Citrus Sinensis ID: 027801

---

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-------22
Protein Sequence
MALNLKTTIHHSPLASSSRQFINGFSPKPTSMSFSRSSSLKGFGTQIAIERKERLSFVQTEAVRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGKSGNKGAEAALTAIEMASLFEHHLK
Secondary Structure (PSIPRED)
cccccEEEEcccccccccccccccccccccccccccccccccccHHHHHHHHccccHHHHHcccEEEEccccccccEEEEEEccccHHHHHHHHHHHHHHHHHccccccccEEEEccccccHHHHHHHHHHcccccEEEEEccEEEccccHHHHHHHHHHHHHHHccccccccEEEEEEccccHHHHHHHccccccccHHHHHHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccEEccccccccccHHcccHHHccccccccccccccccccccccccEEEEEccccccEEHHHHHHEcccccccccccEEEEEEcccHHHHHHHHHHHHHHHHHccccHHHEEEEEEccHHHHHHHHHHHHccccccEEEEEEEEEcccccHHHHHHHHHHHHHHHHHHHHcccEEEEEEEEccHHHHHHHEEEccEEHHHHHHHHHHHHHHHHHHHHc
Coil and Loop (DISEMBL)
malnlkttihhsplasssrqfingfspkptsmsfsrssslkgfgTQIAIERKERLSFVQTEAVRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKkysvkeenidvvwvpgSFEIGVVAQQLGKSGKYTAVLCIGavvrgdtthydAVANSAASGVlsagvnsgvpcifgVLTCDNMDQAlnraggksgnkgAEAALTAIEMASLFEHHLK
Flexible Loop (DISEMBL)
malnlkttihhsplasssrqfINGFSPKPTSMSFSRSSSLKGFGTQIAIERKERLSFVQTEAVRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGKSGNKGAEAALTAIEMASLFEHHLK
Low Complexity Region (SEG)
MALNLKTTIHHSPLASSSRQFINGFSPKPTSMSFSRSSSLKGFGTQIAIERKERLSFVQTEAVRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGKSGNKGAEAALTAIEMASLFEHHLK
Disordered region (IsUnstruct)
******************************************FGTQIAIERKERLSFVQTEAVRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQ********************************
Disordered Region (DISOPRED)
********IHHSPL************************************************VRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGKSGNKGAEAALTAIEMASLFEHHL*
Disordered Region (DISEMBL)
MALNLKTTIHHSPLASSSRQFINGFSPKP************GFGTQIAIERKERLSFVQTEAVRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRA********AEAALTAIEMASLFEHHLK
Disordered Region (DISPRO)
********IHHSPLASSSRQFINGF****************GFGTQIAIERKERLSFVQTEAVRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGKSGNKGAEAALTAIEMASLFEHHLK
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MALNLKTTIHHSPLASSSRQFINGFSPKPTSMSFSRSSSLKGFGTQIAIERKERLSFVQTEAVRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGKSGNKGAEAALTAIEMASLFEHHLK
Positional Conservation
no confident homologs detected

---

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	218	2.2.26 [Sep-21-2011]
O80575	227	6,7-dimethyl-8-ribityllum	yes	no	0.931	0.894	0.758	4e-86
Q9XH32	222	6,7-dimethyl-8-ribityllum	N/A	no	0.866	0.851	0.717	2e-74
B1YEJ3	152	6,7-dimethyl-8-ribityllum	yes	no	0.665	0.953	0.568	1e-41
B7GKI1	154	6,7-dimethyl-8-ribityllum	yes	no	0.637	0.902	0.568	2e-41
A5D1C7	155	6,7-dimethyl-8-ribityllum	yes	no	0.665	0.935	0.52	3e-41
A6LSS9	154	6,7-dimethyl-8-ribityllum	yes	no	0.646	0.915	0.524	7e-41
B3H0P9	153	6,7-dimethyl-8-ribityllum	yes	no	0.642	0.915	0.528	1e-40
B0K0Z0	154	6,7-dimethyl-8-ribityllum	yes	no	0.651	0.922	0.521	2e-40
Q0TTN7	153	6,7-dimethyl-8-ribityllum	yes	no	0.637	0.908	0.503	3e-40
B8F5Z8	153	6,7-dimethyl-8-ribityllum	yes	no	0.678	0.967	0.510	4e-40

>sp|O80575|RISB_ARATH 6,7-dimethyl-8-ribityllumazine synthase, chloroplastic OS=Arabidopsis thaliana GN=At2g44050 PE=2 SV=1

 Score =  317 bits (812), Expect = 4e-86,   Method: Compositional matrix adjust.
 Identities = 154/203 (75%), Positives = 179/203 (88%)

Query: 16  SSSRQFINGFSPKPTSMSFSRSSSLKGFGTQIAIERKERLSFVQTEAVRHLTGFLTKNEG 75
           SSS  +I+G S    S + S SSS  GF + +A+E++ R SFVQT AVRH+TG L + EG
Sbjct: 25  SSSACYIHGGSSVNKSNNLSFSSSTSGFASPLAVEKELRSSFVQTAAVRHVTGSLIRGEG 84

Query: 76  LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKY 135
           LRFA+VVARFNE+VTKLLLEGA+ETFKKYSV+EE+I+V+WVPGSFEIGVVAQ LGKSGK+
Sbjct: 85  LRFAIVVARFNEVVTKLLLEGAIETFKKYSVREEDIEVIWVPGSFEIGVVAQNLGKSGKF 144

Query: 136 TAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGKS 195
            AVLCIGAV+RGDTTHYDAVANSAASGVLSA +NSGVPCIFGVLTC++MDQALNR+GGK+
Sbjct: 145 HAVLCIGAVIRGDTTHYDAVANSAASGVLSASINSGVPCIFGVLTCEDMDQALNRSGGKA 204

Query: 196 GNKGAEAALTAIEMASLFEHHLK 218
           GNKGAE ALTA+EMASLFEHHLK
Sbjct: 205 GNKGAETALTALEMASLFEHHLK 227

Catalyzes the condensation of 5-amino-6-(1'-D)-ribityl-amino-2,4(1H,3H)-pyrimidinedione with L-3,4-dihydrohy-2-butanone-4-phosphate yielding 6,7-dimethyl-8-lumazine.
Arabidopsis thaliana (taxid: 3702)
EC: 2EC: .EC: 5EC: .EC: 1EC: .EC: 9

>sp|Q9XH32|RISB_SPIOL 6,7-dimethyl-8-ribityllumazine synthase, chloroplastic OS=Spinacia oleracea PE=1 SV=1

 Score =  278 bits (711), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 137/191 (71%), Positives = 161/191 (84%), Gaps = 2/191 (1%)

Query: 29  PTSMSFSRSSSLKGFG-TQIAIERKERLSFVQTEAVRHLTGFLTKNEGLRFALVVARFNE 87
           P S   S SSS  G G   +A  +K R SFV T AVR L G++TK +  RFA+VVARFNE
Sbjct: 32  PFSAPLSSSSSFPGCGLVHVASNKKNRASFVVTNAVRELEGYVTKAQSFRFAIVVARFNE 91

Query: 88  LVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVVRG 147
            VT+ L+EGAL+TFKKYSV E+ IDVVWVPG++E+GV AQ LGKSGKY A++C+GAVV+G
Sbjct: 92  FVTRRLMEGALDTFKKYSVNED-IDVVWVPGAYELGVTAQALGKSGKYHAIVCLGAVVKG 150

Query: 148 DTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGKSGNKGAEAALTAI 207
           DT+HYDAV NSA+SGVLSAG+NSGVPC+FGVLTCDNMDQA+NRAGGK+GNKGAE+ALTAI
Sbjct: 151 DTSHYDAVVNSASSGVLSAGLNSGVPCVFGVLTCDNMDQAINRAGGKAGNKGAESALTAI 210

Query: 208 EMASLFEHHLK 218
           EMASLFEHHLK
Sbjct: 211 EMASLFEHHLK 221

Catalyzes the condensation of 5-amino-6-(1'-D)-ribityl-amino-2,4(1H,3H)-pyrimidinedione with L-3,4-dihydrohy-2-butanone-4-phosphate yielding 6,7-dimethyl-8-lumazine.

Spinacia oleracea (taxid: 3562)

EC: 2

EC: .

EC: 5

EC: .

EC: 1

EC: .

EC: 9

>sp|B1YEJ3|RISB_EXIS2 6,7-dimethyl-8-ribityllumazine synthase OS=Exiguobacterium sibiricum (strain DSM 17290 / JCM 13490 / 255-15) GN=ribH PE=3 SV=1

 Score =  169 bits (428), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 83/146 (56%), Positives = 109/146 (74%), Gaps = 1/146 (0%)

Query: 68  GFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQ 127
           GFLT  EGLR A+V ARFNEL+T  L+ GA + F+++ V  + +D  WVPG+FEI +VA+
Sbjct: 5   GFLT-GEGLRVAIVAARFNELITSKLVGGANDAFRRHGVAADAVDTAWVPGAFEIPLVAE 63

Query: 128 QLGKSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQA 187
           +L KSG Y AV+ +GAV+RG T+HYD V N  A GV  A   +GVP IFGVLT D+++QA
Sbjct: 64  KLAKSGNYDAVITLGAVIRGATSHYDYVCNEVAKGVAGASRETGVPIIFGVLTTDSIEQA 123

Query: 188 LNRAGGKSGNKGAEAALTAIEMASLF 213
           + RAG K+GNKG EAA++AIEMA+L 
Sbjct: 124 VERAGTKAGNKGYEAAVSAIEMANLL 149

Riboflavin synthase is a bifunctional enzyme complex catalyzing the formation of riboflavin from 5-amino-6-(1'-D)-ribityl-amino-2,4(1H,3H)-pyrimidinedione and L-3,4-dihydrohy-2-butanone-4-phosphate via 6,7-dimethyl-8-lumazine. The beta subunit catalyzes the condensation of 5-amino-6-(1'-D)-ribityl-amino-2,4(1H,3H)-pyrimidinedione with L-3,4-dihydrohy-2-butanone-4-phosphate yielding 6,7-dimethyl-8-lumazine.

Exiguobacterium sibiricum (strain DSM 17290 / JCM 13490 / 255-15) (taxid: 262543)

EC: 2

EC: .

EC: 5

EC: .

EC: 1

EC: .

EC: 9

>sp|B7GKI1|RISB_ANOFW 6,7-dimethyl-8-ribityllumazine synthase OS=Anoxybacillus flavithermus (strain DSM 21510 / WK1) GN=ribH PE=3 SV=1

 Score =  169 bits (427), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 79/139 (56%), Positives = 107/139 (76%)

Query: 75  GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGK 134
           GL+  +VVARFNE +T  LL GAL+  K++ V+E++IDV WVPG+FEI +VA+++ +S K
Sbjct: 12  GLKIGIVVARFNEFITSKLLSGALDGLKRHGVEEQHIDVAWVPGAFEIPLVAKKMAESKK 71

Query: 135 YTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGK 194
           Y AV+ +GAV+RG T+HYD V N  A G   A ++SGVP IFGVLT D ++QA+ RAG K
Sbjct: 72  YDAVITLGAVIRGATSHYDYVCNEVAKGTSHAALSSGVPVIFGVLTTDTIEQAIERAGTK 131

Query: 195 SGNKGAEAALTAIEMASLF 213
           +GNKG EAAL+AIEMA++ 
Sbjct: 132 AGNKGWEAALSAIEMANVM 150

Riboflavin synthase is a bifunctional enzyme complex catalyzing the formation of riboflavin from 5-amino-6-(1'-D)-ribityl-amino-2,4(1H,3H)-pyrimidinedione and L-3,4-dihydrohy-2-butanone-4-phosphate via 6,7-dimethyl-8-lumazine. The beta subunit catalyzes the condensation of 5-amino-6-(1'-D)-ribityl-amino-2,4(1H,3H)-pyrimidinedione with L-3,4-dihydrohy-2-butanone-4-phosphate yielding 6,7-dimethyl-8-lumazine.

Anoxybacillus flavithermus (strain DSM 21510 / WK1) (taxid: 491915)

EC: 2

EC: .

EC: 5

EC: .

EC: 1

EC: .

EC: 9

>sp|A5D1C7|RISB_PELTS 6,7-dimethyl-8-ribityllumazine synthase OS=Pelotomaculum thermopropionicum (strain DSM 13744 / JCM 10971 / SI) GN=ribH PE=3 SV=1

 Score =  168 bits (425), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 78/150 (52%), Positives = 110/150 (73%), Gaps = 5/150 (3%)

Query: 65  HLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV 124
           HL G     +GLRF +V+ RFNE +T  LL GAL+   ++ V +++I+V WVPG+FEI +
Sbjct: 8   HLIG-----QGLRFGIVIGRFNEFITNKLLSGALDALNRHGVADQDIEVAWVPGAFEIPM 62

Query: 125 VAQQLGKSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNM 184
           VA+++  + KY AV+C+GAV+RG T H+D VA   A GV   G+ SGVP IFGV+T D++
Sbjct: 63  VARKMASAMKYDAVICLGAVIRGATPHFDYVAGEVAKGVARIGLESGVPTIFGVITADSI 122

Query: 185 DQALNRAGGKSGNKGAEAALTAIEMASLFE 214
           +QA+ RAG K+GNKG +AA+TAIEMA+L +
Sbjct: 123 EQAIERAGAKAGNKGWDAAVTAIEMANLMK 152

Riboflavin synthase is a bifunctional enzyme complex catalyzing the formation of riboflavin from 5-amino-6-(1'-D)-ribityl-amino-2,4(1H,3H)-pyrimidinedione and L-3,4-dihydrohy-2-butanone-4-phosphate via 6,7-dimethyl-8-lumazine. The beta subunit catalyzes the condensation of 5-amino-6-(1'-D)-ribityl-amino-2,4(1H,3H)-pyrimidinedione with L-3,4-dihydrohy-2-butanone-4-phosphate yielding 6,7-dimethyl-8-lumazine.

Pelotomaculum thermopropionicum (strain DSM 13744 / JCM 10971 / SI) (taxid: 370438)

EC: 2

EC: .

EC: 5

EC: .

EC: 1

EC: .

EC: 9

>sp|A6LSS9|RISB_CLOB8 6,7-dimethyl-8-ribityllumazine synthase OS=Clostridium beijerinckii (strain ATCC 51743 / NCIMB 8052) GN=ribH PE=3 SV=1

 Score =  167 bits (422), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 74/141 (52%), Positives = 108/141 (76%)

Query: 73  NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKS 132
           +EGL+F +VV RFNE +   LLEGA++  K++ VKEE+ID+ WVPG+FEI ++A+++ KS
Sbjct: 10  SEGLKFGIVVGRFNEFIGGKLLEGAIDGLKRHGVKEEDIDIAWVPGAFEIPLIAKKMAKS 69

Query: 133 GKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAG 192
            KY  V+C+GAV++G T+HYD V +  + G+ S  + SG P IFGVLT + ++QA+ RAG
Sbjct: 70  PKYDGVICLGAVIKGSTSHYDYVCSEVSKGIASVSLESGKPVIFGVLTTNTIEQAIERAG 129

Query: 193 GKSGNKGAEAALTAIEMASLF 213
            K+GNKG E+A++AIEMA+L 
Sbjct: 130 TKAGNKGYESAVSAIEMANLL 150

Riboflavin synthase is a bifunctional enzyme complex catalyzing the formation of riboflavin from 5-amino-6-(1'-D)-ribityl-amino-2,4(1H,3H)-pyrimidinedione and L-3,4-dihydrohy-2-butanone-4-phosphate via 6,7-dimethyl-8-lumazine. The beta subunit catalyzes the condensation of 5-amino-6-(1'-D)-ribityl-amino-2,4(1H,3H)-pyrimidinedione with L-3,4-dihydrohy-2-butanone-4-phosphate yielding 6,7-dimethyl-8-lumazine.

Clostridium beijerinckii (strain ATCC 51743 / NCIMB 8052) (taxid: 290402)

EC: 2

EC: .

EC: 5

EC: .

EC: 1

EC: .

EC: 9

>sp|B3H0P9|RISB_ACTP7 6,7-dimethyl-8-ribityllumazine synthase OS=Actinobacillus pleuropneumoniae serotype 7 (strain AP76) GN=ribH PE=3 SV=1

 Score =  166 bits (419), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 74/140 (52%), Positives = 103/140 (73%)

Query: 75  GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGK 134
           GL+F +V ARFN+ +   LL GA++T  ++   E NID  WVPG+FEI +VA+++  SGK
Sbjct: 12  GLKFGIVTARFNDFINDKLLSGAIDTLVRHGADENNIDTAWVPGAFEIPLVAKKMATSGK 71

Query: 135 YTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGK 194
           Y AV+C+G V+RG TTHYD V N AA G+ +  + +GVP IFGVLT +N++QA+ RAG K
Sbjct: 72  YDAVICLGTVIRGSTTHYDYVCNEAAKGIGAVALETGVPVIFGVLTTENIEQAIERAGTK 131

Query: 195 SGNKGAEAALTAIEMASLFE 214
           +GNKG+E AL AIEM ++ +
Sbjct: 132 AGNKGSECALGAIEMVNVLK 151

Riboflavin synthase is a bifunctional enzyme complex catalyzing the formation of riboflavin from 5-amino-6-(1'-D)-ribityl-amino-2,4(1H,3H)-pyrimidinedione and L-3,4-dihydrohy-2-butanone-4-phosphate via 6,7-dimethyl-8-lumazine. The beta subunit catalyzes the condensation of 5-amino-6-(1'-D)-ribityl-amino-2,4(1H,3H)-pyrimidinedione with L-3,4-dihydrohy-2-butanone-4-phosphate yielding 6,7-dimethyl-8-lumazine.

Actinobacillus pleuropneumoniae serotype 7 (strain AP76) (taxid: 537457)

EC: 2

EC: .

EC: 5

EC: .

EC: 1

EC: .

EC: 9

>sp|B0K0Z0|RISB_THEPX 6,7-dimethyl-8-ribityllumazine synthase OS=Thermoanaerobacter sp. (strain X514) GN=ribH PE=3 SV=1

 Score =  165 bits (417), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 74/142 (52%), Positives = 106/142 (74%)

Query: 74  EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSG 133
           EG +F +VV+RFNE +T  LLEGAL+  K++    ENI++ WVPG+FEI ++A+++ +S 
Sbjct: 11  EGKKFGIVVSRFNEFITNKLLEGALDALKRHGALNENIEIAWVPGAFEIPLIAKKMAESK 70

Query: 134 KYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGG 193
           +Y AV+ +GAV+RG+T H+D VAN  + G+    +++ VP IFGVLT D ++QA+ RAG 
Sbjct: 71  RYDAVIALGAVIRGETPHFDYVANEVSKGIAKISLDTEVPVIFGVLTTDTIEQAIVRAGT 130

Query: 194 KSGNKGAEAALTAIEMASLFEH 215
           K GNKG EAA+TAIEMA+L E 
Sbjct: 131 KGGNKGFEAAVTAIEMANLMEE 152

Riboflavin synthase is a bifunctional enzyme complex catalyzing the formation of riboflavin from 5-amino-6-(1'-D)-ribityl-amino-2,4(1H,3H)-pyrimidinedione and L-3,4-dihydrohy-2-butanone-4-phosphate via 6,7-dimethyl-8-lumazine. The beta subunit catalyzes the condensation of 5-amino-6-(1'-D)-ribityl-amino-2,4(1H,3H)-pyrimidinedione with L-3,4-dihydrohy-2-butanone-4-phosphate yielding 6,7-dimethyl-8-lumazine.

Thermoanaerobacter sp. (strain X514) (taxid: 399726)

EC: 2

EC: .

EC: 5

EC: .

EC: 1

EC: .

EC: 9

>sp|Q0TTN7|RISB_CLOP1 6,7-dimethyl-8-ribityllumazine synthase OS=Clostridium perfringens (strain ATCC 13124 / NCTC 8237 / Type A) GN=ribH PE=3 SV=1

 Score =  164 bits (416), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 70/139 (50%), Positives = 107/139 (76%)

Query: 77  RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYT 136
           +FA+V  RFNE +   L++GAL+ FK++ V+E+NID+ WVPG+FEI ++A++L KSGKY 
Sbjct: 14  KFAIVAGRFNEFIVSKLIDGALDAFKRHGVEEDNIDLAWVPGAFEIPLIAKKLAKSGKYA 73

Query: 137 AVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGKSG 196
            V+C+G V+RG T+HYD V    + G+ +  +++ VP IFG++T +N++QA+ RAG K+G
Sbjct: 74  GVVCLGTVIRGATSHYDYVCGEVSKGIANVSLDTEVPVIFGIVTTENIEQAIERAGTKAG 133

Query: 197 NKGAEAALTAIEMASLFEH 215
           NKG +AA+ AIEMA+L E+
Sbjct: 134 NKGFDAAMAAIEMANLLEN 152

Riboflavin synthase is a bifunctional enzyme complex catalyzing the formation of riboflavin from 5-amino-6-(1'-D)-ribityl-amino-2,4(1H,3H)-pyrimidinedione and L-3,4-dihydrohy-2-butanone-4-phosphate via 6,7-dimethyl-8-lumazine. The beta subunit catalyzes the condensation of 5-amino-6-(1'-D)-ribityl-amino-2,4(1H,3H)-pyrimidinedione with L-3,4-dihydrohy-2-butanone-4-phosphate yielding 6,7-dimethyl-8-lumazine.

Clostridium perfringens (strain ATCC 13124 / NCTC 8237 / Type A) (taxid: 195103)

EC: 2

EC: .

EC: 5

EC: .

EC: 1

EC: .

EC: 9

>sp|B8F5Z8|RISB_HAEPS 6,7-dimethyl-8-ribityllumazine synthase OS=Haemophilus parasuis serovar 5 (strain SH0165) GN=ribH PE=3 SV=1

 Score =  164 bits (415), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 76/149 (51%), Positives = 108/149 (72%), Gaps = 1/149 (0%)

Query: 66  LTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVV 125
           +TG L   E L+F +V ARFN+ +   LL GA++T  ++   E +ID  WVPG+FEI +V
Sbjct: 4   ITGNLVATE-LKFGIVCARFNDFINDKLLSGAIDTLVRHGASESDIDTAWVPGAFEIPLV 62

Query: 126 AQQLGKSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMD 185
           A+++ +SGKY AV+C+G V+RG TTHYD V N AA G+ +  + +GVP IFGVLT +N++
Sbjct: 63  AKKMAESGKYDAVICLGTVIRGSTTHYDYVCNEAAKGIGAVSLQTGVPVIFGVLTTENIE 122

Query: 186 QALNRAGGKSGNKGAEAALTAIEMASLFE 214
           QA+ RAG K+GNKG+E AL AIEM ++ +
Sbjct: 123 QAIERAGTKAGNKGSECALGAIEMVNVLK 151

Riboflavin synthase is a bifunctional enzyme complex catalyzing the formation of riboflavin from 5-amino-6-(1'-D)-ribityl-amino-2,4(1H,3H)-pyrimidinedione and L-3,4-dihydrohy-2-butanone-4-phosphate via 6,7-dimethyl-8-lumazine. The beta subunit catalyzes the condensation of 5-amino-6-(1'-D)-ribityl-amino-2,4(1H,3H)-pyrimidinedione with L-3,4-dihydrohy-2-butanone-4-phosphate yielding 6,7-dimethyl-8-lumazine.

Haemophilus parasuis serovar 5 (strain SH0165) (taxid: 557723)

EC: 2

EC: .

EC: 5

EC: .

EC: 1

EC: .

EC: 9

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	218
225434247	222	PREDICTED: 6,7-dimethyl-8-ribityllumazin	0.917	0.900	0.792	3e-86
15224809	227	6,7-dimethyl-8-ribityllumazine synthase	0.931	0.894	0.758	2e-84
296084377	181	unnamed protein product [Vitis vinifera]	0.816	0.983	0.849	5e-83
255581426	221	6,7-dimethyl-8-ribityllumazine synthase,	0.931	0.918	0.755	8e-83
297824393	227	hypothetical protein ARALYDRAFT_903810 [	0.931	0.894	0.743	2e-82
224117846	221	predicted protein [Populus trichocarpa]	0.885	0.873	0.808	4e-82
388517513	228	unknown [Medicago truncatula]	0.990	0.947	0.657	4e-78
224095325	180	predicted protein [Populus trichocarpa]	0.821	0.994	0.795	5e-77
147853194	681	hypothetical protein VITISV_042207 [Viti	0.793	0.254	0.683	4e-74
5532608	225	6,7-dimethyl-8-ribityllumazine synthase	0.931	0.902	0.684	9e-74

>gi|225434247|ref|XP_002280427.1| PREDICTED: 6,7-dimethyl-8-ribityllumazine synthase, chloroplastic-like [Vitis vinifera]

 Score =  323 bits (828), Expect = 3e-86,   Method: Compositional matrix adjust.
 Identities = 164/207 (79%), Positives = 182/207 (87%), Gaps = 7/207 (3%)

Query: 12  SPLASSSRQFINGFSPKPTSMSFSRSSSLKGFGTQ-IAIERKERLSFVQTEAVRHLTGFL 70
           SPL  ++R  I+  S KP S S    SS+ GFG   IAIE K+R SFVQT AVRHL G L
Sbjct: 20  SPL--TNRPAISSLSYKPLSFS----SSMTGFGQAGIAIELKDRGSFVQTAAVRHLMGSL 73

Query: 71  TKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLG 130
           T+ EGLRFA+VVARFNE+VTKLLLEGALETFK+YSVKEE+IDVVWVPGSFEIGVVA++LG
Sbjct: 74  TRAEGLRFAVVVARFNEIVTKLLLEGALETFKRYSVKEEDIDVVWVPGSFEIGVVAERLG 133

Query: 131 KSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNR 190
           KS KY A+LCIGAV+RGDT+HYDAVANSAASGVLSAG+NSGVPCIFGVLTCD+MDQALNR
Sbjct: 134 KSKKYQAILCIGAVIRGDTSHYDAVANSAASGVLSAGLNSGVPCIFGVLTCDDMDQALNR 193

Query: 191 AGGKSGNKGAEAALTAIEMASLFEHHL 217
           +GGKSGNKGAEAALTAIEMASLFEHHL
Sbjct: 194 SGGKSGNKGAEAALTAIEMASLFEHHL 220

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15224809|ref|NP_181933.1| 6,7-dimethyl-8-ribityllumazine synthase [Arabidopsis thaliana] gi|20139375|sp|O80575.1|RISB_ARATH RecName: Full=6,7-dimethyl-8-ribityllumazine synthase, chloroplastic; Short=DMRL synthase; Short=LS; Short=Lumazine synthase; Flags: Precursor gi|5532610|gb|AAD44810.1|AF148649_1 6,7-dimethyl-8-ribityllumazine synthase precursor [Arabidopsis thaliana] gi|3212862|gb|AAC23413.1| 6,7-dimethyl-8-ribityllumazine synthase precursor [Arabidopsis thaliana] gi|15292959|gb|AAK93590.1| putative 6,7-dimethyl-8-ribityllumazine synthase precursor [Arabidopsis thaliana] gi|20259133|gb|AAM14282.1| putative 6,7-dimethyl-8-ribityllumazine synthase precursor [Arabidopsis thaliana] gi|330255271|gb|AEC10365.1| 6,7-dimethyl-8-ribityllumazine synthase [Arabidopsis thaliana]

 Score =  317 bits (812), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 154/203 (75%), Positives = 179/203 (88%)

Query: 16  SSSRQFINGFSPKPTSMSFSRSSSLKGFGTQIAIERKERLSFVQTEAVRHLTGFLTKNEG 75
           SSS  +I+G S    S + S SSS  GF + +A+E++ R SFVQT AVRH+TG L + EG
Sbjct: 25  SSSACYIHGGSSVNKSNNLSFSSSTSGFASPLAVEKELRSSFVQTAAVRHVTGSLIRGEG 84

Query: 76  LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKY 135
           LRFA+VVARFNE+VTKLLLEGA+ETFKKYSV+EE+I+V+WVPGSFEIGVVAQ LGKSGK+
Sbjct: 85  LRFAIVVARFNEVVTKLLLEGAIETFKKYSVREEDIEVIWVPGSFEIGVVAQNLGKSGKF 144

Query: 136 TAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGKS 195
            AVLCIGAV+RGDTTHYDAVANSAASGVLSA +NSGVPCIFGVLTC++MDQALNR+GGK+
Sbjct: 145 HAVLCIGAVIRGDTTHYDAVANSAASGVLSASINSGVPCIFGVLTCEDMDQALNRSGGKA 204

Query: 196 GNKGAEAALTAIEMASLFEHHLK 218
           GNKGAE ALTA+EMASLFEHHLK
Sbjct: 205 GNKGAETALTALEMASLFEHHLK 227

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296084377|emb|CBI24765.3| unnamed protein product [Vitis vinifera]

 Score =  312 bits (800), Expect = 5e-83,   Method: Compositional matrix adjust.
 Identities = 152/179 (84%), Positives = 167/179 (93%), Gaps = 1/179 (0%)

Query: 40  LKGFGTQ-IAIERKERLSFVQTEAVRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGAL 98
           + GFG   IAIE K+R SFVQT AVRHL G LT+ EGLRFA+VVARFNE+VTKLLLEGAL
Sbjct: 1   MTGFGQAGIAIELKDRGSFVQTAAVRHLMGSLTRAEGLRFAVVVARFNEIVTKLLLEGAL 60

Query: 99  ETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVVRGDTTHYDAVANS 158
           ETFK+YSVKEE+IDVVWVPGSFEIGVVA++LGKS KY A+LCIGAV+RGDT+HYDAVANS
Sbjct: 61  ETFKRYSVKEEDIDVVWVPGSFEIGVVAERLGKSKKYQAILCIGAVIRGDTSHYDAVANS 120

Query: 159 AASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGKSGNKGAEAALTAIEMASLFEHHL 217
           AASGVLSAG+NSGVPCIFGVLTCD+MDQALNR+GGKSGNKGAEAALTAIEMASLFEHHL
Sbjct: 121 AASGVLSAGLNSGVPCIFGVLTCDDMDQALNRSGGKSGNKGAEAALTAIEMASLFEHHL 179

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255581426|ref|XP_002531521.1| 6,7-dimethyl-8-ribityllumazine synthase, putative [Ricinus communis] gi|223528874|gb|EEF30875.1| 6,7-dimethyl-8-ribityllumazine synthase, putative [Ricinus communis]

 Score =  312 bits (799), Expect = 8e-83,   Method: Compositional matrix adjust.
 Identities = 161/213 (75%), Positives = 184/213 (86%), Gaps = 10/213 (4%)

Query: 16  SSSRQFI------NGF-SPKPTSMSFSRSSS-LKGFGTQ-IAIE-RKERLSFVQTEAVRH 65
           SSS Q +      +GF S KP ++SFS SSS + G GT  I+ E +K+R SFV+T AV+H
Sbjct: 9   SSSTQIVRHSHVRHGFPSHKPVNLSFSTSSSFIPGIGTSSISFETKKDRSSFVETAAVKH 68

Query: 66  LTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVV 125
           L G LT+ EGLRFA+VVARFNE+VTK LLEGALETF++YSV EE++DVVWVPGSFEIGVV
Sbjct: 69  LIGSLTRTEGLRFAVVVARFNEIVTKKLLEGALETFERYSVNEEDVDVVWVPGSFEIGVV 128

Query: 126 AQQLGKSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMD 185
           A++LGKS KY A+LCIGAVVRGDTTHYDAVANSAASGVLSAG+NSGVPCIFGVLTCD+MD
Sbjct: 129 AERLGKSRKYHAILCIGAVVRGDTTHYDAVANSAASGVLSAGLNSGVPCIFGVLTCDDMD 188

Query: 186 QALNRAGGKSGNKGAEAALTAIEMASLFEHHLK 218
           QALNRAGGK+GNKGAE ALTAIEMASLFEHHLK
Sbjct: 189 QALNRAGGKAGNKGAEGALTAIEMASLFEHHLK 221

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297824393|ref|XP_002880079.1| hypothetical protein ARALYDRAFT_903810 [Arabidopsis lyrata subsp. lyrata] gi|297325918|gb|EFH56338.1| hypothetical protein ARALYDRAFT_903810 [Arabidopsis lyrata subsp. lyrata]

 Score =  310 bits (795), Expect = 2e-82,   Method: Compositional matrix adjust.
 Identities = 151/203 (74%), Positives = 177/203 (87%)

Query: 16  SSSRQFINGFSPKPTSMSFSRSSSLKGFGTQIAIERKERLSFVQTEAVRHLTGFLTKNEG 75
           SSS   I+G S    S + S SSS  GF + + +E++ R SF+QT AVRH+TG L + EG
Sbjct: 25  SSSACSIHGGSSVNKSNNLSFSSSTSGFASPLTVEKELRSSFLQTAAVRHVTGSLIRGEG 84

Query: 76  LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKY 135
           LRFA+VVARFNE+VTKLLLEGA+ETFKKYSV+EE+I+V+WVPGSFEIGVVAQ LGKSGK+
Sbjct: 85  LRFAIVVARFNEVVTKLLLEGAIETFKKYSVREEDIEVIWVPGSFEIGVVAQNLGKSGKF 144

Query: 136 TAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGKS 195
            AVLCIGAV+RGDTTHYDAVANSAASGVLSA +NSGVPCIFGVLTC++MDQALNR+GGK+
Sbjct: 145 HAVLCIGAVIRGDTTHYDAVANSAASGVLSASINSGVPCIFGVLTCEDMDQALNRSGGKA 204

Query: 196 GNKGAEAALTAIEMASLFEHHLK 218
           GNKG+E ALTA+EMASLFEHHLK
Sbjct: 205 GNKGSETALTALEMASLFEHHLK 227

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224117846|ref|XP_002331646.1| predicted protein [Populus trichocarpa] gi|222874042|gb|EEF11173.1| predicted protein [Populus trichocarpa]

 Score =  309 bits (792), Expect = 4e-82,   Method: Compositional matrix adjust.
 Identities = 160/198 (80%), Positives = 178/198 (89%), Gaps = 5/198 (2%)

Query: 25  FSP---KPTSMSFSRSSSLKGFGT-QIAIERKERLSFVQTEAVRHLTGFLTKNEGLRFAL 80
           FSP   KPT +SFS SSS+ GFGT  I  ERKER S V+T AVRHL G +TK EG RFAL
Sbjct: 25  FSPPYHKPTQLSFSSSSSI-GFGTTSIGFERKERSSIVETAAVRHLEGSVTKTEGFRFAL 83

Query: 81  VVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLC 140
           VVARFNE++T+ LLEGA+ TFKKYSVKEE+IDVVWVPGSFEIG+VA++LGKSGKY AV+C
Sbjct: 84  VVARFNEIITRPLLEGAVATFKKYSVKEEDIDVVWVPGSFEIGIVAERLGKSGKYHAVVC 143

Query: 141 IGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGKSGNKGA 200
           IGAVVRGDTTHYDAVANSAASGVLSAG+NSGVPCIFGVLTC++M+QA+NRAGGKSGNKGA
Sbjct: 144 IGAVVRGDTTHYDAVANSAASGVLSAGLNSGVPCIFGVLTCEDMEQAINRAGGKSGNKGA 203

Query: 201 EAALTAIEMASLFEHHLK 218
           EAALTAIEMASLFEHHLK
Sbjct: 204 EAALTAIEMASLFEHHLK 221

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388517513|gb|AFK46818.1| unknown [Medicago truncatula]

 Score =  296 bits (758), Expect = 4e-78,   Method: Compositional matrix adjust.
 Identities = 150/228 (65%), Positives = 181/228 (79%), Gaps = 12/228 (5%)

Query: 1   MALNLKTT--------IHHSP---LASSSRQFINGFSPKPTSMSFSRSSSLKGFGTQIAI 49
           MAL++ T         +HH P   +A+ +  F    +PK T+ S S S S++    +   
Sbjct: 1   MALSVSTDCFLPVLGFVHHHPQHRIAAPTNFFNLQKAPK-TATSLSFSLSMRALEVKPHA 59

Query: 50  ERKERLSFVQTEAVRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEE 109
           + K R SF QT+AV+HLTG +T+ EGLRFA+VVARFNE++T+ LLEGAL TFK YSV++E
Sbjct: 60  QSKGRSSFAQTDAVKHLTGSVTRTEGLRFAIVVARFNEIITRPLLEGALGTFKNYSVQDE 119

Query: 110 NIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVN 169
           ++DVVWVPG FEIG  A +LGKSGKY AV+CIGAV+RGDTTHYDAVANSAASGVLSAG+N
Sbjct: 120 DVDVVWVPGCFEIGAAATRLGKSGKYHAVICIGAVIRGDTTHYDAVANSAASGVLSAGLN 179

Query: 170 SGVPCIFGVLTCDNMDQALNRAGGKSGNKGAEAALTAIEMASLFEHHL 217
           SGVPCIFGVLTC++MDQA+NRAGGKSGNKGAEAALTAIEMASLFEHHL
Sbjct: 180 SGVPCIFGVLTCEDMDQAINRAGGKSGNKGAEAALTAIEMASLFEHHL 227

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224095325|ref|XP_002310376.1| predicted protein [Populus trichocarpa] gi|222853279|gb|EEE90826.1| predicted protein [Populus trichocarpa]

 Score =  293 bits (749), Expect = 5e-77,   Method: Compositional matrix adjust.
 Identities = 144/181 (79%), Positives = 163/181 (90%), Gaps = 2/181 (1%)

Query: 39  SLKGFGT-QIAIERKERLSFVQTEAVRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGA 97
           +  GFGT  IA ERK R S V T AVRHL G +T+ EGLRFA+VVARFNE++T+ LLEGA
Sbjct: 1   NFSGFGTISIAFERKGRPSLVGTAAVRHLEGSVTRTEGLRFAVVVARFNEIITRPLLEGA 60

Query: 98  LETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVVRGDTTHYDAVAN 157
           + TFKKYSVKE +IDVVWVPGSFEIG+VA++LGKSGKY AV+CIGAVVRGDTTHYDAVAN
Sbjct: 61  VATFKKYSVKE-DIDVVWVPGSFEIGIVAERLGKSGKYNAVVCIGAVVRGDTTHYDAVAN 119

Query: 158 SAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGKSGNKGAEAALTAIEMASLFEHHL 217
           SAASGVLSAG+ SGVPC+FGVLTC++M+QA+NRAGGKSGNKGAEAALTAIEMASLFEHHL
Sbjct: 120 SAASGVLSAGLKSGVPCVFGVLTCEDMEQAINRAGGKSGNKGAEAALTAIEMASLFEHHL 179

Query: 218 K 218
           K
Sbjct: 180 K 180

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147853194|emb|CAN78555.1| hypothetical protein VITISV_042207 [Vitis vinifera]

 Score =  283 bits (724), Expect = 4e-74,   Method: Compositional matrix adjust.
 Identities = 149/218 (68%), Positives = 163/218 (74%), Gaps = 45/218 (20%)

Query: 42  GFGTQ-IAIERKERLSFVQTEAVRHLTGFLTKNEGLRFALV------------------- 81
           GFG   IAIE K+R SFVQT AVRHL G LT+ EGLRFA+V                   
Sbjct: 7   GFGQAGIAIELKDRGSFVQTAAVRHLMGSLTRAEGLRFAVVSFSIPPQFLPFIFISSVYA 66

Query: 82  -------------------------VARFNELVTKLLLEGALETFKKYSVKEENIDVVWV 116
                                    VARFNE+VTKLLLEGALETFK+YSVKEE+IDVVWV
Sbjct: 67  CDSMKLRYCFTMNLRNSAGEHTNKVVARFNEIVTKLLLEGALETFKRYSVKEEDIDVVWV 126

Query: 117 PGSFEIGVVAQQLGKSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIF 176
           PGSFEIGVVA++LGKS KY A+LCIGAV+RGDT+HYDAVANSAASGVLSAG+NSGVPCIF
Sbjct: 127 PGSFEIGVVAERLGKSKKYQAILCIGAVIRGDTSHYDAVANSAASGVLSAGLNSGVPCIF 186

Query: 177 GVLTCDNMDQALNRAGGKSGNKGAEAALTAIEMASLFE 214
           GVLTCD+MDQALNR+GGKSGNKGAEAALTAIEMASLFE
Sbjct: 187 GVLTCDDMDQALNRSGGKSGNKGAEAALTAIEMASLFE 224

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|5532608|gb|AAD44809.1|AF148648_1 6,7-dimethyl-8-ribityllumazine synthase precursor [Nicotiana tabacum]

 Score =  281 bits (720), Expect = 9e-74,   Method: Compositional matrix adjust.
 Identities = 143/209 (68%), Positives = 166/209 (79%), Gaps = 6/209 (2%)

Query: 11  HSPLASSSRQFINGFSPKPTSMSFSRSSSLKGFGTQIAIERK-ERLSFVQTEAVRHLTGF 69
           HSPL S S  F         ++SF++S   +G G+  AIER  +R    QT AVR LTG 
Sbjct: 21  HSPLYSLSLPFHRQSITSSPALSFTQS---QGLGS--AIERHCDRSDLFQTCAVRQLTGS 75

Query: 70  LTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQL 129
           +T  +G RFA+VVARFN+L+TK LLEGAL+TFK YSV+EE+IDVVWVPG FEIGVVAQQL
Sbjct: 76  VTSAKGHRFAVVVARFNDLITKKLLEGALDTFKNYSVREEDIDVVWVPGCFEIGVVAQQL 135

Query: 130 GKSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALN 189
           GKS KY A+LCIGAV+RGDT+HYDAV N+A SGVLSAG+NSG PCIFGVLTCD ++QA N
Sbjct: 136 GKSQKYQAILCIGAVIRGDTSHYDAVVNAATSGVLSAGLNSGTPCIFGVLTCDTLEQAFN 195

Query: 190 RAGGKSGNKGAEAALTAIEMASLFEHHLK 218
           R GGK+GNKGAE ALTAIEMASLFEHHLK
Sbjct: 196 RVGGKAGNKGAETALTAIEMASLFEHHLK 224

Source: Nicotiana tabacum

Species: Nicotiana tabacum

Genus: Nicotiana

Family: Solanaceae

Order: Solanales

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	218
TAIR|locus:2051739	227	COS1 "AT2G44050" [Arabidopsis	0.990	0.951	0.724	1.8e-78
TIGR_CMR|BA_4334	153	BA_4334 "6,7-dimethyl-8-ribity	0.646	0.921	0.531	1.9e-37
TIGR_CMR|DET_1187	155	DET_1187 "6,7-dimethyl-8-ribit	0.692	0.974	0.480	1.9e-37
TIGR_CMR|CHY_1472	152	CHY_1472 "6,7-dimethyl-8-ribit	0.642	0.921	0.510	2.4e-35
TIGR_CMR|GSU_1691	155	GSU_1691 "6,7-dimethyl-8-ribit	0.683	0.961	0.486	3.6e-34
UNIPROTKB|P61714	156	ribE "RibE" [Escherichia coli	0.633	0.884	0.489	2.5e-33
TIGR_CMR|CPS_1531	154	CPS_1531 "6,7-dimethyl-8-ribit	0.637	0.902	0.442	3.8e-30
TIGR_CMR|CJE_0432	154	CJE_0432 "6,7-dimethyl-8-ribit	0.674	0.954	0.414	4.9e-30
TIGR_CMR|VC_2268	156	VC_2268 "6,7-dimethyl-8-ribity	0.655	0.916	0.431	7.9e-30
TIGR_CMR|SO_3466	158	SO_3466 "6,7-dimethyl-8-ribity	0.633	0.873	0.431	5.6e-29

TAIR|locus:2051739 COS1 "AT2G44050" [Arabidopsis thaliana (taxid:3702)]

 Score = 789 (282.8 bits), Expect = 1.8e-78, P = 1.8e-78
 Identities = 158/218 (72%), Positives = 184/218 (84%)

Query:     3 LNLKTTIHH--SPLASSSRQFINGFSPKPTSMSFSRSSSLKGFGTQIAIERKERLSFVQT 60
             L L  T H   +   SSS  +I+G S    S + S SSS  GF + +A+E++ R SFVQT
Sbjct:    10 LRLIPTAHRQLNSRQSSSACYIHGGSSVNKSNNLSFSSSTSGFASPLAVEKELRSSFVQT 69

Query:    61 EAVRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSF 120
              AVRH+TG L + EGLRFA+VVARFNE+VTKLLLEGA+ETFKKYSV+EE+I+V+WVPGSF
Sbjct:    70 AAVRHVTGSLIRGEGLRFAIVVARFNEVVTKLLLEGAIETFKKYSVREEDIEVIWVPGSF 129

Query:   121 EIGVVAQQLGKSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLT 180
             EIGVVAQ LGKSGK+ AVLCIGAV+RGDTTHYDAVANSAASGVLSA +NSGVPCIFGVLT
Sbjct:   130 EIGVVAQNLGKSGKFHAVLCIGAVIRGDTTHYDAVANSAASGVLSASINSGVPCIFGVLT 189

Query:   181 CDNMDQALNRAGGKSGNKGAEAALTAIEMASLFEHHLK 218
             C++MDQALNR+GGK+GNKGAE ALTA+EMASLFEHHLK
Sbjct:   190 CEDMDQALNRSGGKAGNKGAETALTALEMASLFEHHLK 227

GO:0000906 "6,7-dimethyl-8-ribityllumazine synthase activity" evidence=IGI;ISS

GO:0009231 "riboflavin biosynthetic process" evidence=IEA;IGI;ISS

GO:0009349 "riboflavin synthase complex" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009867 "jasmonic acid mediated signaling pathway" evidence=IGI

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0006007 "glucose catabolic process" evidence=RCA

TIGR_CMR|BA_4334 BA_4334 "6,7-dimethyl-8-ribityllumazine synthase" [Bacillus anthracis str. Ames (taxid:198094)]

 Score = 402 (146.6 bits), Expect = 1.9e-37, P = 1.9e-37
 Identities = 75/141 (53%), Positives = 103/141 (73%)

Query:    75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGK 134
             GL+  +VV RFNE +T  LL GAL+  K++ V+E +IDV WVPG+FEI ++A+++  SGK
Sbjct:    11 GLKVGVVVGRFNEFITSKLLGGALDGLKRHGVEENDIDVAWVPGAFEIPLIAKKMANSGK 70

Query:   135 YTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGK 194
             Y AV+ +G V+RG TTHYD V N  A GV S  + + +P IFGVLT + ++QA+ RAG K
Sbjct:    71 YDAVITLGTVIRGATTHYDYVCNEVAKGVASLSLQTDIPVIFGVLTTETIEQAIERAGTK 130

Query:   195 SGNKGAEAALTAIEMASLFEH 215
             +GNKG E+A+ AIEMA L +H
Sbjct:   131 AGNKGYESAVAAIEMAHLSKH 151

GO:0000906 "6,7-dimethyl-8-ribityllumazine synthase activity" evidence=ISS

GO:0009231 "riboflavin biosynthetic process" evidence=ISS

TIGR_CMR|DET_1187 DET_1187 "6,7-dimethyl-8-ribityllumazine synthase" [Dehalococcoides ethenogenes 195 (taxid:243164)]

 Score = 402 (146.6 bits), Expect = 1.9e-37, P = 1.9e-37
 Identities = 73/152 (48%), Positives = 112/152 (73%)

Query:    64 RHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG 123
             +  +G L   +GL+ ALVV+RFNE +T  LL GA ++ +++ V  +N DV WVPG+FEI 
Sbjct:     3 KEFSGVLN-GQGLKVALVVSRFNEFITSKLLSGAKDSLERHGVSADNTDVAWVPGAFEIP 61

Query:   124 VVAQQLGKSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDN 183
             +VAQ+L KSG+Y AV+C+GAV+RG T H++ V++  + G+   G+++ +P IFGV+T D+
Sbjct:    62 LVAQKLAKSGRYDAVICLGAVIRGSTPHFEYVSSEVSKGIARVGLDASLPVIFGVITADS 121

Query:   184 MDQALNRAGGKSGNKGAEAALTAIEMASLFEH 215
             ++QA+ RAG K GNKG +AA  AIE+A+L ++
Sbjct:   122 IEQAIERAGTKMGNKGFDAATQAIEVANLMKN 153

GO:0000906 "6,7-dimethyl-8-ribityllumazine synthase activity" evidence=ISS

GO:0009231 "riboflavin biosynthetic process" evidence=ISS

TIGR_CMR|CHY_1472 CHY_1472 "6,7-dimethyl-8-ribityllumazine synthase" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]

 Score = 382 (139.5 bits), Expect = 2.4e-35, P = 2.4e-35
 Identities = 72/141 (51%), Positives = 103/141 (73%)

Query:    74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSG 133
             +GL+  ++V+RFNE +T+ LL GAL+   ++ V+  NIDV+WVPG+FEI +VA++     
Sbjct:    11 KGLKIGIIVSRFNEFITQKLLAGALDCLTRHEVENTNIDVIWVPGAFEIPLVAKRAVHKD 70

Query:   134 KYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGG 193
              Y A++C+GAV+RG T H+D VA   A G+ + G+ +  P IFGVLT D ++QA+ RAG 
Sbjct:    71 -YDAIICLGAVIRGATPHFDYVAAEVAKGIAAVGLEANKPVIFGVLTTDTIEQAIERAGT 129

Query:   194 KSGNKGAEAALTAIEMASLFE 214
             K+GNKG EAAL AIEMA+LF+
Sbjct:   130 KAGNKGWEAALAAIEMANLFK 150

GO:0000906 "6,7-dimethyl-8-ribityllumazine synthase activity" evidence=ISS

GO:0009231 "riboflavin biosynthetic process" evidence=ISS

TIGR_CMR|GSU_1691 GSU_1691 "6,7-dimethyl-8-ribityllumazine synthase" [Geobacter sulfurreducens PCA (taxid:243231)]

 Score = 371 (135.7 bits), Expect = 3.6e-34, P = 3.6e-34
 Identities = 73/150 (48%), Positives = 104/150 (69%)

Query:    64 RHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG 123
             R + G L    GLRF ++V+RFN  + + LLEGAL+   ++   + +IDVV VPG+FEI 
Sbjct:     3 RFIEGKLDAT-GLRFGIIVSRFNSFIGERLLEGALDALVRHGGDDGDIDVVRVPGAFEIP 61

Query:   124 VVAQQLGKSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDN 183
             + AQ+L + G Y AV+C+GAV+RG T H+D VA   + G+    + +GVP +FGVLT D 
Sbjct:    62 LTAQKLVQKGNYDAVICLGAVIRGSTPHFDYVAAEVSKGIAHVSLATGVPVVFGVLTTDT 121

Query:   184 MDQALNRAGGKSGNKGAEAALTAIEMASLF 213
             ++QA+ RAG K+GNKG +AA+TAIE A L+
Sbjct:   122 IEQAIERAGTKAGNKGFDAAVTAIETARLY 151

GO:0000906 "6,7-dimethyl-8-ribityllumazine synthase activity" evidence=ISS

GO:0009231 "riboflavin biosynthetic process" evidence=ISS

UNIPROTKB|P61714 ribE "RibE" [Escherichia coli K-12 (taxid:83333)]

 Score = 363 (132.8 bits), Expect = 2.5e-33, P = 2.5e-33
 Identities = 68/139 (48%), Positives = 100/139 (71%)

Query:    77 RFALVVARFNELVTKLLLEGALETFKKYS-VKEENIDVVWVPGSFEIGVVAQQLGKSGKY 135
             R A+ +ARFN  +   LLEGA++  K+   VK+ENI VVWVPG++E+ + A  L K+GKY
Sbjct:    14 RVAITIARFNNFINDSLLEGAIDALKRIGQVKDENITVVWVPGAYELPLAAGALAKTGKY 73

Query:   136 TAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGKS 195
              AV+ +G V+RG T H++ VA  A++G+     +S +P  FGVLT ++++QA+ RAG K+
Sbjct:    74 DAVIALGTVIRGGTAHFEYVAGGASNGLAHVAQDSEIPVAFGVLTTESIEQAIERAGTKA 133

Query:   196 GNKGAEAALTAIEMASLFE 214
             GNKGAEAALTA+EM ++ +
Sbjct:   134 GNKGAEAALTALEMINVLK 152

GO:0009349 "riboflavin synthase complex" evidence=IEA

GO:0016740 "transferase activity" evidence=IEA

GO:0009231 "riboflavin biosynthetic process" evidence=IEA

GO:0000906 "6,7-dimethyl-8-ribityllumazine synthase activity" evidence=IDA

TIGR_CMR|CPS_1531 CPS_1531 "6,7-dimethyl-8-ribityllumazine synthase" [Colwellia psychrerythraea 34H (taxid:167879)]

 Score = 333 (122.3 bits), Expect = 3.8e-30, P = 3.8e-30
 Identities = 62/140 (44%), Positives = 101/140 (72%)

Query:    74 EGLRFALVVARFNELVTKLLLEGALETFKKY-SVKEENIDVVWVPGSFEIGVVAQQLGKS 132
             +G +FA+VV+RFN  +   LL+GA++  K++ +V +E+I +V VPG++E+ + A+++ K 
Sbjct:    11 KGKKFAIVVSRFNHFIVDSLLDGAVDALKRHGNVNDEDITIVRVPGAYELPLAAKKIAKK 70

Query:   133 GKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAG 192
             G+  A++ IGAV+RG T H+D VA  +  G+    + S +P  FGV+T D+++QA+ RAG
Sbjct:    71 GEADAIIAIGAVIRGGTPHFDFVAGESNKGLAQVCLESEIPVSFGVITTDSIEQAIERAG 130

Query:   193 GKSGNKGAEAALTAIEMASL 212
              K+GNKGAEAAL A+EM ++
Sbjct:   131 TKAGNKGAEAALGALEMVNV 150

GO:0009231 "riboflavin biosynthetic process" evidence=ISS

TIGR_CMR|CJE_0432 CJE_0432 "6,7-dimethyl-8-ribityllumazine synthase" [Campylobacter jejuni RM1221 (taxid:195099)]

 Score = 332 (121.9 bits), Expect = 4.9e-30, P = 4.9e-30
 Identities = 61/147 (41%), Positives = 95/147 (64%)

Query:    66 LTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVV 125
             + G L  +   + A++ ARFN ++T  L+EGA + F ++  KEEN+ ++ VPG+FE+   
Sbjct:     4 IEGKLNLDSNTKIAIINARFNHIITDRLVEGAKDAFLRHGGKEENLSLILVPGAFELPYA 63

Query:   126 AQQLGKSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMD 185
              ++  +S K+ A+ C+GAV+RG T H+D V+     G+ +  +N  +P  FGVLT D ++
Sbjct:    64 LKKAIESKKFDAICCVGAVIRGSTPHFDYVSAETTKGIANVSLNHNIPVSFGVLTTDTIE 123

Query:   186 QALNRAGGKSGNKGAEAALTAIEMASL 212
             QA+ RAG K+GNKG EA  T IEM +L
Sbjct:   124 QAIERAGSKAGNKGFEAMTTVIEMLNL 150

GO:0000906 "6,7-dimethyl-8-ribityllumazine synthase activity" evidence=ISS

GO:0009231 "riboflavin biosynthetic process" evidence=ISS

TIGR_CMR|VC_2268 VC_2268 "6,7-dimethyl-8-ribityllumazine synthase" [Vibrio cholerae O1 biovar El Tor (taxid:686)]

 Score = 330 (121.2 bits), Expect = 7.9e-30, P = 7.9e-30
 Identities = 63/146 (43%), Positives = 98/146 (67%)

Query:    68 GFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYS-VKEENIDVVWVPGSFEIGVVA 126
             GF   N   + A+V++RFN  + + LL GA++T K++  + ++NI VV  PG+ E+ +VA
Sbjct:     7 GFPAPNA--KIAIVISRFNSFINESLLSGAIDTLKRHGQISDDNITVVRCPGAVELPLVA 64

Query:   127 QQLGKSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQ 186
             Q++ K+G Y A++ +G V+RG T H+D V +    G+    +   +P  FGVLT D +DQ
Sbjct:    65 QRVAKTGDYDAIVSLGCVIRGGTPHFDYVCSEMNKGLAQVSLEFSIPVAFGVLTVDTIDQ 124

Query:   187 ALNRAGGKSGNKGAEAALTAIEMASL 212
             A+ RAG K+GNKGAEAAL+A+EM ++
Sbjct:   125 AIERAGTKAGNKGAEAALSALEMINV 150

GO:0000906 "6,7-dimethyl-8-ribityllumazine synthase activity" evidence=ISS

GO:0009231 "riboflavin biosynthetic process" evidence=ISS

TIGR_CMR|SO_3466 SO_3466 "6,7-dimethyl-8-ribityllumazine synthase" [Shewanella oneidensis MR-1 (taxid:211586)]

 Score = 322 (118.4 bits), Expect = 5.6e-29, P = 5.6e-29
 Identities = 60/139 (43%), Positives = 95/139 (68%)

Query:    77 RFALVVARFNELVTKLLLEGALETFKKYS-VKEENIDVVWVPGSFEIGVVAQQLGKSGKY 135
             + A+V++RFN  + + LLEGAL+T K++  V +ENI VV VPG+ E+ + A+++  SGK+
Sbjct:    14 KVAIVISRFNSFLVESLLEGALDTLKRFGQVSDENITVVRVPGAVELPLAARRVAASGKF 73

Query:   136 TAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGKS 195
               ++ +GAV+RG T H+D VA     G+    +   +P  FGVLT D ++QA+ R+G K+
Sbjct:    74 DGIIALGAVIRGGTPHFDFVAGECNKGLAQIALEFDLPVAFGVLTTDTIEQAIERSGTKA 133

Query:   196 GNKGAEAALTAIEMASLFE 214
             GNKG EAAL+ +EM ++ +
Sbjct:   134 GNKGGEAALSLLEMVNVLQ 152

GO:0000906 "6,7-dimethyl-8-ribityllumazine synthase activity" evidence=ISS

GO:0009231 "riboflavin biosynthetic process" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
B0KAI3	RISB_THEP3	2, ., 5, ., 1, ., 9	0.5140	0.6513	0.9220	yes	no
C3LIX8	RISB_BACAC	2, ., 5, ., 1, ., 9	0.5165	0.6697	0.9542	yes	no
Q9XH32	RISB_SPIOL	2, ., 5, ., 1, ., 9	0.7172	0.8669	0.8513	N/A	no
A0LI20	RISB_SYNFM	2, ., 5, ., 1, ., 9	0.5281	0.6513	0.9220	yes	no
A9WFR1	RISB_CHLAA	2, ., 5, ., 1, ., 9	0.5214	0.6422	0.9032	yes	no
O80575	RISB_ARATH	2, ., 5, ., 1, ., 9	0.7586	0.9311	0.8942	yes	no
Q8XMW9	RISB_CLOPE	2, ., 5, ., 1, ., 9	0.5107	0.6376	0.9084	yes	no
B3H0P9	RISB_ACTP7	2, ., 5, ., 1, ., 9	0.5285	0.6422	0.9150	yes	no
A5MZ82	RISB_CLOK5	2, ., 5, ., 1, ., 9	0.5071	0.6422	0.9090	yes	no
C3P7P8	RISB_BACAA	2, ., 5, ., 1, ., 9	0.5165	0.6697	0.9542	yes	no
A0RIB4	RISB_BACAH	2, ., 5, ., 1, ., 9	0.5202	0.6559	0.9346	yes	no
P50856	RISB_ACTPL	2, ., 5, ., 1, ., 9	0.5142	0.6422	0.9150	yes	no
A8FER2	RISB_BACP2	2, ., 5, ., 1, ., 9	0.5395	0.6376	0.9025	yes	no
Q0TTN7	RISB_CLOP1	2, ., 5, ., 1, ., 9	0.5035	0.6376	0.9084	yes	no
B9E377	RISB_CLOK1	2, ., 5, ., 1, ., 9	0.5071	0.6422	0.9090	yes	no
B8I3K7	RISB_CLOCE	2, ., 5, ., 1, ., 9	0.5177	0.6467	0.9096	yes	no
A5D1C7	RISB_PELTS	2, ., 5, ., 1, ., 9	0.52	0.6651	0.9354	yes	no
B7GKI1	RISB_ANOFW	2, ., 5, ., 1, ., 9	0.5683	0.6376	0.9025	yes	no
B8F5Z8	RISB_HAEPS	2, ., 5, ., 1, ., 9	0.5100	0.6788	0.9673	yes	no
B7JLW7	RISB_BACC0	2, ., 5, ., 1, ., 9	0.5165	0.6697	0.9542	yes	no
A9VG51	RISB_BACWK	2, ., 5, ., 1, ., 9	0.5202	0.6559	0.9346	yes	no
B1YEJ3	RISB_EXIS2	2, ., 5, ., 1, ., 9	0.5684	0.6651	0.9539	yes	no
B7GN04	RISB_BIFLS	2, ., 5, ., 1, ., 9	0.5071	0.6422	0.9032	yes	no
Q7VM44	RISB_HAEDU	2, ., 5, ., 1, ., 9	0.5033	0.6788	0.9673	yes	no
B0K0Z0	RISB_THEPX	2, ., 5, ., 1, ., 9	0.5211	0.6513	0.9220	yes	no
B0BTN9	RISB_ACTPJ	2, ., 5, ., 1, ., 9	0.5214	0.6422	0.9150	yes	no
C5D3M9	RISB_GEOSW	2, ., 5, ., 1, ., 9	0.5251	0.6376	0.9025	yes	no
C1EQY6	RISB_BACC3	2, ., 5, ., 1, ., 9	0.5202	0.6559	0.9346	yes	no
B9LIH3	RISB_CHLSY	2, ., 5, ., 1, ., 9	0.5214	0.6422	0.9032	yes	no
A0Q3H6	RISB_CLONN	2, ., 5, ., 1, ., 9	0.5035	0.6467	0.9215	yes	no
Q81MB5	RISB_BACAN	2, ., 5, ., 1, ., 9	0.5165	0.6697	0.9542	yes	no
Q635G9	RISB_BACCZ	2, ., 5, ., 1, ., 9	0.5202	0.6559	0.9346	yes	no
A6LSS9	RISB_CLOB8	2, ., 5, ., 1, ., 9	0.5248	0.6467	0.9155	yes	no
Q6HE53	RISB_BACHK	2, ., 5, ., 1, ., 9	0.5202	0.6559	0.9346	yes	no
Q0SVI9	RISB_CLOPS	2, ., 5, ., 1, ., 9	0.5107	0.6376	0.9084	yes	no

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
4th Layer	2.5.1.9	0.991
3rd Layer	2.5.1	0.976

---

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	218
PLN02404	141	PLN02404, PLN02404, 6,7-dimethyl-8-ribityllumazine	7e-91
cd09209	133	cd09209, Lumazine_synthase-I, lumazine synthase (6	1e-73
PRK00061	154	PRK00061, ribH, 6,7-dimethyl-8-ribityllumazine syn	5e-72
pfam00885	144	pfam00885, DMRL_synthase, 6,7-dimethyl-8-ribityllu	8e-69
COG0054	152	COG0054, RibH, Riboflavin synthase beta-chain [Coe	1e-63
TIGR00114	138	TIGR00114, lumazine-synth, 6,7-dimethyl-8-ribityll	8e-54
cd08371	129	cd08371, Lumazine_synthase-like, lumazine synthase	6e-26
cd09211	131	cd09211, Lumazine_synthase_archaeal, lumazine synt	7e-15
PRK12419	158	PRK12419, PRK12419, riboflavin synthase subunit be	4e-14
cd09208	137	cd09208, Lumazine_synthase-II, lumazine synthase (	2e-12

>gnl|CDD|178026 PLN02404, PLN02404, 6,7-dimethyl-8-ribityllumazine synthase

 Score =  262 bits (672), Expect = 7e-91
 Identities = 120/140 (85%), Positives = 132/140 (94%)

Query: 70  LTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQL 129
           L   EGLRF +VVARFNE++TK LLEGALETFK+YSVKEENIDVVWVPGSFEI VVAQ+L
Sbjct: 2   LLDGEGLRFGVVVARFNEIITKNLLEGALETFKRYSVKEENIDVVWVPGSFEIPVVAQRL 61

Query: 130 GKSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALN 189
            KSGKY A+LCIGAV+RGDTTHYDAVANSAASGVLSAG+NSGVPCIFGVLTCD+M+QALN
Sbjct: 62  AKSGKYDAILCIGAVIRGDTTHYDAVANSAASGVLSAGLNSGVPCIFGVLTCDDMEQALN 121

Query: 190 RAGGKSGNKGAEAALTAIEM 209
           RAGGK+GNKGAEAALTA+EM
Sbjct: 122 RAGGKAGNKGAEAALTAVEM 141

Length = 141

>gnl|CDD|187742 cd09209, Lumazine_synthase-I, lumazine synthase (6,7-dimethyl-8-ribityllumazine synthase, LS), catalyzes the penultimate step in the biosynthesis of riboflavin (vitamin B2); type-I

 Score =  218 bits (559), Expect = 1e-73
 Identities = 79/133 (59%), Positives = 103/133 (77%)

Query: 78  FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTA 137
            A+VV+RFNE +T  LLEGAL+  K++ VKEENIDVV VPG+FEI + A++L +SGKY A
Sbjct: 1   IAIVVSRFNEEITDALLEGALDALKRHGVKEENIDVVRVPGAFEIPLAAKRLARSGKYDA 60

Query: 138 VLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGKSGN 197
           ++ +G V+RG+T H+D V N    G++   + +GVP IFGVLT DN +QAL RAGGK+GN
Sbjct: 61  IIALGCVIRGETPHFDYVCNEVTRGLMRLSLETGVPVIFGVLTTDNEEQALERAGGKAGN 120

Query: 198 KGAEAALTAIEMA 210
           KGAEAAL A+EMA
Sbjct: 121 KGAEAALAALEMA 133

Type-I LS, also known as RibH1, catalyzes the penultimate step in the biosynthesis of riboflavin in plants and microorganisms. LS catalyse the formation of 6,7-dimethyl-8-ribityllumazine by the condensation of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione with 3,4-dihydroxy- 2-butanone-4-phosphate. Subsequently, the lumazine intermediate dismutates to yield riboflavin and 5-amino-6-ribitylamino- 2,4(1H,3H)-pyrimidinedione, in a reaction catalyzed by riboflavin synthase synthase (RS); RS belongs to a different family of the Lumazine-synthase-like superfamily. Riboflavin is the precursor of flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) which are essential cofactors for the catalysis of a wide range of redox reactions. These cofactors are also involved in many other processes involving DNA repair, circadian time-keeping, light sensing, and bioluminescence. Riboflavin is biosynthesized in plants, fungi and certain microorganisms; as animals lack the necessary enzymes to produce this vitamin, they acquire it from dietary sources. Type II LSs are distinct from type-I LS not only in protein sequence, but in that they exhibit different quaternary assemblies; type-I LSs form pentamers. The pathogen Brucella spp. encode both a Type-I LS and a Type-II LS called RibH1 and RibH2, respectively. RibH1/type-I LS appears to be the functional LS in Brucella spp., whereas RibH2/type-II LS has much lower catalytic activity as LS. The pathogen Brucella spp. have both a type-I LS and a type-II LS called RibH1 and RibH2, respectively. RibH1/type-I LS appears to be a functional LS in Brucella spp., whereas RibH2/type-II LS has much lower catalytic activity as LS. Length = 133

>gnl|CDD|234606 PRK00061, ribH, 6,7-dimethyl-8-ribityllumazine synthase; Provisional

 Score =  215 bits (550), Expect = 5e-72
 Identities = 81/141 (57%), Positives = 108/141 (76%)

Query: 74  EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSG 133
           +GLR  +VVARFN+ +T  LLEGAL+  K++ V EENIDVV VPG+FEI + A++L +SG
Sbjct: 11  KGLRIGIVVARFNDFITDALLEGALDALKRHGVSEENIDVVRVPGAFEIPLAAKKLAESG 70

Query: 134 KYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGG 193
           KY AV+ +GAV+RG+T H+D VAN  A G+    + +GVP  FGVLT D ++QA+ RAG 
Sbjct: 71  KYDAVIALGAVIRGETPHFDYVANEVAKGLADVSLETGVPVGFGVLTTDTIEQAIERAGT 130

Query: 194 KSGNKGAEAALTAIEMASLFE 214
           K+GNKGAEAAL A+EMA+L +
Sbjct: 131 KAGNKGAEAALAALEMANLLK 151

Length = 154

>gnl|CDD|201491 pfam00885, DMRL_synthase, 6,7-dimethyl-8-ribityllumazine synthase

 Score =  206 bits (528), Expect = 8e-69
 Identities = 80/141 (56%), Positives = 106/141 (75%)

Query: 74  EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSG 133
            GLR A+VVARFN  +T  LLEGAL+  K++ V EE+IDVV VPG+FE+ + A++L KSG
Sbjct: 2   TGLRIAIVVARFNADITDRLLEGALDALKRHGVSEEDIDVVRVPGAFELPLAAKKLAKSG 61

Query: 134 KYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGG 193
           +Y AV+ +GAV+RG T H+D VA   + G++   + +GVP  FGVLT D  +QAL RAGG
Sbjct: 62  RYDAVVALGAVIRGGTYHFDYVAQEVSRGLMQVSLETGVPVGFGVLTTDTFEQALERAGG 121

Query: 194 KSGNKGAEAALTAIEMASLFE 214
           K+GNKGAEAAL A+EMA+L +
Sbjct: 122 KAGNKGAEAALAALEMANLLK 142

This family includes the beta chain of 6,7-dimethyl-8- ribityllumazine synthase EC:2.5.1.9, an enzyme involved in riboflavin biosynthesis. The family also includes a subfamily of distant archaebacterial proteins that may also have the same function. Length = 144

>gnl|CDD|223132 COG0054, RibH, Riboflavin synthase beta-chain [Coenzyme metabolism]

 Score =  194 bits (495), Expect = 1e-63
 Identities = 77/141 (54%), Positives = 108/141 (76%)

Query: 74  EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSG 133
           +GLR A+VVARFN+ +T  LLEGA++  K++    +NIDVV VPG+FEI + A++L ++G
Sbjct: 11  KGLRIAIVVARFNDDITDALLEGAVDALKRHGADVDNIDVVRVPGAFEIPLAAKKLARTG 70

Query: 134 KYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGG 193
           KY AV+ +GAV+RG+T H+D VAN  A G++   + +GVP  FGVLT DN++QA+ RAG 
Sbjct: 71  KYDAVVALGAVIRGETYHFDYVANEVARGLMDVSLETGVPVTFGVLTTDNIEQAIERAGT 130

Query: 194 KSGNKGAEAALTAIEMASLFE 214
           K+GNKGAEAA  A+EMA+L +
Sbjct: 131 KAGNKGAEAAEAALEMANLLK 151

Length = 152

>gnl|CDD|211550 TIGR00114, lumazine-synth, 6,7-dimethyl-8-ribityllumazine synthase

 Score =  168 bits (428), Expect = 8e-54
 Identities = 65/138 (47%), Positives = 101/138 (73%)

Query: 76  LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKY 135
           +R  +V+ARFN  +T +LL+GA++  K+   + +NIDV+WVPG+FE+ +  ++L +SGKY
Sbjct: 1   VRVGIVIARFNRFITDMLLKGAIDALKRLGAEVDNIDVIWVPGAFELPLAVKKLAESGKY 60

Query: 136 TAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGKS 195
            AV+ +G V+RG T H++ VA+ AA G+    ++ G P IFG+LT + ++QA+ RAG K+
Sbjct: 61  DAVIALGTVIRGGTPHFEYVADEAAKGIADLALDYGKPVIFGILTTETIEQAIERAGTKA 120

Query: 196 GNKGAEAALTAIEMASLF 213
           GNKG EAA+ A+EMA+L 
Sbjct: 121 GNKGVEAAVKALEMANLL 138

This enzyme catalyzes the cyclo-ligation of 3,4-dihydroxy-2-butanone-4-P and 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione to form 6,7-dimethyl-8-ribityllumazine, the immediate precursor of riboflavin. Sometimes referred to as riboflavin synthase, beta subunit, this should not be confused with the alpha subunit which carries out the subsequent reaction. Archaeal members of this family are considered putative, although included in the seed and scoring above the trusted cutoff [Biosynthesis of cofactors, prosthetic groups, and carriers, Riboflavin, FMN, and FAD]. Length = 138

>gnl|CDD|187740 cd08371, Lumazine_synthase-like, lumazine synthase and riboflavin synthase; involved in the riboflavin (vitamin B2) biosynthetic pathway

 Score = 97.1 bits (242), Expect = 6e-26
 Identities = 53/132 (40%), Positives = 80/132 (60%), Gaps = 4/132 (3%)

Query: 78  FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTA 137
             +V ARFN  +   L++GA+    +       I VV VPG++EI + A++L +   Y A
Sbjct: 1   VGIVDARFNRDIVDALVKGAIAELAELGG-NIKIIVVTVPGAYEIPLAAKKLLEKEDYDA 59

Query: 138 VLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMD-QALNRAGGKSG 196
           V+ IG V++G+T H++ VA+  + G+++  + +  P IFGVLT DN + QA  RA  K G
Sbjct: 60  VVAIGVVIKGETYHFEIVAHEVSRGLMNLQLETDKPVIFGVLTPDNAEEQADERA--KRG 117

Query: 197 NKGAEAALTAIE 208
           NKG EAA  A+E
Sbjct: 118 NKGEEAARAAVE 129

This superfamily contains lumazine synthase (6,7-dimethyl-8-ribityllumazine synthase, LS) and riboflavin synthase (RS). Both enzymes play important roles in the riboflavin biosynthetic pathway. Riboflavin is the precursor of flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) which are essential cofactors for the catalysis of a wide range of redox reactions. These cofactors are also involved in many other processes involving DNA repair, circadian time-keeping, light sensing, and bioluminescence. Riboflavin is biosynthesized in plants, fungi and certain microorganisms; as animals lack the necessary enzymes to produce this vitamin, they acquire it from dietary sources. In the final steps of the riboflavin biosynthetic pathway, LS catalyzes the condensation of the 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione with 3,4-dihydroxy- 2-butanone-4-phosphate to release water, inorganic phosphate and 6,7-dimethyl-8-ribityllumazine (DMRL), and RS catalyzes a dismutation of DMRL which yields riboflavin and 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione. In the latter reaction, a four-carbon moiety is transferred between two DMRL molecules serving as donor and acceptor, respectively. Both the LS and RS catalyzed reactions are thermodynamically irreversible and can proceed in the absence of a catalyst. In bacteria and eukaryotes, there are two types of LS: type-I LS forms homo-pentamers or icosahedrally arranged dodecamers of pentamers, type-II LS forms decamers (dimers of pentamers). In archaea LSs and RSs appear to have diverged early in the evolution of archaea from a common ancestor. Length = 129

>gnl|CDD|187744 cd09211, Lumazine_synthase_archaeal, lumazine synthase (6,7-dimethyl-8-ribityllumazine synthase, LS); catalyzes the penultimate step in the biosynthesis of riboflavin (vitamin B2)

 Score = 68.1 bits (167), Expect = 7e-15
 Identities = 42/134 (31%), Positives = 68/134 (50%), Gaps = 8/134 (5%)

Query: 79  ALVVARFNELVTKLLLEGALET--FKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYT 136
            +VVA FN  +T ++ E ALE   F    VK     V+ VPG F++ +  ++L +     
Sbjct: 2   GIVVAEFNYDITYMMEEKALEHAKFLGAEVKY----VLRVPGVFDMPLAVKKLLEKDDID 57

Query: 137 AVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVL-TCDNMDQALNRAGGKS 195
           AV+ +GAV++G+T H + +AN AA  +L   +  G P   G+     +  QAL R     
Sbjct: 58  AVVTLGAVIKGETKHDELIANQAARKILDLSLEYGKPVTLGISGPGMSRLQALERI-EYY 116

Query: 196 GNKGAEAALTAIEM 209
             +  EAA+  ++ 
Sbjct: 117 AKRAVEAAVKMVKR 130

Archaeal LS is an important enzyme in the riboflavin biosynthetic pathway. Riboflavin is the precursor of flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) which are essential cofactors for the catalysis of a wide range of redox reactions. These cofactors are also involved in many other processes involving DNA repair, circadian time-keeping, light sensing, and bioluminescence. In the final steps of the riboflavin biosynthetic pathway LS catalyzes the condensation of the 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione with 3,4-dihydroxy- 2-butanone-4-phosphate to release water, inorganic phosphate and 6,7-dimethyl-8-ribityllumazine (DMRL), and riboflavin synthase (RS) catalyzes a dismutation of DMRL which yields riboflavin and 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione. In the latter reaction, a four-carbon moiety is transferred between two DMRL molecules serving as donor and acceptor, respectively. Both the LS and RS catalyzed reactions are thermodynamically irreversible and can proceed in the absence of a catalyst. LS from Methanococcus jannaschii forms capsids with icosahedral 532 symmetry consisting of 60 subunits. Archaeal LSs share sequence similarity with archaeal RSs, both appear to have diverged early in the evolution of archaea from a common ancestor. Length = 131

>gnl|CDD|237096 PRK12419, PRK12419, riboflavin synthase subunit beta; Provisional

 Score = 67.0 bits (164), Expect = 4e-14
 Identities = 39/146 (26%), Positives = 63/146 (43%), Gaps = 7/146 (4%)

Query: 74  EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSG 133
              R A + AR++  +     +G +            +D+  VPG+FEI + AQ L K+G
Sbjct: 9   TPQRIAFIQARWHADIVDQARKGFVAEIAARGGAASQVDIFDVPGAFEIPLHAQTLAKTG 68

Query: 134 KYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMD-----QAL 188
           +Y A++    VV G    ++ VA +   G++   +++ VP    VLT  +          
Sbjct: 69  RYAAIVAAALVVDGGIYRHEFVAQAVIDGLMRVQLDTEVPVFSVVLTPHHFHESEEHHDF 128

Query: 189 NRAGGKSGNKGAEAALTAIEMASLFE 214
            RA      KGAEAA    +     E
Sbjct: 129 FRAHFVV--KGAEAAHACADTLLSRE 152

Length = 158

>gnl|CDD|187741 cd09208, Lumazine_synthase-II, lumazine synthase (6,7-dimethyl-8-ribityllumazine synthase, LS), catalyzes the penultimate step in the biosynthesis of riboflavin (vitamin B2); type-II

 Score = 61.7 bits (150), Expect = 2e-12
 Identities = 32/137 (23%), Positives = 60/137 (43%), Gaps = 3/137 (2%)

Query: 76  LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKY 135
            R A + AR++  +     +G            + +D+  VPG+FEI + A++L ++G+Y
Sbjct: 1   FRIAFIQARWHADIVDQARKGFEAEMAAKGGASDEVDIFDVPGAFEIPLHAKRLARTGRY 60

Query: 136 TAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNM---DQALNRAG 192
            A++    VV G    ++ VA +   G++   + + VP    VLT  +     +      
Sbjct: 61  AAIVGAALVVDGGIYRHEFVAQAVIDGLMRVQLETEVPVFSVVLTPHHFHEHKEHHEFFF 120

Query: 193 GKSGNKGAEAALTAIEM 209
                KG E A   + +
Sbjct: 121 AHFKKKGVEVAHACLAI 137

Type-II LS also known as RibH2, catalyzes the penultimate step in the biosynthesis of riboflavin in plants and microorganisms. LS catalyses the formation of 6,7-dimethyl-8-ribityllumazine by the condensation of 5-amino-6-ribitylamino- 2,4(1H,3H)-pyrimidinedione with 3,4-dihydroxy- 2-butanone-4-phosphate. Subsequently, the lumazine intermediate dismutates yielding riboflavin and 5-amino-6-ribitylamino- 2,4(1H,3H)-pyrimidinedione, in a reaction catalyzed by riboflavin synthase (RS); RS belongs to a different family of the Lumazine-synthase-like superfamily. Riboflavin is the precursor of flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) which are essential cofactors for the catalysis of a wide range of redox reactions. These cofactors are also involved in many other processes involving DNA repair, circadian time-keeping, light sensing, and bioluminescence. Riboflavin is biosynthesized in plants, fungi and certain microorganisms; as animals lack the necessary enzymes to produce this vitamin, they acquire it from dietary sources. Type II LSs are distinct from type-I LS not only in protein sequence, but in that they exhibit different quaternary assemblies; type-II LSs form decamers (dimers of pentamers). The pathogen Brucella spp. have both a type-I LS and a type-II LS called RibH1 and RibH2, respectively. RibH1/type-I LS appears to be a functional LS in Brucella spp., whereas RibH2/type-II LS has much lower catalytic activity as LS and may be regulated by a riboswitch that senses FMN, suggesting that the type-II LSs may have evolved into very poor catalysts or, that they may harbor a new, as-yet-unknown function. Length = 137

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	218
COG0054	152	RibH Riboflavin synthase beta-chain [Coenzyme meta	100.0
PLN02404	141	6,7-dimethyl-8-ribityllumazine synthase	100.0
PRK00061	154	ribH 6,7-dimethyl-8-ribityllumazine synthase; Prov	100.0
TIGR00114	138	lumazine-synth 6,7-dimethyl-8-ribityllumazine synt	100.0
PRK12419	158	riboflavin synthase subunit beta; Provisional	100.0
PF00885	144	DMRL_synthase: 6,7-dimethyl-8-ribityllumazine synt	100.0
KOG3243	158	consensus 6,7-dimethyl-8-ribityllumazine synthase	100.0
TIGR01506	151	ribC_arch riboflavin synthase. This archaeal prote	100.0
PRK06455	155	riboflavin synthase; Provisional	100.0
COG1731	154	Archaeal riboflavin synthase [Coenzyme metabolism]	99.61
PF04392	294	ABC_sub_bind: ABC transporter substrate binding pr	95.7
cd01541	273	PBP1_AraR Ligand-binding domain of DNA transcripti	94.68
PRK11041	309	DNA-binding transcriptional regulator CytR; Provis	94.59
cd06300	272	PBP1_ABC_sugar_binding_like_1 Periplasmic sugar-bi	94.35
cd06320	275	PBP1_allose_binding Periplasmic allose-binding dom	94.33
cd06318	282	PBP1_ABC_sugar_binding_like_9 Periplasmic sugar-bi	94.1
cd06305	273	PBP1_methylthioribose_binding_like Methylthioribos	94.03
cd06301	272	PBP1_rhizopine_binding_like Periplasmic binding pr	93.89
cd06325	281	PBP1_ABC_uncharacterized_transporter Type I peripl	93.87
TIGR01481	329	ccpA catabolite control protein A. Catabolite cont	93.86
cd06310	273	PBP1_ABC_sugar_binding_like_2 Periplasmic sugar-bi	93.66
cd06319	277	PBP1_ABC_sugar_binding_like_10 Periplasmic sugar-b	93.63
cd01391	269	Periplasmic_Binding_Protein_Type_1 Type 1 periplas	93.6
cd06284	267	PBP1_LacI_like_6 Ligand-binding domain of an uncha	93.53
PF13377	160	Peripla_BP_3: Periplasmic binding protein-like dom	93.43
cd01575	268	PBP1_GntR Ligand-binding domain of DNA transcripti	93.23
cd06317	275	PBP1_ABC_sugar_binding_like_8 Periplasmic sugar-bi	93.1
cd06273	268	PBP1_GntR_like_1 This group includes the ligand-bi	92.99
cd06316	294	PBP1_ABC_sugar_binding_like_7 Periplasmic sugar-bi	92.96
cd01539	303	PBP1_GGBP Periplasmic glucose/galactose-binding pr	92.91
cd06271	268	PBP1_AglR_RafR_like Ligand-binding domain of DNA t	92.89
cd06291	265	PBP1_Qymf_like Ligand binding domain of the lacI-l	92.78
cd06277	268	PBP1_LacI_like_1 Ligand-binding domain of uncharac	92.74
cd01538	288	PBP1_ABC_xylose_binding Periplasmic xylose-binding	92.74
cd06315	280	PBP1_ABC_sugar_binding_like_6 Periplasmic sugar-bi	92.62
cd06270	268	PBP1_GalS_like Ligand binding domain of DNA transc	92.61
cd01542	259	PBP1_TreR_like Ligand-binding domain of DNA transc	92.47
cd06271	268	PBP1_AglR_RafR_like Ligand-binding domain of DNA t	92.33
cd06297	269	PBP1_LacI_like_12 Ligand-binding domain of unchara	92.29
cd06293	269	PBP1_LacI_like_11 Ligand-binding domain of unchara	92.15
cd01540	289	PBP1_arabinose_binding Periplasmic L-arabinose-bin	92.12
cd01536	267	PBP1_ABC_sugar_binding_like Periplasmic sugar-bind	92.08
PRK10014	342	DNA-binding transcriptional repressor MalI; Provis	92.02
cd06292	273	PBP1_LacI_like_10 Ligand-binding domain of unchara	91.95
cd06307	275	PBP1_uncharacterized_sugar_binding Periplasmic sug	91.88
cd06323	268	PBP1_ribose_binding Periplasmic sugar-binding doma	91.88
cd06270	268	PBP1_GalS_like Ligand binding domain of DNA transc	91.87
PRK10355	330	xylF D-xylose transporter subunit XylF; Provisiona	91.7
cd06283	267	PBP1_RegR_EndR_KdgR_like Ligand-binding domain of	91.68
TIGR01016	386	sucCoAbeta succinyl-CoA synthetase, beta subunit.	91.62
PRK15395	330	methyl-galactoside ABC transporter galactose-bindi	91.56
cd06302	298	PBP1_LsrB_Quorum_Sensing Periplasmic binding domai	91.54
TIGR02634	302	xylF D-xylose ABC transporter, substrate-binding p	91.51
cd06322	267	PBP1_ABC_sugar_binding_like_12 Periplasmic sugar-b	91.47
cd06312	271	PBP1_ABC_sugar_binding_like_4 Periplasmic sugar-bi	91.04
cd01537	264	PBP1_Repressors_Sugar_Binding_like Ligand-binding	90.95
cd06312	271	PBP1_ABC_sugar_binding_like_4 Periplasmic sugar-bi	90.89
cd06299	265	PBP1_LacI_like_13 Ligand-binding domain of DNA-bin	90.86
cd06281	269	PBP1_LacI_like_5 Ligand-binding domain of uncharac	90.66
cd06293	269	PBP1_LacI_like_11 Ligand-binding domain of unchara	90.62
PRK00696	388	sucC succinyl-CoA synthetase subunit beta; Provisi	90.43
TIGR02637	302	RhaS rhamnose ABC transporter, rhamnose-binding pr	90.43
cd06267	264	PBP1_LacI_sugar_binding_like Ligand binding domain	90.18
PRK10653	295	D-ribose transporter subunit RbsB; Provisional	90.1
cd06309	273	PBP1_YtfQ_like Periplasmic binding domain of ABC-t	89.92
cd06275	269	PBP1_PurR Ligand-binding domain of purine represso	89.91
cd06294	270	PBP1_ycjW_transcription_regulator_like Ligand-bind	89.85
cd01545	270	PBP1_SalR Ligand-binding domain of DNA transcripti	89.68
cd06280	263	PBP1_LacI_like_4 Ligand-binding domain of uncharac	89.68
cd06290	265	PBP1_LacI_like_9 Ligand-binding domain of uncharac	89.51
PRK09492	315	treR trehalose repressor; Provisional	89.5
cd06289	268	PBP1_MalI_like Ligand-binding domain of MalI, a tr	89.41
PF00532	279	Peripla_BP_1: Periplasmic binding proteins and sug	89.3
cd06286	260	PBP1_CcpB_like Ligand-binding domain of a novel tr	89.21
cd06296	270	PBP1_CatR_like Ligand-binding domain of a LacI-lik	89.19
PF02601	319	Exonuc_VII_L: Exonuclease VII, large subunit; Inte	89.13
PRK10423	327	transcriptional repressor RbsR; Provisional	89.08
PRK10014	342	DNA-binding transcriptional repressor MalI; Provis	88.96
PRK10423	327	transcriptional repressor RbsR; Provisional	88.91
cd06287	269	PBP1_LacI_like_8 Ligand-binding domain of uncharac	88.83
PF00532	279	Peripla_BP_1: Periplasmic binding proteins and sug	88.8
cd06273	268	PBP1_GntR_like_1 This group includes the ligand-bi	88.74
cd06354	265	PBP1_BmpA_PnrA_like Periplasmic binding domain of	88.43
cd01574	264	PBP1_LacI Ligand-binding domain of DNA transcripti	88.24
cd06323	268	PBP1_ribose_binding Periplasmic sugar-binding doma	88.09
cd06298	268	PBP1_CcpA_like Ligand-binding domain of the catabo	88.07
PRK10727	343	DNA-binding transcriptional regulator GalR; Provis	88.05
cd06275	269	PBP1_PurR Ligand-binding domain of purine represso	87.98
PRK15408	336	autoinducer 2-binding protein lsrB; Provisional	87.93
cd06290	265	PBP1_LacI_like_9 Ligand-binding domain of uncharac	87.84
cd06274	264	PBP1_FruR Ligand binding domain of DNA transcripti	87.61
cd06285	265	PBP1_LacI_like_7 Ligand-binding domain of uncharac	87.54
COG1609	333	PurR Transcriptional regulators [Transcription]	87.52
PRK15395	330	methyl-galactoside ABC transporter galactose-bindi	87.43
cd06306	268	PBP1_TorT-like TorT-like proteins, a periplasmic b	87.41
cd06295	275	PBP1_CelR Ligand binding domain of a transcription	87.39
cd06306	268	PBP1_TorT-like TorT-like proteins, a periplasmic b	87.27
PRK10401	346	DNA-binding transcriptional regulator GalS; Provis	87.27
PRK09701	311	D-allose transporter subunit; Provisional	87.24
cd06311	274	PBP1_ABC_sugar_binding_like_3 Periplasmic sugar-bi	87.23
cd01538	288	PBP1_ABC_xylose_binding Periplasmic xylose-binding	87.04
cd06281	269	PBP1_LacI_like_5 Ligand-binding domain of uncharac	86.97
TIGR02955	295	TMAO_TorT TMAO reductase system periplasmic protei	86.92
PRK11303	328	DNA-binding transcriptional regulator FruR; Provis	86.6
PRK10703	341	DNA-binding transcriptional repressor PurR; Provis	86.54
TIGR02417	327	fruct_sucro_rep D-fructose-responsive transcriptio	86.47
cd06272	261	PBP1_hexuronate_repressor_like Ligand-binding doma	86.45
cd06278	266	PBP1_LacI_like_2 Ligand-binding domain of uncharac	86.44
TIGR01481	329	ccpA catabolite control protein A. Catabolite cont	86.44
PRK14987	331	gluconate operon transcriptional regulator; Provis	86.42
cd06304	260	PBP1_BmpA_like Periplasmic binding component of a	86.29
cd06272	261	PBP1_hexuronate_repressor_like Ligand-binding doma	86.27
cd06299	265	PBP1_LacI_like_13 Ligand-binding domain of DNA-bin	86.16
TIGR02405	311	trehalos_R_Ecol trehalose operon repressor, proteo	86.08
cd06282	266	PBP1_GntR_like_2 Ligand-binding domain of putative	85.96
cd06267	264	PBP1_LacI_sugar_binding_like Ligand binding domain	85.94
cd06292	273	PBP1_LacI_like_10 Ligand-binding domain of unchara	85.69
cd06308	270	PBP1_sensor_kinase_like Periplasmic binding domain	85.49
COG1609	333	PurR Transcriptional regulators [Transcription]	85.15
cd06321	271	PBP1_ABC_sugar_binding_like_11 Periplasmic sugar-b	85.09
cd06279	283	PBP1_LacI_like_3 Ligand-binding domain of uncharac	85.0
COG2984	322	ABC-type uncharacterized transport system, peripla	84.98
cd06319	277	PBP1_ABC_sugar_binding_like_10 Periplasmic sugar-b	84.91
cd06285	265	PBP1_LacI_like_7 Ligand-binding domain of uncharac	84.85
PRK14046	392	malate--CoA ligase subunit beta; Provisional	84.83
cd06289	268	PBP1_MalI_like Ligand-binding domain of MalI, a tr	84.66
cd06313	272	PBP1_ABC_sugar_binding_like_5 Periplasmic sugar-bi	84.6
PF04392	294	ABC_sub_bind: ABC transporter substrate binding pr	84.58
PRK10936	343	TMAO reductase system periplasmic protein TorT; Pr	84.48
cd06294	270	PBP1_ycjW_transcription_regulator_like Ligand-bind	84.08
PRK10936	343	TMAO reductase system periplasmic protein TorT; Pr	84.06
PRK10703	341	DNA-binding transcriptional repressor PurR; Provis	83.99
PRK10727	343	DNA-binding transcriptional regulator GalR; Provis	83.84
PRK09526	342	lacI lac repressor; Reviewed	83.79
TIGR02637	302	RhaS rhamnose ABC transporter, rhamnose-binding pr	83.54
cd06300	272	PBP1_ABC_sugar_binding_like_1 Periplasmic sugar-bi	83.49
cd06297	269	PBP1_LacI_like_12 Ligand-binding domain of unchara	83.39
cd06307	275	PBP1_uncharacterized_sugar_binding Periplasmic sug	83.08
cd01575	268	PBP1_GntR Ligand-binding domain of DNA transcripti	82.7
PF13407	257	Peripla_BP_4: Periplasmic binding protein domain;	82.43
COG2039	207	Pcp Pyrrolidone-carboxylate peptidase (N-terminal	82.25
cd00886	152	MogA_MoaB MogA_MoaB family. Members of this family	82.19
PRK10401	346	DNA-binding transcriptional regulator GalS; Provis	81.67
PF13407	257	Peripla_BP_4: Periplasmic binding protein domain;	81.55
TIGR02667	163	moaB_proteo molybdenum cofactor biosynthesis prote	81.3
cd06291	265	PBP1_Qymf_like Ligand binding domain of the lacI-l	81.02
PRK14987	331	gluconate operon transcriptional regulator; Provis	80.59
cd01544	270	PBP1_GalR Ligand-binding domain of DNA transcripti	80.55
cd06325	281	PBP1_ABC_uncharacterized_transporter Type I peripl	80.5
cd06286	260	PBP1_CcpB_like Ligand-binding domain of a novel tr	80.42
PF03358	152	FMN_red: NADPH-dependent FMN reductase; InterPro:	80.34
cd06274	264	PBP1_FruR Ligand binding domain of DNA transcripti	80.24
cd01537	264	PBP1_Repressors_Sugar_Binding_like Ligand-binding	80.22
cd06288	269	PBP1_sucrose_transcription_regulator Ligand-bindin	80.16
TIGR02417	327	fruct_sucro_rep D-fructose-responsive transcriptio	80.09

>COG0054 RibH Riboflavin synthase beta-chain [Coenzyme metabolism]

Probab=100.00  E-value=1.1e-58  Score=383.94  Aligned_cols=152  Identities=52%  Similarity=0.860  Sum_probs=147.1

Q ss_pred             HhhhcccCCCCCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEe
Q 027801           63 VRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIG  142 (218)
Q Consensus        63 ~~~~~~~~~~~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG  142 (218)
                      |+.+++.+. +++.|||||++|||++|+|+|+++|+++|+++|...+||+++||||+||||+++++|+++++||||||||
T Consensus         1 m~~~~g~~~-~~~~riaIV~arfn~~I~d~ll~gA~~~l~~~G~~~~~i~vv~VPGa~EiPl~a~~La~~~~yDAvv~lG   79 (152)
T COG0054           1 MNIIEGNLV-AKGLRIAIVVARFNDDITDALLEGAVDALKRHGADVDNIDVVRVPGAFEIPLAAKKLARTGKYDAVVALG   79 (152)
T ss_pred             CCccCCCcC-CCCceEEEEEeehhHHHHHHHHHHHHHHHHHcCCCcccceEEEeCCcchhHHHHHHHHhcCCcceEEEEe
Confidence            566777775 8899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeeeCCchhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHhhCCCCCCcHHHHHHHHHHHHHHHhh
Q 027801          143 AVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGKSGNKGAEAALTAIEMASLFEH  215 (218)
Q Consensus       143 ~VIrGeT~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~Rag~k~gnKG~EAA~aAleM~~L~~~  215 (218)
                      |||||+|+||||||+++++|||++||++++||+|||||++|+|||++|+|.+.+|||.|||.+||||++++++
T Consensus        80 ~VIrG~T~Hfd~Va~~~~~gl~~vsl~~~~PV~~GVLt~~~~eqA~~rag~~~gnkG~~Aa~aAlem~~l~~~  152 (152)
T COG0054          80 AVIRGETYHFDYVANEVARGLMDVSLETGVPVTFGVLTTDNIEQAIERAGTKAGNKGAEAAEAALEMANLLKK  152 (152)
T ss_pred             eEEeCCCccHHHHHHHHHHHHHHHHHhhCCCeEeeecCCCcHHHHHHHhCccccccHHHHHHHHHHHHHHhcC
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999874

>PLN02404 6,7-dimethyl-8-ribityllumazine synthase

Probab=100.00  E-value=1.4e-58  Score=379.57  Aligned_cols=138  Identities=86%  Similarity=1.315  Sum_probs=135.9

Q ss_pred             CCCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEeeeeeCCchh
Q 027801           72 KNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVVRGDTTH  151 (218)
Q Consensus        72 ~~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~VIrGeT~H  151 (218)
                      +++++||+||+||||++|+++|+++|+++|+++|+++++++++|||||||||+++++|+++++|||||||||||||+|+|
T Consensus         4 ~~~~~ri~IV~s~fn~~I~~~Ll~ga~~~l~~~gv~~~~i~v~~VPGa~EiP~a~~~l~~s~~~DavIaLG~VIrGeT~H   83 (141)
T PLN02404          4 DGEGLRFGVVVARFNEIITKNLLEGALETFKRYSVKEENIDVVWVPGSFEIPVVAQRLAKSGKYDAILCIGAVIRGDTTH   83 (141)
T ss_pred             CCCCCEEEEEEecCcHHHHHHHHHHHHHHHHHcCCCccceEEEEcCcHHHHHHHHHHHHhcCCCCEEEEEEEEEeCCCch
Confidence            57889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHhhCCCCCCcHHHHHHHHHHH
Q 027801          152 YDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGKSGNKGAEAALTAIEM  209 (218)
Q Consensus       152 ~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~Rag~k~gnKG~EAA~aAleM  209 (218)
                      |||||+++++|||+++|++++||+|||||++|+|||++|++++.+|||.|||++||||
T Consensus        84 ~e~V~~~v~~gl~~vsl~~~~PV~~GVLt~~~~eQA~~Rag~~~~nkG~eaA~aalem  141 (141)
T PLN02404         84 YDAVANSAASGVLSAGLNSGVPCIFGVLTCDDMEQALNRAGGKAGNKGAEAALTAVEM  141 (141)
T ss_pred             hHHHHHHHHHHHHHHHhccCCCEEEEEcCCCCHHHHHHHhCCcccCcHHHHHHHHHhC
Confidence            9999999999999999999999999999999999999999999999999999999998

>PRK00061 ribH 6,7-dimethyl-8-ribityllumazine synthase; Provisional

Probab=100.00  E-value=7.1e-58  Score=379.68  Aligned_cols=150  Identities=55%  Similarity=0.899  Sum_probs=144.5

Q ss_pred             hhcccCCCCCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEeee
Q 027801           65 HLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAV  144 (218)
Q Consensus        65 ~~~~~~~~~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~V  144 (218)
                      .+++++. .++.||+||+||||++|++.|+++|+++|+++|+++++++++||||+||||+++++|+++++||||||||||
T Consensus         3 ~~~~~~~-~~~~riaIV~s~~n~~i~~~l~~ga~~~l~~~gv~~~~i~v~~VPGa~EiP~a~~~l~~~~~~DavIalG~V   81 (154)
T PRK00061          3 IIEGNLV-AKGLRIGIVVARFNDFITDALLEGALDALKRHGVSEENIDVVRVPGAFEIPLAAKKLAESGKYDAVIALGAV   81 (154)
T ss_pred             ccCCCcC-CCCCEEEEEEecCcHHHHHHHHHHHHHHHHHcCCCccceEEEECCCHHHHHHHHHHHHHcCCCCEEEEEeeE
Confidence            3456664 788999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeCCchhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHhhCCCCCCcHHHHHHHHHHHHHHHhh
Q 027801          145 VRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGKSGNKGAEAALTAIEMASLFEH  215 (218)
Q Consensus       145 IrGeT~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~Rag~k~gnKG~EAA~aAleM~~L~~~  215 (218)
                      |||+|+||||||+++++|||++||++++||+|||||++|+|||++|+|++.+|||.|||++|++|++++++
T Consensus        82 IrG~T~H~e~V~~~v~~gl~~v~l~~~~PV~~GVLt~~~~eQa~~R~~~~~~nkG~eaa~aal~m~~l~~~  152 (154)
T PRK00061         82 IRGETPHFDYVANEVAKGLADVSLETGVPVGFGVLTTDTIEQAIERAGTKAGNKGAEAALAALEMANLLKQ  152 (154)
T ss_pred             EcCCCchHHHHHHHHHHHHHHHHhccCCCEEEEecCCCCHHHHHHHhCccccccHHHHHHHHHHHHHHHHh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999886

>TIGR00114 lumazine-synth 6,7-dimethyl-8-ribityllumazine synthase

Probab=100.00  E-value=6.1e-58  Score=374.34  Aligned_cols=138  Identities=46%  Similarity=0.870  Sum_probs=135.7

Q ss_pred             CEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEeeeeeCCchhHHHH
Q 027801           76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVVRGDTTHYDAV  155 (218)
Q Consensus        76 ~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~VIrGeT~H~e~V  155 (218)
                      +||+||+||||++|+++|+++|+++|+++|+.+++|+++||||+||||+++++|+++++|||||||||||||+|+|||||
T Consensus         1 ~ri~IV~s~~n~~i~~~L~~ga~~~l~~~g~~~~~i~v~~VPGa~EiP~a~~~l~~~~~~DavI~LG~VIrG~T~H~e~v   80 (138)
T TIGR00114         1 VRVGIVIARFNRDITDMLLKGAIDALKRLGAEVDNIDVIWVPGAFELPLAVKKLAETGKYDAVIALGCVIRGGTPHFEYV   80 (138)
T ss_pred             CEEEEEEecCCHHHHHHHHHHHHHHHHHcCCCccceEEEECCcHHHHHHHHHHHHhcCCCCEEEEEeeEEeCCCchhHHH
Confidence            59999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHhhCCCCCCcHHHHHHHHHHHHHHH
Q 027801          156 ANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGKSGNKGAEAALTAIEMASLF  213 (218)
Q Consensus       156 a~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~Rag~k~gnKG~EAA~aAleM~~L~  213 (218)
                      |+++++|||++||++++||+|||||++|+|||++|++++.+|||.|||++|+||++++
T Consensus        81 ~~~v~~gl~~~sl~~~~PV~~GvLt~~~~eQa~~R~~~~~~nkG~eaA~aal~m~~~~  138 (138)
T TIGR00114        81 ADEAAKGIADLALDYDKPVIFGILTTGTIEQAIERAGDKAGNKGVEAAVAALEMAKLL  138 (138)
T ss_pred             HHHHHHHHHHHHhhhCCCEEEEecCCCCHHHHHHHccccccccHHHHHHHHHHHHhcC
Confidence            9999999999999999999999999999999999999999999999999999999875

Archaeal members of this family are considered putative, although included in the seed and scoring above the trusted cutoff.

