGKRVLDIGCNNGYYSFRMLGRGAKS-VIGID  145 (315)
T ss_pred             cCCCEEEEecCCCcHHHHHHhhcCCCE-EEEEC
Confidence            357899999999999999999995543 56665

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

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

Probab=95.59  E-value=0.033  Score=45.61  Aligned_cols=42  Identities=17%  Similarity=0.213  Sum_probs=32.7

Q ss_pred             HHHhhcccccCCCCcEEeecCCchHHHHHHHHHC-CCCeEEEecC
Q 040620          169 VLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAF-PDTKCTVFAC  212 (214)
Q Consensus       169 ~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl  212 (214)
                      .+++..+  ..+..+|||||||+|..+..+++.. ++.+++.+|.
T Consensus        67 ~~~~~l~--~~~g~~VLdIG~GsG~~t~~la~~~~~~~~V~~vE~  109 (212)
T PRK13942         67 IMCELLD--LKEGMKVLEIGTGSGYHAAVVAEIVGKSGKVVTIER  109 (212)
T ss_pred             HHHHHcC--CCCcCEEEEECCcccHHHHHHHHhcCCCCEEEEEeC
Confidence            3455555  5567899999999999999998875 4568888875

>PLN02490 MPBQ/MSBQ methyltransferase

Probab=95.55  E-value=0.018  Score=50.77  Aligned_cols=33  Identities=27%  Similarity=0.342  Sum_probs=30.0

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+|||||||+|.++..+++.+|..+++++|+
T Consensus       113 ~~~~VLDLGcGtG~~~l~La~~~~~~~VtgVD~  145 (340)
T PLN02490        113 RNLKVVDVGGGTGFTTLGIVKHVDAKNVTILDQ  145 (340)
T ss_pred             CCCEEEEEecCCcHHHHHHHHHCCCCEEEEEEC
Confidence            356999999999999999999999999999986

>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=95.53  E-value=0.0066  Score=39.34  Aligned_cols=46  Identities=13%  Similarity=0.243  Sum_probs=37.9

Q ss_pred             cCcchhhhcCCCC--CCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           39 LRIPDIINNSGQP--MTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        39 lglfd~L~~~~~p--~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      ..|+-.|... ++  +|..|||+.+++++   ..+.++++.|...|+++...
T Consensus         8 ~~vL~~l~~~-~~~~~t~~~la~~l~~~~---~~vs~~v~~L~~~Glv~r~~   55 (62)
T PF12802_consen    8 FRVLMALARH-PGEELTQSELAERLGISK---STVSRIVKRLEKKGLVERER   55 (62)
T ss_dssp             HHHHHHHHHS-TTSGEEHHHHHHHHTS-H---HHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHC-CCCCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEeC
Confidence            3445556665 34  89999999999999   99999999999999999876

...

>COG2345 Predicted transcriptional regulator [Transcription]

Probab=95.51  E-value=0.027  Score=46.41  Aligned_cols=72  Identities=13%  Similarity=0.212  Sum_probs=54.0

Q ss_pred             cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCC--CccceeeCCCCCccccccccccchH
Q 040620           41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNE--QEEESILLPPHLDFFSRISLQLQGS  118 (214)
Q Consensus        41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~--~~~~~y~~t~~~~~~s~~l~~~~~~  118 (214)
                      |.-.|..+ +|+|+.|||+++|+++   ..+++-|..|...|++.....+ .+  --...|++|..    +...++..+.
T Consensus        16 il~lL~~~-g~~sa~elA~~Lgis~---~avR~HL~~Le~~Glv~~~~~~-~g~GRP~~~y~Lt~~----g~~~f~~~y~   86 (218)
T COG2345          16 ILELLKKS-GPVSADELAEELGISP---MAVRRHLDDLEAEGLVEVERQQ-GGRGRPAKLYRLTEK----GREQFPKRYG   86 (218)
T ss_pred             HHHHHhcc-CCccHHHHHHHhCCCH---HHHHHHHHHHHhCcceeeeecc-CCCCCCceeeeeccc----chhhcchhhH
Confidence            44556655 9999999999999999   9999999999999999865321 11  01356999999    8876655544


Q ss_pred             HHH
Q 040620          119 TIL  121 (214)
Q Consensus       119 ~~~  121 (214)
                      .+.
T Consensus        87 ~l~   89 (218)
T COG2345          87 ELA   89 (218)
T ss_pred             HHH
Confidence            443

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=95.47  E-value=0.019  Score=35.54  Aligned_cols=44  Identities=11%  Similarity=0.210  Sum_probs=37.9

Q ss_pred             cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      |++.|..+ ++++..+||+.+++++   ..+++.|..|...|++....
T Consensus         5 il~~l~~~-~~~s~~~l~~~l~~s~---~tv~~~l~~L~~~g~i~~~~   48 (53)
T smart00420        5 ILELLAQQ-GKVSVEELAELLGVSE---MTIRRDLNKLEEQGLLTRVH   48 (53)
T ss_pred             HHHHHHHc-CCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEEee
Confidence            44555555 6799999999999999   99999999999999998764

>PRK03902 manganese transport transcriptional regulator; Provisional

Probab=95.46  E-value=0.019  Score=44.04  Aligned_cols=54  Identities=22%  Similarity=0.400  Sum_probs=46.1

Q ss_pred             hhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCccccccc
Q 040620           44 IINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRIS  112 (214)
Q Consensus        44 ~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l  112 (214)
                      ++... ++.++.+||+.+++++   ..+.+.++.|...|++.+..       ...|.+|+.    ++.+
T Consensus        16 l~~~~-~~~~~~ela~~l~vs~---~svs~~l~~L~~~Gli~~~~-------~~~i~LT~~----G~~~   69 (142)
T PRK03902         16 LIEEK-GYARVSDIAEALSVHP---SSVTKMVQKLDKDEYLIYEK-------YRGLVLTPK----GKKI   69 (142)
T ss_pred             HHhcC-CCcCHHHHHHHhCCCh---hHHHHHHHHHHHCCCEEEec-------CceEEECHH----HHHH
Confidence            34444 8899999999999999   99999999999999999765       478999999    6655

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=95.44  E-value=0.021  Score=42.99  Aligned_cols=43  Identities=16%  Similarity=0.246  Sum_probs=37.7

Q ss_pred             hhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecC
Q 040620           43 DIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKD   89 (214)
Q Consensus        43 d~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~   89 (214)
                      .+|..+ +|+|+++||+.++.+.   ..++|-|+-|...|++.....
T Consensus        35 ~LL~~~-~~~tvdelae~lnr~r---Stv~rsl~~L~~~GlV~Rek~   77 (126)
T COG3355          35 ALLEEN-GPLTVDELAEILNRSR---STVYRSLQNLLEAGLVEREKV   77 (126)
T ss_pred             HHHhhc-CCcCHHHHHHHHCccH---HHHHHHHHHHHHcCCeeeeee
Confidence            445344 9999999999999998   999999999999999998763

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

Probab=95.41  E-value=0.014  Score=48.64  Aligned_cols=34  Identities=24%  Similarity=0.342  Sum_probs=24.7

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHC-CCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAF-PDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl  212 (214)
                      ....+|||||||+|.++..++++. |+.++++.|.
T Consensus        46 ~~g~~vLDv~~GtG~~~~~l~~~~~~~~~v~~vD~   80 (233)
T PF01209_consen   46 RPGDRVLDVACGTGDVTRELARRVGPNGKVVGVDI   80 (233)
T ss_dssp             -S--EEEEET-TTSHHHHHHGGGSS---EEEEEES
T ss_pred             CCCCEEEEeCCChHHHHHHHHHHCCCccEEEEecC
Confidence            446799999999999999999875 6789999986

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.

>PHA03411 putative methyltransferase; Provisional

Probab=95.40  E-value=0.021  Score=48.77  Aligned_cols=32  Identities=9%  Similarity=0.126  Sum_probs=29.3

Q ss_pred             CCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          181 LKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       181 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+|+|+|||+|.++..++++.+..+++.+|+
T Consensus        65 ~grVLDLGcGsGilsl~la~r~~~~~V~gVDi   96 (279)
T PHA03411         65 TGKVLDLCAGIGRLSFCMLHRCKPEKIVCVEL   96 (279)
T ss_pred             CCeEEEcCCCCCHHHHHHHHhCCCCEEEEEEC
Confidence            46999999999999999999988889999986

>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator)

Probab=95.33  E-value=0.023  Score=42.68  Aligned_cols=47  Identities=11%  Similarity=0.179  Sum_probs=40.0

Q ss_pred             CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      +|+|.++||+.+++++   ..++++++.|...|++.....    . .+.|.++.-
T Consensus        24 ~~~s~~eia~~~~i~~---~~v~~il~~L~~~gli~~~~g----~-~ggy~l~~~   70 (132)
T TIGR00738        24 GPVSVKEIAERQGISR---SYLEKILRTLRRAGLVESVRG----P-GGGYRLARP   70 (132)
T ss_pred             CcCcHHHHHHHHCcCH---HHHHHHHHHHHHCCcEEeccC----C-CCCccCCCC
Confidence            5999999999999999   999999999999999986521    1 457887766

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.

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

Probab=95.32  E-value=0.018  Score=48.04  Aligned_cols=32  Identities=19%  Similarity=0.231  Sum_probs=28.1

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                      ...+|||||||-|.++..+++.  +.+++..|+-
T Consensus        59 ~g~~vLDvGCGgG~Lse~mAr~--Ga~VtgiD~s   90 (243)
T COG2227          59 PGLRVLDVGCGGGILSEPLARL--GASVTGIDAS   90 (243)
T ss_pred             CCCeEEEecCCccHhhHHHHHC--CCeeEEecCC
Confidence            4679999999999999999999  4888888863

>TIGR00122 birA_repr_reg BirA biotin operon repressor domain

Probab=95.28  E-value=0.021  Score=38.11  Aligned_cols=54  Identities=20%  Similarity=0.271  Sum_probs=44.0

Q ss_pred             cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      +.|+..|.+  ++.+..+||+++|++.   ..+++.++.|...|+.....       ...|.+.+.
T Consensus         3 ~~il~~L~~--~~~~~~eLa~~l~vS~---~tv~~~l~~L~~~g~~i~~~-------~~g~~l~~~   56 (69)
T TIGR00122         3 LRLLALLAD--NPFSGEKLGEALGMSR---TAVNKHIQTLREWGVDVLTV-------GKGYRLPPP   56 (69)
T ss_pred             HHHHHHHHc--CCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCeEEec-------CCceEecCc
Confidence            456677886  7899999999999999   99999999999999976554       355666555

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.

>PLN02396 hexaprenyldihydroxybenzoate methyltransferase

Probab=95.26  E-value=0.023  Score=49.75  Aligned_cols=31  Identities=16%  Similarity=0.235  Sum_probs=26.5

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+|||||||.|.++..+++  ++.+++++|.
T Consensus       131 ~g~~ILDIGCG~G~~s~~La~--~g~~V~GID~  161 (322)
T PLN02396        131 EGLKFIDIGCGGGLLSEPLAR--MGATVTGVDA  161 (322)
T ss_pred             CCCEEEEeeCCCCHHHHHHHH--cCCEEEEEeC
Confidence            346899999999999998886  4778999885

>smart00138 MeTrc Methyltransferase, chemotaxis proteins

Probab=95.22  E-value=0.097  Score=44.38  Aligned_cols=33  Identities=27%  Similarity=0.309  Sum_probs=26.4

Q ss_pred             CCCcEEeecCCchH----HHHHHHHHCC-----CCeEEEecC
Q 040620          180 GLKPLVDVGGSTGT----MARAIATAFP-----DTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~----~~~~l~~~~P-----~l~~~v~Dl  212 (214)
                      +..+|+|+|||+|.    +++.+++..|     +.+++..|+
T Consensus        99 ~~~ri~d~GCgtGee~YslA~~l~e~~~~~~~~~~~I~g~Di  140 (264)
T smart00138       99 RRVRIWSAGCSTGEEPYSLAMLLAETLPKAREPDVKILATDI  140 (264)
T ss_pred             CCEEEEeccccCChHHHHHHHHHHHHhhhcCCCCeEEEEEEC
Confidence            45699999999996    6777888766     467888886

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

>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=95.20  E-value=0.0072  Score=38.89  Aligned_cols=45  Identities=16%  Similarity=0.294  Sum_probs=37.9

Q ss_pred             CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      .+...|..+ ++++..+||+.+++++   ..+.++++.|...|++....
T Consensus         7 ~iL~~l~~~-~~~~~~~la~~~~~~~---~~~t~~i~~L~~~g~I~r~~   51 (59)
T PF01047_consen    7 RILRILYEN-GGITQSELAEKLGISR---STVTRIIKRLEKKGLIERER   51 (59)
T ss_dssp             HHHHHHHHH-SSEEHHHHHHHHTS-H---HHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHc-CCCCHHHHHHHHCCCh---hHHHHHHHHHHHCCCEEecc
Confidence            344455565 7899999999999999   99999999999999999765

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 ....

>PLN02672 methionine S-methyltransferase

Probab=95.17  E-value=0.022  Score=57.04  Aligned_cols=32  Identities=22%  Similarity=0.257  Sum_probs=30.0

Q ss_pred             CCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          181 LKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       181 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+|+|||||+|..++.+++++|+.+++..|+
T Consensus       119 ~~~VLDlG~GSG~Iai~La~~~~~~~v~avDi  150 (1082)
T PLN02672        119 DKTVAELGCGNGWISIAIAEKWLPSKVYGLDI  150 (1082)
T ss_pred             CCEEEEEecchHHHHHHHHHHCCCCEEEEEEC
Confidence            46899999999999999999999999999986

>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR

Probab=95.09  E-value=0.044  Score=44.58  Aligned_cols=67  Identities=13%  Similarity=0.114  Sum_probs=50.3

Q ss_pred             CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecC-CCCCCccceeeCCCCCccccccccc
Q 040620           40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKD-GKNEQEEESILLPPHLDFFSRISLQ  114 (214)
Q Consensus        40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~-~~~~~~~~~y~~t~~~~~~s~~l~~  114 (214)
                      .|+..|... +++|..+||+.+|+++   ..+++.|+.|...|++..... ...|--...|.+|+.    ++.+++
T Consensus         5 ~IL~~L~~~-~~~t~~eLA~~lgis~---~tV~~~L~~Le~~GlV~r~~~~~~~gRp~~~y~LT~~----G~~~~~   72 (203)
T TIGR02702         5 DILSYLLKQ-GQATAAALAEALAISP---QAVRRHLKDLETEGLIEYEAVVQGMGRPQYHYQLSRQ----GREQFP   72 (203)
T ss_pred             HHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeEEeecccCCCCCceEEEECcc----hhhhcc
Confidence            456666655 7899999999999999   999999999999999987631 001111234889988    777653

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=95.08  E-value=0.029  Score=43.90  Aligned_cols=50  Identities=16%  Similarity=0.131  Sum_probs=46.0

Q ss_pred             CCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCccccccc
Q 040620           49 GQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRIS  112 (214)
Q Consensus        49 ~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l  112 (214)
                      ++++...+||+.++++|   ..+..+++-|...|++.+.+       .+.+.+|+.    ++..
T Consensus        22 ~~~~~~~diA~~L~Vsp---~sVt~ml~rL~~~GlV~~~~-------y~gi~LT~~----G~~~   71 (154)
T COG1321          22 KGFARTKDIAERLKVSP---PSVTEMLKRLERLGLVEYEP-------YGGVTLTEK----GREK   71 (154)
T ss_pred             cCcccHHHHHHHhCCCc---HHHHHHHHHHHHCCCeEEec-------CCCeEEChh----hHHH
Confidence            38999999999999999   99999999999999999987       689999999    6655

>PRK06266 transcription initiation factor E subunit alpha; Validated

Probab=95.07  E-value=0.039  Score=44.16  Aligned_cols=45  Identities=7%  Similarity=0.050  Sum_probs=40.6

Q ss_pred             CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      .|+++|..+ |++|.++||..+|++.   ..++++|..|...|++....
T Consensus        26 ~Vl~~L~~~-g~~tdeeLA~~Lgi~~---~~VRk~L~~L~e~gLv~~~r   70 (178)
T PRK06266         26 EVLKALIKK-GEVTDEEIAEQTGIKL---NTVRKILYKLYDARLADYKR   70 (178)
T ss_pred             HHHHHHHHc-CCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCeEEee
Confidence            377888876 8999999999999999   99999999999999999654

>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=95.06  E-value=0.026  Score=35.74  Aligned_cols=44  Identities=20%  Similarity=0.259  Sum_probs=34.5

Q ss_pred             cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620           41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ   87 (214)
Q Consensus        41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~   87 (214)
                      |+..|..+++++|.++||+.++++.   +.+++-+..|...|+..+.
T Consensus         5 il~~L~~~~~~it~~eLa~~l~vS~---rTi~~~i~~L~~~~~~I~~   48 (55)
T PF08279_consen    5 ILKLLLESKEPITAKELAEELGVSR---RTIRRDIKELREWGIPIES   48 (55)
T ss_dssp             HHHHHHHTTTSBEHHHHHHHCTS-H---HHHHHHHHHHHHTT-EEEE
T ss_pred             HHHHHHHcCCCcCHHHHHHHhCCCH---HHHHHHHHHHHHCCCeEEe
Confidence            4556644447899999999999999   9999999999999944444

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 ....

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

Probab=95.05  E-value=0.031  Score=48.28  Aligned_cols=53  Identities=25%  Similarity=0.213  Sum_probs=34.6

Q ss_pred             HHHHhhhhhhhhHHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          155 FYEAMITDFELIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       155 f~~am~~~~~~~~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      |..+-...+++..+. +..+.   .+.++|+|||||+|.++++-++.-. -+++.+|.
T Consensus       140 FGTG~H~TT~lcl~~-l~~~~---~~g~~vLDvG~GSGILaiaA~klGA-~~v~a~Di  192 (295)
T PF06325_consen  140 FGTGHHPTTRLCLEL-LEKYV---KPGKRVLDVGCGSGILAIAAAKLGA-KKVVAIDI  192 (295)
T ss_dssp             S-SSHCHHHHHHHHH-HHHHS---STTSEEEEES-TTSHHHHHHHHTTB-SEEEEEES
T ss_pred             ccCCCCHHHHHHHHH-HHHhc---cCCCEEEEeCCcHHHHHHHHHHcCC-CeEEEecC
Confidence            334444555555443 34443   3457999999999999999888733 35777776

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 ....

>PLN02336 phosphoethanolamine N-methyltransferase

Probab=95.04  E-value=0.041  Score=50.33  Aligned_cols=41  Identities=10%  Similarity=0.165  Sum_probs=31.3

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+++.++  ..+..++||||||+|.++..+++.+.  +++.+|.
T Consensus        27 ~~il~~l~--~~~~~~vLDlGcG~G~~~~~la~~~~--~v~giD~   67 (475)
T PLN02336         27 PEILSLLP--PYEGKSVLELGAGIGRFTGELAKKAG--QVIALDF   67 (475)
T ss_pred             hHHHhhcC--ccCCCEEEEeCCCcCHHHHHHHhhCC--EEEEEeC
Confidence            44555555  34467999999999999999999854  6777775

>TIGR00406 prmA ribosomal protein L11 methyltransferase

Probab=95.00  E-value=0.037  Score=47.48  Aligned_cols=33  Identities=21%  Similarity=0.225  Sum_probs=26.9

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                      +..+|+|||||+|.+++.+++. +..+++.+|+-
T Consensus       159 ~g~~VLDvGcGsG~lai~aa~~-g~~~V~avDid  191 (288)
T TIGR00406       159 KDKNVIDVGCGSGILSIAALKL-GAAKVVGIDID  191 (288)
T ss_pred             CCCEEEEeCCChhHHHHHHHHc-CCCeEEEEECC
Confidence            3589999999999999988764 45688888863

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.

>PLN02366 spermidine synthase

Probab=94.99  E-value=0.027  Score=48.93  Aligned_cols=34  Identities=24%  Similarity=0.360  Sum_probs=28.4

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCC-CeEEEecCC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPD-TKCTVFACH  213 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dlp  213 (214)
                      ++.++||+||||.|..+..+++. |. .+++++|+.
T Consensus        90 ~~pkrVLiIGgG~G~~~rellk~-~~v~~V~~VEiD  124 (308)
T PLN02366         90 PNPKKVLVVGGGDGGVLREIARH-SSVEQIDICEID  124 (308)
T ss_pred             CCCCeEEEEcCCccHHHHHHHhC-CCCCeEEEEECC
Confidence            35789999999999999999865 65 578888864

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

Probab=94.98  E-value=0.045  Score=44.39  Aligned_cols=41  Identities=20%  Similarity=0.152  Sum_probs=31.2

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +.+++.++  ..+..++||+|||.|.-+.-|+++  +..++.+|.
T Consensus        20 s~v~~a~~--~~~~g~~LDlgcG~GRNalyLA~~--G~~VtAvD~   60 (192)
T PF03848_consen   20 SEVLEAVP--LLKPGKALDLGCGEGRNALYLASQ--GFDVTAVDI   60 (192)
T ss_dssp             HHHHHHCT--TS-SSEEEEES-TTSHHHHHHHHT--T-EEEEEES
T ss_pred             HHHHHHHh--hcCCCcEEEcCCCCcHHHHHHHHC--CCeEEEEEC
Confidence            44556665  456789999999999999999998  888888885

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.

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

Probab=94.93  E-value=0.0084  Score=41.24  Aligned_cols=56  Identities=16%  Similarity=0.186  Sum_probs=42.3

Q ss_pred             cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      |...+..  ++.+..+|+..++++.   ..+.++|..|...|++...        .+.|.+|+.    +..++
T Consensus        11 IL~~l~~--~~~~~t~i~~~~~L~~---~~~~~yL~~L~~~gLI~~~--------~~~Y~lTek----G~~~l   66 (77)
T PF14947_consen   11 ILKILSK--GGAKKTEIMYKANLNY---STLKKYLKELEEKGLIKKK--------DGKYRLTEK----GKEFL   66 (77)
T ss_dssp             HHHHH-T--T-B-HHHHHTTST--H---HHHHHHHHHHHHTTSEEEE--------TTEEEE-HH----HHHHH
T ss_pred             HHHHHHc--CCCCHHHHHHHhCcCH---HHHHHHHHHHHHCcCeeCC--------CCEEEECcc----HHHHH
Confidence            3344443  8999999999999999   9999999999999999775        589999999    76654

>PRK00811 spermidine synthase; Provisional

Probab=94.92  E-value=0.029  Score=48.04  Aligned_cols=33  Identities=21%  Similarity=0.259  Sum_probs=28.4

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +.++|||||||.|..+..++++.+..+++++|+
T Consensus        76 ~p~~VL~iG~G~G~~~~~~l~~~~~~~V~~VEi  108 (283)
T PRK00811         76 NPKRVLIIGGGDGGTLREVLKHPSVEKITLVEI  108 (283)
T ss_pred             CCCEEEEEecCchHHHHHHHcCCCCCEEEEEeC
Confidence            568999999999999999997655668998886

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

Probab=94.89  E-value=0.03  Score=51.92  Aligned_cols=33  Identities=18%  Similarity=0.124  Sum_probs=30.6

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +...+||||||.|.+...+++++|+..++++|.
T Consensus       347 ~~p~~lEIG~G~G~~~~~~A~~~p~~~~iGiE~  379 (506)
T PRK01544        347 KRKVFLEIGFGMGEHFINQAKMNPDALFIGVEV  379 (506)
T ss_pred             CCceEEEECCCchHHHHHHHHhCCCCCEEEEEe
Confidence            467999999999999999999999999999885

>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=94.88  E-value=0.044  Score=40.22  Aligned_cols=32  Identities=13%  Similarity=0.203  Sum_probs=23.6

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .....+||||||.|.+.--|.+.  .-++.++|.
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            35679999999999988777665  445555553

; GO: 0008168 methyltransferase activity

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=94.85  E-value=0.023  Score=41.12  Aligned_cols=46  Identities=15%  Similarity=0.262  Sum_probs=41.0

Q ss_pred             HhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceee
Q 040620           37 IQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQ   86 (214)
Q Consensus        37 ~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~   86 (214)
                      .+..|+.+|..+ +++|..+||+++|+++   ..+++.++.|...|++..
T Consensus         4 ~D~~il~~L~~~-~~~~~~~la~~l~~s~---~tv~~~l~~L~~~g~i~~   49 (108)
T smart00344        4 IDRKILEELQKD-ARISLAELAKKVGLSP---STVHNRVKRLEEEGVIKG   49 (108)
T ss_pred             HHHHHHHHHHHh-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeec
Confidence            356677888886 7899999999999999   999999999999999983

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

>PRK03573 transcriptional regulator SlyA; Provisional

Probab=94.85  E-value=0.076  Score=40.49  Aligned_cols=65  Identities=12%  Similarity=0.113  Sum_probs=46.8

Q ss_pred             cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      ++..|...++++|..+||+.+++++   ..+.++++-|...|+++.....+|.- .-.+.+|+.    ++.+.
T Consensus        36 vL~~l~~~~~~~t~~eLa~~l~~~~---~tvt~~v~~Le~~GlV~r~~~~~DrR-~~~l~LT~~----G~~~~  100 (144)
T PRK03573         36 TLHNIHQLPPEQSQIQLAKAIGIEQ---PSLVRTLDQLEEKGLISRQTCASDRR-AKRIKLTEK----AEPLI  100 (144)
T ss_pred             HHHHHHHcCCCCCHHHHHHHhCCCh---hhHHHHHHHHHHCCCEeeecCCCCcC-eeeeEEChH----HHHHH
Confidence            3455554335689999999999999   99999999999999999875321111 234667777    55553

>PRK11727 23S rRNA mA1618 methyltransferase; Provisional

Probab=94.84  E-value=0.036  Score=48.43  Aligned_cols=33  Identities=9%  Similarity=-0.034  Sum_probs=29.8

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...++||||||+|.....++.+.|+++++..|+
T Consensus       114 ~~~~vLDIGtGag~I~~lLa~~~~~~~~~atDI  146 (321)
T PRK11727        114 ANVRVLDIGVGANCIYPLIGVHEYGWRFVGSDI  146 (321)
T ss_pred             CCceEEEecCCccHHHHHHHhhCCCCEEEEEeC
Confidence            357999999999999999999999999999986

>PRK14967 putative methyltransferase; Provisional

Probab=94.83  E-value=0.048  Score=44.80  Aligned_cols=35  Identities=20%  Similarity=0.165  Sum_probs=28.3

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                      .....+|+|+|||+|.++..+++. +..+++.+|+-
T Consensus        34 ~~~~~~vLDlGcG~G~~~~~la~~-~~~~v~~vD~s   68 (223)
T PRK14967         34 LGPGRRVLDLCTGSGALAVAAAAA-GAGSVTAVDIS   68 (223)
T ss_pred             cCCCCeEEEecCCHHHHHHHHHHc-CCCeEEEEECC
Confidence            344579999999999999999876 44588888863

>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein

Probab=94.82  E-value=0.039  Score=44.88  Aligned_cols=58  Identities=12%  Similarity=0.143  Sum_probs=47.7

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      +..|+..|..+ ++++..+||+.+++++   ..+++.|..|...|++...+..     ...|.+|+.
T Consensus       145 ~~~IL~~l~~~-g~~s~~eia~~l~is~---stv~r~L~~Le~~GlI~r~~~r-----~~~~~lT~~  202 (203)
T TIGR01884       145 ELKVLEVLKAE-GEKSVKNIAKKLGKSL---STISRHLRELEKKGLVEQKGRK-----GKRYSLTKL  202 (203)
T ss_pred             HHHHHHHHHHc-CCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEEcCC-----ccEEEeCCC
Confidence            34566677765 6899999999999999   9999999999999999988511     467888875

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.

>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=94.82  E-value=0.028  Score=36.80  Aligned_cols=37  Identities=24%  Similarity=0.351  Sum_probs=34.1

Q ss_pred             CCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           49 GQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        49 ~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      +++++..+||+.++++|   ..+...++-|...|++...+
T Consensus        20 ~~~v~~~~iA~~L~vs~---~tvt~ml~~L~~~GlV~~~~   56 (60)
T PF01325_consen   20 GGPVRTKDIAERLGVSP---PTVTEMLKRLAEKGLVEYEP   56 (60)
T ss_dssp             TSSBBHHHHHHHHTS-H---HHHHHHHHHHHHTTSEEEET
T ss_pred             CCCccHHHHHHHHCCCh---HHHHHHHHHHHHCCCEEecC
Confidence            48999999999999999   99999999999999999885

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 ....

>PRK11050 manganese transport regulator MntR; Provisional

Probab=94.80  E-value=0.031  Score=43.45  Aligned_cols=58  Identities=19%  Similarity=0.250  Sum_probs=48.1

Q ss_pred             cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      |..++... ++++..+||+.+++++   ..+.++++.|...|++....       ...+.+|+.    +..+.
T Consensus        42 I~~~l~~~-~~~t~~eLA~~l~is~---stVsr~l~~Le~~GlI~r~~-------~~~v~LT~~----G~~l~   99 (152)
T PRK11050         42 IADLIAEV-GEARQVDIAARLGVSQ---PTVAKMLKRLARDGLVEMRP-------YRGVFLTPE----GEKLA   99 (152)
T ss_pred             HHHHHHhc-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEEec-------CCceEECch----HHHHH
Confidence            55566654 7899999999999999   99999999999999998765       467888888    66553

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=94.79  E-value=0.057  Score=34.36  Aligned_cols=43  Identities=9%  Similarity=0.201  Sum_probs=36.9

Q ss_pred             cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      |+..|..  ++.|..+|++.+++++   ..+++.++.|...|++....
T Consensus         2 il~~l~~--~~~~~~~i~~~l~is~---~~v~~~l~~L~~~g~i~~~~   44 (66)
T smart00418        2 ILKLLAE--GELCVCELAEILGLSQ---STVSHHLKKLREAGLVESRR   44 (66)
T ss_pred             HHHHhhc--CCccHHHHHHHHCCCH---HHHHHHHHHHHHCCCeeeee
Confidence            3445553  7899999999999999   99999999999999998654

>PLN02585 magnesium protoporphyrin IX methyltransferase

Probab=94.78  E-value=0.033  Score=48.60  Aligned_cols=32  Identities=19%  Similarity=0.205  Sum_probs=27.4

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                      +..+|||||||+|.++..++++  +.+++.+|+-
T Consensus       144 ~~~~VLDlGcGtG~~a~~la~~--g~~V~gvD~S  175 (315)
T PLN02585        144 AGVTVCDAGCGTGSLAIPLALE--GAIVSASDIS  175 (315)
T ss_pred             CCCEEEEecCCCCHHHHHHHHC--CCEEEEEECC
Confidence            3579999999999999999986  5788988863

>PRK10901 16S rRNA methyltransferase B; Provisional

Probab=94.76  E-value=0.044  Score=49.66  Aligned_cols=35  Identities=11%  Similarity=0.193  Sum_probs=31.0

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .....+|+|+|||+|..+..+++..|+.+++.+|+
T Consensus       242 ~~~g~~VLDlgaG~G~~t~~la~~~~~~~v~a~D~  276 (427)
T PRK10901        242 PQNGERVLDACAAPGGKTAHILELAPQAQVVALDI  276 (427)
T ss_pred             CCCCCEEEEeCCCCChHHHHHHHHcCCCEEEEEeC
Confidence            34567999999999999999999998888998886

>KOG3115 consensus Methyltransferase-like protein [General function prediction only]

Probab=94.73  E-value=0.014  Score=47.60  Aligned_cols=32  Identities=25%  Similarity=0.346  Sum_probs=28.5

Q ss_pred             CCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          181 LKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       181 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      -..++|||||-|.+.+.|+..||+.-+.++++
T Consensus        61 kvefaDIGCGyGGLlv~Lsp~fPdtLiLGmEI   92 (249)
T KOG3115|consen   61 KVEFADIGCGYGGLLMKLAPKFPDTLILGMEI   92 (249)
T ss_pred             cceEEeeccCccchhhhccccCccceeeeehh
Confidence            36899999999999999999999998877654

>PRK11873 arsM arsenite S-adenosylmethyltransferase; Reviewed

Probab=94.66  E-value=0.052  Score=45.82  Aligned_cols=35  Identities=20%  Similarity=0.153  Sum_probs=29.0

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHC-CCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAF-PDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl  212 (214)
                      .....+|||||||.|..+..+++.. |+.+++.+|+
T Consensus        75 ~~~g~~VLDiG~G~G~~~~~~a~~~g~~~~v~gvD~  110 (272)
T PRK11873         75 LKPGETVLDLGSGGGFDCFLAARRVGPTGKVIGVDM  110 (272)
T ss_pred             CCCCCEEEEeCCCCCHHHHHHHHHhCCCCEEEEECC
Confidence            4467899999999999988777764 6678999986

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

Probab=94.64  E-value=0.04  Score=47.61  Aligned_cols=54  Identities=24%  Similarity=0.161  Sum_probs=35.7

Q ss_pred             HHHHHhhhhhhhhHHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          154 IFYEAMITDFELIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       154 ~f~~am~~~~~~~~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .|..+-...+.+..+ +++.+.   .+.++++|||||+|.++++.++--. .+++.+|+
T Consensus       140 AFGTG~HpTT~lcL~-~Le~~~---~~g~~vlDvGcGSGILaIAa~kLGA-~~v~g~Di  193 (300)
T COG2264         140 AFGTGTHPTTSLCLE-ALEKLL---KKGKTVLDVGCGSGILAIAAAKLGA-KKVVGVDI  193 (300)
T ss_pred             ccCCCCChhHHHHHH-HHHHhh---cCCCEEEEecCChhHHHHHHHHcCC-ceEEEecC
Confidence            343444444455443 445554   3688999999999999999888622 24666665

>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial

Probab=94.63  E-value=0.041  Score=41.40  Aligned_cols=47  Identities=15%  Similarity=0.228  Sum_probs=39.1

Q ss_pred             CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      +++|+.|||+++++++   ..++++|+.|...|++.....    . .+.|.+...
T Consensus        24 ~~~s~~eia~~l~is~---~~v~~~l~~L~~~Gli~~~~g----~-~ggy~l~~~   70 (130)
T TIGR02944        24 QPYSAAEIAEQTGLNA---PTVSKILKQLSLAGIVTSKRG----V-EGGYTLARA   70 (130)
T ss_pred             CCccHHHHHHHHCcCH---HHHHHHHHHHHHCCcEEecCC----C-CCChhhcCC
Confidence            7899999999999999   999999999999999976421    0 356776655

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.

>PHA00738 putative HTH transcription regulator

Probab=94.61  E-value=0.042  Score=40.20  Aligned_cols=60  Identities=12%  Similarity=0.141  Sum_probs=48.3

Q ss_pred             HhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           37 IQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        37 ~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      .++.|+..|... +++++.+|++.++++.   ..+.+-|+.|...|++.....   |. ...|++++.
T Consensus        13 tRr~IL~lL~~~-e~~~V~eLae~l~lSQ---ptVS~HLKvLreAGLV~srK~---Gr-~vyY~Ln~~   72 (108)
T PHA00738         13 LRRKILELIAEN-YILSASLISHTLLLSY---TTVLRHLKILNEQGYIELYKE---GR-TLYAKIREN   72 (108)
T ss_pred             HHHHHHHHHHHc-CCccHHHHHHhhCCCH---HHHHHHHHHHHHCCceEEEEE---CC-EEEEEECCC
Confidence            456678888873 5799999999999999   999999999999999998762   11 244777776

>COG1959 Predicted transcriptional regulator [Transcription]

Probab=94.58  E-value=0.039  Score=42.92  Aligned_cols=47  Identities=13%  Similarity=0.220  Sum_probs=40.8

Q ss_pred             CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      ++.|+++||++.+++|   .+|.+++..|...|++.-....     .|-|.+..-
T Consensus        24 ~~~s~~~IA~~~~is~---~~L~kil~~L~kaGlV~S~rG~-----~GGy~Lar~   70 (150)
T COG1959          24 GPVSSAEIAERQGISP---SYLEKILSKLRKAGLVKSVRGK-----GGGYRLARP   70 (150)
T ss_pred             CcccHHHHHHHhCcCH---HHHHHHHHHHHHcCCEEeecCC-----CCCccCCCC
Confidence            4899999999999999   9999999999999999866421     577888777

>TIGR00478 tly hemolysin TlyA family protein

Probab=94.57  E-value=0.088  Score=43.80  Aligned_cols=42  Identities=21%  Similarity=0.196  Sum_probs=30.8

Q ss_pred             HHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          169 VLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       169 ~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+++.++- ....++++|||||+|.++..++++ +-.+++.+|.
T Consensus        65 ~~l~~~~~-~~~~~~vlDiG~gtG~~t~~l~~~-ga~~v~avD~  106 (228)
T TIGR00478        65 EALEEFNI-DVKNKIVLDVGSSTGGFTDCALQK-GAKEVYGVDV  106 (228)
T ss_pred             HHHHhcCC-CCCCCEEEEcccCCCHHHHHHHHc-CCCEEEEEeC
Confidence            34454431 124679999999999999999986 5557888885

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=94.56  E-value=0.029  Score=37.48  Aligned_cols=48  Identities=15%  Similarity=0.235  Sum_probs=38.1

Q ss_pred             cchhhhcCCCCCCHHHHHHHcCCCCCC--cccHHHHHHHHHhCCceeeec
Q 040620           41 IPDIINNSGQPMTLTQIIVALNVHPNK--TRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        41 lfd~L~~~~~p~t~~eLA~~~g~~~~~--~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      |+++|.+.++|++..+|++.++....+  ++.+++.|+.|-..|++....
T Consensus         3 IL~~L~~~~~P~g~~~l~~~L~~~g~~~se~avRrrLr~me~~Glt~~~g   52 (66)
T PF08461_consen    3 ILRILAESDKPLGRKQLAEELKLRGEELSEEAVRRRLRAMERDGLTRKVG   52 (66)
T ss_pred             HHHHHHHcCCCCCHHHHHHHHHhcChhhhHHHHHHHHHHHHHCCCccccC
Confidence            456777777999999999998753322  288999999999999777654

>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=94.52  E-value=0.027  Score=37.55  Aligned_cols=41  Identities=24%  Similarity=0.374  Sum_probs=33.0

Q ss_pred             hhcCCCCCCHHHHHHHcCCC-CCCcccHHHHHHHHHhCCceeeec
Q 040620           45 INNSGQPMTLTQIIVALNVH-PNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        45 L~~~~~p~t~~eLA~~~g~~-~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      +.++|-|-|+.|||+.+|+. +   ..+++.|+.|...|++...+
T Consensus        19 ~~~~G~~Pt~rEIa~~~g~~S~---~tv~~~L~~Le~kG~I~r~~   60 (65)
T PF01726_consen   19 IEENGYPPTVREIAEALGLKST---STVQRHLKALERKGYIRRDP   60 (65)
T ss_dssp             HHHHSS---HHHHHHHHTSSSH---HHHHHHHHHHHHTTSEEEGC
T ss_pred             HHHcCCCCCHHHHHHHhCCCCh---HHHHHHHHHHHHCcCccCCC
Confidence            34455677999999999996 7   89999999999999999875

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.

>PHA03412 putative methyltransferase; Provisional

Probab=94.46  E-value=0.045  Score=45.80  Aligned_cols=32  Identities=13%  Similarity=0.171  Sum_probs=27.8

Q ss_pred             CCcEEeecCCchHHHHHHHHHC---CCCeEEEecC
Q 040620          181 LKPLVDVGGSTGTMARAIATAF---PDTKCTVFAC  212 (214)
Q Consensus       181 ~~~vvDVGGG~G~~~~~l~~~~---P~l~~~v~Dl  212 (214)
                      ..+|||+|||+|.++..++++.   ++.+++.+|+
T Consensus        50 ~grVLDlG~GSG~Lalala~~~~~~~~~~V~aVEI   84 (241)
T PHA03412         50 SGSVVDLCAGIGGLSFAMVHMMMYAKPREIVCVEL   84 (241)
T ss_pred             CCEEEEccChHHHHHHHHHHhcccCCCcEEEEEEC
Confidence            5799999999999999999985   4668888886

>KOG1270 consensus Methyltransferases [Coenzyme transport and metabolism]

Probab=94.40  E-value=0.044  Score=46.39  Aligned_cols=30  Identities=20%  Similarity=0.296  Sum_probs=25.6

Q ss_pred             CCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          181 LKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       181 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .++|||||||.|.++..|++.  ...++..|.
T Consensus        90 g~~ilDvGCGgGLLSepLArl--ga~V~GID~  119 (282)
T KOG1270|consen   90 GMKILDVGCGGGLLSEPLARL--GAQVTGIDA  119 (282)
T ss_pred             CceEEEeccCccccchhhHhh--CCeeEeecc
Confidence            367999999999999999998  467777775

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

Probab=94.39  E-value=0.066  Score=34.18  Aligned_cols=42  Identities=19%  Similarity=0.135  Sum_probs=34.5

Q ss_pred             HHHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHH
Q 040620           30 SLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLL   78 (214)
Q Consensus        30 ~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L   78 (214)
                      -.+|.+|++.|-||.=.    ..|.+|||+.+|+++   ..+...||-.
T Consensus         6 ~e~L~~A~~~GYfd~PR----~~tl~elA~~lgis~---st~~~~LRra   47 (53)
T PF04967_consen    6 REILKAAYELGYFDVPR----RITLEELAEELGISK---STVSEHLRRA   47 (53)
T ss_pred             HHHHHHHHHcCCCCCCC----cCCHHHHHHHhCCCH---HHHHHHHHHH
Confidence            46899999999998644    489999999999998   7776666643

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

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

Probab=94.35  E-value=0.08  Score=43.51  Aligned_cols=31  Identities=3%  Similarity=-0.231  Sum_probs=27.9

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+++|+|||.|..++.|+++  ..++|.+|+
T Consensus        34 ~~~rvLd~GCG~G~da~~LA~~--G~~V~gvD~   64 (213)
T TIGR03840        34 AGARVFVPLCGKSLDLAWLAEQ--GHRVLGVEL   64 (213)
T ss_pred             CCCeEEEeCCCchhHHHHHHhC--CCeEEEEeC
Confidence            4579999999999999999986  888999986

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.

>KOG2904 consensus Predicted methyltransferase [General function prediction only]

Probab=94.28  E-value=0.05  Score=46.43  Aligned_cols=33  Identities=15%  Similarity=0.399  Sum_probs=29.9

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ....++|+|||+|..+..++..-|+.+++-.|+
T Consensus       148 ~~~~ildlgtGSGaIslsll~~L~~~~v~AiD~  180 (328)
T KOG2904|consen  148 KHTHILDLGTGSGAISLSLLHGLPQCTVTAIDV  180 (328)
T ss_pred             ccceEEEecCCccHHHHHHHhcCCCceEEEEec
Confidence            345899999999999999999999999998886

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

Probab=94.27  E-value=0.0087  Score=41.53  Aligned_cols=64  Identities=13%  Similarity=0.173  Sum_probs=45.6

Q ss_pred             HhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           37 IQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        37 ~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      ++++|..+|... +.+++.+|.+.+|++.   -.+.+-|..|...|++.....-.+..-.-.|++|+.
T Consensus         1 vRl~Il~~L~~~-~~~~f~~L~~~l~lt~---g~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~~lT~~   64 (80)
T PF13601_consen    1 VRLAILALLYAN-EEATFSELKEELGLTD---GNLSKHLKKLEEAGYVEVEKEFEGRRPRTWYSLTDK   64 (80)
T ss_dssp             HHHHHHHHHHHH-SEEEHHHHHHHTT--H---HHHHHHHHHHHHTTSEEEEEE-SSS--EEEEEE-HH
T ss_pred             CHHHHHHHHhhc-CCCCHHHHHHHhCcCH---HHHHHHHHHHHHCCCEEEEEeccCCCCeEEEEECHH
Confidence            456777788876 7899999999999999   999999999999999997753111100123666666

>TIGR00373 conserved hypothetical protein TIGR00373

Probab=94.26  E-value=0.047  Score=42.85  Aligned_cols=44  Identities=11%  Similarity=0.039  Sum_probs=38.9

Q ss_pred             CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620           40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ   87 (214)
Q Consensus        40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~   87 (214)
                      .|+++|..+ +.+|-++||+.+|++.   ..++++|..|...|++.+.
T Consensus        18 ~Vl~aL~~~-~~~tdEeLa~~Lgi~~---~~VRk~L~~L~e~~Lv~~~   61 (158)
T TIGR00373        18 LVLFSLGIK-GEFTDEEISLELGIKL---NEVRKALYALYDAGLADYK   61 (158)
T ss_pred             HHHHHHhcc-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCceee
Confidence            366777765 7999999999999999   9999999999999999754

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.

>PRK14902 16S rRNA methyltransferase B; Provisional

Probab=94.26  E-value=0.062  Score=48.90  Aligned_cols=35  Identities=20%  Similarity=0.261  Sum_probs=30.4

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHC-CCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAF-PDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl  212 (214)
                      ..+..+|+|+|||+|..+..+++.. |+.+++.+|+
T Consensus       248 ~~~g~~VLDlgaG~G~~t~~la~~~~~~~~v~avDi  283 (444)
T PRK14902        248 PKGGDTVLDACAAPGGKTTHIAELLKNTGKVVALDI  283 (444)
T ss_pred             CCCCCEEEEeCCCCCHHHHHHHHHhCCCCEEEEEeC
Confidence            3456799999999999999999987 7788999987

>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=94.22  E-value=0.14  Score=42.17  Aligned_cols=64  Identities=19%  Similarity=0.136  Sum_probs=37.4

Q ss_pred             CChhhHHHHHHHHHhhhhhhhhHHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          145 QTLFGTADGIFYEAMITDFELIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       145 ~~~f~~~~g~f~~am~~~~~~~~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      |..|+..|.-|.+.+..+.......+++.+. ..++...|.|.|||.+.++.++.+.   .++--|||
T Consensus        38 P~~F~~YH~Gfr~Qv~~WP~nPvd~iI~~l~-~~~~~~viaD~GCGdA~la~~~~~~---~~V~SfDL  101 (219)
T PF05148_consen   38 PELFDIYHEGFRQQVKKWPVNPVDVIIEWLK-KRPKSLVIADFGCGDAKLAKAVPNK---HKVHSFDL  101 (219)
T ss_dssp             HHHHHHHHHHHHHHHCTSSS-HHHHHHHHHC-TS-TTS-EEEES-TT-HHHHH--S------EEEEES
T ss_pred             HHHHHHHHHHHHHHHhcCCCCcHHHHHHHHH-hcCCCEEEEECCCchHHHHHhcccC---ceEEEeec
Confidence            4567766656888888777666666666554 2344579999999999999765422   34555554

; GO: 0008168 methyltransferase activity; PDB: 2ZFU_B.

>PTZ00338 dimethyladenosine transferase-like protein; Provisional

Probab=94.19  E-value=0.1  Score=45.01  Aligned_cols=41  Identities=15%  Similarity=0.294  Sum_probs=30.8

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+++..+  .....+|+|||||.|.++..+++...  +++.+|+
T Consensus        26 ~~Iv~~~~--~~~~~~VLEIG~G~G~LT~~Ll~~~~--~V~avEi   66 (294)
T PTZ00338         26 DKIVEKAA--IKPTDTVLEIGPGTGNLTEKLLQLAK--KVIAIEI   66 (294)
T ss_pred             HHHHHhcC--CCCcCEEEEecCchHHHHHHHHHhCC--cEEEEEC
Confidence            44555554  45567999999999999999999854  5666664

>PRK11512 DNA-binding transcriptional repressor MarR; Provisional

Probab=94.14  E-value=0.054  Score=41.44  Aligned_cols=65  Identities=11%  Similarity=0.087  Sum_probs=47.9

Q ss_pred             CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      .|+-.|... +++|..+||+.+++++   ..+.++++-|...|++......+|.- .-.+.+|+.    ++.+.
T Consensus        44 ~vL~~l~~~-~~~t~~eLa~~l~i~~---~tvsr~l~~Le~~GlI~R~~~~~DrR-~~~l~LT~~----G~~~~  108 (144)
T PRK11512         44 KVLCSIRCA-ACITPVELKKVLSVDL---GALTRMLDRLVCKGWVERLPNPNDKR-GVLVKLTTS----GAAIC  108 (144)
T ss_pred             HHHHHHHHc-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEeccCcccCC-eeEeEEChh----HHHHH
Confidence            345566654 7899999999999999   99999999999999999775321111 223566777    55543

>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function

Probab=94.07  E-value=0.058  Score=40.50  Aligned_cols=51  Identities=12%  Similarity=0.253  Sum_probs=46.1

Q ss_pred             HHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           34 KRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        34 ~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      +..++..|.+.+.++ |.+|..|++..+|++.   ..+.++++-|++.|-+...+
T Consensus        10 r~eLk~rIvElVRe~-GRiTi~ql~~~TGasR---~Tvk~~lreLVa~G~l~~~G   60 (127)
T PF06163_consen   10 REELKARIVELVREH-GRITIKQLVAKTGASR---NTVKRYLRELVARGDLYRHG   60 (127)
T ss_pred             HHHHHHHHHHHHHHc-CCccHHHHHHHHCCCH---HHHHHHHHHHHHcCCeEeCC
Confidence            456677888999998 9999999999999998   89999999999999999885

>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators

Probab=94.04  E-value=0.15  Score=32.81  Aligned_cols=34  Identities=12%  Similarity=0.109  Sum_probs=30.9

Q ss_pred             CCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           52 MTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        52 ~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      .|..+||+.+++++   ..+++.+..|...|++....
T Consensus        26 ~~~~~la~~~~is~---~~v~~~l~~L~~~G~i~~~~   59 (66)
T cd07377          26 PSERELAEELGVSR---TTVREALRELEAEGLVERRP   59 (66)
T ss_pred             CCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEecC
Confidence            35999999999999   99999999999999998664

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

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

Probab=94.02  E-value=0.12  Score=42.46  Aligned_cols=32  Identities=22%  Similarity=0.258  Sum_probs=26.5

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                      +..+|||||||.|.++..+++.  ..++++.|..
T Consensus        48 ~~~~vLdiG~G~G~~~~~l~~~--~~~v~~iD~s   79 (233)
T PRK05134         48 FGKRVLDVGCGGGILSESMARL--GADVTGIDAS   79 (233)
T ss_pred             CCCeEEEeCCCCCHHHHHHHHc--CCeEEEEcCC
Confidence            4678999999999999999886  4678888763

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

Probab=94.02  E-value=0.062  Score=48.91  Aligned_cols=32  Identities=9%  Similarity=0.040  Sum_probs=26.9

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+..+|+|+|||+|.+++.+++..  .+++.+|.
T Consensus       296 ~~~~~VLDlgcGtG~~sl~la~~~--~~V~gvD~  327 (443)
T PRK13168        296 QPGDRVLDLFCGLGNFTLPLARQA--AEVVGVEG  327 (443)
T ss_pred             CCCCEEEEEeccCCHHHHHHHHhC--CEEEEEeC
Confidence            345799999999999999999986  57777775

>COG4190 Predicted transcriptional regulator [Transcription]

Probab=93.95  E-value=0.063  Score=40.63  Aligned_cols=47  Identities=13%  Similarity=0.301  Sum_probs=42.1

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      .+.|...|+.. +|.|+.|+|+.+|-+.   ..|.|-|+.|+..|++.-..
T Consensus        66 nleLl~~Ia~~-~P~Si~ElAe~vgRdv---~nvhr~Ls~l~~~GlI~fe~  112 (144)
T COG4190          66 NLELLELIAQE-EPASINELAELVGRDV---KNVHRTLSTLADLGLIFFEE  112 (144)
T ss_pred             HHHHHHHHHhc-CcccHHHHHHHhCcch---HHHHHHHHHHHhcCeEEEec
Confidence            35567788887 9999999999999999   99999999999999998775

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

Probab=93.93  E-value=0.13  Score=45.03  Aligned_cols=35  Identities=14%  Similarity=0.198  Sum_probs=28.9

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCC-CeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPD-TKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dl  212 (214)
                      ..+..+|||||||+|.++..+++..+. -+++.+|.
T Consensus        78 i~~g~~VLDIG~GtG~~a~~LA~~~~~~g~VvgVDi  113 (322)
T PRK13943         78 LDKGMRVLEIGGGTGYNAAVMSRVVGEKGLVVSVEY  113 (322)
T ss_pred             CCCCCEEEEEeCCccHHHHHHHHhcCCCCEEEEEEC
Confidence            445679999999999999999998875 46777775

>PRK11014 transcriptional repressor NsrR; Provisional

Probab=93.93  E-value=0.077  Score=40.59  Aligned_cols=61  Identities=13%  Similarity=0.251  Sum_probs=45.3

Q ss_pred             HHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           32 SLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        32 ~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      +++..+.++.   +.. |.+++.++||++.|+++   ..++++++.|...|++.-....     .+.|.+...
T Consensus        10 Al~~~i~la~---~~~-g~~~s~~~ia~~~~is~---~~vrk~l~~L~~~Glv~s~~G~-----~GG~~l~~~   70 (141)
T PRK11014         10 GLRALIYMAS---LPE-GRMTSISEVTEVYGVSR---NHMVKIINQLSRAGYVTAVRGK-----NGGIRLGKP   70 (141)
T ss_pred             HHHHHHHHhc---CCC-CCccCHHHHHHHHCcCH---HHHHHHHHHHHhCCEEEEecCC-----CCCeeecCC
Confidence            4555554443   222 26789999999999999   9999999999999999877521     356766655

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

Probab=93.90  E-value=0.084  Score=34.58  Aligned_cols=44  Identities=16%  Similarity=0.309  Sum_probs=37.0

Q ss_pred             CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      .|+..+..  ++++..+||+.++++.   ..+++.++.|...|++....
T Consensus        11 ~il~~l~~--~~~~~~ei~~~~~i~~---~~i~~~l~~L~~~g~i~~~~   54 (78)
T cd00090          11 RILRLLLE--GPLTVSELAERLGLSQ---STVSRHLKKLEEAGLVESRR   54 (78)
T ss_pred             HHHHHHHH--CCcCHHHHHHHHCcCH---hHHHHHHHHHHHCCCeEEEE
Confidence            34555555  3499999999999998   99999999999999999764

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.

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

Probab=93.81  E-value=0.14  Score=40.59  Aligned_cols=37  Identities=19%  Similarity=0.174  Sum_probs=28.7

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCCC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACHL  214 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~  214 (214)
                      ....++|+++|+|.|..++.+++..+..++++-|.|+
T Consensus        43 ~~~~~~VLELGaG~Gl~gi~~a~~~~~~~Vv~TD~~~   79 (173)
T PF10294_consen   43 LFRGKRVLELGAGTGLPGIAAAKLFGAARVVLTDYNE   79 (173)
T ss_dssp             GTTTSEEEETT-TTSHHHHHHHHT-T-SEEEEEE-S-
T ss_pred             hcCCceEEEECCccchhHHHHHhccCCceEEEeccch
Confidence            4457899999999999999999998888999998874

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.

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=93.81  E-value=0.14  Score=32.32  Aligned_cols=36  Identities=11%  Similarity=0.201  Sum_probs=32.7

Q ss_pred             CCC-CHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           50 QPM-TLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        50 ~p~-t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      ..+ |..+||+.+++++   ..+++.+..|...|++....
T Consensus        18 ~~l~s~~~la~~~~vs~---~tv~~~l~~L~~~g~i~~~~   54 (60)
T smart00345       18 DKLPSERELAAQLGVSR---TTVREALSRLEAEGLVQRRP   54 (60)
T ss_pred             CcCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEEec
Confidence            456 8999999999999   99999999999999998764

>PRK01581 speE spermidine synthase; Validated

Probab=93.76  E-value=0.082  Score=47.00  Aligned_cols=35  Identities=14%  Similarity=0.137  Sum_probs=29.3

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                      .++++||+||||.|..+..+++..|..+++++|+-
T Consensus       149 ~~PkrVLIIGgGdG~tlrelLk~~~v~~It~VEID  183 (374)
T PRK01581        149 IDPKRVLILGGGDGLALREVLKYETVLHVDLVDLD  183 (374)
T ss_pred             CCCCEEEEECCCHHHHHHHHHhcCCCCeEEEEeCC
Confidence            45789999999999999999986556789988863

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

Probab=93.70  E-value=0.15  Score=41.46  Aligned_cols=33  Identities=15%  Similarity=0.178  Sum_probs=25.7

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+..+|+|||||+|..+..+++...  +++.+|.
T Consensus        76 ~~~~~~VLeiG~GsG~~t~~la~~~~--~v~~vd~  108 (212)
T PRK00312         76 LKPGDRVLEIGTGSGYQAAVLAHLVR--RVFSVER  108 (212)
T ss_pred             CCCCCEEEEECCCccHHHHHHHHHhC--EEEEEeC
Confidence            45568999999999999988777753  5666664

>COG4742 Predicted transcriptional regulator [Transcription]

Probab=93.65  E-value=0.069  Score=45.18  Aligned_cols=64  Identities=19%  Similarity=0.238  Sum_probs=57.2

Q ss_pred             HHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCccccccc
Q 040620           33 LKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRIS  112 (214)
Q Consensus        33 L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l  112 (214)
                      +...-+.+|+-.|.+  ||.|.+||-..+++++   ..+..=+.-|...|++.++        ++.|++|+.    ++..
T Consensus        10 f~SekRk~lLllL~e--gPkti~EI~~~l~vs~---~ai~pqiKkL~~~~LV~~~--------~~~Y~LS~~----G~ii   72 (260)
T COG4742          10 FLSEKRKDLLLLLKE--GPKTIEEIKNELNVSS---SAILPQIKKLKDKGLVVQE--------GDRYSLSSL----GKII   72 (260)
T ss_pred             HccHHHHHHHHHHHh--CCCCHHHHHHHhCCCc---HHHHHHHHHHhhCCCEEec--------CCEEEecch----HHHH
Confidence            345566777888887  9999999999999999   9999999999999999999        489999999    9988


Q ss_pred             c
Q 040620          113 L  113 (214)
Q Consensus       113 ~  113 (214)
                      +
T Consensus        73 v   73 (260)
T COG4742          73 V   73 (260)
T ss_pred             H
Confidence            7

>PRK04148 hypothetical protein; Provisional

Probab=93.58  E-value=0.15  Score=38.93  Aligned_cols=40  Identities=15%  Similarity=0.178  Sum_probs=28.8

Q ss_pred             HHHhhcccccCCCCcEEeecCCchH-HHHHHHHHCCCCeEEEecC
Q 040620          169 VLIEDCNEVSKGLKPLVDVGGSTGT-MARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       169 ~~l~~~~~~~~~~~~vvDVGGG~G~-~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+.+.++  -.+..+++|||+|.|. ++..|.+.  +..++..|.
T Consensus         7 ~l~~~~~--~~~~~kileIG~GfG~~vA~~L~~~--G~~ViaIDi   47 (134)
T PRK04148          7 FIAENYE--KGKNKKIVELGIGFYFKVAKKLKES--GFDVIVIDI   47 (134)
T ss_pred             HHHHhcc--cccCCEEEEEEecCCHHHHHHHHHC--CCEEEEEEC
Confidence            3445454  2234789999999996 88888765  678888885

>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed

Probab=93.55  E-value=0.11  Score=40.47  Aligned_cols=47  Identities=13%  Similarity=0.104  Sum_probs=40.5

Q ss_pred             CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      +++|+++||++.++++   .+|.+++..|...|++.-....     .|-|.++.-
T Consensus        23 ~~~s~~eIA~~~~is~---~~L~kIl~~L~~aGlv~S~rG~-----~GGy~La~~   69 (153)
T PRK11920         23 KLSRIPEIARAYGVSE---LFLFKILQPLVEAGLVETVRGR-----NGGVRLGRP   69 (153)
T ss_pred             CcCcHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEeecCC-----CCCeeecCC
Confidence            6789999999999999   9999999999999999866521     467777776

>TIGR00563 rsmB ribosomal RNA small subunit methyltransferase RsmB

Probab=93.46  E-value=0.11  Score=47.08  Aligned_cols=35  Identities=11%  Similarity=0.231  Sum_probs=30.7

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .....+|+|+|||+|..+..+++..|+.+++.+|.
T Consensus       236 ~~~g~~VLDlcag~G~kt~~la~~~~~~~v~a~D~  270 (426)
T TIGR00563       236 PQNEETILDACAAPGGKTTHILELAPQAQVVALDI  270 (426)
T ss_pred             CCCCCeEEEeCCCccHHHHHHHHHcCCCeEEEEeC
Confidence            34567999999999999999999998788888886

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.

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

Probab=93.46  E-value=0.08  Score=44.77  Aligned_cols=34  Identities=29%  Similarity=0.355  Sum_probs=30.6

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCC------CeEEEecCC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPD------TKCTVFACH  213 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~------l~~~v~Dlp  213 (214)
                      ..-++|||+||+|-.+..|+++-++      .+++|.|+-
T Consensus       100 ~~m~~lDvaGGTGDiaFril~~v~s~~~~~~~~V~v~Din  139 (296)
T KOG1540|consen  100 KGMKVLDVAGGTGDIAFRILRHVKSQFGDRESKVTVLDIN  139 (296)
T ss_pred             CCCeEEEecCCcchhHHHHHHhhccccCCCCceEEEEeCC
Confidence            3479999999999999999999999      789999974

>PRK13255 thiopurine S-methyltransferase; Reviewed

Probab=93.44  E-value=0.15  Score=42.02  Aligned_cols=32  Identities=3%  Similarity=-0.234  Sum_probs=28.1

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ....+|+|+|||.|..+..|+++  ..+++.+|+
T Consensus        36 ~~~~rvL~~gCG~G~da~~LA~~--G~~V~avD~   67 (218)
T PRK13255         36 PAGSRVLVPLCGKSLDMLWLAEQ--GHEVLGVEL   67 (218)
T ss_pred             CCCCeEEEeCCCChHhHHHHHhC--CCeEEEEcc
Confidence            34579999999999999999985  888999986

>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family

Probab=93.40  E-value=0.067  Score=39.06  Aligned_cols=37  Identities=16%  Similarity=0.365  Sum_probs=34.6

Q ss_pred             CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecC
Q 040620           50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKD   89 (214)
Q Consensus        50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~   89 (214)
                      +++|..+||+.+++++   ..+.++++.|...|++.....
T Consensus        42 ~~~t~~eL~~~l~~~~---stvs~~i~~Le~kg~I~r~~~   78 (109)
T TIGR01889        42 GKLTLKEIIKEILIKQ---SALVKIIKKLSKKGYLSKERS   78 (109)
T ss_pred             CcCcHHHHHHHHCCCH---HHHHHHHHHHHHCCCEeccCC
Confidence            7899999999999999   999999999999999997653

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.

>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators

Probab=93.36  E-value=0.086  Score=38.58  Aligned_cols=59  Identities=17%  Similarity=0.183  Sum_probs=44.4

Q ss_pred             cCcchhhhcCCCCCCHHHHHHHc-----CCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCC
Q 040620           39 LRIPDIINNSGQPMTLTQIIVAL-----NVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPP  103 (214)
Q Consensus        39 lglfd~L~~~~~p~t~~eLA~~~-----g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~  103 (214)
                      ..|++.|...++++|++||.+++     +++.   ..+.|.|+.|+..|++.+...  ++. ..+|..+.
T Consensus         4 ~~Il~~l~~~~~~~sa~ei~~~l~~~~~~i~~---~TVYR~L~~L~~~Gli~~~~~--~~~-~~~y~~~~   67 (116)
T cd07153           4 LAILEVLLESDGHLTAEEIYERLRKKGPSISL---ATVYRTLELLEEAGLVREIEL--GDG-KARYELNT   67 (116)
T ss_pred             HHHHHHHHhCCCCCCHHHHHHHHHhcCCCCCH---HHHHHHHHHHHhCCCEEEEEe--CCC-ceEEEeCC
Confidence            34677777655899999999998     4666   899999999999999998753  111 35676543

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.

>PRK06474 hypothetical protein; Provisional

Probab=93.34  E-value=0.13  Score=41.16  Aligned_cols=71  Identities=14%  Similarity=0.188  Sum_probs=53.4

Q ss_pred             HHHHHHHhcCcchhhhcCCCCCCHHHHHHHc-CCCCCCcccHHHHHHHHHhCCceeeecCCC-CCCccceeeCCCC
Q 040620           31 LSLKRAIQLRIPDIINNSGQPMTLTQIIVAL-NVHPNKTRCTQILVCLLAHSGFFVQQKDGK-NEQEEESILLPPH  104 (214)
Q Consensus        31 ~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~-g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~-~~~~~~~y~~t~~  104 (214)
                      .+|.--.++.|++.|...++++|+.+|++.+ +++.   ..+.|.|+.|...|++....... .+..+..|+.++.
T Consensus         6 ~~La~p~R~~Il~~L~~~~~~~ta~el~~~l~~is~---aTvYrhL~~L~e~GLI~~~~~~~~~~~~ek~y~~~~~   78 (178)
T PRK06474          6 EILMHPVRMKICQVLMRNKEGLTPLELVKILKDVPQ---ATLYRHLQTMVDSGILHVVKEKKVRSVSEKYYAINEE   78 (178)
T ss_pred             HhhCCHHHHHHHHHHHhCCCCCCHHHHHHHhcCCCH---HHHHHHHHHHHHCCCEEEeecccccCceeEEEEeccc
Confidence            4555566778888888764459999999999 6777   78999999999999999865321 1111356888887

>TIGR00417 speE spermidine synthase

Probab=93.23  E-value=0.11  Score=44.08  Aligned_cols=34  Identities=21%  Similarity=0.302  Sum_probs=28.6

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                      +.++|++||||.|..+..+++..|..++++.|+-
T Consensus        72 ~p~~VL~iG~G~G~~~~~ll~~~~~~~v~~veid  105 (270)
T TIGR00417        72 NPKHVLVIGGGDGGVLREVLKHKSVEKATLVDID  105 (270)
T ss_pred             CCCEEEEEcCCchHHHHHHHhCCCcceEEEEeCC
Confidence            4579999999999999999987666778888763

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.

>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=93.19  E-value=0.077  Score=30.23  Aligned_cols=31  Identities=23%  Similarity=0.303  Sum_probs=25.7

Q ss_pred             CCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCce
Q 040620           51 PMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFF   84 (214)
Q Consensus        51 p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l   84 (214)
                      |+|-+|||+.+|+.+   .-+.|+|..|...|++
T Consensus         2 ~mtr~diA~~lG~t~---ETVSR~l~~l~~~glI   32 (32)
T PF00325_consen    2 PMTRQDIADYLGLTR---ETVSRILKKLERQGLI   32 (32)
T ss_dssp             E--HHHHHHHHTS-H---HHHHHHHHHHHHTTSE
T ss_pred             CcCHHHHHHHhCCcH---HHHHHHHHHHHHcCCC
Confidence            589999999999999   9999999999988874

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 ....

>TIGR01983 UbiG ubiquinone biosynthesis O-methyltransferase

Probab=93.00  E-value=0.11  Score=42.35  Aligned_cols=32  Identities=19%  Similarity=0.135  Sum_probs=26.1

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                      ...+|+|+|||+|.++..+++..+  ++++.|+.
T Consensus        45 ~~~~vLdlG~G~G~~~~~l~~~~~--~v~~iD~s   76 (224)
T TIGR01983        45 FGLRVLDVGCGGGLLSEPLARLGA--NVTGIDAS   76 (224)
T ss_pred             CCCeEEEECCCCCHHHHHHHhcCC--eEEEEeCC
Confidence            467999999999999999988754  47777753

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.

>PRK15431 ferrous iron transport protein FeoC; Provisional

Probab=92.98  E-value=0.15  Score=35.11  Aligned_cols=44  Identities=20%  Similarity=0.208  Sum_probs=40.0

Q ss_pred             cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      |=|+|+.+ |-+++.+||.++++++   ..++.+|..++..|-+++..
T Consensus         7 lRd~l~~~-gr~s~~~Ls~~~~~p~---~~VeaMLe~l~~kGkverv~   50 (78)
T PRK15431          7 VRDLLALR-GRMEAAQISQTLNTPQ---PMINAMLQQLESMGKAVRIQ   50 (78)
T ss_pred             HHHHHHHc-CcccHHHHHHHHCcCH---HHHHHHHHHHHHCCCeEeec
Confidence            34778887 8999999999999999   99999999999999999875

>PRK03522 rumB 23S rRNA methyluridine methyltransferase; Reviewed

Probab=92.89  E-value=0.14  Score=44.39  Aligned_cols=30  Identities=17%  Similarity=0.091  Sum_probs=26.0

Q ss_pred             CCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          181 LKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       181 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+|+|+|||+|.++..+++.  ..+++.+|.
T Consensus       174 ~~~VLDl~cG~G~~sl~la~~--~~~V~gvD~  203 (315)
T PRK03522        174 PRSMWDLFCGVGGFGLHCATP--GMQLTGIEI  203 (315)
T ss_pred             CCEEEEccCCCCHHHHHHHhc--CCEEEEEeC
Confidence            579999999999999999984  467888875

>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element

Probab=92.54  E-value=0.14  Score=36.03  Aligned_cols=46  Identities=22%  Similarity=0.243  Sum_probs=40.2

Q ss_pred             HHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           54 LTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        54 ~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      +.+||+.+++++   ..+.+.++.|...|++...+       ...|.+|+.    +..+.
T Consensus         2 ~~ela~~l~is~---stvs~~l~~L~~~glI~r~~-------~~~~~lT~~----g~~~~   47 (96)
T smart00529        2 TSEIAERLNVSP---PTVTQMLKKLEKDGLVEYEP-------YRGITLTEK----GRRLA   47 (96)
T ss_pred             HHHHHHHhCCCh---HHHHHHHHHHHHCCCEEEcC-------CCceEechh----HHHHH
Confidence            579999999999   99999999999999999986       468999998    65553

iron dependent repressor

>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=92.52  E-value=0.052  Score=39.37  Aligned_cols=44  Identities=16%  Similarity=0.264  Sum_probs=33.7

Q ss_pred             cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      |++.|... +.++-++||+.+|+++   ..++++|..|...|++....
T Consensus        18 Il~~L~~~-~~l~de~la~~~~l~~---~~vRkiL~~L~~~~lv~~~~   61 (105)
T PF02002_consen   18 ILDALLRK-GELTDEDLAKKLGLKP---KEVRKILYKLYEDGLVSYRR   61 (105)
T ss_dssp             HHHHHHHH---B-HHHHHHTT-S-H---HHHHHHHHHHHHHSS-EEEE
T ss_pred             HHHHHHHc-CCcCHHHHHHHhCCCH---HHHHHHHHHHHHCCCeEEEE
Confidence            56777765 7899999999999999   99999999999999997664

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.

>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=92.31  E-value=0.051  Score=38.31  Aligned_cols=62  Identities=13%  Similarity=0.162  Sum_probs=45.6

Q ss_pred             chhhhcCCCCCCHHHHHHHc-CCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           42 PDIINNSGQPMTLTQIIVAL-NVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        42 fd~L~~~~~p~t~~eLA~~~-g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      ...|..  ++....||.+.+ ++++   +.|.+-|+.|...|++.......... .-.|.+|+.    ++.|.
T Consensus        11 L~~l~~--g~~rf~el~~~l~~is~---~~L~~~L~~L~~~GLv~r~~~~~~p~-~v~Y~LT~~----G~~l~   73 (90)
T PF01638_consen   11 LRALFQ--GPMRFSELQRRLPGISP---KVLSQRLKELEEAGLVERRVYPEVPP-RVEYSLTEK----GKELL   73 (90)
T ss_dssp             HHHHTT--SSEEHHHHHHHSTTS-H---HHHHHHHHHHHHTTSEEEEEESSSSS-EEEEEE-HH----HHHHH
T ss_pred             HHHHHh--CCCcHHHHHHhcchhHH---HHHHHHHHHHHHcchhhcccccCCCC-CCccCCCcC----HHHHH
Confidence            334555  899999999999 8999   99999999999999998764210000 235999998    77764

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.

>COG4189 Predicted transcriptional regulator [Transcription]

Probab=92.17  E-value=0.19  Score=41.90  Aligned_cols=55  Identities=15%  Similarity=0.295  Sum_probs=49.3

Q ss_pred             HHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620           29 KSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ   87 (214)
Q Consensus        29 ~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~   87 (214)
                      ..++|...++..|..+|+.. +|+.+.|||+++|++.   ..+..-+..|...|+++..
T Consensus        16 v~kalaS~vRv~Il~lL~~k-~plNvneiAe~lgLpq---st~s~~ik~Le~aGlirT~   70 (308)
T COG4189          16 VLKALASKVRVAILQLLHRK-GPLNVNEIAEALGLPQ---STMSANIKVLEKAGLIRTE   70 (308)
T ss_pred             HHHHHHHHHHHHHHHHHHHh-CCCCHHHHHHHhCCch---hhhhhhHHHHHhcCceeee
Confidence            35678888999999999997 8999999999999998   8888899999999999754

>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain

Probab=92.16  E-value=0.29  Score=34.92  Aligned_cols=44  Identities=14%  Similarity=-0.007  Sum_probs=38.6

Q ss_pred             CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCC
Q 040620           50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLP  102 (214)
Q Consensus        50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t  102 (214)
                      .++|..|||+.+|+++   ..+.|.|..|...|++.....      .+.|..|
T Consensus        46 ~~is~~eLa~~~g~sr---~tVsr~L~~Le~~GlI~r~~~------~~~~~~n   89 (95)
T TIGR01610        46 DRVTATVIAELTGLSR---THVSDAIKSLARRRIIFRQGM------MGIVGVN   89 (95)
T ss_pred             CccCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeeeecC------CceeecC
Confidence            7899999999999999   999999999999999997642      3667666

This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.

>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=92.03  E-value=0.18  Score=35.79  Aligned_cols=63  Identities=8%  Similarity=0.057  Sum_probs=47.6

Q ss_pred             HHHhcCcchhhhcC-CCCCCHHHHHHHcCCCCCCcccHHHHH----------HHHHhCCce-eeecCCCCCCccceeeCC
Q 040620           35 RAIQLRIPDIINNS-GQPMTLTQIIVALNVHPNKTRCTQILV----------CLLAHSGFF-VQQKDGKNEQEEESILLP  102 (214)
Q Consensus        35 ~a~~lglfd~L~~~-~~p~t~~eLA~~~g~~~~~~~~l~rlL----------r~L~~~g~l-~~~~~~~~~~~~~~y~~t  102 (214)
                      .-++..|+..|.+. +.+.++.|||..+++++   ..+.--|          +.|+.+|++ .+...  ++  ...|++|
T Consensus         8 S~~R~~vl~~L~~~yp~~~~~~eIar~v~~~~---snV~GaL~G~g~rY~~e~SLv~lGLV~~~~~~--~g--~k~Y~lT   80 (90)
T PF07381_consen    8 SKVRKKVLEYLCSIYPEPAYPSEIARSVGSDY---SNVLGALRGDGKRYNKEDSLVGLGLVEEEEEK--GG--FKYYRLT   80 (90)
T ss_pred             HHHHHHHHHHHHHcCCCcCCHHHHHHHHCCCH---HHHHHHHhcCCCCcCcchhHHHcCCeeEeeec--CC--eeEEEeC
Confidence            44566677788776 68899999999999999   7776666          459999999 33321  12  4579999


Q ss_pred             CC
Q 040620          103 PH  104 (214)
Q Consensus       103 ~~  104 (214)
                      +.
T Consensus        81 ~~   82 (90)
T PF07381_consen   81 EK   82 (90)
T ss_pred             hh
Confidence            88

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

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

Probab=92.02  E-value=0.19  Score=44.72  Aligned_cols=31  Identities=19%  Similarity=0.125  Sum_probs=25.6

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+|+|+|||+|.+++.++..  ..+++.+|.
T Consensus       233 ~~~~vLDL~cG~G~~~l~la~~--~~~v~~vE~  263 (374)
T TIGR02085       233 PVTQMWDLFCGVGGFGLHCAGP--DTQLTGIEI  263 (374)
T ss_pred             CCCEEEEccCCccHHHHHHhhc--CCeEEEEEC
Confidence            3478999999999999999964  467888775

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.

>PRK11169 leucine-responsive transcriptional regulator; Provisional

Probab=91.92  E-value=0.15  Score=40.05  Aligned_cols=47  Identities=15%  Similarity=0.178  Sum_probs=42.8

Q ss_pred             HHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceee
Q 040620           36 AIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQ   86 (214)
Q Consensus        36 a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~   86 (214)
                      .++..|..+|..+ +.+|..+||+++|+++   ..+++=++-|...|++..
T Consensus        14 ~~D~~IL~~Lq~d-~R~s~~eiA~~lglS~---~tv~~Ri~rL~~~GvI~~   60 (164)
T PRK11169         14 RIDRNILNELQKD-GRISNVELSKRVGLSP---TPCLERVRRLERQGFIQG   60 (164)
T ss_pred             HHHHHHHHHhccC-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeEE
Confidence            3677889999987 8999999999999999   999999999999999973

>KOG1271 consensus Methyltransferases [General function prediction only]

Probab=91.91  E-value=0.23  Score=40.13  Aligned_cols=22  Identities=18%  Similarity=0.297  Sum_probs=19.3

Q ss_pred             CCcEEeecCCchHHHHHHHHHC
Q 040620          181 LKPLVDVGGSTGTMARAIATAF  202 (214)
Q Consensus       181 ~~~vvDVGGG~G~~~~~l~~~~  202 (214)
                      ..+|||+|||.|+++..|++.-
T Consensus        68 A~~VlDLGtGNG~~L~~L~~eg   89 (227)
T KOG1271|consen   68 ADRVLDLGTGNGHLLFQLAKEG   89 (227)
T ss_pred             ccceeeccCCchHHHHHHHHhc
Confidence            3499999999999999999863

>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=91.85  E-value=0.15  Score=34.43  Aligned_cols=36  Identities=25%  Similarity=0.355  Sum_probs=33.9

Q ss_pred             CCCCHHHHHHHc---CC--CCCCcccHHHHHHHHHhCCceeeec
Q 040620           50 QPMTLTQIIVAL---NV--HPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        50 ~p~t~~eLA~~~---g~--~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      +.+++.++|+.+   ++  ..   |+++.++..|.+.|++.+..
T Consensus        23 ~~i~l~~ia~~l~~~~~k~~~---RRlYDI~NVLealgli~K~~   63 (71)
T PF02319_consen   23 KSISLNEIADKLISENVKTQR---RRLYDIINVLEALGLIEKQS   63 (71)
T ss_dssp             TEEEHHHHHHHCHHHCCHHHC---HHHHHHHHHHHHCTSEEEEE
T ss_pred             CcccHHHHHHHHccccccccc---chhhHHHHHHHHhCceeecC
Confidence            789999999999   98  88   99999999999999999965

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.

>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=91.85  E-value=0.32  Score=37.58  Aligned_cols=36  Identities=11%  Similarity=0.194  Sum_probs=34.5

Q ss_pred             CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      |++|.+|||-+.|++.   |.+.--|..+.+.|-+....
T Consensus         5 Ga~T~eELA~~FGvtt---RkvaStLa~~ta~Grl~Rv~   40 (155)
T PF07789_consen    5 GAKTAEELAGKFGVTT---RKVASTLAMVTATGRLIRVN   40 (155)
T ss_pred             CcccHHHHHHHhCcch---hhhHHHHHHHHhcceeEEec
Confidence            8999999999999999   99999999999999999875

The region in question is approximately 150 amino acid residues long.

>PRK03612 spermidine synthase; Provisional

Probab=91.82  E-value=0.2  Score=46.71  Aligned_cols=33  Identities=21%  Similarity=0.463  Sum_probs=28.5

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCC-CeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPD-TKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dl  212 (214)
                      ++.++|+|||||.|..+..+++ +|. .+++++|+
T Consensus       296 ~~~~rVL~IG~G~G~~~~~ll~-~~~v~~v~~VEi  329 (521)
T PRK03612        296 ARPRRVLVLGGGDGLALREVLK-YPDVEQVTLVDL  329 (521)
T ss_pred             CCCCeEEEEcCCccHHHHHHHh-CCCcCeEEEEEC
Confidence            3568999999999999999996 576 78999886

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

Probab=91.76  E-value=0.31  Score=39.68  Aligned_cols=32  Identities=9%  Similarity=0.123  Sum_probs=25.1

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+++|+|||+|.+++..+.+.. .+++.+|.
T Consensus        53 ~~~~vLDl~~GsG~l~l~~lsr~a-~~V~~vE~   84 (199)
T PRK10909         53 VDARCLDCFAGSGALGLEALSRYA-AGATLLEM   84 (199)
T ss_pred             CCCEEEEcCCCccHHHHHHHHcCC-CEEEEEEC
Confidence            346999999999999997666654 57777764

>PF02527 GidB: rRNA small subunit methyltransferase G; InterPro: IPR003682 This entry represents a rRNA small subunit methyltransferase G

Probab=91.73  E-value=0.35  Score=38.92  Aligned_cols=30  Identities=27%  Similarity=0.445  Sum_probs=27.2

Q ss_pred             cEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          183 PLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       183 ~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +++|||.|-|.=++.++=.+|+++++.+|-
T Consensus        51 ~~lDiGSGaGfPGipLaI~~p~~~~~LvEs   80 (184)
T PF02527_consen   51 KVLDIGSGAGFPGIPLAIARPDLQVTLVES   80 (184)
T ss_dssp             EEEEETSTTTTTHHHHHHH-TTSEEEEEES
T ss_pred             eEEecCCCCCChhHHHHHhCCCCcEEEEeC
Confidence            799999999999999999999999999873

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.

>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]

Probab=91.54  E-value=0.18  Score=41.38  Aligned_cols=42  Identities=14%  Similarity=0.272  Sum_probs=35.7

Q ss_pred             hhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620           43 DIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ   87 (214)
Q Consensus        43 d~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~   87 (214)
                      +.|...+.+.|.+|+|+++|++.   ...+|.|.+|++.|++...
T Consensus       165 ~~~~~~~~~~Taeela~~~giSR---vTaRRYLeyl~~~~~l~a~  206 (224)
T COG4565         165 EALKEPDQELTAEELAQALGISR---VTARRYLEYLVSNGILEAE  206 (224)
T ss_pred             HHHhCcCCccCHHHHHHHhCccH---HHHHHHHHHHHhcCeeeEE
Confidence            44442238999999999999998   8999999999999999854

>PRK10870 transcriptional repressor MprA; Provisional

Probab=91.53  E-value=0.43  Score=37.94  Aligned_cols=65  Identities=9%  Similarity=0.124  Sum_probs=47.4

Q ss_pred             cchhhhcC-CCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           41 IPDIINNS-GQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        41 lfd~L~~~-~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      ++-.|... ++++|..+||+.+++++   ..+.+++.-|...|++......+|.- .-.+.+|+.    ++.++
T Consensus        60 iL~~L~~~~~~~it~~eLa~~l~l~~---~tvsr~v~rLe~kGlV~R~~~~~DrR-~~~v~LT~~----G~~~~  125 (176)
T PRK10870         60 ALITLESQENHSIQPSELSCALGSSR---TNATRIADELEKRGWIERRESDNDRR-CLHLQLTEK----GHEFL  125 (176)
T ss_pred             HHHHHhcCCCCCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEecCCCCCCC-eeEEEECHH----HHHHH
Confidence            44455432 26799999999999999   99999999999999999875321111 134667777    66654

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=91.50  E-value=0.17  Score=39.24  Aligned_cols=46  Identities=11%  Similarity=0.227  Sum_probs=42.0

Q ss_pred             HhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceee
Q 040620           37 IQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQ   86 (214)
Q Consensus        37 ~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~   86 (214)
                      ++..|.++|..+ +..|..+||+++|+++   ..+++=++-|...|++..
T Consensus        10 ~D~~Il~~Lq~d-~R~s~~eiA~~lglS~---~tV~~Ri~rL~~~GvI~~   55 (153)
T PRK11179         10 LDRGILEALMEN-ARTPYAELAKQFGVSP---GTIHVRVEKMKQAGIITG   55 (153)
T ss_pred             HHHHHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeee
Confidence            566788899987 8999999999999999   999999999999999974

>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2

Probab=91.31  E-value=0.13  Score=33.88  Aligned_cols=43  Identities=12%  Similarity=0.254  Sum_probs=34.7

Q ss_pred             cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620           41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ   87 (214)
Q Consensus        41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~   87 (214)
                      |++.|-.. |+.|..+|++.+++++   +.++.-|-.|...+++.+.
T Consensus        18 V~~~Ll~~-G~ltl~~i~~~t~l~~---~~Vk~~L~~LiQh~~v~y~   60 (62)
T PF08221_consen   18 VGEVLLSR-GRLTLREIVRRTGLSP---KQVKKALVVLIQHNLVQYF   60 (62)
T ss_dssp             HHHHHHHC--SEEHHHHHHHHT--H---HHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHc-CCcCHHHHHHHhCCCH---HHHHHHHHHHHHcCCeeee
Confidence            44555555 8999999999999999   9999999999999999875

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.

>PF14394 DUF4423: Domain of unknown function (DUF4423)

Probab=91.17  E-value=0.62  Score=37.01  Aligned_cols=61  Identities=8%  Similarity=0.076  Sum_probs=49.1

Q ss_pred             HHhHHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHc--CCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCC
Q 040620           26 NYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVAL--NVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPP  103 (214)
Q Consensus        26 g~~~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~--g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~  103 (214)
                      .-|...+++..+.+     .+   +.-++++||+++  +++.   ..++.-|..|...|++..++       ++.|..|.
T Consensus        22 ~~W~~~~ir~l~~l-----~~---~~~d~~~iak~l~p~is~---~ev~~sL~~L~~~gli~k~~-------~g~y~~t~   83 (171)
T PF14394_consen   22 SSWYHPAIRELLPL-----MP---FAPDPEWIAKRLRPKISA---EEVRDSLEFLEKLGLIKKDG-------DGKYVQTD   83 (171)
T ss_pred             hhhHHHHHHHHhhc-----CC---CCCCHHHHHHHhcCCCCH---HHHHHHHHHHHHCCCeEECC-------CCcEEEec
Confidence            45666666665432     22   334999999999  9999   99999999999999999997       67999998


Q ss_pred             C
Q 040620          104 H  104 (214)
Q Consensus       104 ~  104 (214)
                      .
T Consensus        84 ~   84 (171)
T PF14394_consen   84 K   84 (171)
T ss_pred             c
Confidence            7

>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed

Probab=91.14  E-value=0.29  Score=44.21  Aligned_cols=46  Identities=17%  Similarity=0.232  Sum_probs=40.3

Q ss_pred             CCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           49 GQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        49 ~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      +.|.|.++|++++++++   +.++++++.|...|++.+.+       ++.|.+..-
T Consensus       308 g~~~t~~~La~~l~~~~---~~v~~iL~~L~~agLI~~~~-------~g~~~l~rd  353 (412)
T PRK04214        308 GKALDVDEIRRLEPMGY---DELGELLCELARIGLLRRGE-------RGQWVLARD  353 (412)
T ss_pred             CCCCCHHHHHHHhCCCH---HHHHHHHHHHHhCCCeEecC-------CCceEecCC
Confidence            48999999999999999   99999999999999999764       466776655

>COG1522 Lrp Transcriptional regulators [Transcription]

Probab=91.10  E-value=0.2  Score=38.43  Aligned_cols=48  Identities=13%  Similarity=0.202  Sum_probs=42.7

Q ss_pred             HhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           37 IQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        37 ~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      ++..|...|..+ ++.|..+||+++|+++   ..+.+-++-|...|++..-.
T Consensus         9 ~D~~IL~~L~~d-~r~~~~eia~~lglS~---~~v~~Ri~~L~~~GiI~~~~   56 (154)
T COG1522           9 IDRRILRLLQED-ARISNAELAERVGLSP---STVLRRIKRLEEEGVIKGYT   56 (154)
T ss_pred             HHHHHHHHHHHh-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCceeeEE
Confidence            456678888887 8899999999999999   99999999999999998653

>COG0357 GidB Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]

Probab=91.08  E-value=0.21  Score=41.25  Aligned_cols=32  Identities=34%  Similarity=0.579  Sum_probs=29.9

Q ss_pred             CCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          181 LKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       181 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+++|||.|.|.=++-++=.+|+++++++|-
T Consensus        68 ~~~~~DIGSGaGfPGipLAI~~p~~~vtLles   99 (215)
T COG0357          68 AKRVLDIGSGAGFPGIPLAIAFPDLKVTLLES   99 (215)
T ss_pred             CCEEEEeCCCCCCchhhHHHhccCCcEEEEcc
Confidence            58999999999999999999999999999883

>PLN02781 Probable caffeoyl-CoA O-methyltransferase

Probab=91.03  E-value=0.32  Score=40.46  Aligned_cols=36  Identities=25%  Similarity=0.265  Sum_probs=30.3

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCC-CCeEEEecCC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFP-DTKCTVFACH  213 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dlp  213 (214)
                      ..+.+++||||+|.|..++.+++..| +.+++.+|..
T Consensus        66 ~~~~~~vLEiGt~~G~s~l~la~~~~~~g~v~tiD~d  102 (234)
T PLN02781         66 IMNAKNTLEIGVFTGYSLLTTALALPEDGRITAIDID  102 (234)
T ss_pred             HhCCCEEEEecCcccHHHHHHHHhCCCCCEEEEEECC
Confidence            34578999999999999999999866 6788888864

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

Probab=90.95  E-value=0.34  Score=43.89  Aligned_cols=33  Identities=18%  Similarity=0.170  Sum_probs=26.8

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+..+|+|+|||+|.++..+++..  .+++.+|.
T Consensus       290 ~~~~~~vLDl~cG~G~~sl~la~~~--~~V~~vE~  322 (431)
T TIGR00479       290 LQGEELVVDAYCGVGTFTLPLAKQA--KSVVGIEV  322 (431)
T ss_pred             cCCCCEEEEcCCCcCHHHHHHHHhC--CEEEEEEc
Confidence            3455799999999999999999875  36777775

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.

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

Probab=90.94  E-value=0.32  Score=41.03  Aligned_cols=43  Identities=12%  Similarity=0.273  Sum_probs=33.1

Q ss_pred             hHHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          166 IASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       166 ~~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+..+++..+  .....+|+|||+|.|.++..|++..  -+++++|.
T Consensus        18 ~~~~Iv~~~~--~~~~~~VlEiGpG~G~lT~~L~~~~--~~v~~vE~   60 (262)
T PF00398_consen   18 IADKIVDALD--LSEGDTVLEIGPGPGALTRELLKRG--KRVIAVEI   60 (262)
T ss_dssp             HHHHHHHHHT--CGTTSEEEEESSTTSCCHHHHHHHS--SEEEEEES
T ss_pred             HHHHHHHhcC--CCCCCEEEEeCCCCccchhhHhccc--CcceeecC
Confidence            3455666665  5577899999999999999999997  55665553

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 ....

>PF09243 Rsm22: Mitochondrial small ribosomal subunit Rsm22; InterPro: IPR015324 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=90.86  E-value=0.48  Score=40.39  Aligned_cols=33  Identities=24%  Similarity=0.360  Sum_probs=28.1

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCe-EEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTK-CTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~-~~v~Dl  212 (214)
                      .+++|||+|+|+|..+-+..+.+|++. ++++|.
T Consensus        33 ~P~~vLD~GsGpGta~wAa~~~~~~~~~~~~vd~   66 (274)
T PF09243_consen   33 RPRSVLDFGSGPGTALWAAREVWPSLKEYTCVDR   66 (274)
T ss_pred             CCceEEEecCChHHHHHHHHHHhcCceeeeeecC
Confidence            367999999999999999999999664 777774

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

>TIGR00095 RNA methyltransferase, RsmD family

Probab=90.78  E-value=0.32  Score=39.09  Aligned_cols=32  Identities=13%  Similarity=-0.008  Sum_probs=26.9

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+++|++||+|.++++++++... +++.+|.
T Consensus        49 ~g~~vLDLfaGsG~lglea~srga~-~v~~vE~   80 (189)
T TIGR00095        49 QGAHLLDVFAGSGLLGEEALSRGAK-VAFLEED   80 (189)
T ss_pred             CCCEEEEecCCCcHHHHHHHhCCCC-EEEEEeC
Confidence            3578999999999999999999764 6777775

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.

>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=90.17  E-value=0.39  Score=32.12  Aligned_cols=36  Identities=19%  Similarity=0.266  Sum_probs=33.8

Q ss_pred             CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      -++|-++||+.+|+++   ..+.++|+.|...|++....
T Consensus        27 ~~lt~~~iA~~~g~sr---~tv~r~l~~l~~~g~I~~~~   62 (76)
T PF13545_consen   27 LPLTQEEIADMLGVSR---ETVSRILKRLKDEGIIEVKR   62 (76)
T ss_dssp             EESSHHHHHHHHTSCH---HHHHHHHHHHHHTTSEEEET
T ss_pred             ecCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEEcC
Confidence            5799999999999999   99999999999999999774

...

>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=90.04  E-value=0.16  Score=36.47  Aligned_cols=47  Identities=15%  Similarity=0.237  Sum_probs=36.6

Q ss_pred             hcCcchhhhc---CCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620           38 QLRIPDIINN---SGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ   87 (214)
Q Consensus        38 ~lglfd~L~~---~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~   87 (214)
                      +-.|++.|..   ...++++++|+++++++.   ..++..|+.|...|++=..
T Consensus        49 ~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~---~~v~~al~~L~~eG~IYsT   98 (102)
T PF08784_consen   49 QDKVLNFIKQQPNSEEGVHVDEIAQQLGMSE---NEVRKALDFLSNEGHIYST   98 (102)
T ss_dssp             HHHHHHHHHC----TTTEEHHHHHHHSTS-H---HHHHHHHHHHHHTTSEEES
T ss_pred             HHHHHHHHHhcCCCCCcccHHHHHHHhCcCH---HHHHHHHHHHHhCCeEecc
Confidence            3445555555   127899999999999998   9999999999999987543

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.

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

Probab=89.92  E-value=0.53  Score=38.52  Aligned_cols=43  Identities=16%  Similarity=0.143  Sum_probs=27.3

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+++.+.  ......++|+|+|.|....+.+-.++=-+++++++
T Consensus        32 ~~il~~~~--l~~~dvF~DlGSG~G~~v~~aal~~~~~~~~GIEi   74 (205)
T PF08123_consen   32 SKILDELN--LTPDDVFYDLGSGVGNVVFQAALQTGCKKSVGIEI   74 (205)
T ss_dssp             HHHHHHTT----TT-EEEEES-TTSHHHHHHHHHH--SEEEEEE-
T ss_pred             HHHHHHhC--CCCCCEEEECCCCCCHHHHHHHHHcCCcEEEEEEe
Confidence            34455554  55678999999999999998887776555777664

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 ....

>COG1378 Predicted transcriptional regulators [Transcription]

Probab=89.86  E-value=0.51  Score=39.75  Aligned_cols=47  Identities=15%  Similarity=0.043  Sum_probs=41.4

Q ss_pred             CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      |+.|+.|||+.+|++.   .++..+|+.|...|++...+.    . +..|+.-+-
T Consensus        29 g~~tA~eis~~sgvP~---~kvY~vl~sLe~kG~v~~~~g----~-P~~y~av~p   75 (247)
T COG1378          29 GEATAKEISEASGVPR---PKVYDVLRSLEKKGLVEVIEG----R-PKKYRAVPP   75 (247)
T ss_pred             CCccHHHHHHHcCCCc---hhHHHHHHHHHHCCCEEeeCC----C-CceEEeCCH
Confidence            8999999999999999   999999999999999998742    1 577877776

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

Probab=89.83  E-value=0.75  Score=37.70  Aligned_cols=41  Identities=15%  Similarity=0.192  Sum_probs=27.6

Q ss_pred             HHHhhcccccCCCCcEEeecCCchHHHHHHHHHCC-CCeEEEec
Q 040620          169 VLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFP-DTKCTVFA  211 (214)
Q Consensus       169 ~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~D  211 (214)
                      .+++..+  ..+..+|+|||+|+|..+..+++..- .-+++.+|
T Consensus        63 ~~l~~L~--l~pg~~VLeIGtGsGY~aAlla~lvg~~g~Vv~vE  104 (209)
T PF01135_consen   63 RMLEALD--LKPGDRVLEIGTGSGYQAALLAHLVGPVGRVVSVE  104 (209)
T ss_dssp             HHHHHTT--C-TT-EEEEES-TTSHHHHHHHHHHSTTEEEEEEE
T ss_pred             HHHHHHh--cCCCCEEEEecCCCcHHHHHHHHhcCccceEEEEC
Confidence            3455555  66778999999999999999988743 33455554

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 ....

>PTZ00146 fibrillarin; Provisional

Probab=89.79  E-value=0.47  Score=40.96  Aligned_cols=35  Identities=11%  Similarity=0.133  Sum_probs=28.1

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCC-CCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFP-DTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl  212 (214)
                      +....+|||+|||+|.++..+++... .=+++.+|.
T Consensus       130 IkpG~~VLDLGaG~G~~t~~lAdiVG~~G~VyAVD~  165 (293)
T PTZ00146        130 IKPGSKVLYLGAASGTTVSHVSDLVGPEGVVYAVEF  165 (293)
T ss_pred             cCCCCEEEEeCCcCCHHHHHHHHHhCCCCEEEEEEC
Confidence            45667999999999999999999874 446777664

>TIGR01177 conserved hypothetical protein TIGR01177

Probab=89.74  E-value=0.64  Score=40.57  Aligned_cols=33  Identities=12%  Similarity=-0.051  Sum_probs=26.5

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +.+..+|+|+|||+|.++++.+..  ..+++..|+
T Consensus       180 ~~~g~~vLDp~cGtG~~lieaa~~--~~~v~g~Di  212 (329)
T TIGR01177       180 VTEGDRVLDPFCGTGGFLIEAGLM--GAKVIGCDI  212 (329)
T ss_pred             CCCcCEEEECCCCCCHHHHHHHHh--CCeEEEEcC
Confidence            445679999999999999886653  677888886

This family is found exclusively in the Archaea.

>PRK14903 16S rRNA methyltransferase B; Provisional

Probab=89.72  E-value=0.52  Score=42.86  Aligned_cols=35  Identities=17%  Similarity=0.101  Sum_probs=29.4

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHC-CCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAF-PDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl  212 (214)
                      ..+..+|+|+|||+|..+..+++.. +..+++.+|+
T Consensus       235 ~~~g~~VLD~cagpGgkt~~la~~~~~~g~V~a~Di  270 (431)
T PRK14903        235 LEPGLRVLDTCAAPGGKTTAIAELMKDQGKILAVDI  270 (431)
T ss_pred             CCCCCEEEEeCCCccHHHHHHHHHcCCCCEEEEEEC
Confidence            3456799999999999999999986 5668888886

>PRK13509 transcriptional repressor UlaR; Provisional

Probab=89.72  E-value=0.41  Score=40.29  Aligned_cols=45  Identities=16%  Similarity=0.247  Sum_probs=40.5

Q ss_pred             CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      .|.+.|.+. +.+++.|||+.+|+++   ..++|.|+.|...|++...-
T Consensus         9 ~Il~~l~~~-~~~~~~ela~~l~vS~---~TirRdL~~Le~~g~i~r~~   53 (251)
T PRK13509          9 ILLELLAQL-GFVTVEKVIERLGISP---ATARRDINKLDESGKLKKVR   53 (251)
T ss_pred             HHHHHHHHc-CCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEec
Confidence            367788876 8999999999999999   99999999999999998765

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

Probab=89.62  E-value=0.41  Score=42.12  Aligned_cols=32  Identities=28%  Similarity=0.209  Sum_probs=24.5

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEec
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFA  211 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~D  211 (214)
                      -..++|+|||||+|-+++-.+++- .-++..+|
T Consensus        59 f~dK~VlDVGcGtGILS~F~akAG-A~~V~aVe   90 (346)
T KOG1499|consen   59 FKDKTVLDVGCGTGILSMFAAKAG-ARKVYAVE   90 (346)
T ss_pred             cCCCEEEEcCCCccHHHHHHHHhC-cceEEEEe
Confidence            357899999999999999988886 33444443

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

Probab=89.58  E-value=0.44  Score=39.86  Aligned_cols=26  Identities=19%  Similarity=0.331  Sum_probs=21.2

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDT  205 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l  205 (214)
                      ..++++|+|||+|..+.+|-..--.+
T Consensus       125 ~F~~~lDLGCGTGL~G~~lR~~a~~l  150 (287)
T COG4976         125 PFRRMLDLGCGTGLTGEALRDMADRL  150 (287)
T ss_pred             ccceeeecccCcCcccHhHHHHHhhc
Confidence            37899999999999999887764433

>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional

Probab=89.42  E-value=0.22  Score=46.09  Aligned_cols=63  Identities=14%  Similarity=0.199  Sum_probs=51.7

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      +..|...|... +++|..+||+++++++   ..+.++++.|.+.|++......     ...|.+|+.    ++.++
T Consensus         8 e~~vL~~L~~~-~~~s~~eLA~~l~l~~---~tVt~~i~~Le~kGlV~~~~~~-----~~~i~LTee----G~~~~   70 (489)
T PRK04172          8 EKKVLKALKEL-KEATLEELAEKLGLPP---EAVMRAAEWLEEKGLVKVEERV-----EEVYVLTEE----GKKYA   70 (489)
T ss_pred             HHHHHHHHHhC-CCCCHHHHHHHhCcCH---HHHHHHHHHHHhCCCEEEEeee-----EEEEEECHH----HHHHH
Confidence            34455666665 7899999999999999   9999999999999999976421     357999999    88876

>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional

Probab=89.29  E-value=0.51  Score=38.98  Aligned_cols=58  Identities=10%  Similarity=0.163  Sum_probs=46.7

Q ss_pred             hhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           44 IINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        44 ~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      .+.+. ..+|..+||+.+++++   ..+.|.|+.|...|++.....   .. ...+.+|+.    ++.++
T Consensus        15 ~l~~~-~~IS~~eLA~~L~iS~---~Tvsr~Lk~LEe~GlI~R~~~---~r-~~~v~LTek----G~~ll   72 (217)
T PRK14165         15 AVNNT-VKISSSEFANHTGTSS---KTAARILKQLEDEGYITRTIV---PR-GQLITITEK----GLDVL   72 (217)
T ss_pred             ccCCC-CCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEEEc---CC-ceEEEECHH----HHHHH
Confidence            45543 5699999999999999   999999999999999987642   01 467888888    77665

>PLN02823 spermine synthase

Probab=89.25  E-value=0.51  Score=41.57  Aligned_cols=33  Identities=21%  Similarity=0.269  Sum_probs=29.2

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +.++||.||||.|..++.+++..|..+++++|+
T Consensus       103 ~pk~VLiiGgG~G~~~re~l~~~~~~~v~~VEi  135 (336)
T PLN02823        103 NPKTVFIMGGGEGSTAREVLRHKTVEKVVMCDI  135 (336)
T ss_pred             CCCEEEEECCCchHHHHHHHhCCCCCeEEEEEC
Confidence            568999999999999999998777778998886

>PRK00215 LexA repressor; Validated

Probab=89.20  E-value=0.48  Score=38.34  Aligned_cols=38  Identities=24%  Similarity=0.374  Sum_probs=34.7

Q ss_pred             CCCCCCHHHHHHHcCC-CCCCcccHHHHHHHHHhCCceeeec
Q 040620           48 SGQPMTLTQIIVALNV-HPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        48 ~~~p~t~~eLA~~~g~-~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      ++.+.|..|||+++|+ ++   ..+.++|..|...|++....
T Consensus        20 ~~~~~s~~ela~~~~~~~~---~tv~~~l~~L~~~g~i~~~~   58 (205)
T PRK00215         20 TGYPPSRREIADALGLRSP---SAVHEHLKALERKGFIRRDP   58 (205)
T ss_pred             hCCCCCHHHHHHHhCCCCh---HHHHHHHHHHHHCCCEEeCC
Confidence            3468899999999999 88   89999999999999998875

>PF13730 HTH_36: Helix-turn-helix domain

Probab=89.20  E-value=0.38  Score=30.24  Aligned_cols=29  Identities=21%  Similarity=0.248  Sum_probs=27.6

Q ss_pred             CHHHHHHHcCCCCCCcccHHHHHHHHHhCCce
Q 040620           53 TLTQIIVALNVHPNKTRCTQILVCLLAHSGFF   84 (214)
Q Consensus        53 t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l   84 (214)
                      |.+.||+.+|+++   +.+++.+..|...|++
T Consensus        27 S~~~la~~~g~s~---~Tv~~~i~~L~~~G~I   55 (55)
T PF13730_consen   27 SQETLAKDLGVSR---RTVQRAIKELEEKGLI   55 (55)
T ss_pred             CHHHHHHHHCcCH---HHHHHHHHHHHHCcCC
Confidence            8999999999999   9999999999999985

>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=89.14  E-value=0.36  Score=32.88  Aligned_cols=49  Identities=24%  Similarity=0.298  Sum_probs=41.2

Q ss_pred             HhcCcchhhhcC-CCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           37 IQLRIPDIINNS-GQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        37 ~~lglfd~L~~~-~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      ++..+++.++.+ ..+++..+|++.+|.|+   +.+...+..|...|++....
T Consensus         3 ~~~~~Le~I~rsR~~Gi~q~~L~~~~~~D~---r~i~~~~k~L~~~gLI~k~~   52 (75)
T PF04182_consen    3 IQYCLLERIARSRYNGITQSDLSKLLGIDP---RSIFYRLKKLEKKGLIVKQS   52 (75)
T ss_pred             hHHHHHHHHHhcCCCCEehhHHHHHhCCCc---hHHHHHHHHHHHCCCEEEEE
Confidence            344556666654 27899999999999999   99999999999999999875

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.

>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=89.10  E-value=0.2  Score=30.28  Aligned_cols=36  Identities=6%  Similarity=0.152  Sum_probs=25.3

Q ss_pred             HhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHH
Q 040620           37 IQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVC   76 (214)
Q Consensus        37 ~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr   76 (214)
                      ++..|...|..+ +..|..+||+++|+++   ..+.+=++
T Consensus         4 ~D~~Il~~Lq~d-~r~s~~~la~~lglS~---~~v~~Ri~   39 (42)
T PF13404_consen    4 LDRKILRLLQED-GRRSYAELAEELGLSE---STVRRRIR   39 (42)
T ss_dssp             HHHHHHHHHHH--TTS-HHHHHHHHTS-H---HHHHHHHH
T ss_pred             HHHHHHHHHHHc-CCccHHHHHHHHCcCH---HHHHHHHH
Confidence            445677888887 8999999999999998   65554433

...

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

Probab=89.06  E-value=0.21  Score=41.45  Aligned_cols=31  Identities=10%  Similarity=0.182  Sum_probs=23.7

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ....|||||||+|..+..|...  ....+++|+
T Consensus        50 ~~~~iLDIGCGsGLSg~vL~~~--Gh~wiGvDi   80 (270)
T KOG1541|consen   50 KSGLILDIGCGSGLSGSVLSDS--GHQWIGVDI   80 (270)
T ss_pred             CCcEEEEeccCCCcchheeccC--CceEEeecC
Confidence            3789999999999988776654  455666665

>PRK14901 16S rRNA methyltransferase B; Provisional

Probab=89.04  E-value=0.6  Score=42.43  Aligned_cols=35  Identities=11%  Similarity=0.072  Sum_probs=29.0

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCC-CCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFP-DTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl  212 (214)
                      ..+..+|+|+|||+|..+..+++..+ .-+++.+|+
T Consensus       250 ~~~g~~VLDl~ag~G~kt~~la~~~~~~g~v~a~D~  285 (434)
T PRK14901        250 PQPGEVILDACAAPGGKTTHIAELMGDQGEIWAVDR  285 (434)
T ss_pred             CCCcCEEEEeCCCCchhHHHHHHHhCCCceEEEEcC
Confidence            34467999999999999999999864 457888886

>PRK00536 speE spermidine synthase; Provisional

Probab=89.01  E-value=0.44  Score=40.49  Aligned_cols=32  Identities=19%  Similarity=0.170  Sum_probs=28.0

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +++++||=||||.|..++++++. |. +++..|+
T Consensus        71 ~~pk~VLIiGGGDGg~~REvLkh-~~-~v~mVeI  102 (262)
T PRK00536         71 KELKEVLIVDGFDLELAHQLFKY-DT-HVDFVQA  102 (262)
T ss_pred             CCCCeEEEEcCCchHHHHHHHCc-CC-eeEEEEC
Confidence            46799999999999999999987 55 8888876

>TIGR00498 lexA SOS regulatory protein LexA

Probab=88.96  E-value=0.52  Score=37.96  Aligned_cols=37  Identities=19%  Similarity=0.405  Sum_probs=33.9

Q ss_pred             CCCCCHHHHHHHcCCC-CCCcccHHHHHHHHHhCCceeeec
Q 040620           49 GQPMTLTQIIVALNVH-PNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        49 ~~p~t~~eLA~~~g~~-~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      +-|.|..|||+.+|++ +   ..+++.|+.|...|++...+
T Consensus        23 ~~~~~~~ela~~~~~~s~---~tv~~~l~~L~~~g~i~~~~   60 (199)
T TIGR00498        23 GYPPSIREIARAVGLRSP---SAAEEHLKALERKGYIERDP   60 (199)
T ss_pred             CCCCcHHHHHHHhCCCCh---HHHHHHHHHHHHCCCEecCC
Confidence            3578999999999998 8   89999999999999999874

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.

>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=88.91  E-value=0.76  Score=31.68  Aligned_cols=35  Identities=20%  Similarity=0.260  Sum_probs=33.0

Q ss_pred             CCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceee
Q 040620           49 GQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQ   86 (214)
Q Consensus        49 ~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~   86 (214)
                      +.|+...+||+.++++|   -.++..+..|..+|++..
T Consensus        21 ~~PVgSk~ia~~l~~s~---aTIRN~M~~Le~lGlve~   55 (78)
T PF03444_consen   21 GEPVGSKTIAEELGRSP---ATIRNEMADLEELGLVES   55 (78)
T ss_pred             CCCcCHHHHHHHHCCCh---HHHHHHHHHHHHCCCccC
Confidence            48999999999999999   999999999999999984

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

>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY

Probab=88.87  E-value=0.48  Score=39.70  Aligned_cols=46  Identities=9%  Similarity=0.112  Sum_probs=41.1

Q ss_pred             CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      .|++.|..+++-++..+||+++|+++   ..+++-++.|.+.|++...+
T Consensus       187 ~IL~~L~~~egrlse~eLAerlGVSR---s~ireAlrkLE~aGvIe~r~  232 (251)
T TIGR02787       187 HIFEELDGNEGLLVASKIADRVGITR---SVIVNALRKLESAGVIESRS  232 (251)
T ss_pred             HHHHHhccccccccHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEecc
Confidence            57888887438899999999999999   99999999999999999774

This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.

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

Probab=88.79  E-value=0.71  Score=40.84  Aligned_cols=29  Identities=17%  Similarity=0.261  Sum_probs=24.6

Q ss_pred             CcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          182 KPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       182 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+++|++||+|.+++.+++...  +++.+|.
T Consensus       199 ~~vlDl~~G~G~~sl~la~~~~--~v~~vE~  227 (353)
T TIGR02143       199 GDLLELYCGNGNFSLALAQNFR--RVLATEI  227 (353)
T ss_pred             CcEEEEeccccHHHHHHHHhCC--EEEEEEC
Confidence            4699999999999999999874  6777764

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.

>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=88.65  E-value=0.54  Score=30.70  Aligned_cols=36  Identities=8%  Similarity=0.123  Sum_probs=31.5

Q ss_pred             CCC-CHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           50 QPM-TLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        50 ~p~-t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      ..+ |..+||++.+++.   .-+++-++.|...|++...+
T Consensus        22 ~~lps~~~la~~~~vsr---~tvr~al~~L~~~g~i~~~~   58 (64)
T PF00392_consen   22 DRLPSERELAERYGVSR---TTVREALRRLEAEGLIERRP   58 (64)
T ss_dssp             SBE--HHHHHHHHTS-H---HHHHHHHHHHHHTTSEEEET
T ss_pred             CEeCCHHHHHHHhccCC---cHHHHHHHHHHHCCcEEEEC
Confidence            567 9999999999999   99999999999999999875

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 ....