>PRK12419 riboflavin synthase subunit beta; Provisional

Probab=100.00  E-value=1.2e-57  Score=380.15  Aligned_cols=145  Identities=27%  Similarity=0.333  Sum_probs=136.9

Q ss_pred             cCCCCCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEeeeeeCC
Q 027801           69 FLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVVRGD  148 (218)
Q Consensus        69 ~~~~~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~VIrGe  148 (218)
                      +.++.++.||+||+||||++|+++|++||+++|+++|+++++++++|||||||||+++++|+++++|||||||||||||+
T Consensus         4 ~~~~~~~~riaIV~srfn~~It~~Ll~gA~~~l~~~G~~~~~i~v~~VPGA~EiP~~a~~l~~~~~yDaiIaLG~VIrGe   83 (158)
T PRK12419          4 SPRFATPQRIAFIQARWHADIVDQARKGFVAEIAARGGAASQVDIFDVPGAFEIPLHAQTLAKTGRYAAIVAAALVVDGG   83 (158)
T ss_pred             CCCCCCCCEEEEEEecCCHHHHHHHHHHHHHHHHHcCCCccceEEEECCcHHHHHHHHHHHHhcCCCCEEEEEEEEEcCC
Confidence            44567889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             chhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHH-----HHHHhhCCCCCCcHHHHHHHHHHHHHHHhh
Q 027801          149 TTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMD-----QALNRAGGKSGNKGAEAALTAIEMASLFEH  215 (218)
Q Consensus       149 T~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~e-----QA~~Rag~k~gnKG~EAA~aAleM~~L~~~  215 (218)
                      |+||||||+++++|||+++|++++||+|||||++|+|     ||++|++.  +|||.|||.+||||++|+++
T Consensus        84 T~H~e~V~~~v~~gl~~vsl~~~~PV~fGVLT~~~~eqA~~rqa~~Ra~~--~nKG~eaA~aalem~~l~~~  153 (158)
T PRK12419         84 IYRHEFVAQAVIDGLMRVQLDTEVPVFSVVLTPHHFHESEEHHDFFRAHF--VVKGAEAAHACADTLLSRER  153 (158)
T ss_pred             CchhHHHHHHHHHHHHHHHhccCCCEEEEecCCCcHHHHHHHHHHhhcCc--cccHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999     55556754  49999999999999999886

>PF00885 DMRL_synthase: 6,7-dimethyl-8-ribityllumazine synthase; InterPro: IPR002180 6,7-dimethyl-8-ribityllumazine synthase (riboflavin synthase) catalyses the biosynthesis of riboflavin according to the reaction: 2 6,7-dimethyl-8-(1-D-ribityl)lumazine = riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine

Probab=100.00  E-value=7.2e-56  Score=363.52  Aligned_cols=142  Identities=54%  Similarity=0.893  Sum_probs=137.4

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEeeeeeCCchhHH
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVVRGDTTHYD  153 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~VIrGeT~H~e  153 (218)
                      +++|||||+||||++|+++|+++|+++|+++|+++++++++||||+||||+++++|+++++|||||||||||||+|+|||
T Consensus         2 ~~~ri~IV~s~~n~~i~~~ll~~a~~~l~~~g~~~~~i~~~~VPGa~ElP~a~~~l~~~~~~Davi~lG~VI~G~T~H~~   81 (144)
T PF00885_consen    2 SGLRIAIVVSRFNEEITDRLLEGALEELKRHGVAEENIEVIRVPGAFELPLAAKRLAESGRYDAVIALGCVIRGETDHFE   81 (144)
T ss_dssp             TTEEEEEEEESTTHHHHHHHHHHHHHHHHHTTTTGGCEEEEEESSGGGHHHHHHHHHHCSTESEEEEEEEEE--SSTHHH
T ss_pred             CCCEEEEEEEeccHHHHHHHHHHHHHHHHHcCCCccceEEEEcCCHHHHHHHHHHHhcccCccEEEEeccccCCCchHHH
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHhhCCCCCCcHHHHHHHHHHHHHHHhh
Q 027801          154 AVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGKSGNKGAEAALTAIEMASLFEH  215 (218)
Q Consensus       154 ~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~Rag~k~gnKG~EAA~aAleM~~L~~~  215 (218)
                      |||+++++|||++|+++++||+|||||++|+|||++|++++.+|||+|||++|++|++++++
T Consensus        82 ~v~~~v~~gl~~lsl~~~~PV~~gvlt~~~~eqa~~R~~~~~~nkG~eaA~aal~m~~l~~~  143 (144)
T PF00885_consen   82 YVANAVSRGLMDLSLEYGIPVIFGVLTPDTEEQALERAGGKAGNKGREAAEAALEMAKLLRQ  143 (144)
T ss_dssp             HHHHHHHHHHHHHHHHHTSEEEEEEEEESSHHHHHHHCEETTEEHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccCCccEEEEecCCCCHHHHHHHhcchhhhhHHHHHHHHHHHHHHHhc
Confidence            99999999999999999999999999999999999999999999999999999999999986

The biosynthesis of one riboflavin molecule requires one molecule of GTP and two molecules of ribulose 5-phosphate as substrates. The final step in the biosynthesis of the vitamin involves the dismutation of 6,7-dimethyl-8-ribityllumazine catalyzed by riboflavin synthase. The second product, 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione, is recycled in the biosynthetic pathway by 6,7-dimethyl-8-ribityllumazine synthase []. N-[2,4-dioxo-6-d-ribitylamino-1,2,3,4-tetrahydropyrimidin-5-yl]oxalamic acid derivatives inhibit riboflavin synthase []. This family includes the beta chain of 6,7-dimethyl-8-ribityllumazine synthase 2.5.1.9 from EC. The family also includes a subfamily of distant archaebacterial proteins that may also have the same function for example O28856 from SWISSPROT.; GO: 0009231 riboflavin biosynthetic process, 0009349 riboflavin synthase complex; PDB: 2O6H_D 1C41_C 2OBX_H 1VSX_H 1VSW_3 3JV8_C 3MK3_r 3NQ4_G 2A58_A 2A57_D ....

>KOG3243 consensus 6,7-dimethyl-8-ribityllumazine synthase [Coenzyme transport and metabolism]

Probab=100.00  E-value=4.6e-52  Score=338.96  Aligned_cols=156  Identities=63%  Similarity=1.043  Sum_probs=150.8

Q ss_pred             hhhhHhhhcccCCCCCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEE
Q 027801           59 QTEAVRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAV  138 (218)
Q Consensus        59 ~~~a~~~~~~~~~~~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaV  138 (218)
                      |++++++.++++.+++++||+||.+|||+.+++.|++||++++++++|.++||++.||||+||||+.+|.+.+++.||+|
T Consensus         1 ~~~gv~~p~~s~~~G~~lR~~IvhARwN~vvi~~LvkGAiEtm~~~~V~eenI~ie~VPGS~Elp~g~~~~~~r~~~daV   80 (158)
T KOG3243|consen    1 QTAGVRHPTGSLIRGEGLRFAIVHARWNEVVIKLLVKGAIETMKKYSVREENIEIEWVPGSFELPVGAQNLGKRGKFDAV   80 (158)
T ss_pred             CccccCCCChhhccCCCeEEEEEeehhHHHHHHHHHHHHHHHHHHhCcchhceeEEEcCCceeccHHHHhhhhccCceEE
Confidence            45677888888888999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEeeeeeCCchhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHhhCCCCC-CcHHHHHHHHHHHHHHHh
Q 027801          139 LCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGKSG-NKGAEAALTAIEMASLFE  214 (218)
Q Consensus       139 IaLG~VIrGeT~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~Rag~k~g-nKG~EAA~aAleM~~L~~  214 (218)
                      ||+|++|||+|.|||||+++++.|||+++++.++|||||+|||+|+|||+.|+|++.+ |+|.||+.+|+||+.++.
T Consensus        81 i~IGvlIkGsTmHfeyis~s~~hglm~~~~~sgvPvIfGlLTc~~eeQAL~RaG~~~ghNhG~dwg~aAvEMa~kf~  157 (158)
T KOG3243|consen   81 ICIGVLIKGSTMHFEYISNSAAHGLMSASINSGVPVIFGLLTCEDEEQALNRAGGKAGHNHGADWGLAAVEMASKFE  157 (158)
T ss_pred             EEEEEEEecCchhHHHHHHHHHHHHhhhcccCCCCEEEEEeeeccHHHHHHhhccccccccchhHHHHHHHHHHhhc
Confidence            9999999999999999999999999999999999999999999999999999999988 999999999999999875

>TIGR01506 ribC_arch riboflavin synthase

Probab=100.00  E-value=7.7e-47  Score=313.24  Aligned_cols=132  Identities=16%  Similarity=0.156  Sum_probs=125.9

Q ss_pred             EEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEeeeeeCCchhHHHHH
Q 027801           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVVRGDTTHYDAVA  156 (218)
Q Consensus        77 RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~VIrGeT~H~e~Va  156 (218)
                      ||+|+.+.|-+.   .|+++|+++|+++| ...+|+++||||+||||+++++|+++++|||||||||||||+|+||||| 
T Consensus         1 ~~~~~~ttf~~~---~M~~gA~~~L~~~g-~g~~i~v~~VPGa~EiP~aak~l~~~~~~DaVIaLG~VIrGeT~Hfd~V-   75 (151)
T TIGR01506         1 KVGIADTTFARY---DMGGAAIDELRKHT-AGIKIIRRTVPGIKDLPVAAKKLLEEEGCEMVITLGWVGPEEKDKLSYH-   75 (151)
T ss_pred             Ccceecchhhhh---hHHHHHHHHHHhcC-CCCeEEEEECCcHhHHHHHHHHHHhcCCCCEEEEeceEEcCCCCcEeHH-
Confidence            589999999998   99999999999965 3346999999999999999999999899999999999999999999999 


Q ss_pred             HHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHhhCCCCCCcHHHHHHHHHHHHHHHhh
Q 027801          157 NSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGKSGNKGAEAALTAIEMASLFEH  215 (218)
Q Consensus       157 ~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~Rag~k~gnKG~EAA~aAleM~~L~~~  215 (218)
                       ++++|||++++++++||+| |||++|+|||++|++.+.+|||+|||.+||+|+.++++
T Consensus        76 -~vs~GL~~lsl~~~~PVi~-VlT~e~eeQA~~Rag~~~~nkG~eaA~aaleMi~l~~~  132 (151)
T TIGR01506        76 -EASTGLIQVQLMTNKHVID-VTVHEDEAEDPEELKVLADNRAREHAQNLIMLLFKPDR  132 (151)
T ss_pred             -HHHHHHHHHHhhhCCCEEE-EEeeCCHHHHHHHhcccccChHHHHHHHHHHHHHHHHH
Confidence             9999999999999999999 99999999999999999999999999999999999765

This archaeal protein catalyzes the same reaction, the final step in riboflavin biosynthesis, as bacterial riboflavin biosynthesis alpha chain. However, it is more similar in sequence to 6,7-dimethyl-8-ribityllumazine synthase, which catalyzes the previous reaction and which (in bacteria) is called the riboflavin synthase beta chain.

>PRK06455 riboflavin synthase; Provisional

Probab=100.00  E-value=2.4e-33  Score=233.53  Aligned_cols=126  Identities=17%  Similarity=0.226  Sum_probs=108.5

Q ss_pred             CEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEeeeeeCCchhHHHH
Q 027801           76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVVRGDTTHYDAV  155 (218)
Q Consensus        76 ~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~VIrGeT~H~e~V  155 (218)
                      .||+||+|+||+.   .|+++|+++|+++| ...+|++++|||+||||+++++|+++++||||||||||  |+|+|||||
T Consensus         2 ~kigIV~s~fn~~---~L~~gAi~~L~~~g-~~~~I~v~~VPGa~ELP~aakkL~~~~~yDaVIaLG~V--G~t~h~d~V   75 (155)
T PRK06455          2 MKIGIADTTFARV---DMGSAAIDELRKLD-PSAKIIRYTVPGIKDLPVAAKKLIEEEGCDIVMALGMP--GPTEKDKYC   75 (155)
T ss_pred             cEEEEEEEecchH---HHHHHHHHHHHhcC-CCCceEEEECCCHHHHHHHHHHHHhcCCCCEEEEecce--eccCcchhH
Confidence            5999999999997   79999999999988 44689999999999999999999999999999999999  899999999


Q ss_pred             HHHHHHHHHHhchhcCCceEEEEcCCC---CHHHHHHhhCCCCCCcHHHHHHHHHHHHH
Q 027801          156 ANSAASGVLSAGVNSGVPCIFGVLTCD---NMDQALNRAGGKSGNKGAEAALTAIEMAS  211 (218)
Q Consensus       156 a~~vs~gLm~lsL~~~vPVifGVLT~~---n~eQA~~Rag~k~gnKG~EAA~aAleM~~  211 (218)
                      |+++++|||++|+++++||+|.-+--+   ++++-..-    ..||.+|-|..++.|+.
T Consensus        76 a~~vS~GL~~lsL~t~~PVi~v~vhede~~~~~~l~~~----~~~r~~~h~~n~~~~~~  130 (155)
T PRK06455         76 AHEASIGLIMAQLMTNKHIIEVFVHEDEAKDEKELKEL----AEDRAREHAENLVKLLF  130 (155)
T ss_pred             HHHHHHHHHHHHhhhCCCEEEEEecccccCCHHHHHHH----HHHHHHHHHHHHHHHHh
Confidence            999999999999999999999877632   22221111    23566888888888764

>COG1731 Archaeal riboflavin synthase [Coenzyme metabolism]

Probab=99.61  E-value=2.1e-15  Score=123.97  Aligned_cols=126  Identities=18%  Similarity=0.169  Sum_probs=106.3

Q ss_pred             CEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEeeeeeCCchhHHHH
Q 027801           76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVVRGDTTHYDAV  155 (218)
Q Consensus        76 ~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~VIrGeT~H~e~V  155 (218)
                      .+|+|+.+.|.+.   .|-.-|+++|+++-.. -.|..++|||..+||+++++|++..+||+||+||+|  |.|.-+.|.
T Consensus         2 ~kvGiaDTTFaRv---dMg~vai~~lk~~~~~-~~i~R~TVPGIKdlpvaakrLieeeGCd~Vi~lG~~--G~t~~Dk~~   75 (154)
T COG1731           2 TKVGIADTTFARV---DMGSVAIDELKKLLPG-IKIKRYTVPGIKDLPVAAKRLIEEEGCDIVIALGWV--GPTEKDKYS   75 (154)
T ss_pred             ceeeeeccceeee---cchHHHHHHHHhhCCC-CceEEeeCCCcccChHHHHHHHHhcCCcEEEEccCc--CcchhhHHH
Confidence            4899999999998   8899999999998543 479999999999999999999999999999999999  999999999


Q ss_pred             HHHHHHHHHHhchhcCCceEEEEcCCC---CHHHHHHhhCCCCCCcHHHHHHHHHHHHH
Q 027801          156 ANSAASGVLSAGVNSGVPCIFGVLTCD---NMDQALNRAGGKSGNKGAEAALTAIEMAS  211 (218)
Q Consensus       156 a~~vs~gLm~lsL~~~vPVifGVLT~~---n~eQA~~Rag~k~gnKG~EAA~aAleM~~  211 (218)
                      +.+.+.||+.+|+.+|+.||..-+--+   ++++-.+-    ..||.+|-|...++|+.
T Consensus        76 ~~~aS~GLi~~QlmTn~hiidV~VHEDEa~dekeL~~l----a~~RareHa~Nlv~ll~  130 (154)
T COG1731          76 YLAASIGLIMAQLMTNKHIIDVTVHEDEAEDEKELKEL----AVDRAREHAENLVKLLF  130 (154)
T ss_pred             HHHHhhHHHHHHHHcCCeEEEEEeeccccCCHHHHHHH----HHHHHHHHHHHHHHHHh
Confidence            999999999999999999998766532   22221111    13556888888888864

>PF04392 ABC_sub_bind: ABC transporter substrate binding protein; InterPro: IPR007487 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems

Probab=95.70  E-value=0.13  Score=45.61  Aligned_cols=87  Identities=17%  Similarity=0.348  Sum_probs=52.6

Q ss_pred             EEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEe--CCcch-HHHHHHHhhhcCCccEEEEEeeeeeCCchhHH
Q 027801           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWV--PGSFE-IGVVAQQLGKSGKYTAVLCIGAVVRGDTTHYD  153 (218)
Q Consensus        77 RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~V--PGA~E-LP~aak~L~~~~~yDaVIaLG~VIrGeT~H~e  153 (218)
                      ||||++.--|+.+. ...+|.++.|++.|+.++++++..-  -|-.+ ++-.++++ ...++|-||++|.-      =  
T Consensus         1 ~v~i~~~~~~~~~~-~~~~gf~~~L~~~g~~~~~~~~~~~~a~~d~~~~~~~~~~l-~~~~~DlIi~~gt~------a--   70 (294)
T PF04392_consen    1 KVGILQFISHPALD-DIVRGFKDGLKELGYDEKNVEIEYKNAEGDPEKLRQIARKL-KAQKPDLIIAIGTP------A--   70 (294)
T ss_dssp             EEEEEESS--HHHH-HHHHHHHHHHHHTT--CCCEEEEEEE-TT-HHHHHHHHHHH-CCTS-SEEEEESHH------H--
T ss_pred             CeEEEEEeccHHHH-HHHHHHHHHHHHcCCccccEEEEEecCCCCHHHHHHHHHHH-hcCCCCEEEEeCcH------H--
Confidence            79999999888755 5589999999999998766665433  34333 44444444 46789999999753      1  


Q ss_pred             HHHHHHHHHHHHhchhcCCceEEEEcC
Q 027801          154 AVANSAASGVLSAGVNSGVPCIFGVLT  180 (218)
Q Consensus       154 ~Va~~vs~gLm~lsL~~~vPVifGVLT  180 (218)
                            ++.+.+- +..++||+|.-++
T Consensus        71 ------a~~~~~~-~~~~iPVVf~~V~   90 (294)
T PF04392_consen   71 ------AQALAKH-LKDDIPVVFCGVS   90 (294)
T ss_dssp             ------HHHHHHH--SS-S-EEEECES
T ss_pred             ------HHHHHHh-cCCCcEEEEEecc
Confidence                  2222222 2223999998885

ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. This family contains many hypothetical proteins and some ABC transporter substrate binding proteins.; PDB: 3LFT_A 3LKV_A.

>cd01541 PBP1_AraR Ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a member of the LacI-GalR family of bacterial transcription regulators

Probab=94.68  E-value=0.37  Score=40.57  Aligned_cols=62  Identities=5%  Similarity=0.053  Sum_probs=44.1

Q ss_pred             EEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHHhhhcCCccEEEEEee
Q 027801           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        78 IaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~L~~~~~yDaVIaLG~  143 (218)
                      ||+|...++...-..+++++.++++++|+.   +.+.....-.+.. -+++.+. ..++||+|..+.
T Consensus         2 igvv~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~i~~l~-~~~vdgii~~~~   64 (273)
T cd01541           2 IGVITTYISDYIFPSIIRGIESVLSEKGYS---LLLASTNNDPERERKCLENML-SQGIDGLIIEPT   64 (273)
T ss_pred             eEEEeCCccchhHHHHHHHHHHHHHHcCCE---EEEEeCCCCHHHHHHHHHHHH-HcCCCEEEEecc
Confidence            789999999988899999999999999874   5444433333322 2334443 467999997653

Ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of AraR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which i

>PRK11041 DNA-binding transcriptional regulator CytR; Provisional

Probab=94.59  E-value=0.18  Score=43.34  Aligned_cols=69  Identities=12%  Similarity=0.059  Sum_probs=50.6

Q ss_pred             CCCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEee
Q 027801           72 KNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        72 ~~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~  143 (218)
                      ..+..+||+|...+.......|++++.++++++|+.   +.+.......+....+-+.+...++||||..++
T Consensus        32 ~~~~~~ig~v~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~i~~l~~~~vDgiIi~~~  100 (309)
T PRK11041         32 RNESRTILVIVPDICDPFFSEIIRGIEVTAAEHGYL---VLIGDCAHQNQQEKTFVNLIITKQIDGMLLLGS  100 (309)
T ss_pred             cCCCcEEEEEeCCCcCccHHHHHHHHHHHHHHCCCE---EEEEeCCCChHHHHHHHHHHHHcCCCEEEEecC
Confidence            345578999999988888899999999999999973   555444444444444333345578999999875

>cd06300 PBP1_ABC_sugar_binding_like_1 Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily

Probab=94.35  E-value=0.54  Score=39.54  Aligned_cols=64  Identities=8%  Similarity=0.020  Sum_probs=47.0

Q ss_pred             EEEEEEcccCHHHHHHHHHHHHHHHHHC---CCCCCCeEEEEeCCcchHHHHHHHh--hhcCCccEEEEEee
Q 027801           77 RFALVVARFNELVTKLLLEGALETFKKY---SVKEENIDVVWVPGSFEIGVVAQQL--GKSGKYTAVLCIGA  143 (218)
Q Consensus        77 RIaIV~Srfn~~It~~Ll~gA~~~L~~~---Gv~~e~I~vv~VPGA~ELP~aak~L--~~~~~yDaVIaLG~  143 (218)
                      |||+|...+.......++++..+.++++   |.   +++++..+...+-....+.+  +...++||||..++
T Consensus         1 ~Ig~i~~~~~~~~~~~~~~~i~~~~~~~~~~g~---~~~l~i~~~~~~~~~~~~~~~~~~~~~vdgiIi~~~   69 (272)
T cd06300           1 KIGLSNSYAGNTWRAQMLDEFKAQAKELKKAGL---ISEFIVTSADGDVAQQIADIRNLIAQGVDAIIINPA   69 (272)
T ss_pred             CeEEeccccCChHHHHHHHHHHHHHHhhhccCC---eeEEEEecCCCCHHHHHHHHHHHHHcCCCEEEEeCC
Confidence            7899998888888889999999999999   75   34556566665544433332  23459999999764

Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their substrate specificity is not known in detail.

>cd06320 PBP1_allose_binding Periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis

Probab=94.33  E-value=0.39  Score=40.42  Aligned_cols=62  Identities=19%  Similarity=0.278  Sum_probs=43.8

Q ss_pred             EEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH---HHHHHhhhcCCccEEEEEe
Q 027801           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGKSGKYTAVLCIG  142 (218)
Q Consensus        77 RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP---~aak~L~~~~~yDaVIaLG  142 (218)
                      |||+|...+.......|++++.++++++|+.   +.+...++..+..   -+++.+. ..++||+|..+
T Consensus         1 ~igvi~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~~~i~~l~-~~~vdgiIi~~   65 (275)
T cd06320           1 KYGVVLKTLSNEFWRSLKEGYENEAKKLGVS---VDIQAAPSEGDQQGQLSIAENMI-NKGYKGLLFSP   65 (275)
T ss_pred             CeeEEEecCCCHHHHHHHHHHHHHHHHhCCe---EEEEccCCCCCHHHHHHHHHHHH-HhCCCEEEECC
Confidence            6899999999889999999999999999974   5555444332221   1233443 45799998643

Periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis. The members of this group are belonging to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Like other periplasmic receptors of the ABC-type transport systems, the allose-binding protein consists of two alpha/beta domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding.

>cd06318 PBP1_ABC_sugar_binding_like_9 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems

Probab=94.10  E-value=0.48  Score=39.96  Aligned_cols=61  Identities=10%  Similarity=0.030  Sum_probs=43.4

Q ss_pred             EEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcch--HH-HHHHHhhhcCCccEEEEEee
Q 027801           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE--IG-VVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        77 RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~E--LP-~aak~L~~~~~yDaVIaLG~  143 (218)
                      |||+|+..+....-..++++..++++++|+.     +.......+  .. -.++.+ ...++||||..++
T Consensus         1 ~igv~~~~~~~~~~~~~~~~i~~~~~~~g~~-----v~~~~~~~~~~~~~~~i~~~-~~~~~Dgiii~~~   64 (282)
T cd06318           1 KIGFSQYTLNSPFFAALTEAAKAHAKALGYE-----LISTDAQGDLTKQIADVEDL-LTRGVNVLIINPV   64 (282)
T ss_pred             CeeEEeccccCHHHHHHHHHHHHHHHHcCCE-----EEEEcCCCCHHHHHHHHHHH-HHcCCCEEEEecC
Confidence            6899999888888999999999999999973     333333222  22 123444 4578999998653

Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.

>cd06305 PBP1_methylthioribose_binding_like Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily

Probab=94.03  E-value=0.4  Score=40.09  Aligned_cols=60  Identities=17%  Similarity=0.041  Sum_probs=43.2

Q ss_pred             EEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHH---HHhhhcCCccEEEEEe
Q 027801           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVA---QQLGKSGKYTAVLCIG  142 (218)
Q Consensus        77 RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aa---k~L~~~~~yDaVIaLG  142 (218)
                      |||+|...+.......++++..++++++|+.   +.+  ++..++.....   +.+. ..++||+|+..
T Consensus         1 ~Ig~i~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~--~~~~~~~~~~~~~l~~~~-~~~vdgii~~~   63 (273)
T cd06305           1 RIAVVRYGGSGDFDQAYLAGTKAEAEALGGD---LRV--YDAGGDDAKQADQIDQAI-AQKVDAIIIQH   63 (273)
T ss_pred             CeEEEeecCCCcHHHHHHHHHHHHHHHcCCE---EEE--ECCCCCHHHHHHHHHHHH-HcCCCEEEEec
Confidence            5899998888888889999999999999874   444  44555543322   3333 45799999875

Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. The sugar-binding domain of the periplasmic proteins in this group is also homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR), DNA-binding transcriptional repressors such as LacI and GalR.

>cd06301 PBP1_rhizopine_binding_like Periplasmic binding proteins specific to rhizopines

Probab=93.89  E-value=0.52  Score=39.49  Aligned_cols=82  Identities=16%  Similarity=0.291  Sum_probs=52.7

Q ss_pred             EEEEEEcccCHHHHHHHHHHHHHHHHH-CCCCCCCeEEEEeCCcchHHH---HHHHhhhcCCccEEEEEeeeeeCCchhH
Q 027801           77 RFALVVARFNELVTKLLLEGALETFKK-YSVKEENIDVVWVPGSFEIGV---VAQQLGKSGKYTAVLCIGAVVRGDTTHY  152 (218)
Q Consensus        77 RIaIV~Srfn~~It~~Ll~gA~~~L~~-~Gv~~e~I~vv~VPGA~ELP~---aak~L~~~~~yDaVIaLG~VIrGeT~H~  152 (218)
                      ||++|...+.+..-..+.+++.+.+++ .|+     +++...+..+.--   .++.+. ..++||+|..++-    +.  
T Consensus         1 ~igvi~~~~~~~~~~~~~~gi~~~~~~~~~~-----~~~~~~~~~~~~~~~~~i~~l~-~~~vdgiii~~~~----~~--   68 (272)
T cd06301           1 KIGVSMANFDDNFLTLLRNAMKEHAKVLGGV-----ELQFEDAKNDVATQLSQVENFI-AQGVDAIIVVPVD----TA--   68 (272)
T ss_pred             CeeEeecccCCHHHHHHHHHHHHHHHHcCCc-----EEEEeCCCCCHHHHHHHHHHHH-HcCCCEEEEecCc----hh--
Confidence            689999999888899999999999999 775     3444444332221   223333 4579999987752    11  


Q ss_pred             HHHHHHHHHHHHHhchhcCCceEE
Q 027801          153 DAVANSAASGVLSAGVNSGVPCIF  176 (218)
Q Consensus       153 e~Va~~vs~gLm~lsL~~~vPVif  176 (218)
                            ....+.+.-.+.++|+++
T Consensus        69 ------~~~~~~~~l~~~~iPvv~   86 (272)
T cd06301          69 ------ATAPIVKAANAAGIPLVY   86 (272)
T ss_pred             ------hhHHHHHHHHHCCCeEEE
Confidence                  111223333567889874

Periplasmic binding proteins specific to rhizopines, which are simple sugar-like compounds produced in the nodules induced by the symbiotic root nodule bacteria, such as Rhizobium and Sinorhizobium. Rhizopine-binding-like proteins from other bacteria are also included. Two inositol based rhizopine compounds are known to date: L-3-O-methly-scyllo-inosamine (3-O-MSI) and scyllo-inosamine. Bacterial strains that can metabolize rhizopine have a greater competitive advantage in nodulation and rhizopine synthesis is regulated by NifA/NtrA regulatory transcription activators which are maximally expressed at the onset of nitrogen fixation in bacteroids. The members of this group belong to the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily.

>cd06325 PBP1_ABC_uncharacterized_transporter Type I periplasmic ligand-binding domain of uncharacterized ABC-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions

Probab=93.87  E-value=0.36  Score=40.54  Aligned_cols=117  Identities=16%  Similarity=0.158  Sum_probs=67.4

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEeeeeeCCchhHH
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVVRGDTTHYD  153 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~VIrGeT~H~e  153 (218)
                      ...||+++....+ .......++..+.++++|+.   +........-+.=-+++++..  ..|+|+|.+          |
T Consensus       130 g~~~i~~l~~~~~-~~~~~r~~g~~~~~~~~g~~---~~~~~~~~~~~~~~~~~~~~~--~~dai~~~~----------d  193 (281)
T cd06325         130 DAKTVGVLYNPSE-ANSVVQVKELKKAAAKLGIE---VVEATVSSSNDVQQAAQSLAG--KVDAIYVPT----------D  193 (281)
T ss_pred             CCcEEEEEeCCCC-ccHHHHHHHHHHHHHhCCCE---EEEEecCCHHHHHHHHHHhcc--cCCEEEEcC----------c
Confidence            4568999976544 22445678999999998874   222223333333234445543  369988743          4


Q ss_pred             HHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHH---HHhhCCCCCCcHHHHHHHHHHHH
Q 027801          154 AVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQA---LNRAGGKSGNKGAEAALTAIEMA  210 (218)
Q Consensus       154 ~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA---~~Rag~k~gnKG~EAA~aAleM~  210 (218)
                      ..+..+.+.+.+..++.++|    |++.++...+   +....-....-|.+|+..+++++
T Consensus       194 ~~a~~~~~~~~~~~~~~~ip----vig~d~~~~~~~~l~tv~~~~~~~G~~a~~~l~~~l  249 (281)
T cd06325         194 NTVASAMEAVVKVANEAKIP----VIASDDDMVKRGGLATYGIDYYELGRQTGKMAAKIL  249 (281)
T ss_pred             hhHHhHHHHHHHHHHHcCCC----EEEcCHHHHhCCceEEecCCHHHHHHHHHHHHHHHH
Confidence            46777888888888777899    4454444321   11111112345666666666654

This group includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); its ligand specificity has not been determined experimentally.

>TIGR01481 ccpA catabolite control protein A

Probab=93.86  E-value=0.52  Score=41.11  Aligned_cols=67  Identities=13%  Similarity=0.157  Sum_probs=47.7

Q ss_pred             CCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHH-HHHhhhcCCccEEEEEee
Q 027801           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVV-AQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~a-ak~L~~~~~yDaVIaLG~  143 (218)
                      .+...|+++...+....-..+++++.+.++++|..   +.+.......+.-.. ++.+ ...++||+|..+.
T Consensus        57 ~~~~~Igvv~~~~~~~f~~~l~~~i~~~~~~~g~~---~~i~~~~~~~~~~~~~~~~l-~~~~vdGiIi~~~  124 (329)
T TIGR01481        57 KRTTTVGVIIPDISNIYYAELARGIEDIATMYKYN---IILSNSDEDPEKEVQVLNTL-LSKQVDGIIFMGG  124 (329)
T ss_pred             CCCCEEEEEeCCCCchhHHHHHHHHHHHHHHcCCE---EEEEeCCCCHHHHHHHHHHH-HhCCCCEEEEeCC
Confidence            34567999999888788889999999999999973   555444444433322 2344 4578999998874

Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.

>cd06310 PBP1_ABC_sugar_binding_like_2 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems

Probab=93.66  E-value=0.59  Score=39.19  Aligned_cols=63  Identities=16%  Similarity=0.096  Sum_probs=42.5

Q ss_pred             EEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH---HHHHHhhhcCCccEEEEEee
Q 027801           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        77 RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP---~aak~L~~~~~yDaVIaLG~  143 (218)
                      |||+|+..+.......++.++.+.++++|..   +.++......+..   -.++.+ ...++||+|..++
T Consensus         1 ~Igvi~~~~~~~~~~~~~~g~~~~~~~~g~~---~~~~~~~~~~~~~~~~~~i~~l-~~~~vdgvii~~~   66 (273)
T cd06310           1 KIALVPKGTTSDFWQAVKAGAEAAAKELGVK---VTFQGPASETDVAGQVNLLENA-IARGPDAILLAPT   66 (273)
T ss_pred             CeEEEecCCCcHHHHHHHHHHHHHHHHcCCE---EEEecCccCCCHHHHHHHHHHH-HHhCCCEEEEcCC
Confidence            7999999987777789999999999999874   3333221122222   223334 3468999998654

Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.

>cd06319 PBP1_ABC_sugar_binding_like_10 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems

Probab=93.63  E-value=0.63  Score=39.03  Aligned_cols=61  Identities=8%  Similarity=0.016  Sum_probs=43.6

Q ss_pred             EEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH---HHHHHhhhcCCccEEEEEee
Q 027801           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        77 RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP---~aak~L~~~~~yDaVIaLG~  143 (218)
                      |||+|...+....-..+++++.+.++++|+.   +  +.+++..+-.   -+++.+. ..++||+|..++
T Consensus         1 ~i~vi~~~~~~~~~~~~~~~i~~~~~~~g~~---~--~~~~~~~~~~~~~~~i~~~~-~~~~dgiii~~~   64 (277)
T cd06319           1 QIAYIVSDLRIPFWQIMGRGVKSKAKALGYD---A--VELSAENSAKKELENLRTAI-DKGVSGIIISPT   64 (277)
T ss_pred             CeEEEeCCCCchHHHHHHHHHHHHHHhcCCe---E--EEecCCCCHHHHHHHHHHHH-hcCCCEEEEcCC
Confidence            6899999888888999999999999999874   3  3344433222   3344443 467999987653

Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.

>cd01391 Periplasmic_Binding_Protein_Type_1 Type 1 periplasmic binding fold superfamily

Probab=93.60  E-value=0.75  Score=36.66  Aligned_cols=85  Identities=9%  Similarity=0.092  Sum_probs=55.4

Q ss_pred             EEEEEEccc-CHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchH--H-HHHHHhhhcCCccEEEEEeeeeeCCchhH
Q 027801           77 RFALVVARF-NELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEI--G-VVAQQLGKSGKYTAVLCIGAVVRGDTTHY  152 (218)
Q Consensus        77 RIaIV~Srf-n~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~EL--P-~aak~L~~~~~yDaVIaLG~VIrGeT~H~  152 (218)
                      |||++...+ +......+.+++.+.+++.|.   ++++..+....+-  . -.++++. ..++|++|..++.-      .
T Consensus         1 ~Ig~i~~~~~~~~~~~~~~~~~~~~~~~~g~---~~~~~~~~~~~~~~~~~~~~~~~~-~~~~d~ii~~~~~~------~   70 (269)
T cd01391           1 KIGVLLPLSGSAPFGAQLLAGIELAAEEIGR---GLEVILADSQSDPERALEALRDLI-QQGVDGIIGPPSSS------S   70 (269)
T ss_pred             CceEEeecCCCcHHHHHHHHHHHHHHHHhCC---ceEEEEecCCCCHHHHHHHHHHHH-HcCCCEEEecCCCH------H
Confidence            588898888 677888999999999999432   3456666665542  2 3334444 45899999988741      1


Q ss_pred             HHHHHHHHHHHHHhchhcCCceEEEE
Q 027801          153 DAVANSAASGVLSAGVNSGVPCIFGV  178 (218)
Q Consensus       153 e~Va~~vs~gLm~lsL~~~vPVifGV  178 (218)
                      .   .    .+.+...+.++|+++--
T Consensus        71 ~---~----~~~~~~~~~~ip~v~~~   89 (269)
T cd01391          71 A---L----AVVELAAAAGIPVVSLD   89 (269)
T ss_pred             H---H----HHHHHHHHcCCcEEEec
Confidence            0   0    13444456788987753

Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins con

>cd06284 PBP1_LacI_like_6 Ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria

Probab=93.53  E-value=0.45  Score=39.44  Aligned_cols=62  Identities=6%  Similarity=0.035  Sum_probs=44.0

Q ss_pred             EEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcch--HHHHHHHhhhcCCccEEEEEeee
Q 027801           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE--IGVVAQQLGKSGKYTAVLCIGAV  144 (218)
Q Consensus        78 IaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~E--LP~aak~L~~~~~yDaVIaLG~V  144 (218)
                      |++|...+.......+.++..+.++++|..   +.+  .+...+  .-..+-..+...++||+|..++.
T Consensus         2 i~~v~~~~~~~~~~~~~~~i~~~~~~~g~~---~~~--~~~~~~~~~~~~~~~~~~~~~vdgiii~~~~   65 (267)
T cd06284           2 ILVLVPDIANPFFSEILKGIEDEAREAGYG---VLL--GDTRSDPEREQEYLDLLRRKQADGIILLDGS   65 (267)
T ss_pred             EEEEECCCCCccHHHHHHHHHHHHHHcCCe---EEE--ecCCCChHHHHHHHHHHHHcCCCEEEEecCC
Confidence            788999999888899999999999999873   433  333333  12222233456789999997753

This group includes the ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria. This group belongs to the the LacI-GalR family repressors and are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding.

>PF13377 Peripla_BP_3: Periplasmic binding protein-like domain; PDB: 3K9C_B 3BIL_B 3JVD_B 1ZAY_A 1VPW_A 1DBQ_A 2PUA_A 1QQA_A 1PNR_A 1JHZ_A

Probab=93.43  E-value=0.71  Score=35.80  Aligned_cols=100  Identities=22%  Similarity=0.226  Sum_probs=67.5

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHH-HhhhcCCccEEEEEeeeeeCCchhHH
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQ-QLGKSGKYTAVLCIGAVVRGDTTHYD  153 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak-~L~~~~~yDaVIaLG~VIrGeT~H~e  153 (218)
                      -.||+++...-+.......++|..+.++++|++..... +..++..+-..... .++++.++|||||..          +
T Consensus         9 ~r~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~l~~~~pdaii~~~----------~   77 (160)
T PF13377_consen    9 HRRIAFIGGPPNSSVSRERLEGFREALKEHGIEFEELI-FFSDDDSEDAREAQLLWLRRLRPDAIICSN----------D   77 (160)
T ss_dssp             -SSEEEEESSTTSHHHHHHHHHHHHHHHHTTSEEEGEE-EEESSSHHHHHHHHHHHHHTCSSSEEEESS----------H
T ss_pred             CCeEEEEecCCCChhHHHHHHHHHHHHHHCCCCCCeeE-eecCCcchhHHHHHHHHHhcCCCcEEEEcC----------H
Confidence            45899999888889999999999999999999744433 33444443333332 234545789999843          4


Q ss_pred             HHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHH
Q 027801          154 AVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQA  187 (218)
Q Consensus       154 ~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA  187 (218)
                      .++..+.+.+.+..++  +|==.+|++.++...+
T Consensus        78 ~~a~~~~~~l~~~g~~--vP~di~vv~~~~~~~~  109 (160)
T PF13377_consen   78 RLALGVLRALRELGIR--VPQDISVVSFDDSPLL  109 (160)
T ss_dssp             HHHHHHHHHHHHTTSC--TTTTSEEEEESSSGHH
T ss_pred             HHHHHHHHHHHHcCCc--ccccccEEEecCcHHH
Confidence            5788888888887664  4433356666654443

...

>cd01575 PBP1_GntR Ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators

Probab=93.23  E-value=0.95  Score=37.51  Aligned_cols=63  Identities=16%  Similarity=0.110  Sum_probs=42.8

Q ss_pred             EEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHHhhhcCCccEEEEEeee
Q 027801           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGAV  144 (218)
Q Consensus        78 IaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~L~~~~~yDaVIaLG~V  144 (218)
                      ||+|...+....-..++++..++++++|+.   +.++.....-+-. -.++.+ ...++||+|..++-
T Consensus         2 Ig~i~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~~~~l-~~~~vdgiii~~~~   65 (268)
T cd01575           2 VAVLVPSLSNSVFADVLQGISDVLEAAGYQ---LLLGNTGYSPEREEELLRTL-LSRRPAGLILTGLE   65 (268)
T ss_pred             EEEEeCCCcchhHHHHHHHHHHHHHHcCCE---EEEecCCCCchhHHHHHHHH-HHcCCCEEEEeCCC
Confidence            788998888888889999999999999873   4333322211211 223444 35779999998753

This group represents the ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of GntR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding,

>cd06317 PBP1_ABC_sugar_binding_like_8 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems

Probab=93.10  E-value=0.86  Score=38.06  Aligned_cols=61  Identities=8%  Similarity=0.020  Sum_probs=44.4

Q ss_pred             EEEEEccc-CHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHh--hhcCCccEEEEEee
Q 027801           78 FALVVARF-NELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQL--GKSGKYTAVLCIGA  143 (218)
Q Consensus        78 IaIV~Srf-n~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L--~~~~~yDaVIaLG~  143 (218)
                      |++|...+ +......+++++.++++++|+.     ++..+..++..-..+.+  +...++||+|..++
T Consensus         2 i~vi~p~~~~~~~~~~~~~g~~~~~~~~g~~-----~~~~~~~~~~~~~~~~~~~l~~~~vdgiii~~~   65 (275)
T cd06317           2 IGYTQNNVGSHSYQTTYNKAFQAAAEEDGVE-----VIVLDANGDVARQAAQVEDLIAQKVDGIILWPT   65 (275)
T ss_pred             eEEEecccCCCHHHHHHHHHHHHHHHhcCCE-----EEEEcCCcCHHHHHHHHHHHHHcCCCEEEEecC
Confidence            78888888 8888999999999999998863     33345555555443332  23457999998764

Pperiplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.

>cd06273 PBP1_GntR_like_1 This group includes the ligand-binding domain of putative DNA transcription repressors which are highly similar to that of the repressor specific for gluconate (GntR), a member of the LacI-GalR family of bacterial transcription regulators

Probab=92.99  E-value=0.87  Score=37.96  Aligned_cols=62  Identities=13%  Similarity=0.112  Sum_probs=42.8

Q ss_pred             EEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHHhhhcCCccEEEEEee
Q 027801           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        78 IaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~L~~~~~yDaVIaLG~  143 (218)
                      ||+|...++...-..++++..++++++|+.   +.+..-....+.- -.++.|. +.++||+|..++
T Consensus         2 i~vv~p~~~~~~~~~~~~~i~~~~~~~g~~---~~~~~~~~~~~~~~~~~~~l~-~~~vdgiii~~~   64 (268)
T cd06273           2 IGAIVPTLDNAIFARVIQAFQETLAAHGYT---LLVASSGYDLDREYAQARKLL-ERGVDGLALIGL   64 (268)
T ss_pred             eEEEeCCCCCchHHHHHHHHHHHHHHCCCE---EEEecCCCCHHHHHHHHHHHH-hcCCCEEEEeCC
Confidence            789998888888889999999999999873   4443222222322 2334554 457999998765

This group includes the ligand-binding domain of putative DNA transcription repressors which are highly similar to that of the repressor specific for gluconate (GntR), a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational

>cd06316 PBP1_ABC_sugar_binding_like_7 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems

Probab=92.96  E-value=0.93  Score=38.94  Aligned_cols=62  Identities=16%  Similarity=0.201  Sum_probs=42.7

Q ss_pred             EEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHh--hhcCCccEEEEEe
Q 027801           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQL--GKSGKYTAVLCIG  142 (218)
Q Consensus        77 RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L--~~~~~yDaVIaLG  142 (218)
                      ||++|+..++......++++..++++++|+.   +.++. ++.++...-.+.+  +..+++||+|..+
T Consensus         1 ~i~~i~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~-~~~~~~~~~~~~l~~~~~~~~dgiii~~   64 (294)
T cd06316           1 KAAIVMHTSGSDWSNAQVRGAKDEFAKLGIE---VVATT-DAQFDPAKQVADIETTISQKPDIIISIP   64 (294)
T ss_pred             CeEEEecCCCChHHHHHHHHHHHHHHHcCCE---EEEec-CCCCCHHHHHHHHHHHHHhCCCEEEEcC
Confidence            7899999998888889999999999999873   33222 4444433222222  1246799998765

Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.

>cd01539 PBP1_GGBP Periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species

Probab=92.91  E-value=0.99  Score=39.42  Aligned_cols=61  Identities=7%  Similarity=0.047  Sum_probs=43.3

Q ss_pred             EEEEEEcccCHHHHHHHHHHHHHHHHH--CCCCCCCeEEEEeCCcch--HH-HHHHHhhhcCCccEEEEEee
Q 027801           77 RFALVVARFNELVTKLLLEGALETFKK--YSVKEENIDVVWVPGSFE--IG-VVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        77 RIaIV~Srfn~~It~~Ll~gA~~~L~~--~Gv~~e~I~vv~VPGA~E--LP-~aak~L~~~~~yDaVIaLG~  143 (218)
                      ||++|+..++...-..++++..+++++  .|+     ++...++-.+  -. -.++.+ ...++||+|..++
T Consensus         1 ~Igviv~~~~~~~~~~~~~gi~~~a~~~~~g~-----~~~~~~~~~~~~~q~~~i~~l-~~~~vdgiii~~~   66 (303)
T cd01539           1 KIGVFLYKFDDTFISLVRKNLEDIQKENGGKV-----EFTFYDAKNNQSTQNEQIDTA-LAKGVDLLAVNLV   66 (303)
T ss_pred             CeEEEeeCCCChHHHHHHHHHHHHHHhhCCCe-----eEEEecCCCCHHHHHHHHHHH-HHcCCCEEEEecC
Confidence            689999999988899999999999999  554     4444454332  22 234444 3568999997653

Periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species. GGBP is a member of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic GGBP is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR.

>cd06271 PBP1_AglR_RafR_like Ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators

Probab=92.89  E-value=0.44  Score=39.51  Aligned_cols=63  Identities=17%  Similarity=0.116  Sum_probs=44.8

Q ss_pred             EEEEEcc----cCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEee
Q 027801           78 FALVVAR----FNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        78 IaIV~Sr----fn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~  143 (218)
                      ||||..+    |....-..|+++..+.++++|+.   +.+...+..-+---.+.+++..+++||+|..++
T Consensus         2 igvi~p~~~~~~~~~~~~~~~~~i~~~~~~~g~~---~~~~~~~~~~~~~~~~~~~~~~~~vdgiii~~~   68 (268)
T cd06271           2 IGLVLPTGEREEGDPFFAEFLSGLSEALAEHGYD---LVLLPVDPDEDPLEVYRRLVESGLVDGVIISRT   68 (268)
T ss_pred             eEEEeCCcccccCCccHHHHHHHHHHHHHHCCce---EEEecCCCcHHHHHHHHHHHHcCCCCEEEEecC
Confidence            5777766    56777788999999999999874   666655554333334555556678999998765

Ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the represso

>cd06291 PBP1_Qymf_like Ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs

Probab=92.78  E-value=1  Score=37.63  Aligned_cols=62  Identities=11%  Similarity=0.059  Sum_probs=42.3

Q ss_pred             EEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcch-HHHHHHHhhhcCCccEEEEEee
Q 027801           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE-IGVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        78 IaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~E-LP~aak~L~~~~~yDaVIaLG~  143 (218)
                      |++|...+.......+++++.++++++|+.   +.+....+.-+ .--.++.+ ...++||+|..++
T Consensus         2 I~vi~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~i~~~-~~~~~dgiii~~~   64 (265)
T cd06291           2 IGLIVPTISNPFFSELARAVEKELYKKGYK---LILCNSDNDPEKEREYLEML-RQNQVDGIIAGTH   64 (265)
T ss_pred             EEEEECCCCChhHHHHHHHHHHHHHHCCCe---EEEecCCccHHHHHHHHHHH-HHcCCCEEEEecC
Confidence            788998888888899999999999999874   33333222221 11222333 4567999998875

This group includes the ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs. Qymf is a strict anaerobe that could be grown in the presence of borax and its cells are straight rods that produce endospores. This group is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription

>cd06277 PBP1_LacI_like_1 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors

Probab=92.74  E-value=0.99  Score=37.84  Aligned_cols=63  Identities=16%  Similarity=0.223  Sum_probs=41.5

Q ss_pred             EEEEEcc---cCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEee
Q 027801           78 FALVVAR---FNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        78 IaIV~Sr---fn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~  143 (218)
                      ||+++..   +....-..++++..+.++++|+.   +.+......-+--..+...+...++||||..++
T Consensus         2 vgv~~~~~~~~~~~~~~~~~~~i~~~~~~~g~~---~~~~~~~~~~~~~~~~~~~l~~~~vdgiii~~~   67 (268)
T cd06277           2 IGLIASKRILNSPAFYSEIYRAIEEEAKKYGYN---LILKFVSDEDEEEFELPSFLEDGKVDGIILLGG   67 (268)
T ss_pred             eEEEEeccccccCCcHHHHHHHHHHHHHHcCCE---EEEEeCCCChHHHHHHHHHHHHCCCCEEEEeCC
Confidence            6888877   67777788999999999999873   555444332222222222234578999998774

This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.

>cd01538 PBP1_ABC_xylose_binding Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily

Probab=92.74  E-value=0.98  Score=38.88  Aligned_cols=63  Identities=8%  Similarity=-0.065  Sum_probs=44.0

Q ss_pred             EEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHHhhhcCCccEEEEEee
Q 027801           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        77 RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~L~~~~~yDaVIaLG~  143 (218)
                      .||+|...+.......++++..++++++|+.   +.++.-.+.-+-. -.++.+. ..++||||..++
T Consensus         1 ~I~vi~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~i~~~~-~~~vdgiii~~~   64 (288)
T cd01538           1 KIGLSLPTKTEERWIRDRPNFEAALKELGAE---VIVQNANGDPAKQISQIENMI-AKGVDVLVIAPV   64 (288)
T ss_pred             CeEEEEeCCCcHHHHHHHHHHHHHHHHcCCE---EEEECCCCCHHHHHHHHHHHH-HcCCCEEEEecC
Confidence            4789998888888899999999999999974   4444332222322 3334443 568999998763

Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic xylose-binding protein is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR.

>cd06315 PBP1_ABC_sugar_binding_like_6 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems

Probab=92.62  E-value=1.2  Score=38.09  Aligned_cols=61  Identities=15%  Similarity=0.017  Sum_probs=44.4

Q ss_pred             EEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchH--H-HHHHHhhhcCCccEEEEEee
Q 027801           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEI--G-VVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        77 RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~EL--P-~aak~L~~~~~yDaVIaLG~  143 (218)
                      +||+|...++......++++..++++++|..     ++...+..+-  - -.++.+ ...++||+|..+.
T Consensus         2 ~ig~i~~~~~~~~~~~~~~gi~~~a~~~gy~-----~~~~~~~~~~~~~~~~i~~l-~~~~vdgiil~~~   65 (280)
T cd06315           2 NIIFVASDLKNGGILGVGEGVREAAKAIGWN-----LRILDGRGSEAGQAAALNQA-IALKPDGIVLGGV   65 (280)
T ss_pred             eEEEEecccCCcHHHHHHHHHHHHHHHcCcE-----EEEECCCCCHHHHHHHHHHH-HHcCCCEEEEcCC
Confidence            6899999999988999999999999999873     3334443321  1 223333 4678999999874

Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.

>cd06270 PBP1_GalS_like Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism

Probab=92.61  E-value=0.52  Score=39.51  Aligned_cols=60  Identities=17%  Similarity=0.180  Sum_probs=41.4

Q ss_pred             EEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH---HHHHHhhhcCCccEEEEEee
Q 027801           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        78 IaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP---~aak~L~~~~~yDaVIaLG~  143 (218)
                      |++|...++...-..+++|..++++++|+.   +.+  +++-++..   -.++.+ .++++||||+.++
T Consensus         2 igvi~p~~~~~~~~~~~~g~~~~a~~~g~~---~~~--~~~~~~~~~~~~~i~~~-~~~~vdgii~~~~   64 (268)
T cd06270           2 IGLVVSDLDGPFFGPLLSGVESVARKAGKH---LII--TAGHHSAEKEREAIEFL-LERRCDALILHSK   64 (268)
T ss_pred             EEEEEccccCcchHHHHHHHHHHHHHCCCE---EEE--EeCCCchHHHHHHHHHH-HHcCCCEEEEecC
Confidence            788888888888888889999999998873   333  33333322   223333 3567999999876

Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism. Transcription of the galactose regulon genes is regulated by Gal iso-repressor (GalS) and Gal repressor (GalR) in different ways, but both repressors recognize the same DNA binding site in the absence of D-galactose. GalS is a dimeric protein like GalR,and its major role is in regulating expression of the high-affinity galactose transporter encoded by the mgl operon, whereas GalR is the exclusive regulator of galactose permease, the low-affinity galactose transporter. GalS and GalR are members of the LacI-GalR family of transcription regulators and both contain the type I periplasmic binding protein-like fold. Hence, they are homologous to the periplasmic sugar bindi

>cd01542 PBP1_TreR_like Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators

Probab=92.47  E-value=0.98  Score=37.46  Aligned_cols=60  Identities=13%  Similarity=0.248  Sum_probs=40.8

Q ss_pred             EEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcch---HHHHHHHhhhcCCccEEEEEee
Q 027801           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE---IGVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        78 IaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~E---LP~aak~L~~~~~yDaVIaLG~  143 (218)
                      ||+|...|.......++++..++++++|+.   +.+  .+...+   .--.+++| ...++||+|..+.
T Consensus         2 igvv~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~--~~~~~~~~~~~~~i~~l-~~~~~dgii~~~~   64 (259)
T cd01542           2 IGVIVPRLDSFSTSRTVKGILAALYENGYQ---MLL--MNTNFSIEKEIEALELL-ARQKVDGIILLAT   64 (259)
T ss_pred             eEEEecCCccchHHHHHHHHHHHHHHCCCE---EEE--EeCCCCHHHHHHHHHHH-HhcCCCEEEEeCC
Confidence            688888888888888999999999998863   333  333332   11233444 3578999998764

Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of TreR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding wh

>cd06271 PBP1_AglR_RafR_like Ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators

Probab=92.33  E-value=2.2  Score=35.37  Aligned_cols=101  Identities=17%  Similarity=0.089  Sum_probs=61.2

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHH-HHHHhhhc-CCccEEEEEeeeeeCCchhH
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV-VAQQLGKS-GKYTAVLCIGAVVRGDTTHY  152 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~-aak~L~~~-~~yDaVIaLG~VIrGeT~H~  152 (218)
                      ..||+++...-+......-++|..+.++++|+......++.-+...+-.. +++++++. ..+|||+|.+-         
T Consensus       120 ~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~d---------  190 (268)
T cd06271         120 HRRIALLNPPEDLTFAQHRRAGYRRALAEAGLPLDPALIVSGDMTEEGGYAAAAELLALPDRPTAIVCSSE---------  190 (268)
T ss_pred             CCcEEEecCccccchHHHHHHHHHHHHHHhCCCCCCceEEeCCCChHHHHHHHHHHHhCCCCCCEEEEcCc---------
Confidence            46899998765544445667999999999998643334444333433322 34455444 45899998654         


Q ss_pred             HHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHH
Q 027801          153 DAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQA  187 (218)
Q Consensus       153 e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA  187 (218)
                       .++..+.+.+.+..+.  +|==..|++.++.+.+
T Consensus       191 -~~a~g~~~al~~~g~~--vp~~i~iig~d~~~~~  222 (268)
T cd06271         191 -LMALGVLAALAEAGLR--PGRDVSVVGFDDSPPL  222 (268)
T ss_pred             -HHHHHHHHHHHHhCCC--CCcceeEEEecCchHH
Confidence             2555666677765543  3322345666665544

Ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the represso

>cd06297 PBP1_LacI_like_12 Ligand-binding domain of uncharacterized transcription regulators from Thermus thermophilus and close homologs

Probab=92.29  E-value=0.74  Score=39.03  Aligned_cols=63  Identities=8%  Similarity=0.001  Sum_probs=43.1

Q ss_pred             EEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEee
Q 027801           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        78 IaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~  143 (218)
                      ||+|...+.......|+++..++++++|+.   +.++.....-+..-.+.+++...++||||..++
T Consensus         2 Igvi~p~~~~~~~~~~~~~i~~~~~~~gy~---~~~~~~~~~~~~~~~~~~~l~~~~vdgvi~~~~   64 (269)
T cd06297           2 ISVLLPVVATEFYRRLLEGIEGALLEQRYD---LALFPLLSLARLKRYLESTTLAYLTDGLLLASY   64 (269)
T ss_pred             EEEEeCCCcChhHHHHHHHHHHHHHHCCCE---EEEEeCCCcHHHHHHHHHHHHhcCCCEEEEecC
Confidence            688888887788888999999999998874   444433332223334444445678999988764

Ligand-binding domain of uncharacterized transcription regulators from Thermus thermophilus and close homologs from other bacteria. This group belongs to the the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding.

>cd06293 PBP1_LacI_like_11 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors

Probab=92.15  E-value=2  Score=35.97  Aligned_cols=102  Identities=20%  Similarity=0.164  Sum_probs=60.0

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHHhhh-cCCccEEEEEeeeeeCCchh
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGK-SGKYTAVLCIGAVVRGDTTH  151 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~L~~-~~~yDaVIaLG~VIrGeT~H  151 (218)
                      ...||+++.+.-+......-.+|.++.++++|.......+++.+-.+|-. -.++.+++ ...+|||+|-          
T Consensus       115 G~~~i~~i~~~~~~~~~~~R~~Gf~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~----------  184 (269)
T cd06293         115 GHRRIAFVGGPDALISARERYAGYREALAEAHIPEVPEYVCFGDYTREFGRAAAAQLLARGDPPTAIFAA----------  184 (269)
T ss_pred             CCceEEEEecCcccccHHHHHHHHHHHHHHcCCCCChheEEecCCCHHHHHHHHHHHHcCCCCCCEEEEc----------
Confidence            45689999765443333345699999999999864333444333333322 12344443 3568999984          


Q ss_pred             HHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHH
Q 027801          152 YDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQA  187 (218)
Q Consensus       152 ~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA  187 (218)
                      .+.++..+.+++.+..+  .+|==..|++.++...+
T Consensus       185 ~d~~a~g~~~al~~~g~--~vp~di~i~g~d~~~~~  218 (269)
T cd06293         185 SDEIAIGLLEVLRERGL--SIPGDMSLVGFDDVGPA  218 (269)
T ss_pred             CcHHHHHHHHHHHHcCC--CCccceEEEeecCchHH
Confidence            34566667777776654  34433455666665544

This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.

>cd01540 PBP1_arabinose_binding Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily

Probab=92.12  E-value=0.99  Score=38.28  Aligned_cols=84  Identities=10%  Similarity=0.054  Sum_probs=51.8

Q ss_pred             EEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEeeeeeCCchhHHHHH
Q 027801           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVVRGDTTHYDAVA  156 (218)
Q Consensus        77 RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~VIrGeT~H~e~Va  156 (218)
                      ||++|...+.......+++++.++++++|+.   +.++.....-+.=-.++.+. ..++||+|..++-    +.      
T Consensus         1 ~Ig~v~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~i~~~~-~~~~dgiii~~~~----~~------   66 (289)
T cd01540           1 KIGFIVKQPEEPWFQTEWKFAKKAAKEKGFT---VVKIDVPDGEKVLSAIDNLG-AQGAKGFVICVPD----VK------   66 (289)
T ss_pred             CeeeecCCCCCcHHHHHHHHHHHHHHHcCCE---EEEccCCCHHHHHHHHHHHH-HcCCCEEEEccCc----hh------
Confidence            5889998877777789999999999999974   44332221111112334443 4779999998742    11      


Q ss_pred             HHHHHHHHHhchhcCCceEE
Q 027801          157 NSAASGVLSAGVNSGVPCIF  176 (218)
Q Consensus       157 ~~vs~gLm~lsL~~~vPVif  176 (218)
                        ....+++...+.++||+.
T Consensus        67 --~~~~~~~~~~~~~iPvV~   84 (289)
T cd01540          67 --LGPAIVAKAKAYNMKVVA   84 (289)
T ss_pred             --hhHHHHHHHHhCCCeEEE
Confidence              112233444457888874

Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. ABP is only involved in transport contrary to other related sugar-binding proteins such as the glucose/galactose-binding protein (GGBP) and the ribose-binding protein (RBP), both of which are involved in chemotaxis as well as transport. The periplasmic ABP consists of two alpha/beta globular domains connected by a three-stranded hinge, a Venus flytrap-like domain, which undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, ABP is homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR) and DNA-binding transcriptional repressors such a

>cd01536 PBP1_ABC_sugar_binding_like Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily

Probab=92.08  E-value=0.72  Score=37.89  Aligned_cols=63  Identities=16%  Similarity=0.116  Sum_probs=41.9

Q ss_pred             EEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchH-HHHHHHhhhcCCccEEEEEee
Q 027801           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEI-GVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        77 RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~EL-P~aak~L~~~~~yDaVIaLG~  143 (218)
                      ||++|...+....-..+++++.+.++++|+.   +.++...+.-+- --.++++.. .++||+|..++
T Consensus         1 ~ig~i~p~~~~~~~~~~~~~~~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~l~~-~~vdgvi~~~~   64 (267)
T cd01536           1 KIGLVVPSLNNPFWQAMNKGAEAAAKELGVE---LIVLDAQNDVSKQIQQIEDLIA-QGVDGIIISPV   64 (267)
T ss_pred             CEEEEeccccCHHHHHHHHHHHHHHHhcCce---EEEECCCCCHHHHHHHHHHHHH-cCCCEEEEeCC
Confidence            5888888887778888889999999887763   444444332221 233444543 37899988764

Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily. The members of this family function as the primary receptors for chemotaxis and transport of many sugar based solutes in bacteria and archaea. The sugar binding domain is also homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR. Moreover, this periplasmic binding domain, also known as Venus flytrap domain, undergoes transition from an open to a closed conformational state upon the binding of ligands such as lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. This family also includes the periplasmic binding domain of autoinducer-2 (AI-2

>PRK10014 DNA-binding transcriptional repressor MalI; Provisional

Probab=92.02  E-value=1.9  Score=37.73  Aligned_cols=67  Identities=15%  Similarity=0.074  Sum_probs=46.2

Q ss_pred             CCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcch-HHHHHHHhhhcCCccEEEEEee
Q 027801           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE-IGVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~E-LP~aak~L~~~~~yDaVIaLG~  143 (218)
                      .....|++|...+....-..++++..+.++++|..   +.++......+ ..-.++.| ...++||||..+.
T Consensus        62 ~~~~~Igvv~~~~~~~~~~~i~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~l-~~~~vdgiIi~~~  129 (342)
T PRK10014         62 GQSGVIGLIVRDLSAPFYAELTAGLTEALEAQGRM---VFLLQGGKDGEQLAQRFSTL-LNQGVDGVVIAGA  129 (342)
T ss_pred             CCCCEEEEEeCCCccchHHHHHHHHHHHHHHcCCE---EEEEeCCCCHHHHHHHHHHH-HhCCCCEEEEeCC
Confidence            34567999999888888888999999999999863   33332222222 23334444 3567999999875

>cd06292 PBP1_LacI_like_10 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors

Probab=91.95  E-value=0.79  Score=38.44  Aligned_cols=63  Identities=11%  Similarity=0.102  Sum_probs=41.9

Q ss_pred             EEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHH-HHHhhhcCCccEEEEEeee
Q 027801           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVV-AQQLGKSGKYTAVLCIGAV  144 (218)
Q Consensus        78 IaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~a-ak~L~~~~~yDaVIaLG~V  144 (218)
                      ||+|...+.......++++..+.+++.|+.   +.+..-...-|...- ++.| ...++||+|.+++.
T Consensus         2 Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~i~~l-~~~~vdgiIi~~~~   65 (273)
T cd06292           2 VGLLVPELSNPIFPAFAEAIEAALAQYGYT---VLLCNTYRGGVSEADYVEDL-LARGVRGVVFISSL   65 (273)
T ss_pred             EEEEeCCCcCchHHHHHHHHHHHHHHCCCE---EEEEeCCCChHHHHHHHHHH-HHcCCCEEEEeCCC
Confidence            788888888888888889999999998863   433332222233322 3444 34578988888753

This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.

>cd06307 PBP1_uncharacterized_sugar_binding Periplasmic sugar-binding domain of uncharacterized transport systems

Probab=91.88  E-value=2  Score=36.24  Aligned_cols=64  Identities=9%  Similarity=0.136  Sum_probs=43.2

Q ss_pred             EEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH---HHHHHhhhcCCccEEEEEee
Q 027801           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        77 RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP---~aak~L~~~~~yDaVIaLG~  143 (218)
                      ||++|+..++......+++++.++++++|...-.+ .++.+..++-+   -.++.+ .. ++||+|..+.
T Consensus         1 ~ig~v~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~-~~~~~~~~~~~~~~~~i~~~-~~-~vdgiii~~~   67 (275)
T cd06307           1 RLGFLLPKGSNAFYRELAAALEAAAAAFPDARIRV-RIHFVESFDPAALAAALLRL-GA-RSDGVALVAP   67 (275)
T ss_pred             CeEEEeCCCCChHHHHHHHHHHHHHhhhhccCceE-EEEEccCCCHHHHHHHHHHH-Hh-cCCEEEEeCC
Confidence            68999999999999999999999999998642111 22223333333   222333 34 8999998653

Periplasmic sugar-binding domain of uncharacterized transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. The members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes.

>cd06323 PBP1_ribose_binding Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs

Probab=91.88  E-value=1.4  Score=36.49  Aligned_cols=59  Identities=17%  Similarity=0.179  Sum_probs=41.2

Q ss_pred             EEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHH---HHHHhhhcCCccEEEEEe
Q 027801           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGKSGKYTAVLCIG  142 (218)
Q Consensus        78 IaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~---aak~L~~~~~yDaVIaLG  142 (218)
                      |++|...+.+.....+++++.+.++++|+.   +.+  .+...+..-   +++.+ ...++||+|..+
T Consensus         2 I~vv~~~~~~~~~~~~~~~i~~~~~~~g~~---v~~--~~~~~~~~~~~~~~~~~-~~~~~dgii~~~   63 (268)
T cd06323           2 IGLSVSTLNNPFFVTLKDGAQKEAKELGYE---LTV--LDAQNDAAKQLNDIEDL-ITRGVDAIIINP   63 (268)
T ss_pred             eeEecccccCHHHHHHHHHHHHHHHHcCce---EEe--cCCCCCHHHHHHHHHHH-HHcCCCEEEEcC
Confidence            788998899999999999999999998863   433  333332221   22333 346799999764

Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs. Members of this group are belonging to the type I periplasmic binding protein superfamily, whose members are involved in chemotaxis, ATP-binding cassette transport, and intercellular communication in central nervous system. The thermophilic and mesophilic ribose-binding proteins are structurally very similar, but differ substantially in thermal stability.

>cd06270 PBP1_GalS_like Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism

Probab=91.87  E-value=3  Score=34.95  Aligned_cols=123  Identities=20%  Similarity=0.222  Sum_probs=69.5

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHH---HHHHhhhc-CCccEEEEEeeeeeCCc
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGKS-GKYTAVLCIGAVVRGDT  149 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~---aak~L~~~-~~yDaVIaLG~VIrGeT  149 (218)
                      ...||+++...........=.+|..+.++++|+..+...++  ++.++..-   +++.++++ .++|||+|.+.      
T Consensus       115 g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~d------  186 (268)
T cd06270         115 GHRKIACITGPLTKEDARLRLQGYRDALAEAGIALDESLII--EGDFTEEGGYAAMQELLARGAPFTAVFCAND------  186 (268)
T ss_pred             CCceEEEEeCCcccccHHHHHHHHHHHHHHcCCCCCcceEE--ECCCCHHHHHHHHHHHHhCCCCCCEEEEcCc------
Confidence            45689999876544444455689999999999764333333  33333222   23444444 46899998763      


Q ss_pred             hhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHhhC--CCCCCcHHHHHHHHHHHH
Q 027801          150 THYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAG--GKSGNKGAEAALTAIEMA  210 (218)
Q Consensus       150 ~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~Rag--~k~gnKG~EAA~aAleM~  210 (218)
                          .++..+.+.+.+..+  .+|==.+|++.++.+.+..=..  ........+.+..|++++
T Consensus       187 ----~~a~g~~~~l~~~g~--~ip~di~v~g~d~~~~~~~~~~~~~ti~~~~~~~g~~a~~~l  243 (268)
T cd06270         187 ----EMAAGAISALREHGI--SVPQDVSIIGFDDVLLARYLYPKLTTVHYPIEEMAQMAAKLA  243 (268)
T ss_pred             ----HHHHHHHHHHHHcCC--CCCCceeEEEecCchHhhhcCCCceEeecCHHHHHHHHHHHH
Confidence                255566666655443  3454556677776555422100  112344455566666655

Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism. Transcription of the galactose regulon genes is regulated by Gal iso-repressor (GalS) and Gal repressor (GalR) in different ways, but both repressors recognize the same DNA binding site in the absence of D-galactose. GalS is a dimeric protein like GalR,and its major role is in regulating expression of the high-affinity galactose transporter encoded by the mgl operon, whereas GalR is the exclusive regulator of galactose permease, the low-affinity galactose transporter. GalS and GalR are members of the LacI-GalR family of transcription regulators and both contain the type I periplasmic binding protein-like fold. Hence, they are homologous to the periplasmic sugar bindi

>PRK10355 xylF D-xylose transporter subunit XylF; Provisional

Probab=91.70  E-value=2.3  Score=38.20  Aligned_cols=65  Identities=5%  Similarity=-0.042  Sum_probs=48.9

Q ss_pred             CCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH---HHHHHhhhcCCccEEEEEee
Q 027801           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP---~aak~L~~~~~yDaVIaLG~  143 (218)
                      ++..+||+|....+...-..++++..++++++|+.     +..+++..+-.   -.++.+ ...++||+|..++
T Consensus        23 ~~~~~Ig~i~~~~~~~f~~~~~~gi~~~a~~~g~~-----l~i~~~~~~~~~~~~~i~~l-~~~~vDGiIi~~~   90 (330)
T PRK10355         23 AKEVKIGMAIDDLRLERWQKDRDIFVKKAESLGAK-----VFVQSANGNEETQMSQIENM-INRGVDVLVIIPY   90 (330)
T ss_pred             CCCceEEEEecCCCchHHHHHHHHHHHHHHHcCCE-----EEEECCCCCHHHHHHHHHHH-HHcCCCEEEEeCC
Confidence            46789999999999999999999999999999873     44456654322   223444 3568999998764

>cd06283 PBP1_RegR_EndR_KdgR_like Ligand-binding domain of DNA transcription repressor RegR and other putative regulators such as KdgR and EndR

Probab=91.68  E-value=1  Score=37.37  Aligned_cols=60  Identities=12%  Similarity=0.140  Sum_probs=41.8

Q ss_pred             EEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH---HHHHHhhhcCCccEEEEEee
Q 027801           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        78 IaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP---~aak~L~~~~~yDaVIaLG~  143 (218)
                      |++|...+.......+++++.++++++|+.   +.++.  ...+-+   -.++.+ ...++||||..+.
T Consensus         2 igvi~~~~~~~~~~~~~~~i~~~a~~~g~~---~~~~~--~~~~~~~~~~~~~~l-~~~~~dgiii~~~   64 (267)
T cd06283           2 IGVIVADITNPFSSLVLKGIEDVCRAHGYQ---VLVCN--SDNDPEKEKEYLESL-LAYQVDGLIVNPT   64 (267)
T ss_pred             EEEEecCCccccHHHHHHHHHHHHHHcCCE---EEEEc--CCCCHHHHHHHHHHH-HHcCcCEEEEeCC
Confidence            688888888878889999999999999863   44433  333322   233444 3568999998775

Ligand-binding domain of DNA transcription repressor RegR and other putative regulators such as KdgR and EndR, all of which are members of the LacI-GalR family of bacterial transcription regulators. RegR regulates bacterial competence and the expression of virulence factors, including hyaluronidase. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA b

>TIGR01016 sucCoAbeta succinyl-CoA synthetase, beta subunit

Probab=91.62  E-value=4.6  Score=37.58  Aligned_cols=110  Identities=20%  Similarity=0.200  Sum_probs=69.5

Q ss_pred             HHHHHHHHHHHCCCCCCCeEEEEeCCc---chHHHHHHHhhhcCCccEEEEEeeeeeCCchhHHHHHHHHHHHHHHhchh
Q 027801           93 LLEGALETFKKYSVKEENIDVVWVPGS---FEIGVVAQQLGKSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVN  169 (218)
Q Consensus        93 Ll~gA~~~L~~~Gv~~e~I~vv~VPGA---~ELP~aak~L~~~~~yDaVIaLG~VIrGeT~H~e~Va~~vs~gLm~lsL~  169 (218)
                      +--.+.+.+..+|..+.|.--+  .|.   -.+--+++.+++..++|+|++   .+-|....++.+++++.+.+.+.  .
T Consensus       268 l~~~t~D~~~~~g~~~aNplDl--gg~a~~~~~~~al~~l~~dp~vd~ilv---~i~gg~~~~~~va~~i~~a~~~~--~  340 (386)
T TIGR01016       268 LAMATMDIIKLYGGEPANFLDV--GGGASAERVREALKLVLSDKSVKVVFI---NIFGGITRCDLVAKGLVEALKEV--G  340 (386)
T ss_pred             HHHHHHHHHHHcCCCCCCcEEe--cCCCCHHHHHHHHHHHHcCCCCCEEEE---ECCCCCCCHHHHHHHHHHHHHhc--C
Confidence            3345778888899877665443  333   224456666777888999994   22266666666665555555442  1


Q ss_pred             cCCceEEEEcCCCCHHHHHH---hhC--CCCCCcHHHHHHHHHHHH
Q 027801          170 SGVPCIFGVLTCDNMDQALN---RAG--GKSGNKGAEAALTAIEMA  210 (218)
Q Consensus       170 ~~vPVifGVLT~~n~eQA~~---Rag--~k~gnKG~EAA~aAleM~  210 (218)
                      .++||..... ..+.+++.+   .+|  ...-.-..+|+++|++++
T Consensus       341 ~~kPvvv~~~-g~~~~~~~~~L~~~G~~ip~~~~~~~Av~~~~~~~  385 (386)
T TIGR01016       341 VNVPVVVRLE-GTNVEEGKKILAESGLNIIFATSMEEAAEKAVEAA  385 (386)
T ss_pred             CCCcEEEEeC-CccHHHHHHHHHHcCCCccccCCHHHHHHHHHHhh
Confidence            2399965554 467777644   445  345567789999999875

This family contains a split seen both in a maximum parsimony tree (which ignores gaps) and in the gap pattern near position 85 of the seed alignment. Eukaryotic and most bacterial sequences are longer and contain a region similar to TXQTXXXG. Sequences from Deinococcus radiodurans, Mycobacterium tuberculosis, Streptomyces coelicolor, and the Archaea are 6 amino acids shorter in that region and contain a motif resembling [KR]G

>PRK15395 methyl-galactoside ABC transporter galactose-binding periplasmic protein MglB; Provisional

Probab=91.56  E-value=2.9  Score=37.39  Aligned_cols=118  Identities=14%  Similarity=0.188  Sum_probs=70.7

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEE-eCCcchHHH---HHHHhhhc---CCccEEEEEeeeeeC
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVW-VPGSFEIGV---VAQQLGKS---GKYTAVLCIGAVVRG  147 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~-VPGA~ELP~---aak~L~~~---~~yDaVIaLG~VIrG  147 (218)
                      ..+|+++.+.-+......-++|..+.|+++|+..   ...+ ..|.++..-   +++.++++   .++|||+|-+..   
T Consensus       162 ~~~i~~i~g~~~~~~~~~R~~G~~~al~~~g~~~---~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~ai~~~~d~---  235 (330)
T PRK15395        162 KIQYVLLKGEPGHPDAEARTTYVIKELNDKGIKT---EQLQLDTAMWDTAQAKDKMDAWLSGPNANKIEVVIANNDA---  235 (330)
T ss_pred             ceEEEEEecCCCCchHHHHHHHHHHHHHhcCCCe---eeeecccCCcCHHHHHHHHHHHHhhCcCCCeeEEEECCch---
Confidence            3456777665544444455689999999999852   2222 346665543   33445544   368999987654   


Q ss_pred             CchhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHH--hhCC-------CCCCcHHHHHHHHHHHH
Q 027801          148 DTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALN--RAGG-------KSGNKGAEAALTAIEMA  210 (218)
Q Consensus       148 eT~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~--Rag~-------k~gnKG~EAA~aAleM~  210 (218)
                             ++..+.+++.+..+ ..+|    |++.++.+.+..  |.+.       ....-|.+++..+++++
T Consensus       236 -------~A~gvl~al~~~Gl-~~vp----Vvg~D~~~~~~~~~~~g~~~ttv~~~~~~~G~~a~~~l~~~l  295 (330)
T PRK15395        236 -------MAMGAVEALKAHNK-SSIP----VFGVDALPEALALVKSGAMAGTVLNDANNQAKATFDLAKNLA  295 (330)
T ss_pred             -------HHHHHHHHHHhcCC-CCCe----EEeeCCCHHHHHHHHhCCceEEEecCHHHHHHHHHHHHHHHh
Confidence                   67788888888776 3567    666676554433  2221       12345666665555554

>cd06302 PBP1_LsrB_Quorum_Sensing Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs

Probab=91.54  E-value=2.1  Score=37.18  Aligned_cols=61  Identities=20%  Similarity=0.160  Sum_probs=43.8

Q ss_pred             EEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEe-CCcchHHHHHHHh--hhcCCccEEEEEe
Q 027801           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWV-PGSFEIGVVAQQL--GKSGKYTAVLCIG  142 (218)
Q Consensus        77 RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~V-PGA~ELP~aak~L--~~~~~yDaVIaLG  142 (218)
                      +|++|...+....-..+++++.++++++|+.     +..+ +.-.+-....+.+  +...++||||..+
T Consensus         1 ~I~vi~~~~~~~f~~~i~~gi~~~a~~~g~~-----v~~~~~~~~d~~~~~~~i~~~~~~~~DgiIi~~   64 (298)
T cd06302           1 TIAFVPKVTGIPYFNRMEEGAKEAAKELGVD-----AIYVGPTTADAAGQVQIIEDLIAQGVDAIAVVP   64 (298)
T ss_pred             CEEEEEcCCCChHHHHHHHHHHHHHHHhCCe-----EEEECCCCCCHHHHHHHHHHHHhcCCCEEEEec
Confidence            5888888877777888999999999998863     4443 6655554443333  1246799999975

Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs from other bacteria. The members of this group are homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transporters of many sugar based solutes in bacteria and archaea and that are a member of the type I periplasmic binding protein superfamily. LsrB binds a chemically distinct form of the AI-2 signal that lacks boron, in contrast to the Vibrio harveyi AI-2 signaling molecule that has an unusual furanosyl borate diester. Hence, many bacteria coordinate their gene expression according to the local density of their population by producing species specific AI-2. This process of quorum sensing allows LsrB to function as a periplasmic AI-2 binding p

>TIGR02634 xylF D-xylose ABC transporter, substrate-binding protein

Probab=91.51  E-value=1.2  Score=38.96  Aligned_cols=59  Identities=7%  Similarity=-0.058  Sum_probs=37.2

Q ss_pred             EEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHH---HHHHhhhcCCccEEEEEe
Q 027801           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGKSGKYTAVLCIG  142 (218)
Q Consensus        78 IaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~---aak~L~~~~~yDaVIaLG  142 (218)
                      ||++..+++.+.-..+.++..+++++.|+.   +.+.  +...+.-.   .++.+ ...++||||..+
T Consensus         1 ig~~~~~~~~~~~~~~~~~i~~~a~~~g~~---v~~~--~~~~~~~~q~~~i~~l-~~~~vDgIIi~~   62 (302)
T TIGR02634         1 IGVSIDDLRLERWQKDRDIFVAAAESLGAK---VFVQ--SANGNEAKQISQIENL-IARGVDVLVIIP   62 (302)
T ss_pred             CeeecCccchhhHHHHHHHHHHHHHhcCCE---EEEE--eCCCCHHHHHHHHHHH-HHcCCCEEEEeC
Confidence            577888888888888888888888888763   3333  33323221   22233 345788888765

Members of this family are periplasmic (when in Gram-negative bacteria) binding proteins for D-xylose import by a high-affinity ATP-binding cassette (ABC) transporter.

>cd06322 PBP1_ABC_sugar_binding_like_12 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems

Probab=91.47  E-value=2  Score=35.92  Aligned_cols=62  Identities=13%  Similarity=0.016  Sum_probs=41.1

Q ss_pred             EEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHHhhhcCCccEEEEEee
Q 027801           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        78 IaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~L~~~~~yDaVIaLG~  143 (218)
                      ||+|...........+++++.+.+++.|+.   +.+....+..+.- -.++.+ ...++||+|..++
T Consensus         2 i~~~~~~~~~~~~~~~~~~i~~~~~~~g~~---~~i~~~~~~~~~~~~~~~~~-~~~~vdgiii~~~   64 (267)
T cd06322           2 IGASLLTQQHPFYIELANAMKEEAKKQKVN---LIVSIANQDLNKQLSDVEDF-ITKKVDAIVLSPV   64 (267)
T ss_pred             eeEeecCcccHHHHHHHHHHHHHHHhcCCE---EEEecCCCCHHHHHHHHHHH-HHcCCCEEEEcCC
Confidence            677887777788889999999999999873   4433322222211 122333 3568999999875

This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consist of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.

>cd06312 PBP1_ABC_sugar_binding_like_4 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems

Probab=91.04  E-value=1.6  Score=36.84  Aligned_cols=62  Identities=13%  Similarity=0.141  Sum_probs=42.9

Q ss_pred             EEEEEEccc-CHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHH---HHHHhhhcCCccEEEEEee
Q 027801           77 RFALVVARF-NELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        77 RIaIV~Srf-n~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~---aak~L~~~~~yDaVIaLG~  143 (218)
                      ||++|...+ .......++++..+.++++|+.   +.++...+ ++..-   .+++|. ..++||+|..++
T Consensus         1 ~i~~i~~~~~~~~~~~~~~~g~~~~~~~~g~~---v~~~~~~~-~~~~~~~~~i~~l~-~~~vdgiii~~~   66 (271)
T cd06312           1 KIAFVTHGPAGDPFWTVVKNGAEDAAKDLGVD---VEYRGPET-FDVADMARLIEAAI-AAKPDGIVVTIP   66 (271)
T ss_pred             CEEEecCCCCCCcHHHHHHHHHHHHHHHhCCE---EEEECCCC-CCHHHHHHHHHHHH-HhCCCEEEEeCC
Confidence            688888887 7778889999999999999874   44443333 23332   233443 458999998774

Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.

>cd01537 PBP1_Repressors_Sugar_Binding_like Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems

Probab=90.95  E-value=1.3  Score=35.95  Aligned_cols=64  Identities=11%  Similarity=0.053  Sum_probs=44.2

Q ss_pred             EEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcch-HHHHHHHhhhcCCccEEEEEeee
Q 027801           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE-IGVVAQQLGKSGKYTAVLCIGAV  144 (218)
Q Consensus        77 RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~E-LP~aak~L~~~~~yDaVIaLG~V  144 (218)
                      |||+|...........+.+++.+.+++.|+.   +.++...+..| ..-.++.+.. .++|++|+.++-
T Consensus         1 ~ig~v~~~~~~~~~~~~~~g~~~~~~~~g~~---l~~~~~~~~~~~~~~~~~~~~~-~~~d~ii~~~~~   65 (264)
T cd01537           1 TIGVLVPDLDNPFFAQVLKGIEEAAKAAGYQ---VLLANSQNDAEKQLSALENLIA-RGVDGIIIAPSD   65 (264)
T ss_pred             CeEEEEcCCCChHHHHHHHHHHHHHHHcCCe---EEEEeCCCCHHHHHHHHHHHHH-cCCCEEEEecCC
Confidence            5788887766667788999999999998863   45554444332 3445556654 479999987753

Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems, all of which contain the type I periplasmic binding protein-like fold. Their specific ligands include lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor; in general the sugar binding domain in this family binds a sugar, which in turn changes the DNA binding activity of the repressor domain. The core structure of the periplasmic binding proteins is classified into two types and they differ in number and order of beta strands in each domain: type I, which has six beta strands, and type II, which has five beta strands. These two distinct structural arrangem

>cd06312 PBP1_ABC_sugar_binding_like_4 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems

Probab=90.89  E-value=6.4  Score=33.16  Aligned_cols=120  Identities=17%  Similarity=0.092  Sum_probs=73.4

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcch-HHHHHHHhhhc-CCccEEEEEeeeeeCCchhH
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE-IGVVAQQLGKS-GKYTAVLCIGAVVRGDTTHY  152 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~E-LP~aak~L~~~-~~yDaVIaLG~VIrGeT~H~  152 (218)
                      ..||+++.+.-+......-++|..+.++++++.   +..+.....++ .--+++.+++. .++|+|+|.+-.        
T Consensus       125 ~~~i~~i~g~~~~~~~~~r~~g~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~l~~~~~~~aI~~~~d~--------  193 (271)
T cd06312         125 GKNVLCVIHEPGNVTLEDRCAGFADGLGGAGIT---EEVIETGADPTEVASRIAAYLRANPDVDAVLTLGAP--------  193 (271)
T ss_pred             CCeEEEEecCCCCccHHHHHHHHHHHHHhcCce---eeEeecCCCHHHHHHHHHHHHHhCCCccEEEEeCCc--------
Confidence            458999987555455556779999999999864   22332233333 22344555443 468999987543        


Q ss_pred             HHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHH--HhhC-------CCCCCcHHHHHHHHHHHHH
Q 027801          153 DAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQAL--NRAG-------GKSGNKGAEAALTAIEMAS  211 (218)
Q Consensus       153 e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~--~Rag-------~k~gnKG~EAA~aAleM~~  211 (218)
                        ++..+.+++.+..+..+++|    ++.++..++.  -+.+       -....-|.+|+..+++|+.
T Consensus       194 --~a~g~~~al~~~g~~~di~v----vg~d~~~~~~~~l~~g~~~~tv~~~~~~~g~~a~~~l~~~~~  255 (271)
T cd06312         194 --SAAPAAKALKQAGLKGKVKL----GGFDLSPATLQAIKAGYIQFAIDQQPYLQGYLPVSLLWLYKR  255 (271)
T ss_pred             --cchHHHHHHHhcCCCCCeEE----EEecCCHHHHHHHhcCceEEEEecCchhhhHHHHHHHHHHHh
Confidence              56677777877776644443    3556555554  2222       2245677788777777765

Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.

>cd06299 PBP1_LacI_like_13 Ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia

Probab=90.86  E-value=6.3  Score=32.72  Aligned_cols=99  Identities=15%  Similarity=0.160  Sum_probs=61.5

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchH--H-HHHHHhhhcCCccEEEEEeeeeeCCchh
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEI--G-VVAQQLGKSGKYTAVLCIGAVVRGDTTH  151 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~EL--P-~aak~L~~~~~yDaVIaLG~VIrGeT~H  151 (218)
                      ..||+++...-+......-.+|..+.++++|++.....+  .+|.+..  . -.++.+++.+ +|||+|.+..       
T Consensus       116 ~~~I~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~-~~av~~~~d~-------  185 (265)
T cd06299         116 HKKIGYISGPQDTSTGRERLEAFRQACASLGLEVNEDLV--VLGGYSQESGYAGATKLLDQG-ATAIIAGDSM-------  185 (265)
T ss_pred             CCcEEEEeCCCCcccHHHHHHHHHHHHHHCCCCCChHhE--EecCcchHHHHHHHHHHHcCC-CCEEEEcCcH-------
Confidence            458999987766556667778999999999964222222  2344332  1 1234455444 8999987653       


Q ss_pred             HHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHH
Q 027801          152 YDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQAL  188 (218)
Q Consensus       152 ~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~  188 (218)
                         .+..+.+++.+..++  +|==..|++.++.+.+.
T Consensus       186 ---~a~gv~~al~~~g~~--vp~dv~v~g~d~~~~~~  217 (265)
T cd06299         186 ---MTIGAIRAIHDAGLV--IGEDISLIGFDDLPVFR  217 (265)
T ss_pred             ---HHHHHHHHHHHhCCC--CCcceeEEEeCCHHHHh
Confidence               566777777765543  33234456667766654

This group includes the ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia. This regulatory protein is a member of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial trans

>cd06281 PBP1_LacI_like_5 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors

Probab=90.66  E-value=1.2  Score=37.53  Aligned_cols=62  Identities=8%  Similarity=0.129  Sum_probs=39.7

Q ss_pred             EEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHHhhhcCCccEEEEEee
Q 027801           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        78 IaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~L~~~~~yDaVIaLG~  143 (218)
                      ||+|...+....-..++++..+.++++|+.   +.+..-....+-. -.++.+ ...++||+|..++
T Consensus         2 Igvv~~~~~~~~~~~~~~~i~~~a~~~g~~---~~~~~~~~~~~~~~~~i~~l-~~~~vdgii~~~~   64 (269)
T cd06281           2 IGCLVSDITNPLLAQLFSGAEDRLRAAGYS---LLIANSLNDPERELEILRSF-EQRRMDGIIIAPG   64 (269)
T ss_pred             EEEEecCCccccHHHHHHHHHHHHHHcCCE---EEEEeCCCChHHHHHHHHHH-HHcCCCEEEEecC
Confidence            788888887777788888888988888863   3333222222222 222333 4567898888775

This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.

>cd06293 PBP1_LacI_like_11 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors

Probab=90.62  E-value=1  Score=37.73  Aligned_cols=63  Identities=10%  Similarity=0.030  Sum_probs=40.0

Q ss_pred             EEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHHhhhcCCccEEEEEee
Q 027801           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        77 RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~L~~~~~yDaVIaLG~  143 (218)
                      .||+|...+....-..+++++.++++++|+.   +.++...+..+-- -.++. +...++||+|..++
T Consensus         1 ~Ig~i~~~~~~~~~~~~~~gi~~~~~~~gy~---v~~~~~~~~~~~~~~~i~~-~~~~~~dgiii~~~   64 (269)
T cd06293           1 TIGLVVPDIANPFFAELADAVEEEADARGLS---LVLCATRNRPERELTYLRW-LDTNHVDGLIFVTN   64 (269)
T ss_pred             CEEEEeCCCCCCcHHHHHHHHHHHHHHCCCE---EEEEeCCCCHHHHHHHHHH-HHHCCCCEEEEeCC
Confidence            3778887777767778888888888888863   4555444333211 12223 34567888888764

This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.

>PRK00696 sucC succinyl-CoA synthetase subunit beta; Provisional

Probab=90.43  E-value=7.2  Score=36.35  Aligned_cols=120  Identities=20%  Similarity=0.230  Sum_probs=71.4

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcc---hHHHHHHHhhhcCCccEEEEEeeeeeCCchh
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSF---EIGVVAQQLGKSGKYTAVLCIGAVVRGDTTH  151 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~---ELP~aak~L~~~~~yDaVIaLG~VIrGeT~H  151 (218)
                      +-||+||..--      .+---+.+.|.++|....|---+  .|..   ..--+++.+++..++|+|+++  +. |...-
T Consensus       256 ~~~i~ii~ng~------G~~~~~~D~l~~~g~~~~NPvDl--~g~~~~e~~~~aL~~l~~d~~vd~vlv~--~~-~~~~~  324 (388)
T PRK00696        256 DGNIGCMVNGA------GLAMATMDIIKLYGGEPANFLDV--GGGATAERVAEAFKIILSDPNVKAILVN--IF-GGITR  324 (388)
T ss_pred             CCcEEEEECCc------hHHHHHHHHHHHcCCCcCCeEEe--cCCCCHHHHHHHHHHHhcCCCCCEEEEE--eC-CCCCC
Confidence            35777776543      22234667888888766664333  3432   244566667778899999975  22 44433


Q ss_pred             HHHHHHHHHHHHHHhchh--cCCceEEEEcCCCCHHHHHH---hhC--CCCCCcHHHHHHHHHHHH
Q 027801          152 YDAVANSAASGVLSAGVN--SGVPCIFGVLTCDNMDQALN---RAG--GKSGNKGAEAALTAIEMA  210 (218)
Q Consensus       152 ~e~Va~~vs~gLm~lsL~--~~vPVifGVLT~~n~eQA~~---Rag--~k~gnKG~EAA~aAleM~  210 (218)
                      .+-++    ++|.++.-+  +++||.... ...+.+++.+   .+|  .-.-+-..+|+++..|++
T Consensus       325 ~~~va----~~i~~~~~~~~~~kPvv~~~-~g~~~~~~~~~L~~~Gi~ip~f~~pe~A~~al~~~~  385 (388)
T PRK00696        325 CDVIA----EGIIAAVKEVGVTVPLVVRL-EGTNVELGKKILAESGLNIIAADTLDDAAQKAVEAA  385 (388)
T ss_pred             HHHHH----HHHHHHHHhcCCCCcEEEEe-CCCCHHHHHHHHHHCCCCceecCCHHHHHHHHHHHh
Confidence            34455    555554444  789995554 4456666644   333  123355678888888876

>TIGR02637 RhaS rhamnose ABC transporter, rhamnose-binding protein

Probab=90.43  E-value=3.2  Score=35.86  Aligned_cols=101  Identities=18%  Similarity=0.097  Sum_probs=60.0

Q ss_pred             CEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEE-EeCCcchHHH---HHHHhhh-cCCccEEEEEeeeeeCCch
Q 027801           76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVV-WVPGSFEIGV---VAQQLGK-SGKYTAVLCIGAVVRGDTT  150 (218)
Q Consensus        76 ~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv-~VPGA~ELP~---aak~L~~-~~~yDaVIaLG~VIrGeT~  150 (218)
                      .||+++...-.....+...+++.+.++++|..  +++++ .+.+.+..--   .++.+++ ..++|||+|          
T Consensus       124 ~~I~~i~g~~~~~~~~~r~~g~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~~ai~~----------  191 (302)
T TIGR02637       124 GEIAILSAASTATNQNAWIEIMKKELKDPKYP--KVKLVATVYGDDDAQKSYQEAQGLLKSYPNLKGIIA----------  191 (302)
T ss_pred             cEEEEEECCCCCccHHHHHHHHHHHHhhccCC--CCEEEeeecCCchHHHHHHHHHHHHHhCCCccEEEe----------
Confidence            59999987544444456678999999987764  33332 2334443221   2334443 457899998          


Q ss_pred             hHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHH
Q 027801          151 HYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALN  189 (218)
Q Consensus       151 H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~  189 (218)
                      +.+..+..+.+++.+..+..++. +.|+=......|++.
T Consensus       192 ~~d~~a~ga~~al~~~g~~~~i~-vvg~d~~~~~~~~l~  229 (302)
T TIGR02637       192 PTTVGIKAAAQAVSDAKLIGKVK-LTGLGLPSEMAKYVK  229 (302)
T ss_pred             CCCchHHHHHHHHHhcCCCCCEE-EEEcCCcHHHHHHHh
Confidence            34667778888888777653433 345432333456664

This sugar-binding component of ABC transporter complexes is found in rhamnose catabolism operon contexts. Mutation of this gene in Rhizobium leguminosarum abolishes rhamnose transport and prevents growth on rhamnose as a carbon source.

>cd06267 PBP1_LacI_sugar_binding_like Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily

Probab=90.18  E-value=4.8  Score=32.75  Aligned_cols=85  Identities=20%  Similarity=0.096  Sum_probs=54.4

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcch-HHHHHHHhh-hcCCccEEEEEeeeeeCCchhH
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE-IGVVAQQLG-KSGKYTAVLCIGAVVRGDTTHY  152 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~E-LP~aak~L~-~~~~yDaVIaLG~VIrGeT~H~  152 (218)
                      ..||+++...-+........++..+.++++|...+...+...+...+ ..-.++.++ +..+.|+|+|.+          
T Consensus       116 ~~~i~~i~~~~~~~~~~~r~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~i~~~~----------  185 (264)
T cd06267         116 HRRIAFIGGPPDLSTARERLEGYREALEEAGIPLDEELIVEGDFSEESGYEAARELLASGERPTAIFAAN----------  185 (264)
T ss_pred             CceEEEecCCCccchHHHHHHHHHHHHHHcCCCCCcceEEecccchhhHHHHHHHHHhcCCCCcEEEEcC----------
Confidence            56899998877766677788999999999986433334443333322 223334444 445699998731          


Q ss_pred             HHHHHHHHHHHHHhchh
Q 027801          153 DAVANSAASGVLSAGVN  169 (218)
Q Consensus       153 e~Va~~vs~gLm~lsL~  169 (218)
                      +.++..+.+++.+..+.
T Consensus       186 ~~~a~~~~~al~~~g~~  202 (264)
T cd06267         186 DLMAIGALRALRELGLR  202 (264)
T ss_pred             cHHHHHHHHHHHHhCCC
Confidence            23556777777777664

Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily. In most cases, ligands are monosaccharide including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the domain sugar binding changes the DNA binding activity of the repressor domain.

>PRK10653 D-ribose transporter subunit RbsB; Provisional

Probab=90.10  E-value=3.5  Score=35.58  Aligned_cols=65  Identities=20%  Similarity=0.072  Sum_probs=44.4

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcc-hHHHHHHHhhhcCCccEEEEEe
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSF-EIGVVAQQLGKSGKYTAVLCIG  142 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~-ELP~aak~L~~~~~yDaVIaLG  142 (218)
                      +...|++|...+.......++++..++++++|+.   +.++...+-- +-.-.++.+ ...++||+|..+
T Consensus        25 ~~~~I~vi~~~~~~~f~~~~~~~i~~~~~~~G~~---~~~~~~~~d~~~~~~~~~~l-~~~~~dgiii~~   90 (295)
T PRK10653         25 AKDTIALVVSTLNNPFFVSLKDGAQKEADKLGYN---LVVLDSQNNPAKELANVQDL-TVRGTKILLINP   90 (295)
T ss_pred             cCCeEEEEecCCCChHHHHHHHHHHHHHHHcCCe---EEEecCCCCHHHHHHHHHHH-HHcCCCEEEEcC
Confidence            4568999999998888899999999999999974   4443322111 122233444 346799998654

>cd06309 PBP1_YtfQ_like Periplasmic binding domain of ABC-type YtfQ-like transport systems

Probab=89.92  E-value=2.1  Score=36.06  Aligned_cols=62  Identities=3%  Similarity=-0.075  Sum_probs=42.1

Q ss_pred             EEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHHhhhcCCccEEEEEee
Q 027801           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        78 IaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~L~~~~~yDaVIaLG~  143 (218)
                      ||+|.-.+....-..++++..+.++++|+.   +.+....+.-|.= -.++.+ ...++||+|..+.
T Consensus         2 ~g~~~~~~~~~~~~~~~~~~~~~a~~~g~~---~~~~~~~~~~~~~~~~i~~l-~~~~vdgiIi~~~   64 (273)
T cd06309           2 VGFSQVGAESPWRTAETKSIKDAAEKRGFD---LKFADAQQKQENQISAIRSF-IAQGVDVIILAPV   64 (273)
T ss_pred             eeeccCCCCCHHHHHHHHHHHHHHHhcCCE---EEEeCCCCCHHHHHHHHHHH-HHcCCCEEEEcCC
Confidence            677887777777888999999999999974   4444333332221 233444 3467999998764

Periplasmic binding domain of ABC-type YtfQ-like transport systems. The YtfQ protein from Escherichia coli is up-regulated under glucose-limited conditions and shares homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their ligand specificity is not determined experimentally.

>cd06275 PBP1_PurR Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli

Probab=89.91  E-value=3.1  Score=34.69  Aligned_cols=100  Identities=20%  Similarity=0.183  Sum_probs=59.2

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHHhhhc-CCccEEEEEeeeeeCCchh
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKS-GKYTAVLCIGAVVRGDTTH  151 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~L~~~-~~yDaVIaLG~VIrGeT~H  151 (218)
                      ...||+++.++-+......-.+|..+.++++|++.....+++-+...+-. -.++.++++ .++|||+|.          
T Consensus       116 G~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~----------  185 (269)
T cd06275         116 GHRRIGCITGPLEKAPAQQRLAGFRRAMAEAGLPVNPGWIVEGDFECEGGYEAMQRLLAQPKRPTAVFCG----------  185 (269)
T ss_pred             CCceEEEEeCCCCCccHHHHHHHHHHHHHHcCCCCCHHHhccCCCChHHHHHHHHHHHcCCCCCcEEEEC----------
Confidence            34689999877666666666799999999998753222222223233322 134455544 468999983          


Q ss_pred             HHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHH
Q 027801          152 YDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMD  185 (218)
Q Consensus       152 ~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~e  185 (218)
                      .+.++..+.+.+.+..++  +|==-.|++.++.+
T Consensus       186 ~d~~a~g~~~~l~~~g~~--vp~di~vvg~d~~~  217 (269)
T cd06275         186 NDLMAMGALCAAQEAGLR--VPQDLSIIGYDDIE  217 (269)
T ss_pred             ChHHHHHHHHHHHHcCCC--CCcceEEEEeCChh
Confidence            244566666777766553  34333455555543

Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli. This dimeric PurR belongs to the LacI-GalR family of transcription regulators and is activated to bind to DNA operator sites by initially binding either of high affinity corepressors, hypoxanthine or guanine. PurR is composed of two functional domains: aan N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the purine transcription repressor undergoes a

>cd06294 PBP1_ycjW_transcription_regulator_like Ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors

Probab=89.85  E-value=2  Score=35.79  Aligned_cols=62  Identities=10%  Similarity=0.074  Sum_probs=39.5

Q ss_pred             EEEEEcc-----cCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEe
Q 027801           78 FALVVAR-----FNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIG  142 (218)
Q Consensus        78 IaIV~Sr-----fn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG  142 (218)
                      ||+|...     +.......+++++.+.++++|..   +.+..-.+.-+..-.+..++.++++||+|..+
T Consensus         2 igli~p~~~~~~~~~~~~~~~~~~~~~~~~~~g~~---~~~~~~~~~~~~~~~~~~~~~~~~~dgiii~~   68 (270)
T cd06294           2 IGVVLPPSADEAFQNPFFIEVLRGISAVANENGYD---ISLATGKNEEELLEEVKKMIQQKRVDGFILLY   68 (270)
T ss_pred             EEEEeCCccccCcCCCCHHHHHHHHHHHHHHCCCE---EEEecCCCcHHHHHHHHHHHHHcCcCEEEEec
Confidence            5666643     55566678889999999998874   44433332222223444555667899999875

This group includes the ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.

>cd01545 PBP1_SalR Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators

Probab=89.68  E-value=1.8  Score=36.07  Aligned_cols=63  Identities=10%  Similarity=0.058  Sum_probs=34.4

Q ss_pred             EEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcch-HHHHHHHhhhcCCccEEEEEee
Q 027801           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE-IGVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        78 IaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~E-LP~aak~L~~~~~yDaVIaLG~  143 (218)
                      |+++....+...-..+++|+.+.++++|+.   +.+++..+..+ .-..+.+++...++||+|...+
T Consensus         2 I~vi~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~~~~~l~~~~vdgiii~~~   65 (270)
T cd01545           2 IGLLYDNPSPGYVSEIQLGALDACRDTGYQ---LVIEPCDSGSPDLAERVRALLQRSRVDGVILTPP   65 (270)
T ss_pred             EEEEEcCCCcccHHHHHHHHHHHHHhCCCe---EEEEeCCCCchHHHHHHHHHHHHCCCCEEEEeCC
Confidence            566666666666667777777777777653   44444443322 1122222234456777766543

Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. The SalR binds to glucose based compound Salicin which is chemically related to aspirin. The ligand-binding of SalR is structurally homologous to the periplasmic sugar-binding domain of ABC-transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand bind

>cd06280 PBP1_LacI_like_4 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors

Probab=89.68  E-value=1.6  Score=36.56  Aligned_cols=62  Identities=10%  Similarity=0.083  Sum_probs=42.2

Q ss_pred             EEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHH-HHHHhhhcCCccEEEEEee
Q 027801           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV-VAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        78 IaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~-aak~L~~~~~yDaVIaLG~  143 (218)
                      ||+|...+....-..|+++..+.++++|..   +.++.-...-+.-. .++.+ ...++||+|..++
T Consensus         2 Ig~i~p~~~~~~~~~~~~~i~~~~~~~g~~---~~~~~~~~~~~~~~~~i~~l-~~~~~dgiii~~~   64 (263)
T cd06280           2 VGLIVADIRNPFFTAVSRAVEDAAYRAGLR---VILCNTDEDPEKEAMYLELM-EEERVTGVIFAPT   64 (263)
T ss_pred             EEEEecccccccHHHHHHHHHHHHHHCCCE---EEEEeCCCCHHHHHHHHHHH-HhCCCCEEEEeCC
Confidence            788888888778888999999999999874   44332222222222 23343 4667999999875

This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.

>cd06290 PBP1_LacI_like_9 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors

Probab=89.51  E-value=1.9  Score=35.90  Aligned_cols=60  Identities=15%  Similarity=0.249  Sum_probs=40.4

Q ss_pred             EEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH---HHHHHhhhcCCccEEEEEee
Q 027801           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        78 IaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP---~aak~L~~~~~yDaVIaLG~  143 (218)
                      ||+|+..++......++++..+.++++|+.   +  +.++.-.+-.   -.++.+ .+.++||+|..++
T Consensus         2 i~vi~~~~~~~~~~~~~~gi~~~~~~~gy~---~--~~~~~~~~~~~~~~~i~~l-~~~~~dgiii~~~   64 (265)
T cd06290           2 IGVLTQDFASPFYGRILKGMERGLNGSGYS---P--IIATGHWNQSRELEALELL-KSRRVDALILLGG   64 (265)
T ss_pred             EEEEECCCCCchHHHHHHHHHHHHHHCCCE---E--EEEeCCCCHHHHHHHHHHH-HHCCCCEEEEeCC
Confidence            788888888888888899999999988863   3  3333333322   122333 4567899998865

This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.

>PRK09492 treR trehalose repressor; Provisional

Probab=89.50  E-value=1.8  Score=37.41  Aligned_cols=67  Identities=16%  Similarity=0.099  Sum_probs=44.4

Q ss_pred             CCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHHhhhcCCccEEEEEee
Q 027801           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~L~~~~~yDaVIaLG~  143 (218)
                      .+...||+|...+....-..++++..+++.++|+.   +.++......+.- -.++.| ...++||+|..+.
T Consensus        60 ~~~~~Ig~i~~~~~~~~~~~~~~~i~~~~~~~gy~---~~~~~~~~~~~~~~~~~~~l-~~~~vdgiIi~~~  127 (315)
T PRK09492         60 QSDKVVGIIVSRLDSLSENQAVRTMLPAFYEQGYD---PIIMESQFSPEKVNEHLGVL-KRRNVDGVILFGF  127 (315)
T ss_pred             CCCCeEEEEecCCcCcccHHHHHHHHHHHHHcCCe---EEEEecCCChHHHHHHHHHH-HhcCCCEEEEeCC
Confidence            34457999999887767778999999999999974   3333322222222 122333 4567999999873

>cd06289 PBP1_MalI_like Ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria

Probab=89.41  E-value=4.2  Score=33.67  Aligned_cols=102  Identities=23%  Similarity=0.171  Sum_probs=57.7

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcch-HHHHHHHhhhc-CCccEEEEEeeeeeCCchh
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE-IGVVAQQLGKS-GKYTAVLCIGAVVRGDTTH  151 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~E-LP~aak~L~~~-~~yDaVIaLG~VIrGeT~H  151 (218)
                      ...||+++...-+......-.+|..+.++++|+......++..+...| .--.++.++++ .++|||+|.+-        
T Consensus       116 g~~~i~~l~~~~~~~~~~~r~~gf~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~i~~~~~--------  187 (268)
T cd06289         116 GHRRIAFIGGLEDSSTRRERLAGYRAALAEAGLPFDSELVVEGPPSRQGGAEAVAQLLDLPPRPTAIVCFND--------  187 (268)
T ss_pred             CCCCEEEecCCccccchHHHHHHHHHHHHHcCCCCCchhEEecCcchhhHHHHHHHHHcCCCCCCEEEEcCc--------
Confidence            345899887654444455667999999999986432223332232222 22334444443 56899998763        


Q ss_pred             HHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHH
Q 027801          152 YDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQA  187 (218)
Q Consensus       152 ~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA  187 (218)
                        ..+..+.+.+.+..++  +|==..|++.++.+.+
T Consensus       188 --~~a~~~~~al~~~g~~--~p~di~iig~d~~~~~  219 (268)
T cd06289         188 --LVAFGAMSGLRRAGLT--PGRDIAVVGFDDVAEA  219 (268)
T ss_pred             --HHHHHHHHHHHHcCCC--CCcceEEEeecCchHH
Confidence              3455566666665543  2212345555555443

This group includes the ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria. They are members of the LacI-GalR family of repressor proteins which are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.

>PF00532 Peripla_BP_1: Periplasmic binding proteins and sugar binding domain of LacI family; InterPro: IPR001761 This family includes the periplasmic binding proteins, and the LacI family transcriptional regulators

Probab=89.30  E-value=3.7  Score=36.16  Aligned_cols=64  Identities=6%  Similarity=0.059  Sum_probs=51.2

Q ss_pred             CEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEee
Q 027801           76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        76 ~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~  143 (218)
                      ..||+|+.......-..++.+..++++++|+.   +-++...+.-|.--.++.| .+.++||+|..+.
T Consensus         2 ~~IGvivp~~~npff~~ii~gIe~~a~~~Gy~---l~l~~t~~~~~~e~~i~~l-~~~~vDGiI~~s~   65 (279)
T PF00532_consen    2 KTIGVIVPDISNPFFAEIIRGIEQEAREHGYQ---LLLCNTGDDEEKEEYIELL-LQRRVDGIILASS   65 (279)
T ss_dssp             CEEEEEESSSTSHHHHHHHHHHHHHHHHTTCE---EEEEEETTTHHHHHHHHHH-HHTTSSEEEEESS
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHHHHHHcCCE---EEEecCCCchHHHHHHHHH-HhcCCCEEEEecc
Confidence            36899999999888889999999999999984   6677777777777444444 5678999998855

The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The LacI family of proteins consist of transcriptional regulators related to the lac repressor. In this case, generally the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain (lacI) [, ].; PDB: 1BAP_A 7ABP_A 6ABP_A 1ABF_A 5ABP_A 2WRZ_B 9ABP_A 1APB_A 1ABE_A 8ABP_A ....

>cd06286 PBP1_CcpB_like Ligand-binding domain of a novel transcription factor implicated in catabolite repression in Bacillus and Clostridium species

Probab=89.21  E-value=2.1  Score=35.62  Aligned_cols=62  Identities=15%  Similarity=0.118  Sum_probs=41.0

Q ss_pred             EEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHH-HHHHhhhcCCccEEEEEee
Q 027801           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV-VAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        78 IaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~-aak~L~~~~~yDaVIaLG~  143 (218)
                      |+++...++......|++++.+.+++.|+.   +.+......-+-.. .++.+ ...++||+|..++
T Consensus         2 i~~i~~~~~~~~~~~i~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~i~~l-~~~~vdgiii~~~   64 (260)
T cd06286           2 IGVVLPYINHPYFSQLVDGIEKAALKHGYK---VVLLQTNYDKEKELEYLELL-KTKQVDGLILCSR   64 (260)
T ss_pred             EEEEeCCCCCchHHHHHHHHHHHHHHcCCE---EEEEeCCCChHHHHHHHHHH-HHcCCCEEEEeCC
Confidence            688888888888889999999999998863   43332222222221 22333 4567899998875

This group includes the ligand-binding domain of a novel transcription factor implicated in catabolite repression in Bacillus and Clostridium species. CcpB is 30% identical in sequence to CcpA which functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. Like CcpA, the DNA-binding protein CcpB exerts its catabolite-repressing effect by a mechanism dependent on the presence of HPr(Ser-P), the small phosphocarrier proteins of the phosphoenolpyruvate-sugar phosphotransferase system, but with a less significant degree.

>cd06296 PBP1_CatR_like Ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in catechol degradation

Probab=89.19  E-value=1.6  Score=36.40  Aligned_cols=62  Identities=11%  Similarity=0.078  Sum_probs=38.9

Q ss_pred             EEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcch-HHHHHHHhhhcCCccEEEEEee
Q 027801           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE-IGVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        78 IaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~E-LP~aak~L~~~~~yDaVIaLG~  143 (218)
                      ||||...++......+.++..+.++++|+.   +.+....+.-| ---.++.+ .++++||+|...+
T Consensus         2 i~vi~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~i~~l-~~~~~dgiii~~~   64 (270)
T cd06296           2 IGLVFPDLDSPWASEVLRGVEEAAAAAGYD---VVLSESGRRTSPERQWVERL-SARRTDGVILVTP   64 (270)
T ss_pred             eEEEECCCCCccHHHHHHHHHHHHHHcCCe---EEEecCCCchHHHHHHHHHH-HHcCCCEEEEecC
Confidence            677777777777777888888888887763   55554444333 22334444 3466888877654

This group includes the ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in catechol degradation. This group belongs to the the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.

>PF02601 Exonuc_VII_L: Exonuclease VII, large subunit; InterPro: IPR020579 Exonuclease VII 3

Probab=89.13  E-value=5.6  Score=35.86  Aligned_cols=92  Identities=18%  Similarity=0.274  Sum_probs=61.7

Q ss_pred             CCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeC----C-cchHHHHHHHhhhcC---CccEEEEEeee
Q 027801           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVP----G-SFEIGVVAQQLGKSG---KYTAVLCIGAV  144 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VP----G-A~ELP~aak~L~~~~---~yDaVIaLG~V  144 (218)
                      .-..|||||.|.==.-+     ...+..+++.+.. -++.++.++    + +-||--+++.+-+.+   .||.||    |
T Consensus        12 ~~p~~I~vITs~~gAa~-----~D~~~~~~~r~~~-~~~~~~p~~vQG~~A~~~I~~al~~~~~~~~~~~~Dvii----i   81 (319)
T PF02601_consen   12 KFPKRIAVITSPTGAAI-----QDFLRTLKRRNPI-VEIILYPASVQGEGAAASIVSALRKANEMGQADDFDVII----I   81 (319)
T ss_pred             CCCCEEEEEeCCchHHH-----HHHHHHHHHhCCC-cEEEEEeccccccchHHHHHHHHHHHHhccccccccEEE----E
Confidence            45579999999754443     4555666666543 356666655    2 345777777776554   799997    6


Q ss_pred             eeCCchhHHHHH---HHHHHHHHHhchhcCCceEEEE
Q 027801          145 VRGDTTHYDAVA---NSAASGVLSAGVNSGVPCIFGV  178 (218)
Q Consensus       145 IrGeT~H~e~Va---~~vs~gLm~lsL~~~vPVifGV  178 (218)
                      +||+=.--|+-|   ..++++|.+    ..+||+-||
T Consensus        82 ~RGGGs~eDL~~FN~e~varai~~----~~~PvisaI  114 (319)
T PF02601_consen   82 IRGGGSIEDLWAFNDEEVARAIAA----SPIPVISAI  114 (319)
T ss_pred             ecCCCChHHhcccChHHHHHHHHh----CCCCEEEec
Confidence            799887666554   455555544    569999999

1.11.6 from EC is composed of two nonidentical subunits; one large subunit and 4 small ones []. Exonuclease VII catalyses exonucleolytic cleavage in either 5'-3' or 3'-5' direction to yield 5'-phosphomononucleotides. The large subunit also contains the OB-fold domains (IPR004365 from INTERPRO) that bind to nucleic acids at the N terminus. This entry represents Exonuclease VII, large subunit, C-terminal. ; GO: 0008855 exodeoxyribonuclease VII activity

>PRK10423 transcriptional repressor RbsR; Provisional

Probab=89.08  E-value=6.4  Score=34.16  Aligned_cols=124  Identities=23%  Similarity=0.214  Sum_probs=73.0

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH---HHHHHhhhc-CCccEEEEEeeeeeCCc
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGKS-GKYTAVLCIGAVVRGDT  149 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP---~aak~L~~~-~~yDaVIaLG~VIrGeT  149 (218)
                      ...||+++.+..+......-.+|..+.|+++|+....  .+...+.++.-   -+++.+++. .++|||+|.+       
T Consensus       173 G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~-------  243 (327)
T PRK10423        173 GYTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPD--GYEVTGDFEFNGGFDAMQQLLALPLRPQAVFTGN-------  243 (327)
T ss_pred             CCCeEEEEeCCccccchHHHHHHHHHHHHHcCCCCCc--ceEEeCCCChHHHHHHHHHHhcCCCCCCEEEEcC-------
Confidence            4468999976554444456679999999999975322  22234555432   233455543 4689999843       


Q ss_pred             hhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHhhC------CCCCCcHHHHHHHHHHHHH
Q 027801          150 THYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAG------GKSGNKGAEAALTAIEMAS  211 (218)
Q Consensus       150 ~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~Rag------~k~gnKG~EAA~aAleM~~  211 (218)
                         |.++..+.+.+.+..+  .+|==..|++.++...+.....      -.....|.+|++..+++++
T Consensus       244 ---d~~A~g~~~~l~~~g~--~vP~dvsvigfd~~~~~~~~~p~lttv~~~~~~~g~~A~~~l~~~i~  306 (327)
T PRK10423        244 ---DAMAVGVYQALYQAGL--SVPQDIAVIGYDDIELARYMTPPLTTIHQPKDELGELAIDVLIHRMA  306 (327)
T ss_pred             ---cHHHHHHHHHHHHcCC--CCCCceEEEEeCChhHHhhCCCCCceeeCCHHHHHHHHHHHHHHHhc
Confidence               4466667777776544  4565667777777655432111      1122456666666665543

>PRK10014 DNA-binding transcriptional repressor MalI; Provisional

Probab=88.96  E-value=4.3  Score=35.56  Aligned_cols=125  Identities=17%  Similarity=0.118  Sum_probs=72.6

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHH-HHHHhhhc-CCccEEEEEeeeeeCCchh
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV-VAQQLGKS-GKYTAVLCIGAVVRGDTTH  151 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~-aak~L~~~-~~yDaVIaLG~VIrGeT~H  151 (218)
                      ...||+++...-+..-...-.+|..+.|+++|+..+...++..+...+-.+ +++.+++. .++|||+|..         
T Consensus       181 G~~~I~~i~g~~~~~~~~~R~~Gf~~al~~~g~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~n---------  251 (342)
T PRK10014        181 GHQRIAWLGGQSSSLTRAERVGGYCATLLKFGLPFHSEWVLECTSSQKQAAEAITALLRHNPTISAVVCYN---------  251 (342)
T ss_pred             CCCEEEEEcCCcccccHHHHHHHHHHHHHHcCCCCCcceEecCCCChHHHHHHHHHHHcCCCCCCEEEECC---------
Confidence            345899997655443334456899999999998643333333344444322 33444443 4689999754         


Q ss_pred             HHHHHHHHHHHHHHhchhcCCce---------EEEEcCCCCHHHHHHhhC------CCCCCcHHHHHHHHHHHH
Q 027801          152 YDAVANSAASGVLSAGVNSGVPC---------IFGVLTCDNMDQALNRAG------GKSGNKGAEAALTAIEMA  210 (218)
Q Consensus       152 ~e~Va~~vs~gLm~lsL~~~vPV---------ifGVLT~~n~eQA~~Rag------~k~gnKG~EAA~aAleM~  210 (218)
                       |.++-.+.+++.+..++  +|-         =..|++.++.+.+.....      -.....|.+|+...++++
T Consensus       252 -d~~A~g~~~~l~~~g~~--vp~~~~~~~~p~di~vigfd~~~~~~~~~p~lttv~~~~~~~g~~a~~~L~~~i  322 (342)
T PRK10014        252 -ETIAMGAWFGLLRAGRQ--SGESGVDRYFEQQVALAAFTDVPEAELDDPPLTWASTPAREIGRTLADRMMQRI  322 (342)
T ss_pred             -cHHHHHHHHHHHHcCCC--CCCccccccccCceEEEEecCchHHhcCCCCceeeecCHHHHHHHHHHHHHHHh
Confidence             45777778888876654  343         346667776655432111      112234666666555544

>PRK10423 transcriptional repressor RbsR; Provisional

Probab=88.91  E-value=1.9  Score=37.38  Aligned_cols=67  Identities=9%  Similarity=0.063  Sum_probs=46.3

Q ss_pred             CCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHHhhhcCCccEEEEEee
Q 027801           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~L~~~~~yDaVIaLG~  143 (218)
                      .+...||+|+..+....-..++++..+.+.++|+.   +.+....+..+-- -.++.+ ...++||+|.++.
T Consensus        54 ~~~~~Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~~~~l-~~~~vdGiI~~~~  121 (327)
T PRK10423         54 NQTRTIGMLITASTNPFYSELVRGVERSCFERGYS---LVLCNTEGDEQRMNRNLETL-MQKRVDGLLLLCT  121 (327)
T ss_pred             CCCCeEEEEeCCCCCCcHHHHHHHHHHHHHHcCCE---EEEEeCCCCHHHHHHHHHHH-HHcCCCEEEEeCC
Confidence            34567999998877667778999999999999974   4454444433322 233444 4567999998764

>cd06287 PBP1_LacI_like_8 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors

Probab=88.83  E-value=5  Score=34.49  Aligned_cols=95  Identities=19%  Similarity=0.057  Sum_probs=59.9

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHH---HHHHhhhc-CCccEEEEEeeeeeCCc
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGKS-GKYTAVLCIGAVVRGDT  149 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~---aak~L~~~-~~yDaVIaLG~VIrGeT  149 (218)
                      ...||+++.+.-+......-.+|..+.++++|+...   .+.+.+.++..-   +++++++. .++|||+|.        
T Consensus       117 G~~~I~~i~~~~~~~~~~~R~~gf~~a~~~~g~~~~---~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~--------  185 (269)
T cd06287         117 GARQIALIVGSARRNSYLEAEAAYRAFAAEHGMPPV---VLRVDEAGGEEAGYAACAQLLAQHPDLDALCVP--------  185 (269)
T ss_pred             CCCcEEEEeCCcccccHHHHHHHHHHHHHHcCCCcc---eeEecCCCChHHHHHHHHHHHhCCCCCCEEEEc--------
Confidence            345899997654433444566899999999998642   333444444322   33445443 468999986        


Q ss_pred             hhHHHHHHHHHHHHHHhchhcCCceEEEEcC-CCC
Q 027801          150 THYDAVANSAASGVLSAGVNSGVPCIFGVLT-CDN  183 (218)
Q Consensus       150 ~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT-~~n  183 (218)
                        .|.++-.+.+++.+..++  +|==..|++ -++
T Consensus       186 --~d~~A~gvl~al~~~gl~--vP~dvsvig~~d~  216 (269)
T cd06287         186 --VDAFAVGAVRAATELGRA--VPDQLRVVTRYDG  216 (269)
T ss_pred             --CcHHHHHHHHHHHHcCCC--CCCceEEEeccCc
Confidence              456777788888776553  565556666 344

This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.

>PF00532 Peripla_BP_1: Periplasmic binding proteins and sugar binding domain of LacI family; InterPro: IPR001761 This family includes the periplasmic binding proteins, and the LacI family transcriptional regulators

Probab=88.80  E-value=3.4  Score=36.38  Aligned_cols=117  Identities=21%  Similarity=0.271  Sum_probs=77.2

Q ss_pred             CCCE-EEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHH---HHHHhhhcC-CccEEEEEeeeeeCC
Q 027801           74 EGLR-FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGKSG-KYTAVLCIGAVVRGD  148 (218)
Q Consensus        74 ~~~R-IaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~---aak~L~~~~-~yDaVIaLG~VIrGe  148 (218)
                      ...| |+++...-+......-++|..+.|+++|.+.+...+.+  |.+..+.   ++++|++.+ .+|||+|..      
T Consensus       117 Gh~~~I~~i~~~~~~~~~~~R~~Gy~~Al~~~Gl~~~~~~i~~--~~~~~~~g~~~~~~ll~~~p~idai~~~n------  188 (279)
T PF00532_consen  117 GHRRPIAFIGGPEDSSTSRERLQGYRDALKEAGLPIDEEWIFE--GDFDYESGYEAARELLESHPDIDAIFCAN------  188 (279)
T ss_dssp             TCCSTEEEEEESTTTHHHHHHHHHHHHHHHHTTSCEEEEEEEE--SSSSHHHHHHHHHHHHHTSTT-SEEEESS------
T ss_pred             ccCCeEEEEecCcchHHHHHHHHHHHHHHHHcCCCCCcccccc--cCCCHHHHHHHHHHHHhhCCCCEEEEEeC------
Confidence            3467 99999988877888888999999999999543444443  5566553   346666655 678999864      


Q ss_pred             chhHHHHHHHHHHHHHHhc-hhcCCceEE-----EEcCCCCH----------------HHHHHhhCCCCCCcHHHHHHHH
Q 027801          149 TTHYDAVANSAASGVLSAG-VNSGVPCIF-----GVLTCDNM----------------DQALNRAGGKSGNKGAEAALTA  206 (218)
Q Consensus       149 T~H~e~Va~~vs~gLm~ls-L~~~vPVif-----GVLT~~n~----------------eQA~~Rag~k~gnKG~EAA~aA  206 (218)
                          |.++-.+.+++.+.. +  .+|--.     +|++-++.                +|-.       ..-|.+||+-.
T Consensus       189 ----d~~A~ga~~~l~~~gr~--~ip~di~~~~~~v~g~d~~~~~~~~~~~~~~lt~i~~~~-------~~~G~~a~~~l  255 (279)
T PF00532_consen  189 ----DMMAIGAIRALRERGRL--KIPEDIVSGFDSVVGFDNLEDPDFSTLEQPPLTTIQQPA-------YEMGRQAAEML  255 (279)
T ss_dssp             ----HHHHHHHHHHHHHTT-T--CTTTEEEECSCCCGGHHHCCTCCT-SCCSCCEEECHHHH-------HHHHHHHHHHH
T ss_pred             ----HHHHHHHHHHHHHcCCc--ccChhheeeeccchhhccccccccccccCCCeeEEecCC-------CchHHHHHHHH
Confidence                457777777777766 3  355333     33332222                2222       24589999998


Q ss_pred             HHHHH
Q 027801          207 IEMAS  211 (218)
Q Consensus       207 leM~~  211 (218)
                      ++++.
T Consensus       256 ~~~I~  260 (279)
T PF00532_consen  256 LERIN  260 (279)
T ss_dssp             HHHHH
T ss_pred             HHHHh
Confidence            88773

The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The LacI family of proteins consist of transcriptional regulators related to the lac repressor. In this case, generally the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain (lacI) [, ].; PDB: 1BAP_A 7ABP_A 6ABP_A 1ABF_A 5ABP_A 2WRZ_B 9ABP_A 1APB_A 1ABE_A 8ABP_A ....

>cd06273 PBP1_GntR_like_1 This group includes the ligand-binding domain of putative DNA transcription repressors which are highly similar to that of the repressor specific for gluconate (GntR), a member of the LacI-GalR family of bacterial transcription regulators

Probab=88.74  E-value=4.4  Score=33.73  Aligned_cols=100  Identities=20%  Similarity=0.221  Sum_probs=59.8

Q ss_pred             CCEEEEEEccc-CHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcch--HHHHHHHhhh-cCCccEEEEEeeeeeCCch
Q 027801           75 GLRFALVVARF-NELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE--IGVVAQQLGK-SGKYTAVLCIGAVVRGDTT  150 (218)
Q Consensus        75 ~~RIaIV~Srf-n~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~E--LP~aak~L~~-~~~yDaVIaLG~VIrGeT~  150 (218)
                      ..||+++...- +......-.+|..+.|+++|+......++..+..++  ...+ +.+++ ..++|||+|.+        
T Consensus       116 ~~~i~~i~~~~~~~~~~~~r~~gf~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~l~~~~~~~ai~~~~--------  186 (268)
T cd06273         116 HRRIAMIFGPTQGNDRARARRAGVRAALAEAGLELPELWQVEAPYSIADGRAAL-RQLLEQPPRPTAVICGN--------  186 (268)
T ss_pred             CCeEEEEeccccCCccHHHHHHHHHHHHHHcCCCCCHHHeeeCCCcHHHHHHHH-HHHHcCCCCCCEEEEcC--------
Confidence            45899997543 222334567899999999997644444555555554  2333 34443 45699999843        


Q ss_pred             hHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHH
Q 027801          151 HYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQA  187 (218)
Q Consensus       151 H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA  187 (218)
                        +.++..+.+.+.+..+  .+|=--.|++.++...+
T Consensus       187 --~~~a~~~~~~l~~~g~--~~p~~i~vig~d~~~~~  219 (268)
T cd06273         187 --DVLALGALYEARRLGL--SVPEDLSIVGFDDIDGS  219 (268)
T ss_pred             --hHHHHHHHHHHHHcCC--CCCCceEEEecCChhHH
Confidence              3356666666665544  34544455556665554

This group includes the ligand-binding domain of putative DNA transcription repressors which are highly similar to that of the repressor specific for gluconate (GntR), a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational

>cd06354 PBP1_BmpA_PnrA_like Periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its homologs from other bacteria and Archaea

Probab=88.43  E-value=2.5  Score=36.21  Aligned_cols=63  Identities=17%  Similarity=0.182  Sum_probs=39.9

Q ss_pred             EEEEEEcc---cCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEee
Q 027801           77 RFALVVAR---FNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        77 RIaIV~Sr---fn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~  143 (218)
                      |||+|..+   .....-..++++..++++++|+.   +.+...-..-+.--.++.| ...++||||.+++
T Consensus         1 ~I~~i~~~~~~~~~~f~~~~~~gi~~~~~~~gy~---~~i~~~~~~~~~~~~i~~l-~~~~vdgiI~~~~   66 (265)
T cd06354           1 KVALVTDVGGLGDKSFNQSAWEGLERAAKELGIE---YKYVESKSDADYEPNLEQL-ADAGYDLIVGVGF   66 (265)
T ss_pred             CEEEEeCCCCcCchhHHHHHHHHHHHHHHHcCCe---EEEEecCCHHHHHHHHHHH-HhCCCCEEEEcCc
Confidence            68888876   56677778889999999998874   3333221111111223443 4578999998765

Periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its homologs from other bacteria and Archaea. The PnrA lipoprotein, also known as Tp0319 or TmpC, represents a novel family of bacterial purine nucleoside receptor encoded within an ATP-binding cassette (ABC) transport system (pnrABCDE). It shows a striking structural similarity to another basic membrane lipoprotein Med which regulates the competence transcription factor gene, comK, in Bacillus subtilis. The members of PnrA-like subgroup are likely to have similar nucleoside-binding functions and a similar type I periplasmic sugar-binding protein-like fold.

>cd01574 PBP1_LacI Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators

Probab=88.24  E-value=2.7  Score=34.88  Aligned_cols=62  Identities=8%  Similarity=0.047  Sum_probs=42.6

Q ss_pred             EEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcc-hHH-HHHHHhhhcCCccEEEEEee
Q 027801           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSF-EIG-VVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        78 IaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~-ELP-~aak~L~~~~~yDaVIaLG~  143 (218)
                      ||+|...++......+++++.+.++++|..   +.++.-...- +.. -.++.+ .+.++||+|..++
T Consensus         2 i~vi~~~~~~~~~~~~~~gi~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~l-~~~~vdgiii~~~   65 (264)
T cd01574           2 IGVVTTDLALHGPSSTLAAIESAAREAGYA---VTLSMLAEADEEALRAAVRRL-LAQRVDGVIVNAP   65 (264)
T ss_pred             EEEEeCCCCcccHHHHHHHHHHHHHHCCCe---EEEEeCCCCchHHHHHHHHHH-HhcCCCEEEEeCC
Confidence            788998888888889999999999998874   4444333211 111 122333 4567999999876

Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of LacI is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA b

>cd06323 PBP1_ribose_binding Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs

Probab=88.09  E-value=10  Score=31.38  Aligned_cols=96  Identities=20%  Similarity=0.202  Sum_probs=57.2

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHC-CCCCCCeEEEEeCCcchH---HHHHHHhhh-cCCccEEEEEeeeeeCC
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKY-SVKEENIDVVWVPGSFEI---GVVAQQLGK-SGKYTAVLCIGAVVRGD  148 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~-Gv~~e~I~vv~VPGA~EL---P~aak~L~~-~~~yDaVIaLG~VIrGe  148 (218)
                      ...||+++.+.-.........+|..+.|+++ |+.   +. ....+.+..   --.+..+++ ..++|+|+|-+      
T Consensus       120 g~~~i~~l~~~~~~~~~~~r~~g~~~~l~~~~~~~---~~-~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~------  189 (268)
T cd06323         120 GKGKVVELQGIPGASAARERGKGFHEVVDKYPGLK---VV-ASQPADFDRAKGLNVMENILQAHPDIKGVFAQN------  189 (268)
T ss_pred             CCceEEEEeCCCCCccHHHHHHHHHHHHHhCCCcE---EE-ecccCCCCHHHHHHHHHHHHHHCCCcCEEEEcC------
Confidence            3468999987544444556679999999985 653   11 112333332   233444443 35689988743      


Q ss_pred             chhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHH
Q 027801          149 TTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQAL  188 (218)
Q Consensus       149 T~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~  188 (218)
                          +.++..+.+++.+..+ .+++|+ |   .++.+++.
T Consensus       190 ----d~~a~~~~~~l~~~g~-~di~ii-g---~d~~~~~~  220 (268)
T cd06323         190 ----DEMALGAIEALKAAGK-DDVKVV-G---FDGTPDAL  220 (268)
T ss_pred             ----CchHHHHHHHHHHcCC-CCcEEE-E---eCCCHHHH
Confidence                4467777788888777 455543 3   45555443

Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs. Members of this group are belonging to the type I periplasmic binding protein superfamily, whose members are involved in chemotaxis, ATP-binding cassette transport, and intercellular communication in central nervous system. The thermophilic and mesophilic ribose-binding proteins are structurally very similar, but differ substantially in thermal stability.

>cd06298 PBP1_CcpA_like Ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation

Probab=88.07  E-value=2.9  Score=34.74  Aligned_cols=61  Identities=11%  Similarity=0.156  Sum_probs=40.6

Q ss_pred             EEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHH---HHHHhhhcCCccEEEEEee
Q 027801           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        77 RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~---aak~L~~~~~yDaVIaLG~  143 (218)
                      .|++|...++...-..++++..+.++++|..   +.++  +...+..-   .++.+. ..++||+|..++
T Consensus         1 ~i~vi~~~~~~~~~~~~~~~~~~~~~~~g~~---~~~~--~~~~~~~~~~~~i~~l~-~~~vdgiii~~~   64 (268)
T cd06298           1 TVGVIIPDITNSYFAELARGIDDIATMYKYN---IILS--NSDNDKEKELKVLNNLL-AKQVDGIIFMGG   64 (268)
T ss_pred             CEEEEECCCcchHHHHHHHHHHHHHHHcCCe---EEEE--eCCCCHHHHHHHHHHHH-HhcCCEEEEeCC
Confidence            3788888888888888889999999988863   3333  33333222   223333 467899998764

Ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. In gram-positive bacteria, CCR is controlled by HPr, a phosphoenolpyruvate:sugar phsophotrasnferase system (PTS) and a transcriptional regulator CcpA. Moreover, CcpA can regulate sporulation and antibiotic resistance as well as play a role in virulence development of certain pathogens such as the group A streptococcus. The ligand binding domain of CcpA is a member of the LacI-GalR family of bacterial transcription regulators.

>PRK10727 DNA-binding transcriptional regulator GalR; Provisional

Probab=88.05  E-value=5.9  Score=34.93  Aligned_cols=100  Identities=17%  Similarity=0.217  Sum_probs=63.6

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH---HHHHHhhhc-CCccEEEEEeeeeeCCc
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGKS-GKYTAVLCIGAVVRGDT  149 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP---~aak~L~~~-~~yDaVIaLG~VIrGeT  149 (218)
                      ...||+++...-+......=.+|..+.|+++|+..+...+  ..|.++.-   -+++.+++. .++|||+|..       
T Consensus       175 G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~gi~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~n-------  245 (343)
T PRK10727        175 GHTRIGYLCSNHSISDAEDRLQGYYDALAESGIPANDRLV--TFGEPDESGGEQAMTELLGRGRNFTAVACYN-------  245 (343)
T ss_pred             CCccEEEEeCCccccchHHHHHHHHHHHHHCCCCCChhhE--EeCCCChhHHHHHHHHHHhCCCCCCEEEEcC-------
Confidence            3468999976554333344558999999999986332222  23544432   234555544 4689998854       


Q ss_pred             hhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHH
Q 027801          150 THYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQA  187 (218)
Q Consensus       150 ~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA  187 (218)
                         |.++-.+.++|.+..+  .+|==..|++.++...+
T Consensus       246 ---D~~A~g~~~al~~~G~--~vP~disVigfD~~~~~  278 (343)
T PRK10727        246 ---DSMAAGAMGVLNDNGI--DVPGEISLIGFDDVLVS  278 (343)
T ss_pred             ---cHHHHHHHHHHHHcCC--CCCcceeEEeecCcHHH
Confidence               4578888888888765  35655566677776654

>cd06275 PBP1_PurR Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli

Probab=87.98  E-value=2.8  Score=34.93  Aligned_cols=62  Identities=10%  Similarity=0.098  Sum_probs=42.0

Q ss_pred             EEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcch-HHHHHHHhhhcCCccEEEEEee
Q 027801           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE-IGVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        78 IaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~E-LP~aak~L~~~~~yDaVIaLG~  143 (218)
                      ||+|...+.......++++..+.+++.|+.   +.+.......+ .--.++.+. ..++||||..++
T Consensus         2 igvi~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~i~~l~-~~~vdgiii~~~   64 (269)
T cd06275           2 IGMLVTTSTNPFFAEVVRGVEQYCYRQGYN---LILCNTEGDPERQRSYLRMLA-QKRVDGLLVMCS   64 (269)
T ss_pred             EEEEeCCCCcchHHHHHHHHHHHHHHcCCE---EEEEeCCCChHHHHHHHHHHH-HcCCCEEEEecC
Confidence            788888887778888889999999998874   44443332222 223334443 467899999876

Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli. This dimeric PurR belongs to the LacI-GalR family of transcription regulators and is activated to bind to DNA operator sites by initially binding either of high affinity corepressors, hypoxanthine or guanine. PurR is composed of two functional domains: aan N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the purine transcription repressor undergoes a

>PRK15408 autoinducer 2-binding protein lsrB; Provisional

Probab=87.93  E-value=7.6  Score=35.39  Aligned_cols=65  Identities=15%  Similarity=0.084  Sum_probs=46.8

Q ss_pred             CCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHH---HHHHhhhcCCccEEEEEe
Q 027801           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGKSGKYTAVLCIG  142 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~---aak~L~~~~~yDaVIaLG  142 (218)
                      ..+.+|++|....+...-..+.+|+.+.++++|+.   +. +.-|.-.+..-   .++.+. ..++||||...
T Consensus        21 ~~~~~i~~v~k~~~~pf~~~~~~Gi~~aa~~~G~~---v~-~~~~~~~d~~~q~~~i~~li-~~~vdgIiv~~   88 (336)
T PRK15408         21 QAAERIAFIPKLVGVGFFTSGGNGAKEAGKELGVD---VT-YDGPTEPSVSGQVQLINNFV-NQGYNAIIVSA   88 (336)
T ss_pred             cCCcEEEEEECCCCCHHHHHHHHHHHHHHHHhCCE---EE-EECCCCCCHHHHHHHHHHHH-HcCCCEEEEec
Confidence            56779999998887788889999999999999974   32 22565444332   233443 57899998853

>cd06290 PBP1_LacI_like_9 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors

Probab=87.84  E-value=6.8  Score=32.63  Aligned_cols=100  Identities=18%  Similarity=0.231  Sum_probs=62.6

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchH---HHHHHHhhhc-CCccEEEEEeeeeeCCc
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEI---GVVAQQLGKS-GKYTAVLCIGAVVRGDT  149 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~EL---P~aak~L~~~-~~yDaVIaLG~VIrGeT  149 (218)
                      ...||+++...-+......-.+|..+.+.++|++....  ..+++.++.   --++++++++ .++|||+|.+       
T Consensus       114 g~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~l~~~~~~~aii~~~-------  184 (265)
T cd06290         114 GHRRIAHITGPRGHIDARDRLAGYRKALEEAGLEVQPD--LIVQGDFEEESGLEAVEELLQRGPDFTAIFAAN-------  184 (265)
T ss_pred             CCCeEEEEeCccccchhhHHHHHHHHHHHHcCCCCCHH--HEEecCCCHHHHHHHHHHHHcCCCCCCEEEEcC-------
Confidence            34689999876555555667799999999998753221  223444432   2245556544 4689999853       


Q ss_pred             hhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHH
Q 027801          150 THYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQA  187 (218)
Q Consensus       150 ~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA  187 (218)
                         +.++..+.+.+.+..+  .+|==..|++.++.+.+
T Consensus       185 ---~~~a~~~~~~l~~~g~--~ip~di~vi~~d~~~~~  217 (265)
T cd06290         185 ---DQTAYGARLALYRRGL--RVPEDVSLIGFDDLPLS  217 (265)
T ss_pred             ---cHHHHHHHHHHHHcCC--CCCcceEEeeecCchHH
Confidence               3356666677766654  35555667777766544

This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.

>cd06274 PBP1_FruR Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs

Probab=87.61  E-value=2.8  Score=35.05  Aligned_cols=29  Identities=3%  Similarity=0.038  Sum_probs=18.4

Q ss_pred             EEEEEcccCHHHHHHHHHHHHHHHHHCCC
Q 027801           78 FALVVARFNELVTKLLLEGALETFKKYSV  106 (218)
Q Consensus        78 IaIV~Srfn~~It~~Ll~gA~~~L~~~Gv  106 (218)
                      ||++...|-...-..+.++..+.++++|+
T Consensus         2 igvi~~~~~~~~~~~~~~~~~~~~~~~g~   30 (264)
T cd06274           2 IGLIIPDLENRSFARIAKRLEALARERGY   30 (264)
T ss_pred             EEEEeccccCchHHHHHHHHHHHHHHCCC
Confidence            55666665555566666666666666665

Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs, all of which are a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to members of the type I periplasmic binding protein superfamily. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor

>cd06285 PBP1_LacI_like_7 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors

Probab=87.54  E-value=6.3  Score=32.90  Aligned_cols=100  Identities=16%  Similarity=0.179  Sum_probs=63.8

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHH---HHHHhhhc-CCccEEEEEeeeeeCCc
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGKS-GKYTAVLCIGAVVRGDT  149 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~---aak~L~~~-~~yDaVIaLG~VIrGeT  149 (218)
                      ...||+++.+.-+......-.+|..+.++++|+..+...++  .+.++..-   .++.+++. .++|||+|.+..     
T Consensus       113 g~~~i~~i~~~~~~~~~~~R~~Gf~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~d~-----  185 (265)
T cd06285         113 GHRRIAVLAGPDYASTARDRLAGFRAALAEAGIEVPPERIV--YSGFDIEGGEAAAEKLLRSDSPPTAIFAVNDF-----  185 (265)
T ss_pred             CCccEEEEeCCcccccHHHHHHHHHHHHHHcCCCCChhhEE--eCCCCHHHHHHHHHHHHcCCCCCCEEEEcCcH-----
Confidence            34689999876655555566899999999999753222222  23344322   23444433 468999998764     


Q ss_pred             hhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHH
Q 027801          150 THYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQA  187 (218)
Q Consensus       150 ~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA  187 (218)
                           ++-.+.+++.+..+  .+|==..|++.++.+.+
T Consensus       186 -----~a~g~~~~l~~~g~--~~p~di~iig~d~~~~~  216 (265)
T cd06285         186 -----AAIGVMGAARDRGL--RVPDDVALVGYNDIPLV  216 (265)
T ss_pred             -----HHHHHHHHHHHcCC--CCCcceEEEeecCcHHH
Confidence                 66677777776654  35556677777776654

This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.

>COG1609 PurR Transcriptional regulators [Transcription]

Probab=87.52  E-value=3.2  Score=37.79  Aligned_cols=66  Identities=12%  Similarity=0.062  Sum_probs=48.4

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEe
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIG  142 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG  142 (218)
                      +..-|++|...+....-..++.|..+.+.++|..   +.+......-|----+...+...++||+|.+|
T Consensus        57 ~s~~Ig~i~p~~~~~~~~~i~~gi~~~~~~~gy~---~~l~~~~~~~~~e~~~~~~l~~~~vdGiIi~~  122 (333)
T COG1609          57 RTKTIGLVVPDITNPFFAEILKGIEEAAREAGYS---LLLANTDDDPEKEREYLETLLQKRVDGLILLG  122 (333)
T ss_pred             CCCEEEEEeCCCCCchHHHHHHHHHHHHHHcCCE---EEEECCCCCHHHHHHHHHHHHHcCCCEEEEec
Confidence            4446899998888888889999999999999974   44444444334333444445678999999999

>PRK15395 methyl-galactoside ABC transporter galactose-binding periplasmic protein MglB; Provisional

Probab=87.43  E-value=9.9  Score=33.97  Aligned_cols=66  Identities=6%  Similarity=0.031  Sum_probs=46.4

Q ss_pred             CCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHH---HHHHhhhcCCccEEEEEee
Q 027801           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~---aak~L~~~~~yDaVIaLG~  143 (218)
                      .++.+||+|...+....-..++++..+.++++|.    +.++.+++..+-..   .++.| ...++||+|..++
T Consensus        22 ~~~~~Igvv~~~~~~~f~~~~~~gi~~~a~~~g~----~~~~~~~~~~~~~~~~~~i~~l-~~~~vdgiIi~~~   90 (330)
T PRK15395         22 AADTRIGVTIYKYDDNFMSVVRKAIEKDAKAAPD----VQLLMNDSQNDQSKQNDQIDVL-LAKGVKALAINLV   90 (330)
T ss_pred             cCCceEEEEEecCcchHHHHHHHHHHHHHHhcCC----eEEEEecCCCCHHHHHHHHHHH-HHcCCCEEEEecc
Confidence            5667899999887777888999999999999863    34444454443222   23333 4578999998754

>cd06306 PBP1_TorT-like TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria

Probab=87.41  E-value=7.7  Score=32.88  Aligned_cols=122  Identities=11%  Similarity=0.108  Sum_probs=70.7

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHH-HHHHhhhc-CCccEEEEEeeeeeCCchh
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV-VAQQLGKS-GKYTAVLCIGAVVRGDTTH  151 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~-aak~L~~~-~~yDaVIaLG~VIrGeT~H  151 (218)
                      ...||+++...-+......-.+|..+.++++|+..  ..+.......|-.+ +++.+++. .++|+|+|        +  
T Consensus       124 ~~~~i~~l~g~~~~~~~~~R~~g~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~l~~~~~~~~i~~--------~--  191 (268)
T cd06306         124 KPAKVAWFPGPKGAGWVKAVEKGFRDALAGSAIEI--SAIKYGDTGKEVQRKLVEEALEAHPDIDYIVG--------S--  191 (268)
T ss_pred             CCceEEEEeCCCCCchHHHHHHHHHHHHhhcCcEE--eeeccCCccHHHHHHHHHHHHHhCCCcCEEee--------c--
Confidence            34799999887666667777899999999988641  12222222333332 33444443 56898763        1  


Q ss_pred             HHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHhhCC----CCC---CcHHHHHHHHHHHH
Q 027801          152 YDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGG----KSG---NKGAEAALTAIEMA  210 (218)
Q Consensus       152 ~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~Rag~----k~g---nKG~EAA~aAleM~  210 (218)
                       +..+..+.+.+.+..+-.++.|+ |.......-+++.. |.    -..   .-|..|+..+++++
T Consensus       192 -d~~a~~~~~~l~~~g~p~di~vi-g~~~~p~~~~~l~~-g~~~ttv~~~~~~~G~~a~~~l~~~l  254 (268)
T cd06306         192 -AVAAEAAVGILRQRGLTDQIKIV-STYLSHAVYRGLKR-GKILAAPTDSMVLQGRLAIDQAVRIL  254 (268)
T ss_pred             -chhhhHHHHHHHhcCCCCCeEEE-ecCCCHHHHHHHHc-CceEEEEecCHHHHHHHHHHHHHHHH
Confidence             45677788888876653344444 55444445566633 31    112   23666666666654

TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria. The Tor respiratory system is consists of three proteins (TorC, TorA, and TorD) and is induced in the presence of TMAO. The TMAO control is tightly regulated by three proteins: TorS, TorT, and TorR. Thus, the disruption of any of these proteins can abolish the Tor respiratory induction. TorT shares homology with the sugar-binding domain of the type I periplasmic binding proteins. The members of TorT-like family bind TMAO or related compounds and are predicted to be involved in signal transduction and/or substrate transport.

>cd06295 PBP1_CelR Ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators

Probab=87.39  E-value=3.4  Score=34.75  Aligned_cols=63  Identities=25%  Similarity=0.354  Sum_probs=41.8

Q ss_pred             CEEEEEEcc-------cCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEee
Q 027801           76 LRFALVVAR-------FNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        76 ~RIaIV~Sr-------fn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~  143 (218)
                      ..||||+.+       +....-..+++++.+.++++|++   +.++..... +...+.+.+ ...++||||..++
T Consensus         4 ~~i~vi~p~~~~~~~~~~~~~~~~~~~gi~~~~~~~g~~---~~v~~~~~~-~~~~~~~~l-~~~~~dgiii~~~   73 (275)
T cd06295           4 DTIALVVPEPHERDQSFSDPFFLSLLGGIADALAERGYD---LLLSFVSSP-DRDWLARYL-ASGRADGVILIGQ   73 (275)
T ss_pred             eEEEEEecCccccccccCCchHHHHHHHHHHHHHHcCCE---EEEEeCCch-hHHHHHHHH-HhCCCCEEEEeCC
Confidence            357888864       45556677888899999998874   555544333 444444433 4578999998775

This group includes the ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators. The binding of CelR to the celE promoter is inhibited specifically by cellobiose. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn chang

>cd06306 PBP1_TorT-like TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria

Probab=87.27  E-value=2.5  Score=35.90  Aligned_cols=62  Identities=11%  Similarity=0.109  Sum_probs=43.0

Q ss_pred             EEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCC--cch-HHHHHHHhhhcCCccEEEEEe
Q 027801           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPG--SFE-IGVVAQQLGKSGKYTAVLCIG  142 (218)
Q Consensus        77 RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPG--A~E-LP~aak~L~~~~~yDaVIaLG  142 (218)
                      ||+||+.+++......++.+..++++++|+.   +.+....+  ..+ .--.++.+. ..++||||..+
T Consensus         1 ~Igvi~~~~~~~f~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~i~~~~-~~~vdgiI~~~   65 (268)
T cd06306           1 KLCVLYPHLKDAYWLSVNYGMVEEAKRLGVS---LKLLEAGGYPNLAKQIAQLEDCA-AWGADAILLGA   65 (268)
T ss_pred             CeEEEcCCCCCHHHHHHHHHHHHHHHHcCCE---EEEecCCCCCCHHHHHHHHHHHH-HcCCCEEEEcC
Confidence            6899999999888999999999999999873   43332111  111 112345554 46899999664

TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria. The Tor respiratory system is consists of three proteins (TorC, TorA, and TorD) and is induced in the presence of TMAO. The TMAO control is tightly regulated by three proteins: TorS, TorT, and TorR. Thus, the disruption of any of these proteins can abolish the Tor respiratory induction. TorT shares homology with the sugar-binding domain of the type I periplasmic binding proteins. The members of TorT-like family bind TMAO or related compounds and are predicted to be involved in signal transduction and/or substrate transport.

>PRK10401 DNA-binding transcriptional regulator GalS; Provisional

Probab=87.27  E-value=5.4  Score=35.24  Aligned_cols=123  Identities=15%  Similarity=0.125  Sum_probs=72.8

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcc--hHHH-HHHHhhhc-CCccEEEEEeeeeeCCc
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSF--EIGV-VAQQLGKS-GKYTAVLCIGAVVRGDT  149 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~--ELP~-aak~L~~~-~~yDaVIaLG~VIrGeT  149 (218)
                      ...||++|.+.-+......-.+|..+.|+++|+......+  ..|.+  |-.+ .++++++. .++|||+|..       
T Consensus       175 G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~gi~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~n-------  245 (346)
T PRK10401        175 GHQRIGYLSSSHGIEDDAMRRAGWMSALKEQGIIPPESWI--GTGTPDMQGGEAAMVELLGRNLQLTAVFAYN-------  245 (346)
T ss_pred             CCCeEEEEeCCCcCcchHHHHHHHHHHHHHcCCCCChhhe--ecCCCChHHHHHHHHHHHcCCCCCcEEEECC-------
Confidence            3568999977655444556678999999999985332222  23433  3222 34455543 4689999864       


Q ss_pred             hhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHhh------CCCCCCcHHHHHHHHHHHH
Q 027801          150 THYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRA------GGKSGNKGAEAALTAIEMA  210 (218)
Q Consensus       150 ~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~Ra------g~k~gnKG~EAA~aAleM~  210 (218)
                         |.++..+.+.+.+..++  +|==..|++.++.+.+..-.      .-....-|.+|+...++++
T Consensus       246 ---d~~A~g~~~al~~~G~~--vP~disvigfD~~~~~~~~~p~lttv~~~~~~~g~~A~~~l~~~i  307 (346)
T PRK10401        246 ---DNMAAGALTALKDNGIA--IPLHLSIIGFDDIPIARYTDPQLTTVRYPIASMAKLATELALQGA  307 (346)
T ss_pred             ---cHHHHHHHHHHHHcCCC--CCCceEEEEeCCchHHhcCCCCCceeecCHHHHHHHHHHHHHHHh
Confidence               45777788888876553  66555666667665443210      0112234666666655554

>PRK09701 D-allose transporter subunit; Provisional

Probab=87.24  E-value=3.7  Score=36.15  Aligned_cols=67  Identities=13%  Similarity=0.180  Sum_probs=48.9

Q ss_pred             CCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHH---HHHhhhcCCccEEEEEee
Q 027801           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVV---AQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~a---ak~L~~~~~yDaVIaLG~  143 (218)
                      ....+|++|...+....-..+.+++.++++++|+.   +.++..|+..+..--   ++.+ ...++||+|..+.
T Consensus        22 ~~~~~Igvi~~~~~~~f~~~~~~gi~~~a~~~g~~---v~~~~~~~~~~~~~~~~~i~~l-~~~~vDgiIi~~~   91 (311)
T PRK09701         22 FAAAEYAVVLKTLSNPFWVDMKKGIEDEAKTLGVS---VDIFASPSEGDFQSQLQLFEDL-SNKNYKGIAFAPL   91 (311)
T ss_pred             ccCCeEEEEeCCCCCHHHHHHHHHHHHHHHHcCCe---EEEecCCCCCCHHHHHHHHHHH-HHcCCCEEEEeCC
Confidence            34569999999988888889999999999999874   444444666655433   2333 3567999998763

>cd06311 PBP1_ABC_sugar_binding_like_3 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems

Probab=87.23  E-value=6  Score=33.33  Aligned_cols=66  Identities=14%  Similarity=0.092  Sum_probs=43.0

Q ss_pred             EEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH---HHHHHhhhcCCccEEEEEee
Q 027801           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        77 RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP---~aak~L~~~~~yDaVIaLG~  143 (218)
                      .|+++...+.......|++++.++++++|-...+++++.+.+..+-.   -.++.+ ...++||||..+.
T Consensus         1 ~Ig~i~~~~~~~f~~~~~~gi~~~a~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~l-~~~~vDgiii~~~   69 (274)
T cd06311           1 TIGVSIPAADHGWTAGIVWHAQAAAKKLEAAYPDVEFILVTASNDTEQQNAQQDLL-INRKIDALVILPF   69 (274)
T ss_pred             CeeeeccCCCCcHHHHHHHHHHHHHHHhhhhCCCeEEEEEcCCCCHHHHHHHHHHH-HHcCCCEEEEeCC
Confidence            36788877777778889999999999875221235666666654322   222223 3467999998653

Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.

>cd01538 PBP1_ABC_xylose_binding Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily

Probab=87.04  E-value=4  Score=35.12  Aligned_cols=122  Identities=20%  Similarity=0.205  Sum_probs=67.7

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEE--EeCCcch---HHHHHHHhhhc-C-CccEEEEEeeeee
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVV--WVPGSFE---IGVVAQQLGKS-G-KYTAVLCIGAVVR  146 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv--~VPGA~E---LP~aak~L~~~-~-~yDaVIaLG~VIr  146 (218)
                      ...||+++...-+......-.+|..+.++++|... .+++.  ...+.+.   -.-+++.++++ . ++|+|+|.     
T Consensus       124 g~~~i~~l~g~~~~~~~~~R~~gf~~~l~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~I~~~-----  197 (288)
T cd01538         124 PPGNIELIAGSPTDNNAKLFFNGAMSVLKPLIDSG-KITIVGEVATPDWDPETAQKRMENALTANYNKVDGVLAA-----  197 (288)
T ss_pred             CCceEEEEECCCCCchHHHHHHHHHHHHHhccccC-CeeEEeccccCCCCHHHHHHHHHHHHHhCCCCccEEEeC-----
Confidence            45689999775444444556789999999987221 12211  1223332   12334455544 3 68999986     


Q ss_pred             CCchhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHhh--CC-------CCCCcHHHHHHHHHHHH
Q 027801          147 GDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRA--GG-------KSGNKGAEAALTAIEMA  210 (218)
Q Consensus       147 GeT~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~Ra--g~-------k~gnKG~EAA~aAleM~  210 (218)
                           .|.++..+.+.|.+..+.-++.    |++.++...++++.  +.       ....-|.+|+...++++
T Consensus       198 -----~d~~a~g~~~al~~~g~~~dv~----vvg~d~~~~~~~~i~~~~~~tti~~~~~~~G~~a~~~l~~~~  261 (288)
T cd01538         198 -----NDGTAGGAIAALKAAGLAGKPP----VTGQDAELAAVQRIVEGTQTMTVYKDIRELAEAAAELAVALL  261 (288)
T ss_pred             -----CcHHHHHHHHHHHHcCCCCCce----EEecCCCHHHHHHHHhCCceEEEecCHHHHHHHHHHHHHHHh
Confidence                 3456777777777766654333    44556555554431  21       13345666665555443

Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic xylose-binding protein is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR.

>cd06281 PBP1_LacI_like_5 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors

Probab=86.97  E-value=7.5  Score=32.61  Aligned_cols=100  Identities=19%  Similarity=0.143  Sum_probs=57.4

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcch--HHHHHHHhhhcCCccEEEEEeeeeeCCchh
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE--IGVVAQQLGKSGKYTAVLCIGAVVRGDTTH  151 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~E--LP~aak~L~~~~~yDaVIaLG~VIrGeT~H  151 (218)
                      ...||+++.+..+......-.+|..+.++++|+......++.. +.++  ...+-+.|.+...+|||+|.          
T Consensus       115 G~~~i~~l~~~~~~~~~~~R~~Gf~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~l~~~~~~~ai~~~----------  183 (269)
T cd06281         115 GHRRIALVGGGSNTRPGRERLEGYKAAFAAAGLPPDPALVRLS-TPAASGFDATRALLALPDRPTAIIAG----------  183 (269)
T ss_pred             CCcEEEEecCccccccHHHHHHHHHHHHHHcCCCCCHHHeecC-cHHHHHHHHHHHHHcCCCCCcEEEEc----------
Confidence            3458999988766555556779999999999975311112221 1122  12232333334568999873          


Q ss_pred             HHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHH
Q 027801          152 YDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQ  186 (218)
Q Consensus       152 ~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQ  186 (218)
                      .+.++..+.++|.+..++  +|==..|++.++.+.
T Consensus       184 ~d~~a~g~~~~l~~~g~~--ip~dv~iig~d~~~~  216 (269)
T cd06281         184 GTQVLVGVLRALREAGLR--IPRDLSVISIGDSDL  216 (269)
T ss_pred             CcHHHHHHHHHHHHcCCC--CCcceeEEEecCchH
Confidence            344566677777665543  443344555565443

This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.

>TIGR02955 TMAO_TorT TMAO reductase system periplasmic protein TorT

Probab=86.92  E-value=2.8  Score=36.32  Aligned_cols=62  Identities=18%  Similarity=0.080  Sum_probs=41.2

Q ss_pred             EEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcch---HHHHHHHhhhcCCccEEEEEe
Q 027801           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE---IGVVAQQLGKSGKYTAVLCIG  142 (218)
Q Consensus        77 RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~E---LP~aak~L~~~~~yDaVIaLG  142 (218)
                      ||++|+..++...-..+++++.++++++|+.   +.+....+-.+   ---.++.+ ...++||+|..+
T Consensus         1 ~igvvvp~~~n~f~~~~~~gi~~~a~~~g~~---v~~~~~~~~~~~~~~~~~i~~l-~~~~vDgiIi~~   65 (295)
T TIGR02955         1 KLCALYPHLKDSYWLSINYGMVEQAKHLGVE---LKVLEAGGYPNLDKQLAQIEQC-KSWGADAILLGT   65 (295)
T ss_pred             CeeEEecCCCcHHHHHHHHHHHHHHHHhCCE---EEEEcCCCCCCHHHHHHHHHHH-HHcCCCEEEEec
Confidence            6888888888888888889999999998873   44443322111   21233444 357799988754

Members of this family are the periplasmic protein TorT which, together with the the TorS/TorR histidine kinase/response regulator system, regulates expression of the torCAD operon for trimethylamine N-oxide reductase (TMAO reductase). It appears to bind an inducer for TMAO reductase, and shows homology to a periplasmic D-ribose binding protein.

>PRK11303 DNA-binding transcriptional regulator FruR; Provisional

Probab=86.60  E-value=3.6  Score=35.79  Aligned_cols=67  Identities=6%  Similarity=0.044  Sum_probs=44.4

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHHhhhcCCccEEEEEeee
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGAV  144 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~L~~~~~yDaVIaLG~V  144 (218)
                      +...|++|...+....-..++++..++++++|+.   +.+...-...+-- -.++.+ ...++||+|.++..
T Consensus        60 ~~~~Igvv~~~~~~~~~~~l~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~~~~l-~~~~vdgiIi~~~~  127 (328)
T PRK11303         60 RTRSIGLIIPDLENTSYARIAKYLERQARQRGYQ---LLIACSDDQPDNEMRCAEHL-LQRQVDALIVSTSL  127 (328)
T ss_pred             CCceEEEEeCCCCCchHHHHHHHHHHHHHHcCCE---EEEEeCCCCHHHHHHHHHHH-HHcCCCEEEEcCCC
Confidence            4457999998877667778999999999999974   4443322112211 223333 45689999988754

>PRK10703 DNA-binding transcriptional repressor PurR; Provisional

Probab=86.54  E-value=4.2  Score=35.67  Aligned_cols=66  Identities=8%  Similarity=0.018  Sum_probs=45.6

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHH-HHHhhhcCCccEEEEEee
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVV-AQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~a-ak~L~~~~~yDaVIaLG~  143 (218)
                      +...|+++...+.......+++|..++++++|+.   +.++.-.+..+-..- ++.+ ...++||+|..+.
T Consensus        58 ~~~~i~vi~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~i~~l-~~~~vdgiii~~~  124 (341)
T PRK10703         58 HTKSIGLLATSSEAPYFAEIIEAVEKNCYQKGYT---LILCNAWNNLEKQRAYLSML-AQKRVDGLLVMCS  124 (341)
T ss_pred             CCCeEEEEeCCCCCchHHHHHHHHHHHHHHCCCE---EEEEeCCCCHHHHHHHHHHH-HHcCCCEEEEecC
Confidence            4568999999988888889999999999999974   444433332332222 2333 4567999998764

>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor

Probab=86.47  E-value=3.6  Score=35.90  Aligned_cols=68  Identities=9%  Similarity=0.131  Sum_probs=46.2

Q ss_pred             CCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchH-HHHHHHhhhcCCccEEEEEeee
Q 027801           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEI-GVVAQQLGKSGKYTAVLCIGAV  144 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~EL-P~aak~L~~~~~yDaVIaLG~V  144 (218)
                      .+...|+++...+....-..++++..++++++|+.   +.+....+.-+- --.++.+ ...++||+|..+..
T Consensus        58 ~~~~~Igvi~~~~~~~~~~~~~~~i~~~~~~~gy~---~~i~~~~~~~~~~~~~~~~l-~~~~vdgiIi~~~~  126 (327)
T TIGR02417        58 GRSRTIGLVIPDLENYSYARIAKELEQQCREAGYQ---LLIACSDDNPDQEKVVIENL-LARQVDALIVASCM  126 (327)
T ss_pred             CCCceEEEEeCCCCCccHHHHHHHHHHHHHHCCCE---EEEEeCCCCHHHHHHHHHHH-HHcCCCEEEEeCCC
Confidence            34568999998887777788999999999999974   444443332221 1233444 45789999988753

Members of this family belong the lacI helix-turn-helix family (pfam00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer.

>cd06272 PBP1_hexuronate_repressor_like Ligand-binding domain of DNA transcription repressor for the hexuronate utilization operon from Bacillus species and its close homologs from other bacteria, all of which are a member of the LacI-GalR family of bacterial transcription regulators

Probab=86.45  E-value=4.5  Score=33.72  Aligned_cols=124  Identities=17%  Similarity=0.121  Sum_probs=67.0

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHHhhhc-CCccEEEEEeeeeeCCchhH
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKS-GKYTAVLCIGAVVRGDTTHY  152 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~L~~~-~~yDaVIaLG~VIrGeT~H~  152 (218)
                      ..||+++...-.......-.+|..+.++++|+......+...+..++-. -+++++++. .++|||+|..-         
T Consensus       111 ~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~d---------  181 (261)
T cd06272         111 HKKIAYIGDLSLDRRQRKRFKGFLETCDENGISISDSHIDVDGLSAEGGDNAAKKLLKESDLPTAIICGSY---------  181 (261)
T ss_pred             chhEEEeecccccccHHHHHHHHHHHHHHcCCCCCHHHeeeCCCCHHHHHHHHHHHHcCCCCCCEEEECCc---------
Confidence            4589999765443333445689999999999742222233344444432 234555544 45899998543         


Q ss_pred             HHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHhhC------CCCCCcHHHHHHHHHHHH
Q 027801          153 DAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAG------GKSGNKGAEAALTAIEMA  210 (218)
Q Consensus       153 e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~Rag------~k~gnKG~EAA~aAleM~  210 (218)
                       .++..+.+++.+..++  +|==..|++.++.+++..--.      -....-|.+|+...++++
T Consensus       182 -~~a~~~~~~l~~~g~~--vp~dv~vvg~d~~~~~~~~~~~lttv~~~~~~~g~~a~~~l~~~l  242 (261)
T cd06272         182 -DIALGVLSALNKQGIS--IPEDIEIISYDNIPQMAIIDPPLTAVDVPIEEIAKKSLELLLKLI  242 (261)
T ss_pred             -HHHHHHHHHHHHhCCC--CCCceEEEeeCChhHHhhcCCCCceeeccHHHHHHHHHHHHHHHh
Confidence             3555666666555442  232234556666655532111      111234555555555544

Ligand-binding domain of DNA transcription repressor for the hexuronate utilization operon from Bacillus species and its close homologs from other bacteria, all of which are a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor

>cd06278 PBP1_LacI_like_2 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors

Probab=86.44  E-value=3.1  Score=34.38  Aligned_cols=62  Identities=15%  Similarity=0.143  Sum_probs=38.6

Q ss_pred             EEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEee
Q 027801           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        78 IaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~  143 (218)
                      ||+|...+.+..-..++++..+.++++|+.   +.++..+..-+.--.++.+. +.++||+|..++
T Consensus         2 I~~i~~~~~~~~~~~~~~~i~~~~~~~g~~---~~~~~~~~~~~~~~~i~~~~-~~~vdgiii~~~   63 (266)
T cd06278           2 IGVVVADLDNPFYSELLEALSRALQARGYQ---PLLINTDDDEDLDAALRQLL-QYRVDGVIVTSG   63 (266)
T ss_pred             EEEEeCCCCCchHHHHHHHHHHHHHHCCCe---EEEEcCCCCHHHHHHHHHHH-HcCCCEEEEecC
Confidence            577777777777777788888888888863   44443333223333344443 466888887654

This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.

>TIGR01481 ccpA catabolite control protein A

Probab=86.44  E-value=12  Score=32.63  Aligned_cols=123  Identities=21%  Similarity=0.155  Sum_probs=71.0

Q ss_pred             CCCEEEEEEcccCHH-HHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH---HHHHHhhhcCCccEEEEEeeeeeCCc
Q 027801           74 EGLRFALVVARFNEL-VTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGKSGKYTAVLCIGAVVRGDT  149 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~-It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP---~aak~L~~~~~yDaVIaLG~VIrGeT  149 (218)
                      ...||+++....+.. ....-.+|..+.|+++|+......++  .+.+...   -+++++++. ++|||+|.+       
T Consensus       175 G~~~I~~i~g~~~~~~~~~~R~~Gf~~~l~~~g~~~~~~~~~--~~~~~~~~~~~~~~~ll~~-~p~ai~~~~-------  244 (329)
T TIGR01481       175 GHKSIAFVGGPLSDSINGEDRLEGYKEALNKAGIQFGEDLVC--EGKYSYDAGYKAFAELKGS-LPTAVFVAS-------  244 (329)
T ss_pred             CCCeEEEEecCcccccchHHHHHHHHHHHHHcCCCCCcceEE--ecCCChHHHHHHHHHHhCC-CCCEEEEcC-------
Confidence            346899997654332 23455689999999999864322222  3444322   223445443 579999854       


Q ss_pred             hhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHhhC------CCCCCcHHHHHHHHHHHHH
Q 027801          150 THYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAG------GKSGNKGAEAALTAIEMAS  211 (218)
Q Consensus       150 ~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~Rag------~k~gnKG~EAA~aAleM~~  211 (218)
                         |.++-.+.+++.+..+  .+|==..|++-++.+.+..-..      -....-|..|+...+++++
T Consensus       245 ---d~~A~g~~~al~~~g~--~vP~dvsvvgfd~~~~~~~~~p~lttv~~~~~~~g~~Av~~L~~~i~  307 (329)
T TIGR01481       245 ---DEMAAGILNAAMDAGI--KVPEDLEVITSNNTRLTEMVRPQLSTIIQPLYDIGAVAMRLLTKYMN  307 (329)
T ss_pred             ---cHHHHHHHHHHHHcCC--CCCCceEEEeeCCchHHhhcCCCCcEEecCHHHHHHHHHHHHHHHhc
Confidence               4577778888877655  4565556666666554421110      0122356666666666554

Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.

>PRK14987 gluconate operon transcriptional regulator; Provisional

Probab=86.42  E-value=3.3  Score=36.24  Aligned_cols=65  Identities=8%  Similarity=-0.010  Sum_probs=44.3

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcc--hHHHHHHHhhhcCCccEEEEEee
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSF--EIGVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~--ELP~aak~L~~~~~yDaVIaLG~  143 (218)
                      ....||+|...+....-..+++++.+.++++|+.   +.+......-  |... ++.+ ...++||+|..++
T Consensus        62 ~~~~Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~-~~~~-~~~~vdgiI~~~~  128 (331)
T PRK14987         62 TSRAIGVLLPSLTNQVFAEVLRGIESVTDAHGYQ---TMLAHYGYKPEMEQER-LESM-LSWNIDGLILTER  128 (331)
T ss_pred             CCCEEEEEeCCCcchhHHHHHHHHHHHHHHCCCE---EEEecCCCCHHHHHHH-HHHH-HhcCCCEEEEcCC
Confidence            4457999999888778889999999999999973   3333222122  2222 2333 4678999998764

>cd06304 PBP1_BmpA_like Periplasmic binding component of a family of basic membrane lipoproteins from Borrelia and various putative lipoproteins from other bacteria

Probab=86.29  E-value=3.7  Score=34.73  Aligned_cols=62  Identities=19%  Similarity=0.201  Sum_probs=34.5

Q ss_pred             EEEEEEcc--cCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEe
Q 027801           77 RFALVVAR--FNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIG  142 (218)
Q Consensus        77 RIaIV~Sr--fn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG  142 (218)
                      ||++|...  +....-..|+++..+.+++.|+.   +.+...++.-+.--..+.| ...++||+|.++
T Consensus         1 ~Igvi~~~~~~~~~f~~~l~~gi~~~~~~~gy~---~~~~~~~~~~~~~~~~~~l-~~~~vdgiii~~   64 (260)
T cd06304           1 KVALVYDGGGGDKSFNQSAYEGLEKAEKELGVE---VKYVESVEDADYEPNLRQL-AAQGYDLIFGVG   64 (260)
T ss_pred             CEEEEecCCCCcchHHHHHHHHHHHHHHhcCce---EEEEecCCHHHHHHHHHHH-HHcCCCEEEECC
Confidence            57777764  44556667777888888877763   4443332111111222333 335678887764

Periplasmic binding component of a family of basic membrane lipoproteins from Borrelia and various putative lipoproteins from other bacteria. These outer membrane proteins include Med, a cell-surface localized protein regulating the competence transcription factor gene comK in Bacillus subtilis, and PnrA, a periplasmic purine nucleoside binding protein of an ATP-binding cassette (ABC) transport system in Treponema pallidum. All contain the type I periplasmic sugar-binding protein-like fold.

>cd06272 PBP1_hexuronate_repressor_like Ligand-binding domain of DNA transcription repressor for the hexuronate utilization operon from Bacillus species and its close homologs from other bacteria, all of which are a member of the LacI-GalR family of bacterial transcription regulators

Probab=86.27  E-value=3.5  Score=34.40  Aligned_cols=59  Identities=17%  Similarity=0.303  Sum_probs=41.5

Q ss_pred             EEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEee
Q 027801           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        78 IaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~  143 (218)
                      ||+|..++.+.....++.+..+.++++|..   +.+...+ ..+  -..+. +.+.++||+|..++
T Consensus         2 igvv~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~~~~~-~~~--~~~~~-l~~~~vdgii~~~~   60 (261)
T cd06272           2 IGLIWPSVSRVALTELVTGINQAISKNGYN---MNVSITP-SLA--EAEDL-FKENRFDGVIIFGE   60 (261)
T ss_pred             EEEEecCCCchhHHHHHHHHHHHHHHcCCE---EEEEecc-cHH--HHHHH-HHHcCcCEEEEeCC
Confidence            788888888888888999999999988863   5555544 211  12233 35567999998775

Ligand-binding domain of DNA transcription repressor for the hexuronate utilization operon from Bacillus species and its close homologs from other bacteria, all of which are a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor

>cd06299 PBP1_LacI_like_13 Ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia

Probab=86.16  E-value=3.4  Score=34.37  Aligned_cols=60  Identities=7%  Similarity=-0.010  Sum_probs=35.5

Q ss_pred             EEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHH---HHHHhhhcCCccEEEEEee
Q 027801           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        78 IaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~---aak~L~~~~~yDaVIaLG~  143 (218)
                      ||+|...+....-..++++..++++++|+.   +.  .++...+-.-   .++.+ ...++||||..+.
T Consensus         2 igvv~~~~~~~~~~~~~~gi~~~~~~~g~~---~~--~~~~~~~~~~~~~~~~~l-~~~~vdgiIi~~~   64 (265)
T cd06299           2 IGVIVPDIRNPYFASLATAIQDAASAAGYS---TI--IGNSDENPETENRYLDNL-LSQRVDGIIVVPH   64 (265)
T ss_pred             EEEEecCCCCccHHHHHHHHHHHHHHcCCE---EE--EEeCCCCHHHHHHHHHHH-HhcCCCEEEEcCC
Confidence            677777665555667778888888887752   33  3333222221   22333 3567888887764

This group includes the ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia. This regulatory protein is a member of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial trans

>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial

Probab=86.08  E-value=4.3  Score=35.42  Aligned_cols=64  Identities=17%  Similarity=0.227  Sum_probs=43.7

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchH---HHHHHHhhhcCCccEEEEEee
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEI---GVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~EL---P~aak~L~~~~~yDaVIaLG~  143 (218)
                      ....||++...+.......++++..+.+.++|..   +.+  .+..++.   --..+.+ ...++||+|.++.
T Consensus        58 ~~~~Ig~i~~~~~~~~~~~~~~~i~~~~~~~gy~---~~i--~~~~~~~~~~~~~~~~l-~~~~vdGvIi~~~  124 (311)
T TIGR02405        58 SDKVVAVIVSRLDSPSENLAVSGMLPVFYTAGYD---PII--MESQFSPQLTNEHLSVL-QKRNVDGVILFGF  124 (311)
T ss_pred             CCCEEEEEeCCcccccHHHHHHHHHHHHHHCCCe---EEE--ecCCCChHHHHHHHHHH-HhcCCCEEEEeCC
Confidence            4457999998876666778899999999999974   333  3332221   1223333 4677999999874

This family consists of repressors of the LacI family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gammaproteobacteria and does not include the GntR family TreR of Bacillus subtilis

>cd06282 PBP1_GntR_like_2 Ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription regulators

Probab=85.96  E-value=4.1  Score=33.65  Aligned_cols=58  Identities=9%  Similarity=0.117  Sum_probs=32.1

Q ss_pred             EEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH---HHHHHhhhcCCccEEEEE
Q 027801           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGKSGKYTAVLCI  141 (218)
Q Consensus        78 IaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP---~aak~L~~~~~yDaVIaL  141 (218)
                      ||+|...+....-..+++++.+.++++|..   +.++.  ..++-.   -+++.| ...++||+|..
T Consensus         2 igvv~~~~~~~~~~~~~~~i~~~~~~~g~~---~~~~~--~~~~~~~~~~~~~~l-~~~~vdgiii~   62 (266)
T cd06282           2 VGVVLPSLANPVFAECVQGIQEEARAAGYS---LLLAT--TDYDAEREADAVETL-LRQRVDGLILT   62 (266)
T ss_pred             eEEEeCCCCcchHHHHHHHHHHHHHHCCCE---EEEee--CCCCHHHHHHHHHHH-HhcCCCEEEEe
Confidence            567776666666666777777777777653   33332  222222   122333 23567777754

This group includes the ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding

>cd06267 PBP1_LacI_sugar_binding_like Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily

Probab=85.94  E-value=4.4  Score=32.97  Aligned_cols=62  Identities=11%  Similarity=0.076  Sum_probs=40.2

Q ss_pred             EEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcch---HHHHHHHhhhcCCccEEEEEeee
Q 027801           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE---IGVVAQQLGKSGKYTAVLCIGAV  144 (218)
Q Consensus        77 RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~E---LP~aak~L~~~~~yDaVIaLG~V  144 (218)
                      +|++|...++......+.+++.+.++++|+.   +.  ..+.-++   .--.++.+. ..++|++|..+.-
T Consensus         1 ~i~~v~~~~~~~~~~~~~~g~~~~~~~~g~~---~~--~~~~~~~~~~~~~~~~~~~-~~~~d~iii~~~~   65 (264)
T cd06267           1 TIGVIVPDISNPFFAELLRGIEEAAREAGYS---VL--LCNSDEDPEKEREALELLL-SRRVDGIILAPSR   65 (264)
T ss_pred             CEEEEECCCCCHHHHHHHHHHHHHHHHcCCE---EE--EEcCCCCHHHHHHHHHHHH-HcCcCEEEEecCC
Confidence            3678887777777888888888888887753   33  3444443   223344443 4578888876553

Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily. In most cases, ligands are monosaccharide including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the domain sugar binding changes the DNA binding activity of the repressor domain.

>cd06292 PBP1_LacI_like_10 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors

Probab=85.69  E-value=12  Score=31.29  Aligned_cols=97  Identities=20%  Similarity=0.216  Sum_probs=56.4

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH---HHHHHhhhcCCccEEEEEeeeeeCCch
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGKSGKYTAVLCIGAVVRGDTT  150 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP---~aak~L~~~~~yDaVIaLG~VIrGeT~  150 (218)
                      ...||+++...-...-...=.+|..+.++++|+......++  ++-+...   -+++.+++.+ +|||+|..        
T Consensus       121 g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~i~--~~~~~~~~~~~~~~~~l~~~-~~ai~~~~--------  189 (273)
T cd06292         121 GHRRIGFASGPGRTVPRRRKIAGFRAALEEAGLEPPEALVA--RGMFSVEGGQAAAVELLGSG-PTAIVAAS--------  189 (273)
T ss_pred             CCceEEEEeCCcccccHHHHHHHHHHHHHHcCCCCChhheE--eCCCCHHHHHHHHHHHhcCC-CCEEEEcC--------
Confidence            34689999765433333444689999999999753222222  3334322   2344555444 89988763        


Q ss_pred             hHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHH
Q 027801          151 HYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMD  185 (218)
Q Consensus       151 H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~e  185 (218)
                        +.++..+.++|.+..+.  +|==..|++.++..
T Consensus       190 --d~~a~g~~~~l~~~g~~--ip~di~ii~~d~~~  220 (273)
T cd06292         190 --DLMALGAIRAARRRGLR--VPEDVSVVGYDDSA  220 (273)
T ss_pred             --cHHHHHHHHHHHHcCCC--CCcceEEEeeCCch
Confidence              34677777888776553  33223344555544

This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.