>COG1497 Predicted transcriptional regulator [Transcription]

Probab=88.49  E-value=0.47  Score=39.67  Aligned_cols=90  Identities=8%  Similarity=0.028  Sum_probs=62.0

Q ss_pred             CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc---ccc
Q 040620           40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL---QLQ  116 (214)
Q Consensus        40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~---~~~  116 (214)
                      .|...|...-+-....|||+++|+.+   +.+...+.-|+..|++.+.+       .++|..|..    +..++   -..
T Consensus        14 qIL~ei~~~qp~v~q~eIA~~lgiT~---QaVsehiK~Lv~eG~i~~~g-------R~~Y~iTkk----G~e~l~~~~~d   79 (260)
T COG1497          14 QILSEIAVRQPRVKQKEIAKKLGITL---QAVSEHIKELVKEGLIEKEG-------RGEYEITKK----GAEWLLEQLSD   79 (260)
T ss_pred             HHHHHHHHhCCCCCHHHHHHHcCCCH---HHHHHHHHHHHhccceeecC-------CeeEEEehh----HHHHHHHHHHH
Confidence            34444443325589999999999999   99999999999999999976       579999999    87766   134


Q ss_pred             hHHHHHHhhc-cchhhhhHhHH-HhhcCC
Q 040620          117 GSTILLLIAD-ATFTTSFHFLS-TWLQND  143 (214)
Q Consensus       117 ~~~~~~~~~~-~~~~~~~~~l~-~~lr~~  143 (214)
                      ++.|...... ..+...|..+. +-++.|
T Consensus        80 lr~f~~ev~~~l~~~~vw~AIA~edI~~G  108 (260)
T COG1497          80 LRRFSEEVELVLDYVMVWTAIAKEDIKEG  108 (260)
T ss_pred             HHHHHHHHHHHHhhHHHHHHhhHhhhccC
Confidence            4444433311 12335566654 334544

>TIGR00446 nop2p NOL1/NOP2/sun family putative RNA methylase

Probab=88.43  E-value=0.86  Score=38.53  Aligned_cols=34  Identities=9%  Similarity=0.145  Sum_probs=28.1

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCC-CeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPD-TKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dl  212 (214)
                      ....+|+|+|||+|..+..+++..++ -+++.+|+
T Consensus        70 ~~g~~VLDl~ag~G~kt~~la~~~~~~g~v~a~D~  104 (264)
T TIGR00446        70 DPPERVLDMAAAPGGKTTQISALMKNEGAIVANEF  104 (264)
T ss_pred             CCcCEEEEECCCchHHHHHHHHHcCCCCEEEEEcC
Confidence            34678999999999999999998764 46787775

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

Probab=88.39  E-value=1.1  Score=38.13  Aligned_cols=43  Identities=9%  Similarity=0.200  Sum_probs=32.8

Q ss_pred             HHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEec
Q 040620          167 ASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFA  211 (214)
Q Consensus       167 ~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~D  211 (214)
                      .+.+++..+  ......|++||+|.|.+...|+++-....++=.|
T Consensus        19 ~~kIv~~a~--~~~~d~VlEIGpG~GaLT~~Ll~~~~~v~aiEiD   61 (259)
T COG0030          19 IDKIVEAAN--ISPGDNVLEIGPGLGALTEPLLERAARVTAIEID   61 (259)
T ss_pred             HHHHHHhcC--CCCCCeEEEECCCCCHHHHHHHhhcCeEEEEEeC
Confidence            455666655  4457899999999999999999997775555444

>COG1846 MarR Transcriptional regulators [Transcription]

Probab=88.38  E-value=0.44  Score=34.34  Aligned_cols=69  Identities=14%  Similarity=0.189  Sum_probs=49.7

Q ss_pred             HHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           36 AIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        36 a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      ..+..+...|... ++.+..+||+++++++   ..+.++++-|...|++.......|.= .-.+.+|+.    ++.+.
T Consensus        22 ~~q~~~L~~l~~~-~~~~~~~la~~l~i~~---~~vt~~l~~Le~~glv~r~~~~~DrR-~~~l~lT~~----G~~~~   90 (126)
T COG1846          22 PPQYQVLLALYEA-GGITVKELAERLGLDR---STVTRLLKRLEDKGLIERLRDPEDRR-AVLVRLTEK----GRELL   90 (126)
T ss_pred             HHHHHHHHHHHHh-CCCcHHHHHHHHCCCH---HHHHHHHHHHHHCCCeeecCCccccc-eeeEEECcc----HHHHH
Confidence            3445566666665 4555599999999999   99999999999999999876321110 235777777    66654

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

Probab=88.14  E-value=0.64  Score=39.95  Aligned_cols=34  Identities=21%  Similarity=0.366  Sum_probs=30.7

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ++.++||=||||.|..++.+++..|--++++.|+
T Consensus        75 ~~pk~VLiiGgGdG~tlRevlkh~~ve~i~~VEI  108 (282)
T COG0421          75 PNPKRVLIIGGGDGGTLREVLKHLPVERITMVEI  108 (282)
T ss_pred             CCCCeEEEECCCccHHHHHHHhcCCcceEEEEEc
Confidence            3457999999999999999999999889999886

>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional

Probab=88.08  E-value=0.4  Score=40.37  Aligned_cols=45  Identities=11%  Similarity=0.217  Sum_probs=40.3

Q ss_pred             CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      .|.++|.+. +.+++.|||+.+++++   .-++|-|..|...|++...-
T Consensus         9 ~Il~~l~~~-~~~~~~ela~~l~vS~---~TiRRdL~~Le~~g~l~r~~   53 (252)
T PRK10906          9 AIIELVKQQ-GYVSTEELVEHFSVSP---QTIRRDLNDLAEQNKILRHH   53 (252)
T ss_pred             HHHHHHHHc-CCEeHHHHHHHhCCCH---HHHHHHHHHHHHCCCEEEec
Confidence            466788776 8899999999999999   99999999999999998764

>KOG3010 consensus Methyltransferase [General function prediction only]

Probab=87.99  E-value=0.38  Score=40.36  Aligned_cols=27  Identities=33%  Similarity=0.534  Sum_probs=22.2

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDT  205 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l  205 (214)
                      .+.+.++|||||+|..++.+++.|.+.
T Consensus        32 ~~h~~a~DvG~G~Gqa~~~iae~~k~V   58 (261)
T KOG3010|consen   32 EGHRLAWDVGTGNGQAARGIAEHYKEV   58 (261)
T ss_pred             CCcceEEEeccCCCcchHHHHHhhhhh
Confidence            355699999999998888888887654

>PHA02943 hypothetical protein; Provisional

Probab=87.80  E-value=0.73  Score=35.87  Aligned_cols=44  Identities=16%  Similarity=0.214  Sum_probs=38.4

Q ss_pred             CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      .|.+.|..  |+.|..|||+++|++-   ..++-.|..|...|.+.+..
T Consensus        15 eILE~Lk~--G~~TtseIAkaLGlS~---~qa~~~LyvLErEG~VkrV~   58 (165)
T PHA02943         15 KTLRLLAD--GCKTTSRIANKLGVSH---SMARNALYQLAKEGMVLKVE   58 (165)
T ss_pred             HHHHHHhc--CCccHHHHHHHHCCCH---HHHHHHHHHHHHcCceEEEe
Confidence            35566643  8899999999999998   89999999999999999875

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

Probab=87.74  E-value=0.39  Score=37.39  Aligned_cols=32  Identities=28%  Similarity=0.404  Sum_probs=25.8

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCe-EEEecCC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTK-CTVFACH  213 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~-~~v~Dlp  213 (214)
                      ..+++.|+|||.|-++  ++-.+|..+ +++||+-
T Consensus        48 Egkkl~DLgcgcGmLs--~a~sm~~~e~vlGfDId   80 (185)
T KOG3420|consen   48 EGKKLKDLGCGCGMLS--IAFSMPKNESVLGFDID   80 (185)
T ss_pred             cCcchhhhcCchhhhH--HHhhcCCCceEEeeecC
Confidence            3689999999999998  555667775 8888873

>PRK14904 16S rRNA methyltransferase B; Provisional

Probab=87.60  E-value=0.87  Score=41.51  Aligned_cols=34  Identities=12%  Similarity=0.124  Sum_probs=27.8

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCC-CCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFP-DTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl  212 (214)
                      ....+|+|+|||+|..+..+++..+ ..+++.+|+
T Consensus       249 ~~g~~VLDlgaG~G~kt~~la~~~~~~~~V~avD~  283 (445)
T PRK14904        249 QPGSTVLDLCAAPGGKSTFMAELMQNRGQITAVDR  283 (445)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHhCCCcEEEEEEC
Confidence            3457999999999999999988764 457888886

>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional

Probab=87.58  E-value=0.46  Score=40.43  Aligned_cols=45  Identities=11%  Similarity=0.163  Sum_probs=40.1

Q ss_pred             CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      .|.++|... +.+++.|||+.+++++   +-++|-|..|...|++...-
T Consensus        21 ~Il~~L~~~-~~vtv~eLa~~l~VS~---~TIRRDL~~Le~~G~l~r~~   65 (269)
T PRK09802         21 QIIQRLRQQ-GSVQVNDLSALYGVST---VTIRNDLAFLEKQGIAVRAY   65 (269)
T ss_pred             HHHHHHHHc-CCEeHHHHHHHHCCCH---HHHHHHHHHHHhCCCeEEEe
Confidence            356777776 7899999999999999   99999999999999999875

>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional

Probab=87.40  E-value=0.62  Score=40.45  Aligned_cols=56  Identities=11%  Similarity=0.062  Sum_probs=44.2

Q ss_pred             cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      ..|.+.|.++ .+++.++||+++|+++   ..+++.++.|...|++.+...      ...|.+.+.
T Consensus         7 ~~il~~L~~~-~~~s~~~LA~~lgvsr---~tV~~~l~~L~~~G~~i~~~~------~~Gy~L~~~   62 (319)
T PRK11886          7 LQLLSLLADG-DFHSGEQLGEELGISR---AAIWKHIQTLEEWGLDIFSVK------GKGYRLAEP   62 (319)
T ss_pred             HHHHHHHHcC-CCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCceEEec------CCeEEecCc
Confidence            3466677764 7899999999999999   999999999999999554431      346776555

>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]

Probab=87.35  E-value=0.59  Score=39.41  Aligned_cols=54  Identities=9%  Similarity=0.217  Sum_probs=45.7

Q ss_pred             CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      .|.++|.++ |-++++|||+.+++++   .-+||=|+.|...|++...-       ++....+..
T Consensus         9 ~Il~~l~~~-g~v~v~eLa~~~~VS~---~TIRRDL~~Le~~g~l~R~h-------GGa~~~~~~   62 (253)
T COG1349           9 KILELLKEK-GKVSVEELAELFGVSE---MTIRRDLNELEEQGLLLRVH-------GGAVLPDSE   62 (253)
T ss_pred             HHHHHHHHc-CcEEHHHHHHHhCCCH---HHHHHhHHHHHHCCcEEEEe-------CCEecCCCc
Confidence            367888887 8999999999999999   99999999999999999965       455554444

>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=87.29  E-value=0.23  Score=30.29  Aligned_cols=23  Identities=13%  Similarity=0.154  Sum_probs=17.1

Q ss_pred             CCCHHHHHHHcCCCCCCcccHHHHHH
Q 040620           51 PMTLTQIIVALNVHPNKTRCTQILVC   76 (214)
Q Consensus        51 p~t~~eLA~~~g~~~~~~~~l~rlLr   76 (214)
                      ++|+.+||+.+|++.   ..+.|+|+
T Consensus        21 G~si~~IA~~~gvsr---~TvyR~l~   43 (45)
T PF02796_consen   21 GMSIAEIAKQFGVSR---STVYRYLN   43 (45)
T ss_dssp             T--HHHHHHHTTS-H---HHHHHHHC
T ss_pred             CCCHHHHHHHHCcCH---HHHHHHHh
Confidence            399999999999998   88888763

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 ....

>PRK10046 dpiA two-component response regulator DpiA; Provisional

Probab=87.11  E-value=0.62  Score=37.95  Aligned_cols=45  Identities=11%  Similarity=0.202  Sum_probs=37.7

Q ss_pred             CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620           40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ   87 (214)
Q Consensus        40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~   87 (214)
                      .|+.++.+...+.|.+|||+++++++   +-+++.+..|+..|++...
T Consensus       166 ~Vl~~~~~g~~g~s~~eIa~~l~iS~---~Tv~~~~~~~~~~~~~~~~  210 (225)
T PRK10046        166 AVRKLFKEPGVQHTAETVAQALTISR---TTARRYLEYCASRHLIIAE  210 (225)
T ss_pred             HHHHHHHcCCCCcCHHHHHHHhCccH---HHHHHHHHHHHhCCeEEEE
Confidence            35566665112689999999999999   9999999999999999876

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

Probab=87.06  E-value=0.93  Score=37.05  Aligned_cols=34  Identities=32%  Similarity=0.382  Sum_probs=29.1

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCC-CCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFP-DTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl  212 (214)
                      .+.++||+||++.|..++.+++..| +.+++.+|.
T Consensus        44 ~~~k~vLEIGt~~GySal~la~~l~~~g~i~tiE~   78 (205)
T PF01596_consen   44 TRPKRVLEIGTFTGYSALWLAEALPEDGKITTIEI   78 (205)
T ss_dssp             HT-SEEEEESTTTSHHHHHHHHTSTTTSEEEEEES
T ss_pred             cCCceEEEeccccccHHHHHHHhhcccceEEEecC
Confidence            3578999999999999999999988 578888775

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 ....

>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function

Probab=86.96  E-value=0.61  Score=33.25  Aligned_cols=46  Identities=15%  Similarity=0.169  Sum_probs=40.8

Q ss_pred             cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      +.|..+|... +|=.+.-||..++++.   ..+.+.|+.|..+|++++..
T Consensus        10 ~~IL~hl~~~-~~Dy~k~ia~~l~~~~---~~v~~~l~~Le~~GLler~~   55 (92)
T PF10007_consen   10 LKILQHLKKA-GPDYAKSIARRLKIPL---EEVREALEKLEEMGLLERVE   55 (92)
T ss_pred             HHHHHHHHHH-CCCcHHHHHHHHCCCH---HHHHHHHHHHHHCCCeEEec
Confidence            4466677776 8899999999999999   99999999999999999886

>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication

Probab=86.80  E-value=0.8  Score=36.17  Aligned_cols=43  Identities=12%  Similarity=0.186  Sum_probs=40.3

Q ss_pred             CCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           52 MTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        52 ~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      +|..+||+.+|++.   ..+.|.+..|...+++....       .+.|..+|.
T Consensus        76 ~t~~~ia~~l~iS~---~Tv~r~ik~L~e~~iI~k~~-------~G~Y~iNP~  118 (165)
T PF05732_consen   76 ATQKEIAEKLGISK---PTVSRAIKELEEKNIIKKIR-------NGAYMINPN  118 (165)
T ss_pred             eeHHHHHHHhCCCH---HHHHHHHHHHHhCCcEEEcc-------CCeEEECcH
Confidence            68999999999999   99999999999999999886       689999998

; GO: 0006260 DNA replication, 0006276 plasmid maintenance

>PRK13777 transcriptional regulator Hpr; Provisional

Probab=86.77  E-value=0.66  Score=37.36  Aligned_cols=65  Identities=15%  Similarity=0.114  Sum_probs=47.7

Q ss_pred             CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      .+...|..+ +++|..+||+.+++++   ..+.++++-|...|++.......|-- .-...+|+.    ++.+.
T Consensus        49 ~iL~~L~~~-~~itq~eLa~~l~l~~---sTvtr~l~rLE~kGlI~R~~~~~DrR-~~~I~LTek----G~~l~  113 (185)
T PRK13777         49 HILWIAYHL-KGASISEIAKFGVMHV---STAFNFSKKLEERGYLTFSKKEDDKR-NTYIELTEK----GEELL  113 (185)
T ss_pred             HHHHHHHhC-CCcCHHHHHHHHCCCH---hhHHHHHHHHHHCCCEEecCCCCCCC-eeEEEECHH----HHHHH
Confidence            355666665 7899999999999998   88999999999999999764211110 223666777    66554

>COG3432 Predicted transcriptional regulator [Transcription]

Probab=86.71  E-value=0.2  Score=35.90  Aligned_cols=62  Identities=23%  Similarity=0.320  Sum_probs=47.3

Q ss_pred             cchhhh-cCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           41 IPDIIN-NSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        41 lfd~L~-~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      +||+|. .+++++...-|.-.++++-   +..+++++.|+..|++.....   +. ...|.+|+.    +..|+
T Consensus        20 i~dIL~~~~~~~~~~Tri~y~aNlny---~~~~~yi~~L~~~Gli~~~~~---~~-~~~y~lT~K----G~~fl   82 (95)
T COG3432          20 IFDILKAISEGGIGITRIIYGANLNY---KRAQKYIEMLVEKGLIIKQDN---GR-RKVYELTEK----GKRFL   82 (95)
T ss_pred             HHHHHHHhcCCCCCceeeeeecCcCH---HHHHHHHHHHHhCCCEEeccC---Cc-cceEEEChh----HHHHH
Confidence            345555 2338899999999999998   999999999999996665541   11 236999999    87774

>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional

Probab=86.65  E-value=0.53  Score=39.72  Aligned_cols=45  Identities=9%  Similarity=0.207  Sum_probs=40.5

Q ss_pred             CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      .|.+.|... +.+++.|||+.+++++   .-+||=|..|...|++...-
T Consensus         9 ~Il~~L~~~-~~v~v~eLa~~l~VS~---~TIRRDL~~Le~~g~l~r~~   53 (256)
T PRK10434          9 AILEYLQKQ-GKTSVEELAQYFDTTG---TTIRKDLVILEHAGTVIRTY   53 (256)
T ss_pred             HHHHHHHHc-CCEEHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEEEE
Confidence            467888887 8899999999999999   99999999999999998764

>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]

Probab=86.59  E-value=0.51  Score=40.02  Aligned_cols=47  Identities=21%  Similarity=0.320  Sum_probs=42.5

Q ss_pred             cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      ..+.++|.++||-++-+||.+++|.+.   ..+.|+|+-|...|+++..+
T Consensus       198 ~~il~~i~~~GGri~Q~eL~r~lglsk---tTvsR~L~~LEk~GlIe~~K  244 (258)
T COG2512         198 KEILDLIRERGGRITQAELRRALGLSK---TTVSRILRRLEKRGLIEKEK  244 (258)
T ss_pred             HHHHHHHHHhCCEEeHHHHHHhhCCCh---HHHHHHHHHHHhCCceEEEE
Confidence            446788888878899999999999999   99999999999999999876

>PRK10411 DNA-binding transcriptional activator FucR; Provisional

Probab=86.45  E-value=0.91  Score=37.95  Aligned_cols=45  Identities=20%  Similarity=0.232  Sum_probs=39.7

Q ss_pred             CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      .|.+.|.++ +.++++|||+.+++++   +.++|.|..|...|.+....
T Consensus         8 ~Il~~l~~~-~~~~~~eLa~~l~VS~---~TiRRdL~~L~~~~~l~r~~   52 (240)
T PRK10411          8 AIVDLLLNH-TSLTTEALAEQLNVSK---ETIRRDLNELQTQGKILRNH   52 (240)
T ss_pred             HHHHHHHHc-CCCcHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEec
Confidence            366777776 8999999999999999   99999999999999998754

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

Probab=86.45  E-value=0.99  Score=40.05  Aligned_cols=29  Identities=17%  Similarity=0.253  Sum_probs=24.5

Q ss_pred             CcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          182 KPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       182 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+++|++||+|.+++.+++...  +++.+|.
T Consensus       208 ~~vLDl~~G~G~~sl~la~~~~--~v~~vE~  236 (362)
T PRK05031        208 GDLLELYCGNGNFTLALARNFR--RVLATEI  236 (362)
T ss_pred             CeEEEEeccccHHHHHHHhhCC--EEEEEEC
Confidence            4799999999999999999865  6777664

>COG1510 Predicted transcriptional regulators [Transcription]

Probab=86.40  E-value=0.74  Score=36.53  Aligned_cols=44  Identities=20%  Similarity=0.162  Sum_probs=37.0

Q ss_pred             chhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           42 PDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        42 fd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      +-+|=-+.+|+|++||++.+|++.   ..+..-++-|-..+++.+.-
T Consensus        32 Ygilyls~~Pmtl~Ei~E~lg~Sk---s~vS~~lkkL~~~~lV~~~~   75 (177)
T COG1510          32 YGILYLSRKPLTLDEIAEALGMSK---SNVSMGLKKLQDWNLVKKVF   75 (177)
T ss_pred             hhhheecCCCccHHHHHHHHCCCc---chHHHHHHHHHhcchHHhhh
Confidence            333333349999999999999999   99999999999999998754

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

Probab=86.17  E-value=1.7  Score=35.75  Aligned_cols=33  Identities=15%  Similarity=0.205  Sum_probs=26.0

Q ss_pred             HHHhhcccccCCCCcEEeecCCchHHHHHHHHHCC
Q 040620          169 VLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFP  203 (214)
Q Consensus       169 ~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P  203 (214)
                      .+++...  .....+||+||+|+|..+.-|++.--
T Consensus        63 ~m~~~L~--~~~g~~VLEIGtGsGY~aAvla~l~~   95 (209)
T COG2518          63 RMLQLLE--LKPGDRVLEIGTGSGYQAAVLARLVG   95 (209)
T ss_pred             HHHHHhC--CCCCCeEEEECCCchHHHHHHHHHhC
Confidence            3455555  66789999999999999998887643

>COG1733 Predicted transcriptional regulators [Transcription]

Probab=85.96  E-value=2.7  Score=31.40  Aligned_cols=81  Identities=11%  Similarity=0.080  Sum_probs=62.7

Q ss_pred             hhHHHHHHHHHHHHhHHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHcC-CCCCCcccHHHHHHHHHhCCceeeecCCCC
Q 040620           14 FQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALN-VHPNKTRCTQILVCLLAHSGFFVQQKDGKN   92 (214)
Q Consensus        14 ~~~~~~l~~~~~g~~~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g-~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~   92 (214)
                      .-+....++++.+-|...+|+...         .  |+....||-..++ +++   +-|.+-|+.|...|++....-.+-
T Consensus        10 ~c~~~~~l~~ig~kW~~lIl~~L~---------~--g~~RF~eL~r~i~~Is~---k~Ls~~Lk~Le~~Glv~R~~~~~~   75 (120)
T COG1733          10 PCPVEEALEVIGGKWTLLILRDLF---------D--GPKRFNELRRSIGGISP---KMLSRRLKELEEDGLVERVVYPEE   75 (120)
T ss_pred             CCCHHHHHHHHcCccHHHHHHHHh---------c--CCCcHHHHHHHccccCH---HHHHHHHHHHHHCCCEEeeecCCC
Confidence            345667788888888888877653         2  7899999999998 999   999999999999999997652100


Q ss_pred             CCccceeeCCCCCcccccccc
Q 040620           93 EQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        93 ~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      -. .-.|++|+.    ++.|.
T Consensus        76 Pp-rveY~LT~~----G~~L~   91 (120)
T COG1733          76 PP-RVEYRLTEK----GRDLL   91 (120)
T ss_pred             Cc-eeEEEEhhh----HHHHH
Confidence            01 356999999    77765

>KOG3045 consensus Predicted RNA methylase involved in rRNA processing [RNA processing and modification]

Probab=85.91  E-value=1.6  Score=37.27  Aligned_cols=55  Identities=18%  Similarity=0.110  Sum_probs=35.7

Q ss_pred             cCCCCChhhHHHHHHHHHhhhhhhhhHHHHHhhcccccCCCCcEEeecCCchHHHH
Q 040620          141 QNDDQTLFGTADGIFYEAMITDFELIASVLIEDCNEVSKGLKPLVDVGGSTGTMAR  196 (214)
Q Consensus       141 r~~~~~~f~~~~g~f~~am~~~~~~~~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~  196 (214)
                      ..++|+.|+..|.-|..-...+.......++..+. .-++...|.|+|||.+-++.
T Consensus       142 fkedp~afdlYH~gfr~QV~kWP~nPld~ii~~ik-~r~~~~vIaD~GCGEakiA~  196 (325)
T KOG3045|consen  142 FKEDPTAFDLYHAGFRSQVKKWPENPLDVIIRKIK-RRPKNIVIADFGCGEAKIAS  196 (325)
T ss_pred             HhcCcHHHHHHHHHHHHHHHhCCCChHHHHHHHHH-hCcCceEEEecccchhhhhh
Confidence            33455667766655666555665555555655443 23456799999999998875

>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term

Probab=85.74  E-value=1.1  Score=33.27  Aligned_cols=36  Identities=19%  Similarity=0.239  Sum_probs=34.3

Q ss_pred             CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      .++|++|||+.+.+++   |.++.+|+-+...|.++-.+
T Consensus        18 ~~vtl~elA~~l~cS~---Rn~r~lLkkm~~~gWi~W~p   53 (115)
T PF12793_consen   18 VEVTLDELAELLFCSR---RNARTLLKKMQEEGWITWQP   53 (115)
T ss_pred             cceeHHHHHHHhCCCH---HHHHHHHHHHHHCCCeeeeC
Confidence            5789999999999999   99999999999999999886

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

Probab=85.56  E-value=1.1  Score=36.49  Aligned_cols=33  Identities=15%  Similarity=0.290  Sum_probs=24.0

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      -..+.+++|||||.|.+...|+.+.  -+.++.|.
T Consensus        41 ~~ry~~alEvGCs~G~lT~~LA~rC--d~LlavDi   73 (201)
T PF05401_consen   41 RRRYRRALEVGCSIGVLTERLAPRC--DRLLAVDI   73 (201)
T ss_dssp             TSSEEEEEEE--TTSHHHHHHGGGE--EEEEEEES
T ss_pred             ccccceeEecCCCccHHHHHHHHhh--CceEEEeC
Confidence            4556899999999999999998875  34566654

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.

>PRK11639 zinc uptake transcriptional repressor; Provisional

Probab=85.21  E-value=1.6  Score=34.54  Aligned_cols=48  Identities=13%  Similarity=0.235  Sum_probs=38.9

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcC-----CCCCCcccHHHHHHHHHhCCceeeec
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALN-----VHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g-----~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      +.-|+++|...++++|+++|.+++.     ++.   ..++|.|+.|+..|++.+..
T Consensus        28 R~~IL~~l~~~~~hlSa~eI~~~L~~~~~~is~---aTVYRtL~~L~e~Glv~~~~   80 (169)
T PRK11639         28 RLEVLRLMSLQPGAISAYDLLDLLREAEPQAKP---PTVYRALDFLLEQGFVHKVE   80 (169)
T ss_pred             HHHHHHHHHhcCCCCCHHHHHHHHHhhCCCCCc---chHHHHHHHHHHCCCEEEEe
Confidence            3446777766558999999998884     344   78999999999999999875

>PF13518 HTH_28: Helix-turn-helix domain

Probab=85.20  E-value=0.79  Score=28.18  Aligned_cols=29  Identities=7%  Similarity=0.103  Sum_probs=26.7

Q ss_pred             CCHHHHHHHcCCCCCCcccHHHHHHHHHhCCc
Q 040620           52 MTLTQIIVALNVHPNKTRCTQILVCLLAHSGF   83 (214)
Q Consensus        52 ~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~   83 (214)
                      .|..++|+.+|+++   ..+.+|++.....|+
T Consensus        13 ~s~~~~a~~~gis~---~tv~~w~~~y~~~G~   41 (52)
T PF13518_consen   13 ESVREIAREFGISR---STVYRWIKRYREGGI   41 (52)
T ss_pred             CCHHHHHHHHCCCH---hHHHHHHHHHHhcCH
Confidence            49999999999999   999999999988875

>smart00531 TFIIE Transcription initiation factor IIE

Probab=84.90  E-value=0.9  Score=35.05  Aligned_cols=41  Identities=12%  Similarity=0.164  Sum_probs=35.4

Q ss_pred             CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCce
Q 040620           40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFF   84 (214)
Q Consensus        40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l   84 (214)
                      -|+++|-.+ +.+|-++||+.+|++.   ..++++|..|...++.
T Consensus         5 ~v~d~L~~~-~~~~dedLa~~l~i~~---n~vRkiL~~L~ed~~~   45 (147)
T smart00531        5 LVLDALMRN-GCVTEEDLAELLGIKQ---KQLRKILYLLYDEKLI   45 (147)
T ss_pred             eehHHHHhc-CCcCHHHHHHHhCCCH---HHHHHHHHHHHhhhcc
Confidence            467777766 7899999999999999   9999999999995554

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

Probab=84.88  E-value=0.82  Score=37.00  Aligned_cols=34  Identities=21%  Similarity=0.206  Sum_probs=25.0

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ....++|+|+|||+|.+++..+-.-|. +++.+|+
T Consensus        43 ~l~g~~V~DlG~GTG~La~ga~~lGa~-~V~~vdi   76 (198)
T COG2263          43 DLEGKTVLDLGAGTGILAIGAALLGAS-RVLAVDI   76 (198)
T ss_pred             CcCCCEEEEcCCCcCHHHHHHHhcCCc-EEEEEec
Confidence            345679999999999999988776443 4555553

>TIGR02147 Fsuc_second hypothetical protein, TIGR02147

Probab=84.63  E-value=1.3  Score=37.93  Aligned_cols=45  Identities=7%  Similarity=-0.011  Sum_probs=39.8

Q ss_pred             CCCCHHHHHHHcC--CCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           50 QPMTLTQIIVALN--VHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        50 ~p~t~~eLA~~~g--~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      +..++++||++++  ++.   ..++.-|+.|...|++..++       ++.|..|..
T Consensus       136 ~~~~~~~ia~~l~p~is~---~ev~~sL~~L~~~glikk~~-------~g~y~~t~~  182 (271)
T TIGR02147       136 FADDPEELAKRCFPKISA---EQVKESLDLLERLGLIKKNE-------DGFYKQTDK  182 (271)
T ss_pred             CCCCHHHHHHHhCCCCCH---HHHHHHHHHHHHCCCeeECC-------CCcEEeecc
Confidence            4457999999998  777   88999999999999999987       689999887

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.

>PF03141 Methyltransf_29: Putative S-adenosyl-L-methionine-dependent methyltransferase; InterPro: IPR004159 Members of this family of hypothetical plant proteins are putative methyltransferases

Probab=84.57  E-value=0.55  Score=43.28  Aligned_cols=23  Identities=17%  Similarity=0.393  Sum_probs=20.9

Q ss_pred             CCCCcEEeecCCchHHHHHHHHH
Q 040620          179 KGLKPLVDVGGSTGTMARAIATA  201 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~  201 (214)
                      ...+++||||||.|+|+..|+++
T Consensus       116 g~iR~~LDvGcG~aSF~a~l~~r  138 (506)
T PF03141_consen  116 GGIRTALDVGCGVASFGAYLLER  138 (506)
T ss_pred             CceEEEEeccceeehhHHHHhhC
Confidence            45789999999999999999987

; GO: 0008168 methyltransferase activity

>PRK12423 LexA repressor; Provisional

Probab=83.69  E-value=1.4  Score=35.72  Aligned_cols=36  Identities=25%  Similarity=0.288  Sum_probs=32.0

Q ss_pred             CCCCHHHHHHHcCC-CCCCcccHHHHHHHHHhCCceeeec
Q 040620           50 QPMTLTQIIVALNV-HPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        50 ~p~t~~eLA~~~g~-~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      -+-|..|||+++|+ ++   ..+++.|+.|...|++...+
T Consensus        24 ~~Ps~~eia~~~g~~s~---~~v~~~l~~L~~~G~l~~~~   60 (202)
T PRK12423         24 QPPSLAEIAQAFGFASR---SVARKHVQALAEAGLIEVVP   60 (202)
T ss_pred             CCCCHHHHHHHhCCCCh---HHHHHHHHHHHHCCCEEecC
Confidence            35699999999995 76   78899999999999999875

>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C

Probab=83.14  E-value=0.57  Score=28.79  Aligned_cols=38  Identities=13%  Similarity=0.197  Sum_probs=22.2

Q ss_pred             CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCc
Q 040620           40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGF   83 (214)
Q Consensus        40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~   83 (214)
                      .+...+.   .+.|..+||+.+|+++   ..+++|++.....|+
T Consensus         9 ~ii~l~~---~G~s~~~ia~~lgvs~---~Tv~~w~kr~~~~G~   46 (50)
T PF13384_consen    9 QIIRLLR---EGWSIREIAKRLGVSR---STVYRWIKRYREEGL   46 (50)
T ss_dssp             -HHHHHH---HT--HHHHHHHHTS-H---HHHHHHHT-------
T ss_pred             HHHHHHH---CCCCHHHHHHHHCcCH---HHHHHHHHHcccccc
Confidence            3444444   3689999999999999   999999887666553

>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=83.12  E-value=1.1  Score=37.66  Aligned_cols=33  Identities=27%  Similarity=0.350  Sum_probs=27.7

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +.++||=||||.|..+..+++..|-.+++++|+
T Consensus        76 ~p~~VLiiGgG~G~~~~ell~~~~~~~i~~VEi  108 (246)
T PF01564_consen   76 NPKRVLIIGGGDGGTARELLKHPPVESITVVEI  108 (246)
T ss_dssp             ST-EEEEEESTTSHHHHHHTTSTT-SEEEEEES
T ss_pred             CcCceEEEcCCChhhhhhhhhcCCcceEEEEec
Confidence            579999999999999999997776778998886

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 ....

>COG3413 Predicted DNA binding protein [General function prediction only]

Probab=83.08  E-value=1.5  Score=35.88  Aligned_cols=42  Identities=12%  Similarity=0.062  Sum_probs=34.3

Q ss_pred             HHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHH
Q 040620           29 KSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCL   77 (214)
Q Consensus        29 ~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~   77 (214)
                      .-.+|+.|++.|-||.=.    ..+..+||+.+|+++   ..+...||-
T Consensus       160 Q~~vL~~A~~~GYFd~PR----~~~l~dLA~~lGISk---st~~ehLRr  201 (215)
T COG3413         160 QLEVLRLAYKMGYFDYPR----RVSLKDLAKELGISK---STLSEHLRR  201 (215)
T ss_pred             HHHHHHHHHHcCCCCCCc----cCCHHHHHHHhCCCH---HHHHHHHHH
Confidence            567899999999999744    489999999999988   666555554

>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A

Probab=82.91  E-value=0.69  Score=27.46  Aligned_cols=27  Identities=22%  Similarity=0.149  Sum_probs=20.6

Q ss_pred             CCCCHHHHHHHcCCCCCCcccHHHHHHHHH
Q 040620           50 QPMTLTQIIVALNVHPNKTRCTQILVCLLA   79 (214)
Q Consensus        50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~   79 (214)
                      .+.++++||+.+|+++   ..+.|..+...
T Consensus         7 ~~~~l~~iA~~~g~S~---~~f~r~Fk~~~   33 (42)
T PF00165_consen    7 QKLTLEDIAEQAGFSP---SYFSRLFKKET   33 (42)
T ss_dssp             SS--HHHHHHHHTS-H---HHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHCCCH---HHHHHHHHHHH
Confidence            5799999999999998   99988877554

>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain

Probab=82.47  E-value=0.83  Score=42.16  Aligned_cols=65  Identities=9%  Similarity=0.015  Sum_probs=53.9

Q ss_pred             HHhcCcchhhhcCCCC-CCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           36 AIQLRIPDIINNSGQP-MTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        36 a~~lglfd~L~~~~~p-~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      +++..|...|... ++ .+.++||+.+|+++   ..+.+.+..|.+.|++......     ...|.+|+.    ++..+
T Consensus         3 ~~e~~iL~~l~~~-~~~~~~~~la~~~g~~~---~~v~~~~~~L~~kg~v~~~~~~-----~~~~~LT~e----G~~~l   68 (492)
T PLN02853          3 MAEEALLGALSNN-EEISDSGQFAASHGLDH---NEVVGVIKSLHGFRYVDAQDIK-----RETWVLTEE----GKKYA   68 (492)
T ss_pred             hHHHHHHHHHHhc-CCCCCHHHHHHHcCCCH---HHHHHHHHHHHhCCCEEEEEEE-----EEEEEECHH----HHHHH
Confidence            4566677788875 54 89999999999999   9999999999999999865431     578999999    88876

>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=82.27  E-value=2  Score=29.14  Aligned_cols=42  Identities=17%  Similarity=0.219  Sum_probs=37.1

Q ss_pred             cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620           41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ   87 (214)
Q Consensus        41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~   87 (214)
                      |...++.  +..|.+||-+++|++.   ..|-..|.-|+..|++...
T Consensus        10 IL~~ls~--~c~TLeeL~ekTgi~k---~~LlV~LsrL~k~GiI~Rk   51 (72)
T PF05584_consen   10 ILIILSK--RCCTLEELEEKTGISK---NTLLVYLSRLAKRGIIERK   51 (72)
T ss_pred             HHHHHHh--ccCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCeeee
Confidence            4556666  6899999999999999   8999999999999999876

>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]

Probab=82.24  E-value=1.4  Score=35.25  Aligned_cols=45  Identities=13%  Similarity=0.189  Sum_probs=39.4

Q ss_pred             CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      .|++.|... |-+|-++||..+|+..   .-++++|..|...|++....
T Consensus        22 ~v~~~l~~k-ge~tDeela~~l~i~~---~~vrriL~~L~e~~li~~~k   66 (176)
T COG1675          22 LVVDALLEK-GELTDEELAELLGIKK---NEVRRILYALYEDGLISYRK   66 (176)
T ss_pred             HHHHHHHhc-CCcChHHHHHHhCccH---HHHHHHHHHHHhCCceEEEe
Confidence            466777774 5699999999999999   99999999999999999664

>PLN02476 O-methyltransferase

Probab=81.80  E-value=2  Score=36.79  Aligned_cols=36  Identities=22%  Similarity=0.229  Sum_probs=30.0

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCC-CCeEEEecCC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFP-DTKCTVFACH  213 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dlp  213 (214)
                      ..+.+++|+||.+.|..++.+++.-| +-+++-+|..
T Consensus       116 ~~~ak~VLEIGT~tGySal~lA~al~~~G~V~TiE~d  152 (278)
T PLN02476        116 ILGAERCIEVGVYTGYSSLAVALVLPESGCLVACERD  152 (278)
T ss_pred             hcCCCeEEEecCCCCHHHHHHHHhCCCCCEEEEEECC
Confidence            44689999999999999999999876 5577777764

>KOG2361 consensus Predicted methyltransferase [General function prediction only]

Probab=81.72  E-value=0.74  Score=38.67  Aligned_cols=30  Identities=17%  Similarity=0.324  Sum_probs=25.7

Q ss_pred             CcEEeecCCchHHHHHHHHHCCC--CeEEEec
Q 040620          182 KPLVDVGGSTGTMARAIATAFPD--TKCTVFA  211 (214)
Q Consensus       182 ~~vvDVGGG~G~~~~~l~~~~P~--l~~~v~D  211 (214)
                      .+|+.||||.|....-|++.+|+  +++...|
T Consensus        73 ~~ilEvGCGvGNtvfPll~~~~n~~l~v~acD  104 (264)
T KOG2361|consen   73 ETILEVGCGVGNTVFPLLKTSPNNRLKVYACD  104 (264)
T ss_pred             hhheeeccCCCcccchhhhcCCCCCeEEEEcC
Confidence            38999999999999999999999  5555554

>PRK05638 threonine synthase; Validated

Probab=81.65  E-value=1.4  Score=40.17  Aligned_cols=60  Identities=17%  Similarity=0.110  Sum_probs=45.1

Q ss_pred             cchhhhcCCCCCCHHHHHHHcC--CCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCccccccc
Q 040620           41 IPDIINNSGQPMTLTQIIVALN--VHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRIS  112 (214)
Q Consensus        41 lfd~L~~~~~p~t~~eLA~~~g--~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l  112 (214)
                      |+.+|.+  ++++.-||++.++  +++   ..+++.|+.|...|+++....  .+. ...|++|+.    ++.+
T Consensus       376 IL~~L~~--~~~~~~el~~~l~~~~s~---~~v~~hL~~Le~~GLV~~~~~--~g~-~~~Y~Lt~~----g~~~  437 (442)
T PRK05638        376 ILKILSE--REMYGYEIWKALGKPLKY---QAVYQHIKELEELGLIEEAYR--KGR-RVYYKLTEK----GRRL  437 (442)
T ss_pred             HHHHHhh--CCccHHHHHHHHcccCCc---chHHHHHHHHHHCCCEEEeec--CCC-cEEEEECcH----HHHH
Confidence            4555554  6899999999998  777   899999999999999975311  011 345889988    6554

>TIGR03879 near_KaiC_dom probable regulatory domain

Probab=81.37  E-value=0.66  Score=31.62  Aligned_cols=34  Identities=15%  Similarity=0.046  Sum_probs=29.9

Q ss_pred             CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceee
Q 040620           50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQ   86 (214)
Q Consensus        50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~   86 (214)
                      ..+|..|||+.+|+++   ..++.++..+...|.+..
T Consensus        31 eGlS~kEIAe~LGIS~---~TVk~~l~~~~~~~~~~~   64 (73)
T TIGR03879        31 AGKTASEIAEELGRTE---QTVRNHLKGETKAGGLVK   64 (73)
T ss_pred             cCCCHHHHHHHHCcCH---HHHHHHHhcCcccchHHH
Confidence            5799999999999999   999999998888877654

This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.

>PF03428 RP-C: Replication protein C N-terminal domain; InterPro: IPR005090 Proteins in this group have homology with the RepC protein of Agrobacterium Ri and Ti plasmids []

Probab=81.29  E-value=2  Score=34.31  Aligned_cols=57  Identities=18%  Similarity=0.247  Sum_probs=41.4

Q ss_pred             HHHHHHHHHhcCcchhhhcCCCC---CCHHHHHHHc-CCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           29 KSLSLKRAIQLRIPDIINNSGQP---MTLTQIIVAL-NVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        29 ~~~~L~~a~~lglfd~L~~~~~p---~t~~eLA~~~-g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      ...+|.+.+.+-=-+-+...+.|   .|-.+||+.+ |+++   +.++|.++.|+..|++...+
T Consensus        45 ~l~vL~aLls~~~~~d~~~~~~piVfpSN~~La~r~~G~s~---~tlrR~l~~LveaGLI~rrD  105 (177)
T PF03428_consen   45 ALAVLDALLSFTPPDDWEPGRRPIVFPSNAQLAERLNGMSE---RTLRRHLARLVEAGLIVRRD  105 (177)
T ss_pred             HHHHHHHHHHhCCcccccCCCCceeecCHHHHHHHHcCCCH---HHHHHHHHHHHHCCCeeecc
Confidence            33445555544444444432233   5779999999 9999   99999999999999999865

They may be involved in plasmid replication and stabilisation functions.

>COG1654 BirA Biotin operon repressor [Transcription]

Probab=81.06  E-value=3  Score=28.81  Aligned_cols=52  Identities=12%  Similarity=0.125  Sum_probs=43.3

Q ss_pred             chhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           42 PDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        42 fd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      +..+..  .++|=++||+++|++.   ..+..-++.|...|+=.+...      ..-|++...
T Consensus        12 l~~~~~--~~~SGe~La~~LgiSR---taVwK~Iq~Lr~~G~~I~s~~------~kGY~L~~~   63 (79)
T COG1654          12 LLLLTG--NFVSGEKLAEELGISR---TAVWKHIQQLREEGVDIESVR------GKGYLLPQL   63 (79)
T ss_pred             HHHcCC--CcccHHHHHHHHCccH---HHHHHHHHHHHHhCCceEecC------CCceeccCc
Confidence            344443  7999999999999999   999999999999999888763      347888777

>PRK10736 hypothetical protein; Provisional

Probab=80.99  E-value=2  Score=38.48  Aligned_cols=50  Identities=6%  Similarity=0.011  Sum_probs=43.0

Q ss_pred             CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeC
Q 040620           40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILL  101 (214)
Q Consensus        40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~  101 (214)
                      .|++.|..  .|+++++|+.++|++.   ..+...|-.|.-.|++.+.+       ++.|+.
T Consensus       312 ~v~~~l~~--~~~~iD~L~~~~~l~~---~~v~~~L~~LEl~G~v~~~~-------g~~~~~  361 (374)
T PRK10736        312 ELLANVGD--EVTPVDVVAERAGQPV---PEVVTQLLELELAGWIAAVP-------GGYVRL  361 (374)
T ss_pred             HHHHhcCC--CCCCHHHHHHHHCcCH---HHHHHHHHHHHhCCcEEEcC-------CcEEEE
Confidence            46677765  7899999999999999   99999999999999999987       566654

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

Probab=80.91  E-value=2  Score=38.75  Aligned_cols=32  Identities=13%  Similarity=0.035  Sum_probs=25.4

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +.++|||+|||+|.+++..+.. +..+++.+|+
T Consensus       220 ~g~rVLDlfsgtG~~~l~aa~~-ga~~V~~VD~  251 (396)
T PRK15128        220 ENKRVLNCFSYTGGFAVSALMG-GCSQVVSVDT  251 (396)
T ss_pred             CCCeEEEeccCCCHHHHHHHhC-CCCEEEEEEC
Confidence            4689999999999998876643 4457888886

>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional

Probab=80.85  E-value=1  Score=41.71  Aligned_cols=66  Identities=9%  Similarity=0.064  Sum_probs=53.6

Q ss_pred             HHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           36 AIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        36 a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      ..+..|+..|...++..+.++||+.+|+++   ..+.+.+..|.+.|+++.....     ...|.+|+.    ++..+
T Consensus         6 ~~e~~iL~~l~~~~~~~~~~~la~~~~~~~---~~v~~~~~~L~~kg~v~~~~~~-----~~~~~LT~e----G~~~~   71 (494)
T PTZ00326          6 LEENTILSKLESENEIVNSLALAESLNIDH---QKVVGAIKSLESANYITTEMKK-----SNTWTLTEE----GEDYL   71 (494)
T ss_pred             HHHHHHHHHHHhcCCCCCHHHHHHHcCCCH---HHHHHHHHHHHhCCCEEEEEEE-----EEEEEECHH----HHHHH
Confidence            345556677776326799999999999999   9999999999999999865431     578999999    88877

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

Probab=80.76  E-value=2.2  Score=37.82  Aligned_cols=33  Identities=15%  Similarity=0.085  Sum_probs=28.6

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +....++||||+++|.++..++++  +.+++.+|.
T Consensus       209 ~~~g~~vlDLGAsPGGWT~~L~~r--G~~V~AVD~  241 (357)
T PRK11760        209 LAPGMRAVDLGAAPGGWTYQLVRR--GMFVTAVDN  241 (357)
T ss_pred             cCCCCEEEEeCCCCcHHHHHHHHc--CCEEEEEec
Confidence            345789999999999999999998  668888884

>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional

Probab=80.68  E-value=2.1  Score=34.12  Aligned_cols=35  Identities=11%  Similarity=0.140  Sum_probs=33.0

Q ss_pred             CCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           51 PMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        51 p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      ++|-++||+.+|+++   ..+.|+|..|...|++....
T Consensus       168 ~~t~~~lA~~lG~tr---~tvsR~l~~l~~~gii~~~~  202 (211)
T PRK11753        168 KITRQEIGRIVGCSR---EMVGRVLKMLEDQGLISAHG  202 (211)
T ss_pred             CCCHHHHHHHhCCCH---HHHHHHHHHHHHCCCEEecC
Confidence            789999999999999   99999999999999998774

>COG4122 Predicted O-methyltransferase [General function prediction only]

Probab=80.51  E-value=2.5  Score=34.95  Aligned_cols=36  Identities=28%  Similarity=0.399  Sum_probs=32.3

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCC-CCeEEEecCC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFP-DTKCTVFACH  213 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dlp  213 (214)
                      .++.+++++||.+.|..++.++..-| +-+.|-+|+.
T Consensus        57 ~~~~k~iLEiGT~~GySal~mA~~l~~~g~l~tiE~~   93 (219)
T COG4122          57 LSGPKRILEIGTAIGYSALWMALALPDDGRLTTIERD   93 (219)
T ss_pred             hcCCceEEEeecccCHHHHHHHhhCCCCCeEEEEeCC
Confidence            45789999999999999999999999 8888888864

>TIGR01321 TrpR trp operon repressor, proteobacterial

Probab=80.45  E-value=1.3  Score=31.73  Aligned_cols=41  Identities=20%  Similarity=0.077  Sum_probs=33.4

Q ss_pred             HHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHH
Q 040620           34 KRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLA   79 (214)
Q Consensus        34 ~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~   79 (214)
                      ..+.+.+|+..|-.  +++|-.|||+++|++.   ..+.|+=+.|-
T Consensus        40 ~l~~R~~i~~~Ll~--~~~tQrEIa~~lGiS~---atIsR~sn~lk   80 (94)
T TIGR01321        40 DLGDRIRIVNELLN--GNMSQREIASKLGVSI---ATITRGSNNLK   80 (94)
T ss_pred             HHHHHHHHHHHHHh--CCCCHHHHHHHhCCCh---hhhhHHHhhcc
Confidence            45667889988776  7899999999999998   88888765554

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.

>PRK09954 putative kinase; Provisional

Probab=80.40  E-value=1.3  Score=38.99  Aligned_cols=43  Identities=14%  Similarity=0.114  Sum_probs=38.6

Q ss_pred             cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCcee
Q 040620           39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFV   85 (214)
Q Consensus        39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~   85 (214)
                      ..|+..|.++ +++|..|||+.+++++   ..+++.++-|...|++.
T Consensus         6 ~~il~~l~~~-~~~s~~~la~~l~~s~---~~v~~~i~~L~~~g~i~   48 (362)
T PRK09954          6 KEILAILRRN-PLIQQNEIADILQISR---SRVAAHIMDLMRKGRIK   48 (362)
T ss_pred             HHHHHHHHHC-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCcC
Confidence            3477788887 7999999999999999   99999999999999984

>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional

Probab=80.36  E-value=0.66  Score=37.23  Aligned_cols=44  Identities=9%  Similarity=0.070  Sum_probs=39.3

Q ss_pred             CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620           40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ   87 (214)
Q Consensus        40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~   87 (214)
                      .|.++|..+ +.+++++||+.+++++   .-++|=|+.|...|.+...
T Consensus        11 ~Il~~l~~~-~~~~~~~La~~~~vS~---~TiRRDl~~L~~~g~~~r~   54 (185)
T PRK04424         11 ALQELIEEN-PFITDEELAEKFGVSI---QTIRLDRMELGIPELRERI   54 (185)
T ss_pred             HHHHHHHHC-CCEEHHHHHHHHCcCH---HHHHHHHHHHhcchHHHHH
Confidence            356777776 8999999999999999   9999999999999999865

>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins

Probab=80.29  E-value=0.89  Score=33.46  Aligned_cols=61  Identities=20%  Similarity=0.247  Sum_probs=44.3

Q ss_pred             HhcCcchhhhcCCCCCCHHHHHHHcC-----CCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCC
Q 040620           37 IQLRIPDIINNSGQPMTLTQIIVALN-----VHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPP  103 (214)
Q Consensus        37 ~~lglfd~L~~~~~p~t~~eLA~~~g-----~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~  103 (214)
                      -+.-|++.|.+.+++.|++||-+.+.     ++.   ..+.|.|+.|...|++.+....  +. ..+|....
T Consensus         9 ~R~~Il~~l~~~~~~~ta~ei~~~l~~~~~~is~---~TVYR~L~~L~e~Gli~~~~~~--~~-~~~Y~~~~   74 (120)
T PF01475_consen    9 QRLAILELLKESPEHLTAEEIYDKLRKKGPRISL---ATVYRTLDLLEEAGLIRKIEFG--DG-ESRYELST   74 (120)
T ss_dssp             HHHHHHHHHHHHSSSEEHHHHHHHHHHTTTT--H---HHHHHHHHHHHHTTSEEEEEET--TS-EEEEEESS
T ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHhhhccCCcCH---HHHHHHHHHHHHCCeEEEEEcC--CC-cceEeecC
Confidence            34456777877667999999999884     333   5799999999999999987531  11 35677654

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 ....

>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=80.04  E-value=0.61  Score=30.13  Aligned_cols=38  Identities=21%  Similarity=0.307  Sum_probs=29.9

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHH
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLA   79 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~   79 (214)
                      ++.|+++|-++ +.+|+++||+.+++++   +.++..+..|-
T Consensus         7 q~~Ll~~L~~~-~~~~~~ela~~l~~S~---rti~~~i~~L~   44 (59)
T PF08280_consen    7 QLKLLELLLKN-KWITLKELAKKLNISE---RTIKNDINELN   44 (59)
T ss_dssp             HHHHHHHHHHH-TSBBHHHHHHHCTS-H---HHHHHHHHHHH
T ss_pred             HHHHHHHHHcC-CCCcHHHHHHHHCCCH---HHHHHHHHHHH
Confidence            34566777664 8999999999999999   88888877765

; PDB: 2WTE_A 3SQN_A.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	214
2qyo_A	357	Crystal Structure Of Isoflavone O-Methyltransferase		4e-28
1fp2_A	352	Crystal Structure Analysis Of Isoflavone O-Methyltr		4e-28
1fpx_A	352	Crystal Structure Analysis Of Selenomethionine Subs		5e-26
1zgj_A	354	Crystal Structure Of Isoflavanone 4'-O-Methyltransf		1e-18
1zga_A	357	Crystal Structure Of Isoflavanone 4'-o-methyltransf		1e-18
1zg3_A	358	Crystal Structure Of The Isoflavanone 4'-O-Methyltr		1e-18

>pdb|2QYO|A Chain A, Crystal Structure Of Isoflavone O-Methyltransferase Homolog In Complex With Biochanin A And Sah Length = 357

Iteration: 1
 Score =  120 bits (302), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 71/214 (33%), Positives = 118/214 (55%), Gaps = 17/214 (7%)
Query: 12  EHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCT 71
           E F+AQA ++   Y ++ S+SLK +I++ IP+II+N G+P+TL+ ++  L +   K    
Sbjct: 12  EIFKAQALLYKNMYAFVDSMSLKWSIEMNIPNIIHNHGKPITLSNLVSILQIPSTKVDNV 71
Query: 72  QILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISLQLQGSTILLLIADATFTT 131
           Q L+  LAH+GFF    + + E EEE+  L    +   +   +L  + ++  + D T +T
Sbjct: 72  QRLMRYLAHNGFFEIITNQELENEEEAYALTVASELLVK-GTELCLAPMVECVLDPTLST 130
Query: 132 SFHFLSTWLQNDDQTLFGTADG---------------IFYEAMITDFELIASVLIEDCNE 176
           SFH L  W+  +D TLF    G               ++ +A+ +D ++I ++ ++DCN 
Sbjct: 131 SFHNLKKWVYEEDLTLFAVNLGCDLWEFLNKNPEYNTLYNDALASDSKMI-NLAMKDCNL 189
Query: 177 VSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
           V +GL+ +VDVGG  GT  + I   FP   C VF
Sbjct: 190 VFEGLESIVDVGGGNGTTGKIICETFPKLTCVVF 223

>pdb|1FP2|A Chain A, Crystal Structure Analysis Of Isoflavone O-Methyltransferase Length = 352

Iteration: 1
 Score =  120 bits (302), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 78/220 (35%), Positives = 120/220 (54%), Gaps = 24/220 (10%)
Query: 8   NGAR--EHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHP 65
           NG +  E F+AQA ++ + Y ++ S+SLK A+++ IP+II N G+P++L+ ++  L V  
Sbjct: 6   NGRKPSEIFKAQALLYKHIYAFIDSMSLKWAVEMNIPNIIQNHGKPISLSNLVSILQVPS 65
Query: 66  NKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISLQLQGSTILLLIA 125
           +K    + L+  LAH+GFF         +EEES  L    +   R S  L  + ++  + 
Sbjct: 66  SKIGNVRRLMRYLAHNGFFEIIT-----KEEESYALTVASELLVRGS-DLCLAPMVECVL 119
Query: 126 DATFTTSFHFLSTWLQNDDQTLFGTADG---------------IFYEAMITDFELIASVL 170
           D T + S+H L  W+  +D TLFG   G                F +AM +D +LI ++ 
Sbjct: 120 DPTLSGSYHELKKWIYEEDLTLFGVTLGSGFWDFLDKNPEYNTSFNDAMASDSKLI-NLA 178
Query: 171 IEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
           + DC+ V  GL+ +VDVGG TGT A+ I   FP  KC VF
Sbjct: 179 LRDCDFVFDGLESIVDVGGGTGTTAKIICETFPKLKCIVF 218

>pdb|1FPX|A Chain A, Crystal Structure Analysis Of Selenomethionine Substituted Isoflavone O-Methyltransferase Length = 352

Iteration: 1
 Score =  114 bits (284), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 77/220 (35%), Positives = 115/220 (52%), Gaps = 24/220 (10%)
Query: 8   NGAR--EHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHP 65
           NG +  E F+AQA ++ + Y ++ S SLK A++  IP+II N G+P++L+ ++  L V  
Sbjct: 6   NGRKPSEIFKAQALLYKHIYAFIDSXSLKWAVEXNIPNIIQNHGKPISLSNLVSILQVPS 65
Query: 66  NKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISLQLQGSTILLLIA 125
           +K    + L   LAH+GFF         +EEES  L    +   R S  L  +  +  + 
Sbjct: 66  SKIGNVRRLXRYLAHNGFFEIIT-----KEEESYALTVASELLVRGS-DLCLAPXVECVL 119
Query: 126 DATFTTSFHFLSTWLQNDDQTLFGTADG---------------IFYEAMITDFELIASVL 170
           D T + S+H L  W+  +D TLFG   G                F +A  +D +LI ++ 
Sbjct: 120 DPTLSGSYHELKKWIYEEDLTLFGVTLGSGFWDFLDKNPEYNTSFNDAXASDSKLI-NLA 178
Query: 171 IEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
           + DC+ V  GL+ +VDVGG TGT A+ I   FP  KC VF
Sbjct: 179 LRDCDFVFDGLESIVDVGGGTGTTAKIICETFPKLKCIVF 218

>pdb|1ZGJ|A Chain A, Crystal Structure Of Isoflavanone 4'-O-Methyltransferase Complexed With (+)-Pisatin Length = 354

Iteration: 1
 Score = 89.7 bits (221), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 75/224 (33%), Positives = 118/224 (52%), Gaps = 31/224 (13%)
Query: 12  EHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCT 71
           E + AQ  ++ + YN++ S++LK A++L I D I+N G+PMTL+++  +L +HP+K    
Sbjct: 2   ELYHAQIHLYKHVYNFVSSMALKSAMELGIADAIHNHGKPMTLSELASSLKLHPSKVNIL 61
Query: 72  QILVCLLAHSGFF----VQQKDGKNEQEEESILLPPHLDFFSRISLQLQGSTILLLIADA 127
              + LL H+GFF    V+ K+G  E+E    L PP     S++ +  + + +  ++  A
Sbjct: 62  HRFLRLLTHNGFFAKTIVKGKEGDEEEEIAYSLTPP-----SKLLISGKPTCLSSIVKGA 116
Query: 128 TFTTSFHFLST---WLQND-DQTLFGTADG-----------------IFYEAMITDFELI 166
              +S    S+   W   D +QTLF  A G                 +F +AM +D  + 
Sbjct: 117 LHPSSLDMWSSSKKWFNEDKEQTLFECATGESFWDFLNKDSESSTLSMFQDAMASDSRMF 176
Query: 167 ASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
             VL E+   V +GL+ LVDVGG TG + + I   FP  KCTVF
Sbjct: 177 KLVLQEN-KRVFEGLESLVDVGGGTGGVTKLIHEIFPHLKCTVF 219

>pdb|1ZGA|A Chain A, Crystal Structure Of Isoflavanone 4'-o-methyltransferase Complexed With (+)-6a-hydroxymaackiain Length = 357

Iteration: 1
 Score = 89.7 bits (221), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 75/224 (33%), Positives = 118/224 (52%), Gaps = 31/224 (13%)
Query: 12  EHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCT 71
           E + AQ  ++ + YN++ S++LK A++L I D I+N G+PMTL+++  +L +HP+K    
Sbjct: 5   ELYHAQIHLYKHVYNFVSSMALKSAMELGIADAIHNHGKPMTLSELASSLKLHPSKVNIL 64
Query: 72  QILVCLLAHSGFF----VQQKDGKNEQEEESILLPPHLDFFSRISLQLQGSTILLLIADA 127
              + LL H+GFF    V+ K+G  E+E    L PP     S++ +  + + +  ++  A
Sbjct: 65  HRFLRLLTHNGFFAKTIVKGKEGDEEEEIAYSLTPP-----SKLLISGKPTCLSSIVKGA 119
Query: 128 TFTTSFHFLST---WLQND-DQTLFGTADG-----------------IFYEAMITDFELI 166
              +S    S+   W   D +QTLF  A G                 +F +AM +D  + 
Sbjct: 120 LHPSSLDMWSSSKKWFNEDKEQTLFECATGESFWDFLNKDSESSTLSMFQDAMASDSRMF 179
Query: 167 ASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
             VL E+   V +GL+ LVDVGG TG + + I   FP  KCTVF
Sbjct: 180 KLVLQEN-KRVFEGLESLVDVGGGTGGVTKLIHEIFPHLKCTVF 222

>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 = 89.4 bits (220), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 75/224 (33%), Positives = 118/224 (52%), Gaps = 31/224 (13%)
Query: 12  EHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCT 71
           E + AQ  ++ + YN++ S++LK A++L I D I+N G+PMTL+++  +L +HP+K    
Sbjct: 6   ELYHAQIHLYKHVYNFVSSMALKSAMELGIADAIHNHGKPMTLSELASSLKLHPSKVNIL 65
Query: 72  QILVCLLAHSGFF----VQQKDGKNEQEEESILLPPHLDFFSRISLQLQGSTILLLIADA 127
              + LL H+GFF    V+ K+G  E+E    L PP     S++ +  + + +  ++  A
Sbjct: 66  HRFLRLLTHNGFFAKTIVKGKEGDEEEEIAYSLTPP-----SKLLISGKPTCLSSIVKGA 120
Query: 128 TFTTSFHFLST---WLQND-DQTLFGTADG-----------------IFYEAMITDFELI 166
              +S    S+   W   D +QTLF  A G                 +F +AM +D  + 
Sbjct: 121 LHPSSLDMWSSSKKWFNEDKEQTLFECATGESFWDFLNKDSESSTLSMFQDAMASDSRMF 180
Query: 167 ASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
             VL E+   V +GL+ LVDVGG TG + + I   FP  KCTVF
Sbjct: 181 KLVLQEN-KRVFEGLESLVDVGGGTGGVTKLIHEIFPHLKCTVF 223

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	214
1fp2_A	352	Isoflavone O-methyltransferase; protein-product co	6e-42
1zg3_A	358	Isoflavanone 4'-O-methyltransferase; rossman fold,	7e-41
1fp1_D	372	Isoliquiritigenin 2'-O-methyltransferase; protein-	4e-37
3lst_A	348	CALO1 methyltransferase; calicheamicin, enediyne,	8e-35
3reo_A	368	(ISO)eugenol O-methyltransferase; directed evoluti	4e-34
3p9c_A	364	Caffeic acid O-methyltransferase; S-adenosylmethio	2e-33
1qzz_A	374	RDMB, aclacinomycin-10-hydroxylase; anthracycline,	4e-33
3gwz_A	369	MMCR; methyltransferase, mitomycin, S-adenosyl met	2e-31
3i53_A	332	O-methyltransferase; CO-complex, rossmann-like fol	6e-31
2ip2_A	334	Probable phenazine-specific methyltransferase; pyo	2e-30
1tw3_A	360	COMT, carminomycin 4-O-methyltransferase; anthracy	9e-30
1x19_A	359	CRTF-related protein; methyltransferase, bacterioc	1e-27
2r3s_A	335	Uncharacterized protein; methyltransferase domain,	1e-26
3dp7_A	363	SAM-dependent methyltransferase; structural genomi	1e-24
3mcz_A	352	O-methyltransferase; adomet_mtases, S-adenosylmeth	2e-21
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-04

>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 =  144 bits (364), Expect = 6e-42
 Identities = 74/227 (32%), Positives = 115/227 (50%), Gaps = 26/227 (11%)

Query: 1   MDVIHGENGAREHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVA 60
           M          E F+AQA ++ + Y ++ S+SLK A+++ IP+II N G+P++L+ ++  
Sbjct: 1   MASSINGRKPSEIFKAQALLYKHIYAFIDSMSLKWAVEMNIPNIIQNHGKPISLSNLVSI 60

Query: 61  LNVHPNKTRCTQILVCLLAHSGFF--VQQKDGKNEQEEESILLPPHLDFFSRISLQLQGS 118
           L V  +K    + L+  LAH+GFF  + +++        S LL    D      L    +
Sbjct: 61  LQVPSSKIGNVRRLMRYLAHNGFFEIITKEEESYALTVASELLVRGSDL----CL----A 112

Query: 119 TILLLIADATFTTSFHFLSTWLQNDDQTLFGTADG---------------IFYEAMITDF 163
            ++  + D T + S+H L  W+  +D TLFG   G                F +AM +D 
Sbjct: 113 PMVECVLDPTLSGSYHELKKWIYEEDLTLFGVTLGSGFWDFLDKNPEYNTSFNDAMASDS 172

Query: 164 ELIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
           +LI   L + C+ V  GL+ +VDVGG TGT A+ I   FP  KC VF
Sbjct: 173 KLINLALRD-CDFVFDGLESIVDVGGGTGTTAKIICETFPKLKCIVF 218

>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 =  141 bits (357), Expect = 7e-41
 Identities = 70/220 (31%), Positives = 106/220 (48%), Gaps = 23/220 (10%)

Query: 12  EHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCT 71
           E + AQ  ++ + YN++ S++LK A++L I D I+N G+PMTL+++  +L +HP+K    
Sbjct: 6   ELYHAQIHLYKHVYNFVSSMALKSAMELGIADAIHNHGKPMTLSELASSLKLHPSKVNIL 65

Query: 72  QILVCLLAHSGFFVQQK---DGKNEQEEESILLPPHLDFFSRISLQLQGSTILLLIADAT 128
              + LL H+GFF +        +E+EE +  L P              S I+      +
Sbjct: 66  HRFLRLLTHNGFFAKTIVKGKEGDEEEEIAYSLTPPSKLLISGKPTCLSS-IVKGALHPS 124

Query: 129 FTTSFHFLSTWLQND-DQTLFGTADG-----------------IFYEAMITDFELIASVL 170
               +     W   D +QTLF  A G                 +F +AM +D  +   VL
Sbjct: 125 SLDMWSSSKKWFNEDKEQTLFECATGESFWDFLNKDSESSTLSMFQDAMASDSRMFKLVL 184

Query: 171 IEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
            E    V +GL+ LVDVGG TG + + I   FP  KCTVF
Sbjct: 185 QE-NKRVFEGLESLVDVGGGTGGVTKLIHEIFPHLKCTVF 223

>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 =  131 bits (332), Expect = 4e-37
 Identities = 38/218 (17%), Positives = 68/218 (31%), Gaps = 23/218 (10%)

Query: 15  QAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQP---MTLTQIIVALNVHPNKTRCT 71
            A       T N +    L  AI L + +II  +  P   M+ ++I   L      +   
Sbjct: 23  SACLSAMVLTTNLVYPAVLNAAIDLNLFEIIAKATPPGAFMSPSEIASKLPASTQHSDLP 82

Query: 72  QILVCL---LAHSGFFVQQK-DGKNEQEEESILLPPHLDFFSRISLQLQGSTILLLIADA 127
             L  +   LA            ++   E    L     +      +   ++    +   
Sbjct: 83  NRLDRMLRLLASYSVLTSTTRTIEDGGAERVYGLSMVGKYLVPDESRGYLASFTTFLCYP 142

Query: 128 TFTTSFHFLSTWLQNDDQTLFGTADG---------------IFYEAMITDFELIASVLIE 172
                +      + ++D  LF    G               IF ++M+         ++E
Sbjct: 143 ALLQVWMNFKEAVVDEDIDLFKNVHGVTKYEFMGKDKKMNQIFNKSMVDVCATEMKRMLE 202

Query: 173 DCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
                 +G+  LVDVGG +G     I + +P  K   F
Sbjct: 203 IY-TGFEGISTLVDVGGGSGRNLELIISKYPLIKGINF 239

>3lst_A CALO1 methyltransferase; calicheamicin, enediyne, SAH, STRU genomics, PSI-2, protein structure initiative; HET: SAH; 2.40A {Micromonospora echinospora} Length = 348

 Score =  125 bits (316), Expect = 8e-35
 Identities = 36/217 (16%), Positives = 70/217 (32%), Gaps = 32/217 (14%)

Query: 9   GAREHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKT 68
           G  +  Q+   ++     Y  + +L+ A  + + D +     P T  ++  A     +  
Sbjct: 15  GDMDRLQSALALYEEAMGYTYAAALRAAAAVGVADHL--VDGPRTPAELAAATGTDADAL 72

Query: 69  RCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISLQLQGSTILLLIADAT 128
           R    ++ LLA      ++ DG+    ++   L        R    +     +L+  D  
Sbjct: 73  RR---VLRLLAVRDVV-RESDGRFALTDKGAAL--------RSDSPVPARAGILMFTDTM 120

Query: 129 FTTSFHFLSTWLQNDDQTLFGTADG---------------IFYEAMITDFELIASVLIED 173
           F T  H +++ L  +    F    G               ++YE M T       +L   
Sbjct: 121 FWTMSHRVASALGPER-PAFADIFGSSLDAYFDGDAEVEALYYEGMETVSAAEHLILARA 179

Query: 174 CNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
                     + DVGG  G     +    P  +  + 
Sbjct: 180 G--DFPATGTVADVGGGRGGFLLTVLREHPGLQGVLL 214

>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 =  123 bits (311), Expect = 4e-34
 Identities = 43/219 (19%), Positives = 80/219 (36%), Gaps = 22/219 (10%)

Query: 12  EHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQP---MTLTQIIVALNV-HPNK 67
              +A           +  ++LK AI+L + +I+  S  P   ++  +I   L   +P  
Sbjct: 17  SDEEANLFAMQLASAAVLPMALKAAIELDVLEIMAKSVPPSGYISPAEIAAQLPTTNPEA 76

Query: 68  TRCTQILVCLLAHSGFF-VQQKDGKNEQEEESILLPPHLDFFSRISLQLQGSTILLLIAD 126
                 ++ LLA         ++  + + E    L P   F ++    +  +  LLL  D
Sbjct: 77  PVMLDRVLRLLASYSVVTYTLRELPSGKVERLYGLAPVCKFLTKNEDGVSLAPFLLLATD 136

Query: 127 ATFTTSFHFLSTWLQNDDQTLFGTADG---------------IFYEAMITDFELIASVLI 171
                 + +L   +  +    F  A G               +F + M ++  +    ++
Sbjct: 137 KVLLEPWFYLKDAIL-EGGIPFNKAYGMNIFDYHGTDHRINKVFNKGMSSNSTITMKKIL 195

Query: 172 EDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
           E      +GL  +VDVGG TG +A  I   +P      F
Sbjct: 196 EMY-NGFEGLTTIVDVGGGTGAVASMIVAKYPSINAINF 233

>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 =  121 bits (306), Expect = 2e-33
 Identities = 51/229 (22%), Positives = 85/229 (37%), Gaps = 21/229 (9%)

Query: 1   MDVIHGENGAREHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDII-NNSGQPMTLTQIIV 59
           M     +  A     A         + +  ++LK AI+L + +I+    G+ +T T++  
Sbjct: 5   MGSTAADMAASADEDACMFALQLASSSVLPMTLKNAIELGLLEILVAAGGKSLTPTEVAA 64

Query: 60  AL--NVHPNKTRCTQILVCLLAHSGFF-VQQKDGKNEQEEESILLPPHLDFFSRISLQLQ 116
            L    +P        ++ LLA         ++GK+ +   S    P   F +     + 
Sbjct: 65  KLPSAANPEAPDMVDRILRLLASYNVVTCLVEEGKDGRLSRSYGAAPVCKFLTPNEDGVS 124

Query: 117 GSTILLLIADATFTTSFHFLSTWLQNDDQTLFGTADG---------------IFYEAMIT 161
            + + L+  D     S+++L   +  D    F  A G               +F E M  
Sbjct: 125 MAALALMNQDKVLMESWYYLKDAVL-DGGIPFNKAYGMSAFEYHGTDPRFNRVFNEGMKN 183

Query: 162 DFELIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
              +I   L+E      +GL  LVDVGG  G    AIA  +P  K   F
Sbjct: 184 HSIIITKKLLELY-HGFEGLGTLVDVGGGVGATVAAIAAHYPTIKGVNF 231

>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 =  121 bits (305), Expect = 4e-33
 Identities = 38/225 (16%), Positives = 69/225 (30%), Gaps = 28/225 (12%)

Query: 1   MDVIHGENGAREHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVA 60
           M             Q    +     N +  ++L+ A  LR+ D +       TL  +   
Sbjct: 1   MSSSSPGEPLEPTDQDLDVLLKNLGNLVTPMALRVAATLRLVDHL--LAGADTLAGLADR 58

Query: 61  LNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISLQLQGSTI 120
            + HP   +    LV  L   G          E++   +         +      Q + +
Sbjct: 59  TDTHP---QALSRLVRHLTVVGVLEGG-----EKQGRPLRPTRLGMLLADGHPAQQRAWL 110

Query: 121 LLLIADATFTTSFHFLSTWLQNDDQTLFGTADG---------------IFYEAMITDFEL 165
            L  A +    +F  L   ++   +  +    G                F   M  D +L
Sbjct: 111 DLNGAVSHADLAFTGLLDVVR-TGRPAYAGRYGRPFWEDLSADVALADSFDALMSCDEDL 169

Query: 166 IASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
                 +  +     ++ ++DVGG  G M  AIA   P  + T+ 
Sbjct: 170 AYEAPADAYD--WSAVRHVLDVGGGNGGMLAAIALRAPHLRGTLV 212

>3gwz_A MMCR; methyltransferase, mitomycin, S-adenosyl methionine, transferase; HET: MSE SAH; 1.91A {Streptomyces lavendulae} PDB: 3gxo_A* Length = 369

 Score =  116 bits (293), Expect = 2e-31
 Identities = 44/215 (20%), Positives = 75/215 (34%), Gaps = 38/215 (17%)

Query: 15  QAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQIL 74
            A+  V        K+ ++  A++L +P+++     P T T +  A   H    R    L
Sbjct: 37  AAEETVNDILQGAWKARAIHVAVELGVPELL--QEGPRTATALAEATGAHEQTLRR---L 91

Query: 75  VCLLAHSGFFVQ-QKDGKNEQEEESILL---PPHLDFFSRISLQLQGSTILLLIADATFT 130
           + LLA  G F     D    Q   S +L   P          +    +T     A     
Sbjct: 92  LRLLATVGVFDDLGHDDLFAQNALSAVLLPDPAS-------PV----ATDARFQAAPWHW 140

Query: 131 TSFHFLSTWLQNDDQTLFGTADG---------------IFYEAMITDFELIASVLIEDCN 175
            ++  L+  ++  +   F  A+G               +F  AM +     A  +     
Sbjct: 141 RAWEQLTHSVRTGE-ASFDVANGTSFWQLTHEDPKARELFNRAMGSVSLTEAGQVAAAY- 198

Query: 176 EVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
               G    VD+GG  G++  A+  AFP  + T+ 
Sbjct: 199 -DFSGAATAVDIGGGRGSLMAAVLDAFPGLRGTLL 232

>3i53_A O-methyltransferase; CO-complex, rossmann-like fold; HET: SAH; 2.08A {Streptomyces carzinostaticus subsp} PDB: 3i58_A* 3i5u_A* 3i64_A* Length = 332

 Score =  114 bits (288), Expect = 6e-31
 Identities = 40/211 (18%), Positives = 66/211 (31%), Gaps = 30/211 (14%)

Query: 15  QAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQIL 74
           +A         +    ++++ A  LR+ D I  +    T  +I  A   H +     ++L
Sbjct: 4   RAAHIGLRALADLATPMAVRVAATLRVADHI--AAGHRTAAEIASAAGAHADSLD--RLL 59

Query: 75  VCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISLQLQGSTILLLIADATFTTSFH 134
              L   G F +   G     E    L        R         + +  A       F 
Sbjct: 60  -RHLVAVGLFTRDGQGVYGLTEFGEQLRDDHAAGKR-------KWLDMNSAVGRGDLGFV 111

Query: 135 FLSTWLQNDDQTLFGTADG---------------IFYEAMITDFELIASVLIEDCNEVSK 179
            L+  ++   Q  +    G                F   M    EL  + +    +    
Sbjct: 112 ELAHSIR-TGQPAYPVRYGTSFWEDLGSDPVLSASFDTLMSHHLELDYTGIAAKYD--WA 168

Query: 180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
            L  +VDVGG +G +  A+ TA  D   TV 
Sbjct: 169 ALGHVVDVGGGSGGLLSALLTAHEDLSGTVL 199

>2ip2_A Probable phenazine-specific methyltransferase; pyocyanin, phenazine-1-carboxy PHZM; 1.80A {Pseudomonas aeruginosa} Length = 334

 Score =  113 bits (284), Expect = 2e-30
 Identities = 36/211 (17%), Positives = 59/211 (27%), Gaps = 33/211 (15%)

Query: 14  FQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQI 73
             A   +        KS  +  A +L + D+I       +   +  A+            
Sbjct: 6   LAAARNLIQVVTGEWKSRCVYVATRLGLADLI--ESGIDSDETLAAAVGSDA---ERIHR 60

Query: 74  LVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISLQLQGSTILLLIADATFTTSF 133
           L+ LL     F             S LL      F            ++L     F  ++
Sbjct: 61  LMRLLVAFEIFQGDTRDGYANTPTSHLLRDVEGSFRD----------MVLFYGEEFHAAW 110

Query: 134 HFLSTWLQNDD---QTLFGT-----------ADGIFYEAMITDFELIASVLIEDCNEVSK 179
                 L +     +  FG            A   F  AM     L    +    +    
Sbjct: 111 TPACEALLSGTPGFELAFGEDFYSYLKRCPDAGRRFLLAM-KASNLAFHEIPRLLDF--- 166

Query: 180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
             +  VDVGG +G + +AI  A P  +  + 
Sbjct: 167 RGRSFVDVGGGSGELTKAILQAEPSARGVML 197

>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 =  112 bits (281), Expect = 9e-30
 Identities = 38/216 (17%), Positives = 64/216 (29%), Gaps = 30/216 (13%)

Query: 10  AREHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTR 69
           AR       +      +    + ++ A  LR+ D I       T+  +    +  P    
Sbjct: 13  ARPQQIDALRTLIRLGSLHTPMVVRTAATLRLVDHI--LAGARTVKALAARTDTRP---E 67

Query: 70  CTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISLQLQGSTILLLIADATF 129
               L+  L   G   +   G+    E   LL        R       +   L  A A  
Sbjct: 68  ALLRLIRHLVAIGLLEEDAPGEFVPTEVGELLADDHPAAQR-------AWHDLTQAVARA 120

Query: 130 TTSFHFLSTWLQNDDQTLFGTADG---------------IFYEAMITDFELIASVLIEDC 174
             SF  L   ++   +  + +  G                F   +  D ++         
Sbjct: 121 DISFTRLPDAIRTG-RPTYESIYGKPFYEDLAGRPDLRASFDSLLACDQDVAFDAPAAAY 179

Query: 175 NEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
           +     ++ ++DVGG  G  A AIA   P    TV 
Sbjct: 180 D--WTNVRHVLDVGGGKGGFAAAIARRAPHVSATVL 213

>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 =  106 bits (267), Expect = 1e-27
 Identities = 28/212 (13%), Positives = 69/212 (32%), Gaps = 30/212 (14%)

Query: 12  EHFQAQAQVWSYTYN-YMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRC 70
           +      +     +   ++   +K AI+L +   +  +  P  L  +       P +   
Sbjct: 26  DLLNYYHRANELVFKGLIEFSCMKAAIELDLFSHM--AEGPKDLATLAADTGSVPPRLE- 82

Query: 71  TQILVCLLAHSGFFVQQKDG-----------KNEQEEESILLPPHLDFFSRISLQLQGST 119
             +L+  L        +                  +E ++   P     + ++       
Sbjct: 83  --MLLETLRQMRVINLEDGKWSLTEFADYMFSPTPKEPNLHQTPVAKAMAFLADDFYMG- 139

Query: 120 ILLLIADATFT-TSFHFLSTWLQNDDQTLFGTADGIFYEAMITDFELIASVLIEDCNEVS 178
               ++ A     +F     +     +      +  F E   ++ +    +L+E+     
Sbjct: 140 ----LSQAVRGQKNFKGQVPYPPVTRE-----DNLYFEEIHRSNAKFAIQLLLEEAK--L 188

Query: 179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
            G+K ++DVGG  G ++ A+   FP+   T+ 
Sbjct: 189 DGVKKMIDVGGGIGDISAAMLKHFPELDSTIL 220

>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 =  103 bits (259), Expect = 1e-26
 Identities = 35/203 (17%), Positives = 65/203 (32%), Gaps = 21/203 (10%)

Query: 16  AQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILV 75
           + A  ++    Y +S ++K A++L +   I  S    +   +           R   +L 
Sbjct: 6   SPALFFNTVNAYQRSAAIKAAVELNVFTAI--SQGIESSQSLAQKCQTSERGMR---MLC 60

Query: 76  CLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISLQLQGSTILLLIADATFTTSFHF 135
             L   GF  +Q +G         L      F  R S    G   +  +     T  F+ 
Sbjct: 61  DYLVIIGFMTKQAEG-------YRLTSDSAMFLDRQSKFYVGD-AIEFLLSPMITNGFND 112

Query: 136 LSTWLQNDDQTLFGT--------ADGIFYEAMITDFELIASVLIEDCNEVSKGLKPLVDV 187
           L+  +      +               F +AM       A ++ +  NE       ++D+
Sbjct: 113 LTAAVLKGGTAISSEGTLSPEHPVWVQFAKAMSPMMANPAQLIAQLVNENKIEPLKVLDI 172

Query: 188 GGSTGTMARAIATAFPDTKCTVF 210
             S G    A+A   P+ +    
Sbjct: 173 SASHGLFGIAVAQHNPNAEIFGV 195

>3dp7_A SAM-dependent methyltransferase; structural genomics, protein structure initiative, NEW YORK structural genomix research; 2.33A {Bacteroides vulgatus} Length = 363

 Score = 98.6 bits (246), Expect = 1e-24
 Identities = 30/214 (14%), Positives = 63/214 (29%), Gaps = 34/214 (15%)

Query: 14  FQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQI 73
            +AQ       +  +     +  ++  I  +++   +  TL +I     +     +   +
Sbjct: 13  AEAQRLAQEIAFGPVVFQVSRLMLKFGIFQLLSGKREGYTLQEISGRTGLTRYAAQ---V 69

Query: 74  LVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISLQLQGSTILLLIADATFTTSF 133
           L+      G            EE+  +L     F     L  + + + +           
Sbjct: 70  LLEASLTIGTI--------LLEEDRYVLAKAGWFL----LNDKMARVNMEFNHDVNYQGL 117

Query: 134 HFLSTWLQNDD---QTLFGTADGIF-------------YEAMITDF-ELIASVLIEDCNE 176
             L   L N       +FG    I+             +      + +      +E    
Sbjct: 118 FHLEEALLNGRPEGLKVFGEWPTIYEGLSQLPEQVQKSWFGFDHFYSDQSFGKALEIVF- 176

Query: 177 VSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
            S   K L+D+GG+TG  A        + + T+ 
Sbjct: 177 -SHHPKRLLDIGGNTGKWATQCVQYNKEVEVTIV 209

>3mcz_A O-methyltransferase; adomet_mtases, S-adenosylmethionine-dependent methyltransfer structural genomics, PSI-2; HET: MSE; 1.90A {Burkholderia thailandensis} Length = 352

 Score = 89.4 bits (222), Expect = 2e-21
 Identities = 27/209 (12%), Positives = 65/209 (31%), Gaps = 27/209 (12%)

Query: 11  REHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRC 70
           +    +   +   +  Y +S  L  A+  ++ D+        T  ++  +  +   K   
Sbjct: 19  KAALTSVVDLVKLSDQYRQSAILHYAVADKLFDLT---QTGRTPAEVAASFGMVEGKAA- 74

Query: 71  TQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISLQLQGSTILLLIADATFT 130
             IL+  LA  G          ++ +          + +  S    G    ++       
Sbjct: 75  --ILLHALAALGLLT-------KEGDAFRNTALTERYLTTTSADYIGP---IVEHQYLQW 122

Query: 131 TSFHFLSTWLQNDDQTLFGTAD---------GIFYEAMITDFELIASVLIEDCNEVSKGL 181
            ++  L   L+++    F               F +AM+   + +  V+ E         
Sbjct: 123 DNWPRLGEILRSEKPLAFQQESRFAHDTRARDAFNDAMVRLSQPMVDVVSELGVF--ARA 180

Query: 182 KPLVDVGGSTGTMARAIATAFPDTKCTVF 210
           + ++D+ G  GT    +    P     ++
Sbjct: 181 RTVIDLAGGHGTYLAQVLRRHPQLTGQIW 209

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 39.8 bits (92), Expect = 4e-04
 Identities = 32/212 (15%), Positives = 57/212 (26%), Gaps = 67/212 (31%)

Query: 21  WSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVAL-----NVH-PNKT------ 68
           W   + ++    L   I+  +     N  +P    ++   L     + H P         
Sbjct: 344 WDN-WKHVNCDKLTTIIESSL-----NVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWF 397

Query: 69  ----RCTQILVCLLA----------------HSGFFVQQKDGKNEQEEESILL------- 101
                   ++V  L                  S +   +   +NE      ++       
Sbjct: 398 DVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPK 457

Query: 102 --------PPHLD--FFSRISLQLQGSTILLLIADATFTT---SFHFLSTWLQNDDQTLF 148
                   PP+LD  F+S I   L    I        F      F FL   +++D     
Sbjct: 458 TFDSDDLIPPYLDQYFYSHIGHHL--KNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWN 515

Query: 149 GTA-------DGIFYEAMITDFELIASVLIED 173
            +           FY+  I D +     L+  
Sbjct: 516 ASGSILNTLQQLKFYKPYICDNDPKYERLVNA 547

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	214
4a6d_A	353	Hydroxyindole O-methyltransferase; melatonin, circ	99.97
3p9c_A	364	Caffeic acid O-methyltransferase; S-adenosylmethio	99.97
3lst_A	348	CALO1 methyltransferase; calicheamicin, enediyne,	99.97
3reo_A	368	(ISO)eugenol O-methyltransferase; directed evoluti	99.96
1fp2_A	352	Isoflavone O-methyltransferase; protein-product co	99.96
1zg3_A	358	Isoflavanone 4'-O-methyltransferase; rossman fold,	99.96
3gwz_A	369	MMCR; methyltransferase, mitomycin, S-adenosyl met	99.96
2ip2_A	334	Probable phenazine-specific methyltransferase; pyo	99.96
3i53_A	332	O-methyltransferase; CO-complex, rossmann-like fol	99.95
1fp1_D	372	Isoliquiritigenin 2'-O-methyltransferase; protein-	99.95
3dp7_A	363	SAM-dependent methyltransferase; structural genomi	99.95
3mcz_A	352	O-methyltransferase; adomet_mtases, S-adenosylmeth	99.94
1x19_A	359	CRTF-related protein; methyltransferase, bacterioc	99.94
1qzz_A	374	RDMB, aclacinomycin-10-hydroxylase; anthracycline,	99.93
2r3s_A	335	Uncharacterized protein; methyltransferase domain,	99.93
1tw3_A	360	COMT, carminomycin 4-O-methyltransferase; anthracy	99.93
2qm3_A	373	Predicted methyltransferase; putative methyltransf	98.62
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	97.59
3mq2_A	218	16S rRNA methyltransferase; methyltranferase, ribo	97.49
3e05_A	204	Precorrin-6Y C5,15-methyltransferase (decarboxyla;	97.44
2fca_A	213	TRNA (guanine-N(7)-)-methyltransferase; 2.10A {Bac	97.43
3g07_A	292	7SK snRNA methylphosphate capping enzyme; structur	97.4
4dzr_A	215	Protein-(glutamine-N5) methyltransferase, release	97.37
1y0u_A	96	Arsenical resistance operon repressor, putative; s	97.37
3dxy_A	218	TRNA (guanine-N(7)-)-methyltransferase; rossmann f	97.37
1yzh_A	214	TRNA (guanine-N(7)-)-methyltransferase; alpha-beta	97.37
3dtn_A	234	Putative methyltransferase MM_2633; structural gen	97.32
3jwh_A	217	HEN1; methyltransferase; HET: SAH; 2.20A {Anabaena	97.3
3mq0_A	275	Transcriptional repressor of the blcabc operon; he	97.3
2p35_A	259	Trans-aconitate 2-methyltransferase; SAM dependent	97.26
3jwg_A	219	HEN1, methyltransferase type 12; 1.90A {Clostridiu	97.26
3ckk_A	235	TRNA (guanine-N(7)-)-methyltransferase; mettl1, S-	97.25
3bkx_A	275	SAM-dependent methyltransferase; YP_807781.1, cycl	97.24
2vdv_E	246	TRNA (guanine-N(7)-)-methyltransferase; S-adenosyl	97.21
3hem_A	302	Cyclopropane-fatty-acyl-phospholipid synthase 2; p	97.17
3g89_A	249	Ribosomal RNA small subunit methyltransferase G; 1	97.13
3mgg_A	276	Methyltransferase; NYSGXRC, PSI-II, protein struct	97.12
1jsx_A	207	Glucose-inhibited division protein B; methyltransf	97.11
3dh0_A	219	SAM dependent methyltransferase; cystal structure,	97.1
4gek_A	261	TRNA (CMO5U34)-methyltransferase; structural genom	97.09
3bus_A	273	REBM, methyltransferase; rebeccamycin synthesis; H	97.08
1fbn_A	230	MJ fibrillarin homologue; MJ proteins, ribosomal R	97.04
3r4k_A	260	Transcriptional regulator, ICLR family; DNA/RNA-bi	97.03
3g5t_A	299	Trans-aconitate 3-methyltransferase; structural ge	97.02
4dcm_A	375	Ribosomal RNA large subunit methyltransferase G; 2	97.02
3dlc_A	219	Putative S-adenosyl-L-methionine-dependent methylt	97.02
1nkv_A	256	Hypothetical protein YJHP; structural genomics, PS	97.02
2b3t_A	276	Protein methyltransferase HEMK; translation termin	97.0
3ujc_A	266	Phosphoethanolamine N-methyltransferase; parasite;	96.99
3mb5_A	255	SAM-dependent methyltransferase; RNA methyltransfe	96.99
3dli_A	240	Methyltransferase; PSI-II, NYSGXRC, structural gen	96.98
1xdz_A	240	Methyltransferase GIDB; MCSG, protein structure in	96.97
3f4k_A	257	Putative methyltransferase; structural genomics, P	96.94
3ou2_A	218	SAM-dependent methyltransferase; O-methyltransfera	96.93
1nt2_A	210	Fibrillarin-like PRE-rRNA processing protein; adeM	96.93
3ege_A	261	Putative methyltransferase from antibiotic biosyn	96.92
1nv8_A	284	HEMK protein; class I adoMet-dependent methyltrans	96.92
1kpg_A	287	CFA synthase;, cyclopropane-fatty-acyl-phospholipi	96.91
2xrn_A	241	HTH-type transcriptional regulator TTGV; DNA-bindi	96.91
3tfw_A	248	Putative O-methyltransferase; PSI-biology, nysgrc,	96.9
2yxd_A	183	Probable cobalt-precorrin-6Y C(15)-methyltransfer	96.89
2o57_A	297	Putative sarcosine dimethylglycine methyltransfera	96.88
1u2z_A	433	Histone-lysine N-methyltransferase, H3 lysine-79 s	96.88
1vl5_A	260	Unknown conserved protein BH2331; putative methylt	96.87
1yb2_A	275	Hypothetical protein TA0852; structural genomics,	96.87
3b73_A	111	PHIH1 repressor-like protein; winged-helix-turn-he	96.86
2pjd_A	343	Ribosomal RNA small subunit methyltransferase C; g	96.85
1jg1_A	235	PIMT;, protein-L-isoaspartate O-methyltransferase;	96.85
3kkz_A	267	Uncharacterized protein Q5LES9; putative methyltra	96.84
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	96.84
1ve3_A	227	Hypothetical protein PH0226; dimer, riken structur	96.81
3vc1_A	312	Geranyl diphosphate 2-C-methyltransferase; rossman	96.79
2fk8_A	318	Methoxy mycolic acid synthase 4; S-adenosylmethion	96.77
3fzg_A	200	16S rRNA methylase; methyltransferase, plasmid, tr	96.77
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	96.76
1mkm_A	249	ICLR transcriptional regulator; structural genomic	96.76
2pwy_A	258	TRNA (adenine-N(1)-)-methyltransferase; mtase, ado	96.75
3g5l_A	253	Putative S-adenosylmethionine dependent methyltran	96.75
2yxe_A	215	Protein-L-isoaspartate O-methyltransferase; rossma	96.74
2ozv_A	260	Hypothetical protein ATU0636; structural genomics,	96.74
2ipx_A	233	RRNA 2'-O-methyltransferase fibrillarin; FBL, stru	96.73
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	96.73
2h00_A	254	Methyltransferase 10 domain containing protein; st	96.73
2esr_A	177	Methyltransferase; structural genomics, hypothetic	96.71
2gpy_A	233	O-methyltransferase; structural genomics, PSI, pro	96.71
3ntv_A	232	MW1564 protein; rossmann fold, putative methyltran	96.7
3iv6_A	261	Putative Zn-dependent alcohol dehydrogenase; alpha	96.69
1m6y_A	301	S-adenosyl-methyltransferase MRAW; SAM-dependent m	96.69
1o54_A	277	SAM-dependent O-methyltransferase; TM0748, structu	96.67
3uwp_A	438	Histone-lysine N-methyltransferase, H3 lysine-79;	96.64
2g7u_A	257	Transcriptional regulator; ICLR family, structural	96.64
3njr_A	204	Precorrin-6Y methylase; methyltransferase, decarbo	96.64
3duw_A	223	OMT, O-methyltransferase, putative; alternating of	96.64
1ws6_A	171	Methyltransferase; structural genomics, riken stru	96.63
2qe6_A	274	Uncharacterized protein TFU_2867; putative methylt	96.63
3ccf_A	279	Cyclopropane-fatty-acyl-phospholipid synthase; YP_	96.62
2o0y_A	260	Transcriptional regulator; ICLR-family, structural	96.62
3tr6_A	225	O-methyltransferase; cellular processes; HET: SAH;	96.62
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	96.62
3ggd_A	245	SAM-dependent methyltransferase; YP_325210.1, stru	96.62
2bm8_A	236	Cephalosporin hydroxylase CMCI; cephamycin biosynt	96.61
1o9g_A	250	RRNA methyltransferase; antibiotic resistance, Se-	96.59
3gjy_A	317	Spermidine synthase; APC62791, structural genomics	96.58
1xmk_A	79	Double-stranded RNA-specific adenosine deaminase;	96.58
3orh_A	236	Guanidinoacetate N-methyltransferase; structura ge	96.58
2xvm_A	199	Tellurite resistance protein TEHB; antibiotic resi	96.56
3opn_A	232	Putative hemolysin; structural genomics, PSI-2, pr	96.56
3grz_A	205	L11 mtase, ribosomal protein L11 methyltransferase	96.56
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	96.56
3hnr_A	220	Probable methyltransferase BT9727_4108; structural	96.55
3c3p_A	210	Methyltransferase; NP_951602.1, structural genomic	96.55
1dus_A	194	MJ0882; hypothetical protein, methanococcus jannas	96.54
1u2w_A	122	CADC repressor, cadmium efflux system accessory pr	96.54
2nxc_A	254	L11 mtase, ribosomal protein L11 methyltransferase	96.53
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	96.53
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	96.52
3cc8_A	230	Putative methyltransferase; structural genomics, j	96.52
1qam_A	244	ERMC' methyltransferase; rRNA methyltransferase ER	96.52
2fhp_A	187	Methylase, putative; alpha-beta-alpha sandwich, st	96.5
2pxx_A	215	Uncharacterized protein MGC2408; structural genomi	96.5
3jth_A	98	Transcription activator HLYU; transcription factor	96.48
1xtp_A	254	LMAJ004091AAA; SGPP, structural genomics, PSI, pro	96.48
3pfg_A	263	N-methyltransferase; N,N-dimethyltransferase, SAM	96.46
3bja_A	139	Transcriptional regulator, MARR family, putative;	96.44
1i9g_A	280	Hypothetical protein RV2118C; mtase, adoMet, cryst	96.44
2ia2_A	265	Putative transcriptional regulator; SAD, PSI-2, st	96.44
2p7i_A	250	Hypothetical protein; putative methyltransferase,	96.43
3adn_A	294	Spermidine synthase; aminopropyltransferase, polya	96.41
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	96.41
1p91_A	269	Ribosomal RNA large subunit methyltransferase A; R	96.41
3ftd_A	249	Dimethyladenosine transferase; KSGA, rossmann-like	96.41
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	96.41
1g8a_A	227	Fibrillarin-like PRE-rRNA processing protein; rRNA	96.4
3lbf_A	210	Protein-L-isoaspartate O-methyltransferase; modifi	96.4
1sui_A	247	Caffeoyl-COA O-methyltransferase; rossmann fold, p	96.39
3r3h_A	242	O-methyltransferase, SAM-dependent; structural gen	96.38
3e8s_A	227	Putative SAM dependent methyltransferase; NP_74470	96.37
3thr_A	293	Glycine N-methyltransferase; GNMT, folate, methylt	96.37
3tma_A	354	Methyltransferase; thump domain; 2.05A {Thermus th	96.36
1wzn_A	252	SAM-dependent methyltransferase; structural genomi	96.34
3bxo_A	239	N,N-dimethyltransferase; desosamine, sugar, carboh	96.34
3uzu_A	279	Ribosomal RNA small subunit methyltransferase A; s	96.33
2hnk_A	239	SAM-dependent O-methyltransferase; modified rossma	96.31
2pbf_A	227	Protein-L-isoaspartate O-methyltransferase beta-A	96.31
1i1n_A	226	Protein-L-isoaspartate O-methyltransferase; S-aden	96.29
3dr5_A	221	Putative O-methyltransferase; Q8NRD3, CGL1119, PF0	96.29
3u81_A	221	Catechol O-methyltransferase; neurotransmitter deg	96.29
1l3i_A	192	Precorrin-6Y methyltransferase/putative decarboxyl	96.28
2avd_A	229	Catechol-O-methyltransferase; structural genomics,	96.28
3ocj_A	305	Putative exported protein; structural genomics, PS	96.26
2yqz_A	263	Hypothetical protein TTHA0223; RNA methyltransfera	96.26
2hzt_A	107	Putative HTH-type transcriptional regulator YTCD;	96.25
1vbf_A	231	231AA long hypothetical protein-L-isoaspartate O-	96.25
3lpm_A	259	Putative methyltransferase; structural genomics, p	96.24
1dl5_A	317	Protein-L-isoaspartate O-methyltransferase; isoasp	96.24
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	96.23
3bgv_A	313	MRNA CAP guanine-N7 methyltransferase; alternative	96.23
3fpf_A	298	Mtnas, putative uncharacterized protein; thermonic	96.21
4fsd_A	383	Arsenic methyltransferase; rossmann fold; 1.75A {C	96.2
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	96.2
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	96.2
4a5n_A	131	Uncharacterized HTH-type transcriptional regulato;	96.19
3bwc_A	304	Spermidine synthase; SAM, SGPP, structura genomics	96.18
3k0l_A	162	Repressor protein; helix-turn-helix, structural ge	96.17
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	96.17
3sm3_A	235	SAM-dependent methyltransferases; NESG, structural	96.16
3b3j_A	480	Histone-arginine methyltransferase CARM1; protein	96.15
2b25_A	336	Hypothetical protein; structural genomics, methyl	96.15
3e23_A	211	Uncharacterized protein RPA2492; alpha-beta protei	96.15
2y75_A	129	HTH-type transcriptional regulator CYMR; DNA bindi	96.14
2kko_A	108	Possible transcriptional regulatory protein (possi	96.13
3c3y_A	237	Pfomt, O-methyltransferase; plant secondary metabo	96.12
2gxg_A	146	146AA long hypothetical transcriptional regulator;	96.11
3m70_A	286	Tellurite resistance protein TEHB homolog; structu	96.11
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	96.11
1iy9_A	275	Spermidine synthase; rossmann fold, structural gen	96.11
3a27_A	272	TYW2, uncharacterized protein MJ1557; wybutosine m	96.1
1xj5_A	334	Spermidine synthase 1; structural genomics, protei	96.08
4e2x_A	416	TCAB9; kijanose, tetronitrose, tetradeoxy sugar, s	96.07
3cbg_A	232	O-methyltransferase; cyanobacterium; HET: SAH FER	96.06
3l8d_A	242	Methyltransferase; structural genomics, PSI, nysgr	96.06
1zq9_A	285	Probable dimethyladenosine transferase; SGC, struc	96.05
1ub9_A	100	Hypothetical protein PH1061; helix-turn-helix moti	96.05
1s3j_A	155	YUSO protein; structural genomics, MARR transcript	96.04
3bkw_A	243	MLL3908 protein, S-adenosylmethionine dependent me	96.01
3gru_A	295	Dimethyladenosine transferase; rossman fold, ribos	96.0
1ne2_A	200	Hypothetical protein TA1320; structural genomics,	96.0
3p9n_A	189	Possible methyltransferase (methylase); RV2966C, a	96.0
1inl_A	296	Spermidine synthase; beta-barrel, rossman fold, st	95.99
3h2b_A	203	SAM-dependent methyltransferase; alpha-beta protei	95.98
3f6o_A	118	Probable transcriptional regulator, ARSR family pr	95.98
4htf_A	285	S-adenosylmethionine-dependent methyltransferase;	95.96
2y1w_A	348	Histone-arginine methyltransferase CARM1; histone	95.96
2pt6_A	321	Spermidine synthase; transferase, structural genom	95.96
2fyt_A	340	Protein arginine N-methyltransferase 3; structural	95.95
3fut_A	271	Dimethyladenosine transferase; methyltransferase,	95.94
1yub_A	245	Ermam, rRNA methyltransferase; MLS antibiotics; NM	95.94
2ih2_A	421	Modification methylase TAQI; DNA, DNA methyltransf	95.93
1uir_A	314	Polyamine aminopropyltransferase; spermidien synth	95.93
3m33_A	226	Uncharacterized protein; structural genomics, PSI-	95.92
2o07_A	304	Spermidine synthase; structural genomics, structur	95.91
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	95.91
2yvl_A	248	TRMI protein, hypothetical protein; tRNA, methyltr	95.91
2i7c_A	283	Spermidine synthase; transferase, structural genom	95.91
2jsc_A	118	Transcriptional regulator RV1994C/MT2050; cadmium,	95.91
3hp7_A	291	Hemolysin, putative; structural genomics, APC64019	95.9
4hg2_A	257	Methyltransferase type 11; structural genomics, PS	95.89
1mjf_A	281	Spermidine synthase; spermidine synthetase, struct	95.88
3evz_A	230	Methyltransferase; NYSGXRC, NEW YORK SGX research	95.87
1y8c_A	246	S-adenosylmethionine-dependent methyltransferase;	95.86
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	95.85
1zx0_A	236	Guanidinoacetate N-methyltransferase; structural g	95.83
3q7e_A	349	Protein arginine N-methyltransferase 1; HET: SAH;	95.83
1on2_A	142	Transcriptional regulator MNTR; helix-turn-helix,	95.82
1wy7_A	207	Hypothetical protein PH1948; seven-stranded beta s	95.81
3g2m_A	299	PCZA361.24; SAM-dependent methyltransferase, glyco	95.81
2b2c_A	314	Spermidine synthase; beta-alpha, transferase; 2.50	95.8
3tqs_A	255	Ribosomal RNA small subunit methyltransferase A; p	95.79
2ex4_A	241	Adrenal gland protein AD-003; methyltransferase, s	95.78
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	95.78
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	95.76
2nnn_A	140	Probable transcriptional regulator; structural gen	95.74
3kp7_A	151	Transcriptional regulator TCAR; multiple drug resi	95.74
2nyx_A	168	Probable transcriptional regulatory protein, RV14;	95.72
3cgg_A	195	SAM-dependent methyltransferase; NP_600671.1, meth	95.71
3r0a_A	123	Putative transcriptional regulator; structural gen	95.69
3lcc_A	235	Putative methyl chloride transferase; halide methy	95.69
3g3z_A	145	NMB1585, transcriptional regulator, MARR family; t	95.68
2hr3_A	147	Probable transcriptional regulator; MCSG, structur	95.68
2gb4_A	252	Thiopurine S-methyltransferase; 18204406, thiopuri	95.68
2wte_A	244	CSA3; antiviral protein, viral resistance, winged	95.68
3deu_A	166	Transcriptional regulator SLYA; MARR, WING-helix,	95.67
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	95.67
2frn_A	278	Hypothetical protein PH0793; structural genomics,	95.66
3e6m_A	161	MARR family transcriptional regulator; APC88769, s	95.65
2ift_A	201	Putative methylase HI0767; NESG, Y767_haein, struc	95.65
1ixk_A	315	Methyltransferase; open beta sheet; 1.90A {Pyrococ	95.64
3fm5_A	150	Transcriptional regulator; MCSG, PF04017, PSI, MAR	95.62
3bzb_A	281	Uncharacterized protein; RED ALGA, protein structu	95.62
2eth_A	154	Transcriptional regulator, putative, MAR family; M	95.61
3gdh_A	241	Trimethylguanosine synthase homolog; M7G, CAP, dim	95.6
2aot_A	292	HMT, histamine N-methyltransferase; classic methyl	95.6
3bj6_A	152	Transcriptional regulator, MARR family; helix-turn	95.59
1g6q_1	328	HnRNP arginine N-methyltransferase; SAM-binding do	95.59
3f6v_A	151	Possible transcriptional regulator, ARSR family pr	95.57
1r18_A	227	Protein-L-isoaspartate(D-aspartate)-O-methyltrans;	95.56
3d2l_A	243	SAM-dependent methyltransferase; ZP_00538691.1, st	95.56
3cdh_A	155	Transcriptional regulator, MARR family; helix-turn	95.55
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	95.55
3ajd_A	274	Putative methyltransferase MJ0026; tRNA, M5C, ross	95.54
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	95.54
2zfu_A	215	Nucleomethylin, cerebral protein 1; nucleolar prot	95.54
3tm4_A	373	TRNA (guanine N2-)-methyltransferase TRM14; rossma	95.52
3ofk_A	216	Nodulation protein S; NODS, N-methyltransferase, S	95.52
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	95.52
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	95.51
1lj9_A	144	Transcriptional regulator SLYA; HTH DNA binding pr	95.51
3boq_A	160	Transcriptional regulator, MARR family; MARR famil	95.49
2fpo_A	202	Methylase YHHF; structural genomics, putative meth	95.48
3id6_C	232	Fibrillarin-like rRNA/TRNA 2'-O-methyltransferase;	95.48
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	95.45
3s2w_A	159	Transcriptional regulator, MARR family; structural	95.44
1ri5_A	298	MRNA capping enzyme; methyltransferase, M7G, messe	95.44
1r7j_A	95	Conserved hypothetical protein SSO10A; winged heli	95.44
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	95.41
4azs_A	569	Methyltransferase WBDD; kinase; HET: AMP SAM; 2.15	95.38
2h1r_A	299	Dimethyladenosine transferase, putative; SGC toron	95.37
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	95.36
3cjn_A	162	Transcriptional regulator, MARR family; silicibact	95.35
3r0q_C	376	Probable protein arginine N-methyltransferase 4.2;	95.34
2avn_A	260	Ubiquinone/menaquinone biosynthesis methyltransfe	95.34
1yyv_A	131	Putative transcriptional regulator; reductive meth	95.33
2kw5_A	202	SLR1183 protein; structural genomics, northeast st	95.31
2g72_A	289	Phenylethanolamine N-methyltransferase; HET: SAM F	95.3
4df3_A	233	Fibrillarin-like rRNA/TRNA 2'-O-methyltransferase;	95.29
1sfx_A	109	Conserved hypothetical protein AF2008; structural	95.28
2oxt_A	265	Nucleoside-2'-O-methyltransferase; flavivirus, vir	95.26
2wa2_A	276	Non-structural protein 5; transferase, S-adenosyl-	95.25
3k69_A	162	Putative transcription regulator; putative transcr	95.23
2bv6_A	142	MGRA, HTH-type transcriptional regulator MGRA; mul	95.21
4aik_A	151	Transcriptional regulator SLYA; transcription, tra	95.19
3lwf_A	159	LIN1550 protein, putative transcriptional regulato	95.18
3jw4_A	148	Transcriptional regulator, MARR/EMRR family; DNA-b	95.18
2cmg_A	262	Spermidine synthase; transferase, putrescine amino	95.17
3lcv_B	281	Sisomicin-gentamicin resistance methylase SGM; ant	95.14
1z7u_A	112	Hypothetical protein EF0647; winged-helix-turn-hel	95.14
3hsr_A	140	HTH-type transcriptional regulator SARZ; helix-tur	95.13
2lnb_A	80	Z-DNA-binding protein 1; structural genomics, nort	95.11
1ylf_A	149	RRF2 family protein; structural genomics, transcri	95.09
3htx_A	950	HEN1; HEN1, small RNA methyltransferase, protein-R	95.08
3frh_A	253	16S rRNA methylase; methyltransferase domain, heli	95.07
2fsw_A	107	PG_0823 protein; alpha-beta structure, helix-turn-	95.05
2pg4_A	95	Uncharacterized protein; structural genomics, join	95.03
2a61_A	145	Transcriptional regulator TM0710; APC4350, MCSG, m	94.98
3dmg_A	381	Probable ribosomal RNA small subunit methyltransf;	94.97
3t8r_A	143	Staphylococcus aureus CYMR; transcriptional regula	94.84
3df8_A	111	Possible HXLR family transcriptional factor; APC89	94.82
1sqg_A	429	SUN protein, FMU protein; rossmann-fold, mixed bet	94.81
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	94.8
2yxl_A	450	PH0851 protein, 450AA long hypothetical FMU protei	94.74
1z91_A	147	Organic hydroperoxide resistance transcriptional;	94.68
2p41_A	305	Type II methyltransferase; vizier, viral enzymes i	94.63
2f2e_A	146	PA1607; transcription factor, helix-TRUN-helix, AP	94.6
2fbi_A	142	Probable transcriptional regulator; MARR, APC5816,	94.57
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	94.57
2w25_A	150	Probable transcriptional regulatory protein; trans	94.56
2pex_A	153	Transcriptional regulator OHRR; transcription regu	94.53
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	94.42
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	94.4
2vdw_A	302	Vaccinia virus capping enzyme D1 subunit; nucleoti	94.38
1xd7_A	145	YWNA; structural genomics, protein structure initi	94.35
2fbk_A	181	Transcriptional regulator, MARR family; winged-hel	94.3
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	94.28
2i62_A	265	Nicotinamide N-methyltransferase; structural genom	94.27
3nqo_A	189	MARR-family transcriptional regulator; structural	94.24
3sso_A	419	Methyltransferase; macrolide, natural product, ros	94.18
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	94.13
3hrs_A	214	Metalloregulator SCAR; DTXR/MNTR family member, tr	94.12
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	94.11
2zkz_A	99	Transcriptional repressor PAGR; protein-DNA, HTH m	94.11
2r6z_A	258	UPF0341 protein in RSP 3' region; alpha-beta prote	94.05
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	94.04
1uwv_A	433	23S rRNA (uracil-5-)-methyltransferase RUMA; RNA m	94.04
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	94.03
3f3x_A	144	Transcriptional regulator, MARR family, putative;	93.99
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	93.97
3u2r_A	168	Regulatory protein MARR; structural genomics, PSI-	93.93
2gs9_A	211	Hypothetical protein TT1324; methyl transferase, s	93.91
2h09_A	155	Transcriptional regulator MNTR; transcription regu	93.88
3q87_B	170	N6 adenine specific DNA methylase; SAM-methyltrans	93.81
1tbx_A	99	ORF F-93, hypothetical 11.0 kDa protein; sulfolobu	93.81
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	93.8
1p6r_A	82	Penicillinase repressor; transcription regulation,	93.79
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	93.77
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	93.74
2dk5_A	91	DNA-directed RNA polymerase III 39 kDa polypeptide	93.7
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	93.69
3ldu_A	385	Putative methylase; structural genomics, PSI-2, pr	93.61
1sfu_A	75	34L protein; protein/Z-DNA complex, DNA binding pr	93.59
2igt_A	332	SAM dependent methyltransferase; alpha-beta sandwi	93.59
2vn2_A	128	DNAD, chromosome replication initiation protein; D	93.54
3k0b_A	393	Predicted N6-adenine-specific DNA methylase; methy	93.52
2qfm_A	364	Spermine synthase; spermidine aminopropyltransfera	93.46
4g6q_A	182	Putative uncharacterized protein; structural genom	93.44
4hc4_A	376	Protein arginine N-methyltransferase 6; HRMT1L6, S	93.42
2frh_A	127	SARA, staphylococcal accessory regulator A; winged	93.39
2fe3_A	145	Peroxide operon regulator; oxidative stress regula	93.38
3giw_A	277	Protein of unknown function DUF574; rossmann-fold	93.38
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	93.36
2f8l_A	344	Hypothetical protein LMO1582; structural genomics,	93.33
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	93.32
1ku9_A	152	Hypothetical protein MJ223; putative transcription	93.22
3m6w_A	464	RRNA methylase; rRNA methyltransferase, 5-methylcy	93.19
1bja_A	95	Transcription regulatory protein MOTA; activation	93.18
2k4b_A	99	Transcriptional regulator; DNA binding protein, wi	93.16
2o03_A	131	Probable zinc uptake regulation protein FURB; DNA-	93.04
1af7_A	274	Chemotaxis receptor methyltransferase CHER; chemot	93.04
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	92.96
2xvc_A	59	ESCRT-III, SSO0910; cell cycle, cell division, cyt	92.95
1j5y_A	187	Transcriptional regulator, biotin repressor famil;	92.88
1uly_A	192	Hypothetical protein PH1932; helix-turn-helix, str	92.88
1vlm_A	219	SAM-dependent methyltransferase; possible histamin	92.82
3ldg_A	384	Putative uncharacterized protein SMU.472; YPSC, me	92.8
2a14_A	263	Indolethylamine N-methyltransferase; SGC,INMT, str	92.67
2dul_A	378	N(2),N(2)-dimethylguanosine tRNA methyltransferas;	92.64
2oyr_A	258	UPF0341 protein YHIQ; alpha-beta protein, structur	92.48
3gcz_A	282	Polyprotein; flavivirus, RNA capping, methyltransf	92.44
2fxa_A	207	Protease production regulatory protein HPR; protea	92.24
2qlz_A	232	Transcription factor PF0095; 2.50A {Pyrococcus fur	92.14
2as0_A	396	Hypothetical protein PH1915; RNA methyltransferase	92.05
3mwm_A	139	ZUR, putative metal uptake regulation protein; FUR	92.03
2okc_A	445	Type I restriction enzyme stysji M protein; NP_813	91.97
3k6r_A	278	Putative transferase PH0793; structural genomics,	91.82
1v4r_A	102	Transcriptional repressor; helix-turn-helix, winge	91.74
3m4x_A	456	NOL1/NOP2/SUN family protein; mtase domain, PUA do	91.7
2p4w_A	202	Transcriptional regulatory protein ARSR family; ar	91.66
4dmg_A	393	Putative uncharacterized protein TTHA1493; rRNA, m	91.54
4b8x_A	147	SCO5413, possible MARR-transcriptional regulator;	91.47
1cf7_A	76	Protein (transcription factor E2F-4); E2F, winged-	91.46
3b5i_A	374	S-adenosyl-L-methionine:salicylic acid carboxyl me	91.45
2hoe_A	380	N-acetylglucosamine kinase; TM1224, structural gen	91.43
1mzb_A	136	Ferric uptake regulation protein; ferric uptake re	91.41
2xig_A	150	Ferric uptake regulation protein; hpfur, transcrip	91.38
2jjq_A	425	Uncharacterized RNA methyltransferase pyrab10780;	91.31
2v79_A	135	DNA replication protein DNAD; primosome, DNA-bindi	91.21
2frx_A	479	Hypothetical protein YEBU; rossmann-type S-adenosy	91.06
3evf_A	277	RNA-directed RNA polymerase NS5; NS5 methyltransfe	91.03
2yx1_A	336	Hypothetical protein MJ0883; methyl transferase, t	91.0
3c0k_A	396	UPF0064 protein YCCW; PUA domain, adoMet dependent	91.0
4fx0_A	148	Probable transcriptional repressor protein; helix-	90.76
1bia_A	321	BIRA bifunctional protein; transcription regulatio	90.69
2b78_A	385	Hypothetical protein SMU.776; structure genomics,	90.59
1okr_A	123	MECI, methicillin resistance regulatory protein ME	90.54
1wxx_A	382	TT1595, hypothetical protein TTHA1280; thermus the	90.35
2efj_A	384	3,7-dimethylxanthine methyltransferase; SAM-depend	90.33
2obp_A	96	Putative DNA-binding protein; structural genomics,	90.32
3ll7_A	410	Putative methyltransferase; methytransferase, stru	90.29
2k4m_A	153	TR8_protein, UPF0146 protein MTH_1000; alpha+beta,	90.28
2g9w_A	138	Conserved hypothetical protein; DNA-binding domain	90.18
2b9e_A	309	NOL1/NOP2/SUN domain family, member 5 isoform 2; m	90.1
3i71_A	68	Ethanolamine utilization protein EUTK; helix-turn-	90.09
1z6r_A	406	MLC protein; transcriptional repressor, ROK family	90.02
1sd4_A	126	Penicillinase repressor; BLAI, MECI, methicillin,	89.62
3o4f_A	294	Spermidine synthase; aminopropyltransferase, polya	89.51
2pjp_A	121	Selenocysteine-specific elongation factor; SELB, p	89.37
2w57_A	150	Ferric uptake regulation protein; gene regulation,	89.16
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	89.05
3bt7_A	369	TRNA (uracil-5-)-methyltransferase; methyluridine,	88.77
1z05_A	429	Transcriptional regulator, ROK family; structural	88.7
2xyq_A	290	Putative 2'-O-methyl transferase; transferase-vira	88.6
3v97_A	703	Ribosomal RNA large subunit methyltransferase L; Y	88.32
3maj_A	382	DNA processing chain A; MCSG, PSI-2, structural ge	88.04
1jhg_A	101	Trp operon repressor; complex (regulatory protein-	87.78
2zig_A	297	TTHA0409, putative modification methylase; methylt	87.43
2o0m_A	345	Transcriptional regulator, SORC family; structural	87.27
3eld_A	300	Methyltransferase; flavivirus, RNA capping, guanyl	87.15
2b0l_A	102	GTP-sensing transcriptional pleiotropic repressor;	87.1
3u1d_A	151	Uncharacterized protein; GNTR-superfamily, structu	86.97
3rkx_A	323	Biotin-[acetyl-COA-carboxylase] ligase; biotin pro	86.74
1m6e_X	359	S-adenosyl-L-methionnine:salicylic acid carboxyl m	85.95
3p8z_A	267	Mtase, non-structural protein 5; methyltransferase	85.78
2qlz_A	232	Transcription factor PF0095; 2.50A {Pyrococcus fur	85.39
3s1s_A	878	Restriction endonuclease bpusi; PD--(D/E)XK cataly	85.31
2yu3_A	95	DNA-directed RNA polymerase III 39 kDa polypeptide	85.25
3cta_A	230	Riboflavin kinase; structural genomics, transferas	85.23
3eyi_A	72	Z-DNA-binding protein 1; alternative splicing, DNA	85.05
2py6_A	409	Methyltransferase FKBM; YP_546752.1, structural ge	84.65
2qq9_A	226	Diphtheria toxin repressor; regulator, DTXR, helix	84.48
3tqn_A	113	Transcriptional regulator, GNTR family; regulatory	84.42
1fx7_A	230	Iron-dependent repressor IDER; DTXR, iron-dependen	84.38
3lkz_A	321	Non-structural protein 5; flavivirus, methyltransf	83.9
2p5k_A	64	Arginine repressor; DNA-binding domain, winged hel	83.88
2w48_A	315	Sorbitol operon regulator; SORC, activator, repres	83.63
2ek5_A	129	Predicted transcriptional regulators; helix-turn-h	83.53
1i4w_A	353	Mitochondrial replication protein MTF1; mitochondr	83.45
3eyy_A	145	Putative iron uptake regulatory protein; NUR, nick	83.41
3v97_A	703	Ribosomal RNA large subunit methyltransferase L; Y	83.03
1hsj_A	487	Fusion protein consisting of staphylococcus access	82.5
4ets_A	162	Ferric uptake regulation protein; metal binding pr	81.96
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	81.87
3by6_A	126	Predicted transcriptional regulator; structural ge	81.82
3neu_A	125	LIN1836 protein; structural genomics, PSI-2, prote	81.72
2p8t_A	200	Hypothetical protein PH0730; pyrococcus horikoshii	81.72
3axs_A	392	Probable N(2),N(2)-dimethylguanosine tRNA methylt	81.05
3elk_A	117	Putative transcriptional regulator TA0346; structu	80.78
4esf_A	117	PADR-like transcriptional regulator; PADR family,	80.59
4auk_A	375	Ribosomal RNA large subunit methyltransferase M; Y	80.49
3dv8_A	220	Transcriptional regulator, CRP/FNR family; cyclic	80.26
3tka_A	347	Ribosomal RNA small subunit methyltransferase H; H	80.21
2ar0_A	541	M.ecoki, type I restriction enzyme ecoki M protein	80.1