>cd06308 PBP1_sensor_kinase_like Periplasmic binding domain of two-component sensor kinase signaling systems

Probab=85.49  E-value=4.2  Score=34.16  Aligned_cols=61  Identities=3%  Similarity=0.040  Sum_probs=34.0

Q ss_pred             EEEEEEcccCHHHHHHHHHHHHHHHHHC-CCCCCCeEEEEeCCcc--hHHHHHHHhhhcCCccEEEEEe
Q 027801           77 RFALVVARFNELVTKLLLEGALETFKKY-SVKEENIDVVWVPGSF--EIGVVAQQLGKSGKYTAVLCIG  142 (218)
Q Consensus        77 RIaIV~Srfn~~It~~Ll~gA~~~L~~~-Gv~~e~I~vv~VPGA~--ELP~aak~L~~~~~yDaVIaLG  142 (218)
                      +|+++...+.......++.+..+.+.++ |+.   +.+...++..  |.... +.+ ...++||||..+
T Consensus         1 ~ig~~~~~~~~~~~~~~~~~i~~~~~~~~g~~---~~~~~~~~~~~~~~~~i-~~~-~~~~vdgiii~~   64 (270)
T cd06308           1 VIGFSQCNLADPWRAAMNDEIQREASNYPDVE---LIIADAADDNSKQVADI-ENF-IRQGVDLLIISP   64 (270)
T ss_pred             CEEEEeeCCCCHHHHHHHHHHHHHHHhcCCcE---EEEEcCCCCHHHHHHHH-HHH-HHhCCCEEEEec
Confidence            4667776666666667777777777775 553   4444333333  22222 222 234677777655

Periplasmic binding domain of two-component sensor kinase signaling systems, some of which are fused with a C-terminal histidine kinase A domain (HisK) and/or a signal receiver domain (REC). Members of this group share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily and are predicted to be involved in sensing of environmental stimuli; their substrate specificities, however, are not known in detail.

>COG1609 PurR Transcriptional regulators [Transcription]

Probab=85.15  E-value=14  Score=33.60  Aligned_cols=125  Identities=21%  Similarity=0.210  Sum_probs=83.0

Q ss_pred             CCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH---HHHHHhhhc-CC-ccEEEEEeeeeeC
Q 027801           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGKS-GK-YTAVLCIGAVVRG  147 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP---~aak~L~~~-~~-yDaVIaLG~VIrG  147 (218)
                      ....||+++...-+......=++|.++.|+++|+...  +...++|.|..-   -++++++.. .+ +|||+|.-     
T Consensus       173 ~G~~~i~~i~~~~~~~~~~~R~~Gf~~al~~~~~~~~--~~~i~~~~~~~~~g~~~~~~ll~~~~~~ptAif~~n-----  245 (333)
T COG1609         173 LGHRRIAFIGGPLDSSASRERLEGYRAALREAGLPIN--PEWIVEGDFSEESGYEAAERLLARGEPRPTAIFCAN-----  245 (333)
T ss_pred             CCCceEEEEeCCCccccHhHHHHHHHHHHHHCCCCCC--cceEEecCCChHHHHHHHHHHHhcCCCCCcEEEEcC-----
Confidence            3457899999996555555668999999999998632  445555655322   333445443 34 99999964     


Q ss_pred             CchhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHhhC------CCCCCcHHHHHHHHHHHHH
Q 027801          148 DTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAG------GKSGNKGAEAALTAIEMAS  211 (218)
Q Consensus       148 eT~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~Rag------~k~gnKG~EAA~aAleM~~  211 (218)
                           |.++-.+.+.+.+..+.  +|==..|++-+|.+.+....-      -.....|.+|+...++++.
T Consensus       246 -----D~~Alg~l~~~~~~g~~--vP~disviGfDd~~~~~~~~P~LTTv~~~~~~~G~~A~~~Ll~~i~  308 (333)
T COG1609         246 -----DLMALGALRALRELGLR--VPEDLSVIGFDDIELARFLTPPLTTVRQPIEELGRRAAELLLERIN  308 (333)
T ss_pred             -----cHHHHHHHHHHHHcCCC--CCCeeEEEEecChhhhhhCCCCCeeecCCHHHHHHHHHHHHHHHHc
Confidence                 45677777777776665  665567888888666543311      1234568888888887776

>cd06321 PBP1_ABC_sugar_binding_like_11 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems

Probab=85.09  E-value=3.6  Score=34.51  Aligned_cols=63  Identities=17%  Similarity=0.215  Sum_probs=39.2

Q ss_pred             EEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHh--hhcCCccEEEEEe
Q 027801           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQL--GKSGKYTAVLCIG  142 (218)
Q Consensus        77 RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L--~~~~~yDaVIaLG  142 (218)
                      +|++|++.+....-..|..+..+++++.|.   ++.++.+++..+..-..+.+  +...++||+|..+
T Consensus         1 ~Ig~v~~~~~~~~~~~~~~gi~~~~~~~~~---~~~~~~~~~~~~~~~~~~~i~~~~~~~~dgiIi~~   65 (271)
T cd06321           1 KIGVSVGDLGNPFFVALAKGAEAAAKKLNP---GVKVTVVSADYDLNKQVSQIDNFIAAKVDLILLNA   65 (271)
T ss_pred             CeEEEecccCCHHHHHHHHHHHHHHHHhCC---CeEEEEccCCCCHHHHHHHHHHHHHhCCCEEEEeC
Confidence            478888887777777888888888888442   34555555554433222221  2346688887654

This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consist of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.

>cd06279 PBP1_LacI_like_3 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors

Probab=85.00  E-value=4.3  Score=34.64  Aligned_cols=59  Identities=20%  Similarity=0.290  Sum_probs=41.3

Q ss_pred             EEEEEcc-----cCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEee
Q 027801           78 FALVVAR-----FNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        78 IaIV~Sr-----fn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~  143 (218)
                      ||+|+..     |.......++++..+.++++|..     +..++...|.. ..+. +...++||+|..++
T Consensus         2 igvi~p~~~~~~~~~~~~~~~~~gi~~~a~~~g~~-----~~~~~~~~~~~-~~~~-~~~~~~dgiii~~~   65 (283)
T cd06279           2 VGVVLTDSLSYAFSDPVASQFLAGVAEVLDAAGVN-----LLLLPASSEDS-DSAL-VVSALVDGFIVYGV   65 (283)
T ss_pred             EEEEeCCcccccccCccHHHHHHHHHHHHHHCCCE-----EEEecCccHHH-HHHH-HHhcCCCEEEEeCC
Confidence            6778777     66777788999999999998863     34444444433 2233 35678999999876

This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.

>COG2984 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]

Probab=84.98  E-value=13  Score=35.14  Aligned_cols=126  Identities=17%  Similarity=0.156  Sum_probs=82.5

Q ss_pred             hhHhhhcccCCCCCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEE
Q 027801           61 EAVRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLC  140 (218)
Q Consensus        61 ~a~~~~~~~~~~~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIa  140 (218)
                      ..++.+.++     -.||+++.+.=- .=...+++.-.+.++..|++   +....||-.-|+|.+.+-|.  ++.|+|..
T Consensus       150 ~lik~~~Pn-----ak~Igv~Y~p~E-~ns~~l~eelk~~A~~~Gl~---vve~~v~~~ndi~~a~~~l~--g~~d~i~~  218 (322)
T COG2984         150 ELIKALLPN-----AKSIGVLYNPGE-ANSVSLVEELKKEARKAGLE---VVEAAVTSVNDIPRAVQALL--GKVDVIYI  218 (322)
T ss_pred             HHHHHhCCC-----CeeEEEEeCCCC-cccHHHHHHHHHHHHHCCCE---EEEEecCcccccHHHHHHhc--CCCcEEEE
Confidence            445555443     348988875422 11236778888899999985   77888999999999999986  78998874


Q ss_pred             EeeeeeCCchhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCC---HHHHHHhhCCCCCCcHHHHHHHHHHHHH
Q 027801          141 IGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDN---MDQALNRAGGKSGNKGAEAALTAIEMAS  211 (218)
Q Consensus       141 LG~VIrGeT~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n---~eQA~~Rag~k~gnKG~EAA~aAleM~~  211 (218)
                             .|+|-.   ......+++.+.+.++||+-    .++   ++-|+.-.|-.-..-|.+++.-+.+.+.
T Consensus       219 -------p~dn~i---~s~~~~l~~~a~~~kiPli~----sd~~~V~~Ga~aA~gvdy~~~G~qtg~~v~~ILk  278 (322)
T COG2984         219 -------PTDNLI---VSAIESLLQVANKAKIPLIA----SDTSSVKEGALAALGVDYKDLGKQTGEMVVKILK  278 (322)
T ss_pred             -------ecchHH---HHHHHHHHHHHHHhCCCeec----CCHHHHhcCcceeeccCHHHHHHHHHHHHHHHHc
Confidence                   344432   23778899999999999863    222   1122322322333346777666666543

>cd06319 PBP1_ABC_sugar_binding_like_10 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems

Probab=84.91  E-value=8.2  Score=32.26  Aligned_cols=98  Identities=13%  Similarity=0.093  Sum_probs=58.1

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcch--HH-HHHHHhhhc-CCccEEEEEeeeeeCCch
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE--IG-VVAQQLGKS-GKYTAVLCIGAVVRGDTT  150 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~E--LP-~aak~L~~~-~~yDaVIaLG~VIrGeT~  150 (218)
                      ..||+++...-.......-++|.++.++++|..   +..+...+.+.  .. -+++.++++ .++|+|+|.+-.      
T Consensus       125 ~~~i~~i~~~~~~~~~~~r~~gf~~~l~~~~~~---~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~d~------  195 (277)
T cd06319         125 DGKVGMVAIPQKRKNGQKRTKGFKEAMKEAGCD---LAGIRQQKDFSYQETFDYTNDLLTANPDIRAIWLQGSD------  195 (277)
T ss_pred             CCcEEEEeccCCCccHHHHHHHHHHHHHhcCCc---eEeeccCCCCCHHHHHHHHHHHHHhCCCCCEEEECCCc------
Confidence            458999975444344556789999999999875   22233334443  22 223445443 568999987654      


Q ss_pred             hHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHH
Q 027801          151 HYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALN  189 (218)
Q Consensus       151 H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~  189 (218)
                          ++..+.+.|.+..+.-++    .|++.++...+..
T Consensus       196 ----~a~g~~~al~~~g~~~di----~vvg~d~~~~~~~  226 (277)
T cd06319         196 ----RYQGALDAIATAGKTGKV----LLICFDAEPEFIE  226 (277)
T ss_pred             ----cchHHHHHHHHcCCCCCE----EEEEcCCCHHHHH
Confidence                355666666666654333    3445565555543

Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.

>cd06285 PBP1_LacI_like_7 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors

Probab=84.85  E-value=4.5  Score=33.78  Aligned_cols=61  Identities=15%  Similarity=0.109  Sum_probs=41.6

Q ss_pred             EEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH---HHHHHhhhcCCccEEEEEeee
Q 027801           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGKSGKYTAVLCIGAV  144 (218)
Q Consensus        78 IaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP---~aak~L~~~~~yDaVIaLG~V  144 (218)
                      ||+|...+.+.....++.+..+.++++|+.   +.+  .++..+..   -.++.+ ...++||+|..++-
T Consensus         2 igvi~p~~~~~~~~~~~~gi~~~~~~~~~~---~~~--~~~~~~~~~~~~~i~~l-~~~~~dgiii~~~~   65 (265)
T cd06285           2 IGVLVPRLTDTVMATMYEGIEEAAAERGYS---TFV--ANTGDNPDAQRRAIEML-LDRRVDGLILGDAR   65 (265)
T ss_pred             EEEEeCCCCCccHHHHHHHHHHHHHHCCCE---EEE--EeCCCCHHHHHHHHHHH-HHcCCCEEEEecCC
Confidence            788888888788889999999999999874   332  33332222   122333 45779999987653

This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.

>PRK14046 malate--CoA ligase subunit beta; Provisional

Probab=84.83  E-value=32  Score=32.62  Aligned_cols=121  Identities=17%  Similarity=0.129  Sum_probs=73.8

Q ss_pred             EEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCc---chHHHHHHHhhhcCCccEEEEEeeeeeCCchhHH
Q 027801           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGS---FEIGVVAQQLGKSGKYTAVLCIGAVVRGDTTHYD  153 (218)
Q Consensus        77 RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA---~ELP~aak~L~~~~~yDaVIaLG~VIrGeT~H~e  153 (218)
                      +|++++.=      -.|.-.+.+.+..+|..+.|.--+  .|.   -.+--+++.+++..++|+|++.=+   |...-.+
T Consensus       258 ~ig~i~nG------aGl~m~t~D~i~~~gg~paNPlDl--gg~a~~e~~~~aL~~ll~Dp~VdaVlv~i~---ggi~~~~  326 (392)
T PRK14046        258 DIGCIVNG------AGLAMATMDMIKLAGGEPANFLDV--GGGASPERVAKAFRLVLSDRNVKAILVNIF---AGINRCD  326 (392)
T ss_pred             cEEEEeCC------ccHHHHHHHHHHhcCCCCcCCEEe--cCCCCHHHHHHHHHHHHcCCCCCEEEEEcC---CCCCCHH
Confidence            56666521      145557789999999877665333  443   224455566677889999996322   5544445


Q ss_pred             HHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHH---hhCC--CCCCcHHHHHHHHHHHHH
Q 027801          154 AVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALN---RAGG--KSGNKGAEAALTAIEMAS  211 (218)
Q Consensus       154 ~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~---Rag~--k~gnKG~EAA~aAleM~~  211 (218)
                      -+++++.+.+.+.  +.++||+... ...+.+++.+   .+|.  -..+==.|||+.|+++++
T Consensus       327 ~vA~~Ii~a~~~~--~~~kPvvv~l-~G~~~e~~~~iL~~~Gipvf~~~~~~~a~~~~v~~~~  386 (392)
T PRK14046        327 WVAEGVVQAAREV--GIDVPLVVRL-AGTNVEEGRKILAESGLPIITADTLAEAAEKAVEAWK  386 (392)
T ss_pred             HHHHHHHHHHHhc--CCCCcEEEEc-CCCCHHHHHHHHHHcCCCeeecCCHHHHHHHHHHHHh
Confidence            5665555544432  3789995544 4467777654   3331  233555899999998874

>cd06289 PBP1_MalI_like Ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria

Probab=84.66  E-value=4.7  Score=33.34  Aligned_cols=60  Identities=12%  Similarity=0.120  Sum_probs=37.8

Q ss_pred             EEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchH---HHHHHHhhhcCCccEEEEEee
Q 027801           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEI---GVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        78 IaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~EL---P~aak~L~~~~~yDaVIaLG~  143 (218)
                      ||+|...|.......+++++.+.++++|+.     ++..++..+.   --.++.+. ..++||+|..++
T Consensus         2 I~vi~~~~~~~~~~~~~~g~~~~a~~~g~~-----~~~~~~~~~~~~~~~~i~~~~-~~~vdgiii~~~   64 (268)
T cd06289           2 IGLVINDLTNPFFAELAAGLEEVLEEAGYT-----VFLANSGEDVERQEQLLSTML-EHGVAGIILCPA   64 (268)
T ss_pred             EEEEecCCCcchHHHHHHHHHHHHHHcCCe-----EEEecCCCChHHHHHHHHHHH-HcCCCEEEEeCC
Confidence            677777777667777888888888888763     3334443322   12334443 467888888765

This group includes the ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria. They are members of the LacI-GalR family of repressor proteins which are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.

>cd06313 PBP1_ABC_sugar_binding_like_5 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems

Probab=84.60  E-value=7.2  Score=33.20  Aligned_cols=62  Identities=10%  Similarity=-0.113  Sum_probs=40.2

Q ss_pred             EEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHHhhhcCCccEEEEEe
Q 027801           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIG  142 (218)
Q Consensus        77 RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~L~~~~~yDaVIaLG  142 (218)
                      |+|++...+....-..++++..++++++|+.   +.+....+..+-- -.++.+ ...++||||..+
T Consensus         1 ~~~~~~~~~~~~f~~~~~~gi~~~~~~~G~~---~~~~~~~~d~~~~~~~i~~~-~~~~vdgiii~~   63 (272)
T cd06313           1 KAAFSNIGLQATWCAQGKQAADEAGKLLGVD---VTWYGGALDAVKQVAAIENM-ASQGWDFIAVDP   63 (272)
T ss_pred             CcceeecccCChHHHHHHHHHHHHHHHcCCE---EEEecCCCCHHHHHHHHHHH-HHcCCCEEEEcC
Confidence            4567777777777888999999999999973   4444332222211 223333 357899998865

Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.

>PF04392 ABC_sub_bind: ABC transporter substrate binding protein; InterPro: IPR007487 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems

Probab=84.58  E-value=14  Score=32.55  Aligned_cols=85  Identities=15%  Similarity=0.183  Sum_probs=56.1

Q ss_pred             CEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEeeeeeCCchhHHHH
Q 027801           76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVVRGDTTHYDAV  155 (218)
Q Consensus        76 ~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~VIrGeT~H~e~V  155 (218)
                      .||+++...-.. -.....+...+.++++|+.   +..+.|+..-|++-+++.|.  ++.|+++.+       +++  ++
T Consensus       132 k~igvl~~~~~~-~~~~~~~~~~~~a~~~g~~---l~~~~v~~~~~~~~~~~~l~--~~~da~~~~-------~~~--~~  196 (294)
T PF04392_consen  132 KRIGVLYDPSEP-NSVAQIEQLRKAAKKLGIE---LVEIPVPSSEDLEQALEALA--EKVDALYLL-------PDN--LV  196 (294)
T ss_dssp             -EEEEEEETT-H-HHHHHHHHHHHHHHHTT-E---EEEEEESSGGGHHHHHHHHC--TT-SEEEE--------S-H--HH
T ss_pred             CEEEEEecCCCc-cHHHHHHHHHHHHHHcCCE---EEEEecCcHhHHHHHHHHhh--ccCCEEEEE-------CCc--ch
Confidence            589988764433 2346677778888888984   77889999999999998874  467877653       222  33


Q ss_pred             HHHHHHHHHHhchhcCCceEE
Q 027801          156 ANSAASGVLSAGVNSGVPCIF  176 (218)
Q Consensus       156 a~~vs~gLm~lsL~~~vPVif  176 (218)
                      .+. ...+.+.+.+.++||+-
T Consensus       197 ~~~-~~~i~~~~~~~~iPv~~  216 (294)
T PF04392_consen  197 DSN-FEAILQLANEAKIPVFG  216 (294)
T ss_dssp             HHT-HHHHHHHCCCTT--EEE
T ss_pred             HhH-HHHHHHHHHhcCCCEEE
Confidence            333 33488899999999954

ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. This family contains many hypothetical proteins and some ABC transporter substrate binding proteins.; PDB: 3LFT_A 3LKV_A.

>PRK10936 TMAO reductase system periplasmic protein TorT; Provisional

Probab=84.48  E-value=5.7  Score=35.68  Aligned_cols=65  Identities=14%  Similarity=0.105  Sum_probs=47.3

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcch---HHHHHHHhhhcCCccEEEEEe
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE---IGVVAQQLGKSGKYTAVLCIG  142 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~E---LP~aak~L~~~~~yDaVIaLG  142 (218)
                      +..+|++|...+.......++++..++++++|+.   +.+...++..+   .--.++.+. ..++||||..+
T Consensus        45 ~t~~Igvv~p~~~~~f~~~~~~gi~~aa~~~G~~---l~i~~~~~~~~~~~q~~~i~~l~-~~~vdgIIl~~  112 (343)
T PRK10936         45 KAWKLCALYPHLKDSYWLSVNYGMVEEAKRLGVD---LKVLEAGGYYNLAKQQQQLEQCV-AWGADAILLGA  112 (343)
T ss_pred             CCeEEEEEecCCCchHHHHHHHHHHHHHHHhCCE---EEEEcCCCCCCHHHHHHHHHHHH-HhCCCEEEEeC
Confidence            4568999999888888889999999999999973   55554444332   323445554 46799999865

>cd06294 PBP1_ycjW_transcription_regulator_like Ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors

Probab=84.08  E-value=13  Score=30.87  Aligned_cols=97  Identities=18%  Similarity=0.186  Sum_probs=57.6

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHH---HHHHhhhc-CCccEEEEEeeeeeCCch
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGKS-GKYTAVLCIGAVVRGDTT  150 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~---aak~L~~~-~~yDaVIaLG~VIrGeT~  150 (218)
                      ..||+++.+.-+......-.+|..+.++++|.......+  +++.+..--   ++..++++ .++|||+|.+        
T Consensus       122 ~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~--------  191 (270)
T cd06294         122 HKKIAFVGGDLDLEVTQDRLQGYKQALEDHGIPDRNEVI--ISLDFSEEGGYKALKKLLEQHPRPTAIVATD--------  191 (270)
T ss_pred             CccEEEecCCcccHHHHHHHHHHHHHHHHcCCCCCcceE--EecCCchHHHHHHHHHHHhCCCCCCEEEECC--------
Confidence            458999987666544555679999999999974222222  234343211   22334444 4699999854        


Q ss_pred             hHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHH
Q 027801          151 HYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMD  185 (218)
Q Consensus       151 H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~e  185 (218)
                        +.++..+.+++.+..+.  +|=-..|++.++.+
T Consensus       192 --d~~a~g~~~al~~~g~~--iP~dv~vig~d~~~  222 (270)
T cd06294         192 --DLLALGVLKVLNELGLK--VPEDLSIIGFNNSI  222 (270)
T ss_pred             --hHHHHHHHHHHHHcCCC--CCcceEEEeeCChh
Confidence              34667778888777664  33223344555544

This group includes the ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.

>PRK10936 TMAO reductase system periplasmic protein TorT; Provisional

Probab=84.06  E-value=13  Score=33.42  Aligned_cols=121  Identities=14%  Similarity=0.085  Sum_probs=67.9

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH--H-HHHHhhhc-CCccEEEEEeeeeeCCc
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG--V-VAQQLGKS-GKYTAVLCIGAVVRGDT  149 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP--~-aak~L~~~-~~yDaVIaLG~VIrGeT  149 (218)
                      ...||+++.+.-.......-.+|..+.+++.|+.   +.- .+.+-++.-  . .++.+++. .++|+|++  .      
T Consensus       171 g~~~i~~i~g~~~~~~~~~R~~Gf~~~l~~~~i~---~~~-~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~--~------  238 (343)
T PRK10936        171 KPLNVALLPGPEGAGGSKAVEQGFRAAIAGSDVR---IVD-IAYGDNDKELQRNLLQELLERHPDIDYIAG--S------  238 (343)
T ss_pred             CCceEEEEECCCCCchHHHHHHHHHHHHhcCCCE---EEE-eecCCCcHHHHHHHHHHHHHhCCCccEEEe--C------
Confidence            3568999987655445556678999999887763   111 234444432  2 33455443 56898742  1      


Q ss_pred             hhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHhhC------CCCCCcHHHHHHHHHHHH
Q 027801          150 THYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAG------GKSGNKGAEAALTAIEMA  210 (218)
Q Consensus       150 ~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~Rag------~k~gnKG~EAA~aAleM~  210 (218)
                         +..+..+.+++.+..+..++. +.|.......-|++.+=.      .....-|.+|+..+++++
T Consensus       239 ---d~~A~ga~~al~~~g~~~di~-Vvg~~~~p~~~~~i~~G~i~~tv~q~~~~~G~~ai~~l~~~l  301 (343)
T PRK10936        239 ---AVAAEAAIGELRGRNLTDKIK-LVSFYLSHQVYRGLKRGKVLAAPSDQMVLQGRLAIDQAVRQL  301 (343)
T ss_pred             ---CHHHHHHHHHHHhcCCCCCeE-EEEeCCCHHHHHHHHcCCeEEEEecCHHHHHHHHHHHHHHHH
Confidence               235666777777766644443 345555555566665411      112234566666665554

>PRK10703 DNA-binding transcriptional repressor PurR; Provisional

Probab=83.99  E-value=9.7  Score=33.40  Aligned_cols=99  Identities=23%  Similarity=0.289  Sum_probs=58.8

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHH---HHHHhhh-cCCccEEEEEeeeeeCCch
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGK-SGKYTAVLCIGAVVRGDTT  150 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~---aak~L~~-~~~yDaVIaLG~VIrGeT~  150 (218)
                      ..||++|.+.-+......-.+|..+.|+++|+......+  ..+.+...-   .++.+++ ..++|||+|.+-.      
T Consensus       178 ~~~i~~i~~~~~~~~~~~R~~Gf~~~l~~~gi~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~nd~------  249 (341)
T PRK10703        178 HRDIGVIPGPLERNTGAGRLAGFMKAMEEANIKVPEEWI--VQGDFEPESGYEAMQQILSQKHRPTAVFCGGDI------  249 (341)
T ss_pred             CCcEEEEeCCccccchHHHHHHHHHHHHHcCCCCChHHe--EeCCCCHHHHHHHHHHHHhCCCCCCEEEECCcH------
Confidence            458999987655555666678999999999986322222  344444221   2334444 3468999986543      


Q ss_pred             hHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHH
Q 027801          151 HYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQA  187 (218)
Q Consensus       151 H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA  187 (218)
                          ++..+.+.|.+..+.  +|==..|++.++.+.+
T Consensus       250 ----~a~g~~~al~~~g~~--ip~dv~vvgfD~~~~~  280 (341)
T PRK10703        250 ----MAMGAICAADEMGLR--VPQDISVIGYDNVRNA  280 (341)
T ss_pred             ----HHHHHHHHHHHcCCC--CCCceEEEEECCCcHH
Confidence                455566666655442  4434455555554443

>PRK10727 DNA-binding transcriptional regulator GalR; Provisional

Probab=83.84  E-value=6  Score=34.92  Aligned_cols=66  Identities=9%  Similarity=-0.041  Sum_probs=44.7

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHHhhhcCCccEEEEEee
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~L~~~~~yDaVIaLG~  143 (218)
                      ....||+|...+....-..|++++.+.++++|..   +.+.......+-- -.++.| ...++||+|..+.
T Consensus        58 ~~~~Igvi~~~~~~~f~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~i~~l-~~~~vdgiIi~~~  124 (343)
T PRK10727         58 STETVGLVVGDVSDPFFGAMVKAVEQVAYHTGNF---LLIGNGYHNEQKERQAIEQL-IRHRCAALVVHAK  124 (343)
T ss_pred             CCCeEEEEeCCCCcchHHHHHHHHHHHHHHcCCE---EEEEeCCCCHHHHHHHHHHH-HhcCCCEEEEecC
Confidence            4457999999888778889999999999999973   3333333222211 233444 3567999998764

>PRK09526 lacI lac repressor; Reviewed

Probab=83.79  E-value=12  Score=32.73  Aligned_cols=96  Identities=22%  Similarity=0.295  Sum_probs=58.6

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHH---HHHHhhh-cCCccEEEEEeeeeeCCc
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGK-SGKYTAVLCIGAVVRGDT  149 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~---aak~L~~-~~~yDaVIaLG~VIrGeT  149 (218)
                      ...||+++.+.-+......-.+|..+.|+++|+..  ..  .+.|.|...-   .++.+++ ..++|||+|.        
T Consensus       180 G~~~I~~l~g~~~~~~~~~R~~Gf~~al~~~gi~~--~~--~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~--------  247 (342)
T PRK09526        180 GHQRIALLAGPESSVSARLRLAGWLEYLTDYQLQP--IA--VREGDWSAMSGYQQTLQMLREGPVPSAILVA--------  247 (342)
T ss_pred             CCCeEEEEeCCCccccHHHHHHHHHHHHHHcCCCc--ce--EEeCCCchHHHHHHHHHHhcCCCCCcEEEEc--------
Confidence            34699999876554444556789999999999852  22  2345554332   2344443 3568999973        


Q ss_pred             hhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHH
Q 027801          150 THYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMD  185 (218)
Q Consensus       150 ~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~e  185 (218)
                        .|.++..+.+.+.+..+.  +|==..|++-++.+
T Consensus       248 --~d~~A~g~~~al~~~g~~--vP~disvig~d~~~  279 (342)
T PRK09526        248 --NDQMALGVLRALHESGLR--VPGQISVIGYDDTE  279 (342)
T ss_pred             --CcHHHHHHHHHHHHcCCC--CCCceEEEeeCCCc
Confidence              355777777888776653  34233444555543

>TIGR02637 RhaS rhamnose ABC transporter, rhamnose-binding protein

Probab=83.54  E-value=10  Score=32.71  Aligned_cols=61  Identities=20%  Similarity=0.104  Sum_probs=39.8

Q ss_pred             EEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHH---HHHHhhhcCCccEEEEEe
Q 027801           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGKSGKYTAVLCIG  142 (218)
Q Consensus        78 IaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~---aak~L~~~~~yDaVIaLG  142 (218)
                      |++|...........+++++.++++++|..   ..++..+...+...   .++.+ ...++||||..+
T Consensus         1 Igvi~~~~~~~f~~~~~~gi~~~a~~~g~~---~~i~~~~~~~d~~~q~~~i~~l-~~~~vdgiIi~~   64 (302)
T TIGR02637         1 IGLVVKSLGNPFFEAANKGAEEAAKELGSV---YIIYTGPTGTTAEGQIEVVNSL-IAQKVDAIAISA   64 (302)
T ss_pred             CEEEeccCCCHHHHHHHHHHHHHHHHhCCe---eEEEECCCCCCHHHHHHHHHHH-HHcCCCEEEEeC
Confidence            467777777777888999999999999952   22332344333322   23334 356799999875

This sugar-binding component of ABC transporter complexes is found in rhamnose catabolism operon contexts. Mutation of this gene in Rhizobium leguminosarum abolishes rhamnose transport and prevents growth on rhamnose as a carbon source.

>cd06300 PBP1_ABC_sugar_binding_like_1 Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily

Probab=83.49  E-value=12  Score=31.37  Aligned_cols=88  Identities=22%  Similarity=0.190  Sum_probs=54.6

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCC-CCCCCeEEEEeCCcchH---HHHHHHhhhc-CCccEEEEEeeeeeCC
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYS-VKEENIDVVWVPGSFEI---GVVAQQLGKS-GKYTAVLCIGAVVRGD  148 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~G-v~~e~I~vv~VPGA~EL---P~aak~L~~~-~~yDaVIaLG~VIrGe  148 (218)
                      ...||+++.+.-+....+.-.+|..+.+.++| +.   +.. .+.+.++.   --.++.++++ .+.|+|+|.+      
T Consensus       124 g~~~i~~i~~~~~~~~~~~R~~g~~~a~~~~~~~~---~~~-~~~~~~~~~~~~~~~~~~l~~~~~~~~i~~~~------  193 (272)
T cd06300         124 GKGNVLVVRGLAGHPVDEDRYAGAKEVLKEYPGIK---IVG-EVYGDWDQAVAQKAVADFLASNPDVDGIWTQG------  193 (272)
T ss_pred             CCceEEEEECCCCCcchHHHHHHHHHHHHHCCCcE---EEe-ecCCCCCHHHHHHHHHHHHHhCCCcCEEEecC------
Confidence            45689999865444455566789999999887 53   211 23344432   1233444444 4689988864      


Q ss_pred             chhHHHHHHHHHHHHHHhchhcCCceEEEE
Q 027801          149 TTHYDAVANSAASGVLSAGVNSGVPCIFGV  178 (218)
Q Consensus       149 T~H~e~Va~~vs~gLm~lsL~~~vPVifGV  178 (218)
                          +. +..+.+++.+..+  ++|.+.|.
T Consensus       194 ----d~-A~g~~~al~~~g~--~~p~v~g~  216 (272)
T cd06300         194 ----GD-AVGAVQAFEQAGR--DIPPVTGE  216 (272)
T ss_pred             ----CC-cHHHHHHHHHcCC--CCcEEEee
Confidence                33 6778888888776  67755553

Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their substrate specificity is not known in detail.

>cd06297 PBP1_LacI_like_12 Ligand-binding domain of uncharacterized transcription regulators from Thermus thermophilus and close homologs

Probab=83.39  E-value=13  Score=31.33  Aligned_cols=125  Identities=18%  Similarity=0.019  Sum_probs=72.3

Q ss_pred             CCEEEEEEcccCHH------HHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHHhhhc-CCccEEEEEeeeee
Q 027801           75 GLRFALVVARFNEL------VTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKS-GKYTAVLCIGAVVR  146 (218)
Q Consensus        75 ~~RIaIV~Srfn~~------It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~L~~~-~~yDaVIaLG~VIr  146 (218)
                      ..||+++.......      ....-++|.++.++++|++.....++...-.++-. -+++++++. .++|||+|..-   
T Consensus       113 ~~~i~~i~~~~~~~~~~~~~~~~~R~~gf~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~d---  189 (269)
T cd06297         113 PGRIGAITVEEEPDRAFRRTVFAERRAGFQQALKDAGRPFSPDLLAITDHSEEGGRLAMRHLLEKASPPLAVFASAD---  189 (269)
T ss_pred             CCceEEEeCccccccccccccHHHHHHHHHHHHHHcCCCCChhhEEeCCCChhhHHHHHHHHHcCCCCCcEEEEcCc---
Confidence            45899997765444      55567899999999999863221233322223222 244555544 46899998653   


Q ss_pred             CCchhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHH-h---hCCCCCCcHHHHHHHHHHHHH
Q 027801          147 GDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALN-R---AGGKSGNKGAEAALTAIEMAS  211 (218)
Q Consensus       147 GeT~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~-R---ag~k~gnKG~EAA~aAleM~~  211 (218)
                             .++..+.+++.+..+  .+|==..|++.++...+.. .   ..-.....|.+|++.++++++
T Consensus       190 -------~~a~g~~~~l~~~g~--~vP~di~vvg~d~~~~~~~~~lttv~~~~~~~g~~av~~l~~~i~  249 (269)
T cd06297         190 -------QQALGALQEAVELGL--TVGEDVRVVGFDDHPFAREAGLSTLAQPVEAMGARAAQLLLERLE  249 (269)
T ss_pred             -------HHHHHHHHHHHHcCC--CCCCceEEEEECCchhhccCCceeeecCHHHHHHHHHHHHHHHhc
Confidence                   377778888877554  3443344555555544421 1   111233456666666666654

Ligand-binding domain of uncharacterized transcription regulators from Thermus thermophilus and close homologs from other bacteria. This group belongs to the the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding.

>cd06307 PBP1_uncharacterized_sugar_binding Periplasmic sugar-binding domain of uncharacterized transport systems

Probab=83.08  E-value=23  Score=29.82  Aligned_cols=120  Identities=8%  Similarity=0.014  Sum_probs=65.4

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH---HHHHHhhh-cCCccEEEEEeeeeeCCch
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGK-SGKYTAVLCIGAVVRGDTT  150 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP---~aak~L~~-~~~yDaVIaLG~VIrGeT~  150 (218)
                      ..||+++....+......-.+|..+.+++++...+...+  ..+.++..   -.++++++ ..++|||+|.+-.      
T Consensus       125 ~~~i~~i~~~~~~~~~~~R~~gf~~a~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~d~------  196 (275)
T cd06307         125 PGKVAVLAGSHRFRGHEEREMGFRSVLREEFPGLRVLET--LEGLDDPARAYEATRKLLARHPDLVGIYNAGGG------  196 (275)
T ss_pred             CCeEEEEecCCCCcchHHHHHHHHHHHHhhCCCcEEEee--ccCCCChHHHHHHHHHHHHhCCCceEEEECCCC------
Confidence            469999988766455667789999999998864222222  23444322   24445543 3568999887531      


Q ss_pred             hHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHh--hC-------CCCCCcHHHHHHHHHHHHH
Q 027801          151 HYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNR--AG-------GKSGNKGAEAALTAIEMAS  211 (218)
Q Consensus       151 H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~R--ag-------~k~gnKG~EAA~aAleM~~  211 (218)
                          + ..+.+++.+..+.-+    --|++.++.+.+...  .+       -....-|.+|+...++++.
T Consensus       197 ----~-~g~~~al~~~g~~~d----i~Ivg~d~~~~~~~~i~~~~l~~tv~~~~~~~g~~a~~~l~~~~~  257 (275)
T cd06307         197 ----N-RGVIRALREAGRAGK----VVFVGHELTPETRAALRDGTIDAVIDQDPGHLARSAVRVLLAACD  257 (275)
T ss_pred             ----h-HHHHHHHHHcCCCCC----cEEEEecCChHHHHHHHcCeeEEEEEcCHHHHHHHHHHHHHHHHh
Confidence                2 245566665554312    224444555554431  11       1122345555555555543

Periplasmic sugar-binding domain of uncharacterized transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. The members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes.

>cd01575 PBP1_GntR Ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators

Probab=82.70  E-value=18  Score=29.87  Aligned_cols=101  Identities=19%  Similarity=0.243  Sum_probs=59.9

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHHhhhc-CCccEEEEEeeeeeCCchh
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKS-GKYTAVLCIGAVVRGDTTH  151 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~L~~~-~~yDaVIaLG~VIrGeT~H  151 (218)
                      ...||+++...-+......-.+|..+.|+++|.....+.....+-.++-. -+++.++++ .++|||+|...        
T Consensus       115 g~~~i~~i~~~~~~~~~~~r~~gf~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~d--------  186 (268)
T cd01575         115 GYRRIGFLGARMDDTRAQQRLEGFRAALRAAGLDPPLVVTTPEPSSFALGRELLAELLARWPDLDAVFCSND--------  186 (268)
T ss_pred             CCCcEEEecCCCCcccHHHHHHHHHHHHHHcCCCCCceeEeccCCCHHHHHHHHHHHHhCCCCCCEEEECCc--------
Confidence            34589999877653444556789999999999753333333333333322 244555544 46899998543        


Q ss_pred             HHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHH
Q 027801          152 YDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQ  186 (218)
Q Consensus       152 ~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQ  186 (218)
                        .++..+.+.+.+..+  .+|==..|++.++...
T Consensus       187 --~~a~~~~~~l~~~g~--~~p~di~vig~d~~~~  217 (268)
T cd01575         187 --DLALGALFECQRRGI--SVPEDIAIAGFGDLEI  217 (268)
T ss_pred             --HHHHHHHHHHHHhCC--CCCcceEEEecCCchh
Confidence              345566666665443  2454455666665544

This group represents the ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of GntR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding,

>PF13407 Peripla_BP_4: Periplasmic binding protein domain; PDB: 3BRS_B 3GBP_A 3GA5_A 1GCG_A 1GCA_A 3H75_A 3D02_A 3L49_B 3EJW_B 3T95_A

Probab=82.43  E-value=14  Score=30.66  Aligned_cols=101  Identities=18%  Similarity=0.205  Sum_probs=67.0

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEE--eCCcchHHHHH---HHhhhcCCccEEEEEeeeeeCCc
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVW--VPGSFEIGVVA---QQLGKSGKYTAVLCIGAVVRGDT  149 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~--VPGA~ELP~aa---k~L~~~~~yDaVIaLG~VIrGeT  149 (218)
                      +.+|+++...-+......-.++..+.|++++    +++++.  .+..+...-+.   +.+++.++.|+|+|..       
T Consensus       122 ~~~v~~~~~~~~~~~~~~r~~g~~~~l~~~~----~~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~i~~~~-------  190 (257)
T PF13407_consen  122 KGKVLILSGSPGNPNTQERLEGFRDALKEYP----GVEIVDEYEYTDWDPEDARQAIENLLQANPVDAIIACN-------  190 (257)
T ss_dssp             TEEEEEEESSTTSHHHHHHHHHHHHHHHHCT----TEEEEEEEEECTTSHHHHHHHHHHHHHHTTEEEEEESS-------
T ss_pred             CceEEeccCCCCchHHHHHHHHHHHHHhhcc----eeeeeeeeeccCCCHHHHHHHHHHhhhcCCceEEEeCC-------
Confidence            3789999888887777777899999999954    355554  23334433333   3444444588888754       


Q ss_pred             hhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHh
Q 027801          150 THYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNR  190 (218)
Q Consensus       150 ~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~R  190 (218)
                         +..+..+.+.|.+..+. +.|.+.|+=..+..-+++.+
T Consensus       191 ---~~~~~g~~~al~~~g~~-~~~~v~g~d~~~~~~~~i~~  227 (257)
T PF13407_consen  191 ---DGMALGAAQALQQAGRA-GKVIVVGFDGSPEALEAIKD  227 (257)
T ss_dssp             ---HHHHHHHHHHHHHTTCT-TTSEEEEEECHHHHHHHHHT
T ss_pred             ---ChHHHHHHHHHHHcCCc-ccceeecCCCCHHHHHHHHC
Confidence               34666899999998884 55667777554444455533

...

>COG2039 Pcp Pyrrolidone-carboxylate peptidase (N-terminal pyroglutamyl peptidase) [Posttranslational modification, protein turnover, chaperones]

Probab=82.25  E-value=4.5  Score=35.84  Aligned_cols=40  Identities=23%  Similarity=0.250  Sum_probs=36.2

Q ss_pred             HHHHHHHHHHHHHhchhcCCceEEEEcCC-CCHHHHHHhhC
Q 027801          153 DAVANSAASGVLSAGVNSGVPCIFGVLTC-DNMDQALNRAG  192 (218)
Q Consensus       153 e~Va~~vs~gLm~lsL~~~vPVifGVLT~-~n~eQA~~Rag  192 (218)
                      -||||.+.++++...-+++-|+-.|.+-. -+.|||.+.-+
T Consensus       139 TyvCNhvmY~~l~~~~~~~~~~~~GFiHvPy~peqa~~~~~  179 (207)
T COG2039         139 TYVCNHVMYGLLHHLAKKGPPVRAGFIHVPYLPEQAARKPN  179 (207)
T ss_pred             hhhhHHHHHHHHHHHHHhCCCCcceeEeecCCHHHHhCCCC
Confidence            69999999999999999999999999876 68999987754

>cd00886 MogA_MoaB MogA_MoaB family

Probab=82.19  E-value=8.4  Score=31.35  Aligned_cols=74  Identities=9%  Similarity=0.091  Sum_probs=49.5

Q ss_pred             HHHHHHCCCCCCCeEEEEeCCcch-HHHHHHHhhhcCCccEEEEEeeeeeCCchhHHHHHHHHHHH-----------HHH
Q 027801           98 LETFKKYSVKEENIDVVWVPGSFE-IGVVAQQLGKSGKYTAVLCIGAVVRGDTTHYDAVANSAASG-----------VLS  165 (218)
Q Consensus        98 ~~~L~~~Gv~~e~I~vv~VPGA~E-LP~aak~L~~~~~yDaVIaLG~VIrGeT~H~e~Va~~vs~g-----------Lm~  165 (218)
                      .+.|+++|..  -.....||.-.| |--+++.+.+..++|-||+.|-+-.|   ++|++.+++.+-           +..
T Consensus        26 ~~~l~~~G~~--v~~~~~v~Dd~~~i~~~l~~~~~~~~~DlVittGG~s~g---~~D~t~~al~~~~~~~l~g~~~~~~~  100 (152)
T cd00886          26 VELLEEAGHE--VVAYEIVPDDKDEIREALIEWADEDGVDLILTTGGTGLA---PRDVTPEATRPLLDKELPGFGEAFRA  100 (152)
T ss_pred             HHHHHHcCCe--eeeEEEcCCCHHHHHHHHHHHHhcCCCCEEEECCCcCCC---CCcCcHHHHHHHhCCcCccHHHHHHH
Confidence            4458888874  455667888886 55556666543479999999998544   445555555543           456


Q ss_pred             hchhcCCceEE
Q 027801          166 AGVNSGVPCIF  176 (218)
Q Consensus       166 lsL~~~vPVif  176 (218)
                      ++++-+.|.++
T Consensus       101 ~~~~pg~~~~~  111 (152)
T cd00886         101 LSLEETGTAML  111 (152)
T ss_pred             hhcccCCcEEE
Confidence            77777766654

Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF) an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea, and eukaryotes. MoCF contains a tricyclic pyranopterin, termed molybdopterin (MPT). MogA, together with MoeA, is responsible for the metal incorporation into MPT, the third step in MoCF biosynthesis. The plant homolog Cnx1 is a MoeA-MogA fusion protein. The mammalian homolog gephyrin is a MogA-MoeA fusion protein, that plays a critical role in postsynaptic anchoring of inhibitory glycine receptors and major GABAa receptor subtypes. In contrast, MoaB shows high similarity to MogA, but little is known about its physiological role. All well studied members of this family form highly stable trimers.

>PRK10401 DNA-binding transcriptional regulator GalS; Provisional

Probab=81.67  E-value=7.5  Score=34.35  Aligned_cols=66  Identities=9%  Similarity=-0.045  Sum_probs=44.1

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcch-HHHHHHHhhhcCCccEEEEEee
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE-IGVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~E-LP~aak~L~~~~~yDaVIaLG~  143 (218)
                      +...|+++...+....-..++++..+.++++|..   +.+..-....+ .--.++.+ ...++||+|.++.
T Consensus        58 ~~~~Igvi~~~~~~~f~~~l~~gi~~~~~~~gy~---~~~~~~~~~~~~~~~~i~~l-~~~~vdGiIi~~~  124 (346)
T PRK10401         58 VSDTIGVVVMDVSDAFFGALVKAVDLVAQQHQKY---VLIGNSYHEAEKERHAIEVL-IRQRCNALIVHSK  124 (346)
T ss_pred             CCCEEEEEeCCCCCccHHHHHHHHHHHHHHCCCE---EEEEcCCCChHHHHHHHHHH-HhcCCCEEEEeCC
Confidence            4457999998887777888999999999999873   33332222211 11233444 3567999998864

>PF13407 Peripla_BP_4: Periplasmic binding protein domain; PDB: 3BRS_B 3GBP_A 3GA5_A 1GCG_A 1GCA_A 3H75_A 3D02_A 3L49_B 3EJW_B 3T95_A

Probab=81.55  E-value=6.4  Score=32.80  Aligned_cols=62  Identities=11%  Similarity=0.193  Sum_probs=45.7

Q ss_pred             EEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhh--hcCCccEEEEEee
Q 027801           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLG--KSGKYTAVLCIGA  143 (218)
Q Consensus        78 IaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~--~~~~yDaVIaLG~  143 (218)
                      |+||........-..+.+++.+.++++|+.   +.++ .++-+...--.+.+-  -..++||||....
T Consensus         1 I~vi~~~~~~~~~~~~~~g~~~~a~~~g~~---~~~~-~~~~~d~~~q~~~i~~~i~~~~d~Iiv~~~   64 (257)
T PF13407_consen    1 IGVIVPSMDNPFWQQVIKGAKAAAKELGYE---VEIV-FDAQNDPEEQIEQIEQAISQGVDGIIVSPV   64 (257)
T ss_dssp             EEEEESSSSSHHHHHHHHHHHHHHHHHTCE---EEEE-EESTTTHHHHHHHHHHHHHTTESEEEEESS
T ss_pred             cEEEeCCCCCHHHHHHHHHHHHHHHHcCCE---EEEe-CCCCCCHHHHHHHHHHHHHhcCCEEEecCC
Confidence            688888888889999999999999999873   3333 577777765554441  2466999995443

...

>TIGR02667 moaB_proteo molybdenum cofactor biosynthesis protein B, proteobacterial

Probab=81.30  E-value=6.9  Score=32.56  Aligned_cols=80  Identities=11%  Similarity=0.040  Sum_probs=52.0

Q ss_pred             HHHHHHCCCCCCCeEEEEeCCcch-HHHHHHHhhhcCCccEEEEEeeeeeCCchhHHHHHHHH--------HHHHHHhch
Q 027801           98 LETFKKYSVKEENIDVVWVPGSFE-IGVVAQQLGKSGKYTAVLCIGAVVRGDTTHYDAVANSA--------ASGVLSAGV  168 (218)
Q Consensus        98 ~~~L~~~Gv~~e~I~vv~VPGA~E-LP~aak~L~~~~~yDaVIaLG~VIrGeT~H~e~Va~~v--------s~gLm~lsL  168 (218)
                      ...|++.|..  -...-.||.-.| |--+++.+++..++|.||+-|-+--|+.++---+-..+        ..-+-.+++
T Consensus        28 ~~~L~~~G~~--v~~~~iv~Dd~~~i~~~l~~~~~~~~~DlVIttGGtg~g~~D~t~eal~~l~~~~l~G~~~~~~~i~~  105 (163)
T TIGR02667        28 VERLTEAGHR--LADRAIVKDDIYQIRAQVSAWIADPDVQVILITGGTGFTGRDVTPEALEPLFDKTVEGFGELFRQLSY  105 (163)
T ss_pred             HHHHHHCCCe--EEEEEEcCCCHHHHHHHHHHHHhcCCCCEEEECCCcCCCCCCCcHHHHHHHHCCcCCcHHHHHHHHhh
Confidence            3447778874  455667898877 55556666545789999999998666555543333322        234677788


Q ss_pred             hc-CCceE-----EEEc
Q 027801          169 NS-GVPCI-----FGVL  179 (218)
Q Consensus       169 ~~-~vPVi-----fGVL  179 (218)
                      +- +.|.+     +|++
T Consensus       106 ~p~G~~~~lsr~~~g~~  122 (163)
T TIGR02667       106 EEIGTSTIQSRALAGLA  122 (163)
T ss_pred             cccCHHHHHhhhhheee
Confidence            84 78864     6654

This model represents the MoaB protein molybdopterin biosynthesis regions in Proteobacteria. This crystallized but incompletely characterized protein is thought to be involved in, though not required for, early steps in molybdopterin biosynthesis. It may bind a molybdopterin precursor. A distinctive conserved motif PCN near the C-terminus helps distinguish this clade from other homologs, including sets of proteins designated MogA.

>cd06291 PBP1_Qymf_like Ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs

Probab=81.02  E-value=30  Score=28.75  Aligned_cols=122  Identities=15%  Similarity=0.087  Sum_probs=66.9

Q ss_pred             CCEEEEEEcccC-HHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH---HHHHHhhh-cCCccEEEEEeeeeeCCc
Q 027801           75 GLRFALVVARFN-ELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGK-SGKYTAVLCIGAVVRGDT  149 (218)
Q Consensus        75 ~~RIaIV~Srfn-~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP---~aak~L~~-~~~yDaVIaLG~VIrGeT  149 (218)
                      ..||+++....+ ......-.+|..+.|+++|...+.   +..++.++..   -.++.+++ ..+.|||+|.+       
T Consensus       112 ~~~i~~i~~~~~~~~~~~~r~~gf~~~l~~~~~~~~~---~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~-------  181 (265)
T cd06291         112 CKHIAHIGGPNNTVSPTNLRYEGFLDVLKENGLEVRI---IEIQENFDDAEKKEEIKELLEEYPDIDGIFASN-------  181 (265)
T ss_pred             CcEEEEEccCcccccchHHHHHHHHHHHHHcCCCCCh---heeeccccchHHHHHHHHHHhCCCCCCEEEECC-------
Confidence            458999987666 355666678999999999986332   2233444322   12334443 34579988843       


Q ss_pred             hhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHh------hCCCCCCcHHHHHHHHHHHHH
Q 027801          150 THYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNR------AGGKSGNKGAEAALTAIEMAS  211 (218)
Q Consensus       150 ~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~R------ag~k~gnKG~EAA~aAleM~~  211 (218)
                         +..+..+.+.+.+..++  +|=-..|++-++.+.+..-      ..-....-|.+|++.+++++.
T Consensus       182 ---d~~a~~~~~al~~~g~~--vp~di~v~g~d~~~~~~~~~~~~~tv~~~~~~~g~~a~~~l~~~i~  244 (265)
T cd06291         182 ---DLTAILVLKEAQQRGIR--VPEDLQIIGYDGTKLTRLYTPELTTIRQPIEEIAKTAVDLLIKQIE  244 (265)
T ss_pred             ---hHHHHHHHHHHHHcCCC--CCcceEEeccCChHHHhhcCCCceeecCCHHHHHHHHHHHHHHHHc
Confidence               33455666677665543  2312234455555443221      111122346666666665544

This group includes the ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs. Qymf is a strict anaerobe that could be grown in the presence of borax and its cells are straight rods that produce endospores. This group is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription

>PRK14987 gluconate operon transcriptional regulator; Provisional

Probab=80.59  E-value=14  Score=32.39  Aligned_cols=98  Identities=20%  Similarity=0.215  Sum_probs=58.8

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHHhhhc-CCccEEEEEeeeeeCCchh
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKS-GKYTAVLCIGAVVRGDTTH  151 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~L~~~-~~yDaVIaLG~VIrGeT~H  151 (218)
                      ...||+++.+.-+.. ...-.+|..+.|+++|+.... .++.....+|-. -+++.+++. .++|||+|.          
T Consensus       179 Gh~~I~~i~~~~~~~-~~~R~~Gf~~al~~~g~~~~~-~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~----------  246 (331)
T PRK14987        179 GHRHIAYLGARLDER-TIIKQKGYEQAMLDAGLVPYS-VMVEQSSSYSSGIELIRQARREYPQLDGVFCT----------  246 (331)
T ss_pred             CCceEEEEcCCCccc-HHHHHHHHHHHHHHcCCCccc-eeecCCCChhhHHHHHHHHHhcCCCCCEEEEC----------
Confidence            346899996554432 234579999999999974322 122223333322 234555544 468999983          


Q ss_pred             HHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHH
Q 027801          152 YDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMD  185 (218)
Q Consensus       152 ~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~e  185 (218)
                      .|.++..+.+++.+..+  .+|==..|++.++.+
T Consensus       247 nD~~A~g~~~al~~~g~--~vP~disvigfD~~~  278 (331)
T PRK14987        247 NDDLAVGAAFECQRLGL--KVPDDMAIAGFHGHD  278 (331)
T ss_pred             CcHHHHHHHHHHHHcCC--CCCCccEEEeeCCch
Confidence            45677777788777655  356444556666554

>cd01544 PBP1_GalR Ligand-binding domain of DNA transcription repressor GalR which is one of two regulatory proteins involved in galactose transport and metabolism

Probab=80.55  E-value=4.6  Score=34.10  Aligned_cols=55  Identities=11%  Similarity=0.189  Sum_probs=37.7

Q ss_pred             EEEEEEc-----ccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEe
Q 027801           77 RFALVVA-----RFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIG  142 (218)
Q Consensus        77 RIaIV~S-----rfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG  142 (218)
                      |||+|..     .+....-..+++++.+.++++|+.   +.+..-++  +..    .  ...++||+|..+
T Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~~~~~~--~~~----~--~~~~vdgii~~~   60 (270)
T cd01544           1 RIAIVQWYSEEEELDDPYYLSIRLGIEKRAQELGIE---LTKFFRDD--DLL----E--ILEDVDGIIAIG   60 (270)
T ss_pred             CeEEEEeccccccccCccHHHHHHHHHHHHHHcCCE---EEEEeccc--hhH----H--hccCcCEEEEec
Confidence            6788887     555667778889999999998874   44443322  111    1  346799999876

Ligand-binding domain of DNA transcription repressor GalR which is one of two regulatory proteins involved in galactose transport and metabolism. Transcription of the galactose regulon genes is regulated by Gal iso-repressor (GalS) and Gal repressor (GalR) in different ways, but both repressors recognize the same DNA binding site in the absence of D-galactose. GalR is a dimeric protein like GalS and is exclusively involved in the regulation of galactose permease, the low-affinity galactose transporter. GalS is involved in regulating expression of the high-affinity galactose transporter encoded by the mgl operon. GalS and GalR are members of the LacI-GalR family of transcription regulators and both contain the type I periplasmic binding protein-like fold. Hence, they are structurally homologous to the periplasmic sugar bindi

>cd06325 PBP1_ABC_uncharacterized_transporter Type I periplasmic ligand-binding domain of uncharacterized ABC-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions

Probab=80.50  E-value=7.3  Score=32.64  Aligned_cols=65  Identities=11%  Similarity=0.181  Sum_probs=44.0

Q ss_pred             EEEEEEcccCHHHHHHHHHHHHHHHHHCCCC-CCCeEEEEeCCcchHH---HHHHHhhhcCCccEEEEEee
Q 027801           77 RFALVVARFNELVTKLLLEGALETFKKYSVK-EENIDVVWVPGSFEIG---VVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        77 RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~-~e~I~vv~VPGA~ELP---~aak~L~~~~~yDaVIaLG~  143 (218)
                      ||||+.. +.......++++..++++++|.. ..++.++......+-.   -.++++. +.++|++|.++.
T Consensus         1 ~igv~~~-~~~~~~~~~~~gi~~~~~~~g~~~g~~v~l~~~~~~~~~~~~~~~~~~l~-~~~vd~iI~~~~   69 (281)
T cd06325           1 KVGILQL-VEHPALDAARKGFKDGLKEAGYKEGKNVKIDYQNAQGDQSNLPTIARKFV-ADKPDLIVAIAT   69 (281)
T ss_pred             CeEEecC-CCCcchHHHHHHHHHHHHHhCccCCceEEEEEecCCCCHHHHHHHHHHHH-hcCCCEEEEcCc
Confidence            6888886 77778889999999999999862 1234554444333322   2334444 468999999864

This group includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); its ligand specificity has not been determined experimentally.

>cd06286 PBP1_CcpB_like Ligand-binding domain of a novel transcription factor implicated in catabolite repression in Bacillus and Clostridium species

Probab=80.42  E-value=23  Score=29.34  Aligned_cols=124  Identities=16%  Similarity=0.134  Sum_probs=70.9

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcch-HHHHHHHhhhc-CCccEEEEEeeeeeCCchh
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE-IGVVAQQLGKS-GKYTAVLCIGAVVRGDTTH  151 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~E-LP~aak~L~~~-~~yDaVIaLG~VIrGeT~H  151 (218)
                      ...||+++...=+......-.+|..+.|+++|.+.....+++-+..++ .--..+.+++. .++|||+|..         
T Consensus       113 g~~~i~~i~~~~~~~~~~~R~~Gf~~~l~~~~~~~~~~~i~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~---------  183 (260)
T cd06286         113 GYRKIAYCIGRKKSLNSQSRKKAYKDALEEYGLTPDEEWIFEGCFTIEDGERIGHQLLKMKDRPDAIFTGS---------  183 (260)
T ss_pred             CCceEEEEcCCcccchhHHHHHHHHHHHHHcCCCCChHheEeCCCCHHHHHHHHHHHHcCCCCCCEEEEcc---------
Confidence            456899997654444455667999999999997533333333222322 12234455543 5799988764         


Q ss_pred             HHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHhhC-----CCCCCcHHHHHHHHHHHH
Q 027801          152 YDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAG-----GKSGNKGAEAALTAIEMA  210 (218)
Q Consensus       152 ~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~Rag-----~k~gnKG~EAA~aAleM~  210 (218)
                       +.++..+.+.+.+..++  +|==..|++.++.+.+ ..-.     -.....|.+|+..+++++
T Consensus       184 -d~~a~~~~~~l~~~g~~--ip~di~v~g~d~~~~~-~~~~~ttv~~~~~~~g~~a~~~l~~~i  243 (260)
T cd06286         184 -DEVAAGIITEAKKQGIR--VPEDLAIIGFDNQPIS-ELLGITTIDQPVKELGEKAFELLLNQL  243 (260)
T ss_pred             -hHHHHHHHHHHHHcCCC--CCcceEEEeecCcccc-cCCCCcccCCCHHHHHHHHHHHHHHHh
Confidence             34666777777765553  3434455555655544 2211     112245666666666655

This group includes the ligand-binding domain of a novel transcription factor implicated in catabolite repression in Bacillus and Clostridium species. CcpB is 30% identical in sequence to CcpA which functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. Like CcpA, the DNA-binding protein CcpB exerts its catabolite-repressing effect by a mechanism dependent on the presence of HPr(Ser-P), the small phosphocarrier proteins of the phosphoenolpyruvate-sugar phosphotransferase system, but with a less significant degree.

>PF03358 FMN_red: NADPH-dependent FMN reductase; InterPro: IPR005025 NADPH-dependent FMN reductase (1

Probab=80.34  E-value=4.4  Score=31.90  Aligned_cols=98  Identities=11%  Similarity=0.158  Sum_probs=58.6

Q ss_pred             CEEEEEEcccC-HHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHH-------------Hhh-hcCCccEEEE
Q 027801           76 LRFALVVARFN-ELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQ-------------QLG-KSGKYTAVLC  140 (218)
Q Consensus        76 ~RIaIV~Srfn-~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak-------------~L~-~~~~yDaVIa  140 (218)
                      +||+||.+.-+ +-.++.|++.+.+.|++.|+   +++++.+..- .+|..-.             .+. +-...|++|.
T Consensus         1 Mkilii~gS~r~~~~t~~l~~~~~~~l~~~g~---e~~~i~l~~~-~~p~~~~~~~~~~~~~d~~~~~~~~l~~aD~iI~   76 (152)
T PF03358_consen    1 MKILIINGSPRKNSNTRKLAEAVAEQLEEAGA---EVEVIDLADY-PLPCCDGDFECPCYIPDDVQELYDKLKEADGIIF   76 (152)
T ss_dssp             -EEEEEESSSSTTSHHHHHHHHHHHHHHHTTE---EEEEEECTTS-HCHHHHHHHHHTGCTSHHHHHHHHHHHHSSEEEE
T ss_pred             CEEEEEECcCCCCCHHHHHHHHHHHHHHHcCC---EEEEEecccc-chhhcccccccccCCcHHHHHHHhceecCCeEEE
Confidence            58899988875 78899999999999999987   4788887776 7774321             121 1246898876


Q ss_pred             EeeeeeCC-chhHHHHHHHHHHHHHHhchhcCCceEEEEc
Q 027801          141 IGAVVRGD-TTHYDAVANSAASGVLSAGVNSGVPCIFGVL  179 (218)
Q Consensus       141 LG~VIrGe-T~H~e~Va~~vs~gLm~lsL~~~vPVifGVL  179 (218)
                      .-=+--|. +..++..-+-...  -.-..-.++|+..-..
T Consensus        77 ~sP~y~~~~s~~lK~~lD~~~~--~~~~~~~~K~~~~i~~  114 (152)
T PF03358_consen   77 ASPVYNGSVSGQLKNFLDRLSC--WFRRALRGKPVAIIAV  114 (152)
T ss_dssp             EEEEBTTBE-HHHHHHHHTHHH--THTTTTTTSEEEEEEE
T ss_pred             eecEEcCcCChhhhHHHHHhcc--ccccccCCCEEEEEEE
Confidence            54432222 2222222222221  1122335788866543

5.1.29 from EC) reduces FMN and also reduces riboflavin and FAD, although more slowly. Members of this entry catalyse the reaction NAD(P)H + FMN = NAD(P)(+) + FMNH(2).; PDB: 3SVL_B 3GFS_F 3GFQ_A 1NNI_1 2GSW_B 3GFR_D 1T0I_B 3D7N_A 2R97_A 3B6K_A ....

>cd06274 PBP1_FruR Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs

Probab=80.24  E-value=19  Score=29.97  Aligned_cols=100  Identities=10%  Similarity=-0.076  Sum_probs=58.1

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHHhhhc--CCccEEEEEeeeeeCCchh
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKS--GKYTAVLCIGAVVRGDTTH  151 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~L~~~--~~yDaVIaLG~VIrGeT~H  151 (218)
                      ..||+++.+.-.......-.+|..+.++++|+..+...++..+-..|-. -+++.++++  ..+|||+|.+-.       
T Consensus       116 ~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~ai~~~~d~-------  188 (264)
T cd06274         116 PEEVLFLGGLPELSPSRERLAGFRQALADAGLPVQPDWIYAEGYSPESGYQLMAELLARLGRLPRALFTTSYT-------  188 (264)
T ss_pred             CCcEEEEeCCCcccchHHHHHHHHHHHHHcCCCCCcceeecCCCChHHHHHHHHHHHccCCCCCcEEEEcChH-------
Confidence            4589999877654455666799999999999753233333333232221 123344444  469999987543       


Q ss_pred             HHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHH
Q 027801          152 YDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQ  186 (218)
Q Consensus       152 ~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQ  186 (218)
                         ++..+.+.+.+..++  +|==..|++.++.+.
T Consensus       189 ---~A~g~~~al~~~g~~--ip~dv~v~g~d~~~~  218 (264)
T cd06274         189 ---LLEGVLRFLRERPGL--APSDLRIATFDDHPL  218 (264)
T ss_pred             ---HHHHHHHHHHHcCCC--CCcceEEEEeCCHHH
Confidence               455666677766554  332234444455443

Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs, all of which are a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to members of the type I periplasmic binding protein superfamily. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor

>cd01537 PBP1_Repressors_Sugar_Binding_like Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems

Probab=80.22  E-value=13  Score=30.17  Aligned_cols=84  Identities=18%  Similarity=0.091  Sum_probs=51.5

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcc-hHHHHHHHhhhcC-CccEEEEEeeeeeCCchhH
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSF-EIGVVAQQLGKSG-KYTAVLCIGAVVRGDTTHY  152 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~-ELP~aak~L~~~~-~yDaVIaLG~VIrGeT~H~  152 (218)
                      ..||+++...-+....+...++..+.++++| ..+.+.+++..... +.--.++.+++.+ +.|+++|.+-         
T Consensus       118 ~~~i~~i~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~i~~~~~---------  187 (264)
T cd01537         118 HRRIALLAGPLGSSTARERVAGFKDALKEAG-PIEIVLVQEGDWDAEKGYQAAEELLTAHPDPTAIFAAND---------  187 (264)
T ss_pred             CCcEEEEECCCCCCcHHHHHHHHHHHHHHcC-CcChhhhccCCCCHHHHHHHHHHHHhcCCCCCEEEEcCc---------
Confidence            5689999876554566677899999999988 21223333333222 2333444555444 4899997632         


Q ss_pred             HHHHHHHHHHHHHhchh
Q 027801          153 DAVANSAASGVLSAGVN  169 (218)
Q Consensus       153 e~Va~~vs~gLm~lsL~  169 (218)
                       ..+..+.+.+.+..++
T Consensus       188 -~~a~~~~~~~~~~g~~  203 (264)
T cd01537         188 -DMALGALRALREAGLR  203 (264)
T ss_pred             -HHHHHHHHHHHHhCCC
Confidence             2455667777777765

Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems, all of which contain the type I periplasmic binding protein-like fold. Their specific ligands include lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor; in general the sugar binding domain in this family binds a sugar, which in turn changes the DNA binding activity of the repressor domain. The core structure of the periplasmic binding proteins is classified into two types and they differ in number and order of beta strands in each domain: type I, which has six beta strands, and type II, which has five beta strands. These two distinct structural arrangem

>cd06288 PBP1_sucrose_transcription_regulator Ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members of the LacI-GalR family of bacterial transcription repressors

Probab=80.16  E-value=8.3  Score=31.99  Aligned_cols=62  Identities=11%  Similarity=0.093  Sum_probs=37.4

Q ss_pred             EEEEEccc-CHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcc-hHHHHHHHhhhcCCccEEEEEee
Q 027801           78 FALVVARF-NELVTKLLLEGALETFKKYSVKEENIDVVWVPGSF-EIGVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        78 IaIV~Srf-n~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~-ELP~aak~L~~~~~yDaVIaLG~  143 (218)
                      ||+|.... ....-..+.++..+.++++|+.   +.++...... +..-.++.+ ...++||+|..++
T Consensus         2 ig~v~~~~~~~~~~~~~~~~i~~~~~~~g~~---~~~~~~~~~~~~~~~~~~~l-~~~~~dgiii~~~   65 (269)
T cd06288           2 IGLISDEIATTPFAVEIILGAQDAAREHGYL---LLVVNTGGDDELEAEAVEAL-LDHRVDGIIYATM   65 (269)
T ss_pred             eEEEeCCCCCCccHHHHHHHHHHHHHHCCCE---EEEEeCCCCHHHHHHHHHHH-HHcCCCEEEEecC
Confidence            67777776 5666677888888888888763   3333322221 112233333 3567888888774

This group includes the ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.

>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor

Probab=80.09  E-value=16  Score=31.90  Aligned_cols=97  Identities=15%  Similarity=0.014  Sum_probs=57.7

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHH-HHHHhhhc-C-CccEEEEEeeeeeCCch
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV-VAQQLGKS-G-KYTAVLCIGAVVRGDTT  150 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~-aak~L~~~-~-~yDaVIaLG~VIrGeT~  150 (218)
                      ...||+++...-+......=.+|..+.|+++|+..  ..++..+...|-.+ +++.+++. . .+|||+|.+        
T Consensus       177 G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~~~~~--~~~~~~~~~~~~~~~~~~~ll~~~~~~~~Ai~~~~--------  246 (327)
T TIGR02417       177 HADEFWYLGAQPELSVSRDRLAGFRQALKQATLEV--EWVYGGNYSRESGYQMFAKLCARLGRLPQALFTTS--------  246 (327)
T ss_pred             CCCeEEEEeCcccchhHHHHHHHHHHHHHHcCCCh--HhEEeCCCChHHHHHHHHHHHhcCCCCCcEEEEcC--------
Confidence            34689999765443334455689999999999852  12222233334332 34555554 3 589999843        


Q ss_pred             hHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHH
Q 027801          151 HYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMD  185 (218)
Q Consensus       151 H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~e  185 (218)
                        |.++-.+.+.|.+..   .+|==..|++.+|.+
T Consensus       247 --D~~A~g~~~al~~~g---~vP~dvsvigfd~~~  276 (327)
T TIGR02417       247 --YTLLEGVLDYMLERP---LLDSQLHLATFGDNY  276 (327)
T ss_pred             --cHHHHHHHHHHHHcC---CCCCcceEEEECCch
Confidence              345666777776654   366445566666554

Members of this family belong the lacI helix-turn-helix family (pfam00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	218
1c2y_A	156	Crystal Structures Of A Pentameric Fungal And An Ic		1e-69
1vsw_A	153	Crystal Structure Of Lumazine Synthase From Bacillu		2e-40
1rvv_A	154	SynthaseRIBOFLAVIN SYNTHASE COMPLEX OF BACILLUS SUB		1e-36
3mk3_A	156	Crystal Structure Of Lumazine Synthase From Salmone		9e-36
1hqk_A	154	Crystal Structure Analysis Of Lumazine Synthase Fro		2e-31
1kz6_A	159	Mutant Enzyme W63y/l119f Lumazine Synthase From S.p		2e-21
1kz9_A	159	Mutant Enzyme L119f Lumazine Synthase From S.pombe		3e-21
2a57_A	159	Structure Of 6,7-dimthyl-8-ribityllumazine Synthase		1e-20
1kz4_A	159	Mutant Enzyme W63y Lumazine Synthase From S.pombe L		1e-20
1kyv_A	159	Lumazine Synthase From S.pombe Bound To Riboflavin		2e-20
1kz1_A	159	Mutant Enzyme W27g Lumazine Synthase From S.pombe L		9e-20
2jfb_A	164	3d Structure Of Lumazine Synthase From Candida Albi		2e-19
4gef_A	179	Product Complex Of Lumazine Synthase From Candida G		6e-19
1c41_A	200	Crystal Structures Of A Pentameric Fungal And An Ic		5e-18
1ejb_A	168	Lumazine Synthase From Saccharomyces Cerevisiae Len		7e-16
1w19_A	160	Lumazine Synthase From Mycobacterium Tuberculosis B		2e-13
2o6h_A	157	Lumazine Synthase Ribh1 From Brucella Melitensis (g		4e-10
2f59_A	157	Lumazine Synthase Ribh1 From Brucella Abortus (gene		2e-09
2obx_A	157	Lumazine Synthase Ribh2 From Mesorhizobium Loti (ge		4e-08
1t13_A	158	Crystal Structure Of Lumazine Synthase From Brucell		9e-07
1di0_A	158	Crystal Structure Of Lumazine Synthase From Brucell		1e-06

>pdb|1C2Y|A Chain A, Crystal Structures Of A Pentameric Fungal And An Icosahedral Plant Lumazine Synthase Reveals The Structural Basis For Differences In Assembly Length = 156

Iteration: 1
 Score =  258 bits (660), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 119/156 (76%), Positives = 142/156 (91%), Gaps = 1/156 (0%)
Query: 63  VRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEI 122
           +  L G++TK +  RFA+VVARFNE VT+ L+EGAL+TFKKYSV E+ IDVVWVPG++E+
Sbjct: 1   MNELEGYVTKAQSFRFAIVVARFNEFVTRRLMEGALDTFKKYSVNED-IDVVWVPGAYEL 59
Query: 123 GVVAQQLGKSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCD 182
           GV AQ LGKSGKY A++C+GAVV+GDT+HYDAV NSA+SGVLSAG+NSGVPC+FGVLTCD
Sbjct: 60  GVTAQALGKSGKYHAIVCLGAVVKGDTSHYDAVVNSASSGVLSAGLNSGVPCVFGVLTCD 119
Query: 183 NMDQALNRAGGKSGNKGAEAALTAIEMASLFEHHLK 218
           NMDQA+NRAGGK+GNKGAE+ALTAIEMASLFEHHLK
Sbjct: 120 NMDQAINRAGGKAGNKGAESALTAIEMASLFEHHLK 155

>pdb|1VSW|A Chain A, Crystal Structure Of Lumazine Synthase From Bacillus Anthracis Length = 153

Iteration: 1
 Score =  162 bits (409), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 78/151 (51%), Positives = 106/151 (70%), Gaps = 5/151 (3%)
Query: 65  HLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV 124
           HL G      GL+  +VV RFNE +T  LL GAL+  K++ V+E +IDV WVPG+FEI +
Sbjct: 6   HLVG-----TGLKVGVVVGRFNEFITSKLLGGALDGLKRHGVEENDIDVAWVPGAFEIPL 60
Query: 125 VAQQLGKSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNM 184
           +A+++  SGKY AV+ +G V+RG TTHYD V N  A GV S  + + +P IFGVLT + +
Sbjct: 61  IAKKMANSGKYDAVITLGTVIRGATTHYDYVCNEVAKGVASLSLQTDIPVIFGVLTTETI 120
Query: 185 DQALNRAGGKSGNKGAEAALTAIEMASLFEH 215
           +QA+ RAG K+GNKG E+A+ AIEMA L +H
Sbjct: 121 EQAIERAGTKAGNKGYESAVAAIEMAHLSKH 151

>pdb|1RVV|A Chain A, SynthaseRIBOFLAVIN SYNTHASE COMPLEX OF BACILLUS SUBTILIS Length = 154

Iteration: 1
 Score =  149 bits (376), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 67/138 (48%), Positives = 98/138 (71%)
Query: 75  GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGK 134
           GL+  +VV RFN+ +T  LL GA +   ++ V   +IDV WVPG+FEI   A+++ ++ K
Sbjct: 12  GLKIGIVVGRFNDFITSKLLSGAEDALLRHGVDTNDIDVAWVPGAFEIPFAAKKMAETKK 71
Query: 135 YTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGK 194
           Y A++ +G V+RG TTHYD V N AA G+  A   +GVP IFG++T +N++QA+ RAG K
Sbjct: 72  YDAIITLGTVIRGATTHYDYVCNEAAKGIAQAANTTGVPVIFGIVTTENIEQAIERAGTK 131
Query: 195 SGNKGAEAALTAIEMASL 212
           +GNKG + A++AIEMA+L
Sbjct: 132 AGNKGVDCAVSAIEMANL 149

>pdb|3MK3|A Chain A, Crystal Structure Of Lumazine Synthase From Salmonella Typhimurium Lt2 Length = 156

Iteration: 1
 Score =  146 bits (368), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 68/139 (48%), Positives = 102/139 (73%), Gaps = 1/139 (0%)
Query: 77  RFALVVARFNELVTKLLLEGALETFKKY-SVKEENIDVVWVPGSFEIGVVAQQLGKSGKY 135
           R A+ +ARFN+ +   LL+GA++   +   VK++NI VVWVPG++E+ +  + L KSGKY
Sbjct: 14  RVAITIARFNQFINDSLLDGAVDALTRIGQVKDDNITVVWVPGAYELPLATEALAKSGKY 73
Query: 136 TAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGKS 195
            AV+ +G V+RG T H++ VA  A++G+ S   +SGVP  FGVLT ++++QA+ RAG K+
Sbjct: 74  DAVVALGTVIRGGTAHFEYVAGGASNGLASVAQDSGVPVAFGVLTTESIEQAIERAGTKA 133
Query: 196 GNKGAEAALTAIEMASLFE 214
           GNKGAEAALTA+EM ++ +
Sbjct: 134 GNKGAEAALTALEMINVLK 152

>pdb|1HQK|A Chain A, Crystal Structure Analysis Of Lumazine Synthase From Aquifex Aeolicus Length = 154

Iteration: 1
 Score =  131 bits (330), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 64/141 (45%), Positives = 95/141 (67%)
Query: 74  EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSG 133
           EGLRF +V +RFN  +   L+EGA++   ++  +EE+I +V VPGS+EI V A +L +  
Sbjct: 11  EGLRFGIVASRFNHALVDRLVEGAIDCIVRHGGREEDITLVRVPGSWEIPVAAGELARKE 70
Query: 134 KYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGG 193
              AV+ IG ++RG T H+D +A+  + G+ +  +    P  FGV+T D ++QA+ RAG 
Sbjct: 71  DIDAVIAIGVLIRGATPHFDYIASEVSKGLANLSLELRKPITFGVITADTLEQAIERAGT 130
Query: 194 KSGNKGAEAALTAIEMASLFE 214
           K GNKG EAAL+AIEMA+LF+
Sbjct: 131 KHGNKGWEAALSAIEMANLFK 151

>pdb|1KZ6|A Chain A, Mutant Enzyme W63y/l119f Lumazine Synthase From S.pombe Length = 159

Iteration: 1
 Score = 98.6 bits (244), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 56/141 (39%), Positives = 85/141 (60%), Gaps = 2/141 (1%)
Query: 72  KNEGLRFALVVARFNELVTKLLLEGALETF-KKYSVKEENIDVVWVPGSFEIGVVAQQLG 130
           K   LR  +V AR+N    + L++GA+ET  +K+ VK ENID+  VPGS+E+    +   
Sbjct: 14  KGPELRILIVHARWNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSYELPQGIRASI 73
Query: 131 KSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNR 190
               Y AV+ IG +++G T H++ ++ +   G++  G++SGVP IFG+LT  N +QAL R
Sbjct: 74  ARNTYDAVIGIGVLIKGSTMHFEYISEAVVHGLMRVGLDSGVPVIFGLLTVLNEEQALYR 133
Query: 191 AGGKSG-NKGAEAALTAIEMA 210
           AG   G N G +    A+EM 
Sbjct: 134 AGLNGGHNHGNDWGSAAVEMG 154

>pdb|1KZ9|A Chain A, Mutant Enzyme L119f Lumazine Synthase From S.pombe Length = 159

Iteration: 1
 Score = 98.2 bits (243), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 56/141 (39%), Positives = 85/141 (60%), Gaps = 2/141 (1%)
Query: 72  KNEGLRFALVVARFNELVTKLLLEGALETF-KKYSVKEENIDVVWVPGSFEIGVVAQQLG 130
           K   LR  +V AR+N    + L++GA+ET  +K+ VK ENID+  VPGS+E+    +   
Sbjct: 14  KGPELRILIVHARWNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSWELPQGIRASI 73
Query: 131 KSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNR 190
               Y AV+ IG +++G T H++ ++ +   G++  G++SGVP IFG+LT  N +QAL R
Sbjct: 74  ARNTYDAVIGIGVLIKGSTMHFEYISEAVVHGLMRVGLDSGVPVIFGLLTVLNEEQALYR 133
Query: 191 AGGKSG-NKGAEAALTAIEMA 210
           AG   G N G +    A+EM 
Sbjct: 134 AGLNGGHNHGNDWGSAAVEMG 154

>pdb|2A57|A Chain A, Structure Of 6,7-dimthyl-8-ribityllumazine Synthase From Schizosaccharomyces Pombe Mutant W27y With Bound Ligand 6- Carboxyethyl-7-oxo-8-ribityllumazine Length = 159

Iteration: 1
 Score = 96.3 bits (238), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 55/141 (39%), Positives = 84/141 (59%), Gaps = 2/141 (1%)
Query: 72  KNEGLRFALVVARFNELVTKLLLEGALETF-KKYSVKEENIDVVWVPGSFEIGVVAQQLG 130
           K   LR  +V AR+N    + L++GA+ET  +K+ VK ENID+  VPGS+E+    +   
Sbjct: 14  KGPELRILIVHARYNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSWELPQGIRASI 73
Query: 131 KSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNR 190
               Y AV+ IG +++G T H++ ++ +   G++  G++SGVP I G+LT  N +QAL R
Sbjct: 74  ARNTYDAVIGIGVLIKGSTMHFEYISEAVVHGLMRVGLDSGVPVILGLLTVLNEEQALYR 133
Query: 191 AGGKSG-NKGAEAALTAIEMA 210
           AG   G N G +    A+EM 
Sbjct: 134 AGLNGGHNHGNDWGSAAVEMG 154

>pdb|1KZ4|A Chain A, Mutant Enzyme W63y Lumazine Synthase From S.pombe Length = 159

Iteration: 1
 Score = 96.3 bits (238), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 55/141 (39%), Positives = 84/141 (59%), Gaps = 2/141 (1%)
Query: 72  KNEGLRFALVVARFNELVTKLLLEGALETF-KKYSVKEENIDVVWVPGSFEIGVVAQQLG 130
           K   LR  +V AR+N    + L++GA+ET  +K+ VK ENID+  VPGS+E+    +   
Sbjct: 14  KGPELRILIVHARWNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSYELPQGIRASI 73
Query: 131 KSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNR 190
               Y AV+ IG +++G T H++ ++ +   G++  G++SGVP I G+LT  N +QAL R
Sbjct: 74  ARNTYDAVIGIGVLIKGSTMHFEYISEAVVHGLMRVGLDSGVPVILGLLTVLNEEQALYR 133
Query: 191 AGGKSG-NKGAEAALTAIEMA 210
           AG   G N G +    A+EM 
Sbjct: 134 AGLNGGHNHGNDWGSAAVEMG 154

>pdb|1KYV|A Chain A, Lumazine Synthase From S.pombe Bound To Riboflavin Length = 159

Iteration: 1
 Score = 95.9 bits (237), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 55/141 (39%), Positives = 84/141 (59%), Gaps = 2/141 (1%)
Query: 72  KNEGLRFALVVARFNELVTKLLLEGALETF-KKYSVKEENIDVVWVPGSFEIGVVAQQLG 130
           K   LR  +V AR+N    + L++GA+ET  +K+ VK ENID+  VPGS+E+    +   
Sbjct: 14  KGPELRILIVHARWNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSWELPQGIRASI 73
Query: 131 KSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNR 190
               Y AV+ IG +++G T H++ ++ +   G++  G++SGVP I G+LT  N +QAL R
Sbjct: 74  ARNTYDAVIGIGVLIKGSTMHFEYISEAVVHGLMRVGLDSGVPVILGLLTVLNEEQALYR 133
Query: 191 AGGKSG-NKGAEAALTAIEMA 210
           AG   G N G +    A+EM 
Sbjct: 134 AGLNGGHNHGNDWGSAAVEMG 154

>pdb|1KZ1|A Chain A, Mutant Enzyme W27g Lumazine Synthase From S.pombe Length = 159

Iteration: 1
 Score = 93.2 bits (230), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 55/141 (39%), Positives = 83/141 (58%), Gaps = 2/141 (1%)
Query: 72  KNEGLRFALVVARFNELVTKLLLEGALETF-KKYSVKEENIDVVWVPGSFEIGVVAQQLG 130
           K   LR  +V AR N    + L++GA+ET  +K+ VK ENID+  VPGS+E+    +   
Sbjct: 14  KGPELRILIVHARGNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSWELPQGIRASI 73
Query: 131 KSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNR 190
               Y AV+ IG +++G T H++ ++ +   G++  G++SGVP I G+LT  N +QAL R
Sbjct: 74  ARNTYDAVIGIGVLIKGSTMHFEYISEAVVHGLMRVGLDSGVPVILGLLTVLNEEQALYR 133
Query: 191 AGGKSG-NKGAEAALTAIEMA 210
           AG   G N G +    A+EM 
Sbjct: 134 AGLNGGHNHGNDWGSAAVEMG 154

>pdb|2JFB|A Chain A, 3d Structure Of Lumazine Synthase From Candida Albicans Length = 164

Iteration: 1
 Score = 92.4 bits (228), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 57/162 (35%), Positives = 88/162 (54%), Gaps = 10/162 (6%)
Query: 62  AVRHLTGFLTKNEG--LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGS 119
           AV+ L     K +G  LR  ++ AR+N  +   L+ GA++  +++ VKEENI +  VPGS
Sbjct: 2   AVKGLGEVDQKYDGSKLRIGILHARWNRKIIDALVAGAVKRLQEFGVKEENIIIETVPGS 61
Query: 120 FEIGV-----VAQQLGKSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPC 174
           FE+       V +Q        A++ IG +++G T H++ + +S    ++      G+P 
Sbjct: 62  FELPYGSKLFVEKQKRLGKPLDAIIPIGVLIKGSTMHFEYICDSTTHQLMKLNFELGIPV 121
Query: 175 IFGVLTCDNMDQALNRAG---GKSGNKGAEAALTAIEMASLF 213
           IFGVLTC   +QA  RAG   GK  N G +    A+EMA+ F
Sbjct: 122 IFGVLTCLTDEQAEARAGLIEGKMHNHGEDWGAAAVEMATKF 163

>pdb|4GEF|A Chain A, Product Complex Of Lumazine Synthase From Candida Glabrata Length = 179

Iteration: 1
 Score = 90.5 bits (223), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 52/147 (35%), Positives = 83/147 (56%), Gaps = 9/147 (6%)
Query: 76  LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV----VAQQLGK 131
           LR  ++ AR+N ++   L++GA++      VKEENI V  VPGSFE+       A++  K
Sbjct: 29  LRVGIIHARWNRVIIDALVKGAIDRMLSLGVKEENIIVETVPGSFELPYGSKRFAEKQAK 88
Query: 132 SGK-YTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNR 190
            G+    V+ IG +++G T H++ +++S    +++      +P IFG+LTC   +QAL R
Sbjct: 89  KGEPLDVVIPIGVLIKGSTMHFEYISDSTTQAIMNLQDKINIPVIFGLLTCLTEEQALAR 148
Query: 191 AGGKSG----NKGAEAALTAIEMASLF 213
           AG   G    N G +    A+EMA+ F
Sbjct: 149 AGIDEGKTMHNHGEDWGAAAVEMATKF 175

>pdb|1C41|A Chain A, Crystal Structures Of A Pentameric Fungal And An Icosahedral Plant Lumazine Synthase Reveals The Structural Basis For Differences In Assembly Length = 200

Iteration: 1
 Score = 87.8 bits (216), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 55/172 (31%), Positives = 83/172 (48%), Gaps = 38/172 (22%)
Query: 76  LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQL------ 129
           LR  +V AR+NE + + LL G         VKE NI V  VPGS+E+ +  Q+L      
Sbjct: 16  LRIGIVHARWNETIIEPLLAGTKAKLLACGVKESNIVVQSVPGSWELPIAVQRLYSASQL 75
Query: 130 ------------------------------GKSGKYTAVLCIGAVVRGDTTHYDAVANSA 159
                                           +G + A++ IG +++G+T H++ +A+S 
Sbjct: 76  QTPSSGPSLSAGDLLGSSTTDLTALPTTTASSTGPFDALIAIGVLIKGETMHFEYIADSV 135
Query: 160 ASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGKSG--NKGAEAALTAIEM 209
           + G++   +++GVP IFGVLT    DQA  RAG   G  N G +  L A+EM
Sbjct: 136 SHGLMRVQLDTGVPVIFGVLTVLTDDQAKARAGVIEGSHNHGEDWGLAAVEM 187

>pdb|1EJB|A Chain A, Lumazine Synthase From Saccharomyces Cerevisiae Length = 168

Iteration: 1
 Score = 80.5 bits (197), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 46/147 (31%), Positives = 77/147 (52%), Gaps = 9/147 (6%)
Query: 76  LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-----VVAQQLG 130
           +R  ++ AR+N ++   L++GA+E      V+E NI +  VPGS+E+       V +Q  
Sbjct: 17  IRVGIIHARWNRVIIDALVKGAIERMASLGVEENNIIIETVPGSYELPWGTKRFVDRQAK 76
Query: 131 KSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNR 190
                  V+ IG +++G T H++ +++S    +++      +P IFG+LTC   +QAL R
Sbjct: 77  LGKPLDVVIPIGVLIKGSTMHFEYISDSTTHALMNLQEKVDMPVIFGLLTCMTEEQALAR 136
Query: 191 AGGKSG----NKGAEAALTAIEMASLF 213
           AG        N G +    A+EMA  F
Sbjct: 137 AGIDEAHSMHNHGEDWGAAAVEMAVKF 163

>pdb|1W19|A Chain A, Lumazine Synthase From Mycobacterium Tuberculosis Bound To 3-(1,3,7-Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl) Propane 1-Phosphate Length = 160

Iteration: 1
 Score = 72.4 bits (176), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 42/118 (35%), Positives = 69/118 (58%), Gaps = 4/118 (3%)
Query: 75  GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGK 134
           G+R A+V + ++  +   LL+GA +      + +    VV V G+ EI VVAQ+L ++  
Sbjct: 17  GVRLAIVASSWHGKICDALLDGARKVAAGCGLDDPT--VVRVLGAIEIPVVAQELARN-- 72
Query: 135 YTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAG 192
           + AV+ +G V+RG T H+D V ++   G+    ++S  P   GVLT +  +QAL+RAG
Sbjct: 73  HDAVVALGVVIRGQTPHFDYVCDAVTQGLTRVSLDSSTPIANGVLTTNTEEQALDRAG 130

>pdb|2O6H|A Chain A, Lumazine Synthase Ribh1 From Brucella Melitensis (gene Bmei1187, Swiss-prot Entry Q8ygh2) Complexed With Inhibitor 5-nitro-6-(d- Ribitylamino)-2,4(1h,3h) Pyrimidinedione Length = 157

Iteration: 1
 Score = 61.6 bits (148), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 44/138 (31%), Positives = 67/138 (48%), Gaps = 8/138 (5%)
Query: 80  LVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVV---AQQLGKSG--K 134
           +V ARF + +   LL+GA     +        DVV VPG+ EI      A     +G  +
Sbjct: 17  IVEARFYDDLADALLDGAKAALDEAGA---TYDVVTVPGALEIPATISFALDGADNGGTE 73
Query: 135 YTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGK 194
           Y   + +G V+RG+T H+D V+N +   +    V   +    G+LT +N +QA  RA  +
Sbjct: 74  YDGFVALGTVIRGETYHFDIVSNESCRALTDLSVEESIAIGNGILTVENEEQAWVRARRE 133
Query: 195 SGNKGAEAALTAIEMASL 212
             +KG  AA  A+ M  L
Sbjct: 134 DKDKGGFAARAALTMIGL 151

>pdb|2F59|A Chain A, Lumazine Synthase Ribh1 From Brucella Abortus (gene Bruab1_0785, Swiss-prot Entry Q57dy1) Complexed With Inhibitor 5-nitro-6-(d- Ribitylamino)-2,4(1h,3h) Pyrimidinedione Length = 157

Iteration: 1
 Score = 58.9 bits (141), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 43/138 (31%), Positives = 66/138 (47%), Gaps = 8/138 (5%)
Query: 80  LVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVV---AQQLGKSG--K 134
           +V ARF + +   LL+GA     +        DVV VPG+ EI      A     +G  +
Sbjct: 17  IVEARFYDDLADALLDGAKAALDEAGA---TYDVVTVPGALEIPATISFALDGADNGGTE 73
Query: 135 YTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGK 194
           Y   + +G V+RG+T H+D V+N +   +    V   +    G+LT +N +QA   A  +
Sbjct: 74  YDGFVALGTVIRGETYHFDIVSNESCRALTDLSVEESIAIGNGILTVENEEQAWVHARRE 133
Query: 195 SGNKGAEAALTAIEMASL 212
             +KG  AA  A+ M  L
Sbjct: 134 DKDKGGFAARAALTMIGL 151

>pdb|2OBX|A Chain A, Lumazine Synthase Ribh2 From Mesorhizobium Loti (gene Mll7281, Swiss- Prot Entry Q986n2) Complexed With Inhibitor 5-nitro-6-(d- Ribitylamino)-2,4(1h,3h) Pyrimidinedione Length = 157

Iteration: 1
 Score = 54.7 bits (130), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 33/110 (30%), Positives = 58/110 (52%)
Query: 74  EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSG 133
           E +R A+V AR++  +    +                +DV  VPG++EI + A+ L ++G
Sbjct: 10  ETVRIAVVRARWHADIVDQCVSAFEAEMADIGGDRFAVDVFDVPGAYEIPLHARTLAETG 69
Query: 134 KYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDN 183
           +Y AVL    VV G    ++ VA++   G+++  +++GVP +  VLT  N
Sbjct: 70  RYGAVLGTAFVVNGGIYRHEFVASAVIDGMMNVQLSTGVPVLSAVLTPHN 119

>pdb|1T13|A Chain A, Crystal Structure Of Lumazine Synthase From Brucella Abortus Bound To 5-nitro-6-(d-ribitylamino)-2,4(1h,3h) Pyrimidinedione Length = 158

Iteration: 1
 Score = 50.1 bits (118), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 28/105 (26%), Positives = 56/105 (53%), Gaps = 3/105 (2%)
Query: 110 NIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVN 169
            +++  VPG++EI + A+ L ++G+Y A++    V+ G    +D VA +  +G++   + 
Sbjct: 45  EVEIFDVPGAYEIPLHAKTLARTGRYAAIVGAAFVIDGGIYRHDFVATAVINGMMQVQLE 104
Query: 170 SGVPCIFGVLTCDNMDQALNRAGGKSGN---KGAEAALTAIEMAS 211
           + VP +  VLT  +  ++         +   KG EAA  A+++ S
Sbjct: 105 TEVPVLSVVLTPHHFHESKEHHDFFHAHFKVKGVEAAHAALQIVS 149

>pdb|1DI0|A Chain A, Crystal Structure Of Lumazine Synthase From Brucella Abortus Length = 158