>4a6d_A Hydroxyindole O-methyltransferase; melatonin, circadian clock; HET: SAM; 2.40A {Homo sapiens} PDB: 4a6e_A*

Probab=99.97  E-value=6.9e-32  Score=235.64  Aligned_cols=186  Identities=16%  Similarity=0.219  Sum_probs=160.0

Q ss_pred             hhHHHHHHHHHHHHhHHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCC
Q 040620           14 FQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNE   93 (214)
Q Consensus        14 ~~~~~~l~~~~~g~~~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~   93 (214)
                      .++...|++++.||+.+++|++|++|||||+|++.++|+|++|||+++|+++   +.++||||+|++.|+|.+...   +
T Consensus         6 ~~~~~~L~~l~~Gf~~s~~L~aa~eLglfd~L~~~~~p~t~~eLA~~~g~~~---~~l~rlLr~L~~~gll~~~~~---~   79 (353)
T 4a6d_A            6 DQAYRLLNDYANGFMVSQVLFAACELGVFDLLAEAPGPLDVAAVAAGVRASA---HGTELLLDICVSLKLLKVETR---G   79 (353)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHSSSCBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEEEE---T
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHcCHHHHHhcCCCCCCHHHHHHhhCcCH---HHHHHHHHHHHHCCCEEEecc---C
Confidence            3788889999999999999999999999999997668999999999999999   999999999999999986542   1


Q ss_pred             CccceeeCCCCCcccccccc----ccchHHHHHHhhccchhhhhHhHHHhhcCCCCChhhHHHH----------------
Q 040620           94 QEEESILLPPHLDFFSRISL----QLQGSTILLLIADATFTTSFHFLSTWLQNDDQTLFGTADG----------------  153 (214)
Q Consensus        94 ~~~~~y~~t~~~~~~s~~l~----~~~~~~~~~~~~~~~~~~~~~~l~~~lr~~~~~~f~~~~g----------------  153 (214)
                      + .++|++|+.    ++.++    +.++..++.++. ...+..|.+|.+.+++++ .+|...+|                
T Consensus        80 ~-~~~y~~t~~----s~~~l~~~~~~~~~~~~~~~~-~~~~~~~~~L~~~vr~g~-~~~~~~~g~~~~~~~~~~~~~~~~  152 (353)
T 4a6d_A           80 G-KAFYRNTEL----SSDYLTTVSPTSQCSMLKYMG-RTSYRCWGHLADAVREGR-NQYLETFGVPAEELFTAIYRSEGE  152 (353)
T ss_dssp             T-EEEEEECHH----HHHHHSTTSTTCCHHHHHHHH-HTHHHHHTTHHHHHHHTS-CCHHHHHSCCCSSHHHHHTSSHHH
T ss_pred             c-cceeeCCHH----HHHHhhcCCchHHHHHHHHhC-HHHHHHHHHHHHHHhcCC-ChhHHhcCCChHHHHHHHhhCHHH
Confidence            1 468999999    87654    467788776654 357889999999999886 33433322                


Q ss_pred             --HHHHHhhhhhhhhHHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCCC
Q 040620          154 --IFYEAMITDFELIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACHL  214 (214)
Q Consensus       154 --~f~~am~~~~~~~~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~  214 (214)
                        .|+++|...+....+.+++.++  +++.++|||||||+|.++++++++||+++++++|+|+
T Consensus       153 ~~~f~~aM~~~~~~~~~~~~~~~~--~~~~~~v~DvGgG~G~~~~~l~~~~p~~~~~~~dlp~  213 (353)
T 4a6d_A          153 RLQFMQALQEVWSVNGRSVLTAFD--LSVFPLMCDLGGGAGALAKECMSLYPGCKITVFDIPE  213 (353)
T ss_dssp             HHHHHHHHHTTHHHHHHHHHHSSC--GGGCSEEEEETCTTSHHHHHHHHHCSSCEEEEEECHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcC--cccCCeEEeeCCCCCHHHHHHHHhCCCceeEeccCHH
Confidence              7999999988888888999998  7888999999999999999999999999999999983

>3p9c_A Caffeic acid O-methyltransferase; S-adenosylmethionine dependent O-methyltransferase; HET: SAH; 1.80A {Lolium perenne} PDB: 3p9i_A* 3p9k_A*

Probab=99.97  E-value=1.1e-30  Score=228.87  Aligned_cols=196  Identities=24%  Similarity=0.320  Sum_probs=167.4

Q ss_pred             CchhhhhHHHHHHHHHHHHhHHHHHHHHHhcCcchhhhcCC-CCCCHHHHHHHcCC--CCCCcc---cHHHHHHHHHhCC
Q 040620            9 GAREHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSG-QPMTLTQIIVALNV--HPNKTR---CTQILVCLLAHSG   82 (214)
Q Consensus         9 ~~~~~~~~~~~l~~~~~g~~~~~~L~~a~~lglfd~L~~~~-~p~t~~eLA~~~g~--~~~~~~---~l~rlLr~L~~~g   82 (214)
                      ...+..+++..+++++.+++.+++|++|+++||||+|++++ +|+|++|||+++|+  +|   +   .|+||||+|++.|
T Consensus        13 ~~~~~~~~~~~~~~l~~~~~~~~~l~~a~~Lgifd~L~~~g~~~~t~~eLA~~~g~~~~~---~~~~~l~rlLr~L~~~g   89 (364)
T 3p9c_A           13 AASADEDACMFALQLASSSVLPMTLKNAIELGLLEILVAAGGKSLTPTEVAAKLPSAANP---EAPDMVDRILRLLASYN   89 (364)
T ss_dssp             CHHHHHHHHHHHHHHTTTTHHHHHHHHHHHHTHHHHHHHTTTCCBCHHHHHHTTTCTTCT---THHHHHHHHHHHHHHTT
T ss_pred             cchHHHHHHHHHHHHHHhHHHHHHHHHHHHCChHHHHhhcCCCCCCHHHHHHhcCCCCCc---cchhhHHHHHHHHHhCC
Confidence            45668899999999999999999999999999999999864 69999999999998  88   7   9999999999999


Q ss_pred             ceeeecCC-CCCCccceeeCCCCCcccccccc-c---cchHHHHHHhhccchhhhhHhHHHhhcCCCCChhhHHHH----
Q 040620           83 FFVQQKDG-KNEQEEESILLPPHLDFFSRISL-Q---LQGSTILLLIADATFTTSFHFLSTWLQNDDQTLFGTADG----  153 (214)
Q Consensus        83 ~l~~~~~~-~~~~~~~~y~~t~~~~~~s~~l~-~---~~~~~~~~~~~~~~~~~~~~~l~~~lr~~~~~~f~~~~g----  153 (214)
                      +|+++..+ .++..+++|++|+.    ++.|+ +   .++++++.++..+.++..|.+|.+++|+++ ++|+..+|    
T Consensus        90 ~l~~~~~~~~~g~~~~~y~~t~~----s~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~~r~g~-~~~~~~~g~~~~  164 (364)
T 3p9c_A           90 VVTCLVEEGKDGRLSRSYGAAPV----CKFLTPNEDGVSMAALALMNQDKVLMESWYYLKDAVLDGG-IPFNKAYGMSAF  164 (364)
T ss_dssp             SEEEEEEECSSSCEEEEEEECGG----GGGSSCCTTSCCTHHHHHHHTSHHHHGGGGGHHHHHHHCS-CHHHHHHSSCHH
T ss_pred             CEEEeccccCCCCcCCEEecCHH----HHHHcCCCCCCCHHHHHHHhcCHHHHHHHhCHHHHHhhCC-ChHHHhcCCCHH
Confidence            99987310 00100268999999    99887 2   478888877766778899999999999886 67766544    


Q ss_pred             -----------HHHHHhhhhhhhhHHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          154 -----------IFYEAMITDFELIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       154 -----------~f~~am~~~~~~~~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                                 .|+++|...+......+++.++ .+++..+|||||||+|.++..+++++|+++++++|+|
T Consensus       165 ~~~~~~~~~~~~f~~~m~~~~~~~~~~~~~~~~-~~~~~~~vlDvG~G~G~~~~~l~~~~p~~~~~~~D~~  234 (364)
T 3p9c_A          165 EYHGTDPRFNRVFNEGMKNHSIIITKKLLELYH-GFEGLGTLVDVGGGVGATVAAIAAHYPTIKGVNFDLP  234 (364)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHHHHHHHHHHHCC-TTTTCSEEEEETCTTSHHHHHHHHHCTTCEEEEEECH
T ss_pred             HHHHhCHHHHHHHHHHHHHhhHHHHHHHHHhcc-cccCCCEEEEeCCCCCHHHHHHHHHCCCCeEEEecCH
Confidence                       6889998888777778888886 3667899999999999999999999999999999986

>3lst_A CALO1 methyltransferase; calicheamicin, enediyne, SAH, STRU genomics, PSI-2, protein structure initiative; HET: SAH; 2.40A {Micromonospora echinospora}

Probab=99.97  E-value=7.6e-30  Score=221.83  Aligned_cols=181  Identities=17%  Similarity=0.244  Sum_probs=161.1

Q ss_pred             hhhHHHHHHHHHHHHhHHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCC
Q 040620           13 HFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKN   92 (214)
Q Consensus        13 ~~~~~~~l~~~~~g~~~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~   92 (214)
                      ..++..++++++.|++.+.+|++++++||||+|++  +|+|++|||+++|+++   +.++||||+|++.|+|++ .    
T Consensus        19 ~~~~~~~l~~~~~~~~~~~~l~~a~~lglf~~l~~--g~~t~~elA~~~g~~~---~~l~rlLr~l~~~g~l~~-~----   88 (348)
T 3lst_A           19 RLQSALALYEEAMGYTYAAALRAAAAVGVADHLVD--GPRTPAELAAATGTDA---DALRRVLRLLAVRDVVRE-S----   88 (348)
T ss_dssp             HHHHHHHHHHHHTTHHHHHHHHHHHHHTGGGGGTT--SCBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEE-E----
T ss_pred             CchHHHHHHHHHHHHHHHHHHHHHHHcCchhHhhC--CCCCHHHHHHHhCcCH---HHHHHHHHHHHhCCCEEe-c----
Confidence            45788899999999999999999999999999986  7999999999999999   999999999999999999 4    


Q ss_pred             CCccceeeCCCCCcccccccc---ccchHHHHHHhhccchhhhhHhHHHhhcCCCCChhhHHHH---------------H
Q 040620           93 EQEEESILLPPHLDFFSRISL---QLQGSTILLLIADATFTTSFHFLSTWLQNDDQTLFGTADG---------------I  154 (214)
Q Consensus        93 ~~~~~~y~~t~~~~~~s~~l~---~~~~~~~~~~~~~~~~~~~~~~l~~~lr~~~~~~f~~~~g---------------~  154 (214)
                         +++|++|+.    ++.|+   +.++.+++.++.++..+..|.+|++++|++. ++|...+|               .
T Consensus        89 ---~~~y~~t~~----s~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~g~-~~~~~~~g~~~~~~~~~~~~~~~~  160 (348)
T 3lst_A           89 ---DGRFALTDK----GAALRSDSPVPARAGILMFTDTMFWTMSHRVASALGPER-PAFADIFGSSLDAYFDGDAEVEAL  160 (348)
T ss_dssp             ---TTEEEECTT----TGGGSTTSSSCSHHHHHHHTSHHHHHHHHTHHHHTCTTC-CCHHHHHSSCHHHHHTTCHHHHHH
T ss_pred             ---CCEEecCHH----HHHHhcCCCccHHHHHHHhcCHHHHHHHHHHHHHHhcCC-ChhhHHhCCCHHHHHHhCHHHHHH
Confidence               689999999    99887   3578888877666667899999999999876 44544333               6


Q ss_pred             HHHHhhhhhhhhHHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          155 FYEAMITDFELIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       155 f~~am~~~~~~~~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                      |.++|...+....+.+++.++  +++..+|||||||+|.++..+++++|+++++++|+|
T Consensus       161 f~~~m~~~~~~~~~~~~~~~~--~~~~~~vLDvG~G~G~~~~~l~~~~p~~~~~~~D~~  217 (348)
T 3lst_A          161 YYEGMETVSAAEHLILARAGD--FPATGTVADVGGGRGGFLLTVLREHPGLQGVLLDRA  217 (348)
T ss_dssp             HHHHHHHHHHTTHHHHHHHSC--CCSSEEEEEETCTTSHHHHHHHHHCTTEEEEEEECH
T ss_pred             HHHHHHHhhhhhHHHHHHhCC--ccCCceEEEECCccCHHHHHHHHHCCCCEEEEecCH
Confidence            889998888877788899988  777899999999999999999999999999999986

>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=99.96  E-value=3.4e-29  Score=219.63  Aligned_cols=199  Identities=21%  Similarity=0.292  Sum_probs=163.2

Q ss_pred             CchhhhhHHHHHHHHHHHHhHHHHHHHHHhcCcchhhhcC---CCCCCHHHHHHHcC-CCCCCcccHHHHHHHHHhCCce
Q 040620            9 GAREHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNS---GQPMTLTQIIVALN-VHPNKTRCTQILVCLLAHSGFF   84 (214)
Q Consensus         9 ~~~~~~~~~~~l~~~~~g~~~~~~L~~a~~lglfd~L~~~---~~p~t~~eLA~~~g-~~~~~~~~l~rlLr~L~~~g~l   84 (214)
                      .+.+..+++..+++++.+++.+++|++|+++||||+|++.   ++|+|++|||+++| .+|.+++.|+||||+|++.|+|
T Consensus        14 ~~~~~~~~~~~~~~l~~~~~~~~~l~~a~~Lglfd~L~~~~gp~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gll   93 (368)
T 3reo_A           14 THSSDEEANLFAMQLASAAVLPMALKAAIELDVLEIMAKSVPPSGYISPAEIAAQLPTTNPEAPVMLDRVLRLLASYSVV   93 (368)
T ss_dssp             ---CHHHHHHHHHHHHTTTHHHHHHHHHHHTTHHHHHHHHCCTTCCBCHHHHHTTSSCCCTTHHHHHHHHHHHHHHTTSE
T ss_pred             CchHHHHHHHHHHHHHHHHHHHHHHHHHHHCCchhHHhhcCCCCCCcCHHHHHHhcCcCCCcchhhHHHHHHHHHhCCCe
Confidence            3446888999999999999999999999999999999973   25799999999998 4772223999999999999999


Q ss_pred             eeecCCC-CCCccceeeCCCCCcccccccc----ccchHHHHHHhhccchhhhhHhHHHhhcCCCCChhhHHHH------
Q 040620           85 VQQKDGK-NEQEEESILLPPHLDFFSRISL----QLQGSTILLLIADATFTTSFHFLSTWLQNDDQTLFGTADG------  153 (214)
Q Consensus        85 ~~~~~~~-~~~~~~~y~~t~~~~~~s~~l~----~~~~~~~~~~~~~~~~~~~~~~l~~~lr~~~~~~f~~~~g------  153 (214)
                      .+..... ++..+++|++|+.    ++.|+    +.++++++.++..+.++..|.+|.+++|+++ ++|+..+|      
T Consensus        94 ~~~~~~~~~g~~~~~y~~t~~----s~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~r~g~-~~~~~~~g~~~~~~  168 (368)
T 3reo_A           94 TYTLRELPSGKVERLYGLAPV----CKFLTKNEDGVSLAPFLLLATDKVLLEPWFYLKDAILEGG-IPFNKAYGMNIFDY  168 (368)
T ss_dssp             EEEEEECTTSCEEEEEEECTT----HHHHSCCTTSCCSHHHHHHHTCHHHHGGGGGHHHHHHHCS-CHHHHHSSSCHHHH
T ss_pred             EEecccCCCCcccceeCcCHH----HHHHhCCCCCCCHHHHHHHhcCHHHHhhhhchHHHHhcCC-CHHHHHhCCCHHHH
Confidence            9872100 0100268999999    99887    2568888877766678899999999999876 56665433      


Q ss_pred             ---------HHHHHhhhhhhhhHHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          154 ---------IFYEAMITDFELIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       154 ---------~f~~am~~~~~~~~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                               .|+++|...+......+++.++ .+++..+|||||||+|.++..+++++|+++++++|+|
T Consensus       169 ~~~~~~~~~~f~~~m~~~~~~~~~~~~~~~~-~~~~~~~vlDvG~G~G~~~~~l~~~~p~~~~~~~D~~  236 (368)
T 3reo_A          169 HGTDHRINKVFNKGMSSNSTITMKKILEMYN-GFEGLTTIVDVGGGTGAVASMIVAKYPSINAINFDLP  236 (368)
T ss_dssp             HTTCHHHHHHHHHHHHHHHHHHHHHHHTTCC-TTTTCSEEEEETCTTSHHHHHHHHHCTTCEEEEEECH
T ss_pred             HhhCHHHHHHHHHHHHhhhhhHHHHHHHhcc-cccCCCEEEEeCCCcCHHHHHHHHhCCCCEEEEEehH
Confidence                     6899999888777778888886 3677899999999999999999999999999999986

>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=99.96  E-value=2.5e-29  Score=218.79  Aligned_cols=194  Identities=38%  Similarity=0.637  Sum_probs=163.8

Q ss_pred             CCchhhhhHHHHHHHHHHHHhHHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620            8 NGAREHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ   87 (214)
Q Consensus         8 ~~~~~~~~~~~~l~~~~~g~~~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~   87 (214)
                      +.++++.+++..+++++.+++.+.+|++++++|||++|+..++|+|++|||+++|++|.+++.++||||+|++.|+|++.
T Consensus         8 ~~~~~~~~a~~~l~~~~~~~~~~~~l~~a~~lgif~~L~~~~~~~t~~ela~~~~~~~~~~~~l~rlLr~L~~~gll~~~   87 (352)
T 1fp2_A            8 RKPSEIFKAQALLYKHIYAFIDSMSLKWAVEMNIPNIIQNHGKPISLSNLVSILQVPSSKIGNVRRLMRYLAHNGFFEII   87 (352)
T ss_dssp             CCSTHHHHHHHHHHHHHTTHHHHHHHHHHHHTTHHHHHHHHTSCEEHHHHHHHHTCCGGGHHHHHHHHHHHHHTTSEEEE
T ss_pred             CChHHHhhHHHHHHHHHHHHHHHHHHHHHHHCChhhhhhhcCCCccHHHHHHHhCcCCCChHHHHHHHHHHHhCCeEEEe
Confidence            34578899999999999999999999999999999999975459999999999999642238999999999999999988


Q ss_pred             c-CCCCCCccceeeCCCCCcccccccc---ccchHHHHHHhhccchhhhhHhHHHhhc-CCCCChhhHHHH---------
Q 040620           88 K-DGKNEQEEESILLPPHLDFFSRISL---QLQGSTILLLIADATFTTSFHFLSTWLQ-NDDQTLFGTADG---------  153 (214)
Q Consensus        88 ~-~~~~~~~~~~y~~t~~~~~~s~~l~---~~~~~~~~~~~~~~~~~~~~~~l~~~lr-~~~~~~f~~~~g---------  153 (214)
                      . .      +++|++|+.    ++.|+   +.+++.++.++.++.++..|.+|++++| ++. ++|...+|         
T Consensus        88 ~~~------~~~y~~t~~----s~~L~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~~g~-~~~~~~~g~~~~~~~~~  156 (352)
T 1fp2_A           88 TKE------EESYALTVA----SELLVRGSDLCLAPMVECVLDPTLSGSYHELKKWIYEEDL-TLFGVTLGSGFWDFLDK  156 (352)
T ss_dssp             ESS------SEEEEECHH----HHTTSTTSSSCCHHHHHHHTCHHHHHGGGGHHHHHTCSSC-CHHHHHHSSCHHHHHHH
T ss_pred             cCC------CCeEeCCHH----HHHHhCCCCccHHHHHHHhcCchHHHHHHHHHHHHHhcCC-ChHHHHcCCCHHHHHHh
Confidence            2 1      589999999    99887   3468888877766667889999999999 654 66655433         


Q ss_pred             ------HHHHHhhhhhhhhHHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          154 ------IFYEAMITDFELIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       154 ------~f~~am~~~~~~~~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                            .|+++|........+. ++.+++.+.+..+|||||||+|.++..+++++|+++++++|+|
T Consensus       157 ~~~~~~~f~~~m~~~~~~~~~~-~~~~~~~~~~~~~vlDvG~G~G~~~~~l~~~~p~~~~~~~D~~  221 (352)
T 1fp2_A          157 NPEYNTSFNDAMASDSKLINLA-LRDCDFVFDGLESIVDVGGGTGTTAKIICETFPKLKCIVFDRP  221 (352)
T ss_dssp             CHHHHHHHHHHHHHTHHHHHHH-HHTCHHHHTTCSEEEEETCTTSHHHHHHHHHCTTCEEEEEECH
T ss_pred             ChHHHHHHHHHHHhcchhhhhH-HHhcccccccCceEEEeCCCccHHHHHHHHHCCCCeEEEeeCH
Confidence                  6888888877766566 7778434777899999999999999999999999999999985

>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=99.96  E-value=2.8e-29  Score=218.85  Aligned_cols=200  Identities=34%  Similarity=0.591  Sum_probs=163.0

Q ss_pred             CchhhhhHHHHHHHHHHHHhHHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620            9 GAREHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus         9 ~~~~~~~~~~~l~~~~~g~~~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      ..+++.+++..+++++.+++.+.+|++++++|||++|+..++|+|++|||+++|++|.+++.|+||||+|++.|+|++..
T Consensus         3 ~~~~~~~~~~~l~~~~~~~~~~~~l~~a~~lgif~~L~~~~~~~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~gll~~~~   82 (358)
T 1zg3_A            3 EESELYHAQIHLYKHVYNFVSSMALKSAMELGIADAIHNHGKPMTLSELASSLKLHPSKVNILHRFLRLLTHNGFFAKTI   82 (358)
T ss_dssp             TTSCCTTHHHHHHHHHTTHHHHHHHHHHHHHTHHHHHHHHTSCEEHHHHHHHTTCCTTTHHHHHHHHHHHHHTTSEEEEE
T ss_pred             chHHhhhHHHHHHHHHHHHHHHHHHHHHHHCChHhHHhhcCCCcCHHHHHHhcCCCCcchHHHHHHHHHHhhCCcEEEec
Confidence            34678899999999999999999999999999999999754599999999999996433489999999999999999871


Q ss_pred             C--CC-CCCccceeeCCCCCcccccccc---ccchHHHHHHhhccchhhhhHhHHHhhcCCC-CChhhHHHH--------
Q 040620           89 D--GK-NEQEEESILLPPHLDFFSRISL---QLQGSTILLLIADATFTTSFHFLSTWLQNDD-QTLFGTADG--------  153 (214)
Q Consensus        89 ~--~~-~~~~~~~y~~t~~~~~~s~~l~---~~~~~~~~~~~~~~~~~~~~~~l~~~lr~~~-~~~f~~~~g--------  153 (214)
                      +  +. +++.+++|++|+.    ++.|+   +.+++.++.++.++.++..|.+|++++|++. .++|+..+|        
T Consensus        83 ~~~~~~~g~~~~~y~~t~~----s~~l~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~g~~~~~~~~~~g~~~~~~~~  158 (358)
T 1zg3_A           83 VKGKEGDEEEEIAYSLTPP----SKLLISGKPTCLSSIVKGALHPSSLDMWSSSKKWFNEDKEQTLFECATGESFWDFLN  158 (358)
T ss_dssp             ECCSSSSCCCEEEEEECHH----HHTTCTTSTTCCHHHHHHHTSHHHHGGGGGHHHHHHCSCCCCHHHHHHSSCHHHHHT
T ss_pred             ccccccCCCCCCEEeCCHH----HHHHhCCCCccHHHHHHHhcCcHHHHHHHHHHHHHhCCCCCChHHHHhCCCHHHHHh
Confidence            0  00 0000279999999    99887   3478888887766677899999999999884 266665433        


Q ss_pred             ---------HHHHHhhhhhhhhHHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          154 ---------IFYEAMITDFELIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       154 ---------~f~~am~~~~~~~~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                               .|+++|...+.... .+++.+++.+.+..+|||||||+|.++..+++++|+++++++|+|
T Consensus       159 ~~p~~~~~~~f~~~m~~~~~~~~-~~~~~~~~~~~~~~~vlDvG~G~G~~~~~l~~~~p~~~~~~~D~~  226 (358)
T 1zg3_A          159 KDSESSTLSMFQDAMASDSRMFK-LVLQENKRVFEGLESLVDVGGGTGGVTKLIHEIFPHLKCTVFDQP  226 (358)
T ss_dssp             SGGGHHHHHHHHHHHHHHHHTHH-HHHHHTHHHHHTCSEEEEETCTTSHHHHHHHHHCTTSEEEEEECH
T ss_pred             cChhhhhHHHHHHHHhcccHHHH-HHHHhcchhccCCCEEEEECCCcCHHHHHHHHHCCCCeEEEeccH
Confidence                     46677877666555 678888433677889999999999999999999999999999986

>3gwz_A MMCR; methyltransferase, mitomycin, S-adenosyl methionine, transferase; HET: MSE SAH; 1.91A {Streptomyces lavendulae} PDB: 3gxo_A*

Probab=99.96  E-value=7e-29  Score=217.54  Aligned_cols=182  Identities=22%  Similarity=0.276  Sum_probs=159.9

Q ss_pred             hhhHHHHHHHHHHHHhHHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCC
Q 040620           13 HFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKN   92 (214)
Q Consensus        13 ~~~~~~~l~~~~~g~~~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~   92 (214)
                      ..+...++++++.+++.+++|++++++||||+|++  +|+|++|||+++|+++   +.++||||+|++.|+|++++    
T Consensus        35 ~~~~~~~l~~l~~~~~~~~~l~~a~~lglf~~l~~--g~~t~~eLA~~~g~~~---~~l~rlLr~L~~~g~l~~~~----  105 (369)
T 3gwz_A           35 RAAAEETVNDILQGAWKARAIHVAVELGVPELLQE--GPRTATALAEATGAHE---QTLRRLLRLLATVGVFDDLG----  105 (369)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHTTGGGGTT--SCEEHHHHHHHHTCCH---HHHHHHHHHHHHTTSSEECS----
T ss_pred             CChHHHHHHHHHHHHHHHHHHHHHHHCChhhhhcC--CCCCHHHHHHHHCcCH---HHHHHHHHHHHhCCCEEEeC----
Confidence            44677889999999999999999999999999995  8999999999999999   99999999999999999976    


Q ss_pred             CCccce-eeCCCCCcccccccc---ccchHHHHHHhhccchhhhhHhHHHhhcCCCCChhhHHHH---------------
Q 040620           93 EQEEES-ILLPPHLDFFSRISL---QLQGSTILLLIADATFTTSFHFLSTWLQNDDQTLFGTADG---------------  153 (214)
Q Consensus        93 ~~~~~~-y~~t~~~~~~s~~l~---~~~~~~~~~~~~~~~~~~~~~~l~~~lr~~~~~~f~~~~g---------------  153 (214)
                         +++ |++|+.    ++.|.   +.++..++.++..+..+..|.++.++++++. ++|...+|               
T Consensus       106 ---~~~~y~~t~~----s~~L~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~g~-~~~~~~~g~~~~~~~~~~~~~~~  177 (369)
T 3gwz_A          106 ---HDDLFAQNAL----SAVLLPDPASPVATDARFQAAPWHWRAWEQLTHSVRTGE-ASFDVANGTSFWQLTHEDPKARE  177 (369)
T ss_dssp             ---STTEEECCHH----HHTTSCCTTCHHHHHHHHHHSHHHHHHHHTHHHHHHHSS-CSHHHHHSSCHHHHHHHCHHHHH
T ss_pred             ---CCceEecCHH----HHHHhcCCchhHHHHHHHcCCHHHHHHHHhHHHHHhCCC-ChhHhhcCCCHHHHHHhCHHHHH
Confidence               578 999999    99987   3568888877766557789999999999876 34443322               


Q ss_pred             HHHHHhhhhhhhhHHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          154 IFYEAMITDFELIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       154 ~f~~am~~~~~~~~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                      .|+++|........+.+++.++  +.+..+|||||||+|.++..+++++|+++++++|+|
T Consensus       178 ~f~~~m~~~~~~~~~~l~~~~~--~~~~~~vlDvG~G~G~~~~~l~~~~p~~~~~~~D~~  235 (369)
T 3gwz_A          178 LFNRAMGSVSLTEAGQVAAAYD--FSGAATAVDIGGGRGSLMAAVLDAFPGLRGTLLERP  235 (369)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSC--CTTCSEEEEETCTTSHHHHHHHHHCTTCEEEEEECH
T ss_pred             HHHHHHHHHHhhhHHHHHHhCC--CccCcEEEEeCCCccHHHHHHHHHCCCCeEEEEcCH
Confidence            6888898887777788888888  777899999999999999999999999999999985

>2ip2_A Probable phenazine-specific methyltransferase; pyocyanin, phenazine-1-carboxy PHZM; 1.80A {Pseudomonas aeruginosa}

Probab=99.96  E-value=3.9e-28  Score=209.24  Aligned_cols=177  Identities=19%  Similarity=0.208  Sum_probs=155.8

Q ss_pred             hHHHHHHHHHHHHhHHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCC
Q 040620           15 QAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQ   94 (214)
Q Consensus        15 ~~~~~l~~~~~g~~~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~   94 (214)
                      .+...+++++.+++.+.+|++++++|||++|.+  +|+|++|||+++|+++   +.++||||+|++.|+|.+.+      
T Consensus         7 ~~~~~l~~~~~~~~~~~~l~~~~~lgi~~~l~~--~~~t~~ela~~~~~~~---~~l~r~Lr~L~~~g~l~~~~------   75 (334)
T 2ip2_A            7 AAARNLIQVVTGEWKSRCVYVATRLGLADLIES--GIDSDETLAAAVGSDA---ERIHRLMRLLVAFEIFQGDT------   75 (334)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHT--TCCSHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEET------
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHcCcHHHHhC--CCCCHHHHHHHhCcCH---HHHHHHHHHHHhCCceEecC------
Confidence            677899999999999999999999999999986  8999999999999999   99999999999999999986      


Q ss_pred             ccceeeCCCCCcccccccc--ccchHHHHHHhhccchhhhhHhHHHhhcCCCCChhhHHHH---------------HHHH
Q 040620           95 EEESILLPPHLDFFSRISL--QLQGSTILLLIADATFTTSFHFLSTWLQNDDQTLFGTADG---------------IFYE  157 (214)
Q Consensus        95 ~~~~y~~t~~~~~~s~~l~--~~~~~~~~~~~~~~~~~~~~~~l~~~lr~~~~~~f~~~~g---------------~f~~  157 (214)
                       ++.|++|+.    ++.|+  +.++..++.++.+... ..|.+|.++++++. ++|+..+|               .|++
T Consensus        76 -~~~y~~t~~----s~~l~~~~~~~~~~~~~~~~~~~-~~~~~l~~~l~~~~-~~~~~~~g~~~~~~~~~~~~~~~~f~~  148 (334)
T 2ip2_A           76 -RDGYANTPT----SHLLRDVEGSFRDMVLFYGEEFH-AAWTPACEALLSGT-PGFELAFGEDFYSYLKRCPDAGRRFLL  148 (334)
T ss_dssp             -TTEEEECHH----HHTTSSSTTCSHHHHHHHTTHHH-HHTTTHHHHHHHCC-CHHHHHHSSCHHHHHHHCHHHHHHHHH
T ss_pred             -CCeEecCHH----HHHHhCCCccHHHHHHHhcCchh-hHHHHHHHHHhcCC-ChhhhhcCCCHHHHHhhChHHHHHHHH
Confidence             589999999    98887  3478888877765444 88999999999876 55554432               6888


Q ss_pred             HhhhhhhhhHHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          158 AMITDFELIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       158 am~~~~~~~~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                      +| ..+....+.+++.++  +.+ .+|||||||+|.++..+++++|+.+++++|+|
T Consensus       149 ~m-~~~~~~~~~~~~~~~--~~~-~~vlDvG~G~G~~~~~l~~~~p~~~~~~~D~~  200 (334)
T 2ip2_A          149 AM-KASNLAFHEIPRLLD--FRG-RSFVDVGGGSGELTKAILQAEPSARGVMLDRE  200 (334)
T ss_dssp             HH-GGGHHHHHHHHHHSC--CTT-CEEEEETCTTCHHHHHHHHHCTTCEEEEEECT
T ss_pred             HH-HHHHHHHHHHHHhCC--CCC-CEEEEeCCCchHHHHHHHHHCCCCEEEEeCcH
Confidence            99 777767778888887  666 99999999999999999999999999999985

>3i53_A O-methyltransferase; CO-complex, rossmann-like fold; HET: SAH; 2.08A {Streptomyces carzinostaticus subsp} PDB: 3i58_A* 3i5u_A* 3i64_A*

Probab=99.95  E-value=9.2e-29  Score=213.31  Aligned_cols=177  Identities=20%  Similarity=0.190  Sum_probs=151.7

Q ss_pred             HHHHHHHHHHhHHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccc
Q 040620           18 AQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEE   97 (214)
Q Consensus        18 ~~l~~~~~g~~~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~   97 (214)
                      ..+++++.||+.+++|++|+++||||+|++  +|+|++|||+++|+++   +.++||||+|++.|++.+++       ++
T Consensus         7 ~~l~~~~~g~~~~~~l~~a~~lglf~~l~~--g~~t~~elA~~~~~~~---~~l~rlLr~l~~~gl~~~~~-------~~   74 (332)
T 3i53_A            7 HIGLRALADLATPMAVRVAATLRVADHIAA--GHRTAAEIASAAGAHA---DSLDRLLRHLVAVGLFTRDG-------QG   74 (332)
T ss_dssp             SSCHHHHTCCHHHHHHHHHHHHTHHHHHHT--TCCBHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEECT-------TS
T ss_pred             HHHHHHHHhhHHHHHHHHHHHcChHHHHhc--CCCCHHHHHHHHCcCH---HHHHHHHHHHHhCCcEEecC-------CC
Confidence            357889999999999999999999999986  7999999999999999   99999999999999999986       68


Q ss_pred             eeeCCCCCcccccccc---ccchHHHHHHhhccchh-hhhHhHHHhhcCCCCChhhHHHH---------------HHHHH
Q 040620           98 SILLPPHLDFFSRISL---QLQGSTILLLIADATFT-TSFHFLSTWLQNDDQTLFGTADG---------------IFYEA  158 (214)
Q Consensus        98 ~y~~t~~~~~~s~~l~---~~~~~~~~~~~~~~~~~-~~~~~l~~~lr~~~~~~f~~~~g---------------~f~~a  158 (214)
                      +|.+|+.    ++.|.   +.++..++.++.....+ ..|.++.++++++. ++|...+|               .|.++
T Consensus        75 ~y~~t~~----s~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~-~~~~~~~g~~~~~~~~~~~~~~~~f~~~  149 (332)
T 3i53_A           75 VYGLTEF----GEQLRDDHAAGKRKWLDMNSAVGRGDLGFVELAHSIRTGQ-PAYPVRYGTSFWEDLGSDPVLSASFDTL  149 (332)
T ss_dssp             BEEECTT----GGGGSTTCTTCCHHHHCTTSHHHHHGGGGGGHHHHHHHSS-CSHHHHHSSCHHHHHHHCHHHHHHHHHH
T ss_pred             eEEcCHh----HHHHhcCCchhHHHHHHHcCCHhHHHHHHHHhHHHHhcCC-CHHHHhhCCCHHHHHHhCHHHHHHHHHH
Confidence            9999999    99987   35688887665444455 78999999999886 34544332               67888


Q ss_pred             hhhhhhhhHHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          159 MITDFELIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       159 m~~~~~~~~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                      |...+....+.+++.++  +.+..+|||||||+|.++..+++++|+++++++|+|
T Consensus       150 m~~~~~~~~~~~~~~~~--~~~~~~vlDvG~G~G~~~~~l~~~~p~~~~~~~D~~  202 (332)
T 3i53_A          150 MSHHLELDYTGIAAKYD--WAALGHVVDVGGGSGGLLSALLTAHEDLSGTVLDLQ  202 (332)
T ss_dssp             HHHHHHHHHTTGGGSSC--CGGGSEEEEETCTTSHHHHHHHHHCTTCEEEEEECH
T ss_pred             HHHhHHhhHHHHHHhCC--CCCCCEEEEeCCChhHHHHHHHHHCCCCeEEEecCH
Confidence            88777666666777777  667789999999999999999999999999999985

>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=99.95  E-value=6.5e-28  Score=211.36  Aligned_cols=199  Identities=20%  Similarity=0.252  Sum_probs=155.7

Q ss_pred             chhhhhHHHHHH--HHHHHHhHHHHHHHHHhcCcchhhhcCCCC---CCHHHHHHHcCC---CCCCcccHHHHHHHHHhC
Q 040620           10 AREHFQAQAQVW--SYTYNYMKSLSLKRAIQLRIPDIINNSGQP---MTLTQIIVALNV---HPNKTRCTQILVCLLAHS   81 (214)
Q Consensus        10 ~~~~~~~~~~l~--~~~~g~~~~~~L~~a~~lglfd~L~~~~~p---~t~~eLA~~~g~---~~~~~~~l~rlLr~L~~~   81 (214)
                      .++..+++..++  +++.+++.+.+|++++++|||++|++.|+|   +|++|||+++|+   +|.+++.++||||+|++.
T Consensus        16 ~~~~~~~~~~l~~~~l~~~~~~~~~l~~a~~lgif~~L~~~g~pg~~~t~~eLA~~~~~~~~~~~~~~~l~rlLr~L~~~   95 (372)
T 1fp1_D           16 TSEQTEDSACLSAMVLTTNLVYPAVLNAAIDLNLFEIIAKATPPGAFMSPSEIASKLPASTQHSDLPNRLDRMLRLLASY   95 (372)
T ss_dssp             ---CCHHHHHHHHHHHHHTTHHHHHHHHHHHTTHHHHHHTCSSTTCCBCHHHHHTTSCGGGCCTTHHHHHHHHHHHHHHT
T ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHCChHHHHHhcCCCCCCcCHHHHHHhcCCCCCCCcChHHHHHHHHHHhhC
Confidence            345778888999  999999999999999999999999975226   999999999999   432238999999999999


Q ss_pred             CceeeecCC-CCCCccceeeCCCCCcccccccc-c---cchHHHHHHhhccchhhhhHhHHHhhcCCCCChhhHHHH---
Q 040620           82 GFFVQQKDG-KNEQEEESILLPPHLDFFSRISL-Q---LQGSTILLLIADATFTTSFHFLSTWLQNDDQTLFGTADG---  153 (214)
Q Consensus        82 g~l~~~~~~-~~~~~~~~y~~t~~~~~~s~~l~-~---~~~~~~~~~~~~~~~~~~~~~l~~~lr~~~~~~f~~~~g---  153 (214)
                      |+|++...+ .++..+++|++|+.    ++.|+ +   .++++++.++.++.++..|.+|+++++++..++|...+|   
T Consensus        96 gll~~~~~~~~~g~~~~~y~~t~~----s~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~g~~~~~~~~~g~~~  171 (372)
T 1fp1_D           96 SVLTSTTRTIEDGGAERVYGLSMV----GKYLVPDESRGYLASFTTFLCYPALLQVWMNFKEAVVDEDIDLFKNVHGVTK  171 (372)
T ss_dssp             TSEEEEEEECTTSCEEEEEEECTT----GGGGSTTCTTCCCTHHHHHHTCHHHHHHHTTHHHHHHSCC------------
T ss_pred             CceEecccccCCCCcCCeEecCHH----HHHHhCCCCCCCHHHHHHHhcCchHHHHHHHHHHHHHcCCCChhHHHhCCCH
Confidence            999987200 00000159999999    99887 2   368888877766667889999999999883366655433   


Q ss_pred             ------------HHHHHhhhhhhhhHHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          154 ------------IFYEAMITDFELIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       154 ------------~f~~am~~~~~~~~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                                  .|+++|...+......+++.++ .+.+..+|||||||+|.++..+++++|+++++++|+|
T Consensus       172 ~~~~~~~~~~~~~f~~~m~~~~~~~~~~l~~~~~-~~~~~~~vLDvG~G~G~~~~~l~~~~~~~~~~~~D~~  242 (372)
T 1fp1_D          172 YEFMGKDKKMNQIFNKSMVDVCATEMKRMLEIYT-GFEGISTLVDVGGGSGRNLELIISKYPLIKGINFDLP  242 (372)
T ss_dssp             --CCSSCHHHHHHHHHHHHHHHHHHHHHHHHHCC-TTTTCSEEEEETCTTSHHHHHHHHHCTTCEEEEEECH
T ss_pred             HHHHHhCHHHHHHHHHHHHhhhHHHHHHHHHHhh-ccCCCCEEEEeCCCCcHHHHHHHHHCCCCeEEEeChH
Confidence                        6889998887777778888885 3667789999999999999999999999999999985

>3dp7_A SAM-dependent methyltransferase; structural genomics, protein structure initiative, NEW YORK structural genomix research; 2.33A {Bacteroides vulgatus}

Probab=99.95  E-value=8.5e-28  Score=210.22  Aligned_cols=183  Identities=15%  Similarity=0.084  Sum_probs=145.9

Q ss_pred             CchhhhhHHHHHHHHHHHHhHHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620            9 GAREHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus         9 ~~~~~~~~~~~l~~~~~g~~~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      .+.++.+++..+++++.|++.+++|++++++||||+|+++++|+|++|||+++|+++   +.++||||+|++.|+|+++ 
T Consensus         8 ~~~~~~~a~~~l~~l~~g~~~~~~l~~a~~lgifd~L~~~~~~~t~~eLA~~~g~~~---~~l~rlLr~l~~~g~l~~~-   83 (363)
T 3dp7_A            8 EQCTAAEAQRLAQEIAFGPVVFQVSRLMLKFGIFQLLSGKREGYTLQEISGRTGLTR---YAAQVLLEASLTIGTILLE-   83 (363)
T ss_dssp             SCCCSTTHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHTCTTCBCHHHHHHHHTCCH---HHHHHHHHHHHHHTSEEEE-
T ss_pred             CchhHHHHHHHHHHHHhhHHHHHHHHHHHHhCHHHHHHhcCCCCCHHHHHHHhCcCH---HHHHHHHHHHhhCCCeEec-
Confidence            345688899999999999999999999999999999998558999999999999999   9999999999999999886 


Q ss_pred             CCCCCCccceeeCCCCCcccccccc-ccchHHHHHHhhccchhhhhHhHHHhhcCCCCChhhHHHH--------------
Q 040620           89 DGKNEQEEESILLPPHLDFFSRISL-QLQGSTILLLIADATFTTSFHFLSTWLQNDDQTLFGTADG--------------  153 (214)
Q Consensus        89 ~~~~~~~~~~y~~t~~~~~~s~~l~-~~~~~~~~~~~~~~~~~~~~~~l~~~lr~~~~~~f~~~~g--------------  153 (214)
                             +++|++|+.    ++.|+ +.....++. +.....+..|.+|++++|++++ ++...+|              
T Consensus        84 -------~~~y~~t~~----s~~L~~~~~~~~~~~-~~~~~~~~~~~~L~~~lr~g~~-~~~~~~g~~~~~~~~~~~~~~  150 (363)
T 3dp7_A           84 -------EDRYVLAKA----GWFLLNDKMARVNME-FNHDVNYQGLFHLEEALLNGRP-EGLKVFGEWPTIYEGLSQLPE  150 (363)
T ss_dssp             -------TTEEEECHH----HHHHHHCHHHHHHHH-HHHHTTHHHHTTHHHHHHHSSC-GGGGGTCCCSSHHHHGGGSCH
T ss_pred             -------CCEEecccc----hHHhhCCCcccchhe-eecHHhhhhHHHHHHHHhcCCC-ccccccCchHhHHHHHhhCHH
Confidence                   489999999    98887 333333333 3344678999999999998863 3333322              


Q ss_pred             -------HHHHHhhhhhhhhHHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          154 -------IFYEAMITDFELIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       154 -------~f~~am~~~~~~~~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                             .|+++|.....   ..++..+.  ..+.++|||||||+|.++..+++++|+++++++|+|
T Consensus       151 ~~~~~~~~f~~~~~~~~~---~~~l~~~~--~~~~~~vlDvG~G~G~~~~~l~~~~p~~~~~~~D~~  212 (363)
T 3dp7_A          151 QVQKSWFGFDHFYSDQSF---GKALEIVF--SHHPKRLLDIGGNTGKWATQCVQYNKEVEVTIVDLP  212 (363)
T ss_dssp             HHHHHHHHHHHHTTCCCC---HHHHHHHG--GGCCSEEEEESCTTCHHHHHHHHHSTTCEEEEEECH
T ss_pred             HHHHHHHHHHHHhhhhhH---HHHHHHhc--ccCCCEEEEeCCCcCHHHHHHHHhCCCCEEEEEeCH
Confidence                   14444443321   12334333  256789999999999999999999999999999986

>3mcz_A O-methyltransferase; adomet_mtases, S-adenosylmethionine-dependent methyltransfer structural genomics, PSI-2; HET: MSE; 1.90A {Burkholderia thailandensis}

Probab=99.94  E-value=1.2e-26  Score=201.13  Aligned_cols=181  Identities=13%  Similarity=0.163  Sum_probs=149.4

Q ss_pred             chhhhhHHHHHHHHHHHHhHHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecC
Q 040620           10 AREHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKD   89 (214)
Q Consensus        10 ~~~~~~~~~~l~~~~~g~~~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~   89 (214)
                      |....+....+++++.+++.+.+|++++++|||++|+   +|+|++|||+++|+++   +.++||||+|++.|+|+++  
T Consensus        18 ~~~~l~~p~~l~~~~~~~~~~~~l~~a~~lgif~~l~---~~~t~~elA~~~~~~~---~~l~rlLr~L~~~gll~~~--   89 (352)
T 3mcz_A           18 DKAALTSVVDLVKLSDQYRQSAILHYAVADKLFDLTQ---TGRTPAEVAASFGMVE---GKAAILLHALAALGLLTKE--   89 (352)
T ss_dssp             SCCCCCSHHHHHHHHHTHHHHHHHHHHHHTTHHHHTT---SCBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEE--
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHHCChHHHhC---CCCCHHHHHHHhCcCh---HHHHHHHHHHHHCCCeEec--
Confidence            3333344445999999999999999999999999997   4999999999999999   9999999999999999998  


Q ss_pred             CCCCCccceeeCCCCCcccccccc----ccchHHHHHHhhccchhhhhHhHHHhhcCCCCChhhHHHH---------HHH
Q 040620           90 GKNEQEEESILLPPHLDFFSRISL----QLQGSTILLLIADATFTTSFHFLSTWLQNDDQTLFGTADG---------IFY  156 (214)
Q Consensus        90 ~~~~~~~~~y~~t~~~~~~s~~l~----~~~~~~~~~~~~~~~~~~~~~~l~~~lr~~~~~~f~~~~g---------~f~  156 (214)
                            +++|.+|+.    ++.++    +.+++.++.+.  ...+..|.+++++++++.+.+|.....         .|.
T Consensus        90 ------~~~y~~t~~----s~~~l~~~~~~~~~~~~~~~--~~~~~~~~~l~~~l~~g~~~~f~~~~~~~~~~~~~~~f~  157 (352)
T 3mcz_A           90 ------GDAFRNTAL----TERYLTTTSADYIGPIVEHQ--YLQWDNWPRLGEILRSEKPLAFQQESRFAHDTRARDAFN  157 (352)
T ss_dssp             ------TTEEEECHH----HHHHHSTTCTTCCHHHHHHH--HTTTTTGGGHHHHHTCSSCCTTSHHHHTTTCHHHHHHHH
T ss_pred             ------CCeeecCHH----HHhhccCCChhhHHHHHHHh--HHHHHHHHHHHHHHhCCCCCCcccccccccCHHHHHHHH
Confidence                  478999999    87654    35577776543  246788999999999997665433211         788


Q ss_pred             HHhhhhhhhhHHHHHhhcccccCC-CCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          157 EAMITDFELIASVLIEDCNEVSKG-LKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       157 ~am~~~~~~~~~~~l~~~~~~~~~-~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                      ++|...... ...+++.++  +.+ ..+|||||||+|.++..+++++|+.+++++|+|
T Consensus       158 ~~m~~~~~~-~~~~l~~~~--~~~~~~~vlDvG~G~G~~~~~l~~~~p~~~~~~~D~~  212 (352)
T 3mcz_A          158 DAMVRLSQP-MVDVVSELG--VFARARTVIDLAGGHGTYLAQVLRRHPQLTGQIWDLP  212 (352)
T ss_dssp             HHHHHHHHH-HHHHHHTCG--GGTTCCEEEEETCTTCHHHHHHHHHCTTCEEEEEECG
T ss_pred             HHHHhhhhh-HHHHHHhCC--CcCCCCEEEEeCCCcCHHHHHHHHhCCCCeEEEEECH
Confidence            899873322 246788888  555 899999999999999999999999999999986

>1x19_A CRTF-related protein; methyltransferase, bacteriochllochlorophyll, BCHU, SAM, SAH, adenosylmethyonine, S-adenosylhomocysteine, ADO-Met; 2.27A {Chlorobium tepidum} PDB: 1x1a_A* 1x1b_A* 1x1c_A* 1x1d_A*

Probab=99.94  E-value=9.8e-27  Score=202.72  Aligned_cols=185  Identities=16%  Similarity=0.266  Sum_probs=158.0

Q ss_pred             CCchhhhhHHHHHHHHHH-HHhHHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceee
Q 040620            8 NGAREHFQAQAQVWSYTY-NYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQ   86 (214)
Q Consensus         8 ~~~~~~~~~~~~l~~~~~-g~~~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~   86 (214)
                      +.+.++.+++.++++++. +++.+.+|++++++|||++|++  +|+|++|||+++|+++   +.++||||+|++.|+|++
T Consensus        22 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~lgif~~L~~--~~~t~~eLA~~~g~~~---~~l~rlLr~L~~~gll~~   96 (359)
T 1x19_A           22 MSNNDLLNYYHRANELVFKGLIEFSCMKAAIELDLFSHMAE--GPKDLATLAADTGSVP---PRLEMLLETLRQMRVINL   96 (359)
T ss_dssp             ECCCHHHHHHHHHHHHHTHHHHHHHHHHHHHHHTHHHHHTT--CCBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEE
T ss_pred             CCccccCCcchHHHHHHHHHHHHHHHHHHHHHcCcHHHHcC--CCCCHHHHHHHhCcCh---HHHHHHHHHHHhCCCeEe
Confidence            456678889999999986 8999999999999999999996  8999999999999999   999999999999999999


Q ss_pred             ecCCCCCCccceeeCCCCCcccccccc---c---cchHHHHHHhhccchhhhhHhHHHhhcCCCCChhhH---------H
Q 040620           87 QKDGKNEQEEESILLPPHLDFFSRISL---Q---LQGSTILLLIADATFTTSFHFLSTWLQNDDQTLFGT---------A  151 (214)
Q Consensus        87 ~~~~~~~~~~~~y~~t~~~~~~s~~l~---~---~~~~~~~~~~~~~~~~~~~~~l~~~lr~~~~~~f~~---------~  151 (214)
                      ++        ++|++|+..   +..+.   +   .++++++.++ ....+..|.+|+++++++.+  |+.         .
T Consensus        97 ~~--------~~y~~t~~~---~~~l~~~~~~~~~~~~~~~~~~-~~~~~~~~~~L~~~l~~g~~--~~~~~~~p~~~~~  162 (359)
T 1x19_A           97 ED--------GKWSLTEFA---DYMFSPTPKEPNLHQTPVAKAM-AFLADDFYMGLSQAVRGQKN--FKGQVPYPPVTRE  162 (359)
T ss_dssp             ET--------TEEEECHHH---HHHSSSSCSBTTBCCHHHHHHH-HHHHHHTGGGHHHHHTTSCC--CCCSSCSSCCSHH
T ss_pred             eC--------CeEecCHHH---HHHhcCCCCCccccHHHHHHHH-HHHHHHHHHHHHHHHhcCCC--CcccccCchhhHH
Confidence            84        699999961   44555   3   4678877665 34578899999999998764  221         1


Q ss_pred             HHHHHHHhhhhhh-hhHHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          152 DGIFYEAMITDFE-LIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       152 ~g~f~~am~~~~~-~~~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                      ...|.++|..... ...+.+++.++  +.+..+|||||||+|.++..+++++|+++++++|+|
T Consensus       163 ~~~f~~~m~~~~~~~~~~~l~~~~~--~~~~~~vLDvG~G~G~~~~~l~~~~p~~~~~~~D~~  223 (359)
T 1x19_A          163 DNLYFEEIHRSNAKFAIQLLLEEAK--LDGVKKMIDVGGGIGDISAAMLKHFPELDSTILNLP  223 (359)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHCC--CTTCCEEEEESCTTCHHHHHHHHHCTTCEEEEEECG
T ss_pred             HHHHHHHHHHhccchhHHHHHHhcC--CCCCCEEEEECCcccHHHHHHHHHCCCCeEEEEecH
Confidence            2278999998887 77778888888  777899999999999999999999999999999985

>1qzz_A RDMB, aclacinomycin-10-hydroxylase; anthracycline, methyltransferase, polyketide, tailoring enzymes, structural proteomics in E spine; HET: SAM; 2.10A {Streptomyces purpurascens} SCOP: a.4.5.29 c.66.1.12 PDB: 1r00_A* 1xds_A* 1xdu_A*

Probab=99.93  E-value=5.4e-26  Score=198.48  Aligned_cols=182  Identities=20%  Similarity=0.202  Sum_probs=152.7

Q ss_pred             hhhHHHHHHHHHHHHhHHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCC
Q 040620           13 HFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKN   92 (214)
Q Consensus        13 ~~~~~~~l~~~~~g~~~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~   92 (214)
                      ..+....+++++.+++.+.+|++++++|||++|.+  +|+|++|||+++|+++   +.++||||+|++.|+|.+..    
T Consensus        13 ~~~~~~~l~~~~~~~~~~~~l~~~~~l~i~~~l~~--~~~t~~eLA~~~g~~~---~~l~r~Lr~L~~~Gll~~~~----   83 (374)
T 1qzz_A           13 TDQDLDVLLKNLGNLVTPMALRVAATLRLVDHLLA--GADTLAGLADRTDTHP---QALSRLVRHLTVVGVLEGGE----   83 (374)
T ss_dssp             CHHHHHHHHHTTTCCHHHHHHHHHHHTTHHHHHHT--TCCSHHHHHHHHTCCH---HHHHHHHHHHHHTTSEECCC----
T ss_pred             CchHHHHHHHHHHhhHHHHHHHHHHHcChHHHHhC--CCCCHHHHHHHhCcCH---HHHHHHHHHHhhCCCEEEeC----
Confidence            34566789999999999999999999999999975  8999999999999999   99999999999999999865    


Q ss_pred             CCccc--eeeCCCCCcccccccc---ccchHHHHHHhhccchh-hhhHhHHHhhcCCCCChhhHHHH-------------
Q 040620           93 EQEEE--SILLPPHLDFFSRISL---QLQGSTILLLIADATFT-TSFHFLSTWLQNDDQTLFGTADG-------------  153 (214)
Q Consensus        93 ~~~~~--~y~~t~~~~~~s~~l~---~~~~~~~~~~~~~~~~~-~~~~~l~~~lr~~~~~~f~~~~g-------------  153 (214)
                         ++  .|++|+.    ++.|.   +.++..++.+...+..+ ..|.++.+.++++. .+|...+|             
T Consensus        84 ---~~~~~y~~t~~----s~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~-~~~~~~~g~~~~~~~~~~~~~  155 (374)
T 1qzz_A           84 ---KQGRPLRPTRL----GMLLADGHPAQQRAWLDLNGAVSHADLAFTGLLDVVRTGR-PAYAGRYGRPFWEDLSADVAL  155 (374)
T ss_dssp             ---C-CCCCEECTT----GGGGSTTCTTCHHHHHCTTSHHHHHHGGGGGHHHHHHHSC-CSHHHHHSSCHHHHHHHCHHH
T ss_pred             ---CCCeEEEEChH----HHhhcCCCcccHHHHHHHcCChhhHHHHHHHHHHHHhcCC-ChhhhhhCCCHHHHHhhChHH
Confidence               46  9999999    98887   34777877665444456 88999999999876 33443332             


Q ss_pred             --HHHHHhhhhhhhhHHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          154 --IFYEAMITDFELIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       154 --~f~~am~~~~~~~~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                        .|.++|........+.+++.++  +.+..+|||||||+|.++..+++++|+.+++++|+|
T Consensus       156 ~~~f~~~~~~~~~~~~~~~~~~~~--~~~~~~vlDvG~G~G~~~~~l~~~~~~~~~~~~D~~  215 (374)
T 1qzz_A          156 ADSFDALMSCDEDLAYEAPADAYD--WSAVRHVLDVGGGNGGMLAAIALRAPHLRGTLVELA  215 (374)
T ss_dssp             HHHHHHTCGGGSTTTTHHHHHTSC--CTTCCEEEEETCTTSHHHHHHHHHCTTCEEEEEECH
T ss_pred             HHHHHHHHHHhhHhHHHHHHHhCC--CCCCCEEEEECCCcCHHHHHHHHHCCCCEEEEEeCH
Confidence              6777787666655677888877  667889999999999999999999999999999973

>2r3s_A Uncharacterized protein; methyltransferase domain, structural genomics, joint center structural genomics, JCSG, protein structure initiative; HET: MSE; 2.15A {Nostoc punctiforme}

Probab=99.93  E-value=4.4e-26  Score=195.95  Aligned_cols=179  Identities=18%  Similarity=0.193  Sum_probs=151.3

Q ss_pred             HHHHHHHHHHhHHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccc
Q 040620           18 AQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEE   97 (214)
Q Consensus        18 ~~l~~~~~g~~~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~   97 (214)
                      ..+++++.+++.+.+|++++++|||++|++  +|+|++|||+++|+++   +.++||||+|++.|+|++.        ++
T Consensus         8 ~~l~~~~~~~~~~~~l~~~~~l~i~~~l~~--~~~t~~ela~~~~~~~---~~l~r~L~~L~~~g~l~~~--------~~   74 (335)
T 2r3s_A            8 ALFFNTVNAYQRSAAIKAAVELNVFTAISQ--GIESSQSLAQKCQTSE---RGMRMLCDYLVIIGFMTKQ--------AE   74 (335)
T ss_dssp             HHHHHHHTTHHHHHHHHHHHHTTHHHHHTT--SEECHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEE--------TT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcChHHHHhc--CCCCHHHHHHHhCCCc---hHHHHHHHHHHhcCCeEec--------CC
Confidence            578899999999999999999999999996  8999999999999999   9999999999999999885        58


Q ss_pred             eeeCCCCCcccc-cccc---ccchHHHHHHhhccchhhhhHhHHHhhcCCCCCh--hhHHH------HHHHHHhhhhhhh
Q 040620           98 SILLPPHLDFFS-RISL---QLQGSTILLLIADATFTTSFHFLSTWLQNDDQTL--FGTAD------GIFYEAMITDFEL  165 (214)
Q Consensus        98 ~y~~t~~~~~~s-~~l~---~~~~~~~~~~~~~~~~~~~~~~l~~~lr~~~~~~--f~~~~------g~f~~am~~~~~~  165 (214)
                      +|++|+.    + +.+.   +.++..++.++.++..+..|.++.++++++.+..  |+...      ..|.++|......
T Consensus        75 ~y~~t~~----~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  150 (335)
T 2r3s_A           75 GYRLTSD----SAMFLDRQSKFYVGDAIEFLLSPMITNGFNDLTAAVLKGGTAISSEGTLSPEHPVWVQFAKAMSPMMAN  150 (335)
T ss_dssp             EEEECHH----HHHHTCTTSTTCCGGGHHHHTCHHHHGGGTTHHHHHHHTSCCSTTTGGGSTTCTHHHHHHHHSGGGGHH
T ss_pred             EEecCHH----HHHHhccCCcHHHHHHHHHhcchhhHHHHHhHHHHHhcCCCCCCCcccccCCHHHHHHHHHHHHHHHhh
Confidence            9999999    8 5665   3457777777655467889999999999876321  22211      1788899888777


Q ss_pred             hHHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          166 IASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       166 ~~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                      ....+++.+++.+.+..+|||||||+|.++..+++++|+.+++++|++
T Consensus       151 ~~~~~~~~~~~~~~~~~~vlDvG~G~G~~~~~l~~~~p~~~~~~~D~~  198 (335)
T 2r3s_A          151 PAQLIAQLVNENKIEPLKVLDISASHGLFGIAVAQHNPNAEIFGVDWA  198 (335)
T ss_dssp             HHHHHHHHHTC--CCCSEEEEETCTTCHHHHHHHHHCTTCEEEEEECH
T ss_pred             hHHHHHHhcccccCCCCEEEEECCCcCHHHHHHHHHCCCCeEEEEecH
Confidence            777788888732267889999999999999999999999999999974

>1tw3_A COMT, carminomycin 4-O-methyltransferase; anthracycline, methylate, tailoring enzyme, polyketide, S-adenosyl-L-homocystein; HET: SAH ERT; 2.35A {Streptomyces peucetius} SCOP: a.4.5.29 c.66.1.12 PDB: 1tw2_A*

Probab=99.93  E-value=2e-25  Score=194.03  Aligned_cols=179  Identities=16%  Similarity=0.191  Sum_probs=151.6

Q ss_pred             HHHHHHHHHHHHhHHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCc
Q 040620           16 AQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQE   95 (214)
Q Consensus        16 ~~~~l~~~~~g~~~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~   95 (214)
                      ...++++++.+++.+.+|++++++|||++|.+  +|+|++|||+++|+++   +.++|+||+|++.|+|.+..       
T Consensus        19 ~~~~~~~~~~~~~~~~~l~~~~~l~i~~~l~~--~~~t~~ela~~~~~~~---~~l~r~L~~L~~~g~~~~~~-------   86 (360)
T 1tw3_A           19 DALRTLIRLGSLHTPMVVRTAATLRLVDHILA--GARTVKALAARTDTRP---EALLRLIRHLVAIGLLEEDA-------   86 (360)
T ss_dssp             HHHHHHHHHHCSHHHHHHHHHHHTTHHHHHHT--TCCBHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEEE-------
T ss_pred             chHHHHHHHHhHHHHHHHHHHHHhCHHHHHhC--CCCCHHHHHHHhCcCH---HHHHHHHHHHHHCCCEEecC-------
Confidence            35678899999999999999999999999975  8999999999999999   99999999999999999976       


Q ss_pred             cceeeCCCCCcccccccc---ccchHHHHHHhhccc-hhhhhHhHHHhhcCCCCChhhHHHH---------------HHH
Q 040620           96 EESILLPPHLDFFSRISL---QLQGSTILLLIADAT-FTTSFHFLSTWLQNDDQTLFGTADG---------------IFY  156 (214)
Q Consensus        96 ~~~y~~t~~~~~~s~~l~---~~~~~~~~~~~~~~~-~~~~~~~l~~~lr~~~~~~f~~~~g---------------~f~  156 (214)
                      +++|.+|+.    ++.|.   +.++..++.+...+. .+..|.++.+.++++.+ +|...+|               .|.
T Consensus        87 ~g~y~~t~~----s~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~g~~-~~~~~~g~~~~~~~~~~p~~~~~f~  161 (360)
T 1tw3_A           87 PGEFVPTEV----GELLADDHPAAQRAWHDLTQAVARADISFTRLPDAIRTGRP-TYESIYGKPFYEDLAGRPDLRASFD  161 (360)
T ss_dssp             TTEEEECTT----GGGGSTTSTTCHHHHTCTTSHHHHHGGGGGGHHHHHHHCCC-CHHHHHSSCHHHHHHTCHHHHHHHH
T ss_pred             CCeEEeCHH----HHHHhcCCchhHHHHHHHhcCchhHHHHHHHHHHHHHcCCC-HHHHhcCCCHHHHHHhChHHHHHHH
Confidence            689999999    99887   347777765554333 57889999999998763 3332222               677


Q ss_pred             HHhhhhhhhhHHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          157 EAMITDFELIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       157 ~am~~~~~~~~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                      ++|........+.+++.++  +.+..+|||||||+|.++..+++++|+.+++++|+|
T Consensus       162 ~~~~~~~~~~~~~l~~~~~--~~~~~~vLDvG~G~G~~~~~l~~~~~~~~~~~~D~~  216 (360)
T 1tw3_A          162 SLLACDQDVAFDAPAAAYD--WTNVRHVLDVGGGKGGFAAAIARRAPHVSATVLEMA  216 (360)
T ss_dssp             HHHTTTTTTTTHHHHHHSC--CTTCSEEEEETCTTSHHHHHHHHHCTTCEEEEEECT
T ss_pred             HHHHHHHHHhHHHHHHhCC--CccCcEEEEeCCcCcHHHHHHHHhCCCCEEEEecCH
Confidence            8887776666677888887  667789999999999999999999999999999985

>2qm3_A Predicted methyltransferase; putative methyltransferase, structural genomics, pyrococcus PSI-2, protein structure initiative; HET: MSE; 2.05A {Pyrococcus furiosus dsm 3638}

Probab=98.62  E-value=2.6e-08  Score=86.89  Aligned_cols=147  Identities=10%  Similarity=0.043  Sum_probs=88.2

Q ss_pred             CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc-c---c
Q 040620           40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL-Q---L  115 (214)
Q Consensus        40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~-~---~  115 (214)
                      ++|..| .  +|.|++|||+++|+++   +.+++||+.|++.|+++..        ++ |++|+.    +..++ .   .
T Consensus        47 ~ll~~L-~--~~~t~~eLa~~~g~~~---~~v~~~L~~l~~~gll~~~--------~~-~~lt~~----~~~~l~~~~~~  107 (373)
T 2qm3_A           47 NVLSAV-L--ASDDIWRIVDLSEEPL---PLVVAILESLNELGYVTFE--------DG-VKLTEK----GEELVAEYGIG  107 (373)
T ss_dssp             HHHHHH-H--HCSCHHHHHHHHTSCH---HHHHHHHHHHHHTTSEECS--------SS-SEECHH----HHHHHHHHTCC
T ss_pred             HHHHHh-c--CCCCHHHHHHHhCCCh---HHHHHHHHHHhhCCcEEEC--------CC-EEECHH----HHHHHHhcCcc
Confidence            678888 4  7999999999999999   9999999999999999875        34 999998    55543 1   1


Q ss_pred             chHHHH-HHhh-----ccchhhhhHhHHHhhcCCCCChhhHHHHHHHHHhhhhhhhhHHHHHhhcccccCCCCcEEeecC
Q 040620          116 QGSTIL-LLIA-----DATFTTSFHFLSTWLQNDDQTLFGTADGIFYEAMITDFELIASVLIEDCNEVSKGLKPLVDVGG  189 (214)
Q Consensus       116 ~~~~~~-~~~~-----~~~~~~~~~~l~~~lr~~~~~~f~~~~g~f~~am~~~~~~~~~~~l~~~~~~~~~~~~vvDVGG  189 (214)
                      .....+ ....     ...+...|..+.+.++... .+...    |.+..... ......++...........+|+||| 
T Consensus       108 ~~~~~~~~~~~g~g~~~~~~~~~~~~l~~~~~~~~-~~~~~----~~~~~~~~-~~~~~~~l~~~~~~~~~~~~VLDlG-  180 (373)
T 2qm3_A          108 KRYDFTCPHCQGKTVDLQAFADLLEQFREIVKDRP-EPLHE----FDQAYVTP-ETTVARVILMHTRGDLENKDIFVLG-  180 (373)
T ss_dssp             CCCC------------CGGGHHHHHHHHHHHTTCC-CCCGG----GTCCCBCH-HHHHHHHHHHHHTTCSTTCEEEEES-
T ss_pred             ccccccchhhcCCCcchhhhHHHHHHHHHHHhcCC-ccchh----cCCeecCH-HHHHHHHHHHhhcCCCCCCEEEEEC-
Confidence            100000 0000     0011123444555555332 11100    11100000 0011111111110122457999999 


Q ss_pred             CchHHHHHHHHHCCCCeEEEecC
Q 040620          190 STGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       190 G~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      |+|.+++.+++..|+.+++++|+
T Consensus       181 G~G~~~~~la~~~~~~~v~~vDi  203 (373)
T 2qm3_A          181 DDDLTSIALMLSGLPKRIAVLDI  203 (373)
T ss_dssp             CTTCHHHHHHHHTCCSEEEEECS
T ss_pred             CCCHHHHHHHHhCCCCEEEEEEC
Confidence            99999999999999999999997

>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A

Probab=97.59  E-value=2e-05  Score=51.89  Aligned_cols=55  Identities=11%  Similarity=0.217  Sum_probs=46.6

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCC
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLP  102 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t  102 (214)
                      +..|+++|..++.|+|..|||+.+|++.   ..+.+.+..|...|++....       .+.|.++
T Consensus        12 ~~~IL~~L~~~~~~~s~~eLA~~lglsr---~tv~~~l~~L~~~G~I~~~~-------~G~y~lg   66 (67)
T 2heo_A           12 EQKILQVLSDDGGPVAIFQLVKKCQVPK---KTLNQVLYRLKKEDRVSSPS-------PKYWSIG   66 (67)
T ss_dssp             HHHHHHHHHHHCSCEEHHHHHHHHCSCH---HHHHHHHHHHHHTTSEEEEE-------TTEEEEC
T ss_pred             HHHHHHHHHHcCCCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCcEecCC-------CceEeeC
Confidence            4457788876546899999999999999   99999999999999987755       5788764

>3mq2_A 16S rRNA methyltransferase; methyltranferase, ribosomal, antibiotic resistance, aminoglycoside, S-adenosyl-L-methionine; HET: SAH; 1.69A {Streptomyces SP}

Probab=97.49  E-value=8.2e-05  Score=59.04  Aligned_cols=36  Identities=19%  Similarity=0.242  Sum_probs=32.3

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                      .....+|||||||+|.++..+++.+|+.+++.+|+-
T Consensus        25 ~~~~~~vLDiGcG~G~~~~~la~~~p~~~v~gvD~s   60 (218)
T 3mq2_A           25 SQYDDVVLDVGTGDGKHPYKVARQNPSRLVVALDAD   60 (218)
T ss_dssp             TTSSEEEEEESCTTCHHHHHHHHHCTTEEEEEEESC
T ss_pred             ccCCCEEEEecCCCCHHHHHHHHHCCCCEEEEEECC
Confidence            345679999999999999999999999999999973

>3e05_A Precorrin-6Y C5,15-methyltransferase (decarboxyla; porphyrin metabolism, S-adenosyl-methionine; 1.80A {Geobacter metallireducens} SCOP: c.66.1.0

Probab=97.44  E-value=0.0002  Score=56.24  Aligned_cols=42  Identities=10%  Similarity=0.196  Sum_probs=35.8

Q ss_pred             HHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          169 VLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       169 ~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .++...+  .....+|||||||+|.++..+++..|..+++.+|+
T Consensus        31 ~~l~~l~--~~~~~~vLDiG~G~G~~~~~la~~~~~~~v~~vD~   72 (204)
T 3e05_A           31 VTLSKLR--LQDDLVMWDIGAGSASVSIEASNLMPNGRIFALER   72 (204)
T ss_dssp             HHHHHTT--CCTTCEEEEETCTTCHHHHHHHHHCTTSEEEEEEC
T ss_pred             HHHHHcC--CCCCCEEEEECCCCCHHHHHHHHHCCCCEEEEEeC
Confidence            3455554  55678999999999999999999999999999996

>2fca_A TRNA (guanine-N(7)-)-methyltransferase; 2.10A {Bacillus subtilis} SCOP: c.66.1.53

Probab=97.43  E-value=0.00013  Score=58.28  Aligned_cols=33  Identities=18%  Similarity=0.246  Sum_probs=30.7

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+|||||||+|.++..+++.+|+.+++.+|+
T Consensus        38 ~~~~vLDiGcG~G~~~~~la~~~p~~~v~giD~   70 (213)
T 2fca_A           38 DNPIHIEVGTGKGQFISGMAKQNPDINYIGIEL   70 (213)
T ss_dssp             CCCEEEEECCTTSHHHHHHHHHCTTSEEEEECS
T ss_pred             CCceEEEEecCCCHHHHHHHHHCCCCCEEEEEe
Confidence            356899999999999999999999999999996

>3g07_A 7SK snRNA methylphosphate capping enzyme; structural genomics consortium (SGC), methyltransferase, phosphoprotein, S-adenosyl-L-methionine; HET: SAM; 2.65A {Homo sapiens}

Probab=97.40  E-value=0.00014  Score=60.77  Aligned_cols=42  Identities=12%  Similarity=0.151  Sum_probs=35.1

Q ss_pred             HhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          171 IEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       171 l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +..+...+...++|||||||+|.++..+++++|..+++.+|+
T Consensus        37 l~~l~~~~~~~~~VLDiGCG~G~~~~~la~~~~~~~v~gvDi   78 (292)
T 3g07_A           37 LRVLKPEWFRGRDVLDLGCNVGHLTLSIACKWGPSRMVGLDI   78 (292)
T ss_dssp             GGTSCGGGTTTSEEEEESCTTCHHHHHHHHHTCCSEEEEEES
T ss_pred             HHhhhhhhcCCCcEEEeCCCCCHHHHHHHHHcCCCEEEEECC
Confidence            344443344578999999999999999999999999999997

>4dzr_A Protein-(glutamine-N5) methyltransferase, release specific; structural genomics, PSI-biology; 2.55A {Alicyclobacillus acidocaldarius subsp}

Probab=97.37  E-value=0.00018  Score=56.16  Aligned_cols=34  Identities=29%  Similarity=0.398  Sum_probs=31.8

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+..+|+|+|||+|.++..+++.+|+.+++.+|+
T Consensus        29 ~~~~~vLDiG~G~G~~~~~l~~~~~~~~v~~vD~   62 (215)
T 4dzr_A           29 PSGTRVIDVGTGSGCIAVSIALACPGVSVTAVDL   62 (215)
T ss_dssp             CTTEEEEEEESSBCHHHHHHHHHCTTEEEEEEEC
T ss_pred             CCCCEEEEecCCHhHHHHHHHHhCCCCeEEEEEC
Confidence            4578999999999999999999999999999997

>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=97.37  E-value=0.00033  Score=48.88  Aligned_cols=60  Identities=8%  Similarity=0.141  Sum_probs=51.2

Q ss_pred             HHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           31 LSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        31 ~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      .++..-.++.|+..| .  +++|+.|||+.+++++   ..+++.|+.|...|++....        +.|.+++.
T Consensus        26 ~~l~~~~r~~Il~~L-~--~~~~~~eLa~~l~is~---~tv~~~L~~L~~~Glv~~~~--------g~y~l~~~   85 (96)
T 1y0u_A           26 YAVTNPVRRKILRML-D--KGRSEEEIMQTLSLSK---KQLDYHLKVLEAGFCIERVG--------ERWVVTDA   85 (96)
T ss_dssp             HHHSCHHHHHHHHHH-H--TTCCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEET--------TEEEECTT
T ss_pred             HHhCCHHHHHHHHHH-c--CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEEC--------CEEEECCC
Confidence            344445566788888 5  8899999999999999   99999999999999999874        58999988

>3dxy_A TRNA (guanine-N(7)-)-methyltransferase; rossmann fold methyltransferase, tRNA modification, S-adenosyl-L-methionine, TR processing; HET: SAM; 1.50A {Escherichia coli} PDB: 3dxx_A* 3dxz_A*

Probab=97.37  E-value=0.00016  Score=58.10  Aligned_cols=33  Identities=15%  Similarity=0.164  Sum_probs=30.9

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+|||||||+|.++..+++.+|+.+++.+|+
T Consensus        34 ~~~~vLDiGcG~G~~~~~lA~~~p~~~v~giD~   66 (218)
T 3dxy_A           34 EAPVTLEIGFGMGASLVAMAKDRPEQDFLGIEV   66 (218)
T ss_dssp             CCCEEEEESCTTCHHHHHHHHHCTTSEEEEECS
T ss_pred             CCCeEEEEeeeChHHHHHHHHHCCCCeEEEEEe
Confidence            457999999999999999999999999999986

>1yzh_A TRNA (guanine-N(7)-)-methyltransferase; alpha-beta-alpha sandwich, S-adenosylmeth dependent, structural genomics, PSI; 2.02A {Streptococcus pneumoniae} SCOP: c.66.1.53

Probab=97.37  E-value=0.00018  Score=57.11  Aligned_cols=33  Identities=21%  Similarity=0.281  Sum_probs=30.8

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+|||||||+|.++..+++.+|+.+++.+|+
T Consensus        41 ~~~~vLDiGcG~G~~~~~la~~~p~~~v~gvD~   73 (214)
T 1yzh_A           41 DNPIHVEVGSGKGAFVSGMAKQNPDINYIGIDI   73 (214)
T ss_dssp             CCCEEEEESCTTSHHHHHHHHHCTTSEEEEEES
T ss_pred             CCCeEEEEccCcCHHHHHHHHHCCCCCEEEEEc
Confidence            357899999999999999999999999999996

>3dtn_A Putative methyltransferase MM_2633; structural genomics, unknown function, PSI-2, protein structure initiative; 2.09A {Methanosarcina mazei}

Probab=97.32  E-value=0.00055  Score=54.62  Aligned_cols=43  Identities=19%  Similarity=0.378  Sum_probs=35.0

Q ss_pred             HHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          169 VLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       169 ~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .++...+ ...+..+|||||||+|.++..+++.+|+.+++++|+
T Consensus        34 ~~~~~~~-~~~~~~~vLDiG~G~G~~~~~l~~~~~~~~v~~vD~   76 (234)
T 3dtn_A           34 VSVSIAS-VDTENPDILDLGAGTGLLSAFLMEKYPEATFTLVDM   76 (234)
T ss_dssp             HHHHTCC-CSCSSCEEEEETCTTSHHHHHHHHHCTTCEEEEEES
T ss_pred             HHHHHhh-cCCCCCeEEEecCCCCHHHHHHHHhCCCCeEEEEEC
Confidence            3444443 234568999999999999999999999999999997

>3jwh_A HEN1; methyltransferase; HET: SAH; 2.20A {Anabaena variabilis} PDB: 3jwj_A

Probab=97.30  E-value=0.00021  Score=56.55  Aligned_cols=34  Identities=12%  Similarity=0.176  Sum_probs=31.2

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+..+|||||||+|.++..++++.|..+++.+|+
T Consensus        28 ~~~~~vLDiGcG~G~~~~~l~~~~~~~~v~gvD~   61 (217)
T 3jwh_A           28 SNARRVIDLGCGQGNLLKILLKDSFFEQITGVDV   61 (217)
T ss_dssp             TTCCEEEEETCTTCHHHHHHHHCTTCSEEEEEES
T ss_pred             cCCCEEEEeCCCCCHHHHHHHhhCCCCEEEEEEC
Confidence            3467999999999999999999999999999996

>3mq0_A Transcriptional repressor of the blcabc operon; helix-turn-helix, GAF fold, transcription repressor; 1.79A {Agrobacterium tumefaciens}

Probab=97.30  E-value=0.00011  Score=61.33  Aligned_cols=62  Identities=19%  Similarity=0.403  Sum_probs=51.5

Q ss_pred             HHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           31 LSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        31 ~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      +++.-+  +.|+++|...++++|+.|||+++|+++   ..+.|+|+.|+..|++.+++       +++|.+++.
T Consensus        27 ~sl~Ra--l~IL~~l~~~~~~ltl~eia~~lgl~k---sTv~RlL~tL~~~G~v~~~~-------~~~Y~LG~~   88 (275)
T 3mq0_A           27 PALRRA--VRILDLVAGSPRDLTAAELTRFLDLPK---SSAHGLLAVMTELDLLARSA-------DGTLRIGPH   88 (275)
T ss_dssp             HHHHHH--HHHHHHHHHCSSCEEHHHHHHHHTCC-----CHHHHHHHHHHTTSEEECT-------TSEEEECTH
T ss_pred             hHHHHH--HHHHHHHhhCCCCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEECC-------CCcEEehHH
Confidence            344444  467888887657899999999999999   99999999999999999986       579999988

>2p35_A Trans-aconitate 2-methyltransferase; SAM dependent methyltrans agrobacterium tumefaciens, structural genomics, PSI-2; HET: SAH; 1.95A {Agrobacterium tumefaciens str}

Probab=97.26  E-value=0.0003  Score=56.90  Aligned_cols=43  Identities=12%  Similarity=0.105  Sum_probs=36.5

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+++.++  .....+|||||||+|.++..+++++|..+++++|+
T Consensus        23 ~~l~~~~~--~~~~~~vLdiG~G~G~~~~~l~~~~~~~~v~~~D~   65 (259)
T 2p35_A           23 RDLLAQVP--LERVLNGYDLGCGPGNSTELLTDRYGVNVITGIDS   65 (259)
T ss_dssp             HHHHTTCC--CSCCSSEEEETCTTTHHHHHHHHHHCTTSEEEEES
T ss_pred             HHHHHhcC--CCCCCEEEEecCcCCHHHHHHHHhCCCCEEEEEEC
Confidence            34566555  45678999999999999999999999999999996

>3jwg_A HEN1, methyltransferase type 12; 1.90A {Clostridium thermocellum} PDB: 3jwi_A

Probab=97.26  E-value=0.00024  Score=56.26  Aligned_cols=34  Identities=15%  Similarity=0.169  Sum_probs=31.3

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+..+|||||||+|.++..++++.|..+++.+|+
T Consensus        28 ~~~~~vLDiGcG~G~~~~~l~~~~~~~~v~gvD~   61 (219)
T 3jwg_A           28 VNAKKVIDLGCGEGNLLSLLLKDKSFEQITGVDV   61 (219)
T ss_dssp             TTCCEEEEETCTTCHHHHHHHTSTTCCEEEEEES
T ss_pred             cCCCEEEEecCCCCHHHHHHHhcCCCCEEEEEEC
Confidence            3467999999999999999999999999999997

>3ckk_A TRNA (guanine-N(7)-)-methyltransferase; mettl1, S-adenosyl-L-methionine, tRNA Pro structural genomics, structural genomics consortium, SGC; HET: SAM; 1.55A {Homo sapiens}

Probab=97.25  E-value=0.00014  Score=59.14  Aligned_cols=33  Identities=21%  Similarity=0.330  Sum_probs=30.7

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +..+|||||||.|.++..+++.+|+.+++++|+
T Consensus        46 ~~~~vLDiGcG~G~~~~~la~~~p~~~v~GiDi   78 (235)
T 3ckk_A           46 AQVEFADIGCGYGGLLVELSPLFPDTLILGLEI   78 (235)
T ss_dssp             CCEEEEEETCTTCHHHHHHGGGSTTSEEEEEES
T ss_pred             CCCeEEEEccCCcHHHHHHHHHCCCCeEEEEEC
Confidence            456899999999999999999999999999986

>3bkx_A SAM-dependent methyltransferase; YP_807781.1, cyclopropane-fatty-acyl-phospholipid synthase-L protein, methyltransferase domain; 1.85A {Lactobacillus casei}

Probab=97.24  E-value=0.00045  Score=56.51  Aligned_cols=42  Identities=14%  Similarity=0.253  Sum_probs=35.0

Q ss_pred             HHHhhcccccCCCCcEEeecCCchHHHHHHHHHC-CCCeEEEecC
Q 040620          169 VLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAF-PDTKCTVFAC  212 (214)
Q Consensus       169 ~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl  212 (214)
                      .+++.++  ..+..+|||||||.|.++..+++++ |+.+++++|+
T Consensus        34 ~l~~~~~--~~~~~~vLDiGcG~G~~~~~l~~~~g~~~~v~gvD~   76 (275)
T 3bkx_A           34 AIAEAWQ--VKPGEKILEIGCGQGDLSAVLADQVGSSGHVTGIDI   76 (275)
T ss_dssp             HHHHHHT--CCTTCEEEEESCTTSHHHHHHHHHHCTTCEEEEECS
T ss_pred             HHHHHcC--CCCCCEEEEeCCCCCHHHHHHHHHhCCCCEEEEEEC
Confidence            3445444  5567899999999999999999996 8899999997

>2vdv_E TRNA (guanine-N(7)-)-methyltransferase; S-adenosyl-L-methionine, phosphorylation, M7G, spout MT, tRNA processing; HET: SAM; 2.30A {Saccharomyces cerevisiae} PDB: 2vdu_E

Probab=97.21  E-value=0.00028  Score=57.36  Aligned_cols=34  Identities=18%  Similarity=0.297  Sum_probs=31.3

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+..+|||||||+|.++..+++.+|+.+++.+|+
T Consensus        48 ~~~~~vLDiGcG~G~~~~~la~~~~~~~v~gvD~   81 (246)
T 2vdv_E           48 TKKVTIADIGCGFGGLMIDLSPAFPEDLILGMEI   81 (246)
T ss_dssp             SCCEEEEEETCTTSHHHHHHHHHSTTSEEEEEES
T ss_pred             CCCCEEEEEcCCCCHHHHHHHHhCCCCCEEEEEc
Confidence            3567999999999999999999999999999996

>3hem_A Cyclopropane-fatty-acyl-phospholipid synthase 2; protein-ligand complex, cytoplasm, lipid synthesis, methyltransferase; HET: D22; 2.39A {Mycobacterium tuberculosis} SCOP: c.66.1.18 PDB: 1kpi_A*

Probab=97.17  E-value=0.00051  Score=57.32  Aligned_cols=42  Identities=14%  Similarity=0.231  Sum_probs=35.0

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+++.++  ..+..+|||||||+|.++..+++++| .+++++|+
T Consensus        62 ~~~~~~~~--~~~~~~vLDiGcG~G~~~~~la~~~~-~~v~gvD~  103 (302)
T 3hem_A           62 KLALDKLN--LEPGMTLLDIGCGWGSTMRHAVAEYD-VNVIGLTL  103 (302)
T ss_dssp             HHHHHTTC--CCTTCEEEEETCTTSHHHHHHHHHHC-CEEEEEEC
T ss_pred             HHHHHHcC--CCCcCEEEEeeccCcHHHHHHHHhCC-CEEEEEEC
Confidence            44555554  55678999999999999999999988 88999986

>3g89_A Ribosomal RNA small subunit methyltransferase G; 16S rRNA methyltransferase, translation, cytoplasm, rRNA processing; HET: HIC SAM AMP; 1.50A {Thermus thermophilus} PDB: 3g88_A* 3g8a_A* 3g8b_A*

Probab=97.13  E-value=0.0003  Score=57.68  Aligned_cols=34  Identities=15%  Similarity=0.291  Sum_probs=31.5

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ....+|+|||||+|..++.++..+|+.+++.+|.
T Consensus        79 ~~~~~vLDiG~G~G~~~i~la~~~~~~~v~~vD~  112 (249)
T 3g89_A           79 QGPLRVLDLGTGAGFPGLPLKIVRPELELVLVDA  112 (249)
T ss_dssp             CSSCEEEEETCTTTTTHHHHHHHCTTCEEEEEES
T ss_pred             CCCCEEEEEcCCCCHHHHHHHHHCCCCEEEEEEC
Confidence            4567999999999999999999999999999996

>3mgg_A Methyltransferase; NYSGXRC, PSI-II, protein structure initiative, structural genomics, NEW YORK SGX research center for structural genomics; 1.86A {Methanosarcina mazei}

Probab=97.12  E-value=0.00059  Score=55.90  Aligned_cols=35  Identities=17%  Similarity=0.205  Sum_probs=32.4

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +.+..+|||||||+|.++..+++.+|+.+++.+|+
T Consensus        35 ~~~~~~vLDiG~G~G~~~~~l~~~~~~~~v~~vD~   69 (276)
T 3mgg_A           35 YPPGAKVLEAGCGIGAQTVILAKNNPDAEITSIDI   69 (276)
T ss_dssp             CCTTCEEEETTCTTSHHHHHHHHHCTTSEEEEEES
T ss_pred             CCCCCeEEEecCCCCHHHHHHHHhCCCCEEEEEEC
Confidence            45678999999999999999999999999999996

>1jsx_A Glucose-inhibited division protein B; methyltransferase fold, structural genomics, PSI, protein structure initiative; 2.40A {Escherichia coli} SCOP: c.66.1.20

Probab=97.11  E-value=0.00033  Score=54.85  Aligned_cols=33  Identities=18%  Similarity=0.329  Sum_probs=30.7

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +..+|+|||||+|.++..+++.+|+.+++++|.
T Consensus        65 ~~~~vLDiG~G~G~~~~~l~~~~~~~~v~~vD~   97 (207)
T 1jsx_A           65 QGERFIDVGTGPGLPGIPLSIVRPEAHFTLLDS   97 (207)
T ss_dssp             CSSEEEEETCTTTTTHHHHHHHCTTSEEEEEES
T ss_pred             CCCeEEEECCCCCHHHHHHHHHCCCCEEEEEeC
Confidence            357999999999999999999999999999996

>3dh0_A SAM dependent methyltransferase; cystal structure, PSI-2, NYSGXRC, structural genomics, protein structure initiative; HET: SAM; 2.72A {Aquifex aeolicus}

Probab=97.10  E-value=0.00034  Score=55.19  Aligned_cols=43  Identities=14%  Similarity=0.186  Sum_probs=36.0

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHC-CCCeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAF-PDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl  212 (214)
                      ..+++.++  .....+|||||||+|.++..+++.. |+.+++++|.
T Consensus        27 ~~~~~~~~--~~~~~~vLDiG~G~G~~~~~l~~~~~~~~~v~~vD~   70 (219)
T 3dh0_A           27 EKVLKEFG--LKEGMTVLDVGTGAGFYLPYLSKMVGEKGKVYAIDV   70 (219)
T ss_dssp             HHHHHHHT--CCTTCEEEESSCTTCTTHHHHHHHHTTTCEEEEEES
T ss_pred             HHHHHHhC--CCCCCEEEEEecCCCHHHHHHHHHhCCCcEEEEEEC
Confidence            44555555  5567899999999999999999997 8899999996

>4gek_A TRNA (CMO5U34)-methyltransferase; structural genomics, PSI-biology, NEW YORK structural genomi research consortium, nysgrc, rossmann fold; HET: GEK; 1.50A {Escherichia coli} PDB: 1im8_A*

Probab=97.09  E-value=0.00044  Score=57.19  Aligned_cols=34  Identities=15%  Similarity=0.184  Sum_probs=30.2

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHC--CCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAF--PDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~--P~l~~~v~Dl  212 (214)
                      .+..+|||||||+|.++..+++++  |+.+++.+|+
T Consensus        69 ~~~~~vLDlGcGtG~~~~~la~~~~~~~~~v~gvD~  104 (261)
T 4gek_A           69 QPGTQVYDLGCSLGAATLSVRRNIHHDNCKIIAIDN  104 (261)
T ss_dssp             CTTCEEEEETCTTTHHHHHHHHTCCSSSCEEEEEES
T ss_pred             CCCCEEEEEeCCCCHHHHHHHHhcCCCCCEEEEEEC
Confidence            456799999999999999999985  6789999996

>3bus_A REBM, methyltransferase; rebeccamycin synthesis; HET: SAH; 2.65A {Lechevalieria aerocolonigenes}

Probab=97.08  E-value=0.00096  Score=54.44  Aligned_cols=42  Identities=26%  Similarity=0.272  Sum_probs=34.6

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+++..+  .....+|||||||.|.++..+++++ ..+++++|+
T Consensus        51 ~~l~~~~~--~~~~~~vLDiGcG~G~~~~~l~~~~-~~~v~gvD~   92 (273)
T 3bus_A           51 DEMIALLD--VRSGDRVLDVGCGIGKPAVRLATAR-DVRVTGISI   92 (273)
T ss_dssp             HHHHHHSC--CCTTCEEEEESCTTSHHHHHHHHHS-CCEEEEEES
T ss_pred             HHHHHhcC--CCCCCEEEEeCCCCCHHHHHHHHhc-CCEEEEEeC
Confidence            44556555  5567899999999999999999987 678999886

>1fbn_A MJ fibrillarin homologue; MJ proteins, ribosomal RNA processing, snoRNP, structural genomics, BSGC structure funded by NIH; 1.60A {Methanocaldococcus jannaschii} SCOP: c.66.1.3 PDB: 1g8s_A

Probab=97.04  E-value=0.00065  Score=54.49  Aligned_cols=35  Identities=17%  Similarity=0.144  Sum_probs=31.4

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+..+|||||||+|.++..+++.+|+.+++.+|.
T Consensus        72 ~~~~~~VLDlGcG~G~~~~~la~~~~~~~v~gvD~  106 (230)
T 1fbn_A           72 IKRDSKILYLGASAGTTPSHVADIADKGIVYAIEY  106 (230)
T ss_dssp             CCTTCEEEEESCCSSHHHHHHHHHTTTSEEEEEES
T ss_pred             CCCCCEEEEEcccCCHHHHHHHHHcCCcEEEEEEC
Confidence            45667999999999999999999999888999886

>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=97.03  E-value=0.00017  Score=59.73  Aligned_cols=57  Identities=19%  Similarity=0.250  Sum_probs=50.2

Q ss_pred             cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      +.|+++|...++++|+.|||+++|+++   ..+.|+|+.|...|++.+++.      .++|++++.
T Consensus         9 l~IL~~l~~~~~~lsl~eia~~lgl~k---sT~~RlL~tL~~~G~v~~~~~------~~~Y~lG~~   65 (260)
T 3r4k_A            9 LTLLTYFNHGRLEIGLSDLTRLSGMNK---ATVYRLMSELQEAGFVEQVEG------ARSYRLGPQ   65 (260)
T ss_dssp             HHHHTTCBTTBSEEEHHHHHHHHCSCH---HHHHHHHHHHHHTTSEEECSS------SSEEEECTT
T ss_pred             HHHHHHHhhCCCCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEcCC------CCcEEcCHH
Confidence            457788876447899999999999999   999999999999999999863      489999998

>3g5t_A Trans-aconitate 3-methyltransferase; structural genomics, protein structure initiative, PSI, center for eukaryotic structural genomics; HET: MSE SAH T8N; 1.12A {Saccharomyces cerevisiae}

Probab=97.02  E-value=0.0012  Score=54.93  Aligned_cols=34  Identities=29%  Similarity=0.255  Sum_probs=31.2

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHC-CCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAF-PDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl  212 (214)
                      .+..+|||||||+|.++..+++++ |..+++++|+
T Consensus        35 ~~~~~vLDiGcG~G~~~~~la~~~~~~~~v~gvD~   69 (299)
T 3g5t_A           35 GERKLLVDVGCGPGTATLQMAQELKPFEQIIGSDL   69 (299)
T ss_dssp             SCCSEEEEETCTTTHHHHHHHHHSSCCSEEEEEES
T ss_pred             CCCCEEEEECCCCCHHHHHHHHhCCCCCEEEEEeC
Confidence            357899999999999999999997 9999999997

>4dcm_A Ribosomal RNA large subunit methyltransferase G; 23S rRNA (guanine1835-N2)-methyltransferase; HET: SAM; 2.30A {Escherichia coli}

Probab=97.02  E-value=0.00086  Score=58.38  Aligned_cols=41  Identities=15%  Similarity=0.245  Sum_probs=34.8

Q ss_pred             HHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          170 LIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       170 ~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +++.++  .....+|+|+|||+|.+++.+++++|..+++.+|.
T Consensus       214 ll~~l~--~~~~~~VLDlGcG~G~~s~~la~~~p~~~V~gvD~  254 (375)
T 4dcm_A          214 FMQHLP--ENLEGEIVDLGCGNGVIGLTLLDKNPQAKVVFVDE  254 (375)
T ss_dssp             HHHTCC--CSCCSEEEEETCTTCHHHHHHHHHCTTCEEEEEES
T ss_pred             HHHhCc--ccCCCeEEEEeCcchHHHHHHHHHCCCCEEEEEEC
Confidence            455555  33347999999999999999999999999999996

>3dlc_A Putative S-adenosyl-L-methionine-dependent methyltransferase; structural genomics, joint center for structural genomics; HET: MSE SAM; 1.15A {Methanococcus maripaludis}

Probab=97.02  E-value=0.00048  Score=53.91  Aligned_cols=41  Identities=17%  Similarity=0.289  Sum_probs=32.7

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+++.++  ..+. +|||||||+|.++..++++ |+.+++++|+
T Consensus        34 ~~~~~~~~--~~~~-~vLdiG~G~G~~~~~l~~~-~~~~v~~~D~   74 (219)
T 3dlc_A           34 ENIINRFG--ITAG-TCIDIGSGPGALSIALAKQ-SDFSIRALDF   74 (219)
T ss_dssp             HHHHHHHC--CCEE-EEEEETCTTSHHHHHHHHH-SEEEEEEEES
T ss_pred             HHHHHhcC--CCCC-EEEEECCCCCHHHHHHHHc-CCCeEEEEEC
Confidence            44445444  3333 9999999999999999999 8999999986

>1nkv_A Hypothetical protein YJHP; structural genomics, PSI, protein structure initiative, northeast structural genomics consortium, NESG; 2.90A {Escherichia coli} SCOP: c.66.1.21

Probab=97.02  E-value=0.00093  Score=53.91  Aligned_cols=42  Identities=19%  Similarity=0.133  Sum_probs=34.2

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+++..+  ..+..+|||||||+|.++..+++.+ +.+++++|+
T Consensus        26 ~~l~~~~~--~~~~~~VLDiGcG~G~~~~~la~~~-~~~v~gvD~   67 (256)
T 1nkv_A           26 ATLGRVLR--MKPGTRILDLGSGSGEMLCTWARDH-GITGTGIDM   67 (256)
T ss_dssp             HHHHHHTC--CCTTCEEEEETCTTCHHHHHHHHHT-CCEEEEEES
T ss_pred             HHHHHhcC--CCCCCEEEEECCCCCHHHHHHHHhc-CCeEEEEeC
Confidence            44555554  5567899999999999999999998 678898886

>2b3t_A Protein methyltransferase HEMK; translation termination, methylation, conformational changes; HET: SAH; 3.10A {Escherichia coli} SCOP: c.66.1.30 PDB: 1t43_A*

Probab=97.00  E-value=0.0012  Score=54.57  Aligned_cols=33  Identities=27%  Similarity=0.378  Sum_probs=30.7

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +..+|+|||||+|..+..+++.+|+.+++.+|.
T Consensus       109 ~~~~vLDlG~GsG~~~~~la~~~~~~~v~~vD~  141 (276)
T 2b3t_A          109 QPCRILDLGTGTGAIALALASERPDCEIIAVDR  141 (276)
T ss_dssp             SCCEEEEETCTTSHHHHHHHHHCTTSEEEEECS
T ss_pred             CCCEEEEecCCccHHHHHHHHhCCCCEEEEEEC
Confidence            457999999999999999999999999999986

>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=96.99  E-value=0.00069  Score=54.79  Aligned_cols=42  Identities=12%  Similarity=0.195  Sum_probs=34.9

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+++.++  ..+..+|||||||+|.++..+++++ +.+++++|+
T Consensus        45 ~~~~~~~~--~~~~~~vLdiG~G~G~~~~~l~~~~-~~~v~~vD~   86 (266)
T 3ujc_A           45 KKILSDIE--LNENSKVLDIGSGLGGGCMYINEKY-GAHTHGIDI   86 (266)
T ss_dssp             HHHTTTCC--CCTTCEEEEETCTTSHHHHHHHHHH-CCEEEEEES
T ss_pred             HHHHHhcC--CCCCCEEEEECCCCCHHHHHHHHHc-CCEEEEEeC
Confidence            44555554  5567899999999999999999988 789999986

>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=96.99  E-value=0.0011  Score=53.60  Aligned_cols=43  Identities=12%  Similarity=0.237  Sum_probs=36.1

Q ss_pred             HHHhhcccccCCCCcEEeecCCchHHHHHHHHH-CCCCeEEEecCC
Q 040620          169 VLIEDCNEVSKGLKPLVDVGGSTGTMARAIATA-FPDTKCTVFACH  213 (214)
Q Consensus       169 ~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~-~P~l~~~v~Dlp  213 (214)
                      .++...+  .....+|||+|||+|.++..+++. .|..+++.+|+-
T Consensus        84 ~i~~~~~--~~~~~~vldiG~G~G~~~~~l~~~~~~~~~v~~~D~~  127 (255)
T 3mb5_A           84 LIVAYAG--ISPGDFIVEAGVGSGALTLFLANIVGPEGRVVSYEIR  127 (255)
T ss_dssp             HHHHHTT--CCTTCEEEEECCTTSHHHHHHHHHHCTTSEEEEECSC
T ss_pred             HHHHhhC--CCCCCEEEEecCCchHHHHHHHHHhCCCeEEEEEecC
Confidence            3445554  556789999999999999999999 899999999973

>3dli_A Methyltransferase; PSI-II, NYSGXRC, structural genomics, protein structure initiative; 2.46A {Archaeoglobus fulgidus}

Probab=96.98  E-value=0.0017  Score=52.11  Aligned_cols=33  Identities=15%  Similarity=0.240  Sum_probs=28.2

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +.+..+|||||||.|.++..+++.  +.+++++|+
T Consensus        39 ~~~~~~vLDiGcG~G~~~~~l~~~--~~~v~gvD~   71 (240)
T 3dli_A           39 FKGCRRVLDIGCGRGEFLELCKEE--GIESIGVDI   71 (240)
T ss_dssp             TTTCSCEEEETCTTTHHHHHHHHH--TCCEEEECS
T ss_pred             hcCCCeEEEEeCCCCHHHHHHHhC--CCcEEEEEC
Confidence            445689999999999999999998  557888886

>1xdz_A Methyltransferase GIDB; MCSG, protein structure initiative, structural genomics, methyltransferase fold, PSI; 1.60A {Bacillus subtilis} SCOP: c.66.1.20

Probab=96.97  E-value=0.00044  Score=55.86  Aligned_cols=34  Identities=24%  Similarity=0.452  Sum_probs=31.4

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+..+|+|||||+|..+..+++..|+.+++.+|.
T Consensus        69 ~~~~~vLDiG~G~G~~~~~la~~~~~~~v~~vD~  102 (240)
T 1xdz_A           69 NQVNTICDVGAGAGFPSLPIKICFPHLHVTIVDS  102 (240)
T ss_dssp             GGCCEEEEECSSSCTTHHHHHHHCTTCEEEEEES
T ss_pred             CCCCEEEEecCCCCHHHHHHHHhCCCCEEEEEeC
Confidence            4568999999999999999999999999999996

>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=96.94  E-value=0.0012  Score=53.33  Aligned_cols=41  Identities=17%  Similarity=0.097  Sum_probs=33.1

Q ss_pred             HHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          170 LIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       170 ~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ++..+. ...+..+|||||||+|.++..+++.+|. +++++|+
T Consensus        37 ~l~~l~-~~~~~~~vLDiG~G~G~~~~~l~~~~~~-~v~~vD~   77 (257)
T 3f4k_A           37 AVSFIN-ELTDDAKIADIGCGTGGQTLFLADYVKG-QITGIDL   77 (257)
T ss_dssp             HHTTSC-CCCTTCEEEEETCTTSHHHHHHHHHCCS-EEEEEES
T ss_pred             HHHHHh-cCCCCCeEEEeCCCCCHHHHHHHHhCCC-eEEEEEC
Confidence            344442 2455679999999999999999999986 8999886

>3ou2_A SAM-dependent methyltransferase; O-methyltransferase, SAH; HET: SAH; 1.50A {Streptomyces luridus} PDB: 3ou6_A* 3ou7_A*

Probab=96.93  E-value=0.0019  Score=50.47  Aligned_cols=33  Identities=12%  Similarity=0.195  Sum_probs=28.6

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .....+|||||||+|.++..++++  ..+++++|+
T Consensus        44 ~~~~~~vLdiG~G~G~~~~~l~~~--~~~v~~~D~   76 (218)
T 3ou2_A           44 GNIRGDVLELASGTGYWTRHLSGL--ADRVTALDG   76 (218)
T ss_dssp             TTSCSEEEEESCTTSHHHHHHHHH--SSEEEEEES
T ss_pred             CCCCCeEEEECCCCCHHHHHHHhc--CCeEEEEeC
Confidence            345579999999999999999999  668999886

>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=96.93  E-value=0.00089  Score=53.34  Aligned_cols=35  Identities=14%  Similarity=0.225  Sum_probs=30.9

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+..+|||||||+|.++..+++..|+.+++.+|+
T Consensus        55 ~~~g~~VLDlGcGtG~~~~~la~~~~~~~V~gvD~   89 (210)
T 1nt2_A           55 LRGDERVLYLGAASGTTVSHLADIVDEGIIYAVEY   89 (210)
T ss_dssp             CCSSCEEEEETCTTSHHHHHHHHHTTTSEEEEECC
T ss_pred             CCCCCEEEEECCcCCHHHHHHHHHcCCCEEEEEEC
Confidence            44567999999999999999999998778999886

>3ege_A Putative methyltransferase from antibiotic biosyn pathway; YP_324569.1, putative methyltransferase from antibiotic BIOS pathway; 2.40A {Anabaena variabilis atcc 29413}

Probab=96.92  E-value=0.00085  Score=54.78  Aligned_cols=42  Identities=19%  Similarity=0.165  Sum_probs=33.8

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                      ..+++.++  ..+..+|||||||+|.++..+++  |+.+++++|+-
T Consensus        24 ~~l~~~~~--~~~~~~vLDiGcG~G~~~~~l~~--~~~~v~gvD~s   65 (261)
T 3ege_A           24 NAIINLLN--LPKGSVIADIGAGTGGYSVALAN--QGLFVYAVEPS   65 (261)
T ss_dssp             HHHHHHHC--CCTTCEEEEETCTTSHHHHHHHT--TTCEEEEECSC
T ss_pred             HHHHHHhC--CCCCCEEEEEcCcccHHHHHHHh--CCCEEEEEeCC
Confidence            44455554  45678999999999999999997  78899999973

>1nv8_A HEMK protein; class I adoMet-dependent methyltransferase; HET: SAM MEQ; 2.20A {Thermotoga maritima} SCOP: c.66.1.30 PDB: 1nv9_A* 1vq1_A* 1sg9_A*

Probab=96.92  E-value=0.0008  Score=56.24  Aligned_cols=32  Identities=22%  Similarity=0.432  Sum_probs=29.7

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+|+|||||+|.+++.+++. |+.+++.+|+
T Consensus       123 ~~~~vLDlG~GsG~~~~~la~~-~~~~v~~vDi  154 (284)
T 1nv8_A          123 GIKTVADIGTGSGAIGVSVAKF-SDAIVFATDV  154 (284)
T ss_dssp             TCCEEEEESCTTSHHHHHHHHH-SSCEEEEEES
T ss_pred             CCCEEEEEeCchhHHHHHHHHC-CCCEEEEEEC
Confidence            4569999999999999999999 9999999996

>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=96.91  E-value=0.0012  Score=54.42  Aligned_cols=42  Identities=12%  Similarity=0.101  Sum_probs=33.5

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+++..+  ..+..+|||||||.|.++..++++++. +++++|+
T Consensus        54 ~~~~~~~~--~~~~~~vLDiGcG~G~~~~~l~~~~~~-~v~gvd~   95 (287)
T 1kpg_A           54 DLALGKLG--LQPGMTLLDVGCGWGATMMRAVEKYDV-NVVGLTL   95 (287)
T ss_dssp             HHHHTTTT--CCTTCEEEEETCTTSHHHHHHHHHHCC-EEEEEES
T ss_pred             HHHHHHcC--CCCcCEEEEECCcccHHHHHHHHHcCC-EEEEEEC
Confidence            34555554  556779999999999999999987764 8999886

>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=96.91  E-value=0.00033  Score=57.29  Aligned_cols=57  Identities=12%  Similarity=0.109  Sum_probs=49.1

Q ss_pred             cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      +.|++.|...++++|+.|||+++|+++   ..+.|+|+.|...|++.+++.      +++|.+++.
T Consensus         9 l~iL~~l~~~~~~~s~~ela~~~gl~~---stv~r~l~~L~~~G~v~~~~~------~~~Y~lg~~   65 (241)
T 2xrn_A            9 ASIMRALGSHPHGLSLAAIAQLVGLPR---STVQRIINALEEEFLVEALGP------AGGFRLGPA   65 (241)
T ss_dssp             HHHHHHHHTCTTCEEHHHHHHHTTSCH---HHHHHHHHHHHTTTSEEECGG------GCEEEECSH
T ss_pred             HHHHHHHHhCCCCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEeCC------CCeEEECHH
Confidence            346677776545899999999999999   999999999999999998762      489999987