Iteration: 1
 Score = 49.7 bits (117), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 28/105 (26%), Positives = 56/105 (53%), Gaps = 3/105 (2%)
Query: 110 NIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVN 169
            +++  VPG++EI + A+ L ++G+Y A++    V+ G    +D VA +  +G++   + 
Sbjct: 45  EVEIFDVPGAYEIPLHAKTLARTGRYAAIVGAAFVIDGGIYDHDFVATAVINGMMQVQLE 104
Query: 170 SGVPCIFGVLTCDNMDQALNRAGGKSGN---KGAEAALTAIEMAS 211
           + VP +  VLT  +  ++         +   KG EAA  A+++ S
Sbjct: 105 TEVPVLSVVLTPHHFHESKEHHDFFHAHFKVKGVEAAHAALQIVS 149

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	218
1c2y_A	156	Protein (lumazine synthase); riboflavin biosynthes	7e-84
1rvv_A	154	Riboflavin synthase; transferase, flavoprotein; HE	1e-82
1hqk_A	154	6,7-dimethyl-8-ribityllumazine synthase; analysi s	8e-82
3nq4_A	156	6,7-dimethyl-8-ribityllumazine synthase; 30MER, ic	7e-80
1kz1_A	159	6,7-dimethyl-8-ribityllumazine synthase; riboflavi	3e-77
1di0_A	158	Lumazine synthase; transferase; 2.70A {Brucella ab	2e-76
1ejb_A	168	Lumazine synthase; analysis, inhibitor complex, vi	7e-75
2obx_A	157	DMRL synthase 1, 6,7-dimethyl-8-ribityllumazine sy	1e-74
2c92_A	160	6,7-dimethyl-8-ribityllumazine synthase; transfera	2e-70
2i0f_A	157	6,7-dimethyl-8-ribityllumazine synthase 1; lumazin	2e-68
1c41_A	200	Lumazine synthase; riboflavin biosynthesis, transf	3e-66
2b99_A	156	Riboflavin synthase; lumazine riboflavin, transfer	1e-16

>1c2y_A Protein (lumazine synthase); riboflavin biosynthesis, transferase; HET: LMZ; 3.30A {Spinacia oleracea} SCOP: c.16.1.1 Length = 156

 Score =  245 bits (627), Expect = 7e-84
 Identities = 119/156 (76%), Positives = 142/156 (91%), Gaps = 1/156 (0%)

Query: 63  VRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEI 122
           +  L G++TK +  RFA+VVARFNE VT+ L+EGAL+TFKKYSV E +IDVVWVPG++E+
Sbjct: 1   MNELEGYVTKAQSFRFAIVVARFNEFVTRRLMEGALDTFKKYSVNE-DIDVVWVPGAYEL 59

Query: 123 GVVAQQLGKSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCD 182
           GV AQ LGKSGKY A++C+GAVV+GDT+HYDAV NSA+SGVLSAG+NSGVPC+FGVLTCD
Sbjct: 60  GVTAQALGKSGKYHAIVCLGAVVKGDTSHYDAVVNSASSGVLSAGLNSGVPCVFGVLTCD 119

Query: 183 NMDQALNRAGGKSGNKGAEAALTAIEMASLFEHHLK 218
           NMDQA+NRAGGK+GNKGAE+ALTAIEMASLFEHHLK
Sbjct: 120 NMDQAINRAGGKAGNKGAESALTAIEMASLFEHHLK 155

>1rvv_A Riboflavin synthase; transferase, flavoprotein; HET: INI; 2.40A {Bacillus subtilis} SCOP: c.16.1.1 PDB: 1zis_A* 1vsw_A 1vsx_A 3jv8_A Length = 154

 Score =  241 bits (618), Expect = 1e-82
 Identities = 69/152 (45%), Positives = 102/152 (67%), Gaps = 1/152 (0%)

Query: 63  VRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEI 122
           +  + G L    GL+  +VV RFN+ +T  LL GA +   ++ V   +IDV WVPG+FEI
Sbjct: 1   MNIIQGNLV-GTGLKIGIVVGRFNDFITSKLLSGAEDALLRHGVDTNDIDVAWVPGAFEI 59

Query: 123 GVVAQQLGKSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCD 182
              A+++ ++ KY A++ +G V+RG TTHYD V N AA G+  A   +GVP IFG++T +
Sbjct: 60  PFAAKKMAETKKYDAIITLGTVIRGATTHYDYVCNEAAKGIAQAANTTGVPVIFGIVTTE 119

Query: 183 NMDQALNRAGGKSGNKGAEAALTAIEMASLFE 214
           N++QA+ RAG K+GNKG + A++AIEMA+L  
Sbjct: 120 NIEQAIERAGTKAGNKGVDCAVSAIEMANLNR 151

>1hqk_A 6,7-dimethyl-8-ribityllumazine synthase; analysi stability, vitamin biosynthesis, transferase; 1.60A {Aquifex aeolicus} SCOP: c.16.1.1 PDB: 1nqu_A* 1nqv_A* 1nqw_A* 1nqx_A* Length = 154

 Score =  239 bits (613), Expect = 8e-82
 Identities = 67/152 (44%), Positives = 100/152 (65%), Gaps = 1/152 (0%)

Query: 63  VRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEI 122
           ++   G LT  EGLRF +V +RFN  +   L+EGA++   ++  +EE+I +V VPGS+EI
Sbjct: 1   MQIYEGKLT-AEGLRFGIVASRFNHALVDRLVEGAIDCIVRHGGREEDITLVRVPGSWEI 59

Query: 123 GVVAQQLGKSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCD 182
            V A +L +     AV+ IG ++RG T H+D +A+  + G+ +  +    P  FGV+T D
Sbjct: 60  PVAAGELARKEDIDAVIAIGVLIRGATPHFDYIASEVSKGLANLSLELRKPITFGVITAD 119

Query: 183 NMDQALNRAGGKSGNKGAEAALTAIEMASLFE 214
            ++QA+ RAG K GNKG EAAL+AIEMA+LF+
Sbjct: 120 TLEQAIERAGTKHGNKGWEAALSAIEMANLFK 151

>3nq4_A 6,7-dimethyl-8-ribityllumazine synthase; 30MER, icosahedral, flavodoxin like fold, transferase, DMRL riboflavin biosynthesis, drug targe; 3.50A {Salmonella typhimurium} PDB: 3mk3_A Length = 156

 Score =  234 bits (600), Expect = 7e-80
 Identities = 68/153 (44%), Positives = 105/153 (68%), Gaps = 2/153 (1%)

Query: 63  VRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKY-SVKEENIDVVWVPGSFE 121
           +  +   +      R A+ +ARFN+ +   LL+GA++   +   VK++NI VVWVPG++E
Sbjct: 1   MNIIKANVA-APDARVAITIARFNQFINDSLLDGAVDALTRIGQVKDDNITVVWVPGAYE 59

Query: 122 IGVVAQQLGKSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTC 181
           + +  + L KSGKY AV+ +G V+RG T H++ VA  A++G+ S   +SGVP  FGVLT 
Sbjct: 60  LPLATEALAKSGKYDAVVALGTVIRGGTAHFEYVAGGASNGLASVAQDSGVPVAFGVLTT 119

Query: 182 DNMDQALNRAGGKSGNKGAEAALTAIEMASLFE 214
           ++++QA+ RAG K+GNKGAEAALTA+EM ++ +
Sbjct: 120 ESIEQAIERAGTKAGNKGAEAALTALEMINVLK 152

>1kz1_A 6,7-dimethyl-8-ribityllumazine synthase; riboflavin biosynthesis, ligand binding, transferase; 2.00A {Schizosaccharomyces pombe} SCOP: c.16.1.1 PDB: 2a59_A* 2a58_A* 2a57_A* 1kyv_A* 1kyx_A* 1kyy_A* 1kz9_A 1kz4_A 1kz6_A Length = 159

 Score =  228 bits (583), Expect = 3e-77
 Identities = 54/144 (37%), Positives = 83/144 (57%), Gaps = 2/144 (1%)

Query: 74  EGLRFALVVARFNELVTKLLLEGALETF-KKYSVKEENIDVVWVPGSFEIGVVAQQLGKS 132
             LR  +V AR N    + L++GA+ET  +K+ VK ENID+  VPGS+E+    +     
Sbjct: 16  PELRILIVHARGNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSWELPQGIRASIAR 75

Query: 133 GKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAG 192
             Y AV+ IG +++G T H++ ++ +   G++  G++SGVP I G+LT  N +QAL RAG
Sbjct: 76  NTYDAVIGIGVLIKGSTMHFEYISEAVVHGLMRVGLDSGVPVILGLLTVLNEEQALYRAG 135

Query: 193 GKSG-NKGAEAALTAIEMASLFEH 215
              G N G +    A+EM     +
Sbjct: 136 LNGGHNHGNDWGSAAVEMGLKALY 159

>1di0_A Lumazine synthase; transferase; 2.70A {Brucella abortus} SCOP: c.16.1.1 PDB: 1t13_A* 1xn1_A Length = 158

 Score =  226 bits (578), Expect = 2e-76
 Identities = 31/144 (21%), Positives = 67/144 (46%), Gaps = 3/144 (2%)

Query: 74  EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSG 133
              + A + AR++  +     +  +      +     +++  VPG++EI + A+ L ++G
Sbjct: 9   TSFKIAFIQARWHADIVDEARKSFVAELAAKTGGSVEVEIFDVPGAYEIPLHAKTLARTG 68

Query: 134 KYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGG 193
           +Y A++    V+ G    +D VA +  +G++   + + VP +  VLT  +  ++      
Sbjct: 69  RYAAIVGAAFVIDGGIYDHDFVATAVINGMMQVQLETEVPVLSVVLTPHHFHESKEHHDF 128

Query: 194 KSGN---KGAEAALTAIEMASLFE 214
              +   KG EAA  A+++ S   
Sbjct: 129 FHAHFKVKGVEAAHAALQIVSERS 152

>1ejb_A Lumazine synthase; analysis, inhibitor complex, vitamin biosynthesis transferase; HET: INJ; 1.85A {Saccharomyces cerevisiae} SCOP: c.16.1.1 PDB: 2jfb_A Length = 168

 Score =  222 bits (568), Expect = 7e-75
 Identities = 44/149 (29%), Positives = 76/149 (51%), Gaps = 9/149 (6%)

Query: 74  EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQL---- 129
             +R  ++ AR+N ++   L++GA+E      V+E NI +  VPGS+E+    ++     
Sbjct: 15  SKIRVGIIHARWNRVIIDALVKGAIERMASLGVEENNIIIETVPGSYELPWGTKRFVDRQ 74

Query: 130 -GKSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQAL 188
                    V+ IG +++G T H++ +++S    +++      +P IFG+LTC   +QAL
Sbjct: 75  AKLGKPLDVVIPIGVLIKGSTMHFEYISDSTTHALMNLQEKVDMPVIFGLLTCMTEEQAL 134

Query: 189 NRAGGKSG----NKGAEAALTAIEMASLF 213
            RAG        N G +    A+EMA  F
Sbjct: 135 ARAGIDEAHSMHNHGEDWGAAAVEMAVKF 163

>2obx_A DMRL synthase 1, 6,7-dimethyl-8-ribityllumazine synthase 1, riboflavin S; alpha-beta, transferase; HET: INI; 2.53A {Mesorhizobium loti} Length = 157

 Score =  221 bits (566), Expect = 1e-74
 Identities = 40/144 (27%), Positives = 69/144 (47%), Gaps = 3/144 (2%)

Query: 74  EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSG 133
           E +R A+V AR++  +    +                +DV  VPG++EI + A+ L ++G
Sbjct: 10  ETVRIAVVRARWHADIVDQCVSAFEAEMADIGGDRFAVDVFDVPGAYEIPLHARTLAETG 69

Query: 134 KYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAG- 192
           +Y AVL    VV G    ++ VA++   G+++  +++GVP +  VLT  N   +      
Sbjct: 70  RYGAVLGTAFVVNGGIYRHEFVASAVIDGMMNVQLSTGVPVLSAVLTPHNYHDSAEHHRF 129

Query: 193 --GKSGNKGAEAALTAIEMASLFE 214
                  KG EAA   +E+ +  E
Sbjct: 130 FFEHFTVKGKEAARACVEILAARE 153

>2c92_A 6,7-dimethyl-8-ribityllumazine synthase; transferase, riboflavin biosynthesis, inhibitor binding; HET: TP6; 1.6A {Mycobacterium tuberculosis} PDB: 1w29_A* 1w19_A* 2c94_A* 2c97_A* 2c9b_A* 2c9d_A* 2vi5_A* Length = 160

 Score =  211 bits (539), Expect = 2e-70
 Identities = 48/143 (33%), Positives = 81/143 (56%), Gaps = 6/143 (4%)

Query: 74  EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSG 133
            G+R A+V + ++  +   LL+GA +      +  ++  VV V G+ EI VVAQ+L ++ 
Sbjct: 16  SGVRLAIVASSWHGKICDALLDGARKVAAGCGL--DDPTVVRVLGAIEIPVVAQELARN- 72

Query: 134 KYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAG- 192
            + AV+ +G V+RG T H+D V ++   G+    ++S  P   GVLT +  +QAL+RAG 
Sbjct: 73  -HDAVVALGVVIRGQTPHFDYVCDAVTQGLTRVSLDSSTPIANGVLTTNTEEQALDRAGL 131

Query: 193 -GKSGNKGAEAALTAIEMASLFE 214
              + +KGA+A + A+  A    
Sbjct: 132 PTSAEDKGAQATVAALATALTLR 154

>2i0f_A 6,7-dimethyl-8-ribityllumazine synthase 1; lumazine synthase RIBH1, transferase; 2.22A {Brucella abortus} PDB: 2f59_A 2o6h_A* Length = 157

 Score =  205 bits (525), Expect = 2e-68
 Identities = 41/146 (28%), Positives = 65/146 (44%), Gaps = 8/146 (5%)

Query: 74  EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSG 133
           +     +V ARF + +   LL+GA     +        DVV VPG+ EI           
Sbjct: 11  DAPHLLIVEARFYDDLADALLDGAKAALDEAGA---TYDVVTVPGALEIPATISFALDGA 67

Query: 134 -----KYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQAL 188
                +Y   + +G V+RG+T H+D V+N +   +    V   +    G+LT +N +QA 
Sbjct: 68  DNGGTEYDGFVALGTVIRGETYHFDIVSNESCRALTDLSVEESIAIGNGILTVENEEQAW 127

Query: 189 NRAGGKSGNKGAEAALTAIEMASLFE 214
             A  +  +KG  AA  A+ M  L +
Sbjct: 128 VHARREDKDKGGFAARAALTMIGLRK 153

>1c41_A Lumazine synthase; riboflavin biosynthesis, transferase; HET: LMZ; 3.10A {Magnaporthe grisea} SCOP: c.16.1.1 Length = 200

 Score =  202 bits (514), Expect = 3e-66
 Identities = 55/178 (30%), Positives = 83/178 (46%), Gaps = 38/178 (21%)

Query: 74  EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQL---- 129
             LR  +V AR+NE + + LL G         VKE NI V  VPGS+E+ +  Q+L    
Sbjct: 14  SALRIGIVHARWNETIIEPLLAGTKAKLLACGVKESNIVVQSVPGSWELPIAVQRLYSAS 73

Query: 130 --------------------------------GKSGKYTAVLCIGAVVRGDTTHYDAVAN 157
                                             +G + A++ IG +++G+T H++ +A+
Sbjct: 74  QLQTPSSGPSLSAGDLLGSSTTDLTALPTTTASSTGPFDALIAIGVLIKGETMHFEYIAD 133

Query: 158 SAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGKSG--NKGAEAALTAIEMASLF 213
           S + G++   +++GVP IFGVLT    DQA  RAG   G  N G +  L A+EM    
Sbjct: 134 SVSHGLMRVQLDTGVPVIFGVLTVLTDDQAKARAGVIEGSHNHGEDWGLAAVEMGVRR 191

>2b99_A Riboflavin synthase; lumazine riboflavin, transferase; HET: RDL; 2.22A {Methanocaldococcus jannaschii} PDB: 2b98_A* Length = 156

 Score = 73.1 bits (179), Expect = 1e-16
 Identities = 22/135 (16%), Positives = 48/135 (35%), Gaps = 7/135 (5%)

Query: 75  GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGK 134
             +  +V   F  +    +   A++  K+ S     I    VPG  ++ V  ++L +   
Sbjct: 2   TKKVGIVDTTFARVD---MASIAIKKLKELSPNI-KIIRKTVPGIKDLPVACKKLLEEEG 57

Query: 135 YTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGK 194
              V+ +G    G        A+ A+ G++ A + +    I  V   ++  +        
Sbjct: 58  CDIVMALGMP--GKAEKDKVCAHEASLGLMLAQLMTNKH-IIEVFVHEDEAKDDKELDWL 114

Query: 195 SGNKGAEAALTAIEM 209
           +  +  E A     +
Sbjct: 115 AKRRAEEHAENVYYL 129

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	218
3nq4_A	156	6,7-dimethyl-8-ribityllumazine synthase; 30MER, ic	100.0
1c2y_A	156	Protein (lumazine synthase); riboflavin biosynthes	100.0
1hqk_A	154	6,7-dimethyl-8-ribityllumazine synthase; analysi s	100.0
1rvv_A	154	Riboflavin synthase; transferase, flavoprotein; HE	100.0
1kz1_A	159	6,7-dimethyl-8-ribityllumazine synthase; riboflavi	100.0
2i0f_A	157	6,7-dimethyl-8-ribityllumazine synthase 1; lumazin	100.0
1ejb_A	168	Lumazine synthase; analysis, inhibitor complex, vi	100.0
2obx_A	157	DMRL synthase 1, 6,7-dimethyl-8-ribityllumazine sy	100.0
1di0_A	158	Lumazine synthase; transferase; 2.70A {Brucella ab	100.0
2c92_A	160	6,7-dimethyl-8-ribityllumazine synthase; transfera	100.0
1c41_A	200	Lumazine synthase; riboflavin biosynthesis, transf	100.0
2b99_A	156	Riboflavin synthase; lumazine riboflavin, transfer	100.0
3e61_A	277	Putative transcriptional repressor of ribose OPER;	96.21
3jy6_A	276	Transcriptional regulator, LACI family; NYSGXRC, P	96.01
3l6u_A	293	ABC-type sugar transport system periplasmic compo;	95.91
3l49_A	291	ABC sugar (ribose) transporter, periplasmic substr	95.84
3hs3_A	277	Ribose operon repressor; PSI-II, NYSGXRC, periplas	95.73
3lft_A	295	Uncharacterized protein; ABC, ATPase, cassette, L-	95.66
3lkv_A	302	Uncharacterized conserved domain protein; ATPase b	95.54
2qh8_A	302	Uncharacterized protein; conserved domain protein,	95.41
3jvd_A	333	Transcriptional regulators; structural genomics, P	95.38
3tb6_A	298	Arabinose metabolism transcriptional repressor; tr	95.15
3egc_A	291	Putative ribose operon repressor; structural genom	95.04
3h75_A	350	Periplasmic sugar-binding domain protein; protein	94.91
3uug_A	330	Multiple sugar-binding periplasmic receptor CHVE;	94.86
2qh8_A	302	Uncharacterized protein; conserved domain protein,	94.81
3k4h_A	292	Putative transcriptional regulator; structural gen	94.8
3ksm_A	276	ABC-type sugar transport system, periplasmic COMP;	94.66
3lft_A	295	Uncharacterized protein; ABC, ATPase, cassette, L-	94.44
3o74_A	272	Fructose transport system repressor FRUR; dual tra	94.42
3rot_A	297	ABC sugar transporter, periplasmic sugar binding;	94.36
3g85_A	289	Transcriptional regulator (LACI family); transcrip	94.27
3kke_A	303	LACI family transcriptional regulator; structural	94.23
3gbv_A	304	Putative LACI-family transcriptional regulator; NY	94.02
3o1i_D	304	Periplasmic protein TORT; ligand free, two compone	93.85
3k9c_A	289	Transcriptional regulator, LACI family protein; PS	93.78
8abp_A	306	L-arabinose-binding protein; binding proteins; HET	93.75
3gv0_A	288	Transcriptional regulator, LACI family; transcript	93.5
3huu_A	305	Transcription regulator like protein; PSI-II, NYSG	93.47
3h5o_A	339	Transcriptional regulator GNTR; transcription regu	93.42
3c3k_A	285	Alanine racemase; structural genomics, protein str	93.3
3miz_A	301	Putative transcriptional regulator protein, LACI f	93.25
3qk7_A	294	Transcriptional regulators; structural genomics, N	93.07
3g1w_A	305	Sugar ABC transporter; sugar-binding protein, baci	92.73
3gyb_A	280	Transcriptional regulators (LACI-family transcript	92.68
3hs3_A	277	Ribose operon repressor; PSI-II, NYSGXRC, periplas	92.66
3hcw_A	295	Maltose operon transcriptional repressor; RNA-bind	92.6
3m9w_A	313	D-xylose-binding periplasmic protein; xylose bindi	92.52
1byk_A	255	Protein (trehalose operon repressor); LACI family,	92.46
2rgy_A	290	Transcriptional regulator, LACI family; 11011J, NY	92.46
2iks_A	293	DNA-binding transcriptional dual regulator; escher	92.43
2fep_A	289	Catabolite control protein A; CCPA, transcriptiona	92.38
3k4h_A	292	Putative transcriptional regulator; structural gen	92.36
3brq_A	296	HTH-type transcriptional regulator ASCG; transcrip	92.31
1dbq_A	289	Purine repressor; transcription regulation, DNA-bi	92.2
3d8u_A	275	PURR transcriptional regulator; APC91343.1, vibrio	92.18
3qk7_A	294	Transcriptional regulators; structural genomics, N	92.06
2x7x_A	325	Sensor protein; transferase, sensor histidine kina	92.04
3e61_A	277	Putative transcriptional repressor of ribose OPER;	91.92
3dbi_A	338	Sugar-binding transcriptional regulator, LACI FAM;	91.75
3hcw_A	295	Maltose operon transcriptional repressor; RNA-bind	91.64
2fn9_A	290	Ribose ABC transporter, periplasmic ribose-bindin;	91.47
2o20_A	332	Catabolite control protein A; CCPA, transcriptiona	91.4
3g85_A	289	Transcriptional regulator (LACI family); transcrip	91.37
2ioy_A	283	Periplasmic sugar-binding protein; ribose binding	91.33
3e3m_A	355	Transcriptional regulator, LACI family; structural	90.95
3rot_A	297	ABC sugar transporter, periplasmic sugar binding;	90.86
3tb6_A	298	Arabinose metabolism transcriptional repressor; tr	90.85
3bil_A	348	Probable LACI-family transcriptional regulator; st	90.83
2fqx_A	318	Membrane lipoprotein TMPC; ABC transport system, l	90.8
3ctp_A	330	Periplasmic binding protein/LACI transcriptional;	90.78
3clk_A	290	Transcription regulator; 11017J, PSI-II, NYSGXRC,	90.72
3bbl_A	287	Regulatory protein of LACI family; protein structu	90.68
3kjx_A	344	Transcriptional regulator, LACI family; LACL famil	90.56
3d8u_A	275	PURR transcriptional regulator; APC91343.1, vibrio	90.52
3egc_A	291	Putative ribose operon repressor; structural genom	90.49
2rgy_A	290	Transcriptional regulator, LACI family; 11011J, NY	90.45
2qu7_A	288	Putative transcriptional regulator; structural gen	90.43
3d02_A	303	Putative LACI-type transcriptional regulator; peri	90.39
2rjo_A	332	Twin-arginine translocation pathway signal protei;	90.03
2vk2_A	306	YTFQ, ABC transporter periplasmic-binding protein	89.95
2qu7_A	288	Putative transcriptional regulator; structural gen	89.88
3kke_A	303	LACI family transcriptional regulator; structural	89.81
1qpz_A	340	PURA, protein (purine nucleotide synthesis repress	89.71
2fvy_A	309	D-galactose-binding periplasmic protein; periplasm	89.66
2fvy_A	309	D-galactose-binding periplasmic protein; periplasm	89.55
3gbv_A	304	Putative LACI-family transcriptional regulator; NY	89.49
3huu_A	305	Transcription regulator like protein; PSI-II, NYSG	89.49
3dbi_A	338	Sugar-binding transcriptional regulator, LACI FAM;	89.37
3miz_A	301	Putative transcriptional regulator protein, LACI f	89.25
2hsg_A	332	Glucose-resistance amylase regulator; CCPA, transc	89.12
3jvd_A	333	Transcriptional regulators; structural genomics, P	89.06
3brs_A	289	Periplasmic binding protein/LACI transcriptional;	88.93
2iks_A	293	DNA-binding transcriptional dual regulator; escher	88.71
3gv0_A	288	Transcriptional regulator, LACI family; transcript	88.65
3snr_A	362	Extracellular ligand-binding receptor; structural	88.52
2dri_A	271	D-ribose-binding protein; sugar transport; HET: RI	88.33
2o20_A	332	Catabolite control protein A; CCPA, transcriptiona	88.19
1pea_A	385	Amidase operon; gene regulator, receptor, binding	88.14
2fep_A	289	Catabolite control protein A; CCPA, transcriptiona	87.97
3h75_A	350	Periplasmic sugar-binding domain protein; protein	87.75
1qpz_A	340	PURA, protein (purine nucleotide synthesis repress	87.74
3gyb_A	280	Transcriptional regulators (LACI-family transcript	87.56
2vk2_A	306	YTFQ, ABC transporter periplasmic-binding protein	87.53
3brq_A	296	HTH-type transcriptional regulator ASCG; transcrip	87.52
3g1w_A	305	Sugar ABC transporter; sugar-binding protein, baci	87.1
3c3k_A	285	Alanine racemase; structural genomics, protein str	87.08
4fe7_A	412	Xylose operon regulatory protein; HTH_ARAC, helix-	87.03
3l6u_A	293	ABC-type sugar transport system periplasmic compo;	87.0
3l49_A	291	ABC sugar (ribose) transporter, periplasmic substr	86.74
2dri_A	271	D-ribose-binding protein; sugar transport; HET: RI	86.71
3k9c_A	289	Transcriptional regulator, LACI family protein; PS	86.45
3bbl_A	287	Regulatory protein of LACI family; protein structu	86.41
3clk_A	290	Transcription regulator; 11017J, PSI-II, NYSGXRC,	86.34
2h0a_A	276	TTHA0807, transcriptional regulator; repressor, st	86.19
1gud_A	288	ALBP, D-allose-binding periplasmic protein; peripl	86.15
3brs_A	289	Periplasmic binding protein/LACI transcriptional;	85.73
1dbq_A	289	Purine repressor; transcription regulation, DNA-bi	85.7
2hsg_A	332	Glucose-resistance amylase regulator; CCPA, transc	85.65
3cs3_A	277	Sugar-binding transcriptional regulator, LACI FAM;	85.64
1gud_A	288	ALBP, D-allose-binding periplasmic protein; peripl	85.57
1jye_A	349	Lactose operon repressor; gene regulation, protein	85.37
4evq_A	375	Putative ABC transporter subunit, substrate-bindi	85.29
3h5t_A	366	Transcriptional regulator, LACI family; DNA-depend	85.05
3h5o_A	339	Transcriptional regulator GNTR; transcription regu	84.99
2h0a_A	276	TTHA0807, transcriptional regulator; repressor, st	84.97
1jye_A	349	Lactose operon repressor; gene regulation, protein	84.9
3kjx_A	344	Transcriptional regulator, LACI family; LACL famil	84.86
2ioy_A	283	Periplasmic sugar-binding protein; ribose binding	84.64
3cs3_A	277	Sugar-binding transcriptional regulator, LACI FAM;	84.39
3o74_A	272	Fructose transport system repressor FRUR; dual tra	84.32
3iwt_A	178	178AA long hypothetical molybdenum cofactor biosy	84.15
3o1i_D	304	Periplasmic protein TORT; ligand free, two compone	84.05
4eyg_A	368	Twin-arginine translocation pathway signal; PSI-bi	83.67
3e3m_A	355	Transcriptional regulator, LACI family; structural	82.98
3ipc_A	356	ABC transporter, substrate binding protein (amino;	82.87
2h3h_A	313	Sugar ABC transporter, periplasmic sugar-binding p	82.04
3hut_A	358	Putative branched-chain amino acid ABC transporter	81.9
3lop_A	364	Substrate binding periplasmic protein; protein str	81.78
3ctp_A	330	Periplasmic binding protein/LACI transcriptional;	81.47
3lkv_A	302	Uncharacterized conserved domain protein; ATPase b	81.46
2rjo_A	332	Twin-arginine translocation pathway signal protei;	81.25
2h3h_A	313	Sugar ABC transporter, periplasmic sugar-binding p	81.24
1jx6_A	342	LUXP protein; protein-ligand complex, signaling pr	81.02
3m9w_A	313	D-xylose-binding periplasmic protein; xylose bindi	80.98
2fp4_B	395	Succinyl-COA ligase [GDP-forming] beta-chain, mito	80.71
2pjk_A	178	178AA long hypothetical molybdenum cofactor biosyn	80.45
3bil_A	348	Probable LACI-family transcriptional regulator; st	80.23
2nu8_B	388	SCS-beta, succinyl-COA synthetase beta chain; citr	80.22
1tjy_A	316	Sugar transport protein; protein-ligand complex, s	80.09

>3nq4_A 6,7-dimethyl-8-ribityllumazine synthase; 30MER, icosahedral, flavodoxin like fold, transferase, DMRL riboflavin biosynthesis, drug targe; 3.50A {Salmonella typhimurium} PDB: 3mk3_A

Probab=100.00  E-value=1.9e-61  Score=401.04  Aligned_cols=152  Identities=45%  Similarity=0.814  Sum_probs=147.9

Q ss_pred             HhhhcccCCCCCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCC-CCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEE
Q 027801           63 VRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYS-VKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCI  141 (218)
Q Consensus        63 ~~~~~~~~~~~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~G-v~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaL  141 (218)
                      |+.++|++. ++++||+||+||||++|+++|+++|+++|+++| +++++|+++||||+||||+++|+|+++++|||||||
T Consensus         1 m~~~~g~~~-~~~~ri~IV~arfn~~I~~~Ll~gA~~~l~~~G~v~~~~i~v~~VPGafEiP~aa~~la~~~~yDavIaL   79 (156)
T 3nq4_A            1 MNIIKANVA-APDARVAITIARFNQFINDSLLDGAVDALTRIGQVKDDNITVVWVPGAYELPLATEALAKSGKYDAVVAL   79 (156)
T ss_dssp             CEEEECCSC-CTTCCEEEEEESTTHHHHHHHHHHHHHHHHHTTCCCTTSEEEEEESSTTTHHHHHHHHHHHCSCSEEEEE
T ss_pred             CceecCccC-CCCCEEEEEEeeCcHHHHHHHHHHHHHHHHHcCCCcccceEEEEcCcHHHHHHHHHHHHhcCCCCEEEEe
Confidence            566788885 899999999999999999999999999999999 999999999999999999999999999999999999


Q ss_pred             eeeeeCCchhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHhhCCCCCCcHHHHHHHHHHHHHHHhh
Q 027801          142 GAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGKSGNKGAEAALTAIEMASLFEH  215 (218)
Q Consensus       142 G~VIrGeT~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~Rag~k~gnKG~EAA~aAleM~~L~~~  215 (218)
                      ||||||+|+||||||+++++|||++||++++||+||||||+|+|||++|+|.+.+|||.|||.+|+||++|+++
T Consensus        80 G~VIrG~T~Hfd~Va~~v~~Gl~~v~L~~~vPV~~GVLT~~~~eQA~~Rag~~~~nKG~eaA~aalem~~l~~~  153 (156)
T 3nq4_A           80 GTVIRGGTAHFEYVAGGASNGLASVAQDSGVPVAFGVLTTESIEQAIERAGTKAGNKGAEAALTALEMINVLKA  153 (156)
T ss_dssp             EEEECCSSTHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEESCHHHHHHHBTSTTCBHHHHHHHHHHHHHHHHHT
T ss_pred             eeeecCCchHHHHHHHHHHHHHHHHHhccCCCEEEEEeCCCCHHHHHHHhCCcccccHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999986

>1c2y_A Protein (lumazine synthase); riboflavin biosynthesis, transferase; HET: LMZ; 3.30A {Spinacia oleracea} SCOP: c.16.1.1

Probab=100.00  E-value=1e-60  Score=396.56  Aligned_cols=153  Identities=77%  Similarity=1.267  Sum_probs=146.3

Q ss_pred             hhhcccCCCCCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEee
Q 027801           64 RHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        64 ~~~~~~~~~~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~  143 (218)
                      +.++|+++++++.|||||+||||++|+++|+++|+++|+++|++ ++|+++||||+||||+++|+|+++++|||||||||
T Consensus         2 ~~~~g~~~~~~~~ri~IV~arfn~~I~~~Ll~ga~~~l~~~Gv~-~~i~v~~VPGafEiP~aa~~la~~~~yDavIaLG~   80 (156)
T 1c2y_A            2 NELEGYVTKAQSFRFAIVVARFNEFVTRRLMEGALDTFKKYSVN-EDIDVVWVPGAYELGVTAQALGKSGKYHAIVCLGA   80 (156)
T ss_dssp             EEECCCSSSCTTCCEEEEEESTTHHHHHHHHHHHHHHHHHTTCC-SCCEEEEESSHHHHHHHHHHHHHTTCCSEEEEEEE
T ss_pred             ccccccccCCCCCEEEEEEEeCcHHHHHHHHHHHHHHHHHcCCC-CceEEEECCcHHHHHHHHHHHHhcCCCCEEEEecc
Confidence            34567764578899999999999999999999999999999998 89999999999999999999999999999999999


Q ss_pred             eeeCCchhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHhhCCCCCCcHHHHHHHHHHHHHHHhhhc
Q 027801          144 VVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGKSGNKGAEAALTAIEMASLFEHHL  217 (218)
Q Consensus       144 VIrGeT~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~Rag~k~gnKG~EAA~aAleM~~L~~~~~  217 (218)
                      ||||+|+||||||+++++|||++||++++||+||||||+|+|||++|+|.+.+|||.|||.+|+||++|+++-.
T Consensus        81 VIrG~T~Hfd~Va~~v~~gl~~v~L~~~vPV~~GVLT~~~~eQA~~Rag~~~~nKG~eaA~aAlem~~l~~~l~  154 (156)
T 1c2y_A           81 VVKGDTSHYDAVVNSASSGVLSAGLNSGVPCVFGVLTCDNMDQAINRAGGKAGNKGAESALTAIEMASLFEHHL  154 (156)
T ss_dssp             CCCCSSTHHHHHHHHHHHHHHHHHHHHTSCEEEEEECCSSHHHHHHHEEETTEEHHHHHHHHHHHHHHHHHHHC
T ss_pred             cccCCchHHHHHHHHHHHHHHHHHhhcCCCEEEEEeCCCCHHHHHHHcCCcccchHHHHHHHHHHHHHHHHHHh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999998754

>1hqk_A 6,7-dimethyl-8-ribityllumazine synthase; analysi stability, vitamin biosynthesis, transferase; 1.60A {Aquifex aeolicus} SCOP: c.16.1.1 PDB: 1nqu_A* 1nqv_A* 1nqw_A* 1nqx_A*

Probab=100.00  E-value=2.1e-60  Score=393.88  Aligned_cols=151  Identities=44%  Similarity=0.720  Sum_probs=145.3

Q ss_pred             hhhcccCCCCCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEee
Q 027801           64 RHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        64 ~~~~~~~~~~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~  143 (218)
                      +.++|++ ++++.|||||+||||++|+++|+++|+++|+++|+++++|+++||||+||||+++|+|+++++|||||||||
T Consensus         2 ~~~~g~~-~~~~~ri~IV~arfn~~I~~~Ll~ga~~~l~~~gv~~~~i~v~~VPGafEiP~aa~~la~~~~yDavIalG~   80 (154)
T 1hqk_A            2 QIYEGKL-TAEGLRFGIVASRFNHALVDRLVEGAIDCIVRHGGREEDITLVRVPGSWEIPVAAGELARKEDIDAVIAIGV   80 (154)
T ss_dssp             EEECCCS-CCTTCCEEEEEECTTHHHHHHHHHHHHHHHHHTTCCGGGEEEEEESSGGGHHHHHHHHHTCTTCCEEEEEEE
T ss_pred             CcccCCc-CCCCCEEEEEEeeCcHHHHHHHHHHHHHHHHHcCCCccceEEEECCcHHHHHHHHHHHHhcCCCCEEEEeee
Confidence            3456766 478899999999999999999999999999999999899999999999999999999999999999999999


Q ss_pred             eeeCCchhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHhhCCCCCCcHHHHHHHHHHHHHHHhh
Q 027801          144 VVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGKSGNKGAEAALTAIEMASLFEH  215 (218)
Q Consensus       144 VIrGeT~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~Rag~k~gnKG~EAA~aAleM~~L~~~  215 (218)
                      ||||+|+||||||+++++|||++||++++||+|||||++|+|||++|+|.+.+|||.|||.+|++|++|+++
T Consensus        81 VIrG~T~Hfd~Va~~vs~gl~~v~l~~~vPV~~GVLT~~~~eQA~~Rag~~~~nkG~eaA~aalem~~l~~~  152 (154)
T 1hqk_A           81 LIRGATPHFDYIASEVSKGLANLSLELRKPITFGVITADTLEQAIERAGTKHGNKGWEAALSAIEMANLFKS  152 (154)
T ss_dssp             EECCSSTHHHHHHHHHHHHHHHHHHHHTSCEEEEEEEESSHHHHHHHEEETTEEHHHHHHHHHHHHHHHHHH
T ss_pred             eecCCchHHHHHHHHHHHHHHHHHhhcCCCEEEEEeCCCCHHHHHHHhcccccchHHHHHHHHHHHHHHHHh
Confidence            999999999999999999999999999999999999999999999999999999999999999999999986

>1rvv_A Riboflavin synthase; transferase, flavoprotein; HET: INI; 2.40A {Bacillus subtilis} SCOP: c.16.1.1 PDB: 1zis_A* 1vsw_A 1vsx_A 3jv8_A

Probab=100.00  E-value=2.1e-60  Score=394.01  Aligned_cols=151  Identities=46%  Similarity=0.814  Sum_probs=145.3

Q ss_pred             hhhcccCCCCCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEee
Q 027801           64 RHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        64 ~~~~~~~~~~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~  143 (218)
                      +.++|++ ++++.|||||+||||++|+++|+++|+++|+++|+++++|+++||||+||||+++|+|+++++|||||||||
T Consensus         2 ~~~~g~~-~~~~~ri~IV~arfn~~I~~~Ll~ga~~~l~~~gv~~~~i~v~~VPGafEiP~aa~~la~~~~yDavIaLG~   80 (154)
T 1rvv_A            2 NIIQGNL-VGTGLKIGIVVGRFNDFITSKLLSGAEDALLRHGVDTNDIDVAWVPGAFEIPFAAKKMAETKKYDAIITLGT   80 (154)
T ss_dssp             EEECCCS-CCTTCCEEEEEESTTHHHHHHHHHHHHHHHHHTTCCGGGEEEEEESSGGGHHHHHHHHHHTSCCSEEEEEEE
T ss_pred             CcccCCc-CCCCCEEEEEEEeCcHHHHHHHHHHHHHHHHHcCCCccceEEEECCcHHHHHHHHHHHHhcCCCCEEEEeee
Confidence            3456766 478899999999999999999999999999999999899999999999999999999999999999999999


Q ss_pred             eeeCCchhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHhhCCCCCCcHHHHHHHHHHHHHHHhh
Q 027801          144 VVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGKSGNKGAEAALTAIEMASLFEH  215 (218)
Q Consensus       144 VIrGeT~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~Rag~k~gnKG~EAA~aAleM~~L~~~  215 (218)
                      ||||+|+||||||+++++|||++||++++||+|||||++|+|||++|+|.+.+|||.|||.+|++|++|+++
T Consensus        81 VIrG~T~Hfd~V~~~vs~Gl~~v~l~~~vPV~~GVLT~~~~eQA~~Rag~~~~nkG~eaA~aalem~~l~~~  152 (154)
T 1rvv_A           81 VIRGATTHYDYVCNEAAKGIAQAANTTGVPVIFGIVTTENIEQAIERAGTKAGNKGVDCAVSAIEMANLNRS  152 (154)
T ss_dssp             EECCSSSHHHHHHHHHHHHHHHHHHHHCSCEEEEEEEESSHHHHHHTEEETTEEHHHHHHHHHHHHHHHHHH
T ss_pred             eecCCchHHHHHHHHHHHHHHHHHhhhCCCEEEEecCCCCHHHHHHHhcccccchHHHHHHHHHHHHHHHHh
Confidence            999999999999999999999999999999999999999999999999999999999999999999999986

>1kz1_A 6,7-dimethyl-8-ribityllumazine synthase; riboflavin biosynthesis, ligand binding, transferase; 2.00A {Schizosaccharomyces pombe} SCOP: c.16.1.1 PDB: 2a59_A* 2a58_A* 2a57_A* 1kyv_A* 1kyx_A* 1kyy_A* 1kz9_A 1kz4_A 1kz6_A

Probab=100.00  E-value=5.5e-59  Score=387.29  Aligned_cols=146  Identities=37%  Similarity=0.521  Sum_probs=140.4

Q ss_pred             ccCCCCCCCEEEEEEcccCHHHHHHHHHHHHHHHHH-CCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEeeeee
Q 027801           68 GFLTKNEGLRFALVVARFNELVTKLLLEGALETFKK-YSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVVR  146 (218)
Q Consensus        68 ~~~~~~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~-~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~VIr  146 (218)
                      +.+ ++++.|||||+||||++|+++|+++|+++|++ +|+++++|+++||||+||||+++|+|+++++||||||||||||
T Consensus        11 ~~~-~~~~~riaIV~arfn~~I~~~Ll~ga~~~l~~~~Gv~~~~i~v~~VPGafEiP~aa~~la~~~~yDavIaLG~VIr   89 (159)
T 1kz1_A           11 SDL-KGPELRILIVHARGNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSWELPQGIRASIARNTYDAVIGIGVLIK   89 (159)
T ss_dssp             CCC-CCTTCCEEEEECCTTHHHHHHHHHHHHHHHHHHHCCCGGGEEEEECSSGGGHHHHHHHHHHHSCCSEEEEEEEEEC
T ss_pred             CCc-CCCCCEEEEEEeeCcHHHHHHHHHHHHHHHHHHcCCCccceEEEECCcHHHHHHHHHHHHhcCCCCEEEEeccccc
Confidence            444 46789999999999999999999999999999 9999899999999999999999999999999999999999999


Q ss_pred             CCchhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHhhC-CCCCCcHHHHHHHHHHHHHHHh
Q 027801          147 GDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAG-GKSGNKGAEAALTAIEMASLFE  214 (218)
Q Consensus       147 GeT~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~Rag-~k~gnKG~EAA~aAleM~~L~~  214 (218)
                      |+|+||||||+++++|||++||++++||+|||||++|+|||++|+| .+.+|||.|||.+|+||++|++
T Consensus        90 G~T~Hfd~Va~~v~~Gl~~v~L~~~vPV~~GVLT~~~~eQA~~Rag~~~~~nKG~eaA~aalem~~l~~  158 (159)
T 1kz1_A           90 GSTMHFEYISEAVVHGLMRVGLDSGVPVILGLLTVLNEEQALYRAGLNGGHNHGNDWGSAAVEMGLKAL  158 (159)
T ss_dssp             CSSSHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEESSHHHHHHHBTCTTCCBHHHHHHHHHHHHHHHTC
T ss_pred             CCchHHHHHHHHHHHHHHHHHhhcCCCEEEEEeCCCCHHHHHHHhCCccccchHHHHHHHHHHHHHhhc
Confidence            9999999999999999999999999999999999999999999999 7779999999999999999975

>2i0f_A 6,7-dimethyl-8-ribityllumazine synthase 1; lumazine synthase RIBH1, transferase; 2.22A {Brucella abortus} PDB: 2f59_A 2o6h_A*

Probab=100.00  E-value=2.9e-58  Score=382.14  Aligned_cols=138  Identities=30%  Similarity=0.440  Sum_probs=135.1

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhc-----CCccEEEEEeeeeeCCc
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKS-----GKYTAVLCIGAVVRGDT  149 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~-----~~yDaVIaLG~VIrGeT  149 (218)
                      ++|||||+||||++|+++|+++|+++|+++|   ++|+++||||+||||+++|+|+++     ++|||||||||||||+|
T Consensus        12 ~~ri~IV~arfn~~I~~~Ll~gA~~~l~~~G---~~i~v~~VPGafEiP~aa~~la~~~~~~~~~yDavIaLG~VIrG~T   88 (157)
T 2i0f_A           12 APHLLIVEARFYDDLADALLDGAKAALDEAG---ATYDVVTVPGALEIPATISFALDGADNGGTEYDGFVALGTVIRGET   88 (157)
T ss_dssp             CCEEEEEEECSSHHHHHHHHHHHHHHHHHTT---CEEEEEEESSGGGHHHHHHHHHHHHHTTCCCCSEEEEEEEEECCSS
T ss_pred             CcEEEEEEEeCcHHHHHHHHHHHHHHHHHcC---CCeEEEECCcHHHHHHHHHHHHhhccccCCCCCEEEEeeeeecCCc
Confidence            4899999999999999999999999999999   489999999999999999999998     99999999999999999


Q ss_pred             hhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHhhCCCCCCcHHHHHHHHHHHHHHHhh
Q 027801          150 THYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGKSGNKGAEAALTAIEMASLFEH  215 (218)
Q Consensus       150 ~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~Rag~k~gnKG~EAA~aAleM~~L~~~  215 (218)
                      +||||||+++++|||++||++++||+||||||+|+|||++|+|.+.+|||.|||.+|+||++|+++
T Consensus        89 ~Hfd~Va~~v~~gl~~vsl~~~vPV~~GVLT~~~~eQA~~Rag~~~~nkG~eaA~aAlem~~l~~~  154 (157)
T 2i0f_A           89 YHFDIVSNESCRALTDLSVEESIAIGNGILTVENEEQAWVHARREDKDKGGFAARAALTMIGLRKK  154 (157)
T ss_dssp             STTHHHHHHHHHHHHHHHHHTTCCEEEEEEEESSHHHHHHHHCTTTTCHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHhhcCCCEEEEEeCCCCHHHHHHHhCccccccHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999999986

>1ejb_A Lumazine synthase; analysis, inhibitor complex, vitamin biosynthesis transferase; HET: INJ; 1.85A {Saccharomyces cerevisiae} SCOP: c.16.1.1 PDB: 2jfb_A

Probab=100.00  E-value=3.5e-58  Score=385.34  Aligned_cols=144  Identities=31%  Similarity=0.541  Sum_probs=139.0

Q ss_pred             CCCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhh-----cCCccEEEEEeeeee
Q 027801           72 KNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGK-----SGKYTAVLCIGAVVR  146 (218)
Q Consensus        72 ~~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~-----~~~yDaVIaLG~VIr  146 (218)
                      +++++|||||+||||++|++.|+++|+++|+++|+++++|+++||||+||||+++|+|++     +++||||||||||||
T Consensus        13 ~~~~~ri~IV~arfn~~I~~~Ll~gA~~~L~~~Gv~~~~i~v~~VPGafEiP~aak~la~~~~~~~~~yDavIaLG~VIr   92 (168)
T 1ejb_A           13 DGSKIRVGIIHARWNRVIIDALVKGAIERMASLGVEENNIIIETVPGSYELPWGTKRFVDRQAKLGKPLDVVIPIGVLIK   92 (168)
T ss_dssp             CCTTCCEEEEECCTTHHHHHHHHHHHHHHHHHTTCCGGGEEEEECSSGGGHHHHHHHHHHHHHHTTCCCSEEEEEEEEEC
T ss_pred             CCCCCEEEEEEEeCcHHHHHHHHHHHHHHHHHcCCCccceEEEECCcHHHHHHHHHHHHhhccccCCCcCEEEEeccccc
Confidence            467899999999999999999999999999999999899999999999999999999998     789999999999999


Q ss_pred             CCchhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHhhCC----CCCCcHHHHHHHHHHHHHHHhh
Q 027801          147 GDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGG----KSGNKGAEAALTAIEMASLFEH  215 (218)
Q Consensus       147 GeT~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~Rag~----k~gnKG~EAA~aAleM~~L~~~  215 (218)
                      |+|+||||||+++++|||++||++++||+|||||++|+|||++|+|.    +.+|||.|||.+||||++++++
T Consensus        93 G~T~Hfd~Va~~vs~Gl~~vsL~~~vPV~~GVLT~~~~eQA~~Rag~~~~~~~~nkG~eaA~aAlem~~l~~~  165 (168)
T 1ejb_A           93 GSTMHFEYISDSTTHALMNLQEKVDMPVIFGLLTCMTEEQALARAGIDEAHSMHNHGEDWGAAAVEMAVKFGK  165 (168)
T ss_dssp             CSSSHHHHHHHHHHHHHHHHHHHHTSCBCCEEEEESSHHHHHHHBTCSTTCCSCBHHHHHHHHHHHHHHHHST
T ss_pred             CCchHHHHHHHHHHHHHHHHHhhcCCCEEEEEecCCCHHHHHHhcCccccccccchHHHHHHHHHHHHHHhcc
Confidence            99999999999999999999999999999999999999999999997    5579999999999999999876

>2obx_A DMRL synthase 1, 6,7-dimethyl-8-ribityllumazine synthase 1, riboflavin S; alpha-beta, transferase; HET: INI; 2.53A {Mesorhizobium loti}

Probab=100.00  E-value=2.1e-58  Score=382.93  Aligned_cols=145  Identities=28%  Similarity=0.372  Sum_probs=139.9

Q ss_pred             CCCCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEeeeeeCCch
Q 027801           71 TKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVVRGDTT  150 (218)
Q Consensus        71 ~~~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~VIrGeT~  150 (218)
                      ++++++|||||+||||++|++.|+++|+++|+++|+++++|+++||||+||||+++|+|+++++|||||||||||||+|+
T Consensus         7 ~~~~~~ri~IV~arfn~~I~~~Ll~gA~~~l~~~Gv~~~~i~v~~VPGafEiP~aa~~la~~~~yDavIaLG~VIrG~T~   86 (157)
T 2obx_A            7 KDYETVRIAVVRARWHADIVDQCVSAFEAEMADIGGDRFAVDVFDVPGAYEIPLHARTLAETGRYGAVLGTAFVVNGGIY   86 (157)
T ss_dssp             CSCCCEEEEEEEECTTHHHHHHHHHHHHHHHHHHHTTSEEEEEEEESSGGGHHHHHHHHHHHTCCSEEEEEEECCCCSSB
T ss_pred             CCCCCCEEEEEEeeCcHHHHHHHHHHHHHHHHHcCCCccceEEEECCcHHHHHHHHHHHHhcCCCCEEEEeeccccCCCc
Confidence            35788999999999999999999999999999999998899999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHhh---CCCCCCcHHHHHHHHHHHHHHHhh
Q 027801          151 HYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRA---GGKSGNKGAEAALTAIEMASLFEH  215 (218)
Q Consensus       151 H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~Ra---g~k~gnKG~EAA~aAleM~~L~~~  215 (218)
                      ||||||+++++|||++||++++||+||||||+|+|||++|+   +.+.+|||.|||.+|++|++|+++
T Consensus        87 Hfd~Va~~vs~Gl~~v~L~~~vPV~~GVLT~~~~eqa~eR~~~~~~~~~nKG~eaA~aalem~~l~~~  154 (157)
T 2obx_A           87 RHEFVASAVIDGMMNVQLSTGVPVLSAVLTPHNYHDSAEHHRFFFEHFTVKGKEAARACVEILAAREK  154 (157)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHCCCEEEEEECBSCCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhhcCCCEEEEecCCCCHHHHHHHhhhhcchhcchHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999998   456689999999999999999986

>1di0_A Lumazine synthase; transferase; 2.70A {Brucella abortus} SCOP: c.16.1.1 PDB: 1t13_A* 1xn1_A

Probab=100.00  E-value=2.5e-58  Score=382.85  Aligned_cols=144  Identities=22%  Similarity=0.350  Sum_probs=138.1

Q ss_pred             CCCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEeeeeeCCchh
Q 027801           72 KNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVVRGDTTH  151 (218)
Q Consensus        72 ~~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~VIrGeT~H  151 (218)
                      +++++|||||+||||++|+++|+++|+++|+++|+++++|+++||||+||||+++|+|+++++|||||||||||||+|+|
T Consensus         7 ~~~~~ri~IV~arfn~~I~~~Ll~gA~~~l~~~gv~~~~i~v~~VPGafEiP~aa~~la~~~~yDavIaLG~VIrG~T~H   86 (158)
T 1di0_A            7 NKTSFKIAFIQARWHADIVDEARKSFVAELAAKTGGSVEVEIFDVPGAYEIPLHAKTLARTGRYAAIVGAAFVIDGGIYD   86 (158)
T ss_dssp             --CCEEEEEEEECTTHHHHHHHHHHHHHHHHHHHTTSEEEEEEEESSGGGHHHHHHHHHHTSCCSEEEEEEECCCCSSBC
T ss_pred             CCCCCEEEEEEEeCcHHHHHHHHHHHHHHHHHcCCCccceEEEECCcHHHHHHHHHHHHhcCCCCEEEEeeccccCCCcH
Confidence            46789999999999999999999999999999999988999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHhh---CCCCCCcHHHHHHHHHHHHHHHhh
Q 027801          152 YDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRA---GGKSGNKGAEAALTAIEMASLFEH  215 (218)
Q Consensus       152 ~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~Ra---g~k~gnKG~EAA~aAleM~~L~~~  215 (218)
                      |||||+++++|||++||++++||+|||||++|+|||++|+   +.+.+|||.|||.+|++|++++++
T Consensus        87 fd~Va~~vs~Gl~~v~L~~~vPV~~GVLT~~~~eqA~er~~~~~~~~~nKG~eaA~aal~m~~l~~~  153 (158)
T 1di0_A           87 HDFVATAVINGMMQVQLETEVPVLSVVLTPHHFHESKEHHDFFHAHFKVKGVEAAHAALQIVSERSR  153 (158)
T ss_dssp             CHHHHHHHHHHHHHHHHHHCCCEEEEEECBSSCCCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhhcCCCEEEEecCCCCHHHHHHHhhhhcchhcchHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999   456689999999999999999986

>2c92_A 6,7-dimethyl-8-ribityllumazine synthase; transferase, riboflavin biosynthesis, inhibitor binding; HET: TP6; 1.6A {Mycobacterium tuberculosis} PDB: 1w29_A* 1w19_A* 2c94_A* 2c97_A* 2c9b_A* 2c9d_A* 2vi5_A*

Probab=100.00  E-value=3.2e-56  Score=370.93  Aligned_cols=140  Identities=34%  Similarity=0.552  Sum_probs=135.1

Q ss_pred             CCCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEeeeeeCCchh
Q 027801           72 KNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVVRGDTTH  151 (218)
Q Consensus        72 ~~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~VIrGeT~H  151 (218)
                      ++++.|||||+||||++|+++|+++|+++|+++|++  +|+++||||+||||+++|+|++  +|||||||||||||+|+|
T Consensus        14 ~~~~~ri~IV~arfn~~I~~~Ll~gA~~~l~~~G~~--~i~v~~VPGafEiP~aak~la~--~yDavIaLG~VIrG~T~H   89 (160)
T 2c92_A           14 DASGVRLAIVASSWHGKICDALLDGARKVAAGCGLD--DPTVVRVLGAIEIPVVAQELAR--NHDAVVALGVVIRGQTPH   89 (160)
T ss_dssp             CCTTCCEEEEEECSSHHHHHHHHHHHHHHHHHTTCS--CCEEEEESSGGGHHHHHHHHHT--SCSEEEEEEEEECCSSTH
T ss_pred             CCCCCEEEEEEEeCcHHHHHHHHHHHHHHHHHcCCC--ceEEEECCcHHHHHHHHHHHHh--cCCEEEEEeeeecCCchH
Confidence            467899999999999999999999999999999986  8999999999999999999986  599999999999999999


Q ss_pred             HHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHhhCC--CCCCcHHHHHHHHHHHHHHHhh
Q 027801          152 YDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGG--KSGNKGAEAALTAIEMASLFEH  215 (218)
Q Consensus       152 ~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~Rag~--k~gnKG~EAA~aAleM~~L~~~  215 (218)
                      |||||+++++|||++||++++||+|||||++|+|||++|+|.  +.+|||.|||.+|++|++++++
T Consensus        90 fd~Va~~vs~Gl~~v~L~~~vPV~~GVLT~~~~eQA~~Rag~~~~~~nKG~eaA~aalem~~l~~~  155 (160)
T 2c92_A           90 FDYVCDAVTQGLTRVSLDSSTPIANGVLTTNTEEQALDRAGLPTSAEDKGAQATVAALATALTLRE  155 (160)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTCCEEEEEEEESSHHHHHTTBTCTTCSCBHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhhcCCCEEEEEcCCCCHHHHHHHhccccccchhHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999985  6899999999999999999886

>1c41_A Lumazine synthase; riboflavin biosynthesis, transferase; HET: LMZ; 3.10A {Magnaporthe grisea} SCOP: c.16.1.1

Probab=100.00  E-value=5.5e-57  Score=386.69  Aligned_cols=145  Identities=38%  Similarity=0.605  Sum_probs=139.8

Q ss_pred             CCCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhh--------------------
Q 027801           72 KNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGK--------------------  131 (218)
Q Consensus        72 ~~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~--------------------  131 (218)
                      +++++||+||++|||++|++.|+++|+++|+++|++++||+++||||+||||+++++|++                    
T Consensus        12 ~g~~lriaIV~arfn~~I~~~Ll~GA~~~L~~~Gv~~~~I~v~~VPGa~ElP~a~~~l~~~~~~~~~~~~~~~~~~~~~~   91 (200)
T 1c41_A           12 DGSALRIGIVHARWNETIIEPLLAGTKAKLLACGVKESNIVVQSVPGSWELPIAVQRLYSASQLQTPSSGPSLSAGDLLG   91 (200)
Confidence            467899999999999999999999999999999999999999999999999999999987                    


Q ss_pred             ----------------cCCccEEEEEeeeeeCCchhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHhhCC--
Q 027801          132 ----------------SGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGG--  193 (218)
Q Consensus       132 ----------------~~~yDaVIaLG~VIrGeT~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~Rag~--  193 (218)
                                      +++|||||||||||||+|+||||||+++++|||+++|++++||+|||||++|+|||++|+|.  
T Consensus        92 ~~~~~~~~~~~~~~~~~~~~DAVIaLG~VIrGeT~HfeyVa~~vs~GLm~v~L~~~vPVifGVLT~~t~eQA~~RAg~~~  171 (200)
T 1c41_A           92 SSTTDLTALPTTTASSTGPFDALIAIGVLIKGETMHFEYIADSVSHGLMRVQLDTGVPVIFGVLTVLTDDQAKARAGVIE  171 (200)
Confidence                            57899999999999999999999999999999999999999999999999999999999997  


Q ss_pred             CCCCcHHHHHHHHHHHHHHHhhh
Q 027801          194 KSGNKGAEAALTAIEMASLFEHH  216 (218)
Q Consensus       194 k~gnKG~EAA~aAleM~~L~~~~  216 (218)
                      +.+|||.|||.+|+||+.++++-
T Consensus       172 k~~NkG~eaA~aAvem~~~~~~~  194 (200)
T 1c41_A          172 GSHNHGEDWGLAAVEMGVRRRDW  194 (200)
Confidence            88999999999999999998863

>2b99_A Riboflavin synthase; lumazine riboflavin, transferase; HET: RDL; 2.22A {Methanocaldococcus jannaschii} PDB: 2b98_A*

Probab=100.00  E-value=4.4e-50  Score=332.94  Aligned_cols=132  Identities=17%  Similarity=0.129  Sum_probs=127.0

Q ss_pred             CEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEeeeeeCCchhHHHH
Q 027801           76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVVRGDTTHYDAV  155 (218)
Q Consensus        76 ~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~VIrGeT~H~e~V  155 (218)
                      +||+||+||||+   +.|+++|+++|+++|+++ +++++||||+||||+++++|+++++||||||||||  |+|+|||||
T Consensus         3 ~ri~IV~arfn~---~~Ll~gA~~~L~~~G~~~-~i~~~~VPGafEiP~aak~la~~~~yDavIaLG~V--G~T~Hfd~V   76 (156)
T 2b99_A            3 KKVGIVDTTFAR---VDMASIAIKKLKELSPNI-KIIRKTVPGIKDLPVACKKLLEEEGCDIVMALGMP--GKAEKDKVC   76 (156)
T ss_dssp             CEEEEEEESSCS---SCCHHHHHHHHHHHCTTC-EEEEEEESSGGGHHHHHHHHHHHSCCSEEEEEECC--CSSHHHHHH
T ss_pred             cEEEEEEEecch---HHHHHHHHHHHHHcCCCC-eEEEEECCcHHHHHHHHHHHHhcCCCCEEEEeccc--CCcchhHHH
Confidence            699999999999   899999999999999986 48889999999999999999999999999999999  999999999


Q ss_pred             HHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHhh-CCCCCCcHHHHHHHHHHHHHHHhh
Q 027801          156 ANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRA-GGKSGNKGAEAALTAIEMASLFEH  215 (218)
Q Consensus       156 a~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~Ra-g~k~gnKG~EAA~aAleM~~L~~~  215 (218)
                      |+++++|||++||++++||+||  |++|.|||++|+ +.+.+|||.|||.+|+||++++++
T Consensus        77 a~~vs~Gl~~v~L~~~vPV~~g--t~~~~eqa~~r~~g~k~~nKG~EaA~aaiem~~l~~~  135 (156)
T 2b99_A           77 AHEASLGLMLAQLMTNKHIIEV--FVHEDEAKDDKELDWLAKRRAEEHAENVYYLLFKPEY  135 (156)
T ss_dssp             HHHHHHHHHHHHHHHTCCEEEE--ECCGGGSSSHHHHHHHHHHHHHHHHHHHHHHHHCHHH
T ss_pred             HHHHHHHHHHHHhhhCCCEEEE--eCCCHHHHHHHhhcchhhhhHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999  999999999999 778899999999999999999775

>3e61_A Putative transcriptional repressor of ribose OPER; structural genomics, DNA-binding, transcripti regulation, PSI-2; 2.00A {Staphylococcus saprophyticus subsp}

Probab=96.21  E-value=0.028  Score=45.88  Aligned_cols=67  Identities=7%  Similarity=-0.003  Sum_probs=50.2

Q ss_pred             CCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEe
Q 027801           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIG  142 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG  142 (218)
                      .+..+||+|...+.......+++++.+.++++|+.   +.++...+..+-....-..+...++||||..+
T Consensus         6 ~~~~~Ig~i~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~~~~l~~~~~dgiIi~~   72 (277)
T 3e61_A            6 RKSKLIGLLLPDMSNPFFTLIARGVEDVALAHGYQ---VLIGNSDNDIKKAQGYLATFVSHNCTGMISTA   72 (277)
T ss_dssp             ----CEEEEESCTTSHHHHHHHHHHHHHHHHTTCC---EEEEECTTCHHHHHHHHHHHHHTTCSEEEECG
T ss_pred             CCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCCE---EEEEeCCCCHHHHHHHHHHHHhCCCCEEEEec
Confidence            45568999999999889999999999999999984   67777776655444333334567899999987

>3jy6_A Transcriptional regulator, LACI family; NYSGXRC, PSI-II, protein S initiative, structural genomics; 1.97A {Lactobacillus brevis}

Probab=96.01  E-value=0.068  Score=43.78  Aligned_cols=69  Identities=10%  Similarity=0.053  Sum_probs=53.2

Q ss_pred             CCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEeee
Q 027801           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAV  144 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~V  144 (218)
                      .+..+||+|...+.......++++..+.++++|+.   +.++...+..+-....-+.+...++||||..+.-
T Consensus         5 ~~s~~Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~~~~l~~~~vdgiIi~~~~   73 (276)
T 3jy6_A            5 QSSKLIAVIVANIDDYFSTELFKGISSILESRGYI---GVLFDANADIEREKTLLRAIGSRGFDGLILQSFS   73 (276)
T ss_dssp             CCCCEEEEEESCTTSHHHHHHHHHHHHHHHTTTCE---EEEEECTTCHHHHHHHHHHHHTTTCSEEEEESSC
T ss_pred             CCCcEEEEEeCCCCchHHHHHHHHHHHHHHHCCCE---EEEEeCCCCHHHHHHHHHHHHhCCCCEEEEecCC
Confidence            45678999999999889999999999999999973   6666666655544333333456789999998864

>3l6u_A ABC-type sugar transport system periplasmic compo; structural genomics, nysgrc, target 11006S, PSI-2, protein S initiative; 1.90A {Exiguobacterium sibiricum}

Probab=95.91  E-value=0.055  Score=44.36  Aligned_cols=67  Identities=9%  Similarity=-0.086  Sum_probs=49.1

Q ss_pred             CCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHH-HHHHhhhcCCccEEEEEee
Q 027801           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV-VAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~-aak~L~~~~~yDaVIaLG~  143 (218)
                      .+..+||+|...+.......+++++.+.++++|+.   +.++...+..+-.. .++.+ ...++||||..+.
T Consensus         6 ~~~~~Ig~i~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~l-~~~~vdgiI~~~~   73 (293)
T 3l6u_A            6 PKRNIVGFTIVNDKHEFAQRLINAFKAEAKANKYE---ALVATSQNSRISEREQILEF-VHLKVDAIFITTL   73 (293)
T ss_dssp             ---CEEEEEESCSCSHHHHHHHHHHHHHHHHTTCE---EEEEECSSCHHHHHHHHHHH-HHTTCSEEEEECS
T ss_pred             CCCcEEEEEEecCCcHHHHHHHHHHHHHHHHcCCE---EEEECCCCCHHHHHHHHHHH-HHcCCCEEEEecC
Confidence            45678999999999999999999999999999983   56665554444332 33444 3578999998876

>3l49_A ABC sugar (ribose) transporter, periplasmic substrate-binding subunit; sugar binding/transporter, structural genomics, PSI; HET: UNL; 2.30A {Rhodobacter sphaeroides}

Probab=95.84  E-value=0.072  Score=43.60  Aligned_cols=67  Identities=10%  Similarity=-0.026  Sum_probs=48.4

Q ss_pred             CCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHH-HHHHhhhcCCccEEEEEee
Q 027801           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV-VAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~-aak~L~~~~~yDaVIaLG~  143 (218)
                      .+..+||+|...+.......+++++.+.++++|+.   +.++...+..+--. .++.+ ...++||||..+.
T Consensus         3 ~~~~~Ig~i~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~l-~~~~vdgiIi~~~   70 (291)
T 3l49_A            3 LEGKTIGITAIGTDHDWDLKAYQAQIAEIERLGGT---AIALDAGRNDQTQVSQIQTL-IAQKPDAIIEQLG   70 (291)
T ss_dssp             CTTCEEEEEESCCSSHHHHHHHHHHHHHHHHTTCE---EEEEECTTCHHHHHHHHHHH-HHHCCSEEEEESS
T ss_pred             CCCcEEEEEeCCCCChHHHHHHHHHHHHHHHcCCE---EEEEcCCCCHHHHHHHHHHH-HHcCCCEEEEeCC
Confidence            35578999999999888889999999999999973   55554444433222 23344 3467999997754

>3hs3_A Ribose operon repressor; PSI-II, NYSGXRC, periplasmic binding protein, structural genomics, protein structure initiative; 1.60A {Lactobacillus acidophilus}

Probab=95.73  E-value=0.026  Score=46.54  Aligned_cols=67  Identities=7%  Similarity=0.063  Sum_probs=49.3

Q ss_pred             CCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCC-eEEEEeCCcchHHHHHHHhhhcCCccEEEEEe
Q 027801           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEEN-IDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIG  142 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~-I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG  142 (218)
                      .+..+||+|...+....-..+++++.+.++++|+   + +.++...+..+-....-..+...++||+|..+
T Consensus         8 ~~~~~Igvi~~~~~~~~~~~~~~gi~~~a~~~g~---~~~~~~~~~~~~~~~~~~~~~l~~~~vdgiIi~~   75 (277)
T 3hs3_A            8 KKSKMIGIIIPDLNNRFYAQIIDGIQEVIQKEGY---TALISFSTNSDVKKYQNAIINFENNNVDGIITSA   75 (277)
T ss_dssp             CCCCEEEEEESCTTSHHHHHHHHHHHHHHHHTTC---EEEEEECSSCCHHHHHHHHHHHHHTTCSEEEEEC
T ss_pred             CCCCEEEEEeCCCCChhHHHHHHHHHHHHHHCCC---CEEEEEeCCCChHHHHHHHHHHHhCCCCEEEEcc
Confidence            4567899999999888899999999999999997   3 44444444444333322334567899999987

>3lft_A Uncharacterized protein; ABC, ATPase, cassette, L-Trp, PSI, MCSG, structural genomics center for structural genomics; HET: MSE TRP; 1.35A {Streptococcus pneumoniae}

Probab=95.66  E-value=0.13  Score=42.90  Aligned_cols=97  Identities=16%  Similarity=0.146  Sum_probs=68.8

Q ss_pred             hhHhhhcccCCCCCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEE
Q 027801           61 EAVRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLC  140 (218)
Q Consensus        61 ~a~~~~~~~~~~~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIa  140 (218)
                      .+++.+....+  ...||+++...-+. -....+++..+.++++|+.   ++..++...-+..-++++|.  .++|||+|
T Consensus       121 ~~~~~l~~~~p--g~~~I~~i~~~~~~-~~~~r~~g~~~al~~~gi~---~~~~~~~~~~~~~~~~~~l~--~~~dai~~  192 (295)
T 3lft_A          121 QQVELIKALTP--NVKTIGALYSSSED-NSKTQVEEFKAYAEKAGLT---VETFAVPSTNEIASTVTVMT--SKVDAIWV  192 (295)
T ss_dssp             HHHHHHHHHCT--TCCEEEEEEETTCH-HHHHHHHHHHHHHHHTTCE---EEEEEESSGGGHHHHHHHHT--TTCSEEEE
T ss_pred             HHHHHHHHhCC--CCcEEEEEeCCCCc-chHHHHHHHHHHHHHcCCE---EEEEecCCHHHHHHHHHHHH--hcCCEEEE
Confidence            34455444332  34699999887553 3556789999999999985   55567776667777788876  47999998


Q ss_pred             EeeeeeCCchhHHHHHHHHHHHHHHhchhcCCceE
Q 027801          141 IGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCI  175 (218)
Q Consensus       141 LG~VIrGeT~H~e~Va~~vs~gLm~lsL~~~vPVi  175 (218)
                      ..          |.++-.+.+.+.+.....++||+
T Consensus       193 ~~----------D~~a~g~~~~l~~~~~~~~i~vi  217 (295)
T 3lft_A          193 PI----------DNTIASGFPTVVSSNQSSKKPIY  217 (295)
T ss_dssp             CS----------CHHHHHTHHHHHHHTTTTCCCEE
T ss_pred             CC----------chhHHHHHHHHHHHHHHcCCCEE
Confidence            42          34555667788888888899953

>3lkv_A Uncharacterized conserved domain protein; ATPase binding cassette, PSI, MCSG, structural genomics, Pro structure initiative; HET: PHE; 2.20A {Vibrio cholerae}

Probab=95.54  E-value=0.21  Score=42.64  Aligned_cols=90  Identities=18%  Similarity=0.227  Sum_probs=62.6

Q ss_pred             CCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCC-CCeEEE--EeCCcch-HHHHHHHhhhcCCccEEEEEeeeeeCC
Q 027801           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKE-ENIDVV--WVPGSFE-IGVVAQQLGKSGKYTAVLCIGAVVRGD  148 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~-e~I~vv--~VPGA~E-LP~aak~L~~~~~yDaVIaLG~VIrGe  148 (218)
                      ++..||||+.---|.-+ |...+|.+++|++.|..+ +|+++.  .--|-.+ ++-.+++|. ..++|.||++|      
T Consensus         6 ~~~~~igi~q~~~hp~l-d~~~~G~~~~L~~~G~~~g~nv~~~~~~a~gd~~~~~~~~~~l~-~~~~DlIiai~------   77 (302)
T 3lkv_A            6 AKTAKVAVSQIVEHPAL-DATRQGLLDGLKAKGYEEGKNLEFDYKTAQGNPAIAVQIARQFV-GENPDVLVGIA------   77 (302)
T ss_dssp             -CCEEEEEEESCCCHHH-HHHHHHHHHHHHHTTCCBTTTEEEEEEECTTCHHHHHHHHHHHH-TTCCSEEEEES------
T ss_pred             cCCceEEEEEeecChhH-HHHHHHHHHHHHhhCcccCCcEEEEEEeCCCCHHHHHHHHHHHH-hcCCcEEEEcC------
Confidence            67789999988778776 788999999999999643 355554  3444333 566667775 57899999875      


Q ss_pred             chhHHHHHHHHHHHHHHhchhcCCceEEEEcC
Q 027801          149 TTHYDAVANSAASGVLSAGVNSGVPCIFGVLT  180 (218)
Q Consensus       149 T~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT  180 (218)
                      |+=        ++.+.+  ...++||+|.-++
T Consensus        78 t~a--------a~a~~~--~~~~iPVVf~~v~   99 (302)
T 3lkv_A           78 TPT--------AQALVS--ATKTIPIVFTAVT   99 (302)
T ss_dssp             HHH--------HHHHHH--HCSSSCEEEEEES
T ss_pred             CHH--------HHHHHh--hcCCCCeEEEecC
Confidence            332        233332  2458999998776

>3jvd_A Transcriptional regulators; structural genomics, PSI-2, sugar binding protein, transcrip regulation, protein structure initiative; 2.30A {Corynebacterium glutamicum}

Probab=95.38  E-value=0.04  Score=47.14  Aligned_cols=67  Identities=9%  Similarity=0.014  Sum_probs=49.5

Q ss_pred             CCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEee
Q 027801           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~  143 (218)
                      .+..+||+|...+....-..+++++.+.++++|+.   +.++...+ .+-....-..+...++||||..+.
T Consensus        62 ~~~~~Igvi~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~-~~~~~~~~~~l~~~~vdGiIi~~~  128 (333)
T 3jvd_A           62 HRSALVGVIVPDLSNEYYSESLQTIQQDLKAAGYQ---MLVAEANS-VQAQDVVMESLISIQAAGIIHVPV  128 (333)
T ss_dssp             --CCEEEEEESCSSSHHHHHHHHHHHHHHHHHTCE---EEEEECCS-HHHHHHHHHHHHHHTCSEEEECCC
T ss_pred             CCCCEEEEEeCCCcChHHHHHHHHHHHHHHHCCCE---EEEECCCC-hHHHHHHHHHHHhCCCCEEEEcch
Confidence            45568999999998888899999999999999974   66666666 443333323334568999998876

>3tb6_A Arabinose metabolism transcriptional repressor; transcription regulation, arabinose binding, DNA binding Pro; HET: ARB; 2.21A {Bacillus subtilis}

Probab=95.15  E-value=0.12  Score=42.22  Aligned_cols=66  Identities=3%  Similarity=-0.021  Sum_probs=50.2

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEee
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~  143 (218)
                      ..+||+|...+.......++++..++++++|+.   +.++...+..+-....-..+...++||||..++
T Consensus        15 ~~~Igvi~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~l~~~~vdgiIi~~~   80 (298)
T 3tb6_A           15 NKTIGVLTTYISDYIFPSIIRGIESYLSEQGYS---MLLTSTNNNPDNERRGLENLLSQHIDGLIVEPT   80 (298)
T ss_dssp             CCEEEEEESCSSSTTHHHHHHHHHHHHHHTTCE---EEEEECTTCHHHHHHHHHHHHHTCCSEEEECCS
T ss_pred             CceEEEEeCCCCchHHHHHHHHHHHHHHHCCCE---EEEEeCCCChHHHHHHHHHHHHCCCCEEEEecc
Confidence            368999999998888889999999999999984   666666655554433322234678999998876

>3egc_A Putative ribose operon repressor; structural genomics, unknown function, DNA-binding, transcri transcription regulation, PSI-2; 2.35A {Burkholderia thailandensis}

Probab=95.04  E-value=0.097  Score=43.04  Aligned_cols=69  Identities=6%  Similarity=-0.039  Sum_probs=52.5

Q ss_pred             CCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEeee
Q 027801           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAV  144 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~V  144 (218)
                      .+..+||+|...+.......+++++.+.++++|+.   +.++...+..+-..-.-..+...++||||..+.-
T Consensus         6 ~~~~~Igvv~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~l~~~~vdgiIi~~~~   74 (291)
T 3egc_A            6 KRSNVVGLIVSDIENVFFAEVASGVESEARHKGYS---VLLANTAEDIVREREAVGQFFERRVDGLILAPSE   74 (291)
T ss_dssp             -CCCEEEEEESCTTSHHHHHHHHHHHHHHHHTTCE---EEEEECTTCHHHHHHHHHHHHHTTCSEEEECCCS
T ss_pred             CCCcEEEEEECCCcchHHHHHHHHHHHHHHHCCCE---EEEEeCCCCHHHHHHHHHHHHHCCCCEEEEeCCC
Confidence            56678999999998888899999999999999973   6677666655544433333456789999988763

>3h75_A Periplasmic sugar-binding domain protein; protein structure initiative II (PSI II), sugar binding PROT alpha/beta fold; 1.60A {Pseudomonas fluorescens pf-5}

Probab=94.91  E-value=0.17  Score=43.09  Aligned_cols=87  Identities=8%  Similarity=0.031  Sum_probs=59.5

Q ss_pred             CCEEEEEEcccCH-HHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHHhhhc-CCccEEEEEeeeeeCCchh
Q 027801           75 GLRFALVVARFNE-LVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKS-GKYTAVLCIGAVVRGDTTH  151 (218)
Q Consensus        75 ~~RIaIV~Srfn~-~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~L~~~-~~yDaVIaLG~VIrGeT~H  151 (218)
                      ..+|++|...+.. ..-..+++++.+.++++|+.   +.++...+..+-- -.++.++.. .++||||..+.    ... 
T Consensus         3 ~~~Ig~i~p~~~~~~f~~~~~~g~~~~a~~~g~~---~~~~~~~~~~~~~~~~i~~~i~~~~~vDgiIi~~~----~~~-   74 (350)
T 3h75_A            3 LTSVVFLNPGNSTETFWVSYSQFMQAAARDLGLD---LRILYAERDPQNTLQQARELFQGRDKPDYLMLVNE----QYV-   74 (350)
T ss_dssp             CCEEEEEECSCTTCHHHHHHHHHHHHHHHHHTCE---EEEEECTTCHHHHHHHHHHHHHSSSCCSEEEEECC----SSH-
T ss_pred             CCEEEEECCCCCCChHHHHHHHHHHHHHHHcCCe---EEEEECCCCHHHHHHHHHHHHhcCCCCCEEEEeCc----hhh-
Confidence            5689999998876 78889999999999999984   6666555544432 245566665 79999998652    111 


Q ss_pred             HHHHHHHHHHHHHHhchhcCCceEEE
Q 027801          152 YDAVANSAASGVLSAGVNSGVPCIFG  177 (218)
Q Consensus       152 ~e~Va~~vs~gLm~lsL~~~vPVifG  177 (218)
                              ...+.+...+.++||++-
T Consensus        75 --------~~~~~~~~~~~giPvV~~   92 (350)
T 3h75_A           75 --------APQILRLSQGSGIKLFIV   92 (350)
T ss_dssp             --------HHHHHHHHTTSCCEEEEE
T ss_pred             --------HHHHHHHHHhCCCcEEEE
Confidence                    122333444679998863

>3uug_A Multiple sugar-binding periplasmic receptor CHVE; periplasmic binding protein, sugar-binding protein, sugar binding protein; HET: BDP; 1.75A {Agrobacterium tumefaciens} PDB: 3urm_A*

Probab=94.86  E-value=0.094  Score=43.82  Aligned_cols=66  Identities=3%  Similarity=-0.030  Sum_probs=48.2

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHH-HHHHhhhcCCccEEEEEee
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV-VAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~-aak~L~~~~~yDaVIaLG~  143 (218)
                      +..+||+|........-..+++++.+.++++|+.   +.++...+..+--. .++.+. ..++||||..+.
T Consensus         2 ~~~~Igvi~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~i~~~~-~~~vdgiIi~~~   68 (330)
T 3uug_A            2 DKGSVGIAMPTKSSARWIDDGNNIVKQLQEAGYK---TDLQYADDDIPNQLSQIENMV-TKGVKVLVIASI   68 (330)
T ss_dssp             CCCEEEEEECCSSSTHHHHHHHHHHHHHHHTTCE---EEEEECTTCHHHHHHHHHHHH-HHTCSEEEECCS
T ss_pred             CCcEEEEEeCCCcchHHHHHHHHHHHHHHHcCCE---EEEeeCCCCHHHHHHHHHHHH-HcCCCEEEEEcC
Confidence            4678999999998778888999999999999973   55655444443222 234443 357999998765

>3k4h_A Putative transcriptional regulator; structural genomics, protein structure INI NEW YORK structural genomix research consortium; HET: MAL; 2.80A {Bacillus cytotoxicus nvh 391-98}

Probab=94.80  E-value=0.056  Score=44.31  Aligned_cols=68  Identities=9%  Similarity=0.000  Sum_probs=49.3

Q ss_pred             CCCCEEEEEEcc-----cCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEee
Q 027801           73 NEGLRFALVVAR-----FNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        73 ~~~~RIaIV~Sr-----fn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~  143 (218)
                      .+..+||+|...     +.......+++++.+.++++|+.   +.++...+.-+....+-+.+...++||||.++.
T Consensus         6 ~~~~~Igvi~~~~~~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~~~~~~vdgiIi~~~   78 (292)
T 3k4h_A            6 QTTKTLGLVMPSSASKAFQNPFFPEVIRGISSFAHVEGYA---LYMSTGETEEEIFNGVVKMVQGRQIGGIILLYS   78 (292)
T ss_dssp             -CCCEEEEECSSCHHHHTTSTHHHHHHHHHHHHHHHTTCE---EEECCCCSHHHHHHHHHHHHHTTCCCEEEESCC
T ss_pred             CCCCEEEEEecCCccccccCHHHHHHHHHHHHHHHHcCCE---EEEEeCCCCHHHHHHHHHHHHcCCCCEEEEeCC
Confidence            566789999999     88888889999999999999973   444444443343333333445688999998775

>3ksm_A ABC-type sugar transport system, periplasmic COMP; periplasmic component, PSI- 11023L, structural genomics, protein structure initiative; HET: BDR; 1.90A {Hahella chejuensis}

Probab=94.66  E-value=0.075  Score=42.91  Aligned_cols=65  Identities=11%  Similarity=-0.013  Sum_probs=47.5

Q ss_pred             CEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH---HHHHHhhhcCCccEEEEEee
Q 027801           76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        76 ~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP---~aak~L~~~~~yDaVIaLG~  143 (218)
                      +|||+|...+.......+++++.+.++++|+.   +.++..+...+..   -.++.+...+++||||..++
T Consensus         1 ~~Ig~i~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~~~i~~l~~~~~vdgii~~~~   68 (276)
T 3ksm_A            1 PKLLLVLKGDSNAYWRQVYLGAQKAADEAGVT---LLHRSTKDDGDIAGQIQILSYHLSQAPPDALILAPN   68 (276)
T ss_dssp             CEEEEECSCSSSTHHHHHHHHHHHHHHHHTCE---EEECCCSSTTCHHHHHHHHHHHHHHSCCSEEEECCS
T ss_pred             CeEEEEeCCCCChHHHHHHHHHHHHHHHcCCE---EEEECCCCCCCHHHHHHHHHHHHHhCCCCEEEEeCC
Confidence            48999999988888889999999999999973   4444333333332   24455655555999999876

>3lft_A Uncharacterized protein; ABC, ATPase, cassette, L-Trp, PSI, MCSG, structural genomics center for structural genomics; HET: MSE TRP; 1.35A {Streptococcus pneumoniae}

Probab=94.44  E-value=0.36  Score=40.22  Aligned_cols=84  Identities=14%  Similarity=0.259  Sum_probs=53.2

Q ss_pred             CEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEE--EeCCcch-HHHHHHHhhhcCCccEEEEEeeeeeCCchhH
Q 027801           76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVV--WVPGSFE-IGVVAQQLGKSGKYTAVLCIGAVVRGDTTHY  152 (218)
Q Consensus        76 ~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv--~VPGA~E-LP~aak~L~~~~~yDaVIaLG~VIrGeT~H~  152 (218)
                      .+|||| ...+...-..+++|..+.|.++|....++.+.  .--+..| ..-.+++| ...++|+||++|      +...
T Consensus         3 ~~Igvi-~~~~~p~~~~i~~gi~~~l~~~gy~g~~v~l~~~~~~~~~~~~~~~~~~l-~~~~vDgII~~~------~~~~   74 (295)
T 3lft_A            3 AKIGVL-QFVSHPSLDLIYKGIQDGLAEEGYKDDQVKIDFMNSEGDQSKVATMSKQL-VANGNDLVVGIA------TPAA   74 (295)
T ss_dssp             EEEEEE-ECSCCHHHHHHHHHHHHHHHHTTCCGGGEEEEEEECTTCHHHHHHHHHHH-TTSSCSEEEEES------HHHH
T ss_pred             eEEEEE-EccCChhHHHHHHHHHHHHHHcCCCCCceEEEEecCCCCHHHHHHHHHHH-HhcCCCEEEECC------cHHH
Confidence            479998 44555666789999999999999833355554  3333333 23344555 467899999875      2222


Q ss_pred             HHHHHHHHHHHHHhchhcCCceEEE
Q 027801          153 DAVANSAASGVLSAGVNSGVPCIFG  177 (218)
Q Consensus       153 e~Va~~vs~gLm~lsL~~~vPVifG  177 (218)
                      +.+        .+  ...++||++.
T Consensus        75 ~~~--------~~--~~~~iPvV~~   89 (295)
T 3lft_A           75 QGL--------AS--ATKDLPVIMA   89 (295)
T ss_dssp             HHH--------HH--HCSSSCEEEE
T ss_pred             HHH--------HH--cCCCCCEEEE
Confidence            221        12  2479999985

>3o74_A Fructose transport system repressor FRUR; dual transcriptional regulator, DNA, transcription; 2.00A {Pseudomonas putida} PDB: 3o75_A*

Probab=94.42  E-value=0.18  Score=40.68  Aligned_cols=67  Identities=6%  Similarity=0.030  Sum_probs=50.5

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEeee
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAV  144 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~V  144 (218)
                      ..+||++...+.......+++++.+.++++|+.   +.++...+..+-..-.-+.+...++||+|..+.-
T Consensus         2 s~~Igvi~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~l~~~~vdgiIi~~~~   68 (272)
T 3o74_A            2 TRTLGFILPDLENPSYARIAKQLEQGARARGYQ---LLIASSDDQPDSERQLQQLFRARRCDALFVASCL   68 (272)
T ss_dssp             CCEEEEEESCTTCHHHHHHHHHHHHHHHHTTCE---EEEEECTTCHHHHHHHHHHHHHTTCSEEEECCCC
T ss_pred             ceEEEEEeCCCcChhHHHHHHHHHHHHHHCCCE---EEEEeCCCCHHHHHHHHHHHHHcCCCEEEEecCc
Confidence            357999999999889999999999999999984   6666666554444333333345789999988754

>3rot_A ABC sugar transporter, periplasmic sugar binding; nysgrc, PSI-biology, structural genomics; 1.91A {Legionella pneumophila subsp}

Probab=94.36  E-value=0.21  Score=41.33  Aligned_cols=65  Identities=9%  Similarity=0.073  Sum_probs=46.1

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeC--CcchHH-HHHHHhhhcCCccEEEEEee
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVP--GSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VP--GA~ELP-~aak~L~~~~~yDaVIaLG~  143 (218)
                      ..+||+|....+......+++++.+.++++|+.   +.+....  +..+-- -.++.+. ..++||||..+.
T Consensus         3 ~~~Igvi~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~i~~l~-~~~vdgiii~~~   70 (297)
T 3rot_A            3 RDKYYLITHGSQDPYWTSLFQGAKKAAEELKVD---LQILAPPGANDVPKQVQFIESAL-ATYPSGIATTIP   70 (297)
T ss_dssp             CCEEEEECSCCCSHHHHHHHHHHHHHHHHHTCE---EEEECCSSSCCHHHHHHHHHHHH-HTCCSEEEECCC
T ss_pred             eEEEEEEecCCCCchHHHHHHHHHHHHHHhCcE---EEEECCCCcCCHHHHHHHHHHHH-HcCCCEEEEeCC
Confidence            578999999998888889999999999999973   4444323  122222 2334443 467999998765

>3g85_A Transcriptional regulator (LACI family); transcription regulator, PSI-II, structural genomics structure initiative; 1.84A {Clostridium acetobutylicum atcc 824}

Probab=94.27  E-value=0.066  Score=43.91  Aligned_cols=68  Identities=15%  Similarity=0.169  Sum_probs=46.6

Q ss_pred             CCCCEEEEEEc-ccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEee
Q 027801           73 NEGLRFALVVA-RFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        73 ~~~~RIaIV~S-rfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~  143 (218)
                      .+..+||++.. .+.......+++++.+.++++|+.   +.++..++..+--...-..+...++||||..+.
T Consensus         9 ~~~~~Igvi~~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~l~~~~vdgiIi~~~   77 (289)
T 3g85_A            9 QSKPTIALYWSSDISVNIISRFLRGLQSKLAKQNYN---YNVVICPYKTDCLHLEKGISKENSFDAAIIANI   77 (289)
T ss_dssp             --CCEEEEEEETTSCGGGHHHHHHHHHHHHHHTTTC---SEEEEEEECTTCGGGCGGGSTTTCCSEEEESSC
T ss_pred             CCCceEEEEeccccchHHHHHHHHHHHHHHHHcCCe---EEEEecCCCchhHHHHHHHHhccCCCEEEEecC
Confidence            56678999998 688888889999999999999985   555544433221111122335678999998765

>3kke_A LACI family transcriptional regulator; structural genomics, DNA-binding, transcription regulation, PSI-2; 2.20A {Mycobacterium smegmatis str}

Probab=94.23  E-value=0.14  Score=42.69  Aligned_cols=68  Identities=15%  Similarity=0.072  Sum_probs=51.2

Q ss_pred             CCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEee
Q 027801           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~  143 (218)
                      .+..+||+|...+....-..+++++.+.++++|+.   +.++...+..+-..-.-..+...++||||..+.
T Consensus        13 ~~s~~Igvi~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~l~~~~vdgiI~~~~   80 (303)
T 3kke_A           13 SRSGTIGLIVPDVNNAVFADMFSGVQMAASGHSTD---VLLGQIDAPPRGTQQLSRLVSEGRVDGVLLQRR   80 (303)
T ss_dssp             ----CEEEEESCTTSTTHHHHHHHHHHHHHHTTCC---EEEEECCSTTHHHHHHHHHHHSCSSSEEEECCC
T ss_pred             CCCCEEEEEeCCCcChHHHHHHHHHHHHHHHCCCE---EEEEeCCCChHHHHHHHHHHHhCCCcEEEEecC
Confidence            34567999999988888889999999999999984   677777766665544434445788999999876

>3gbv_A Putative LACI-family transcriptional regulator; NYSGXRC, PSI-II, 11231J, structur genomics, protein structure initiative; 2.20A {Bacteroides fragilis}

Probab=94.02  E-value=0.35  Score=39.48  Aligned_cols=67  Identities=13%  Similarity=0.175  Sum_probs=47.7

Q ss_pred             CCCCEEEEEEccc-CHHHHHHHHHHHHHHHHHC-CCCCCCeEEEEeC-CcchH---HHHHHHhhhcCCccEEEEEee
Q 027801           73 NEGLRFALVVARF-NELVTKLLLEGALETFKKY-SVKEENIDVVWVP-GSFEI---GVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        73 ~~~~RIaIV~Srf-n~~It~~Ll~gA~~~L~~~-Gv~~e~I~vv~VP-GA~EL---P~aak~L~~~~~yDaVIaLG~  143 (218)
                      .+..+||+|...+ ....-..+++++.+.++++ |..   +.+.... ...+.   --.++.+ ...++||||..+.
T Consensus         6 ~~~~~Igvi~~~~~~~~~~~~~~~gi~~~a~~~~g~~---~~~~~~~~~~~~~~~~~~~i~~l-~~~~vdgiii~~~   78 (304)
T 3gbv_A            6 NKKYTFACLLPKHLEGEYWTDVQKGIREAVTTYSDFN---ISANITHYDPYDYNSFVATSQAV-IEEQPDGVMFAPT   78 (304)
T ss_dssp             -CCEEEEEEEECCCTTSHHHHHHHHHHHHHHHTGGGC---EEEEEEEECSSCHHHHHHHHHHH-HTTCCSEEEECCS
T ss_pred             CCcceEEEEecCCCCchHHHHHHHHHHHHHHHHHhCC---eEEEEEcCCCCCHHHHHHHHHHH-HhcCCCEEEECCC
Confidence            5667899999998 7778889999999999998 764   6666542 22222   1223444 4578999999876

>3o1i_D Periplasmic protein TORT; ligand free, two component sensor, periplasmic binding prote signaling protein; HET: PE4; 2.80A {Vibrio parahaemolyticus} PDB: 3o1h_B* 3o1j_C

Probab=93.85  E-value=0.15  Score=41.76  Aligned_cols=68  Identities=9%  Similarity=-0.032  Sum_probs=49.5

Q ss_pred             CCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCC--cchHHH-HHHHhhhcCCccEEEEEeee
Q 027801           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPG--SFEIGV-VAQQLGKSGKYTAVLCIGAV  144 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPG--A~ELP~-aak~L~~~~~yDaVIaLG~V  144 (218)
                      ++..+||+|........-..+++++.+.++++|+.   +.++...+  ..+--. .++.+. ..++||||..+.-
T Consensus         3 ~~~~~Igvi~~~~~~~~~~~~~~g~~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~~~~~-~~~vdgiii~~~~   73 (304)
T 3o1i_D            3 GSDEKICAIYPHLKDSYWLSVNYGMVSEAEKQGVN---LRVLEAGGYPNKSRQEQQLALCT-QWGANAIILGTVD   73 (304)
T ss_dssp             --CCEEEEEESCSCSHHHHHHHHHHHHHHHHHTCE---EEEEECSSTTCHHHHHHHHHHHH-HHTCSEEEECCSS
T ss_pred             CCCcEEEEEeCCCCCcHHHHHHHHHHHHHHHcCCe---EEEEcCCCCCCHHHHHHHHHHHH-HcCCCEEEEeCCC
Confidence            45679999999998888999999999999999984   66666665  333222 233343 4679999988754

>3k9c_A Transcriptional regulator, LACI family protein; PSI-II, 11026W, structural genomics, PR structure initiative; 2.14A {Rhodococcus jostii}

Probab=93.78  E-value=0.24  Score=40.92  Aligned_cols=67  Identities=15%  Similarity=0.121  Sum_probs=50.0