>3tfw_A Putative O-methyltransferase; PSI-biology, nysgrc, structural genomics, NEW YORK structura genomics research consortium; 1.88A {Klebsiella pneumoniae subsp}

Probab=96.90  E-value=0.0014  Score=53.36  Aligned_cols=34  Identities=18%  Similarity=0.295  Sum_probs=31.2

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCC-CCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFP-DTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl  212 (214)
                      .+..+|||||||+|..+..+++.+| +.+++.+|+
T Consensus        62 ~~~~~VLdiG~G~G~~~~~la~~~~~~~~v~~vD~   96 (248)
T 3tfw_A           62 TQAKRILEIGTLGGYSTIWMARELPADGQLLTLEA   96 (248)
T ss_dssp             HTCSEEEEECCTTSHHHHHHHTTSCTTCEEEEEEC
T ss_pred             cCCCEEEEecCCchHHHHHHHHhCCCCCEEEEEEC
Confidence            3578999999999999999999999 889999997

>2yxd_A Probable cobalt-precorrin-6Y C(15)-methyltransfer [decarboxylating]; alpha and beta protein (A/B) class; HET: MES; 2.30A {Methanocaldococcus jannaschii}

Probab=96.89  E-value=0.0011  Score=50.16  Aligned_cols=40  Identities=28%  Similarity=0.214  Sum_probs=32.3

Q ss_pred             HHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          169 VLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       169 ~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+++.++  ..+..+|+|||||+|.++..+++  |..+++.+|.
T Consensus        26 ~~~~~~~--~~~~~~vLdiG~G~G~~~~~l~~--~~~~v~~vD~   65 (183)
T 2yxd_A           26 VSIGKLN--LNKDDVVVDVGCGSGGMTVEIAK--RCKFVYAIDY   65 (183)
T ss_dssp             HHHHHHC--CCTTCEEEEESCCCSHHHHHHHT--TSSEEEEEEC
T ss_pred             HHHHHcC--CCCCCEEEEeCCCCCHHHHHHHh--cCCeEEEEeC
Confidence            3444444  44567999999999999999998  8889999986

>2o57_A Putative sarcosine dimethylglycine methyltransferase; structural genomics, protein structure initiative, PSI-2; 1.95A {Galdieria sulphuraria} SCOP: c.66.1.18

Probab=96.88  E-value=0.00075  Score=55.92  Aligned_cols=45  Identities=18%  Similarity=0.197  Sum_probs=34.1

Q ss_pred             HHHHhhccc--ccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          168 SVLIEDCNE--VSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       168 ~~~l~~~~~--~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                      ..+++.++|  ......+|||||||.|.++..+++++ +.+++++|+-
T Consensus        68 ~~l~~~l~~~~~~~~~~~vLDiGcG~G~~~~~l~~~~-~~~v~gvD~s  114 (297)
T 2o57_A           68 EWLASELAMTGVLQRQAKGLDLGAGYGGAARFLVRKF-GVSIDCLNIA  114 (297)
T ss_dssp             HHHHHHHHHTTCCCTTCEEEEETCTTSHHHHHHHHHH-CCEEEEEESC
T ss_pred             HHHHHHhhhccCCCCCCEEEEeCCCCCHHHHHHHHHh-CCEEEEEeCC
Confidence            445555511  25567899999999999999999987 4589998873

>1u2z_A Histone-lysine N-methyltransferase, H3 lysine-79 specific; histone methyltransferase, nucleosome; HET: SAH; 2.20A {Saccharomyces cerevisiae} SCOP: c.66.1.31

Probab=96.88  E-value=0.0011  Score=58.96  Aligned_cols=43  Identities=16%  Similarity=0.149  Sum_probs=35.4

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+++..+  .....+|||||||+|.++..+++.+|..+++++|+
T Consensus       232 ~~ml~~l~--l~~g~~VLDLGCGsG~la~~LA~~~g~~~V~GVDi  274 (433)
T 1u2z_A          232 SDVYQQCQ--LKKGDTFMDLGSGVGNCVVQAALECGCALSFGCEI  274 (433)
T ss_dssp             HHHHHHTT--CCTTCEEEEESCTTSHHHHHHHHHHCCSEEEEEEC
T ss_pred             HHHHHhcC--CCCCCEEEEeCCCcCHHHHHHHHHCCCCEEEEEeC
Confidence            33445444  55678999999999999999999999889999986

>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=96.87  E-value=0.00067  Score=55.11  Aligned_cols=42  Identities=26%  Similarity=0.325  Sum_probs=33.7

Q ss_pred             HHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          167 ASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       167 ~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+++.++  .....+|||||||+|.++..++++.+  +++++|+
T Consensus        26 ~~~l~~~l~--~~~~~~vLDiGcG~G~~~~~l~~~~~--~v~gvD~   67 (260)
T 1vl5_A           26 LAKLMQIAA--LKGNEEVLDVATGGGHVANAFAPFVK--KVVAFDL   67 (260)
T ss_dssp             HHHHHHHHT--CCSCCEEEEETCTTCHHHHHHGGGSS--EEEEEES
T ss_pred             HHHHHHHhC--CCCCCEEEEEeCCCCHHHHHHHHhCC--EEEEEeC
Confidence            345556555  45678999999999999999999986  8888886

>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=96.87  E-value=0.0012  Score=54.45  Aligned_cols=42  Identities=24%  Similarity=0.273  Sum_probs=32.9

Q ss_pred             HHHhhcccccCCCCcEEeecCCchHHHHHHHHH-CCCCeEEEecC
Q 040620          169 VLIEDCNEVSKGLKPLVDVGGSTGTMARAIATA-FPDTKCTVFAC  212 (214)
Q Consensus       169 ~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~-~P~l~~~v~Dl  212 (214)
                      .++...+  ..+..+|||+|||+|.++..+++. +|..+++.+|+
T Consensus       101 ~~~~~~~--~~~~~~VLD~G~G~G~~~~~la~~~~~~~~v~~vD~  143 (275)
T 1yb2_A          101 YIIMRCG--LRPGMDILEVGVGSGNMSSYILYALNGKGTLTVVER  143 (275)
T ss_dssp             -----CC--CCTTCEEEEECCTTSHHHHHHHHHHTTSSEEEEECS
T ss_pred             HHHHHcC--CCCcCEEEEecCCCCHHHHHHHHHcCCCCEEEEEEC
Confidence            3444444  556789999999999999999998 89999999997

>3b73_A PHIH1 repressor-like protein; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 2.12A {Haloarcula marismortui atcc 43049}

Probab=96.86  E-value=0.00014  Score=52.76  Aligned_cols=61  Identities=11%  Similarity=0.066  Sum_probs=52.8

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHc--CCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVAL--NVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~--g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      +..|+..|..+ +++|+.+||+.+  ++++   ..+++-|+.|...|++...+       .+.|.+|+.    ++.++
T Consensus        15 d~~IL~~L~~~-g~~s~~eLA~~l~~giS~---~aVs~rL~~Le~~GLV~~~~-------rg~Y~LT~~----G~~~l   77 (111)
T 3b73_A           15 DDRILEIIHEE-GNGSPKELEDRDEIRISK---SSVSRRLKKLADHDLLQPLA-------NGVYVITEE----GEAYL   77 (111)
T ss_dssp             HHHHHHHHHHH-SCBCHHHHHTSTTCCSCH---HHHHHHHHHHHHTTSEEECS-------TTCEEECHH----HHHHH
T ss_pred             HHHHHHHHHHc-CCCCHHHHHHHHhcCCCH---HHHHHHHHHHHHCCCEEecC-------CceEEECch----HHHHH
Confidence            34577788766 899999999999  9999   99999999999999999876       468999999    76665

>2pjd_A Ribosomal RNA small subunit methyltransferase C; gene duplication, RNA modification, SAM binding; 2.10A {Escherichia coli}

Probab=96.85  E-value=0.00085  Score=57.40  Aligned_cols=43  Identities=21%  Similarity=0.341  Sum_probs=35.3

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+++.++  .....+|+|||||+|.++..+++++|+.+++.+|.
T Consensus       186 ~~ll~~l~--~~~~~~VLDlGcG~G~~~~~la~~~~~~~v~~vD~  228 (343)
T 2pjd_A          186 QLLLSTLT--PHTKGKVLDVGCGAGVLSVAFARHSPKIRLTLCDV  228 (343)
T ss_dssp             HHHHHHSC--TTCCSBCCBTTCTTSHHHHHHHHHCTTCBCEEEES
T ss_pred             HHHHHhcC--cCCCCeEEEecCccCHHHHHHHHHCCCCEEEEEEC
Confidence            44555554  22356999999999999999999999999999996

>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=96.85  E-value=0.00054  Score=55.09  Aligned_cols=42  Identities=21%  Similarity=0.239  Sum_probs=34.2

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+++.++  ..+..+|||||||+|.++..+++..| .+++++|.
T Consensus        81 ~~~~~~l~--~~~~~~vLdiG~G~G~~~~~la~~~~-~~v~~vD~  122 (235)
T 1jg1_A           81 AIMLEIAN--LKPGMNILEVGTGSGWNAALISEIVK-TDVYTIER  122 (235)
T ss_dssp             HHHHHHHT--CCTTCCEEEECCTTSHHHHHHHHHHC-SCEEEEES
T ss_pred             HHHHHhcC--CCCCCEEEEEeCCcCHHHHHHHHHhC-CEEEEEeC
Confidence            34445444  45677999999999999999999998 88999885

>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=96.84  E-value=0.0011  Score=54.05  Aligned_cols=41  Identities=15%  Similarity=0.106  Sum_probs=33.7

Q ss_pred             HHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          170 LIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       170 ~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ++..++ ...+..+|||||||+|.++..+++. |..+++++|+
T Consensus        37 ~l~~l~-~~~~~~~vLDiGcG~G~~~~~la~~-~~~~v~gvD~   77 (267)
T 3kkz_A           37 ALSFID-NLTEKSLIADIGCGTGGQTMVLAGH-VTGQVTGLDF   77 (267)
T ss_dssp             HHTTCC-CCCTTCEEEEETCTTCHHHHHHHTT-CSSEEEEEES
T ss_pred             HHHhcc-cCCCCCEEEEeCCCCCHHHHHHHhc-cCCEEEEEeC
Confidence            344443 3456789999999999999999998 8899999997

>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=96.84  E-value=0.0023  Score=47.18  Aligned_cols=49  Identities=6%  Similarity=0.105  Sum_probs=39.2

Q ss_pred             HHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           36 AIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        36 a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      ..+..|+..|..+ +++|..+||+.+++++   ..+.++++.|...|++....
T Consensus        37 ~~~~~vL~~l~~~-~~~t~~eLa~~l~~~~---~tvs~~l~~L~~~Glv~r~~   85 (142)
T 3ech_A           37 PPDVHVLKLIDEQ-RGLNLQDLGRQMCRDK---ALITRKIRELEGRNLVRRER   85 (142)
T ss_dssp             HHHHHHHHHHHHT-TTCCHHHHHHHHC------CHHHHHHHHHHHTTSEEC--
T ss_pred             HHHHHHHHHHHhC-CCcCHHHHHHHhCCCH---HHHHHHHHHHHHCCCEeecc
Confidence            4455677888876 7999999999999999   99999999999999999765

>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=96.81  E-value=0.00082  Score=53.09  Aligned_cols=31  Identities=6%  Similarity=-0.040  Sum_probs=27.8

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+|||||||+|.++..++++.|  +++++|+
T Consensus        38 ~~~~vLDlG~G~G~~~~~l~~~~~--~v~~vD~   68 (227)
T 1ve3_A           38 KRGKVLDLACGVGGFSFLLEDYGF--EVVGVDI   68 (227)
T ss_dssp             SCCEEEEETCTTSHHHHHHHHTTC--EEEEEES
T ss_pred             CCCeEEEEeccCCHHHHHHHHcCC--EEEEEEC
Confidence            367999999999999999999988  8888886

>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=96.79  E-value=0.0022  Score=53.74  Aligned_cols=46  Identities=17%  Similarity=0.176  Sum_probs=35.3

Q ss_pred             hhHHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          165 LIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       165 ~~~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .....+++.++ ......+|||||||.|.++..+++++ ..+++++|+
T Consensus       103 ~~~~~l~~~l~-~~~~~~~vLDiGcG~G~~~~~la~~~-~~~v~gvD~  148 (312)
T 3vc1_A          103 AQAEFLMDHLG-QAGPDDTLVDAGCGRGGSMVMAHRRF-GSRVEGVTL  148 (312)
T ss_dssp             HHHHHHHTTSC-CCCTTCEEEEESCTTSHHHHHHHHHH-CCEEEEEES
T ss_pred             HHHHHHHHHhc-cCCCCCEEEEecCCCCHHHHHHHHHc-CCEEEEEeC
Confidence            33344555553 24567899999999999999999986 678999986

>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=96.77  E-value=0.0017  Score=54.34  Aligned_cols=42  Identities=21%  Similarity=0.280  Sum_probs=34.0

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+++..+  ..+..+|||||||.|.++..+++++ +.+++++|+
T Consensus        80 ~~~~~~~~--~~~~~~vLDiGcG~G~~~~~la~~~-~~~v~gvD~  121 (318)
T 2fk8_A           80 DLNLDKLD--LKPGMTLLDIGCGWGTTMRRAVERF-DVNVIGLTL  121 (318)
T ss_dssp             HHHHTTSC--CCTTCEEEEESCTTSHHHHHHHHHH-CCEEEEEES
T ss_pred             HHHHHhcC--CCCcCEEEEEcccchHHHHHHHHHC-CCEEEEEEC
Confidence            44555554  5567799999999999999999987 568999886

>3fzg_A 16S rRNA methylase; methyltransferase, plasmid, transferase; HET: SAM; 2.00A {Escherichia coli}

Probab=96.77  E-value=0.00091  Score=53.24  Aligned_cols=34  Identities=12%  Similarity=0.098  Sum_probs=31.8

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ....+|+|+|||.|.++..++...|+.+++..|+
T Consensus        48 ~~~~~VLDlGCG~GplAl~l~~~~p~a~~~A~Di   81 (200)
T 3fzg_A           48 KHVSSILDFGCGFNPLALYQWNENEKIIYHAYDI   81 (200)
T ss_dssp             CCCSEEEEETCTTHHHHHHHHCSSCCCEEEEECS
T ss_pred             CCCCeEEEecCCCCHHHHHHHhcCCCCEEEEEeC
Confidence            4578999999999999999999999999999986

>1qgp_A Protein (double stranded RNA adenosine deaminase); Z-alpha-Z-DNA binding domain, RNA-editing, Z-DNA recognition, ADAR1, helix- turn-helix; NMR {Homo sapiens} SCOP: a.4.5.19

Probab=96.76  E-value=0.00062  Score=45.93  Aligned_cols=57  Identities=12%  Similarity=0.099  Sum_probs=46.8

Q ss_pred             hcCcchhhhcCCC---CCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCC
Q 040620           38 QLRIPDIINNSGQ---PMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPP  103 (214)
Q Consensus        38 ~lglfd~L~~~~~---p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~  103 (214)
                      +..|+++|..+ +   ++|+.|||+++|++.   ..+++.|..|...|++...+..     .+.|..++
T Consensus        16 ~~~IL~~L~~~-~~~~~~t~~eLA~~Lgvs~---~tV~~~L~~L~~~G~I~~~g~~-----~~~W~i~~   75 (77)
T 1qgp_A           16 EQRILKFLEEL-GEGKATTAHDLSGKLGTPK---KEINRVLYSLAKKGKLQKEAGT-----PPLWKIAV   75 (77)
T ss_dssp             HHHHHHHHHHH-CSSSCEEHHHHHHHHCCCH---HHHHHHHHHHHHHTSEEEECSS-----SCEEEECC
T ss_pred             HHHHHHHHHHc-CCCCCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEecCCC-----CCceEecC
Confidence            45577778876 4   899999999999999   9999999999999999886521     46776655

>1mkm_A ICLR transcriptional regulator; structural genomics, winged helix-turn-helix, PSI, protein structure initiative; 2.20A {Thermotoga maritima} SCOP: a.4.5.33 d.110.2.2

Probab=96.76  E-value=0.00063  Score=55.77  Aligned_cols=56  Identities=16%  Similarity=0.282  Sum_probs=48.6

Q ss_pred             cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      +.|++.|...++++|+.|||+++|+++   ..+.|+|+.|...|++..+.       .++|.+++.
T Consensus        11 l~iL~~l~~~~~~~~~~ela~~~gl~~---stv~r~l~~L~~~G~v~~~~-------~~~Y~lg~~   66 (249)
T 1mkm_A           11 FEILDFIVKNPGDVSVSEIAEKFNMSV---SNAYKYMVVLEEKGFVLRKK-------DKRYVPGYK   66 (249)
T ss_dssp             HHHHHHHHHCSSCBCHHHHHHHTTCCH---HHHHHHHHHHHHTTSEEECT-------TSCEEECTH
T ss_pred             HHHHHHHHhCCCCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCcEEECC-------CCcEEECHH
Confidence            346677776545899999999999999   99999999999999999883       689999887

>2pwy_A TRNA (adenine-N(1)-)-methyltransferase; mtase, adoMet, TRMI, tRNA-M1A58; HET: SAH; 1.70A {Thermus thermophilus}

Probab=96.75  E-value=0.0023  Score=51.64  Aligned_cols=43  Identities=12%  Similarity=0.124  Sum_probs=35.9

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHH-CCCCeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATA-FPDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~-~P~l~~~v~Dl  212 (214)
                      ..++...+  .....+|||+|||+|.++..+++. .|..+++.+|.
T Consensus        86 ~~~~~~~~--~~~~~~vLdiG~G~G~~~~~l~~~~~~~~~v~~~D~  129 (258)
T 2pwy_A           86 SAMVTLLD--LAPGMRVLEAGTGSGGLTLFLARAVGEKGLVESYEA  129 (258)
T ss_dssp             HHHHHHTT--CCTTCEEEEECCTTSHHHHHHHHHHCTTSEEEEEES
T ss_pred             HHHHHHcC--CCCCCEEEEECCCcCHHHHHHHHHhCCCCEEEEEeC
Confidence            34555555  556789999999999999999999 78999999986

>3g5l_A Putative S-adenosylmethionine dependent methyltransferase; structural genomics, PSI-2, protein structure initiative; 2.35A {Listeria monocytogenes str}

Probab=96.75  E-value=0.0016  Score=52.47  Aligned_cols=40  Identities=18%  Similarity=0.017  Sum_probs=32.2

Q ss_pred             HHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          170 LIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       170 ~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +.+.++  .....+|||||||+|.++..+++..+. +++++|+
T Consensus        36 l~~~~~--~~~~~~vLD~GcG~G~~~~~l~~~~~~-~v~~vD~   75 (253)
T 3g5l_A           36 LKKMLP--DFNQKTVLDLGCGFGWHCIYAAEHGAK-KVLGIDL   75 (253)
T ss_dssp             HHTTCC--CCTTCEEEEETCTTCHHHHHHHHTTCS-EEEEEES
T ss_pred             HHHhhh--ccCCCEEEEECCCCCHHHHHHHHcCCC-EEEEEEC
Confidence            444444  345789999999999999999999775 8888886

>2yxe_A Protein-L-isoaspartate O-methyltransferase; rossman-type fold, alpha/beta/alpha sandwich structure, STRU genomics, NPPSFA; 2.00A {Methanocaldococcus jannaschii}

Probab=96.74  E-value=0.0018  Score=50.85  Aligned_cols=42  Identities=17%  Similarity=0.134  Sum_probs=34.0

Q ss_pred             HHHhhcccccCCCCcEEeecCCchHHHHHHHHHC-CCCeEEEecC
Q 040620          169 VLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAF-PDTKCTVFAC  212 (214)
Q Consensus       169 ~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl  212 (214)
                      .+++...  .....+|||||||+|.++..+++.. |+.+++.+|.
T Consensus        68 ~~~~~~~--~~~~~~vLdiG~G~G~~~~~l~~~~~~~~~v~~vD~  110 (215)
T 2yxe_A           68 MMCELLD--LKPGMKVLEIGTGCGYHAAVTAEIVGEDGLVVSIER  110 (215)
T ss_dssp             HHHHHTT--CCTTCEEEEECCTTSHHHHHHHHHHCTTSEEEEEES
T ss_pred             HHHHhhC--CCCCCEEEEECCCccHHHHHHHHHhCCCCEEEEEeC
Confidence            3444444  4556799999999999999999998 7789999886

>2ozv_A Hypothetical protein ATU0636; structural genomics, predicted transferase, predicted O-methyltransferase, PFAM PF05175; HET: MSE; 1.70A {Agrobacterium tumefaciens str}

Probab=96.74  E-value=0.0013  Score=54.12  Aligned_cols=35  Identities=17%  Similarity=0.352  Sum_probs=31.6

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .....+|||+|||+|.+++.+++++|+.+++.+|+
T Consensus        34 ~~~~~~VLDlG~G~G~~~l~la~~~~~~~v~gvDi   68 (260)
T 2ozv_A           34 DDRACRIADLGAGAGAAGMAVAARLEKAEVTLYER   68 (260)
T ss_dssp             CCSCEEEEECCSSSSHHHHHHHHHCTTEEEEEEES
T ss_pred             ccCCCEEEEeCChHhHHHHHHHHhCCCCeEEEEEC
Confidence            34467999999999999999999999999999986

>2ipx_A RRNA 2'-O-methyltransferase fibrillarin; FBL, structural genomics, structural genomics consortium, SGC; HET: MTA; 1.82A {Homo sapiens}

Probab=96.73  E-value=0.00096  Score=53.48  Aligned_cols=35  Identities=17%  Similarity=0.234  Sum_probs=31.2

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHC-CCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAF-PDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl  212 (214)
                      .....+|||||||+|.++..+++++ |+.+++.+|+
T Consensus        75 ~~~~~~vLDlG~G~G~~~~~la~~~g~~~~v~gvD~  110 (233)
T 2ipx_A           75 IKPGAKVLYLGAASGTTVSHVSDIVGPDGLVYAVEF  110 (233)
T ss_dssp             CCTTCEEEEECCTTSHHHHHHHHHHCTTCEEEEECC
T ss_pred             CCCCCEEEEEcccCCHHHHHHHHHhCCCcEEEEEEC
Confidence            4456799999999999999999997 7889999986

>1qbj_A Protein (double-stranded RNA specific adenosine D (ADAR1)); protein-Z-DNA complex, hydrolase-DNA complex; HET: DNA; 2.10A {Homo sapiens} SCOP: a.4.5.19 PDB: 3f21_A* 3f22_A* 3f23_A* 3irr_A* 3irq_D* 2gxb_A 2acj_A 2l54_A

Probab=96.73  E-value=0.00085  Score=45.79  Aligned_cols=59  Identities=12%  Similarity=0.084  Sum_probs=47.2

Q ss_pred             HhcCcchhhhcCCC---CCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           37 IQLRIPDIINNSGQ---PMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        37 ~~lglfd~L~~~~~---p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      .+..|.++|.++ +   ++|+.|||+++|++.   +.+++.|..|...|+++..+..     .+.|...+.
T Consensus        11 ~~~~IL~~L~~~-~pg~~~t~~eLA~~Lgvsr---~tV~~~L~~Le~~G~I~~~g~~-----~~~W~i~~~   72 (81)
T 1qbj_A           11 QEQRILKFLEEL-GEGKATTAHDLSGKLGTPK---KEINRVLYSLAKKGKLQKEAGT-----PPLWKIAVS   72 (81)
T ss_dssp             HHHHHHHHHHHH-CTTCCBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEESSS-----SCEEEEC--
T ss_pred             HHHHHHHHHHHc-CCCCCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEecCCC-----CCeeEEeCc
Confidence            455577778776 5   799999999999999   9999999999999999876421     467887776

>2h00_A Methyltransferase 10 domain containing protein; structural genomics, structural genomics consortium, SGC; HET: SAH; 2.00A {Homo sapiens} SCOP: c.66.1.54

Probab=96.73  E-value=0.00079  Score=54.63  Aligned_cols=33  Identities=9%  Similarity=0.120  Sum_probs=30.5

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +..+|||||||+|.++..+++++|+.+++.+|+
T Consensus        65 ~~~~vLDlG~G~G~~~~~la~~~~~~~v~gvD~   97 (254)
T 2h00_A           65 TLRRGIDIGTGASCIYPLLGATLNGWYFLATEV   97 (254)
T ss_dssp             CCCEEEEESCTTTTHHHHHHHHHHCCEEEEEES
T ss_pred             CCCEEEEeCCChhHHHHHHHHhCCCCeEEEEEC
Confidence            467999999999999999999999999999996

>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=96.71  E-value=0.0019  Score=49.12  Aligned_cols=33  Identities=9%  Similarity=0.029  Sum_probs=29.0

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ....+|+|+|||+|.++..++++ |..+++.+|+
T Consensus        30 ~~~~~vLDlGcG~G~~~~~l~~~-~~~~v~~vD~   62 (177)
T 2esr_A           30 FNGGRVLDLFAGSGGLAIEAVSR-GMSAAVLVEK   62 (177)
T ss_dssp             CCSCEEEEETCTTCHHHHHHHHT-TCCEEEEECC
T ss_pred             cCCCeEEEeCCCCCHHHHHHHHc-CCCEEEEEEC
Confidence            35679999999999999999987 7788999986

>2gpy_A O-methyltransferase; structural genomics, PSI, protein structure initiative, NEW research center for structural genomics, nysgxrc; HET: MSE; 1.90A {Bacillus halodurans}

Probab=96.71  E-value=0.0015  Score=52.23  Aligned_cols=33  Identities=18%  Similarity=0.335  Sum_probs=30.8

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +..+|||||||.|..+..+++.+|+.+++.+|+
T Consensus        54 ~~~~vLdiG~G~G~~~~~la~~~~~~~v~~vD~   86 (233)
T 2gpy_A           54 APARILEIGTAIGYSAIRMAQALPEATIVSIER   86 (233)
T ss_dssp             CCSEEEEECCTTSHHHHHHHHHCTTCEEEEECC
T ss_pred             CCCEEEEecCCCcHHHHHHHHHCCCCEEEEEEC
Confidence            467999999999999999999999999999986

>3ntv_A MW1564 protein; rossmann fold, putative methyltransferase, transferase; HET: MSE; 1.55A {Staphylococcus aureus}

Probab=96.70  E-value=0.0011  Score=53.40  Aligned_cols=34  Identities=18%  Similarity=0.304  Sum_probs=31.3

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+..+|||||||.|..+..+++.+|..+++.+|+
T Consensus        70 ~~~~~vLDiG~G~G~~~~~la~~~~~~~v~~vD~  103 (232)
T 3ntv_A           70 NNVKNILEIGTAIGYSSMQFASISDDIHVTTIER  103 (232)
T ss_dssp             HTCCEEEEECCSSSHHHHHHHTTCTTCEEEEEEC
T ss_pred             cCCCEEEEEeCchhHHHHHHHHhCCCCEEEEEEC
Confidence            3568999999999999999999999999999996

>3iv6_A Putative Zn-dependent alcohol dehydrogenase; alpha/beta fold, rossmann-fold, structural genomics, PSI-2, structure initiative; HET: SAM; 2.70A {Rhodobacter sphaeroides}

Probab=96.69  E-value=0.0025  Score=52.86  Aligned_cols=41  Identities=20%  Similarity=0.037  Sum_probs=33.1

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+++..+  .....+|||||||+|.++..++++  ..+++.+|+
T Consensus        35 ~~il~~l~--l~~g~~VLDlGcGtG~~a~~La~~--g~~V~gvD~   75 (261)
T 3iv6_A           35 ENDIFLEN--IVPGSTVAVIGASTRFLIEKALER--GASVTVFDF   75 (261)
T ss_dssp             HHHHHTTT--CCTTCEEEEECTTCHHHHHHHHHT--TCEEEEEES
T ss_pred             HHHHHhcC--CCCcCEEEEEeCcchHHHHHHHhc--CCEEEEEEC
Confidence            45556555  556789999999999999999987  568888886

>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=96.69  E-value=0.0019  Score=54.57  Aligned_cols=43  Identities=21%  Similarity=0.203  Sum_probs=35.3

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+++.++  .....++||+|||.|.++..+++++|+.+++.+|+
T Consensus        16 ~e~l~~L~--~~~g~~vLD~g~G~G~~s~~la~~~~~~~VigvD~   58 (301)
T 1m6y_A           16 REVIEFLK--PEDEKIILDCTVGEGGHSRAILEHCPGCRIIGIDV   58 (301)
T ss_dssp             HHHHHHHC--CCTTCEEEETTCTTSHHHHHHHHHCTTCEEEEEES
T ss_pred             HHHHHhcC--CCCCCEEEEEeCCcCHHHHHHHHHCCCCEEEEEEC
Confidence            33445444  44567999999999999999999999999999996

>1o54_A SAM-dependent O-methyltransferase; TM0748, structural genomi PSI, protein structure initiative, joint center for structu genomics; 1.65A {Thermotoga maritima} SCOP: c.66.1.13

Probab=96.67  E-value=0.0026  Score=52.34  Aligned_cols=43  Identities=21%  Similarity=0.229  Sum_probs=35.6

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHH-CCCCeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATA-FPDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~-~P~l~~~v~Dl  212 (214)
                      ..++...+  .....+|||+|||+|.++..++++ .|..+++.+|.
T Consensus       102 ~~i~~~~~--~~~~~~VLDiG~G~G~~~~~la~~~~~~~~v~~vD~  145 (277)
T 1o54_A          102 SFIAMMLD--VKEGDRIIDTGVGSGAMCAVLARAVGSSGKVFAYEK  145 (277)
T ss_dssp             HHHHHHTT--CCTTCEEEEECCTTSHHHHHHHHHTTTTCEEEEECC
T ss_pred             HHHHHHhC--CCCCCEEEEECCcCCHHHHHHHHHhCCCcEEEEEEC
Confidence            34455555  556779999999999999999999 78999999986

>3uwp_A Histone-lysine N-methyltransferase, H3 lysine-79; epigenetics, tubercidin, structu genomics, structural genomics consortium, SGC; HET: 5ID; 2.05A {Homo sapiens} PDB: 4eqz_A* 3sx0_A* 4er0_A* 4er7_A* 1nw3_A* 4er6_A* 4er5_A* 3qow_A* 3qox_A* 4ek9_A* 4ekg_A* 4eki_A* 4er3_A* 3sr4_A*

Probab=96.64  E-value=0.0023  Score=56.62  Aligned_cols=43  Identities=16%  Similarity=0.183  Sum_probs=35.6

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+++..+  .....+|+|||||.|..++.++..+|..+++++|+
T Consensus       163 ~~il~~l~--l~~gd~VLDLGCGtG~l~l~lA~~~g~~kVvGIDi  205 (438)
T 3uwp_A          163 AQMIDEIK--MTDDDLFVDLGSGVGQVVLQVAAATNCKHHYGVEK  205 (438)
T ss_dssp             HHHHHHHC--CCTTCEEEEESCTTSHHHHHHHHHCCCSEEEEEEC
T ss_pred             HHHHHhcC--CCCCCEEEEeCCCCCHHHHHHHHHCCCCEEEEEeC
Confidence            44555554  55678999999999999999999998778999987

>2g7u_A Transcriptional regulator; ICLR family, structural genomics, PSI, protein structure initiative, midwest center for struc genomics; 2.30A {Rhodococcus SP}

Probab=96.64  E-value=0.00083  Score=55.32  Aligned_cols=55  Identities=11%  Similarity=0.167  Sum_probs=48.1

Q ss_pred             cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      +.|++.|...++++|+.|||+++|+++   ..+.|+|+.|...|++.++        +++|++++.
T Consensus        17 l~iL~~l~~~~~~~~~~eia~~~gl~~---stv~r~l~~L~~~G~v~~~--------~~~Y~Lg~~   71 (257)
T 2g7u_A           17 FAVLLAFDAQRPNPTLAELATEAGLSR---PAVRRILLTLQKLGYVAGS--------GGRWSLTPR   71 (257)
T ss_dssp             HHHHHTCSSSCSSCBHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEE--------TTEEEECGG
T ss_pred             HHHHHHHHhCCCCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEeC--------CCEEEEcHH
Confidence            356677775447899999999999999   9999999999999999987        479999987

>3njr_A Precorrin-6Y methylase; methyltransferase, decarboxylase, transferase; HET: SAH PG4; 2.70A {Rhodobacter capsulatus}

Probab=96.64  E-value=0.0024  Score=50.38  Aligned_cols=39  Identities=15%  Similarity=0.245  Sum_probs=31.9

Q ss_pred             HHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          170 LIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       170 ~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ++...+  .....+|+|||||+|.++..+++.  ..+++.+|+
T Consensus        47 ~l~~l~--~~~~~~vLDlGcG~G~~~~~la~~--~~~v~~vD~   85 (204)
T 3njr_A           47 TLAALA--PRRGELLWDIGGGSGSVSVEWCLA--GGRAITIEP   85 (204)
T ss_dssp             HHHHHC--CCTTCEEEEETCTTCHHHHHHHHT--TCEEEEEES
T ss_pred             HHHhcC--CCCCCEEEEecCCCCHHHHHHHHc--CCEEEEEeC
Confidence            344444  455689999999999999999998  788999986

>3duw_A OMT, O-methyltransferase, putative; alternating of alpha and beta with complex SAH; HET: SAH; 1.20A {Bacillus cereus} PDB: 3dul_A*

Probab=96.64  E-value=0.0013  Score=52.12  Aligned_cols=34  Identities=12%  Similarity=0.309  Sum_probs=31.0

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCC-CCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFP-DTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl  212 (214)
                      .+..+|||||||+|..+..+++++| +.+++.+|+
T Consensus        57 ~~~~~vLdiG~G~G~~~~~la~~~~~~~~v~~vD~   91 (223)
T 3duw_A           57 QGARNILEIGTLGGYSTIWLARGLSSGGRVVTLEA   91 (223)
T ss_dssp             HTCSEEEEECCTTSHHHHHHHTTCCSSCEEEEEES
T ss_pred             hCCCEEEEecCCccHHHHHHHHhCCCCCEEEEEEC
Confidence            3568999999999999999999999 789999986

>1ws6_A Methyltransferase; structural genomics, riken structural genomics/proteomics initiative, RSGI; 2.50A {Thermus thermophilus} SCOP: c.66.1.46

Probab=96.63  E-value=0.0017  Score=48.78  Aligned_cols=31  Identities=10%  Similarity=0.013  Sum_probs=27.6

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+|+|+|||+|.++..++++.|+  ++.+|+
T Consensus        41 ~~~~vLD~GcG~G~~~~~l~~~~~~--v~~vD~   71 (171)
T 1ws6_A           41 RRGRFLDPFAGSGAVGLEAASEGWE--AVLVEK   71 (171)
T ss_dssp             TCCEEEEETCSSCHHHHHHHHTTCE--EEEECC
T ss_pred             CCCeEEEeCCCcCHHHHHHHHCCCe--EEEEeC
Confidence            4679999999999999999999876  888886

>2qe6_A Uncharacterized protein TFU_2867; putative methyltransferase, structural genomics, joint cente structural genomics, JCSG; HET: NEP SAM; 1.95A {Thermobifida fusca}

Probab=96.63  E-value=0.0032  Score=52.24  Aligned_cols=33  Identities=15%  Similarity=0.355  Sum_probs=30.5

Q ss_pred             CCCcEEeecCCc---hHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGST---GTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~---G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +..+|||||||.   |.++..+.+.+|+.+++.+|+
T Consensus        77 ~~~~vLDlGcG~pt~G~~~~~~~~~~p~~~v~~vD~  112 (274)
T 2qe6_A           77 GISQFLDLGSGLPTVQNTHEVAQSVNPDARVVYVDI  112 (274)
T ss_dssp             CCCEEEEETCCSCCSSCHHHHHHHHCTTCEEEEEES
T ss_pred             CCCEEEEECCCCCCCChHHHHHHHhCCCCEEEEEEC
Confidence            468999999999   999988889999999999997

>3ccf_A Cyclopropane-fatty-acyl-phospholipid synthase; YP_321342.1, putative methyltransferase; 1.90A {Anabaena variabilis atcc 29413}

Probab=96.62  E-value=0.0021  Score=52.87  Aligned_cols=39  Identities=21%  Similarity=0.245  Sum_probs=31.9

Q ss_pred             HHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          170 LIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       170 ~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +++.++  .....+|||||||+|.++..+++  |..+++++|+
T Consensus        49 l~~~l~--~~~~~~vLDiGcG~G~~~~~l~~--~~~~v~gvD~   87 (279)
T 3ccf_A           49 LLQLLN--PQPGEFILDLGCGTGQLTEKIAQ--SGAEVLGTDN   87 (279)
T ss_dssp             HHHHHC--CCTTCEEEEETCTTSHHHHHHHH--TTCEEEEEES
T ss_pred             HHHHhC--CCCCCEEEEecCCCCHHHHHHHh--CCCeEEEEEC
Confidence            444444  44567999999999999999999  8889999986

>2o0y_A Transcriptional regulator; ICLR-family, structural genomics, protein structure initiative, midwest center for structural genomics, MCSG; 2.00A {Rhodococcus SP}

Probab=96.62  E-value=0.00064  Score=56.14  Aligned_cols=56  Identities=11%  Similarity=0.243  Sum_probs=47.9

Q ss_pred             cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      +.|++.|...++++|+.|||+++|+++   ..+.|+|+.|...|++.+++       .++|.+++.
T Consensus        26 l~iL~~l~~~~~~~~~~eia~~~gl~k---stv~r~l~tL~~~G~v~~~~-------~~~Y~lg~~   81 (260)
T 2o0y_A           26 IDLLELFDAAHPTRSLKELVEGTKLPK---TTVVRLVATMCARSVLTSRA-------DGSYSLGPE   81 (260)
T ss_dssp             HHHHTTCBTTBSSBCHHHHHHHHCCCH---HHHHHHHHHHHHTTSEEECT-------TSCEEECHH
T ss_pred             HHHHHHHhhCCCCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEECC-------CCeEEecHH
Confidence            456777764337899999999999999   99999999999999999986       348999877

>3tr6_A O-methyltransferase; cellular processes; HET: SAH; 2.70A {Coxiella burnetii} SCOP: c.66.1.0

Probab=96.62  E-value=0.0014  Score=51.98  Aligned_cols=33  Identities=30%  Similarity=0.387  Sum_probs=30.4

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCC-CCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFP-DTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl  212 (214)
                      +..+|||||||+|..+..+++.+| +.+++.+|.
T Consensus        64 ~~~~vLdiG~G~G~~~~~la~~~~~~~~v~~vD~   97 (225)
T 3tr6_A           64 QAKKVIDIGTFTGYSAIAMGLALPKDGTLITCDV   97 (225)
T ss_dssp             TCSEEEEECCTTSHHHHHHHTTCCTTCEEEEEES
T ss_pred             CCCEEEEeCCcchHHHHHHHHhCCCCCEEEEEeC
Confidence            467999999999999999999998 889999986

>3pqk_A Biofilm growth-associated repressor; helix-turn-helix motif, winged-helix fold, transcriptional R DNA binding, transcription; 2.09A {Xylella fastidiosa} PDB: 3pqj_A

Probab=96.62  E-value=0.0023  Score=44.89  Aligned_cols=60  Identities=8%  Similarity=0.123  Sum_probs=46.6

Q ss_pred             HHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           36 AIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        36 a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      -.++.|+..|.+  +|+|+.|||+.+|+++   ..+.+.|+.|...|++.....   +. ...|.+++.
T Consensus        23 ~~r~~Il~~L~~--~~~~~~ela~~l~is~---~tvs~~L~~L~~~Glv~~~~~---g~-~~~y~l~~~   82 (102)
T 3pqk_A           23 PVRLMLVCTLVE--GEFSVGELEQQIGIGQ---PTLSQQLGVLRESGIVETRRN---IK-QIFYRLTEA   82 (102)
T ss_dssp             HHHHHHHHHHHT--CCBCHHHHHHHHTCCT---THHHHHHHHHHHTTSEEEECS---SS-CCEEEECSS
T ss_pred             HHHHHHHHHHHh--CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeEEEEe---CC-EEEEEECcH
Confidence            344556666755  7899999999999999   999999999999999987652   11 345776665

>3ggd_A SAM-dependent methyltransferase; YP_325210.1, structural GEN joint center for structural genomics, JCSG; HET: SAH; 2.11A {Anabaena variabilis atcc 29413}

Probab=96.62  E-value=0.0026  Score=51.03  Aligned_cols=33  Identities=21%  Similarity=0.367  Sum_probs=28.9

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .....+|||||||+|.++..+++..+  +++.+|.
T Consensus        54 ~~~~~~vLD~GcG~G~~~~~la~~~~--~v~gvD~   86 (245)
T 3ggd_A           54 FNPELPLIDFACGNGTQTKFLSQFFP--RVIGLDV   86 (245)
T ss_dssp             SCTTSCEEEETCTTSHHHHHHHHHSS--CEEEEES
T ss_pred             cCCCCeEEEEcCCCCHHHHHHHHhCC--CEEEEEC
Confidence            34567999999999999999999998  7888886

>2bm8_A Cephalosporin hydroxylase CMCI; cephamycin biosynthesis; 2.5A {Streptomyces clavuligerus} SCOP: c.66.1.50 PDB: 2bm9_A* 2br5_A* 2br4_A* 2br3_A*

Probab=96.61  E-value=0.0019  Score=52.30  Aligned_cols=32  Identities=13%  Similarity=0.039  Sum_probs=29.7

Q ss_pred             CCcEEeecCCchHHHHHHHHH----CCCCeEEEecC
Q 040620          181 LKPLVDVGGSTGTMARAIATA----FPDTKCTVFAC  212 (214)
Q Consensus       181 ~~~vvDVGGG~G~~~~~l~~~----~P~l~~~v~Dl  212 (214)
                      ..+|||||||+|..+..+++.    .|+.+++.+|+
T Consensus        82 ~~~VLDiG~GtG~~t~~la~~~~~~~~~~~V~gvD~  117 (236)
T 2bm8_A           82 PRTIVELGVYNGGSLAWFRDLTKIMGIDCQVIGIDR  117 (236)
T ss_dssp             CSEEEEECCTTSHHHHHHHHHHHHTTCCCEEEEEES
T ss_pred             CCEEEEEeCCCCHHHHHHHHhhhhcCCCCEEEEEeC
Confidence            579999999999999999998    79999999997

>1o9g_A RRNA methyltransferase; antibiotic resistance, Se-MAD; 1.5A {Streptomyces viridochromogenes} SCOP: c.66.1.29 PDB: 1o9h_A

Probab=96.59  E-value=0.0016  Score=52.79  Aligned_cols=33  Identities=12%  Similarity=0.031  Sum_probs=30.1

Q ss_pred             CCCcEEeecCCchHHHHHHHHH--CCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATA--FPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~--~P~l~~~v~Dl  212 (214)
                      ...+|+|+|||+|.++..+++.  +|..+++.+|+
T Consensus        51 ~~~~vLD~gcGsG~~~~~la~~~~~~~~~v~gvDi   85 (250)
T 1o9g_A           51 GPVTLWDPCCGSGYLLTVLGLLHRRSLRQVIASDV   85 (250)
T ss_dssp             SCEEEEETTCTTSHHHHHHHHHTGGGEEEEEEEES
T ss_pred             CCCeEEECCCCCCHHHHHHHHHhccCCCeEEEEEC
Confidence            4579999999999999999999  88889999997

>3gjy_A Spermidine synthase; APC62791, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.47A {Corynebacterium glutamicum atcc 13032}

Probab=96.58  E-value=0.0016  Score=55.61  Aligned_cols=31  Identities=32%  Similarity=0.537  Sum_probs=29.4

Q ss_pred             CcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          182 KPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       182 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+|||||||.|.++..+++.+|+.+++++|+
T Consensus        91 ~rVLdIG~G~G~la~~la~~~p~~~v~~VEi  121 (317)
T 3gjy_A           91 LRITHLGGGACTMARYFADVYPQSRNTVVEL  121 (317)
T ss_dssp             CEEEEESCGGGHHHHHHHHHSTTCEEEEEES
T ss_pred             CEEEEEECCcCHHHHHHHHHCCCcEEEEEEC
Confidence            4999999999999999999999999999987

>1xmk_A Double-stranded RNA-specific adenosine deaminase; winged helix-turn-helix, RNA editing, interferon, ADAR1, hydrolase; 0.97A {Homo sapiens} SCOP: a.4.5.19

Probab=96.58  E-value=0.00079  Score=45.74  Aligned_cols=58  Identities=10%  Similarity=0.059  Sum_probs=47.6

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcc-cHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTR-CTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~-~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      +-.|.++|... +|.|+.+||+.+|+++   . .+++.|..|...|+++..+.   +  .-.|.+|+.
T Consensus        13 ~~~IL~~Lk~~-g~~ta~eiA~~Lgit~---~~aVr~hL~~Le~eGlV~~~~~---g--RP~w~LT~~   71 (79)
T 1xmk_A           13 KEKICDYLFNV-SDSSALNLAKNIGLTK---ARDINAVLIDMERQGDVYRQGT---T--PPIWHLTDK   71 (79)
T ss_dssp             HHHHHHHHHHT-CCEEHHHHHHHHCGGG---HHHHHHHHHHHHHTTSEEEECS---S--SCEEEECHH
T ss_pred             HHHHHHHHHHc-CCcCHHHHHHHcCCCc---HHHHHHHHHHHHHCCCEEecCC---C--CCCeEeCHh
Confidence            44566778877 8999999999999998   8 99999999999999986542   1  237888876

>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=96.58  E-value=0.001  Score=53.88  Aligned_cols=33  Identities=18%  Similarity=0.204  Sum_probs=28.4

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ....+|||||||.|..+..+++..|. +++++|+
T Consensus        59 ~~G~rVLdiG~G~G~~~~~~~~~~~~-~v~~id~   91 (236)
T 3orh_A           59 SKGGRVLEVGFGMAIAASKVQEAPID-EHWIIEC   91 (236)
T ss_dssp             TTCEEEEEECCTTSHHHHHHTTSCEE-EEEEEEC
T ss_pred             cCCCeEEEECCCccHHHHHHHHhCCc-EEEEEeC
Confidence            34679999999999999999998885 6888886

>2xvm_A Tellurite resistance protein TEHB; antibiotic resistance, transferase; HET: SAH; 1.48A {Escherichia coli} PDB: 2xva_A* 4dq0_A* 2i6g_A*

Probab=96.56  E-value=0.0029  Score=48.69  Aligned_cols=39  Identities=13%  Similarity=0.165  Sum_probs=31.1

Q ss_pred             HHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          170 LIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       170 ~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +++.++  ..+..+|||||||+|.++..+++.  ..+++.+|.
T Consensus        24 l~~~~~--~~~~~~vLdiG~G~G~~~~~l~~~--~~~v~~vD~   62 (199)
T 2xvm_A           24 VLEAVK--VVKPGKTLDLGCGNGRNSLYLAAN--GYDVDAWDK   62 (199)
T ss_dssp             HHHHTT--TSCSCEEEEETCTTSHHHHHHHHT--TCEEEEEES
T ss_pred             HHHHhh--ccCCCeEEEEcCCCCHHHHHHHHC--CCeEEEEEC
Confidence            444444  345679999999999999999988  668898886

>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=96.56  E-value=0.0037  Score=50.64  Aligned_cols=43  Identities=14%  Similarity=0.183  Sum_probs=32.0

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...++.++. ....++|||||||+|.++..+++. +..+++.+|+
T Consensus        26 ~~~L~~~~~-~~~g~~VLDiGcGtG~~t~~la~~-g~~~V~gvDi   68 (232)
T 3opn_A           26 EKALKEFHL-EINGKTCLDIGSSTGGFTDVMLQN-GAKLVYALDV   68 (232)
T ss_dssp             HHHHHHTTC-CCTTCEEEEETCTTSHHHHHHHHT-TCSEEEEECS
T ss_pred             HHHHHHcCC-CCCCCEEEEEccCCCHHHHHHHhc-CCCEEEEEcC
Confidence            344555541 224569999999999999999988 4348999986

>3grz_A L11 mtase, ribosomal protein L11 methyltransferase; methylase, SAM-binding domain, PSI-2, nysgxrc; 2.00A {Lactobacillus delbrueckii subsp}

Probab=96.56  E-value=0.0035  Score=48.90  Aligned_cols=32  Identities=19%  Similarity=0.181  Sum_probs=28.1

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+|||||||+|.++..+++ +|..+++.+|+
T Consensus        60 ~~~~vLDiG~G~G~~~~~l~~-~~~~~v~~vD~   91 (205)
T 3grz_A           60 KPLTVADVGTGSGILAIAAHK-LGAKSVLATDI   91 (205)
T ss_dssp             SCCEEEEETCTTSHHHHHHHH-TTCSEEEEEES
T ss_pred             CCCEEEEECCCCCHHHHHHHH-CCCCEEEEEEC
Confidence            567999999999999999776 58889999986

>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2}

Probab=96.56  E-value=0.0009  Score=45.22  Aligned_cols=37  Identities=16%  Similarity=0.214  Sum_probs=35.0

Q ss_pred             CCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           49 GQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        49 ~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      |+|.|+.|||+.+|+++   ..+++-|..|...|++....
T Consensus        22 g~~psv~EIa~~lgvS~---~TVrr~L~~Le~kG~I~R~~   58 (77)
T 2jt1_A           22 GAPVKTRDIADAAGLSI---YQVRLYLEQLHDVGVLEKVN   58 (77)
T ss_dssp             TSCEEHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEES
T ss_pred             CCCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCcEEecC
Confidence            68999999999999998   89999999999999999875

>3hnr_A Probable methyltransferase BT9727_4108; structural genomics, PSI-2, protein structure initiative; 2.80A {Bacillus thuringiensis serovarkonkukian}

Probab=96.55  E-value=0.0022  Score=50.42  Aligned_cols=32  Identities=16%  Similarity=0.231  Sum_probs=28.2

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ....+|||||||.|.++..++++  +.+++++|.
T Consensus        44 ~~~~~vLDiGcG~G~~~~~l~~~--~~~v~~vD~   75 (220)
T 3hnr_A           44 KSFGNVLEFGVGTGNLTNKLLLA--GRTVYGIEP   75 (220)
T ss_dssp             TCCSEEEEECCTTSHHHHHHHHT--TCEEEEECS
T ss_pred             cCCCeEEEeCCCCCHHHHHHHhC--CCeEEEEeC
Confidence            35679999999999999999998  678998886

>3c3p_A Methyltransferase; NP_951602.1, structural genomics, joint for structural genomics, JCSG, protein structure initiative transferase; 1.90A {Geobacter sulfurreducens pca}

Probab=96.55  E-value=0.0017  Score=51.14  Aligned_cols=33  Identities=15%  Similarity=0.148  Sum_probs=30.2

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCC-CCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFP-DTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl  212 (214)
                      +..+|||||||.|..+..+++..| +.+++.+|+
T Consensus        56 ~~~~vLdiG~G~G~~~~~la~~~~~~~~v~~vD~   89 (210)
T 3c3p_A           56 QPQLVVVPGDGLGCASWWFARAISISSRVVMIDP   89 (210)
T ss_dssp             CCSEEEEESCGGGHHHHHHHTTSCTTCEEEEEES
T ss_pred             CCCEEEEEcCCccHHHHHHHHhCCCCCEEEEEEC
Confidence            467999999999999999999998 889999986

>1dus_A MJ0882; hypothetical protein, methanococcus jannaschii, structural genomics, BSGC structure funded by NIH; 1.80A {Methanocaldococcus jannaschii} SCOP: c.66.1.4

Probab=96.54  E-value=0.0026  Score=48.53  Aligned_cols=41  Identities=20%  Similarity=0.281  Sum_probs=32.9

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+++.++  ..+..+|+|||||+|.++..+++.  ..+++.+|+
T Consensus        42 ~~l~~~~~--~~~~~~vLdiG~G~G~~~~~~~~~--~~~v~~~D~   82 (194)
T 1dus_A           42 KILVENVV--VDKDDDILDLGCGYGVIGIALADE--VKSTTMADI   82 (194)
T ss_dssp             HHHHHHCC--CCTTCEEEEETCTTSHHHHHHGGG--SSEEEEEES
T ss_pred             HHHHHHcc--cCCCCeEEEeCCCCCHHHHHHHHc--CCeEEEEEC
Confidence            44555555  446789999999999999999998  778888886

>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=96.54  E-value=0.001  Score=48.57  Aligned_cols=67  Identities=12%  Similarity=0.064  Sum_probs=49.6

Q ss_pred             HHHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           30 SLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        30 ~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      ..+|.--.++.|+..|..+ +++|+.|||+.+|+++   ..+.+.|+.|...|++.....   +. ...|.+++.
T Consensus        36 ~~al~~~~rl~IL~~L~~~-~~~s~~eLa~~l~is~---stvs~~L~~L~~~Glv~~~~~---gr-~~~y~l~~~  102 (122)
T 1u2w_A           36 LKAIADENRAKITYALCQD-EELCVCDIANILGVTI---ANASHHLRTLYKQGVVNFRKE---GK-LALYSLGDE  102 (122)
T ss_dssp             HHHHHSHHHHHHHHHHHHS-SCEEHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEC--------CCEEEESCH
T ss_pred             HHHhCCHHHHHHHHHHHHC-CCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeEEEEE---CC-EEEEEECHH
Confidence            3344444566788888754 8999999999999999   999999999999999987641   10 224666655

>2nxc_A L11 mtase, ribosomal protein L11 methyltransferase; transferase S-adenosly-L-methionine dependent methyltransfer posttranslational modification; 1.59A {Thermus thermophilus} SCOP: c.66.1.39 PDB: 1ufk_A 2nxe_A* 2nxj_A 2nxn_A 2zbp_A* 2zbq_A* 2zbr_A* 3cjq_A* 3cjr_A* 3cju_A* 3egv_A* 3cjt_A*

Probab=96.53  E-value=0.0027  Score=51.88  Aligned_cols=32  Identities=19%  Similarity=0.158  Sum_probs=28.0

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+..+|+|||||+|.+++.+++..+  +++.+|+
T Consensus       119 ~~~~~VLDiGcG~G~l~~~la~~g~--~v~gvDi  150 (254)
T 2nxc_A          119 RPGDKVLDLGTGSGVLAIAAEKLGG--KALGVDI  150 (254)
T ss_dssp             CTTCEEEEETCTTSHHHHHHHHTTC--EEEEEES
T ss_pred             CCCCEEEEecCCCcHHHHHHHHhCC--eEEEEEC
Confidence            3567999999999999999999876  8888886

>2oqg_A Possible transcriptional regulator, ARSR family P; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 1.54A {Rhodococcus SP}

Probab=96.53  E-value=0.00096  Score=47.52  Aligned_cols=59  Identities=12%  Similarity=0.045  Sum_probs=46.0

Q ss_pred             HhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           37 IQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        37 ~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      .++.|+..|..  +|+|+.+||+.+|+++   ..+.+.|+.|...|++.....   +. ...|.+++.
T Consensus        22 ~r~~IL~~L~~--~~~~~~ela~~l~is~---~tv~~~l~~L~~~gli~~~~~---gr-~~~y~l~~~   80 (114)
T 2oqg_A           22 TRWEILTELGR--ADQSASSLATRLPVSR---QAIAKHLNALQACGLVESVKV---GR-EIRYRALGA   80 (114)
T ss_dssp             HHHHHHHHHHH--SCBCHHHHHHHSSSCH---HHHHHHHHHHHHTTSEEEEEE---TT-EEEEEECSH
T ss_pred             HHHHHHHHHHc--CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeeEEec---CC-EEEEEechH
Confidence            44556677744  7899999999999999   999999999999999987641   00 233777776

>3cuo_A Uncharacterized HTH-type transcriptional regulato; DNA-binding transcriptional regulator, structural genomics, MCSG; 2.00A {Escherichia coli K12}

Probab=96.52  E-value=0.00097  Score=46.11  Aligned_cols=50  Identities=12%  Similarity=0.153  Sum_probs=42.6

Q ss_pred             HHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           35 RAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        35 ~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      .-.++.|+..|... +++|..|||+.+|+++   ..+.+.|+.|...|++....
T Consensus        23 ~~~~~~il~~l~~~-~~~s~~ela~~l~is~---~tvs~~l~~L~~~glv~~~~   72 (99)
T 3cuo_A           23 HPKRLLILCMLSGS-PGTSAGELTRITGLSA---SATSQHLARMRDEGLIDSQR   72 (99)
T ss_dssp             SHHHHHHHHHHTTC-CSEEHHHHHHHHCCCH---HHHHHHHHHHHHTTSEEEEE
T ss_pred             ChHHHHHHHHHHhC-CCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEEe
Confidence            34456677777763 6999999999999999   99999999999999998765

>3cc8_A Putative methyltransferase; structural genomics, joint center for structural genomics, JCSG, protein structure initiative, PS transferase; 1.64A {Bacillus cereus}

Probab=96.52  E-value=0.0016  Score=51.26  Aligned_cols=40  Identities=25%  Similarity=0.411  Sum_probs=31.9

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+++.++   .+..+|+|||||.|.++..+++. | .+++++|.
T Consensus        23 ~~l~~~~~---~~~~~vLdiG~G~G~~~~~l~~~-~-~~~~~~D~   62 (230)
T 3cc8_A           23 PNLLKHIK---KEWKEVLDIGCSSGALGAAIKEN-G-TRVSGIEA   62 (230)
T ss_dssp             HHHHTTCC---TTCSEEEEETCTTSHHHHHHHTT-T-CEEEEEES
T ss_pred             HHHHHHhc---cCCCcEEEeCCCCCHHHHHHHhc-C-CeEEEEeC
Confidence            34555443   35679999999999999999998 5 88999886

>1qam_A ERMC' methyltransferase; rRNA methyltransferase ERMC', cofactor analogs; 2.20A {Bacillus subtilis} SCOP: c.66.1.24 PDB: 1qan_A* 1qao_A* 1qaq_A* 2erc_A

Probab=96.52  E-value=0.0037  Score=50.87  Aligned_cols=42  Identities=7%  Similarity=0.192  Sum_probs=33.4

Q ss_pred             HHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          167 ASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       167 ~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+++..+  .....+|||||||+|.++..++++.  .+++.+|+
T Consensus        19 ~~~i~~~~~--~~~~~~VLDiG~G~G~lt~~l~~~~--~~v~~vD~   60 (244)
T 1qam_A           19 IDKIMTNIR--LNEHDNIFEIGSGKGHFTLELVQRC--NFVTAIEI   60 (244)
T ss_dssp             HHHHHTTCC--CCTTCEEEEECCTTSHHHHHHHHHS--SEEEEECS
T ss_pred             HHHHHHhCC--CCCCCEEEEEeCCchHHHHHHHHcC--CeEEEEEC
Confidence            345556555  4566799999999999999999996  67888875

>2fhp_A Methylase, putative; alpha-beta-alpha sandwich, structural genomics, PSI, protein structure initiative; HET: MSE; 1.60A {Enterococcus faecalis} SCOP: c.66.1.46

Probab=96.50  E-value=0.0038  Score=47.62  Aligned_cols=33  Identities=12%  Similarity=-0.033  Sum_probs=28.5

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ....+|||+|||+|.++..+++ .+..+++.+|+
T Consensus        43 ~~~~~vLD~GcG~G~~~~~~~~-~~~~~v~~vD~   75 (187)
T 2fhp_A           43 FDGGMALDLYSGSGGLAIEAVS-RGMDKSICIEK   75 (187)
T ss_dssp             CSSCEEEETTCTTCHHHHHHHH-TTCSEEEEEES
T ss_pred             cCCCCEEEeCCccCHHHHHHHH-cCCCEEEEEEC
Confidence            3467999999999999999888 57788999986

>2pxx_A Uncharacterized protein MGC2408; structural genomics consortium, SGC, methyltransferase, LOC84291, transferase; HET: SAH; 1.30A {Homo sapiens}

Probab=96.50  E-value=0.0028  Score=49.34  Aligned_cols=33  Identities=6%  Similarity=0.019  Sum_probs=28.7

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ....+|||||||+|.++..+++..+. +++++|+
T Consensus        41 ~~~~~vLdiGcG~G~~~~~l~~~~~~-~v~~~D~   73 (215)
T 2pxx_A           41 RPEDRILVLGCGNSALSYELFLGGFP-NVTSVDY   73 (215)
T ss_dssp             CTTCCEEEETCTTCSHHHHHHHTTCC-CEEEEES
T ss_pred             CCCCeEEEECCCCcHHHHHHHHcCCC-cEEEEeC
Confidence            45679999999999999999999775 8888886

>3jth_A Transcription activator HLYU; transcription factor, RTXA, DNA-binding, transcription regulation; 2.00A {Vibrio vulnificus}

Probab=96.48  E-value=0.0014  Score=45.67  Aligned_cols=64  Identities=16%  Similarity=0.273  Sum_probs=49.0

Q ss_pred             HHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           32 SLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        32 ~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      +|.--.++.|+..|.+  +++|+.|||+.+|+++   ..+.+.|+.|...|++.....   +. ...|.+++.
T Consensus        19 ~l~~~~r~~Il~~L~~--~~~~~~ela~~l~is~---~tvs~~L~~L~~~Glv~~~~~---g~-~~~y~l~~~   82 (98)
T 3jth_A           19 AMANERRLQILCMLHN--QELSVGELCAKLQLSQ---SALSQHLAWLRRDGLVTTRKE---AQ-TVYYTLKSE   82 (98)
T ss_dssp             HHCSHHHHHHHHHTTT--SCEEHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEECC---TT-CCEEEECCH
T ss_pred             HcCCHHHHHHHHHHhc--CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeEEEEe---CC-EEEEEECHH
Confidence            3444455667778876  7999999999999999   999999999999999987752   11 234666554

>1xtp_A LMAJ004091AAA; SGPP, structural genomics, PSI, protein structure initiative dependent methyltransferase; HET: SAI; 1.94A {Leishmania major} SCOP: c.66.1.42

Probab=96.48  E-value=0.0035  Score=50.31  Aligned_cols=42  Identities=14%  Similarity=0.280  Sum_probs=32.9

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+++.++  ..+..+|||||||+|.++..++++. ..+++++|.
T Consensus        83 ~~~l~~l~--~~~~~~vLDiG~G~G~~~~~l~~~~-~~~v~~vD~  124 (254)
T 1xtp_A           83 RNFIASLP--GHGTSRALDCGAGIGRITKNLLTKL-YATTDLLEP  124 (254)
T ss_dssp             HHHHHTST--TCCCSEEEEETCTTTHHHHHTHHHH-CSEEEEEES
T ss_pred             HHHHHhhc--ccCCCEEEEECCCcCHHHHHHHHhh-cCEEEEEeC
Confidence            34555554  4567899999999999999999987 556888885

>3pfg_A N-methyltransferase; N,N-dimethyltransferase, SAM binding, DTDP-linked sugar BIND transferase; HET: SAM TLO; 1.35A {Streptomyces fradiae} PDB: 3pfh_A* 3px3_A* 3px2_A*

Probab=96.46  E-value=0.0028  Score=51.50  Aligned_cols=32  Identities=25%  Similarity=0.300  Sum_probs=27.4

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+..+|||||||+|.++..++++.+  +++++|+
T Consensus        49 ~~~~~vLDiGcG~G~~~~~l~~~~~--~v~gvD~   80 (263)
T 3pfg_A           49 PKAASLLDVACGTGMHLRHLADSFG--TVEGLEL   80 (263)
T ss_dssp             TTCCEEEEETCTTSHHHHHHTTTSS--EEEEEES
T ss_pred             CCCCcEEEeCCcCCHHHHHHHHcCC--eEEEEEC
Confidence            3568999999999999999999854  6888886

>3bja_A Transcriptional regulator, MARR family, putative; NP_978771.1, putative MARR-like transcription regulator, MAR structural genomics; 2.38A {Bacillus cereus}

Probab=96.44  E-value=0.0029  Score=46.06  Aligned_cols=67  Identities=12%  Similarity=0.336  Sum_probs=49.2

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      ++.|+..|... +++|..+||+.+++++   ..+.+.++.|...|++.......+.- ...+.+|+.    ++.+.
T Consensus        35 ~~~iL~~l~~~-~~~~~~ela~~l~~~~---~tvs~~l~~L~~~gli~r~~~~~d~r-~~~~~lT~~----G~~~~  101 (139)
T 3bja_A           35 QFGVIQVLAKS-GKVSMSKLIENMGCVP---SNMTTMIQRMKRDGYVMTEKNPNDQR-ETLVYLTKK----GEETK  101 (139)
T ss_dssp             HHHHHHHHHHS-CSEEHHHHHHHCSSCC---TTHHHHHHHHHHTTSEEEEECSSCTT-CEEEEECHH----HHHHH
T ss_pred             HHHHHHHHHHc-CCcCHHHHHHHHCCCh---hHHHHHHHHHHHCCCeeeccCCCCCc-eeEEEECHH----HHHHH
Confidence            44466777765 7899999999999999   99999999999999998764211111 223666766    55543

>1i9g_A Hypothetical protein RV2118C; mtase, adoMet, crystal, structural genomics, protein structure initiative; HET: SAM; 1.98A {Mycobacterium tuberculosis} SCOP: c.66.1.13

Probab=96.44  E-value=0.0047  Score=50.55  Aligned_cols=43  Identities=9%  Similarity=0.224  Sum_probs=35.1

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHH-CCCCeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATA-FPDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~-~P~l~~~v~Dl  212 (214)
                      ..++...+  .....+|||||||+|.++..+++. .|..+++.+|+
T Consensus        89 ~~i~~~~~--~~~~~~vLdiG~G~G~~~~~l~~~~~~~~~v~~vD~  132 (280)
T 1i9g_A           89 AQIVHEGD--IFPGARVLEAGAGSGALTLSLLRAVGPAGQVISYEQ  132 (280)
T ss_dssp             HHHHHHTT--CCTTCEEEEECCTTSHHHHHHHHHHCTTSEEEEECS
T ss_pred             HHHHHHcC--CCCCCEEEEEcccccHHHHHHHHHhCCCCEEEEEeC
Confidence            34555555  556779999999999999999996 68899999986

>2ia2_A Putative transcriptional regulator; SAD, PSI-2, structural genomics, structure initiative, midwest center for structural genomic transcription; 2.10A {Rhodococcus SP}

Probab=96.44  E-value=0.0008  Score=55.71  Aligned_cols=55  Identities=16%  Similarity=0.294  Sum_probs=48.1

Q ss_pred             cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      +.|++.|...++++|+.|||+++|+++   ..+.|+|+.|...|++.++        +++|.+++.
T Consensus        24 l~iL~~l~~~~~~~~~~eia~~~gl~~---stv~r~l~tL~~~G~v~~~--------~~~Y~Lg~~   78 (265)
T 2ia2_A           24 LAVIRCFDHRNQRRTLSDVARATDLTR---ATARRFLLTLVELGYVATD--------GSAFWLTPR   78 (265)
T ss_dssp             HHHHHTCCSSCSSEEHHHHHHHHTCCH---HHHHHHHHHHHHHTSEEES--------SSEEEECGG
T ss_pred             HHHHHHHHhCCCCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEec--------CCEEEEcHH
Confidence            456777775447899999999999999   9999999999999999987        479999987

>2p7i_A Hypothetical protein; putative methyltransferase, structural genomics, joint cente structural genomics, JCSG; 1.74A {Pectobacterium atrosepticum SCRI1043} SCOP: c.66.1.41 PDB: 2p7h_A

Probab=96.43  E-value=0.0022  Score=50.99  Aligned_cols=31  Identities=16%  Similarity=0.298  Sum_probs=26.8

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +..+|||||||+|.++..++++.|  +++++|+
T Consensus        42 ~~~~vLDiGcG~G~~~~~l~~~~~--~v~gvD~   72 (250)
T 2p7i_A           42 RPGNLLELGSFKGDFTSRLQEHFN--DITCVEA   72 (250)
T ss_dssp             CSSCEEEESCTTSHHHHHHTTTCS--CEEEEES
T ss_pred             CCCcEEEECCCCCHHHHHHHHhCC--cEEEEeC
Confidence            457899999999999999999987  5777775

>1xn7_A Hypothetical protein YHGG; alpha+beta, GFT structural genomics, protein structure initiative, PSI, NESG; NMR {Escherichia coli} SCOP: a.4.5.62

Probab=96.41  E-value=0.0017  Score=43.89  Aligned_cols=43  Identities=21%  Similarity=0.201  Sum_probs=39.8

Q ss_pred             cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620           41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ   87 (214)
Q Consensus        41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~   87 (214)
                      |.+.|.++ +.++++|||+.+++++   ..++|.|+.|...|++...
T Consensus         7 Il~~L~~~-g~vsv~eLa~~l~VS~---~TIRrdL~~Le~~G~l~R~   49 (78)
T 1xn7_A            7 VRDLLALR-GRMEAAQISQTLNTPQ---PMINAMLQQLESMGKAVRI   49 (78)
T ss_dssp             HHHHHHHS-CSBCHHHHHHHTTCCH---HHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHc-CCCcHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEe
Confidence            56778877 8999999999999999   9999999999999999887

>1p91_A Ribosomal RNA large subunit methyltransferase A; RLMA, RRMA, 23S rRNA, NESG, structural genomics, PSI, protein structure initiative; HET: SAM; 2.80A {Escherichia coli} SCOP: c.66.1.33

Probab=96.41  E-value=0.002  Score=52.48  Aligned_cols=33  Identities=21%  Similarity=0.363  Sum_probs=30.6

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+|||||||.|.++..+++.+|..+++++|.
T Consensus        85 ~~~~vLdiG~G~G~~~~~l~~~~~~~~v~~vD~  117 (269)
T 1p91_A           85 KATAVLDIGCGEGYYTHAFADALPEITTFGLDV  117 (269)
T ss_dssp             TCCEEEEETCTTSTTHHHHHHTCTTSEEEEEES
T ss_pred             CCCEEEEECCCCCHHHHHHHHhCCCCeEEEEeC
Confidence            467999999999999999999999999999986

>3ftd_A Dimethyladenosine transferase; KSGA, rossmann-like fold, RNA methyltransferase, mtase, anti resistance, methyltransferase, RNA-binding; 1.44A {Aquifex aeolicus} PDB: 3ftc_A 3fte_A 3ftf_A* 3r9x_B*

Probab=96.41  E-value=0.0026  Score=52.24  Aligned_cols=43  Identities=26%  Similarity=0.395  Sum_probs=34.2

Q ss_pred             HHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          167 ASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       167 ~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+++..+  .....+|+|||||.|.++..++++ +..+++.+|+
T Consensus        20 ~~~iv~~~~--~~~~~~VLDiG~G~G~lt~~L~~~-~~~~v~avEi   62 (249)
T 3ftd_A           20 LKKIAEELN--IEEGNTVVEVGGGTGNLTKVLLQH-PLKKLYVIEL   62 (249)
T ss_dssp             HHHHHHHTT--CCTTCEEEEEESCHHHHHHHHTTS-CCSEEEEECC
T ss_pred             HHHHHHhcC--CCCcCEEEEEcCchHHHHHHHHHc-CCCeEEEEEC
Confidence            345666655  455679999999999999999987 5678888886

>2qww_A Transcriptional regulator, MARR family; YP_013417.1, multiple antibiotic-resistance repressor (MARR) structural genomics; HET: MSE; 2.07A {Listeria monocytogenes str}

Probab=96.41  E-value=0.013  Score=43.54  Aligned_cols=67  Identities=13%  Similarity=0.144  Sum_probs=48.8

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceee--ecCCCCCCccceeeCCCCCcccccccc
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQ--QKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~--~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      ++.|+..|... +++|..+||+.+++++   ..+.++++.|...|++..  .....+.- ...+.+|+.    ++.+.
T Consensus        43 ~~~iL~~l~~~-~~~t~~eLa~~l~~~~---~tvs~~l~~Le~~Glv~r~~~~~~~d~R-~~~~~LT~~----G~~~~  111 (154)
T 2qww_A           43 QLAMINVIYST-PGISVADLTKRLIITG---SSAAANVDGLISLGLVVKLNKTIPNDSM-DLTLKLSKK----GEDLS  111 (154)
T ss_dssp             HHHHHHHHHHS-TTEEHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEESCC--CTTCT-TCEEEECHH----HHHHH
T ss_pred             HHHHHHHHHHC-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEecCcCCCCCCc-eeEeEECHH----HHHHH
Confidence            44567777776 7899999999999999   999999999999999998  43211111 224667776    55543

>1g8a_A Fibrillarin-like PRE-rRNA processing protein; rRNA binding, RNA binding, structural genomics, BSGC structure funded by NIH; 1.40A {Pyrococcus horikoshii} SCOP: c.66.1.3 PDB: 2nnw_B 3nmu_F* 3nvk_I* 3nvm_B 1pry_A

Probab=96.40  E-value=0.0025  Score=50.66  Aligned_cols=35  Identities=20%  Similarity=0.127  Sum_probs=30.3

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHC-CCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAF-PDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl  212 (214)
                      ..+..+|+|+|||+|.++..++++. |+.+++.+|.
T Consensus        71 ~~~~~~vLDlG~G~G~~~~~la~~~~~~~~v~~vD~  106 (227)
T 1g8a_A           71 IKPGKSVLYLGIASGTTASHVSDIVGWEGKIFGIEF  106 (227)
T ss_dssp             CCTTCEEEEETTTSTTHHHHHHHHHCTTSEEEEEES
T ss_pred             CCCCCEEEEEeccCCHHHHHHHHHhCCCeEEEEEEC
Confidence            4456799999999999999999985 6788998886

>3lbf_A Protein-L-isoaspartate O-methyltransferase; modified rossman-type fold, S-adenosyl-L- methionine; HET: SAH; 1.80A {Escherichia coli}

Probab=96.40  E-value=0.0055  Score=47.86  Aligned_cols=40  Identities=10%  Similarity=0.091  Sum_probs=32.1

Q ss_pred             HHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          169 VLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       169 ~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+++..+  ..+..+|||||||+|.++..+++.  ..+++.+|.
T Consensus        68 ~~~~~l~--~~~~~~vLdiG~G~G~~~~~la~~--~~~v~~vD~  107 (210)
T 3lbf_A           68 RMTELLE--LTPQSRVLEIGTGSGYQTAILAHL--VQHVCSVER  107 (210)
T ss_dssp             HHHHHTT--CCTTCEEEEECCTTSHHHHHHHHH--SSEEEEEES
T ss_pred             HHHHhcC--CCCCCEEEEEcCCCCHHHHHHHHh--CCEEEEEec
Confidence            3445444  456789999999999999999998  678888886

>1sui_A Caffeoyl-COA O-methyltransferase; rossmann fold, protein-cofactor-substrate complex; HET: SAH FRE; 2.70A {Medicago sativa} SCOP: c.66.1.1 PDB: 1sus_A*

Probab=96.39  E-value=0.0032  Score=51.36  Aligned_cols=34  Identities=29%  Similarity=0.307  Sum_probs=30.8

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCC-CCeEEEecCC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFP-DTKCTVFACH  213 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dlp  213 (214)
                      +.++|||||||+|..++.+++..| +.+++.+|+-
T Consensus        79 ~~~~VLeiG~G~G~~~~~la~~~~~~~~v~~iD~s  113 (247)
T 1sui_A           79 NAKNTMEIGVYTGYSLLATALAIPEDGKILAMDIN  113 (247)
T ss_dssp             TCCEEEEECCGGGHHHHHHHHHSCTTCEEEEEESC
T ss_pred             CcCEEEEeCCCcCHHHHHHHHhCCCCCEEEEEECC
Confidence            467999999999999999999998 7899999873

>3r3h_A O-methyltransferase, SAM-dependent; structural genomics, PSI-biology, NEW YORK structural genomi research consortium, nysgrc; 2.65A {Legionella pneumophila subsp}

Probab=96.38  E-value=0.0026  Score=51.73  Aligned_cols=34  Identities=26%  Similarity=0.368  Sum_probs=30.6

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCC-CCeEEEecCC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFP-DTKCTVFACH  213 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dlp  213 (214)
                      +.++|||||||+|..+..+++..| +.+++.+|+-
T Consensus        60 ~~~~VLDiG~G~G~~t~~la~~~~~~~~v~~iD~~   94 (242)
T 3r3h_A           60 RAKKVLELGTFTGYSALAMSLALPDDGQVITCDIN   94 (242)
T ss_dssp             TCSEEEEEESCCSHHHHHHHHTSCTTCEEEEEECC
T ss_pred             CcCEEEEeeCCcCHHHHHHHHhCCCCCEEEEEECC
Confidence            467999999999999999999997 8899999863

>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=96.37  E-value=0.0025  Score=50.01  Aligned_cols=40  Identities=15%  Similarity=0.216  Sum_probs=31.3

Q ss_pred             HHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          169 VLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       169 ~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .++..+.  .....+|||||||+|.++..+++.  ..+++.+|+
T Consensus        43 ~~~~~~~--~~~~~~vLdiG~G~G~~~~~l~~~--~~~v~~vD~   82 (227)
T 3e8s_A           43 AILLAIL--GRQPERVLDLGCGEGWLLRALADR--GIEAVGVDG   82 (227)
T ss_dssp             HHHHHHH--HTCCSEEEEETCTTCHHHHHHHTT--TCEEEEEES
T ss_pred             HHHHHhh--cCCCCEEEEeCCCCCHHHHHHHHC--CCEEEEEcC
Confidence            3444443  334589999999999999999998  668888886

>3thr_A Glycine N-methyltransferase; GNMT, folate, methyltransferase binding, liver cytosol, transferase-transferase inhibitor C; HET: C2F TAM; 2.00A {Rattus norvegicus} SCOP: c.66.1.5 PDB: 3ths_A* 1xva_A* 1d2c_A 1kia_A* 1nbh_A* 1bhj_A* 2idj_A 2idk_A* 1d2g_A 1d2h_A* 1nbi_A* 1r8x_A 1r8y_A 1r74_A* 2azt_A*

Probab=96.37  E-value=0.0026  Score=52.48  Aligned_cols=32  Identities=19%  Similarity=0.167  Sum_probs=27.7

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+..+|||||||+|.++..+++..+  +++.+|+
T Consensus        56 ~~~~~vLDiGcG~G~~~~~l~~~~~--~v~gvD~   87 (293)
T 3thr_A           56 HGCHRVLDVACGTGVDSIMLVEEGF--SVTSVDA   87 (293)
T ss_dssp             TTCCEEEETTCTTSHHHHHHHHTTC--EEEEEES
T ss_pred             cCCCEEEEecCCCCHHHHHHHHCCC--eEEEEEC
Confidence            3467999999999999999999844  8888886

>3tma_A Methyltransferase; thump domain; 2.05A {Thermus thermophilus}

Probab=96.36  E-value=0.0039  Score=53.35  Aligned_cols=44  Identities=18%  Similarity=0.179  Sum_probs=36.3

Q ss_pred             HHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHC-CCCeEEEecC
Q 040620          167 ASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAF-PDTKCTVFAC  212 (214)
Q Consensus       167 ~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl  212 (214)
                      +..++....  +.+..+|+|+|||+|.+++.++... |+.+++.+|+
T Consensus       192 a~~l~~~~~--~~~~~~vLD~gcGsG~~~ie~a~~~~~~~~v~g~Di  236 (354)
T 3tma_A          192 AQALLRLAD--ARPGMRVLDPFTGSGTIALEAASTLGPTSPVYAGDL  236 (354)
T ss_dssp             HHHHHHHTT--CCTTCCEEESSCTTSHHHHHHHHHHCTTSCEEEEES
T ss_pred             HHHHHHHhC--CCCCCEEEeCCCCcCHHHHHHHHhhCCCceEEEEEC
Confidence            344455544  5567899999999999999999998 9999999996

>1wzn_A SAM-dependent methyltransferase; structural genomics, riken structural genomics/proteomics initiative, RSGI; HET: SAH; 1.90A {Pyrococcus horikoshii} SCOP: c.66.1.43

Probab=96.34  E-value=0.0049  Score=49.53  Aligned_cols=32  Identities=13%  Similarity=0.208  Sum_probs=28.0

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+..+|||||||+|.++..+++.  ..+++++|+
T Consensus        40 ~~~~~vLDlGcG~G~~~~~l~~~--~~~v~gvD~   71 (252)
T 1wzn_A           40 REVRRVLDLACGTGIPTLELAER--GYEVVGLDL   71 (252)
T ss_dssp             SCCCEEEEETCTTCHHHHHHHHT--TCEEEEEES
T ss_pred             cCCCEEEEeCCCCCHHHHHHHHC--CCeEEEEEC
Confidence            45679999999999999999987  668998886

>3bxo_A N,N-dimethyltransferase; desosamine, sugar, carbohydrate, antibiotic, SAM, adoMet; HET: SAM UPP; 2.00A {Streptomyces venezuelae}

Probab=96.34  E-value=0.0063  Score=48.22  Aligned_cols=32  Identities=22%  Similarity=0.255  Sum_probs=28.1

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+..+|||||||+|.++..++++.+  +++++|+
T Consensus        39 ~~~~~vLdiG~G~G~~~~~l~~~~~--~v~~~D~   70 (239)
T 3bxo_A           39 PEASSLLDVACGTGTHLEHFTKEFG--DTAGLEL   70 (239)
T ss_dssp             TTCCEEEEETCTTSHHHHHHHHHHS--EEEEEES
T ss_pred             CCCCeEEEecccCCHHHHHHHHhCC--cEEEEeC
Confidence            3567999999999999999999987  7888876

>3uzu_A Ribosomal RNA small subunit methyltransferase A; ssgcid, seattle structural genomics center for infectio disease; 1.75A {Burkholderia pseudomallei}

Probab=96.33  E-value=0.0025  Score=53.31  Aligned_cols=43  Identities=7%  Similarity=0.237  Sum_probs=33.6

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCC--CeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPD--TKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~--l~~~v~Dl  212 (214)
                      ..+++..+  .....+|||||||+|.++..|+++.+.  .+++.+|+
T Consensus        32 ~~iv~~~~--~~~~~~VLEIG~G~G~lt~~La~~~~~~~~~V~avDi   76 (279)
T 3uzu_A           32 DAIVAAIR--PERGERMVEIGPGLGALTGPVIARLATPGSPLHAVEL   76 (279)
T ss_dssp             HHHHHHHC--CCTTCEEEEECCTTSTTHHHHHHHHCBTTBCEEEEEC
T ss_pred             HHHHHhcC--CCCcCEEEEEccccHHHHHHHHHhCCCcCCeEEEEEC
Confidence            44555554  455779999999999999999998765  56888875

>2hnk_A SAM-dependent O-methyltransferase; modified rossman fold; HET: SAH; 2.30A {Leptospira interrogans}

Probab=96.31  E-value=0.0037  Score=50.26  Aligned_cols=33  Identities=30%  Similarity=0.481  Sum_probs=30.1

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCC-CCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFP-DTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl  212 (214)
                      +..+|||||||+|..+..+++..| ..+++.+|.
T Consensus        60 ~~~~VLdiG~G~G~~~~~la~~~~~~~~v~~vD~   93 (239)
T 2hnk_A           60 GAKRIIEIGTFTGYSSLCFASALPEDGKILCCDV   93 (239)
T ss_dssp             TCSEEEEECCTTCHHHHHHHHHSCTTCEEEEEES
T ss_pred             CcCEEEEEeCCCCHHHHHHHHhCCCCCEEEEEEC
Confidence            467999999999999999999998 688999886

>2pbf_A Protein-L-isoaspartate O-methyltransferase beta-A methyltransferase; protein repair, isoaspartyl formation, P. falciparum; HET: SAH; 2.00A {Plasmodium falciparum}

Probab=96.31  E-value=0.0062  Score=48.24  Aligned_cols=35  Identities=17%  Similarity=0.213  Sum_probs=30.4

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHC-----CCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAF-----PDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~-----P~l~~~v~Dl  212 (214)
                      ..+..+|||||||+|.++..+++..     |+.+++.+|.
T Consensus        78 ~~~~~~VLdiG~G~G~~~~~la~~~~~~~~~~~~v~~vD~  117 (227)
T 2pbf_A           78 LKPGSRAIDVGSGSGYLTVCMAIKMNVLENKNSYVIGLER  117 (227)
T ss_dssp             SCTTCEEEEESCTTSHHHHHHHHHTTTTTCTTCEEEEEES
T ss_pred             CCCCCEEEEECCCCCHHHHHHHHHhcccCCCCCEEEEEeC
Confidence            3456799999999999999999987     6789999886

>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=96.29  E-value=0.0054  Score=48.58  Aligned_cols=35  Identities=17%  Similarity=0.157  Sum_probs=30.2

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHC-CCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAF-PDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl  212 (214)
                      .....+|||||||+|..+..+++.. |+.+++.+|+
T Consensus        75 ~~~~~~vLDiG~G~G~~~~~la~~~~~~~~v~~vD~  110 (226)
T 1i1n_A           75 LHEGAKALDVGSGSGILTACFARMVGCTGKVIGIDH  110 (226)
T ss_dssp             SCTTCEEEEETCTTSHHHHHHHHHHCTTCEEEEEES
T ss_pred             CCCCCEEEEEcCCcCHHHHHHHHHhCCCcEEEEEeC
Confidence            3456799999999999999999985 7789999886

>3dr5_A Putative O-methyltransferase; Q8NRD3, CGL1119, PF01596, CGR117, NESG, structural genomics, PSI-2, protein structure initiative; 2.25A {Corynebacterium glutamicum}

Probab=96.29  E-value=0.0068  Score=48.54  Aligned_cols=31  Identities=13%  Similarity=0.160  Sum_probs=28.3

Q ss_pred             CcEEeecCCchHHHHHHHHHCC-CCeEEEecC
Q 040620          182 KPLVDVGGSTGTMARAIATAFP-DTKCTVFAC  212 (214)
Q Consensus       182 ~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl  212 (214)
                      .+|||||||+|..+..++++.| +.+++.+|+
T Consensus        58 ~~vLdiG~G~G~~~~~la~~~~~~~~v~~vD~   89 (221)
T 3dr5_A           58 TGAIAITPAAGLVGLYILNGLADNTTLTCIDP   89 (221)
T ss_dssp             CEEEEESTTHHHHHHHHHHHSCTTSEEEEECS
T ss_pred             CCEEEEcCCchHHHHHHHHhCCCCCEEEEEEC
Confidence            3999999999999999999986 889999986

>3u81_A Catechol O-methyltransferase; neurotransmitter degradation, transferase transferase inhibitor complex; HET: SAH; 1.13A {Rattus norvegicus} SCOP: c.66.1.1 PDB: 3nwe_A* 3oe5_A* 3ozr_A* 3oe4_A* 3ozt_A* 3ozs_A* 3r6t_A* 3hvi_A* 1jr4_A* 1vid_A* 1h1d_A* 2cl5_A* 3hvh_A* 3hvj_A* 3hvk_A* 3nw9_A* 3nwb_A* 3s68_A* 2zlb_A 2zth_A* ...

Probab=96.29  E-value=0.0028  Score=50.29  Aligned_cols=33  Identities=12%  Similarity=0.186  Sum_probs=29.9

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCC-CCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFP-DTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl  212 (214)
                      +..+|||||||+|..+..+++..| +.+++.+|+
T Consensus        58 ~~~~vLdiG~G~G~~~~~la~~~~~~~~v~~vD~   91 (221)
T 3u81_A           58 SPSLVLELGAYCGYSAVRMARLLQPGARLLTMEI   91 (221)
T ss_dssp             CCSEEEEECCTTSHHHHHHHTTSCTTCEEEEEES
T ss_pred             CCCEEEEECCCCCHHHHHHHHhCCCCCEEEEEeC
Confidence            468999999999999999999875 889999986

>1l3i_A Precorrin-6Y methyltransferase/putative decarboxylase; structural genomics, beta barrel, rossmann fold, tetramer; HET: SAH; 1.95A {Methanothermobacterthermautotrophicus} SCOP: c.66.1.22 PDB: 1kxz_A 1l3b_A 1f38_A 1l3c_A*

Probab=96.28  E-value=0.0046  Score=47.02  Aligned_cols=33  Identities=21%  Similarity=0.204  Sum_probs=28.8

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .....+|+|+|||+|.++..+++..  .+++++|.
T Consensus        31 ~~~~~~vldiG~G~G~~~~~l~~~~--~~v~~~D~   63 (192)
T 1l3i_A           31 PGKNDVAVDVGCGTGGVTLELAGRV--RRVYAIDR   63 (192)
T ss_dssp             CCTTCEEEEESCTTSHHHHHHHTTS--SEEEEEES
T ss_pred             CCCCCEEEEECCCCCHHHHHHHHhc--CEEEEEEC
Confidence            4556799999999999999999987  78888886

>2avd_A Catechol-O-methyltransferase; structural genomics, structural genomics consortium, SGC; HET: SAM; 1.70A {Homo sapiens} SCOP: c.66.1.1

Probab=96.28  E-value=0.0031  Score=50.03  Aligned_cols=34  Identities=32%  Similarity=0.373  Sum_probs=30.7

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCC-CCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFP-DTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl  212 (214)
                      .+..+|||||||.|..+..+++..| +.+++.+|.
T Consensus        68 ~~~~~vLdiG~G~G~~~~~la~~~~~~~~v~~vD~  102 (229)
T 2avd_A           68 IQAKKALDLGTFTGYSALALALALPADGRVVTCEV  102 (229)
T ss_dssp             TTCCEEEEECCTTSHHHHHHHTTSCTTCEEEEEES
T ss_pred             cCCCEEEEEcCCccHHHHHHHHhCCCCCEEEEEEC
Confidence            3568999999999999999999988 789999987

>3ocj_A Putative exported protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; HET: PLM; 1.39A {Bordetella parapertussis}

Probab=96.26  E-value=0.0013  Score=54.95  Aligned_cols=35  Identities=11%  Similarity=-0.051  Sum_probs=31.2

Q ss_pred             cCCCCcEEeecCCchHHHHHHH-HHCCCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIA-TAFPDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~-~~~P~l~~~v~Dl  212 (214)
                      ..+..+|||||||+|.++..++ ..+|+.+++.+|+
T Consensus       116 l~~~~~vLDiGcG~G~~~~~la~~~~~~~~v~gvD~  151 (305)
T 3ocj_A          116 LRPGCVVASVPCGWMSELLALDYSACPGVQLVGIDY  151 (305)
T ss_dssp             CCTTCEEEETTCTTCHHHHTSCCTTCTTCEEEEEES
T ss_pred             CCCCCEEEEecCCCCHHHHHHHHhcCCCCeEEEEEC
Confidence            4467899999999999999996 7899999999997

>2yqz_A Hypothetical protein TTHA0223; RNA methyltransferase, SAM, structural genomics, NPPSFA; HET: SAM; 1.80A {Thermus thermophilus} PDB: 2yr0_A

Probab=96.26  E-value=0.0064  Score=48.94  Aligned_cols=33  Identities=12%  Similarity=0.214  Sum_probs=28.1

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+..+|||||||+|.++..+++.  ..+++++|.
T Consensus        37 ~~~~~~vLDiG~G~G~~~~~l~~~--~~~v~~vD~   69 (263)
T 2yqz_A           37 KGEEPVFLELGVGTGRIALPLIAR--GYRYIALDA   69 (263)
T ss_dssp             SSSCCEEEEETCTTSTTHHHHHTT--TCEEEEEES
T ss_pred             CCCCCEEEEeCCcCCHHHHHHHHC--CCEEEEEEC
Confidence            456789999999999999999987  567888875

>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=96.25  E-value=0.0029  Score=44.92  Aligned_cols=77  Identities=9%  Similarity=-0.002  Sum_probs=55.2

Q ss_pred             HHHHHHHHHHhHHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHc-CCCCCCcccHHHHHHHHHhCCceeeecCCCCCCcc
Q 040620           18 AQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVAL-NVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEE   96 (214)
Q Consensus        18 ~~l~~~~~g~~~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~-g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~   96 (214)
                      ..+++++.+.|...+|.         .|..  ++++..|||+.+ ++++   ..+.+.|+.|...|++.......+.. .
T Consensus         5 ~~~l~~l~~~~~~~IL~---------~L~~--~~~~~~eLa~~l~~is~---~tls~~L~~Le~~GlI~r~~~~~d~r-~   69 (107)
T 2hzt_A            5 EATLEVIGGKWKXVILX---------HLTH--GKKRTSELKRLMPNITQ---KMLTQQLRELEADGVINRIVYNQVPP-K   69 (107)
T ss_dssp             HHHHHHHCSTTHHHHHH---------HHTT--CCBCHHHHHHHCTTSCH---HHHHHHHHHHHHTTSEEEEEECSSSC-E
T ss_pred             HHHHHHHcCccHHHHHH---------HHHh--CCCCHHHHHHHhcCCCH---HHHHHHHHHHHHCCCEEEeecCCCCC-e
Confidence            34455555555544443         3343  789999999999 9999   99999999999999999765321111 2


Q ss_pred             ceeeCCCCCcccccccc
Q 040620           97 ESILLPPHLDFFSRISL  113 (214)
Q Consensus        97 ~~y~~t~~~~~~s~~l~  113 (214)
                      -.|.+|+.    ++.+.
T Consensus        70 ~~y~LT~~----G~~l~   82 (107)
T 2hzt_A           70 VEYELSEY----GRSLE   82 (107)
T ss_dssp             EEEEECTT----GGGGH
T ss_pred             EEEEECcc----HHHHH
Confidence            46999999    77664

>1vbf_A 231AA long hypothetical protein-L-isoaspartate O- methyltransferase; trimeric coiled coil assembly; 2.80A {Sulfolobus tokodaii} SCOP: c.66.1.7

Probab=96.25  E-value=0.0066  Score=48.16  Aligned_cols=41  Identities=12%  Similarity=0.235  Sum_probs=32.3

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+++...  ..+..+|||||||+|.++..+++..  .+++.+|.
T Consensus        60 ~~~~~~~~--~~~~~~vLdiG~G~G~~~~~l~~~~--~~v~~vD~  100 (231)
T 1vbf_A           60 IFMLDELD--LHKGQKVLEIGTGIGYYTALIAEIV--DKVVSVEI  100 (231)
T ss_dssp             HHHHHHTT--CCTTCEEEEECCTTSHHHHHHHHHS--SEEEEEES
T ss_pred             HHHHHhcC--CCCCCEEEEEcCCCCHHHHHHHHHc--CEEEEEeC
Confidence            34455544  4566799999999999999999986  67888875

>3lpm_A Putative methyltransferase; structural genomics, protein structure initiative, NEW YORK structural genomix research consortium, nysgxrc; 2.40A {Listeria monocytogenes}

Probab=96.24  E-value=0.0038  Score=50.90  Aligned_cols=34  Identities=12%  Similarity=0.101  Sum_probs=30.1

Q ss_pred             cC-CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          178 SK-GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       178 ~~-~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .. +..+|||+|||+|.++..++++.|. +++.+|+
T Consensus        46 ~~~~~~~vLDlG~G~G~~~~~la~~~~~-~v~gvDi   80 (259)
T 3lpm_A           46 LPIRKGKIIDLCSGNGIIPLLLSTRTKA-KIVGVEI   80 (259)
T ss_dssp             CCSSCCEEEETTCTTTHHHHHHHTTCCC-EEEEECC
T ss_pred             CCCCCCEEEEcCCchhHHHHHHHHhcCC-cEEEEEC
Confidence            44 5789999999999999999999876 8999886

>1dl5_A Protein-L-isoaspartate O-methyltransferase; isoaspartyl residues, protein repair, deamidation, post-translational modification; HET: SAH; 1.80A {Thermotoga maritima} SCOP: c.66.1.7 d.197.1.1

Probab=96.24  E-value=0.0051  Score=51.84  Aligned_cols=42  Identities=14%  Similarity=0.206  Sum_probs=33.8

Q ss_pred             HHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCC-CeEEEecC
Q 040620          169 VLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPD-TKCTVFAC  212 (214)
Q Consensus       169 ~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dl  212 (214)
                      .+++..+  ..+..+|||||||.|.++..+++..+. .+++.+|+
T Consensus        66 ~l~~~l~--~~~~~~VLDiGcG~G~~~~~la~~~~~~~~v~gvD~  108 (317)
T 1dl5_A           66 LFMEWVG--LDKGMRVLEIGGGTGYNAAVMSRVVGEKGLVVSVEY  108 (317)
T ss_dssp             HHHHHTT--CCTTCEEEEECCTTSHHHHHHHHHHCTTCEEEEEES
T ss_pred             HHHHhcC--CCCcCEEEEecCCchHHHHHHHHhcCCCCEEEEEEC
Confidence            3445444  455689999999999999999999884 78888886

>2k02_A Ferrous iron transport protein C; FEOC, iron-sulfur, metal-binding, metal binding protein; NMR {Klebsiella pneumoniae subsp}

Probab=96.23  E-value=0.0018  Score=44.79  Aligned_cols=43  Identities=14%  Similarity=0.160  Sum_probs=39.8

Q ss_pred             cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620           41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ   87 (214)
Q Consensus        41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~   87 (214)
                      |.++|.+. +.+++.|||+.+++++   ..++|.|+.|...|++...
T Consensus         7 Il~~L~~~-g~vsv~eLA~~l~VS~---~TIRrDL~~Le~~G~l~R~   49 (87)
T 2k02_A            7 VRDMLALQ-GRMEAKQLSARLQTPQ---PLIDAMLERMEAMGKVVRI   49 (87)
T ss_dssp             HHHHHHHS-CSEEHHHHHHHTTCCH---HHHHHHHHHHHTTCCSEEE
T ss_pred             HHHHHHHc-CCCcHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEE
Confidence            56778877 8999999999999999   9999999999999999987

>3bgv_A MRNA CAP guanine-N7 methyltransferase; alternative splicing, mRNA capping, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: SAH; 2.30A {Homo sapiens} PDB: 3epp_A*

Probab=96.23  E-value=0.0058  Score=51.09  Aligned_cols=33  Identities=15%  Similarity=-0.031  Sum_probs=27.7

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ....+|||||||+|.++..+++ .|..+++.+|+
T Consensus        33 ~~~~~VLDlGcG~G~~~~~l~~-~~~~~v~gvD~   65 (313)
T 3bgv_A           33 KRDITVLDLGCGKGGDLLKWKK-GRINKLVCTDI   65 (313)
T ss_dssp             --CCEEEEETCTTTTTHHHHHH-TTCSEEEEEES
T ss_pred             CCCCEEEEECCCCcHHHHHHHh-cCCCEEEEEeC
Confidence            3567999999999999999988 47788999986

>3fpf_A Mtnas, putative uncharacterized protein; thermonicotianamine, nicotianamine, biosynthetic protein; HET: TNA MTA; 1.66A {Methanothermobacter thermautotrophicusorganism_taxid} PDB: 3fpe_A* 3fph_A* 3fpg_A* 3fpj_A* 3o31_A*

Probab=96.21  E-value=0.004  Score=52.64  Aligned_cols=35  Identities=11%  Similarity=0.107  Sum_probs=30.5

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .....+|+|||||+|.++..++.+.|+.+++.+|+
T Consensus       120 l~~g~rVLDIGcG~G~~ta~~lA~~~ga~V~gIDi  154 (298)
T 3fpf_A          120 FRRGERAVFIGGGPLPLTGILLSHVYGMRVNVVEI  154 (298)
T ss_dssp             CCTTCEEEEECCCSSCHHHHHHHHTTCCEEEEEES
T ss_pred             CCCcCEEEEECCCccHHHHHHHHHccCCEEEEEEC
Confidence            55688999999999988877777789999999996

>4fsd_A Arsenic methyltransferase; rossmann fold; 1.75A {Cyanidioschyzon SP} PDB: 4fr0_A* 4fs8_A 3p7e_A 3qnh_A 3qhu_A

Probab=96.20  E-value=0.0032  Score=54.57  Aligned_cols=34  Identities=15%  Similarity=0.069  Sum_probs=30.8

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHC-CCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAF-PDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl  212 (214)
                      .+..+|||||||+|.++..+++.+ |+.+++.+|+
T Consensus        82 ~~~~~VLDlGcG~G~~~~~la~~~~~~~~v~gvD~  116 (383)
T 4fsd_A           82 LEGATVLDLGCGTGRDVYLASKLVGEHGKVIGVDM  116 (383)
T ss_dssp             GTTCEEEEESCTTSHHHHHHHHHHTTTCEEEEEEC
T ss_pred             CCCCEEEEecCccCHHHHHHHHHhCCCCEEEEEEC
Confidence            356799999999999999999997 8999999997

>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19

Probab=96.20  E-value=0.0026  Score=43.39  Aligned_cols=58  Identities=17%  Similarity=0.114  Sum_probs=46.5

Q ss_pred             HhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           37 IQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        37 ~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      ....|.++|..+ + +|+.|||+++|+++   ..+++.|..|...|++...+.+     +-.|.++..
T Consensus        18 ~~~~IL~lL~~~-g-~sa~eLAk~LgiSk---~aVr~~L~~Le~eG~I~~~~~~-----PP~W~~~~~   75 (82)
T 1oyi_A           18 IVCEAIKTIGIE-G-ATAAQLTRQLNMEK---REVNKALYDLQRSAMVYSSDDI-----PPRWFMTTE   75 (82)
T ss_dssp             HHHHHHHHHSSS-T-EEHHHHHHHSSSCH---HHHHHHHHHHHHHTSSEECSSS-----SCEEESCC-
T ss_pred             HHHHHHHHHHHc-C-CCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEeCCCC-----CCcceeccC
Confidence            334567788875 4 99999999999999   9999999999999999987521     456777765

>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=96.20  E-value=0.0016  Score=46.12  Aligned_cols=47  Identities=15%  Similarity=0.209  Sum_probs=40.4

Q ss_pred             HhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           37 IQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        37 ~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      .++.|+..|..  +++|+.|||+.+|+++   ..+.+.|+.|...|++....
T Consensus        27 ~r~~IL~~L~~--~~~~~~ela~~l~is~---stvs~~L~~L~~~Glv~~~~   73 (106)
T 1r1u_A           27 NRIRIMELLSV--SEASVGHISHQLNLSQ---SNVSHQLKLLKSVHLVKAKR   73 (106)
T ss_dssp             HHHHHHHHHHH--CCBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHHh--CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeEEEE
Confidence            44556666764  7899999999999999   99999999999999998765

>4a5n_A Uncharacterized HTH-type transcriptional regulato; activator, DNA binding, MARR-like; 1.81A {Bacillus subtilis} PDB: 4a5m_A

Probab=96.19  E-value=0.0077  Score=44.70  Aligned_cols=79  Identities=8%  Similarity=-0.016  Sum_probs=60.9

Q ss_pred             HHHHHHHHHHHHhHHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHc-CCCCCCcccHHHHHHHHHhCCceeeecCCCCCC
Q 040620           16 AQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVAL-NVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQ   94 (214)
Q Consensus        16 ~~~~l~~~~~g~~~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~-g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~   94 (214)
                      +...+++++.+-|...+|...         ..  +++++.||++.+ |+++   ..|.+.|+.|...|++.......+..
T Consensus        15 pi~~~l~~lg~kW~l~IL~~L---------~~--g~~rf~eL~~~l~gIs~---~~Ls~~L~~Le~~GLV~R~~~~~d~r   80 (131)
T 4a5n_A           15 PVEFTLDVIGGKWKGILFYHM---------ID--GKKRFNEFRRICPSITQ---RMLTLQLRELEADGIVHREVYHQVPP   80 (131)
T ss_dssp             HHHHHHHHHCSSSHHHHHHHH---------TT--SCBCHHHHHHHCTTSCH---HHHHHHHHHHHHTTSEEEEEECSSSC
T ss_pred             cHHHHHHHHcCcCHHHHHHHH---------hc--CCcCHHHHHHHhcccCH---HHHHHHHHHHHHCCCEEEEecCCCCC
Confidence            456667777777776666543         23  899999999999 9999   99999999999999999765311111


Q ss_pred             ccceeeCCCCCcccccccc
Q 040620           95 EEESILLPPHLDFFSRISL  113 (214)
Q Consensus        95 ~~~~y~~t~~~~~~s~~l~  113 (214)
                       .-.|.+|+.    ++.+.
T Consensus        81 -~v~y~LT~~----G~~l~   94 (131)
T 4a5n_A           81 -KVEYSLTEF----GRTLE   94 (131)
T ss_dssp             -EEEEEECTT----GGGGH
T ss_pred             -eEEEEECHh----HHHHH
Confidence             246999999    88886

>3bwc_A Spermidine synthase; SAM, SGPP, structura genomics, PSI, protein structure initiative, structural GEN pathogenic protozoa consortium; HET: MSE SAM; 2.30A {Trypanosoma cruzi} PDB: 3bwb_A*

Probab=96.18  E-value=0.0031  Score=53.10  Aligned_cols=34  Identities=15%  Similarity=0.284  Sum_probs=30.6

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+.++|||||||.|..+..+++..|..+++++|+
T Consensus        94 ~~~~~VLdiG~G~G~~~~~l~~~~~~~~v~~vDi  127 (304)
T 3bwc_A           94 PKPERVLIIGGGDGGVLREVLRHGTVEHCDLVDI  127 (304)
T ss_dssp             SSCCEEEEEECTTSHHHHHHHTCTTCCEEEEEES
T ss_pred             CCCCeEEEEcCCCCHHHHHHHhCCCCCEEEEEEC
Confidence            3468999999999999999999888889999987

>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=96.17  E-value=0.0046  Score=46.66  Aligned_cols=67  Identities=10%  Similarity=0.188  Sum_probs=49.9

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      +..|+..|..+ +++|..+||+.+++++   ..+.++++.|...|++.......|.- ...+.+|+.    ++.++
T Consensus        48 q~~iL~~l~~~-~~~t~~eLa~~l~~~~---~tvs~~l~~Le~~Glv~r~~~~~DrR-~~~l~LT~~----G~~~~  114 (162)
T 3k0l_A           48 QFTALSVLAAK-PNLSNAKLAERSFIKP---QSANKILQDLLANGWIEKAPDPTHGR-RILVTVTPS----GLDKL  114 (162)
T ss_dssp             HHHHHHHHHHC-TTCCHHHHHHHHTSCG---GGHHHHHHHHHHTTSEEEEECCSSSC-CEEEEECHH----HHHHH
T ss_pred             HHHHHHHHHHC-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCcCeEecCCCCcCC-eeEeEECHh----HHHHH
Confidence            34467777776 7999999999999999   99999999999999999775311110 123667776    55553

>2htj_A P fimbrial regulatory protein KS71A; winged helix-turn-helix, PAP PILI, transcription activator; NMR {Escherichia coli} SCOP: a.4.5.73

Probab=96.17  E-value=0.003  Score=42.49  Aligned_cols=44  Identities=20%  Similarity=0.264  Sum_probs=38.8

Q ss_pred             CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620           40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ   87 (214)
Q Consensus        40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~   87 (214)
                      .|++.|..+ +++|..|||+.+|+++   ..+++.|+.|...|++...
T Consensus         4 ~Il~~L~~~-~~~s~~eLa~~lgvs~---~tv~r~L~~L~~~GlI~~~   47 (81)
T 2htj_A            4 EILEFLNRH-NGGKTAEIAEALAVTD---YQARYYLLLLEKAGMVQRS   47 (81)
T ss_dssp             HHHHHHHHS-CCCCHHHHHHHHTSCH---HHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEe
Confidence            356677765 7899999999999999   9999999999999999854

>3sm3_A SAM-dependent methyltransferases; NESG, structural genomics, PSI-biology, protein structure in northeast structural genomics; 2.20A {Methanosarcina mazei}

Probab=96.16  E-value=0.0044  Score=48.91  Aligned_cols=32  Identities=16%  Similarity=0.284  Sum_probs=28.3

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ....+|||||||+|.++..++++  ..+++++|+
T Consensus        29 ~~~~~vLdiG~G~G~~~~~l~~~--~~~v~~vD~   60 (235)
T 3sm3_A           29 QEDDEILDIGCGSGKISLELASK--GYSVTGIDI   60 (235)
T ss_dssp             CTTCEEEEETCTTSHHHHHHHHT--TCEEEEEES
T ss_pred             CCCCeEEEECCCCCHHHHHHHhC--CCeEEEEEC
Confidence            35679999999999999999998  678999886

>3b3j_A Histone-arginine methyltransferase CARM1; protein arginine methyltransferase 4, APO catalytic domain, regulator, mRNA processing; 2.55A {Rattus norvegicus}

Probab=96.15  E-value=0.0077  Score=54.10  Aligned_cols=43  Identities=16%  Similarity=0.171  Sum_probs=33.9

Q ss_pred             HHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          167 ASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       167 ~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+++.++  ..+..+|+|||||+|.+++.+++ .|..+++.+|+
T Consensus       147 ~~~il~~l~--~~~~~~VLDiGcGtG~la~~la~-~~~~~V~gvD~  189 (480)
T 3b3j_A          147 QRAILQNHT--DFKDKIVLDVGCGSGILSFFAAQ-AGARKIYAVEA  189 (480)
T ss_dssp             HHHHHHTGG--GTTTCEEEEESCSTTHHHHHHHH-TTCSEEEEEEC
T ss_pred             HHHHHHhhh--hcCCCEEEEecCcccHHHHHHHH-cCCCEEEEEEc
Confidence            344555554  44567999999999999998887 68889999986

>2b25_A Hypothetical protein; structural genomics, methyl transferase, SAM, structural GEN consortium, SGC, transferase; HET: SAM; 2.50A {Homo sapiens} SCOP: c.66.1.13

Probab=96.15  E-value=0.0068  Score=51.36  Aligned_cols=41  Identities=12%  Similarity=0.237  Sum_probs=33.5

Q ss_pred             HHhhcccccCCCCcEEeecCCchHHHHHHHHH-CCCCeEEEecC
Q 040620          170 LIEDCNEVSKGLKPLVDVGGSTGTMARAIATA-FPDTKCTVFAC  212 (214)
Q Consensus       170 ~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~-~P~l~~~v~Dl  212 (214)
                      ++...+  .....+|||||||+|.++..+++. .|+.+++.+|+
T Consensus        97 ~l~~l~--~~~g~~VLDiG~G~G~~~~~la~~~g~~~~v~~vD~  138 (336)
T 2b25_A           97 ILSMMD--INPGDTVLEAGSGSGGMSLFLSKAVGSQGRVISFEV  138 (336)
T ss_dssp             HHHHHT--CCTTCEEEEECCTTSHHHHHHHHHHCTTCEEEEEES
T ss_pred             HHHhcC--CCCCCEEEEeCCCcCHHHHHHHHHhCCCceEEEEeC
Confidence            344444  455779999999999999999998 58899999986

>3e23_A Uncharacterized protein RPA2492; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; HET: SAM; 1.60A {Rhodopseudomonas palustris}

Probab=96.15  E-value=0.005  Score=48.14  Aligned_cols=32  Identities=16%  Similarity=0.173  Sum_probs=28.0

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ....+|||||||+|.++..++++  ..+++++|+
T Consensus        42 ~~~~~vLDiGcG~G~~~~~l~~~--~~~v~~vD~   73 (211)
T 3e23_A           42 PAGAKILELGCGAGYQAEAMLAA--GFDVDATDG   73 (211)
T ss_dssp             CTTCEEEESSCTTSHHHHHHHHT--TCEEEEEES
T ss_pred             CCCCcEEEECCCCCHHHHHHHHc--CCeEEEECC
Confidence            35679999999999999999988  568888886

>2y75_A HTH-type transcriptional regulator CYMR; DNA binding protein; 2.00A {Bacillus subtilis}

Probab=96.14  E-value=0.0026  Score=46.65  Aligned_cols=47  Identities=19%  Similarity=0.247  Sum_probs=39.3

Q ss_pred             CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      +++|+++||+++++++   ..++++++.|...|++.....    . .+.|.+..-
T Consensus        25 ~~~s~~ela~~~~i~~---~~v~~il~~L~~~Glv~~~~g----~-~ggy~L~~~   71 (129)
T 2y75_A           25 GPTSLKSIAQTNNLSE---HYLEQLVSPLRNAGLVKSIRG----A-YGGYVLGSE   71 (129)
T ss_dssp             CCBCHHHHHHHTTSCH---HHHHHHHHHHHHTTSEEEC---------CCEEESSC
T ss_pred             CcCCHHHHHHHHCcCH---HHHHHHHHHHHHCCceEecCC----C-CCceEeCCC
Confidence            7899999999999999   999999999999999987631    0 367887766

>2kko_A Possible transcriptional regulatory protein (possibly ARSR-family); NESG, DNA-binding, transcription regulation, WHTH, homodimer; NMR {Mycobacterium bovis} PDB: 3gw2_A

Probab=96.13  E-value=0.001  Score=47.47  Aligned_cols=45  Identities=16%  Similarity=0.232  Sum_probs=38.7

Q ss_pred             cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      +.|+..|..  +++|+.|||+.+|+++   ..+.+.|+.|...|++....
T Consensus        28 ~~IL~~L~~--~~~s~~eLa~~lgis~---stvs~~L~~L~~~GlV~~~~   72 (108)
T 2kko_A           28 LQILDLLAQ--GERAVEAIATATGMNL---TTASANLQALKSGGLVEARR   72 (108)
T ss_dssp             HHHHHHHTT--CCEEHHHHHHHHTCCH---HHHHHHHHHHHHHTSEEEEE
T ss_pred             HHHHHHHHc--CCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeEEEE
Confidence            345556664  7899999999999999   99999999999999998764

>3c3y_A Pfomt, O-methyltransferase; plant secondary metabolism; HET: SAH; 1.37A {Mesembryanthemum crystallinum}

Probab=96.12  E-value=0.0053  Score=49.54  Aligned_cols=34  Identities=29%  Similarity=0.277  Sum_probs=30.7

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCC-CCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFP-DTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl  212 (214)
                      .+.++|||||||.|..+..+++..| +.+++.+|+
T Consensus        69 ~~~~~VLeiG~G~G~~~~~la~~~~~~~~v~~iD~  103 (237)
T 3c3y_A           69 VNAKKTIEVGVFTGYSLLLTALSIPDDGKITAIDF  103 (237)
T ss_dssp             TTCCEEEEECCTTSHHHHHHHHHSCTTCEEEEEES
T ss_pred             hCCCEEEEeCCCCCHHHHHHHHhCCCCCEEEEEEC
Confidence            3568999999999999999999998 789999886

>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=96.11  E-value=0.025  Score=41.30  Aligned_cols=61  Identities=15%  Similarity=0.176  Sum_probs=46.0

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      ++.|+..|. . +++|..+||+.+++++   ..+.+.++.|...|++.......|.- ...+.+|+.
T Consensus        39 ~~~iL~~l~-~-~~~~~~ela~~l~~s~---~tvs~~l~~Le~~glv~r~~~~~d~r-~~~~~lT~~   99 (146)
T 2gxg_A           39 DFLVLRATS-D-GPKTMAYLANRYFVTQ---SAITASVDKLEEMGLVVRVRDREDRR-KILIEITEK   99 (146)
T ss_dssp             HHHHHHHHT-T-SCBCHHHHHHHTTCCH---HHHHHHHHHHHHTTSEEEEECSSCTT-CEEEEECHH
T ss_pred             HHHHHHHHh-c-CCcCHHHHHHHhCCCc---hhHHHHHHHHHHCCCEEeecCCCCCc-eEEEEECHH
Confidence            444666777 4 8999999999999999   99999999999999999764211111 123666666

>3m70_A Tellurite resistance protein TEHB homolog; structural genomics, PSI-2, protein ST initiative; 1.95A {Haemophilus influenzae}

Probab=96.11  E-value=0.0048  Score=50.77  Aligned_cols=32  Identities=13%  Similarity=0.129  Sum_probs=28.2

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ....+|||||||.|.++..++++  ..+++.+|.
T Consensus       119 ~~~~~vLD~GcG~G~~~~~l~~~--g~~v~~vD~  150 (286)
T 3m70_A          119 ISPCKVLDLGCGQGRNSLYLSLL--GYDVTSWDH  150 (286)
T ss_dssp             SCSCEEEEESCTTCHHHHHHHHT--TCEEEEEES
T ss_pred             cCCCcEEEECCCCCHHHHHHHHC--CCeEEEEEC
Confidence            35789999999999999999998  568999886

>2fbh_A Transcriptional regulator PA3341; MARR, transcription regulator, APC5857, structural genomics, protein structure initiative; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=96.11  E-value=0.0055  Score=44.90  Aligned_cols=66  Identities=12%  Similarity=0.168  Sum_probs=48.8

Q ss_pred             cCcchhh-hcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           39 LRIPDII-NNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        39 lglfd~L-~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      +.|+..| ... +++|..+||+.+++++   ..+.++++.|...|++.......|.- ...+.+|+.    ++.++
T Consensus        40 ~~iL~~l~~~~-~~~t~~~la~~l~~s~---~~vs~~l~~L~~~glv~r~~~~~d~R-~~~~~lT~~----G~~~~  106 (146)
T 2fbh_A           40 WLVLLHLARHR-DSPTQRELAQSVGVEG---PTLARLLDGLESQGLVRRLAVAEDRR-AKHIVLTPK----ADVLI  106 (146)
T ss_dssp             HHHHHHHHHCS-SCCBHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEECCBTTBC-SCEEEECTT----HHHHH
T ss_pred             HHHHHHHHHcC-CCCCHHHHHHHhCCCh---hhHHHHHHHHHHCCCeeecCCCcccC-eeeeEECHh----HHHHH
Confidence            3366677 544 8999999999999999   99999999999999999864211111 233777777    65554

>1iy9_A Spermidine synthase; rossmann fold, structural genomics, PSI, protein structure initiative, northeast structural genomics consortium, NESG; 2.30A {Bacillus subtilis} SCOP: c.66.1.17

Probab=96.11  E-value=0.0031  Score=52.37  Aligned_cols=33  Identities=24%  Similarity=0.300  Sum_probs=30.1

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +.++|||||||.|..++.+++..|..+++++|+
T Consensus        75 ~~~~VLdiG~G~G~~~~~l~~~~~~~~v~~vEi  107 (275)
T 1iy9_A           75 NPEHVLVVGGGDGGVIREILKHPSVKKATLVDI  107 (275)
T ss_dssp             SCCEEEEESCTTCHHHHHHTTCTTCSEEEEEES
T ss_pred             CCCEEEEECCchHHHHHHHHhCCCCceEEEEEC
Confidence            468999999999999999998878889999987

>3a27_A TYW2, uncharacterized protein MJ1557; wybutosine modification, transferase; HET: SAM; 2.00A {Methanocaldococcus jannaschii}

Probab=96.10  E-value=0.004  Score=51.52  Aligned_cols=35  Identities=14%  Similarity=0.035  Sum_probs=31.5

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +.+..+|+|+|||+|.+++.++++.|..+++.+|+
T Consensus       117 ~~~~~~VLDlgcG~G~~s~~la~~~~~~~V~~vD~  151 (272)
T 3a27_A          117 SNENEVVVDMFAGIGYFTIPLAKYSKPKLVYAIEK  151 (272)
T ss_dssp             CCTTCEEEETTCTTTTTHHHHHHHTCCSEEEEEEC
T ss_pred             cCCCCEEEEecCcCCHHHHHHHHhCCCCEEEEEeC
Confidence            34567999999999999999999999889999886

>1xj5_A Spermidine synthase 1; structural genomics, protein structure initiative, CESG, AT1G23820, putrescine aminopropyl transferase, SPDS1; 2.70A {Arabidopsis thaliana} SCOP: c.66.1.17 PDB: 2q41_A

Probab=96.08  E-value=0.0033  Score=53.91  Aligned_cols=34  Identities=18%  Similarity=0.265  Sum_probs=30.9

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+.++|||||||.|..++.++++.|..+++.+|+
T Consensus       119 ~~~~~VLdIG~G~G~~a~~la~~~~~~~V~~VDi  152 (334)
T 1xj5_A          119 PNPKKVLVIGGGDGGVLREVARHASIEQIDMCEI  152 (334)
T ss_dssp             SCCCEEEEETCSSSHHHHHHTTCTTCCEEEEEES
T ss_pred             CCCCEEEEECCCccHHHHHHHHcCCCCEEEEEEC
Confidence            3568999999999999999999888899999986

>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=96.07  E-value=0.0054  Score=53.42  Aligned_cols=43  Identities=21%  Similarity=0.235  Sum_probs=34.0

Q ss_pred             hHHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          166 IASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       166 ~~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+..+++.++  .....+|||||||+|.++..++++  ..+++.+|.
T Consensus        95 ~~~~l~~~~~--~~~~~~VLDiGcG~G~~~~~l~~~--g~~v~gvD~  137 (416)
T 4e2x_A           95 LARDFLATEL--TGPDPFIVEIGCNDGIMLRTIQEA--GVRHLGFEP  137 (416)
T ss_dssp             HHHHHHHTTT--CSSSCEEEEETCTTTTTHHHHHHT--TCEEEEECC
T ss_pred             HHHHHHHHhC--CCCCCEEEEecCCCCHHHHHHHHc--CCcEEEECC
Confidence            4455666665  556789999999999999999987  448888886

>3cbg_A O-methyltransferase; cyanobacterium; HET: SAH FER 4FE; 2.00A {Synechocystis SP}

Probab=96.06  E-value=0.0044  Score=49.80  Aligned_cols=33  Identities=27%  Similarity=0.375  Sum_probs=29.9

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCC-CCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFP-DTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl  212 (214)
                      +.++|||||||.|..+..+++..| +.+++.+|.
T Consensus        72 ~~~~vLdiG~G~G~~~~~la~~~~~~~~v~~iD~  105 (232)
T 3cbg_A           72 GAKQVLEIGVFRGYSALAMALQLPPDGQIIACDQ  105 (232)
T ss_dssp             TCCEEEEECCTTSHHHHHHHTTSCTTCEEEEEES
T ss_pred             CCCEEEEecCCCCHHHHHHHHhCCCCCEEEEEEC
Confidence            467999999999999999999998 788999886

>3l8d_A Methyltransferase; structural genomics, PSI, nysgrc, protein structure initiative, NEW YORK SGX research center for STRU genomics; 1.70A {Bacillus thuringiensis}

Probab=96.06  E-value=0.0046  Score=49.21  Aligned_cols=31  Identities=16%  Similarity=0.143  Sum_probs=27.6

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +..+|||||||+|.++..+++.  ..+++++|+
T Consensus        53 ~~~~vLDiG~G~G~~~~~l~~~--~~~v~~vD~   83 (242)
T 3l8d_A           53 KEAEVLDVGCGDGYGTYKLSRT--GYKAVGVDI   83 (242)
T ss_dssp             TTCEEEEETCTTSHHHHHHHHT--TCEEEEEES
T ss_pred             CCCeEEEEcCCCCHHHHHHHHc--CCeEEEEEC
Confidence            5679999999999999999998  668888886

>1zq9_A Probable dimethyladenosine transferase; SGC, structural genomics, structural genomics consortium; HET: SAM; 1.90A {Homo sapiens} SCOP: c.66.1.24

Probab=96.05  E-value=0.0065  Score=50.60  Aligned_cols=42  Identities=17%  Similarity=0.256  Sum_probs=33.2

Q ss_pred             HHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          167 ASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       167 ~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+++..+  .....+|||||||+|.++..++++..  +++.+|+
T Consensus        17 ~~~i~~~~~--~~~~~~VLDiG~G~G~lt~~L~~~~~--~v~~vD~   58 (285)
T 1zq9_A           17 INSIIDKAA--LRPTDVVLEVGPGTGNMTVKLLEKAK--KVVACEL   58 (285)
T ss_dssp             HHHHHHHTC--CCTTCEEEEECCTTSTTHHHHHHHSS--EEEEEES
T ss_pred             HHHHHHhcC--CCCCCEEEEEcCcccHHHHHHHhhCC--EEEEEEC
Confidence            355666665  45667999999999999999999854  7888775

>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=96.05  E-value=0.0016  Score=44.98  Aligned_cols=69  Identities=14%  Similarity=0.163  Sum_probs=50.2

Q ss_pred             HHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           31 LSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        31 ~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      .++..-.++.|+..|..+ +++|..+||+.+++++   ..+.+.|+.|...|++.......++. ...|.+|+.
T Consensus        11 ~~l~~~~~~~iL~~L~~~-~~~~~~ela~~l~is~---~tvs~~l~~L~~~gli~~~~~~~~~r-~~~~~lt~~   79 (100)
T 1ub9_A           11 HILGNPVRLGIMIFLLPR-RKAPFSQIQKVLDLTP---GNLDSHIRVLERNGLVKTYKVIADRP-RTVVEITDF   79 (100)
T ss_dssp             HHHHSHHHHHHHHHHHHH-SEEEHHHHHHHTTCCH---HHHHHHHHHHHHTTSEEEEEECSSSC-EEEEEECHH
T ss_pred             cccCChHHHHHHHHHHhc-CCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEEecCCCcc-eEEEEECHH
Confidence            344445566677777644 7899999999999999   99999999999999998643110111 245677766

>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=96.04  E-value=0.012  Score=43.54  Aligned_cols=46  Identities=11%  Similarity=0.281  Sum_probs=40.2

Q ss_pred             cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      +.|+..|... +++|..+||+.+++++   ..+.+.++.|...|++....
T Consensus        40 ~~iL~~l~~~-~~~t~~ela~~l~~s~---~tvs~~l~~Le~~glv~r~~   85 (155)
T 1s3j_A           40 LFVLASLKKH-GSLKVSEIAERMEVKP---SAVTLMADRLEQKNLIARTH   85 (155)
T ss_dssp             HHHHHHHHHH-SEEEHHHHHHHHTSCH---HHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHc-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEeecC
Confidence            3366677665 7899999999999999   99999999999999999865

>3bkw_A MLL3908 protein, S-adenosylmethionine dependent methyltransferase; NP_104914.1; HET: MSE; 1.60A {Mesorhizobium loti}

Probab=96.01  E-value=0.0089  Score=47.48  Aligned_cols=40  Identities=18%  Similarity=0.030  Sum_probs=30.6

Q ss_pred             HHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          170 LIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       170 ~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +...++  .....+|||||||+|.++..++++.+ .+++++|+
T Consensus        35 l~~~~~--~~~~~~vLdiG~G~G~~~~~l~~~~~-~~v~~vD~   74 (243)
T 3bkw_A           35 LRAMLP--EVGGLRIVDLGCGFGWFCRWAHEHGA-SYVLGLDL   74 (243)
T ss_dssp             HHHHSC--CCTTCEEEEETCTTCHHHHHHHHTTC-SEEEEEES
T ss_pred             HHHhcc--ccCCCEEEEEcCcCCHHHHHHHHCCC-CeEEEEcC
Confidence            444444  34567999999999999999998833 38888886

>3gru_A Dimethyladenosine transferase; rossman fold, ribosomal assem adenosyl-L-methionine, rRNA, methyltransferase, RNA-binding processing; HET: AMP; 1.60A {Methanocaldococcus jannaschii} PDB: 3grr_A* 3grv_A* 3gry_A* 3fyd_A 3fyc_A*

Probab=96.00  E-value=0.0098  Score=50.09  Aligned_cols=42  Identities=17%  Similarity=0.260  Sum_probs=33.3

Q ss_pred             HHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          167 ASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       167 ~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+++..+  .....+|||||||+|.++..++++  ..+++.+|+
T Consensus        39 ~~~Iv~~l~--~~~~~~VLEIG~G~G~lT~~La~~--~~~V~aVEi   80 (295)
T 3gru_A           39 VNKAVESAN--LTKDDVVLEIGLGKGILTEELAKN--AKKVYVIEI   80 (295)
T ss_dssp             HHHHHHHTT--CCTTCEEEEECCTTSHHHHHHHHH--SSEEEEEES
T ss_pred             HHHHHHhcC--CCCcCEEEEECCCchHHHHHHHhc--CCEEEEEEC
Confidence            455666655  556679999999999999999998  567888875

>1ne2_A Hypothetical protein TA1320; structural genomics, conserved hypothetical protein, PSI, protein structure initiative; 1.75A {Thermoplasma acidophilum} SCOP: c.66.1.32

Probab=96.00  E-value=0.005  Score=47.89  Aligned_cols=33  Identities=21%  Similarity=0.291  Sum_probs=28.2

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ....+|+|+|||+|.++..+++. +..+++.+|+
T Consensus        50 ~~~~~vlD~gcG~G~~~~~l~~~-~~~~v~~vD~   82 (200)
T 1ne2_A           50 IGGRSVIDAGTGNGILACGSYLL-GAESVTAFDI   82 (200)
T ss_dssp             SBTSEEEEETCTTCHHHHHHHHT-TBSEEEEEES
T ss_pred             CCCCEEEEEeCCccHHHHHHHHc-CCCEEEEEEC
Confidence            34679999999999999999987 6567999886

>3p9n_A Possible methyltransferase (methylase); RV2966C, adoMet binding, RNA methylase, RSMD, SAM-fold, RNA methyltransferase; 1.90A {Mycobacterium tuberculosis}

Probab=96.00  E-value=0.0066  Score=46.79  Aligned_cols=32  Identities=6%  Similarity=0.067  Sum_probs=27.3

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+|+|+|||+|.++..+++. +..+++.+|+
T Consensus        44 ~~~~vLDlgcG~G~~~~~~~~~-~~~~v~~vD~   75 (189)
T 3p9n_A           44 TGLAVLDLYAGSGALGLEALSR-GAASVLFVES   75 (189)
T ss_dssp             TTCEEEEETCTTCHHHHHHHHT-TCSEEEEEEC
T ss_pred             CCCEEEEeCCCcCHHHHHHHHC-CCCeEEEEEC
Confidence            4679999999999999988774 6678999886

>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=95.99  E-value=0.0037  Score=52.47  Aligned_cols=33  Identities=18%  Similarity=0.242  Sum_probs=30.2

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +..+|||||||+|..+..+++..|..+++++|+
T Consensus        90 ~~~~VLdiG~G~G~~~~~l~~~~~~~~v~~vDi  122 (296)
T 1inl_A           90 NPKKVLIIGGGDGGTLREVLKHDSVEKAILCEV  122 (296)
T ss_dssp             SCCEEEEEECTTCHHHHHHTTSTTCSEEEEEES
T ss_pred             CCCEEEEEcCCcCHHHHHHHhcCCCCEEEEEEC
Confidence            357999999999999999999888899999986

>3h2b_A SAM-dependent methyltransferase; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; HET: SAH; 2.00A {Corynebacterium glutamicum atcc 13032}

Probab=95.98  E-value=0.0054  Score=47.59  Aligned_cols=30  Identities=20%  Similarity=0.236  Sum_probs=26.8

Q ss_pred             CCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          181 LKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       181 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+|||||||+|.++..++++  +.+++++|+
T Consensus        42 ~~~vLDiGcG~G~~~~~l~~~--~~~v~gvD~   71 (203)
T 3h2b_A           42 DGVILDVGSGTGRWTGHLASL--GHQIEGLEP   71 (203)
T ss_dssp             CSCEEEETCTTCHHHHHHHHT--TCCEEEECC
T ss_pred             CCeEEEecCCCCHHHHHHHhc--CCeEEEEeC
Confidence            579999999999999999998  558888886

>3f6o_A Probable transcriptional regulator, ARSR family protein; transcriptional regulator,RHA00566,MCSG, structural genomics, PSI-2; 1.90A {Rhodococcus SP}

Probab=95.98  E-value=0.002  Score=46.55  Aligned_cols=65  Identities=11%  Similarity=0.196  Sum_probs=50.2

Q ss_pred             HHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           31 LSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        31 ~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      .+|.--.++.|+..|.+  +|+++.+||+.+|+++   ..+.+.|+.|...|++.....   +. ...|.+++.
T Consensus        13 ~al~~~~R~~Il~~L~~--~~~~~~eLa~~l~is~---~tvs~hL~~L~~~GlV~~~~~---gr-~~~y~l~~~   77 (118)
T 3f6o_A           13 QALADPTRRAVLGRLSR--GPATVSELAKPFDMAL---PSFMKHIHFLEDSGWIRTHKQ---GR-VRTCAIEKE   77 (118)
T ss_dssp             HHHTSHHHHHHHHHHHT--CCEEHHHHHTTCCSCH---HHHHHHHHHHHHTTSEEEEEE---TT-EEEEEECSH
T ss_pred             HHhCCHHHHHHHHHHHh--CCCCHHHHHHHhCcCH---HHHHHHHHHHHHCCCeEEEec---CC-EEEEEECHH
Confidence            44444556667777775  8999999999999999   999999999999999987651   11 234666665

>4htf_A S-adenosylmethionine-dependent methyltransferase; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; HET: MSE SAM; 1.60A {Escherichia coli}

Probab=95.96  E-value=0.0088  Score=49.09  Aligned_cols=39  Identities=15%  Similarity=0.256  Sum_probs=31.0

Q ss_pred             HHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          169 VLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       169 ~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .++..++   .+..+|||||||.|.++..+++.  ..+++++|+
T Consensus        60 ~~l~~~~---~~~~~vLDiGcG~G~~~~~l~~~--~~~v~gvD~   98 (285)
T 4htf_A           60 RVLAEMG---PQKLRVLDAGGGEGQTAIKMAER--GHQVILCDL   98 (285)
T ss_dssp             HHHHHTC---SSCCEEEEETCTTCHHHHHHHHT--TCEEEEEES
T ss_pred             HHHHhcC---CCCCEEEEeCCcchHHHHHHHHC--CCEEEEEEC
Confidence            3445444   23579999999999999999998  678999886

>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=95.96  E-value=0.01  Score=50.80  Aligned_cols=43  Identities=19%  Similarity=0.207  Sum_probs=32.7

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                      ..+++...  ..+..+|||||||+|.++..++++ +..+++.+|..
T Consensus        40 ~~i~~~l~--~~~~~~VLDiGcGtG~ls~~la~~-g~~~V~~vD~s   82 (348)
T 2y1w_A           40 RAILQNHT--DFKDKIVLDVGCGSGILSFFAAQA-GARKIYAVEAS   82 (348)
T ss_dssp             HHHHHTGG--GTTTCEEEEETCTTSHHHHHHHHT-TCSEEEEEECS
T ss_pred             HHHHhccc--cCCcCEEEEcCCCccHHHHHHHhC-CCCEEEEECCH
Confidence            33445443  345679999999999999998885 66789988863

>2pt6_A Spermidine synthase; transferase, structural genomics consor SGC,dcadoMet complex; HET: S4M 1PG; 2.00A {Plasmodium falciparum} PDB: 2pss_A* 2pt9_A*

Probab=95.96  E-value=0.0037  Score=53.18  Aligned_cols=33  Identities=18%  Similarity=0.254  Sum_probs=30.2

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +.++|+|||||+|..++.+++..|..+++.+|+
T Consensus       116 ~~~~VLdiG~G~G~~~~~l~~~~~~~~v~~vDi  148 (321)
T 2pt6_A          116 EPKNVLVVGGGDGGIIRELCKYKSVENIDICEI  148 (321)
T ss_dssp             SCCEEEEEECTTCHHHHHHTTCTTCCEEEEEES
T ss_pred             CCCEEEEEcCCccHHHHHHHHcCCCCEEEEEEC
Confidence            457999999999999999999888899999986

>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=95.95  E-value=0.0099  Score=50.75  Aligned_cols=35  Identities=26%  Similarity=0.139  Sum_probs=29.4

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                      ..+..+|||||||+|.++..++++ +..+++.+|.-
T Consensus        62 ~~~~~~VLDiGcGtG~ls~~la~~-g~~~v~gvD~s   96 (340)
T 2fyt_A           62 IFKDKVVLDVGCGTGILSMFAAKA-GAKKVLGVDQS   96 (340)
T ss_dssp             GTTTCEEEEETCTTSHHHHHHHHT-TCSEEEEEESS
T ss_pred             hcCCCEEEEeeccCcHHHHHHHHc-CCCEEEEEChH
Confidence            445689999999999999999987 55689998863

>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=95.94  E-value=0.0082  Score=49.93  Aligned_cols=41  Identities=22%  Similarity=0.302  Sum_probs=31.5

Q ss_pred             HHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          167 ASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       167 ~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+++..+  .... +|||||||+|.++..++++.  .+++.+|+
T Consensus        36 ~~~Iv~~~~--~~~~-~VLEIG~G~G~lt~~L~~~~--~~V~avEi   76 (271)
T 3fut_A           36 LRRIVEAAR--PFTG-PVFEVGPGLGALTRALLEAG--AEVTAIEK   76 (271)
T ss_dssp             HHHHHHHHC--CCCS-CEEEECCTTSHHHHHHHHTT--CCEEEEES
T ss_pred             HHHHHHhcC--CCCC-eEEEEeCchHHHHHHHHHcC--CEEEEEEC
Confidence            345555554  4445 99999999999999999985  56777775

>1yub_A Ermam, rRNA methyltransferase; MLS antibiotics; NMR {Streptococcus pneumoniae} SCOP: c.66.1.24

Probab=95.94  E-value=0.0039  Score=50.57  Aligned_cols=42  Identities=17%  Similarity=0.279  Sum_probs=33.5

Q ss_pred             HHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          167 ASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       167 ~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+++..+  .....+|||||||.|.++..++++.  .+++.+|+
T Consensus        18 ~~~i~~~~~--~~~~~~VLDiG~G~G~~~~~l~~~~--~~v~~id~   59 (245)
T 1yub_A           18 LNQIIKQLN--LKETDTVYEIGTGKGHLTTKLAKIS--KQVTSIEL   59 (245)
T ss_dssp             HHHHHHHCC--CCSSEEEEECSCCCSSCSHHHHHHS--SEEEESSS
T ss_pred             HHHHHHhcC--CCCCCEEEEEeCCCCHHHHHHHHhC--CeEEEEEC
Confidence            345566555  4556799999999999999999985  77888886

>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=95.93  E-value=0.0093  Score=51.77  Aligned_cols=44  Identities=9%  Similarity=0.106  Sum_probs=33.9

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHC-CCCeEEEecCC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAF-PDTKCTVFACH  213 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dlp  213 (214)
                      ..+++.++  .....+|+|+|||+|.++..+++++ |..+++.+|+-
T Consensus        29 ~~~~~~~~--~~~~~~vLD~gcGtG~~~~~~~~~~~~~~~i~gvDi~   73 (421)
T 2ih2_A           29 DFMVSLAE--APRGGRVLEPACAHGPFLRAFREAHGTAYRFVGVEID   73 (421)
T ss_dssp             HHHHHHCC--CCTTCEEEEETCTTCHHHHHHHHHHCSCSEEEEEESC
T ss_pred             HHHHHhhc--cCCCCEEEECCCCChHHHHHHHHHhCCCCeEEEEECC
Confidence            33444443  2345699999999999999999988 77899999873

>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=95.93  E-value=0.0041  Score=52.62  Aligned_cols=33  Identities=21%  Similarity=0.249  Sum_probs=30.3

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +.++|||||||.|..+..+++..|..+++++|+
T Consensus        77 ~~~~VLdiG~G~G~~~~~l~~~~~~~~v~~vDi  109 (314)
T 1uir_A           77 EPKRVLIVGGGEGATLREVLKHPTVEKAVMVDI  109 (314)
T ss_dssp             CCCEEEEEECTTSHHHHHHTTSTTCCEEEEEES
T ss_pred             CCCeEEEEcCCcCHHHHHHHhcCCCCEEEEEEC
Confidence            458999999999999999999888899999986

>3m33_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, MCSG, midwest center for structural genomics; 2.19A {Deinococcus radiodurans}

Probab=95.92  E-value=0.0049  Score=49.07  Aligned_cols=31  Identities=10%  Similarity=0.218  Sum_probs=27.6

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+|||||||+|.++..++++  ..+++.+|+
T Consensus        48 ~~~~vLDiGcG~G~~~~~l~~~--~~~v~~vD~   78 (226)
T 3m33_A           48 PQTRVLEAGCGHGPDAARFGPQ--AARWAAYDF   78 (226)
T ss_dssp             TTCEEEEESCTTSHHHHHHGGG--SSEEEEEES
T ss_pred             CCCeEEEeCCCCCHHHHHHHHc--CCEEEEEEC
Confidence            4679999999999999999998  678888886

>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=95.91  E-value=0.004  Score=52.52  Aligned_cols=34  Identities=12%  Similarity=0.193  Sum_probs=30.8

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+.++|||||||.|..++.++++.|..+++.+|+
T Consensus        94 ~~~~~VLdiG~G~G~~~~~l~~~~~~~~v~~vDi  127 (304)
T 2o07_A           94 PNPRKVLIIGGGDGGVLREVVKHPSVESVVQCEI  127 (304)
T ss_dssp             SSCCEEEEEECTTSHHHHHHTTCTTCCEEEEEES
T ss_pred             CCCCEEEEECCCchHHHHHHHHcCCCCEEEEEEC
Confidence            3468999999999999999999988899999986

>3oop_A LIN2960 protein; protein structure initiative, PSI-2, structural genomics, MI center for structural genomics, MCSG, unknown function; 1.78A {Listeria innocua}

Probab=95.91  E-value=0.0025  Score=46.95  Aligned_cols=68  Identities=13%  Similarity=0.175  Sum_probs=49.2

Q ss_pred             HhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           37 IQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        37 ~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      .+..|+..|..+ +++|..+||+.+++++   ..+.++++.|...|++.......|.- ...+.+|+.    ++.+.
T Consensus        38 ~~~~iL~~l~~~-~~~t~~eLa~~l~~~~---~~vs~~l~~L~~~Glv~r~~~~~D~R-~~~~~LT~~----G~~~~  105 (143)
T 3oop_A           38 EQWSVLEGIEAN-EPISQKEIALWTKKDT---PTVNRIVDVLLRKELIVREISTEDRR-ISLLSLTDK----GRKET  105 (143)
T ss_dssp             HHHHHHHHHHHH-SSEEHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEEC----CC-SCEEEECHH----HHHHH
T ss_pred             HHHHHHHHHHHc-CCcCHHHHHHHHCCCH---hhHHHHHHHHHHCCCeeccCCCccCc-eeeeeECHH----HHHHH
Confidence            344466677766 8999999999999999   99999999999999999764211111 234667776    55553

>2yvl_A TRMI protein, hypothetical protein; tRNA, methyltransferase, S-adenosylmethionine, structural GE NPPSFA; HET: SAM; 2.20A {Aquifex aeolicus}

Probab=95.91  E-value=0.012  Score=47.02  Aligned_cols=40  Identities=13%  Similarity=0.234  Sum_probs=32.5

Q ss_pred             HHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          169 VLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       169 ~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .++...+  .....+|+|+|||+|.++..+++.  ..+++.+|.
T Consensus        82 ~~~~~~~--~~~~~~vldiG~G~G~~~~~l~~~--~~~v~~vD~  121 (248)
T 2yvl_A           82 YIALKLN--LNKEKRVLEFGTGSGALLAVLSEV--AGEVWTFEA  121 (248)
T ss_dssp             HHHHHTT--CCTTCEEEEECCTTSHHHHHHHHH--SSEEEEECS
T ss_pred             HHHHhcC--CCCCCEEEEeCCCccHHHHHHHHh--CCEEEEEec
Confidence            3444444  456779999999999999999999  778999886

>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=95.91  E-value=0.0041  Score=51.79  Aligned_cols=33  Identities=18%  Similarity=0.254  Sum_probs=30.3

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +.++|||||||.|..+..+++..|..+++++|+
T Consensus        78 ~~~~VLdiG~G~G~~~~~l~~~~~~~~v~~vDi  110 (283)
T 2i7c_A           78 EPKNVLVVGGGDGGIIRELCKYKSVENIDICEI  110 (283)
T ss_dssp             SCCEEEEEECTTSHHHHHHTTCTTCCEEEEEES
T ss_pred             CCCeEEEEeCCcCHHHHHHHHcCCCCEEEEEEC
Confidence            468999999999999999999888899999986

>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=95.90  E-value=0.011  Score=49.72  Aligned_cols=42  Identities=17%  Similarity=0.105  Sum_probs=31.7

Q ss_pred             HHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          169 VLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       169 ~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+++.+.. .....++||||||+|.++..+++. +..+++.+|+
T Consensus        75 ~~l~~~~~-~~~g~~vLDiGcGTG~~t~~L~~~-ga~~V~aVDv  116 (291)
T 3hp7_A           75 KALAVFNL-SVEDMITIDIGASTGGFTDVMLQN-GAKLVYAVDV  116 (291)
T ss_dssp             HHHHHTTC-CCTTCEEEEETCTTSHHHHHHHHT-TCSEEEEECS
T ss_pred             HHHHhcCC-CccccEEEecCCCccHHHHHHHhC-CCCEEEEEEC
Confidence            34555541 124579999999999999998887 5668999886

>4hg2_A Methyltransferase type 11; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; HET: MES; 1.60A {Anaeromyxobacter dehalogenans}

Probab=95.89  E-value=0.0042  Score=51.16  Aligned_cols=31  Identities=16%  Similarity=0.239  Sum_probs=26.3

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+|||||||+|.++..|++++.  +++.+|.
T Consensus        39 ~~~~vLDvGcGtG~~~~~l~~~~~--~v~gvD~   69 (257)
T 4hg2_A           39 ARGDALDCGCGSGQASLGLAEFFE--RVHAVDP   69 (257)
T ss_dssp             CSSEEEEESCTTTTTHHHHHTTCS--EEEEEES
T ss_pred             CCCCEEEEcCCCCHHHHHHHHhCC--EEEEEeC
Confidence            457899999999999999998864  6777775

>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=95.88  E-value=0.0044  Score=51.53  Aligned_cols=32  Identities=16%  Similarity=0.259  Sum_probs=29.4

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +.++|||||||.|..+..++++ |..+++++|+
T Consensus        75 ~~~~VLdiG~G~G~~~~~l~~~-~~~~v~~vDi  106 (281)
T 1mjf_A           75 KPKRVLVIGGGDGGTVREVLQH-DVDEVIMVEI  106 (281)
T ss_dssp             CCCEEEEEECTTSHHHHHHTTS-CCSEEEEEES
T ss_pred             CCCeEEEEcCCcCHHHHHHHhC-CCCEEEEEEC
Confidence            4579999999999999999998 9899999986

>3evz_A Methyltransferase; NYSGXRC, NEW YORK SGX research CE structural genomics, protein structure initiative, pyrococc furiosus, PSI-2; 2.20A {Pyrococcus furiosus}

Probab=95.87  E-value=0.0066  Score=48.11  Aligned_cols=34  Identities=24%  Similarity=0.296  Sum_probs=29.7

Q ss_pred             cCCCCcEEeecCC-chHHHHHHHHHCCCCeEEEecC
Q 040620          178 SKGLKPLVDVGGS-TGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG-~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+..+||||||| +|.++..+++.. ..+++.+|+
T Consensus        53 ~~~~~~vLDlG~G~~G~~~~~la~~~-~~~v~~vD~   87 (230)
T 3evz_A           53 LRGGEVALEIGTGHTAMMALMAEKFF-NCKVTATEV   87 (230)
T ss_dssp             CCSSCEEEEECCTTTCHHHHHHHHHH-CCEEEEEEC
T ss_pred             cCCCCEEEEcCCCHHHHHHHHHHHhc-CCEEEEEEC
Confidence            3457899999999 999999999987 778898886

>1y8c_A S-adenosylmethionine-dependent methyltransferase; structural genomics, protein structure initiative, PSI; 2.50A {Clostridium acetobutylicum} SCOP: c.66.1.43

Probab=95.86  E-value=0.011  Score=46.83  Aligned_cols=31  Identities=10%  Similarity=0.138  Sum_probs=27.0

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +..+|||||||+|.++..+++.  ..+++++|.
T Consensus        37 ~~~~vLdiG~G~G~~~~~l~~~--~~~~~~~D~   67 (246)
T 1y8c_A           37 VFDDYLDLACGTGNLTENLCPK--FKNTWAVDL   67 (246)
T ss_dssp             CTTEEEEETCTTSTTHHHHGGG--SSEEEEECS
T ss_pred             CCCeEEEeCCCCCHHHHHHHHC--CCcEEEEEC
Confidence            4679999999999999999998  467888886

>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=95.85  E-value=0.0042  Score=45.24  Aligned_cols=67  Identities=12%  Similarity=0.102  Sum_probs=48.9

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      ++.++..|..+ +++|..+||+.+++++   ..+.++++.|...|++.......+.- ...+.+|+.    ++.+.
T Consensus        36 ~~~iL~~l~~~-~~~~~~~la~~l~~~~---~tvs~~l~~L~~~gli~r~~~~~d~R-~~~~~lT~~----G~~~~  102 (138)
T 1jgs_A           36 QFKVLCSIRCA-ACITPVELKKVLSVDL---GALTRMLDRLVCKGWVERLPNPNDKR-GVLVKLTTG----GAAIC  102 (138)
T ss_dssp             HHHHHHHHHHH-SSBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEEECTTCSS-CEEEEECHH----HHHHH
T ss_pred             HHHHHHHHHhc-CCCCHHHHHHHHCCCh---HHHHHHHHHHHHCCCEEecCCcccCc-eeEeEEChh----HHHHH
Confidence            33456666655 7899999999999999   99999999999999999864211111 123677777    65554

>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=95.83  E-value=0.0051  Score=49.25  Aligned_cols=32  Identities=16%  Similarity=0.160  Sum_probs=26.2

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+|||||||+|.++..+++..+ .+++.+|+
T Consensus        60 ~~~~vLDiGcGtG~~~~~l~~~~~-~~v~gvD~   91 (236)
T 1zx0_A           60 KGGRVLEVGFGMAIAASKVQEAPI-DEHWIIEC   91 (236)
T ss_dssp             TCEEEEEECCTTSHHHHHHHTSCE-EEEEEEEC
T ss_pred             CCCeEEEEeccCCHHHHHHHhcCC-CeEEEEcC
Confidence            457999999999999999966544 37888886

>3q7e_A Protein arginine N-methyltransferase 1; HET: SAH; 2.20A {Rattus norvegicus} PDB: 1orh_A* 1ori_A* 1or8_A*

Probab=95.83  E-value=0.0068  Score=51.95  Aligned_cols=34  Identities=29%  Similarity=0.330  Sum_probs=29.5

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                      .+.++|||||||+|.++..++++ +..+++.+|+-
T Consensus        65 ~~~~~VLDvGcG~G~~~~~la~~-g~~~v~gvD~s   98 (349)
T 3q7e_A           65 FKDKVVLDVGSGTGILCMFAAKA-GARKVIGIECS   98 (349)
T ss_dssp             HTTCEEEEESCTTSHHHHHHHHT-TCSEEEEEECS
T ss_pred             CCCCEEEEEeccchHHHHHHHHC-CCCEEEEECcH
Confidence            34689999999999999999998 77799999863

>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=95.82  E-value=0.0025  Score=47.21  Aligned_cols=50  Identities=20%  Similarity=0.289  Sum_probs=44.8

Q ss_pred             CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      +++|..+||+.+++++   ..+.+.++.|...|++....       ...|.+|+.    +..+.
T Consensus        21 ~~~~~~ela~~l~vs~---~tvs~~l~~Le~~Glv~r~~-------~~~~~LT~~----g~~~~   70 (142)
T 1on2_A           21 GYARVSDIAEALAVHP---SSVTKMVQKLDKDEYLIYEK-------YRGLVLTSK----GKKIG   70 (142)
T ss_dssp             SSCCHHHHHHHHTSCH---HHHHHHHHHHHHTTSEEEET-------TTEEEECHH----HHHHH
T ss_pred             CCCCHHHHHHHhCCCH---HHHHHHHHHHHHCCCEEEee-------CceEEEchh----HHHHH
Confidence            7899999999999999   99999999999999999886       578899988    66654

>1wy7_A Hypothetical protein PH1948; seven-stranded beta sheet, methyltransferase fold, structura genomics, transferase; HET: SAH; 2.20A {Pyrococcus horikoshii} SCOP: c.66.1.32

Probab=95.81  E-value=0.0081  Score=46.78  Aligned_cols=33  Identities=15%  Similarity=0.134  Sum_probs=27.4

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ....+|+|+|||+|.++..+++..+ .+++.+|+
T Consensus        48 ~~~~~vlD~g~G~G~~~~~l~~~~~-~~v~~vD~   80 (207)
T 1wy7_A           48 IEGKVVADLGAGTGVLSYGALLLGA-KEVICVEV   80 (207)
T ss_dssp             STTCEEEEETCTTCHHHHHHHHTTC-SEEEEEES
T ss_pred             CCcCEEEEeeCCCCHHHHHHHHcCC-CEEEEEEC
Confidence            3467999999999999999998743 37888886

>3g2m_A PCZA361.24; SAM-dependent methyltransferase, glycopeptide antibiotics biosynthesis, structural genomics; 2.00A {Amycolatopsis orientalis} PDB: 3g2o_A* 3g2p_A* 3g2q_A*

Probab=95.81  E-value=0.0064  Score=50.44  Aligned_cols=40  Identities=8%  Similarity=0.130  Sum_probs=31.0

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+++.++  . ...+|||||||+|.++..++++  ..+++.+|+
T Consensus        73 ~~~~~~~~--~-~~~~vLDlGcG~G~~~~~l~~~--~~~v~gvD~  112 (299)
T 3g2m_A           73 REFATRTG--P-VSGPVLELAAGMGRLTFPFLDL--GWEVTALEL  112 (299)
T ss_dssp             HHHHHHHC--C-CCSCEEEETCTTTTTHHHHHTT--TCCEEEEES
T ss_pred             HHHHHhhC--C-CCCcEEEEeccCCHHHHHHHHc--CCeEEEEEC
Confidence            44555544  2 3449999999999999999998  578888886

>2b2c_A Spermidine synthase; beta-alpha, transferase; 2.50A {Caenorhabditis elegans} SCOP: c.66.1.17

Probab=95.80  E-value=0.0051  Score=52.23  Aligned_cols=33  Identities=21%  Similarity=0.286  Sum_probs=30.3

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +.++|||||||.|..++.+++..|..+++++|+
T Consensus       108 ~~~~VLdIG~G~G~~~~~l~~~~~~~~v~~vDi  140 (314)
T 2b2c_A          108 DPKRVLIIGGGDGGILREVLKHESVEKVTMCEI  140 (314)
T ss_dssp             SCCEEEEESCTTSHHHHHHTTCTTCCEEEEECS
T ss_pred             CCCEEEEEcCCcCHHHHHHHHcCCCCEEEEEEC
Confidence            457999999999999999999888999999986

>3tqs_A Ribosomal RNA small subunit methyltransferase A; protein synthesis; 1.98A {Coxiella burnetii} SCOP: c.66.1.0

Probab=95.79  E-value=0.0055  Score=50.48  Aligned_cols=41  Identities=12%  Similarity=0.286  Sum_probs=32.3

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+++..+  .....+|+|||||+|.++..++++.  .+++.+|+
T Consensus        19 ~~iv~~~~--~~~~~~VLEIG~G~G~lt~~La~~~--~~V~avEi   59 (255)
T 3tqs_A           19 QKIVSAIH--PQKTDTLVEIGPGRGALTDYLLTEC--DNLALVEI   59 (255)
T ss_dssp             HHHHHHHC--CCTTCEEEEECCTTTTTHHHHTTTS--SEEEEEEC
T ss_pred             HHHHHhcC--CCCcCEEEEEcccccHHHHHHHHhC--CEEEEEEC
Confidence            44555554  4557799999999999999999985  57888775

>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=95.78  E-value=0.0047  Score=49.49  Aligned_cols=32  Identities=13%  Similarity=0.267  Sum_probs=28.2

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +..+|||||||+|.++..++++. ..+++++|+
T Consensus        79 ~~~~vLDiGcG~G~~~~~l~~~~-~~~v~~vD~  110 (241)
T 2ex4_A           79 GTSCALDCGAGIGRITKRLLLPL-FREVDMVDI  110 (241)
T ss_dssp             CCSEEEEETCTTTHHHHHTTTTT-CSEEEEEES
T ss_pred             CCCEEEEECCCCCHHHHHHHHhc-CCEEEEEeC
Confidence            46799999999999999999887 568888886

>2fu4_A Ferric uptake regulation protein; DNA binding domain, helix-turn-helix, DNA binding protein; 1.80A {Escherichia coli}

Probab=95.78  E-value=0.0045  Score=41.65  Aligned_cols=47  Identities=9%  Similarity=0.253  Sum_probs=40.8

Q ss_pred             cCcchhhhcCC-CCCCHHHHHHHc-----CCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           39 LRIPDIINNSG-QPMTLTQIIVAL-----NVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        39 lglfd~L~~~~-~p~t~~eLA~~~-----g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      ..|++.|...+ +++|++||++.+     +++.   ..++|.|+.|...|++....
T Consensus        20 ~~IL~~l~~~~~~~~s~~el~~~l~~~~~~is~---~TVyR~L~~L~~~Glv~~~~   72 (83)
T 2fu4_A           20 LKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGL---ATVYRVLNQFDDAGIVTRHN   72 (83)
T ss_dssp             HHHHHHHTSGGGSSBCHHHHHHHHHHTTCCCCH---HHHHHHHHHHHHHTSEEEEE
T ss_pred             HHHHHHHHhCCCCCCCHHHHHHHHHHhCCCCCH---hhHHHHHHHHHHCCCeEEEe
Confidence            34777887654 689999999999     8988   99999999999999999764

>3nrv_A Putative transcriptional regulator (MARR/EMRR FAM; PSI-2, protein structure initiati structural genomics; HET: MSE; 2.00A {Acinetobacter SP}

Probab=95.76  E-value=0.0035  Score=46.33  Aligned_cols=48  Identities=13%  Similarity=0.171  Sum_probs=40.5

Q ss_pred             HhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           37 IQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        37 ~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      .++.++..|... +++|..+||+.+++++   ..+.++++.|...|++....
T Consensus        41 ~~~~iL~~l~~~-~~~t~~ela~~l~~~~---~tvs~~l~~Le~~Glv~r~~   88 (148)
T 3nrv_A           41 TEWRIISVLSSA-SDCSVQKISDILGLDK---AAVSRTVKKLEEKKYIEVNG   88 (148)
T ss_dssp             HHHHHHHHHHHS-SSBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEC--
T ss_pred             HHHHHHHHHHcC-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEeec
Confidence            344566777776 7999999999999999   99999999999999999764

>2nnn_A Probable transcriptional regulator; structural genomics, PSI-2, protein structure initiative, M center for structural genomics, MCSG; 2.40A {Pseudomonas aeruginosa}

Probab=95.74  E-value=0.0024  Score=46.53  Aligned_cols=67  Identities=16%  Similarity=0.168  Sum_probs=49.4

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      ++.|+..|... +++|..+||+.+++++   ..+.+.++.|...|++.......+.- ...|.+|+.    ++.+.
T Consensus        40 ~~~iL~~l~~~-~~~t~~ela~~l~~~~---~tvs~~l~~L~~~glv~r~~~~~d~R-~~~~~lT~~----G~~~~  106 (140)
T 2nnn_A           40 QWAALVRLGET-GPCPQNQLGRLTAMDA---ATIKGVVERLDKRGLIQRSADPDDGR-RLLVSLSPA----GRAEL  106 (140)
T ss_dssp             HHHHHHHHHHH-SSBCHHHHHHHTTCCH---HHHHHHHHHHHHTTCEEEEEETTEEE-EEEEEECHH----HHHHH
T ss_pred             HHHHHHHHHHc-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEeeCCCCCCC-eeeeEECHh----HHHHH
Confidence            45577777765 7999999999999999   99999999999999999754210000 123677777    55543

>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=95.74  E-value=0.029  Score=41.46  Aligned_cols=43  Identities=14%  Similarity=0.138  Sum_probs=38.6

Q ss_pred             cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceee
Q 040620           39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQ   86 (214)
Q Consensus        39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~   86 (214)
                      ..++..| .. +++|..+||+.+++++   ..+.++++.|...|++..
T Consensus        41 ~~iL~~l-~~-~~~t~~eLa~~l~~~~---~~vs~~l~~Le~~Glv~r   83 (151)
T 3kp7_A           41 SHVLNML-SI-EALTVGQITEKQGVNK---AAVSRRVKKLLNAELVKL   83 (151)
T ss_dssp             HHHHHHH-HH-SCBCHHHHHHHHCSCS---SHHHHHHHHHHHTTSEEC
T ss_pred             HHHHHHH-Hc-CCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEe
Confidence            3467777 54 8999999999999999   999999999999999996

>2nyx_A Probable transcriptional regulatory protein, RV14; alpha/beta, structural genomics, PSI-2; 2.30A {Mycobacterium tuberculosis}

Probab=95.72  E-value=0.014  Score=44.29  Aligned_cols=67  Identities=22%  Similarity=0.269  Sum_probs=49.6

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      ++.|+..|... +++|..+||+.+++++   ..+.++++.|...|++.......|.- ...+.+|+.    ++.+.
T Consensus        47 ~~~iL~~L~~~-~~~t~~eLa~~l~is~---~tvs~~l~~Le~~GlV~r~~~~~DrR-~~~~~LT~~----G~~~~  113 (168)
T 2nyx_A           47 QFRTLVILSNH-GPINLATLATLLGVQP---SATGRMVDRLVGAELIDRLPHPTSRR-ELLAALTKR----GRDVV  113 (168)
T ss_dssp             HHHHHHHHHHH-CSEEHHHHHHHHTSCH---HHHHHHHHHHHHTTSEEEEECSSCSS-CEEEEECHH----HHHHH
T ss_pred             HHHHHHHHHHc-CCCCHHHHHHHhCCCH---HHHHHHHHHHHHCCCEEeccCCCCCC-eeEEEECHH----HHHHH
Confidence            44567777765 7899999999999999   99999999999999999864211111 223667777    55544

>3cgg_A SAM-dependent methyltransferase; NP_600671.1, methyltransferase domain, structural genomics; HET: NHE CIT; 2.00A {Corynebacterium glutamicum atcc 13032}

Probab=95.71  E-value=0.0098  Score=45.25  Aligned_cols=32  Identities=9%  Similarity=0.097  Sum_probs=27.5

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ....+|+|||||.|.++..+++.  +.+++.+|.
T Consensus        45 ~~~~~vLdiG~G~G~~~~~l~~~--~~~v~~~D~   76 (195)
T 3cgg_A           45 PRGAKILDAGCGQGRIGGYLSKQ--GHDVLGTDL   76 (195)
T ss_dssp             CTTCEEEEETCTTTHHHHHHHHT--TCEEEEEES
T ss_pred             cCCCeEEEECCCCCHHHHHHHHC--CCcEEEEcC
Confidence            35679999999999999999988  568888875

>3r0a_A Putative transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; 2.31A {Methanosarcina mazei}

Probab=95.69  E-value=0.0036  Score=45.72  Aligned_cols=48  Identities=13%  Similarity=0.108  Sum_probs=40.5

Q ss_pred             hcCcchhhhcCCCC-CCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           38 QLRIPDIINNSGQP-MTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        38 ~lglfd~L~~~~~p-~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      +..|+..|..+++| +|+.|||+++++++   ..+.|.|+.|...|++....
T Consensus        28 e~~il~~L~~~~~~~~t~~eLa~~l~~s~---sTV~r~L~~L~~~GlV~r~~   76 (123)
T 3r0a_A           28 DLNVMKSFLNEPDRWIDTDALSKSLKLDV---STVQRSVKKLHEKEILQRSQ   76 (123)
T ss_dssp             HHHHHHHHHHSTTCCEEHHHHHHHHTSCH---HHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHHCCCCCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEeeC
Confidence            34466666665466 99999999999999   99999999999999998753

>3lcc_A Putative methyl chloride transferase; halide methyltransferase; HET: SAH; 1.80A {Arabidopsis thaliana}

Probab=95.69  E-value=0.0052  Score=48.98  Aligned_cols=29  Identities=17%  Similarity=0.141  Sum_probs=25.8

Q ss_pred             CcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          182 KPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       182 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+|||||||+|.++..+++  +..+++++|+
T Consensus        68 ~~vLDiGcG~G~~~~~l~~--~~~~v~gvD~   96 (235)
T 3lcc_A           68 GRALVPGCGGGHDVVAMAS--PERFVVGLDI   96 (235)
T ss_dssp             EEEEEETCTTCHHHHHHCB--TTEEEEEECS
T ss_pred             CCEEEeCCCCCHHHHHHHh--CCCeEEEEEC
Confidence            5999999999999999976  6778999886

>3g3z_A NMB1585, transcriptional regulator, MARR family; transcription factor, structur genomics, oxford protein production facility; 2.10A {Neisseria meningitidis serogroup B}

Probab=95.68  E-value=0.0039  Score=45.95  Aligned_cols=68  Identities=10%  Similarity=0.057  Sum_probs=49.8

Q ss_pred             HhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           37 IQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        37 ~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      .+..|+..|... +++|..+||+.+++++   ..+.++++.|...|++.......|.- ...+.+|+.    ++.+.
T Consensus        32 ~q~~iL~~l~~~-~~~t~~eLa~~l~~~~---~tvs~~l~~Le~~Glv~r~~~~~D~R-~~~~~LT~~----G~~~~   99 (145)
T 3g3z_A           32 NLFAVLYTLATE-GSRTQKHIGEKWSLPK---QTVSGVCKTLAGQGLIEWQEGEQDRR-KRLLSLTET----GKAYA   99 (145)
T ss_dssp             HHHHHHHHHHHH-CSBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEECCCSSCGG-GSCEEECHH----HHHHH
T ss_pred             HHHHHHHHHHHC-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEeeccCCCCCc-eeeeeEChh----HHHHH
Confidence            345566777665 7899999999999999   99999999999999999764211110 224667777    55543

>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=95.68  E-value=0.025  Score=41.49  Aligned_cols=69  Identities=19%  Similarity=0.261  Sum_probs=49.9

Q ss_pred             HHhcCcchhhhc-CCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           36 AIQLRIPDIINN-SGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        36 a~~lglfd~L~~-~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      ..++.|+..|.. . +++|..+||+.+++++   ..+.+.++.|...|++.......|.- ...+.+|+.    ++.+.
T Consensus        35 ~~~~~iL~~l~~~~-~~~~~~~la~~l~i~~---~~vs~~l~~Le~~glv~r~~~~~d~R-~~~~~lT~~----G~~~~  104 (147)
T 2hr3_A           35 FSQLVVLGAIDRLG-GDVTPSELAAAERMRS---SNLAALLRELERGGLIVRHADPQDGR-RTRVSLSSE----GRRNL  104 (147)
T ss_dssp             HHHHHHHHHHHHTT-SCBCHHHHHHHTTCCH---HHHHHHHHHHHHTTSEEEEC-------CCEEEECHH----HHHHH
T ss_pred             HHHHHHHHHHHHcC-CCCCHHHHHHHhCCCh---hhHHHHHHHHHHCCCEeeCCCCCCCC-ceeeEECHH----HHHHH
Confidence            344567777776 5 8999999999999999   99999999999999999764211111 223667777    55543

>2gb4_A Thiopurine S-methyltransferase; 18204406, thiopurine methyltransferase, structural genomics, PSI, protein structure initiative; HET: SAH; 1.25A {Mus musculus} PDB: 3bgi_A* 3bgd_A* 2bzg_A* 2h11_A*

Probab=95.68  E-value=0.007  Score=49.57  Aligned_cols=31  Identities=3%  Similarity=-0.240  Sum_probs=27.7

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+|||||||.|..+..|+++  ..+++.+|+
T Consensus        68 ~~~~vLD~GCG~G~~~~~La~~--G~~V~gvD~   98 (252)
T 2gb4_A           68 SGLRVFFPLCGKAIEMKWFADR--GHTVVGVEI   98 (252)
T ss_dssp             CSCEEEETTCTTCTHHHHHHHT--TCEEEEECS
T ss_pred             CCCeEEEeCCCCcHHHHHHHHC--CCeEEEEEC
Confidence            4679999999999999999987  668999986

>2wte_A CSA3; antiviral protein, viral resistance, winged helix-turn-helix prnai nucleotide-binding domain; HET: MSE; 1.80A {Sulfolobus solfataricus}

Probab=95.68  E-value=0.0024  Score=52.42  Aligned_cols=61  Identities=10%  Similarity=0.185  Sum_probs=50.6

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCccccccc
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRIS  112 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l  112 (214)
                      ++.|+..|..+ +++|..|||+++|+++   ..+.|.|+.|...|++...+.      ...|.+|+.    ++.+
T Consensus       154 ~~~IL~~L~~~-~~~s~~eLA~~lglsk---sTv~r~L~~Le~~GlV~r~~r------~~~~~LT~~----G~~l  214 (244)
T 2wte_A          154 EMKLLNVLYET-KGTGITELAKMLDKSE---KTLINKIAELKKFGILTQKGK------DRKVELNEL----GLNV  214 (244)
T ss_dssp             HHHHHHHHHHH-TCBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEETT------TTEEEECHH----HHHH
T ss_pred             HHHHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEeCC------ccEEEECHH----HHHH
Confidence            34456666555 7899999999999999   999999999999999998753      578999988    5555

>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=95.67  E-value=0.0056  Score=46.64  Aligned_cols=68  Identities=12%  Similarity=0.100  Sum_probs=48.8

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      ++.|+..|...++++|..+||+.+++++   ..+.++++.|...|++.......|.- ...+.+|+.    ++.++
T Consensus        55 q~~vL~~L~~~~~~~t~~eLa~~l~i~~---~tvs~~l~~Le~~GlV~r~~~~~DrR-~~~l~LT~~----G~~~~  122 (166)
T 3deu_A           55 HWVTLHNIHQLPPDQSQIQLAKAIGIEQ---PSLVRTLDQLEDKGLISRQTCASDRR-AKRIKLTEK----AEPLI  122 (166)
T ss_dssp             HHHHHHHHHHSCSSEEHHHHHHHHTSCH---HHHHHHHHHHHHTTSEEEC---------CEEEECGG----GHHHH
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHCCCH---hhHHHHHHHHHHCCCEEeeCCCCCCC-eeEEEECHH----HHHHH
Confidence            4446667765337899999999999999   99999999999999999765211110 234777777    66654

>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=95.67  E-value=0.0086  Score=43.65  Aligned_cols=67  Identities=9%  Similarity=0.210  Sum_probs=48.8

Q ss_pred             cCcchhhhcCCC-CCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           39 LRIPDIINNSGQ-PMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        39 lglfd~L~~~~~-p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      ..++..|...++ ++|..+||+.+++++   ..+.++++.|...|++.......|.- ...+.+|+.    ++.+.
T Consensus        37 ~~iL~~l~~~~~~~~~~~ela~~l~~~~---~tvs~~l~~Le~~Gli~r~~~~~d~R-~~~i~lT~~----G~~~~  104 (141)
T 3bro_A           37 MTIIDYLSRNKNKEVLQRDLESEFSIKS---STATVLLQRMEIKKLLYRKVSGKDSR-QKCLKLTKK----ANKLE  104 (141)
T ss_dssp             HHHHHHHHHTTTSCCBHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEEECSSCTT-SEEEEECHH----HHTTH
T ss_pred             HHHHHHHHHCCCCCcCHHHHHHHHCCCc---chHHHHHHHHHHCCCEEeeCCCcCCC-eeeeEECHH----HHHHH
Confidence            345666766522 899999999999999   99999999999999998765211111 224667777    66554

>2frn_A Hypothetical protein PH0793; structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; 2.10A {Pyrococcus horikoshii OT3} PDB: 3k6r_A 3a25_A* 3a26_A*

Probab=95.66  E-value=0.0075  Score=49.93  Aligned_cols=32  Identities=19%  Similarity=0.077  Sum_probs=29.1

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +..+|+|+|||+|.+++.+++..+. +++.+|+
T Consensus       125 ~~~~VLDlgcG~G~~~~~la~~~~~-~V~~vD~  156 (278)
T 2frn_A          125 PDELVVDMFAGIGHLSLPIAVYGKA-KVIAIEK  156 (278)
T ss_dssp             TTCEEEETTCTTTTTHHHHHHHTCC-EEEEECC
T ss_pred             CCCEEEEecccCCHHHHHHHHhCCC-EEEEEEC
Confidence            4679999999999999999999887 8888886

>3e6m_A MARR family transcriptional regulator; APC88769, silicibacter pomeroyi DSS, structural genomics, PSI-2, protein structure initiative; 2.20A {Silicibacter pomeroyi}

Probab=95.65  E-value=0.017  Score=43.43  Aligned_cols=67  Identities=15%  Similarity=0.222  Sum_probs=48.9

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      ++.|+..|... +++|..+||+.+++++   ..+.++++.|...|++.......|.- ...+.+|+.    ++.+.
T Consensus        55 q~~vL~~l~~~-~~~t~~eLa~~l~~~~---~~vs~~l~~Le~~Glv~r~~~~~DrR-~~~~~LT~~----G~~~~  121 (161)
T 3e6m_A           55 KLRLLSSLSAY-GELTVGQLATLGVMEQ---STTSRTVDQLVDEGLAARSISDADQR-KRTVVLTRK----GKKKL  121 (161)
T ss_dssp             HHHHHHHHHHH-SEEEHHHHHHHTTCCH---HHHHHHHHHHHHTTSEEECC---CCC-SCEEEECHH----HHHHH
T ss_pred             HHHHHHHHHhC-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEeeCCcccCC-eeEeeECHH----HHHHH
Confidence            34466777765 7899999999999999   99999999999999999765211111 234667776    55543

>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=95.65  E-value=0.0089  Score=46.86  Aligned_cols=31  Identities=13%  Similarity=0.089  Sum_probs=26.3

Q ss_pred             CCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          181 LKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       181 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+|||+|||+|.++..++++.+ .+++.+|+
T Consensus        54 ~~~vLDlGcGtG~~~~~~~~~~~-~~v~gvD~   84 (201)
T 2ift_A           54 QSECLDGFAGSGSLGFEALSRQA-KKVTFLEL   84 (201)
T ss_dssp             TCEEEETTCTTCHHHHHHHHTTC-SEEEEECS
T ss_pred             CCeEEEcCCccCHHHHHHHHccC-CEEEEEEC
Confidence            57999999999999999887754 57888886

>1ixk_A Methyltransferase; open beta sheet; 1.90A {Pyrococcus horikoshii} SCOP: c.66.1.38

Probab=95.64  E-value=0.012  Score=49.70  Aligned_cols=35  Identities=17%  Similarity=0.186  Sum_probs=30.4

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCC-CCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFP-DTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl  212 (214)
                      .....+|+|+|||+|..+..+++..+ ..+++.+|+
T Consensus       116 ~~~g~~VLDlg~G~G~~t~~la~~~~~~~~v~avD~  151 (315)
T 1ixk_A          116 PKPGEIVADMAAAPGGKTSYLAQLMRNDGVIYAFDV  151 (315)
T ss_dssp             CCTTCEEEECCSSCSHHHHHHHHHTTTCSEEEEECS
T ss_pred             CCCCCEEEEeCCCCCHHHHHHHHHhCCCCEEEEEcC
Confidence            44567999999999999999999976 478999986

>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=95.62  E-value=0.0034  Score=46.62  Aligned_cols=69  Identities=13%  Similarity=0.137  Sum_probs=46.7

Q ss_pred             HhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           37 IQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        37 ~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      .++.++..|...++++|..+||+.+++++   ..+.++++.|...|++.......|.- .-.+.+|+.    ++.+.
T Consensus        40 ~q~~vL~~l~~~~~~~t~~eLa~~l~i~~---~tvs~~l~~Le~~Glv~r~~~~~D~R-~~~~~LT~~----G~~~~  108 (150)
T 3fm5_A           40 RSYSVLVLACEQAEGVNQRGVAATMGLDP---SQIVGLVDELEERGLVVRTLDPSDRR-NKLIAATEE----GRRLR  108 (150)
T ss_dssp             HHHHHHHHHHHSTTCCCSHHHHHHHTCCH---HHHHHHHHHHHTTTSEEC------------CEECHH----HHHHH
T ss_pred             HHHHHHHHHHhCCCCcCHHHHHHHHCCCH---hHHHHHHHHHHHCCCEEeeCCccccc-hheeeECHH----HHHHH
Confidence            34446667765546899999999999999   99999999999999999764210100 112666666    55554

>3bzb_A Uncharacterized protein; RED ALGA, protein structure initiat center for eukaryotic structural genomics, CESG, structural genomics; 2.79A {Cyanidioschyzon merolae}

Probab=95.62  E-value=0.015  Score=48.07  Aligned_cols=33  Identities=12%  Similarity=0.124  Sum_probs=27.7

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...++|||||||+|.+++.+++. ...+++.+|+
T Consensus        78 ~~~~~vLDlG~G~G~~~~~~a~~-~~~~v~~~D~  110 (281)
T 3bzb_A           78 IAGKTVCELGAGAGLVSIVAFLA-GADQVVATDY  110 (281)
T ss_dssp             TTTCEEEETTCTTSHHHHHHHHT-TCSEEEEEEC
T ss_pred             cCCCeEEEecccccHHHHHHHHc-CCCEEEEEeC
Confidence            35679999999999999988886 3458999997

>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=95.61  E-value=0.006  Score=45.55  Aligned_cols=63  Identities=16%  Similarity=0.155  Sum_probs=47.5

Q ss_pred             HhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           37 IQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        37 ~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      .++.|+..|... +++|..+||+.+++++   ..+.++++.|...|++.......+.- ...+.+|+.
T Consensus        45 ~~~~iL~~l~~~-~~~t~~ela~~l~is~---~tvs~~l~~Le~~Gli~r~~~~~d~R-~~~~~lT~~  107 (154)
T 2eth_A           45 TELYAFLYVALF-GPKKMKEIAEFLSTTK---SNVTNVVDSLEKRGLVVREMDPVDRR-TYRVVLTEK  107 (154)
T ss_dssp             HHHHHHHHHHHH-CCBCHHHHHHHTTSCH---HHHHHHHHHHHHTTSEEEEECTTTSS-CEEEEECHH
T ss_pred             HHHHHHHHHHHc-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEeeCCCCCcc-eeEEEECHH
Confidence            355577777765 7899999999999999   99999999999999999864211111 123666666

>3gdh_A Trimethylguanosine synthase homolog; M7G, CAP, dimethyltransferase, usnRNA, snoRNA, telomerase, cytoplasm, methyltransferase, nucleus; HET: MGP SAH; 2.00A {Homo sapiens} PDB: 3egi_A*

Probab=95.60  E-value=0.0086  Score=47.85  Aligned_cols=31  Identities=13%  Similarity=-0.005  Sum_probs=27.5

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+|||||||+|.++..+++..  .+++.+|+
T Consensus        78 ~~~~vLD~gcG~G~~~~~la~~~--~~v~~vD~  108 (241)
T 3gdh_A           78 KCDVVVDAFCGVGGNTIQFALTG--MRVIAIDI  108 (241)
T ss_dssp             CCSEEEETTCTTSHHHHHHHHTT--CEEEEEES
T ss_pred             CCCEEEECccccCHHHHHHHHcC--CEEEEEEC
Confidence            46799999999999999999974  78888886

>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=95.60  E-value=0.014  Score=48.27  Aligned_cols=33  Identities=15%  Similarity=0.364  Sum_probs=25.1

Q ss_pred             CCCcEEeecCCchHHHH----HHHHHCCCCeE--EEecC
Q 040620          180 GLKPLVDVGGSTGTMAR----AIATAFPDTKC--TVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~----~l~~~~P~l~~--~v~Dl  212 (214)
                      +..+|||||||+|.++.    .++.++|+.++  ++.|.
T Consensus        52 ~~~~VLDiG~GtG~~~~~~l~~l~~~~~~~~v~~~~vD~   90 (292)
T 2aot_A           52 SEIKILSIGGGAGEIDLQILSKVQAQYPGVCINNEVVEP   90 (292)
T ss_dssp             SEEEEEEETCTTSHHHHHHHHHHHHHSTTCEEEEEEECS
T ss_pred             CCCeEEEEcCCCCHHHHHHHHHHHhhCCCceeeEEEEeC
Confidence            34689999999997654    45667788854  88874

>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=95.59  E-value=0.006  Score=45.16  Aligned_cols=62  Identities=15%  Similarity=0.206  Sum_probs=46.7

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      ++.|+..|... +++|..+||+.+++++   ..+.++++.|...|++.......+.- ...+.+|+.
T Consensus        42 ~~~iL~~l~~~-~~~t~~ela~~l~~~~---~~vs~~l~~Le~~Glv~r~~~~~d~R-~~~~~lT~~  103 (152)
T 3bj6_A           42 QRAILEGLSLT-PGATAPQLGAALQMKR---QYISRILQEVQRAGLIERRTNPEHAR-SHRYWLTPR  103 (152)
T ss_dssp             HHHHHHHHHHS-TTEEHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEECCSSSTT-SCEEEECHH
T ss_pred             HHHHHHHHHhC-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCeeecCCccccc-ceeeEEChh
Confidence            34466777766 7899999999999999   99999999999999999865211111 124566666

>1g6q_1 HnRNP arginine N-methyltransferase; SAM-binding domain, beta-barrel, mixed alpha-beta, hexamer; 2.90A {Saccharomyces cerevisiae} SCOP: c.66.1.6

Probab=95.59  E-value=0.011  Score=50.17  Aligned_cols=33  Identities=21%  Similarity=0.155  Sum_probs=28.0

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                      +.++|||||||+|.++..++++ +..+++.+|..
T Consensus        38 ~~~~VLDiGcGtG~ls~~la~~-g~~~v~~vD~s   70 (328)
T 1g6q_1           38 KDKIVLDVGCGTGILSMFAAKH-GAKHVIGVDMS   70 (328)
T ss_dssp             TTCEEEEETCTTSHHHHHHHHT-CCSEEEEEESS
T ss_pred             CCCEEEEecCccHHHHHHHHHC-CCCEEEEEChH
Confidence            4679999999999999998886 66689988863

>3f6v_A Possible transcriptional regulator, ARSR family protein; probable transcriptional repressor ARSR family, structural genomics, PSI-2; 1.48A {Rhodococcus SP}

Probab=95.57  E-value=0.0038  Score=47.45  Aligned_cols=67  Identities=12%  Similarity=0.188  Sum_probs=53.5

Q ss_pred             HHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           29 KSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        29 ~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      ...+|.--.++.|+..|..  +|+|+.|||+.+|+++   ..+.+.|+.|...|++.....   +. ...|.+++.
T Consensus        51 ~l~aL~~p~R~~IL~~L~~--~~~t~~eLa~~lgls~---stvs~hL~~L~~aGlV~~~~~---Gr-~~~y~lt~~  117 (151)
T 3f6v_A           51 QLEVAAEPTRRRLVQLLTS--GEQTVNNLAAHFPASR---SAISQHLRVLTEAGLVTPRKD---GR-FRYYRLDPQ  117 (151)
T ss_dssp             HHHHHTSHHHHHHHHHGGG--CCEEHHHHHTTSSSCH---HHHHHHHHHHHHTTSEEEEEE---TT-EEEEEECHH
T ss_pred             HHHHhCCHHHHHHHHHHHh--CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEEec---CC-EEEEEEChH
Confidence            4566666778888888985  8999999999999999   999999999999999987651   11 234666655

>1r18_A Protein-L-isoaspartate(D-aspartate)-O-methyltrans; methyltransferase, isomerization, protein repair, S-adenosyl homocysteine; HET: SAH; 2.20A {Drosophila melanogaster} SCOP: c.66.1.7

Probab=95.56  E-value=0.011  Score=47.05  Aligned_cols=35  Identities=20%  Similarity=0.244  Sum_probs=29.1

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCC------CCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFP------DTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P------~l~~~v~Dl  212 (214)
                      .....+|||||||+|.++..+++..+      ..+++.+|+
T Consensus        82 ~~~~~~VLdiG~G~G~~~~~la~~~~~~~~~~~~~v~~vD~  122 (227)
T 1r18_A           82 LKPGARILDVGSGSGYLTACFYRYIKAKGVDADTRIVGIEH  122 (227)
T ss_dssp             CCTTCEEEEESCTTSHHHHHHHHHHHHSCCCTTCEEEEEES
T ss_pred             CCCCCEEEEECCCccHHHHHHHHhcccccCCccCEEEEEEc
Confidence            34567999999999999999999766      368888885

>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=95.56  E-value=0.0072  Score=48.01  Aligned_cols=30  Identities=27%  Similarity=0.238  Sum_probs=26.3

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+|||||||+|.++..+++.   .+++++|+
T Consensus        33 ~~~~vLdiG~G~G~~~~~l~~~---~~v~~vD~   62 (243)
T 3d2l_A           33 PGKRIADIGCGTGTATLLLADH---YEVTGVDL   62 (243)
T ss_dssp             TTCEEEEESCTTCHHHHHHTTT---SEEEEEES
T ss_pred             CCCeEEEecCCCCHHHHHHhhC---CeEEEEEC
Confidence            3579999999999999999887   68888886

>3cdh_A Transcriptional regulator, MARR family; helix-turn-hleix, structura genomics, PSI-2, protein structure initiative; 2.69A {Silicibacter pomeroyi dss-3}

Probab=95.55  E-value=0.0051  Score=45.85  Aligned_cols=67  Identities=13%  Similarity=0.198  Sum_probs=48.3

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      ++.|+..|... +++|..+||+.+++++   ..+.++++.|...|++.......+.- ...+.+|+.    ++.+.
T Consensus        45 ~~~iL~~l~~~-~~~t~~ela~~l~i~~---~tvs~~l~~Le~~Glv~r~~~~~d~R-~~~~~lT~~----G~~~~  111 (155)
T 3cdh_A           45 EWRVLACLVDN-DAMMITRLAKLSLMEQ---SRMTRIVDQMDARGLVTRVADAKDKR-RVRVRLTDD----GRALA  111 (155)
T ss_dssp             HHHHHHHHSSC-SCBCHHHHHHHTTCCH---HHHHHHHHHHHHTTSEEECC-------CCCEEECHH----HHHHH
T ss_pred             HHHHHHHHHHC-CCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEeccCCCcCC-eeEeEECHH----HHHHH
Confidence            34466777765 7899999999999999   99999999999999998764211110 123667776    55543

>2rdp_A Putative transcriptional regulator MARR; PFAM PF01047, winged-helix binding motif, structural genomics, PSI-2; 2.30A {Geobacillus stearothermophilus}

Probab=95.55  E-value=0.0055  Score=45.29  Aligned_cols=66  Identities=12%  Similarity=0.123  Sum_probs=48.2

Q ss_pred             cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      +.|+..|..+ +++|..+||+.+++++   ..+.+.++.|...|++.......+.- ...+.+|+.    ++.++
T Consensus        45 ~~iL~~l~~~-~~~t~~ela~~l~~~~---~tvs~~l~~Le~~Glv~r~~~~~d~R-~~~~~lT~~----G~~~~  110 (150)
T 2rdp_A           45 FVALQWLLEE-GDLTVGELSNKMYLAC---STTTDLVDRMERNGLVARVRDEHDRR-VVRIRLLEK----GERII  110 (150)
T ss_dssp             HHHHHHHHHH-CSBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEEECCC----CEEEEECHH----HHHHH
T ss_pred             HHHHHHHHHc-CCCCHHHHHHHHCCCc---hhHHHHHHHHHHCCCeeecCCCCCcc-eeEeEECHh----HHHHH
Confidence            3456677665 7899999999999999   99999999999999999764211110 123667776    55543

>3ajd_A Putative methyltransferase MJ0026; tRNA, M5C, rossmann fold, structural genomics, riken structu genomics/proteomics initiative; 1.27A {Methanocaldococcus jannaschii} PDB: 3a4t_A

Probab=95.54  E-value=0.009  Score=49.30  Aligned_cols=35  Identities=9%  Similarity=0.131  Sum_probs=30.8

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCC-CeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPD-TKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dl  212 (214)
                      .....+|+|+|||+|..+..+++..++ .+++.+|+
T Consensus        81 ~~~g~~VLDlgaG~G~~t~~la~~~~~~~~v~avD~  116 (274)
T 3ajd_A           81 PREDDFILDMCAAPGGKTTHLAQLMKNKGTIVAVEI  116 (274)
T ss_dssp             CCTTCEEEETTCTTCHHHHHHHHHTTTCSEEEEEES
T ss_pred             CCCcCEEEEeCCCccHHHHHHHHHcCCCCEEEEECC
Confidence            345679999999999999999999887 78999986

>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=95.54  E-value=0.0054  Score=44.76  Aligned_cols=68  Identities=15%  Similarity=0.084  Sum_probs=49.1

Q ss_pred             hcCcchhhhcCC-CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           38 QLRIPDIINNSG-QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        38 ~lglfd~L~~~~-~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      +..++..|..++ +++|..+||+.+++++   ..+.++++.|...|++.......|.- ...+.+|+.    ++.+.
T Consensus        33 ~~~vL~~l~~~~~~~~t~~ela~~l~~~~---~tvs~~l~~Le~~Gli~r~~~~~D~R-~~~~~LT~~----G~~~~  101 (139)
T 3eco_A           33 QGHTLGYLYAHQQDGLTQNDIAKALQRTG---PTVSNLLRNLERKKLIYRYVDAQDTR-RKNIGLTTS----GIKLV  101 (139)
T ss_dssp             HHHHHHHHHHSTTTCEEHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEEECCC--C-CEEEEECHH----HHHHH
T ss_pred             HHHHHHHHHhcCCCCcCHHHHHHHhCCCc---ccHHHHHHHHHHCCCEeecCCCCCCC-eeeeEECHH----HHHHH
Confidence            444666676653 5999999999999999   99999999999999999765211111 223566666    55554

>2zfu_A Nucleomethylin, cerebral protein 1; nucleolar protein, SAM-binding protein, protein structure, N phosphoprotein, nuclear protein; HET: SAH; 2.00A {Homo sapiens}

Probab=95.54  E-value=0.017  Score=45.16  Aligned_cols=30  Identities=17%  Similarity=0.190  Sum_probs=24.2

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                      ....+|||||||+|.++..++     .+++.+|+-
T Consensus        66 ~~~~~vLDiG~G~G~~~~~l~-----~~v~~~D~s   95 (215)
T 2zfu_A           66 PASLVVADFGCGDCRLASSIR-----NPVHCFDLA   95 (215)
T ss_dssp             CTTSCEEEETCTTCHHHHHCC-----SCEEEEESS
T ss_pred             CCCCeEEEECCcCCHHHHHhh-----ccEEEEeCC
Confidence            456799999999999998873     578888763

>3tm4_A TRNA (guanine N2-)-methyltransferase TRM14; rossmann fold, thump domain, tRNA methyltransferase; HET: SAM; 1.95A {Pyrococcus furiosus} PDB: 3tlj_A* 3tm5_A*

Probab=95.52  E-value=0.011  Score=51.22  Aligned_cols=34  Identities=12%  Similarity=-0.050  Sum_probs=30.5

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+..+|+|+|||+|.+++.+++..+..+++.+|+
T Consensus       216 ~~~~~vLD~gCGsG~~~i~~a~~~~~~~v~g~Di  249 (373)
T 3tm4_A          216 LDGGSVLDPMCGSGTILIELALRRYSGEIIGIEK  249 (373)
T ss_dssp             CCSCCEEETTCTTCHHHHHHHHTTCCSCEEEEES
T ss_pred             CCCCEEEEccCcCcHHHHHHHHhCCCCeEEEEeC
Confidence            3567999999999999999999998778998886

>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=95.52  E-value=0.0076  Score=47.19  Aligned_cols=33  Identities=18%  Similarity=0.336  Sum_probs=27.6

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .....+|||||||+|.++..+++..  .+++.+|+
T Consensus        49 ~~~~~~vLDiGcG~G~~~~~l~~~~--~~v~~vD~   81 (216)
T 3ofk_A           49 SGAVSNGLEIGCAAGAFTEKLAPHC--KRLTVIDV   81 (216)
T ss_dssp             TSSEEEEEEECCTTSHHHHHHGGGE--EEEEEEES
T ss_pred             cCCCCcEEEEcCCCCHHHHHHHHcC--CEEEEEEC
Confidence            3446799999999999999999885  47888876

>3bpv_A Transcriptional regulator; MARR, DNA binding, transcription factor, winged helix motif, DNA-binding; 1.40A {Methanobacterium thermoautotrophicum} PDB: 3bpx_A*

Probab=95.52  E-value=0.0045  Score=45.03  Aligned_cols=67  Identities=13%  Similarity=0.145  Sum_probs=48.4

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      ++.|+..|..+ +++|..+||+.+++++   ..+.+.++.|...|++.......+.- ...+.+|+.    ++.+.
T Consensus        31 ~~~iL~~l~~~-~~~~~~ela~~l~~s~---~tvs~~l~~L~~~glv~~~~~~~d~R-~~~~~lT~~----G~~~~   97 (138)
T 3bpv_A           31 QVACLLRIHRE-PGIKQDELATFFHVDK---GTIARTLRRLEESGFIEREQDPENRR-RYILEVTRR----GEEII   97 (138)
T ss_dssp             HHHHHHHHHHS-TTCBHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEEEETTEEE-EEEEEECHH----HHHTH
T ss_pred             HHHHHHHHHHc-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEeecCCCCce-eEEeeECHh----HHHHH
Confidence            34456667665 8899999999999999   99999999999999999854210000 122667776    55553

>1r1t_A Transcriptional repressor SMTB; zinc, transcriptional regulation, winged HTH protein, DNA binding, transcription repressor; 1.70A {Synechococcus elongatus pcc 7942} SCOP: a.4.5.5 PDB: 1r23_A 1smt_A 1r22_A

Probab=95.51  E-value=0.0068  Score=44.19  Aligned_cols=47  Identities=13%  Similarity=0.188  Sum_probs=41.2

Q ss_pred             HhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           37 IQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        37 ~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      .++.|+..|.+  +++++.+||+.+|+++   ..+.+.|+.|...|++....
T Consensus        47 ~rl~IL~~L~~--~~~s~~ela~~lgis~---stvs~~L~~Le~~Glv~~~~   93 (122)
T 1r1t_A           47 NRLRLLSLLAR--SELCVGDLAQAIGVSE---SAVSHQLRSLRNLRLVSYRK   93 (122)
T ss_dssp             HHHHHHHHHTT--CCBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHHc--CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeEEEE
Confidence            45567777775  7899999999999999   99999999999999998764

>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=95.51  E-value=0.0061  Score=44.72  Aligned_cols=60  Identities=15%  Similarity=0.168  Sum_probs=45.2

Q ss_pred             CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      .++..|..+ +++|..+||+.+++++   ..+.+.++.|...|++.......+.- ...+.+|+.
T Consensus        33 ~iL~~l~~~-~~~t~~~la~~l~~s~---~~vs~~l~~Le~~gli~r~~~~~d~R-~~~~~lT~~   92 (144)
T 1lj9_A           33 LYLVRVCEN-PGIIQEKIAELIKVDR---TTAARAIKRLEEQGFIYRQEDASNKK-IKRIYATEK   92 (144)
T ss_dssp             HHHHHHHHS-TTEEHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEEECSSCTT-CEEEEECHH
T ss_pred             HHHHHHHHC-cCcCHHHHHHHHCCCH---hHHHHHHHHHHHCCCEEeecCCCCCc-eeeeEEChh
Confidence            356666665 7899999999999999   99999999999999999865211110 123666666

>3boq_A Transcriptional regulator, MARR family; MARR famil structural genomics, PSI-2, protein structure initiative; 2.39A {Silicibacter pomeroyi dss-3}

Probab=95.49  E-value=0.035  Score=41.34  Aligned_cols=48  Identities=17%  Similarity=0.182  Sum_probs=40.2

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      ++.|+..|...++++|..+||+.+++++   ..+.++++.|...|++....
T Consensus        49 ~~~iL~~L~~~~~~~~~~ela~~l~i~~---~tvs~~l~~Le~~Gli~r~~   96 (160)
T 3boq_A           49 KFDAMAQLARNPDGLSMGKLSGALKVTN---GNVSGLVNRLIKDGMVVKAM   96 (160)
T ss_dssp             HHHHHHHHHHCTTCEEHHHHHHHCSSCC---SCHHHHHHHHHHHTSEEEC-
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHCCCh---hhHHHHHHHHHHCCCEEeec
Confidence            4457778832237899999999999999   99999999999999999764

>2fpo_A Methylase YHHF; structural genomics, putative methyltransferase, PSI, protei structure initiative; HET: MSE; 2.05A {Escherichia coli} SCOP: c.66.1.46

Probab=95.48  E-value=0.011  Score=46.37  Aligned_cols=31  Identities=10%  Similarity=0.159  Sum_probs=26.2

Q ss_pred             CCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          181 LKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       181 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+|||+|||+|.+++.++++.. .+++.+|+
T Consensus        55 ~~~vLDlgcG~G~~~~~l~~~~~-~~V~~vD~   85 (202)
T 2fpo_A           55 DAQCLDCFAGSGALGLEALSRYA-AGATLIEM   85 (202)
T ss_dssp             TCEEEETTCTTCHHHHHHHHTTC-SEEEEECS
T ss_pred             CCeEEEeCCCcCHHHHHHHhcCC-CEEEEEEC
Confidence            57999999999999999888754 37888886

>3id6_C Fibrillarin-like rRNA/TRNA 2'-O-methyltransferase; C/D guide RNA, 2'-O-methylation, coiled-coil, methyltransfer binding, rRNA processing; HET: SAM; 2.60A {Sulfolobus solfataricus} SCOP: c.66.1.0 PDB: 3id5_B* 3pla_E*

Probab=95.48  E-value=0.024  Score=46.03  Aligned_cols=45  Identities=9%  Similarity=0.119  Sum_probs=33.9

Q ss_pred             HHHHhhcc-cccCCCCcEEeecCCchHHHHHHHHH-CCCCeEEEecC
Q 040620          168 SVLIEDCN-EVSKGLKPLVDVGGSTGTMARAIATA-FPDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~-~~~~~~~~vvDVGGG~G~~~~~l~~~-~P~l~~~v~Dl  212 (214)
                      ..++..++ .......+|+|+|||+|..+..+++. -|+-+++.+|+
T Consensus        63 ~~ll~~l~~~~l~~g~~VLDlG~GtG~~t~~la~~v~~~G~V~avD~  109 (232)
T 3id6_C           63 GAILKGLKTNPIRKGTKVLYLGAASGTTISHVSDIIELNGKAYGVEF  109 (232)
T ss_dssp             HHHHTTCSCCSCCTTCEEEEETCTTSHHHHHHHHHHTTTSEEEEEEC
T ss_pred             HHHHhhhhhcCCCCCCEEEEEeecCCHHHHHHHHHhCCCCEEEEEEC
Confidence            33444443 12556789999999999999999987 46778888886

>2fa5_A Transcriptional regulator MARR/EMRR family; multiple antibiotics resistance repressor, XCC structural genomics, X-RAY diffraction; 1.80A {Xanthomonas campestris}

Probab=95.45  E-value=0.006  Score=45.75  Aligned_cols=47  Identities=13%  Similarity=0.154  Sum_probs=39.9

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      ++.|+..|... +++|..+||+.+++++   ..+.++++.|...|++....
T Consensus        51 ~~~iL~~l~~~-~~~t~~ela~~l~is~---~tvs~~l~~Le~~glv~r~~   97 (162)
T 2fa5_A           51 EWRVITILALY-PGSSASEVSDRTAMDK---VAVSRAVARLLERGFIRRET   97 (162)
T ss_dssp             HHHHHHHHHHS-TTCCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEC--
T ss_pred             HHHHHHHHHhC-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEeeec
Confidence            34467777765 7999999999999999   99999999999999998764

>3s2w_A Transcriptional regulator, MARR family; structural genomics, PSI-biology, protein structure initiati midwest center for structural genomics; 2.45A {Methanosarcina mazei}

Probab=95.44  E-value=0.0053  Score=46.09  Aligned_cols=64  Identities=13%  Similarity=0.173  Sum_probs=47.1

Q ss_pred             cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      ++..|..+ +++|..+||+.+++++   ..+.++++.|...|++.......|.- ...+.+|+.    ++.+.
T Consensus        55 vL~~l~~~-~~~t~~eLa~~l~~~~---~tvs~~l~~Le~~Glv~r~~~~~DrR-~~~l~LT~~----G~~~~  118 (159)
T 3s2w_A           55 FLMRLYRE-DGINQESLSDYLKIDK---GTTARAIQKLVDEGYVFRQRDEKDRR-SYRVFLTEK----GKKLE  118 (159)
T ss_dssp             HHHHHHHS-CSEEHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEEECC---C-CEEEEECHH----HHHHH
T ss_pred             HHHHHHHC-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEEecCCCCCC-eeEEEECHH----HHHHH
Confidence            55666665 8899999999999999   99999999999999999765211110 124666666    55543

>1ri5_A MRNA capping enzyme; methyltransferase, M7G, messenger RNA CAP, structural genomics, PSI, protein structure initiative; 2.10A {Encephalitozoon cuniculi} SCOP: c.66.1.34 PDB: 1ri2_A* 1ri3_A* 1ri1_A* 1ri4_A 1z3c_A* 2hv9_A*

Probab=95.44  E-value=0.011  Score=48.38  Aligned_cols=33  Identities=15%  Similarity=0.021  Sum_probs=28.0

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+..+|||||||+|.++..+++. +..+++++|+
T Consensus        63 ~~~~~vLDiGcG~G~~~~~l~~~-~~~~v~gvD~   95 (298)
T 1ri5_A           63 KRGDSVLDLGCGKGGDLLKYERA-GIGEYYGVDI   95 (298)
T ss_dssp             CTTCEEEEETCTTTTTHHHHHHH-TCSEEEEEES
T ss_pred             CCCCeEEEECCCCCHHHHHHHHC-CCCEEEEEEC
Confidence            35679999999999999998876 6668999886

>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=95.44  E-value=0.0051  Score=43.04  Aligned_cols=55  Identities=16%  Similarity=0.139  Sum_probs=47.2

Q ss_pred             cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      |...+..  + ++..+||..+|+++   +.+++.++.|...|++....        +.|.+|+.    +..++
T Consensus        13 IL~~i~~--~-~~~t~La~~~~ls~---~~~~~~l~~L~~~GLI~~~~--------~~~~LT~k----G~~~l   67 (95)
T 1r7j_A           13 ILEACKS--G-SPKTRIMYGANLSY---ALTGRYIKMLMDLEIIRQEG--------KQYMLTKK----GEELL   67 (95)
T ss_dssp             HHHHHTT--C-BCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEET--------TEEEECHH----HHHHH
T ss_pred             HHHHHHc--C-CCHHHHHHHhCcCH---HHHHHHHHHHHHCCCeEEEC--------CeeEEChh----HHHHH
Confidence            3344443  5 89999999999999   99999999999999999984        67999999    88775

>3bdd_A Regulatory protein MARR; putative multiple antibiotic-resistance repressor, structura genomics, joint center for structural genomics, JCSG; 2.20A {Streptococcus suis}

Probab=95.41  E-value=0.013  Score=42.67  Aligned_cols=62  Identities=15%  Similarity=0.282  Sum_probs=47.5

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      ++.|+..|..+ +++|..+||+.+++++   ..+.+.++.|...|++.......|.- ...|.+|+.
T Consensus        33 ~~~iL~~l~~~-~~~~~~ela~~l~is~---~~vs~~l~~L~~~gli~~~~~~~d~r-~~~~~lT~~   94 (142)
T 3bdd_A           33 RYSILQTLLKD-APLHQLALQERLQIDR---AAVTRHLKLLEESGYIIRKRNPDNQR-EVLVWPTEQ   94 (142)
T ss_dssp             HHHHHHHHHHH-CSBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEEECSSSTT-CEEEEECHH
T ss_pred             HHHHHHHHHhC-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEecCCCCCCC-eeEEEECHH
Confidence            44467777765 7899999999999999   99999999999999998775211111 234667766

>4azs_A Methyltransferase WBDD; kinase; HET: AMP SAM; 2.15A {Escherichia coli} PDB: 4azt_A* 4azv_A* 4azw_A*

Probab=95.38  E-value=0.011  Score=53.99  Aligned_cols=31  Identities=13%  Similarity=0.197  Sum_probs=28.0

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+|||||||.|.++..+++.  ..++|++|+
T Consensus        66 ~~~~vLDvGCG~G~~~~~la~~--ga~V~giD~   96 (569)
T 4azs_A           66 RPLNVLDLGCAQGFFSLSLASK--GATIVGIDF   96 (569)
T ss_dssp             SCCEEEEETCTTSHHHHHHHHT--TCEEEEEES
T ss_pred             CCCeEEEECCCCcHHHHHHHhC--CCEEEEECC
Confidence            4569999999999999999998  788999996

>2h1r_A Dimethyladenosine transferase, putative; SGC toronto dimethyladenosine transferase, structural genomics, structural genomics consortium; 1.89A {Plasmodium falciparum}

Probab=95.37  E-value=0.009  Score=50.14  Aligned_cols=41  Identities=15%  Similarity=0.238  Sum_probs=31.8

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+++..+  .....+|||||||+|.++..++++  ..+++.+|+
T Consensus        32 ~~i~~~~~--~~~~~~VLDiG~G~G~lt~~La~~--~~~v~~vDi   72 (299)
T 2h1r_A           32 DKIIYAAK--IKSSDIVLEIGCGTGNLTVKLLPL--AKKVITIDI   72 (299)
T ss_dssp             HHHHHHHC--CCTTCEEEEECCTTSTTHHHHTTT--SSEEEEECS
T ss_pred             HHHHHhcC--CCCcCEEEEEcCcCcHHHHHHHhc--CCEEEEEEC
Confidence            44555444  455679999999999999999987  457888876

>3tgn_A ADC operon repressor ADCR; helix-turn-helix, transcriptional regulator, transcription; 2.00A {Streptococcus pneumoniae}

Probab=95.36  E-value=0.01  Score=43.54  Aligned_cols=62  Identities=19%  Similarity=0.202  Sum_probs=43.5

Q ss_pred             HhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           37 IQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        37 ~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      .+..|+..|... + +|..+||+.+++++   ..+.+.++.|...|++.......|.- ...+.+|+.
T Consensus        39 ~~~~iL~~l~~~-~-~t~~eLa~~l~~s~---~tvs~~l~~L~~~Glv~r~~~~~d~R-~~~~~lT~~  100 (146)
T 3tgn_A           39 TQEHILMLLSEE-S-LTNSELARRLNVSQ---AAVTKAIKSLVKEGMLETSKDSKDAR-VIFYQLTDL  100 (146)
T ss_dssp             HHHHHHHHHTTC-C-CCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEC-----------CCEECGG
T ss_pred             HHHHHHHHHHhC-C-CCHHHHHHHHCCCH---HHHHHHHHHHHHCCCeEeccCCCCCc-eeEEEECHh
Confidence            344566677764 4 99999999999999   99999999999999999764211111 234666666

>3cjn_A Transcriptional regulator, MARR family; silicibacter pomeroy structural genomics, PSI-2, protein structure initiative; 1.95A {Silicibacter pomeroyi dss-3}

Probab=95.35  E-value=0.0068  Score=45.50  Aligned_cols=62  Identities=13%  Similarity=0.228  Sum_probs=46.6

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      ++.|+..|... +++|..+||+.+++++   ..+.++++.|...|++.......+.- ...+.+|+.
T Consensus        54 ~~~iL~~l~~~-~~~t~~ela~~l~is~---~tvs~~l~~Le~~Gli~r~~~~~d~R-~~~~~lT~~  115 (162)
T 3cjn_A           54 KMRALAILSAK-DGLPIGTLGIFAVVEQ---STLSRALDGLQADGLVRREVDSDDQR-SSRVYLTPA  115 (162)
T ss_dssp             HHHHHHHHHHS-CSEEHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEEEC--CCS-SEEEEECHH
T ss_pred             HHHHHHHHHHC-CCCCHHHHHHHHCCCh---hHHHHHHHHHHHCCCEEecCCCCCCC-eeEEEECHH
Confidence            44567777766 7899999999999999   99999999999999998764211110 123666666

>3r0q_C Probable protein arginine N-methyltransferase 4.2; arginine methyltransferase, methylation; HET: SAH; 2.61A {Arabidopsis thaliana}

Probab=95.34  E-value=0.023  Score=49.11  Aligned_cols=34  Identities=26%  Similarity=0.216  Sum_probs=28.3

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+.++|||||||+|.+++.++++ ...+++.+|.
T Consensus        61 ~~~~~~VLDlGcGtG~ls~~la~~-g~~~V~gvD~   94 (376)
T 3r0q_C           61 HFEGKTVLDVGTGSGILAIWSAQA-GARKVYAVEA   94 (376)
T ss_dssp             TTTTCEEEEESCTTTHHHHHHHHT-TCSEEEEEES
T ss_pred             cCCCCEEEEeccCcCHHHHHHHhc-CCCEEEEEcc
Confidence            445789999999999999999998 3348888886

>2avn_A Ubiquinone/menaquinone biosynthesis methyltransfe related protein; ubiquinone/menaquinone biosynthesis methyltransferase-relate protein; HET: SAI; 2.35A {Thermotoga maritima} SCOP: c.66.1.41

Probab=95.34  E-value=0.011  Score=48.04  Aligned_cols=31  Identities=16%  Similarity=0.243  Sum_probs=27.2

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+|||||||+|.++..+++.  ..+++++|.
T Consensus        54 ~~~~vLDiGcG~G~~~~~l~~~--~~~v~gvD~   84 (260)
T 2avn_A           54 NPCRVLDLGGGTGKWSLFLQER--GFEVVLVDP   84 (260)
T ss_dssp             SCCEEEEETCTTCHHHHHHHTT--TCEEEEEES
T ss_pred             CCCeEEEeCCCcCHHHHHHHHc--CCeEEEEeC
Confidence            5679999999999999999987  568888886

>1yyv_A Putative transcriptional regulator; reductive methylation, D lysine, structural genomics, PSI; HET: MLY; 2.35A {Salmonella typhimurium} SCOP: a.4.5.69

Probab=95.33  E-value=0.016  Score=42.70  Aligned_cols=80  Identities=11%  Similarity=0.052  Sum_probs=57.7

Q ss_pred             hHHHHHHHHHHHHhHHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHc-CCCCCCcccHHHHHHHHHhCCceeeecCCCCC
Q 040620           15 QAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVAL-NVHPNKTRCTQILVCLLAHSGFFVQQKDGKNE   93 (214)
Q Consensus        15 ~~~~~l~~~~~g~~~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~-g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~   93 (214)
                      -+...+++++.+.|...+|..         |..  ++++..||++.+ |+++   ..|.+.|+.|...|++.......+.
T Consensus        23 c~~~~~l~~l~~~w~l~IL~~---------L~~--g~~~~~eLa~~l~gis~---~tls~~L~~Le~~GlV~r~~~~~d~   88 (131)
T 1yyv_A           23 CPSREVLKHVTSRWGVLILVA---------LRD--GTHRFSDLRRXMGGVSE---XMLAQSLQALEQDGFLNRVSYPVVP   88 (131)
T ss_dssp             CTHHHHHHHHHSHHHHHHHHH---------GGG--CCEEHHHHHHHSTTCCH---HHHHHHHHHHHHHTCEEEEEECSSS
T ss_pred             CCHHHHHHHHcCCcHHHHHHH---------HHc--CCCCHHHHHHHhccCCH---HHHHHHHHHHHHCCcEEEEecCCCC
Confidence            345566677777766555433         333  789999999999 7999   9999999999999999976521111


Q ss_pred             CccceeeCCCCCcccccccc
Q 040620           94 QEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        94 ~~~~~y~~t~~~~~~s~~l~  113 (214)
                      . .-.|.+|+.    ++.+.
T Consensus        89 r-~~~y~LT~~----G~~l~  103 (131)
T 1yyv_A           89 P-HVEYSLTPL----GEQVS  103 (131)
T ss_dssp             C-EEEEEECHH----HHHHH
T ss_pred             C-eEEEEECcc----HHHHH
Confidence            1 235888888    66654

>2kw5_A SLR1183 protein; structural genomics, northeast structural genomics consortium (NESG), PSI-2, protein structure initiative, unknown function; NMR {Synechocystis} PDB: 3mer_A

Probab=95.31  E-value=0.012  Score=45.58  Aligned_cols=28  Identities=14%  Similarity=0.116  Sum_probs=25.2

Q ss_pred             cEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          183 PLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       183 ~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +|||||||.|.++..+++.  ..+++++|.
T Consensus        32 ~vLdiGcG~G~~~~~l~~~--~~~v~~vD~   59 (202)
T 2kw5_A           32 KILCLAEGEGRNACFLASL--GYEVTAVDQ   59 (202)
T ss_dssp             EEEECCCSCTHHHHHHHTT--TCEEEEECS
T ss_pred             CEEEECCCCCHhHHHHHhC--CCeEEEEEC
Confidence            9999999999999999987  568888886

>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=95.30  E-value=0.0059  Score=50.38  Aligned_cols=32  Identities=13%  Similarity=0.160  Sum_probs=24.5

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+|||||||+|.++ .++...+..+++.+|+
T Consensus        71 ~~~~vLDiGcG~G~~~-~l~~~~~~~~v~gvD~  102 (289)
T 2g72_A           71 SGRTLIDIGSGPTVYQ-LLSACSHFEDITMTDF  102 (289)
T ss_dssp             CCSEEEEETCTTCCGG-GTTGGGGCSEEEEECS
T ss_pred             CCCeEEEECCCcChHH-HHhhccCCCeEEEeCC
Confidence            4679999999999944 4444455668999986

>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=95.29  E-value=0.012  Score=47.90  Aligned_cols=35  Identities=17%  Similarity=0.197  Sum_probs=31.0

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHC-CCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAF-PDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl  212 (214)
                      .....+|+|+|||+|.++..+++.- |+=+++.+|.
T Consensus        75 ikpG~~VldlG~G~G~~~~~la~~VG~~G~V~avD~  110 (233)
T 4df3_A           75 VKEGDRILYLGIASGTTASHMSDIIGPRGRIYGVEF  110 (233)
T ss_dssp             CCTTCEEEEETCTTSHHHHHHHHHHCTTCEEEEEEC
T ss_pred             CCCCCEEEEecCcCCHHHHHHHHHhCCCceEEEEeC
Confidence            6678899999999999999999974 8888888886

>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=95.28  E-value=0.0065  Score=42.19  Aligned_cols=47  Identities=19%  Similarity=0.314  Sum_probs=40.1

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      +..|+..|... +++|..+||+.+++++   ..+.+.|+.|...|++....
T Consensus        22 ~~~il~~l~~~-~~~s~~ela~~l~is~---~tv~~~l~~L~~~glv~~~~   68 (109)
T 1sfx_A           22 DVRIYSLLLER-GGMRVSEIARELDLSA---RFVRDRLKVLLKRGFVRREI   68 (109)
T ss_dssp             HHHHHHHHHHH-CCBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHHc-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEEEe
Confidence            34455666554 7899999999999999   99999999999999999764

>2oxt_A Nucleoside-2'-O-methyltransferase; flavivirus, viral enzyme, RNA capping, S-adenosyl-L-methionine, viral protein; HET: SAM; 2.90A {Meaban virus}

Probab=95.26  E-value=0.0077  Score=49.83  Aligned_cols=32  Identities=16%  Similarity=0.110  Sum_probs=26.9

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +.+..+|||||||+|.++..++++   -+++.+|+
T Consensus        72 ~~~g~~VLDlGcGtG~~s~~la~~---~~V~gvD~  103 (265)
T 2oxt_A           72 VELTGRVVDLGCGRGGWSYYAASR---PHVMDVRA  103 (265)
T ss_dssp             CCCCEEEEEESCTTSHHHHHHHTS---TTEEEEEE
T ss_pred             CCCCCEEEEeCcCCCHHHHHHHHc---CcEEEEEC
Confidence            445679999999999999999887   57888875

>2wa2_A Non-structural protein 5; transferase, S-adenosyl-L- methionine, virion, membrane, flavivirus, N7-methyltransferase, 2'-O-methyltransferase; HET: SAM; 1.80A {Modoc virus} PDB: 2wa1_A*

Probab=95.25  E-value=0.0077  Score=50.16  Aligned_cols=32  Identities=16%  Similarity=0.161  Sum_probs=27.0

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +.+..+|||||||+|.++..++++   -+++.+|+
T Consensus        80 ~~~g~~VLDlGcGtG~~s~~la~~---~~V~gVD~  111 (276)
T 2wa2_A           80 VELKGTVVDLGCGRGSWSYYAASQ---PNVREVKA  111 (276)
T ss_dssp             CCCCEEEEEESCTTCHHHHHHHTS---TTEEEEEE
T ss_pred             CCCCCEEEEeccCCCHHHHHHHHc---CCEEEEEC
Confidence            445679999999999999999987   57888875

>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=95.23  E-value=0.026  Score=43.24  Aligned_cols=47  Identities=11%  Similarity=0.249  Sum_probs=40.5

Q ss_pred             CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      +++|.++||+++++++   ..+++++..|...|++.-...    . .|-|.+..-
T Consensus        27 ~~~s~~~IA~~~~is~---~~l~kil~~L~~aGlv~s~rG----~-~GGy~Lar~   73 (162)
T 3k69_A           27 SKVASRELAQSLHLNP---VMIRNILSVLHKHGYLTGTVG----K-NGGYQLDLA   73 (162)
T ss_dssp             SCBCHHHHHHHHTSCG---GGTHHHHHHHHHTTSSEEECS----T-TCEEECCSC
T ss_pred             CCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEeecC----C-CCCeEecCC
Confidence            7899999999999999   999999999999999976541    1 456888777

>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=95.21  E-value=0.015  Score=42.52  Aligned_cols=62  Identities=13%  Similarity=0.270  Sum_probs=46.7

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      ++.|+..|... +++|..+||+.+++++   ..+.+.++.|...|++.......+.- ...+.+|+.
T Consensus        39 ~~~iL~~l~~~-~~~~~~ela~~l~~~~---~tvs~~l~~L~~~gli~r~~~~~d~R-~~~~~lT~~  100 (142)
T 2bv6_A           39 QFLVLTILWDE-SPVNVKKVVTELALDT---GTVSPLLKRMEQVDLIKRERSEVDQR-EVFIHLTDK  100 (142)
T ss_dssp             HHHHHHHHHHS-SEEEHHHHHHHTTCCT---TTHHHHHHHHHHTTSEEEEECSSSTT-CEEEEECHH
T ss_pred             HHHHHHHHHHc-CCcCHHHHHHHHCCCh---hhHHHHHHHHHHCCCEEeecCCCCcc-eEEEEEChH
Confidence            44566777765 7899999999999999   99999999999999999765211111 124566666

>4aik_A Transcriptional regulator SLYA; transcription, transcription factor; 1.85A {Yersinia pseudotuberculosis} PDB: 4aih_A 4aij_A 3qpt_A* 3q5f_A*

Probab=95.19  E-value=0.021  Score=42.86  Aligned_cols=65  Identities=14%  Similarity=0.135  Sum_probs=47.5

Q ss_pred             cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      +.-.|...+++.+..+||+.+++++   ..+.++++.|...|++.......|.- .-.+.+|+.    ++.+.
T Consensus        36 vL~~L~~~~~~~~~~eLa~~l~~~~---~tvs~~v~~Le~~GlV~R~~~~~DrR-~~~l~LT~~----G~~~~  100 (151)
T 4aik_A           36 TLYNINRLPPEQSQIQLAKAIGIEQ---PSLVRTLDQLEEKGLITRHTSANDRR-AKRIKLTEQ----SSPII  100 (151)
T ss_dssp             HHHHHHHSCTTSCHHHHHHHHTSCH---HHHHHHHHHHHHTTSEEEEECSSCTT-CEEEEECGG----GHHHH
T ss_pred             HHHHHHHcCCCCcHHHHHHHHCcCH---HHHHHHHHHHHhCCCeEeecCCCCCc-chhhhcCHH----HHHHH
Confidence            4455655446688899999999999   99999999999999999765311111 124777777    66554

>3lwf_A LIN1550 protein, putative transcriptional regulator; structural genomics, JOI for structural genomics, JCSG; HET: SO4; 2.06A {Listeria innocua}

Probab=95.18  E-value=0.02  Score=43.84  Aligned_cols=47  Identities=17%  Similarity=0.256  Sum_probs=40.4

Q ss_pred             CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      +|+|+++||+++++++   ..+++++..|...|++.-...    . .|-|.+..-
T Consensus        43 ~~~s~~eIA~~~~i~~---~~l~kil~~L~~aGlv~s~rG----~-~GGy~Lar~   89 (159)
T 3lwf_A           43 GPISLRSIAQDKNLSE---HYLEQLIGPLRNAGIVKSIRG----A-HGGYVLNGD   89 (159)
T ss_dssp             CCBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEECS----T-TCEEEECSC
T ss_pred             CCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCeEEEecC----C-CCceEecCC
Confidence            7899999999999999   999999999999999986642    1 466877766

>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=95.18  E-value=0.037  Score=40.72  Aligned_cols=46  Identities=9%  Similarity=0.120  Sum_probs=32.9

Q ss_pred             CcchhhhcCC-CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           40 RIPDIINNSG-QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        40 glfd~L~~~~-~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      .++..|..++ +++|..+||+.+++++   ..+.++++.|...|++....
T Consensus        45 ~vL~~l~~~~~~~~t~~eLa~~l~~~~---~~vs~~l~~L~~~Glv~r~~   91 (148)
T 3jw4_A           45 RMIGYIYENQESGIIQKDLAQFFGRRG---ASITSMLQGLEKKGYIERRI   91 (148)
T ss_dssp             HHHHHHHHHTTTCCCHHHHHHC---------CHHHHHHHHHHTTSBCCC-
T ss_pred             HHHHHHHhCCCCCCCHHHHHHHHCCCh---hHHHHHHHHHHHCCCEEeeC
Confidence            3555665542 6899999999999999   99999999999999998764

>2cmg_A Spermidine synthase; transferase, putrescine aminopropyltransferase, spermidine biosynthesis, polyamine biosynthesis, SPEE; 2.0A {Helicobacter pylori} PDB: 2cmh_A

Probab=95.17  E-value=0.011  Score=48.83  Aligned_cols=31  Identities=19%  Similarity=0.156  Sum_probs=28.1

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +.++|||||||.|..+..+++. | .+++++|+
T Consensus        72 ~~~~VL~iG~G~G~~~~~ll~~-~-~~v~~vei  102 (262)
T 2cmg_A           72 ELKEVLIVDGFDLELAHQLFKY-D-THIDFVQA  102 (262)
T ss_dssp             CCCEEEEESSCCHHHHHHHTTS-S-CEEEEECS
T ss_pred             CCCEEEEEeCCcCHHHHHHHhC-C-CEEEEEEC
Confidence            4579999999999999999998 8 88999886

>3lcv_B Sisomicin-gentamicin resistance methylase SGM; antibiotic resistance, methyltransferase, transferase; HET: SAM; 2.00A {Micromonospora zionensis} PDB: 3lcu_A*

Probab=95.14  E-value=0.0034  Score=52.33  Aligned_cols=34  Identities=12%  Similarity=-0.012  Sum_probs=31.7

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ....+|+|||||.|-++..+...+|+.+++.+|+
T Consensus       131 ~~p~~VLDLGCG~GpLAl~~~~~~p~a~y~a~DI  164 (281)
T 3lcv_B          131 PRPNTLRDLACGLNPLAAPWMGLPAETVYIASDI  164 (281)
T ss_dssp             CCCSEEEETTCTTGGGCCTTTTCCTTCEEEEEES
T ss_pred             CCCceeeeeccCccHHHHHHHhhCCCCEEEEEeC
Confidence            4578999999999999999999999999999996

>1z7u_A Hypothetical protein EF0647; winged-helix-turn-helix, MARR, structural genomics, PSI, Pro structure initiative; 2.20A {Enterococcus faecalis} SCOP: a.4.5.69

Probab=95.14  E-value=0.0044  Score=44.33  Aligned_cols=78  Identities=10%  Similarity=0.015  Sum_probs=54.1

Q ss_pred             HHHHHHHHHHHhHHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHc-CCCCCCcccHHHHHHHHHhCCceeeecCCCCCCc
Q 040620           17 QAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVAL-NVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQE   95 (214)
Q Consensus        17 ~~~l~~~~~g~~~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~-g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~   95 (214)
                      ...++++..+.|...+|.         .|..  ++++..+||+.+ ++++   ..+.+.|+.|...|++.......+.. 
T Consensus        12 ~~~~l~~l~~~~~~~IL~---------~L~~--~~~~~~eLa~~l~~is~---~tvs~~L~~Le~~GlI~r~~~~~d~r-   76 (112)
T 1z7u_A           12 INLALSTINGKWKLSLMD---------ELFQ--GTKRNGELMRALDGITQ---RVLTDRLREMEKDGLVHRESFNELPP-   76 (112)
T ss_dssp             HHHHHHTTCSTTHHHHHH---------HHHH--SCBCHHHHHHHSTTCCH---HHHHHHHHHHHHHTSEEEEEECCSSC-
T ss_pred             HHHHHHHHcCccHHHHHH---------HHHh--CCCCHHHHHHHhccCCH---HHHHHHHHHHHHCCCEEEeecCCCCC-
Confidence            344555555555544443         3444  789999999999 9999   99999999999999999765211111 


Q ss_pred             cceeeCCCCCcccccccc
Q 040620           96 EESILLPPHLDFFSRISL  113 (214)
Q Consensus        96 ~~~y~~t~~~~~~s~~l~  113 (214)
                      .-.|.+|+.    ++.+.
T Consensus        77 ~~~~~LT~~----G~~~~   90 (112)
T 1z7u_A           77 RVEYTLTPE----GYALY   90 (112)
T ss_dssp             EEEEEECHH----HHHHH
T ss_pred             eEEEEECHh----HHHHH
Confidence            234888888    66553

>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=95.13  E-value=0.0037  Score=46.03  Aligned_cols=66  Identities=14%  Similarity=0.197  Sum_probs=48.7

Q ss_pred             cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      ..|+..|..+ +++|..+||+.+++++   ..+.++++.|...|++.......|.- ...+.+|+.    ++.+.
T Consensus        39 ~~vL~~l~~~-~~~t~~eLa~~l~~~~---~tvs~~l~~L~~~Glv~r~~~~~D~R-~~~~~LT~~----G~~~~  104 (140)
T 3hsr_A           39 YIVLMAIEND-EKLNIKKLGERVFLDS---GTLTPLLKKLEKKDYVVRTREEKDER-NLQISLTEQ----GKAIK  104 (140)
T ss_dssp             HHHHHHSCTT-CEEEHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEEC--------CEEEECHH----HHHTH
T ss_pred             HHHHHHHHHc-CCcCHHHHHHHHCCCh---hhHHHHHHHHHHCCCeEecCCCCCcc-eeeeeEChH----HHHHH
Confidence            3456666665 8999999999999999   99999999999999999775211111 234777777    66664

>2lnb_A Z-DNA-binding protein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, immune system; NMR {Homo sapiens}

Probab=95.11  E-value=0.011  Score=39.55  Aligned_cols=56  Identities=14%  Similarity=0.196  Sum_probs=47.4

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCC
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPP  103 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~  103 (214)
                      +-.|++.|.++|.|+...|||+++|++.   ..+.+.+..|-..|.+.-+.       .-.|.++.
T Consensus        21 eekVLe~LkeaG~PlkageIae~~GvdK---KeVdKaik~LKkEgkI~SPk-------RCyw~~~~   76 (80)
T 2lnb_A           21 EQRILQVLTEAGSPVKLAQLVKECQAPK---RELNQVLYRMKKELKVSLTS-------PATWCLGG   76 (80)
T ss_dssp             HHHHHHHHHHHTSCEEHHHHHHHHTSCH---HHHHHHHHHHHHTTSEEEEE-------TTEEEESS
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHCCCH---HHHHHHHHHHHHcCCccCCC-------CceeeCCC
Confidence            3456777888889999999999999999   99999999999999998776       45676653

>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=95.09  E-value=0.012  Score=44.29  Aligned_cols=46  Identities=15%  Similarity=0.206  Sum_probs=38.9

Q ss_pred             CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      +++|+++||+++++++   ..+++++..|...|++.....      .+.|.+..-
T Consensus        29 ~~~~~~~iA~~~~i~~---~~l~kil~~L~~~Glv~s~rG------~GGy~L~~~   74 (149)
T 1ylf_A           29 SLCTSDYMAESVNTNP---VVIRKIMSYLKQAGFVYVNRG------PGGAGLLKD   74 (149)
T ss_dssp             GGCCHHHHHHHHTSCH---HHHHHHHHHHHHTTSEEEC---------CCEEESSC
T ss_pred             CCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCcEEEccC------CCceEeCCC
Confidence            7899999999999999   999999999999999986641      356777666