Q ss_pred             CCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEeee
Q 027801           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAV  144 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~V  144 (218)
                      .+..+||+|. .+....-..+++++.+.++++|+.   +.++...+.-+-.-.++.| ...++||||..+.-
T Consensus        10 ~~~~~Igvi~-~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~l-~~~~vdgiIi~~~~   76 (289)
T 3k9c_A           10 ASSRLLGVVF-ELQQPFHGDLVEQIYAAATRRGYD---VMLSAVAPSRAEKVAVQAL-MRERCEAAILLGTR   76 (289)
T ss_dssp             ---CEEEEEE-ETTCHHHHHHHHHHHHHHHHTTCE---EEEEEEBTTBCHHHHHHHH-TTTTEEEEEEETCC
T ss_pred             CCCCEEEEEE-ecCCchHHHHHHHHHHHHHHCCCE---EEEEeCCCCHHHHHHHHHH-HhCCCCEEEEECCC
Confidence            4567899999 888888899999999999999974   6677666655533344555 45789999998763

>8abp_A L-arabinose-binding protein; binding proteins; HET: GLA GAL; 1.49A {Escherichia coli} SCOP: c.93.1.1 PDB: 7abp_A* 6abp_A* 1abe_A* 1abf_A* 5abp_A* 1bap_A* 1apb_A* 9abp_A* 2wrz_A

Probab=93.75  E-value=0.19  Score=41.37  Aligned_cols=64  Identities=13%  Similarity=-0.017  Sum_probs=45.1

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcch-HHHHHHHhhhcCCccEEEEEee
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE-IGVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~E-LP~aak~L~~~~~yDaVIaLG~  143 (218)
                      ..+||+|........-..+++++.++++++|+.   +.++.- +..+ ---.++.+.. .++||||..+.
T Consensus         2 ~~~Ig~i~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~-~~~~~~~~~i~~l~~-~~vdgiii~~~   66 (306)
T 8abp_A            2 NLKLGFLVKQPEEPWFQTEWKFADKAGKDLGFE---VIKIAV-PDGEKTLNAIDSLAA-SGAKGFVICTP   66 (306)
T ss_dssp             CEEEEEEESCTTSHHHHHHHHHHHHHHHHHTEE---EEEEEC-CSHHHHHHHHHHHHH-TTCCEEEEECS
T ss_pred             CeEEEEEeCCCCchHHHHHHHHHHHHHHHcCCE---EEEeCC-CCHHHHHHHHHHHHH-cCCCEEEEeCC
Confidence            468999999998888899999999999999873   433322 2222 1123444543 56999998774

>3gv0_A Transcriptional regulator, LACI family; transcription regulator, PSI-II, structural genomics structure initiative; 2.35A {Agrobacterium tumefaciens str}

Probab=93.50  E-value=0.091  Score=43.37  Aligned_cols=68  Identities=16%  Similarity=0.043  Sum_probs=48.5

Q ss_pred             CCCCEEEEEEcccCH--HHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEee
Q 027801           73 NEGLRFALVVARFNE--LVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~--~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~  143 (218)
                      .+..+||+|......  .....+++++.+.++++|+.   +.++...+.-+-...+..++.+.++||||..+.
T Consensus         6 ~~s~~Igvv~~~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~l~~~~vdgiIi~~~   75 (288)
T 3gv0_A            6 GKTNVIALVLSVDEELMGFTSQMVFGITEVLSTTQYH---LVVTPHIHAKDSMVPIRYILETGSADGVIISKI   75 (288)
T ss_dssp             -CCCEEEEECBCCCCSSCHHHHHHHHHHHHHTTSSCE---EEECCBSSGGGTTHHHHHHHHHTCCSEEEEESC
T ss_pred             CCCCEEEEEecCCccccHHHHHHHHHHHHHHHHcCCE---EEEecCCcchhHHHHHHHHHHcCCccEEEEecC
Confidence            566789999997654  66778999999999999973   555544444443344445556789999998764

>3huu_A Transcription regulator like protein; PSI-II, NYSGXRC, LAC I, STR genomics, protein structure initiative; 1.95A {Staphylococcus haemolyticus}

Probab=93.47  E-value=0.13  Score=42.83  Aligned_cols=69  Identities=10%  Similarity=0.057  Sum_probs=50.3

Q ss_pred             CCCCEEEEEEcc-----cCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEeee
Q 027801           73 NEGLRFALVVAR-----FNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAV  144 (218)
Q Consensus        73 ~~~~RIaIV~Sr-----fn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~V  144 (218)
                      .+..+||+|...     +....-..+++++.+.++++|+.   +.++...+.-+...-+-..+...++||||.++.-
T Consensus        20 ~~~~~Igvi~~~~~~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~l~~~~vdgiIi~~~~   93 (305)
T 3huu_A           20 NKTLTIGLIQKSSAPEIRQNPFNSDVLNGINQACNVRGYS---TRMTVSENSGDLYHEVKTMIQSKSVDGFILLYSL   93 (305)
T ss_dssp             -CCCEEEEECSCCSHHHHTSHHHHHHHHHHHHHHHHHTCE---EEECCCSSHHHHHHHHHHHHHTTCCSEEEESSCB
T ss_pred             CCCCEEEEEeCCCccccccCcHHHHHHHHHHHHHHHCCCE---EEEEeCCCChHHHHHHHHHHHhCCCCEEEEeCCc
Confidence            455689999998     77788889999999999999973   5555444444443333344467899999998764

>3h5o_A Transcriptional regulator GNTR; transcription regulator, GNTR,chromobacterium violaceum, PSI, SGX, DNA-binding; 2.30A {Chromobacterium violaceum}

Probab=93.42  E-value=0.37  Score=40.87  Aligned_cols=68  Identities=9%  Similarity=-0.030  Sum_probs=47.2

Q ss_pred             CCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEee
Q 027801           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~  143 (218)
                      .+..+||+|...+....-..+++++.+.+.++|+.   +.+....+..+-....-+.+...++||||..+.
T Consensus        60 ~~~~~Igvi~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~l~~~~vdGiIi~~~  127 (339)
T 3h5o_A           60 AKSRTVLVLIPSLANTVFLETLTGIETVLDAAGYQ---MLIGNSHYDAGQELQLLRAYLQHRPDGVLITGL  127 (339)
T ss_dssp             ---CEEEEEESCSTTCTTHHHHHHHHHHHHHTTCE---EEEEECTTCHHHHHHHHHHHHTTCCSEEEEECS
T ss_pred             CCCCEEEEEeCCCCCHHHHHHHHHHHHHHHHCCCE---EEEEeCCCChHHHHHHHHHHHcCCCCEEEEeCC
Confidence            34567999998877777778899999999999974   555555555443333222334678999999875

>3c3k_A Alanine racemase; structural genomics, protein structure initiative, NEW YORK research center for structural genomics, nysgxrc; 1.99A {Actinobacillus succinogenes}

Probab=93.30  E-value=0.33  Score=39.93  Aligned_cols=67  Identities=12%  Similarity=0.107  Sum_probs=46.6

Q ss_pred             CCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHHhhhcCCccEEEEEee
Q 027801           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~L~~~~~yDaVIaLG~  143 (218)
                      .+..+||+|...+....-..+++++.+.++++|+.   +.++...+..+-- -.++.+ ...++||||..+.
T Consensus         6 ~~~~~Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~~~~l-~~~~vdgiI~~~~   73 (285)
T 3c3k_A            6 AKTGMLLVMVSNIANPFCAAVVKGIEKTAEKNGYR---ILLCNTESDLARSRSCLTLL-SGKMVDGVITMDA   73 (285)
T ss_dssp             -CCCEEEEEESCTTSHHHHHHHHHHHHHHHHTTCE---EEEEECTTCHHHHHHHTHHH-HTTCCSEEEECCC
T ss_pred             CCCCEEEEEeCCCCCchHHHHHHHHHHHHHHcCCE---EEEEeCCCCHHHHHHHHHHH-HhCCCCEEEEeCC
Confidence            45678999999888888889999999999999973   4444333322211 223444 3578999998764

>3miz_A Putative transcriptional regulator protein, LACI family; LACL family, protein structure initiative II (PSI II), NYSGXRC, structural genomics; 1.91A {Rhizobium etli}

Probab=93.25  E-value=0.17  Score=41.93  Aligned_cols=69  Identities=14%  Similarity=0.095  Sum_probs=49.1

Q ss_pred             CCCCEEEEEEcccCHHHHH-HHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEeee
Q 027801           73 NEGLRFALVVARFNELVTK-LLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAV  144 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~-~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~V  144 (218)
                      .+..+||+|...+....-. .+++++.+.++++|+.   +.++...+..+-....-+.+...++||||..+.-
T Consensus        11 ~~s~~Igvi~~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~l~~~~vdGiIi~~~~   80 (301)
T 3miz_A           11 SRSNTFGIITDYVSTTPYSVDIVRGIQDWANANGKT---ILIANTGGSSEREVEIWKMFQSHRIDGVLYVTMY   80 (301)
T ss_dssp             -CCCEEEEEESSTTTCCSCHHHHHHHHHHHHHTTCE---EEEEECTTCHHHHHHHHHHHHHTTCSEEEEEEEE
T ss_pred             CCCCEEEEEeCCCcCcccHHHHHHHHHHHHHHCCCE---EEEEeCCCChHHHHHHHHHHHhCCCCEEEEecCC
Confidence            4567899999877654455 7889999999999974   6666666555544333333456789999988864

>3qk7_A Transcriptional regulators; structural genomics, NEW YORK structural genomix research CO NYSGXRC, PSI-2, protein structur initiative; 2.70A {Yersinia pestis}

Probab=93.07  E-value=0.23  Score=41.14  Aligned_cols=68  Identities=9%  Similarity=-0.045  Sum_probs=49.2

Q ss_pred             CCCCEEEEEEc----ccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEeee
Q 027801           73 NEGLRFALVVA----RFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAV  144 (218)
Q Consensus        73 ~~~~RIaIV~S----rfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~V  144 (218)
                      .+..+||+|..    .+....-..+++++.+.++++|+.   +.++...+.-+. ..+.+++...++||||..+.-
T Consensus         4 ~~s~~Igvi~~~~~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~-~~~~~~l~~~~vdGiIi~~~~   75 (294)
T 3qk7_A            4 GRTDAIALAYPSRPRVLNNSTFLEMISWIGIELGKRGLD---LLLIPDEPGEKY-QSLIHLVETRRVDALIVAHTQ   75 (294)
T ss_dssp             -CCCEEEEEEESCSGGGSCHHHHHHHHHHHHHHHHTTCE---EEEEEECTTCCC-HHHHHHHHHTCCSEEEECSCC
T ss_pred             CccceEEEEecCCCccccChhHHHHHHHHHHHHHHCCCE---EEEEeCCChhhH-HHHHHHHHcCCCCEEEEeCCC
Confidence            45668999998    777778889999999999999984   666665542222 233344456789999998764

>3g1w_A Sugar ABC transporter; sugar-binding protein, bacillus halod target 11229F, transport protein, structural genomics; 2.02A {Bacillus halodurans c-125}

Probab=92.73  E-value=0.28  Score=40.39  Aligned_cols=65  Identities=11%  Similarity=0.071  Sum_probs=45.2

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH---HHHHHhhhcCCccEEEEEee
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP---~aak~L~~~~~yDaVIaLG~  143 (218)
                      ++.+|++|........-..+++++.+.++++|+.   +.++ .+...+.-   -.++.+. ..++||||..++
T Consensus         3 ~~~~I~~i~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~-~~~~~~~~~~~~~i~~l~-~~~vdgiIi~~~   70 (305)
T 3g1w_A            3 LNETYMMITFQSGMDYWKRCLKGFEDAAQALNVT---VEYR-GAAQYDIQEQITVLEQAI-AKNPAGIAISAI   70 (305)
T ss_dssp             --CEEEEEESSTTSTHHHHHHHHHHHHHHHHTCE---EEEE-ECSSSCHHHHHHHHHHHH-HHCCSEEEECCS
T ss_pred             CCceEEEEEccCCChHHHHHHHHHHHHHHHcCCE---EEEe-CCCcCCHHHHHHHHHHHH-HhCCCEEEEcCC
Confidence            3578999999998888899999999999999973   3332 23333322   2234443 468999998875

>3gyb_A Transcriptional regulators (LACI-family transcriptional regulatory protein); protein structure initiative II(PSI II), nysgxrc; 1.60A {Corynebacterium glutamicum}

Probab=92.68  E-value=0.12  Score=42.12  Aligned_cols=65  Identities=8%  Similarity=0.031  Sum_probs=46.4

Q ss_pred             CCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchH-HHHHHHhhhcCCccEEEEEee
Q 027801           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEI-GVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~EL-P~aak~L~~~~~yDaVIaLG~  143 (218)
                      .+..+||++...+....-..+++++.++++++|+.   +.++... ..+- --.++.+ ...++|||| ++.
T Consensus         3 ~~~~~Igvi~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~-~~~~~~~~~~~l-~~~~vdgiI-~~~   68 (280)
T 3gyb_A            3 LRTQLIAVLIDDYSNPWFIDLIQSLSDVLTPKGYR---LSVIDSL-TSQAGTDPITSA-LSMRPDGII-IAQ   68 (280)
T ss_dssp             -CCCEEEEEESCTTSGGGHHHHHHHHHHHGGGTCE---EEEECSS-SSCSSSCHHHHH-HTTCCSEEE-EES
T ss_pred             CccCEEEEEeCCCCChHHHHHHHHHHHHHHHCCCE---EEEEeCC-CchHHHHHHHHH-HhCCCCEEE-ecC
Confidence            45678999999888888889999999999999973   5555444 2221 1233444 467899999 775

>3hs3_A Ribose operon repressor; PSI-II, NYSGXRC, periplasmic binding protein, structural genomics, protein structure initiative; 1.60A {Lactobacillus acidophilus}

Probab=92.66  E-value=1.4  Score=36.08  Aligned_cols=97  Identities=12%  Similarity=0.071  Sum_probs=68.1

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhc-CCccEEEEEeeeeeCCchhH
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKS-GKYTAVLCIGAVVRGDTTHY  152 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~-~~yDaVIaLG~VIrGeT~H~  152 (218)
                      ...||+++....+......-.+|..+.|+++|+.   ++...+.|.++ --+++.+++. .++|||+|.          .
T Consensus       121 G~~~I~~i~~~~~~~~~~~R~~Gf~~~l~~~g~~---~~~~~~~~~~~-~~~~~~~l~~~~~~~ai~~~----------~  186 (277)
T 3hs3_A          121 KIEKVLIQHWPLSLPTIRERIEAMTAEASKLKID---YLLEETPENNP-YISAQSALNKSNQFDAIITV----------N  186 (277)
T ss_dssp             TCCEEEEEESCTTSHHHHHHHHHHHHHHHHTTCE---EEEEECCSSCH-HHHHHHHHHTGGGCSEEECS----------S
T ss_pred             CCCEEEEEeCCCcCccHHHHHHHHHHHHHHCCCC---CCCCCccCCch-HHHHHHHHcCCCCCCEEEEC----------C
Confidence            4559999998877667777779999999999985   22215678888 4455666544 679999875          3


Q ss_pred             HHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHH
Q 027801          153 DAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQ  186 (218)
Q Consensus       153 e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQ  186 (218)
                      |.++-.+.+++.+..++  +|==..|++.++.+.
T Consensus       187 d~~A~g~~~al~~~g~~--vP~di~vig~d~~~~  218 (277)
T 3hs3_A          187 DLYAAEIIKEAKRRNLK--IPDDFQLVGYDNNIL  218 (277)
T ss_dssp             HHHHHHHHHHHHHTTCC--TTTTCEEECSBCCGG
T ss_pred             HHHHHHHHHHHHHcCCC--CCCceEEEeeCCcHH
Confidence            56888888888888775  332234556665543

>3hcw_A Maltose operon transcriptional repressor; RNA-binding, PSI-2, NYSGXRC, STRU genomics, protein structure initiative; 2.20A {Staphylococcus aureus subsp}

Probab=92.60  E-value=0.23  Score=41.21  Aligned_cols=68  Identities=13%  Similarity=0.013  Sum_probs=47.8

Q ss_pred             CCCCEEEEEE-----cccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEee
Q 027801           73 NEGLRFALVV-----ARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        73 ~~~~RIaIV~-----Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~  143 (218)
                      .+..+||+|.     ..+....-..+++++.+.++++|+.   +.++...+..+...-+-+.+...++||||..+.
T Consensus         5 ~~s~~Igvi~~~~~~~~~~~~f~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~l~~~~vdGiI~~~~   77 (295)
T 3hcw_A            5 NQTYKIGLVLKGSEEPIRLNPFYINVLLGISETCNQHGYG---TQTTVSNNMNDLMDEVYKMIKQRMVDAFILLYS   77 (295)
T ss_dssp             CCSCEEEEECSCCCHHHHSCHHHHHHHHHHHHHHHTTTCE---EEECCCCSHHHHHHHHHHHHHTTCCSEEEESCC
T ss_pred             CCCcEEEEEeecCCcccccChHHHHHHHHHHHHHHHCCCE---EEEEcCCCChHHHHHHHHHHHhCCcCEEEEcCc
Confidence            4556899999     4455667778999999999999973   445444444444433334446789999998865

>3m9w_A D-xylose-binding periplasmic protein; xylose binding protein, conformational changes, SUGA protein; 2.15A {Escherichia coli} PDB: 3m9x_A* 3ma0_A*

Probab=92.52  E-value=0.27  Score=40.87  Aligned_cols=65  Identities=8%  Similarity=0.011  Sum_probs=45.3

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHH-HHHHhhhcCCccEEEEEee
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV-VAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~-aak~L~~~~~yDaVIaLG~  143 (218)
                      ..+||+|...+....-..+++++.+.++++|+.   +.+....+..+--. .++.+ ...++||||..+.
T Consensus         2 ~~~Igvi~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~i~~l-~~~~vdgiIi~~~   67 (313)
T 3m9w_A            2 EVKIGMAIDDLRLERWQKDRDIFVKKAESLGAK---VFVQSANGNEETQMSQIENM-INRGVDVLVIIPY   67 (313)
T ss_dssp             -CEEEEEESCCSSSTTHHHHHHHHHHHHHTSCE---EEEEECTTCHHHHHHHHHHH-HHTTCSEEEEECS
T ss_pred             CcEEEEEeCCCCChHHHHHHHHHHHHHHHcCCE---EEEECCCCCHHHHHHHHHHH-HHcCCCEEEEeCC
Confidence            457999998877767778889999999999973   55555544443332 23333 3568999998875

>1byk_A Protein (trehalose operon repressor); LACI family, phosphate binding, protein structure, trehalose repressor, gene regulation; HET: T6P; 2.50A {Escherichia coli} SCOP: c.93.1.1

Probab=92.46  E-value=0.6  Score=37.44  Aligned_cols=65  Identities=18%  Similarity=0.144  Sum_probs=45.6

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHHhhhcCCccEEEEEee
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~L~~~~~yDaVIaLG~  143 (218)
                      ..+||+|........-..++++..+.++++|+.   +.++...+..+-- -.++.+ ...++||+|..++
T Consensus         2 s~~Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~~~~l-~~~~vdgiI~~~~   67 (255)
T 1byk_A            2 DKVVAIIVTRLDSLSENLAVQTMLPAFYEQGYD---PIMMESQFSPQLVAEHLGVL-KRRNIDGVVLFGF   67 (255)
T ss_dssp             CCEEEEEESCTTCHHHHHHHHHHHHHHHHHTCE---EEEEECTTCHHHHHHHHHHH-HTTTCCEEEEECC
T ss_pred             CCEEEEEeCCCCCccHHHHHHHHHHHHHHcCCE---EEEEeCCCcHHHHHHHHHHH-HhcCCCEEEEecC
Confidence            357999999888778889999999999999973   4444433322221 123444 4578999998875

>2rgy_A Transcriptional regulator, LACI family; 11011J, NYSGXRC, transctiptional regulator, SUG binding protein, structural genomics, PSI-2; 2.05A {Burkholderia phymatum}

Probab=92.46  E-value=0.35  Score=39.84  Aligned_cols=67  Identities=13%  Similarity=-0.009  Sum_probs=47.0

Q ss_pred             CCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHH----HHHHhhhcCCccEEEEEee
Q 027801           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV----VAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~----aak~L~~~~~yDaVIaLG~  143 (218)
                      .+..+||+|...+....-..+++++.+.++++|+.   +.++...+..+--.    .++.+. ..++||+|..+.
T Consensus         6 ~~~~~Ig~i~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~~~~l~-~~~vdgiIi~~~   76 (290)
T 2rgy_A            6 QQLGIIGLFVPTFFGSYYGTILKQTDLELRAVHRH---VVVATGCGESTPREQALEAVRFLI-GRDCDGVVVISH   76 (290)
T ss_dssp             --CCEEEEECSCSCSHHHHHHHHHHHHHHHHTTCE---EEEECCCSSSCHHHHHHHHHHHHH-HTTCSEEEECCS
T ss_pred             CCCCeEEEEeCCCCCchHHHHHHHHHHHHHHCCCE---EEEEeCCCchhhhhhHHHHHHHHH-hcCccEEEEecC
Confidence            45568999998888888889999999999999973   44444433333222    345553 568999998775

>2iks_A DNA-binding transcriptional dual regulator; escherichia coli structural genomics, PSI-2, protein structure initiative; 1.85A {Escherichia coli}

Probab=92.43  E-value=0.58  Score=38.48  Aligned_cols=67  Identities=6%  Similarity=0.006  Sum_probs=47.1

Q ss_pred             CCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchH-HHHHHHhhhcCCccEEEEEee
Q 027801           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEI-GVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~EL-P~aak~L~~~~~yDaVIaLG~  143 (218)
                      .+..+||+|...+....-..+++++.+.++++|+.   +.+....+..+- --.++.+. ..++||||..+.
T Consensus        18 ~~~~~Ig~i~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~~~~l~-~~~vdgii~~~~   85 (293)
T 2iks_A           18 GRTRSIGLVIPDLENTSYTRIANYLERQARQRGYQ---LLIACSEDQPDNEMRCIEHLL-QRQVDAIIVSTS   85 (293)
T ss_dssp             CCCCEEEEEESCSCSHHHHHHHHHHHHHHHHTTCE---EEEEECTTCHHHHHHHHHHHH-HTTCSEEEECCS
T ss_pred             CCCcEEEEEeCCCcCcHHHHHHHHHHHHHHHCCCE---EEEEcCCCCHHHHHHHHHHHH-HcCCCEEEEeCC
Confidence            45668999999888888889999999999999973   444433332221 12334443 467999998775

>2fep_A Catabolite control protein A; CCPA, transcriptional regulator; HET: SEP; 2.45A {Bacillus subtilis} PDB: 2nzu_G* 1sxh_A 1sxi_A 1sxg_A* 2nzv_G* 2oen_G*

Probab=92.38  E-value=0.54  Score=38.79  Aligned_cols=67  Identities=9%  Similarity=0.152  Sum_probs=46.8

Q ss_pred             CCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHHhhhcCCccEEEEEee
Q 027801           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~L~~~~~yDaVIaLG~  143 (218)
                      .+..+||+|...+....-..+++++.+.++++|+.   +.++...+..+-- -.++.+. ..++||||..+.
T Consensus        14 ~~s~~Igvi~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~l~-~~~vdgiIi~~~   81 (289)
T 2fep_A           14 KKTTTVGVIIPDISSIFYSELARGIEDIATMYKYN---IILSNSDQNMEKELHLLNTML-GKQVDGIVFMGG   81 (289)
T ss_dssp             --CCEEEEEESCTTSHHHHHHHHHHHHHHHHTTCE---EEEEECTTCHHHHHHHHHHHH-HTTCSEEEECCS
T ss_pred             CCCCeEEEEeCCCCCchHHHHHHHHHHHHHHcCCE---EEEEeCCCCHHHHHHHHHHHH-hCCCCEEEEecC
Confidence            45668999999988888889999999999999973   5554433332211 2234443 578999998775

>3k4h_A Putative transcriptional regulator; structural genomics, protein structure INI NEW YORK structural genomix research consortium; HET: MAL; 2.80A {Bacillus cytotoxicus nvh 391-98}

Probab=92.36  E-value=1.2  Score=36.19  Aligned_cols=85  Identities=19%  Similarity=0.119  Sum_probs=59.3

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHHhhhc-CCccEEEEEeeeeeCCchhH
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKS-GKYTAVLCIGAVVRGDTTHY  152 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~L~~~-~~yDaVIaLG~VIrGeT~H~  152 (218)
                      ..||+++....+......-++|..+.|+++|+......++..+...+-- -+++.+++. .++|||+|.          .
T Consensus       131 ~~~i~~i~~~~~~~~~~~R~~gf~~~l~~~g~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~----------~  200 (292)
T 3k4h_A          131 HKQIAFIGGGSDLLVTRDRLAGMSDALKLADIVLPKEYILHFDFSRESGQQAVEELMGLQQPPTAIMAT----------D  200 (292)
T ss_dssp             CCCEEEEESCTTBHHHHHHHHHHHHHHHHTTCCCCGGGEEECCSSHHHHHHHHHHHHTSSSCCSEEEES----------S
T ss_pred             CceEEEEeCcccchhHHHHHHHHHHHHHHcCCCCChheEEecCCCHHHHHHHHHHHHcCCCCCcEEEEc----------C
Confidence            3489999988776666677899999999999864433344333333322 234455544 589999975          3


Q ss_pred             HHHHHHHHHHHHHhchh
Q 027801          153 DAVANSAASGVLSAGVN  169 (218)
Q Consensus       153 e~Va~~vs~gLm~lsL~  169 (218)
                      |.++-.+.++|.+..++
T Consensus       201 d~~a~g~~~al~~~g~~  217 (292)
T 3k4h_A          201 DLIGLGVLSALSKKGFV  217 (292)
T ss_dssp             HHHHHHHHHHHHHTTCC
T ss_pred             hHHHHHHHHHHHHhCCC
Confidence            56788888999888875

>3brq_A HTH-type transcriptional regulator ASCG; transcriptional repressor structure escherichia coli, struct genomics, PSI-2; HET: FRU; 2.00A {Escherichia coli}

Probab=92.31  E-value=0.41  Score=38.87  Aligned_cols=67  Identities=16%  Similarity=0.038  Sum_probs=43.4

Q ss_pred             CCCCEEEEEEcc--cCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchH-HHHHHHhhhcCCccEEEEEee
Q 027801           73 NEGLRFALVVAR--FNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEI-GVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        73 ~~~~RIaIV~Sr--fn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~EL-P~aak~L~~~~~yDaVIaLG~  143 (218)
                      .+..+||+|...  +.......+++++.+.++++|+.   +.++...+..+- --.++.+. ..++||||..+.
T Consensus        17 ~~~~~Ig~i~~~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~~~~l~-~~~vdgii~~~~   86 (296)
T 3brq_A           17 KSTQTLGLVVTNTLYHGIYFSELLFHAARMAEEKGRQ---LLLADGKHSAEEERQAIQYLL-DLRCDAIMIYPR   86 (296)
T ss_dssp             --CCEEEEEECGGGCC--CHHHHHHHHHHHHHHTTCE---EEEECCTTSHHHHHHHHHHHH-HTTCSEEEEECS
T ss_pred             CCCceEEEEeCCcccCCchHHHHHHHHHHHHHHCCCE---EEEEeCCCCHHHHHHHHHHHH-hcCCCEEEEecC
Confidence            455789999988  77777888999999999999873   444433222221 12334444 468999998775

>1dbq_A Purine repressor; transcription regulation, DNA-binding regulatory protein; 2.20A {Escherichia coli} SCOP: c.93.1.1 PDB: 1jhz_A

Probab=92.20  E-value=0.52  Score=38.35  Aligned_cols=67  Identities=7%  Similarity=0.023  Sum_probs=44.7

Q ss_pred             CCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchH-HHHHHHhhhcCCccEEEEEee
Q 027801           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEI-GVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~EL-P~aak~L~~~~~yDaVIaLG~  143 (218)
                      .+..+||++...+.......+++++.+.++++|+.   +.+....+..+- --.++.+. ..++||||..+.
T Consensus         5 ~~~~~Ig~i~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~~~~l~-~~~vdgii~~~~   72 (289)
T 1dbq_A            5 NHTKSIGLLATSSEAAYFAEIIEAVEKNCFQKGYT---LILGNAWNNLEKQRAYLSMMA-QKRVDGLLVMCS   72 (289)
T ss_dssp             ---CEEEEEESCTTSHHHHHHHHHHHHHHHHHTCE---EEEEECTTCHHHHHHHHHHHH-HTTCSEEEEECS
T ss_pred             CCCCEEEEEeCCCCChHHHHHHHHHHHHHHHcCCe---EEEEcCCCChHHHHHHHHHHH-hCCCCEEEEEec
Confidence            45568999998888888889999999999999973   444433222221 12234443 568999998774

>3d8u_A PURR transcriptional regulator; APC91343.1, vibrio parahaem RIMD 2210633, structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.88A {Vibrio parahaemolyticus}

Probab=92.18  E-value=0.38  Score=38.90  Aligned_cols=65  Identities=14%  Similarity=0.172  Sum_probs=45.1

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHHhhhcCCccEEEEEee
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~L~~~~~yDaVIaLG~  143 (218)
                      ..+||+|...+.......+++++.+.++++|+.   +.++...+..+-- -.++.+ ...++||+|..+.
T Consensus         3 s~~Ig~i~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~~~~l-~~~~vdgii~~~~   68 (275)
T 3d8u_A            3 AYSIALIIPSLFEKACAHFLPSFQQALNKAGYQ---LLLGYSDYSIEQEEKLLSTF-LESRPAGVVLFGS   68 (275)
T ss_dssp             -CEEEEEESCSSCHHHHHHHHHHHHHHHHTSCE---ECCEECTTCHHHHHHHHHHH-HTSCCCCEEEESS
T ss_pred             ceEEEEEeCCCccccHHHHHHHHHHHHHHCCCE---EEEEcCCCCHHHHHHHHHHH-HhcCCCEEEEeCC
Confidence            458999999888888889999999999999974   4444333332222 223444 3578999998775

>3qk7_A Transcriptional regulators; structural genomics, NEW YORK structural genomix research CO NYSGXRC, PSI-2, protein structur initiative; 2.70A {Yersinia pestis}

Probab=92.06  E-value=1.6  Score=35.93  Aligned_cols=125  Identities=14%  Similarity=0.048  Sum_probs=76.5

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHHhhhc-CCccEEEEEeeeeeCCchh
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKS-GKYTAVLCIGAVVRGDTTH  151 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~L~~~-~~yDaVIaLG~VIrGeT~H  151 (218)
                      ...||+++....+......-++|..+.|+++|+..+...++..+...|-- -+++++++. .++|||+|.          
T Consensus       125 G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~g~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~----------  194 (294)
T 3qk7_A          125 GHQRIAFVSTDARISYVDQRLQGYVQTMSEAGLMPLAGYLQKADPTRPGGYLAASRLLALEVPPTAIITD----------  194 (294)
T ss_dssp             TCCCEEEEEESSCCHHHHHHHHHHHHHHHTTTCCCCTTCEEEECSSHHHHHHHHHHHHHSSSCCSEEEES----------
T ss_pred             CCceEEEEeCCcccchHHHHHHHHHHHHHHCCCCCChhHeecCCCCHHHHHHHHHHHHcCCCCCcEEEEC----------
Confidence            44589999988776666666899999999999875443444444343432 244555544 689999985          


Q ss_pred             HHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHh------hCCCC-CCcHHHHHHHHHHHH
Q 027801          152 YDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNR------AGGKS-GNKGAEAALTAIEMA  210 (218)
Q Consensus       152 ~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~R------ag~k~-gnKG~EAA~aAleM~  210 (218)
                      .|.++-.+.++|.+..++  +|==..|++.++.+.+..-      ..-.. ..-|..|+...++++
T Consensus       195 nd~~A~g~~~al~~~G~~--vP~di~vig~D~~~~~~~~~p~lttv~~~~~~~~g~~av~~L~~~i  258 (294)
T 3qk7_A          195 CNMLGDGVASALDKAGLL--GGEGISLIAYDGLPDDSLLDIAVTPIVQNTRTSVGKQIASMICDLL  258 (294)
T ss_dssp             SHHHHHHHHHHHHHTTCS--STTSCEEEEETCSCTTCSCCSCCEEEECCCHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCC--CCCceEEEeecCccHHhhcCCCceeEecCcHHHHHHHHHHHHHHHh
Confidence            367888888888887765  3422233344444332110      11112 234667776666655

>2x7x_A Sensor protein; transferase, sensor histidine kinase; HET: FRU; 2.64A {Bacteroides thetaiotaomicron}

Probab=92.04  E-value=1.2  Score=37.51  Aligned_cols=66  Identities=6%  Similarity=0.023  Sum_probs=44.0

Q ss_pred             CCCCEEEEEEcccCHHHHHHHHHHHHHHHHHC-CCCCCCeEEEEeCCcchHH-HHHHHhhhcCCccEEEEEee
Q 027801           73 NEGLRFALVVARFNELVTKLLLEGALETFKKY-SVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~-Gv~~e~I~vv~VPGA~ELP-~aak~L~~~~~yDaVIaLG~  143 (218)
                      .+..+||++... ....-..+++++.+.++++ |+.   +.+....+..+-- -.++.+. ..++||||..+.
T Consensus         4 ~~~~~Igvi~~~-~~~~~~~~~~gi~~~a~~~~g~~---l~i~~~~~~~~~~~~~i~~l~-~~~vdgiIi~~~   71 (325)
T 2x7x_A            4 TPHFRIGVAQCS-DDSWRHKMNDEILREAMFYNGVS---VEIRSAGDDNSKQAEDVHYFM-DEGVDLLIISAN   71 (325)
T ss_dssp             --CCEEEEEESC-CSHHHHHHHHHHHHHHTTSSSCE---EEEEECTTCHHHHHHHHHHHH-HTTCSEEEECCS
T ss_pred             CCCeEEEEEecC-CCHHHHHHHHHHHHHHHHcCCcE---EEEeCCCCCHHHHHHHHHHHH-HcCCCEEEEeCC
Confidence            455689999987 6666778999999999988 873   5554444333322 2345554 467999998764

>3e61_A Putative transcriptional repressor of ribose OPER; structural genomics, DNA-binding, transcripti regulation, PSI-2; 2.00A {Staphylococcus saprophyticus subsp}

Probab=91.92  E-value=0.84  Score=36.95  Aligned_cols=98  Identities=13%  Similarity=0.110  Sum_probs=67.3

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEeeeeeCCchhHH
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVVRGDTTHYD  153 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~VIrGeT~H~e  153 (218)
                      ...||+++....+......-.+|..+.|+++|+.   +.. .+++.+...-+.+.|.+..++|||+|.          .|
T Consensus       121 G~~~i~~i~~~~~~~~~~~R~~gf~~~l~~~~~~---~~~-~~~~~~~~~~~~~~l~~~~~~~ai~~~----------~d  186 (277)
T 3e61_A          121 KGKNVLIVHENLLIDAFHQRVQGIKYILDQQRID---YKM-LEATLLDNDKKFIDLIKELSIDSIICS----------ND  186 (277)
T ss_dssp             TCCSEEEEESCTTSHHHHHHHHHHHHHHHC---C---EEE-EEGGGGGSHHHHHHHHHHHTCCEEEES----------SH
T ss_pred             CCCeEEEEeCCCCCccHHHHHHHHHHHHHHcCCC---ccc-eecCCCCHHHHHHHhhcCCCCCEEEEC----------Cc
Confidence            3458999998877667777789999999999985   333 567777766666556556789999975          35


Q ss_pred             HHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHH
Q 027801          154 AVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQA  187 (218)
Q Consensus       154 ~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA  187 (218)
                      .++-.+.+.+.+..++  +|==..|++.++.+.+
T Consensus       187 ~~a~g~~~al~~~g~~--vP~di~vig~d~~~~~  218 (277)
T 3e61_A          187 LLAINVLGIVQRYHFK--VPAEIQIIGYDNIPFS  218 (277)
T ss_dssp             HHHHHHHHHHHHTTCC--TTTTCEEECSBCCGGG
T ss_pred             HHHHHHHHHHHHcCCC--CCCceEEEeeCCchHH
Confidence            6788888888887765  3422345566665543

>3dbi_A Sugar-binding transcriptional regulator, LACI FAM; structural genomics, sugar-binding transcriptional regulator structure initiative, PSI-2; HET: MSE; 2.45A {Escherichia coli K12}

Probab=91.75  E-value=0.63  Score=39.26  Aligned_cols=67  Identities=16%  Similarity=0.048  Sum_probs=48.8

Q ss_pred             CCCCEEEEEEcc--cCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHH-HHHHhhhcCCccEEEEEee
Q 027801           73 NEGLRFALVVAR--FNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV-VAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        73 ~~~~RIaIV~Sr--fn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~-aak~L~~~~~yDaVIaLG~  143 (218)
                      .+..+||+|...  +....-..+++++.+.++++|+.   +.++...+..+--. .++.+ ...++||||..+.
T Consensus        59 ~~~~~Igvi~~~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~l-~~~~vdgiIi~~~  128 (338)
T 3dbi_A           59 KSTQTLGLVVTNTLYHGIYFSELLFHAARMAEEKGRQ---LLLADGKHSAEEERQAIQYL-LDLRCDAIMIYPR  128 (338)
T ss_dssp             -CCSEEEEEECTTTTSTTHHHHHHHHHHHHHHHTTCE---EEEEECTTSHHHHHHHHHHH-HHTTCSEEEECCS
T ss_pred             CCCCEEEEEecCCcccChhHHHHHHHHHHHHHHCCCE---EEEEeCCCChHHHHHHHHHH-HhCCCCEEEEeCC
Confidence            456689999998  78888889999999999999973   55655444444333 33444 4568999998764

>3hcw_A Maltose operon transcriptional repressor; RNA-binding, PSI-2, NYSGXRC, STRU genomics, protein structure initiative; 2.20A {Staphylococcus aureus subsp}

Probab=91.64  E-value=1.5  Score=36.16  Aligned_cols=123  Identities=11%  Similarity=0.065  Sum_probs=75.5

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHHhhhc----CCccEEEEEeeeeeCC
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKS----GKYTAVLCIGAVVRGD  148 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~L~~~----~~yDaVIaLG~VIrGe  148 (218)
                      ...||+++....+......-++|..+.|+++|+.   ++++...-..|-- -+++.+++.    .++|||+|..      
T Consensus       130 G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~g~~---~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~ai~~~~------  200 (295)
T 3hcw_A          130 GVDELIFITEKGNFEVSKDRIQGFETVASQFNLD---YQIIETSNEREVILNYMQNLHTRLKDPNIKQAIISLD------  200 (295)
T ss_dssp             CCSEEEEEEESSCCHHHHHHHHHHHHHHHHTTCE---EEEEEECSCHHHHHHHHHHHHHHHTCTTSCEEEEESS------
T ss_pred             CCccEEEEcCCccchhHHHHHHHHHHHHHHcCCC---eeEEeccCCHHHHHHHHHHHHhhcccCCCCcEEEECC------
Confidence            3469999998877666677789999999999985   3343333333322 234555543    2799999743      


Q ss_pred             chhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHhh------CCCCCCcHHHHHHHHHHHHH
Q 027801          149 TTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRA------GGKSGNKGAEAALTAIEMAS  211 (218)
Q Consensus       149 T~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~Ra------g~k~gnKG~EAA~aAleM~~  211 (218)
                          |.++-.+.++|.+..++  +|==..|++.++.+.+..-.      .-....-|..|+...+++++
T Consensus       201 ----d~~A~g~~~al~~~g~~--vP~di~vig~D~~~~~~~~~p~lttv~~~~~~~g~~a~~~l~~~i~  263 (295)
T 3hcw_A          201 ----AMLHLAILSVLYELNIE--IPKDVMTATFNDSYLTEIASPPQTCIDIKPRMLGQQAGSAILNILK  263 (295)
T ss_dssp             ----HHHHHHHHHHHHHTTCC--TTTTEEEEEECCSHHHHTSSSCCEEEECCHHHHHHHHHHHHHHHHH
T ss_pred             ----hHHHHHHHHHHHHcCCC--CCCceEEEEeCChhHHhhCCCCeeEEEECHHHHHHHHHHHHHHHhc
Confidence                66888888888887664  45334555666655442211      01122345666666665543

>2fn9_A Ribose ABC transporter, periplasmic ribose-bindin; RBP, ribose binding protein, periplasmic binding protein, thermophilic proteins; 1.40A {Thermotoga maritima} PDB: 2fn8_A*

Probab=91.47  E-value=0.76  Score=37.50  Aligned_cols=64  Identities=13%  Similarity=0.100  Sum_probs=43.5

Q ss_pred             CEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHHhhhcCCccEEEEEee
Q 027801           76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        76 ~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~L~~~~~yDaVIaLG~  143 (218)
                      .+||+|...+....-..+++++.+.++++|+.   +.++...+..+-- -.++.+. ..++||+|..+.
T Consensus         3 ~~Ig~i~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~~~~l~-~~~vdgiI~~~~   67 (290)
T 2fn9_A            3 GKMAIVISTLNNPWFVVLAETAKQRAEQLGYE---ATIFDSQNDTAKESAHFDAII-AAGYDAIIFNPT   67 (290)
T ss_dssp             CEEEEEESCSSSHHHHHHHHHHHHHHHHTTCE---EEEEECTTCHHHHHHHHHHHH-HTTCSEEEECCS
T ss_pred             eEEEEEeCCCCChHHHHHHHHHHHHHHHcCCE---EEEeCCCCCHHHHHHHHHHHH-HcCCCEEEEecC
Confidence            47999998887778888999999999999873   4444333322221 2334444 467999988764

>2o20_A Catabolite control protein A; CCPA, transcriptional regulator, helix-turn-helix, transcrip; 1.90A {Lactococcus lactis}

Probab=91.40  E-value=0.79  Score=38.66  Aligned_cols=67  Identities=9%  Similarity=0.129  Sum_probs=47.5

Q ss_pred             CCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHHhhhcCCccEEEEEee
Q 027801           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~L~~~~~yDaVIaLG~  143 (218)
                      .+..+||++...+....-..+++++.+.++++|+.   +.+....+..+-- -.++.+. ..++||+|..+.
T Consensus        61 ~~~~~Ig~i~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~~~~l~-~~~vdgiI~~~~  128 (332)
T 2o20_A           61 KRTTTVGVILPTITSTYFAAITRGVDDIASMYKYN---MILANSDNDVEKEEKVLETFL-SKQVDGIVYMGS  128 (332)
T ss_dssp             -CCCEEEEEESCTTCHHHHHHHHHHHHHHHHTTCE---EEEEECTTCHHHHHHHHHHHH-HTTCSEEEECSS
T ss_pred             CCCCEEEEEeCCCCCcHHHHHHHHHHHHHHHcCCE---EEEEECCCChHHHHHHHHHHH-hCCCCEEEEeCC
Confidence            45568999999888888889999999999999973   5555443333221 2344443 578999998875

>3g85_A Transcriptional regulator (LACI family); transcription regulator, PSI-II, structural genomics structure initiative; 1.84A {Clostridium acetobutylicum atcc 824}

Probab=91.37  E-value=1.3  Score=36.00  Aligned_cols=103  Identities=17%  Similarity=0.130  Sum_probs=67.3

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHHhhhc-CCccEEEEEeeeeeCCchh
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKS-GKYTAVLCIGAVVRGDTTH  151 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~L~~~-~~yDaVIaLG~VIrGeT~H  151 (218)
                      ...||+++...-+......-.+|..+.|+++|+..+...++..+...|-. -+++++++. .++|||+|.          
T Consensus       126 G~~~i~~i~~~~~~~~~~~R~~gf~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~----------  195 (289)
T 3g85_A          126 RYKSAAAILTESLNDAMDNRNKGFIETCHKNGIKISENHIIAAENSIHGGVDAAKKLMKLKNTPKALFCN----------  195 (289)
T ss_dssp             TCCBCEEEECCCSSHHHHHHHHHHHHHHHHTTCBCCGGGEEECCSSHHHHHHHHHHHTTSSSCCSEEEES----------
T ss_pred             CCCEEEEEeCCcccccHHHHHHHHHHHHHHcCCCCChhheeccCCCHHHHHHHHHHHHcCCCCCcEEEEc----------
Confidence            44689999988776666677799999999999864443444433333322 234555544 579999985          


Q ss_pred             HHHHHHHHHHHHHHhchhcCCceEEEEcCCC--CHHHHH
Q 027801          152 YDAVANSAASGVLSAGVNSGVPCIFGVLTCD--NMDQAL  188 (218)
Q Consensus       152 ~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~--n~eQA~  188 (218)
                      .|.++-.+.+.+.+..++  +|==..|++.+  +.+.+.
T Consensus       196 ~d~~a~g~~~al~~~g~~--vP~di~vig~d~~~~~~~~  232 (289)
T 3g85_A          196 SDSIALGVISVLNKRQIS--IPDDIEIVAIGMNDREYTE  232 (289)
T ss_dssp             SHHHHHHHHHHHHHTTCC--TTTTCEEEEEECSCHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCC--CCCceEEEEeCCCCcchhh
Confidence            356888888888887765  44222344445  665543

>2ioy_A Periplasmic sugar-binding protein; ribose binding protein, thermophilic proteins; HET: RIP; 1.90A {Thermoanaerobacter tengcongensis}

Probab=91.33  E-value=1.1  Score=36.69  Aligned_cols=64  Identities=22%  Similarity=0.100  Sum_probs=44.0

Q ss_pred             CEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHHhhhcCCccEEEEEee
Q 027801           76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        76 ~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~L~~~~~yDaVIaLG~  143 (218)
                      .+||+|........-..+++++.++++++|+.   +.+....+..+-- -.++.+. ..++||+|..+.
T Consensus         2 ~~Igvi~~~~~~~f~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~i~~l~-~~~vdgiIi~~~   66 (283)
T 2ioy_A            2 KTIGLVISTLNNPFFVTLKNGAEEKAKELGYK---IIVEDSQNDSSKELSNVEDLI-QQKVDVLLINPV   66 (283)
T ss_dssp             CEEEEEESCSSSHHHHHHHHHHHHHHHHHTCE---EEEEECTTCHHHHHHHHHHHH-HTTCSEEEECCS
T ss_pred             eEEEEEecCCCCHHHHHHHHHHHHHHHhcCcE---EEEecCCCCHHHHHHHHHHHH-HcCCCEEEEeCC
Confidence            37999999888888889999999999999973   3333222222221 2244454 578999998653

>3e3m_A Transcriptional regulator, LACI family; structural genomics, DNA-binding, plasmid, transcription regulation, PSI-2; 1.60A {Silicibacter pomeroyi}

Probab=90.95  E-value=0.84  Score=38.97  Aligned_cols=67  Identities=9%  Similarity=0.034  Sum_probs=47.3

Q ss_pred             CCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHH-HHHHhhhcCCccEEEEEee
Q 027801           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV-VAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~-aak~L~~~~~yDaVIaLG~  143 (218)
                      .+...||+|...+....-..++++..+.++++|+.   +.+....+..+--. .++.+ ...++||+|..+.
T Consensus        68 ~~~~~Igvi~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~l-~~~~vdGiI~~~~  135 (355)
T 3e3m_A           68 KRSGFVGLLLPSLNNLHFAQTAQSLTDVLEQGGLQ---LLLGYTAYSPEREEQLVETM-LRRRPEAMVLSYD  135 (355)
T ss_dssp             ---CEEEEEESCSBCHHHHHHHHHHHHHHHHTTCE---EEEEECTTCHHHHHHHHHHH-HHTCCSEEEEECS
T ss_pred             CCCCEEEEEeCCCCchHHHHHHHHHHHHHHHCCCE---EEEEeCCCChHHHHHHHHHH-HhCCCCEEEEeCC
Confidence            34567999999988888889999999999999984   55555544444332 23333 4578999998764

>3rot_A ABC sugar transporter, periplasmic sugar binding; nysgrc, PSI-biology, structural genomics; 1.91A {Legionella pneumophila subsp}

Probab=90.86  E-value=2.9  Score=34.34  Aligned_cols=95  Identities=5%  Similarity=-0.005  Sum_probs=63.8

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH---HHHHHhh-hcCCccEEEEEeeeeeCCch
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLG-KSGKYTAVLCIGAVVRGDTT  150 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP---~aak~L~-~~~~yDaVIaLG~VIrGeT~  150 (218)
                      ..||+++...-.......-.+|..+.|+++|+.   +  ..+.+.+...   -+++.++ +..++|||+|..        
T Consensus       130 ~~~i~~i~g~~~~~~~~~R~~Gf~~~l~~~g~~---~--~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~--------  196 (297)
T 3rot_A          130 AKRALVLNPQPGHIGLEKRAYGIKTILQDKGIF---F--EELDVGTDPNQVQSRVKSYFKIHPETNIIFCLT--------  196 (297)
T ss_dssp             CCEEEEEESCTTCHHHHHHHHHHHHHHHHTTCE---E--EEEECCSCHHHHHHHHHHHHHHCTTCCEEEESS--------
T ss_pred             CceEEEEeCCCCcHHHHHHHHHHHHHHHhcCCe---E--EEeecCCChHHHHHHHHHHHHhCCCCCEEEEcC--------
Confidence            569999988776666667789999999999874   2  2333333322   2334433 456799999853        


Q ss_pred             hHHHHHHHHHHHHHHhchh---cCCceEEEEcCCCCHHHHH
Q 027801          151 HYDAVANSAASGVLSAGVN---SGVPCIFGVLTCDNMDQAL  188 (218)
Q Consensus       151 H~e~Va~~vs~gLm~lsL~---~~vPVifGVLT~~n~eQA~  188 (218)
                        |.++-.+.++|.+..+.   .++.|    ++.++...++
T Consensus       197 --d~~A~g~~~al~~~g~~vP~~dv~v----ig~D~~~~~~  231 (297)
T 3rot_A          197 --SQALDPLGQMLLHPDRYDFNYQPQV----YSFDKTPNTV  231 (297)
T ss_dssp             --HHHHHHHHHHHHSHHHHTCCCCCEE----EEECCCHHHH
T ss_pred             --CcchHHHHHHHHhcCCccCCCceEE----EEeCCCHHHH
Confidence              66888999999998886   45544    3446555543

>3tb6_A Arabinose metabolism transcriptional repressor; transcription regulation, arabinose binding, DNA binding Pro; HET: ARB; 2.21A {Bacillus subtilis}

Probab=90.85  E-value=1.7  Score=35.18  Aligned_cols=101  Identities=13%  Similarity=0.088  Sum_probs=64.6

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcch---HHHHHHHhhh-cCC--ccEEEEEeeeeeC
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE---IGVVAQQLGK-SGK--YTAVLCIGAVVRG  147 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~E---LP~aak~L~~-~~~--yDaVIaLG~VIrG  147 (218)
                      ...||+++...-+ .....-.+|..+.|+++|+......+++.+....   .--+++.+++ ..+  +|||+|..     
T Consensus       136 G~~~i~~i~~~~~-~~~~~R~~gf~~~l~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~ai~~~~-----  209 (298)
T 3tb6_A          136 GHTHMMGIFKADD-TQGVKRMNGFIQAHRERELFPSPDMIVTFTTEEKESKLLEKVKATLEKNSKHMPTAILCYN-----  209 (298)
T ss_dssp             TCCSEEEEEESSS-HHHHHHHHHHHHHHHHTTCCCCGGGEEEECHHHHTTHHHHHHHHHHHHTTTSCCSEEECSS-----
T ss_pred             CCCcEEEEcCCCC-ccHHHHHHHHHHHHHHcCCCCCcceEEEecccchhhhHHHHHHHHHhcCCCCCCeEEEEeC-----
Confidence            3458999987766 4455667999999999998755544555443322   1234455554 345  99999753     


Q ss_pred             CchhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHH
Q 027801          148 DTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQA  187 (218)
Q Consensus       148 eT~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA  187 (218)
                           |.++-.+.++|.+..++  +|==..|++.++.+.+
T Consensus       210 -----d~~a~g~~~al~~~g~~--vP~di~vvg~d~~~~~  242 (298)
T 3tb6_A          210 -----DEIALKVIDMLREMDLK--VPEDMSIVGYDDSHFA  242 (298)
T ss_dssp             -----HHHHHHHHHHHHHTTCC--TTTTCEEECSBCCTHH
T ss_pred             -----cHHHHHHHHHHHHcCCC--CCCceEEEecCCcHHH
Confidence                 56788888888887765  3422345555655443

>3bil_A Probable LACI-family transcriptional regulator; structural genomics, unknown function, PSI-2, protein structure initiative; 2.50A {Corynebacterium glutamicum atcc 13032}

Probab=90.83  E-value=0.69  Score=39.61  Aligned_cols=67  Identities=9%  Similarity=0.043  Sum_probs=46.0

Q ss_pred             CCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHHhhhcCCccEEEEEee
Q 027801           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~L~~~~~yDaVIaLG~  143 (218)
                      .+..+||+|...+....-..+++++.+.++++|+.   +.++...+..+-- -.++.+ ...++||+|..+.
T Consensus        64 ~~s~~Igvi~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~l-~~~~vdgiI~~~~  131 (348)
T 3bil_A           64 SRSNTIGVIVPSLINHYFAAMVTEIQSTASKAGLA---TIITNSNEDATTMSGSLEFL-TSHGVDGIICVPN  131 (348)
T ss_dssp             ----CEEEEESCSSSHHHHHHHHHHHHHHHHTTCC---EEEEECTTCHHHHHHHHHHH-HHTTCSCEEECCC
T ss_pred             CCCCEEEEEeCCCCCcHHHHHHHHHHHHHHHcCCE---EEEEeCCCCHHHHHHHHHHH-HhCCCCEEEEeCC
Confidence            34457999999888888889999999999999984   5555544433322 233444 3568999998764

>2fqx_A Membrane lipoprotein TMPC; ABC transport system, ligand-binding protein, guanosine, TP0319, transport protein; HET: GMP; 1.70A {Treponema pallidum} PDB: 2fqw_A* 2fqy_A*

Probab=90.80  E-value=0.97  Score=38.70  Aligned_cols=66  Identities=12%  Similarity=0.122  Sum_probs=43.6

Q ss_pred             CCCEEEEEEc--ccCH-HHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEee
Q 027801           74 EGLRFALVVA--RFNE-LVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        74 ~~~RIaIV~S--rfn~-~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~  143 (218)
                      +..+||+|..  ..++ .....+++|..+.++++|+.   +.++.....-+.--.++.|++ .++|+||+.|.
T Consensus         3 ~~~~Ig~v~~~g~~~d~~f~~~~~~Gi~~~~~~~g~~---~~~~~~~~~~~~~~~l~~l~~-~~~dgIi~~~~   71 (318)
T 2fqx_A            3 GDFVVGMVTDSGDIDDKSFNQQVWEGISRFAQENNAK---CKYVTASTDAEYVPSLSAFAD-ENMGLVVACGS   71 (318)
T ss_dssp             CCCEEEEEESSSCTTSSSHHHHHHHHHHHHHHHTTCE---EEEEECCSGGGHHHHHHHHHH-TTCSEEEEEST
T ss_pred             CCcEEEEEEcCCCCCCccHHHHHHHHHHHHHHHhCCe---EEEEeCCCHHHHHHHHHHHHH-cCCCEEEECCh
Confidence            4578999986  5555 57778888999999999873   444433222222234566654 56999998764

>3ctp_A Periplasmic binding protein/LACI transcriptional; structural genomics, protein structure initiative; HET: XLF; 1.41A {Alkaliphilus metalliredigens}

Probab=90.78  E-value=1.1  Score=37.74  Aligned_cols=66  Identities=11%  Similarity=0.039  Sum_probs=46.2

Q ss_pred             CCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHHhhhcCCccEEEEEee
Q 027801           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~L~~~~~yDaVIaLG~  143 (218)
                      .+..+||+|...+....-..+++++.+.++++|+.   +.++...+..+-- -.++.+. ..++|||| .+.
T Consensus        58 ~~~~~Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~~~~l~-~~~vdgiI-~~~  124 (330)
T 3ctp_A           58 KNSKTIGLMVPNISNPFFNQMASVIEEYAKNKGYT---LFLCNTDDDKEKEKTYLEVLQ-SHRVAGII-ASR  124 (330)
T ss_dssp             --CCEEEEEESCTTSHHHHHHHHHHHHHHHHTTCE---EEEEECTTCHHHHHHHHHHHH-HTTCSEEE-EET
T ss_pred             CCCCEEEEEeCCCCCcHHHHHHHHHHHHHHHCCCE---EEEEeCCCChHHHHHHHHHHH-hCCCCEEE-ECC
Confidence            45568999999887777889999999999999973   5555444333322 2334443 56899999 775

>3clk_A Transcription regulator; 11017J, PSI-II, NYSGXRC, dimer, structural genomics, protein structure initiative; 2.08A {Lactobacillus plantarum WCFS1}

Probab=90.72  E-value=0.39  Score=39.48  Aligned_cols=67  Identities=15%  Similarity=0.066  Sum_probs=42.8

Q ss_pred             CCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEE-EeCCcchH-HHHHHHhhhcCCccEEEEEee
Q 027801           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVV-WVPGSFEI-GVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv-~VPGA~EL-P~aak~L~~~~~yDaVIaLG~  143 (218)
                      .+..+||+|...+....-..+++++.+.++++|+.   +.+. ...+..+- --.++.+. ..++||+|..+.
T Consensus         6 ~~~~~Ig~i~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~~l~-~~~vdgiI~~~~   74 (290)
T 3clk_A            6 KSSNVIAAVVSSVRTNFAQQILDGIQEEAHKNGYN---LIIVYSGSADPEEQKHALLTAI-ERPVMGILLLSI   74 (290)
T ss_dssp             --CCEEEEECCCCSSSHHHHHHHHHHHHHHTTTCE---EEEEC----------CHHHHHH-SSCCSEEEEESC
T ss_pred             ccCCEEEEEeCCCCChHHHHHHHHHHHHHHHcCCe---EEEEeCCCCCHHHHHHHHHHHH-hcCCCEEEEecc
Confidence            45568999998888778889999999999999873   4333 22222221 11234443 568999998775

>3bbl_A Regulatory protein of LACI family; protein structure initiative II, PSI-II, NYSGXRC, transcript regulator, periplasmic binding protein; 2.35A {Chloroflexus aggregans}

Probab=90.68  E-value=2  Score=35.13  Aligned_cols=83  Identities=20%  Similarity=0.209  Sum_probs=55.9

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH---HHHHHhhh-c-C-CccEEEEEeeeeeCC
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGK-S-G-KYTAVLCIGAVVRGD  148 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP---~aak~L~~-~-~-~yDaVIaLG~VIrGe  148 (218)
                      ..||+++...-+......-.+|..+.|+++|+......++  +|.+...   -+++.+++ . . ++|||+|..      
T Consensus       125 ~~~I~~i~~~~~~~~~~~R~~Gf~~~l~~~g~~~~~~~~~--~~~~~~~~~~~~~~~~l~~~~~~~~~ai~~~~------  196 (287)
T 3bbl_A          125 HRRIAILAWPEDSRVGNDRLQGYLEAMQTAQLPIETGYIL--RGEGTFEVGRAMTLHLLDLSPERRPTAIMTLN------  196 (287)
T ss_dssp             CCCEEEEECCTTCHHHHHHHHHHHHHHHHTTCCCCGGGEE--ECCSSHHHHHHHHHHHHTSCTTTSCSEEEESS------
T ss_pred             CCeEEEEeCCcccccHHHHHHHHHHHHHHcCCCCChhhEE--eCCCCHHHHHHHHHHHHhhCCCCCCcEEEECC------
Confidence            4589999877555555666799999999999763322233  3444432   23455655 4 4 799999853      


Q ss_pred             chhHHHHHHHHHHHHHHhchh
Q 027801          149 TTHYDAVANSAASGVLSAGVN  169 (218)
Q Consensus       149 T~H~e~Va~~vs~gLm~lsL~  169 (218)
                          |.++-.+.+++.+..++
T Consensus       197 ----d~~a~g~~~al~~~G~~  213 (287)
T 3bbl_A          197 ----DTMAIGAMAAARERGLT  213 (287)
T ss_dssp             ----HHHHHHHHHHHHHTTCC
T ss_pred             ----cHHHHHHHHHHHHcCCC
Confidence                56778888888887764

>3kjx_A Transcriptional regulator, LACI family; LACL family, protein structure initiative II(PSI II), NYSGXRC, structural genomics; 2.33A {Silicibacter pomeroyi}

Probab=90.56  E-value=0.73  Score=39.09  Aligned_cols=67  Identities=16%  Similarity=0.096  Sum_probs=47.8

Q ss_pred             CCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHH-HHHHhhhcCCccEEEEEee
Q 027801           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV-VAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~-aak~L~~~~~yDaVIaLG~  143 (218)
                      .+..+||+|...+....-..+++++.+.++++|+.   +.+....+..+--. .++.+ ...++||||..+.
T Consensus        66 ~~~~~Ig~i~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~i~~l-~~~~vdGiIi~~~  133 (344)
T 3kjx_A           66 NRVNLVAVIIPSLSNMVFPEVLTGINQVLEDTELQ---PVVGVTDYLPEKEEKVLYEM-LSWRPSGVIIAGL  133 (344)
T ss_dssp             SCCSEEEEEESCSSSSSHHHHHHHHHHHHTSSSSE---EEEEECTTCHHHHHHHHHHH-HTTCCSEEEEECS
T ss_pred             CCCCEEEEEeCCCCcHHHHHHHHHHHHHHHHCCCE---EEEEeCCCCHHHHHHHHHHH-HhCCCCEEEEECC
Confidence            44568999998887777788999999999999974   55554444444322 23333 4578999998764

>3d8u_A PURR transcriptional regulator; APC91343.1, vibrio parahaem RIMD 2210633, structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.88A {Vibrio parahaemolyticus}

Probab=90.52  E-value=2.1  Score=34.39  Aligned_cols=99  Identities=12%  Similarity=0.074  Sum_probs=63.6

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHH---HHHHhhhc-CCccEEEEEeeeeeCCch
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGKS-GKYTAVLCIGAVVRGDTT  150 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~---aak~L~~~-~~yDaVIaLG~VIrGeT~  150 (218)
                      ..||+++....+......-.+|..+.|+++|+..+..  +..++.+...-   +++.+++. .++|||+|.         
T Consensus       120 ~~~i~~i~~~~~~~~~~~R~~gf~~~l~~~g~~~~~~--~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~---------  188 (275)
T 3d8u_A          120 FKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTPDHF--LTTHEAPSSQLGAEGLAKLLLRDSSLNALVCS---------  188 (275)
T ss_dssp             CCCEEEEECSCSSHHHHHHHHHHHHHHHHTTCCCCCE--EECSSCCCHHHHHHHHHHHHTTCTTCCEEEES---------
T ss_pred             CCeEEEEcCCCCCchHHHHHHHHHHHHHHcCCCCCcc--EEEeCCCChhHHHHHHHHHHhCCCCCCEEEEc---------
Confidence            4689999987665555666799999999999863322  22356555432   23445544 579999874         


Q ss_pred             hHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHH
Q 027801          151 HYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQA  187 (218)
Q Consensus       151 H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA  187 (218)
                       .|.++..+.+++.+..++  +|==..|++.++.+.+
T Consensus       189 -~d~~a~g~~~al~~~g~~--vP~di~vvg~d~~~~~  222 (275)
T 3d8u_A          189 -HEEIAIGALFECHRRVLK--VPTDIAIICLEGSSMG  222 (275)
T ss_dssp             -SHHHHHHHHHHHHHTTCC--TTTTCEEEESSCCHHH
T ss_pred             -CcHHHHHHHHHHHHcCCC--CCCceEEEecCCchHh
Confidence             345777888888877654  4411235556665554

>3egc_A Putative ribose operon repressor; structural genomics, unknown function, DNA-binding, transcri transcription regulation, PSI-2; 2.35A {Burkholderia thailandensis}

Probab=90.49  E-value=1.6  Score=35.63  Aligned_cols=99  Identities=13%  Similarity=0.114  Sum_probs=61.9

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH---HHHHHhh-hcCCccEEEEEeeeeeCCc
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLG-KSGKYTAVLCIGAVVRGDT  149 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP---~aak~L~-~~~~yDaVIaLG~VIrGeT  149 (218)
                      ...||+++....+......-.+|..+.|+++|+..+...++  ++.++..   -+++.++ +..++|||+|..       
T Consensus       124 G~~~i~~i~~~~~~~~~~~R~~gf~~~l~~~g~~~~~~~~~--~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~-------  194 (291)
T 3egc_A          124 GHTRIGAIVGSAGLMTSRERLKGFRAAMSAAGLPVRQEWIA--AGGVRADNGRDGAIKVLTGADRPTALLTSS-------  194 (291)
T ss_dssp             TCCSEEEECSCTTSHHHHHHHHHHHHHHHHTTCCCCGGGEE--C------CCHHHHHHHHTC-CCCSEEEESS-------
T ss_pred             CCCEEEEEeCCCCCcCHHHHHHHHHHHHHHcCCCCCHHHeE--eCCCChhHHHHHHHHHHhCCCCCcEEEECC-------
Confidence            45689999988776677778899999999999864322222  3433321   2345555 456899999754       


Q ss_pred             hhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHH
Q 027801          150 THYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQ  186 (218)
Q Consensus       150 ~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQ  186 (218)
                         |.++-.+.++|.+..++  +|==..|++.++.+.
T Consensus       195 ---d~~a~g~~~al~~~g~~--vP~di~vvg~d~~~~  226 (291)
T 3egc_A          195 ---HRITEGAMQALNVLGLR--YGPDVEIVSFDNLPW  226 (291)
T ss_dssp             ---HHHHHHHHHHHHHHTCC--BTTTBEEEEESCCGG
T ss_pred             ---cHHHHHHHHHHHHcCCC--CCCceEEEEecCchh
Confidence               56788888888888775  332123344455443

>2rgy_A Transcriptional regulator, LACI family; 11011J, NYSGXRC, transctiptional regulator, SUG binding protein, structural genomics, PSI-2; 2.05A {Burkholderia phymatum}

Probab=90.45  E-value=1.8  Score=35.44  Aligned_cols=83  Identities=17%  Similarity=0.315  Sum_probs=55.8

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHH---HHHHhhh-cCCccEEEEEeeeeeCCch
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGK-SGKYTAVLCIGAVVRGDTT  150 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~---aak~L~~-~~~yDaVIaLG~VIrGeT~  150 (218)
                      ..||+++...-.......-++|..+.|+++|++.+...++  +|.+...-   +++.+++ ..++|||+|.         
T Consensus       128 ~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~g~~~~~~~~~--~~~~~~~~~~~~~~~~l~~~~~~~ai~~~---------  196 (290)
T 2rgy_A          128 HRKLAVISGPFTASDNVERLDGFFDELARHGIARDSVPLI--ESDFSPEGGYAATCQLLESKAPFTGLFCA---------  196 (290)
T ss_dssp             CCSEEEEESCTTCHHHHHHHHHHHHHHHTTTCCGGGSCEE--ECCSSHHHHHHHHHHHHHHTCCCSEEEES---------
T ss_pred             CceEEEEeCCCCCccHHHHHHHHHHHHHHcCCCCCcccEE--ecCCChhHHHHHHHHHHhCCCCCcEEEEC---------
Confidence            4689999887554445566799999999999753322233  35454332   3345554 3579999974         


Q ss_pred             hHHHHHHHHHHHHHHhchh
Q 027801          151 HYDAVANSAASGVLSAGVN  169 (218)
Q Consensus       151 H~e~Va~~vs~gLm~lsL~  169 (218)
                       .|.++-.+.+++.+..++
T Consensus       197 -~d~~A~g~~~al~~~G~~  214 (290)
T 2rgy_A          197 -NDTMAVSALARFQQLGIS  214 (290)
T ss_dssp             -SHHHHHHHHHHHHHTTCC
T ss_pred             -CcHHHHHHHHHHHHcCCC
Confidence             356788888888887765

>2qu7_A Putative transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 2.30A {Staphylococcus saprophyticus subsp}

Probab=90.43  E-value=2.3  Score=34.63  Aligned_cols=84  Identities=10%  Similarity=0.047  Sum_probs=55.6

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcc----hHH---HHHHHhhhcCCccEEEEEeeeeeC
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSF----EIG---VVAQQLGKSGKYTAVLCIGAVVRG  147 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~----ELP---~aak~L~~~~~yDaVIaLG~VIrG  147 (218)
                      ..||+++...-+......-.+|..+.|+++|+......++..+|.|    ...   -+++.+++. ++|||+|..     
T Consensus       122 ~~~I~~i~~~~~~~~~~~R~~gf~~~l~~~g~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~l~~-~~~ai~~~~-----  195 (288)
T 2qu7_A          122 CKEVGLLLANPNISTTIGRKNGYNKAISEFDLNVNPSLIHYSDQQLGTNAQIYSGYEATKTLLSK-GIKGIVATN-----  195 (288)
T ss_dssp             CCCEEEEECCTTSHHHHHHHHHHHHHHHHTTCCCCGGGEEECCSSCSHHHHHHHHHHHHHHHHHT-TCCEEEECS-----
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHHHHHHHcCCCCCcceEEeccCCccccCCHHHHHHHHHHHHhc-CCCEEEECC-----
Confidence            4689999887655555666799999999999753221122115666    332   234555555 899999842     


Q ss_pred             CchhHHHHHHHHHHHHHHhchh
Q 027801          148 DTTHYDAVANSAASGVLSAGVN  169 (218)
Q Consensus       148 eT~H~e~Va~~vs~gLm~lsL~  169 (218)
                           |.++-.+.+.+.+..++
T Consensus       196 -----d~~a~g~~~al~~~g~~  212 (288)
T 2qu7_A          196 -----HLLLLGALQAIKESEKE  212 (288)
T ss_dssp             -----HHHHHHHHHHHHHSSCC
T ss_pred             -----cHHHHHHHHHHHHhCCC
Confidence                 45777788888876664

>3d02_A Putative LACI-type transcriptional regulator; periplasmic sugar-binding protein, structura genomics; HET: MSE GOL; 1.30A {Klebsiella pneumoniae subsp}

Probab=90.39  E-value=1.4  Score=35.99  Aligned_cols=64  Identities=13%  Similarity=0.064  Sum_probs=44.3

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEE-eCCcchHH---HHHHHhhhcCCccEEEEEee
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVW-VPGSFEIG---VVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~-VPGA~ELP---~aak~L~~~~~yDaVIaLG~  143 (218)
                      +..+||++........-..+++++.+.++++|+     ++.. .+...+..   -.++.+. ..++||||..+.
T Consensus         3 ~~~~Ig~i~~~~~~~~~~~~~~g~~~~~~~~g~-----~~~~~~~~~~~~~~~~~~~~~l~-~~~vdgiii~~~   70 (303)
T 3d02_A            3 AEKTVVNISKVDGMPWFNRMGEGVVQAGKEFNL-----NASQVGPSSTDAPQQVKIIEDLI-ARKVDAITIVPN   70 (303)
T ss_dssp             -CEEEEEECSCSSCHHHHHHHHHHHHHHHHTTE-----EEEEECCSSSCHHHHHHHHHHHH-HTTCSEEEECCS
T ss_pred             CceEEEEEeccCCChHHHHHHHHHHHHHHHcCC-----EEEEECCCCCCHHHHHHHHHHHH-HcCCCEEEEecC
Confidence            456899999888878888999999999999985     3432 33333322   2334454 467999988764

>2rjo_A Twin-arginine translocation pathway signal protei; PSI-2, NYSGXRC, twin arginine translocation pathway signal P structural genomics; HET: GAL; 2.05A {Burkholderia phytofirmans}

Probab=90.03  E-value=0.95  Score=38.05  Aligned_cols=68  Identities=13%  Similarity=-0.033  Sum_probs=47.5

Q ss_pred             CCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHHhhhcC-CccEEEEEee
Q 027801           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSG-KYTAVLCIGA  143 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~L~~~~-~yDaVIaLG~  143 (218)
                      ++..+||+|...+....-..+++++.+.++++|+.   +.++...+..+-- -.++.+...+ ++||||..+.
T Consensus         3 ~~s~~Igvi~~~~~~~~~~~~~~gi~~~a~~~g~~---l~~~~~~~~~~~~~~~i~~l~~~~~~vdgiIi~~~   72 (332)
T 2rjo_A            3 LGQTTLACSFRSLTNPYYTAFNKGAQSFAKSVGLP---YVPLTTEGSSEKGIADIRALLQKTGGNLVLNVDPN   72 (332)
T ss_dssp             CCCCEEEEEESCTTSHHHHHHHHHHHHHHHHHTCC---EEEEECTTCHHHHHHHHHHHHHHTTTCEEEEECCS
T ss_pred             CCccEEEEEecCCCcHHHHHHHHHHHHHHHHcCCE---EEEecCCCCHHHHHHHHHHHHHCCCCCCEEEEeCC
Confidence            45578999999888888889999999999999984   5555443333322 2345554433 2999998764

>2vk2_A YTFQ, ABC transporter periplasmic-binding protein YTFQ; transport protein, galactofuranose; HET: GZL; 1.20A {Escherichia coli}

Probab=89.95  E-value=0.81  Score=37.94  Aligned_cols=65  Identities=8%  Similarity=-0.099  Sum_probs=44.8

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchH-HHHHHHhhhcCCccEEEEEee
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEI-GVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~EL-P~aak~L~~~~~yDaVIaLG~  143 (218)
                      ..+||++...........+++++.+.++++|+.   +.+....+..+- --.++.+. ..++||||..+.
T Consensus         2 ~~~Ig~i~~~~~~~~~~~~~~gi~~~a~~~g~~---l~~~~~~~~~~~~~~~i~~l~-~~~vdgiIi~~~   67 (306)
T 2vk2_A            2 PLTVGFSQVGSESGWRAAETNVAKSEAEKRGIT---LKIADGQQKQENQIKAVRSFV-AQGVDAIFIAPV   67 (306)
T ss_dssp             CCEEEEEECCCCSHHHHHHHHHHHHHHHHHTCE---EEEEECTTCHHHHHHHHHHHH-HHTCSEEEECCS
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHHHHcCCE---EEEeCCCCCHHHHHHHHHHHH-HcCCCEEEEeCC
Confidence            368999999888888888999999999999973   444433332221 12334444 457999998764

>2qu7_A Putative transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 2.30A {Staphylococcus saprophyticus subsp}

Probab=89.88  E-value=0.68  Score=37.83  Aligned_cols=66  Identities=11%  Similarity=0.078  Sum_probs=44.3

Q ss_pred             CCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHHhhhcCCccEEEEEee
Q 027801           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~L~~~~~yDaVIaLG~  143 (218)
                      .+..+||++... ....-..+++++.+.++++|+.   +.++...+..+-- -.++.+. ..++||||..+.
T Consensus         6 ~~~~~Igvi~~~-~~~~~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~~~~l~-~~~vdgiI~~~~   72 (288)
T 2qu7_A            6 GRSNIIAFIVPD-QNPFFTEVLTEISHECQKHHLH---VAVASSEENEDKQQDLIETFV-SQNVSAIILVPV   72 (288)
T ss_dssp             -CEEEEEEEESS-CCHHHHHHHHHHHHHHGGGTCE---EEEEECTTCHHHHHHHHHHHH-HTTEEEEEECCS
T ss_pred             CCCCEEEEEECC-CCchHHHHHHHHHHHHHHCCCE---EEEEeCCCCHHHHHHHHHHHH-HcCccEEEEecC
Confidence            345689999988 7677788999999999999873   4444333322221 2344443 567999998765

>3kke_A LACI family transcriptional regulator; structural genomics, DNA-binding, transcription regulation, PSI-2; 2.20A {Mycobacterium smegmatis str}

Probab=89.81  E-value=2.5  Score=34.95  Aligned_cols=102  Identities=22%  Similarity=0.121  Sum_probs=66.5

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHHh-----hh-cCCccEEEEEeeeee
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQL-----GK-SGKYTAVLCIGAVVR  146 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~L-----~~-~~~yDaVIaLG~VIr  146 (218)
                      ...||+++....+......-++|..+.|+++|+..+...++......|-- -+++.+     ++ ..++|||+|.     
T Consensus       130 G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~g~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~ai~~~-----  204 (303)
T 3kke_A          130 GHSRIAFISGTAIHDTAQRRKEGYLETLASAGLRSEAAWVVDAGWEADAGSAALNTLYRGANLGKPDGPTAVVVA-----  204 (303)
T ss_dssp             TCCSEEEEESCSSCHHHHHHHHHHHHHHHHTTCCCCGGGEEECCSSHHHHHHHHHHHHHHHCTTSTTSCSEEEES-----
T ss_pred             CCCeEEEEeCCCcCccHHHHHHHHHHHHHHcCCCCCcceEEecCCChHHHHHHHHHhcchhhhcCCCCCcEEEEC-----
Confidence            34589999988776667777899999999999864433344333333322 234555     54 4579999985     


Q ss_pred             CCchhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHH
Q 027801          147 GDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQA  187 (218)
Q Consensus       147 GeT~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA  187 (218)
                           .|.++-.+.++|.+..++  +|==..|++.++.+.+
T Consensus       205 -----nd~~A~g~~~al~~~G~~--vP~di~vig~D~~~~~  238 (303)
T 3kke_A          205 -----SVNAAVGALSTALRLGLR--VPEDLSIVGINTTWVS  238 (303)
T ss_dssp             -----SHHHHHHHHHHHHHTTCC--TTTTCEEEEESCCHHH
T ss_pred             -----CHHHHHHHHHHHHHcCCC--CCCceEEEEEcChhHh
Confidence                 356888888888887765  4422334455655543

>1qpz_A PURA, protein (purine nucleotide synthesis repressor); transcription regulation, DNA-binding, purine biosynthesis; HET: DNA HPA; 2.50A {Escherichia coli} SCOP: a.35.1.5 c.93.1.1 PDB: 1bdi_A* 1qp0_A* 1qp4_A* 1pnr_A* 1wet_A* 1zay_A* 1vpw_A* 2pue_A* 2puf_A* 2pug_A* 1bdh_A* 1qp7_A* 1qqa_A* 1qqb_A* 2puc_A* 2pua_A* 2pub_A* 2pud_A* 1jfs_A* 1jh9_A* ...

Probab=89.71  E-value=1.5  Score=37.10  Aligned_cols=67  Identities=7%  Similarity=0.023  Sum_probs=46.7

Q ss_pred             CCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHHhhhcCCccEEEEEee
Q 027801           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~L~~~~~yDaVIaLG~  143 (218)
                      .+..+||++...+....-..+++++.+.++++|+.   +.+....+..+-- -.++.|. ..++||+|..+.
T Consensus        56 ~~~~~Igvi~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~l~-~~~vdgiI~~~~  123 (340)
T 1qpz_A           56 NHTKSIGLLATSSEAAYFAEIIEAVEKNCFQKGYT---LILGNAWNNLEKQRAYLSMMA-QKRVDGLLVMCS  123 (340)
T ss_dssp             TCCSEEEEEESCSCSHHHHHHHHHHHHHHHHTTCE---EEEEECTTCHHHHHHHHHHHH-HTTCSEEEECCS
T ss_pred             CCCCEEEEEeCCCCChHHHHHHHHHHHHHHHcCCE---EEEEeCCCCHHHHHHHHHHHH-cCCCCEEEEeCC
Confidence            35568999999888888889999999999999973   4444333322221 1234443 568999998765

>2fvy_A D-galactose-binding periplasmic protein; periplasmic binding protien, hinge, chemotaxis, transport,; HET: BGC; 0.92A {Escherichia coli} SCOP: c.93.1.1 PDB: 1glg_A* 2fw0_A* 2gbp_A* 2qw1_A* 2hph_A* 2ipn_A* 2ipm_A* 2ipl_A* 1gca_A* 1gcg_A 3ga5_A* 3gbp_A*

Probab=89.66  E-value=3  Score=34.01  Aligned_cols=96  Identities=16%  Similarity=0.205  Sum_probs=63.1

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEE-EeCCcchHH---HHHHHhhhc-C--CccEEEEEeeeeeC
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVV-WVPGSFEIG---VVAQQLGKS-G--KYTAVLCIGAVVRG  147 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv-~VPGA~ELP---~aak~L~~~-~--~yDaVIaLG~VIrG  147 (218)
                      ..||+++...-.......-.+|..+.|+++|..   ++.. .+.|.+...   -+++.+++. .  ++|||+|.      
T Consensus       140 ~~~i~~i~~~~~~~~~~~R~~gf~~~l~~~g~~---~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~ai~~~------  210 (309)
T 2fvy_A          140 QIQFVLLKGEPGHPDAEARTTYVIKELNDKGIK---TEQLQLDTAMWDTAQAKDKMDAWLSGPNANKIEVVIAN------  210 (309)
T ss_dssp             SEEEEEEECSTTCHHHHHHHHHHHHHHHHTTCC---EEEEEEEECTTCHHHHHHHHHHHHTSTTGGGCCEEEES------
T ss_pred             ceEEEEEEcCCCCccHHHHHHHHHHHHHhcCCc---eEEEEEecCCCCHHHHHHHHHHHHHhCCCCCccEEEEC------
Confidence            347999987655555667789999999999975   3322 234555433   234556655 2  79999974      


Q ss_pred             CchhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHH
Q 027801          148 DTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQAL  188 (218)
Q Consensus       148 eT~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~  188 (218)
                          .|.++..+.+++.+.. +.+++    |++.++...+.
T Consensus       211 ----~d~~a~g~~~al~~~g-~~di~----vig~d~~~~~~  242 (309)
T 2fvy_A          211 ----NDAMAMGAVEALKAHN-KSSIP----VFGVDALPEAL  242 (309)
T ss_dssp             ----SHHHHHHHHHHHHHTT-CTTSC----EECSBCCHHHH
T ss_pred             ----CchhHHHHHHHHHHcC-CCCce----EEecCCCHHHH
Confidence                3567778888888877 22566    44566655554

>2fvy_A D-galactose-binding periplasmic protein; periplasmic binding protien, hinge, chemotaxis, transport,; HET: BGC; 0.92A {Escherichia coli} SCOP: c.93.1.1 PDB: 1glg_A* 2fw0_A* 2gbp_A* 2qw1_A* 2hph_A* 2ipn_A* 2ipm_A* 2ipl_A* 1gca_A* 1gcg_A 3ga5_A* 3gbp_A*

Probab=89.55  E-value=1.1  Score=36.58  Aligned_cols=64  Identities=6%  Similarity=-0.054  Sum_probs=42.6

Q ss_pred             CEEEEEEcccCHHHHHHHHHHHHHHHHHCCC-CCCCeEEEEeCCcchHH-HHHHHhhhcCCccEEEEEee
Q 027801           76 LRFALVVARFNELVTKLLLEGALETFKKYSV-KEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        76 ~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv-~~e~I~vv~VPGA~ELP-~aak~L~~~~~yDaVIaLG~  143 (218)
                      .+||+|...+.......+++++.+.++++|. .   +.++...+..+-- -.++.+. ..++||||..+.
T Consensus         3 ~~Igvi~~~~~~~~~~~~~~gi~~~a~~~g~~~---~~~~~~~~~~~~~~~~~~~~~-~~~vdgiii~~~   68 (309)
T 2fvy_A            3 TRIGVTIYKYDDNFMSVVRKAIEQDAKAAPDVQ---LLMNDSQNDQSKQNDQIDVLL-AKGVKALAINLV   68 (309)
T ss_dssp             EEEEEEESCTTSHHHHHHHHHHHHHHHTCTTEE---EEEEECTTCHHHHHHHHHHHH-HTTCSEEEECCS
T ss_pred             cEEEEEeccCCcHHHHHHHHHHHHHHHhcCCeE---EEEecCCCCHHHHHHHHHHHH-HcCCCEEEEeCC
Confidence            4789999888888888899999999999885 3   3333333322211 1234443 567999988654

>3gbv_A Putative LACI-family transcriptional regulator; NYSGXRC, PSI-II, 11231J, structur genomics, protein structure initiative; 2.20A {Bacteroides fragilis}

Probab=89.49  E-value=1.9  Score=34.97  Aligned_cols=88  Identities=2%  Similarity=-0.127  Sum_probs=55.2

Q ss_pred             CCCEEEEEEc----ccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcch-HHHHHHHhhhc-CCccEEEEEeeeeeC
Q 027801           74 EGLRFALVVA----RFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE-IGVVAQQLGKS-GKYTAVLCIGAVVRG  147 (218)
Q Consensus        74 ~~~RIaIV~S----rfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~E-LP~aak~L~~~-~~yDaVIaLG~VIrG  147 (218)
                      ...||+++..    .-.......-.+|..+.|+++|...+...++.-....| ---+++.+++. .++|||+|..     
T Consensus       134 ~~~~i~~i~~~~~g~~~~~~~~~R~~gf~~~l~~~g~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~-----  208 (304)
T 3gbv_A          134 NDREIVIFRKIHEGVIGSNQQESREIGFRQYMQEHHPACNILELNLHADLNIEDSRMLDDFFREHPDVKHGITFN-----  208 (304)
T ss_dssp             TCSEEEEEEEEBTTBCCCHHHHHHHHHHHHHHHHHCTTSEEEEEEEESSCSSCHHHHHHHHHHHCTTCCEEEESS-----
T ss_pred             CCCeEEEEEecccCCccchhHHHHHHHHHHHHHhhCCCcEEEEeeecCCCHHHHHHHHHHHHHhCCCeEEEEEcC-----
Confidence            3479999984    33445556677999999999998643333333333333 33344555544 5799999853     


Q ss_pred             CchhHHHHHHHHHHHHHHhchhcCCc
Q 027801          148 DTTHYDAVANSAASGVLSAGVNSGVP  173 (218)
Q Consensus       148 eT~H~e~Va~~vs~gLm~lsL~~~vP  173 (218)
                           |. +-.+.+++.+..+ .++.
T Consensus       209 -----d~-a~g~~~al~~~g~-~di~  227 (304)
T 3gbv_A          209 -----SK-VYIIGEYLQQRRK-SDFS  227 (304)
T ss_dssp             -----SC-THHHHHHHHHTTC-CSCE
T ss_pred             -----cc-hHHHHHHHHHcCC-CCcE
Confidence                 22 4457777888777 4544

>3huu_A Transcription regulator like protein; PSI-II, NYSGXRC, LAC I, STR genomics, protein structure initiative; 1.95A {Staphylococcus haemolyticus}

Probab=89.49  E-value=1.6  Score=36.07  Aligned_cols=98  Identities=9%  Similarity=-0.073  Sum_probs=62.9

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchH-HHHHHHh-hh-cCCccEEEEEeeeeeCCch
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEI-GVVAQQL-GK-SGKYTAVLCIGAVVRGDTT  150 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~EL-P~aak~L-~~-~~~yDaVIaLG~VIrGeT~  150 (218)
                      ...||+++....+......-.+|..+.|+++|+....    .+.|.+.- --+++.+ ++ ..++|||+|.         
T Consensus       143 G~~~I~~i~~~~~~~~~~~R~~Gf~~~l~~~g~~~~~----~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~---------  209 (305)
T 3huu_A          143 GHRHILFLQESGHYAVTEDRSVGFKQYCDDVKISNDC----VVIKSMNDLRDFIKQYCIDASHMPSVIITS---------  209 (305)
T ss_dssp             TCCSEEEEEESSCBHHHHHHHHHHHHHHHHTTCCCCE----EEECSHHHHHHHC--------CCCSEEEES---------
T ss_pred             CCCeEEEEcCCcccchhHHHHHHHHHHHHHcCCCccc----EEecCcHHHHHHHHHhhhcCCCCCCEEEEC---------
Confidence            3468999998877766667789999999999986432    34555553 1123344 43 4689999983         


Q ss_pred             hHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHH
Q 027801          151 HYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQA  187 (218)
Q Consensus       151 H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA  187 (218)
                       .|.++-.+.+++.+..++  +|==..|++.++.+.+
T Consensus       210 -nd~~A~g~~~al~~~g~~--vP~di~vig~D~~~~~  243 (305)
T 3huu_A          210 -DVMLNMQLLNVLYEYQLR--IPEDIQTATFNTSFLT  243 (305)
T ss_dssp             -SHHHHHHHHHHHHHTTCC--TTTTCEEEEESCSHHH
T ss_pred             -ChHHHHHHHHHHHHcCCC--CCcceEEEEECCcchh
Confidence             467888888888888775  3422234455665543

>3dbi_A Sugar-binding transcriptional regulator, LACI FAM; structural genomics, sugar-binding transcriptional regulator structure initiative, PSI-2; HET: MSE; 2.45A {Escherichia coli K12}

Probab=89.37  E-value=2.3  Score=35.81  Aligned_cols=84  Identities=14%  Similarity=0.194  Sum_probs=59.5

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH---HHHHHhh-hcCCccEEEEEeeeeeCCc
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLG-KSGKYTAVLCIGAVVRGDT  149 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP---~aak~L~-~~~~yDaVIaLG~VIrGeT  149 (218)
                      ...||+++....+......-++|..+.|+++|+..+...+  ++|.|...   -+++.++ +..++|||+|..       
T Consensus       180 G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~g~~~~~~~~--~~~~~~~~~~~~~~~~ll~~~~~~~ai~~~n-------  250 (338)
T 3dbi_A          180 GHQEIAFLTGSMDSPTSIERLAGYKDALAQHGIALNEKLI--ANGKWTPASGAEGVEMLLERGAKFSALVASN-------  250 (338)
T ss_dssp             TCCSEEEECCCTTCHHHHHHHHHHHHHHHHTTCCCCGGGE--ECCCSSHHHHHHHHHHHHHTTCCCSEEEESS-------
T ss_pred             CCCEEEEEeCCCCCccHHHHHHHHHHHHHHCCCCCCcceE--EeCCCCHHHHHHHHHHHHcCCCCCeEEEECC-------
Confidence            4468999988766666667789999999999986433333  35555443   2344455 446799999732       


Q ss_pred             hhHHHHHHHHHHHHHHhchh
Q 027801          150 THYDAVANSAASGVLSAGVN  169 (218)
Q Consensus       150 ~H~e~Va~~vs~gLm~lsL~  169 (218)
                         |.++-.+.++|.+..++
T Consensus       251 ---d~~A~g~~~al~~~G~~  267 (338)
T 3dbi_A          251 ---DDMAIGAMKALHERGVA  267 (338)
T ss_dssp             ---HHHHHHHHHHHHHTTCC
T ss_pred             ---hHHHHHHHHHHHHcCCC
Confidence               56888888999888775

>3miz_A Putative transcriptional regulator protein, LACI family; LACL family, protein structure initiative II (PSI II), NYSGXRC, structural genomics; 1.91A {Rhizobium etli}

Probab=89.25  E-value=1.3  Score=36.58  Aligned_cols=100  Identities=17%  Similarity=0.187  Sum_probs=66.4

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEe---CCcchH---HHHHHHhhhc-CCccEEEEEeeeee
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWV---PGSFEI---GVVAQQLGKS-GKYTAVLCIGAVVR  146 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~V---PGA~EL---P~aak~L~~~-~~yDaVIaLG~VIr  146 (218)
                      ...||+++....+......-++|..+.|+++|+..+...++..   +-..|-   .-+++.+++. .++|||+|.     
T Consensus       130 G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~-----  204 (301)
T 3miz_A          130 GHRRIGYIRLNPILLGAELRLDAFRRTTSEFGLTENDLSISLGMDGPVGAENNYVFAAATEMLKQDDRPTAIMSG-----  204 (301)
T ss_dssp             TCCSEEEEECCTTSHHHHHHHHHHHHHHHHHTCCGGGEEEEECEESSTTSCEECHHHHHHHHHTSTTCCSEEEES-----
T ss_pred             CCCeEEEEecCccchhHHHHHHHHHHHHHHcCCCCCcceEEEcCCCCcCccccHHHHHHHHHHcCCCCCcEEEEC-----
Confidence            3458999998877767777789999999999986444444433   222221   1345556544 589999975     


Q ss_pred             CCchhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHH
Q 027801          147 GDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMD  185 (218)
Q Consensus       147 GeT~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~e  185 (218)
                           .|.++-.+.+++.+..++  +|==..|++.++.+
T Consensus       205 -----~d~~A~g~~~al~~~g~~--vP~di~vig~D~~~  236 (301)
T 3miz_A          205 -----NDEMAIQIYIAAMALGLR--IPQDVSIVGFDDFR  236 (301)
T ss_dssp             -----SHHHHHHHHHHHHTTTCC--HHHHCEEECSBCCH
T ss_pred             -----CHHHHHHHHHHHHHcCCC--CCCCeeEEEeCCcH
Confidence                 356777888888877654  34223566666665

>2hsg_A Glucose-resistance amylase regulator; CCPA, transcriptional regulator, transcription regulator; 2.50A {Bacillus megaterium} SCOP: a.35.1.5 c.93.1.1 PDB: 1rzr_G 2jcg_A 1zvv_A 3oqo_A* 3oqm_A* 3oqn_A*

Probab=89.12  E-value=0.63  Score=39.18  Aligned_cols=67  Identities=6%  Similarity=0.117  Sum_probs=44.2

Q ss_pred             CCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHHhhhcCCccEEEEEee
Q 027801           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~L~~~~~yDaVIaLG~  143 (218)
                      .+..+||++...+....-..+++++.+.++++|+.   +.+....+..+-- -.++.+ ...++||+|..+.
T Consensus        58 ~~~~~Ig~i~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~l-~~~~vdgiI~~~~  125 (332)
T 2hsg_A           58 KKTTTVGVIIPDISNIFYAELARGIEDIATMYKYN---IILSNSDQNQDKELHLLNNM-LGKQVDGIIFMSG  125 (332)
T ss_dssp             C-CCEEEEEEC--CCSHHHHHHHHHHHHHHHHTCE---EEEEECCSHHHHHHHHHHHT-SCCSSCCEEECCS
T ss_pred             CCCCEEEEEeCCCCCcHHHHHHHHHHHHHHHcCCE---EEEEeCCCChHHHHHHHHHH-HhCCCcEEEEecC
Confidence            45678999998877777788999999999999973   4444333322221 123444 3578999998774

>3jvd_A Transcriptional regulators; structural genomics, PSI-2, sugar binding protein, transcrip regulation, protein structure initiative; 2.30A {Corynebacterium glutamicum}

Probab=89.06  E-value=4.5  Score=34.22  Aligned_cols=95  Identities=17%  Similarity=0.170  Sum_probs=63.9