>3htx_A HEN1; HEN1, small RNA methyltransferase, protein-RNA complex; HET: SAH; 3.10A {Arabidopsis thaliana}

Probab=95.08  E-value=0.013  Score=56.19  Aligned_cols=33  Identities=15%  Similarity=0.148  Sum_probs=30.0

Q ss_pred             CCCcEEeecCCchHHHHHHHHHC-CCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAF-PDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl  212 (214)
                      +..+|||||||+|.++..+++.. |..+++.+|+
T Consensus       721 ~g~rVLDVGCGTG~lai~LAr~g~p~a~VtGVDI  754 (950)
T 3htx_A          721 SASTLVDFGCGSGSLLDSLLDYPTSLQTIIGVDI  754 (950)
T ss_dssp             CCSEEEEETCSSSHHHHHHTSSCCCCCEEEEEES
T ss_pred             CCCEEEEECCCCCHHHHHHHHhCCCCCeEEEEEC
Confidence            57899999999999999999998 6679999996

>3frh_A 16S rRNA methylase; methyltransferase domain, helical N-terminal domain, methyltransferase, plasmid, transferase; HET: SAH; 1.20A {Escherichia coli} PDB: 3fri_A* 3b89_A*

Probab=95.07  E-value=0.017  Score=47.49  Aligned_cols=31  Identities=6%  Similarity=-0.073  Sum_probs=28.1

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ....+|+|||||.|-++..+.   |..+++.+|+
T Consensus       104 ~~p~~VLDlGCG~gpLal~~~---~~~~y~a~DI  134 (253)
T 3frh_A          104 ETPRRVLDIACGLNPLALYER---GIASVWGCDI  134 (253)
T ss_dssp             CCCSEEEEETCTTTHHHHHHT---TCSEEEEEES
T ss_pred             CCCCeEEEecCCccHHHHHhc---cCCeEEEEeC
Confidence            457899999999999999888   9999999986

>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=95.05  E-value=0.0077  Score=42.62  Aligned_cols=80  Identities=11%  Similarity=0.052  Sum_probs=57.2

Q ss_pred             hHHHHHHHHHHHHhHHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHc-CCCCCCcccHHHHHHHHHhCCceeeecCCCCC
Q 040620           15 QAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVAL-NVHPNKTRCTQILVCLLAHSGFFVQQKDGKNE   93 (214)
Q Consensus        15 ~~~~~l~~~~~g~~~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~-g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~   93 (214)
                      -+...+++++.+.|...+|.         .|..  ++++..|||+.+ |+++   ..+.+.|+.|...|++.......+.
T Consensus        13 c~~~~~l~~l~~~~~~~IL~---------~L~~--~~~~~~eL~~~l~gis~---~~ls~~L~~Le~~GlV~r~~~~~d~   78 (107)
T 2fsw_A           13 CPVRKSMQIFAGKWTLLIIF---------QINR--RIIRYGELKRAIPGISE---KMLIDELKFLCGKGLIKKKQYPEVP   78 (107)
T ss_dssp             CHHHHHHHHHTSSSHHHHHH---------HHTT--SCEEHHHHHHHSTTCCH---HHHHHHHHHHHHTTSEEEEEECSSS
T ss_pred             CCHHHHHHHHcCccHHHHHH---------HHHh--CCcCHHHHHHHcccCCH---HHHHHHHHHHHHCCCEEEeecCCCC
Confidence            34556666666666655544         3333  789999999999 5999   9999999999999999976521111


Q ss_pred             CccceeeCCCCCcccccccc
Q 040620           94 QEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        94 ~~~~~y~~t~~~~~~s~~l~  113 (214)
                      . .-.|.+|+.    ++.+.
T Consensus        79 r-~~~y~LT~~----G~~l~   93 (107)
T 2fsw_A           79 P-RVEYSLTPL----GEKVL   93 (107)
T ss_dssp             C-EEEEEECHH----HHTTH
T ss_pred             C-eeEEEECcc----HHHHH
Confidence            1 245889988    76654

>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=95.03  E-value=0.023  Score=39.08  Aligned_cols=57  Identities=16%  Similarity=0.123  Sum_probs=41.5

Q ss_pred             chhhhcCCCCCCHHHHHHHcCCCCCCccc-HHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           42 PDIINNSGQPMTLTQIIVALNVHPNKTRC-TQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        42 fd~L~~~~~p~t~~eLA~~~g~~~~~~~~-l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      +..|...+.++|..|||+.+++++   .. +.++++.|...|++..++.  +.- ...+.+|+.
T Consensus        21 L~~l~~~~~~~t~~eLa~~l~is~---~t~vs~~l~~Le~~Glv~~~~~--drR-~~~~~LT~~   78 (95)
T 2pg4_A           21 LLEFEKKGYEPSLAEIVKASGVSE---KTFFMGLKDRLIRAGLVKEETL--SYR-VKTLKLTEK   78 (95)
T ss_dssp             HHHHHHTTCCCCHHHHHHHHCCCH---HHHHTTHHHHHHHTTSEEEEEE--ETT-EEEEEECHH
T ss_pred             HHHHHhcCCCCCHHHHHHHHCCCc---hHHHHHHHHHHHHCCCeecCCC--CCC-eEEEEECHh
Confidence            344555423899999999999999   99 9999999999999994431  000 223566666

>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=94.98  E-value=0.0041  Score=45.65  Aligned_cols=67  Identities=18%  Similarity=0.208  Sum_probs=48.9

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      ++.|+..|..+ +++|..+||+.+++++   ..+.+.++.|...|++.......+.- ...|.+|+.    ++.+.
T Consensus        35 ~~~iL~~l~~~-~~~~~~~la~~l~~s~---~tvs~~l~~L~~~glv~r~~~~~d~r-~~~~~lT~~----G~~~~  101 (145)
T 2a61_A           35 QFDILQKIYFE-GPKRPGELSVLLGVAK---STVTGLVKRLEADGYLTRTPDPADRR-AYFLVITRK----GEEVI  101 (145)
T ss_dssp             HHHHHHHHHHH-CCBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEEEETTEEE-EEEEEECHH----HHHHH
T ss_pred             HHHHHHHHHHc-CCCCHHHHHHHHCCCc---hhHHHHHHHHHHCCCeeecCCCCCCc-eEEEEECHH----HHHHH
Confidence            44566677665 7899999999999999   99999999999999999764210000 123667777    55543

>3dmg_A Probable ribosomal RNA small subunit methyltransf; monomethyltranserase, 16S rRNA methyltransferase, N2 G1207 methyltransferase; HET: SAH; 1.55A {Thermus thermophilus} PDB: 3dmf_A* 3dmh_A* 2zul_A* 2zwv_A*

Probab=94.97  E-value=0.023  Score=49.39  Aligned_cols=31  Identities=13%  Similarity=0.231  Sum_probs=27.4

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+|+|+|||+|.++..+++.  +.+++.+|.
T Consensus       233 ~~~~VLDlGcG~G~~~~~la~~--g~~V~gvDi  263 (381)
T 3dmg_A          233 RGRQVLDLGAGYGALTLPLARM--GAEVVGVED  263 (381)
T ss_dssp             TTCEEEEETCTTSTTHHHHHHT--TCEEEEEES
T ss_pred             CCCEEEEEeeeCCHHHHHHHHc--CCEEEEEEC
Confidence            4679999999999999999998  568888885

>3t8r_A Staphylococcus aureus CYMR; transcriptional regulator protein, dimer, sulfenic acid, UNK function; 1.70A {Staphylococcus aureus} PDB: 3t8t_A

Probab=94.84  E-value=0.021  Score=42.80  Aligned_cols=47  Identities=17%  Similarity=0.140  Sum_probs=40.2

Q ss_pred             CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      +++|+++||+++++++   ..+++++..|...|++.-...    . .+-|.+..-
T Consensus        27 ~~~s~~~IA~~~~i~~---~~l~kil~~L~~aGlv~s~rG----~-~GGy~Lar~   73 (143)
T 3t8r_A           27 GCISLKSIAEENNLSD---LYLEQLVGPLRNAGLIRSVRG----A-KGGYQLRVP   73 (143)
T ss_dssp             CCEEHHHHHHHTTCCH---HHHHHHHHHHHHTTSEEECSS----S-SSEEEESSC
T ss_pred             CCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCEEEecCC----C-CCCeeecCC
Confidence            6899999999999999   999999999999999985531    1 467887776

>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=94.82  E-value=0.0071  Score=43.31  Aligned_cols=74  Identities=12%  Similarity=0.077  Sum_probs=56.8

Q ss_pred             HHHHHHHHHHHhHHHHHHHHHhcCcchhhhcCCCCCC--HHHHHHHc-CCCCCCcccHHHHHHHHHhCCceeeecCCCCC
Q 040620           17 QAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMT--LTQIIVAL-NVHPNKTRCTQILVCLLAHSGFFVQQKDGKNE   93 (214)
Q Consensus        17 ~~~l~~~~~g~~~~~~L~~a~~lglfd~L~~~~~p~t--~~eLA~~~-g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~   93 (214)
                      ...+++++.+.|...+|..         |..  ++.+  +.||++.+ |+++   ..+.+.|+.|...|++.....    
T Consensus        17 ~~~~l~~l~~~wrl~IL~~---------L~~--g~~~~~~~eL~~~l~gis~---~~ls~~L~~Le~~GlV~r~~~----   78 (111)
T 3df8_A           17 SESVLHLLGKKYTMLIISV---------LGN--GSTRQNFNDIRSSIPGISS---TILSRRIKDLIDSGLVERRSG----   78 (111)
T ss_dssp             TSSTHHHHHSTTHHHHHHH---------HTS--SSSCBCHHHHHHTSTTCCH---HHHHHHHHHHHHTTSEEEEES----
T ss_pred             HHHHHHHHcCccHHHHHHH---------Hhc--CCCCCCHHHHHHHccCCCH---HHHHHHHHHHHHCCCEEEeec----
Confidence            3455667777776665543         343  7877  99999999 9999   999999999999999998741    


Q ss_pred             CccceeeCCCCCcccccccc
Q 040620           94 QEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        94 ~~~~~y~~t~~~~~~s~~l~  113 (214)
                      . ...|.+|+.    ++.+.
T Consensus        79 r-~~~y~LT~~----G~~l~   93 (111)
T 3df8_A           79 Q-ITTYALTEK----GMNVR   93 (111)
T ss_dssp             S-SEEEEECHH----HHHHH
T ss_pred             C-cEEEEECcc----HHHHH
Confidence            1 357888888    76664

>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=94.81  E-value=0.018  Score=50.64  Aligned_cols=36  Identities=11%  Similarity=0.230  Sum_probs=31.8

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                      .....+|+|+|||+|..+..+++..|+.+++.+|+-
T Consensus       244 ~~~g~~VLDlgaG~G~~t~~la~~~~~~~v~a~D~~  279 (429)
T 1sqg_A          244 PQNGEHILDLCAAPGGKTTHILEVAPEAQVVAVDID  279 (429)
T ss_dssp             CCTTCEEEEESCTTCHHHHHHHHHCTTCEEEEEESS
T ss_pred             CCCcCeEEEECCCchHHHHHHHHHcCCCEEEEECCC
Confidence            345679999999999999999999999899999863

>4hbl_A Transcriptional regulator, MARR family; HTH, transcription factor, DNA binding; 2.50A {Staphylococcus epidermidis}

Probab=94.80  E-value=0.017  Score=42.79  Aligned_cols=68  Identities=16%  Similarity=0.197  Sum_probs=48.2

Q ss_pred             HhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           37 IQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        37 ~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      .++.|+..|..+ +++|..+||+.+++++   ..+.++++.|...|++.......|.- ...+.+|+.    ++.+.
T Consensus        42 ~q~~iL~~l~~~-~~~~~~eLa~~l~~~~---~~vs~~l~~L~~~Glv~r~~~~~D~R-~~~~~LT~~----G~~~~  109 (149)
T 4hbl_A           42 SQYLVMLTLWEE-NPQTLNSIGRHLDLSS---NTLTPMLKRLEQSGWVKRERQQSDKR-QLIITLTDN----GQQQQ  109 (149)
T ss_dssp             HHHHHHHHHHHS-SSEEHHHHHHHHTCCH---HHHHHHHHHHHHHTSEEC----------CEEEECSH----HHHHH
T ss_pred             HHHHHHHHHHHC-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEeeCCCCCCcc-eeeeeECHH----HHHHH
Confidence            344566777766 8999999999999999   99999999999999999764211110 234777777    55553

>2yxl_A PH0851 protein, 450AA long hypothetical FMU protein; FMU-homolog, methyltransferase, structural genomics, NPPSFA; HET: SFG; 2.55A {Pyrococcus horikoshii}

Probab=94.74  E-value=0.03  Score=49.62  Aligned_cols=36  Identities=19%  Similarity=0.278  Sum_probs=31.4

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCC-CeEEEecCC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPD-TKCTVFACH  213 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dlp  213 (214)
                      .....+|+|+|||+|..+..+++..|+ .+++.+|+-
T Consensus       257 ~~~g~~VLDlgaG~G~~t~~la~~~~~~~~v~a~D~s  293 (450)
T 2yxl_A          257 PKPGETVVDLAAAPGGKTTHLAELMKNKGKIYAFDVD  293 (450)
T ss_dssp             CCTTCEEEESSCTTCHHHHHHHHHTTTCSEEEEECSC
T ss_pred             CCCcCEEEEeCCCccHHHHHHHHHcCCCCEEEEEcCC
Confidence            445679999999999999999999988 789998863

>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=94.68  E-value=0.012  Score=43.19  Aligned_cols=67  Identities=10%  Similarity=0.152  Sum_probs=50.7

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      ++.|+..|... +++|..+||+.+++++   ..+.++++.|...|++.......+.- ...+.+|+.    ++.+.
T Consensus        42 ~~~iL~~l~~~-~~~~~~~la~~l~~~~---~tvs~~l~~L~~~glv~r~~~~~d~R-~~~~~LT~~----G~~~~  108 (147)
T 1z91_A           42 QYLALLLLWEH-ETLTVKKMGEQLYLDS---GTLTPMLKRMEQQGLITRKRSEEDER-SVLISLTED----GALLK  108 (147)
T ss_dssp             HHHHHHHHHHH-SEEEHHHHHHTTTCCH---HHHHHHHHHHHHHTSEECCBCSSCTT-SBEEEECHH----HHSGG
T ss_pred             HHHHHHHHHHC-CCCCHHHHHHHHCCCc---CcHHHHHHHHHHCCCEEeccCCCCCC-eeEEEECHh----HHHHH
Confidence            34466666665 6899999999999999   99999999999999999765211111 234778888    77665

>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=94.63  E-value=0.014  Score=49.18  Aligned_cols=32  Identities=13%  Similarity=0.051  Sum_probs=26.5

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +.+..+|||||||+|.++..++++   -+++.+|+
T Consensus        80 ~~~g~~VLDlGcG~G~~s~~la~~---~~V~gvD~  111 (305)
T 2p41_A           80 VTPEGKVVDLGCGRGGWSYYCGGL---KNVREVKG  111 (305)
T ss_dssp             SCCCEEEEEETCTTSHHHHHHHTS---TTEEEEEE
T ss_pred             CCCCCEEEEEcCCCCHHHHHHHhc---CCEEEEec
Confidence            345679999999999999999987   36777776

>2f2e_A PA1607; transcription factor, helix-TRUN-helix, APC5613, structural genomics, PSI, protein structure initiative; HET: GLC; 1.85A {Pseudomonas aeruginosa} SCOP: a.4.5.69

Probab=94.60  E-value=0.017  Score=43.34  Aligned_cols=75  Identities=9%  Similarity=0.029  Sum_probs=54.8

Q ss_pred             HHHHHHHHHhHHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccce
Q 040620           19 QVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEES   98 (214)
Q Consensus        19 ~l~~~~~g~~~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~   98 (214)
                      ..++++.+.|...+|..         |..  ++++..||++.+|+++   ..+.+.|+.|...|++....... +. ...
T Consensus        16 ~~l~~l~~~w~l~IL~~---------L~~--g~~~~~eLa~~lgis~---~tls~~L~~Le~~GlI~r~~~~~-d~-~~~   79 (146)
T 2f2e_A           16 RPLDVIGDGWSMLIVRD---------AFE--GLTRFGEFQKSLGLAK---NILAARLRNLVEHGVMVAVPAES-GS-HQE   79 (146)
T ss_dssp             TTHHHHCSSSHHHHHHH---------HHT--TCCSHHHHHHHHCCCH---HHHHHHHHHHHHTTSEEEEECSS-SS-CEE
T ss_pred             HHHHHhCCchHHHHHHH---------HHh--CCCCHHHHHHHhCCCH---HHHHHHHHHHHHCCCEEEEecCC-CC-eEE
Confidence            34555555555544433         333  7899999999999999   99999999999999999875311 11 247


Q ss_pred             eeCCCCCcccccccc
Q 040620           99 ILLPPHLDFFSRISL  113 (214)
Q Consensus        99 y~~t~~~~~~s~~l~  113 (214)
                      |.+|+.    ++.+.
T Consensus        80 y~LT~~----G~~l~   90 (146)
T 2f2e_A           80 YRLTDK----GRALF   90 (146)
T ss_dssp             EEECHH----HHTTH
T ss_pred             EEECch----HHHHH
Confidence            899998    77764

>2fbi_A Probable transcriptional regulator; MARR, APC5816, structural genomic protein structure initiative; 2.10A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=94.57  E-value=0.0046  Score=45.15  Aligned_cols=47  Identities=17%  Similarity=0.158  Sum_probs=40.8

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      +..|+..|... +++|..+||+.+++++   ..+.++++.|...|++....
T Consensus        38 ~~~iL~~l~~~-~~~t~~ela~~l~~s~---~~vs~~l~~Le~~glv~r~~   84 (142)
T 2fbi_A           38 QWRVIRILRQQ-GEMESYQLANQACILR---PSMTGVLARLERDGIVRRWK   84 (142)
T ss_dssp             HHHHHHHHHHH-CSEEHHHHHHHTTCCH---HHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHHc-CCCCHHHHHHHHCCCH---hHHHHHHHHHHHCCCEEeec
Confidence            44566777765 7899999999999999   99999999999999998764

>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=94.57  E-value=0.018  Score=42.90  Aligned_cols=46  Identities=15%  Similarity=0.226  Sum_probs=40.5

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ   87 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~   87 (214)
                      +..|+..|..+ +++|..|||+++|+++   ..+++.++.|...|++...
T Consensus         7 d~~il~~L~~~-~~~s~~ela~~lg~s~---~tv~~~l~~L~~~G~i~~~   52 (144)
T 2cfx_A            7 DLNIIEELKKD-SRLSMRELGRKIKLSP---PSVTERVRQLESFGIIKQY   52 (144)
T ss_dssp             HHHHHHHHHHC-SCCCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeEEE
Confidence            34567778776 8899999999999999   9999999999999999854

>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=94.56  E-value=0.017  Score=43.16  Aligned_cols=46  Identities=13%  Similarity=0.065  Sum_probs=40.2

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ   87 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~   87 (214)
                      +..|...|..+ +++|..|||+++|+++   ..+.+.++.|...|++...
T Consensus         9 ~~~iL~~L~~~-~~~s~~ela~~lg~s~---~tv~~~l~~L~~~G~i~~~   54 (150)
T 2w25_A            9 DRILVRELAAD-GRATLSELATRAGLSV---SAVQSRVRRLESRGVVQGY   54 (150)
T ss_dssp             HHHHHHHHHHC-TTCCHHHHHHHHTSCH---HHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEE
Confidence            44567777766 7899999999999999   9999999999999999754

>2pex_A Transcriptional regulator OHRR; transcription regulator; 1.90A {Xanthomonas campestris} PDB: 2pfb_A

Probab=94.53  E-value=0.0086  Score=44.47  Aligned_cols=67  Identities=15%  Similarity=0.170  Sum_probs=49.1

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      ++.|+..|... +++|..+||+.+++++   ..+.++++.|...|++.......+.- ...+.+|+.    ++.+.
T Consensus        49 ~~~iL~~l~~~-~~~t~~ela~~l~~s~---~tvs~~l~~Le~~glv~r~~~~~d~R-~~~~~lT~~----G~~~~  115 (153)
T 2pex_A           49 QYLVMLVLWET-DERSVSEIGERLYLDS---ATLTPLLKRLQAAGLVTRTRAASDER-QVIIALTET----GRALR  115 (153)
T ss_dssp             HHHHHHHHHHS-CSEEHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEEC--------CEEEECHH----HHHGG
T ss_pred             HHHHHHHHHhC-CCcCHHHHHHHhCCCc---ccHHHHHHHHHHCCCEeecCCcccCC-eeEeeECHH----HHHHH
Confidence            34466677765 7899999999999999   99999999999999999864211100 124777777    66654

>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=94.42  E-value=0.017  Score=43.11  Aligned_cols=46  Identities=17%  Similarity=0.235  Sum_probs=40.9

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ   87 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~   87 (214)
                      +..|...|..+ +++|..+||+++|+++   ..+.+.++.|...|++...
T Consensus         5 ~~~il~~L~~~-~~~~~~ela~~lg~s~---~tv~~~l~~L~~~G~i~~~   50 (150)
T 2pn6_A            5 DLRILKILQYN-AKYSLDEIAREIRIPK---ATLSYRIKKLEKDGVIKGY   50 (150)
T ss_dssp             HHHHHHHHTTC-TTSCHHHHHHHHTSCH---HHHHHHHHHHHHTTSSCCC
T ss_pred             HHHHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCcEEEE
Confidence            45677888876 7899999999999999   9999999999999999864

>2lkp_A Transcriptional regulator, ARSR family; symmetric homodimer, NI(II) binding protein, DNA binding Pro transcription regulator; NMR {Mycobacterium tuberculosis}

Probab=94.40  E-value=0.015  Score=41.57  Aligned_cols=48  Identities=19%  Similarity=0.324  Sum_probs=41.1

Q ss_pred             HHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           36 AIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        36 a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      -.++.|+..|.+  +++|+.+||+.+++++   ..+.+.|+.|...|++....
T Consensus        32 ~~~~~il~~L~~--~~~s~~ela~~l~is~---stvsr~l~~Le~~Glv~~~~   79 (119)
T 2lkp_A           32 PSRLMILTQLRN--GPLPVTDLAEAIGMEQ---SAVSHQLRVLRNLGLVVGDR   79 (119)
T ss_dssp             HHHHHHHHHHHH--CCCCHHHHHHHHSSCH---HHHHHHHHHHHHHCSEEEEE
T ss_pred             HHHHHHHHHHHH--CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEEe
Confidence            345666777776  6899999999999999   99999999999999998664

>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=94.38  E-value=0.024  Score=47.56  Aligned_cols=32  Identities=3%  Similarity=-0.118  Sum_probs=25.4

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+|||||||.|..+..+++. ...+++++|+
T Consensus        48 ~~~~VLDlGCG~G~~l~~~~~~-~~~~v~GiD~   79 (302)
T 2vdw_A           48 NKRKVLAIDFGNGADLEKYFYG-EIALLVATDP   79 (302)
T ss_dssp             SCCEEEETTCTTTTTHHHHHHT-TCSEEEEEES
T ss_pred             CCCeEEEEecCCcHhHHHHHhc-CCCeEEEEEC
Confidence            4579999999999877776664 3468999986

>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=94.35  E-value=0.022  Score=42.67  Aligned_cols=45  Identities=13%  Similarity=0.224  Sum_probs=38.0

Q ss_pred             CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      ++ |+++||++.++++   ..|+++|..|...|++.....      .+-|.+..-
T Consensus        23 ~~-s~~~IA~~~~i~~---~~l~kIl~~L~~aGlv~s~rG------~GGy~Lar~   67 (145)
T 1xd7_A           23 KT-SSEIIADSVNTNP---VVVRRMISLLKKADILTSRAG------VPGASLKKD   67 (145)
T ss_dssp             CC-CHHHHHHHHTSCH---HHHHHHHHHHHHTTSEECCSS------SSSCEESSC
T ss_pred             CC-CHHHHHHHHCcCH---HHHHHHHHHHHHCCceEeecC------CCCceecCC
Confidence            35 9999999999999   999999999999999986641      356777666

>2fbk_A Transcriptional regulator, MARR family; winged-helix-turn-helix; 2.30A {Deinococcus radiodurans} SCOP: a.4.5.28

Probab=94.30  E-value=0.011  Score=45.37  Aligned_cols=48  Identities=13%  Similarity=0.161  Sum_probs=40.2

Q ss_pred             hcCcchhhhcCCCC--CCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           38 QLRIPDIINNSGQP--MTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        38 ~lglfd~L~~~~~p--~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      ++.|+..|...++|  +|..+||+.+++++   ..+.++++.|...|++....
T Consensus        71 ~~~iL~~L~~~~~~~~~t~~eLa~~l~is~---~tvs~~l~~Le~~GlV~r~~  120 (181)
T 2fbk_A           71 GWDLLLTLYRSAPPEGLRPTELSALAAISG---PSTSNRIVRLLEKGLIERRE  120 (181)
T ss_dssp             HHHHHHHHHHHCCSSCBCHHHHHHHCSCCS---GGGSSHHHHHHHHTSEECCC
T ss_pred             HHHHHHHHHHcCCCCCCCHHHHHHHHCCCH---HHHHHHHHHHHHCcCEEecC
Confidence            44467777765333  99999999999999   99999999999999998764

>2p5v_A Transcriptional regulator, LRP/ASNC family; NMB0573, structu genomics; 1.99A {Neisseria meningitidis} PDB: 2p6s_A 2p6t_A

Probab=94.28  E-value=0.021  Score=43.25  Aligned_cols=46  Identities=13%  Similarity=0.207  Sum_probs=40.3

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ   87 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~   87 (214)
                      +..|...|..+ +++|..|||+++|+++   ..+++.++.|...|++...
T Consensus        12 ~~~il~~L~~~-~~~s~~ela~~lg~s~---~tv~~~l~~L~~~G~i~~~   57 (162)
T 2p5v_A           12 DIKILQVLQEN-GRLTNVELSERVALSP---SPCLRRLKQLEDAGIVRQY   57 (162)
T ss_dssp             HHHHHHHHHHC-TTCCHHHHHHHHTSCH---HHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEeee
Confidence            34567777776 7899999999999999   9999999999999999854

>2i62_A Nicotinamide N-methyltransferase; structural genomics, structural genomics consortium, SGC; HET: SAH; 1.80A {Mus musculus} PDB: 2iip_A* 3rod_A*

Probab=94.27  E-value=0.005  Score=49.61  Aligned_cols=33  Identities=18%  Similarity=0.042  Sum_probs=28.1

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+..+|||||||+|.++..+++..+ .+++++|.
T Consensus        55 ~~~~~vLDlGcG~G~~~~~l~~~~~-~~v~gvD~   87 (265)
T 2i62_A           55 VKGELLIDIGSGPTIYQLLSACESF-TEIIVSDY   87 (265)
T ss_dssp             CCEEEEEEESCTTCCGGGTTGGGTE-EEEEEEES
T ss_pred             cCCCEEEEECCCccHHHHHHhhccc-CeEEEecC
Confidence            3457999999999999999998876 67888886

>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=94.24  E-value=0.021  Score=44.30  Aligned_cols=70  Identities=13%  Similarity=0.097  Sum_probs=51.7

Q ss_pred             HHhcCcchhhhcC-CCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           36 AIQLRIPDIINNS-GQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        36 a~~lglfd~L~~~-~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      ..+..|+..|... ++++|..+||+.+++++   ..+.++++.|...|++.......|.- ...+.+|+.    ++.++
T Consensus        41 ~~q~~vL~~L~~~~~~~~t~~eLa~~l~is~---~tvs~~l~~Le~~GlV~r~~~~~DrR-~~~l~LT~~----G~~~~  111 (189)
T 3nqo_A           41 SRQYMTILSILHLPEEETTLNNIARKMGTSK---QNINRLVANLEKNGYVDVIPSPHDKR-AINVKVTDL----GKKVM  111 (189)
T ss_dssp             HHHHHHHHHHHHSCGGGCCHHHHHHHHTSCH---HHHHHHHHHHHHTTSEEEEECSSCSS-CEEEEECHH----HHHHH
T ss_pred             HHHHHHHHHHHhccCCCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEeccCCCCCC-eeEEEECHH----HHHHH
Confidence            3445566777642 27899999999999999   99999999999999999865311111 234777777    76665

>3sso_A Methyltransferase; macrolide, natural product, rossman fold; HET: SAH; 1.90A {Micromonospora griseorubida} PDB: 3ssn_A* 3ssm_A*

Probab=94.18  E-value=0.03  Score=49.32  Aligned_cols=33  Identities=12%  Similarity=0.142  Sum_probs=27.3

Q ss_pred             CCCcEEeecCC------chHHHHHHHHH-CCCCeEEEecC
Q 040620          180 GLKPLVDVGGS------TGTMARAIATA-FPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG------~G~~~~~l~~~-~P~l~~~v~Dl  212 (214)
                      +..+|||||||      +|..+..++++ +|+.+++.+|+
T Consensus       216 ~~~rVLDIGCG~~~~~~TGG~Sl~la~~~fP~a~V~GVDi  255 (419)
T 3sso_A          216 QQVRVLEIGVGGYKHPEWGGGSLRMWKSFFPRGQIYGLDI  255 (419)
T ss_dssp             SCCEEEEECCSCTTCSSCCCHHHHHHHHHCTTCEEEEEES
T ss_pred             CCCEEEEEecCCCcCCCCCHHHHHHHHHhCCCCEEEEEEC
Confidence            46799999999      66667777765 69999999997

>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=94.13  E-value=0.013  Score=41.42  Aligned_cols=45  Identities=24%  Similarity=0.318  Sum_probs=37.6

Q ss_pred             CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620           40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ   87 (214)
Q Consensus        40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~   87 (214)
                      .|+..+...|.++|..+||+.+|+++   ..+++.|..|...|++...
T Consensus        22 ~Il~~l~~~g~~~s~~eLa~~lgvs~---~tV~~~L~~L~~~GlV~~~   66 (110)
T 1q1h_A           22 DVLRILLDKGTEMTDEEIANQLNIKV---NDVRKKLNLLEEQGFVSYR   66 (110)
T ss_dssp             HHHHHHHHHCSCBCHHHHHHTTTSCH---HHHHHHHHHHHHHTSCEEE
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEE
Confidence            35555533334899999999999999   9999999999999999876

>3hrs_A Metalloregulator SCAR; DTXR/MNTR family member, transcription; 2.70A {Streptococcus gordonii} PDB: 3hrt_A 3hru_A

Probab=94.12  E-value=0.025  Score=45.19  Aligned_cols=51  Identities=16%  Similarity=0.198  Sum_probs=46.2

Q ss_pred             CCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           49 GQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        49 ~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      +++++..+||+.+++++   ..+.+.++.|...|++....       ...+.+|+.    ++.+.
T Consensus        18 ~~~~~~~~lA~~l~vs~---~tvs~~l~~Le~~GlV~r~~-------~~~i~LT~~----G~~~~   68 (214)
T 3hrs_A           18 HNKITNKEIAQLMQVSP---PAVTEMMKKLLAEELLIKDK-------KAGYLLTDL----GLKLV   68 (214)
T ss_dssp             CSCCCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEET-------TTEEEECHH----HHHHH
T ss_pred             CCCcCHHHHHHHHCCCh---hHHHHHHHHHHHCCCEEEec-------CCCeEECHH----HHHHH
Confidence            38999999999999999   99999999999999999987       578999999    77764

>2x4h_A Hypothetical protein SSO2273; transcription; 2.30A {Sulfolobus solfataricus}

Probab=94.11  E-value=0.033  Score=40.73  Aligned_cols=44  Identities=14%  Similarity=0.289  Sum_probs=40.4

Q ss_pred             CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      +++|..+||+.+++++   ..+.+.++.|...|++....        ..|.+|+.
T Consensus        30 ~~~s~~ela~~l~is~---~tv~~~l~~Le~~Gli~r~~--------~~~~Lt~~   73 (139)
T 2x4h_A           30 EGAKINRIAKDLKIAP---SSVFEEVSHLEEKGLVKKKE--------DGVWITNN   73 (139)
T ss_dssp             SCBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEET--------TEEEECHH
T ss_pred             CCcCHHHHHHHhCCCh---HHHHHHHHHHHHCCCEEecC--------CeEEEChh
Confidence            7899999999999999   99999999999999999873        57888888

>2zkz_A Transcriptional repressor PAGR; protein-DNA, HTH motif, dimer, DN binding, transcription regulation; 2.00A {Bacillus anthracis}

Probab=94.11  E-value=0.011  Score=41.23  Aligned_cols=59  Identities=15%  Similarity=0.257  Sum_probs=42.4

Q ss_pred             HhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           37 IQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        37 ~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      .++.|+..|..+ +++++.|||+.+|+++   ..+.+.|+.|... ++.....   |. ...|++++.
T Consensus        28 ~Rl~IL~~l~~~-~~~~~~ela~~l~is~---stvs~hL~~L~~~-lv~~~~~---gr-~~~y~l~~~   86 (99)
T 2zkz_A           28 MRLKIVNELYKH-KALNVTQIIQILKLPQ---STVSQHLCKMRGK-VLKRNRQ---GL-EIYYSINNP   86 (99)
T ss_dssp             HHHHHHHHHHHH-SCEEHHHHHHHHTCCH---HHHHHHHHHHBTT-TBEEEEE---TT-EEEEECCCH
T ss_pred             HHHHHHHHHHHC-CCcCHHHHHHHHCcCH---HHHHHHHHHHHHH-hhhheEe---Cc-EEEEEEChH
Confidence            344455333323 7899999999999999   9999999999999 8876541   11 234666654

>2r6z_A UPF0341 protein in RSP 3' region; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 1.80A {Neisseria gonorrhoeae}

Probab=94.05  E-value=0.044  Score=45.02  Aligned_cols=31  Identities=16%  Similarity=0.148  Sum_probs=27.0

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+|||+|||.|.+++.+++.  ..+++.+|+
T Consensus        83 ~~~~VLDlgcG~G~~a~~lA~~--g~~V~~vD~  113 (258)
T 2r6z_A           83 AHPTVWDATAGLGRDSFVLASL--GLTVTAFEQ  113 (258)
T ss_dssp             GCCCEEETTCTTCHHHHHHHHT--TCCEEEEEC
T ss_pred             CcCeEEEeeCccCHHHHHHHHh--CCEEEEEEC
Confidence            4579999999999999999996  568888886

>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=94.04  E-value=0.024  Score=39.22  Aligned_cols=36  Identities=17%  Similarity=0.252  Sum_probs=34.4

Q ss_pred             CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      +++|..|||+.+|+++   ..+.+.|+.|...|++....
T Consensus        35 ~~~t~~ela~~l~is~---~tv~~~l~~L~~~g~v~~~~   70 (109)
T 2d1h_A           35 KPITSEELADIFKLSK---TTVENSLKKLIELGLVVRTK   70 (109)
T ss_dssp             SCEEHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeEeec
Confidence            7899999999999999   99999999999999999875

>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=94.04  E-value=0.041  Score=48.52  Aligned_cols=33  Identities=12%  Similarity=0.088  Sum_probs=28.1

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+..+|+|+|||+|.++..+++.  ..+++.+|.
T Consensus       284 ~~~~~~VLDlgcG~G~~~~~la~~--~~~V~gvD~  316 (433)
T 1uwv_A          284 VQPEDRVLDLFCGMGNFTLPLATQ--AASVVGVEG  316 (433)
T ss_dssp             CCTTCEEEEESCTTTTTHHHHHTT--SSEEEEEES
T ss_pred             CCCCCEEEECCCCCCHHHHHHHhh--CCEEEEEeC
Confidence            345679999999999999999988  678888886

>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=94.03  E-value=0.014  Score=40.28  Aligned_cols=48  Identities=10%  Similarity=0.064  Sum_probs=39.3

Q ss_pred             CCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccc---eeeCCCCCccccccc
Q 040620           51 PMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEE---SILLPPHLDFFSRIS  112 (214)
Q Consensus        51 p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~---~y~~t~~~~~~s~~l  112 (214)
                      ++|..+||+.+++++   ..+.++++.|...|++....       ++   .|.+|+.    ++.+
T Consensus        30 ~~t~~eLa~~l~i~~---~tvs~~l~~Le~~Glv~~~~-------d~R~~~v~LT~~----G~~~   80 (95)
T 2qvo_A           30 DVYIQYIASKVNSPH---SYVWLIIKKFEEAKMVECEL-------EGRTKIIRLTDK----GQKI   80 (95)
T ss_dssp             CEEHHHHHHHSSSCH---HHHHHHHHHHHHTTSEEEEE-------ETTEEEEEECHH----HHHH
T ss_pred             CcCHHHHHHHHCcCH---HHHHHHHHHHHHCcCccCCC-------CCCeEEEEEChh----HHHH
Confidence            499999999999999   99999999999999994332       23   4778877    5554

>3f3x_A Transcriptional regulator, MARR family, putative; DNA binding protein, DNA-binding, transcription regulation; 1.90A {Sulfolobus solfataricus}

Probab=93.99  E-value=0.088  Score=38.39  Aligned_cols=67  Identities=15%  Similarity=0.203  Sum_probs=49.5

Q ss_pred             HhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           37 IQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        37 ~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      .++.|+..|... ++ |..+||+.+++++   ..+.+.++.|...|++.......|.- .-.+.+|+.    ++.+.
T Consensus        38 ~~~~iL~~l~~~-~~-~~~~la~~l~~~~---~tvs~~l~~Le~~Glv~r~~~~~D~R-~~~~~LT~~----G~~~~  104 (144)
T 3f3x_A           38 LDFSILKATSEE-PR-SMVYLANRYFVTQ---SAITAAVDKLEAKGLVRRIRDSKDRR-IVIVEITPK----GRQVL  104 (144)
T ss_dssp             HHHHHHHHHHHS-CE-EHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEEEETTEEE-EEEEEECHH----HHHHH
T ss_pred             HHHHHHHHHHHC-CC-CHHHHHHHHCCCh---hHHHHHHHHHHHCCCEEeccCCCCCc-eEEEEECHH----HHHHH
Confidence            345577778776 55 9999999999999   99999999999999999765210000 114777877    66654

>2dbb_A Putative HTH-type transcriptional regulator PH006; ASNC family, helix-turn-helix (HTH) domain, structural genom NPPSFA; 2.00A {Pyrococcus horikoshii}

Probab=93.97  E-value=0.024  Score=42.35  Aligned_cols=46  Identities=13%  Similarity=0.194  Sum_probs=40.7

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ   87 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~   87 (214)
                      +..|+..|..+ +++|..+||+++|+++   ..+++.++.|...|++...
T Consensus        11 d~~il~~L~~~-~~~s~~ela~~lg~s~---~tv~~~l~~L~~~G~i~~~   56 (151)
T 2dbb_A           11 DMQLVKILSEN-SRLTYRELADILNTTR---QRIARRIDKLKKLGIIRKF   56 (151)
T ss_dssp             HHHHHHHHHHC-TTCCHHHHHHHTTSCH---HHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEE
Confidence            44577788876 8899999999999999   9999999999999999854

>3u2r_A Regulatory protein MARR; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, helix-turn-helix; 2.20A {Planctomyces limnophilus}

Probab=93.93  E-value=0.036  Score=41.80  Aligned_cols=68  Identities=16%  Similarity=0.138  Sum_probs=45.9

Q ss_pred             hcCcchhhhcC-CCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           38 QLRIPDIINNS-GQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        38 ~lglfd~L~~~-~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      ++.|+..|... ++++|..+||+.+++++   ..+.++++.|...|++.......|.- .-.+.+|+.    ++.++
T Consensus        48 q~~vL~~l~~~~~~~~t~~eLa~~l~~~~---~tvs~~l~~Le~~Glv~r~~~~~DrR-~~~l~LT~~----G~~~~  116 (168)
T 3u2r_A           48 QYNTLRLLRSVHPEGMATLQIADRLISRA---PDITRLIDRLDDRGLVLRTRKPENRR-VVEVALTDA----GLKLL  116 (168)
T ss_dssp             HHHHHHHHHHHTTSCEEHHHHHHHC---C---THHHHHHHHHHHTTSEEEEEETTEEE-EEEEEECHH----HHHHH
T ss_pred             HHHHHHHHHhcCCCCcCHHHHHHHHCCCh---hhHHHHHHHHHHCCCEeecCCCCCCC-eeEeEECHH----HHHHH
Confidence            34466667664 26999999999999999   99999999999999999764210000 113667776    55554

>2gs9_A Hypothetical protein TT1324; methyl transferase, structural genomics, NPPSFA, national PR protein structural and functional analyses; HET: SAH; 2.60A {Thermus thermophilus}

Probab=93.91  E-value=0.034  Score=43.18  Aligned_cols=28  Identities=21%  Similarity=0.201  Sum_probs=23.5

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCC-eEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDT-KCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l-~~~v~Dl  212 (214)
                      +..+|+|||||+|.++..+     .. +++.+|.
T Consensus        36 ~~~~vLdiG~G~G~~~~~l-----~~~~v~~vD~   64 (211)
T 2gs9_A           36 PGESLLEVGAGTGYWLRRL-----PYPQKVGVEP   64 (211)
T ss_dssp             CCSEEEEETCTTCHHHHHC-----CCSEEEEECC
T ss_pred             CCCeEEEECCCCCHhHHhC-----CCCeEEEEeC
Confidence            5679999999999999887     44 7888875

>2h09_A Transcriptional regulator MNTR; transcription regulator, diphtheria toxin, manganese transport, structural genomics, NPPSFA; 2.10A {Escherichia coli}

Probab=93.88  E-value=0.018  Score=43.16  Aligned_cols=56  Identities=14%  Similarity=0.144  Sum_probs=45.8

Q ss_pred             hhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           43 DIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        43 d~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      ..|... +++|..+||+.+++++   ..+++.++.|...|++....       ...+.+|+.    +..+.
T Consensus        47 ~~l~~~-~~~~~~~la~~l~vs~---~tvs~~l~~Le~~Glv~r~~-------~~~~~lT~~----g~~~~  102 (155)
T 2h09_A           47 DLIREV-GEARQVDMAARLGVSQ---PTVAKMLKRLATMGLIEMIP-------WRGVFLTAE----GEKLA  102 (155)
T ss_dssp             HHHHHH-SCCCHHHHHHHHTSCH---HHHHHHHHHHHHTTCEEEET-------TTEEEECHH----HHHHH
T ss_pred             HHHHhC-CCcCHHHHHHHhCcCH---HHHHHHHHHHHHCCCEEEec-------CCceEEChh----HHHHH
Confidence            355544 6799999999999999   99999999999999998875       456778877    65543

>3q87_B N6 adenine specific DNA methylase; SAM-methyltransferase, methyltransferase, methylation, trans activator-transferase complex; HET: SAM; 2.00A {Encephalitozoon cuniculi}

Probab=93.81  E-value=0.023  Score=43.20  Aligned_cols=21  Identities=29%  Similarity=0.561  Sum_probs=18.6

Q ss_pred             CCcEEeecCCchHHHHHHHHH
Q 040620          181 LKPLVDVGGSTGTMARAIATA  201 (214)
Q Consensus       181 ~~~vvDVGGG~G~~~~~l~~~  201 (214)
                      ..+|+|||||+|.++..++++
T Consensus        24 ~~~vLD~GcG~G~~~~~l~~~   44 (170)
T 3q87_B           24 MKIVLDLGTSTGVITEQLRKR   44 (170)
T ss_dssp             SCEEEEETCTTCHHHHHHTTT
T ss_pred             CCeEEEeccCccHHHHHHHhc
Confidence            469999999999999988764

>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=93.81  E-value=0.026  Score=38.92  Aligned_cols=62  Identities=8%  Similarity=0.155  Sum_probs=47.7

Q ss_pred             CcchhhhcCCCCCCHHHH----HHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           40 RIPDIINNSGQPMTLTQI----IVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        40 glfd~L~~~~~p~t~~eL----A~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      .|+..|..+ +++|..+|    |+.+++++   ..+.++++.|...|++......   . ...|.+|+.    ++.++
T Consensus        12 ~iL~~l~~~-~~~~~~el~~~la~~l~is~---~tvs~~l~~Le~~gli~r~~~~---r-~~~~~LT~~----G~~~~   77 (99)
T 1tbx_A           12 IVLAYLYDN-EGIATYDLYKKVNAEFPMST---ATFYDAKKFLIQEGFVKERQER---G-EKRLYLTEK----GKLFA   77 (99)
T ss_dssp             HHHHHHTTC-TTCBHHHHHHHHHTTSCCCH---HHHHHHHHHHHHTTSEEEEEET---T-EEEEEECHH----HHHHH
T ss_pred             HHHHHHHHc-CCcCHHHHHHHHHHHcCCCH---HHHHHHHHHHHHCCCEEEEecC---C-ceEEEECHH----HHHHH
Confidence            345556655 78999999    99999999   9999999999999999876420   0 345777777    66554

>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=93.80  E-value=0.025  Score=42.38  Aligned_cols=46  Identities=11%  Similarity=0.216  Sum_probs=40.5

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ   87 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~   87 (214)
                      +..|...|..+ +++|..|||+++|+++   ..+++.++.|...|++...
T Consensus        10 d~~il~~L~~~-~~~s~~ela~~lg~s~---~tv~~~l~~L~~~G~i~~~   55 (152)
T 2cg4_A           10 DRGILEALMGN-ARTAYAELAKQFGVSP---ETIHVRVEKMKQAGIITGA   55 (152)
T ss_dssp             HHHHHHHHHHC-TTSCHHHHHHHHTSCH---HHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHcCCcceE
Confidence            34567778776 8999999999999999   9999999999999999864

>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=93.79  E-value=0.021  Score=38.18  Aligned_cols=46  Identities=20%  Similarity=0.346  Sum_probs=38.3

Q ss_pred             cCcchhhhcCCCCCCHHHHHHHcC----CCCCCcccHHHHHHHHHhCCceeeec
Q 040620           39 LRIPDIINNSGQPMTLTQIIVALN----VHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        39 lglfd~L~~~~~p~t~~eLA~~~g----~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      ..|+..|... +++|+.||++.++    +++   ..+.++|+.|...|++....
T Consensus        12 ~~vL~~L~~~-~~~t~~ei~~~l~~~~~~s~---~Tv~~~l~rL~~kGlv~r~~   61 (82)
T 1p6r_A           12 LEVMKVIWKH-SSINTNEVIKELSKTSTWSP---KTIQTMLLRLIKKGALNHHK   61 (82)
T ss_dssp             HHHHHHHHTS-SSEEHHHHHHHHHHHSCCCH---HHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHcC-CCCCHHHHHHHHhhcCCccH---HHHHHHHHHHHHCCCeEEEe
Confidence            4455666654 7999999999997    566   89999999999999999875

>3i4p_A Transcriptional regulator, ASNC family; PSI, structural genom protein structure initiative, midwest center for structural genomics; 2.30A {Agrobacterium tumefaciens str}

Probab=93.77  E-value=0.027  Score=42.81  Aligned_cols=47  Identities=6%  Similarity=0.181  Sum_probs=41.7

Q ss_pred             HhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620           37 IQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ   87 (214)
Q Consensus        37 ~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~   87 (214)
                      ++..|.++|..+ +++|..+||+++|+++   ..+++-++.|...|++..-
T Consensus         4 ~d~~il~~L~~~-~~~s~~~la~~lg~s~---~tv~~rl~~L~~~g~i~~~   50 (162)
T 3i4p_A            4 LDRKILRILQED-STLAVADLAKKVGLST---TPCWRRIQKMEEDGVIRRR   50 (162)
T ss_dssp             HHHHHHHHHTTC-SCSCHHHHHHHHTCCH---HHHHHHHHHHHHTTSSCCC
T ss_pred             HHHHHHHHHHHC-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeeec
Confidence            345678888887 8999999999999999   9999999999999999843

>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=93.74  E-value=0.022  Score=42.65  Aligned_cols=46  Identities=17%  Similarity=0.165  Sum_probs=40.3

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ   87 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~   87 (214)
                      +..|...|..+ +++|..+||+++|+++   ..+++.++.|...|++...
T Consensus         9 ~~~il~~L~~~-~~~s~~ela~~lg~s~---~tv~~~l~~L~~~G~i~~~   54 (151)
T 2cyy_A            9 DKKIIKILQND-GKAPLREISKITGLAE---STIHERIRKLRESGVIKKF   54 (151)
T ss_dssp             HHHHHHHHHHC-TTCCHHHHHHHHCSCH---HHHHHHHHHHHHHTSSCCC
T ss_pred             HHHHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeEEE
Confidence            34567778776 7999999999999999   9999999999999999764

>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=93.70  E-value=0.048  Score=37.72  Aligned_cols=46  Identities=13%  Similarity=0.100  Sum_probs=38.5

Q ss_pred             CcchhhhcCC-CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           40 RIPDIINNSG-QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        40 glfd~L~~~~-~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      .|+..|.+.+ .+++..+||++++++.   ..+.++|+.|...|++....
T Consensus        24 ~Vl~~I~~~g~~gi~qkeLa~~~~l~~---~tvt~iLk~LE~kglIkr~~   70 (91)
T 2dk5_A           24 LVYQIIEDAGNKGIWSRDVRYKSNLPL---TEINKILKNLESKKLIKAVK   70 (91)
T ss_dssp             HHHHHHHHHCTTCEEHHHHHHHTTCCH---HHHHHHHHHHHHTTSEEEEC
T ss_pred             HHHHHHHHcCCCCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEEec
Confidence            3556666531 5899999999999999   99999999999999999554

>2ia0_A Putative HTH-type transcriptional regulator PF086; ASNC, PSI, structural genomics, southeast collaboratory for structural genomics; 2.37A {Pyrococcus furiosus}

Probab=93.69  E-value=0.032  Score=42.94  Aligned_cols=46  Identities=11%  Similarity=0.185  Sum_probs=40.0

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ   87 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~   87 (214)
                      +..|...|..+ +++|..|||+++|+++   ..+++.++.|...|++...
T Consensus        19 d~~IL~~L~~~-~~~s~~eLA~~lglS~---~tv~~~l~~L~~~G~I~~~   64 (171)
T 2ia0_A           19 DRNILRLLKKD-ARLTISELSEQLKKPE---STIHFRIKKLQERGVIERY   64 (171)
T ss_dssp             HHHHHHHHHHC-TTCCHHHHHHHHTSCH---HHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEee
Confidence            34567777776 7899999999999999   9999999999999999754

>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=93.61  E-value=0.077  Score=46.10  Aligned_cols=34  Identities=29%  Similarity=0.068  Sum_probs=26.3

Q ss_pred             HHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHC
Q 040620          167 ASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAF  202 (214)
Q Consensus       167 ~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~  202 (214)
                      +..++....  +.+..+|+|.+||+|.+++..+..-
T Consensus       184 Aa~ll~~~~--~~~~~~vlDp~CGSGt~lieaa~~~  217 (385)
T 3ldu_A          184 AAGLIYLTP--WKAGRVLVDPMCGSGTILIEAAMIG  217 (385)
T ss_dssp             HHHHHHTSC--CCTTSCEEETTCTTCHHHHHHHHHH
T ss_pred             HHHHHHhhC--CCCCCeEEEcCCCCCHHHHHHHHHH
Confidence            444555555  5567899999999999999988764

>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=93.59  E-value=0.051  Score=36.23  Aligned_cols=43  Identities=9%  Similarity=-0.008  Sum_probs=37.6

Q ss_pred             chhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           42 PDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        42 fd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      ++.|.++ +..|+.+||.++|++.   +.++|.|-.|...|.+...+
T Consensus        21 i~~L~~~-~~~Ta~~IAkkLg~sK---~~vNr~LY~L~kkG~V~~~~   63 (75)
T 1sfu_A           21 VLSLNTN-DYTTAISLSNRLKINK---KKINQQLYKLQKEDTVKMVP   63 (75)
T ss_dssp             HHTSCTT-CEECHHHHHHHTTCCH---HHHHHHHHHHHHTTSEEEEC
T ss_pred             HHhCCCC-cchHHHHHHHHHCCCH---HHHHHHHHHHHHCCCEecCC
Confidence            3467763 5599999999999999   99999999999999998875

>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=93.59  E-value=0.056  Score=46.03  Aligned_cols=31  Identities=19%  Similarity=0.112  Sum_probs=26.8

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +..+|||+|||+|.+++.+++..+  +++.+|+
T Consensus       153 ~~~~VLDlgcGtG~~sl~la~~ga--~V~~VD~  183 (332)
T 2igt_A          153 RPLKVLNLFGYTGVASLVAAAAGA--EVTHVDA  183 (332)
T ss_dssp             SCCEEEEETCTTCHHHHHHHHTTC--EEEEECS
T ss_pred             CCCcEEEcccccCHHHHHHHHcCC--EEEEEEC
Confidence            356999999999999999999744  8898886

>2vn2_A DNAD, chromosome replication initiation protein; DNA replication, primosome; 2.3A {Geobacillus kaustophilus HTA426}

Probab=93.54  E-value=0.028  Score=41.26  Aligned_cols=51  Identities=16%  Similarity=0.141  Sum_probs=36.7

Q ss_pred             CCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCC-CCccceeeCCCC
Q 040620           51 PMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKN-EQEEESILLPPH  104 (214)
Q Consensus        51 p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~-~~~~~~y~~t~~  104 (214)
                      ..|..+||+++++++   ..+.+.++.|...|++.......+ |.....|.++|+
T Consensus        51 ~ps~~~LA~~l~~s~---~~V~~~l~~Le~kGlI~~~~~~~~~g~~~~~Ydl~pl  102 (128)
T 2vn2_A           51 FPTPAELAERMTVSA---AECMEMVRRLLQKGMIAIEEHTDEQGIRNEKYTLEPL  102 (128)
T ss_dssp             SCCHHHHHHTSSSCH---HHHHHHHHHHHHTTSSEECC----------CEECHHH
T ss_pred             CCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEEeEECCCCcEEEEEehHHH
Confidence            379999999999999   999999999999999998643211 112234555555

>3k0b_A Predicted N6-adenine-specific DNA methylase; methylase,PF01170, putative RNA methylase, PSI,MCSG, structu genomics; 1.50A {Listeria monocytogenes str}

Probab=93.52  E-value=0.083  Score=46.08  Aligned_cols=36  Identities=19%  Similarity=0.118  Sum_probs=27.4

Q ss_pred             HHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCC
Q 040620          167 ASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPD  204 (214)
Q Consensus       167 ~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~  204 (214)
                      +..++....  +.+...|+|.+||+|++++..+....+
T Consensus       190 Aa~ll~l~~--~~~~~~vlDp~CGSGt~~ieaa~~~~~  225 (393)
T 3k0b_A          190 AAALVLLTS--WHPDRPFYDPVCGSGTIPIEAALIGQN  225 (393)
T ss_dssp             HHHHHHHSC--CCTTSCEEETTCTTSHHHHHHHHHHTT
T ss_pred             HHHHHHHhC--CCCCCeEEEcCCCCCHHHHHHHHHhcC
Confidence            444555555  556789999999999999988876554

>4g6q_A Putative uncharacterized protein; structural genomics, PSI-biology, protein structure initiati midwest center for structural genomics, MCSG; 2.08A {Kribbella flavida}

Probab=93.44  E-value=0.059  Score=41.93  Aligned_cols=66  Identities=15%  Similarity=0.233  Sum_probs=48.9

Q ss_pred             HHHHhcCcchhhhcCCCCCCHHHHHHHcC-CCCCCcccHHHHHHHHHhCCceeeecCC-CCCCccceeeCCCC
Q 040620           34 KRAIQLRIPDIINNSGQPMTLTQIIVALN-VHPNKTRCTQILVCLLAHSGFFVQQKDG-KNEQEEESILLPPH  104 (214)
Q Consensus        34 ~~a~~lglfd~L~~~~~p~t~~eLA~~~g-~~~~~~~~l~rlLr~L~~~g~l~~~~~~-~~~~~~~~y~~t~~  104 (214)
                      .-=.++.|+.+|.+  +|+|+.+||+.++ ++.   ..+.+-|+.|...|++...... ..+..+..|++++.
T Consensus        21 a~P~Rl~il~~L~~--~~~~~~~l~~~l~~~~~---~~~s~Hl~~L~~aglv~~~~e~~~~g~~er~y~~~~~   88 (182)
T 4g6q_A           21 HHPLRWRITQLLIG--RSLTTRELAELLPDVAT---TTLYRQVGILVKAGVLMVTAEHQVRGAVERTYTLNTQ   88 (182)
T ss_dssp             TSHHHHHHHHHTTT--SCEEHHHHHHHCTTBCH---HHHHHHHHHHHHHTSEEEEEEEEETTEEEEEEEECTT
T ss_pred             CCHHHHHHHHHHHh--CCCCHHHHHHHhcCCCH---HHHHHHHHHHHHCCCeEEEEeecccCcceeEEEeccc
Confidence            33356777888876  8999999999996 887   7899999999999999855421 01111346888777

>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=93.42  E-value=0.063  Score=46.69  Aligned_cols=32  Identities=25%  Similarity=0.261  Sum_probs=24.4

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +.++|||||||+|.+++..+++-. -+++.+|.
T Consensus        83 ~~k~VLDvG~GtGiLs~~Aa~aGA-~~V~ave~  114 (376)
T 4hc4_A           83 RGKTVLDVGAGTGILSIFCAQAGA-RRVYAVEA  114 (376)
T ss_dssp             TTCEEEEETCTTSHHHHHHHHTTC-SEEEEEEC
T ss_pred             CCCEEEEeCCCccHHHHHHHHhCC-CEEEEEeC
Confidence            367999999999999987776532 36777764

>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=93.39  E-value=0.026  Score=40.93  Aligned_cols=65  Identities=20%  Similarity=0.310  Sum_probs=47.8

Q ss_pred             cchhhhcC-CCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           41 IPDIINNS-GQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        41 lfd~L~~~-~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      ++..|... ++++|..+||+.+++++   ..+.++++.|...|++.......|.- ...+.+|+.    ++.+.
T Consensus        42 vL~~l~~~~~~~~t~~eLa~~l~~~~---~tvs~~l~~Le~~Glv~r~~~~~D~R-~~~i~LT~~----G~~~~  107 (127)
T 2frh_A           42 VLTYISENKEKEYYLKDIINHLNYKQ---PQVVKAVKILSQEDYFDKKRNEHDER-TVLILVNAQ----QRKKI  107 (127)
T ss_dssp             HHHHHHHTCCSEEEHHHHHHHSSSHH---HHHHHHHHHHHHTTSSCCBCCSSSSC-CCEEECCSH----HHHHH
T ss_pred             HHHHHHhccCCCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEecCCCCCCC-eeEEEECHH----HHHHH
Confidence            45555543 26799999999999999   99999999999999999864211111 234678887    66654

>2fe3_A Peroxide operon regulator; oxidative stress regulator, DNA binding protein; 1.75A {Bacillus subtilis} PDB: 3f8n_A 2rgv_A*

Probab=93.38  E-value=0.087  Score=39.33  Aligned_cols=59  Identities=17%  Similarity=0.091  Sum_probs=45.2

Q ss_pred             cCcchhhhcCCCCCCHHHHHHHc-----CCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCC
Q 040620           39 LRIPDIINNSGQPMTLTQIIVAL-----NVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPP  103 (214)
Q Consensus        39 lglfd~L~~~~~p~t~~eLA~~~-----g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~  103 (214)
                      .-|++.|...++++|++||.+.+     +++.   ..++|.|+.|+..|++.+...  +++ ..+|..+.
T Consensus        25 ~~Il~~L~~~~~~~sa~ei~~~l~~~~~~is~---aTVYR~L~~L~e~Glv~~~~~--~~~-~~~Y~~~~   88 (145)
T 2fe3_A           25 HAILEYLVNSMAHPTADDIYKALEGKFPNMSV---ATVYNNLRVFRESGLVKELTY--GDA-SSRFDFVT   88 (145)
T ss_dssp             HHHHHHHHHCSSCCCHHHHHHHHGGGCTTCCH---HHHHHHHHHHHHTTSEEEECC--TTS-CCEEEECC
T ss_pred             HHHHHHHHhCCCCCCHHHHHHHHHHhCCCCCh---hhHHHHHHHHHHCCCEEEEee--CCC-ceEEECCC
Confidence            33677787655899999999999     6777   899999999999999998753  111 34676543

>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=93.38  E-value=0.12  Score=42.98  Aligned_cols=33  Identities=12%  Similarity=0.395  Sum_probs=25.8

Q ss_pred             CCCcEEeecCCc---hHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGST---GTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~---G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +..+|||||||.   |.......+..|+.+++.+|.
T Consensus        78 g~~q~LDLGcG~pT~~~~~~la~~~~P~arVv~VD~  113 (277)
T 3giw_A           78 GIRQFLDIGTGIPTSPNLHEIAQSVAPESRVVYVDN  113 (277)
T ss_dssp             CCCEEEEESCCSCCSSCHHHHHHHHCTTCEEEEEEC
T ss_pred             CCCEEEEeCCCCCcccHHHHHHHHHCCCCEEEEEeC
Confidence            578999999997   344444455789999999986

>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=93.36  E-value=0.028  Score=41.33  Aligned_cols=45  Identities=18%  Similarity=0.200  Sum_probs=39.0

Q ss_pred             cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620           39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ   87 (214)
Q Consensus        39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~   87 (214)
                      ..|...|..+ +++|..+||+++|+++   ..+++.++.|...|++...
T Consensus         7 ~~il~~L~~~-~~~~~~ela~~lg~s~---~tv~~~l~~L~~~G~i~~~   51 (141)
T 1i1g_A            7 KIILEILEKD-ARTPFTEIAKKLGISE---TAVRKRVKALEEKGIIEGY   51 (141)
T ss_dssp             HHHHHHHHHC-TTCCHHHHHHHHTSCH---HHHHHHHHHHHHHTSSCCC
T ss_pred             HHHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEecc
Confidence            4456677665 7899999999999999   9999999999999999754

>2f8l_A Hypothetical protein LMO1582; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE SAM; 2.20A {Listeria monocytogenes} SCOP: c.66.1.45

Probab=93.33  E-value=0.032  Score=47.40  Aligned_cols=33  Identities=6%  Similarity=0.060  Sum_probs=28.7

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCC-----CeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPD-----TKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~-----l~~~v~Dl  212 (214)
                      ...+|+|+|||+|.++..+++..|.     .+++++|+
T Consensus       130 ~~~~VlDp~cGsG~~l~~~~~~~~~~~~~~~~v~GiDi  167 (344)
T 2f8l_A          130 KNVSILDPACGTANLLTTVINQLELKGDVDVHASGVDV  167 (344)
T ss_dssp             SEEEEEETTCTTSHHHHHHHHHHHTTSSCEEEEEEEES
T ss_pred             CCCEEEeCCCCccHHHHHHHHHHHHhcCCCceEEEEEC
Confidence            3579999999999999999999876     67888886

>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=93.22  E-value=0.03  Score=40.89  Aligned_cols=44  Identities=18%  Similarity=0.327  Sum_probs=37.5

Q ss_pred             cchhhh-cCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           41 IPDIIN-NSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        41 lfd~L~-~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      ++..|. .. +|+|..+||+.+|+++   ..+.++++.|...|++....
T Consensus        31 il~~L~~~~-~~~t~~ela~~l~~~~---stvs~~l~~L~~~G~v~r~~   75 (152)
T 1ku9_A           31 VYAILYLSD-KPLTISDIMEELKISK---GNVSMSLKKLEELGFVRKVW   75 (152)
T ss_dssp             HHHHHHHCS-SCEEHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEEC
T ss_pred             HHHHHHHcC-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEEe
Confidence            344553 23 7899999999999999   99999999999999999864

>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=93.19  E-value=0.066  Score=47.86  Aligned_cols=35  Identities=11%  Similarity=0.099  Sum_probs=30.3

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCC-CeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPD-TKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dl  212 (214)
                      .....+|||+|||+|..+..+++..++ .+++.+|+
T Consensus        99 ~~~g~~VLDlgaGpG~kt~~LA~~~~~~g~V~AvDi  134 (464)
T 3m6w_A           99 PKPGERVLDLAAAPGGKTTHLAARMGGKGLLLANEV  134 (464)
T ss_dssp             CCTTCEEEESSCTTCHHHHHHHHHTTTCSEEEEECS
T ss_pred             cCCCCEEEEEcCCcCHHHHHHHHhCCCCCEEEEEEC
Confidence            345679999999999999999999876 68888886

>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=93.18  E-value=0.018  Score=40.35  Aligned_cols=60  Identities=8%  Similarity=0.111  Sum_probs=48.5

Q ss_pred             hcCcchhhhcCCCCCCHHHHHH-HcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           38 QLRIPDIINNSGQPMTLTQIIV-ALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~-~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      ++.|+-.|..+ ++.|+.+||+ ..+++.   ..+.|-++.|...|++..++       ++ +.+|+.    ++.++
T Consensus        18 QfsiL~~L~~~-~~~t~~~Lae~~l~~dr---stvsrnl~~L~r~GlVe~~~-------~D-l~LT~~----G~~~l   78 (95)
T 1bja_A           18 TATILITIAKK-DFITAAEVREVHPDLGN---AVVNSNIGVLIKKGLVEKSG-------DG-LIITGE----AQDII   78 (95)
T ss_dssp             HHHHHHHHHHS-TTBCHHHHHHTCTTSCH---HHHHHHHHHHHTTTSEEEET-------TE-EEECHH----HHHHH
T ss_pred             HHHHHHHHHHC-CCCCHHHHHHHHhcccH---HHHHHHHHHHHHCCCeecCC-------CC-eeeCHh----HHHHH
Confidence            34455667777 6999999999 999998   89999999999999999443       34 888888    66654

>2k4b_A Transcriptional regulator; DNA binding protein, winged helix; NMR {Lactococcus lactis subsp}

Probab=93.16  E-value=0.021  Score=40.20  Aligned_cols=47  Identities=13%  Similarity=0.152  Sum_probs=39.1

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCC----CCCCcccHHHHHHHHHhCCceeeec
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNV----HPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~----~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      +..|+..|-+. +++|+.||+++++.    ++   ..+.++|+-|...|++....
T Consensus        37 e~~VL~~L~~~-~~~t~~eL~~~l~~~~~~s~---sTVt~~L~rLe~KGlV~R~~   87 (99)
T 2k4b_A           37 ELIVMRVIWSL-GEARVDEIYAQIPQELEWSL---ATVKTLLGRLVKKEMLSTEK   87 (99)
T ss_dssp             CSHHHHHHHHH-SCEEHHHHHHTCCGGGCCCH---HHHHHHHHHHHHTTSCEEEE
T ss_pred             HHHHHHHHHhC-CCCCHHHHHHHHhcccCCCH---hhHHHHHHHHHHCCCEEEEe
Confidence            34466777665 79999999999985    45   78999999999999999876

>2o03_A Probable zinc uptake regulation protein FURB; DNA-binding, helix-turn-helix, zinc binding, GE regulation; 2.70A {Mycobacterium tuberculosis}

Probab=93.04  E-value=0.041  Score=40.40  Aligned_cols=58  Identities=12%  Similarity=0.079  Sum_probs=44.9

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHc-----CCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeC
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVAL-----NVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILL  101 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~-----g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~  101 (214)
                      +.-|++.|.+.++++|++||.+.+     +++.   ..++|.|+.|+..|++.+...  +++ ..+|..
T Consensus        13 R~~Il~~l~~~~~~~sa~ei~~~l~~~~~~is~---~TVYR~L~~L~e~Glv~~~~~--~~~-~~~y~~   75 (131)
T 2o03_A           13 RAAISTLLETLDDFRSAQELHDELRRRGENIGL---TTVYRTLQSMASSGLVDTLHT--DTG-ESVYRR   75 (131)
T ss_dssp             HHHHHHHHHHCCSCEEHHHHHHHHHHTTCCCCH---HHHHHHHHHHHTTTSEEEEEC--TTS-CEEEEE
T ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHHHhCCCCCH---hhHHHHHHHHHHCCCEEEEEe--CCC-ceEEEe
Confidence            445677776655799999999999     7777   899999999999999998753  111 356764

>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=93.04  E-value=0.054  Score=44.98  Aligned_cols=32  Identities=22%  Similarity=0.111  Sum_probs=26.2

Q ss_pred             CCcEEeecCCchH----HHHHHHHHCC----CCeEEEecC
Q 040620          181 LKPLVDVGGSTGT----MARAIATAFP----DTKCTVFAC  212 (214)
Q Consensus       181 ~~~vvDVGGG~G~----~~~~l~~~~P----~l~~~v~Dl  212 (214)
                      ..+|+|+|||+|.    +++.+++..|    +.+++..|+
T Consensus       106 ~~rIld~GCgTGee~ysiAi~L~e~~~~~~~~~~I~atDi  145 (274)
T 1af7_A          106 EYRVWSAAASTGEEPYSIAITLADALGMAPGRWKVFASDI  145 (274)
T ss_dssp             CEEEEESCCTTTHHHHHHHHHHHHHHCSCTTSEEEEEEES
T ss_pred             CcEEEEeeccCChhHHHHHHHHHHhcccCCCCeEEEEEEC
Confidence            4689999999998    6777888766    468888886

>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=92.96  E-value=0.047  Score=42.76  Aligned_cols=42  Identities=19%  Similarity=0.455  Sum_probs=35.9

Q ss_pred             hhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           44 IINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        44 ~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      .+.+.|.|.|..|||+++|+++   ..+++.|+.|...|++....
T Consensus        17 ~~~~~g~~~s~~eia~~lgl~~---~tv~~~l~~Le~~G~i~~~~   58 (196)
T 3k2z_A           17 FIEKNGYPPSVREIARRFRITP---RGALLHLIALEKKGYIERKN   58 (196)
T ss_dssp             HHHHHSSCCCHHHHHHHHTSCH---HHHHHHHHHHHHTTSEECC-
T ss_pred             HHHHhCCCCCHHHHHHHcCCCc---HHHHHHHHHHHHCCCEEecC
Confidence            3444446899999999999998   88999999999999998774

>2xvc_A ESCRT-III, SSO0910; cell cycle, cell division, cytokinesis, winged-helix; 2.15A {Sulfolobus solfataricus}

Probab=92.95  E-value=0.04  Score=34.61  Aligned_cols=46  Identities=17%  Similarity=0.221  Sum_probs=41.0

Q ss_pred             cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620           39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ   87 (214)
Q Consensus        39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~   87 (214)
                      -.|++.|..+||-+.++..|++.|+++   +.+..+||-|...|++.-.
T Consensus        13 ~~lL~yIr~sGGildI~~~a~kygV~k---deV~~~LrrLe~KGLI~le   58 (59)
T 2xvc_A           13 RELLDYIVNNGGFLDIEHFSKVYGVEK---QEVVKLLEALKNKGLIAVE   58 (59)
T ss_dssp             HHHHHHHHHTTSEEEHHHHHHHHCCCH---HHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHcCCEEeHHHHHHHhCCCH---HHHHHHHHHHHHCCCeecc
Confidence            346788888888899999999999999   9999999999999998743

>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=92.88  E-value=0.075  Score=41.35  Aligned_cols=56  Identities=20%  Similarity=0.255  Sum_probs=45.6

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCc-eeeecCCCCCCccceeeCCCC
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGF-FVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~-l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      ...|..+|.++++++|..|||+++|+++   +.++|-++.|...|+ +...        .+.|.+.+.
T Consensus        23 ~~~Il~~L~~~~~~~s~~eLa~~l~vS~---~Ti~rdi~~L~~~G~~I~~~--------~~Gy~l~~~   79 (187)
T 1j5y_A           23 LKSIVRILERSKEPVSGAQLAEELSVSR---QVIVQDIAYLRSLGYNIVAT--------PRGYVLAGG   79 (187)
T ss_dssp             HHHHHHHHHHCSSCBCHHHHHHHHTSCH---HHHHHHHHHHHHHTCCCEEE--------TTEEECCTT
T ss_pred             HHHHHHHHHHcCCCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeEEEE--------CCEEEECCc
Confidence            3457778876446799999999999999   999999999999999 6554        356777766

>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=92.88  E-value=0.067  Score=42.04  Aligned_cols=49  Identities=16%  Similarity=0.247  Sum_probs=42.8

Q ss_pred             HHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620           34 KRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ   87 (214)
Q Consensus        34 ~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~   87 (214)
                      ....+..|+..|. + +++|..|||+.+|+++   ..+++.++.|...|++...
T Consensus        18 ~d~~~~~IL~~L~-~-~~~s~~eLA~~lglS~---stv~~~l~~Le~~GlI~~~   66 (192)
T 1uly_A           18 LEDTRRKILKLLR-N-KEMTISQLSEILGKTP---QTIYHHIEKLKEAGLVEVK   66 (192)
T ss_dssp             HSHHHHHHHHHHT-T-CCBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHH-c-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEE
Confidence            3445666788888 4 7999999999999999   9999999999999999876

>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=92.82  E-value=0.085  Score=41.34  Aligned_cols=21  Identities=24%  Similarity=0.261  Sum_probs=18.3

Q ss_pred             CCcEEeecCCchHHHHHHHHH
Q 040620          181 LKPLVDVGGSTGTMARAIATA  201 (214)
Q Consensus       181 ~~~vvDVGGG~G~~~~~l~~~  201 (214)
                      ..+|||||||+|.++..+++.
T Consensus        48 ~~~vLDiG~G~G~~~~~l~~~   68 (219)
T 1vlm_A           48 EGRGVEIGVGTGRFAVPLKIK   68 (219)
T ss_dssp             SSCEEEETCTTSTTHHHHTCC
T ss_pred             CCcEEEeCCCCCHHHHHHHHH
Confidence            679999999999999887654

>3ldg_A Putative uncharacterized protein SMU.472; YPSC, methyltransferase, transferase; HET: SAH; 1.96A {Streptococcus mutans}

Probab=92.80  E-value=0.12  Score=44.88  Aligned_cols=36  Identities=28%  Similarity=0.157  Sum_probs=27.2

Q ss_pred             HHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCC
Q 040620          167 ASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPD  204 (214)
Q Consensus       167 ~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~  204 (214)
                      +..++....  +.+...|+|.+||+|+++++.+....+
T Consensus       183 Aaall~l~~--~~~~~~llDp~CGSGt~lIEAa~~a~~  218 (384)
T 3ldg_A          183 AAAIILLSN--WFPDKPFVDPTCGSGTFCIEAAMIGMN  218 (384)
T ss_dssp             HHHHHHHTT--CCTTSCEEETTCTTSHHHHHHHHHHTT
T ss_pred             HHHHHHHhC--CCCCCeEEEeCCcCCHHHHHHHHHhcC
Confidence            444555555  556789999999999999988876554

>2a14_A Indolethylamine N-methyltransferase; SGC,INMT, structural genomics, structural genomics consortium; HET: SAH; 1.70A {Homo sapiens} SCOP: c.66.1.15

Probab=92.67  E-value=0.021  Score=46.53  Aligned_cols=32  Identities=16%  Similarity=0.097  Sum_probs=23.5

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCC-eEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDT-KCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l-~~~v~Dl  212 (214)
                      .+..+|||||||+|.++..+++.  .. +++..|+
T Consensus        54 ~~g~~vLDiGCG~G~~~~~~~~~--~~~~v~g~D~   86 (263)
T 2a14_A           54 LQGDTLIDIGSGPTIYQVLAACD--SFQDITLSDF   86 (263)
T ss_dssp             CCEEEEEESSCTTCCGGGTTGGG--TEEEEEEEES
T ss_pred             CCCceEEEeCCCccHHHHHHHHh--hhcceeeccc
Confidence            34579999999999887765544  33 5787775

>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=92.64  E-value=0.1  Score=45.21  Aligned_cols=32  Identities=19%  Similarity=0.109  Sum_probs=29.7

Q ss_pred             CCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          181 LKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       181 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+|||+|||+|..++.++++.|..+++..|+
T Consensus        48 ~~~VLDl~aGtG~~~l~~a~~~~~~~V~avDi   79 (378)
T 2dul_A           48 PKIVLDALSATGIRGIRFALETPAEEVWLNDI   79 (378)
T ss_dssp             CSEEEESSCTTSHHHHHHHHHSSCSEEEEEES
T ss_pred             CCEEEECCCchhHHHHHHHHhCCCCeEEEEEC
Confidence            57999999999999999999999889998886

>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=92.48  E-value=0.15  Score=41.85  Aligned_cols=29  Identities=17%  Similarity=0.234  Sum_probs=26.2

Q ss_pred             CcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          182 KPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       182 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+|+|+|||.|..+..++++  ..+++.+|+
T Consensus        90 ~~VLDl~~G~G~dal~lA~~--g~~V~~vE~  118 (258)
T 2oyr_A           90 PDVVDATAGLGRDAFVLASV--GCRVRMLER  118 (258)
T ss_dssp             CCEEETTCTTCHHHHHHHHH--TCCEEEEEC
T ss_pred             CEEEEcCCcCCHHHHHHHHc--CCEEEEEEC
Confidence            79999999999999999998  567888886

>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=92.44  E-value=0.11  Score=43.41  Aligned_cols=42  Identities=21%  Similarity=0.120  Sum_probs=31.7

Q ss_pred             HHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          169 VLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       169 ~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+.+.+.  +....+|||+|||+|.++.-.++..|-.+++.+|+
T Consensus        81 ei~eK~~--Lk~~~~VLDLGaAPGGWsQvAa~~~gv~sV~Gvdv  122 (282)
T 3gcz_A           81 WMEERGY--VKPTGIVVDLGCGRGGWSYYAASLKNVKKVMAFTL  122 (282)
T ss_dssp             HHHHTTS--CCCCEEEEEETCTTCHHHHHHHTSTTEEEEEEECC
T ss_pred             HHHHhcC--CCCCCEEEEeCCCCCHHHHHHHHhcCCCeeeeEEe
Confidence            3445553  55667999999999999998888777666666665

>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=92.24  E-value=0.077  Score=41.91  Aligned_cols=66  Identities=12%  Similarity=0.058  Sum_probs=48.3

Q ss_pred             cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      ..|+..|..+ +++|..+||+.+++++   ..+.++++.|...|++.......|.- .-.+.+|+.    ++.++
T Consensus        51 ~~iL~~L~~~-~~~t~~eLa~~l~i~~---stvs~~l~~Le~~GlV~r~~~~~DrR-~~~l~LT~~----G~~~~  116 (207)
T 2fxa_A           51 HHILWIAYQL-NGASISEIAKFGVMHV---STAFNFSKKLEERGYLRFSKRLNDKR-NTYVQLTEE----GTEVF  116 (207)
T ss_dssp             HHHHHHHHHH-TSEEHHHHHHHTTCCH---HHHHHHHHHHHHHTSEEEECC-------CEEEECHH----HHHHH
T ss_pred             HHHHHHHHHC-CCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEEecCCCCCc-eEEEEECHH----HHHHH
Confidence            3456667665 7899999999999999   99999999999999999875211110 124667777    65554

>2qlz_A Transcription factor PF0095; 2.50A {Pyrococcus furiosus} PDB: 2quf_A

Probab=92.14  E-value=0.019  Score=46.66  Aligned_cols=51  Identities=6%  Similarity=0.105  Sum_probs=43.3

Q ss_pred             HHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceee
Q 040620           31 LSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQ   86 (214)
Q Consensus        31 ~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~   86 (214)
                      .+|.--.++.|+..|..  +|+|+.+||+.+|+++   ..+.+.|+.|...|++..
T Consensus         7 kaL~~~~R~~IL~~L~~--g~~s~~ELa~~lglS~---stVs~hL~~Le~aGLV~~   57 (232)
T 2qlz_A            7 YILGNKVRRDLLSHLTC--MECYFSLLSSKVSVSS---TAVAKHLKIMEREGVLQS   57 (232)
T ss_dssp             HHHTSHHHHHHHHHHTT--TTTCSSSSCTTCCCCH---HHHHHHHHHHHHTTSEEE
T ss_pred             HHhCCHHHHHHHHHHHh--CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEE
Confidence            34444455667777875  8999999999999999   999999999999999998

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

Probab=92.05  E-value=0.12  Score=44.68  Aligned_cols=32  Identities=22%  Similarity=0.030  Sum_probs=27.7

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +..+|+|+|||+|.++..+++. +..+++.+|+
T Consensus       217 ~~~~VLDl~~G~G~~~~~la~~-g~~~v~~vD~  248 (396)
T 2as0_A          217 PGDRVLDVFTYTGGFAIHAAIA-GADEVIGIDK  248 (396)
T ss_dssp             TTCEEEETTCTTTHHHHHHHHT-TCSEEEEEES
T ss_pred             CCCeEEEecCCCCHHHHHHHHC-CCCEEEEEeC
Confidence            5679999999999999999987 4557888886

>3mwm_A ZUR, putative metal uptake regulation protein; FUR, regulatory metal, graded transcription regulation, transcription; 2.40A {Streptomyces coelicolor}

Probab=92.03  E-value=0.13  Score=38.17  Aligned_cols=60  Identities=12%  Similarity=-0.002  Sum_probs=45.8

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHc-----CCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCC
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVAL-----NVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPP  103 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~-----g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~  103 (214)
                      +.-|++.|.++++++|++||.+.+     +++.   .-++|.|+.|+..|++.+...  +++ ..+|....
T Consensus        16 R~~Il~~L~~~~~h~sa~eI~~~l~~~~~~is~---aTVYR~L~~L~e~Glv~~~~~--~~g-~~~Y~~~~   80 (139)
T 3mwm_A           16 RAAVSAALQEVEEFRSAQELHDMLKHKGDAVGL---TTVYRTLQSLADAGEVDVLRT--AEG-ESVYRRCS   80 (139)
T ss_dssp             HHHHHHHHTTCSSCEEHHHHHHHHHHTTCCCCH---HHHHHHHHHHHHTTSSEEEEC--TTS-CEEEECCS
T ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHHHhCCCCCH---HHHHHHHHHHHHCCCEEEEEc--CCC-ceEEEECC
Confidence            444677777655799999999988     4666   899999999999999998752  111 35787654

>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=91.97  E-value=0.094  Score=46.27  Aligned_cols=43  Identities=12%  Similarity=0.056  Sum_probs=31.2

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHC-------------CCCeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAF-------------PDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-------------P~l~~~v~Dl  212 (214)
                      ..+++...  .....+|+|.|||+|.++..+++..             +..+++++|+
T Consensus       161 ~~mv~~l~--~~~~~~VlDpacGsG~fl~~~~~~l~~~~~~~~~~~~~~~~~i~G~Ei  216 (445)
T 2okc_A          161 QAMVDCIN--PQMGETVCDPACGTGGFLLTAYDYMKGQSASKEKRDFLRDKALHGVDN  216 (445)
T ss_dssp             HHHHHHHC--CCTTCCEEETTCTTCHHHHHHHHHHHTCC-CCHHHHHHHHTTEEEEES
T ss_pred             HHHHHHhC--CCCCCEEeccCCCcchHHHHHHHHHHHhcCCHHHHHhhcCeEEEEEeC
Confidence            33444443  3345699999999999999988764             4567888876

>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=91.82  E-value=0.1  Score=43.50  Aligned_cols=33  Identities=21%  Similarity=0.164  Sum_probs=28.2

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ....+|||+|||+|.+++.++++ +..+++.+|+
T Consensus       124 ~~g~~VlD~~aG~G~~~i~~a~~-g~~~V~avD~  156 (278)
T 3k6r_A          124 KPDELVVDMFAGIGHLSLPIAVY-GKAKVIAIEK  156 (278)
T ss_dssp             CTTCEEEETTCTTTTTTHHHHHH-TCCEEEEECC
T ss_pred             CCCCEEEEecCcCcHHHHHHHHh-cCCeEEEEEC
Confidence            35789999999999999999987 5568888886

>1v4r_A Transcriptional repressor; helix-turn-helix, winged-helix, gene regulation; NMR {Streptomyces} SCOP: a.4.5.6

Probab=91.74  E-value=0.16  Score=35.20  Aligned_cols=54  Identities=11%  Similarity=0.238  Sum_probs=42.3

Q ss_pred             HHHHHHHhcCcch-hhhcCCCCC-CHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           31 LSLKRAIQLRIPD-IINNSGQPM-TLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        31 ~~L~~a~~lglfd-~L~~~~~p~-t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      ..++-.++..|.+ .+.. |..+ |..+||+.+|++.   ..+++-|+.|...|++....
T Consensus        14 ~~l~~~i~~~I~~~~l~~-g~~lps~~eLa~~~~vSr---~tvr~al~~L~~~Gli~~~~   69 (102)
T 1v4r_A           14 ADVATHFRTLIKSGELAP-GDTLPSVADIRAQFGVAA---KTVSRALAVLKSEGLVSSRG   69 (102)
T ss_dssp             HHHHHHHHHHTTTTSCCT-TSBCCCHHHHHHHSSSCT---THHHHHTTTTTTSSCCEEET
T ss_pred             HHHHHHHHHHHHhCCCCC-cCCCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEeC
Confidence            3444555556665 4444 2566 9999999999999   99999999999999998775

>3m4x_A NOL1/NOP2/SUN family protein; mtase domain, PUA domain, RRM motif, transferase; 2.28A {Enterococcus faecium}

Probab=91.70  E-value=0.11  Score=46.40  Aligned_cols=35  Identities=11%  Similarity=0.110  Sum_probs=29.7

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCC-CeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPD-TKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dl  212 (214)
                      .....+|||+|||+|..+..+++..++ .+++.+|+
T Consensus       103 ~~~g~~VLDlcaGpGgkt~~lA~~~~~~g~V~AvDi  138 (456)
T 3m4x_A          103 AKPGEKVLDLCAAPGGKSTQLAAQMKGKGLLVTNEI  138 (456)
T ss_dssp             CCTTCEEEESSCTTCHHHHHHHHHHTTCSEEEEECS
T ss_pred             CCCCCEEEEECCCcCHHHHHHHHHcCCCCEEEEEeC
Confidence            345679999999999999999998765 67888886

>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=91.66  E-value=0.073  Score=42.20  Aligned_cols=65  Identities=11%  Similarity=0.203  Sum_probs=46.8

Q ss_pred             HHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCC-CCCccceeeCCCC
Q 040620           35 RAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGK-NEQEEESILLPPH  104 (214)
Q Consensus        35 ~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~-~~~~~~~y~~t~~  104 (214)
                      --.++.|+..|..  +|+|+.+||+.+|+++   ..+.+.|+.|...|++....... .+.-.-.|.+++.
T Consensus        14 ~~~rl~IL~~L~~--~~~s~~eLa~~l~is~---stvs~hLk~Le~~GLV~~~~~~~~~g~~~~~Y~Lt~~   79 (202)
T 2p4w_A           14 NETRRRILFLLTK--RPYFVSELSRELGVGQ---KAVLEHLRILEEAGLIESRVEKIPRGRPRKYYMIKKG   79 (202)
T ss_dssp             SHHHHHHHHHHHH--SCEEHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEEECCBTTBCCCEEEEECTT
T ss_pred             CHHHHHHHHHHHh--CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCceEEEeeccCCCCceEEEEEChH
Confidence            3344455556654  8999999999999999   99999999999999999764210 0011334666665

>4dmg_A Putative uncharacterized protein TTHA1493; rRNA, methyltransferase, S-adenosyl-methionine, 23S ribosoma transferase; HET: SAM; 1.70A {Thermus thermophilus}

Probab=91.54  E-value=0.13  Score=44.92  Aligned_cols=31  Identities=16%  Similarity=-0.021  Sum_probs=26.5

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +..+|||+|||+|.+++.+++.-  .+++.+|+
T Consensus       214 ~g~~VLDlg~GtG~~sl~~a~~g--a~V~avDi  244 (393)
T 4dmg_A          214 PGERVLDVYSYVGGFALRAARKG--AYALAVDK  244 (393)
T ss_dssp             TTCEEEEESCTTTHHHHHHHHTT--CEEEEEES
T ss_pred             CCCeEEEcccchhHHHHHHHHcC--CeEEEEEC
Confidence            36799999999999999999974  44888886

>4b8x_A SCO5413, possible MARR-transcriptional regulator; winged helix motif; HET: CME; 1.25A {Streptomyces coelicolor}

Probab=91.47  E-value=0.038  Score=41.08  Aligned_cols=51  Identities=18%  Similarity=0.243  Sum_probs=39.4

Q ss_pred             CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      +++|..+||+.+++++   ..+.++++-|...|++......+|.- .-.+.+|+.
T Consensus        50 ~~~t~~eLa~~l~~~~---~tvs~~v~~Le~~Glv~r~~~~~DrR-~~~l~LT~~  100 (147)
T 4b8x_A           50 GELPMSKIGERLMVHP---TSVTNTVDRLVRSGLVAKRPNPNDGR-GTLATITDK  100 (147)
T ss_dssp             GEEEHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEEECC-----CEEEEECHH
T ss_pred             CCcCHHHHHHHHCCCH---HHHHHHHHHHHhCCCEEEeecCCcCc-eeEEEECHH
Confidence            7899999999999999   99999999999999999775311110 123666666

>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=91.46  E-value=0.15  Score=34.01  Aligned_cols=36  Identities=17%  Similarity=0.160  Sum_probs=34.2

Q ss_pred             CCCCHHHHHHHcCC-CCCCcccHHHHHHHHHhCCceeeec
Q 040620           50 QPMTLTQIIVALNV-HPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        50 ~p~t~~eLA~~~g~-~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      +.+++.++|+.+++ ..   |+++.++..|.++|++.+..
T Consensus        29 ~~i~l~~aa~~L~v~~k---RRiYDI~NVLe~igli~K~~   65 (76)
T 1cf7_A           29 GVLDLKLAADTLAVRQK---RRIYDITNVLEGIGLIEKKS   65 (76)
T ss_dssp             TEEEHHHHHHHTTTCCT---HHHHHHHHHHHHHTSEEEEE
T ss_pred             CcCcHHHHHHHhCCccc---eehhhHHHHHhHhcceeecC
Confidence            78999999999999 88   99999999999999999986

>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=91.45  E-value=0.19  Score=43.68  Aligned_cols=35  Identities=23%  Similarity=0.222  Sum_probs=28.0

Q ss_pred             CCCcEEeecCCchHHHHHH--------HHHC-------CCCeEEEecCCC
Q 040620          180 GLKPLVDVGGSTGTMARAI--------ATAF-------PDTKCTVFACHL  214 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l--------~~~~-------P~l~~~v~Dlp~  214 (214)
                      +.-+|+|+|||+|..+..+        .+++       |.+++..=|||.
T Consensus        52 ~~~~IaDlGCssG~Nt~~~v~~ii~~i~~~~~~~~~~~pe~~v~~nDLp~  101 (374)
T 3b5i_A           52 PPFTAVDLGCSSGANTVHIIDFIVKHISKRFDAAGIDPPEFTAFFSDLPS  101 (374)
T ss_dssp             CCEEEEEETCCSSHHHHHHHHHHHHHHHHHHHHTTCCCCCEEEEEEECTT
T ss_pred             CceEEEecCCCCChhHHHHHHHHHHHHHHHHhhcCCCCCceeEEecCCCc
Confidence            3568999999999887765        3344       889999999984

>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=91.43  E-value=0.086  Score=45.45  Aligned_cols=70  Identities=17%  Similarity=0.267  Sum_probs=49.2

Q ss_pred             HHHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCC--ccceeeCCCC
Q 040620           30 SLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQ--EEESILLPPH  104 (214)
Q Consensus        30 ~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~--~~~~y~~t~~  104 (214)
                      ..+++...+..|+++|. + +++|..|||+++|+++   ..+.++++-|...|++.+.+......  -...|+.++.
T Consensus        14 ~~~~~~~~~~~il~~l~-~-~~~sr~~la~~~gls~---~tv~~~v~~L~~~gli~~~~~~~~~~GR~~~~l~~~~~   85 (380)
T 2hoe_A           14 PKSVRAENISRILKRIM-K-SPVSRVELAEELGLTK---TTVGEIAKIFLEKGIVVEEKDSPKGVGRPTKSLKISPN   85 (380)
T ss_dssp             --------CCCSHHHHH-H-SCBCHHHHHHHHTCCH---HHHHHHHHHHHHHTSEEEEECCC----CCCEEEEECGG
T ss_pred             chhHHHHHHHHHHHHHH-c-CCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEeecCCCCCCCCCceEEEEccC
Confidence            45677778888999999 6 9999999999999999   99999999999999999875321110  0223666666

>1mzb_A Ferric uptake regulation protein; ferric uptake regulator, iron, DTXR, gene regulation; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.42

Probab=91.41  E-value=0.1  Score=38.43  Aligned_cols=57  Identities=14%  Similarity=0.249  Sum_probs=43.8

Q ss_pred             cCcchhhhcCC-CCCCHHHHHHHc-----CCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeC
Q 040620           39 LRIPDIINNSG-QPMTLTQIIVAL-----NVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILL  101 (214)
Q Consensus        39 lglfd~L~~~~-~p~t~~eLA~~~-----g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~  101 (214)
                      .-|++.|.+++ +++|++||.+.+     +++.   ..++|.|+.|+..|++.+...  +++ ..+|..
T Consensus        21 ~~Il~~L~~~~~~~~sa~ei~~~l~~~~~~is~---aTVYR~L~~L~e~Glv~~~~~--~~~-~~~Y~~   83 (136)
T 1mzb_A           21 VKILQMLDSAEQRHMSAEDVYKALMEAGEDVGL---ATVYRVLTQFEAAGLVVRHNF--DGG-HAVFEL   83 (136)
T ss_dssp             HHHHHHHHCC-CCSBCHHHHHHHHHHTTCCCCH---HHHHHHHHHHHHHTSEEEECS--SSS-SCEEEE
T ss_pred             HHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCH---HHHHHHHHHHHHCCcEEEEEe--CCC-ceEEEe
Confidence            33677887665 789999999998     6777   899999999999999998752  111 356875

>2xig_A Ferric uptake regulation protein; hpfur, transcription, homeostasis; HET: CIT; 1.85A {Helicobacter pylori}

Probab=91.38  E-value=0.12  Score=38.84  Aligned_cols=59  Identities=10%  Similarity=0.190  Sum_probs=45.2

Q ss_pred             HhcCcchhhhcCCCCCCHHHHHHHc-----CCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeC
Q 040620           37 IQLRIPDIINNSGQPMTLTQIIVAL-----NVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILL  101 (214)
Q Consensus        37 ~~lglfd~L~~~~~p~t~~eLA~~~-----g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~  101 (214)
                      -+.-|++.|..+++++|++||.+.+     ++++   .-++|.|+.|+..|++.+...  +++ ..+|..
T Consensus        28 qR~~IL~~l~~~~~~~sa~ei~~~l~~~~~~is~---aTVYR~L~~L~e~Glv~~~~~--~~~-~~~Y~~   91 (150)
T 2xig_A           28 QREEVVSVLYRSGTHLSPEEITHSIRQKDKNTSI---SSVYRILNFLEKENFISVLET--SKS-GRRYEI   91 (150)
T ss_dssp             HHHHHHHHHHHCSSCBCHHHHHHHHHHHSTTCCH---HHHHHHHHHHHHTTSEEEEEE--TTT-EEEEEE
T ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHHHHhCCCCCH---hhHHHHHHHHHHCCcEEEEEe--CCC-ceEEEe
Confidence            3344778887655799999999998     6777   899999999999999997652  111 346775

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

Probab=91.31  E-value=0.17  Score=44.63  Aligned_cols=32  Identities=16%  Similarity=0.158  Sum_probs=26.9

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+..+|+|+|||+|.++..+++.  ..+++.+|.
T Consensus       289 ~~~~~VLDlgcG~G~~sl~la~~--~~~V~gvD~  320 (425)
T 2jjq_A          289 VEGEKILDMYSGVGTFGIYLAKR--GFNVKGFDS  320 (425)
T ss_dssp             CCSSEEEEETCTTTHHHHHHHHT--TCEEEEEES
T ss_pred             CCCCEEEEeeccchHHHHHHHHc--CCEEEEEEC
Confidence            34679999999999999999987  457888875

>2v79_A DNA replication protein DNAD; primosome, DNA-binding protein; HET: DNA; 2.00A {Bacillus subtilis}

Probab=91.21  E-value=0.061  Score=39.95  Aligned_cols=52  Identities=15%  Similarity=0.128  Sum_probs=39.4

Q ss_pred             CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCC-CCCCccceeeCCCC
Q 040620           50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDG-KNEQEEESILLPPH  104 (214)
Q Consensus        50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~-~~~~~~~~y~~t~~  104 (214)
                      ...|.++||+++|+++   +.+.++++.|...|++...... .+|.....|.++|+
T Consensus        50 ~~ps~~~LA~~~~~s~---~~v~~~L~~L~~KGlI~i~~~~d~~g~~~~~ydL~pL  102 (135)
T 2v79_A           50 YFPTPNQLQEGMSISV---EECTNRLRMFIQKGFLFIEECEDQNGIKFEKYSLQPL  102 (135)
T ss_dssp             CSCCHHHHHTTSSSCH---HHHHHHHHHHHHHTSCEEEEEECTTCCEEEEEECHHH
T ss_pred             CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEEeEecCCCceEEEeeHHHH
Confidence            4579999999999999   9999999999999999974311 11212345666666

>2frx_A Hypothetical protein YEBU; rossmann-type S-adenosylmethionine-dependent methyltransfera domain; 2.90A {Escherichia coli}

Probab=91.06  E-value=0.22  Score=44.59  Aligned_cols=33  Identities=12%  Similarity=0.206  Sum_probs=29.0

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCC-CCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFP-DTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl  212 (214)
                      ...+|||+|||+|..+..+++..+ ..+++.+|+
T Consensus       117 ~g~~VLDl~aGpG~kt~~lA~~~~~~g~V~avDi  150 (479)
T 2frx_A          117 APQRVMDVAAAPGSKTTQISARMNNEGAILANEF  150 (479)
T ss_dssp             CCSEEEESSCTTSHHHHHHHHHTTTCSEEEEECS
T ss_pred             CCCEEEEeCCCCCHHHHHHHHhCCCCCEEEEEEC
Confidence            567999999999999999999976 478888886

>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=91.03  E-value=0.19  Score=41.80  Aligned_cols=34  Identities=18%  Similarity=0.103  Sum_probs=25.9

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEec
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFA  211 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~D  211 (214)
                      +....+|||+|||+|.++.-++++.|-.+++.+|
T Consensus        72 l~~~~~VLDLGaAPGGWSQvAa~~~~~~~v~g~d  105 (277)
T 3evf_A           72 VKLEGRVIDLGCGRGGWCYYAAAQKEVSGVKGFT  105 (277)
T ss_dssp             SCCCEEEEEETCTTCHHHHHHHTSTTEEEEEEEC
T ss_pred             CCCCCEEEEecCCCCHHHHHHHHhcCCCcceeEE
Confidence            5566799999999999999888876654444333

>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=91.00  E-value=0.13  Score=43.70  Aligned_cols=31  Identities=16%  Similarity=0.082  Sum_probs=26.5

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+..+|+|+|||+|.+++. ++  +..+++.+|+
T Consensus       194 ~~~~~VLDlg~G~G~~~l~-a~--~~~~V~~vD~  224 (336)
T 2yx1_A          194 SLNDVVVDMFAGVGPFSIA-CK--NAKKIYAIDI  224 (336)
T ss_dssp             CTTCEEEETTCTTSHHHHH-TT--TSSEEEEEES
T ss_pred             CCCCEEEEccCccCHHHHh-cc--CCCEEEEEEC
Confidence            3567999999999999999 77  5778998886

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

Probab=91.00  E-value=0.16  Score=43.97  Aligned_cols=32  Identities=13%  Similarity=-0.003  Sum_probs=27.3

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +..+|+|+|||+|.++..+++.. ..+++.+|+
T Consensus       220 ~~~~VLDl~cG~G~~sl~la~~g-~~~V~~vD~  251 (396)
T 3c0k_A          220 ENKRVLNCFSYTGGFAVSALMGG-CSQVVSVDT  251 (396)
T ss_dssp             TTCEEEEESCTTCSHHHHHHHTT-CSEEEEEES
T ss_pred             CCCeEEEeeccCCHHHHHHHHCC-CCEEEEEEC
Confidence            46799999999999999999874 457888886

>4fx0_A Probable transcriptional repressor protein; helix-turn-helix, DNA binding, transcription regulator; 2.70A {Mycobacterium tuberculosis} PDB: 4fx4_A*

Probab=90.76  E-value=0.13  Score=38.14  Aligned_cols=35  Identities=9%  Similarity=0.164  Sum_probs=29.2

Q ss_pred             CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620           50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ   87 (214)
Q Consensus        50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~   87 (214)
                      +++|..+||+.+++++   ..+.++++.|...|++...
T Consensus        51 ~~~t~~eLa~~l~~~~---~tvsr~v~~Le~~glVr~~   85 (148)
T 4fx0_A           51 IDLTMSELAARIGVER---TTLTRNLEVMRRDGLVRVM   85 (148)
T ss_dssp             ---CHHHHHHHHTCCH---HHHHHHHHHHHHTTSBC--
T ss_pred             CCcCHHHHHHHHCCCh---hhHHHHHHHHHHCCCEEee
Confidence            5699999999999999   9999999999999999554

>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=90.69  E-value=0.23  Score=41.94  Aligned_cols=55  Identities=15%  Similarity=0.092  Sum_probs=45.5

Q ss_pred             CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      .|..+|.+. +++|.++||+++++++   +.++|-++.|...|+..+...      ...|.+.+.
T Consensus         9 ~Il~~L~~~-~~~s~~eLa~~l~vS~---~ti~r~l~~L~~~G~~i~~~~------g~GY~l~~~   63 (321)
T 1bia_A            9 KLIALLANG-EFHSGEQLGETLGMSR---AAINKHIQTLRDWGVDVFTVP------GKGYSLPEP   63 (321)
T ss_dssp             HHHHHHTTS-SCBCHHHHHHHHTSCH---HHHHHHHHHHHHTTCCCEEET------TTEEECSSC
T ss_pred             HHHHHHHcC-CCcCHHHHHHHHCCCH---HHHHHHHHHHHhCCCcEEEec------CCCcEEeec
Confidence            466777654 7899999999999999   999999999999999976542      457888765

>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=90.59  E-value=0.19  Score=43.46  Aligned_cols=32  Identities=16%  Similarity=0.016  Sum_probs=26.6

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +..+|||+|||+|.+++.+++.. ..+++.+|+
T Consensus       212 ~~~~VLDl~cGtG~~sl~la~~g-a~~V~~vD~  243 (385)
T 2b78_A          212 AGKTVLNLFSYTAAFSVAAAMGG-AMATTSVDL  243 (385)
T ss_dssp             BTCEEEEETCTTTHHHHHHHHTT-BSEEEEEES
T ss_pred             CCCeEEEEeeccCHHHHHHHHCC-CCEEEEEEC
Confidence            46799999999999999999863 237888886

>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=90.54  E-value=0.053  Score=38.69  Aligned_cols=44  Identities=23%  Similarity=0.351  Sum_probs=37.0

Q ss_pred             cchhhhcCCCCCCHHHHHHHcC----CCCCCcccHHHHHHHHHhCCceeeec
Q 040620           41 IPDIINNSGQPMTLTQIIVALN----VHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        41 lfd~L~~~~~p~t~~eLA~~~g----~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      |+..|... +|+|..+||+.++    +++   ..+.++|+.|...|++....
T Consensus        15 vL~~l~~~-~~~t~~ela~~l~~~~~~s~---~tv~~~l~~L~~~Glv~r~~   62 (123)
T 1okr_A           15 VMNIIWMK-KYASANNIIEEIQMQKDWSP---KTIRTLITRLYKKGFIDRKK   62 (123)
T ss_dssp             HHHHHHHH-SSEEHHHHHHHHHHHCCCCH---HHHHHHHHHHHHHTSEEEEE
T ss_pred             HHHHHHhC-CCcCHHHHHHHHhccCCCcH---hhHHHHHHHHHHCCCeEEEe
Confidence            44445444 7899999999999    667   89999999999999999875

>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=90.35  E-value=0.16  Score=43.75  Aligned_cols=31  Identities=16%  Similarity=0.055  Sum_probs=27.2

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +..+|+|+|||+|.++..+++.  ..+++.+|+
T Consensus       209 ~~~~VLDlg~G~G~~~~~la~~--~~~v~~vD~  239 (382)
T 1wxx_A          209 RGERALDVFSYAGGFALHLALG--FREVVAVDS  239 (382)
T ss_dssp             CEEEEEEETCTTTHHHHHHHHH--EEEEEEEES
T ss_pred             CCCeEEEeeeccCHHHHHHHHh--CCEEEEEEC
Confidence            4579999999999999999998  567888886

>2efj_A 3,7-dimethylxanthine methyltransferase; SAM-dependant methyltransferase, SAH, theobromine; HET: SAH 37T; 2.00A {Coffea canephora} PDB: 2eg5_A*

Probab=90.33  E-value=0.18  Score=43.87  Aligned_cols=34  Identities=12%  Similarity=0.061  Sum_probs=28.4

Q ss_pred             CCcEEeecCCchHHHHHHHHH-----------------CCCCeEEEecCCC
Q 040620          181 LKPLVDVGGSTGTMARAIATA-----------------FPDTKCTVFACHL  214 (214)
Q Consensus       181 ~~~vvDVGGG~G~~~~~l~~~-----------------~P~l~~~v~Dlp~  214 (214)
                      .-+|+|+||++|..+..+++.                 .|.+++..-|||.
T Consensus        53 ~~~IaDlGCssG~NT~~~v~~ii~~i~~~~~~~~~~~~~pe~~v~~nDLp~  103 (384)
T 2efj_A           53 CFKVGDLGCASGPNTFSTVRDIVQSIDKVGQEKKNELERPTIQIFLNDLFQ  103 (384)
T ss_dssp             EEEEEEETCCSSHHHHHHHHHHHHHHTCC----------CEEEEEEECCTT
T ss_pred             ceEEEecCCCCCchHHHHHHHHHHHHHHHhhhcccCCCCCceEEEecCCCc
Confidence            568999999999988877766                 5888899999984

>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=90.32  E-value=0.15  Score=35.66  Aligned_cols=49  Identities=12%  Similarity=0.141  Sum_probs=39.7

Q ss_pred             CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      ++.+..+||++++++.   ..|.|.|..|...|++..... .++  -+...+|+.
T Consensus        35 ~~~s~~eLa~~l~l~~---stLsR~l~rLe~~GLV~r~~~-~D~--R~~v~LT~~   83 (96)
T 2obp_A           35 TPWSLPKIAKRAQLPM---SVLRRVLTQLQAAGLADVSVE-ADG--RGHASLTQE   83 (96)
T ss_dssp             CCCBHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEEEC-TTS--CEEEEECHH
T ss_pred             CCcCHHHHHHHhCCch---hhHHHHHHHHHHCCCEEeecC-CCC--ceeEEECHH
Confidence            7899999999999999   999999999999999998653 121  234566665

>3ll7_A Putative methyltransferase; methytransferase, structural genomics, MCSG, PSI-2, protein initiative; HET: MSE; 1.80A {Porphyromonas gingivalis}

Probab=90.29  E-value=0.17  Score=44.44  Aligned_cols=30  Identities=17%  Similarity=0.148  Sum_probs=26.3

Q ss_pred             CCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          181 LKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       181 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+|+|+|||.|..++.+++.  ..+++.+|+
T Consensus        94 g~~VLDLgcG~G~~al~LA~~--g~~V~~VD~  123 (410)
T 3ll7_A           94 GTKVVDLTGGLGIDFIALMSK--ASQGIYIER  123 (410)
T ss_dssp             TCEEEESSCSSSHHHHHHHTT--CSEEEEEES
T ss_pred             CCEEEEeCCCchHHHHHHHhc--CCEEEEEEC
Confidence            689999999999999999887  468888886

>2k4m_A TR8_protein, UPF0146 protein MTH_1000; alpha+beta, rossman fold, structural genomics, PSI-2; NMR {Methanothermobacterthermautotrophicus str}

Probab=90.28  E-value=0.23  Score=37.58  Aligned_cols=32  Identities=13%  Similarity=0.068  Sum_probs=25.3

Q ss_pred             CCCcEEeecCCchH-HHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGT-MARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~-~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...++||||||+|. .+..|++. -+..++..|+
T Consensus        35 ~~~rVlEVG~G~g~~vA~~La~~-~g~~V~atDI   67 (153)
T 2k4m_A           35 PGTRVVEVGAGRFLYVSDYIRKH-SKVDLVLTDI   67 (153)
T ss_dssp             SSSEEEEETCTTCCHHHHHHHHH-SCCEEEEECS
T ss_pred             CCCcEEEEccCCChHHHHHHHHh-CCCeEEEEEC
Confidence            45799999999995 77777764 4677888885

>2g9w_A Conserved hypothetical protein; DNA-binding domain, bacterial transcription repressor, DNA B protein; 1.80A {Mycobacterium tuberculosis} SCOP: a.4.5.39

Probab=90.18  E-value=0.11  Score=38.14  Aligned_cols=48  Identities=19%  Similarity=0.221  Sum_probs=39.1

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcC----CCCCCcccHHHHHHHHHhCCceeeec
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALN----VHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g----~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      +..|+..|....+|+|..+|++.++    +++   ..+.++|+-|...|++....
T Consensus        11 e~~vL~~L~~~~~~~t~~el~~~l~~~~~~~~---~Tvt~~l~rLe~kGlv~r~~   62 (138)
T 2g9w_A           11 ERAVMDHLWSRTEPQTVRQVHEALSARRDLAY---TTVMAVLQRLAKKNLVLQIR   62 (138)
T ss_dssp             HHHHHHHHHTCSSCEEHHHHHHHHTTTCCCCH---HHHHHHHHHHHHTTSEEEEC
T ss_pred             HHHHHHHHHhcCCCCCHHHHHHHHhccCCCCH---HHHHHHHHHHHHCCCEEEEe
Confidence            3445556655227899999999998    677   89999999999999999875

>2b9e_A NOL1/NOP2/SUN domain family, member 5 isoform 2; methytransferase, structural genomics, structural genomics consortium, SGC; HET: SAM; 1.65A {Homo sapiens} SCOP: c.66.1.38

Probab=90.10  E-value=0.23  Score=41.80  Aligned_cols=35  Identities=14%  Similarity=0.175  Sum_probs=29.5

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHC-CCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAF-PDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl  212 (214)
                      .....+|+|+|||+|..+..+++.. +..+++.+|+
T Consensus       100 ~~~g~~VLDlcaG~G~kt~~la~~~~~~g~V~a~D~  135 (309)
T 2b9e_A          100 PPPGSHVIDACAAPGNKTSHLAALLKNQGKIFAFDL  135 (309)
T ss_dssp             CCTTCEEEESSCTTCHHHHHHHHHHTTCSEEEEEES
T ss_pred             CCCCCEEEEeCCChhHHHHHHHHHhCCCCEEEEEeC
Confidence            3456799999999999999999985 5678888886

>3i71_A Ethanolamine utilization protein EUTK; helix-turn-helix, unknown function; HET: FLC; 2.10A {Escherichia coli}

Probab=90.09  E-value=0.37  Score=30.33  Aligned_cols=50  Identities=16%  Similarity=0.185  Sum_probs=42.1

Q ss_pred             hhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           44 IINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        44 ~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      .|++...+||+.|+|...+.+-   ...+.-|..|.+.|-+.+.+        .+|++.|.
T Consensus        11 ll~s~~QGMTaGEVAA~f~w~L---e~ar~aLeqLf~~G~LRKRs--------SRYrlkph   60 (68)
T 3i71_A           11 LLTSVRQGMTAGEVAAHFGWPL---EKARNALEQLFSAGTLRKRS--------SRYRLKPH   60 (68)
T ss_dssp             HHHHCTTCBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEEC--------CEEEECC-
T ss_pred             HHHHHhccccHHHHHHHhCCcH---HHHHHHHHHHHhcchhhhhc--------cccccCcc
Confidence            4444347899999999999988   88899999999999999995        79988775

>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=90.02  E-value=0.18  Score=43.74  Aligned_cols=52  Identities=10%  Similarity=0.153  Sum_probs=44.0

Q ss_pred             HHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           33 LKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        33 L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      ++..-+..|+++|..+ +++|..|||+++|+++   ..+.++++-|...|++.+.+
T Consensus        13 ~r~~n~~~il~~l~~~-~~~sr~~la~~~~ls~---~tv~~~v~~L~~~g~i~~~~   64 (406)
T 1z6r_A           13 IKQTNAGAVYRLIDQL-GPVSRIDLSRLAQLAP---ASITKIVHEMLEAHLVQELE   64 (406)
T ss_dssp             HHHHHHHHHHHHHHSS-CSCCHHHHHHHTTCCH---HHHHHHHHHHHHHTSEEEC-
T ss_pred             HHHhHHHHHHHHHHHc-CCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCcEEeec
Confidence            3444445578888877 8999999999999999   99999999999999999865

>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=89.62  E-value=0.11  Score=37.15  Aligned_cols=47  Identities=15%  Similarity=0.282  Sum_probs=38.8

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCC----CCCCcccHHHHHHHHHhCCceeeec
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNV----HPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~----~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      +..|+..|..+ +|+|..|||+.++.    ++   ..+.++|+-|...|++....
T Consensus        12 q~~vL~~L~~~-~~~t~~el~~~l~~~~~~~~---~Tvt~~l~rLe~kGlv~R~~   62 (126)
T 1sd4_A           12 EWDVMNIIWDK-KSVSANEIVVEIQKYKEVSD---KTIRTLITRLYKKEIIKRYK   62 (126)
T ss_dssp             HHHHHHHHHHS-SSEEHHHHHHHHHTTSCCCH---HHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHhc-CCCCHHHHHHHHhhcCCCCh---hhHHHHHHHHHHCCceEEEe
Confidence            34455566665 78999999999975    66   89999999999999999875

>3o4f_A Spermidine synthase; aminopropyltransferase, polyamine synthase, rossmann fold, P biosynthesis, spermidine biosynthesis, transferase; 2.90A {Escherichia coli}

Probab=89.51  E-value=0.27  Score=41.23  Aligned_cols=34  Identities=21%  Similarity=0.271  Sum_probs=30.4

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +++++||=||||.|..++.+++..|-.+++++|+
T Consensus        82 p~pk~VLIiGgGdG~~~revlk~~~v~~v~~VEI  115 (294)
T 3o4f_A           82 GHAKHVLIIGGGDGAMLREVTRHKNVESITMVEI  115 (294)
T ss_dssp             SCCCEEEEESCTTSHHHHHHHTCTTCCEEEEEES
T ss_pred             CCCCeEEEECCCchHHHHHHHHcCCcceEEEEcC
Confidence            3578999999999999999999888888998886

>2pjp_A Selenocysteine-specific elongation factor; SELB, protein-RNA complex, elongation factor, winged- helix, bulge, translation/RNA complex; 2.30A {Escherichia coli}

Probab=89.37  E-value=0.27  Score=35.45  Aligned_cols=54  Identities=6%  Similarity=0.136  Sum_probs=43.2

Q ss_pred             cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      -.|.+.+..  .|.++.+||+.+++++   ..++++|+.|+..|.+....       .+.|-++..
T Consensus        10 ~~i~~~~~~--~p~~~~~la~~~~~~~---~~~~~~l~~l~~~G~l~~i~-------~~~~~~~~~   63 (121)
T 2pjp_A           10 QKAEPLFGD--EPWWVRDLAKETGTDE---QAMRLTLRQAAQQGIITAIV-------KDRYYRNDR   63 (121)
T ss_dssp             HHHGGGCSS--SCEEHHHHHHHTTCCH---HHHHHHHHHHHHTTSEEEEE-------TTEEEEHHH
T ss_pred             HHHHHHHHh--CCCCHHHHHHHhCCCH---HHHHHHHHHHHHCCCEEEec-------CCceECHHH
Confidence            345566654  5779999999999999   99999999999999999887       455555444

>2w57_A Ferric uptake regulation protein; gene regulation, transcription regulation, transport, iron, repressor, DNA-binding, transcription; 2.60A {Vibrio cholerae}

Probab=89.16  E-value=0.15  Score=38.20  Aligned_cols=57  Identities=11%  Similarity=0.205  Sum_probs=43.5

Q ss_pred             cCcchhhhcCC-CCCCHHHHHHHc-----CCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeC
Q 040620           39 LRIPDIINNSG-QPMTLTQIIVAL-----NVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILL  101 (214)
Q Consensus        39 lglfd~L~~~~-~p~t~~eLA~~~-----g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~  101 (214)
                      .-|++.|.+++ +++|++||.+.+     +++.   .-++|.|+.|+..|++.+...  +++ ..+|..
T Consensus        20 ~~Il~~L~~~~~~h~sa~ei~~~l~~~~~~is~---aTVYR~L~~L~e~Glv~~~~~--~~~-~~~Y~~   82 (150)
T 2w57_A           20 LKILEVLQQPECQHISAEELYKKLIDLGEEIGL---ATVYRVLNQFDDAGIVTRHHF--EGG-KSVFEL   82 (150)
T ss_dssp             HHHHHHHTSGGGSSEEHHHHHHHHHHTTCCCCH---HHHHHHHHHHHHTTSEEEEEC--GGG-CEEEEE
T ss_pred             HHHHHHHHhCCCCCCCHHHHHHHHHHhCCCCCH---HHHHHHHHHHHHCCcEEEEEe--CCC-ceEEEe
Confidence            33677777655 689999999998     5676   899999999999999997642  111 346874

>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=89.05  E-value=0.099  Score=42.77  Aligned_cols=63  Identities=16%  Similarity=0.258  Sum_probs=46.3

Q ss_pred             hcCcchhhhcCC-CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           38 QLRIPDIINNSG-QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        38 ~lglfd~L~~~~-~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      +..|+..|..++ +++|..+||+.+++++   ..+.++++-|...|++......+|.- .-...+|+.
T Consensus       160 q~~vL~~L~~~~~~~~t~~eLa~~l~i~~---~tvt~~v~rLe~~GlV~R~~~~~DrR-~~~i~LT~~  223 (250)
T 1p4x_A          160 EFTILAIITSQNKNIVLLKDLIETIHHKY---PQTVRALNNLKKQGYLIKERSTEDER-KILIHMDDA  223 (250)
T ss_dssp             HHHHHHHHHTTTTCCEEHHHHHHHSSSCH---HHHHHHHHHHHHHTSSEEEECSSSTT-CEEEECCHH
T ss_pred             HHHHHHHHHhCCCCCcCHHHHHHHHCCCh---hhHHHHHHHHHHCCCEEeeCCCCCCC-eEEEEECHH
Confidence            344666776653 3699999999999999   99999999999999999875321111 123566666

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

Probab=88.77  E-value=0.48  Score=40.58  Aligned_cols=30  Identities=17%  Similarity=0.237  Sum_probs=24.8

Q ss_pred             CCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          181 LKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       181 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+|+|+|||+|.+++.+++..  .+++.+|.
T Consensus       214 ~~~vLDl~cG~G~~~l~la~~~--~~V~gvd~  243 (369)
T 3bt7_A          214 KGDLLELYCGNGNFSLALARNF--DRVLATEI  243 (369)
T ss_dssp             CSEEEEESCTTSHHHHHHGGGS--SEEEEECC
T ss_pred             CCEEEEccCCCCHHHHHHHhcC--CEEEEEEC
Confidence            3689999999999999998853  46777775

>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=88.70  E-value=0.21  Score=43.72  Aligned_cols=52  Identities=12%  Similarity=0.197  Sum_probs=45.9

Q ss_pred             HHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           33 LKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        33 L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      ++..-+..|+++|..+ +++|..|||+++|+++   ..+.++++-|...|++.+.+
T Consensus        36 ~r~~n~~~il~~l~~~-~~~sr~ela~~~gls~---~tv~~~v~~L~~~gli~~~~   87 (429)
T 1z05_A           36 IKQINAGRVYKLIDQK-GPISRIDLSKESELAP---ASITKITRELIDAHLIHETT   87 (429)
T ss_dssp             HHHHHHHHHHHHHHHH-CSBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEEC
T ss_pred             HHHHHHHHHHHHHHHc-CCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEecc
Confidence            5555666688888887 8999999999999999   99999999999999999864

>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=88.60  E-value=0.43  Score=39.88  Aligned_cols=34  Identities=15%  Similarity=0.123  Sum_probs=25.9

Q ss_pred             cCCCCcEEeecC------CchHHHHHHHHHCC-CCeEEEecCC
Q 040620          178 SKGLKPLVDVGG------STGTMARAIATAFP-DTKCTVFACH  213 (214)
Q Consensus       178 ~~~~~~vvDVGG------G~G~~~~~l~~~~P-~l~~~v~Dlp  213 (214)
                      .....+|||+||      |+|.  ..+++..| +.+++.+|+-
T Consensus        61 l~~g~~VLDLGcGsg~~~GpGs--~~~a~~~~~~~~V~gvDis  101 (290)
T 2xyq_A           61 VPYNMRVIHFGAGSDKGVAPGT--AVLRQWLPTGTLLVDSDLN  101 (290)
T ss_dssp             CCTTCEEEEESCCCTTSBCHHH--HHHHHHSCTTCEEEEEESS
T ss_pred             CCCCCEEEEeCCCCCCCCCcHH--HHHHHHcCCCCEEEEEECC
Confidence            455679999999      5577  55677777 6899999973

>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=88.32  E-value=0.51  Score=44.19  Aligned_cols=33  Identities=21%  Similarity=0.212  Sum_probs=25.1

Q ss_pred             HHHHHhhcccccCCCCcEEeecCCchHHHHHHHHH
Q 040620          167 ASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATA  201 (214)
Q Consensus       167 ~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~  201 (214)
                      +..++....  +.+..+|+|.+||+|+++++.+..
T Consensus       179 Aa~ll~~~~--~~~~~~llDP~CGSGt~lIeAa~~  211 (703)
T 3v97_A          179 AAAIVMRSG--WQPGTPLLDPMCGSGTLLIEAAML  211 (703)
T ss_dssp             HHHHHHHTT--CCTTSCEEETTCTTSHHHHHHHHH
T ss_pred             HHHHHHhhC--CCCCCeEEecCCCCcHHHHHHHHH
Confidence            444555555  456689999999999999987765

>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=88.04  E-value=0.26  Score=42.88  Aligned_cols=52  Identities=15%  Similarity=0.296  Sum_probs=45.4

Q ss_pred             cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCC
Q 040620           39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLP  102 (214)
Q Consensus        39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t  102 (214)
                      ..|++.|..  +|+++++|++++|++.   ..+...|-.|.-.|++...+       ++.|+++
T Consensus       331 ~~vl~~l~~--~~~~~D~l~~~~gl~~---~~v~~~L~~LEl~G~v~~~~-------Gg~~~~~  382 (382)
T 3maj_A          331 TRILALLGP--SPVGIDDLIRLSGISP---AVVRTILLELELAGRLERHG-------GSLVSLS  382 (382)
T ss_dssp             HHHHHHCCS--SCEEHHHHHHHHCCCH---HHHHHHHHHHHHTTCCEECT-------TSEEEC-
T ss_pred             HHHHHhhCC--CCCCHHHHHHHHCcCH---HHHHHHHHHHHhCCcEEeCC-------CceEecC
Confidence            357888875  8999999999999999   99999999999999999987       6788764

>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=87.78  E-value=0.27  Score=34.65  Aligned_cols=42  Identities=12%  Similarity=-0.002  Sum_probs=35.0

Q ss_pred             HHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHh
Q 040620           34 KRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAH   80 (214)
Q Consensus        34 ~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~   80 (214)
                      ..+.++||+..|..  +.+|-.|||+.+|++.   ..+.|+=|.|-.
T Consensus        43 ~l~~R~~l~~~L~~--ge~TQREIA~~lGiS~---stISRi~r~L~~   84 (101)
T 1jhg_A           43 ALGTRVRIIEELLR--GEMSQRELKNELGAGI---ATITRGSNSLKA   84 (101)
T ss_dssp             HHHHHHHHHHHHHH--CCSCHHHHHHHHCCCH---HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHc--CCcCHHHHHHHHCCCh---hhhhHHHHHHHH
Confidence            34566889999987  7899999999999998   888888776644

>2zig_A TTHA0409, putative modification methylase; methyltransferase, S- adenosylmethionine, structural genomics, NPPSFA; 2.10A {Thermus thermophilus} PDB: 2zie_A* 2zif_A

Probab=87.43  E-value=0.41  Score=39.75  Aligned_cols=32  Identities=19%  Similarity=-0.040  Sum_probs=27.3

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                      ....|||++||+|+.+.++++.  +-+++++|+.
T Consensus       235 ~~~~vlD~f~GsGt~~~~a~~~--g~~~~g~e~~  266 (297)
T 2zig_A          235 VGDVVLDPFAGTGTTLIAAARW--GRRALGVELV  266 (297)
T ss_dssp             TTCEEEETTCTTTHHHHHHHHT--TCEEEEEESC
T ss_pred             CCCEEEECCCCCCHHHHHHHHc--CCeEEEEeCC
Confidence            4579999999999999998886  5688988874

>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=87.27  E-value=0.11  Score=44.27  Aligned_cols=60  Identities=13%  Similarity=0.135  Sum_probs=0.0

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      +..|...|... +++|..|||+++++++   ..++|.|+.|...|++....        ....+|+.    ++.+.
T Consensus        22 ~~~iL~~l~~~-~~~t~~eLa~~l~vs~---~Tv~r~l~~Le~~Glv~~~~--------~gi~LT~~----G~~~~   81 (345)
T 2o0m_A           22 RFQILRNIYWM-QPIGRRSLSETMGITE---RVLRTETDVLKQLNLIEPSK--------SGMTLTER----GLEVY   81 (345)
T ss_dssp             ----------------------------------------------------------------------------
T ss_pred             HHHHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEEe--------cceEEcHH----HHHHH
Confidence            34577777776 8999999999999999   99999999999999998553        45778888    77765

>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=87.15  E-value=0.3  Score=41.05  Aligned_cols=35  Identities=11%  Similarity=0.051  Sum_probs=28.4

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +.+..++||+||++|.++.-++++.+-..++.+|+
T Consensus        79 ~~~g~~vlDLGaaPGgWsqva~~~~gv~sV~Gvdl  113 (300)
T 3eld_A           79 LRITGRVLDLGCGRGGWSYYAAAQKEVMSVKGYTL  113 (300)
T ss_dssp             CCCCEEEEEETCTTCHHHHHHHTSTTEEEEEEECC
T ss_pred             CCCCCEEEEcCCCCCHHHHHHHHhcCCceeeeEEe
Confidence            45678999999999999999998766556666665

>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=87.10  E-value=0.41  Score=33.50  Aligned_cols=45  Identities=9%  Similarity=0.145  Sum_probs=36.8

Q ss_pred             CcchhhhcCCCCC-CHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           40 RIPDIINNSGQPM-TLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        40 glfd~L~~~~~p~-t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      .|...|... +.+ |..+||+.+|++.   ..+++-|+.|...|++....
T Consensus        32 ~I~~~l~~g-~~lps~~eLa~~lgVSr---~tVr~al~~L~~~GlI~~~~   77 (102)
T 2b0l_A           32 HIFEELDGN-EGLLVASKIADRVGITR---SVIVNALRKLESAGVIESRS   77 (102)
T ss_dssp             HHTTSSBTT-EEEECHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHhhhcCC-CcCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEEe
Confidence            334455542 455 9999999999998   99999999999999998764

>3u1d_A Uncharacterized protein; GNTR-superfamily, structural genomics, PSI-biology, midwest for structural genomics, MCSG; 1.80A {Halomicrobium mukohataei}

Probab=86.97  E-value=0.92  Score=34.24  Aligned_cols=88  Identities=7%  Similarity=-0.012  Sum_probs=55.7

Q ss_pred             cCcchhhhcC-CCCCCHHHHHHHcC-CCCCCcccHHHHHHHHHhCCceeeecCCCC----CCccceeeCCCCCccccccc
Q 040620           39 LRIPDIINNS-GQPMTLTQIIVALN-VHPNKTRCTQILVCLLAHSGFFVQQKDGKN----EQEEESILLPPHLDFFSRIS  112 (214)
Q Consensus        39 lglfd~L~~~-~~p~t~~eLA~~~g-~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~----~~~~~~y~~t~~~~~~s~~l  112 (214)
                      +.|+..|-.+ .+..|+++|++.++ +++   ..+++-|+.|+..|++.+.....+    +.-...|.+|+.    ++.+
T Consensus        32 ~~IL~~Ll~~p~~~~ta~eL~~~l~~lS~---aTVyrhL~~L~eaGLV~~~~~~~~~~~rGrP~k~Y~LT~~----Gr~~  104 (151)
T 3u1d_A           32 LDVLHQILAQPDGVLSVEELLYRNPDETE---ANLRYHVDELVDRGIVEKIPVPRAKSVDDPPTTFYAVTGE----GIAL  104 (151)
T ss_dssp             HHHHHHHHHSTTSCBCHHHHHHHCTTSCH---HHHHHHHHHHHHTTSEEEEECCCCTTSSSCCCEEEEECHH----HHHH
T ss_pred             HHHHHHHHcCCCCCCCHHHHHHhcCCCCH---HHHHHHHHHHHHCCCeEEeecCcCcccCCCCceEEEECHH----HHHH
Confidence            3344444432 15689999999999 998   999999999999999997642100    000125777777    5554


Q ss_pred             cccchHHHHHHhhccchh-hhhHhHHHhhcC
Q 040620          113 LQLQGSTILLLIADATFT-TSFHFLSTWLQN  142 (214)
Q Consensus       113 ~~~~~~~~~~~~~~~~~~-~~~~~l~~~lr~  142 (214)
                      +        .. .+.... ..|..+.+.+.+
T Consensus       105 l--------~~-y~~la~~~alr~l~~~v~~  126 (151)
T 3u1d_A          105 L--------RA-VSMYEEAAVWRSVYEQMER  126 (151)
T ss_dssp             H--------HH-TTCSTHHHHTHHHHHHSCC
T ss_pred             H--------HH-hHHHhHHHHHHHHHHHhhc
Confidence            3        11 111222 567777777743

>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=86.74  E-value=0.34  Score=41.06  Aligned_cols=57  Identities=12%  Similarity=0.162  Sum_probs=45.6

Q ss_pred             cCcchhhhc-CCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           39 LRIPDIINN-SGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        39 lglfd~L~~-~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      ..|+++|.+ .+.++|.++||+++|++.   ..+++-++.|...|+..+...      ..-|++.+.
T Consensus         6 ~~iL~~L~~~~g~~~Sg~eLa~~lgvSr---~aV~k~i~~L~~~G~~i~~~~------~~GY~L~~~   63 (323)
T 3rkx_A            6 QDVLQLLYKNKPNYISGQSIAESLNISR---TAVKKVIDQLKLEGCKIDSVN------HKGHLLQQL   63 (323)
T ss_dssp             HHHHHHHHHHTTSCBCHHHHHHHHTSCH---HHHHHHHHHHHHTTCEEEEET------TTEEEEEEC
T ss_pred             HHHHHHHHhCCCCccCHHHHHHHHCCCH---HHHHHHHHHHHhcCCeEEEeC------CCeEEEecC
Confidence            346677743 236899999999999999   999999999999999777532      467887765

>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=85.95  E-value=0.24  Score=42.79  Aligned_cols=36  Identities=17%  Similarity=0.114  Sum_probs=26.2

Q ss_pred             CCCCcEEeecCCchHHHHH--------HHHH--------CCCCeEEEecCCC
Q 040620          179 KGLKPLVDVGGSTGTMARA--------IATA--------FPDTKCTVFACHL  214 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~--------l~~~--------~P~l~~~v~Dlp~  214 (214)
                      ++.-+|+|+||++|..+..        +.++        .|..++..-|||.
T Consensus        50 ~~~~~IaDlGCs~G~Nt~~~v~~ii~~i~~~~~~~~~~~~pe~~v~~nDLp~  101 (359)
T 1m6e_X           50 TTRLAIADLGCSSGPNALFAVTELIKTVEELRKKMGRENSPEYQIFLNDLPG  101 (359)
T ss_dssp             SSEECCEEESCCSSTTTTTGGGTTHHHHHHHHHSSSCSSCCEEEEEEEECTT
T ss_pred             CCceEEEecCCCCCcchHHHHHHHHHHHHHHHHhcCCCCCCceEEEecCCCc
Confidence            3456899999999975543        3322        5778889999984

>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=85.78  E-value=0.74  Score=37.67  Aligned_cols=43  Identities=14%  Similarity=0.046  Sum_probs=33.2

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+.+.+.  +....+|||+||++|.++.-.+....-.++..+|+
T Consensus        68 ~ei~ek~~--l~~g~~VvDLGaapGGWSq~~a~~~g~~~V~avdv  110 (267)
T 3p8z_A           68 QWFVERNM--VIPEGRVIDLGCGRGGWSYYCAGLKKVTEVRGYTK  110 (267)
T ss_dssp             HHHHHTTS--SCCCEEEEEESCTTSHHHHHHHTSTTEEEEEEECC
T ss_pred             HHHHHhcC--CCCCCEEEEcCCCCCcHHHHHHHhcCCCEEEEEec
Confidence            44555553  55667999999999999998877776667888876

>2qlz_A Transcription factor PF0095; 2.50A {Pyrococcus furiosus} PDB: 2quf_A

Probab=85.39  E-value=0.82  Score=36.91  Aligned_cols=44  Identities=14%  Similarity=0.029  Sum_probs=38.6

Q ss_pred             CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      -|.-.|..  ++.|+++||+.+|+++   .-+...|.-|...|++....
T Consensus       169 ~l~~~l~~--~~~t~~~la~~~~l~~---~~V~~~l~~L~~~~~v~~~~  212 (232)
T 2qlz_A          169 ILHYLLLN--GRATVEELSDRLNLKE---REVREKISEMARFVPVKIIN  212 (232)
T ss_dssp             HHHHHHHS--SEEEHHHHHHHHTCCH---HHHHHHHHHHTTTSCEEEET
T ss_pred             HHHHHHhc--CCCCHHHHHHHhCcCH---HHHHHHHHHHHhcCCeEEec
Confidence            34555665  8999999999999999   99999999999999998765

>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=85.31  E-value=0.79  Score=43.81  Aligned_cols=34  Identities=9%  Similarity=0.168  Sum_probs=28.7

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCC---CeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPD---TKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~---l~~~v~Dl  212 (214)
                      ....+|+|.|||+|.++.+++++.++   .++.++|+
T Consensus       320 ~~g~rVLDPaCGSG~FLIaaA~~l~ei~~~~IyGvEI  356 (878)
T 3s1s_A          320 TEDEVISDPAAGSGNLLATVSAGFNNVMPRQIWANDI  356 (878)
T ss_dssp             CTTCEEEETTCTTSHHHHHHHHTSTTCCGGGEEEECS
T ss_pred             CCCCEEEECCCCccHHHHHHHHHhcccCCCeEEEEEC
Confidence            35679999999999999999998873   46888876

>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=85.25  E-value=0.3  Score=33.98  Aligned_cols=48  Identities=13%  Similarity=0.093  Sum_probs=40.6

Q ss_pred             hcCcchhhhcCC-CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           38 QLRIPDIINNSG-QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        38 ~lglfd~L~~~~-~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      +.-|+.++.++| .+++..+|+.+++++.   ..+.+.|..|...+++....
T Consensus        39 E~lVy~~I~~aGn~GIw~kdL~~~tnL~~---~~vtkiLK~LE~k~lIK~Vk   87 (95)
T 2yu3_A           39 EKLVYQIIEDAGNKGIWSRDVRYKSNLPL---TEINKILKNLESKKLIKAVK   87 (95)
T ss_dssp             HHHHHHHHHHHTTSCEEHHHHHHHHTCCH---HHHHHHHHHHHHHTSEEEEC
T ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHhCCCH---HHHHHHHHHHHhCCCEEEec
Confidence            344566776642 6799999999999999   99999999999999999875

>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=85.23  E-value=0.2  Score=40.04  Aligned_cols=53  Identities=9%  Similarity=0.186  Sum_probs=44.0

Q ss_pred             CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      +++|..++|+++++++   ..+.+.++.|...|+|.....   .- ...+.+|+.    ++.+.
T Consensus        26 ~~~s~s~aA~~L~isq---~avSr~I~~LE~~~L~~R~~~---~R-~~~v~LT~~----G~~l~   78 (230)
T 3cta_A           26 AYLTSSKLADMLGISQ---QSASRIIIDLEKNGYITRTVT---KR-GQILNITEK----GLDVL   78 (230)
T ss_dssp             EECCHHHHHHHHTSCH---HHHHHHHHHHHHTTSEEEEEE---TT-EEEEEECHH----HHHHH
T ss_pred             CCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEEEEc---CC-eEEEEECHH----HHHHH
Confidence            6799999999999999   999999999999999998731   00 256888888    77765

>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=85.05  E-value=0.9  Score=29.59  Aligned_cols=47  Identities=11%  Similarity=0.099  Sum_probs=39.6

Q ss_pred             cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      -.|++.|..+ ||.++=.||+.+|+..  +..+++.|-.|...|++..+.
T Consensus        13 e~I~~fL~~~-Gp~~AL~IAK~LGlkt--AK~VNp~LY~m~~~~lL~~De   59 (72)
T 3eyi_A           13 EDIYRFLKDN-GPQRALVIAQALGMRT--AKDVNRDLYRMKSRHLLDMDE   59 (72)
T ss_dssp             HHHHHHHHHH-CSEEHHHHHHHTTCCS--GGGTHHHHHHHHHTTSEEECT
T ss_pred             HHHHHHHHHc-CCchHHHHHHHhCcch--hhhcCHHHHHHHHccCcCCCC
Confidence            3467788877 9999999999999965  245999999999999997664

>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=84.65  E-value=1  Score=39.26  Aligned_cols=33  Identities=15%  Similarity=0.224  Sum_probs=28.0

Q ss_pred             CCCCcEEeecCCchHHHHHHH-HHCCC-CeEEEec
Q 040620          179 KGLKPLVDVGGSTGTMARAIA-TAFPD-TKCTVFA  211 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~-~~~P~-l~~~v~D  211 (214)
                      .+..+++|||++.|.++..++ +..|+ .+++.|+
T Consensus       225 ~~~~~viDvGAn~G~~s~~~a~~~~~~~~~V~afE  259 (409)
T 2py6_A          225 SDSEKMVDCGASIGESLAGLIGVTKGKFERVWMIE  259 (409)
T ss_dssp             CSSCEEEEETCTTSHHHHHHHHHHTSCCSEEEEEC
T ss_pred             CCCCEEEECCCCcCHHHHHHHHHhcCCCCEEEEEc
Confidence            467899999999999999988 67776 6788776

>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=84.48  E-value=0.51  Score=37.64  Aligned_cols=50  Identities=16%  Similarity=0.180  Sum_probs=43.8

Q ss_pred             CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      .+.+..+||+++++++   ..+.++++.|...|++....       ...+.+|+.    ++.+.
T Consensus        23 ~~~~~~~la~~l~vs~---~tvs~~l~~Le~~GlV~r~~-------~~~v~LT~~----G~~~~   72 (226)
T 2qq9_A           23 VTPLRARIAERLEQSG---PTVSQTVARMERDGLVVVAS-------DRSLQMTPT----GRTLA   72 (226)
T ss_dssp             CCCBHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEECT-------TSBEEECHH----HHHHH
T ss_pred             CCccHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEEeC-------CCCeEECHH----HHHHH
Confidence            3446699999999999   99999999999999999986       567999999    88775

>3tqn_A Transcriptional regulator, GNTR family; regulatory functions; 2.80A {Coxiella burnetii}

Probab=84.42  E-value=0.73  Score=32.59  Aligned_cols=36  Identities=8%  Similarity=0.185  Sum_probs=32.8

Q ss_pred             CCC-CHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           50 QPM-TLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        50 ~p~-t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      ..+ |..+||+.+|++.   ..+++-++.|...|++....
T Consensus        31 ~~lPs~~~La~~~~vSr---~tvr~al~~L~~~Gli~~~~   67 (113)
T 3tqn_A           31 EMIPSIRKISTEYQINP---LTVSKAYQSLLDDNVIEKRR   67 (113)
T ss_dssp             CEECCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEET
T ss_pred             CcCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEec
Confidence            445 8999999999999   99999999999999998775

>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=84.38  E-value=0.36  Score=38.58  Aligned_cols=48  Identities=13%  Similarity=0.103  Sum_probs=42.3

Q ss_pred             CCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           52 MTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        52 ~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      .+..+||+++++++   ..+.+.++.|...|++....       ...+.+|+.    ++.+.
T Consensus        25 ~~~~~La~~l~vs~---~tvs~~l~~Le~~GlV~r~~-------~~~v~LT~~----G~~~~   72 (230)
T 1fx7_A           25 PLRARIAERLDQSG---PTVSQTVSRMERDGLLRVAG-------DRHLELTEK----GRALA   72 (230)
T ss_dssp             CCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEECT-------TSCEEECHH----HHHHH
T ss_pred             CcHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEeC-------CccEEECHH----HHHHH
Confidence            34599999999999   99999999999999999986       567889998    77765

>3lkz_A Non-structural protein 5; flavivirus, methyltransferase, inhibitor, P nucleotide-binding, RNA replication, viral protein; HET: SFG; 2.00A {West nile virus}

Probab=83.90  E-value=0.77  Score=38.69  Aligned_cols=43  Identities=16%  Similarity=0.140  Sum_probs=32.0

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+.+.+.  +.....|||+||++|.++.-++....-.++..+|+
T Consensus        84 ~ei~~~~~--l~~~~~VlDLGaapGGwsq~~~~~~gv~~V~avdv  126 (321)
T 3lkz_A           84 RWLVERRF--LEPVGKVIDLGCGRGGWCYYMATQKRVQEVRGYTK  126 (321)
T ss_dssp             HHHHHTTS--CCCCEEEEEETCTTCHHHHHHTTCTTEEEEEEECC
T ss_pred             HHHHHhcC--CCCCCEEEEeCCCCCcHHHHHHhhcCCCEEEEEEc
Confidence            34445544  55566999999999999997777766557888876

>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=83.88  E-value=0.9  Score=28.16  Aligned_cols=35  Identities=14%  Similarity=0.142  Sum_probs=28.4

Q ss_pred             hhhhcCCCCCCHHHHHHHc-----CCCCCCcccHHHHHHHHHhCCce
Q 040620           43 DIINNSGQPMTLTQIIVAL-----NVHPNKTRCTQILVCLLAHSGFF   84 (214)
Q Consensus        43 d~L~~~~~p~t~~eLA~~~-----g~~~~~~~~l~rlLr~L~~~g~l   84 (214)
                      .++..+ +++|++||++.+     +++.   .-++|.|.   ..|++
T Consensus        12 ~ll~~~-~~~t~~el~~~l~~~~~~vs~---~Tv~R~L~---~lg~v   51 (64)
T 2p5k_A           12 EIITSN-EIETQDELVDMLKQDGYKVTQ---ATVSRDIK---ELHLV   51 (64)
T ss_dssp             HHHHHS-CCCSHHHHHHHHHHTTCCCCH---HHHHHHHH---HHTCE
T ss_pred             HHHHcC-CCCCHHHHHHHHHHhCCCcCH---HHHHHHHH---HcCCE
Confidence            345554 789999999999     9988   88888887   66887

>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding, transcription, transcription regulator, transcription regulation; 3.20A {Klebsiella pneumoniae}

Probab=83.63  E-value=0.76  Score=38.48  Aligned_cols=35  Identities=23%  Similarity=0.141  Sum_probs=33.0

Q ss_pred             CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCcee-ee
Q 040620           50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFV-QQ   87 (214)
Q Consensus        50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~-~~   87 (214)
                      +++|.+|||+++|+++   ..++|.|..|...|++. ..
T Consensus        20 ~~~~~~ela~~l~vS~---~tIrRdL~~l~~~G~v~iri   55 (315)
T 2w48_A           20 QDMTQAQIARELGIYR---TTISRLLKRGREQGIVTIAI   55 (315)
T ss_dssp             SCCCHHHHHHHTTCCH---HHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCcEEEEe
Confidence            7899999999999999   99999999999999997 54

>2ek5_A Predicted transcriptional regulators; helix-turn-helix, interwined alpha helices; 2.20A {Corynebacterium glutamicum atcc 13032} PDB: 2du9_A

Probab=83.53  E-value=1.1  Score=32.59  Aligned_cols=36  Identities=14%  Similarity=0.324  Sum_probs=33.0

Q ss_pred             CCC-CHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           50 QPM-TLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        50 ~p~-t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      ..+ |..+||+.+|+++   ..+++-++.|...|++...+
T Consensus        26 ~~LPse~~La~~~gvSr---~tVr~Al~~L~~~Gli~~~~   62 (129)
T 2ek5_A           26 QRVPSTNELAAFHRINP---ATARNGLTLLVEAGILYKKR   62 (129)
T ss_dssp             SCBCCHHHHHHHTTCCH---HHHHHHHHHHHTTTSEEEET
T ss_pred             CcCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCcEEEec
Confidence            556 8999999999998   89999999999999998876

>1i4w_A Mitochondrial replication protein MTF1; mitochondrial transcription factor, transcription initiation; 2.60A {Saccharomyces cerevisiae} SCOP: c.66.1.24

Probab=83.45  E-value=1.2  Score=38.29  Aligned_cols=32  Identities=6%  Similarity=0.081  Sum_probs=25.4

Q ss_pred             CCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          181 LKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       181 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+|||||.|.|.+...|+++..--+++++++
T Consensus        59 ~~~VlEIGPG~G~LT~~Ll~~~~~~~vvavE~   90 (353)
T 1i4w_A           59 ELKVLDLYPGVGIQSAIFYNKYCPRQYSLLEK   90 (353)
T ss_dssp             TCEEEEESCTTCHHHHHHHHHHCCSEEEEECC
T ss_pred             CCEEEEECCCCCHHHHHHHhhCCCCEEEEEec
Confidence            47899999999999999999744345666553

>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=83.41  E-value=0.45  Score=35.35  Aligned_cols=46  Identities=11%  Similarity=0.142  Sum_probs=37.6

Q ss_pred             cCcchhhhcCCCCCCHHHHHHHc-----CCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           39 LRIPDIINNSGQPMTLTQIIVAL-----NVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        39 lglfd~L~~~~~p~t~~eLA~~~-----g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      .-|++.|.++ ++.|++||.+.+     ++++   .-++|.|+.|+..|++.+..
T Consensus        22 ~~Il~~l~~~-~h~ta~ei~~~l~~~~~~is~---~TVYR~L~~L~e~Glv~~i~   72 (145)
T 3eyy_A           22 QLVLEAVDTL-EHATPDDILGEVRKTASGINI---STVYRTLELLEELGLVSHAH   72 (145)
T ss_dssp             HHHHHHHHHH-SSBCHHHHHHHHHTTCTTCCH---HHHHHHHHHHHHHTSEEEEE
T ss_pred             HHHHHHHHhc-CCCCHHHHHHHHHhhCCCCCH---hHHHHHHHHHHHCCcEEEEE
Confidence            3366777766 489999999987     4566   79999999999999998865

>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=83.03  E-value=1.1  Score=41.99  Aligned_cols=32  Identities=13%  Similarity=0.009  Sum_probs=26.4

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..++|||+|||+|.+++.+++... .+++.+|+
T Consensus       539 ~g~~VLDlg~GtG~~sl~aa~~ga-~~V~aVD~  570 (703)
T 3v97_A          539 KGKDFLNLFSYTGSATVHAGLGGA-RSTTTVDM  570 (703)
T ss_dssp             TTCEEEEESCTTCHHHHHHHHTTC-SEEEEEES
T ss_pred             CCCcEEEeeechhHHHHHHHHCCC-CEEEEEeC
Confidence            467999999999999999998532 35888886

>1hsj_A Fusion protein consisting of staphylococcus accessary regulator protein R and maltose...; novel fold for DNA binding; HET: GLC; 2.30A {Escherichia coli} SCOP: a.4.5.28 c.94.1.1

Probab=82.50  E-value=0.57  Score=41.16  Aligned_cols=65  Identities=11%  Similarity=0.129  Sum_probs=47.4

Q ss_pred             CcchhhhcC-CCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCccccccc
Q 040620           40 RIPDIINNS-GQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRIS  112 (214)
Q Consensus        40 glfd~L~~~-~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l  112 (214)
                      .|+..|.++ ++++|..|||+++++++   ..+.|+++-|...|++.+....+|.- .-...+|+.    ++.+
T Consensus       408 ~vl~~l~~~~~~~~~~~~l~~~~~~~~---~~~t~~~~~le~~g~v~r~~~~~D~R-~~~i~lT~~----g~~~  473 (487)
T 1hsj_A          408 YILNHILRSESNEISSKEIAKCSEFKP---YYLTKALQKLKDLKLLSKKRSLQDER-TVIVYVTDT----QKAN  473 (487)
T ss_dssp             HHHHHHHTCSCSEEEHHHHHHSSCCCH---HHHHHHHHHHHTTTTSCCEECCSSSS-CCEEECCSS----HHHH
T ss_pred             HHHHHHHhCCCCCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEeecCCCCCCC-eEEEEECHH----HHHH
Confidence            355566553 26799999999999999   99999999999999998765321111 234677777    5554

>4ets_A Ferric uptake regulation protein; metal binding protein, transcription factor; 2.10A {Campylobacter jejuni subsp}

Probab=81.96  E-value=0.98  Score=34.23  Aligned_cols=59  Identities=12%  Similarity=0.060  Sum_probs=42.2

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHc-------CCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCC
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVAL-------NVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLP  102 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~-------g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t  102 (214)
                      +.-|++.|.+++++.|++||.+.+       +++.   .-++|.|+.|+..|++.+...  +++ ..+|..+
T Consensus        35 R~~IL~~L~~~~~h~sA~eI~~~l~~~~~~~~is~---aTVYRtL~~L~e~Glv~~i~~--~~~-~~~Y~~~  100 (162)
T 4ets_A           35 REVLLKTLYHSDTHYTPESLYMEIKQAEPDLNVGI---ATVYRTLNLLEEAEMVTSISF--GSA-GKKYELA  100 (162)
T ss_dssp             HHHHHHHHHSCCSCBCHHHHHHHHHHHCGGGCCCH---HHHHHHHHHHHHTTSEEECC--------CCEEEC
T ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHHhhcCCCCCCH---HHHHHHHHHHHHCCCEEEEEe--CCC-ceEEEeC
Confidence            344677777665899999998866       3555   799999999999999998742  111 3467654

>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=81.87  E-value=0.46  Score=38.72  Aligned_cols=65  Identities=9%  Similarity=0.171  Sum_probs=47.3

Q ss_pred             cchhhhcCC-CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           41 IPDIINNSG-QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        41 lfd~L~~~~-~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      +...|.+.+ +++|..|||+++++++   ..+.++++-|...|++......+|.= .-...+|+.    ++.+.
T Consensus        39 vL~~L~~~~~~~~~~~el~~~l~~~~---~t~t~~l~rLe~~G~i~R~~~~~DrR-~~~i~LT~~----G~~~~  104 (250)
T 1p4x_A           39 LLTYLFHQQENTLPFKKIVSDLCYKQ---SDLVQHIKVLVKHSYISKVRSKIDER-NTYISISEE----QREKI  104 (250)
T ss_dssp             HHHHHHSCSCSEEEHHHHHHHSSSCG---GGTHHHHHHHHHTTSCEEEECSSSTT-SEEEECCHH----HHHHH
T ss_pred             HHHHHHhcCCCCcCHHHHHHHHCCCH---hhHHHHHHHHHHCCCEEecCCCCCCC-eEEEEECHH----HHHHH
Confidence            455565532 5899999999999999   99999999999999998765321110 123667777    66654

>3by6_A Predicted transcriptional regulator; structural genomics, PSI-2, MCSG, structure initiative, midwest center for structural genomic binding; 2.20A {Oenococcus oeni}

Probab=81.82  E-value=1  Score=32.51  Aligned_cols=36  Identities=6%  Similarity=0.066  Sum_probs=33.1

Q ss_pred             CCC-CHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           50 QPM-TLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        50 ~p~-t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      ..+ |..+||+.+|+++   ..+++-++.|...|++....
T Consensus        33 ~~lPse~~La~~~~vSr---~tvr~Al~~L~~~Gli~~~~   69 (126)
T 3by6_A           33 DQLPSVRETALQEKINP---NTVAKAYKELEAQKVIRTIP   69 (126)
T ss_dssp             CEECCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEET
T ss_pred             CcCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEEec
Confidence            456 9999999999998   89999999999999998876

>3neu_A LIN1836 protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG, unknown function; 1.58A {Listeria innocua}

Probab=81.72  E-value=1.5  Score=31.60  Aligned_cols=36  Identities=17%  Similarity=0.337  Sum_probs=32.8

Q ss_pred             CCC-CHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           50 QPM-TLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        50 ~p~-t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      ..+ |..+||+.+|+++   .-+++-+..|...|++....
T Consensus        35 ~~Lps~~~La~~~~vSr---~tvr~Al~~L~~~G~i~~~~   71 (125)
T 3neu_A           35 DKLPSVREMGVKLAVNP---NTVSRAYQELERAGYIYAKR   71 (125)
T ss_dssp             CBCCCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEET
T ss_pred             CCCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCeEEEec
Confidence            455 6999999999999   99999999999999999875

>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=81.72  E-value=0.51  Score=37.36  Aligned_cols=49  Identities=16%  Similarity=0.201  Sum_probs=41.8

Q ss_pred             CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      +|++..+||+++++.+   ..++..++.|...|++...+        +...+|+.    ++.+.
T Consensus        29 ~~V~~~~LA~~LgvS~---~SV~~~lkkL~e~GLV~~~~--------~Gv~LTe~----G~~~A   77 (200)
T 2p8t_A           29 EPLGRKQISERLELGE---GSVRTLLRKLSHLDIIRSKQ--------RGHFLTLK----GKEIR   77 (200)
T ss_dssp             SCBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEC----------CEEECHH----HHHHH
T ss_pred             CCccHHHHHHHhCCCH---HHHHHHHHHHHHCCCEEEeC--------CCeEECHH----HHHHH
Confidence            6899999999999999   99999999999999999884        56777777    66543

>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=81.05  E-value=1.2  Score=38.82  Aligned_cols=33  Identities=12%  Similarity=-0.075  Sum_probs=28.1

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCC-CeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPD-TKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dl  212 (214)
                      +..+|||+++|+|.+++.++++.++ .+++..|+
T Consensus        52 ~g~~VLDlfaGtG~~sl~aa~~~~ga~~V~avDi   85 (392)
T 3axs_A           52 RPVKVADPLSASGIRAIRFLLETSCVEKAYANDI   85 (392)
T ss_dssp             SCEEEEESSCTTSHHHHHHHHHCSCEEEEEEECS
T ss_pred             CCCEEEECCCcccHHHHHHHHhCCCCCEEEEEEC
Confidence            4579999999999999999998776 46788775

>3elk_A Putative transcriptional regulator TA0346; structural genomics, PSI-2, prote structure initiative; 1.70A {Thermoplasma acidophilum}

Probab=80.78  E-value=0.44  Score=34.17  Aligned_cols=73  Identities=16%  Similarity=0.187  Sum_probs=51.5

Q ss_pred             HHHHHHhcCcchhhhcCCCCCCHHHHHHHcC------CCCCCcccHHHHHHHHHhCCceeeecCC-CCCCccceeeCCCC
Q 040620           32 SLKRAIQLRIPDIINNSGQPMTLTQIIVALN------VHPNKTRCTQILVCLLAHSGFFVQQKDG-KNEQEEESILLPPH  104 (214)
Q Consensus        32 ~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g------~~~~~~~~l~rlLr~L~~~g~l~~~~~~-~~~~~~~~y~~t~~  104 (214)
                      .++-.+++-|..+|..  +|++.-+|++.+.      +++   ..+...|+-|...|++...... .++.....|++|+.
T Consensus        10 l~~g~l~~~IL~lL~~--~p~~gyel~~~l~~~~~~~i~~---gtly~~L~~Le~~GlI~~~~~~~~~~~~rk~Y~lT~~   84 (117)
T 3elk_A           10 ILHGLITLYILKELVK--RPMHGYELQKSMFETTGQALPQ---GSIYILLKTMKERGFVISESSVNEKGQQLTVYHITDA   84 (117)
T ss_dssp             HHHHHHHHHHHHHHHH--SCEEHHHHHHHHHHHHSCCCCT---THHHHHHHHHHHHTSEEEEEEEC-CCCEEEEEEECHH
T ss_pred             HHhhHHHHHHHHHHHc--CCCCHHHHHHHHHHHhCCCCCc---chHHHHHHHHHHCCCEEEEeeecCCCCCceEEEECHH
Confidence            3344445556667776  8999999999886      777   9999999999999999865321 11111245888888


Q ss_pred             Ccccccccc
Q 040620          105 LDFFSRISL  113 (214)
Q Consensus       105 ~~~~s~~l~  113 (214)
                          ++..+
T Consensus        85 ----G~~~l   89 (117)
T 3elk_A           85 ----GKKFL   89 (117)
T ss_dssp             ----HHHHH
T ss_pred             ----HHHHH
Confidence                76654

>4esf_A PADR-like transcriptional regulator; PADR family, DNA binding protein, HTH fold; 2.20A {Bacillus cereus}

Probab=80.59  E-value=0.93  Score=32.42  Aligned_cols=71  Identities=15%  Similarity=0.097  Sum_probs=49.4

Q ss_pred             HHHHhcCcchhhhcCCCCCCHHHHHHHc------CCCCCCcccHHHHHHHHHhCCceeeecCC-CCCCccceeeCCCCCc
Q 040620           34 KRAIQLRIPDIINNSGQPMTLTQIIVAL------NVHPNKTRCTQILVCLLAHSGFFVQQKDG-KNEQEEESILLPPHLD  106 (214)
Q Consensus        34 ~~a~~lglfd~L~~~~~p~t~~eLA~~~------g~~~~~~~~l~rlLr~L~~~g~l~~~~~~-~~~~~~~~y~~t~~~~  106 (214)
                      +-.+++=|..+|..  +|++--+|++.+      ++++   ..+...|+-|...|++...... .++.....|++|+.  
T Consensus         9 ~g~l~~~IL~lL~~--~p~~Gyei~~~l~~~g~~~is~---gtlY~~L~rLe~~GlI~~~~~~~~~g~~rk~Y~LT~~--   81 (117)
T 4esf_A            9 KGSLEGCVLEIISR--RETYGYEITRHLNDLGFTEVVE---GTVYTILVRLEKKKLVNIEKKPSDMGPPRKFYSLNEA--   81 (117)
T ss_dssp             HHHHHHHHHHHHHH--SCBCHHHHHHHHHHHTCTTCCH---HHHHHHHHHHHHTTCEEEEEEC-----CEEEEEECHH--
T ss_pred             HChHHHHHHHHHHc--CCCCHHHHHHHHHHcCCCCCCc---cHHHHHHHHHHHCCCEEEEeecCCCCCCceEEEECHH--
Confidence            33344445556666  899999999998      6787   9999999999999999875321 01111245888888  


Q ss_pred             ccccccc
Q 040620          107 FFSRISL  113 (214)
Q Consensus       107 ~~s~~l~  113 (214)
                        ++..+
T Consensus        82 --G~~~l   86 (117)
T 4esf_A           82 --GRQEL   86 (117)
T ss_dssp             --HHHHH
T ss_pred             --HHHHH
Confidence              66654

>4auk_A Ribosomal RNA large subunit methyltransferase M; YGDE; HET: TLA PGE; 1.90A {Escherichia coli} PDB: 4atn_A* 4b17_A*

Probab=80.49  E-value=1.6  Score=37.85  Aligned_cols=33  Identities=12%  Similarity=0.021  Sum_probs=29.3

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +....++||+|+++|.++..++++  +.+++.+|.
T Consensus       209 l~~G~~vlDLGAaPGGWT~~l~~r--g~~V~aVD~  241 (375)
T 4auk_A          209 LANGMWAVDLGACPGGWTYQLVKR--NMWVYSVDN  241 (375)
T ss_dssp             SCTTCEEEEETCTTCHHHHHHHHT--TCEEEEECS
T ss_pred             CCCCCEEEEeCcCCCHHHHHHHHC--CCEEEEEEh
Confidence            456789999999999999999998  688999985

>3dv8_A Transcriptional regulator, CRP/FNR family; cyclic nucleotide-binding domain, structural genomics, joint for structural genomics; 2.55A {Eubacterium rectale atcc 33656}

Probab=80.26  E-value=1.7  Score=33.27  Aligned_cols=35  Identities=14%  Similarity=0.185  Sum_probs=33.2

Q ss_pred             CCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           51 PMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        51 p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      ++|-++||+.+|+++   ..+.|++..|...|++....
T Consensus       169 ~~t~~~lA~~lg~sr---~tvsR~l~~L~~~g~I~~~~  203 (220)
T 3dv8_A          169 KITHETIANHLGSHR---EVITRMLRYFQVEGLVKLSR  203 (220)
T ss_dssp             CCCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEET
T ss_pred             cCCHHHHHHHhCCCH---HHHHHHHHHHHHCCCEEeCC
Confidence            899999999999999   99999999999999998774

>3tka_A Ribosomal RNA small subunit methyltransferase H; HET: SAM CTN PG4; 2.25A {Escherichia coli}

Probab=80.21  E-value=2.1  Score=36.67  Aligned_cols=44  Identities=11%  Similarity=0.068  Sum_probs=36.2

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHC-CCCeEEEecCC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAF-PDTKCTVFACH  213 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dlp  213 (214)
                      ..+++.+.  ......+||..+|.|..+..|+++. |+.+++.+|.-
T Consensus        47 ~Evl~~L~--i~pggiyVD~TlG~GGHS~~iL~~lg~~GrVig~D~D   91 (347)
T 3tka_A           47 DEAVNGLN--IRPDGIYIDGTFGRGGHSRLILSQLGEEGRLLAIDRD   91 (347)
T ss_dssp             HHHHHHTC--CCTTCEEEESCCTTSHHHHHHHTTCCTTCEEEEEESC
T ss_pred             HHHHHhhC--CCCCCEEEEeCcCCCHHHHHHHHhCCCCCEEEEEECC
Confidence            45566665  4556799999999999999999985 88999999963

>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=80.10  E-value=1.2  Score=40.38  Aligned_cols=23  Identities=9%  Similarity=-0.045  Sum_probs=19.6

Q ss_pred             CCCcEEeecCCchHHHHHHHHHC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAF  202 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~  202 (214)
                      ...+|+|.+||+|.++..+++..
T Consensus       169 ~~~~VlDPaCGSG~fLi~a~~~l  191 (541)
T 2ar0_A          169 PREVVQDPAAGTAGFLIEADRYV  191 (541)
T ss_dssp             TTCCEEETTCTTTHHHHHHHHHH
T ss_pred             CCCeEecCCcccchHHHHHHHHH
Confidence            45699999999999999888753

---

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	214
d1fp2a1	101	a.4.5.29 (A:8-108) Isoflavone O-methyltransferase	5e-19
d1fp2a2	244	c.66.1.12 (A:109-352) Isoflavone O-methyltransfera	2e-16
d1fp1d2	244	c.66.1.12 (D:129-372) Chalcone O-methyltransferase	2e-14
d1fp1d1	110	a.4.5.29 (D:19-128) Chalcone O-methyltransferase {	2e-12
d1kyza1	107	a.4.5.29 (A:13-119) Caffeic acid/5-hydroxyferulic	1e-11
d1kyza2	243	c.66.1.12 (A:120-362) Caffeic acid/5-hydroxyferuli	5e-10
d1qzza1	92	a.4.5.29 (A:10-101) Aclacinomycin-10-hydroxylase R	3e-09
d1qzza2	256	c.66.1.12 (A:102-357) Aclacinomycin-10-hydroxylase	0.002
d1mkma1	75	a.4.5.33 (A:1-75) Transcriptional regulator IclR,	0.004

>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 = 76.5 bits (188), Expect = 5e-19
 Identities = 29/76 (38%), Positives = 50/76 (65%)

Query: 9  GAREHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKT 68
             E F+AQA ++ + Y ++ S+SLK A+++ IP+II N G+P++L+ ++  L V  +K 
Sbjct: 2  KPSEIFKAQALLYKHIYAFIDSMSLKWAVEMNIPNIIQNHGKPISLSNLVSILQVPSSKI 61

Query: 69 RCTQILVCLLAHSGFF 84
             + L+  LAH+GFF
Sbjct: 62 GNVRRLMRYLAHNGFF 77

>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 = 73.2 bits (179), Expect = 2e-16
 Identities = 40/108 (37%), Positives = 55/108 (50%), Gaps = 16/108 (14%)

Query: 118 STILLLIADATFTTSFHFLSTWLQNDDQTLFGTADG---------------IFYEAMITD 162
           + ++  + D T + S+H L  W+  +D TLFG   G                F +AM +D
Sbjct: 4   APMVECVLDPTLSGSYHELKKWIYEEDLTLFGVTLGSGFWDFLDKNPEYNTSFNDAMASD 63

Query: 163 FELIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
            +LI   L  DC+ V  GL+ +VDVGG TGT A+ I   FP  KC VF
Sbjct: 64  SKLINLAL-RDCDFVFDGLESIVDVGGGTGTTAKIICETFPKLKCIVF 110

>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 = 67.4 bits (164), Expect = 2e-14
 Identities = 20/108 (18%), Positives = 36/108 (33%), Gaps = 16/108 (14%)

Query: 118 STILLLIADATFTTSFHFLSTWLQNDDQTLFGTADG---------------IFYEAMITD 162
           ++    +        +      + ++D  LF    G               IF ++M+  
Sbjct: 5   ASFTTFLCYPALLQVWMNFKEAVVDEDIDLFKNVHGVTKYEFMGKDKKMNQIFNKSMVDV 64

Query: 163 FELIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
                  ++E       G+  LVDVGG +G     I + +P  K   F
Sbjct: 65  CATEMKRMLEIYTGFE-GISTLVDVGGGSGRNLELIISKYPLIKGINF 111

>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 = 59.4 bits (144), Expect = 2e-12
 Identities = 18/89 (20%), Positives = 29/89 (32%), Gaps = 6/89 (6%)

Query: 15 QAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQP---MTLTQIIVALNV---HPNKT 68
           A       T N +    L  AI L + +II  +  P   M+ ++I   L     H +  
Sbjct: 5  SACLSAMVLTTNLVYPAVLNAAIDLNLFEIIAKATPPGAFMSPSEIASKLPASTQHSDLP 64

Query: 69 RCTQILVCLLAHSGFFVQQKDGKNEQEEE 97
               ++ LLA             +   E
Sbjct: 65 NRLDRMLRLLASYSVLTSTTRTIEDGGAE 93

>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 = 57.1 bits (138), Expect = 1e-11
 Identities = 13/74 (17%), Positives = 32/74 (43%), Gaps = 3/74 (4%)

Query: 27 YMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNV---HPNKTRCTQILVCLLAHSGF 83
           +  + LK A++L + +II  +G    ++ I +A  +   +P+       ++ LLA    
Sbjct: 18 SVLPMILKSALELDLLEIIAKAGPGAQISPIEIASQLPTTNPDAPVMLDRMLRLLACYII 77

Query: 84 FVQQKDGKNEQEEE 97
                 + + + +
Sbjct: 78 LTCSVRTQQDGKVQ 91

>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 = 55.2 bits (132), Expect = 5e-10
 Identities = 26/106 (24%), Positives = 39/106 (36%), Gaps = 17/106 (16%)

Query: 120 ILLLIADATFTTSFHFLSTWLQNDDQTLFGTADG---------------IFYEAMITDFE 164
           + L+  D     S++ L   +  D    F  A G               +F + M     
Sbjct: 8   LNLMNQDKVLMESWYHLKDAVL-DGGIPFNKAYGMTAFEYHGTDPRFNKVFNKGMSDHST 66

Query: 165 LIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
           +    ++E       GLK LVDVGG TG +   I + +P  K   F
Sbjct: 67  ITMKKILETYTGFE-GLKSLVDVGGGTGAVINTIVSKYPTIKGINF 111

>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 = 50.1 bits (120), Expect = 3e-09
 Identities = 15/77 (19%), Positives = 26/77 (33%), Gaps = 5/77 (6%)

Query: 15 QAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQIL 74
          Q    +     N +  ++L+ A  LR+ D +       TL  +    + HP   +    L
Sbjct: 6  QDLDVLLKNLGNLVTPMALRVAATLRLVDHL--LAGADTLAGLADRTDTHP---QALSRL 60

Query: 75 VCLLAHSGFFVQQKDGK 91
          V  L   G     +   
Sbjct: 61 VRHLTVVGVLEGGEKQG 77

>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 = 35.7 bits (81), Expect = 0.002
 Identities = 15/57 (26%), Positives = 24/57 (42%), Gaps = 2/57 (3%)

Query: 154 IFYEAMITDFELIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVF 210
            F   M  D +L      +  +     ++ ++DVGG  G M  AIA   P  + T+ 
Sbjct: 57  SFDALMSCDEDLAYEAPADAYD--WSAVRHVLDVGGGNGGMLAAIALRAPHLRGTLV 111

>d1mkma1 a.4.5.33 (A:1-75) Transcriptional regulator IclR, N-terminal domain {Thermotoga maritima [TaxId: 2336]} Length = 75

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]

 Score = 32.7 bits (75), Expect = 0.004
 Identities = 14/60 (23%), Positives = 30/60 (50%), Gaps = 5/60 (8%)

Query: 32 SLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGK 91
          +LK+A    I D I  +   +++++I    N+    +   + +V L    GF +++KD +
Sbjct: 3  TLKKA--FEILDFIVKNPGDVSVSEIAEKFNMS--VSNAYKYMVVLEEK-GFVLRKKDKR 57

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	214
d1fp2a1	101	Isoflavone O-methyltransferase {Alfalfa (Medicago	99.79
d1kyza2	243	Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltra	99.75
d1fp1d2	244	Chalcone O-methyltransferase {Alfalfa (Medicago sa	99.74
d1fp2a2	244	Isoflavone O-methyltransferase {Alfalfa (Medicago	99.67
d1tw3a1	85	Carminomycin 4-O-methyltransferase {Streptomyces p	99.65
d1qzza1	92	Aclacinomycin-10-hydroxylase RdmB {Streptomyces pu	99.62
d1fp1d1	110	Chalcone O-methyltransferase {Alfalfa (Medicago sa	99.59
d1kyza1	107	Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltra	99.54
d1qzza2	256	Aclacinomycin-10-hydroxylase RdmB {Streptomyces pu	99.53
d1tw3a2	253	Carminomycin 4-O-methyltransferase {Streptomyces p	99.46
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	98.19
d2o57a1	282	Putative sarcosine dimethylglycine methyltransfera	97.69
d1nkva_	245	Hypothetical Protein YjhP {Escherichia coli [TaxId	97.52
d2fcaa1	204	tRNA (guanine-N(7)-)-methyltransferase TrmB {Bacil	97.48
d1yzha1	204	tRNA (guanine-N(7)-)-methyltransferase TrmB {Strep	97.46
d1im8a_	225	Hypothetical protein HI0319 (YecO) {Haemophilus in	97.46
d1p91a_	268	rRNA methyltransferase RlmA {Escherichia coli [Tax	97.28
d1g8sa_	230	Fibrillarin homologue {Archaeon Methanococcus jann	97.15
d1u2za_	406	Catalytic, N-terminal domain of histone methyltran	97.12
d2b3ta1	274	N5-glutamine methyltransferase, HemK {Escherichia	97.1
d2gh1a1	281	Methyltransferase BC2162 {Bacillus cereus [TaxId:	97.09
d1kpia_	291	CmaA2 {Mycobacterium tuberculosis [TaxId: 1773]}	97.05
d1wzna1	251	Hypothetical methyltransferase PH1305 {Archaeon Py	97.04
d1nt2a_	209	Fibrillarin homologue {Archaeon Archaeoglobus fulg	97.03
d1dusa_	194	Hypothetical protein MJ0882 {Archaeon Methanococcu	97.02
d2fk8a1	280	Methoxy mycolic acid synthase 4, Mma4 {Mycobacteri	97.02
d1kpga_	285	CmaA1 {Mycobacterium tuberculosis [TaxId: 1773]}	96.95
d1nw3a_	328	Catalytic, N-terminal domain of histone methyltran	96.95
d1l3ia_	186	Precorrin-6Y methyltransferase (CbiT) {Archaeon Me	96.92
d1ve3a1	226	Hypothetical protein PH0226 {Archaeon Pyrococcus h	96.85
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	96.84
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	96.84
d1y8ca_	246	Putative methyltransferase CAC2371 {Clostridium ac	96.83
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	96.78
d2i6ga1	198	Putative methyltransferase TehB {Salmonella typhim	96.78
d2nxca1	254	PrmA-like protein TTHA0656 (TT0836) {Thermus therm	96.7
d1zx0a1	229	Guanidinoacetate methyltransferase {Human (Homo sa	96.7
d2avna1	246	Hypothetical methyltransferase TM1389 {Thermotoga	96.67
d1xtpa_	254	Hypothetical protein Lmaj004091aaa (LmjF30.0810) {	96.61
d2h00a1	250	Methyltransferase 10 domain containing protein MET	96.6
d2hoea1	62	N-acetylglucosamine kinase {Thermotoga maritima [T	96.55
d1yb2a1	250	Hypothetical protein Ta0852 {Thermoplasma acidophi	96.52
d1xvaa_	292	Glycine N-methyltransferase {Rat (Rattus norvegicu	96.51
d2ex4a1	222	Adrenal gland protein AD-003 (C9orf32) {Human (Hom	96.51
d1dl5a1	213	Protein-L-isoaspartyl O-methyltransferase {Thermot	96.49
d1lnwa_	141	MexR repressor {Pseudomonas aeruginosa [TaxId: 287	96.48
d1z6ra1	70	Mlc protein N-terminal domain {Escherichia coli [T	96.41
d1ub9a_	100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	96.39
d2fyta1	311	Protein arginine N-methyltransferase 3, PRMT3 {Hum	96.35
d1lvaa3	64	C-terminal fragment of elongation factor SelB {Moo	96.34
d1i9ga_	264	Probable methyltransferase Rv2118c {Mycobacterium	96.33
d1o54a_	266	Hypothetical protein TM0748 {Thermotoga maritima [	96.29
d1r1ua_	94	Metal-sensing transcriptional repressor CzrA {Stap	96.2
d1r1ta_	98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	96.17
d2bzga1	229	Thiopurine S-methyltransferase {Human (Homo sapien	96.13
d1jqea_	280	Histamine methyltransferase {Human (Homo sapiens)	96.12
d2etha1	140	Putative transcriptional regulator TM0816 {Thermot	96.08
d1ne2a_	197	Hypothetical protein Ta1320 {Archaeon Thermoplasma	96.01
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	95.92
d1u2wa1	108	Cadmium efflux system accessory protein CadC {Stap	95.87
d1ulya_	190	Hypothetical protein PH1932 {Pyrococcus horikoshii	95.85
d1xd7a_	127	Hypothetical protein ywnA {Bacillus subtilis [TaxI	95.84
d1s3ja_	143	Putative transcriptional regulator YusO {Bacillus	95.82
d1oria_	316	Protein arginine N-methyltransferase 1, PRMT1 {Rat	95.75
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	95.74
d1wy7a1	201	Hypothetical protein PH1948 {Archaeon Pyrococcus h	95.7
d2b25a1	324	Hypothetical protein FLJ20628 {Human (Homo sapiens	95.63
d1vlma_	208	Possible histamine N-methyltransferase TM1293 {The	95.55
d1i1na_	224	Protein-L-isoaspartyl O-methyltransferase {Human (	95.51
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	95.39
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	95.37
d1g6q1_	328	Arginine methyltransferase, HMT1 {Baker's yeast (S	95.37
d2fbha1	137	Transcriptional regulator PA3341 {Pseudomonas aeru	95.37
d2bv6a1	136	Transcriptional regulator MgrA {Staphylococcus aur	95.32
d1g8aa_	227	Fibrillarin homologue {Archaeon Pyrococcus horikos	95.26
d2p4wa1	194	Transcriptional regulatory protein PF1790 {Pyrococ	95.22
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	95.16
d2hr3a1	145	Probable transcriptional regulator PA3067 {Pseudom	95.1
d2a14a1	257	Indolethylamine N-methyltransferase, INMT {Human (	95.02
d2a61a1	139	Transcriptional regulator TM0710 {Thermotoga marit	95.02
d1lj9a_	144	Transcriptional regulator SlyA {Enterococcus faeca	94.87
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	94.86
d1ylfa1	138	Hypothetical protein BC1842 {Bacillus cereus [TaxI	94.83
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	94.83
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	94.81
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	94.77
d1nv8a_	271	N5-glutamine methyltransferase, HemK {Thermotoga m	94.7
d3deua1	140	Transcriptional regulator SlyA {Salmonella typhimu	94.62
d1jgsa_	138	Multiple antibiotic resistance repressor, MarR {Es	94.55
d2ev0a1	61	Manganese transport regulator MntR {Bacillus subti	94.53
d3ctaa1	85	Ta1064 (RFK), N-terminal domain {Thermoplasma acid	94.41
d1ws6a1	171	Methyltransferase TTHA0928 {Thermus thermophilus [	94.32
d2g72a1	263	Phenylethanolamine N-methyltransferase, PNMTase {H	94.25
d1j75a_	57	Dlm-1 {Mouse (Mus musculus) [TaxId: 10090]}	94.13
d1r7ja_	90	Sso10a (SSO10449) {Archaeon Sulfolobus solfataricu	94.02
d1jsxa_	207	Glucose-inhibited division protein B (GidB) {Esche	94.02
d1vbfa_	224	Protein-L-isoaspartyl O-methyltransferase {Sulfolo	93.99
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	93.95
d1r18a_	223	Protein-L-isoaspartyl O-methyltransferase {Fruit f	93.77
d2hzta1	95	Putative transcriptional regulator YtcD {Bacillus	93.5
d1dpua_	69	C-terminal domain of RPA32 {Human (Homo sapiens) [	93.38
d2frna1	260	Hypothetical protein PH0793 {Pyrococcus horikoshii	93.32
d2fbia1	136	Probable transcriptional regulator PA4135 {Pseudom	93.07
d1z91a1	137	Organic hydroperoxide resistance transcriptional r	92.67
d1xdza_	239	Glucose-inhibited division protein B (GidB) {Bacil	92.3
d1jg1a_	215	Protein-L-isoaspartyl O-methyltransferase {Archaeo	92.27
d2gxba1	59	Z-alpha domain of dsRNA-specific adenosine deamina	92.26
d1yuba_	245	rRNA adenine dimethylase {Streptococcus pneumoniae	92.16
d1yyva1	114	Putative transcriptional regulator YtfH {Salmonell	91.81
d1hsja1	115	Staphylococcal accessory regulator A homolog, SarR	91.76
d2fpoa1	183	Methylase YhhF {Escherichia coli [TaxId: 562]}	91.67
d2frha1	115	Pleiotropic regulator of virulence genes, SarA {St	91.54
d1uira_	312	Spermidine synthase {Thermus thermophilus [TaxId:	91.37
d2cl5a1	214	Catechol O-methyltransferase, COMT {Rat (Rattus no	91.33
d1q1ha_	88	Transcription factor E/IIe-alpha, N-terminal domai	91.22
d1bl0a1	54	MarA {Escherichia coli [TaxId: 562]}	91.11
d1p4xa2	125	Staphylococcal accessory regulator A homolog, SarS	91.05
d1xmka1	73	Z-alpha domain of dsRNA-specific adenosine deamina	90.6
d2fxaa1	162	Protease production regulatory protein Hpr {Bacill	90.44
d1p4xa1	125	Staphylococcal accessory regulator A homolog, SarS	90.21
d2fbka1	172	Transcriptional regulator DR1159 {Deinococcus radi	90.17
d2fswa1	102	Hypothetical protein PG0823 {Porphyromonas gingiva	90.15
d2f2ea1	142	Hypothetical protein PA1607 {Pseudomonas aeruginos	89.98
d1sfua_	70	34L {Yaba-like disease virus, YLDV [TaxId: 132475]	89.72
d1zyba1	73	Probable transcription regulator BT4300, C-termina	89.29
d2hs5a1	69	Putative transcriptional regulator RHA1_ro03477 {R	89.25
d2avda1	219	COMT domain-containing protein 1, COMTD1 {Human (H	89.14
d2gaua1	81	Transcriptional regulator PG0396, C-terminal domai	89.14
d2zcwa1	82	Transcriptional regulator TTHA1359, C-terminal dom	88.99
d1i5za1	69	Catabolite gene activator protein (CAP), C-termina	88.83
d2p41a1	257	An RNA cap (nucleoside-2'-O-)-methyltransferase do	88.61
d1mjfa_	276	Putative spermidine synthetase PF0127 (SpeE) {Arch	88.53
d1z7ua1	108	Hypothetical protein EF0647 {Enterococcus faecalis	88.32
d1cf7a_	67	Cell cycle transcription factor E2F-4 {Human (Homo	88.27
d2as0a2	324	Hypothetical protein PH1915, middle and C-terminal	88.16
d1iy9a_	274	Spermidine synthase {Bacillus subtilis [TaxId: 142	88.1
d2o07a1	285	Spermidine synthase {Human (Homo sapiens) [TaxId:	87.68
d3bwga1	78	Transcriptional regulator YydK {Bacillus subtilis	87.64
d1d5ya1	54	Rob transcription factor, N-terminal domain {Esche	87.54
d1inla_	295	Spermidine synthase {Thermotoga maritima [TaxId: 2	87.42
d2b2ca1	312	Spermidine synthase {Caenorhabditis elegans [TaxId	87.31
d1hw1a1	74	Fatty acid responsive transcription factor FadR, N	87.29
d1ft9a1	80	CO-sensing protein CooA, C-terminal domain {Rhodos	87.09
d2fhpa1	182	Putative methylase EF2452 {Enterococcus faecalis [	86.49
d1xj5a_	290	Spermidine synthase {Thale cress (Arabidopsis thal	85.27
d3e5ua1	80	Chlorophenol reduction protein CprK {Desulfitobact	84.92
d1stza1	87	Heat-inducible transcription repressor HrcA, N-ter	84.69
d2f8la1	328	Hypothetical protein Lmo1582 {Listeria monocytogen	83.33
d1susa1	227	Caffeoyl-CoA O-methyltransferase {Alfalfa (Medicag	82.41
d1okra_	120	Methicillin resistance regulatory protein MecI {St	82.06
d2dk5a1	78	DNA-directed RNA polymerase III subunit RPC6, RPO3	81.54
d1wxxa2	318	Hypothetical protein TTHA1280, middle and C-termin	80.17

>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=99.79  E-value=1.7e-20  Score=133.94  Aligned_cols=95  Identities=36%  Similarity=0.585  Sum_probs=85.2

Q ss_pred             chhhhhHHHHHHHHHHHHhHHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecC
Q 040620           10 AREHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKD   89 (214)
Q Consensus        10 ~~~~~~~~~~l~~~~~g~~~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~   89 (214)
                      +.|..+++..+|++++||+.+++|++|+++||||+|+++++|+|++|||+++++++.+.+.|.|+||+|++.|+|.++.+
T Consensus         3 ~~e~~qaq~~l~~~~~gf~~s~aL~~aveLgi~d~l~~~~~p~t~~eLa~~~~~~~~~~~~L~RlLR~L~~~gi~~~~~~   82 (101)
T d1fp2a1           3 PSEIFKAQALLYKHIYAFIDSMSLKWAVEMNIPNIIQNHGKPISLSNLVSILQVPSSKIGNVRRLMRYLAHNGFFEIITK   82 (101)
T ss_dssp             STHHHHHHHHHHHHHTTHHHHHHHHHHHHTTHHHHHHHHTSCEEHHHHHHHHTCCGGGHHHHHHHHHHHHHTTSEEEEES
T ss_pred             hHHHHHHHHHHHHHHHhHHHHHHHHHHHHcCcHHHHHHcCCCCCHHHHHHHcCCCCccchHHHHHHHHHHhCCceeeecC
Confidence            56788999999999999999999999999999999987778999999999999987444679999999999999987653


Q ss_pred             CCCCCccceeeCCCCCcccccccc
Q 040620           90 GKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        90 ~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      .     +++|++|+.    |+.|+
T Consensus        83 ~-----~~~Y~lt~~----s~~Lv   97 (101)
T d1fp2a1          83 E-----EESYALTVA----SELLV   97 (101)
T ss_dssp             S-----SEEEEECHH----HHTTS
T ss_pred             C-----CCeEecCHH----HHHhh
Confidence            1     579999999    99887

>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=99.75  E-value=2.5e-18  Score=140.72  Aligned_cols=98  Identities=27%  Similarity=0.398  Sum_probs=87.2

Q ss_pred             cchHHHHHHhhccchhhhhHhHHHhhcCCCCChhhHHHH---------------HHHHHhhhhhhhhHHHHHhhcccccC
Q 040620          115 LQGSTILLLIADATFTTSFHFLSTWLQNDDQTLFGTADG---------------IFYEAMITDFELIASVLIEDCNEVSK  179 (214)
Q Consensus       115 ~~~~~~~~~~~~~~~~~~~~~l~~~lr~~~~~~f~~~~g---------------~f~~am~~~~~~~~~~~l~~~~~~~~  179 (214)
                      .++++++.+..++.++..|.+|.+++|+|+ ++|+..+|               .|+++|...+...+..+++.++| ++
T Consensus         3 ~s~~~~~~~~~~~~~~~~W~~L~~avrtG~-~~f~~~~G~~~~~~~~~~p~~~~~F~~aM~~~~~~~~~~~~~~~~~-~~   80 (243)
T d1kyza2           3 VSISALNLMNQDKVLMESWYHLKDAVLDGG-IPFNKAYGMTAFEYHGTDPRFNKVFNKGMSDHSTITMKKILETYTG-FE   80 (243)
T ss_dssp             CCTHHHHHHHTSHHHHGGGGGHHHHHHHCS-CHHHHHHSSCHHHHGGGCHHHHHHHHHHHHHHHHHHHHHHHHHCCT-TS
T ss_pred             CcHHHHHHHhcCHHHHHHHHHHHHHHhhCC-CHHHhhcCCCHHHHHHhCHHHHHHHHHHHhHhhhhHHHHHHHhccc-cc
Confidence            578899988888889999999999999997 57777665               79999999888888889999983 45


Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecCCC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFACHL  214 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~  214 (214)
                      +.++|||||||+|.++++++++||+++++++|+|+
T Consensus        81 ~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~  115 (243)
T d1kyza2          81 GLKSLVDVGGGTGAVINTIVSKYPTIKGINFDLPH  115 (243)
T ss_dssp             SCSEEEEETCTTSHHHHHHHHHCTTSEEEEEECTT
T ss_pred             CCcEEEEecCCCcHHHHHHHHHCCCCeEEEcccHH
Confidence            68899999999999999999999999999999995

>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=99.74  E-value=1.4e-18  Score=142.46  Aligned_cols=99  Identities=20%  Similarity=0.277  Sum_probs=83.2

Q ss_pred             cchHHHHHHhhccchhhhhHhHHHhhcCCCCChhhHHHH---------------HHHHHhhhhhhhhHHHHHhhcccccC
Q 040620          115 LQGSTILLLIADATFTTSFHFLSTWLQNDDQTLFGTADG---------------IFYEAMITDFELIASVLIEDCNEVSK  179 (214)
Q Consensus       115 ~~~~~~~~~~~~~~~~~~~~~l~~~lr~~~~~~f~~~~g---------------~f~~am~~~~~~~~~~~l~~~~~~~~  179 (214)
                      .++++++.++..+.++..|.+|.++++++++++|+.++|               .|+++|.+.+...++.+++.|+ .|+
T Consensus         2 g~l~~~~~~~~~p~~~~~w~~l~~~v~~g~~~~f~~~~G~~~~e~l~~~p~~~~~F~~aM~~~s~~~~~~l~~~~~-~f~   80 (244)
T d1fp1d2           2 GYLASFTTFLCYPALLQVWMNFKEAVVDEDIDLFKNVHGVTKYEFMGKDKKMNQIFNKSMVDVCATEMKRMLEIYT-GFE   80 (244)
T ss_dssp             CCCTHHHHHHTCHHHHHHHTTHHHHHHSCC--------------CCSSCHHHHHHHHHHHHHHHHHHHHHHHHHCC-TTT
T ss_pred             ccHHHHHHHHhCHHHHHHHHHHHHHHhcCCCCHhHHhcCCCHHHHHhhCHHHHHHHHHHHHHHHHHHHHHHHHhcc-ccc
Confidence            467889999989999999999999999998888988776               7999999998888888999998 478


Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecCCC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFACHL  214 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~  214 (214)
                      +.++|||||||+|.++++++++||++++|++|+|+
T Consensus        81 ~~~~vlDiGGG~G~~~~~l~~~~P~l~~~v~Dlp~  115 (244)
T d1fp1d2          81 GISTLVDVGGGSGRNLELIISKYPLIKGINFDLPQ  115 (244)
T ss_dssp             TCSEEEEETCTTSHHHHHHHHHCTTCEEEEEECHH
T ss_pred             CCcEEEEecCCCcHHHHHHHHHCCCCeEEEecchh
Confidence            89999999999999999999999999999999984

>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=99.67  E-value=5.3e-17  Score=132.95  Aligned_cols=98  Identities=40%  Similarity=0.669  Sum_probs=84.9

Q ss_pred             chHHHHHHhhccchhhhhHhHHHhhcCCCCChhhHHHH---------------HHHHHhhhhhhhhHHHHHhhcccccCC
Q 040620          116 QGSTILLLIADATFTTSFHFLSTWLQNDDQTLFGTADG---------------IFYEAMITDFELIASVLIEDCNEVSKG  180 (214)
Q Consensus       116 ~~~~~~~~~~~~~~~~~~~~l~~~lr~~~~~~f~~~~g---------------~f~~am~~~~~~~~~~~l~~~~~~~~~  180 (214)
                      ++.+++.++.++.++.+|..+++++|++.+++|+.++|               .|+++|...+......+.+ +.|.+++
T Consensus         2 s~ap~~~~~~~p~~~~~w~~l~~~~~~~~~~~f~~a~G~~~~e~l~~~pe~~~~F~~aM~~~s~~~~~~~~~-~~~~~~~   80 (244)
T d1fp2a2           2 CLAPMVECVLDPTLSGSYHELKKWIYEEDLTLFGVTLGSGFWDFLDKNPEYNTSFNDAMASDSKLINLALRD-CDFVFDG   80 (244)
T ss_dssp             CCHHHHHHHTCHHHHHGGGGHHHHHTCSSCCHHHHHHSSCHHHHHHHCHHHHHHHHHHHHHTHHHHHHHHHT-CHHHHTT
T ss_pred             ChHHHHHHHhCHHHHHHHHHHHHHHhcCCCCHHHHhhCCCHHHHHHhCHHHHHHHHHHhhhhhhhhhhhHhh-hcccccC
Confidence            56788888889999999999999999998899988876               7999998887766555544 3344888


Q ss_pred             CCcEEeecCCchHHHHHHHHHCCCCeEEEecCCC
Q 040620          181 LKPLVDVGGSTGTMARAIATAFPDTKCTVFACHL  214 (214)
Q Consensus       181 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~  214 (214)
                      .++|||||||+|.++++++++||+++++|||+|+
T Consensus        81 ~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~  114 (244)
T d1fp2a2          81 LESIVDVGGGTGTTAKIICETFPKLKCIVFDRPQ  114 (244)
T ss_dssp             CSEEEEETCTTSHHHHHHHHHCTTCEEEEEECHH
T ss_pred             ceEEEEecCCccHHHHHHHHhCCCCeEEEecCHH
Confidence            9999999999999999999999999999999984

>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=99.65  E-value=9.5e-17  Score=110.85  Aligned_cols=77  Identities=13%  Similarity=0.140  Sum_probs=71.5

Q ss_pred             HHHHHHHhHHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceee
Q 040620           21 WSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESIL  100 (214)
Q Consensus        21 ~~~~~g~~~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~  100 (214)
                      +..+.+++.+.+|++|+++||||+|++  +|+|++|||+++|+++   +.+.|+||+|++.|+|.+++       ++.|.
T Consensus         6 l~~l~~~~~~~aL~~av~L~ifd~l~~--gp~s~~eLA~~~g~~~---~~l~rlLr~l~a~gl~~e~~-------~~~y~   73 (85)
T d1tw3a1           6 LIRLGSLHTPMVVRTAATLRLVDHILA--GARTVKALAARTDTRP---EALLRLIRHLVAIGLLEEDA-------PGEFV   73 (85)
T ss_dssp             HHHHHCSHHHHHHHHHHHTTHHHHHHT--TCCBHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEEE-------TTEEE
T ss_pred             HHHHHchHHHHHHHHHHHcCcHHHhcc--CCCCHHHHHHHhCcCh---hHHHHHHHHHHHCCCeEecC-------CCeEe
Confidence            444578999999999999999999986  8999999999999999   99999999999999999987       68999


Q ss_pred             CCCCCcccccccc
Q 040620          101 LPPHLDFFSRISL  113 (214)
Q Consensus       101 ~t~~~~~~s~~l~  113 (214)
                      +|+.    |+.|.
T Consensus        74 lt~~----s~~L~   82 (85)
T d1tw3a1          74 PTEV----GELLA   82 (85)
T ss_dssp             ECTT----GGGGS
T ss_pred             cCHH----HHHhh
Confidence            9999    98886

>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=99.62  E-value=1.9e-16  Score=110.78  Aligned_cols=85  Identities=18%  Similarity=0.157  Sum_probs=77.0

Q ss_pred             hHHHHHHHHHHHHhHHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCC
Q 040620           15 QAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQ   94 (214)
Q Consensus        15 ~~~~~l~~~~~g~~~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~   94 (214)
                      +....+++++.+++.+.+|++|+++||||+|++  +|+|++|||+++|+++   +.+.|+||+|++.|+|+++++.    
T Consensus         6 ~~~d~ll~~~~~~~~~~~L~~aveL~ifd~L~~--gp~t~~eLA~~~g~~~---~~l~rLlr~L~a~gll~~~~d~----   76 (92)
T d1qzza1           6 QDLDVLLKNLGNLVTPMALRVAATLRLVDHLLA--GADTLAGLADRTDTHP---QALSRLVRHLTVVGVLEGGEKQ----   76 (92)
T ss_dssp             HHHHHHHHTTTCCHHHHHHHHHHHTTHHHHHHT--TCCSHHHHHHHHTCCH---HHHHHHHHHHHHTTSEECCCC-----
T ss_pred             hhHHHHHHHHHchHHHHHHHHHHHcCchHHHhC--CCCCHHHHHHHHCcCc---hHHHHHHHHHHHCCCeeeecCC----
Confidence            667889999999999999999999999999987  8999999999999999   9999999999999999988621    


Q ss_pred             ccceeeCCCCCcccccccc
Q 040620           95 EEESILLPPHLDFFSRISL  113 (214)
Q Consensus        95 ~~~~y~~t~~~~~~s~~l~  113 (214)
                       .+.|++|+.    +..|.
T Consensus        77 -~~~~~~t~~----g~lL~   90 (92)
T d1qzza1          77 -GRPLRPTRL----GMLLA   90 (92)
T ss_dssp             -CCCCEECTT----GGGGS
T ss_pred             -CceecccHH----HHhcc
Confidence             457888999    88775

>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=99.59  E-value=9.2e-16  Score=110.05  Aligned_cols=98  Identities=19%  Similarity=0.192  Sum_probs=80.6

Q ss_pred             hhhhHHHHHHHHHHHHhHHHHHHHHHhcCcchhhhcCCCC---CCHHHHHHHcCC---CCCCcccHHHHHHHHHhCCcee
Q 040620           12 EHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQP---MTLTQIIVALNV---HPNKTRCTQILVCLLAHSGFFV   85 (214)
Q Consensus        12 ~~~~~~~~l~~~~~g~~~~~~L~~a~~lglfd~L~~~~~p---~t~~eLA~~~g~---~~~~~~~l~rlLr~L~~~g~l~   85 (214)
                      +.+++....++++.+++.+++|++|++|||+|+|+.+|+|   +|+.|||.++.+   +|..+..|.|+||.|++.|+|.
T Consensus         2 ~~~~~~l~a~~L~~~~v~pMaLk~AieLgI~diI~~~G~~~~~ls~~ela~~lp~~~~~p~~~~~L~RiLRlLas~~vf~   81 (110)
T d1fp1d1           2 TEDSACLSAMVLTTNLVYPAVLNAAIDLNLFEIIAKATPPGAFMSPSEIASKLPASTQHSDLPNRLDRMLRLLASYSVLT   81 (110)
T ss_dssp             CHHHHHHHHHHHHHTTHHHHHHHHHHHTTHHHHHHTCSSTTCCBCHHHHHTTSCGGGCCTTHHHHHHHHHHHHHHTTSEE
T ss_pred             chHHHHHHHHHHHHhhHHHHHHHHHHHcCCHHHHHHcCCCCCCCCHHHHHHhCCCCCCCccHHHHHHHHHHHHHHcCccc
Confidence            5678899999999999999999999999999999987544   899999999886   3422246999999999999998


Q ss_pred             eecCC-CCCCccceeeCCCCCcccccccc
Q 040620           86 QQKDG-KNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        86 ~~~~~-~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      +...+ .+++.+..|.+||.    |++|+
T Consensus        82 ~~~~~~~~g~~e~~Y~Ltpv----sk~Lv  106 (110)
T d1fp1d1          82 STTRTIEDGGAERVYGLSMV----GKYLV  106 (110)
T ss_dssp             EEEEECTTSCEEEEEEECTT----GGGGS
T ss_pred             cccccCCCCCeeeEEecchh----hHhhc
Confidence            66432 22222457999999    99998

>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=99.54  E-value=1.6e-15  Score=108.38  Aligned_cols=98  Identities=15%  Similarity=0.170  Sum_probs=80.3

Q ss_pred             hhhhHHHHHHHHHHHHhHHHHHHHHHhcCcchhhhcCC--CCCCHHHHHHHcCC-CCCCcccHHHHHHHHHhCCceeeec
Q 040620           12 EHFQAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSG--QPMTLTQIIVALNV-HPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        12 ~~~~~~~~l~~~~~g~~~~~~L~~a~~lglfd~L~~~~--~p~t~~eLA~~~g~-~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      +.+++....++++.+++.+++|++|++|||+|+|+..|  .++|..|||.++.. +|+++..|+|+||.|++.|+|.+..
T Consensus         3 ~dee~~l~a~~L~~~~v~pmaLk~AieLgI~DiI~~~G~~~~ls~~eia~~l~~~~p~~~~~L~RilR~Las~~vf~~~~   82 (107)
T d1kyza1           3 SDEEANLFAMQLASASVLPMILKSALELDLLEIIAKAGPGAQISPIEIASQLPTTNPDAPVMLDRMLRLLACYIILTCSV   82 (107)
T ss_dssp             CHHHHHHHHHHHHTTTHHHHHHHHHHHTTHHHHHHTTCTTCCBCHHHHHHTSSCCCTTHHHHHHHHHHHHHHTTSEEEEE
T ss_pred             ccHHHHHHHHHHHHhhHHHHHHHHHHHcCCHHHHHHcCCCCCCCHHHHHHhcCCCCCcchHHHHHHHHHHHhcCceEEee
Confidence            34667788889999999999999999999999999874  47899999999988 4433357999999999999998754


Q ss_pred             CC-CCCCccceeeCCCCCcccccccc
Q 040620           89 DG-KNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        89 ~~-~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      .. .+|+.+.+|.+||.    |++|+
T Consensus        83 ~~~~dg~~~~~Y~LTpv----sk~Lv  104 (107)
T d1kyza1          83 RTQQDGKVQRLYGLATV----AKYLV  104 (107)
T ss_dssp             EECTTSCEEEEEEECHH----HHHHS
T ss_pred             ecCCCCCeeeEEecchh----HHhhc
Confidence            32 22222457999999    99987

>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=99.53  E-value=3.2e-15  Score=122.80  Aligned_cols=98  Identities=21%  Similarity=0.217  Sum_probs=80.0

Q ss_pred             ccchHHHHHHhhccc-hhhhhHhHHHhhcCCCCChhhHHHH---------------HHHHHhhhhhhhhHHHHHhhcccc
Q 040620          114 QLQGSTILLLIADAT-FTTSFHFLSTWLQNDDQTLFGTADG---------------IFYEAMITDFELIASVLIEDCNEV  177 (214)
Q Consensus       114 ~~~~~~~~~~~~~~~-~~~~~~~l~~~lr~~~~~~f~~~~g---------------~f~~am~~~~~~~~~~~l~~~~~~  177 (214)
                      |.++++++.+..... ...+|.+|.+.+|+|.+ .|...+|               .|+++|...+...++.+++.+|  
T Consensus         2 p~~~~~~~~l~~~~~~~~~~~~~L~~~~rtG~~-~~~~~~G~~~~e~~~~~p~~~~~f~~~m~~~~~~~~~~~~~~~d--   78 (256)
T d1qzza2           2 PAQQRAWLDLNGAVSHADLAFTGLLDVVRTGRP-AYAGRYGRPFWEDLSADVALADSFDALMSCDEDLAYEAPADAYD--   78 (256)
T ss_dssp             TTCHHHHHCTTSHHHHHHGGGGGHHHHHHHSCC-SHHHHHSSCHHHHHHHCHHHHHHHHHTCGGGSTTTTHHHHHTSC--
T ss_pred             cHHHHHHHhhcCchhhhHhhHHHHHHHHHhCCc-hhhhhhCCCHHHHHHhCHHHHHHHHHHHHhhHHHHHHHHHhcCC--
Confidence            345677765543322 23579999999999974 4555444               7899999888888888999999  


Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCCC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACHL  214 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp~  214 (214)
                      |++.++|||||||+|.++..++++||+++++++|+|+
T Consensus        79 ~~~~~~vlDvG~G~G~~~~~l~~~~P~~~~~~~Dlp~  115 (256)
T d1qzza2          79 WSAVRHVLDVGGGNGGMLAAIALRAPHLRGTLVELAG  115 (256)
T ss_dssp             CTTCCEEEEETCTTSHHHHHHHHHCTTCEEEEEECHH
T ss_pred             CccCCEEEEECCCCCHHHHHHHHhhcCcEEEEecChH
Confidence            8899999999999999999999999999999999973

>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=99.46  E-value=5.5e-14  Score=114.77  Aligned_cols=83  Identities=22%  Similarity=0.291  Sum_probs=73.0

Q ss_pred             hhhhhHhHHHhhcCCCCChhhHHHH---------------HHHHHhhhhhhhhHHHHHhhcccccCCCCcEEeecCCchH
Q 040620          129 FTTSFHFLSTWLQNDDQTLFGTADG---------------IFYEAMITDFELIASVLIEDCNEVSKGLKPLVDVGGSTGT  193 (214)
Q Consensus       129 ~~~~~~~l~~~lr~~~~~~f~~~~g---------------~f~~am~~~~~~~~~~~l~~~~~~~~~~~~vvDVGGG~G~  193 (214)
                      ...+|.+|++.+|+|+ .+|..++|               .|.++|...+...++.+++.+|  |++.++|||||||+|.
T Consensus        17 ~~~~~~~L~~~vr~G~-~~~~~~~G~~~~~~~~~~~~~~~~f~~~m~~~~~~~~~~~~~~~d--~~~~~~VLDvGcG~G~   93 (253)
T d1tw3a2          17 ADISFTRLPDAIRTGR-PTYESIYGKPFYEDLAGRPDLRASFDSLLACDQDVAFDAPAAAYD--WTNVRHVLDVGGGKGG   93 (253)
T ss_dssp             HGGGGGGHHHHHHHCC-CCHHHHHSSCHHHHHHTCHHHHHHHHHHHTTTTTTTTHHHHHHSC--CTTCSEEEEETCTTSH
T ss_pred             ccccHHHHHHHHHhCC-chhhhccCCCHHHHHhhCHHHHHHHHHHHHHhHHHHHHHHHhhcC--CccCCEEEEeCCCCCH
Confidence            3467999999999997 45665554               6899999888888888999999  8899999999999999


Q ss_pred             HHHHHHHHCCCCeEEEecCCC
Q 040620          194 MARAIATAFPDTKCTVFACHL  214 (214)
Q Consensus       194 ~~~~l~~~~P~l~~~v~Dlp~  214 (214)
                      ++..+++++|+++++++|+|+
T Consensus        94 ~~~~la~~~p~~~~~~~D~~~  114 (253)
T d1tw3a2          94 FAAAIARRAPHVSATVLEMAG  114 (253)
T ss_dssp             HHHHHHHHCTTCEEEEEECTT
T ss_pred             HHHHHHHhcceeEEEEccCHH
Confidence            999999999999999999984

>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=98.19  E-value=3.3e-07  Score=60.45  Aligned_cols=56  Identities=16%  Similarity=0.282  Sum_probs=50.5

Q ss_pred             cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      +.|.+.+..++.|+|+.|||+++|+++   ..++|+|..|...|++.+++       +++|.+++.
T Consensus         8 l~IL~~~a~~~~~~s~~eia~~~~~~~---st~~rll~tL~~~g~l~~~~-------~g~y~lG~~   63 (75)
T d1mkma1           8 FEILDFIVKNPGDVSVSEIAEKFNMSV---SNAYKYMVVLEEKGFVLRKK-------DKRYVPGYK   63 (75)
T ss_dssp             HHHHHHHHHCSSCBCHHHHHHHTTCCH---HHHHHHHHHHHHTTSEEECT-------TSCEEECTH
T ss_pred             HHHHHHHHhCCCCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEECC-------CCCEeecHH
Confidence            457788887768999999999999999   99999999999999999986       688999887

>d2o57a1 c.66.1.18 (A:16-297) Putative sarcosine dimethylglycine methyltransferase {Red algae (Galdieria sulphuraria) [TaxId: 130081]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Mycolic acid cyclopropane synthase
domain: Putative sarcosine dimethylglycine methyltransferase
species: Red algae (Galdieria sulphuraria) [TaxId: 130081]

Probab=97.69  E-value=2.9e-05  Score=62.58  Aligned_cols=54  Identities=22%  Similarity=0.188  Sum_probs=40.4

Q ss_pred             HHHhhhhhhhhHHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          156 YEAMITDFELIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       156 ~~am~~~~~~~~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..++.......+..+....+  +++..+|||||||+|.++..|++++ +.+++++|+
T Consensus        45 ~~a~~~~~~~~~~~l~~~~~--l~~~~~vLDiGcG~G~~~~~la~~~-~~~v~gvD~   98 (282)
T d2o57a1          45 REASLRTDEWLASELAMTGV--LQRQAKGLDLGAGYGGAARFLVRKF-GVSIDCLNI   98 (282)
T ss_dssp             HHHHHHHHHHHHHHHHHTTC--CCTTCEEEEETCTTSHHHHHHHHHH-CCEEEEEES
T ss_pred             HHHHHHHHHHHHHHHHHhcC--CCCCCEEEEeCCCCcHHHhhhhccC-CcEEEEEec
Confidence            34444444444455555555  7778999999999999999999875 678999986

>d1nkva_ c.66.1.21 (A:) Hypothetical Protein YjhP {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Hypothetical Protein YjhP
domain: Hypothetical Protein YjhP
species: Escherichia coli [TaxId: 562]

Probab=97.52  E-value=6.2e-05  Score=59.25  Aligned_cols=42  Identities=19%  Similarity=0.120  Sum_probs=34.8

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+.+.+.  +.+..+|||||||+|.++..++++++ .+++.+|+
T Consensus        23 ~~l~~~~~--l~pg~~VLDiGCG~G~~~~~la~~~~-~~v~GvD~   64 (245)
T d1nkva_          23 ATLGRVLR--MKPGTRILDLGSGSGEMLCTWARDHG-ITGTGIDM   64 (245)
T ss_dssp             HHHHHHTC--CCTTCEEEEETCTTCHHHHHHHHHTC-CEEEEEES
T ss_pred             HHHHHHcC--CCCCCEEEEEcCCCCHHHHHHHHhcC-CEEEEEec
Confidence            34556555  66788999999999999999998876 78999987

>d2fcaa1 c.66.1.53 (A:10-213) tRNA (guanine-N(7)-)-methyltransferase TrmB {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: TrmB-like
domain: tRNA (guanine-N(7)-)-methyltransferase TrmB
species: Bacillus subtilis [TaxId: 1423]

Probab=97.48  E-value=4.8e-05  Score=59.06  Aligned_cols=32  Identities=19%  Similarity=0.253  Sum_probs=29.8

Q ss_pred             CCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          181 LKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       181 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+||||||.|.++..+++.+|+..++++|+
T Consensus        30 ~PlvLeIGcG~G~~~~~lA~~~p~~~~iGiD~   61 (204)
T d2fcaa1          30 NPIHIEVGTGKGQFISGMAKQNPDINYIGIEL   61 (204)
T ss_dssp             CCEEEEECCTTSHHHHHHHHHCTTSEEEEECS
T ss_pred             CceEEEEEecCcHHHHHHHHhCCCCcEEEeec
Confidence            34789999999999999999999999999996

>d1yzha1 c.66.1.53 (A:8-211) tRNA (guanine-N(7)-)-methyltransferase TrmB {Streptococcus pneumoniae [TaxId: 1313]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: TrmB-like
domain: tRNA (guanine-N(7)-)-methyltransferase TrmB
species: Streptococcus pneumoniae [TaxId: 1313]

Probab=97.46  E-value=5.1e-05  Score=58.88  Aligned_cols=32  Identities=22%  Similarity=0.288  Sum_probs=29.9

Q ss_pred             CCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          181 LKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       181 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+||||||.|.++..+++.+|+..++++|+
T Consensus        32 ~plvLdIGcG~G~~~~~lA~~~p~~~~iGid~   63 (204)
T d1yzha1          32 NPIHVEVGSGKGAFVSGMAKQNPDINYIGIDI   63 (204)
T ss_dssp             CCEEEEESCTTSHHHHHHHHHCTTSEEEEEES
T ss_pred             CCeEEEEeccCCHHHHHHHHHCCCCceEEEec
Confidence            45799999999999999999999999999986

>d1im8a_ c.66.1.14 (A:) Hypothetical protein HI0319 (YecO) {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Hypothetical protein HI0319 (YecO)
domain: Hypothetical protein HI0319 (YecO)
species: Haemophilus influenzae [TaxId: 727]

Probab=97.46  E-value=4.6e-05  Score=59.26  Aligned_cols=34  Identities=18%  Similarity=0.179  Sum_probs=30.5

Q ss_pred             CCCCcEEeecCCchHHHHHHHHH--CCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATA--FPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~--~P~l~~~v~Dl  212 (214)
                      .+..+|||||||+|..+..|++.  +|+.+++++|+
T Consensus        38 ~~~~~vLDlGCGtG~~~~~l~~~~~~~~~~v~giD~   73 (225)
T d1im8a_          38 TADSNVYDLGCSRGAATLSARRNINQPNVKIIGIDN   73 (225)
T ss_dssp             CTTCEEEEESCTTCHHHHHHHHTCCCSSCEEEEECS
T ss_pred             CCCCEEEEeccchhhHHHHHHHhhcCCCCceEEeCC
Confidence            45679999999999999999986  58999999997

>d1p91a_ c.66.1.33 (A:) rRNA methyltransferase RlmA {Escherichia coli [TaxId: 562]}

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

Probab=97.28  E-value=0.00013  Score=58.54  Aligned_cols=34  Identities=21%  Similarity=0.357  Sum_probs=31.5

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+..+|||||||+|.++..+++.+|+.+++.+|+
T Consensus        83 ~~~~~iLDiGcG~G~~~~~l~~~~~~~~~~giD~  116 (268)
T d1p91a_          83 DKATAVLDIGCGEGYYTHAFADALPEITTFGLDV  116 (268)
T ss_dssp             TTCCEEEEETCTTSTTHHHHHHTCTTSEEEEEES
T ss_pred             CCCCEEEEeCCCCcHHHHHHHHHCCCCEEEEecc
Confidence            3567999999999999999999999999999996

>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=97.15  E-value=0.00016  Score=57.04  Aligned_cols=35  Identities=17%  Similarity=0.144  Sum_probs=32.7

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+..+|||||||+|..+..+++..|+-+++.+|+
T Consensus        72 ikpG~~VLDlGcGsG~~~~~la~~~~~g~V~aVDi  106 (230)
T d1g8sa_          72 IKRDSKILYLGASAGTTPSHVADIADKGIVYAIEY  106 (230)
T ss_dssp             CCTTCEEEEESCCSSHHHHHHHHHTTTSEEEEEES
T ss_pred             CCCCCEEEEeCEEcCHHHHHHHHhCCCCEEEEEeC
Confidence            66788999999999999999999999999999986

>d1u2za_ c.66.1.31 (A:) Catalytic, N-terminal domain of histone methyltransferase Dot1l {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Catalytic, N-terminal domain of histone methyltransferase Dot1l
domain: Catalytic, N-terminal domain of histone methyltransferase Dot1l
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.12  E-value=0.00023  Score=60.68  Aligned_cols=45  Identities=16%  Similarity=0.124  Sum_probs=37.2

Q ss_pred             HHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          167 ASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       167 ~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                      +..+++..+  .....+|||||||.|..+..+++.+|..+++++|+-
T Consensus       205 i~~Il~~l~--Lkpgd~fLDLGCG~G~~vl~aA~~~g~~~v~GIDiS  249 (406)
T d1u2za_         205 LSDVYQQCQ--LKKGDTFMDLGSGVGNCVVQAALECGCALSFGCEIM  249 (406)
T ss_dssp             HHHHHHHTT--CCTTCEEEEESCTTSHHHHHHHHHHCCSEEEEEECC
T ss_pred             HHHHHHHhC--CCCCCEEEeCCCCCcHHHHHHHHHcCCCeEEEEeCC
Confidence            344555554  666789999999999999999999998899999863

>d2b3ta1 c.66.1.30 (A:2-275) N5-glutamine methyltransferase, HemK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: N5-glutamine methyltransferase, HemK
domain: N5-glutamine methyltransferase, HemK
species: Escherichia coli [TaxId: 562]

Probab=97.10  E-value=0.00039  Score=56.21  Aligned_cols=34  Identities=26%  Similarity=0.379  Sum_probs=31.0

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ....+|+|+|||+|..++.+++.+|+++++..|.
T Consensus       107 ~~~~~vlDlGtGSG~I~i~la~~~p~~~v~avDi  140 (274)
T d2b3ta1         107 EQPCRILDLGTGTGAIALALASERPDCEIIAVDR  140 (274)
T ss_dssp             SSCCEEEEETCTTSHHHHHHHHHCTTSEEEEECS
T ss_pred             ccccceeeeehhhhHHHHHHHhhCCcceeeeccc
Confidence            3456899999999999999999999999999986

>d2gh1a1 c.66.1.49 (A:13-293) Methyltransferase BC2162 {Bacillus cereus [TaxId: 1396]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: BC2162-like
domain: Methyltransferase BC2162
species: Bacillus cereus [TaxId: 1396]

Probab=97.09  E-value=0.00014  Score=58.60  Aligned_cols=44  Identities=20%  Similarity=0.250  Sum_probs=36.0

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCC-CeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPD-TKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dl  212 (214)
                      +.+++.. |...+..+|||||||+|.++..+++.+|. .+++++|+
T Consensus        16 ~~l~~~~-~~~~~~~~ILDiGcG~G~~~~~la~~~~~~~~v~giD~   60 (281)
T d2gh1a1          16 SFLVNTV-WKITKPVHIVDYGCGYGYLGLVLMPLLPEGSKYTGIDS   60 (281)
T ss_dssp             HHHHHTT-SCCCSCCEEEEETCTTTHHHHHHTTTSCTTCEEEEEEC
T ss_pred             HHHHHHH-hccCCcCEEEEecCcCCHHHHHHHHhCCCCCEEEEEec
Confidence            4455544 34677889999999999999999999985 78999996

>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=97.05  E-value=0.00037  Score=56.72  Aligned_cols=43  Identities=14%  Similarity=0.221  Sum_probs=35.9

Q ss_pred             HHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          167 ASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       167 ~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+++...  ..+..+|||||||.|.+++.++++++ .+++++++
T Consensus        50 ~~~~~~~l~--l~~G~~VLDiGCG~G~~~~~~a~~~g-~~v~git~   92 (291)
T d1kpia_          50 RKLALDKLN--LEPGMTLLDIGCGWGSTMRHAVAEYD-VNVIGLTL   92 (291)
T ss_dssp             HHHHHHTTC--CCTTCEEEEETCTTSHHHHHHHHHHC-CEEEEEES
T ss_pred             HHHHHHhcC--CCCCCEEEEecCcchHHHHHHHHhcC-cceeeccc
Confidence            345666666  77889999999999999999999997 58888876

>d1wzna1 c.66.1.43 (A:1-251) Hypothetical methyltransferase PH1305 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: CAC2371-like
domain: Hypothetical methyltransferase PH1305
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=97.04  E-value=0.00036  Score=54.44  Aligned_cols=41  Identities=10%  Similarity=0.141  Sum_probs=32.3

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+++.+.  ..+.++|||||||+|..+..++++.  .+++++|+
T Consensus        31 ~~~~~~~~--~~~~~~iLDiGcGtG~~~~~l~~~~--~~v~gvD~   71 (251)
T d1wzna1          31 EEIFKEDA--KREVRRVLDLACGTGIPTLELAERG--YEVVGLDL   71 (251)
T ss_dssp             HHHHHHTC--SSCCCEEEEETCTTCHHHHHHHHTT--CEEEEEES
T ss_pred             HHHHHHhc--CCCCCEEEEeCCCCCccchhhcccc--eEEEEEee
Confidence            34455554  5567899999999999999999974  47888886

>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=97.03  E-value=0.00044  Score=53.50  Aligned_cols=35  Identities=14%  Similarity=0.225  Sum_probs=32.8

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+..+|||||||+|..+..+++..|+.+++.+|.
T Consensus        54 lkpg~~VLDlGcG~G~~~~~la~~v~~g~V~gvDi   88 (209)
T d1nt2a_          54 LRGDERVLYLGAASGTTVSHLADIVDEGIIYAVEY   88 (209)
T ss_dssp             CCSSCEEEEETCTTSHHHHHHHHHTTTSEEEEECC
T ss_pred             CCCCCEEEEeCCcCCHHHHHHHHhccCCeEEEEeC
Confidence            66788999999999999999999999999999996

>d1dusa_ c.66.1.4 (A:) Hypothetical protein MJ0882 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Hypothetical protein MJ0882
domain: Hypothetical protein MJ0882
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=97.02  E-value=0.0003  Score=53.44  Aligned_cols=39  Identities=21%  Similarity=0.291  Sum_probs=30.7

Q ss_pred             HHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          170 LIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       170 ~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +++.++  ..+..+|||||||+|.+++.+++..|+  ++++|+
T Consensus        44 Li~~l~--~~~~~~VLDiGcG~G~~~~~la~~~~~--v~~iD~   82 (194)
T d1dusa_          44 LVENVV--VDKDDDILDLGCGYGVIGIALADEVKS--TTMADI   82 (194)
T ss_dssp             HHHHCC--CCTTCEEEEETCTTSHHHHHHGGGSSE--EEEEES
T ss_pred             HHHhCC--cCCCCeEEEEeecCChhHHHHHhhccc--cceeee
Confidence            455555  456789999999999999999999885  555564

>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=97.02  E-value=0.0004  Score=56.13  Aligned_cols=43  Identities=19%  Similarity=0.230  Sum_probs=35.9

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                      ..+++...  ..+..+|||||||.|.++..++++++ .+++++|+-
T Consensus        42 ~~~~~~l~--l~~g~~VLDiGCG~G~~a~~~a~~~g-~~v~gi~ls   84 (280)
T d2fk8a1          42 DLNLDKLD--LKPGMTLLDIGCGWGTTMRRAVERFD-VNVIGLTLS   84 (280)
T ss_dssp             HHHHTTSC--CCTTCEEEEESCTTSHHHHHHHHHHC-CEEEEEESC
T ss_pred             HHHHHHcC--CCCCCEEEEecCCchHHHHHHHHhCc-eeEEEecch
Confidence            45667766  77789999999999999999988875 599998863

>d1kpga_ c.66.1.18 (A:) CmaA1 {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Mycolic acid cyclopropane synthase
domain: CmaA1
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=96.95  E-value=0.00049  Score=55.85  Aligned_cols=42  Identities=12%  Similarity=0.124  Sum_probs=35.2

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+++...  ..+..+|||||||.|..++.++++++ .+++++++
T Consensus        52 ~~~~~~l~--l~~G~~VLDiGCG~G~~a~~~a~~~g-~~v~git~   93 (285)
T d1kpga_          52 DLALGKLG--LQPGMTLLDVGCGWGATMMRAVEKYD-VNVVGLTL   93 (285)
T ss_dssp             HHHHTTTT--CCTTCEEEEETCTTSHHHHHHHHHHC-CEEEEEES
T ss_pred             HHHHHHcC--CCCCCEEEEecCcchHHHHHHHhcCC-cceEEEec
Confidence            44566665  67789999999999999999999995 89888875

>d1nw3a_ c.66.1.31 (A:) Catalytic, N-terminal domain of histone methyltransferase Dot1l {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Catalytic, N-terminal domain of histone methyltransferase Dot1l
domain: Catalytic, N-terminal domain of histone methyltransferase Dot1l
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.95  E-value=0.00055  Score=56.47  Aligned_cols=43  Identities=16%  Similarity=0.183  Sum_probs=37.1

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+++...  ..+..+|+|||||.|.++..+++.+|..+++++|+
T Consensus       141 ~~~~~~~~--l~~~~~vlD~GcG~G~~~~~~a~~~~~~~~~Gid~  183 (328)
T d1nw3a_         141 AQMIDEIK--MTDDDLFVDLGSGVGQVVLQVAAATNCKHHYGVEK  183 (328)
T ss_dssp             HHHHHHSC--CCTTCEEEEETCTTSHHHHHHHHHCCCSEEEEEEC
T ss_pred             HHHHHHcC--CCCCCEEEEcCCCCCHHHHHHHHHhCCCeEEEEeC
Confidence            44566665  66778999999999999999999999999999986

>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=96.92  E-value=0.00036  Score=52.67  Aligned_cols=39  Identities=18%  Similarity=0.164  Sum_probs=30.8

Q ss_pred             HHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          170 LIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       170 ~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ++....  ..+..+|||||||+|.+++.+++..+  +++.+|+
T Consensus        25 il~~l~--~~~g~~VLDiGcGsG~~s~~lA~~~~--~V~avD~   63 (186)
T d1l3ia_          25 IMCLAE--PGKNDVAVDVGCGTGGVTLELAGRVR--RVYAIDR   63 (186)
T ss_dssp             HHHHHC--CCTTCEEEEESCTTSHHHHHHHTTSS--EEEEEES
T ss_pred             HHHhcC--CCCCCEEEEEECCeEcccccccccce--EEEEecC
Confidence            344444  55678999999999999999988754  7888886

>d1ve3a1 c.66.1.43 (A:2-227) Hypothetical protein PH0226 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: CAC2371-like
domain: Hypothetical protein PH0226
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=96.85  E-value=0.00064  Score=51.74  Aligned_cols=31  Identities=6%  Similarity=0.034  Sum_probs=27.0

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+|||||||+|.++..+++.  +.+++++|+
T Consensus        37 ~~~~ILDiGcG~G~~~~~la~~--~~~v~giD~   67 (226)
T d1ve3a1          37 KRGKVLDLACGVGGFSFLLEDY--GFEVVGVDI   67 (226)
T ss_dssp             SCCEEEEETCTTSHHHHHHHHT--TCEEEEEES
T ss_pred             CCCEEEEECCCcchhhhhHhhh--hcccccccc
Confidence            4579999999999999999985  668899886

>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=96.84  E-value=0.00027  Score=45.22  Aligned_cols=47  Identities=11%  Similarity=0.190  Sum_probs=41.7

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      +..|+.+|..+ +|+|..|||+.+|+++   ..+.++++.|...|++.+.+
T Consensus         8 ~~~Il~~l~~~-g~~sr~eLa~~~glS~---~Tv~~~l~~L~~~Glv~e~~   54 (71)
T d1z05a1           8 AGRVYKLIDQK-GPISRIDLSKESELAP---ASITKITRELIDAHLIHETT   54 (71)
T ss_dssp             HHHHHHHHHHH-CSBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEEC
T ss_pred             HHHHHHHHHHc-CCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEEec
Confidence            34577788876 8999999999999999   99999999999999998764

>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=96.84  E-value=0.00043  Score=43.36  Aligned_cols=55  Identities=16%  Similarity=0.125  Sum_probs=44.7

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCC
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLP  102 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t  102 (214)
                      ++.|..+|.++ +.+|.+|||+++|++.   +.+++-+..|...|+..+...      ..-|+++
T Consensus         7 ~~~iL~~L~~~-~~~s~~eLa~~l~vS~---~ti~r~i~~L~~~G~~I~~~~------g~GY~L~   61 (63)
T d1biaa1           7 PLKLIALLANG-EFHSGEQLGETLGMSR---AAINKHIQTLRDWGVDVFTVP------GKGYSLP   61 (63)
T ss_dssp             HHHHHHHHTTS-SCBCHHHHHHHHTSCH---HHHHHHHHHHHHTTCCCEEET------TTEEECS
T ss_pred             HHHHHHHHHHC-CcCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCcEEEeC------CCeEEeC
Confidence            35577888775 8899999999999999   999999999999998665542      3457765

>d1y8ca_ c.66.1.43 (A:) Putative methyltransferase CAC2371 {Clostridium acetobutylicum [TaxId: 1488]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: CAC2371-like
domain: Putative methyltransferase CAC2371
species: Clostridium acetobutylicum [TaxId: 1488]

Probab=96.83  E-value=0.00031  Score=54.94  Aligned_cols=32  Identities=13%  Similarity=0.224  Sum_probs=27.4

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...++|||||||+|.++..++++.+  +++++|+
T Consensus        36 ~~~~~vLDiGCG~G~~~~~l~~~g~--~v~GvD~   67 (246)
T d1y8ca_          36 LVFDDYLDLACGTGNLTENLCPKFK--NTWAVDL   67 (246)
T ss_dssp             CCTTEEEEETCTTSTTHHHHGGGSS--EEEEECS
T ss_pred             CCCCeEEEEeCcCCHHHHHHHHhCC--ccEeecc
Confidence            3457999999999999999999865  6888886

>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=96.78  E-value=0.00047  Score=43.37  Aligned_cols=55  Identities=18%  Similarity=0.242  Sum_probs=44.4

Q ss_pred             cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCC
Q 040620           39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPP  103 (214)
Q Consensus        39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~  103 (214)
                      ..|..+|.++.+++|.++||+.+++++   +.++|-+..|...|+-....       .+-|.+.+
T Consensus        10 ~~Il~~L~~~~~~vs~~~La~~l~VS~---~TI~rdi~~L~~~G~~I~~~-------~gGY~L~~   64 (65)
T d1j5ya1          10 KSIVRILERSKEPVSGAQLAEELSVSR---QVIVQDIAYLRSLGYNIVAT-------PRGYVLAG   64 (65)
T ss_dssp             HHHHHHHHHCSSCBCHHHHHHHHTSCH---HHHHHHHHHHHHHTCCCEEE-------TTEEECCT
T ss_pred             HHHHHHHHHcCCCCcHHHHHHHHCCCH---HHHHHHHHHHHHCCCeEEEe-------CCCEEeCC
Confidence            456777766547899999999999999   99999999999999854444       36787764

>d2i6ga1 c.66.1.44 (A:1-198) Putative methyltransferase TehB {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: TehB-like
domain: Putative methyltransferase TehB
species: Salmonella typhimurium [TaxId: 90371]

Probab=96.78  E-value=0.00067  Score=51.35  Aligned_cols=33  Identities=15%  Similarity=0.092  Sum_probs=27.5

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +....+|||||||+|..+..++++.  .+++.+|+
T Consensus        28 ~~~~grvLDiGcG~G~~~~~la~~g--~~v~gvD~   60 (198)
T d2i6ga1          28 VVAPGRTLDLGCGNGRNSLYLAANG--YDVTAWDK   60 (198)
T ss_dssp             TSCSCEEEEETCTTSHHHHHHHHTT--CEEEEEES
T ss_pred             cCCCCcEEEECCCCCHHHHHHHHHh--hhhccccC
Confidence            3345799999999999999999985  56788876