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeC-CcchHH---HHHHHhhhcCCccEEEEEeeeeeCCc
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVP-GSFEIG---VVAQQLGKSGKYTAVLCIGAVVRGDT  149 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VP-GA~ELP---~aak~L~~~~~yDaVIaLG~VIrGeT  149 (218)
                      ...||+++...-+......=++|..+.|+++|+.      ..++ |.+...   -+++.+++.+++|||+|.        
T Consensus       173 G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~g~~------~~~~~~~~~~~~~~~~~~~ll~~~~~~ai~~~--------  238 (333)
T 3jvd_A          173 SGMNIAALVGEESLSTTQERMRGISHAASIYGAE------VTFHFGHYSVESGEEMAQVVFNNGLPDALIVA--------  238 (333)
T ss_dssp             SSCEEEEEESCTTSHHHHHHHHHHHHHHHHTTCE------EEEEECCSSHHHHHHHHHHHHHTCCCSEEEEC--------
T ss_pred             CCCeEEEEeCCCCCccHHHHHHHHHHHHHHCCCC------EEEecCCCCHHHHHHHHHHHhcCCCCcEEEEC--------
Confidence            4568999998866666667789999999999974      2233 555433   234555555449999984        


Q ss_pred             hhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHH
Q 027801          150 THYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQ  186 (218)
Q Consensus       150 ~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQ  186 (218)
                        .|.++-.+.++|.+..++  +|==..|++.++...
T Consensus       239 --nd~~A~g~~~al~~~G~~--vP~disvig~D~~~~  271 (333)
T 3jvd_A          239 --SPRLMAGVMRAFTRLNVR--VPHDVVIGGYDDPEW  271 (333)
T ss_dssp             --CHHHHHHHHHHHHHTTCC--TTTTCEEEEESCCGG
T ss_pred             --CHHHHHHHHHHHHHcCCC--CCCceEEEEECChHH
Confidence              467888888999888775  342223444455543

>3brs_A Periplasmic binding protein/LACI transcriptional; structural genomics, protein structure initiative; 2.00A {Clostridium phytofermentans}

Probab=88.93  E-value=0.77  Score=37.33  Aligned_cols=67  Identities=15%  Similarity=0.151  Sum_probs=44.0

Q ss_pred             CCCCEEEEEEcccC--HHHHHHHHHHHHHHHHHCCCCCCCeEEEEeC--Ccch-HHHHHHHhhhcCCccEEEEEee
Q 027801           73 NEGLRFALVVARFN--ELVTKLLLEGALETFKKYSVKEENIDVVWVP--GSFE-IGVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        73 ~~~~RIaIV~Srfn--~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VP--GA~E-LP~aak~L~~~~~yDaVIaLG~  143 (218)
                      .+..+||+|...+.  ...-..+++++.+.++++|+.   +.++...  +..+ .--.++.+. ..++||||..+.
T Consensus         3 ~~~~~Ig~v~~~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~~~l~-~~~vdgii~~~~   74 (289)
T 3brs_A            3 LKQYYMICIPKVLDDSSDFWSVLVEGAQMAAKEYEIK---LEFMAPEKEEDYLVQNELIEEAI-KRKPDVILLAAA   74 (289)
T ss_dssp             --CCEEEEECSCCCSSSHHHHHHHHHHHHHHHHHTCE---EEECCCSSTTCHHHHHHHHHHHH-HTCCSEEEECCS
T ss_pred             CCCcEEEEEeCCCCCCchHHHHHHHHHHHHHHHcCCE---EEEecCCCCCCHHHHHHHHHHHH-HhCCCEEEEeCC
Confidence            34568999998877  777788999999999999863   3333221  2222 122345554 467999998765

>2iks_A DNA-binding transcriptional dual regulator; escherichia coli structural genomics, PSI-2, protein structure initiative; 1.85A {Escherichia coli}

Probab=88.71  E-value=3.3  Score=33.83  Aligned_cols=82  Identities=12%  Similarity=0.015  Sum_probs=56.1

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHH---HHHHhhhc-CCccEEEEEeeeeeCCc
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGKS-GKYTAVLCIGAVVRGDT  149 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~---aak~L~~~-~~yDaVIaLG~VIrGeT  149 (218)
                      ...||+++...-+......-.+|..+.|+++|..   ...+ ++|.|...-   +++.+++. .++|||+|.        
T Consensus       137 G~~~I~~i~~~~~~~~~~~R~~Gf~~~l~~~g~~---~~~~-~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~--------  204 (293)
T 2iks_A          137 PAETVLYLGALPELSVSFLREQGFRTAWKDDPRE---VHFL-YANSYEREAAAQLFEKWLETHPMPQALFTT--------  204 (293)
T ss_dssp             CCSSEEEEEECTTSHHHHHHHHHHHHHHTTCCCC---EEEE-EESSSCHHHHHHHHHHHTTTSCCCSEEEES--------
T ss_pred             CCCEEEEEecCcccccHHHHHHHHHHHHHHcCCC---ccEE-EcCCCChhhHHHHHHHHHhcCCCCCEEEEC--------
Confidence            3468999988755555566679999999999972   3322 355555432   34455544 479999984        


Q ss_pred             hhHHHHHHHHHHHHHHhchh
Q 027801          150 THYDAVANSAASGVLSAGVN  169 (218)
Q Consensus       150 ~H~e~Va~~vs~gLm~lsL~  169 (218)
                        .|.++-.+.+++.+..++
T Consensus       205 --~d~~a~g~~~al~~~g~~  222 (293)
T 2iks_A          205 --SFALLQGVMDVTLRRDGK  222 (293)
T ss_dssp             --SHHHHHHHHHHHHHHHSS
T ss_pred             --ChHHHHHHHHHHHHcCCC
Confidence              356788888888887765

>3gv0_A Transcriptional regulator, LACI family; transcription regulator, PSI-II, structural genomics structure initiative; 2.35A {Agrobacterium tumefaciens str}

Probab=88.65  E-value=1.2  Score=36.52  Aligned_cols=84  Identities=19%  Similarity=0.204  Sum_probs=57.3

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH---HHHHHhhhc-CCccEEEEEeeeeeCCc
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGKS-GKYTAVLCIGAVVRGDT  149 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP---~aak~L~~~-~~yDaVIaLG~VIrGeT  149 (218)
                      ...||+++...-.......-++|..+.|+++|+..+...+  +++.+...   -+++.+++. .++|||+|..       
T Consensus       126 G~~~I~~i~~~~~~~~~~~R~~gf~~~l~~~g~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~-------  196 (288)
T 3gv0_A          126 GRKRIAVIVPPSRFSFHDHARKGFNRGIRDFGLTEFPIDA--VTIETPLEKIRDFGQRLMQSSDRPDGIVSIS-------  196 (288)
T ss_dssp             TCCEEEEECCCTTSHHHHHHHHHHHHHHHHTTCEECCCCS--CCTTSCHHHHHHHHHHHTTSSSCCSEEEESC-------
T ss_pred             CCCeEEEEcCCcccchHHHHHHHHHHHHHHcCCCcchhhe--eccccchHHHHHHHHHHHhCCCCCcEEEEcC-------
Confidence            3469999988766656666779999999999975322222  34544432   334555544 5799999863       


Q ss_pred             hhHHHHHHHHHHHHHHhchh
Q 027801          150 THYDAVANSAASGVLSAGVN  169 (218)
Q Consensus       150 ~H~e~Va~~vs~gLm~lsL~  169 (218)
                         |.++-.+.+.|.+..++
T Consensus       197 ---d~~A~g~~~al~~~g~~  213 (288)
T 3gv0_A          197 ---GSSTIALVAGFEAAGVK  213 (288)
T ss_dssp             ---HHHHHHHHHHHHTTTCC
T ss_pred             ---cHHHHHHHHHHHHcCCC
Confidence               56788888888877764

>2dri_A D-ribose-binding protein; sugar transport; HET: RIP; 1.60A {Escherichia coli} SCOP: c.93.1.1 PDB: 1urp_A* 1ba2_A 1dbp_A* 1drj_A* 1drk_A* 2gx6_A*

Probab=88.33  E-value=1.7  Score=35.22  Aligned_cols=63  Identities=21%  Similarity=0.095  Sum_probs=43.3

Q ss_pred             CEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHHhhhcCCccEEEEEe
Q 027801           76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIG  142 (218)
Q Consensus        76 ~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~L~~~~~yDaVIaLG  142 (218)
                      .+||++...+....-..+++++.++++++|+.   +.+....+..+-- -.++.+ ...++||+|..+
T Consensus         2 ~~Igvi~~~~~~~f~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~i~~l-~~~~vdgiIi~~   65 (271)
T 2dri_A            2 DTIALVVSTLNNPFFVSLKDGAQKEADKLGYN---LVVLDSQNNPAKELANVQDL-TVRGTKILLINP   65 (271)
T ss_dssp             CEEEEEESCSSSHHHHHHHHHHHHHHHHHTCE---EEEEECTTCHHHHHHHHHHH-TTTTEEEEEECC
T ss_pred             cEEEEEecCCCCHHHHHHHHHHHHHHHHcCcE---EEEeCCCCCHHHHHHHHHHH-HHcCCCEEEEeC
Confidence            47999999888888889999999999999973   4443333332221 123444 356799998765

>2o20_A Catabolite control protein A; CCPA, transcriptional regulator, helix-turn-helix, transcrip; 1.90A {Lactococcus lactis}

Probab=88.19  E-value=2.7  Score=35.29  Aligned_cols=98  Identities=18%  Similarity=0.263  Sum_probs=63.0

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH---HHHHHhhhcCCccEEEEEeeeeeCCchh
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGKSGKYTAVLCIGAVVRGDTTH  151 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP---~aak~L~~~~~yDaVIaLG~VIrGeT~H  151 (218)
                      ..||+++...-+......-++|..+.|+++|++.+...+  ++|.|...   -+++.+++. ++|||+|.          
T Consensus       180 ~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~g~~~~~~~~--~~~~~~~~~~~~~~~~ll~~-~~~ai~~~----------  246 (332)
T 2o20_A          180 NKKIAYIMGSLKDVENTERMVGYQEALLEANIEFDENLV--FEGNYSYEQGKALAERLLER-GATSAVVS----------  246 (332)
T ss_dssp             CSSEEEECSCTTSHHHHHHHHHHHHHHHHTTCCCCGGGE--ECSCCSHHHHHHHHHHHHHT-TCCEEEES----------
T ss_pred             CCeEEEEeCCcccccHHHHHHHHHHHHHHcCCCCChhhE--EeCCCCHHHHHHHHHHHhcc-CCCEEEEC----------
Confidence            468999987755444556679999999999986432222  35555433   234556666 89999984          


Q ss_pred             HHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHH
Q 027801          152 YDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQA  187 (218)
Q Consensus       152 ~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA  187 (218)
                      .|.++-.+.+++.+..++  +|==..|++.++.+.+
T Consensus       247 ~d~~A~g~~~al~~~G~~--vP~disvig~D~~~~~  280 (332)
T 2o20_A          247 HDTVAVGLLSAMMDKGVK--VPEDFEIISGANSPIT  280 (332)
T ss_dssp             CHHHHHHHHHHHHHTTCC--TTTTCEEEESSCCGGG
T ss_pred             ChHHHHHHHHHHHHcCCC--CccCEEEEEeCChHHH
Confidence            356777888888877664  4422234455555543

>1pea_A Amidase operon; gene regulator, receptor, binding protein; 2.10A {Pseudomonas aeruginosa} SCOP: c.93.1.1 PDB: 1qo0_A 1qnl_A

Probab=88.14  E-value=3.9  Score=34.94  Aligned_cols=87  Identities=6%  Similarity=0.087  Sum_probs=57.4

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeC---CcchHHHHHHHhhhcCCccEEEEEeeeeeCCchh
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVP---GSFEIGVVAQQLGKSGKYTAVLCIGAVVRGDTTH  151 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VP---GA~ELP~aak~L~~~~~yDaVIaLG~VIrGeT~H  151 (218)
                      ..||++|...  ........++..+.|+++|+.  .....++|   |..+.--+++++.+. +.|+|+|.+.        
T Consensus       140 ~~~ia~i~~~--~~~~~~~~~~~~~~l~~~G~~--v~~~~~~~~~~~~~d~~~~~~~l~~~-~pdaI~~~~~--------  206 (385)
T 1pea_A          140 GERVVFIGSD--YIYPRESNHVMRHLYRQHGGT--VLEEIYIPLYPSDDDLQRAVERIYQA-RADVVFSTVV--------  206 (385)
T ss_dssp             CSEEEEEEES--SHHHHHHHHHHHHHHHHTTCE--EEEEEEECSSCCHHHHHHHHHHHHHH-TCSEEEEECC--------
T ss_pred             CcEEEEEeCC--ChHHHHHHHHHHHHHHHcCCE--EEEEEeecCCCCcchHHHHHHHHHHC-CCCEEEEecc--------
Confidence            4799999873  455677889999999999974  12223454   666665566776543 6899998642        


Q ss_pred             HHHHHHHHHHHHHHhchhc-CCceE
Q 027801          152 YDAVANSAASGVLSAGVNS-GVPCI  175 (218)
Q Consensus       152 ~e~Va~~vs~gLm~lsL~~-~vPVi  175 (218)
                       +..+-.+.+.+.+..++. .+|++
T Consensus       207 -~~~a~~~~~~~~~~G~~~~~~~~~  230 (385)
T 1pea_A          207 -GTGTAELYRAIARRYGDGRRPPIA  230 (385)
T ss_dssp             -THHHHHHHHHHHHHHCSSCCCCEE
T ss_pred             -cccHHHHHHHHHHcCCCcCCceEE
Confidence             124556666777776652 25554

>2fep_A Catabolite control protein A; CCPA, transcriptional regulator; HET: SEP; 2.45A {Bacillus subtilis} PDB: 2nzu_G* 1sxh_A 1sxi_A 1sxg_A* 2nzv_G* 2oen_G*

Probab=87.97  E-value=2.9  Score=34.27  Aligned_cols=83  Identities=18%  Similarity=0.173  Sum_probs=56.5

Q ss_pred             CCEEEEEEccc-CHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH---HHHHHhhhc-CCccEEEEEeeeeeCCc
Q 027801           75 GLRFALVVARF-NELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGKS-GKYTAVLCIGAVVRGDT  149 (218)
Q Consensus        75 ~~RIaIV~Srf-n~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP---~aak~L~~~-~~yDaVIaLG~VIrGeT  149 (218)
                      ..||+++.... .......-++|..+.|+++|++.....++  +|.|...   -+++.+++. .++|||+|.        
T Consensus       133 ~~~I~~i~~~~~~~~~~~~R~~Gf~~al~~~g~~~~~~~~~--~~~~~~~~~~~~~~~~l~~~~~~~ai~~~--------  202 (289)
T 2fep_A          133 HTDIAFVSGPMAEPINRSKKLQGYKRALEEANLPFNEQFVA--EGDYTYDSGLEALQHLMSLDKKPTAILSA--------  202 (289)
T ss_dssp             CSSEEEEESCTTSHHHHTTHHHHHHHHHHHTTCCCCGGGEE--ECCSCHHHHHHHHHHHTTSSSCCSEEEES--------
T ss_pred             CCeEEEEeCCccccccHHHHHHHHHHHHHHcCCCCChheEe--eCCCCHHHHHHHHHHHHcCCCCCCEEEEC--------
Confidence            46899999876 55555666799999999999864332233  4545433   234555544 579999984        


Q ss_pred             hhHHHHHHHHHHHHHHhchh
Q 027801          150 THYDAVANSAASGVLSAGVN  169 (218)
Q Consensus       150 ~H~e~Va~~vs~gLm~lsL~  169 (218)
                        .|.++-.+.+++.+..++
T Consensus       203 --~d~~A~g~~~al~~~G~~  220 (289)
T 2fep_A          203 --TDEMALGIIHAAQDQGLS  220 (289)
T ss_dssp             --SHHHHHHHHHHHHHTTCC
T ss_pred             --CHHHHHHHHHHHHHcCCC
Confidence              355788888888887664

>3h75_A Periplasmic sugar-binding domain protein; protein structure initiative II (PSI II), sugar binding PROT alpha/beta fold; 1.60A {Pseudomonas fluorescens pf-5}

Probab=87.75  E-value=4.9  Score=33.88  Aligned_cols=122  Identities=18%  Similarity=0.048  Sum_probs=75.3

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHH---HHHhhh-cCCccEEEEEeeeeeCCc
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVV---AQQLGK-SGKYTAVLCIGAVVRGDT  149 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~a---ak~L~~-~~~yDaVIaLG~VIrGeT  149 (218)
                      ...||+++...-.......-.+|..+.|+++|..   ..+..+++.+...-+   ++.+++ ..++|||+|..       
T Consensus       144 ~~~~i~~i~g~~~~~~~~~R~~Gf~~~l~~~~~~---~~~~~~~~~~~~~~~~~~~~~~L~~~~~~~aI~~~~-------  213 (350)
T 3h75_A          144 HGIELLAFSGLKVTPAAQLRERGLRRALAEHPQV---HLRQLVYGEWNRERAYRQAQQLLKRYPKTQLVWSAN-------  213 (350)
T ss_dssp             CCEEEEEEESCTTSHHHHHHHHHHHHHHHHCTTE---EEEEEEECTTCHHHHHHHHHHHHHHCTTEEEEEESS-------
T ss_pred             CCceEEEEeCCCCCHHHHHHHHHHHHHHHHCCCe---EEEEEeeCCCcHHHHHHHHHHHHHhCCCcCEEEECC-------
Confidence            3369999988776666777789999999999862   122345666654433   334443 45799998753       


Q ss_pred             hhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHhh--CC------CCCCcHHHHHHHHHHHH
Q 027801          150 THYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRA--GG------KSGNKGAEAALTAIEMA  210 (218)
Q Consensus       150 ~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~Ra--g~------k~gnKG~EAA~aAleM~  210 (218)
                         |.++-.+.++|.+..++  +|==..|++.++..++++..  +.      ....-|..|+..+++++
T Consensus       214 ---d~~a~g~~~al~~~G~~--vP~di~vvg~d~~~~~l~~~~~~~lttv~~~~~~~G~~av~~l~~~l  277 (350)
T 3h75_A          214 ---DEMALGAMQAARELGRK--PGTDLLFSGVNSSPEALQALIDGKLSVLEAGHFTLGGWALVALHDDA  277 (350)
T ss_dssp             ---HHHHHHHHHHHHHTTCC--BTTTBEEEEESCCHHHHHHHHHTSSCEEEECGGGHHHHHHHHHHHHH
T ss_pred             ---hHHHHHHHHHHHHcCCC--CCCCeEEEecCCCHHHHHHHHcCCeeEEEcCchhhHHHHHHHHHHHH
Confidence               56888888888888775  22112344556666653322  21      13344555555555544

>1qpz_A PURA, protein (purine nucleotide synthesis repressor); transcription regulation, DNA-binding, purine biosynthesis; HET: DNA HPA; 2.50A {Escherichia coli} SCOP: a.35.1.5 c.93.1.1 PDB: 1bdi_A* 1qp0_A* 1qp4_A* 1pnr_A* 1wet_A* 1zay_A* 1vpw_A* 2pue_A* 2puf_A* 2pug_A* 1bdh_A* 1qp7_A* 1qqa_A* 1qqb_A* 2puc_A* 2pua_A* 2pub_A* 2pud_A* 1jfs_A* 1jh9_A* ...

Probab=87.74  E-value=2.5  Score=35.66  Aligned_cols=83  Identities=20%  Similarity=0.207  Sum_probs=56.1

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHH---HHHHhhhc-CCccEEEEEeeeeeCCch
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGKS-GKYTAVLCIGAVVRGDTT  150 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~---aak~L~~~-~~yDaVIaLG~VIrGeT~  150 (218)
                      ..||+++...-+......-++|..+.|+++|+..+...+  ++|.|...-   +++.+++. .++|||+|.         
T Consensus       177 ~~~I~~i~g~~~~~~~~~R~~Gf~~al~~~g~~~~~~~~--~~~~~~~~~~~~~~~~ll~~~~~~~ai~~~---------  245 (340)
T 1qpz_A          177 HREIGVIPGPLERNTGAGRLAGFMKAMEEAMIKVPESWI--VQGDFEPESGYRAMQQILSQPHRPTAVFCG---------  245 (340)
T ss_dssp             CCCEEEECCCTTSHHHHHHHHHHHHHHHHTTCCCCGGGB--CCCCSSHHHHHHHHHHHHTSSSCCSEEEES---------
T ss_pred             CCEEEEEeCCCccccHHHHHHHHHHHHHHCCCCCChhhe--EeCCCCHHHHHHHHHHHHcCCCCCcEEEEC---------
Confidence            458999987655445556679999999999976332222  356554432   34555554 579999984         


Q ss_pred             hHHHHHHHHHHHHHHhchh
Q 027801          151 HYDAVANSAASGVLSAGVN  169 (218)
Q Consensus       151 H~e~Va~~vs~gLm~lsL~  169 (218)
                       .|.++-.+.+++.+..++
T Consensus       246 -nd~~A~g~~~al~~~G~~  263 (340)
T 1qpz_A          246 -GDIMAMGALCAADEMGLR  263 (340)
T ss_dssp             -SHHHHHHHHHHHHHTTCC
T ss_pred             -CHHHHHHHHHHHHHcCCC
Confidence             356788888888887664

>3gyb_A Transcriptional regulators (LACI-family transcriptional regulatory protein); protein structure initiative II(PSI II), nysgxrc; 1.60A {Corynebacterium glutamicum}

Probab=87.56  E-value=3.3  Score=33.40  Aligned_cols=96  Identities=17%  Similarity=0.038  Sum_probs=64.5

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHH---HHHhhh-cCCccEEEEEeeeeeCCc
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVV---AQQLGK-SGKYTAVLCIGAVVRGDT  149 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~a---ak~L~~-~~~yDaVIaLG~VIrGeT  149 (218)
                      ...||+++......  ...-++|..+.|+++|...   ...++++.+...-+   ++.+++ ..++|||+|.        
T Consensus       117 G~~~i~~i~~~~~~--~~~R~~gf~~~l~~~~~~~---~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~--------  183 (280)
T 3gyb_A          117 GHTHIAHLRVGSGA--GLRRFESFEATMRAHGLEP---LSNDYLGPAVEHAGYTETLALLKEHPEVTAIFSS--------  183 (280)
T ss_dssp             TCCSEEEECCSSHH--HHHHHHHHHHHHHHTTCCC---EECCCCSCCCHHHHHHHHHHHHHHCTTCCEEEES--------
T ss_pred             CCCeEEEEeCCCch--HHHHHHHHHHHHHHcCcCC---CcccccCCCCHHHHHHHHHHHHhCCCCCCEEEEC--------
Confidence            34589999887666  6677899999999999863   32237777765433   344443 4679999986        


Q ss_pred             hhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHH
Q 027801          150 THYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQ  186 (218)
Q Consensus       150 ~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQ  186 (218)
                        .|.++-.+.+++.+..++  +|==..|++.++.+.
T Consensus       184 --~d~~a~g~~~al~~~g~~--vP~di~vvg~d~~~~  216 (280)
T 3gyb_A          184 --NDITAIGALGAARELGLR--VPEDLSIIGYDNTPL  216 (280)
T ss_dssp             --SHHHHHHHHHHHHHHTCC--TTTTCEEEEESCCHH
T ss_pred             --ChHHHHHHHHHHHHcCCC--CCCeeEEEEECCchH
Confidence              356788888888888775  332223455555553

>2vk2_A YTFQ, ABC transporter periplasmic-binding protein YTFQ; transport protein, galactofuranose; HET: GZL; 1.20A {Escherichia coli}

Probab=87.53  E-value=4  Score=33.68  Aligned_cols=121  Identities=15%  Similarity=0.076  Sum_probs=75.8

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEE-eCCcchHH---HHHHHhhhc----CCccEEEEEeeeee
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVW-VPGSFEIG---VVAQQLGKS----GKYTAVLCIGAVVR  146 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~-VPGA~ELP---~aak~L~~~----~~yDaVIaLG~VIr  146 (218)
                      ..||+++...-.......-.+|..+.|+++|.    ++++. ++|.|...   -+++.+++.    .++|||+|.     
T Consensus       128 ~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~g~----~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~ai~~~-----  198 (306)
T 2vk2_A          128 PCNVVELQGTVGASVAIDRKKGFAEAIKNAPN----IKIIRSQSGDFTRSKGKEVMESFIKAENNGKNICMVYAH-----  198 (306)
T ss_dssp             CEEEEEEECSTTCHHHHHHHHHHHHHTTTCTT----EEEEEEEECTTCHHHHHHHHHHHHHHTTTTTTCCEEEES-----
T ss_pred             CCeEEEEEcCCCChhHHHHHHHHHHHHhhCCC----eEEEEeccCCCcHHHHHHHHHHHHHhCCCCCCeeEEEEC-----
Confidence            46899998875555555667999999999884    23332 35655433   234555554    479999984     


Q ss_pred             CCchhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHh--hC------CCCCCcHHHHHHHHHHHHH
Q 027801          147 GDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNR--AG------GKSGNKGAEAALTAIEMAS  211 (218)
Q Consensus       147 GeT~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~R--ag------~k~gnKG~EAA~aAleM~~  211 (218)
                           .|.++-.+.+++.+..++  +|==..|++.++...++++  .+      .....-|..|+...+++++
T Consensus       199 -----nd~~A~g~~~al~~~G~~--vP~di~vig~D~~~~~~~~~~~p~lttv~~~~~~~g~~a~~~l~~~i~  264 (306)
T 2vk2_A          199 -----NDDMVIGAIQAIKEAGLK--PGKDILTGSIDGVPDIYKAMMDGEANASVELTPNMAGPAFDALEKYKK  264 (306)
T ss_dssp             -----SHHHHHHHHHHHHHTTCC--BTTTBEEEEEECCHHHHHHHHTTCCCEEEECCSCCHHHHHHHHHHHHH
T ss_pred             -----CchHHHHHHHHHHHcCCC--CCCCeEEEeecCCHHHHHHHHcCCceEEEecCHHHHHHHHHHHHHHHc
Confidence                 255777888888887664  3411234455665555322  11      1244678888888877664

>3brq_A HTH-type transcriptional regulator ASCG; transcriptional repressor structure escherichia coli, struct genomics, PSI-2; HET: FRU; 2.00A {Escherichia coli}

Probab=87.52  E-value=2.4  Score=34.30  Aligned_cols=83  Identities=14%  Similarity=0.191  Sum_probs=54.7

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH---HHHHHhhhc-CCccEEEEEeeeeeCCch
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGKS-GKYTAVLCIGAVVRGDTT  150 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP---~aak~L~~~-~~yDaVIaLG~VIrGeT~  150 (218)
                      ..||+++...-.......-.+|..+.|+++|+......+  ++|.+...   -+++.+++. .++|||+|..        
T Consensus       139 ~~~I~~i~~~~~~~~~~~R~~gf~~~l~~~g~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~--------  208 (296)
T 3brq_A          139 HQEIAFLTGSMDSPTSIERLAGYKDALAQHGIALNEKLI--ANGKWTPASGAEGVEMLLERGAKFSALVASN--------  208 (296)
T ss_dssp             CCSEEEECCCTTCHHHHHHHHHHHHHHHTTTCCCCGGGE--ECCCSSHHHHHHHHHHHHTC--CCSEEEESS--------
T ss_pred             CceEEEEcCCCCCccHHHHHHHHHHHHHHcCCCCChhhE--EeCCCChhHHHHHHHHHHhCCCCCCEEEECC--------
Confidence            468999987655445566679999999999976332222  35555433   233455543 5799999742        


Q ss_pred             hHHHHHHHHHHHHHHhchh
Q 027801          151 HYDAVANSAASGVLSAGVN  169 (218)
Q Consensus       151 H~e~Va~~vs~gLm~lsL~  169 (218)
                        |.++..+.+.+.+..++
T Consensus       209 --d~~a~g~~~al~~~g~~  225 (296)
T 3brq_A          209 --DDMAIGAMKALHERGVA  225 (296)
T ss_dssp             --HHHHHHHHHHHHHHTCC
T ss_pred             --hHHHHHHHHHHHHcCCC
Confidence              45677888888887765

>3g1w_A Sugar ABC transporter; sugar-binding protein, bacillus halod target 11229F, transport protein, structural genomics; 2.02A {Bacillus halodurans c-125}

Probab=87.10  E-value=3.4  Score=33.78  Aligned_cols=96  Identities=16%  Similarity=0.062  Sum_probs=62.4

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEe-CCcchHH---HHHHHhhh-cCCccEEEEEeeeeeCC
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWV-PGSFEIG---VVAQQLGK-SGKYTAVLCIGAVVRGD  148 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~V-PGA~ELP---~aak~L~~-~~~yDaVIaLG~VIrGe  148 (218)
                      ...||+++...-+ .....-.+|..+.|+++|..   ++..++ .|.+...   -+++.+++ ..++|||+|.       
T Consensus       126 g~~~i~~i~~~~~-~~~~~R~~gf~~~l~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~-------  194 (305)
T 3g1w_A          126 GEGEVAVITLPNQ-LNHQERTTGFKETLEAEFPA---IEVIAVEDGRGDSLHSRRVAHQLLEDYPNLAGIFAT-------  194 (305)
T ss_dssp             TCEEEEEEECTTC-HHHHHHHHHHHHHHHHHCTT---EEEEEEEECTTCHHHHHHHHHHHHHHCTTEEEEEES-------
T ss_pred             CCcEEEEEeCCCc-ccHHHHHHHHHHHHHhhCCC---CEEEEEecCCCCHHHHHHHHHHHHHhCCCceEEEEC-------
Confidence            4468999987644 45666779999999999875   444333 4554433   23444444 4579999874       


Q ss_pred             chhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHH
Q 027801          149 TTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQA  187 (218)
Q Consensus       149 T~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA  187 (218)
                         .|.++-.+.+++.+..+..++.|    ++.++.+++
T Consensus       195 ---~d~~a~g~~~al~~~g~~~di~v----ig~d~~~~~  226 (305)
T 3g1w_A          195 ---EANGGVGVGDAVRLESRAGEIQI----ISFDTDKGT  226 (305)
T ss_dssp             ---SHHHHHHHHHHHHHTTCTTTSEE----EEESCCHHH
T ss_pred             ---CCcchhhHHHHHHhcCCCCCeEE----EEeCCCHHH
Confidence               34578888899999888744433    334555433

>3c3k_A Alanine racemase; structural genomics, protein structure initiative, NEW YORK research center for structural genomics, nysgxrc; 1.99A {Actinobacillus succinogenes}

Probab=87.08  E-value=5.3  Score=32.52  Aligned_cols=98  Identities=20%  Similarity=0.186  Sum_probs=62.0

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHH--hhhc-CCccEEEEEeeeeeCCch
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQ--LGKS-GKYTAVLCIGAVVRGDTT  150 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~--L~~~-~~yDaVIaLG~VIrGeT~  150 (218)
                      ..||+++...-.......-.+|..+.|+++|++..   ++..+...+-- -+++.  +++. .++|||+|.         
T Consensus       124 ~~~I~~i~~~~~~~~~~~R~~gf~~~l~~~g~~~~---~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~---------  191 (285)
T 3c3k_A          124 KKRIALINHDLAYQYAQHRESGYLNRLKFHGLDYS---RISYAENLDYMAGKLATFSLLKSAVKPDAIFAI---------  191 (285)
T ss_dssp             CCCEEEEECCTTSHHHHHHHHHHHHHHHHHTCCCC---EEEECSSSSHHHHHHHHHHHHSSSSCCSEEEES---------
T ss_pred             CCeEEEEeCCCccccHHHHHHHHHHHHHHcCCCce---EeecCCChHHHHHHHHHHHHHcCCCCCeEEEEC---------
Confidence            46899998875544555667999999999998633   33333333322 23455  5554 479999984         


Q ss_pred             hHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHH
Q 027801          151 HYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQA  187 (218)
Q Consensus       151 H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA  187 (218)
                       .|.++-.+.+++.+..++  +|==..|++.++...+
T Consensus       192 -~d~~A~g~~~al~~~g~~--vP~di~vvg~d~~~~~  225 (285)
T 3c3k_A          192 -SDVLAAGAIQALTESGLS--IPQDVAVVGFDGVDIS  225 (285)
T ss_dssp             -SHHHHHHHHHHHHHTTCC--TTTTCEEECSBCCGGG
T ss_pred             -CHHHHHHHHHHHHHcCCC--CCCceEEEEeCChHHH
Confidence             255777888888877664  4422344555655443

>4fe7_A Xylose operon regulatory protein; HTH_ARAC, helix-turn-helix, PBP, periplasmic binding protein binding transcription regulator, DNA xylose; HET: XYS; 2.90A {Escherichia coli} PDB: 4fe4_A

Probab=87.03  E-value=1.4  Score=38.77  Aligned_cols=60  Identities=15%  Similarity=0.134  Sum_probs=40.4

Q ss_pred             CCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEE
Q 027801           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLC  140 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIa  140 (218)
                      .+..+||+|.. .+...-..+++++.+.++++|+.   +.++......+.   ++.+ ...++||||.
T Consensus        23 ~~s~~Igvv~~-~~~~f~~~l~~gi~~~a~~~g~~---~~i~~~~~~~~~---i~~l-~~~~vDGiIi   82 (412)
T 4fe7_A           23 TKRHRITLLFN-ANKAYDRQVVEGVGEYLQASQSE---WDIFIEEDFRAR---IDKI-KDWLGDGVIA   82 (412)
T ss_dssp             CCCEEEEEECC-TTSHHHHHHHHHHHHHHHHHTCC---EEEEECC-CC------------CCCSEEEE
T ss_pred             CCCceEEEEeC-CcchhhHHHHHHHHHHHHhcCCC---eEEEecCCccch---hhhH-hcCCCCEEEE
Confidence            45567999996 67777788999999999999974   666665443332   3444 4578999996

>3l6u_A ABC-type sugar transport system periplasmic compo; structural genomics, nysgrc, target 11006S, PSI-2, protein S initiative; 1.90A {Exiguobacterium sibiricum}

Probab=87.00  E-value=3.9  Score=33.10  Aligned_cols=94  Identities=21%  Similarity=0.213  Sum_probs=63.5

Q ss_pred             CEEEEEEcccCHHHHHHHHHHHHHHHHHC-CCCCCCeEEEEeCCcchHHH---HHHHhhhc-CCccEEEEEeeeeeCCch
Q 027801           76 LRFALVVARFNELVTKLLLEGALETFKKY-SVKEENIDVVWVPGSFEIGV---VAQQLGKS-GKYTAVLCIGAVVRGDTT  150 (218)
Q Consensus        76 ~RIaIV~Srfn~~It~~Ll~gA~~~L~~~-Gv~~e~I~vv~VPGA~ELP~---aak~L~~~-~~yDaVIaLG~VIrGeT~  150 (218)
                      .||+++...-.......-.+|..+.|+++ |+.   +.. .+++.+...-   +++.+++. .++|||+|.         
T Consensus       136 ~~i~~i~g~~~~~~~~~R~~gf~~~l~~~~g~~---~~~-~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~---------  202 (293)
T 3l6u_A          136 GRIVEITGTANVYTTNERHRGFLKGIENEPTLS---IVD-SVSGNYDPVTSERVMRQVIDSGIPFDAVYCH---------  202 (293)
T ss_dssp             EEEEEEECSTTCHHHHHHHHHHHHHHTTCTTEE---EEE-EEECTTCHHHHHHHHHHHHHTTCCCSEEEES---------
T ss_pred             ceEEEEECCCCCchHHHHHHHHHHHHHhCCCcE---Eee-eccCCCCHHHHHHHHHHHHHhCCCCCEEEEC---------
Confidence            39999997776666777789999999998 763   222 2455554443   23444443 679999975         


Q ss_pred             hHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHH
Q 027801          151 HYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQAL  188 (218)
Q Consensus       151 H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~  188 (218)
                       .|.++-.+.+++.+..++ ++.|    ++.++.+.+.
T Consensus       203 -~d~~a~g~~~al~~~g~~-di~v----ig~d~~~~~~  234 (293)
T 3l6u_A          203 -NDDIAMGVLEALKKAKIS-GKIV----VGIDGNRAIL  234 (293)
T ss_dssp             -SHHHHHHHHHHHHHTTCC-CCEE----EEEECCHHHH
T ss_pred             -CchHHHHHHHHHHhCCCC-CeEE----EEecCCHHHH
Confidence             356788888999988887 5544    3445555443

>3l49_A ABC sugar (ribose) transporter, periplasmic substrate-binding subunit; sugar binding/transporter, structural genomics, PSI; HET: UNL; 2.30A {Rhodobacter sphaeroides}

Probab=86.74  E-value=2.4  Score=34.31  Aligned_cols=99  Identities=12%  Similarity=0.039  Sum_probs=63.2

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHC-CCC-CCCeEEEEeCCcchHH---HHHHHhhhc-C---CccEEEEEeee
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKY-SVK-EENIDVVWVPGSFEIG---VVAQQLGKS-G---KYTAVLCIGAV  144 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~-Gv~-~e~I~vv~VPGA~ELP---~aak~L~~~-~---~yDaVIaLG~V  144 (218)
                      ...||+++...-.......-++|..+.|+++ |+. .+...+  ..+.+..-   -+++.+++. .   ++|||+|.   
T Consensus       124 g~~~i~~i~~~~~~~~~~~R~~gf~~~l~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~~~~ai~~~---  198 (291)
T 3l49_A          124 GKGNVLVFNGFYSVPVCKIRYDQMKYVLEAFPDVKIIEPELR--DVIPNTIQSAYSNVTDMLTKYPNEGDVGAIWAC---  198 (291)
T ss_dssp             TCEEEEEECSCTTSHHHHHHHHHHHHHHHTCTTEEECSSCBC--CCSSSHHHHHHHHHHHHHHHCCSTTSCCEEEES---
T ss_pred             CCceEEEEeCCCCCchHHHHHHHHHHHHHHCCCCEEEeeecc--CCCCCCHHHHHHHHHHHHHhCCCcCCcCEEEEC---
Confidence            3468999987766666667789999999998 442 111111  23433322   334555544 4   79999874   


Q ss_pred             eeCCchhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHH
Q 027801          145 VRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALN  189 (218)
Q Consensus       145 IrGeT~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~  189 (218)
                             .|.++-.+.++|.+..++ ++.|+    +.++...+.+
T Consensus       199 -------~d~~a~g~~~al~~~g~~-di~vv----g~d~~~~~~~  231 (291)
T 3l49_A          199 -------WDVPMIGATQALQAAGRT-DIRTY----GVDGSPEFVE  231 (291)
T ss_dssp             -------SHHHHHHHHHHHHHTTCC-SCEEE----EEECCHHHHH
T ss_pred             -------CCchHHHHHHHHHHcCCC-CeEEE----EecCCHHHHH
Confidence                   367888899999999888 66654    3455544433

>2dri_A D-ribose-binding protein; sugar transport; HET: RIP; 1.60A {Escherichia coli} SCOP: c.93.1.1 PDB: 1urp_A* 1ba2_A 1dbp_A* 1drj_A* 1drk_A* 2gx6_A*

Probab=86.71  E-value=6.8  Score=31.63  Aligned_cols=95  Identities=19%  Similarity=0.129  Sum_probs=63.4

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHH---HHHHhhh-cCCccEEEEEeeeeeCCch
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGK-SGKYTAVLCIGAVVRGDTT  150 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~---aak~L~~-~~~yDaVIaLG~VIrGeT~  150 (218)
                      ..||+++...-+......=.+|..+.|+++|+.   +.. ..+|.|...-   +++.+++ ..++|||+|..        
T Consensus       123 ~~~I~~i~g~~~~~~~~~R~~Gf~~al~~~g~~---~~~-~~~~~~~~~~~~~~~~~ll~~~~~~~ai~~~n--------  190 (271)
T 2dri_A          123 GAKVIELQGIAGTSAARERGEGFQQAVAAHKFN---VLA-SQPADFDRIKGLNVMQNLLTAHPDVQAVFAQN--------  190 (271)
T ss_dssp             TCEEEEEECCTTCHHHHHHHHHHHHHHHHHTCE---EEE-EEECTTCHHHHHHHHHHHHHHCTTCCEEEESS--------
T ss_pred             CCeEEEEECCCCCccHhHHHHHHHHHHhcCCCE---EEE-ecCCCCCHHHHHHHHHHHHHhCCCccEEEECC--------
Confidence            369999987655445556678999999999874   221 2456555432   3344544 45799999874        


Q ss_pred             hHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHH
Q 027801          151 HYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQAL  188 (218)
Q Consensus       151 H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~  188 (218)
                        |.++-.+.+++.+..+ .++.|    ++-++.+.+.
T Consensus       191 --D~~A~g~~~al~~~g~-~dv~v----vGfD~~~~~~  221 (271)
T 2dri_A          191 --DEMALGALRALQTAGK-SDVMV----VGFDGTPDGE  221 (271)
T ss_dssp             --HHHHHHHHHHHHHHTC-CSCEE----EEEECCHHHH
T ss_pred             --CcHHHHHHHHHHHcCC-CCcEE----EEecCCHHHH
Confidence              6788999999999888 35544    3445555543

>3k9c_A Transcriptional regulator, LACI family protein; PSI-II, 11026W, structural genomics, PR structure initiative; 2.14A {Rhodococcus jostii}

Probab=86.45  E-value=3.9  Score=33.55  Aligned_cols=82  Identities=15%  Similarity=0.045  Sum_probs=58.5

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHH---HHHHhhh-cCCccEEEEEeeeeeCCc
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGK-SGKYTAVLCIGAVVRGDT  149 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~---aak~L~~-~~~yDaVIaLG~VIrGeT  149 (218)
                      ...||+++....+. ....-++|..+.|+++|...+   ...++|.+..--   +++.+++ ..++|||+|.        
T Consensus       125 G~~~I~~i~~~~~~-~~~~R~~Gf~~al~~~g~~~~---~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~--------  192 (289)
T 3k9c_A          125 GHRNIAHIDGADAP-GGADRRAGFLAAMDRHGLSAS---ATVVTGGTTETEGAEGMHTLLEMPTPPTAVVAF--------  192 (289)
T ss_dssp             TCCSEEEECCTTST-THHHHHHHHHHHHHHTTCGGG---EEEECCCSSHHHHHHHHHHHHTSSSCCSEEEES--------
T ss_pred             CCCcEEEEeCCCCc-cHHHHHHHHHHHHHHCCCCCC---ccEEECCCCHHHHHHHHHHHHcCCCCCCEEEEC--------
Confidence            34589999987766 556677999999999998532   234567665443   3344554 4689999985        


Q ss_pred             hhHHHHHHHHHHHHHHhchh
Q 027801          150 THYDAVANSAASGVLSAGVN  169 (218)
Q Consensus       150 ~H~e~Va~~vs~gLm~lsL~  169 (218)
                        .|.++-.+.+++.+..++
T Consensus       193 --~d~~A~g~~~al~~~g~~  210 (289)
T 3k9c_A          193 --NDRCATGVLDLLVRSGRD  210 (289)
T ss_dssp             --SHHHHHHHHHHHHHTTCC
T ss_pred             --ChHHHHHHHHHHHHcCCC
Confidence              356888888889888775

>3bbl_A Regulatory protein of LACI family; protein structure initiative II, PSI-II, NYSGXRC, transcript regulator, periplasmic binding protein; 2.35A {Chloroflexus aggregans}

Probab=86.41  E-value=0.57  Score=38.50  Aligned_cols=65  Identities=5%  Similarity=-0.101  Sum_probs=43.1

Q ss_pred             CCCEEEEEEcc-c---CHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcc--hHHHHHHHhhhcCCccEEEEEee
Q 027801           74 EGLRFALVVAR-F---NELVTKLLLEGALETFKKYSVKEENIDVVWVPGSF--EIGVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        74 ~~~RIaIV~Sr-f---n~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~--ELP~aak~L~~~~~yDaVIaLG~  143 (218)
                      +..+||+|... +   ....-..+++++.+.++++|+.   +.+....+..  |.- .++.+ ...++||+|..+.
T Consensus         3 ~s~~Ig~i~~~~~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~-~~~~l-~~~~vdgiIi~~~   73 (287)
T 3bbl_A            3 LSFMIGYSWTQTEPGQVNHILDQFLSSMVREAGAVNYF---VLPFPFSEDRSQIDI-YRDLI-RSGNVDGFVLSSI   73 (287)
T ss_dssp             CCCEEEECCCCCCTTCSCCTHHHHHHHHHHHHHHTTCE---EEECCCCSSTTCCHH-HHHHH-HTTCCSEEEECSC
T ss_pred             ceeEEEEEecccccccCChhHHHHHHHHHHHHHHcCCE---EEEEeCCCchHHHHH-HHHHH-HcCCCCEEEEeec
Confidence            34589999887 6   6666778999999999999873   3333222221  222 23444 4577999998764

>3clk_A Transcription regulator; 11017J, PSI-II, NYSGXRC, dimer, structural genomics, protein structure initiative; 2.08A {Lactobacillus plantarum WCFS1}

Probab=86.34  E-value=2.6  Score=34.43  Aligned_cols=83  Identities=14%  Similarity=0.187  Sum_probs=54.8

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHH---HHHHhhhcCCccEEEEEeeeeeCCchh
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGKSGKYTAVLCIGAVVRGDTTH  151 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~---aak~L~~~~~yDaVIaLG~VIrGeT~H  151 (218)
                      ..||+++...-+......-.+|..+.|+++|+......+  ++|.+...-   +++.+++..++|||+|.          
T Consensus       125 ~~~i~~i~~~~~~~~~~~R~~gf~~~l~~~g~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~ai~~~----------  192 (290)
T 3clk_A          125 HRQIGIAGIDQYPYTGRKRLAGYKKALKEANIAINQEWI--KPGDYSYTSGEQAMKAFGKNTDLTGIIAA----------  192 (290)
T ss_dssp             CCSEEEESCCCCTTTHHHHHHHHHHHHHHTTCCCCGGGE--ECCCSSHHHHHHHHHHHCTTCCCSEEEES----------
T ss_pred             CCEEEEEeCCCCCcchHHHHHHHHHHHHHcCCCCCcceE--EcCCCChhhHHHHHHHHhccCCCcEEEEC----------
Confidence            468999987654444456679999999999976322212  356554432   33444444579999984          


Q ss_pred             HHHHHHHHHHHHHHhchh
Q 027801          152 YDAVANSAASGVLSAGVN  169 (218)
Q Consensus       152 ~e~Va~~vs~gLm~lsL~  169 (218)
                      .|.++-.+.+.+.+..++
T Consensus       193 ~d~~a~g~~~al~~~g~~  210 (290)
T 3clk_A          193 SDMTAIGILNQASSFGIE  210 (290)
T ss_dssp             SHHHHHHHHHHHHHTTCC
T ss_pred             CcHHHHHHHHHHHHcCCC
Confidence            355777888888887664

>2h0a_A TTHA0807, transcriptional regulator; repressor, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.80A {Thermus thermophilus}

Probab=86.19  E-value=3.6  Score=33.04  Aligned_cols=100  Identities=18%  Similarity=0.065  Sum_probs=58.9

Q ss_pred             CCEEEEEEccc-C---HHHHH-HHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHHhhhc-CCccEEEEEeeeeeC
Q 027801           75 GLRFALVVARF-N---ELVTK-LLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKS-GKYTAVLCIGAVVRG  147 (218)
Q Consensus        75 ~~RIaIV~Srf-n---~~It~-~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~L~~~-~~yDaVIaLG~VIrG  147 (218)
                      ..||+++...- .   ..... .-.+|..+.|+++|++.....++..+...+-- -+++.+++. .++|||+|.      
T Consensus       114 ~~~i~~i~~~~~~~~~~~~~~~~R~~gf~~~l~~~g~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~------  187 (276)
T 2h0a_A          114 GPIFAIAVEEEPDRAFRRTVFAERMAGFQEALKEAGRPFSPDRLYITRHSQEGGRLALRHFLEKASPPLNVFAG------  187 (276)
T ss_dssp             SCEEEEEECCSCCC---CCHHHHHHHHHHHHHHHTTCCCCGGGEEEECSSHHHHHHHHHHHHTTCCSSEEEECS------
T ss_pred             CCeEEEEecCcccccccchhHHHHHHHHHHHHHHcCCCCChHHeeecCCChHHHHHHHHHHHhCCCCCCEEEEC------
Confidence            45999998765 4   33344 55789999999999864332233333233322 234555544 469999863      


Q ss_pred             CchhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHH
Q 027801          148 DTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQ  186 (218)
Q Consensus       148 eT~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQ  186 (218)
                          .|.++-.+.+.+.+..++  +|==..|++.++...
T Consensus       188 ----~d~~a~g~~~al~~~g~~--vP~di~vvg~d~~~~  220 (276)
T 2h0a_A          188 ----ADQVALGVLEEAVRLGLT--PGRDVRVLGFDGHPF  220 (276)
T ss_dssp             ----SHHHHHHHHHHHHTTSCT--TTTSEEEEEESCCTH
T ss_pred             ----CcHHHHHHHHHHHHcCCC--CCCCeEEEEeCCCch
Confidence                356777788888776654  442223444454433

>1gud_A ALBP, D-allose-binding periplasmic protein; periplasmic binding protein, X-RAY crystallography, hinge bending, conformational change; 1.7A {Escherichia coli} SCOP: c.93.1.1 PDB: 1gub_A 1rpj_A*

Probab=86.15  E-value=2.9  Score=34.31  Aligned_cols=64  Identities=14%  Similarity=0.218  Sum_probs=44.1

Q ss_pred             CEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH---HHHHHhhhcCCccEEEEEee
Q 027801           76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        76 ~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP---~aak~L~~~~~yDaVIaLG~  143 (218)
                      .+||+|........-..+++++.++++++|+.   +.+...+...+.-   -.++.+. ..++||+|..+.
T Consensus         2 ~~Igvi~~~~~~~f~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~~~~~-~~~vdgiIi~~~   68 (288)
T 1gud_A            2 AEYAVVLKTLSNPFWVDMKKGIEDEAKTLGVS---VDIFASPSEGDFQSQLQLFEDLS-NKNYKGIAFAPL   68 (288)
T ss_dssp             CEEEEEESCSSSHHHHHHHHHHHHHHHHHTCC---EEEEECSSTTCHHHHHHHHHHHH-TSSEEEEEECCS
T ss_pred             cEEEEEeCCCCchHHHHHHHHHHHHHHHcCCE---EEEeCCCCCCCHHHHHHHHHHHH-HcCCCEEEEeCC
Confidence            47999998888888889999999999999974   5554422222221   1234443 467999998754

>3brs_A Periplasmic binding protein/LACI transcriptional; structural genomics, protein structure initiative; 2.00A {Clostridium phytofermentans}

Probab=85.73  E-value=5.9  Score=31.98  Aligned_cols=86  Identities=12%  Similarity=-0.036  Sum_probs=57.3

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH---HHHHHhhh-cCCccEEEEEeeeeeCCch
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGK-SGKYTAVLCIGAVVRGDTT  150 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP---~aak~L~~-~~~yDaVIaLG~VIrGeT~  150 (218)
                      ..||+++...-+......-.+|..+.|+++|..  -..+  +++.+...   -+++.+++ ..++|||+|.         
T Consensus       131 ~~~i~~i~~~~~~~~~~~R~~gf~~~l~~~g~~--~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~---------  197 (289)
T 3brs_A          131 SGKIGVISFVKNSKTAMDREEGLKIGLSDDSNK--IEAI--YYCDSNYDKAYDGTVELLTKYPDISVMVGL---------  197 (289)
T ss_dssp             SCEEEEEESCTTSHHHHHHHHHHHHHHGGGGGG--EEEE--EECTTCHHHHHHHHHHHHHHCTTEEEEEES---------
T ss_pred             CceEEEEECCCCCccHHHHHHHHHHHHHhCCCc--EEee--ecCCCCHHHHHHHHHHHHHhCCCceEEEEC---------
Confidence            569999988755555666779999999998863  1222  34444332   23344444 4579999874         


Q ss_pred             hHHHHHHHHHHHHHHhchhcCCce
Q 027801          151 HYDAVANSAASGVLSAGVNSGVPC  174 (218)
Q Consensus       151 H~e~Va~~vs~gLm~lsL~~~vPV  174 (218)
                       .|.++..+.+.+.+..++.++.|
T Consensus       198 -~d~~a~g~~~al~~~G~~~di~v  220 (289)
T 3brs_A          198 -NQYSATGAARAIKDMSLEAKVKL  220 (289)
T ss_dssp             -SHHHHHHHHHHHHHTTCTTTSEE
T ss_pred             -CCcchHHHHHHHHhcCCCCCEEE
Confidence             25577788888888887745555

>1dbq_A Purine repressor; transcription regulation, DNA-binding regulatory protein; 2.20A {Escherichia coli} SCOP: c.93.1.1 PDB: 1jhz_A

Probab=85.70  E-value=2.2  Score=34.61  Aligned_cols=83  Identities=20%  Similarity=0.183  Sum_probs=51.9

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH---HHHHHhhhc-CCccEEEEEeeeeeCCch
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGKS-GKYTAVLCIGAVVRGDTT  150 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP---~aak~L~~~-~~yDaVIaLG~VIrGeT~  150 (218)
                      ..||+++....+......-++|..+.|+++|+......  .++|.|+..   -+++.+++. .++|||+|.         
T Consensus       126 ~~~i~~i~~~~~~~~~~~R~~g~~~~l~~~g~~~~~~~--~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~---------  194 (289)
T 1dbq_A          126 HREIGVIPGPLERNTGAGRLAGFMKAMEEAMIKVPESW--IVQGDFEPESGYRAMQQILSQPHRPTAVFCG---------  194 (289)
T ss_dssp             CCSEEEECCC------CHHHHHHHHHHHHTTCCCCGGG--BCCCCSSHHHHHHHHHHHHTSSSCCSEEEES---------
T ss_pred             CCeEEEEecCCccccHHHHHHHHHHHHHHCCCCCChHH--eEeCCCCHHHHHHHHHHHHhCCCCCCEEEEC---------
Confidence            45899998765544455667999999999997532221  235555432   234455543 679999985         


Q ss_pred             hHHHHHHHHHHHHHHhchh
Q 027801          151 HYDAVANSAASGVLSAGVN  169 (218)
Q Consensus       151 H~e~Va~~vs~gLm~lsL~  169 (218)
                       .|.++..+.+.+.+..++
T Consensus       195 -~d~~a~g~~~al~~~G~~  212 (289)
T 1dbq_A          195 -GDIMAMGALCAADEMGLR  212 (289)
T ss_dssp             -CHHHHHHHHHHHHHTTCC
T ss_pred             -CcHHHHHHHHHHHHcCCC
Confidence             245777888888887664

>2hsg_A Glucose-resistance amylase regulator; CCPA, transcriptional regulator, transcription regulator; 2.50A {Bacillus megaterium} SCOP: a.35.1.5 c.93.1.1 PDB: 1rzr_G 2jcg_A 1zvv_A 3oqo_A* 3oqm_A* 3oqn_A*

Probab=85.65  E-value=3.5  Score=34.52  Aligned_cols=84  Identities=17%  Similarity=0.212  Sum_probs=56.1

Q ss_pred             CCCEEEEEEccc-CHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH---HHHHHhhhc-CCccEEEEEeeeeeCC
Q 027801           74 EGLRFALVVARF-NELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGKS-GKYTAVLCIGAVVRGD  148 (218)
Q Consensus        74 ~~~RIaIV~Srf-n~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP---~aak~L~~~-~~yDaVIaLG~VIrGe  148 (218)
                      ...||+++...- .......-++|..+.|+++|++.+...++  +|.|...   -+++.+++. .++|||+|.       
T Consensus       176 G~~~I~~i~~~~~~~~~~~~R~~Gf~~al~~~g~~~~~~~~~--~~~~~~~~~~~~~~~ll~~~~~~~ai~~~-------  246 (332)
T 2hsg_A          176 GHKNIAFVSGTLEEPINHAKKVKGYKRALTESGLPVRDSYIV--EGDYTYDSGIEAVEKLLEEDEKPTAIFVG-------  246 (332)
T ss_dssp             TCSCEEEEESCTTSHHHHTTHHHHHHHHHHTTTCCCCGGGEE--ECCSSHHHHHHHHHHHHHSSSCCSEEEES-------
T ss_pred             CCCEEEEEeCCcccCccHHHHHHHHHHHHHHcCCCCChheEE--eCCCCHHHHHHHHHHHHcCCCCCeEEEEC-------
Confidence            346899998876 55555566799999999999864322233  4445433   234555554 479999973       


Q ss_pred             chhHHHHHHHHHHHHHHhchh
Q 027801          149 TTHYDAVANSAASGVLSAGVN  169 (218)
Q Consensus       149 T~H~e~Va~~vs~gLm~lsL~  169 (218)
                         .|.++-.+.+++.+..++
T Consensus       247 ---nd~~A~g~~~al~~~G~~  264 (332)
T 2hsg_A          247 ---TDEMALGVIHGAQDRGLN  264 (332)
T ss_dssp             ---SHHHHHHHHHHHHHTTCC
T ss_pred             ---ChHHHHHHHHHHHHcCCC
Confidence               356777788888876653

>3cs3_A Sugar-binding transcriptional regulator, LACI FAM; structural genomics, sugar-binding transcriptional regulator structure initiative; 2.40A {Enterococcus faecalis}

Probab=85.64  E-value=0.75  Score=37.46  Aligned_cols=61  Identities=11%  Similarity=0.043  Sum_probs=42.5

Q ss_pred             CCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEee
Q 027801           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~  143 (218)
                      .+..+||+|...+.......+++++.+.++++|+.   +.++...+..+..      .+- ++||||..+.
T Consensus         6 ~~~~~Igvi~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~------~~~-~vdgiI~~~~   66 (277)
T 3cs3_A            6 RQTNIIGVYLADYGGSFYGELLEGIKKGLALFDYE---MIVCSGKKSHLFI------PEK-MVDGAIILDW   66 (277)
T ss_dssp             CCCCEEEEEECSSCTTTHHHHHHHHHHHHHTTTCE---EEEEESTTTTTCC------CTT-TCSEEEEECT
T ss_pred             cCCcEEEEEecCCCChhHHHHHHHHHHHHHHCCCe---EEEEeCCCCHHHH------hhc-cccEEEEecC
Confidence            55678999999888878888999999999999973   4554443322210      001 7888887764

>1gud_A ALBP, D-allose-binding periplasmic protein; periplasmic binding protein, X-RAY crystallography, hinge bending, conformational change; 1.7A {Escherichia coli} SCOP: c.93.1.1 PDB: 1gub_A 1rpj_A*

Probab=85.57  E-value=6  Score=32.35  Aligned_cols=96  Identities=25%  Similarity=0.313  Sum_probs=62.0

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHC-CCCCCCeEEEEeCCcchHHH---HHHHhhh-cCCccEEEEEeeeeeCCc
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKY-SVKEENIDVVWVPGSFEIGV---VAQQLGK-SGKYTAVLCIGAVVRGDT  149 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~-Gv~~e~I~vv~VPGA~ELP~---aak~L~~-~~~yDaVIaLG~VIrGeT  149 (218)
                      ..||+++...-+..-...=.+|..+.|+++ |+.   +. ..++|.|...-   +++.+++ ..++|||+|.        
T Consensus       133 ~~~I~~i~g~~~~~~~~~R~~Gf~~al~~~~g~~---~~-~~~~~~~~~~~~~~~~~~ll~~~~~~~ai~~~--------  200 (288)
T 1gud_A          133 GGEVAIIEGKAGNASGEARRNGATEAFKKASQIK---LV-ASQPADWDRIKALDVATNVLQRNPNIKAIYCA--------  200 (288)
T ss_dssp             CEEEEEEECSTTCHHHHHHHHHHHHHHHTCTTEE---EE-EEEECTTCHHHHHHHHHHHHHHCTTCCEEEES--------
T ss_pred             CCEEEEEeCCCCCchHhHHHHHHHHHHHhCCCcE---EE-EeecCCccHHHHHHHHHHHHHhCCCceEEEEC--------
Confidence            468999987655444445578999999987 653   21 23466665443   2344554 3579999986        


Q ss_pred             hhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHH
Q 027801          150 THYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQAL  188 (218)
Q Consensus       150 ~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~  188 (218)
                        .|.++-.+.+++.+..+..++.    |++-++...+.
T Consensus       201 --nD~~A~g~~~al~~~G~~~dv~----vvGfD~~~~~~  233 (288)
T 1gud_A          201 --NDTMAMGVAQAVANAGKTGKVL----VVGTDGIPEAR  233 (288)
T ss_dssp             --SHHHHHHHHHHHHHTTCTTTSE----EEEESCCHHHH
T ss_pred             --CCchHHHHHHHHHhcCCCCCeE----EEEeCCCHHHH
Confidence              4567888888888777653443    34557766553

>1jye_A Lactose operon repressor; gene regulation, protein stability, protein DNA-binding, transcription; 1.70A {Escherichia coli} SCOP: c.93.1.1 PDB: 1lbi_A 1lbg_A* 1lbh_A 1jyf_A 3edc_A 1efa_A* 1jwl_A* 2pe5_A* 1tlf_A* 2p9h_A* 2paf_A* 1cjg_A* 1l1m_A 1osl_A 2kei_A* 2kej_A* 2kek_A* 2bjc_A 1lqc_A 1lcc_A* ...

Probab=85.37  E-value=3.2  Score=35.27  Aligned_cols=67  Identities=10%  Similarity=0.116  Sum_probs=45.3

Q ss_pred             CCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCc-ch-HHHHHHHhhhcCCccEEEEEee
Q 027801           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGS-FE-IGVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA-~E-LP~aak~L~~~~~yDaVIaLG~  143 (218)
                      ....+||+|........-..+++++.+.++++|+.   +.+....+. .+ .--.++.+. ..++||+|..+.
T Consensus        59 ~~~~~Igvi~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~l~~l~-~~~vdGiIi~~~  127 (349)
T 1jye_A           59 KQSLLIGVATSSLALHAPSQIVAAILSRADQLGAS---VVVSMVERSGVEACKTAVHNLL-AQRVSGLIINYP  127 (349)
T ss_dssp             ---CEEEEEESCTTSHHHHHHHHHHHHHHHHTTCE---EEEEECCSSSHHHHHHHHHHHH-TTTCSCEEEESC
T ss_pred             CCCCEEEEEeCCCCcccHHHHHHHHHHHHHHcCCE---EEEEeCCCCcHHHHHHHHHHHH-HCCCCEEEEecC
Confidence            34568999998877677778999999999999974   555544432 22 223345554 567999998764

>4evq_A Putative ABC transporter subunit, substrate-bindi component; structural genomics, PSI-biology, midwest center for structu genomics; HET: MSE PHB; 1.40A {Rhodopseudomonas palustris} PDB: 4evr_A

Probab=85.29  E-value=3.7  Score=34.44  Aligned_cols=87  Identities=10%  Similarity=-0.024  Sum_probs=59.2

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEE-eCCcchHHHHHHHhhhcCCccEEEEEeeeeeCCchhH
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVW-VPGSFEIGVVAQQLGKSGKYTAVLCIGAVVRGDTTHY  152 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~-VPGA~ELP~aak~L~~~~~yDaVIaLG~VIrGeT~H~  152 (218)
                      ...||++|..  +........++..+.|+++|+.  .+...+ -+|..+.--.++++.+ .+.|+|++.+.         
T Consensus       150 g~~~ia~i~~--~~~~~~~~~~~~~~~l~~~G~~--v~~~~~~~~~~~d~~~~~~~l~~-~~~dai~~~~~---------  215 (375)
T 4evq_A          150 GLKKAVTVTW--KYAAGEEMVSGFKKSFTAGKGE--VVKDITIAFPDVEFQSALAEIAS-LKPDCVYAFFS---------  215 (375)
T ss_dssp             TCCEEEEEEE--SSHHHHHHHHHHHHHHHHTTCE--EEEEEEECTTCCCCHHHHHHHHH-HCCSEEEEECC---------
T ss_pred             CCcEEEEEec--CchHHHHHHHHHHHHHHHcCCe--EEEEEecCCCCccHHHHHHHHHh-cCCCEEEEecC---------
Confidence            4569999974  4556778899999999999984  222333 4576666666676643 46899998653         


Q ss_pred             HHHHHHHHHHHHHhchhcCCceEE
Q 027801          153 DAVANSAASGVLSAGVNSGVPCIF  176 (218)
Q Consensus       153 e~Va~~vs~gLm~lsL~~~vPVif  176 (218)
                      +..+-.+.+.+.+..++  +|++-
T Consensus       216 ~~~a~~~~~~~~~~g~~--vp~~~  237 (375)
T 4evq_A          216 GGGALKFIKDYAAANLG--IPLWG  237 (375)
T ss_dssp             THHHHHHHHHHHHTTCC--CCEEE
T ss_pred             cchHHHHHHHHHHcCCC--ceEEe
Confidence            12455666777777665  78754

>3h5t_A Transcriptional regulator, LACI family; DNA-dependent, protein structure initiative II(PSI II), NYSGXRC, 11232D), structural genomics; 2.53A {Corynebacterium glutamicum}

Probab=85.05  E-value=2.3  Score=36.27  Aligned_cols=65  Identities=8%  Similarity=0.138  Sum_probs=41.9

Q ss_pred             CCCCEEEEEEcc-----cCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcch--HHHHHHHhhhcCCccEEEEEee
Q 027801           73 NEGLRFALVVAR-----FNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE--IGVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        73 ~~~~RIaIV~Sr-----fn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~E--LP~aak~L~~~~~yDaVIaLG~  143 (218)
                      .+...||+|...     |....-..+++++.+.++  |.   ++.++......+  .--.++.+ ...++||||.++.
T Consensus        66 ~~s~~Igvi~~~~~~~~~~~~~~~~~~~gi~~~a~--g~---~~~~~~~~~~~~~~~~~~~~~l-~~~~vdGiIi~~~  137 (366)
T 3h5t_A           66 RRAGAIGVLLTEDLTYAFEDMASVDFLAGVAQAAG--DT---QLTLIPASPASSVDHVSAQQLV-NNAAVDGVVIYSV  137 (366)
T ss_dssp             --CCEEEEEESSCTTHHHHSHHHHHHHHHHHHHSS--SC---EEEEEECCCCTTCCHHHHHHHH-HTCCCSCEEEESC
T ss_pred             CCCCEEEEEecCCccccccCHHHHHHHHHHHHHHh--hC---CEEEEEcCCCccHHHHHHHHHH-HhCCCCEEEEecC
Confidence            345679999987     555566688889888887  54   366666553321  22223444 5678999998875

>3h5o_A Transcriptional regulator GNTR; transcription regulator, GNTR,chromobacterium violaceum, PSI, SGX, DNA-binding; 2.30A {Chromobacterium violaceum}

Probab=84.99  E-value=7  Score=32.85  Aligned_cols=100  Identities=16%  Similarity=0.265  Sum_probs=65.4

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHH---HHHHhhhc-CCccEEEEEeeeeeCCc
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGKS-GKYTAVLCIGAVVRGDT  149 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~---aak~L~~~-~~yDaVIaLG~VIrGeT  149 (218)
                      ...||+++....+... ..-++|..+.|+++|....+...+ .++.+....   +++.+++. .++|||+|..       
T Consensus       177 G~~~I~~i~~~~~~~~-~~R~~Gf~~al~~~g~~~~~~~~~-~~~~~~~~~~~~~~~~ll~~~~~~~ai~~~n-------  247 (339)
T 3h5o_A          177 GKRRIGFLGAQLDERV-MKRLDGYRAALDAADCRDAGLEWL-DPQPSSMQMGADMLDRALAERPDCDALFCCN-------  247 (339)
T ss_dssp             TCCSEEEEEESCCHHH-HHHHHHHHHHHHHTTCCCGGGEEE-ECSCCCHHHHHHHHHHHHHHCTTCCEEEESS-------
T ss_pred             CCCeEEEEeCCCCccH-HHHHHHHHHHHHHCCCCCCChheE-ecCCCCHHHHHHHHHHHHcCCCCCcEEEECC-------
Confidence            4568999998876543 455699999999999843344433 466665432   34445544 5799998742       


Q ss_pred             hhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHH
Q 027801          150 THYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQA  187 (218)
Q Consensus       150 ~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA  187 (218)
                         |.++-.+.+++.+..++  +|==..|++.++.+.+
T Consensus       248 ---D~~A~g~~~al~~~G~~--vP~disvvgfD~~~~~  280 (339)
T 3h5o_A          248 ---DDLAIGALARSQQLGIA--VPERLAIAGFNDLQPA  280 (339)
T ss_dssp             ---HHHHHHHHHHHHHTTCC--TTTTCEEECSBCCGGG
T ss_pred             ---hHHHHHHHHHHHHcCCC--CCCCEEEEEECCHHHH
Confidence               56788888888887765  4432345566665543

>2h0a_A TTHA0807, transcriptional regulator; repressor, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.80A {Thermus thermophilus}

Probab=84.97  E-value=0.73  Score=37.19  Aligned_cols=62  Identities=5%  Similarity=-0.045  Sum_probs=38.9

Q ss_pred             EEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcc--hHHHHHHHhhhcCCccEEEEEee
Q 027801           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSF--EIGVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        77 RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~--ELP~aak~L~~~~~yDaVIaLG~  143 (218)
                      .||+|...+....-..+++++.+.++++|+.   +.++...+..  |.- .++.+. ..++||+|..+.
T Consensus         1 ~Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~-~~~~l~-~~~vdgiI~~~~   64 (276)
T 2h0a_A            1 TVSVLLPFVATEFYRRLVEGIEGVLLEQRYD---LALFPILSLARLKRY-LENTTL-AYLTDGLILASY   64 (276)
T ss_dssp             CEEEEECCSCCHHHHHHHHHHHHHHGGGTCE---EEECCCCSCCCCC-----------CCCSEEEEESC
T ss_pred             CEEEEECCCCCHHHHHHHHHHHHHHHHCCCE---EEEEeCCCchhhHHH-HHHHHH-hCCCCEEEEecC
Confidence            3789998888888889999999999999873   3333222221  222 234443 467999998775

>1jye_A Lactose operon repressor; gene regulation, protein stability, protein DNA-binding, transcription; 1.70A {Escherichia coli} SCOP: c.93.1.1 PDB: 1lbi_A 1lbg_A* 1lbh_A 1jyf_A 3edc_A 1efa_A* 1jwl_A* 2pe5_A* 1tlf_A* 2p9h_A* 2paf_A* 1cjg_A* 1l1m_A 1osl_A 2kei_A* 2kej_A* 2kek_A* 2bjc_A 1lqc_A 1lcc_A* ...

Probab=84.90  E-value=9.9  Score=32.21  Aligned_cols=97  Identities=19%  Similarity=0.231  Sum_probs=62.7

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHH---HHHHhhhc-CCccEEEEEeeeeeCCch
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGKS-GKYTAVLCIGAVVRGDTT  150 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~---aak~L~~~-~~yDaVIaLG~VIrGeT~  150 (218)
                      ..||+++....+......=++|..+.|+++|+..  ..+  .+|.|...-   +++.+++. .++|||+|.         
T Consensus       179 ~~~I~~i~g~~~~~~~~~R~~Gf~~al~~~gi~~--~~~--~~~~~~~~~~~~~~~~ll~~~~~~~ai~~~---------  245 (349)
T 1jye_A          179 HQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQP--IAE--REGDWSAMSGFQQTMQMLNEGIVPTAMLVA---------  245 (349)
T ss_dssp             CCSEEEEECCTTSHHHHHHHHHHHHHHHHTTCCC--SEE--EECCSSHHHHHHHHHHHHHTTCCCSEEEES---------
T ss_pred             CCEEEEEeCCCCCccHHHHHHHHHHHHHHcCCCc--ccc--ccCCCChHHHHHHHHHHHhCCCCCCEEEEC---------
Confidence            4589999987665555566799999999999853  222  345554322   33444443 579999985         


Q ss_pred             hHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHH
Q 027801          151 HYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQA  187 (218)
Q Consensus       151 H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA  187 (218)
                       .|.++-.+.++|.+..++  +|==..|++.++.+.+
T Consensus       246 -nD~~A~g~~~al~~~G~~--vP~disvvGfD~~~~~  279 (349)
T 1jye_A          246 -NDQMALGAMRAITESGLR--VGADISVVGYDDTEDS  279 (349)
T ss_dssp             -SHHHHHHHHHHHHHTTCC--BTTTBEEECSBCCGGG
T ss_pred             -ChHHHHHHHHHHHHcCCC--CCCcEEEEEECCcHHH
Confidence             356788888888887664  3422245566665544

>3kjx_A Transcriptional regulator, LACI family; LACL family, protein structure initiative II(PSI II), NYSGXRC, structural genomics; 2.33A {Silicibacter pomeroyi}

Probab=84.86  E-value=4.1  Score=34.37  Aligned_cols=98  Identities=17%  Similarity=0.272  Sum_probs=63.5

Q ss_pred             CCEEEEEEcccC-HHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHH---HHHHhhh-cCCccEEEEEeeeeeCCc
Q 027801           75 GLRFALVVARFN-ELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGK-SGKYTAVLCIGAVVRGDT  149 (218)
Q Consensus        75 ~~RIaIV~Srfn-~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~---aak~L~~-~~~yDaVIaLG~VIrGeT  149 (218)
                      ..||+++..... ......=++|..+.|+++|+......  ..+|.+....   +++.+++ ..++|||+|.        
T Consensus       185 ~~~I~~i~~~~~~~~~~~~R~~Gf~~al~~~g~~~~~~~--~~~~~~~~~~~~~~~~~ll~~~~~~~ai~~~--------  254 (344)
T 3kjx_A          185 YRRIGFMGTKMPLDYRARKRFEGFTEVLGKNGVEIEDRE--FYSGGSALAKGREMTQAMLERSPDLDFLYYS--------  254 (344)
T ss_dssp             CCSCCEEESSTTTCHHHHHHHHHHHHHHHHTTCCCSCEE--ECSSCCCHHHHHHHHHHHHHHSTTCCEEEES--------
T ss_pred             CCeEEEEecCcccCccHHHHHHHHHHHHHHcCCCCChhe--EEeCCCCHHHHHHHHHHHHhcCCCCCEEEEC--------
Confidence            458999998762 24445556999999999998644333  3456554432   3444554 4589999975        


Q ss_pred             hhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHH
Q 027801          150 THYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQ  186 (218)
Q Consensus       150 ~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQ  186 (218)
                        .|.++-.+.+++.+..++  +|==..|++.++.+.
T Consensus       255 --nd~~A~g~~~al~~~g~~--vP~disvvg~D~~~~  287 (344)
T 3kjx_A          255 --NDMIAAGGLLYLLEQGID--IPGQIGLAGFNNVEL  287 (344)
T ss_dssp             --SHHHHHHHHHHHHHTTCC--TTTTCEEECSBCCGG
T ss_pred             --CHHHHHHHHHHHHHcCCC--CCCceEEEEECChHH
Confidence              356888888888887764  442234556665544

>2ioy_A Periplasmic sugar-binding protein; ribose binding protein, thermophilic proteins; HET: RIP; 1.90A {Thermoanaerobacter tengcongensis}

Probab=84.64  E-value=6.3  Score=32.06  Aligned_cols=95  Identities=20%  Similarity=0.178  Sum_probs=61.9

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHC-CCCCCCeEEEEeCCcchHHH---HHHHhhh-cCCccEEEEEeeeeeCCc
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKY-SVKEENIDVVWVPGSFEIGV---VAQQLGK-SGKYTAVLCIGAVVRGDT  149 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~-Gv~~e~I~vv~VPGA~ELP~---aak~L~~-~~~yDaVIaLG~VIrGeT  149 (218)
                      ..||+++...-+......=.+|..+.|+++ |+.   +. ...+|.|...-   +++.+++ ..++|||+|..       
T Consensus       123 ~~~I~~i~g~~~~~~~~~R~~Gf~~al~~~~~~~---~~-~~~~~~~~~~~~~~~~~~ll~~~~~~~ai~~~n-------  191 (283)
T 2ioy_A          123 KGNVVELEGIPGASAARDRGKGFDEAIAKYPDIK---IV-AKQAADFDRSKGLSVMENILQAQPKIDAVFAQN-------  191 (283)
T ss_dssp             CEEEEEEECCTTCHHHHHHHHHHHHHHTTCTTEE---EE-EEEECTTCHHHHHHHHHHHHHHCSCCCEEEESS-------
T ss_pred             CceEEEEECCCCCccHHHHHHHHHHHHHhCCCCE---EE-eeccCCCCHHHHHHHHHHHHHhCCCccEEEECC-------
Confidence            469999987654444455568999999987 653   21 12456554432   3445554 45799999874       


Q ss_pred             hhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHH
Q 027801          150 THYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQAL  188 (218)
Q Consensus       150 ~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~  188 (218)
                         |.++-.+.+++.+..+ .++.|    ++.++.+.+.
T Consensus       192 ---D~~A~g~~~al~~~G~-~di~v----iG~D~~~~~~  222 (283)
T 2ioy_A          192 ---DEMALGAIKAIEAANR-QGIIV----VGFDGTEDAL  222 (283)
T ss_dssp             ---HHHHHHHHHHHHHTTC-CCCEE----EEEECCHHHH
T ss_pred             ---chHHHHHHHHHHHCCC-CCcEE----EEeCCCHHHH
Confidence               6688888899988888 46654    3445655553

>3cs3_A Sugar-binding transcriptional regulator, LACI FAM; structural genomics, sugar-binding transcriptional regulator structure initiative; 2.40A {Enterococcus faecalis}

Probab=84.39  E-value=4.2  Score=32.89  Aligned_cols=96  Identities=11%  Similarity=0.150  Sum_probs=62.6

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH---HHHHHhhhc--CCccEEEEEeeeeeCCc
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGKS--GKYTAVLCIGAVVRGDT  149 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP---~aak~L~~~--~~yDaVIaLG~VIrGeT  149 (218)
                      ..||+++...-.......-.+|..+.|+++|++   +++  +.+.|...   -+++.+++.  .++|||+|.        
T Consensus       118 ~~~i~~i~~~~~~~~~~~R~~gf~~~l~~~g~~---~~~--~~~~~~~~~~~~~~~~~l~~~~~~~~ai~~~--------  184 (277)
T 3cs3_A          118 SKKVLLLSGPEKGYDSQERLAVSTRELTRFGIP---YEI--IQGDFTEPSGYAAAKKILSQPQTEPVDVFAF--------  184 (277)
T ss_dssp             CSCEEEEECCTTSHHHHHHHHHHHHHHHHTTCC---EEE--EECCSSHHHHHHHHHHHTTSCCCSSEEEEES--------
T ss_pred             CceEEEEeCCccCccHHHHHHHHHHHHHHcCCC---eeE--EeCCCChhHHHHHHHHHHhcCCCCCcEEEEc--------
Confidence            468999988765555566679999999999975   332  34555433   234555554  579999975        


Q ss_pred             hhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHH
Q 027801          150 THYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQA  187 (218)
Q Consensus       150 ~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA  187 (218)
                        .|.++-.+.+++.+..++  +|==..|++.++.+.+
T Consensus       185 --~d~~a~g~~~al~~~g~~--vP~di~vvg~d~~~~~  218 (277)
T 3cs3_A          185 --NDEMAIGVYKYVAETNYQ--MGKDIRIIGFDNSELG  218 (277)
T ss_dssp             --SHHHHHHHHHHHTTSSCC--BTTTEEEECSSCCHHH
T ss_pred             --ChHHHHHHHHHHHHcCCC--CCCcEEEEEeCCcHHH
Confidence              245677777777665543  4433456777776655

>3o74_A Fructose transport system repressor FRUR; dual transcriptional regulator, DNA, transcription; 2.00A {Pseudomonas putida} PDB: 3o75_A*

Probab=84.32  E-value=1.8  Score=34.66  Aligned_cols=95  Identities=17%  Similarity=0.076  Sum_probs=61.4

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH---HHHHHhhhc-C-CccEEEEEeeeeeCC
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGKS-G-KYTAVLCIGAVVRGD  148 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP---~aak~L~~~-~-~yDaVIaLG~VIrGe  148 (218)
                      ...||+++...........-.+|..+.|+++|+.   +..+ ..+.+...   -+++.+++. . ++|||+|.       
T Consensus       119 G~~~i~~i~~~~~~~~~~~R~~gf~~~l~~~~~~---~~~~-~~~~~~~~~~~~~~~~~l~~~~~~~~ai~~~-------  187 (272)
T 3o74_A          119 APRSIALIGARPELSVSQARAGGFDEALQGYTGE---VRRY-QGEAFSRECGQRLMQQLIDDLGGLPDALVTT-------  187 (272)
T ss_dssp             CCSEEEEEEECTTSHHHHHHHHHHHHHTTTCCSE---EEEE-EESSSSHHHHHHHHHHHHHHHTSCCSEEEES-------
T ss_pred             CCcEEEEEecCCCCccHHHHHHHHHHHHHHcCCC---hhee-ecCCCCHHHHHHHHHHHHhcCCCCCcEEEEe-------
Confidence            4469999998776666777789999999999974   2322 34444332   234445544 4 69999985       


Q ss_pred             chhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHH
Q 027801          149 TTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMD  185 (218)
Q Consensus       149 T~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~e  185 (218)
                         .|.++-.+.+++.+..+   +|==..|++.++.+
T Consensus       188 ---~d~~a~g~~~al~~~g~---vp~di~vvg~d~~~  218 (272)
T 3o74_A          188 ---SYVLLQGVFDTLQARPV---DSRQLQLGTFGDNQ  218 (272)
T ss_dssp             ---SHHHHHHHHHHHHTSCG---GGCCCEEEEESCCG
T ss_pred             ---CchHHHHHHHHHHHcCC---CccceEEEEeCChH
Confidence               35677777788877765   35333445555544

>3iwt_A 178AA long hypothetical molybdenum cofactor biosy protein B; biosynthesis, structural genomics, UNKN function, NPPSFA; HET: PEG; 1.90A {Sulfolobus tokodaii}

Probab=84.15  E-value=3.8  Score=32.55  Aligned_cols=82  Identities=13%  Similarity=0.116  Sum_probs=51.6

Q ss_pred             CCCEEEEEEc---ccCHHH-----HHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHHhhhcCCccEEEEEeee
Q 027801           74 EGLRFALVVA---RFNELV-----TKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGAV  144 (218)
Q Consensus        74 ~~~RIaIV~S---rfn~~I-----t~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~L~~~~~yDaVIaLG~V  144 (218)
                      +.+|++||..   ++..++     +|.=-.-..+.|.+.|+.  -++...||.-.|.- -+++.+...+++|.||+-|-+
T Consensus        14 ~~~~v~iitvsd~~~~~~~~~g~i~D~ng~~L~~~L~~~G~~--v~~~~iV~Dd~~~i~~al~~~~a~~~~DlVittGG~   91 (178)
T 3iwt_A           14 KSLNFYVITISTSRYEKLLKKEPIVDESGDIIKQLLIENGHK--IIGYSLVPDDKIKILKAFTDALSIDEVDVIISTGGT   91 (178)
T ss_dssp             CCCEEEEEEECHHHHHHHHTTCCCCCHHHHHHHHHHHHTTCE--EEEEEEECSCHHHHHHHHHHHHTCTTCCEEEEESCC
T ss_pred             CCCEEEEEEEcCCCccccccCCCCCcchHHHHHHHHHHCCCE--EEEEEEeCCCHHHHHHHHHHHHhcCCCCEEEecCCc
Confidence            5689999963   222221     122112345677888984  57777899988744 445555556889999999998


Q ss_pred             eeCCchhHHHHHHHHH
Q 027801          145 VRGDTTHYDAVANSAA  160 (218)
Q Consensus       145 IrGeT~H~e~Va~~vs  160 (218)
                        |-| ++|+..+++.
T Consensus        92 --g~~-~~D~t~ea~~  104 (178)
T 3iwt_A           92 --GYS-PTDITVETIR  104 (178)
T ss_dssp             --SSS-TTCCHHHHHG
T ss_pred             --ccC-CCCchHHHHH
Confidence              433 4555554443

>3o1i_D Periplasmic protein TORT; ligand free, two component sensor, periplasmic binding prote signaling protein; HET: PE4; 2.80A {Vibrio parahaemolyticus} PDB: 3o1h_B* 3o1j_C

Probab=84.05  E-value=1.2  Score=36.30  Aligned_cols=88  Identities=17%  Similarity=0.084  Sum_probs=55.7

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHH---HHHhhhcCCccEEEEEeeeeeCCchh
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVV---AQQLGKSGKYTAVLCIGAVVRGDTTH  151 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~a---ak~L~~~~~yDaVIaLG~VIrGeT~H  151 (218)
                      ..||+++...-.......-++|..+.|+++|+.   +.. .+.+.+....+   ++.+++..++|| ||.          
T Consensus       136 ~~~i~~i~~~~~~~~~~~R~~gf~~~l~~~~~~---~~~-~~~~~~~~~~~~~~~~~~l~~~~~~a-i~~----------  200 (304)
T 3o1i_D          136 KTNIALLLGPRTRGGTKPVTTGFYEAIKNSDIH---IVD-SFWADNDKELQRNLVQRVIDMGNIDY-IVG----------  200 (304)
T ss_dssp             CEEEEEECCCC-----CHHHHHHHHTTTTBTEE---EEE-CCCCCSCHHHHHHHHHHHHHHSCCSE-EEE----------
T ss_pred             CCEEEEEECCCCcchHHHHHHHHHHHHhcCCCE---EEE-eecCCCcHHHHHHHHHHHHcCCCCCE-EEe----------
Confidence            568999987765555556678999999988764   221 23565554322   333446678999 652          


Q ss_pred             HHHHHHHHHHHHHHhchhcCCceEEEE
Q 027801          152 YDAVANSAASGVLSAGVNSGVPCIFGV  178 (218)
Q Consensus       152 ~e~Va~~vs~gLm~lsL~~~vPVifGV  178 (218)
                      .|.++-.+.++|.+..++.++.|+ |.
T Consensus       201 ~d~~a~g~~~al~~~g~~~di~vv-g~  226 (304)
T 3o1i_D          201 SAVAIEAAISELRSADKTHDIGLV-SV  226 (304)
T ss_dssp             CHHHHHHHHHHHTTTTCGGGSEEB-CS
T ss_pred             cCcchHHHHHHHHhcCCCCCeEEE-Ee
Confidence            256888888999988887556554 44

>4eyg_A Twin-arginine translocation pathway signal; PSI-biology, MCSG, midwest center for structural genomics, transporter; HET: VNL; 1.86A {Rhodopseudomonas palustris} PDB: 4ey3_A* 3t0n_A* 4eyk_A*

Probab=83.67  E-value=7.8  Score=32.32  Aligned_cols=89  Identities=11%  Similarity=0.035  Sum_probs=60.3

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEe-CCcchHHHHHHHhhhcCCccEEEEEeeeeeCCchhH
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWV-PGSFEIGVVAQQLGKSGKYTAVLCIGAVVRGDTTHY  152 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~V-PGA~ELP~aak~L~~~~~yDaVIaLG~VIrGeT~H~  152 (218)
                      ...||++|..  +......+.++..+.|+++|+.  .+....+ +|..+.--.++++.+ .+.|+|++.+.   +.    
T Consensus       138 g~~~ia~i~~--~~~~g~~~~~~~~~~l~~~g~~--v~~~~~~~~~~~d~~~~~~~l~~-~~~d~v~~~~~---~~----  205 (368)
T 4eyg_A          138 GIKKVATLTS--DYAPGNDALAFFKERFTAGGGE--IVEEIKVPLANPDFAPFLQRMKD-AKPDAMFVFVP---AG----  205 (368)
T ss_dssp             TCCEEEEEEE--SSHHHHHHHHHHHHHHHHTTCE--EEEEEEECSSSCCCHHHHHHHHH-HCCSEEEEECC---TT----
T ss_pred             CCCEEEEEec--CchHhHHHHHHHHHHHHHcCCE--EEEEEeCCCCCCcHHHHHHHHHh-cCCCEEEEecc---ch----
Confidence            3469999984  4556778889999999999974  2333344 466666666677654 46899998653   22    


Q ss_pred             HHHHHHHHHHHHHhchhcC-CceEE
Q 027801          153 DAVANSAASGVLSAGVNSG-VPCIF  176 (218)
Q Consensus       153 e~Va~~vs~gLm~lsL~~~-vPVif  176 (218)
                        .+..+.+.+.+..+... +|++.
T Consensus       206 --~a~~~~~~~~~~g~~~~~v~~~~  228 (368)
T 4eyg_A          206 --QGGNFMKQFAERGLDKSGIKVIG  228 (368)
T ss_dssp             --CHHHHHHHHHHTTGGGTTCEEEE
T ss_pred             --HHHHHHHHHHHcCCCcCCceEEe
Confidence              34556677777777655 77654

>3e3m_A Transcriptional regulator, LACI family; structural genomics, DNA-binding, plasmid, transcription regulation, PSI-2; 1.60A {Silicibacter pomeroyi}

Probab=82.98  E-value=6  Score=33.56  Aligned_cols=101  Identities=14%  Similarity=0.178  Sum_probs=65.8

Q ss_pred             CCCEEEEEEcccCHHH-HHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH---HHHHHhhh-cCCccEEEEEeeeeeCC
Q 027801           74 EGLRFALVVARFNELV-TKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGK-SGKYTAVLCIGAVVRGD  148 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~I-t~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP---~aak~L~~-~~~yDaVIaLG~VIrGe  148 (218)
                      ...||+++........ ...-++|..+.|+++|+..+. .+....+.+..-   -+++.+++ ..++|||+|.       
T Consensus       186 G~r~I~~i~~~~~~~~~~~~R~~Gf~~al~~~g~~~~~-~~~~~~~~~~~~~~~~~~~~ll~~~~~~~ai~~~-------  257 (355)
T 3e3m_A          186 GFRKIVFLGEKDDDWTRGAARRAGFKRAMREAGLNPDQ-EIRLGAPPLSIEDGVAAAELILQEYPDTDCIFCV-------  257 (355)
T ss_dssp             TCCSEEEEEESSCTTSHHHHHHHHHHHHHHHTTSCSCC-EEEESCSSCCHHHHHHHHHHHHHHCTTCCEEEES-------
T ss_pred             CCCeEEEEccCcccChhHHHHHHHHHHHHHHCCcCCCc-cEEEecCCCCHHHHHHHHHHHHcCCCCCcEEEEC-------
Confidence            3458999998655432 445579999999999987432 233344444322   23444544 4689999984       


Q ss_pred             chhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHH
Q 027801          149 TTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQA  187 (218)
Q Consensus       149 T~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA  187 (218)
                         .|.++-.+.+++.+..++  +|==..|++.++.+.+
T Consensus       258 ---nD~~A~g~~~al~~~G~~--vP~disvigfD~~~~~  291 (355)
T 3e3m_A          258 ---SDMPAFGLLSRLKSIGVA--VPEQVSVVGFGNFEVS  291 (355)
T ss_dssp             ---SHHHHHHHHHHHHHHTCC--TTTTCEEECSSCCHHH
T ss_pred             ---ChHHHHHHHHHHHHcCCC--CCCceEEEEECChHHH
Confidence               367888888999888764  4433456677776554

>3ipc_A ABC transporter, substrate binding protein (amino; venus flytrap domain, transport protein; 1.30A {Agrobacterium tumefaciens} PDB: 3ip5_A 3ip6_A 3ip7_A 3ip9_A 3ipa_A

Probab=82.87  E-value=12  Score=31.15  Aligned_cols=85  Identities=9%  Similarity=0.079  Sum_probs=57.5

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEE-eCCcchHHHHHHHhhhcCCccEEEEEeeeeeCCchhHH
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVW-VPGSFEIGVVAQQLGKSGKYTAVLCIGAVVRGDTTHYD  153 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~-VPGA~ELP~aak~L~~~~~yDaVIaLG~VIrGeT~H~e  153 (218)
                      ..||++|..  +......+.++..+.|+++|+..  +.... -+|..+.--.++++. ..+.|+|++.+.         +
T Consensus       138 ~~~iaii~~--~~~~~~~~~~~~~~~l~~~g~~v--~~~~~~~~~~~d~~~~~~~l~-~~~~d~v~~~~~---------~  203 (356)
T 3ipc_A          138 DAKVAIIHD--KTPYGQGLADETKKAANAAGVTE--VMYEGVNVGDKDFSALISKMK-EAGVSIIYWGGL---------H  203 (356)
T ss_dssp             TCCEEEEEC--SSHHHHHHHHHHHHHHHHTTCCC--SEEEECCTTCCCCHHHHHHHH-HTTCCEEEEESC---------H
T ss_pred             CCEEEEEeC--CChHHHHHHHHHHHHHHHcCCEE--EEEEeeCCCCCCHHHHHHHHH-hcCCCEEEEccC---------c
Confidence            468999987  45667888999999999999863  23333 457777666777764 457899886543         1


Q ss_pred             HHHHHHHHHHHHhchhcCCceE
Q 027801          154 AVANSAASGVLSAGVNSGVPCI  175 (218)
Q Consensus       154 ~Va~~vs~gLm~lsL~~~vPVi  175 (218)
                      -.+..+.+.+.+..++  +|++
T Consensus       204 ~~a~~~~~~~~~~g~~--~~~~  223 (356)
T 3ipc_A          204 TEAGLIIRQAADQGLK--AKLV  223 (356)
T ss_dssp             HHHHHHHHHHHHHTCC--CEEE
T ss_pred             hHHHHHHHHHHHCCCC--CcEE
Confidence            1233566666666654  6754

>2h3h_A Sugar ABC transporter, periplasmic sugar-binding protein; glucose binding protein, periplasmic binding protein, GBP; HET: BGC; 1.70A {Thermotoga maritima} PDB: 2qvc_A* 3c6q_B*

Probab=82.04  E-value=11  Score=31.08  Aligned_cols=96  Identities=11%  Similarity=0.099  Sum_probs=58.2

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH---HHHHHhhhc-CCccEEEEEeeeeeCCc
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGKS-GKYTAVLCIGAVVRGDT  149 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP---~aak~L~~~-~~yDaVIaLG~VIrGeT  149 (218)
                      ...||+++...-+......-.+|..+.|++.|+..  ..+  +++.+...   -+++.+++. .++|||+|..       
T Consensus       122 G~~~I~~i~~~~~~~~~~~R~~gf~~~l~~~g~~~--~~~--~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~-------  190 (313)
T 2h3h_A          122 GKGKVVIGTGSLTAMNSLQRIQGFKDAIKDSEIEI--VDI--LNDEEDGARAVSLAEAALNAHPDLDAFFGVY-------  190 (313)
T ss_dssp             SCSEEEEEESCSSCHHHHHHHHHHHHHHTTSSCEE--EEE--EECSSCHHHHHHHHHHHHHHCTTCCEEEECS-------
T ss_pred             CCCEEEEEECCCCCccHHHHHHHHHHHhcCCCCEE--EEe--ecCCCCHHHHHHHHHHHHHHCcCceEEEEcC-------
Confidence            34699999987555556667799999999988741  222  34445432   233444443 5799999853       


Q ss_pred             hhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHH
Q 027801          150 THYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQA  187 (218)
Q Consensus       150 ~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA  187 (218)
                         |.++-.+.+++.+..+-.+++    |++.++...+
T Consensus       191 ---d~~a~g~~~al~~~G~p~dv~----vvg~d~~~~~  221 (313)
T 2h3h_A          191 ---AYNGPAQALVVKNAGKVGKVK----IVCFDTTPDI  221 (313)
T ss_dssp             ---TTHHHHHHHHHHHTTCTTTSE----EEEECCCHHH
T ss_pred             ---CCccHHHHHHHHHcCCCCCeE----EEEeCCCHHH
Confidence               235666777777766433333    3445555443