>d2nxca1 c.66.1.39 (A:1-254) PrmA-like protein TTHA0656 (TT0836) {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Ribosomal protein L11 methyltransferase PrmA
domain: PrmA-like protein TTHA0656 (TT0836)
species: Thermus thermophilus [TaxId: 274]

Probab=96.70  E-value=0.00094  Score=53.20  Aligned_cols=53  Identities=17%  Similarity=0.125  Sum_probs=35.5

Q ss_pred             HHHHHhhhhhhhhHHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          154 IFYEAMITDFELIASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       154 ~f~~am~~~~~~~~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .|..+-...+++..+.+.+ +.   .+.++|||||||+|.+++.+++.  ..+++.+|+
T Consensus        98 aFGTG~H~TT~l~l~~l~~-~~---~~g~~VLDiGcGsG~l~i~aa~~--g~~V~gvDi  150 (254)
T d2nxca1          98 AFGTGHHETTRLALKALAR-HL---RPGDKVLDLGTGSGVLAIAAEKL--GGKALGVDI  150 (254)
T ss_dssp             ----CCSHHHHHHHHHHHH-HC---CTTCEEEEETCTTSHHHHHHHHT--TCEEEEEES
T ss_pred             ccCccccchhhHHHHHHHh-hc---CccCEEEEcccchhHHHHHHHhc--CCEEEEEEC
Confidence            3545555556665554433 22   35689999999999999988875  467888886

>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=96.70  E-value=0.00042  Score=53.99  Aligned_cols=32  Identities=16%  Similarity=0.160  Sum_probs=27.2

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+|||||||.|..+..++++.| .+++++|+
T Consensus        53 ~g~~VLdIGcG~G~~a~~~a~~~~-~~v~~id~   84 (229)
T d1zx0a1          53 KGGRVLEVGFGMAIAASKVQEAPI-DEHWIIEC   84 (229)
T ss_dssp             TCEEEEEECCTTSHHHHHHHTSCE-EEEEEEEC
T ss_pred             CCCeEEEeeccchHHHHHHHHcCC-CeEEEeCC
Confidence            457999999999999999998766 47888886

>d2avna1 c.66.1.41 (A:1-246) Hypothetical methyltransferase TM1389 {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: UbiE/COQ5-like
domain: Hypothetical methyltransferase TM1389
species: Thermotoga maritima [TaxId: 2336]

Probab=96.67  E-value=0.00054  Score=52.87  Aligned_cols=32  Identities=19%  Similarity=0.268  Sum_probs=27.7

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ++..+|||||||+|.++..+++.  ..+++++|.
T Consensus        41 ~~~~~vLDiGcG~G~~~~~l~~~--~~~v~giD~   72 (246)
T d2avna1          41 KNPCRVLDLGGGTGKWSLFLQER--GFEVVLVDP   72 (246)
T ss_dssp             CSCCEEEEETCTTCHHHHHHHTT--TCEEEEEES
T ss_pred             CCCCEEEEECCCCchhccccccc--ceEEEEeec
Confidence            45679999999999999999876  678999886

>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=96.61  E-value=0.00084  Score=53.21  Aligned_cols=42  Identities=14%  Similarity=0.271  Sum_probs=32.9

Q ss_pred             HHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          168 SVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       168 ~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+++.++  ..+..++||||||+|.++..|++.+++ +++++|.
T Consensus        83 ~~fl~~l~--~~~~~~vLD~GcG~G~~t~~ll~~~~~-~v~~vD~  124 (254)
T d1xtpa_          83 RNFIASLP--GHGTSRALDCGAGIGRITKNLLTKLYA-TTDLLEP  124 (254)
T ss_dssp             HHHHHTST--TCCCSEEEEETCTTTHHHHHTHHHHCS-EEEEEES
T ss_pred             HHHHhhCC--CCCCCeEEEecccCChhhHHHHhhcCc-eEEEEcC
Confidence            34556665  556789999999999999999988776 6777774

>d2h00a1 c.66.1.54 (A:5-254) Methyltransferase 10 domain containing protein METT10D {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Methyltransferase 10 domain
domain: Methyltransferase 10 domain containing protein METT10D
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.60  E-value=0.00072  Score=53.69  Aligned_cols=34  Identities=9%  Similarity=0.118  Sum_probs=31.4

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ....+++|||+|+|..+..|++++|+++++..|+
T Consensus        60 ~~~~~~LDiGtGsg~I~~~l~~~~~~~~~~~~Di   93 (250)
T d2h00a1          60 STLRRGIDIGTGASCIYPLLGATLNGWYFLATEV   93 (250)
T ss_dssp             CCCCEEEEESCTTTTHHHHHHHHHHCCEEEEEES
T ss_pred             cccceEEEeCCCchHHHHHHHHhCCCccccceec
Confidence            4467999999999999999999999999999986

>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=96.55  E-value=0.0007  Score=42.19  Aligned_cols=45  Identities=20%  Similarity=0.335  Sum_probs=41.0

Q ss_pred             CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecC
Q 040620           40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKD   89 (214)
Q Consensus        40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~   89 (214)
                      .|+..|..  +|+|..|||+.+|+++   ..+.++++-|...|++.+.+.
T Consensus         3 ~Il~~i~~--~pisr~eLa~~~gls~---~TVs~~v~~L~~~GlV~e~~~   47 (62)
T d2hoea1           3 RILKRIMK--SPVSRVELAEELGLTK---TTVGEIAKIFLEKGIVVEEKD   47 (62)
T ss_dssp             CSHHHHHH--SCBCHHHHHHHHTCCH---HHHHHHHHHHHHHTSEEEEEC
T ss_pred             HHHHHHHH--CCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEECCC
Confidence            57788876  7999999999999999   999999999999999998764

>d1yb2a1 c.66.1.13 (A:6-255) Hypothetical protein Ta0852 {Thermoplasma acidophilum [TaxId: 2303]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: tRNA(1-methyladenosine) methyltransferase-like
domain: Hypothetical protein Ta0852
species: Thermoplasma acidophilum [TaxId: 2303]

Probab=96.52  E-value=0.0015  Score=51.90  Aligned_cols=57  Identities=25%  Similarity=0.300  Sum_probs=35.3

Q ss_pred             HHHHhhhhhhhh----HHHHHhhcccccCCCCcEEeecCCchHHHHHHHHH-CCCCeEEEecCC
Q 040620          155 FYEAMITDFELI----ASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATA-FPDTKCTVFACH  213 (214)
Q Consensus       155 f~~am~~~~~~~----~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~-~P~l~~~v~Dlp  213 (214)
                      |...|...++..    +..++...+  .....+|||+|||+|.++..+++. .|+-+++.+|.-
T Consensus        58 ~~~~~~r~~qiiypkD~~~Ii~~l~--i~pG~rVLEiG~GsG~lt~~la~~v~~~g~V~~vD~~  119 (250)
T d1yb2a1          58 FGRVIRRNTQIISEIDASYIIMRCG--LRPGMDILEVGVGSGNMSSYILYALNGKGTLTVVERD  119 (250)
T ss_dssp             HHHHC------------------CC--CCTTCEEEEECCTTSHHHHHHHHHHTTSSEEEEECSC
T ss_pred             HHhhCCCCCcccCHHHHHHHHHHcC--CCCcCEEEEeeeeCcHHHHHHHHHhCCCcEEEEEECC
Confidence            445565444332    233444444  666789999999999999999987 688899998863

>d1xvaa_ c.66.1.5 (A:) Glycine N-methyltransferase {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Glycine N-methyltransferase
domain: Glycine N-methyltransferase
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=96.51  E-value=0.00093  Score=53.68  Aligned_cols=32  Identities=19%  Similarity=0.238  Sum_probs=28.4

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+.++|||||||+|.++..|+++  +.+++.+|+
T Consensus        55 ~~~~~vLD~GcG~G~~~~~la~~--g~~v~gvD~   86 (292)
T d1xvaa_          55 HGCHRVLDVACGTGVDSIMLVEE--GFSVTSVDA   86 (292)
T ss_dssp             TTCCEEEESSCTTSHHHHHHHHT--TCEEEEEES
T ss_pred             cCCCEEEEecCCCcHHHHHHHHc--CCeeeeccC
Confidence            34679999999999999999987  678999996

>d2ex4a1 c.66.1.42 (A:2-224) Adrenal gland protein AD-003 (C9orf32) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: AD-003 protein-like
domain: Adrenal gland protein AD-003 (C9orf32)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.51  E-value=0.00057  Score=52.69  Aligned_cols=34  Identities=12%  Similarity=0.260  Sum_probs=28.5

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+..+|||||||+|.++..++++.+. +++++|+
T Consensus        58 ~~~~~~vLDiGcG~G~~~~~l~~~~~~-~v~~vD~   91 (222)
T d2ex4a1          58 KTGTSCALDCGAGIGRITKRLLLPLFR-EVDMVDI   91 (222)
T ss_dssp             CCCCSEEEEETCTTTHHHHHTTTTTCS-EEEEEES
T ss_pred             CCCCCEEEEeccCCCHhhHHHHHhcCC-EEEEeec
Confidence            345679999999999999999888774 7888886

>d1dl5a1 c.66.1.7 (A:1-213) Protein-L-isoaspartyl O-methyltransferase {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Protein-L-isoaspartyl O-methyltransferase
domain: Protein-L-isoaspartyl O-methyltransferase
species: Thermotoga maritima [TaxId: 2336]

Probab=96.49  E-value=0.0016  Score=50.17  Aligned_cols=42  Identities=14%  Similarity=0.197  Sum_probs=34.4

Q ss_pred             HHHhhcccccCCCCcEEeecCCchHHHHHHHHHC-CCCeEEEecC
Q 040620          169 VLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAF-PDTKCTVFAC  212 (214)
Q Consensus       169 ~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl  212 (214)
                      .+++..+  ..+..+|||||||+|..+..+++.. |+.+++.+|.
T Consensus        66 ~~l~~l~--l~~g~~VLdiG~GtG~~s~~la~~~~~~g~V~~id~  108 (213)
T d1dl5a1          66 LFMEWVG--LDKGMRVLEIGGGTGYNAAVMSRVVGEKGLVVSVEY  108 (213)
T ss_dssp             HHHHHTT--CCTTCEEEEECCTTSHHHHHHHHHHCTTCEEEEEES
T ss_pred             HHHHhhh--ccccceEEEecCccchhHHHHHHHhCCCCcEEEeec
Confidence            3556665  6678899999999999999999876 6778888875

>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=96.48  E-value=0.0031  Score=45.17  Aligned_cols=62  Identities=6%  Similarity=0.156  Sum_probs=46.4

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      +..+...|... +++|..+||+.+++++   ..+.++++.|+..|+++.....+|.- ...+.+|+.
T Consensus        38 q~~vL~~l~~~-~~~t~~~la~~l~~~~---~~vsr~l~~L~~~G~v~r~~~~~D~R-~~~l~lT~~   99 (141)
T d1lnwa_          38 DVHVLKLIDEQ-RGLNLQDLGRQMCRDK---ALITRKIRELEGRNLVRRERNPSDQR-SFQLFLTDE   99 (141)
T ss_dssp             HHHHHHHHHSS-TTCBHHHHHHHTTCCH---HHHHHHHHHHHHTTSEEEEECSSSSS-SEEEEECHH
T ss_pred             HHHHHHHHHHC-CCCCHHHHHHHHCccH---hHHHHHHHHHHHhhceeeeccCCCCc-chhhccCHH
Confidence            44466677665 6799999999999999   99999999999999999776322211 223555555

>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=96.41  E-value=0.001  Score=42.35  Aligned_cols=47  Identities=9%  Similarity=0.132  Sum_probs=41.6

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      ...|+.+|..+ +|+|..|||+.+|+++   ..+.++++.|...|++.+.+
T Consensus         7 ~~~Il~~i~~~-g~~sr~eLa~~~gLS~---~Tvs~iv~~L~~~glv~e~g   53 (70)
T d1z6ra1           7 AGAVYRLIDQL-GPVSRIDLSRLAQLAP---ASITKIVHEMLEAHLVQELE   53 (70)
T ss_dssp             HHHHHHHHHSS-CSCCHHHHHHHTTCCH---HHHHHHHHHHHHHTSEEEC-
T ss_pred             HHHHHHHHHHc-CCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEeeC
Confidence            34477888887 9999999999999999   99999999999999999865

>d1ub9a_ a.4.5.28 (A:) Hypothetical protein PH1061 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Hypothetical protein PH1061
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=96.39  E-value=0.00025  Score=48.30  Aligned_cols=64  Identities=14%  Similarity=0.178  Sum_probs=49.7

Q ss_pred             HHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           36 AIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        36 a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      -.++.|..+|..+ +++|+.|||+.+++++   ..+.+.|+.|...|+++......+.. .-.|.+|+.
T Consensus        16 p~r~~IL~~L~~~-~~~~~~eLa~~l~is~---~~vs~~l~~L~~~glV~~~~~~~d~r-~~~~~LT~~   79 (100)
T d1ub9a_          16 PVRLGIMIFLLPR-RKAPFSQIQKVLDLTP---GNLDSHIRVLERNGLVKTYKVIADRP-RTVVEITDF   79 (100)
T ss_dssp             HHHHHHHHHHHHH-SEEEHHHHHHHTTCCH---HHHHHHHHHHHHTTSEEEEEECSSSC-EEEEEECHH
T ss_pred             HHHHHHHHHhccC-CCeeHHHHHHHHhhcc---ccccHHHHHHhhhceeEEEEcCcCCc-cccccCCHH
Confidence            3466778888766 8999999999999999   99999999999999998654211111 224888887

>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=96.35  E-value=0.0035  Score=50.76  Aligned_cols=35  Identities=26%  Similarity=0.111  Sum_probs=28.3

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                      ..+.++|||||||+|.+++.++++.+ -+++.+|.-
T Consensus        33 ~~~~~~VLDiGcG~G~lsl~aa~~Ga-~~V~aid~s   67 (311)
T d2fyta1          33 IFKDKVVLDVGCGTGILSMFAAKAGA-KKVLGVDQS   67 (311)
T ss_dssp             GTTTCEEEEETCTTSHHHHHHHHTTC-SEEEEEESS
T ss_pred             cCCcCEEEEECCCCCHHHHHHHHcCC-CEEEEEeCH
Confidence            34578999999999999999998855 378877753

>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=96.34  E-value=0.0012  Score=41.42  Aligned_cols=45  Identities=22%  Similarity=0.363  Sum_probs=38.8

Q ss_pred             cchhhhcCC-CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           41 IPDIINNSG-QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        41 lfd~L~~~~-~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      |.+++...| .|-++.|||+.+|+++   ..++.+|+.|+..|.+.+..
T Consensus        12 I~~~~~~~g~~PP~vrdl~~~l~~~e---~~~~~lL~~l~~~G~lvkI~   57 (64)
T d1lvaa3          12 LEDKYRVSRWQPPSFKEVAGSFNLDP---SELEELLHYLVREGVLVKIN   57 (64)
T ss_dssp             HHHHHHHHTTSCCBHHHHHHHTTCCH---HHHHHHHHHHHHTTSEEESS
T ss_pred             HHHHHHHcCCCCCcHHHHHHHhCCCH---HHHHHHHHHHHHCCCEEEec
Confidence            334444443 7899999999999999   99999999999999999987

>d1i9ga_ c.66.1.13 (A:) Probable methyltransferase Rv2118c {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: tRNA(1-methyladenosine) methyltransferase-like
domain: Probable methyltransferase Rv2118c
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=96.33  E-value=0.0028  Score=50.64  Aligned_cols=44  Identities=11%  Similarity=0.237  Sum_probs=37.3

Q ss_pred             HHHHHhhcccccCCCCcEEeecCCchHHHHHHHHH-CCCCeEEEecC
Q 040620          167 ASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATA-FPDTKCTVFAC  212 (214)
Q Consensus       167 ~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~-~P~l~~~v~Dl  212 (214)
                      +..++...+  ..+..+|||+|||+|.++..|++. .|+-+++.+|.
T Consensus        85 ~s~Ii~~l~--i~PG~~VLE~G~GsG~lt~~La~~vgp~G~V~~~d~  129 (264)
T d1i9ga_          85 AAQIVHEGD--IFPGARVLEAGAGSGALTLSLLRAVGPAGQVISYEQ  129 (264)
T ss_dssp             HHHHHHHTT--CCTTCEEEEECCTTSHHHHHHHHHHCTTSEEEEECS
T ss_pred             HHHHHHHhC--CCCCCEEEecCcCCcHHHHHHHHhhCCCcEEEEecC
Confidence            345566666  677899999999999999999998 79999999886

>d1o54a_ c.66.1.13 (A:) Hypothetical protein TM0748 {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: tRNA(1-methyladenosine) methyltransferase-like
domain: Hypothetical protein TM0748
species: Thermotoga maritima [TaxId: 2336]

Probab=96.29  E-value=0.003  Score=50.50  Aligned_cols=44  Identities=20%  Similarity=0.272  Sum_probs=36.9

Q ss_pred             HHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHC-CCCeEEEecC
Q 040620          167 ASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAF-PDTKCTVFAC  212 (214)
Q Consensus       167 ~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl  212 (214)
                      +..++...+  ..+..+|||+|||+|.++..+++.. |+-+++.+|.
T Consensus        92 ~~~Ii~~l~--i~pG~~VLDiG~GsG~lt~~lA~~~~~~G~V~~vD~  136 (266)
T d1o54a_          92 SSFIAMMLD--VKEGDRIIDTGVGSGAMCAVLARAVGSSGKVFAYEK  136 (266)
T ss_dssp             HHHHHHHTT--CCTTCEEEEECCTTSHHHHHHHHHTTTTCEEEEECC
T ss_pred             HHHHHHhhC--CCCCCEEEECCCCCCHHHHHHHHHhCCCcEEEEEeC
Confidence            344566666  7778999999999999999999985 8889999886

>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=96.20  E-value=0.00077  Score=45.57  Aligned_cols=54  Identities=15%  Similarity=0.161  Sum_probs=46.4

Q ss_pred             HHHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           30 SLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        30 ~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      +.+|.--.++.|+..|..  +++++.|||+.+|+++   ..+.+-|+.|...|++....
T Consensus        12 fkaL~d~~Rl~Il~~L~~--~~~~v~el~~~l~~s~---~~vS~HL~~L~~~glv~~~r   65 (94)
T d1r1ua_          12 FKALGDYNRIRIMELLSV--SEASVGHISHQLNLSQ---SNVSHQLKLLKSVHLVKAKR   65 (94)
T ss_dssp             HHHTCSHHHHHHHHHHHH--CCBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHhCCHHHHHHHHHHHc--CCccHHHHHHHHCCCH---HHHHHHHHHHHHCCceEEEE
Confidence            345555566777888887  8999999999999999   99999999999999998776

>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=96.17  E-value=0.0011  Score=45.02  Aligned_cols=53  Identities=13%  Similarity=0.176  Sum_probs=46.0

Q ss_pred             HHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           31 LSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        31 ~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      .+|.--.++.|+..|..  +++++.|||+.+|+++   ..+..-|+.|...|++....
T Consensus        18 kaL~~p~Rl~Il~~L~~--~~~~v~ela~~l~is~---stvS~HL~~L~~aglV~~~r   70 (98)
T d1r1ta_          18 AVLADPNRLRLLSLLAR--SELCVGDLAQAIGVSE---SAVSHQLRSLRNLRLVSYRK   70 (98)
T ss_dssp             HHHCCHHHHHHHHHHTT--CCBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEEE
T ss_pred             HHhCCHHHHHHHHHHHc--CCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCceEEEE
Confidence            45555566778888876  8999999999999999   99999999999999998776

>d2bzga1 c.66.1.36 (A:17-245) Thiopurine S-methyltransferase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Thiopurine S-methyltransferase
domain: Thiopurine S-methyltransferase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.13  E-value=0.0025  Score=49.20  Aligned_cols=33  Identities=6%  Similarity=-0.183  Sum_probs=29.1

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .....+|||+|||.|..+..|+++  ..++|.+|+
T Consensus        43 ~~~~~rvLd~GCG~G~~a~~LA~~--G~~V~gvD~   75 (229)
T d2bzga1          43 GKSGLRVFFPLCGKAVEMKWFADR--GHSVVGVEI   75 (229)
T ss_dssp             TCCSCEEEETTCTTCTHHHHHHHT--TCEEEEECS
T ss_pred             CCCCCEEEEeCCCCcHHHHHHHhC--CCcEEEEeC
Confidence            445679999999999999999997  788999986

>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=96.12  E-value=0.0025  Score=50.55  Aligned_cols=31  Identities=19%  Similarity=0.416  Sum_probs=23.3

Q ss_pred             CcEEeecCCchHHHHHHHH----HCCCCe--EEEecC
Q 040620          182 KPLVDVGGSTGTMARAIAT----AFPDTK--CTVFAC  212 (214)
Q Consensus       182 ~~vvDVGGG~G~~~~~l~~----~~P~l~--~~v~Dl  212 (214)
                      .+|||||||+|.++..|++    ++|+..  ++++|.
T Consensus        42 ~~VLDiGcG~G~~~~~ll~~l~~~~~~~~~~~~~vD~   78 (280)
T d1jqea_          42 IKILSIGGGAGEIDLQILSKVQAQYPGVCINNEVVEP   78 (280)
T ss_dssp             EEEEEETCTTSHHHHHHHHHHHHHSTTCEEEEEEECC
T ss_pred             CeEEEEcCCCCHHHHHHHHHhhhhccCCceEEEEEeC
Confidence            3799999999998776654    577664  577774

>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=96.08  E-value=0.0016  Score=46.61  Aligned_cols=68  Identities=15%  Similarity=0.147  Sum_probs=51.3

Q ss_pred             HhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           37 IQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        37 ~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      .+..++..|..+ +++|+.+||+.+++++   ..+.++++.|...|++.......|.- .-.+.+|+.    ++.++
T Consensus        33 ~q~~iL~~l~~~-~~~t~~~La~~l~i~~---~~vs~~v~~L~~~gli~r~~~~~D~R-~~~l~lT~~----G~~~~  100 (140)
T d2etha1          33 TELYAFLYVALF-GPKKMKEIAEFLSTTK---SNVTNVVDSLEKRGLVVREMDPVDRR-TYRVVLTEK----GKEIF  100 (140)
T ss_dssp             HHHHHHHHHHHH-CCBCHHHHHHHTTSCH---HHHHHHHHHHHHTTSEEEEECTTTSS-CEEEEECHH----HHHHH
T ss_pred             HHHHHHHHHHHc-CCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeeeeecccccc-hhhhhcCHH----HHHHH
Confidence            344467777777 7899999999999999   99999999999999999776321111 235677777    55543

>d1ne2a_ c.66.1.32 (A:) Hypothetical protein Ta1320 {Archaeon Thermoplasma acidophilum [TaxId: 2303]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Ta1320-like
domain: Hypothetical protein Ta1320
species: Archaeon Thermoplasma acidophilum [TaxId: 2303]

Probab=96.01  E-value=0.0021  Score=49.17  Aligned_cols=31  Identities=19%  Similarity=0.259  Sum_probs=25.8

Q ss_pred             CCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          181 LKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       181 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .++|||+|||+|.+++.++...+. +++.+|.
T Consensus        49 Gk~VLDlGcGtG~l~i~a~~~ga~-~V~~vDi   79 (197)
T d1ne2a_          49 GRSVIDAGTGNGILACGSYLLGAE-SVTAFDI   79 (197)
T ss_dssp             TSEEEEETCTTCHHHHHHHHTTBS-EEEEEES
T ss_pred             CCEEEEeCCCCcHHHHHHHHcCCC-ccccccc
Confidence            689999999999999887776544 6888875

>d1sfxa_ a.4.5.50 (A:) Hypothetical protein AF2008 {Archaeoglobus fulgidus [TaxId: 2234]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: TrmB-like
domain: Hypothetical protein AF2008
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=95.92  E-value=0.0011  Score=45.77  Aligned_cols=44  Identities=18%  Similarity=0.280  Sum_probs=38.0

Q ss_pred             cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      |+-.|... +++|+.|||+.+|+++   ..+.+.|+-|...|++....
T Consensus        25 v~~~L~~~-g~~t~~eia~~~~i~~---~~v~~~l~~L~~~GlV~r~~   68 (109)
T d1sfxa_          25 IYSLLLER-GGMRVSEIARELDLSA---RFVRDRLKVLLKRGFVRREI   68 (109)
T ss_dssp             HHHHHHHH-CCBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHhc-CCCCHHHHHHHhCCCc---chHHHHHHHHHhCCCEEEEe
Confidence            44455554 8999999999999999   99999999999999998653

>d1u2wa1 a.4.5.5 (A:12-119) Cadmium efflux system accessory protein CadC {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: Cadmium efflux system accessory protein CadC
species: Staphylococcus aureus [TaxId: 1280]

Probab=95.87  E-value=0.0015  Score=45.16  Aligned_cols=56  Identities=13%  Similarity=0.077  Sum_probs=48.2

Q ss_pred             HHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           29 KSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        29 ~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      .+.+|.--.++.|+..|... +++++.|||+.+|+++   ..+.+-|+.|...|++....
T Consensus        24 ~~kaLadp~Rl~Il~~L~~~-~~~~v~ela~~l~~s~---s~vS~HL~~L~~aGlv~~~r   79 (108)
T d1u2wa1          24 ILKAIADENRAKITYALCQD-EELCVCDIANILGVTI---ANASHHLRTLYKQGVVNFRK   79 (108)
T ss_dssp             HHHHHHSHHHHHHHHHHHHS-SCEEHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEC-
T ss_pred             HHHHhCCHHHHHHHHHHHhC-CCccHHHHHHHHccCh---hHHHHHHHHHHHCCeeEEEE
Confidence            35667777788888888654 8999999999999999   99999999999999999876

>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=95.85  E-value=0.0024  Score=48.13  Aligned_cols=70  Identities=14%  Similarity=0.152  Sum_probs=52.5

Q ss_pred             HHHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCC-CCCccceeeCCCC
Q 040620           30 SLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGK-NEQEEESILLPPH  104 (214)
Q Consensus        30 ~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~-~~~~~~~y~~t~~  104 (214)
                      ..+|.--.+..|+.+|..  +|+|+.|||+.+|+++   ..+.+-|+.|...|++....... .+-....|.+|+.
T Consensus        13 ~~~l~~p~R~~Il~~L~~--~~~s~~ela~~lg~s~---~~v~~hl~~L~~~glv~~~~~~~~~g~~~k~y~~~~~   83 (190)
T d1ulya_          13 IKVMLEDTRRKILKLLRN--KEMTISQLSEILGKTP---QTIYHHIEKLKEAGLVEVKRTEMKGNLVEKYYGRTAD   83 (190)
T ss_dssp             HHHHHSHHHHHHHHHHTT--CCBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEEEEEEETTEEEEEEEESSS
T ss_pred             HHHhCCHHHHHHHHHHHh--CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeEEEEeeccCCcceEEEEEccc
Confidence            445555667778899975  8999999999999999   99999999999999997543100 0000234888876

>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=95.84  E-value=0.0024  Score=45.14  Aligned_cols=43  Identities=14%  Similarity=0.271  Sum_probs=37.4

Q ss_pred             chhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           42 PDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        42 fd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      .-.|+.+ +++|.++||+.++++|   ..++++|+.|...|++.-..
T Consensus        10 L~~la~~-~~~ss~~IA~~~~~~~---~~v~kIl~~L~~aglV~s~r   52 (127)
T d1xd7a_          10 LSLISMD-EKTSSEIIADSVNTNP---VVVRRMISLLKKADILTSRA   52 (127)
T ss_dssp             HHHHHTC-SCCCHHHHHHHHTSCH---HHHHHHHHHHHHTTSEECCS
T ss_pred             HHHHhcC-CCCCHHHHHHHhCcCH---HHHHHHHHHHHHhCcccccC
Confidence            4445555 7899999999999999   99999999999999998554

>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=95.82  E-value=0.0086  Score=42.66  Aligned_cols=65  Identities=11%  Similarity=0.255  Sum_probs=48.8

Q ss_pred             CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      .++..|... +|+|+.+||+.+++++   ..+.+++..|...|++......+|.= .-.+.+|+.    ++.+.
T Consensus        39 ~iL~~l~~~-~~~t~~~la~~~~i~~---~~vs~~l~~L~~~glv~r~~~~~D~R-~~~v~lT~~----G~~~~  103 (143)
T d1s3ja_          39 FVLASLKKH-GSLKVSEIAERMEVKP---SAVTLMADRLEQKNLIARTHNTKDRR-VIDLSLTDE----GDIKF  103 (143)
T ss_dssp             HHHHHHHHH-SEEEHHHHHHHHTSCH---HHHHHHHHHHHHTTSEEEEECSSCTT-SEEEEECHH----HHHHH
T ss_pred             HHHHHHHHC-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHhhhheeeeecCCCC-ceEEEECHH----HHHHH
Confidence            356667665 7899999999999999   99999999999999998765321110 123777777    66554

>d1oria_ c.66.1.6 (A:) Protein arginine N-methyltransferase 1, PRMT1 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Arginine methyltransferase
domain: Protein arginine N-methyltransferase 1, PRMT1
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=95.75  E-value=0.0039  Score=50.70  Aligned_cols=33  Identities=30%  Similarity=0.342  Sum_probs=26.9

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                      +.++|||||||+|.+++.++++-+. +++.+|..
T Consensus        33 ~~~~VLDiGcG~G~ls~~aa~~Ga~-~V~avd~s   65 (316)
T d1oria_          33 KDKVVLDVGSGTGILCMFAAKAGAR-KVIGIECS   65 (316)
T ss_dssp             TTCEEEEETCTTSHHHHHHHHTTCS-EEEEEECS
T ss_pred             CcCEEEEEecCCcHHHHHHHHhCCC-EEEEEcCc
Confidence            4689999999999999988887443 78888853

>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=95.74  E-value=0.0013  Score=45.22  Aligned_cols=36  Identities=17%  Similarity=0.252  Sum_probs=34.3

Q ss_pred             CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      +|+|+.+||+.+++++   ..+.+.++-|...|++....
T Consensus        35 ~~~t~~eLa~~~~i~~---~tvs~~l~~L~~~GlV~r~~   70 (109)
T d2d1ha1          35 KPITSEELADIFKLSK---TTVENSLKKLIELGLVVRTK   70 (109)
T ss_dssp             SCEEHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCCHHHHHHHHCccH---hHHHHHHHHHHHCCCEEEee
Confidence            8999999999999999   99999999999999998765

>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=95.70  E-value=0.0042  Score=47.36  Aligned_cols=32  Identities=16%  Similarity=0.192  Sum_probs=26.4

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..++|||+|||+|.+++.++.+ +..+++.+|.
T Consensus        46 ~g~~vLDlg~GtG~l~i~a~~~-g~~~v~~vdi   77 (201)
T d1wy7a1          46 EGKVVADLGAGTGVLSYGALLL-GAKEVICVEV   77 (201)
T ss_dssp             TTCEEEEETCTTCHHHHHHHHT-TCSEEEEEES
T ss_pred             CCCEEEECcCcchHHHHHHHHc-CCCEEEEEcC
Confidence            3579999999999999988765 4458888886

>d2b25a1 c.66.1.13 (A:6-329) Hypothetical protein FLJ20628 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: tRNA(1-methyladenosine) methyltransferase-like
domain: Hypothetical protein FLJ20628
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.63  E-value=0.0073  Score=49.53  Aligned_cols=56  Identities=11%  Similarity=0.183  Sum_probs=41.5

Q ss_pred             HHHHhhhhhhh----hHHHHHhhcccccCCCCcEEeecCCchHHHHHHHHH-CCCCeEEEecC
Q 040620          155 FYEAMITDFEL----IASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATA-FPDTKCTVFAC  212 (214)
Q Consensus       155 f~~am~~~~~~----~~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~-~P~l~~~v~Dl  212 (214)
                      |...|...++.    .+..++...+  ..+..+|||+|||+|.++..|++. .|+-+++.+|.
T Consensus        71 ~~~~~~r~tqiiypkD~~~Il~~l~--i~pG~rVLE~GtGsG~lt~~LAr~vg~~G~V~t~E~  131 (324)
T d2b25a1          71 YVVLMKRGTAITFPKDINMILSMMD--INPGDTVLEAGSGSGGMSLFLSKAVGSQGRVISFEV  131 (324)
T ss_dssp             HHHHSCCSSCCCCHHHHHHHHHHHT--CCTTCEEEEECCTTSHHHHHHHHHHCTTCEEEEEES
T ss_pred             HhhccCCCCcccccccHHHHHHHhC--CCCCCEEEEecccccHHHHHHHHHhCCCcEEEEecC
Confidence            44555544332    2344556665  667899999999999999999987 68989988886

>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=95.55  E-value=0.0074  Score=45.32  Aligned_cols=26  Identities=19%  Similarity=0.073  Sum_probs=20.1

Q ss_pred             CCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          181 LKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       181 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+|||||||+|.++..+.      +.+++|.
T Consensus        37 ~~~vLDiGcG~G~~~~~~~------~~~giD~   62 (208)
T d1vlma_          37 EGRGVEIGVGTGRFAVPLK------IKIGVEP   62 (208)
T ss_dssp             SSCEEEETCTTSTTHHHHT------CCEEEES
T ss_pred             CCeEEEECCCCcccccccc------eEEEEeC
Confidence            4589999999999988774      3456664

>d1i1na_ c.66.1.7 (A:) Protein-L-isoaspartyl O-methyltransferase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Protein-L-isoaspartyl O-methyltransferase
domain: Protein-L-isoaspartyl O-methyltransferase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.51  E-value=0.012  Score=45.47  Aligned_cols=43  Identities=16%  Similarity=0.071  Sum_probs=33.0

Q ss_pred             HHhhcccccCCCCcEEeecCCchHHHHHHHHH-CCCCeEEEecC
Q 040620          170 LIEDCNEVSKGLKPLVDVGGSTGTMARAIATA-FPDTKCTVFAC  212 (214)
Q Consensus       170 ~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~-~P~l~~~v~Dl  212 (214)
                      +++.......+..+|||||||+|..+..+++. .|.-+++.+|+
T Consensus        66 ~le~L~~~l~~g~~VLdiG~GsGy~ta~la~l~~~~g~V~~ie~  109 (224)
T d1i1na_          66 ALELLFDQLHEGAKALDVGSGSGILTACFARMVGCTGKVIGIDH  109 (224)
T ss_dssp             HHHHTTTTSCTTCEEEEETCTTSHHHHHHHHHHCTTCEEEEEES
T ss_pred             HHHHHhhccCCCCeEEEecCCCCHHHHHHHHHhCCCceEEEEcC
Confidence            44544222556789999999999999988885 67888888885

>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=95.39  E-value=0.0051  Score=44.16  Aligned_cols=46  Identities=20%  Similarity=0.294  Sum_probs=39.3

Q ss_pred             CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      .|+.+|-.+++|+|+.|||+++|+++   ..+.+.++.|...|++....
T Consensus        30 ~i~~~L~~~~~plt~~ela~~l~vsk---~~vs~~l~~L~~~GlV~r~~   75 (151)
T d1ku9a_          30 AVYAILYLSDKPLTISDIMEELKISK---GNVSMSLKKLEELGFVRKVW   75 (151)
T ss_dssp             HHHHHHHHCSSCEEHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEEC
T ss_pred             HHHHHHHhCCCCcCHHHHHHHhCCCc---chHHHHHHHHHHCCCEEEEE
Confidence            45555644448999999999999999   99999999999999998764

>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=95.37  E-value=0.0093  Score=42.00  Aligned_cols=67  Identities=9%  Similarity=0.222  Sum_probs=50.1

Q ss_pred             cCcchhhhcC-CCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           39 LRIPDIINNS-GQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        39 lglfd~L~~~-~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      +.++..|..+ ++++|..+||+.+++++   ..+.++++.|...|++......+|.- ...+.+|+.    ++.+.
T Consensus        32 ~~vL~~l~~~~~~~it~~ela~~~~~~~---~~vs~~l~~L~~~g~v~r~~~~~D~R-~~~i~lT~~----G~~~~   99 (135)
T d3broa1          32 MTIIDYLSRNKNKEVLQRDLESEFSIKS---STATVLLQRMEIKKLLYRKVSGKDSR-QKCLKLTKK----ANKLE   99 (135)
T ss_dssp             HHHHHHHHHTTTSCCBHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEEECSSCTT-SEEEEECHH----HHTTH
T ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHCcCH---hHHHHHHHHHHHHHHHHHHhhhhhhh-hhhhcccHH----HHHHH
Confidence            3345555554 36799999999999999   99999999999999998765321111 235888888    77765

>d1g6q1_ c.66.1.6 (1:) Arginine methyltransferase, HMT1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Arginine methyltransferase
domain: Arginine methyltransferase, HMT1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.37  E-value=0.0065  Score=49.52  Aligned_cols=33  Identities=21%  Similarity=0.124  Sum_probs=26.1

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                      +.++|||||||+|.+++.++++.. -+++..|..
T Consensus        38 ~~~~VLDlGcGtG~ls~~aa~~Ga-~~V~avd~s   70 (328)
T d1g6q1_          38 KDKIVLDVGCGTGILSMFAAKHGA-KHVIGVDMS   70 (328)
T ss_dssp             TTCEEEEETCTTSHHHHHHHHTCC-SEEEEEESS
T ss_pred             CcCEEEEeCCCCCHHHHHHHHhCC-CEEEEEeCC
Confidence            367999999999999988877643 377877753

>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=95.37  E-value=0.0075  Score=42.63  Aligned_cols=64  Identities=13%  Similarity=0.159  Sum_probs=46.8

Q ss_pred             chhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           42 PDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        42 fd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      .-.|..+++++|..+||+.+++++   ..+.++++-|+..|+++.....+|.- .-.+.+|+.    ++.++
T Consensus        34 L~~l~~~~~~~t~~~la~~~~~~~---~~vs~~v~~L~~~gli~r~~~~~D~R-~~~i~lT~~----G~~~~   97 (137)
T d2fbha1          34 LLHLARHRDSPTQRELAQSVGVEG---PTLARLLDGLESQGLVRRLAVAEDRR-AKHIVLTPK----ADVLI   97 (137)
T ss_dssp             HHHHHHCSSCCBHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEECCBTTBC-SCEEEECTT----HHHHH
T ss_pred             HHHHHHcCCCCcHHHHHHHHCCCH---HHHHHHHHHHHHcCCccccCCCCCCC-chhhhcCHH----HHHHH
Confidence            344544435789999999999999   99999999999999999775311111 124777777    65554

>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=95.32  E-value=0.005  Score=43.69  Aligned_cols=61  Identities=11%  Similarity=0.260  Sum_probs=46.7

Q ss_pred             cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      ..++..|..+ +++|..+||+.+++++   ..+.++++-|+..|+++.....+|.- ...+.+|+.
T Consensus        37 ~~vL~~i~~~-~~~t~~~la~~l~~~~---~~~s~~l~~L~~~Gli~r~~~~~D~R-~~~l~lT~~   97 (136)
T d2bv6a1          37 FLVLTILWDE-SPVNVKKVVTELALDT---GTVSPLLKRMEQVDLIKRERSEVDQR-EVFIHLTDK   97 (136)
T ss_dssp             HHHHHHHHHS-SEEEHHHHHHHTTCCT---TTHHHHHHHHHHTTSEEEEECSSSTT-CEEEEECHH
T ss_pred             HHHHHHHHcC-CCCCHHHHHHHHCCCH---hHHHHHHHHHHHCCCEEEeecCCccc-chhhccCHH
Confidence            3455667776 7899999999999999   99999999999999998765321111 124566777

>d1g8aa_ c.66.1.3 (A:) Fibrillarin homologue {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Fibrillarin homologue
domain: Fibrillarin homologue
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=95.26  E-value=0.0053  Score=47.83  Aligned_cols=35  Identities=20%  Similarity=0.127  Sum_probs=31.5

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHC-CCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAF-PDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl  212 (214)
                      ..+..+|||+|||+|..+..+++.- |+-+++.+|+
T Consensus        71 i~pG~~VLDlGaGsG~~t~~la~~VG~~G~V~aVD~  106 (227)
T d1g8aa_          71 IKPGKSVLYLGIASGTTASHVSDIVGWEGKIFGIEF  106 (227)
T ss_dssp             CCTTCEEEEETTTSTTHHHHHHHHHCTTSEEEEEES
T ss_pred             cCCCCEEEEeccCCCHHHHHHHHHhCCCCEEEEEeC
Confidence            6678899999999999999999986 8888998886

>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=95.22  E-value=0.0052  Score=46.52  Aligned_cols=64  Identities=11%  Similarity=0.205  Sum_probs=48.5

Q ss_pred             HHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCC-CCCccceeeCCCC
Q 040620           36 AIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGK-NEQEEESILLPPH  104 (214)
Q Consensus        36 a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~-~~~~~~~y~~t~~  104 (214)
                      =.+..|+..|..  +|+|+.|||+.+|+++   ..+++-|+.|...|++....... .|.....|.++..
T Consensus        15 ~~R~~Il~~L~~--~~~~~~ela~~l~~s~---~~v~~HL~~L~~~Glv~~~~~~~~~G~~~~~y~l~~~   79 (194)
T d2p4wa1          15 ETRRRILFLLTK--RPYFVSELSRELGVGQ---KAVLEHLRILEEAGLIESRVEKIPRGRPRKYYMIKKG   79 (194)
T ss_dssp             HHHHHHHHHHHH--SCEEHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEEECCBTTBCCCEEEEECTT
T ss_pred             HHHHHHHHHHHh--CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeEEEEeecCCCCceEEEEeccc
Confidence            344556677776  8999999999999999   99999999999999998654221 1111236888776

>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=95.16  E-value=0.0052  Score=38.10  Aligned_cols=46  Identities=15%  Similarity=0.226  Sum_probs=41.0

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ   87 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~   87 (214)
                      +..|.++|..+ +.+|..+||+.+|+++   ..+.+=++-|...|++..-
T Consensus         7 D~~IL~~L~~n-~r~s~~~iA~~lgis~---~tv~~Ri~~L~~~giI~~~   52 (63)
T d2cfxa1           7 DLNIIEELKKD-SRLSMRELGRKIKLSP---PSVTERVRQLESFGIIKQY   52 (63)
T ss_dssp             HHHHHHHHHHC-SCCCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeeeE
Confidence            45677888887 8999999999999999   9999999999999999743

>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=95.10  E-value=0.0037  Score=44.90  Aligned_cols=69  Identities=20%  Similarity=0.292  Sum_probs=49.0

Q ss_pred             HhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           37 IQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        37 ~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      .++.+...|...++++|..+||+.+++++   ..+.++++-|...|++.......|.- .-.+.+|+.    ++.++
T Consensus        35 ~q~~vL~~L~~~~g~~t~~~La~~~~~~~---~~vs~~i~~L~~~glv~r~~~~~DrR-~~~i~LT~~----G~~~~  103 (145)
T d2hr3a1          35 SQLVVLGAIDRLGGDVTPSELAAAERMRS---SNLAALLRELERGGLIVRHADPQDGR-RTRVSLSSE----GRRNL  103 (145)
T ss_dssp             HHHHHHHHHHHTTSCBCHHHHHHHTTCCH---HHHHHHHHHHHHTTSEEEEC-------CCEEEECHH----HHHHH
T ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHCCCH---HHHHHHHHHHHHcCCeEeeeCccchh-HHHhccCHH----HHHHH
Confidence            34556666665447899999999999999   99999999999999998765211111 234667776    55543

>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=95.02  E-value=0.0023  Score=49.74  Aligned_cols=34  Identities=15%  Similarity=0.048  Sum_probs=25.7

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..+..+|||||||+|.++..+++... .+++..|+
T Consensus        49 ~~~g~~vLDlGcG~G~~~~~~~~~~~-~~v~giD~   82 (257)
T d2a14a1          49 GLQGDTLIDIGSGPTIYQVLAACDSF-QDITLSDF   82 (257)
T ss_dssp             SCCEEEEEESSCTTCCGGGTTGGGTE-EEEEEEES
T ss_pred             CCCCCEEEEECCCCCHhHHHHhcccc-CcEEEecC
Confidence            34567999999999998876666532 26888886

>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=95.02  E-value=0.0076  Score=42.78  Aligned_cols=65  Identities=17%  Similarity=0.190  Sum_probs=47.9

Q ss_pred             CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      .++..|... +|+|+.+||+.+++++   ..+.+++.-|...|+++.....+|.- .-.+.+|+.    ++.++
T Consensus        34 ~iL~~i~~~-~~~t~~~la~~l~i~~---~tvs~~l~~L~~~gli~r~~~~~D~R-~~~i~LT~~----G~~~~   98 (139)
T d2a61a1          34 DILQKIYFE-GPKRPGELSVLLGVAK---STVTGLVKRLEADGYLTRTPDPADRR-AYFLVITRK----GEEVI   98 (139)
T ss_dssp             HHHHHHHHH-CCBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEEEETTEEE-EEEEEECHH----HHHHH
T ss_pred             HHHHHHHHc-CCCCHHHHHHHhCCCc---ccchHHHHHHHhcCeeeeeeccCCCC-eEEEEECHH----HHHHH
Confidence            345556555 7899999999999999   99999999999999998765211100 234777777    66554

>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=94.87  E-value=0.0058  Score=43.86  Aligned_cols=59  Identities=15%  Similarity=0.183  Sum_probs=44.0

Q ss_pred             cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      +...|..+ +++|..+||+.+++++   ..+.++++-|...|++......+|.- .-.+.+|+.
T Consensus        34 iL~~i~~~-~~~t~~~la~~l~i~~---~tvs~~l~~L~~~glI~r~~~~~D~R-~~~l~LT~~   92 (144)
T d1lj9a_          34 YLVRVCEN-PGIIQEKIAELIKVDR---TTAARAIKRLEEQGFIYRQEDASNKK-IKRIYATEK   92 (144)
T ss_dssp             HHHHHHHS-TTEEHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEEECSSCTT-CEEEEECHH
T ss_pred             HHHHHHhC-CCCCHHHHHHHHCccH---hhHHHHHHHHHhhhcccccCCCCCCC-ccccccCHH
Confidence            33446666 6899999999999999   99999999999999999776321111 124556666

>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=94.86  E-value=0.0052  Score=37.65  Aligned_cols=47  Identities=19%  Similarity=0.190  Sum_probs=41.2

Q ss_pred             HhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620           37 IQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ   87 (214)
Q Consensus        37 ~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~   87 (214)
                      ++..|..+|..+ +.+|..+||+++|+++   ..+.+=++.|...|++..-
T Consensus         4 ~D~~Il~~L~~n-~r~s~~eiA~~l~ls~---~~v~~Ri~~L~~~giI~~~   50 (60)
T d2cyya1           4 IDKKIIKILQND-GKAPLREISKITGLAE---STIHERIRKLRESGVIKKF   50 (60)
T ss_dssp             HHHHHHHHHHHC-TTCCHHHHHHHHCSCH---HHHHHHHHHHHHHTSSCCC
T ss_pred             HHHHHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeEeE
Confidence            455678888887 8999999999999999   9999999999999998743

>d1ylfa1 a.4.5.55 (A:5-142) Hypothetical protein BC1842 {Bacillus cereus [TaxId: 1396]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcriptional regulator Rrf2
domain: Hypothetical protein BC1842
species: Bacillus cereus [TaxId: 1396]

Probab=94.83  E-value=0.0075  Score=43.04  Aligned_cols=46  Identities=15%  Similarity=0.206  Sum_probs=37.6

Q ss_pred             CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      .++|+++||+.+++++   ..++++|+.|...|++.-...      .|-|.+..-
T Consensus        22 ~~vss~~IA~~~~i~~---~~l~kil~~L~~aGlv~S~rG------~GG~~L~~~   67 (138)
T d1ylfa1          22 SLCTSDYMAESVNTNP---VVIRKIMSYLKQAGFVYVNRG------PGGAGLLKD   67 (138)
T ss_dssp             GGCCHHHHHHHHTSCH---HHHHHHHHHHHHTTSEEEC---------CCEEESSC
T ss_pred             CcCcHHHHHHHHCcCH---HHHHHHHHHHHHCCCeEeecC------CCCceecCC
Confidence            6899999999999999   999999999999999987652      344555544

>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=94.83  E-value=0.0048  Score=37.85  Aligned_cols=46  Identities=17%  Similarity=0.203  Sum_probs=40.2

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ   87 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~   87 (214)
                      +..|..+|..+ +.+|..+||+++|+++   ..+.+=++.|...|++..-
T Consensus         5 D~kIl~~L~~n-~r~s~~~lA~~~gls~---~~v~~Ri~~L~~~giI~~~   50 (60)
T d1i1ga1           5 DKIILEILEKD-ARTPFTEIAKKLGISE---TAVRKRVKALEEKGIIEGY   50 (60)
T ss_dssp             HHHHHHHHHHC-TTCCHHHHHHHHTSCH---HHHHHHHHHHHHHTSSCCC
T ss_pred             HHHHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeEeE
Confidence            45577788887 8899999999999999   9999999999999998743

>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=94.81  E-value=0.013  Score=36.33  Aligned_cols=37  Identities=14%  Similarity=0.107  Sum_probs=34.9

Q ss_pred             CCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           49 GQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        49 ~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      +++.+..+||+.+|+.|   ..+.+.++-|...|++.+.+
T Consensus        21 ~~~v~~~~iA~~L~vs~---~SVt~mvkrL~~~Glv~~~~   57 (63)
T d2isya1          21 GVTPLRARIAERLDQSG---PTVSQTVSRMERDGLLRVAG   57 (63)
T ss_dssp             TCCCCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEECT
T ss_pred             CCCCcHHHHHHHhCCCc---hhHHHHHHHHHHCCCEEEcC
Confidence            48899999999999999   99999999999999999886

>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=94.77  E-value=0.0059  Score=37.79  Aligned_cols=46  Identities=11%  Similarity=0.216  Sum_probs=40.9

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeee
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQ   87 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~   87 (214)
                      +..|...|..+ +.+|..+||+++|+++   ..+++=++.|...|++..-
T Consensus         7 D~~IL~~L~~~-~r~s~~eiA~~l~ls~---~~v~~Ri~rL~~~GiI~~~   52 (63)
T d2cg4a1           7 DRGILEALMGN-ARTAYAELAKQFGVSP---ETIHVRVEKMKQAGIITGA   52 (63)
T ss_dssp             HHHHHHHHHHC-TTSCHHHHHHHHTSCH---HHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeEeE
Confidence            45577888887 8999999999999999   9999999999999999854

>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=94.70  E-value=0.012  Score=47.09  Aligned_cols=32  Identities=25%  Similarity=0.524  Sum_probs=28.2

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +..+++|+|||+|..++.++ ++|+.+++..|.
T Consensus       110 ~~~~vld~g~GsG~i~~~la-~~~~~~v~a~Di  141 (271)
T d1nv8a_         110 GIKTVADIGTGSGAIGVSVA-KFSDAIVFATDV  141 (271)
T ss_dssp             TCCEEEEESCTTSHHHHHHH-HHSSCEEEEEES
T ss_pred             cccEEEEeeeeeehhhhhhh-hcccceeeechh
Confidence            45689999999999999987 579999999886

>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=94.62  E-value=0.0086  Score=42.45  Aligned_cols=65  Identities=12%  Similarity=0.112  Sum_probs=46.0

Q ss_pred             cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      +.-.|...++++|..+||+.+++++   ..+.++++.|...|+++.....+|.- ...+.+|+.    ++.+.
T Consensus        36 ~L~~l~~~~~~~t~~~la~~l~i~~---~~vs~~l~~L~~~glI~~~~~~~D~R-~~~l~lT~~----G~~~~  100 (140)
T d3deua1          36 TLHNIHQLPPDQSQIQLAKAIGIEQ---PSLVRTLDQLEDKGLISRQTCASDRR-AKRIKLTEK----AEPLI  100 (140)
T ss_dssp             HHHHHHHSCSSEEHHHHHHHHTSCH---HHHHHHHHHHHHTTSEEEC---------CEEEECGG----GHHHH
T ss_pred             HHHHHHHcCCCccHHHHHHHHCCCH---hHHHHHHHHHHhCCCEEecccCCCCC-ceeeEECHH----HHHHH
Confidence            4444554336799999999999999   99999999999999998765311111 125888888    66654

>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=94.55  E-value=0.0086  Score=42.51  Aligned_cols=66  Identities=11%  Similarity=0.090  Sum_probs=48.9

Q ss_pred             cCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           39 LRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        39 lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      ..+...|..+ +++|..+||+.+++++   ..+.+++..|...|+++..+...|.- ...+.+|+.    ++.+.
T Consensus        37 ~~vL~~l~~~-~~~t~~ela~~~~i~~---~~vs~~v~~L~~~glv~r~~~~~D~R-~~~i~lT~~----G~~~~  102 (138)
T d1jgsa_          37 FKVLCSIRCA-ACITPVELKKVLSVDL---GALTRMLDRLVCKGWVERLPNPNDKR-GVLVKLTTG----GAAIC  102 (138)
T ss_dssp             HHHHHHHHHH-SSBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEEECTTCSS-CEEEEECHH----HHHHH
T ss_pred             HHHHHhHHhC-cCCCHHHHHHHHCCCH---hHHHHHHHHHhhCCCEEEeeccCCCC-eeEEEECHH----HHHHH
Confidence            3345555555 7899999999999999   99999999999999998765321211 235777777    55553

>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=94.53  E-value=0.0092  Score=36.75  Aligned_cols=43  Identities=23%  Similarity=0.335  Sum_probs=35.7

Q ss_pred             chhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           42 PDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        42 fd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      +.+..+. ++.+..+||+.+|+++   ..+.+.++-|...|++.+.+
T Consensus        13 ~~l~~~~-~~v~~~~iA~~L~vs~---~SVs~mikrL~~~GlV~~~~   55 (61)
T d2ev0a1          13 YMLIEEK-GYARVSDIAEALAVHP---SSVTKMVQKLDKDEYLIYEK   55 (61)
T ss_dssp             HHHHHHH-SSCCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEC--
T ss_pred             HHHHhcC-CCccHHHHHHHhCCCc---hhHHHHHHHHHHCCCEEEcc
Confidence            3333343 8899999999999999   99999999999999999875

>d3ctaa1 a.4.5.28 (A:5-89) Ta1064 (RFK), N-terminal domain {Thermoplasma acidophilum [TaxId: 2303]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Ta1064 (RFK), N-terminal domain
species: Thermoplasma acidophilum [TaxId: 2303]

Probab=94.41  E-value=0.0088  Score=39.26  Aligned_cols=48  Identities=8%  Similarity=0.223  Sum_probs=40.0

Q ss_pred             CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      +++|..+||+.+++++   ..+.++|.-|...|++....+   +- .-.|.+|+.
T Consensus        20 ~~lt~~eLa~~l~i~~---~~vs~~l~~Le~~GlV~r~~D---~R-~~~i~LT~~   67 (85)
T d3ctaa1          20 AYLTSSKLADMLGISQ---QSASRIIIDLEKNGYITRTVT---KR-GQILNITEK   67 (85)
T ss_dssp             EECCHHHHHHHHTSCH---HHHHHHHHHHHHTTSEEEEEE---TT-EEEEEECHH
T ss_pred             CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCeeeecc---cc-cccceECHH
Confidence            7899999999999999   999999999999999998651   11 233667777

>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=94.32  E-value=0.02  Score=42.23  Aligned_cols=33  Identities=9%  Similarity=0.041  Sum_probs=26.9

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .....+|||+|||+|.++++.+++  ..+++.+|.
T Consensus        39 ~~~g~~vLDl~~G~G~~~i~a~~~--ga~vv~vD~   71 (171)
T d1ws6a1          39 YPRRGRFLDPFAGSGAVGLEAASE--GWEAVLVEK   71 (171)
T ss_dssp             CTTCCEEEEETCSSCHHHHHHHHT--TCEEEEECC
T ss_pred             ccCCCeEEEeccccchhhhhhhhc--cchhhhccc
Confidence            345679999999999999998887  457777775

>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=94.25  E-value=0.0071  Score=47.69  Aligned_cols=40  Identities=13%  Similarity=0.104  Sum_probs=27.4

Q ss_pred             hhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          172 EDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       172 ~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +.++.+..+..+|||||||+|.+....+.++.. +++..|.
T Consensus        46 ~~f~~g~~~g~~vLDiGcG~g~~~~~~~~~~~~-~v~~~D~   85 (263)
T d2g72a1          46 QTFATGEVSGRTLIDIGSGPTVYQLLSACSHFE-DITMTDF   85 (263)
T ss_dssp             HHHHTSCSCCSEEEEETCTTCCGGGTTGGGGCS-EEEEECS
T ss_pred             HHcCCCCCCCcEEEEeccCCCHHHHHHhcccCC-eEEEEeC
Confidence            334333446789999999999887655555443 6888775

>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=94.13  E-value=0.009  Score=35.40  Aligned_cols=48  Identities=13%  Similarity=0.287  Sum_probs=42.4

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      |-+|...|.++|+|+-+.+|+++++++.   ..|+++|..|-..+=+...+
T Consensus         3 EQkILQVL~dagspvk~~ql~k~cqVpk---k~lNqVL~rlkke~kVsl~~   50 (57)
T d1j75a_           3 EQKILQVLSDDGGPVKIGQLVKKCQVPK---KTLNQVLYRLKKEDRVSSPE   50 (57)
T ss_dssp             HHHHHHHHHHHCSCEEHHHHHHHHCSCH---HHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHhcCCchHHHHHHHHHCCCH---HHHHHHHHHHHhccccccCC
Confidence            4456778888889999999999999999   99999999999988888776

>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=94.02  E-value=0.0075  Score=40.18  Aligned_cols=49  Identities=16%  Similarity=0.127  Sum_probs=44.1

Q ss_pred             CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      ++.+...|..+++++.   +.+.++|..|...|++.+.        ++.|.+|+.    +..|+
T Consensus        17 ~g~~kT~i~~~aNLs~---~~~~kyl~~L~~~GLI~~~--------~~~Y~iT~k----G~~~L   65 (90)
T d1r7ja_          17 SGSPKTRIMYGANLSY---ALTGRYIKMLMDLEIIRQE--------GKQYMLTKK----GEELL   65 (90)
T ss_dssp             TCBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEE--------TTEEEECHH----HHHHH
T ss_pred             CCCCccHHHHHcCCCH---HHHHHHHHHHHHCCCeeec--------CCEEEECcc----HHHHH
Confidence            3457899999999999   9999999999999999877        589999999    88775

>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=94.02  E-value=0.028  Score=42.99  Aligned_cols=34  Identities=18%  Similarity=0.299  Sum_probs=30.5

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ....+++|||.|.|.=++-++=.+|+.+++++|-
T Consensus        64 ~~~~~ilDiGsGaG~PGi~laI~~p~~~~~Lves   97 (207)
T d1jsxa_          64 LQGERFIDVGTGPGLPGIPLSIVRPEAHFTLLDS   97 (207)
T ss_dssp             CCSSEEEEETCTTTTTHHHHHHHCTTSEEEEEES
T ss_pred             hcCCceeeeeccCCceeeehhhhcccceEEEEec
Confidence            3457999999999999999999999999999884

>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=93.99  E-value=0.037  Score=42.75  Aligned_cols=39  Identities=13%  Similarity=0.272  Sum_probs=29.7

Q ss_pred             HHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEec
Q 040620          169 VLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFA  211 (214)
Q Consensus       169 ~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~D  211 (214)
                      .+++..+  ..+..+|||||||+|.++..|++.-  -+++.+|
T Consensus        61 ~ml~~L~--l~~g~~VLdIG~GsGy~ta~La~l~--~~V~aiE   99 (224)
T d1vbfa_          61 FMLDELD--LHKGQKVLEIGTGIGYYTALIAEIV--DKVVSVE   99 (224)
T ss_dssp             HHHHHTT--CCTTCEEEEECCTTSHHHHHHHHHS--SEEEEEE
T ss_pred             HHHHHhh--hcccceEEEecCCCCHHHHHHHHHh--ccccccc
Confidence            3556666  6778899999999999998888874  3555555

>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=93.95  E-value=0.017  Score=36.54  Aligned_cols=40  Identities=23%  Similarity=0.297  Sum_probs=35.0

Q ss_pred             hcCCCCCCHHHHHHHcCC-CCCCcccHHHHHHHHHhCCceeeec
Q 040620           46 NNSGQPMTLTQIIVALNV-HPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        46 ~~~~~p~t~~eLA~~~g~-~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      ..+|-|-|+.|||+.+|+ ++   ..+++.|..|...|++...+
T Consensus        19 ~~~G~~Ps~rei~~~~g~~S~---stv~~~l~~Le~kG~I~r~~   59 (71)
T d1jhfa1          19 SQTGMPPTRAEIAQRLGFRSP---NAAEEHLKALARKGVIEIVS   59 (71)
T ss_dssp             HHHSSCCCHHHHHHHTTCSSH---HHHHHHHHHHHHTTSEEECS
T ss_pred             HHhCCCCCHHHHHHHcCCCCH---HHHHHHHHHHHHCcCeecCC
Confidence            345578899999999999 56   78999999999999999874

>d1r18a_ c.66.1.7 (A:) Protein-L-isoaspartyl O-methyltransferase {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Protein-L-isoaspartyl O-methyltransferase
domain: Protein-L-isoaspartyl O-methyltransferase
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=93.77  E-value=0.047  Score=42.01  Aligned_cols=43  Identities=19%  Similarity=0.178  Sum_probs=31.2

Q ss_pred             HHhhcccccCCCCcEEeecCCchHHHHHHHHH------CCCCeEEEecC
Q 040620          170 LIEDCNEVSKGLKPLVDVGGSTGTMARAIATA------FPDTKCTVFAC  212 (214)
Q Consensus       170 ~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~------~P~l~~~v~Dl  212 (214)
                      +++.......+..+|||||||+|..+..+++.      ++..+++.+|.
T Consensus        70 ~l~~L~~~l~~g~~VLeIGtGsGY~ta~la~l~g~~g~~~~~~V~~iE~  118 (223)
T d1r18a_          70 ALEYLRDHLKPGARILDVGSGSGYLTACFYRYIKAKGVDADTRIVGIEH  118 (223)
T ss_dssp             HHHHTTTTCCTTCEEEEESCTTSHHHHHHHHHHHHSCCCTTCEEEEEES
T ss_pred             HHHHHhhccCCCCeEEEecCCCCHHHHHHHHHhhhccCCcccEEEEEec
Confidence            44544212556789999999999999888775      46677777764

>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=93.50  E-value=0.034  Score=37.07  Aligned_cols=74  Identities=9%  Similarity=-0.001  Sum_probs=53.7

Q ss_pred             HHHHHHHhHHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHc-CCCCCCcccHHHHHHHHHhCCceeeecCCCCCCcccee
Q 040620           21 WSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVAL-NVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESI   99 (214)
Q Consensus        21 ~~~~~g~~~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~-g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y   99 (214)
                      ++++.+-|...+|..         |..  |+....||.+.+ |+++   +-|.+=|+.|...|++......+.-. .-.|
T Consensus         5 l~ilg~kW~l~Il~~---------L~~--g~~rF~el~~~l~gis~---~~Ls~rLk~Le~~glv~r~~~~~~p~-~veY   69 (95)
T d2hzta1           5 LEVIGGKWKCVILCH---------LTH--GKKRTSELKRLMPNITQ---KMLTQQLRELEADGVINRIVYNQVPP-KVEY   69 (95)
T ss_dssp             HHHHCSTTHHHHHHH---------HTT--CCBCHHHHHHHCTTSCH---HHHHHHHHHHHHTTSEEEEEECSSSC-EEEE
T ss_pred             HHHHcCCCHHHHHHH---------HHc--CCCCHHHHHHHhhcCCh---hHHHHHHHHHHHhHHHhheecccccc-chhh
Confidence            444555555555543         223  899999999998 9999   99999999999999998764310000 2349


Q ss_pred             eCCCCCcccccccc
Q 040620          100 LLPPHLDFFSRISL  113 (214)
Q Consensus       100 ~~t~~~~~~s~~l~  113 (214)
                      .+|+.    ++.|.
T Consensus        70 ~LT~~----G~~L~   79 (95)
T d2hzta1          70 ELSEY----GRSLE   79 (95)
T ss_dssp             EECTT----GGGGH
T ss_pred             hhhhh----HHHHH
Confidence            99999    88875

>d1dpua_ a.4.5.16 (A:) C-terminal domain of RPA32 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: C-terminal domain of RPA32
domain: C-terminal domain of RPA32
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.38  E-value=0.025  Score=35.65  Aligned_cols=45  Identities=11%  Similarity=0.200  Sum_probs=39.0

Q ss_pred             CCCCHHHHHHHc-CCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCC
Q 040620           50 QPMTLTQIIVAL-NVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPP  103 (214)
Q Consensus        50 ~p~t~~eLA~~~-g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~  103 (214)
                      .++++++|++++ +++.   ..++..++.|...|++--.-+      +++|+.|.
T Consensus        22 eGi~~~el~~~l~~~~~---~~i~~aid~L~~eG~IYsTiD------ddHfkstd   67 (69)
T d1dpua_          22 EGLNFQDLKNQLKHMSV---SSIKQAVDFLSNEGHIYSTVD------DDHFKSTD   67 (69)
T ss_dssp             TTEEHHHHHHHSTTSCH---HHHHHHHHHHHHTTSEEECSS------TTEEEESS
T ss_pred             cCcCHHHHHHHccCCCH---HHHHHHHHHHHhCCceecccc------cchhcccC
Confidence            789999999999 7998   999999999999999975543      68888764

>d2frna1 c.66.1.47 (A:19-278) Hypothetical protein PH0793 {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Met-10+ protein-like
domain: Hypothetical protein PH0793
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=93.32  E-value=0.028  Score=44.38  Aligned_cols=33  Identities=21%  Similarity=0.164  Sum_probs=28.5

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+..+|||+|||+|.+++.++++ +..+++..|+
T Consensus       106 ~~g~~VlD~~aG~G~~~l~~a~~-~~~~V~avd~  138 (260)
T d2frna1         106 KPDELVVDMFAGIGHLSLPIAVY-GKAKVIAIEK  138 (260)
T ss_dssp             CTTCEEEETTCTTTTTHHHHHHH-TCCEEEEECC
T ss_pred             CCccEEEECcceEcHHHHHHHHh-CCcEEEEecC
Confidence            35789999999999999999987 5678888886

>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=93.07  E-value=0.0059  Score=43.22  Aligned_cols=65  Identities=14%  Similarity=0.154  Sum_probs=47.7

Q ss_pred             CcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           40 RIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        40 glfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      .++..|... +++|..+||+.+++++   ..+.++++-|...|+++.....+|.- .-.+.+|+.    +..+.
T Consensus        34 ~vL~~l~~~-~~~t~~~la~~~~i~~---~~vs~~i~~L~~~gli~r~~~~~D~R-~~~l~lT~~----G~~~~   98 (136)
T d2fbia1          34 RVIRILRQQ-GEMESYQLANQACILR---PSMTGVLARLERDGIVRRWKAPKDQR-RVYVNLTEK----GQQCF   98 (136)
T ss_dssp             HHHHHHHHH-CSEEHHHHHHHTTCCH---HHHHHHHHHHHHTTSEEEEEETTEEE-EEEEEECHH----HHHHH
T ss_pred             HHHHHHHHc-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEEeecCccCc-hhhhccCHH----HHHHH
Confidence            345556665 7899999999999999   99999999999999998765321110 123666776    55554

>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=92.67  E-value=0.0091  Score=42.28  Aligned_cols=64  Identities=9%  Similarity=0.156  Sum_probs=48.5

Q ss_pred             cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      +...|... +++|..+||+.+++++   ..+.+++..|...|++.......|.- .-...+|+.    ++.+.
T Consensus        38 vL~~l~~~-~~~t~~~La~~~~i~~---~~vsr~i~~L~~~glv~r~~~~~D~R-~~~i~lT~~----G~~~~  101 (137)
T d1z91a1          38 ALLLLWEH-ETLTVKKMGEQLYLDS---GTLTPMLKRMEQQGLITRKRSEEDER-SVLISLTED----GALLK  101 (137)
T ss_dssp             HHHHHHHH-SEEEHHHHHHTTTCCH---HHHHHHHHHHHHHTSEECCBCSSCTT-SBEEEECHH----HHSGG
T ss_pred             HHHHHHcC-CCCCHHHHHHHHCcCH---HHHHHHHHHHhhccceEEeecCCCCC-eEEEEECHH----HHHHH
Confidence            34455554 7899999999999999   99999999999999998775311111 234778888    76665

>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=92.30  E-value=0.043  Score=42.82  Aligned_cols=35  Identities=23%  Similarity=0.413  Sum_probs=30.9

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +....+++|||.|.|.=++-++=.+|+++++.+|-
T Consensus        68 ~~~~~~ilDiGSGaGfPGi~laI~~p~~~v~Lves  102 (239)
T d1xdza_          68 FNQVNTICDVGAGAGFPSLPIKICFPHLHVTIVDS  102 (239)
T ss_dssp             GGGCCEEEEECSSSCTTHHHHHHHCTTCEEEEEES
T ss_pred             ccCCCeEEeecCCCchHHHHHHHhCCCccceeecc
Confidence            34567999999999999999999999999999873

>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=92.27  E-value=0.083  Score=40.38  Aligned_cols=41  Identities=22%  Similarity=0.245  Sum_probs=29.9

Q ss_pred             HHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          169 VLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       169 ~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+++..+  ..+..+|||||||+|..+..+++.. +.+++.+|.
T Consensus        69 ~ml~~L~--l~~g~~VLeIGsGsGY~taila~l~-g~~V~~ie~  109 (215)
T d1jg1a_          69 IMLEIAN--LKPGMNILEVGTGSGWNAALISEIV-KTDVYTIER  109 (215)
T ss_dssp             HHHHHHT--CCTTCCEEEECCTTSHHHHHHHHHH-CSCEEEEES
T ss_pred             HHHHhhc--cCccceEEEecCCCChhHHHHHHhh-CceeEEEec
Confidence            3455555  6678899999999999999888764 344655553

>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=92.26  E-value=0.057  Score=32.49  Aligned_cols=44  Identities=11%  Similarity=0.141  Sum_probs=38.1

Q ss_pred             cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      ++..|.+. ...|+..||.+++++.   +.++|.|-.|...|.+++.+
T Consensus         7 ~l~~lg~~-~~~tA~~LA~kl~vpK---k~iNr~LYsL~~kgkl~k~~   50 (59)
T d2gxba1           7 FLEELGEG-KATTAHDLSGKLGTPK---KEINRVLYSLAKKGKLQKEA   50 (59)
T ss_dssp             HHHHHCTT-CCBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEEC
T ss_pred             HHHhcCCc-cchhHHHHHHHhCCcH---HHHHHHHHHHHHccchhhcC
Confidence            34555543 7899999999999999   99999999999999999875

>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=92.16  E-value=0.018  Score=45.25  Aligned_cols=42  Identities=17%  Similarity=0.273  Sum_probs=32.9

Q ss_pred             HHHHHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          167 ASVLIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       167 ~~~~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+++..+  ..+..+|++||+|.|.+...|+++-+  +++.+|+
T Consensus        18 i~kIv~~~~--~~~~d~VLEIGpG~G~LT~~L~~~~~--~v~aIE~   59 (245)
T d1yuba_          18 LNQIIKQLN--LKETDTVYEIGTGKGHLTTKLAKISK--QVTSIEL   59 (245)
T ss_dssp             HHHHHHHCC--CCSSEEEEECSCCCSSCSHHHHHHSS--EEEESSS
T ss_pred             HHHHHHhcC--CCCCCeEEEECCCccHHHHHHHhhcC--ceeEeee
Confidence            456677665  66778999999999999999999844  5666554

>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=91.81  E-value=0.043  Score=37.85  Aligned_cols=79  Identities=11%  Similarity=0.077  Sum_probs=60.2

Q ss_pred             HHHHHHHHHHHHhHHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHc-CCCCCCcccHHHHHHHHHhCCceeeecCCCCCC
Q 040620           16 AQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVAL-NVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQ   94 (214)
Q Consensus        16 ~~~~l~~~~~g~~~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~-g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~   94 (214)
                      +....++++.+-|...+|..         |..  |+....||.+.+ |+++   +-|.+=|+.|...|++......+.-.
T Consensus        13 pv~~~l~~ig~kW~l~Il~~---------L~~--g~~RF~el~~~l~gis~---~~Ls~rL~~Le~~glv~R~~~~~~p~   78 (114)
T d1yyva1          13 PSREVLKHVTSRWGVLILVA---------LRD--GTHRFSDLRRKMGGVSE---KMLAQSLQALEQDGFLNRVSYPVVPP   78 (114)
T ss_dssp             THHHHHHHHHSHHHHHHHHH---------GGG--CCEEHHHHHHHSTTCCH---HHHHHHHHHHHHHTCEEEEEECSSSC
T ss_pred             CHHHHHHHHcCCCHHHHHHH---------Hhc--CCCCHHHHHHHccccch---hHHHHHHHHHHHHHHHhhcccCCCCc
Confidence            35667788888888777754         233  899999999999 7998   99999999999999998764210000


Q ss_pred             ccceeeCCCCCcccccccc
Q 040620           95 EEESILLPPHLDFFSRISL  113 (214)
Q Consensus        95 ~~~~y~~t~~~~~~s~~l~  113 (214)
                       .-.|.+|+.    ++.|.
T Consensus        79 -~veY~LT~~----G~~L~   92 (114)
T d1yyva1          79 -HVEYSLTPL----GEQVS   92 (114)
T ss_dssp             -EEEEEECHH----HHHHH
T ss_pred             -hhHhHhhHh----HHHHH
Confidence             234999999    77775

>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=91.76  E-value=0.039  Score=37.87  Aligned_cols=51  Identities=8%  Similarity=0.120  Sum_probs=40.9

Q ss_pred             CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      +++|..+||+.+++++   ..+.+++..|...|++......+|.- .-...+|+.
T Consensus        47 ~~~t~~ela~~l~~~~---~~vs~~i~~Le~~gli~r~~~~~D~R-~~~i~LT~~   97 (115)
T d1hsja1          47 NEISSKEIAKCSEFKP---YYLTKALQKLKDLKLLSKKRSLQDER-TVIVYVTDT   97 (115)
T ss_dssp             SEEEHHHHHHSSCCCH---HHHHHHHHHHHTTTTSCCEECCSSSS-CCEEECCSS
T ss_pred             CCcCHHHHHHHHCCCh---hhHHHHHHHHHHcCCeEEEeecCCCc-eEEEEECHH
Confidence            6899999999999999   99999999999999999765322211 234677777

>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=91.67  E-value=0.071  Score=39.45  Aligned_cols=31  Identities=10%  Similarity=0.149  Sum_probs=25.7

Q ss_pred             CCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          181 LKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       181 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..++||++||+|.++++.+++-.. +++.+|.
T Consensus        44 ~~~vLDlfaGsG~~giealsrGa~-~v~~VE~   74 (183)
T d2fpoa1          44 DAQCLDCFAGSGALGLEALSRYAA-GATLIEM   74 (183)
T ss_dssp             TCEEEETTCTTCHHHHHHHHTTCS-EEEEECS
T ss_pred             hhhhhhhhccccceeeeEEecCcc-eeEEEEE
Confidence            579999999999999999988654 6776664

>d2frha1 a.4.5.28 (A:102-216) Pleiotropic regulator of virulence genes, SarA {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Pleiotropic regulator of virulence genes, SarA
species: Staphylococcus aureus [TaxId: 1280]

Probab=91.54  E-value=0.038  Score=37.89  Aligned_cols=62  Identities=21%  Similarity=0.305  Sum_probs=46.2

Q ss_pred             hhhhcC-CCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCccccccc
Q 040620           43 DIINNS-GQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRIS  112 (214)
Q Consensus        43 d~L~~~-~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l  112 (214)
                      ..|..+ ++++|..+||+.+++++   ..+.++++.|...|++......+|.- .-.+.+|+.    ++..
T Consensus        40 ~~l~~~~~~~~t~~~la~~l~~~~---~tvs~~i~~Le~~gli~r~~~~~D~R-~~~i~LT~~----G~~~  102 (115)
T d2frha1          40 TYISENKEKEYYLKDIINHLNYKQ---PQVVKAVKILSQEDYFDKKRNEHDER-TVLILVNAQ----QRKK  102 (115)
T ss_dssp             HHHHHTCCSEEEHHHHHHHSSSHH---HHHHHHHHHHHHTTSSCCBCCSSSSC-CCEEECCSH----HHHH
T ss_pred             HHHHcCCCCCCCHHHHHHHHCCCH---hHHHHHHHHHHhhhhheeeecccCCc-eEEEEECHH----HHHH
Confidence            344433 26799999999999999   99999999999999999876422221 234777777    6554

>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=91.37  E-value=0.056  Score=43.74  Aligned_cols=34  Identities=21%  Similarity=0.236  Sum_probs=30.6

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ++.++||.||||.|..+..+++..|..+++++|+
T Consensus        76 ~~pk~VLiiG~G~G~~~~~ll~~~~~~~v~~VEi  109 (312)
T d1uira_          76 PEPKRVLIVGGGEGATLREVLKHPTVEKAVMVDI  109 (312)
T ss_dssp             SCCCEEEEEECTTSHHHHHHTTSTTCCEEEEEES
T ss_pred             CCcceEEEeCCCchHHHHHHHhcCCcceEEEecC
Confidence            3578999999999999999999888889999886

>d2cl5a1 c.66.1.1 (A:3-216) Catechol O-methyltransferase, COMT {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: COMT-like
domain: Catechol O-methyltransferase, COMT
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=91.33  E-value=0.077  Score=40.39  Aligned_cols=34  Identities=12%  Similarity=0.194  Sum_probs=29.9

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCC-CCeEEEecCC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFP-DTKCTVFACH  213 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dlp  213 (214)
                      ++++||+||+|.|..++.++++.| +.+++.+|..
T Consensus        56 kpk~ILEiGt~~G~Sti~la~al~~~g~v~sid~~   90 (214)
T d2cl5a1          56 SPSLVLELGAYCGYSAVRMARLLQPGARLLTMEMN   90 (214)
T ss_dssp             CCSEEEEECCTTSHHHHHHHTTCCTTCEEEEEESC
T ss_pred             CCCEEEEEccCchhHHHHHHHhCCCccEEEEEecc
Confidence            478999999999999999999875 5789998864

>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=91.22  E-value=0.039  Score=36.27  Aligned_cols=45  Identities=27%  Similarity=0.344  Sum_probs=37.9

Q ss_pred             cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      |++.|.+.++-+|=++||+++|+..   ..++++|..|...|++....
T Consensus        23 v~~~L~~~~~evtDe~iA~~tgi~i---n~VRk~Ly~L~~~~L~~y~R   67 (88)
T d1q1ha_          23 VLRILLDKGTEMTDEEIANQLNIKV---NDVRKKLNLLEEQGFVSYRK   67 (88)
T ss_dssp             HHHHHHHHCSCBCHHHHHHTTTSCH---HHHHHHHHHHHHHTSCEEEE
T ss_pred             HHHHHHhccCcCCHHHHHHHhCCcH---HHHHHHHHHHHhCCceEEEE
Confidence            5666654335799999999999998   99999999999999998654

>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=91.11  E-value=0.03  Score=33.06  Aligned_cols=40  Identities=13%  Similarity=0.069  Sum_probs=31.2

Q ss_pred             chhhhcC-CCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCce
Q 040620           42 PDIINNS-GQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFF   84 (214)
Q Consensus        42 fd~L~~~-~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l   84 (214)
                      .+.|.++ ..++|+++||+.+|+++   +.+.|+.+......+.
T Consensus         9 ~~yI~~~~~~~~tl~~lA~~~~~s~---~~l~r~Fk~~~g~tp~   49 (54)
T d1bl0a1           9 LDWIEDNLESPLSLEKVSERSGYSK---WHLQRMFKKETGHSLG   49 (54)
T ss_dssp             HHHHHTTTTSCCCCHHHHHHSSSCH---HHHHHHHHHHHSSCHH
T ss_pred             HHHHHhccCCCCCHHHHHHHHCcCH---HHHHHHHHHHHCcCHH
Confidence            3445543 37899999999999999   9999998877665543

>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=91.05  E-value=0.026  Score=39.53  Aligned_cols=60  Identities=17%  Similarity=0.243  Sum_probs=44.2

Q ss_pred             cchhhhcC-CCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCC
Q 040620           41 IPDIINNS-GQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPH  104 (214)
Q Consensus        41 lfd~L~~~-~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~  104 (214)
                      +...|... ++++|..+||+.+++++   ..+.+.++-|...|++......+|.- .-...+|+.
T Consensus        38 vL~~l~~~~~~~~~~~~ia~~l~~~~---~~vs~~v~~L~~~glV~r~~~~~D~R-~v~i~LT~~   98 (125)
T d1p4xa2          38 ILAIITSQNKNIVLLKDLIETIHHKY---PQTVRALNNLKKQGYLIKERSTEDER-KILIHMDDA   98 (125)
T ss_dssp             HHHHHHTTTTCCEEHHHHHHHSSSCH---HHHHHHHHHHHHHTSSEEEECSSSTT-CEEEECCHH
T ss_pred             HHHHHHHccCCCccHHHHHHHHCCCc---chHHHHHHHHHhccCEeeeecCCCCC-eEEEEECHH
Confidence            45566432 26789999999999999   99999999999999998765322211 223666666

>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=90.60  E-value=0.066  Score=33.87  Aligned_cols=58  Identities=12%  Similarity=0.073  Sum_probs=45.8

Q ss_pred             HhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcc-cHHHHHHHHHhCCceeeecCCCCCCccceeeCCC
Q 040620           37 IQLRIPDIINNSGQPMTLTQIIVALNVHPNKTR-CTQILVCLLAHSGFFVQQKDGKNEQEEESILLPP  103 (214)
Q Consensus        37 ~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~-~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~  103 (214)
                      ++-.|++.|... +|.++-+||+.+|++.   . -+++.|-.|...|-+...+.+     +-.|.++.
T Consensus         6 ~eekI~~~L~~~-g~~~Al~iak~lGl~k---akeVN~~LY~L~k~g~v~k~~~t-----PP~W~L~~   64 (73)
T d1xmka1           6 IKEKICDYLFNV-SDSSALNLAKNIGLTK---ARDINAVLIDMERQGDVYRQGTT-----PPIWHLTD   64 (73)
T ss_dssp             HHHHHHHHHHHT-CCEEHHHHHHHHCGGG---HHHHHHHHHHHHHTTSEEEECSS-----SCEEEECH
T ss_pred             HHHHHHHHHHHc-CCchHHHHHHHhCCCc---HHHHhHHHHHHHHCCCeecCCCC-----CCceeeec
Confidence            455678888887 8999999999999975   4 499999999999999987521     33566554

>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=90.44  E-value=0.018  Score=42.23  Aligned_cols=64  Identities=13%  Similarity=0.067  Sum_probs=46.8

Q ss_pred             cchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccceeeCCCCCcccccccc
Q 040620           41 IPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        41 lfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~y~~t~~~~~~s~~l~  113 (214)
                      |...|... +++|..+||+.+++++   ..+.+++.-|...|++......+|.- .-.+.+|+.    ++.++
T Consensus        46 vL~~l~~~-~~~t~~~la~~~~l~~---~tvs~~i~rL~~~gli~r~~~~~D~R-~~~l~lT~~----G~~~~  109 (162)
T d2fxaa1          46 ILWIAYQL-NGASISEIAKFGVMHV---STAFNFSKKLEERGYLRFSKRLNDKR-NTYVQLTEE----GTEVF  109 (162)
T ss_dssp             HHHHHHHH-TSEEHHHHHHHTTCCH---HHHHHHHHHHHHHTSEEEECC-------CEEEECHH----HHHHH
T ss_pred             HHhhhccC-CCcCHHHHHHHHcCCc---hhhHHHHHHHHHCCCceeecccccCe-eeeeccCHh----HHHHH
Confidence            55667665 7899999999999999   99999999999999999775311111 224666666    55543

>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=90.21  E-value=0.084  Score=36.61  Aligned_cols=47  Identities=6%  Similarity=0.127  Sum_probs=39.1

Q ss_pred             CcchhhhcC-CCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecC
Q 040620           40 RIPDIINNS-GQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKD   89 (214)
Q Consensus        40 glfd~L~~~-~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~   89 (214)
                      .|+..|... ++++|..+||+.+++++   ..+.+.++.|...|++.....
T Consensus        38 ~iL~~l~~~~~~~~t~~eia~~~~~~~---~~vs~~l~~L~~~g~v~r~~~   85 (125)
T d1p4xa1          38 ILLTYLFHQQENTLPFKKIVSDLCYKQ---SDLVQHIKVLVKHSYISKVRS   85 (125)
T ss_dssp             HHHHHHHSCSCSEEEHHHHHHHSSSCG---GGTHHHHHHHHHTTSCEEEEC
T ss_pred             HHHHHHHHhccCCcCHHHHHHHhCCCc---chHHHHHHHHHHCCCceeecc
Confidence            345555443 26899999999999999   999999999999999998763

>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=90.17  E-value=0.037  Score=40.69  Aligned_cols=36  Identities=11%  Similarity=0.162  Sum_probs=33.5

Q ss_pred             CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      .++|..+||+.+++++   ..+.++++-|...|++....
T Consensus        78 ~~lt~~eLa~~l~i~~---~tvsr~l~~Le~~GlV~r~~  113 (172)
T d2fbka1          78 EGLRPTELSALAAISG---PSTSNRIVRLLEKGLIERRE  113 (172)
T ss_dssp             SCBCHHHHHHHCSCCS---GGGSSHHHHHHHHTSEECCC
T ss_pred             CCcCHHHHHHHHCcCH---hHHHHHHHHHHhCCCeeeec
Confidence            3589999999999999   99999999999999999875

>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=90.15  E-value=0.045  Score=36.99  Aligned_cols=79  Identities=10%  Similarity=0.057  Sum_probs=59.7

Q ss_pred             HHHHHHHHHHHHhHHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHc-CCCCCCcccHHHHHHHHHhCCceeeecCCCCCC
Q 040620           16 AQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVAL-NVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQ   94 (214)
Q Consensus        16 ~~~~l~~~~~g~~~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~-g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~   94 (214)
                      +....++++.+-|...+|...         ..  |+....||.+.+ |+++   +-|.+=|+-|...|++........-.
T Consensus         9 pv~~~l~ilg~kW~l~Il~~L---------~~--g~~rF~el~~~l~gIs~---~~Ls~rLkeL~~~glv~r~~~~~~p~   74 (102)
T d2fswa1           9 PVRKSMQIFAGKWTLLIIFQI---------NR--RIIRYGELKRAIPGISE---KMLIDELKFLCGKGLIKKKQYPEVPP   74 (102)
T ss_dssp             HHHHHHHHHTSSSHHHHHHHH---------TT--SCEEHHHHHHHSTTCCH---HHHHHHHHHHHHTTSEEEEEECSSSC
T ss_pred             CHHHHHHHHcCCCHHHHHHHH---------cc--CCCCHHHHHhhCcccch---hHHHHHHHHHHHCCceeecccCCCCC
Confidence            466677788888877766542         33  789999999998 8999   99999999999999998764210000


Q ss_pred             ccceeeCCCCCcccccccc
Q 040620           95 EEESILLPPHLDFFSRISL  113 (214)
Q Consensus        95 ~~~~y~~t~~~~~~s~~l~  113 (214)
                       .-.|.+|+.    +..|.
T Consensus        75 -~veY~LT~~----G~~L~   88 (102)
T d2fswa1          75 -RVEYSLTPL----GEKVL   88 (102)
T ss_dssp             -EEEEEECHH----HHTTH
T ss_pred             -eehhhhhHh----HHHHH
Confidence             234999999    88775

>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=89.98  E-value=0.084  Score=37.78  Aligned_cols=75  Identities=11%  Similarity=0.066  Sum_probs=56.9

Q ss_pred             HHHHHHHHHhHHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeecCCCCCCccce
Q 040620           19 QVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQKDGKNEQEEES   98 (214)
Q Consensus        19 ~l~~~~~g~~~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~~~~~~   98 (214)
                      ..++++..-|...+|+.+.         .  |+..+.||.+.+|+++   .-|.+=|+.|...|++.+.....+-  ...
T Consensus        12 ~~l~ilg~kW~l~Il~~l~---------~--G~~rf~el~~~lgis~---~vLs~rL~~L~~~gLv~r~~~~~p~--r~~   75 (142)
T d2f2ea1          12 RPLDVIGDGWSMLIVRDAF---------E--GLTRFGEFQKSLGLAK---NILAARLRNLVEHGVMVAVPAESGS--HQE   75 (142)
T ss_dssp             TTHHHHCSSSHHHHHHHHH---------T--TCCSHHHHHHHHCCCH---HHHHHHHHHHHHTTSEEEEECSSSS--CEE
T ss_pred             HHHHHHcCCCHHHHHHHHH---------c--CCCCHHHHHHHhhccH---HHHHHHHHHHHHhcceeeecCCCCC--eeE
Confidence            3455666677777666542         3  8999999999999999   9999999999999999874321111  245


Q ss_pred             eeCCCCCcccccccc
Q 040620           99 ILLPPHLDFFSRISL  113 (214)
Q Consensus        99 y~~t~~~~~~s~~l~  113 (214)
                      |.+|+.    ++.|.
T Consensus        76 Y~LT~~----G~~L~   86 (142)
T d2f2ea1          76 YRLTDK----GRALF   86 (142)
T ss_dssp             EEECHH----HHTTH
T ss_pred             EecCcC----cchHH
Confidence            999999    88875

>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=89.72  E-value=0.12  Score=32.23  Aligned_cols=43  Identities=9%  Similarity=-0.008  Sum_probs=38.2

Q ss_pred             chhhhcCCCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           42 PDIINNSGQPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        42 fd~L~~~~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      .+.|..+ +..|+.+||+++|++.   +.+.|.|-.|...|.+...+
T Consensus        16 l~~L~~~-~~~tA~~LAk~Lg~~K---k~VNr~LY~L~~~G~v~~~~   58 (70)
T d1sfua_          16 VLSLNTN-DYTTAISLSNRLKINK---KKINQQLYKLQKEDTVKMVP   58 (70)
T ss_dssp             HHTSCTT-CEECHHHHHHHTTCCH---HHHHHHHHHHHHTTSEEEEC
T ss_pred             HHhcCCC-CCchHHHHHHHhCCCH---HHHHHHHHHHHHCCCeecCC
Confidence            4566665 8899999999999988   99999999999999999885

>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=89.29  E-value=0.17  Score=31.73  Aligned_cols=35  Identities=9%  Similarity=0.115  Sum_probs=32.8

Q ss_pred             CCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           51 PMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        51 p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      ++|-++||+-+|+++   ..+.|.|..|...|++....
T Consensus        27 ~lt~~elA~~lg~sr---~tvsr~l~~l~~~g~I~~~~   61 (73)
T d1zyba1          27 KVKMDDLARCLDDTR---LNISKTLNELQDNGLIELHR   61 (73)
T ss_dssp             ECCHHHHHHHHTSCH---HHHHHHHHHHHHTTSCEEET
T ss_pred             ecCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEecC
Confidence            589999999999999   99999999999999998774

>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=89.25  E-value=0.19  Score=31.03  Aligned_cols=36  Identities=14%  Similarity=0.181  Sum_probs=33.4

Q ss_pred             CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      ..++..+||+..|++.   .-+++-++.|...|++...+
T Consensus        24 ~~l~~~~La~~~~vSr---~tvr~Al~~L~~~Gli~~~~   59 (69)
T d2hs5a1          24 ARLSEPDICAALDVSR---NTVREAFQILIEDRLVAHEL   59 (69)
T ss_dssp             CEECHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEET
T ss_pred             CccCHHHHHHHHCCCH---HHHHHHHHHHHHCCcEEEEc
Confidence            5678999999999999   99999999999999999886

>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=89.14  E-value=0.16  Score=38.67  Aligned_cols=36  Identities=31%  Similarity=0.337  Sum_probs=31.1

Q ss_pred             cCCCCcEEeecCCchHHHHHHHHHCC-CCeEEEecCC
Q 040620          178 SKGLKPLVDVGGSTGTMARAIATAFP-DTKCTVFACH  213 (214)
Q Consensus       178 ~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dlp  213 (214)
                      ..+.++||+||++.|..++.+++.-| +.+++.+|..
T Consensus        57 ~~~~k~vLEiGt~~GyStl~~a~al~~~g~i~tie~~   93 (219)
T d2avda1          57 LIQAKKALDLGTFTGYSALALALALPADGRVVTCEVD   93 (219)
T ss_dssp             HTTCCEEEEECCTTSHHHHHHHTTSCTTCEEEEEESC
T ss_pred             ccCCCeEEEEechhhHHHHHHHHhCCCCceEEEEeec
Confidence            34589999999999999999999987 6788888864

>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=89.14  E-value=0.23  Score=31.31  Aligned_cols=36  Identities=3%  Similarity=-0.022  Sum_probs=33.8

Q ss_pred             CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      -|+|-+|||.-+|+++   ..+.|.|..|...|++....
T Consensus        28 ~~lt~~eLA~~~G~sr---etvsr~L~~l~~~glI~~~~   63 (81)
T d2gaua1          28 IYLSREELATLSNMTV---SNAIRTLSTFVSERMLALDG   63 (81)
T ss_dssp             CCCCHHHHHHHTTSCH---HHHHHHHHHHHHTTSEEEET
T ss_pred             ecCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEecC
Confidence            5799999999999999   99999999999999999874

>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=88.83  E-value=0.15  Score=31.42  Aligned_cols=35  Identities=9%  Similarity=0.099  Sum_probs=33.1

Q ss_pred             CCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           51 PMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        51 p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      |+|-+|||+-+|+++   ..+.|.|+-|...|++....
T Consensus        29 ~lt~~~lA~~~G~sR---etvsr~L~~l~~~glI~~~~   63 (69)
T d1i5za1          29 KITRQEIGQIVGCSR---ETVGRILKMLEDQNLISAHG   63 (69)
T ss_dssp             ECCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEET
T ss_pred             CCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEEcC
Confidence            699999999999999   99999999999999999874

>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=88.61  E-value=0.19  Score=39.34  Aligned_cols=41  Identities=12%  Similarity=0.021  Sum_probs=30.5

Q ss_pred             HHhhcccccCCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          170 LIEDCNEVSKGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       170 ~l~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +.+.+-  +....+|||+|||+|..+..+++.-+..++..+|+
T Consensus        58 ~~~~~~--~~~~~~vvDlG~~pGgws~~~a~~~~v~~V~g~~i   98 (257)
T d2p41a1          58 FVERNL--VTPEGKVVDLGCGRGGWSYYCGGLKNVREVKGLTK   98 (257)
T ss_dssp             HHHTTS--SCCCEEEEEETCTTSHHHHHHHTSTTEEEEEEECC
T ss_pred             HHHhcC--ccCCCeEEEecCCCChHHHHHHhhcCCCceeEEEe
Confidence            444443  45566899999999999999998877666555554

>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=88.53  E-value=0.15  Score=40.26  Aligned_cols=33  Identities=15%  Similarity=0.252  Sum_probs=28.3

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+.++||.||||.|..+..+++ +|..+++++|+
T Consensus        71 ~~p~~vLiiG~G~G~~~~~~l~-~~~~~v~~VEi  103 (276)
T d1mjfa_          71 PKPKRVLVIGGGDGGTVREVLQ-HDVDEVIMVEI  103 (276)
T ss_dssp             SCCCEEEEEECTTSHHHHHHTT-SCCSEEEEEES
T ss_pred             CCCceEEEecCCchHHHHHHHH-hCCceEEEecC
Confidence            4578999999999999999986 67778888876

>d1z7ua1 a.4.5.69 (A:1-108) Hypothetical protein EF0647 {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: HxlR-like
domain: Hypothetical protein EF0647
species: Enterococcus faecalis [TaxId: 1351]

Probab=88.32  E-value=0.06  Score=36.71  Aligned_cols=80  Identities=10%  Similarity=0.032  Sum_probs=58.0

Q ss_pred             hHHHHHHHHHHHHhHHHHHHHHHhcCcchhhhcCCCCCCHHHHHHHc-CCCCCCcccHHHHHHHHHhCCceeeecCCCCC
Q 040620           15 QAQAQVWSYTYNYMKSLSLKRAIQLRIPDIINNSGQPMTLTQIIVAL-NVHPNKTRCTQILVCLLAHSGFFVQQKDGKNE   93 (214)
Q Consensus        15 ~~~~~l~~~~~g~~~~~~L~~a~~lglfd~L~~~~~p~t~~eLA~~~-g~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~   93 (214)
                      -+....++++.+-|...+|..         |..  |+....||.+.+ |+++   +-|.+=|+.|...|++.........
T Consensus         7 c~i~~al~iig~kW~~~Il~~---------L~~--g~~RF~el~~~l~gIS~---~~Ls~rLk~L~~~glv~R~~~~~~p   72 (108)
T d1z7ua1           7 TSINLALSTINGKWKLSLMDE---------LFQ--GTKRNGELMRALDGITQ---RVLTDRLREMEKDGLVHRESFNELP   72 (108)
T ss_dssp             HHHHHHHHTTCSTTHHHHHHH---------HHH--SCBCHHHHHHHSTTCCH---HHHHHHHHHHHHHTSEEEEEECCSS
T ss_pred             CcHHHHHHHHcCCCHHHHHHH---------HHc--CCCCHHHHHHHCcCCCh---hHHHHHHHHHHHCCcceeeccCCCc
Confidence            344556666667777666654         333  789999999998 7999   9999999999999999875421000


Q ss_pred             CccceeeCCCCCcccccccc
Q 040620           94 QEEESILLPPHLDFFSRISL  113 (214)
Q Consensus        94 ~~~~~y~~t~~~~~~s~~l~  113 (214)
                      . .-.|.+|+.    ++.|.
T Consensus        73 ~-~veY~LT~~----G~~L~   87 (108)
T d1z7ua1          73 P-RVEYTLTPE----GYALY   87 (108)
T ss_dssp             C-EEEEEECHH----HHHHH
T ss_pred             c-eehhhhchh----HHHHH
Confidence            0 123999999    77775

>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=88.27  E-value=0.2  Score=31.08  Aligned_cols=36  Identities=17%  Similarity=0.160  Sum_probs=33.5

Q ss_pred             CCCCHHHHHHHcCC-CCCCcccHHHHHHHHHhCCceeeec
Q 040620           50 QPMTLTQIIVALNV-HPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        50 ~p~t~~eLA~~~g~-~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      +-++.++.|+++++ ..   |+++.+...|.++|++.+..
T Consensus        24 ~~~~L~~aa~~L~v~~k---RRiYDI~NVLe~igli~K~~   60 (67)
T d1cf7a_          24 GVLDLKLAADTLAVRQK---RRIYDITNVLEGIGLIEKKS   60 (67)
T ss_dssp             TEEEHHHHHHHTTTCCT---HHHHHHHHHHHHHTSEEEEE
T ss_pred             CeeeHHHHHHHhcCcch---hhHHHHHHHHhhhhhhhccc
Confidence            67899999999999 67   99999999999999999886

>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=88.16  E-value=0.2  Score=40.39  Aligned_cols=33  Identities=21%  Similarity=0.014  Sum_probs=27.7

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .+..+|||++||+|.+++.+++..+ .+++.+|+
T Consensus       144 ~~g~~VLDl~~g~G~~si~~a~~ga-~~V~~vD~  176 (324)
T d2as0a2         144 QPGDRVLDVFTYTGGFAIHAAIAGA-DEVIGIDK  176 (324)
T ss_dssp             CTTCEEEETTCTTTHHHHHHHHTTC-SEEEEEES
T ss_pred             CCCCeeecccCcccchhhhhhhcCC-cEEEeecC
Confidence            4578999999999999999998754 37888886

>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=88.10  E-value=0.15  Score=40.31  Aligned_cols=34  Identities=24%  Similarity=0.285  Sum_probs=30.2

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      .++++||-||||.|..+..+++..|..+++++|+
T Consensus        74 ~~p~~vLiiGgG~G~~~~~~l~~~~~~~i~~VEI  107 (274)
T d1iy9a_          74 PNPEHVLVVGGGDGGVIREILKHPSVKKATLVDI  107 (274)
T ss_dssp             SSCCEEEEESCTTCHHHHHHTTCTTCSEEEEEES
T ss_pred             CCcceEEecCCCCcHHHHHHHhcCCcceEEEecC
Confidence            3578999999999999999998888888988886

>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=87.68  E-value=0.16  Score=40.47  Aligned_cols=34  Identities=12%  Similarity=0.193  Sum_probs=30.3

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +++++|+-||||.|..+..+++..|..++++.|+
T Consensus        77 ~~pk~vLiiGgG~G~~~~~~l~~~~~~~v~~vEi  110 (285)
T d2o07a1          77 PNPRKVLIIGGGDGGVLREVVKHPSVESVVQCEI  110 (285)
T ss_dssp             SSCCEEEEEECTTSHHHHHHTTCTTCCEEEEEES
T ss_pred             cCcCeEEEeCCCchHHHHHHHHcCCcceeeeccC
Confidence            3578999999999999999998888889998876

>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=87.64  E-value=0.31  Score=30.66  Aligned_cols=36  Identities=17%  Similarity=0.276  Sum_probs=33.3

Q ss_pred             CCC-CHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           50 QPM-TLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        50 ~p~-t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      ..+ |..+||+..+++.   .-+++-++.|...|++....
T Consensus        20 ~~LPse~~La~~~~vSr---~tvr~Al~~L~~~Gli~~~~   56 (78)
T d3bwga1          20 DKLPVLETLMAQFEVSK---STITKSLELLEQKGAIFQVR   56 (78)
T ss_dssp             CBCCCHHHHHHHTTCCH---HHHHHHHHHHHHTTSEEEET
T ss_pred             CCCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCcEEEEc
Confidence            556 8999999999999   99999999999999999886

>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=87.54  E-value=0.08  Score=31.06  Aligned_cols=38  Identities=11%  Similarity=0.094  Sum_probs=29.9

Q ss_pred             cchhhhcC-CCCCCHHHHHHHcCCCCCCcccHHHHHHHHHhC
Q 040620           41 IPDIINNS-GQPMTLTQIIVALNVHPNKTRCTQILVCLLAHS   81 (214)
Q Consensus        41 lfd~L~~~-~~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~   81 (214)
                      +.+.|.++ ..|+|+++||+.+++++   +.+.|+.+.....
T Consensus         8 i~~yi~~~~~~~itl~~lA~~~~~S~---~~l~r~Fk~~~g~   46 (54)
T d1d5ya1           8 LLIWLEGHLDQPLSLDNVAAKAGYSK---WHLQRMFKDVTGH   46 (54)
T ss_dssp             HHHHHHTTSSSSCCCHHHHTTTSSCH---HHHHHHHHHHHSS
T ss_pred             HHHHHHHccCCCCCHHHHHHHHCcCH---HHHHHHHHHHHCc
Confidence            44555554 48999999999999999   9999987766544

>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=87.42  E-value=0.17  Score=40.51  Aligned_cols=35  Identities=17%  Similarity=0.227  Sum_probs=30.7

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                      +++++|+-||||.|..+..+++..|..+++++|+-
T Consensus        88 ~~pk~VLiiGgG~G~~~r~~l~~~~~~~i~~VEID  122 (295)
T d1inla_          88 PNPKKVLIIGGGDGGTLREVLKHDSVEKAILCEVD  122 (295)
T ss_dssp             SSCCEEEEEECTTCHHHHHHTTSTTCSEEEEEESC
T ss_pred             CCCceEEEecCCchHHHHHHHhcCCCceEEEecCC
Confidence            35789999999999999999998888889988863

>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=87.31  E-value=0.18  Score=40.74  Aligned_cols=34  Identities=21%  Similarity=0.272  Sum_probs=29.8

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      +++++||-||||.|..+..+++..|-.+++++|+
T Consensus       105 ~~pk~VLIiGgG~G~~~rellk~~~v~~v~~VEI  138 (312)
T d2b2ca1         105 PDPKRVLIIGGGDGGILREVLKHESVEKVTMCEI  138 (312)
T ss_dssp             SSCCEEEEESCTTSHHHHHHTTCTTCCEEEEECS
T ss_pred             CCCCeEEEeCCCchHHHHHHHHcCCcceEEEEcc
Confidence            3578999999999999999998777778998886

>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=87.29  E-value=0.29  Score=30.67  Aligned_cols=36  Identities=14%  Similarity=0.184  Sum_probs=33.3

Q ss_pred             CCC-CHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           50 QPM-TLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        50 ~p~-t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      ..+ |..+||+.++++.   .-+++-++.|+..|++....
T Consensus        25 ~~LPs~~eLa~~~~vSr---~tvr~Al~~L~~~G~i~~~~   61 (74)
T d1hw1a1          25 TILPAERELSELIGVTR---TTLREVLQRLARDGWLTIQH   61 (74)
T ss_dssp             SBCCCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEEET
T ss_pred             CCCccHHHHHHHHCCCH---HHHHHHHHHHHHCCcEEEEe
Confidence            556 7999999999999   99999999999999999886

>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=87.09  E-value=0.34  Score=30.51  Aligned_cols=36  Identities=17%  Similarity=0.231  Sum_probs=33.6

Q ss_pred             CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      -|+|-+|||.-+|+++   ..+.|.|..|...|++....
T Consensus        29 ~~~t~~eiA~~lG~sr---etvsr~l~~l~~~g~I~~~~   64 (80)
T d1ft9a1          29 VDFTVEEIANLIGSSR---QTTSTALNSLIKEGYISRQG   64 (80)
T ss_dssp             ECCCHHHHHHHHCSCH---HHHHHHHHHHHHTTSSEECS
T ss_pred             cCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEECC
Confidence            4799999999999999   99999999999999999764

>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=86.49  E-value=0.41  Score=35.08  Aligned_cols=32  Identities=16%  Similarity=0.045  Sum_probs=25.8

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ...+|||+.||+|.++++.+++-.. +++.+|.
T Consensus        41 ~~~~vLDlfaGsG~~g~ea~srGa~-~v~~ve~   72 (182)
T d2fhpa1          41 DGGMALDLYSGSGGLAIEAVSRGMD-KSICIEK   72 (182)
T ss_dssp             SSCEEEETTCTTCHHHHHHHHTTCS-EEEEEES
T ss_pred             CCCEEEEcccccccccceeeecchh-HHHHHHH
Confidence            4689999999999999999998543 5666664

>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=85.27  E-value=0.27  Score=39.11  Aligned_cols=35  Identities=17%  Similarity=0.262  Sum_probs=30.4

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCCCCeEEEecCC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFPDTKCTVFACH  213 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dlp  213 (214)
                      +++++||=||||.|..+..+++..|-.+++++|+-
T Consensus        79 ~~pk~VLiiGgG~G~~~r~~l~~~~~~~i~~VEiD  113 (290)
T d1xj5a_          79 PNPKKVLVIGGGDGGVLREVARHASIEQIDMCEID  113 (290)
T ss_dssp             SCCCEEEEETCSSSHHHHHHTTCTTCCEEEEEESC
T ss_pred             CCCcceEEecCCchHHHHHHHhcccceeeEEecCC
Confidence            45789999999999999999998787788888863

>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=84.92  E-value=0.35  Score=30.42  Aligned_cols=36  Identities=17%  Similarity=0.207  Sum_probs=32.5

Q ss_pred             CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           50 QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        50 ~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      -|+|-+|||.-+|+++   ..+.|+|..|...|++....
T Consensus        29 ~~lt~~elA~~~g~sr---etvsr~l~~l~~~glI~~~~   64 (80)
T d3e5ua1          29 MPLSQKSIGEITGVHH---VTVSRVLASLKRENILDKKK   64 (80)
T ss_dssp             SCCCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEC--
T ss_pred             eCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCcEEecC
Confidence            5899999999999999   99999999999999998764

>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=84.69  E-value=0.26  Score=32.05  Aligned_cols=37  Identities=14%  Similarity=0.218  Sum_probs=32.9

Q ss_pred             CCCCCCHHHHHHHcCC--CCCCcccHHHHHHHHHhCCceeee
Q 040620           48 SGQPMTLTQIIVALNV--HPNKTRCTQILVCLLAHSGFFVQQ   87 (214)
Q Consensus        48 ~~~p~t~~eLA~~~g~--~~~~~~~l~rlLr~L~~~g~l~~~   87 (214)
                      .|.|++..+||+..++  ++   ..++..|..|...|++...
T Consensus        20 ~g~Pv~s~~i~~~~~l~~S~---aTIRn~m~~LE~~G~l~~~   58 (87)
T d1stza1          20 NKKPVSSQRVLEVSNIEFSS---ATIRNDMKKLEYLGYIYQP   58 (87)
T ss_dssp             HCSCBCHHHHHHHSCCCSCH---HHHHHHHHHHHHTTSEECC
T ss_pred             cCCccCHHHHHHHhCCCCCH---HHHHHHHHHHHHCCcccCC
Confidence            3599999999999776  57   8999999999999999875

>d2f8la1 c.66.1.45 (A:2-329) Hypothetical protein Lmo1582 {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: N-6 DNA Methylase-like
domain: Hypothetical protein Lmo1582
species: Listeria monocytogenes [TaxId: 1639]

Probab=83.33  E-value=0.46  Score=37.74  Aligned_cols=33  Identities=9%  Similarity=0.069  Sum_probs=26.0

Q ss_pred             CCCcEEeecCCchHHHHHHHHH-----CCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATA-----FPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~-----~P~l~~~v~Dl  212 (214)
                      ...+|+|.+||+|.++.++.++     .++.+++++|+
T Consensus       117 ~~~~vlDp~~GsG~~l~~~~~~l~~~~~~~~~~~g~di  154 (328)
T d2f8la1         117 KNVSILDPACGTANLLTTVINQLELKGDVDVHASGVDV  154 (328)
T ss_dssp             SEEEEEETTCTTSHHHHHHHHHHHTTSSCEEEEEEEES
T ss_pred             CCCEEEeCCCCcchhHHHHHHHHHhccCccceEEEecc
Confidence            4568999999999999998764     35556777775

>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=82.41  E-value=0.82  Score=34.77  Aligned_cols=34  Identities=29%  Similarity=0.275  Sum_probs=29.6

Q ss_pred             CCCCcEEeecCCchHHHHHHHHHCC-CCeEEEecC
Q 040620          179 KGLKPLVDVGGSTGTMARAIATAFP-DTKCTVFAC  212 (214)
Q Consensus       179 ~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl  212 (214)
                      .+.++||+||.+.|..++.+++..| +.+++.+|.
T Consensus        58 ~~~k~iLEiGT~~GyStl~la~al~~~g~v~tie~   92 (227)
T d1susa1          58 INAKNTMEIGVYTGYSLLATALAIPEDGKILAMDI   92 (227)
T ss_dssp             HTCCEEEEECCGGGHHHHHHHHHSCTTCEEEEEES
T ss_pred             cCCCcEEEecchhhhhHHHHHhhCCCCcEEEEEec
Confidence            3589999999999999999999988 567887775

>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=82.06  E-value=0.18  Score=34.52  Aligned_cols=47  Identities=21%  Similarity=0.349  Sum_probs=38.2

Q ss_pred             hcCcchhhhcCCCCCCHHHHHHHc----CCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           38 QLRIPDIINNSGQPMTLTQIIVAL----NVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        38 ~lglfd~L~~~~~p~t~~eLA~~~----g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      |..|..+|=+. +|+|+.||.+.+    +.++   ..+..+|+-|...|++....
T Consensus         9 E~~VM~~lW~~-~~~t~~ei~~~l~~~~~~~~---sTv~t~L~rL~~Kg~l~r~~   59 (120)
T d1okra_           9 EWEVMNIIWMK-KYASANNIIEEIQMQKDWSP---KTIRTLITRLYKKGFIDRKK   59 (120)
T ss_dssp             HHHHHHHHHHH-SSEEHHHHHHHHHHHCCCCH---HHHHHHHHHHHHHTSEEEEE
T ss_pred             HHHHHHHHHcC-CCCCHHHHHHHHhcccCccH---HhHHHHHHHHHHCCCeEEEe
Confidence            44556666665 799999988887    5666   79999999999999998775

>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=81.54  E-value=0.35  Score=30.80  Aligned_cols=45  Identities=13%  Similarity=0.118  Sum_probs=39.3

Q ss_pred             cchhhhcCC-CCCCHHHHHHHcCCCCCCcccHHHHHHHHHhCCceeeec
Q 040620           41 IPDIINNSG-QPMTLTQIIVALNVHPNKTRCTQILVCLLAHSGFFVQQK   88 (214)
Q Consensus        41 lfd~L~~~~-~p~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g~l~~~~   88 (214)
                      |++++.++| .++...+|-.+++++.   ..+.+.|..|.+.+++....
T Consensus        18 VY~~I~~ag~~GIW~~dir~ktnL~~---~~l~K~LK~Lesk~lIK~Vk   63 (78)
T d2dk5a1          18 VYQIIEDAGNKGIWSRDVRYKSNLPL---TEINKILKNLESKKLIKAVK   63 (78)
T ss_dssp             HHHHHHHHCTTCEEHHHHHHHTTCCH---HHHHHHHHHHHHTTSEEEEC
T ss_pred             HHHHHHHccccceeHHHHHHHcCCCH---HHHHHHHHHHHhcCCceeec
Confidence            456666554 7899999999999999   99999999999999999875

>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=80.17  E-value=0.42  Score=38.25  Aligned_cols=31  Identities=16%  Similarity=0.055  Sum_probs=25.7

Q ss_pred             CCCcEEeecCCchHHHHHHHHHCCCCeEEEecC
Q 040620          180 GLKPLVDVGGSTGTMARAIATAFPDTKCTVFAC  212 (214)
Q Consensus       180 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl  212 (214)
                      ..++|+|++||+|.+++++++.  ..+++.+|.
T Consensus       145 ~g~rVLDl~~gtG~~s~~~a~g--~~~V~~vD~  175 (318)
T d1wxxa2         145 RGERALDVFSYAGGFALHLALG--FREVVAVDS  175 (318)
T ss_dssp             CEEEEEEETCTTTHHHHHHHHH--EEEEEEEES
T ss_pred             CCCeeeccCCCCcHHHHHHHhc--CCcEEeecc
Confidence            4689999999999999998865  456777775