>3hut_A Putative branched-chain amino acid ABC transporter; extracellular ligand-binding receptor,transport protein; 1.93A {Rhodospirillum rubrum atcc 11170}

Probab=81.90  E-value=7.9  Score=32.26  Aligned_cols=86  Identities=12%  Similarity=-0.004  Sum_probs=58.7

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEE-EEeCCcchHHHHHHHhhhcCCccEEEEEeeeeeCCchhH
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDV-VWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVVRGDTTHY  152 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~v-v~VPGA~ELP~aak~L~~~~~yDaVIaLG~VIrGeT~H~  152 (218)
                      ...||++|.  -+......+.++..+.|+++|+..  ... ..-+|..+.--.++++.+ .+.|+|++.+-.        
T Consensus       138 g~~~ia~i~--~~~~~~~~~~~~~~~~l~~~g~~v--~~~~~~~~~~~~~~~~~~~l~~-~~~d~i~~~~~~--------  204 (358)
T 3hut_A          138 GFTSVAVIG--VTTDWGLSSAQAFRKAFELRGGAV--VVNEEVPPGNRRFDDVIDEIED-EAPQAIYLAMAY--------  204 (358)
T ss_dssp             TCCEEEEEE--ESSHHHHHHHHHHHHHHHHTTCEE--EEEEEECTTCCCCHHHHHHHHH-HCCSEEEEESCH--------
T ss_pred             CCCEEEEEe--cCcHHHHHHHHHHHHHHHHcCCEE--EEEEecCCCCccHHHHHHHHHh-cCCCEEEEccCc--------
Confidence            346999997  355667888999999999999852  222 234566776667777754 568999886531        


Q ss_pred             HHHHHHHHHHHHHhchhcCCceE
Q 027801          153 DAVANSAASGVLSAGVNSGVPCI  175 (218)
Q Consensus       153 e~Va~~vs~gLm~lsL~~~vPVi  175 (218)
                       -.+-.+.+.+.+..+  .+|++
T Consensus       205 -~~a~~~~~~~~~~g~--~~p~~  224 (358)
T 3hut_A          205 -EDAAPFLRALRARGS--ALPVY  224 (358)
T ss_dssp             -HHHHHHHHHHHHTTC--CCCEE
T ss_pred             -hHHHHHHHHHHHcCC--CCcEE
Confidence             244566677777666  47764

>3lop_A Substrate binding periplasmic protein; protein structure initiative II(PSI II), NYSGXRC, structural genomics; 1.55A {Ralstonia solanacearum}

Probab=81.78  E-value=16  Score=30.67  Aligned_cols=86  Identities=12%  Similarity=0.092  Sum_probs=57.1

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEeeeeeCCchhHH
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVVRGDTTHYD  153 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~VIrGeT~H~e  153 (218)
                      ...||++|...  ......++++..+.|+++|+.. ......-+|..+.--.++++. ..+.|+|++.+.         +
T Consensus       140 g~~~iaii~~~--~~~g~~~~~~~~~~~~~~G~~v-~~~~~~~~~~~d~~~~~~~l~-~~~~d~v~~~~~---------~  206 (364)
T 3lop_A          140 GVTRIGVLYQE--DALGKEAITGVERTLKAHALAI-TAMASYPRNTANVGPAVDKLL-AADVQAIFLGAT---------A  206 (364)
T ss_dssp             TCCCEEEEEET--THHHHHHHHHHHHHHHTTTCCC-SEEEEECTTSCCCHHHHHHHH-HSCCSEEEEESC---------H
T ss_pred             CCceEEEEEeC--chhhHHHHHHHHHHHHHcCCcE-EEEEEecCCCccHHHHHHHHH-hCCCCEEEEecC---------c
Confidence            34689999764  4667788999999999999863 223333467777666667764 467899988653         1


Q ss_pred             HHHHHHHHHHHHhchhcCCce
Q 027801          154 AVANSAASGVLSAGVNSGVPC  174 (218)
Q Consensus       154 ~Va~~vs~gLm~lsL~~~vPV  174 (218)
                      -.+..+.+.+.+..+  .+|+
T Consensus       207 ~~a~~~~~~~~~~g~--~~~~  225 (364)
T 3lop_A          207 EPAAQFVRQYRARGG--EAQL  225 (364)
T ss_dssp             HHHHHHHHHHHHTTC--CCEE
T ss_pred             HHHHHHHHHHHHcCC--CCeE
Confidence            234556666666655  4564

>3ctp_A Periplasmic binding protein/LACI transcriptional; structural genomics, protein structure initiative; HET: XLF; 1.41A {Alkaliphilus metalliredigens}

Probab=81.47  E-value=3.1  Score=34.96  Aligned_cols=121  Identities=12%  Similarity=0.088  Sum_probs=71.5

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHH---HHHHhhhcCCccEEEEEeeeeeCCchh
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGKSGKYTAVLCIGAVVRGDTTH  151 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~---aak~L~~~~~yDaVIaLG~VIrGeT~H  151 (218)
                      ..||+++...-+......-++|..+.|+++|++.   +...++|.|...-   +++.+++..++|||+|.          
T Consensus       172 ~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~g~~~---~~~~~~~~~~~~~~~~~~~~ll~~~~~~ai~~~----------  238 (330)
T 3ctp_A          172 CRKILHIKGPEVFEATELRYKGFLDGARAKDLEI---DFIEFQHDFQVKMLEEDINSMKDIVNYDGIFVF----------  238 (330)
T ss_dssp             CCSEEEEECCTTCHHHHHHHHHHHHHHHHTTCCC---EEEECSSSCCGGGGGCCCTTGGGGGGSSEEEES----------
T ss_pred             CCeEEEEeCCccCccHHHHHHHHHHHHHHcCCCc---ceeEEcCCCCHHHHHHHHHHHhcCCCCcEEEEC----------
Confidence            4589999887554445566799999999999863   2223466554321   22344433579999983          


Q ss_pred             HHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHhhCC-------CCCCcHHHHHHHHHHHHH
Q 027801          152 YDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGG-------KSGNKGAEAALTAIEMAS  211 (218)
Q Consensus       152 ~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~Rag~-------k~gnKG~EAA~aAleM~~  211 (218)
                      .|.++-.+.+++.+..++  +|==..|++.++.+.+.. ..+       ....-|..|+...+++++
T Consensus       239 ~d~~A~g~~~al~~~G~~--vP~disvvg~D~~~~~~~-~~p~lttv~~~~~~~g~~a~~~l~~~i~  302 (330)
T 3ctp_A          239 NDIAAATVMRALKKRGVS--IPQEVQIIGFDNSFIGEL-LYPSLTTINQPIEALAYTIIELLIKIIN  302 (330)
T ss_dssp             SHHHHHHHHHHHHHTTCC--TTTTCEEECSBCCTHHHH-SSSCCBEEECCHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCC--CCCCeEEEEECChHHHhc-CCCCcceEECCHHHHHHHHHHHHHHHhc
Confidence            355777788888877664  442224556666555421 111       122345556655555543

>3lkv_A Uncharacterized conserved domain protein; ATPase binding cassette, PSI, MCSG, structural genomics, Pro structure initiative; HET: PHE; 2.20A {Vibrio cholerae}

Probab=81.46  E-value=16  Score=30.70  Aligned_cols=114  Identities=16%  Similarity=0.093  Sum_probs=74.8

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEeeeeeCCchhHH
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVVRGDTTHYD  153 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~VIrGeT~H~e  153 (218)
                      ...||+|+...-... .....+...+.++++|+.   +..+.+....|+.-+++.+.  ++.|++.+..         +.
T Consensus       139 ~~k~vgvi~~~~~~~-s~~~~~~~~~~~~~~g~~---~v~~~~~~~~~~~~~~~~l~--~~~d~i~~~~---------d~  203 (302)
T 3lkv_A          139 NVKSIGVVYNPGEAN-AVSLMELLKLSAAKHGIK---LVEATALKSADVQSATQAIA--EKSDVIYALI---------DN  203 (302)
T ss_dssp             TCCEEEEEECTTCHH-HHHHHHHHHHHHHHTTCE---EEEEECSSGGGHHHHHHHHH--TTCSEEEECS---------CH
T ss_pred             CCCEEEEEeCCCccc-HHHHHHHHHHHHHHcCCE---EEEEecCChHHHHHHHHhcc--CCeeEEEEeC---------Cc
Confidence            346899997654322 234567788888898984   77788999999999988885  5688886532         22


Q ss_pred             HHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHhhCC------CCCCcHHHHHHHHHHHH
Q 027801          154 AVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGG------KSGNKGAEAALTAIEMA  210 (218)
Q Consensus       154 ~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~Rag~------k~gnKG~EAA~aAleM~  210 (218)
                      .+. .....+..++.+.++||+-+     + +..+. .|.      ....-|..||..|.+++
T Consensus       204 ~~~-~~~~~i~~~~~~~~iPv~~~-----~-~~~v~-~G~l~~~~~~~~~~G~~aa~~a~~IL  258 (302)
T 3lkv_A          204 TVA-SAIEGMIVAANQAKTPVFGA-----A-TSYVE-RGAIASLGFDYYQIGVQTADYVAAIL  258 (302)
T ss_dssp             HHH-HTHHHHHHHHHHTTCCEEES-----S-HHHHH-TTCSEEEECCHHHHHHHHHHHHHHHH
T ss_pred             chh-hHHHHHHHHHhhcCCceeec-----c-ccccc-CCceEEEecCHHHHHHHHHHHHHHHH
Confidence            233 35678889999999998643     1 12222 231      12234666666666654

>2rjo_A Twin-arginine translocation pathway signal protei; PSI-2, NYSGXRC, twin arginine translocation pathway signal P structural genomics; HET: GAL; 2.05A {Burkholderia phytofirmans}

Probab=81.25  E-value=8.3  Score=32.20  Aligned_cols=96  Identities=16%  Similarity=0.175  Sum_probs=63.8

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHC-CCCCCCeEEEEeCCcchHH---HHHHHhhh--cCCccEEEEEeeeeeCC
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKY-SVKEENIDVVWVPGSFEIG---VVAQQLGK--SGKYTAVLCIGAVVRGD  148 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~-Gv~~e~I~vv~VPGA~ELP---~aak~L~~--~~~yDaVIaLG~VIrGe  148 (218)
                      ..||+++...-+......-.+|..+.|+++ |+.   +.. .+.|.+...   -+++.+++  ..++|||+|.       
T Consensus       136 ~~~I~~i~g~~~~~~~~~R~~Gf~~al~~~pgi~---~~~-~~~~~~~~~~~~~~~~~ll~~~~~~~~aI~~~-------  204 (332)
T 2rjo_A          136 KGGVVALGGIFSNVPAIERKAGLDAALKKFPGIQ---LLD-FQVADWNSQKAFPIMQAWMTRFNSKIKGVWAA-------  204 (332)
T ss_dssp             CEEEEEEECCTTCHHHHHHHHHHHHHHHTCTTEE---EEE-EEECTTCHHHHHHHHHHHHHHHGGGEEEEEES-------
T ss_pred             CCeEEEEECCCCCccHHHHHHHHHHHHHhCCCcE---EEe-eccCCCCHHHHHHHHHHHHHhcCCCeeEEEEC-------
Confidence            458999988765555667789999999998 764   221 134555433   23445554  3579999973       


Q ss_pred             chhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHH
Q 027801          149 TTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQAL  188 (218)
Q Consensus       149 T~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~  188 (218)
                         .|.++-.+.+++.+..++.+++    |++.++...+.
T Consensus       205 ---nd~~A~g~~~al~~~G~~~di~----vvg~D~~~~~~  237 (332)
T 2rjo_A          205 ---NDDMALGAIEALRAEGLAGQIP----VTGMDGTQPGL  237 (332)
T ss_dssp             ---SHHHHHHHHHHHHHTTCBTTBC----EECSBCCHHHH
T ss_pred             ---CCchHHHHHHHHHHcCCCCCCE----EEeecCCHHHH
Confidence               3567888888998888764444    45667766654

>2h3h_A Sugar ABC transporter, periplasmic sugar-binding protein; glucose binding protein, periplasmic binding protein, GBP; HET: BGC; 1.70A {Thermotoga maritima} PDB: 2qvc_A* 3c6q_B*

Probab=81.24  E-value=3.9  Score=33.87  Aligned_cols=62  Identities=11%  Similarity=0.105  Sum_probs=43.2

Q ss_pred             CEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH---HHHHHhhhcCCccEEEEEee
Q 027801           76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        76 ~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP---~aak~L~~~~~yDaVIaLG~  143 (218)
                      .+|++|...+.. .-..+++++.+.++++|+.   +.++ .+...+..   -.++.+. ..++||||..+.
T Consensus         2 ~~Ig~i~~~~~~-~~~~~~~gi~~~~~~~g~~---~~~~-~~~~~~~~~~~~~i~~l~-~~~vdgiIi~~~   66 (313)
T 2h3h_A            2 LTIGVIGKSVHP-YWSQVEQGVKAAGKALGVD---TKFF-VPQKEDINAQLQMLESFI-AEGVNGIAIAPS   66 (313)
T ss_dssp             CEEEEECSCSSH-HHHHHHHHHHHHHHHHTCE---EEEE-CCSSSCHHHHHHHHHHHH-HTTCSEEEECCS
T ss_pred             eEEEEEeCCCcH-HHHHHHHHHHHHHHHcCCE---EEEE-CCCCCCHHHHHHHHHHHH-HcCCCEEEEeCC
Confidence            579999988888 8889999999999999873   3333 24333322   2344454 467999998765

>1jx6_A LUXP protein; protein-ligand complex, signaling protein; HET: AI2; 1.50A {Vibrio harveyi} SCOP: c.93.1.1 PDB: 1zhh_A* 2hj9_A*

Probab=81.02  E-value=8.5  Score=32.12  Aligned_cols=92  Identities=7%  Similarity=-0.052  Sum_probs=61.4

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHH---HHHHhhh-cCCccEEEEEeeeeeCCch
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGK-SGKYTAVLCIGAVVRGDTT  150 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~---aak~L~~-~~~yDaVIaLG~VIrGeT~  150 (218)
                      ..||+++....+. ....-.+|..+.|+++|. .+ .. ..++|.+..--   +++.+++ ..++|||+|.         
T Consensus       175 ~~~I~~i~~~~~~-~~~~R~~Gf~~~l~~~~~-~~-~~-~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~---------  241 (342)
T 1jx6_A          175 HTYYSVLYFSEGY-ISDVRGDTFIHQVNRDNN-FE-LQ-SAYYTKATKQSGYDAAKASLAKHPDVDFIYAC---------  241 (342)
T ss_dssp             TCEEEEECCSTTH-HHHHHHHHHHHHHHHHHC-CE-EE-EEECCCSSHHHHHHHHHHHHHHCCCCSEEEES---------
T ss_pred             CceEEEEEcCCcc-hhhHHHHHHHHHHHhCCC-cE-EE-EEecCCCCHHHHHHHHHHHHHhCCCccEEEEC---------
Confidence            5799999877664 455667999999999986 21 22 23456554332   3344554 4579999984         


Q ss_pred             hHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHH
Q 027801          151 HYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMD  185 (218)
Q Consensus       151 H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~e  185 (218)
                       .|.++-.+.+++.+..+ .++.    |++.++..
T Consensus       242 -nd~~A~g~~~al~~~g~-~di~----vvg~D~~~  270 (342)
T 1jx6_A          242 -STDVALGAVDALAELGR-EDIM----INGWGGGS  270 (342)
T ss_dssp             -SHHHHHHHHHHHHHHTC-TTSE----EBCSBCCH
T ss_pred             -CChhHHHHHHHHHHcCC-CCcE----EEEeCCCH
Confidence             35678888888888888 4554    45666665

>3m9w_A D-xylose-binding periplasmic protein; xylose binding protein, conformational changes, SUGA protein; 2.15A {Escherichia coli} PDB: 3m9x_A* 3ma0_A*

Probab=80.98  E-value=9  Score=31.52  Aligned_cols=99  Identities=19%  Similarity=0.180  Sum_probs=65.3

Q ss_pred             CEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEE--eCCcchHH---HHHHHhhhc--CCccEEEEEeeeeeCC
Q 027801           76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVW--VPGSFEIG---VVAQQLGKS--GKYTAVLCIGAVVRGD  148 (218)
Q Consensus        76 ~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~--VPGA~ELP---~aak~L~~~--~~yDaVIaLG~VIrGe  148 (218)
                      .||+++...-.......-.+|..+.|+++|.. .++.++.  ..+.+...   -+++.+++.  .++|||+|..      
T Consensus       124 ~~i~~i~g~~~~~~~~~R~~Gf~~~l~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~ai~~~~------  196 (313)
T 3m9w_A          124 GNYFLMGGSPVDNNAKLFRAGQMKVLKPYVDS-GKIKVVGDQWVDGWLPENALKIMENALTANNNKIDAVVASN------  196 (313)
T ss_dssp             EEEEEEESCTTCHHHHHHHHHHHHHHHHHHHT-TSEEEEEEEECGGGCHHHHHHHHHHHHHHTTTCCCEEEESS------
T ss_pred             CcEEEEECCCCCccHHHHHHHHHHHHHhhccC-CCEEEEeeccCCCcCHHHHHHHHHHHHHhCCCCeeEEEECC------
Confidence            39999987766666666679999999998432 1344432  25555433   334555554  5899999853      


Q ss_pred             chhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHH
Q 027801          149 TTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALN  189 (218)
Q Consensus       149 T~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~  189 (218)
                          |.++-.+.++|.+..+..++    .|++.++...+..
T Consensus       197 ----d~~a~g~~~al~~~G~~~di----~vig~d~~~~~~~  229 (313)
T 3m9w_A          197 ----DATAGGAIQALSAQGLSGKV----AISGQDADLAGIK  229 (313)
T ss_dssp             ----HHHHHHHHHHHHTTTCTTTS----EECCCSCCHHHHH
T ss_pred             ----CchHHHHHHHHHHcCCCCCc----EEEecCCCHHHHH
Confidence                56888888888888887344    3556676665543

>2fp4_B Succinyl-COA ligase [GDP-forming] beta-chain, mitochondrial; active site phosphohistidine residue; HET: NEP GTP; 2.08A {Sus scrofa} SCOP: c.23.4.1 d.142.1.4 PDB: 2fpg_B* 2fpi_B* 2fpp_B* 1euc_B* 1eud_B*

Probab=80.71  E-value=20  Score=32.65  Aligned_cols=120  Identities=19%  Similarity=0.110  Sum_probs=80.6

Q ss_pred             EEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCc-c-h-HHHHHHHhhhcCCccEEEEEeeeeeCCchhHH
Q 027801           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGS-F-E-IGVVAQQLGKSGKYTAVLCIGAVVRGDTTHYD  153 (218)
Q Consensus        77 RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA-~-E-LP~aak~L~~~~~yDaVIaLG~VIrGeT~H~e  153 (218)
                      +|++++.-      -.|.-...+.++.+|..+.|.--  +-|. . | +--+.+.+++..++|+|++.   |=|....++
T Consensus       265 ~Ig~~~nG------aGlam~t~D~i~~~Gg~paNflD--vgG~a~~e~~~~al~~il~d~~v~~ilvn---i~ggi~~~d  333 (395)
T 2fp4_B          265 NIACFVNG------AGLAMATCDIIFLNGGKPANFLD--LGGGVKESQVYQAFKLLTADPKVEAILVN---IFGGIVNCA  333 (395)
T ss_dssp             SEEEEESS------HHHHHHHHHHHHHTTCCBCEEEE--CCSSCCHHHHHHHHHHHHHCTTCCEEEEE---EEESSSCHH
T ss_pred             eEEEEecC------chHHHHHHHHHHHcCCCcCCcEE--ECCCCCHHHHHHHHHHHhCCCCCCEEEEE---ecCCccCcH
Confidence            89888742      14444677889999987655433  3333 2 2 34456667778899999973   335667789


Q ss_pred             HHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHh---hCCCCC--CcHHHHHHHHHHHH
Q 027801          154 AVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNR---AGGKSG--NKGAEAALTAIEMA  210 (218)
Q Consensus       154 ~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~R---ag~k~g--nKG~EAA~aAleM~  210 (218)
                      .|++.+.+++.+++  .++||+.- |...|.+++.+.   +|-..-  +-=.|||+.+++++
T Consensus       334 ~vA~gii~a~~~~~--~~~Pivvr-l~G~n~~~g~~~L~~~gl~~~~~~~~~~Aa~~~v~~~  392 (395)
T 2fp4_B          334 IIANGITKACRELE--LKVPLVVR-LEGTNVHEAQNILTNSGLPITSAVDLEDAAKKAVASV  392 (395)
T ss_dssp             HHHHHHHHHHHHHT--CCSCEEEE-EEETTHHHHHHHHHHTCSCCEECSSHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHhcC--CCCeEEEE-cCCCCHHHHHHHHHHCCCceEeCCCHHHHHHHHHHHh
Confidence            99999999998874  68999974 455778776554   332222  34578888887754

>3bil_A Probable LACI-family transcriptional regulator; structural genomics, unknown function, PSI-2, protein structure initiative; 2.50A {Corynebacterium glutamicum atcc 13032}

Probab=80.23  E-value=11  Score=31.86  Aligned_cols=80  Identities=16%  Similarity=0.175  Sum_probs=54.1

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHH---HHHHhhhcCCccEEEEEeeeeeCCchh
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGKSGKYTAVLCIGAVVRGDTTH  151 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~---aak~L~~~~~yDaVIaLG~VIrGeT~H  151 (218)
                      ..||+++...-.......-++|..+.|+++|+.+   +.+ ++|.|...-   +++.+++.+++ ||+|.          
T Consensus       184 ~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~g~~~---~~v-~~~~~~~~~~~~~~~~ll~~~~~-ai~~~----------  248 (348)
T 3bil_A          184 ALPIGYLSGPMDTSTGRERLEDFKAACANSKIGE---QLV-FLGGYEQSVGFEGATKLLDQGAK-TLFAG----------  248 (348)
T ss_dssp             CCSEEEECCCTTSHHHHHHHHHHHHHHHHTTCCC---CEE-ECCCSSHHHHHHHHHHHHHTTCS-EEEES----------
T ss_pred             CCeEEEEeCCCCCccHHHHHHHHHHHHHHcCcCc---cEE-EcCCCCHHHHHHHHHHHHcCCCC-EEEEc----------
Confidence            4589999877555556667799999999999832   222 356655332   34555554446 77763          


Q ss_pred             HHHHHHHHHHHHHHhchh
Q 027801          152 YDAVANSAASGVLSAGVN  169 (218)
Q Consensus       152 ~e~Va~~vs~gLm~lsL~  169 (218)
                      .|.++-.+.+++.+..++
T Consensus       249 nD~~A~g~~~al~~~G~~  266 (348)
T 3bil_A          249 DSMMTIGVIEACHKAGLV  266 (348)
T ss_dssp             SHHHHHHHHHHHHHTTCC
T ss_pred             ChHHHHHHHHHHHHcCCC
Confidence            466888888888887764

>2nu8_B SCS-beta, succinyl-COA synthetase beta chain; citric acid cycle, heterotetramer, ligase, ATP-grAsp fold, R fold; HET: COA; 2.15A {Escherichia coli} SCOP: c.23.4.1 d.142.1.4 PDB: 1scu_B* 2nu6_B* 1jkj_B* 2nu7_B* 2nu9_B* 2nua_B* 2scu_B* 1jll_B* 1cqj_B* 1cqi_B*

Probab=80.22  E-value=8.4  Score=34.95  Aligned_cols=121  Identities=19%  Similarity=0.176  Sum_probs=79.8

Q ss_pred             EEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcc-h-HHHHHHHhhhcCCccEEEEEeeeeeCCchhHHH
Q 027801           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSF-E-IGVVAQQLGKSGKYTAVLCIGAVVRGDTTHYDA  154 (218)
Q Consensus        77 RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~-E-LP~aak~L~~~~~yDaVIaLG~VIrGeT~H~e~  154 (218)
                      +|++++.-      -.|.-...+.++.+|..+.|.--+. -|+- | +=-+.+.+++..++|+|+..  + =|....++.
T Consensus       258 ~Ig~~~nG------aGl~m~t~D~i~~~Gg~~aNflD~g-G~a~~~~~~~~~~~il~d~~v~~ilvn--i-~ggi~~~~~  327 (388)
T 2nu8_B          258 NIGCMVNG------AGLAMGTMDIVKLHGGEPANFLDVG-GGATKERVTEAFKIILSDDKVKAVLVN--I-FGGIVRCDL  327 (388)
T ss_dssp             SEEEEESS------HHHHHHHHHHHHHTTCCBCEEEECC-SCCCHHHHHHHHHHHHTSTTCCEEEEE--E-ESCSSCHHH
T ss_pred             EEEEEeCC------CchhhhhhHHHHHcCCCcCceeEec-CCCCHHHHHHHHHHHhcCCCCCEEEEE--e-cCCcCCchH
Confidence            78888632      1344456788999998665543331 2222 2 33455666777889999983  2 277778899


Q ss_pred             HHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHhh---CCCCC--CcHHHHHHHHHHHH
Q 027801          155 VANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRA---GGKSG--NKGAEAALTAIEMA  210 (218)
Q Consensus       155 Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~Ra---g~k~g--nKG~EAA~aAleM~  210 (218)
                      |++.+.+.+.++  +.++||+.- |...|.+++.+.-   |-...  +-=.+||+.+++++
T Consensus       328 vA~gii~a~~~~--~~~~pivvr-l~G~n~~~g~~~l~~~g~~~~~~~~~~~aa~~~v~~~  385 (388)
T 2nu8_B          328 IADGIIGAVAEV--GVNVPVVVR-LEGNNAELGAKKLADSGLNIIAAKGLTDAAQQVVAAV  385 (388)
T ss_dssp             HHHHHHHHHHHH--TCCSCEEEE-EESTTHHHHHHHHHTTCSSEEECSSHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhc--CCCCeEEEE-eCCCCHHHHHHHHHHCCCceecCCCHHHHHHHHHHHh
Confidence            999999888886  468999984 4557788875543   22211  33477888877764

>1tjy_A Sugar transport protein; protein-ligand complex, signaling protein; HET: PAV; 1.30A {Salmonella typhimurium} SCOP: c.93.1.1 PDB: 1tm2_A 3t95_A* 3ejw_A*

Probab=80.09  E-value=5.8  Score=33.16  Aligned_cols=64  Identities=17%  Similarity=0.158  Sum_probs=44.7

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEe-CCcchHHH---HHHHhhhcCCccEEEEEee
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWV-PGSFEIGV---VAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~V-PGA~ELP~---aak~L~~~~~yDaVIaLG~  143 (218)
                      +..+||++........-..+++++.+.++++|+     ++... |...+..-   .++.|+ ..++||+|..+.
T Consensus         2 ~~~~Igvi~~~~~~~~~~~~~~g~~~~~~~~g~-----~~~~~~~~~~d~~~q~~~i~~li-~~~vdgiii~~~   69 (316)
T 1tjy_A            2 SAERIAFIPKLVGVGFFTSGGNGAQEAGKALGI-----DVTYDGPTEPSVSGQVQLVNNFV-NQGYDAIIVSAV   69 (316)
T ss_dssp             CCCEEEEECSSSSSHHHHHHHHHHHHHHHHHTC-----EEEECCCSSCCHHHHHHHHHHHH-HTTCSEEEECCS
T ss_pred             CCCEEEEEeCCCCChHHHHHHHHHHHHHHHhCC-----EEEEECCCCCCHHHHHHHHHHHH-HcCCCEEEEeCC
Confidence            346899999888777788899999999999886     34433 44444332   234454 467999987653

---

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	218
d1c2ya_	155	c.16.1.1 (A:) Lumazine synthase {Spinach (Spinacia	3e-51
d1c41a_	195	c.16.1.1 (A:) Lumazine synthase {Rice blast fungus	3e-47
d1ejba_	168	c.16.1.1 (A:) Lumazine synthase {Baker's yeast (Sa	5e-44
d1nqua_	154	c.16.1.1 (A:) Lumazine synthase {Aquifex aeolicus	3e-43
d1rvv1_	154	c.16.1.1 (1:) Lumazine synthase {Bacillus subtilis	7e-43
d1kz1a_	150	c.16.1.1 (A:) Lumazine synthase {Fission yeast (Sc	1e-42
d1di0a_	148	c.16.1.1 (A:) Lumazine synthase {Brucella abortus	1e-40

>d1c2ya_ c.16.1.1 (A:) Lumazine synthase {Spinach (Spinacia oleracea) [TaxId: 3562]} Length = 155

class: Alpha and beta proteins (a/b)
fold: Lumazine synthase
superfamily: Lumazine synthase
family: Lumazine synthase
domain: Lumazine synthase
species: Spinach (Spinacia oleracea) [TaxId: 3562]

 Score =  161 bits (408), Expect = 3e-51
 Identities = 118/156 (75%), Positives = 141/156 (90%), Gaps = 1/156 (0%)

Query: 63  VRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEI 122
           +  L G++TK +  RFA+VVARFNE VT+ L+EGAL+TFKKYSV E+  DVVWVPG++E+
Sbjct: 1   MNELEGYVTKAQSFRFAIVVARFNEFVTRRLMEGALDTFKKYSVNEDI-DVVWVPGAYEL 59

Query: 123 GVVAQQLGKSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCD 182
           GV AQ LGKSGKY A++C+GAVV+GDT+HYDAV NSA+SGVLSAG+NSGVPC+FGVLTCD
Sbjct: 60  GVTAQALGKSGKYHAIVCLGAVVKGDTSHYDAVVNSASSGVLSAGLNSGVPCVFGVLTCD 119

Query: 183 NMDQALNRAGGKSGNKGAEAALTAIEMASLFEHHLK 218
           NMDQA+NRAGGK+GNKGAE+ALTAIEMASLFEHHLK
Sbjct: 120 NMDQAINRAGGKAGNKGAESALTAIEMASLFEHHLK 155

>d1c41a_ c.16.1.1 (A:) Lumazine synthase {Rice blast fungus (Magnaporthe grisea) [TaxId: 148305]} Length = 195

class: Alpha and beta proteins (a/b)
fold: Lumazine synthase
superfamily: Lumazine synthase
family: Lumazine synthase
domain: Lumazine synthase
species: Rice blast fungus (Magnaporthe grisea) [TaxId: 148305]

 Score =  152 bits (385), Expect = 3e-47
 Identities = 55/177 (31%), Positives = 83/177 (46%), Gaps = 38/177 (21%)

Query: 74  EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLG--- 130
             LR  +V AR+NE + + LL G         VKE NI V  VPGS+E+ +  Q+L    
Sbjct: 10  SALRIGIVHARWNETIIEPLLAGTKAKLLACGVKESNIVVQSVPGSWELPIAVQRLYSAS 69

Query: 131 ---------------------------------KSGKYTAVLCIGAVVRGDTTHYDAVAN 157
                                             +G + A++ IG +++G+T H++ +A+
Sbjct: 70  QLQTPSSGPSLSAGDLLGSSTTDLTALPTTTASSTGPFDALIAIGVLIKGETMHFEYIAD 129

Query: 158 SAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGKSG--NKGAEAALTAIEMASL 212
           S + G++   +++GVP IFGVLT    DQA  RAG   G  N G +  L A+EM   
Sbjct: 130 SVSHGLMRVQLDTGVPVIFGVLTVLTDDQAKARAGVIEGSHNHGEDWGLAAVEMGVR 186

>d1ejba_ c.16.1.1 (A:) Lumazine synthase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 168

class: Alpha and beta proteins (a/b)
fold: Lumazine synthase
superfamily: Lumazine synthase
family: Lumazine synthase
domain: Lumazine synthase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  143 bits (361), Expect = 5e-44
 Identities = 44/150 (29%), Positives = 76/150 (50%), Gaps = 9/150 (6%)

Query: 74  EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQL---- 129
             +R  ++ AR+N ++   L++GA+E      V+E NI +  VPGS+E+    ++     
Sbjct: 15  SKIRVGIIHARWNRVIIDALVKGAIERMASLGVEENNIIIETVPGSYELPWGTKRFVDRQ 74

Query: 130 -GKSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQAL 188
                    V+ IG +++G T H++ +++S    +++      +P IFG+LTC   +QAL
Sbjct: 75  AKLGKPLDVVIPIGVLIKGSTMHFEYISDSTTHALMNLQEKVDMPVIFGLLTCMTEEQAL 134

Query: 189 NRAGGKSG----NKGAEAALTAIEMASLFE 214
            RAG        N G +    A+EMA  F 
Sbjct: 135 ARAGIDEAHSMHNHGEDWGAAAVEMAVKFG 164

>d1nqua_ c.16.1.1 (A:) Lumazine synthase {Aquifex aeolicus [TaxId: 63363]} Length = 154

class: Alpha and beta proteins (a/b)
fold: Lumazine synthase
superfamily: Lumazine synthase
family: Lumazine synthase
domain: Lumazine synthase
species: Aquifex aeolicus [TaxId: 63363]

 Score =  140 bits (355), Expect = 3e-43
 Identities = 64/141 (45%), Positives = 95/141 (67%)

Query: 74  EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSG 133
           EGLRF +V +RFN  +   L+EGA++   ++  +EE+I +V VPGS+EI V A +L +  
Sbjct: 11  EGLRFGIVASRFNHALVDRLVEGAIDCIVRHGGREEDITLVRVPGSWEIPVAAGELARKE 70

Query: 134 KYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGG 193
              AV+ IG ++RG T H+D +A+  + G+ +  +    P  FGV+T D ++QA+ RAG 
Sbjct: 71  DIDAVIAIGVLIRGATPHFDYIASEVSKGLANLSLELRKPITFGVITADTLEQAIERAGT 130

Query: 194 KSGNKGAEAALTAIEMASLFE 214
           K GNKG EAAL+AIEMA+LF+
Sbjct: 131 KHGNKGWEAALSAIEMANLFK 151

>d1rvv1_ c.16.1.1 (1:) Lumazine synthase {Bacillus subtilis [TaxId: 1423]} Length = 154

class: Alpha and beta proteins (a/b)
fold: Lumazine synthase
superfamily: Lumazine synthase
family: Lumazine synthase
domain: Lumazine synthase
species: Bacillus subtilis [TaxId: 1423]

 Score =  139 bits (352), Expect = 7e-43
 Identities = 67/139 (48%), Positives = 98/139 (70%)

Query: 74  EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSG 133
            GL+  +VV RFN+ +T  LL GA +   ++ V   +IDV WVPG+FEI   A+++ ++ 
Sbjct: 11  TGLKIGIVVGRFNDFITSKLLSGAEDALLRHGVDTNDIDVAWVPGAFEIPFAAKKMAETK 70

Query: 134 KYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGG 193
           KY A++ +G V+RG TTHYD V N AA G+  A   +GVP IFG++T +N++QA+ RAG 
Sbjct: 71  KYDAIITLGTVIRGATTHYDYVCNEAAKGIAQAANTTGVPVIFGIVTTENIEQAIERAGT 130

Query: 194 KSGNKGAEAALTAIEMASL 212
           K+GNKG + A++AIEMA+L
Sbjct: 131 KAGNKGVDCAVSAIEMANL 149

>d1kz1a_ c.16.1.1 (A:) Lumazine synthase {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]} Length = 150

class: Alpha and beta proteins (a/b)
fold: Lumazine synthase
superfamily: Lumazine synthase
family: Lumazine synthase
domain: Lumazine synthase
species: Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]

 Score =  138 bits (350), Expect = 1e-42
 Identities = 54/139 (38%), Positives = 82/139 (58%), Gaps = 2/139 (1%)

Query: 74  EGLRFALVVARFNELVTKLLLEGALETF-KKYSVKEENIDVVWVPGSFEIGVVAQQLGKS 132
             LR  +V AR N    + L++GA+ET  +K+ VK ENID+  VPGS+E+    +     
Sbjct: 8   PELRILIVHARGNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSWELPQGIRASIAR 67

Query: 133 GKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAG 192
             Y AV+ IG +++G T H++ ++ +   G++  G++SGVP I G+LT  N +QAL RAG
Sbjct: 68  NTYDAVIGIGVLIKGSTMHFEYISEAVVHGLMRVGLDSGVPVILGLLTVLNEEQALYRAG 127

Query: 193 GKSG-NKGAEAALTAIEMA 210
              G N G +    A+EM 
Sbjct: 128 LNGGHNHGNDWGSAAVEMG 146

>d1di0a_ c.16.1.1 (A:) Lumazine synthase {Brucella abortus [TaxId: 235]} Length = 148

class: Alpha and beta proteins (a/b)
fold: Lumazine synthase
superfamily: Lumazine synthase
family: Lumazine synthase
domain: Lumazine synthase
species: Brucella abortus [TaxId: 235]

 Score =  133 bits (337), Expect = 1e-40
 Identities = 31/143 (21%), Positives = 67/143 (46%), Gaps = 3/143 (2%)

Query: 75  GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGK 134
             + A + AR++  +     +  +      +     +++  VPG++EI + A+ L ++G+
Sbjct: 2   SFKIAFIQARWHADIVDEARKSFVAELAAKTGGSVEVEIFDVPGAYEIPLHAKTLARTGR 61

Query: 135 YTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGK 194
           Y A++    V+ G    +D VA +  +G++   + + VP +  VLT  +  ++       
Sbjct: 62  YAAIVGAAFVIDGGIYDHDFVATAVINGMMQVQLETEVPVLSVVLTPHHFHESKEHHDFF 121

Query: 195 SGN---KGAEAALTAIEMASLFE 214
             +   KG EAA  A+++ S   
Sbjct: 122 HAHFKVKGVEAAHAALQIVSERS 144

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	218
d1c2ya_	155	Lumazine synthase {Spinach (Spinacia oleracea) [Ta	100.0
d1rvv1_	154	Lumazine synthase {Bacillus subtilis [TaxId: 1423]	100.0
d1nqua_	154	Lumazine synthase {Aquifex aeolicus [TaxId: 63363]	100.0
d1ejba_	168	Lumazine synthase {Baker's yeast (Saccharomyces ce	100.0
d1di0a_	148	Lumazine synthase {Brucella abortus [TaxId: 235]}	100.0
d1kz1a_	150	Lumazine synthase {Fission yeast (Schizosaccharomy	100.0
d1c41a_	195	Lumazine synthase {Rice blast fungus (Magnaporthe	100.0
d1dbqa_	282	Purine repressor (PurR), C-terminal domain {Escher	94.94
d8abpa_	305	L-arabinose-binding protein {Escherichia coli [Tax	94.54
d2nzug1	275	Glucose-resistance amylase regulator CcpA, C-termi	94.54
d1tjya_	316	AI-2 receptor LsrB {Salmonella typhi [TaxId: 90370	92.79
d1jyea_	271	Lac-repressor (lacR) core (C-terminal domain) {Esc	91.67
d1byka_	255	Trehalose repressor, C-terminal domain {Escherichi	91.1
d1guda_	288	D-allose-binding protein {Escherichia coli [TaxId:	91.04
d1jyea_	271	Lac-repressor (lacR) core (C-terminal domain) {Esc	88.97
d2csua3	163	Acetate-CoA ligase alpha chain, AcdA, domains 2 an	87.79
d2fvya1	305	Galactose/glucose-binding protein {Escherichia col	87.05
d2dria_	271	D-ribose-binding protein {Escherichia coli, strain	85.01
d2fvya1	305	Galactose/glucose-binding protein {Escherichia col	84.33
d2f7wa1	173	MogA {Shewanella oneidensis [TaxId: 70863]}	83.6
d1ydga_	201	Trp repressor binding protein WrbA {Deinococcus ra	82.69
d1jlja_	169	Gephyrin N-terminal domain {Human (Homo sapiens) [	80.81
d2dria_	271	D-ribose-binding protein {Escherichia coli, strain	80.81
d1mxsa_	216	KDPG aldolase {Pseudomonas putida [TaxId: 303]}	80.5
d2pjua1	186	Propionate catabolism operon regulatory protein Pr	80.14

>d1c2ya_ c.16.1.1 (A:) Lumazine synthase {Spinach (Spinacia oleracea) [TaxId: 3562]}

class: Alpha and beta proteins (a/b)
fold: Lumazine synthase
superfamily: Lumazine synthase
family: Lumazine synthase
domain: Lumazine synthase
species: Spinach (Spinacia oleracea) [TaxId: 3562]

Probab=100.00  E-value=5e-60  Score=389.88  Aligned_cols=155  Identities=77%  Similarity=1.261  Sum_probs=150.6

Q ss_pred             HhhhcccCCCCCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEe
Q 027801           63 VRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIG  142 (218)
Q Consensus        63 ~~~~~~~~~~~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG  142 (218)
                      |+.++|++.+.++.||+||+|+||++|++.|+++|+++|+++|++ ++++++|||||||||+++++|+++++||||||||
T Consensus         1 m~~~~~~~~~~~~~ki~IV~s~~n~~It~~L~~ga~~~l~~~g~~-~~i~~~~VPGa~EiP~~~~~l~~~~~~daiIaLG   79 (155)
T d1c2ya_           1 MNELEGYVTKAQSFRFAIVVARFNEFVTRRLMEGALDTFKKYSVN-EDIDVVWVPGAYELGVTAQALGKSGKYHAIVCLG   79 (155)
T ss_dssp             CEEECCCSSSCTTCCEEEEEESTTHHHHHHHHHHHHHHHHHTTCC-SCCEEEEESSHHHHHHHHHHHHHTTCCSEEEEEE
T ss_pred             CceEEeeccCCCCCEEEEEEeeCcHHHHHHHHHHHHHHHHHcCCC-CCcEEEEeccHHHHHHHHHHHHhcCCCCeEEEEE
Confidence            567889998899999999999999999999999999999999996 6899999999999999999999999999999999


Q ss_pred             eeeeCCchhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHhhCCCCCCcHHHHHHHHHHHHHHHhhhcC
Q 027801          143 AVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGKSGNKGAEAALTAIEMASLFEHHLK  218 (218)
Q Consensus       143 ~VIrGeT~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~Rag~k~gnKG~EAA~aAleM~~L~~~~~~  218 (218)
                      |||||||+||||||+++++|||++++++++||+||||||+|++||++|++++.+|||.|||++||+|++|++|+||
T Consensus        80 ~VIkGeT~H~e~I~~~v~~gl~~lsl~~~~PV~~GILT~~n~~QA~~R~~~~~~nkG~eaa~aal~m~~l~~~~~k  155 (155)
T d1c2ya_          80 AVVKGDTSHYDAVVNSASSGVLSAGLNSGVPCVFGVLTCDNMDQAINRAGGKAGNKGAESALTAIEMASLFEHHLK  155 (155)
T ss_dssp             ECCCCSSTHHHHHHHHHHHHHHHHHHHHTSCEEEEEECCSSHHHHHHHEEETTEEHHHHHHHHHHHHHHHHHHHCC
T ss_pred             EEEcCCchHHHHHHHHHHHHHHHHHhhcCCCEEecccCCCCHHHHHHHhccccccHHHHHHHHHHHHHHHHHHhcC
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999999987

>d1rvv1_ c.16.1.1 (1:) Lumazine synthase {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: Lumazine synthase
superfamily: Lumazine synthase
family: Lumazine synthase
domain: Lumazine synthase
species: Bacillus subtilis [TaxId: 1423]

Probab=100.00  E-value=5.1e-59  Score=383.37  Aligned_cols=152  Identities=45%  Similarity=0.816  Sum_probs=148.1

Q ss_pred             HhhhcccCCCCCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEe
Q 027801           63 VRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIG  142 (218)
Q Consensus        63 ~~~~~~~~~~~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG  142 (218)
                      |+.++|++. ++++||+||+|+||++|++.|+++|.++|+++|++.++++++|||||||||+++++++++++||||||||
T Consensus         1 m~~~~g~~~-~~~~ki~IV~s~~n~~I~~~l~~ga~~~l~~~g~~~~~i~v~~VPGa~EiP~~~~~~~~~~~~daiIalG   79 (154)
T d1rvv1_           1 MNIIQGNLV-GTGLKIGIVVGRFNDFITSKLLSGAEDALLRHGVDTNDIDVAWVPGAFEIPFAAKKMAETKKYDAIITLG   79 (154)
T ss_dssp             CEEECCCSC-CTTCCEEEEEESTTHHHHHHHHHHHHHHHHHTTCCGGGEEEEEESSGGGHHHHHHHHHHTSCCSEEEEEE
T ss_pred             CceeecccC-CCCCEEEEEEeeCcHHHHHHHHHHHHHHHHHcCCCccCcEEEEECceeeHHHHHHHHhcccccceEEEEE
Confidence            667889885 8999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeeeCCchhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHhhCCCCCCcHHHHHHHHHHHHHHHhh
Q 027801          143 AVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGKSGNKGAEAALTAIEMASLFEH  215 (218)
Q Consensus       143 ~VIrGeT~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~Rag~k~gnKG~EAA~aAleM~~L~~~  215 (218)
                      |||||||+||||||+++++|||++++++++||+|||||++|++||++|++++.+|||.|||++|++|++|+|+
T Consensus        80 ~VIkGeT~H~e~I~~~v~~gl~~lsl~~~~PV~~GILt~~n~~QA~~R~~~~~~nKG~eaA~aal~m~~l~r~  152 (154)
T d1rvv1_          80 TVIRGATTHYDYVCNEAAKGIAQAANTTGVPVIFGIVTTENIEQAIERAGTKAGNKGVDCAVSAIEMANLNRS  152 (154)
T ss_dssp             EEECCSSSHHHHHHHHHHHHHHHHHHHHCSCEEEEEEEESSHHHHHHTEEETTEEHHHHHHHHHHHHHHHHHH
T ss_pred             EEEcCCChhHHHHHHHHHHHHHHHhccCCCCEEEeecCCCCHHHHHHHhcCcccccHHHHHHHHHHHHHHHhh
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999986

>d1nqua_ c.16.1.1 (A:) Lumazine synthase {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: Lumazine synthase
superfamily: Lumazine synthase
family: Lumazine synthase
domain: Lumazine synthase
species: Aquifex aeolicus [TaxId: 63363]

Probab=100.00  E-value=7.7e-59  Score=382.32  Aligned_cols=152  Identities=44%  Similarity=0.724  Sum_probs=148.0

Q ss_pred             HhhhcccCCCCCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEe
Q 027801           63 VRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIG  142 (218)
Q Consensus        63 ~~~~~~~~~~~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG  142 (218)
                      |+.++|++. ++++||+||+|+||++|+++|+++|+++|+++|+..++|+++|||||||||+++++++++++||||||||
T Consensus         1 m~~~~g~~~-~~~~ri~IV~s~~n~~I~~~Ll~ga~~~l~~~g~~~~~i~v~~VPGa~EiP~~~~~l~~~~~~daiIaLG   79 (154)
T d1nqua_           1 MQIYEGKLT-AEGLRFGIVASRFNHALVDRLVEGAIDCIVRHGGREEDITLVRVPGSWEIPVAAGELARKEDIDAVIAIG   79 (154)
T ss_dssp             CEEECCCSC-CTTCCEEEEEECTTHHHHHHHHHHHHHHHHHTTCCGGGEEEEEESSGGGHHHHHHHHHTCTTCCEEEEEE
T ss_pred             CceEecccc-CCCCEEEEEEeeCcHHHHHHHHHHHHHHHHHcCCChhheeeEEeCCHHHhHHHHHHHHhhcCCCeEEEEE
Confidence            567889885 8999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeeeCCchhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHhhCCCCCCcHHHHHHHHHHHHHHHhh
Q 027801          143 AVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGKSGNKGAEAALTAIEMASLFEH  215 (218)
Q Consensus       143 ~VIrGeT~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~Rag~k~gnKG~EAA~aAleM~~L~~~  215 (218)
                      |||||||+||||||+++++|||++++++++||+|||||++|++||++|++++.+|||.|||++|++|++|+|+
T Consensus        80 ~VIkGeT~H~e~I~~~v~~gl~~lsl~~~~Pi~~GILt~~n~~QA~eR~~~~~~nkG~eaA~aal~mi~l~r~  152 (154)
T d1nqua_          80 VLIRGATPHFDYIASEVSKGLANLSLELRKPITFGVITADTLEQAIERAGTKHGNKGWEAALSAIEMANLFKS  152 (154)
T ss_dssp             EEECCSSTHHHHHHHHHHHHHHHHHHHHTSCEEEEEEEESSHHHHHHTEEETTEEHHHHHHHHHHHHHHHHHH
T ss_pred             EEEeCCchHHHHHHHHHHHHHHHHHHhcCCCEEEeecCCCCHHHHHHHhCCcccccHHHHHHHHHHHHHHHHh
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999986

>d1ejba_ c.16.1.1 (A:) Lumazine synthase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: Lumazine synthase
superfamily: Lumazine synthase
family: Lumazine synthase
domain: Lumazine synthase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=4.8e-56  Score=370.12  Aligned_cols=145  Identities=30%  Similarity=0.534  Sum_probs=138.5

Q ss_pred             CCCCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhh-----cCCccEEEEEeeee
Q 027801           71 TKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGK-----SGKYTAVLCIGAVV  145 (218)
Q Consensus        71 ~~~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~-----~~~yDaVIaLG~VI  145 (218)
                      .|++++||+||+|+||++|++.|+++|++.|+++|++.++|+++||||+||||+++++|++     +++|||||||||||
T Consensus        12 ~d~~~~rI~IV~s~~n~~I~~~Ll~ga~~~L~~~gi~~~~i~~~~VPGa~EiP~~~~~l~~~~~~~~~~~D~iI~LG~VI   91 (168)
T d1ejba_          12 YDGSKIRVGIIHARWNRVIIDALVKGAIERMASLGVEENNIIIETVPGSYELPWGTKRFVDRQAKLGKPLDVVIPIGVLI   91 (168)
T ss_dssp             CCCTTCCEEEEECCTTHHHHHHHHHHHHHHHHHTTCCGGGEEEEECSSGGGHHHHHHHHHHHHHHTTCCCSEEEEEEEEE
T ss_pred             cCCcCCEEEEEEccCCHHHHHHHHHHHHHHHHHcCCCccCceEEecCChhHHHHHHHHHHHHhHhhcCCcceEEEEeeEe
Confidence            3689999999999999999999999999999999999999999999999999999999985     47899999999999


Q ss_pred             eCCchhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHhhCCC----CCCcHHHHHHHHHHHHHHHhh
Q 027801          146 RGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGK----SGNKGAEAALTAIEMASLFEH  215 (218)
Q Consensus       146 rGeT~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~Rag~k----~gnKG~EAA~aAleM~~L~~~  215 (218)
                      ||||+||||||+++++|||++++++++||+|||||++|++||++|++.+    ..|||.|||++|+||+.++++
T Consensus        92 kGeT~H~e~I~~~v~~gl~~lsl~~~~PI~~GVLT~~n~~QA~~R~~~~~~~~~~nKG~EaA~aaleM~~~~~k  165 (168)
T d1ejba_          92 KGSTMHFEYISDSTTHALMNLQEKVDMPVIFGLLTCMTEEQALARAGIDEAHSMHNHGEDWGAAAVEMAVKFGK  165 (168)
T ss_dssp             CCSSSHHHHHHHHHHHHHHHHHHHHTSCBCCEEEEESSHHHHHHHBTCSTTCCSCBHHHHHHHHHHHHHHHHST
T ss_pred             ccCchHHHHHHHHHHHHHHHHHHhcCCCEEEEEecCCCHHHHHHHcCccccccccCcHHHHHHHHHHHHHHhhh
Confidence            9999999999999999999999999999999999999999999999865    359999999999999999875

>d1di0a_ c.16.1.1 (A:) Lumazine synthase {Brucella abortus [TaxId: 235]}

class: Alpha and beta proteins (a/b)
fold: Lumazine synthase
superfamily: Lumazine synthase
family: Lumazine synthase
domain: Lumazine synthase
species: Brucella abortus [TaxId: 235]

Probab=100.00  E-value=1.1e-56  Score=367.17  Aligned_cols=142  Identities=22%  Similarity=0.342  Sum_probs=136.5

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEeeeeeCCchhHH
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVVRGDTTHYD  153 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~VIrGeT~H~e  153 (218)
                      +++||+||.|+||++|+++|+++|.++|.++|+..++++++||||+||||+++++++++++|||||||||||||+|+|||
T Consensus         1 ss~rI~IV~s~~n~~i~~~ll~~a~~~l~~~g~~~~~i~~~~VPGa~EiP~aa~~l~~~~~~daiI~lG~VIkGeT~H~e   80 (148)
T d1di0a_           1 TSFKIAFIQARWHADIVDEARKSFVAELAAKTGGSVEVEIFDVPGAYEIPLHAKTLARTGRYAAIVGAAFVIDGGIYDHD   80 (148)
T ss_dssp             CCEEEEEEEECTTHHHHHHHHHHHHHHHHHHHTTSEEEEEEEESSGGGHHHHHHHHHHTSCCSEEEEEEECCCCSSBCCH
T ss_pred             CCCEEEEEEeeCCHHHHHHHHHHHHHHHHHcCCCcceeEEEEcCChhhhHHHHHHHHhhcccCeEEEEEEEecCCchHHH
Confidence            36899999999999999999999999999999998899999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHhhCCCCC---CcHHHHHHHHHHHHHHHhh
Q 027801          154 AVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGKSG---NKGAEAALTAIEMASLFEH  215 (218)
Q Consensus       154 ~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~Rag~k~g---nKG~EAA~aAleM~~L~~~  215 (218)
                      |||+++++|||++++++++||+||||||+|++||++|++++.+   |||.|||.+|++|++++++
T Consensus        81 ~I~~~v~~gl~~v~l~~~~Pv~~gVLt~~n~~QA~~R~~~~~~~~~nKG~EaA~aal~mi~~~~~  145 (148)
T d1di0a_          81 FVATAVINGMMQVQLETEVPVLSVVLTPHHFHESKEHHDFFHAHFKVKGVEAAHAALQIVSERSR  145 (148)
T ss_dssp             HHHHHHHHHHHHHHHHHCCCEEEEEECBSSCCCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhhCCcEEEEeccCCCHHHHHHHhccccccccccHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999986554   4999999999999999875

>d1kz1a_ c.16.1.1 (A:) Lumazine synthase {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]}

class: Alpha and beta proteins (a/b)
fold: Lumazine synthase
superfamily: Lumazine synthase
family: Lumazine synthase
domain: Lumazine synthase
species: Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]

Probab=100.00  E-value=4.3e-55  Score=358.58  Aligned_cols=139  Identities=40%  Similarity=0.587  Sum_probs=133.5

Q ss_pred             CCCCCEEEEEEcccCHHHHHHHHHHHHHHHH-HCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEeeeeeCCch
Q 027801           72 KNEGLRFALVVARFNELVTKLLLEGALETFK-KYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVVRGDTT  150 (218)
Q Consensus        72 ~~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~-~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~VIrGeT~  150 (218)
                      +++++||+||.|+||++|+++|+++|+++|+ +.|+..++++++||||+||||+++++++++++|||||||||||||||+
T Consensus         6 ~~~~~rI~IV~s~~n~~i~~~L~~ga~~~l~~~~~~~~~~i~v~~VPGa~EiP~~~~~~~~~~~~D~iIalG~VIkGeT~   85 (150)
T d1kz1a_           6 KGPELRILIVHARGNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSWELPQGIRASIARNTYDAVIGIGVLIKGSTM   85 (150)
T ss_dssp             CCTTCCEEEEECCTTHHHHHHHHHHHHHHHHHHHCCCGGGEEEEECSSGGGHHHHHHHHHHHSCCSEEEEEEEEECCSSS
T ss_pred             CCCCCEEEEEEccCCHHHHHHHHHHHHHHHHHhcCCCccccEEEEeCCHHHHHHHHHHHHhccccceEEEEEEEecCcch
Confidence            5789999999999999999999999999996 468998999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHhhCCCCC-CcHHHHHHHHHHHH
Q 027801          151 HYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGKSG-NKGAEAALTAIEMA  210 (218)
Q Consensus       151 H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~Rag~k~g-nKG~EAA~aAleM~  210 (218)
                      ||||||+++++|||++|+++++||+||||||+|++||++|++.+.+ |||.|||++|++|+
T Consensus        86 H~e~I~~~v~~gl~~lsl~~~~PI~~GILt~~n~~QA~~R~~~~~~~nkG~eaa~aal~ma  146 (150)
T d1kz1a_          86 HFEYISEAVVHGLMRVGLDSGVPVILGLLTVLNEEQALYRAGLNGGHNHGNDWGSAAVEMG  146 (150)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHCCCEEEEEEEESSHHHHHHHBTCTTCCBHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhccCCccEEEEECCCCCHHHHHHHhCCcCCCccHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999987644 89999999999997

>d1c41a_ c.16.1.1 (A:) Lumazine synthase {Rice blast fungus (Magnaporthe grisea) [TaxId: 148305]}

class: Alpha and beta proteins (a/b)
fold: Lumazine synthase
superfamily: Lumazine synthase
family: Lumazine synthase
domain: Lumazine synthase
species: Rice blast fungus (Magnaporthe grisea) [TaxId: 148305]

Probab=100.00  E-value=1.4e-54  Score=368.29  Aligned_cols=145  Identities=38%  Similarity=0.628  Sum_probs=138.0

Q ss_pred             CCCCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHh---------------------
Q 027801           71 TKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQL---------------------  129 (218)
Q Consensus        71 ~~~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L---------------------  129 (218)
                      .|++++||+||.|+||++|++.|+++|.++|+++|++.++|++++|||+||||+++++|                     
T Consensus         7 ~d~s~lrI~IV~s~~n~~I~d~Ll~ga~~~L~~~Gv~~~~i~v~~VPGa~ElP~a~~~l~~~~~~~~~~~~~~~~~~~~~   86 (195)
T d1c41a_           7 HDGSALRIGIVHARWNETIIEPLLAGTKAKLLACGVKESNIVVQSVPGSWELPIAVQRLYSASQLQTPSSGPSLSAGDLL   86 (195)
T ss_dssp             CCCSSCCEEEEEECTTHHHHHHHHHHHHHHHHHTTCCGGGEEEEEESSTTHHHHHHHHHHHHHHHC--------------
T ss_pred             CCCCCCEEEEEEccCCHHHHHHHHHHHHHHHHHcCCCcccCeEEECCcHHHHHHHHHHHHhhcccccccccccccccccc
Confidence            36889999999999999999999999999999999999999999999999999999998                     


Q ss_pred             ---------------hhcCCccEEEEEeeeeeCCchhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHHhhCCC
Q 027801          130 ---------------GKSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGK  194 (218)
Q Consensus       130 ---------------~~~~~yDaVIaLG~VIrGeT~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~Rag~k  194 (218)
                                     +++++|||||||||||||||+||||||+++++|||++++++++||+|||||++|++||++|++.+
T Consensus        87 ~~~~~~~~~~~~~~~a~~~~yDaiIaLG~VIkGeT~Hfe~I~~~v~~gL~~lsl~~~~PIi~GILTv~n~eQA~~Ra~~~  166 (195)
T d1c41a_          87 GSSTTDLTALPTTTASSTGPFDALIAIGVLIKGETMHFEYIADSVSHGLMRVQLDTGVPVIFGVLTVLTDDQAKARAGVI  166 (195)
T ss_dssp             ----------------CCSCCSEEEEEEEEECCSSTHHHHHHHHHHHHHHHHHHHHTSCEEEEEEEESSHHHHHHHTTCS
T ss_pred             ccccccccchhhhhhhhcCCccEEEEEEEEEecCchHHHHHHHHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHcCCC
Confidence                           34678999999999999999999999999999999999999999999999999999999999865


Q ss_pred             CC--CcHHHHHHHHHHHHHHHhh
Q 027801          195 SG--NKGAEAALTAIEMASLFEH  215 (218)
Q Consensus       195 ~g--nKG~EAA~aAleM~~L~~~  215 (218)
                      .+  |||.|||.+||+|+.++|+
T Consensus       167 ~~~~NKG~EAA~Aal~M~~l~r~  189 (195)
T d1c41a_         167 EGSHNHGEDWGLAAVEMGVRRRD  189 (195)
T ss_dssp             TTCCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCccHHHHHHHHHHHHHHHHH
Confidence            44  9999999999999999886

>d1dbqa_ c.93.1.1 (A:) Purine repressor (PurR), C-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like I
superfamily: Periplasmic binding protein-like I
family: L-arabinose binding protein-like
domain: Purine repressor (PurR), C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=94.94  E-value=0.042  Score=42.73  Aligned_cols=64  Identities=6%  Similarity=0.005  Sum_probs=50.4

Q ss_pred             CEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHHhhhcCCccEEEEEee
Q 027801           76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        76 ~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~L~~~~~yDaVIaLG~  143 (218)
                      ..||+|+..+++..-..++++..++++++|+   ++.++...+..|.= -.++.| ...++||+|.++.
T Consensus         1 ktIg~i~~~~~~pf~~~~~~gi~~~~~~~gy---~~~~~~~~~d~~~~~~~~~~l-~~~~vdgiIi~~~   65 (282)
T d1dbqa_           1 KSIGLLATSSEAAYFAEIIEAVEKNCFQKGY---TLILGNAWNNLEKQRAYLSMM-AQKRVDGLLVMCS   65 (282)
T ss_dssp             CEEEEEESCTTSHHHHHHHHHHHHHHHHHTC---EEEEEECTTCHHHHHHHHHHH-HHTTCSEEEEECS
T ss_pred             CEEEEEeCCCCCHHHHHHHHHHHHHHHHcCC---EEEEEeCCCCHHHHHHHHHHH-HhcCCCEEeeecc
Confidence            3699999999999999999999999999998   46677666666643 344555 5678999998766

>d8abpa_ c.93.1.1 (A:) L-arabinose-binding protein {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like I
superfamily: Periplasmic binding protein-like I
family: L-arabinose binding protein-like
domain: L-arabinose-binding protein
species: Escherichia coli [TaxId: 562]

Probab=94.54  E-value=0.066  Score=42.35  Aligned_cols=87  Identities=11%  Similarity=0.027  Sum_probs=60.1

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhhhcCCccEEEEEeeeeeCCchhHHH
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVVRGDTTHYDA  154 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~~~~~yDaVIaLG~VIrGeT~H~e~  154 (218)
                      ++|||+|+...+...-..+++++.++.+++|+.   +.....+..=+---.++.++ ..++||||....-   .      
T Consensus         1 ~~kIg~v~~~~~~p~~~~~~~g~~~aa~~~G~~---~i~~~~~d~~~q~~~i~~li-~~~vDgiIi~~~~---~------   67 (305)
T d8abpa_           1 NLKLGFLVKQPEEPWFQTEWKFADKAGKDLGFE---VIKIAVPDGEKTLNAIDSLA-ASGAKGFVICTPD---P------   67 (305)
T ss_dssp             CEEEEEEESCTTSHHHHHHHHHHHHHHHHHTEE---EEEEECCSHHHHHHHHHHHH-HTTCCEEEEECSC---G------
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHHHHcCCE---EEEEcCCCHHHHHHHHHHHH-HcCCCEEEEcccc---c------
Confidence            479999999999999999999999999999984   44443333222333445554 4679999987542   1      


Q ss_pred             HHHHHHHHHHHhchhcCCceEEE
Q 027801          155 VANSAASGVLSAGVNSGVPCIFG  177 (218)
Q Consensus       155 Va~~vs~gLm~lsL~~~vPVifG  177 (218)
                         .....+.+...+.++||++-
T Consensus        68 ---~~~~~~~~~a~~~giPVV~~   87 (305)
T d8abpa_          68 ---KLGSAIVAKARGYDMKVIAV   87 (305)
T ss_dssp             ---GGHHHHHHHHHHTTCEEEEE
T ss_pred             ---cccHHHHHHHHhcCCCEEEE
Confidence               12233445556689999873

>d2nzug1 c.93.1.1 (G:58-332) Glucose-resistance amylase regulator CcpA, C-terminal domain {Bacillus megaterium [TaxId: 1404]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like I
superfamily: Periplasmic binding protein-like I
family: L-arabinose binding protein-like
domain: Glucose-resistance amylase regulator CcpA, C-terminal domain
species: Bacillus megaterium [TaxId: 1404]

Probab=94.54  E-value=0.11  Score=40.33  Aligned_cols=65  Identities=6%  Similarity=0.105  Sum_probs=48.6

Q ss_pred             CEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHH-HHHHHhhhcCCccEEEEEeee
Q 027801           76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGAV  144 (218)
Q Consensus        76 ~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP-~aak~L~~~~~yDaVIaLG~V  144 (218)
                      .-||+|+....+..-..+++++.++++++|+.   +.++...+.-|.= -.+..+ ...++||+|..++.
T Consensus         4 ~tIgvvvp~l~~~f~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~e~~~i~~~-~~~~vdgii~~~~~   69 (275)
T d2nzug1           4 TTVGVIIPDISNIFYAELARGIEDIATMYKYN---IILSNSDQNQDKELHLLNNM-LGKQVDGIIFMSGN   69 (275)
T ss_dssp             SEEEEEESCTTSHHHHHHHHHHHHHHHHTTCE---EEEEECTTCHHHHHHHHHHH-HTTCCSEEEECCSC
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHHHcCCE---EEEEECCCCHHHHHHHHHHH-HhcCCceeeccccc
Confidence            35999999988888889999999999999984   5555555554432 233333 45789999999875

>d1tjya_ c.93.1.1 (A:) AI-2 receptor LsrB {Salmonella typhi [TaxId: 90370]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like I
superfamily: Periplasmic binding protein-like I
family: L-arabinose binding protein-like
domain: AI-2 receptor LsrB
species: Salmonella typhi [TaxId: 90370]

Probab=92.79  E-value=0.17  Score=39.29  Aligned_cols=66  Identities=14%  Similarity=0.078  Sum_probs=49.1

Q ss_pred             CCCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHH---HHHHhhhcCCccEEEEEee
Q 027801           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        73 ~~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~---aak~L~~~~~yDaVIaLG~  143 (218)
                      ++..||++|+...+...-..+.+|+.++++++|+.   +. +.-|+-.+..-   .++.++ ..++||||....
T Consensus         1 G~~~kI~~i~~~~~npf~~~~~~g~~~~a~~~G~~---v~-~~~~~~~d~~~q~~~i~~~i-~~~~dgIIi~~~   69 (316)
T d1tjya_           1 GSAERIAFIPKLVGVGFFTSGGNGAQEAGKALGID---VT-YDGPTEPSVSGQVQLVNNFV-NQGYDAIIVSAV   69 (316)
T ss_dssp             CCCCEEEEECSSSSSHHHHHHHHHHHHHHHHHTCE---EE-ECCCSSCCHHHHHHHHHHHH-HTTCSEEEECCS
T ss_pred             CCCCEEEEEeCCCCCHHHHHHHHHHHHHHHHcCCE---EE-EEECCCCCHHHHHHHHHHHH-hcCCCeeeeccc
Confidence            46789999999999999999999999999999973   22 22365555443   234443 468999998765

>d1jyea_ c.93.1.1 (A:) Lac-repressor (lacR) core (C-terminal domain) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like I
superfamily: Periplasmic binding protein-like I
family: L-arabinose binding protein-like
domain: Lac-repressor (lacR) core (C-terminal domain)
species: Escherichia coli [TaxId: 562]

Probab=91.67  E-value=0.89  Score=35.44  Aligned_cols=62  Identities=8%  Similarity=0.075  Sum_probs=47.6

Q ss_pred             EEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeC--CcchHHHHHHHhhhcCCccEEEEEee
Q 027801           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVP--GSFEIGVVAQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        78 IaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VP--GA~ELP~aak~L~~~~~yDaVIaLG~  143 (218)
                      ||++.+.........++++..++++++|+.   +.+...-  +.-+..-.+++|.+ .++||+|..+.
T Consensus         3 igv~~~~l~~~~~~~i~~~i~~~a~~~Gy~---v~v~~~~~~~~~~~~~~l~~l~~-~~vdgiIl~~~   66 (271)
T d1jyea_           3 IGVATSSLALHAPSQIVAAILSRADQLGAS---VVVSMVERSGVEACKTAVHNLLA-QRVSGLIINYP   66 (271)
T ss_dssp             EEEEESCTTSHHHHHHHHHHHHHHHHTTCE---EEEEECCSSSHHHHHHHHHHHHT-TTCSCEEEESC
T ss_pred             EEEEeCCCCChHHHHHHHHHHHHHHHcCCE---EEEEECCCCCHHHHHHHHHHHHh-cCCCEEEeccc
Confidence            799999999999999999999999999984   5444432  23345566777764 47999988664

>d1byka_ c.93.1.1 (A:) Trehalose repressor, C-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like I
superfamily: Periplasmic binding protein-like I
family: L-arabinose binding protein-like
domain: Trehalose repressor, C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=91.10  E-value=0.47  Score=36.83  Aligned_cols=65  Identities=18%  Similarity=0.155  Sum_probs=48.0

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHH-HHHhhhcCCccEEEEEee
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVV-AQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~a-ak~L~~~~~yDaVIaLG~  143 (218)
                      ..-|||++.+........++++..+.++++|+.   +.++.--..-|.-.- ++.| .+.++||+|..++
T Consensus         2 ~k~Igvi~p~~~~~~~~~~~~~i~~~~~~~Gy~---~~~~~s~~d~~~~~~~i~~l-~~~~vdgiIi~~~   67 (255)
T d1byka_           2 DKVVAIIVTRLDSLSENLAVQTMLPAFYEQGYD---PIMMESQFSPQLVAEHLGVL-KRRNIDGVVLFGF   67 (255)
T ss_dssp             CCEEEEEESCTTCHHHHHHHHHHHHHHHHHTCE---EEEEECTTCHHHHHHHHHHH-HTTTCCEEEEECC
T ss_pred             CCEEEEEeCCCCCHHHHHHHHHHHHHHHHcCCE---EEEEeCCCCHHHHHHHHHHH-Hhccccceeeccc
Confidence            456999999888888889999999999999974   555554444444333 3444 5678999998764

>d1guda_ c.93.1.1 (A:) D-allose-binding protein {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like I
superfamily: Periplasmic binding protein-like I
family: L-arabinose binding protein-like
domain: D-allose-binding protein
species: Escherichia coli [TaxId: 562]

Probab=91.04  E-value=0.39  Score=37.19  Aligned_cols=64  Identities=14%  Similarity=0.203  Sum_probs=50.6

Q ss_pred             CEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHH---HHHhhhcCCccEEEEEee
Q 027801           76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVV---AQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        76 ~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~a---ak~L~~~~~yDaVIaLG~  143 (218)
                      .++|+|....++..-..+.+|+.+.++++|+.   +.++..++-.+..--   ++.++ ..++||||..+.
T Consensus         2 ~~~a~i~~~~~npff~~i~~g~~~~a~~~g~~---~~i~~~~~~~d~~~q~~~i~~~i-~~~~DgIi~~~~   68 (288)
T d1guda_           2 AEYAVVLKTLSNPFWVDMKKGIEDEAKTLGVS---VDIFASPSEGDFQSQLQLFEDLS-NKNYKGIAFAPL   68 (288)
T ss_dssp             CEEEEEESCSSSHHHHHHHHHHHHHHHHHTCC---EEEEECSSTTCHHHHHHHHHHHH-TSSEEEEEECCS
T ss_pred             cEEEEEeCCCCCHHHHHHHHHHHHHHHHcCCE---EEEEecCCCCCHHHHHHHHHHHH-hcCCCEEEEecC
Confidence            47899999999999999999999999999974   777777776666543   33343 567999888754

>d1jyea_ c.93.1.1 (A:) Lac-repressor (lacR) core (C-terminal domain) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like I
superfamily: Periplasmic binding protein-like I
family: L-arabinose binding protein-like
domain: Lac-repressor (lacR) core (C-terminal domain)
species: Escherichia coli [TaxId: 562]

Probab=88.97  E-value=0.38  Score=37.69  Aligned_cols=97  Identities=20%  Similarity=0.209  Sum_probs=62.4

Q ss_pred             CEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHH-HH-HHhhhcCCccEEEEEeeeeeCCchhHH
Q 027801           76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV-VA-QQLGKSGKYTAVLCIGAVVRGDTTHYD  153 (218)
Q Consensus        76 ~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~-aa-k~L~~~~~yDaVIaLG~VIrGeT~H~e  153 (218)
                      .||++|.+..+......-++|+.+.+++++...  ......+...+--+ ++ +.+.+...+|+|+|...          
T Consensus       119 ~~i~~i~~~~~~~~~~~R~~g~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~ai~~~~~----------  186 (271)
T d1jyea_         119 QQIALLAGPLSSVSARLRLAGWHKYLTRNQIQP--IAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVAND----------  186 (271)
T ss_dssp             CSEEEEECCTTSHHHHHHHHHHHHHHHHTTCCC--SEEEECCSSHHHHHHHHHHHHHTTCCCSEEEESSH----------
T ss_pred             ccccccccccccchHHhhhHHHHHHhhhccccc--cceeccccccccccchhhhhhhcccccchhhccch----------
Confidence            489999988888888889999999999999863  33333443333221 12 22334567999998654          


Q ss_pred             HHHHHHHHHHHHhchhcCCceEEEEcCCCCHHH
Q 027801          154 AVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQ  186 (218)
Q Consensus       154 ~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQ  186 (218)
                      .++..+.+.+.+..++-+-.+  .|++.++...
T Consensus       187 ~~a~~~~~~l~~~g~~vp~di--~Ii~~d~~~~  217 (271)
T d1jyea_         187 QMALGAMRAITESGLRVGADI--SVVGYDDTED  217 (271)
T ss_dssp             HHHHHHHHHHHHTTCCBTTTB--EEECSBCCGG
T ss_pred             hhhhHHHHhHHHhhccCCceE--EEEeeeccHH
Confidence            466667777777766533332  4556555444

>d2csua3 c.23.4.1 (A:291-453) Acetate-CoA ligase alpha chain, AcdA, domains 2 and 3 {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: Succinyl-CoA synthetase domains
family: Succinyl-CoA synthetase domains
domain: Acetate-CoA ligase alpha chain, AcdA, domains 2 and 3
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=87.79  E-value=1.4  Score=32.51  Aligned_cols=86  Identities=13%  Similarity=0.073  Sum_probs=48.9

Q ss_pred             HHHHHhhhcCCccEEEEEeeeeeCCchhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHHH---hhCCCCCCcHH
Q 027801          124 VVAQQLGKSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALN---RAGGKSGNKGA  200 (218)
Q Consensus       124 ~aak~L~~~~~yDaVIaLG~VIrGeT~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~~---Rag~k~gnKG~  200 (218)
                      -+++.+++...+|+|+++...-........-++..+.+.+.+..  .++||....+..+..+++.+   ++|--.-.-=.
T Consensus        68 ~~l~~~~~d~~vd~v~v~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~kpv~~~~~~~~~~~~~~~~l~~~Gip~f~~pe  145 (163)
T d2csua3          68 RTAKLLLQDPNVDMLIAICVVPTFAGMTLTEHAEGIIRAVKEVN--NEKPVLAMFMAGYVSEKAKELLEKNGIPTYERPE  145 (163)
T ss_dssp             HHHHHHHHSTTCSEEEEEEECCCSTTCCSSHHHHHHHHHHHHHC--CCCCEEEEEECTTTTHHHHHHHHTTTCCEESSHH
T ss_pred             HHHHHHHcCCCcCEEEEeeccCCcccccHHHHHHHHHHHHHHhc--CCCcEEEEECCCCChHHHHHHHHHCCCCcCCCHH
Confidence            44566678899999988766532222333445566666555543  46899988887666555543   34322222223


Q ss_pred             HHHHHHHHHHH
Q 027801          201 EAALTAIEMAS  211 (218)
Q Consensus       201 EAA~aAleM~~  211 (218)
                      +|+++.-.|.+
T Consensus       146 ~a~~Al~~l~~  156 (163)
T d2csua3         146 DVASAAYALVE  156 (163)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            44444444443

>d2fvya1 c.93.1.1 (A:2-306) Galactose/glucose-binding protein {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like I
superfamily: Periplasmic binding protein-like I
family: L-arabinose binding protein-like
domain: Galactose/glucose-binding protein
species: Escherichia coli [TaxId: 562]

Probab=87.05  E-value=2  Score=32.84  Aligned_cols=103  Identities=13%  Similarity=0.076  Sum_probs=63.7

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHhh----hcCCccEEEEEeeeeeCCc
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLG----KSGKYTAVLCIGAVVRGDT  149 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L~----~~~~yDaVIaLG~VIrGeT  149 (218)
                      ...||+++...-.......-.+|..+.++++|.......+.......+-........    ...++|+|+|         
T Consensus       138 g~~~i~~i~g~~~~~~~~~r~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~---------  208 (305)
T d2fvya1         138 GQIQFVLLKGEPGHPDAEARTTYVIKELNDKGIKTEQLQLDTAMWDTAQAKDKMDAWLSGPNANKIEVVIA---------  208 (305)
T ss_dssp             SSEEEEEEECSTTCHHHHHHHHHHHHHHHHTTCCEEEEEEEECTTCHHHHHHHHHHHHTSTTGGGCCEEEE---------
T ss_pred             CCceEEEEeCCCcccchHHHHHHHHHHhhhcCCcccceeEeeccccchhhHHHHHHHHhhccCCCceEEEe---------
Confidence            455899998877777777888999999999998632333333333333333322211    2246788887         


Q ss_pred             hhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHHH
Q 027801          150 THYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQAL  188 (218)
Q Consensus       150 ~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA~  188 (218)
                       ..|.++-.+.+++.+..++  .|.+.|+-..+...+++
T Consensus       209 -~~d~~a~g~~~a~~~~g~~--~i~~vg~d~~~~~~~~i  244 (305)
T d2fvya1         209 -NNDAMAMGAVEALKAHNKS--SIPVFGVDALPEALALV  244 (305)
T ss_dssp             -SSHHHHHHHHHHHHHTTCT--TSCEECSBCCHHHHHHH
T ss_pred             -cchHHhHHHHHHHHHhCCC--CCcEEEEeCCchhhhhe
Confidence             4566788888888888764  34444554333333444

>d2dria_ c.93.1.1 (A:) D-ribose-binding protein {Escherichia coli, strain k-12 [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like I
superfamily: Periplasmic binding protein-like I
family: L-arabinose binding protein-like
domain: D-ribose-binding protein
species: Escherichia coli, strain k-12 [TaxId: 562]

Probab=85.01  E-value=1.4  Score=33.15  Aligned_cols=60  Identities=18%  Similarity=0.097  Sum_probs=41.6

Q ss_pred             EEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHHh--hhcCCccEEEEEe
Q 027801           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQL--GKSGKYTAVLCIG  142 (218)
Q Consensus        78 IaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~L--~~~~~yDaVIaLG  142 (218)
                      ||+|+...++..-..+++|+.++++++|+.   +  +..+...+...-.+.+  +...++|++|...
T Consensus         4 Igvvvp~~~~~f~~~~~~gi~~~a~~~g~~---~--~i~~~~~~~~~~~~~i~~~~~~~~d~ii~~~   65 (271)
T d2dria_           4 IALVVSTLNNPFFVSLKDGAQKEADKLGYN---L--VVLDSQNNPAKELANVQDLTVRGTKILLINP   65 (271)
T ss_dssp             EEEEESCSSSHHHHHHHHHHHHHHHHHTCE---E--EEEECTTCHHHHHHHHHHHTTTTEEEEEECC
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHHHHcCCE---E--EEEeCCCCHHHHHHHHHHHHhcCCccccccc
Confidence            899999998888889999999999999973   3  3444444433322222  1346788877544

>d2fvya1 c.93.1.1 (A:2-306) Galactose/glucose-binding protein {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like I
superfamily: Periplasmic binding protein-like I
family: L-arabinose binding protein-like
domain: Galactose/glucose-binding protein
species: Escherichia coli [TaxId: 562]

Probab=84.33  E-value=1.8  Score=33.16  Aligned_cols=64  Identities=6%  Similarity=0.050  Sum_probs=44.8

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHH---HHHhhhcCCccEEEEEee
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVV---AQQLGKSGKYTAVLCIGA  143 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~a---ak~L~~~~~yDaVIaLG~  143 (218)
                      +.|||+++...++..-..+.+++.+++++++    .+++....+..+.---   ++.|+ +.++||+|....
T Consensus         1 ~~kIgv~~~~~~~~f~~~i~~gi~~~a~~~~----~~~l~~~~~~~~~~~q~~~i~~li-~~~vDgiii~~~   67 (305)
T d2fvya1           1 DTRIGVTIYKYDDNFMSVVRKAIEQDAKAAP----DVQLLMNDSQNDQSKQNDQIDVLL-AKGVKALAINLV   67 (305)
T ss_dssp             CEEEEEEESCTTSHHHHHHHHHHHHHHHTCT----TEEEEEEECTTCHHHHHHHHHHHH-HTTCSEEEECCS
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHHHHHHcC----CcEEEEEcCCCCHHHHHHHHHHHH-HcCCCEEEeecc
Confidence            3699999999999999999999999998763    2344444444443332   34444 357999997654

>d2f7wa1 c.57.1.1 (A:2-174) MogA {Shewanella oneidensis [TaxId: 70863]}

class: Alpha and beta proteins (a/b)
fold: Molybdenum cofactor biosynthesis proteins
superfamily: Molybdenum cofactor biosynthesis proteins
family: MogA-like
domain: MogA
species: Shewanella oneidensis [TaxId: 70863]

Probab=83.60  E-value=0.36  Score=36.84  Aligned_cols=83  Identities=11%  Similarity=0.192  Sum_probs=53.7

Q ss_pred             CCCEEEEEEcc---cCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcch-HHHHHHHhhhcCCccEEEEEeeeeeCCc
Q 027801           74 EGLRFALVVAR---FNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE-IGVVAQQLGKSGKYTAVLCIGAVVRGDT  149 (218)
Q Consensus        74 ~~~RIaIV~Sr---fn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~E-LP~aak~L~~~~~yDaVIaLG~VIrGeT  149 (218)
                      +..|||||...   ++....|.--....+.|.++|.....+..--||.-.| |=-+++++..+.+||-|++-|-+  |-+
T Consensus         1 s~~rv~IitvsD~~~~G~~~D~~gp~l~~~L~~~G~~~~~v~~~ivpDd~~~I~~~l~~~~~~~~~dlIittGGt--G~~   78 (173)
T d2f7wa1           1 SKAKIGIVTVSDRASAGIYEDISGKAIIDTLNDYLTSEWEPIYQVIPDEQDVIETTLIKMADEQDCCLIVTTGGT--GPA   78 (173)
T ss_dssp             CCEEEEEEEECHHHHHCCSCCHHHHHHHHHHHHHBCSCEEEEEEEECSCHHHHHHHHHHHHHTSCEEEEEEESCC--SSS
T ss_pred             CCCEEEEEEeCCCCcCCCccCCCHHHHHHHHHHhCCCceEEEEEEcCCcHHHHHHHhhhhhhcccccEEEEeccc--ccc
Confidence            35799988742   2222234445566778888888632333335898876 55556777778899999999987  433


Q ss_pred             hhHHHHHHHH
Q 027801          150 THYDAVANSA  159 (218)
Q Consensus       150 ~H~e~Va~~v  159 (218)
                       |.|...+++
T Consensus        79 -~~D~T~ea~   87 (173)
T d2f7wa1          79 -KRDVTPEAT   87 (173)
T ss_dssp             -TTCCHHHHH
T ss_pred             -cchhHHHHH
Confidence             555555555

>d1ydga_ c.23.5.8 (A:) Trp repressor binding protein WrbA {Deinococcus radiodurans [TaxId: 1299]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: Flavoproteins
family: WrbA-like
domain: Trp repressor binding protein WrbA
species: Deinococcus radiodurans [TaxId: 1299]

Probab=82.69  E-value=1.5  Score=33.38  Aligned_cols=41  Identities=12%  Similarity=0.108  Sum_probs=33.8

Q ss_pred             CCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCc
Q 027801           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGS  119 (218)
Q Consensus        75 ~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA  119 (218)
                      ++||+||....+-. |+.|.+.+.+.+++.|++   ++++.|+-.
T Consensus         2 ~mkilivy~S~~Gn-T~~la~~ia~g~~~~G~e---v~~~~~~~~   42 (201)
T d1ydga_           2 PVKLAIVFYSSTGT-GYAMAQEAAEAGRAAGAE---VRLLKVRET   42 (201)
T ss_dssp             CCEEEEEECCSSSH-HHHHHHHHHHHHHHTTCE---EEEEECCCC
T ss_pred             CcEEEEEEeCCCcH-HHHHHHHHHHHHHhcCCE---EEEEEcccc
Confidence            68999998776644 788999999999999984   788888753

>d1jlja_ c.57.1.1 (A:) Gephyrin N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Molybdenum cofactor biosynthesis proteins
superfamily: Molybdenum cofactor biosynthesis proteins
family: MogA-like
domain: Gephyrin N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.81  E-value=1.3  Score=33.09  Aligned_cols=83  Identities=13%  Similarity=0.123  Sum_probs=53.0

Q ss_pred             CCEEEEEEcc---cC---HHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcch-HHHHHHHhhhcCCccEEEEEeeeeeC
Q 027801           75 GLRFALVVAR---FN---ELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE-IGVVAQQLGKSGKYTAVLCIGAVVRG  147 (218)
Q Consensus        75 ~~RIaIV~Sr---fn---~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~E-LP~aak~L~~~~~yDaVIaLG~VIrG  147 (218)
                      .+|++||..-   ++   ++-...++...++++...|..  -++...||--.| |--+++++....+||.||+-|-+   
T Consensus         2 ~~rv~iit~gDe~~~G~~~D~ng~~L~~~l~~~~~~G~~--v~~~~iV~Dd~~~i~~al~~~~~~~~~D~ViTtGG~---   76 (169)
T d1jlja_           2 QIRVGVLTVSDSCFRNLAEDRSGINLKDLVQDPSLLGGT--ISAYKIVPDEIEEIKETLIDWCDEKELNLILTTGGT---   76 (169)
T ss_dssp             CCEEEEEEECHHHHTTSSCCHHHHHHHHHHHCTTTTCCE--EEEEEEECSCHHHHHHHHHHHHHTSCCSEEEEESCC---
T ss_pred             ceEEEEEEeCCCcccCCcCCccHHHHHHHHHhhccCCcE--EEEEEEeccchhhHHHHHHHHhhcccccEEEEecCc---
Confidence            5788888521   12   222333444333333335663  566677999866 55666777677899999999998   


Q ss_pred             CchhHHHHHHHHHHH
Q 027801          148 DTTHYDAVANSAASG  162 (218)
Q Consensus       148 eT~H~e~Va~~vs~g  162 (218)
                      ...|+|+..+++...
T Consensus        77 g~~~~D~T~~a~~~~   91 (169)
T d1jlja_          77 GFAPRDVTPEATKEV   91 (169)
T ss_dssp             SSSTTCCHHHHHHHH
T ss_pred             cccccccchhheehh
Confidence            566777777766544

>d2dria_ c.93.1.1 (A:) D-ribose-binding protein {Escherichia coli, strain k-12 [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like I
superfamily: Periplasmic binding protein-like I
family: L-arabinose binding protein-like
domain: D-ribose-binding protein
species: Escherichia coli, strain k-12 [TaxId: 562]

Probab=80.81  E-value=8.9  Score=28.42  Aligned_cols=98  Identities=16%  Similarity=0.101  Sum_probs=63.9

Q ss_pred             CCCEEEEEEcccCHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeCCcchHHHHHHH----hhhcCCccEEEEEeeeeeCCc
Q 027801           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQ----LGKSGKYTAVLCIGAVVRGDT  149 (218)
Q Consensus        74 ~~~RIaIV~Srfn~~It~~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~ELP~aak~----L~~~~~yDaVIaLG~VIrGeT  149 (218)
                      .+.||+++...-+......-.++..+.++.++..    .....++.+.-....+.    +....+.|||+|..       
T Consensus       122 ~~~~i~~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ai~~~~-------  190 (271)
T d2dria_         122 EGAKVIELQGIAGTSAARERGEGFQQAVAAHKFN----VLASQPADFDRIKGLNVMQNLLTAHPDVQAVFAQN-------  190 (271)
T ss_dssp             TTCEEEEEECCTTCHHHHHHHHHHHHHHHHHTCE----EEEEEECTTCHHHHHHHHHHHHHHCTTCCEEEESS-------
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHhHHHHhhccccc----ccceeeecchhhhhhhhHHHHHhcccCceEEeccc-------
Confidence            4568999888777777777778999999988763    23334444444433332    23456899999875       


Q ss_pred             hhHHHHHHHHHHHHHHhchhcCCceEEEEcCCCCHHHH
Q 027801          150 THYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQA  187 (218)
Q Consensus       150 ~H~e~Va~~vs~gLm~lsL~~~vPVifGVLT~~n~eQA  187 (218)
                         |.++..+.+++.+...  +.|.+.|+-..+...++
T Consensus       191 ---d~~a~g~~~al~~~g~--~di~iig~d~~~~~~~~  223 (271)
T d2dria_         191 ---DEMALGALRALQTAGK--SDVMVVGFDGTPDGEKA  223 (271)
T ss_dssp             ---HHHHHHHHHHHHHHTC--CSCEEEEEECCHHHHHH
T ss_pred             ---HHHHHHHHHHHHHhCC--CCCceEECcCCHHHHHH
Confidence               4577788888888764  34555555554333344

>d1mxsa_ c.1.10.1 (A:) KDPG aldolase {Pseudomonas putida [TaxId: 303]}

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: Aldolase
family: Class I aldolase
domain: KDPG aldolase
species: Pseudomonas putida [TaxId: 303]

Probab=80.50  E-value=0.73  Score=37.33  Aligned_cols=87  Identities=17%  Similarity=0.284  Sum_probs=61.4

Q ss_pred             HHHHHHHHCCCCCCCeEEEE-eCCcchHHHHHHHhhhcCCccEEEEEeeeeeCCchhHHHHHHH---------HHHHHHH
Q 027801           96 GALETFKKYSVKEENIDVVW-VPGSFEIGVVAQQLGKSGKYTAVLCIGAVVRGDTTHYDAVANS---------AASGVLS  165 (218)
Q Consensus        96 gA~~~L~~~Gv~~e~I~vv~-VPGA~ELP~aak~L~~~~~yDaVIaLG~VIrGeT~H~e~Va~~---------vs~gLm~  165 (218)
                      ...+.|.+.|+.  .+++-+ .|+++|.   ++.+.++ ..|.+|..|.|+.  ..+.+-..++         ....+.+
T Consensus        33 ~~~~al~~~Gi~--~iEitl~~p~a~~~---i~~l~~~-~p~~~vGaGTV~~--~~~~~~a~~aGa~FivsP~~~~~v~~  104 (216)
T d1mxsa_          33 PLADALAAGGIR--TLEVTLRSQHGLKA---IQVLREQ-RPELCVGAGTVLD--RSMFAAVEAAGAQFVVTPGITEDILE  104 (216)
T ss_dssp             HHHHHHHHTTCC--EEEEESSSTHHHHH---HHHHHHH-CTTSEEEEECCCS--HHHHHHHHHHTCSSEECSSCCHHHHH
T ss_pred             HHHHHHHHCCCC--EEEEeCCChhHHHH---HHHHHHh-CCCcceeeeeeec--HHHHHHHHhCCCCEEECCCCcHHHHH
Confidence            445677777986  455543 7888874   3444332 2488999999975  4444433332         4567889


Q ss_pred             hchhcCCceEEEEcCCCCHHHHHHh
Q 027801          166 AGVNSGVPCIFGVLTCDNMDQALNR  190 (218)
Q Consensus       166 lsL~~~vPVifGVLT~~n~eQA~~R  190 (218)
                      ...+.++|.+=|++|+....+|++.
T Consensus       105 ~a~~~~i~~iPGv~TpsEi~~A~~~  129 (216)
T d1mxsa_         105 AGVDSEIPLLPGISTPSEIMMGYAL  129 (216)
T ss_dssp             HHHHCSSCEECEECSHHHHHHHHTT
T ss_pred             HHHhcCCCccCCcCCHHHHHHHHHC
Confidence            9999999999999999888888866

>d2pjua1 c.92.3.1 (A:11-196) Propionate catabolism operon regulatory protein PrpR {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Chelatase-like
superfamily: PrpR receptor domain-like
family: PrpR receptor domain-like
domain: Propionate catabolism operon regulatory protein PrpR
species: Escherichia coli [TaxId: 562]

Probab=80.14  E-value=2  Score=33.64  Aligned_cols=80  Identities=19%  Similarity=0.242  Sum_probs=54.5

Q ss_pred             HHHHHHHHHHHHCCCCCCCeEEEEeCCcch--HHHHHHHhhhcCCccEEEEEeeeeeCCchhHHHHHHHHHHHHHHhchh
Q 027801           92 LLLEGALETFKKYSVKEENIDVVWVPGSFE--IGVVAQQLGKSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVN  169 (218)
Q Consensus        92 ~Ll~gA~~~L~~~Gv~~e~I~vv~VPGA~E--LP~aak~L~~~~~yDaVIaLG~VIrGeT~H~e~Va~~vs~gLm~lsL~  169 (218)
                      +|.+-+.+...++.   +..++.-+-|.||  ++.+.+++ +.+++|.||+=     |.|.++             +.-.
T Consensus        11 rL~~l~~~i~~ey~---~~~~i~v~~~~~e~av~~~~~~~-~~~~~DviISR-----G~ta~~-------------ir~~   68 (186)
T d2pjua1          11 RLFELFRDISLEFD---HLANITPIQLGFEKAVTYIRKKL-ANERCDAIIAA-----GSNGAY-------------LKSR   68 (186)
T ss_dssp             HHHHHHHHHHTTTT---TTCEEEEECCCHHHHHHHHHHHT-TTSCCSEEEEE-----HHHHHH-------------HHTT
T ss_pred             HHHHHHHHHHHHhc---CCceEEeecCcHHHHHHHHHHHH-HcCCCCEEEEC-----chHHHH-------------HHHh
Confidence            45555566655543   2356777889999  55555544 67899999984     445432             1224


Q ss_pred             cCCceEEEEcCCCCHHHHHHhhCC
Q 027801          170 SGVPCIFGVLTCDNMDQALNRAGG  193 (218)
Q Consensus       170 ~~vPVifGVLT~~n~eQA~~Rag~  193 (218)
                      .++||+.-=+|..+.-||+.++..
T Consensus        69 ~~iPVV~I~vs~~Dil~al~~a~~   92 (186)
T d2pjua1          69 LSVPVILIKPSGYDVLQFLAKAGK   92 (186)
T ss_dssp             CSSCEEEECCCHHHHHHHHHHTTC
T ss_pred             CCCCEEEEcCCHhHHHHHHHHHHH
Confidence            579998888888899999999864