Citrus Sinensis ID: 032216

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-----
Protein Sequence
MALNLKTTIHHSPLASSSRQFINGFSPKPTSMSFSRSSSLKGFGTQIAIERKERLSFVQTEAVRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVV
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHcccHHHHHcccEEEcEEccccccEEEEEEccccHHHHHHHHHHHHHHHHHccccccccEEEEcccccHHHHHHHHHHHcccccEEEEEEEEc
Secondary Structure Prediction (SSPRO)
ccEEEEEEEccccccccccHHccccccccccccccccccccccccccEEEccccccHHHHHHHHHHcccccccccccEEEEEEcccHHHHHHHHHHHHHHHHHccccHHHEEEEEEccHHHHHHHHHHHHccccccEEEEEEEEE
Coil and Loop (DISEMBL)
malnlkttihhsplasssrqfingfspkptsmsfsrssslkgfgTQIAIERKERLSFVQTEAVRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKkysvkeenidvvwvpgSFEIGVVAQQLGKSGKYTAVLCIGAVV
Flexible Loop (DISEMBL)
malnlkttihhsplasssrqfINGFSPKPTSMSFSRSSSLKGFGTQIAIERKERLSFVQTEAVRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQqlgksgkytAVLCIGAVV
Low Complexity Region (SEG)
MALNLKTTIHHSPLASSSRQFINGFSPKPTSMSFSRSSSLKGFGTQIAIERKERLSFVQTEAVRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVV
Disordered region (IsUnstruct)
******************************************FGTQIAIERKERLSFVQTEAVRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA**
Disordered Region (DISOPRED)
***************************************************************RHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVV
Disordered Region (DISEMBL)
MALNLKTTIHHSPLASSSRQFINGFSPKP************GFGTQIAIERKERLSFVQTEAVRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVV
Disordered Region (DISPRO)
*ALNLKTTIHHS*LASSSR*************************TQIAIERKERLSFVQTEAVRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVV
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MALNLKTTIHHSPLASSSRQFINGFSPKPTSMSFSRSSSLKGFGTQIAIERKERLSFVQTEAVRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVV
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	145	2.2.26 [Sep-21-2011]
O80575	227	6,7-dimethyl-8-ribityllum	yes	no	0.896	0.572	0.684	5e-45
Q9XH32	222	6,7-dimethyl-8-ribityllum	N/A	no	0.8	0.522	0.618	3e-33
A6LSS9	154	6,7-dimethyl-8-ribityllum	yes	no	0.503	0.474	0.534	9e-20
Q3Z799	155	6,7-dimethyl-8-ribityllum	yes	no	0.558	0.522	0.512	2e-19
Q3ZY85	155	6,7-dimethyl-8-ribityllum	yes	no	0.558	0.522	0.512	2e-19
A5FQE3	155	6,7-dimethyl-8-ribityllum	yes	no	0.558	0.522	0.512	2e-19
C3L2U0	154	6,7-dimethyl-8-ribityllum	yes	no	0.496	0.467	0.5	1e-18
B1IL45	154	6,7-dimethyl-8-ribityllum	yes	no	0.496	0.467	0.5	1e-18
B1KZ46	154	6,7-dimethyl-8-ribityllum	yes	no	0.496	0.467	0.5	1e-18
A7GH84	154	6,7-dimethyl-8-ribityllum	yes	no	0.496	0.467	0.5	1e-18

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

 Score =  179 bits (454), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 89/130 (68%), Positives = 108/130 (83%)

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 TAVLCIGAVV 145
            AVLCIGAV+
Sbjct: 145 HAVLCIGAVI 154

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 =  140 bits (353), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 73/118 (61%), Positives = 89/118 (75%), Gaps = 2/118 (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  LVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVV 145
            VT+ L+EGAL+TFKKYSV E+ IDVVWVPG++E+GV AQ LGKSGKY A++C+GAVV
Sbjct: 92  FVTRRLMEGALDTFKKYSVNED-IDVVWVPGAYELGVTAQALGKSGKYHAIVCLGAVV 148

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

 Score = 95.5 bits (236), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 39/73 (53%), Positives = 58/73 (79%)

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

Query: 133 GKYTAVLCIGAVV 145
            KY  V+C+GAV+
Sbjct: 70  PKYDGVICLGAVI 82

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|Q3Z799|RISB_DEHE1 6,7-dimethyl-8-ribityllumazine synthase OS=Dehalococcoides ethenogenes (strain 195) GN=ribH PE=3 SV=1

 Score = 94.7 bits (234), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 42/82 (51%), Positives = 61/82 (74%), Gaps = 1/82 (1%)

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

Query: 124 VVAQQLGKSGKYTAVLCIGAVV 145
           +VAQ+L KSG+Y AV+C+GAV+
Sbjct: 62  LVAQKLAKSGRYDAVICLGAVI 83

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.

Dehalococcoides ethenogenes (strain 195) (taxid: 243164)

EC: 2

EC: .

EC: 5

EC: .

EC: 1

EC: .

EC: 9

>sp|Q3ZY85|RISB_DEHSC 6,7-dimethyl-8-ribityllumazine synthase OS=Dehalococcoides sp. (strain CBDB1) GN=ribH PE=3 SV=1

 Score = 94.7 bits (234), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 42/82 (51%), Positives = 61/82 (74%), Gaps = 1/82 (1%)

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

Query: 124 VVAQQLGKSGKYTAVLCIGAVV 145
           +VAQ+L KSG+Y AV+C+GAV+
Sbjct: 62  LVAQKLAKSGRYDAVVCLGAVI 83

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.

Dehalococcoides sp. (strain CBDB1) (taxid: 255470)

EC: 2

EC: .

EC: 5

EC: .

EC: 1

EC: .

EC: 9

>sp|A5FQE3|RISB_DEHSB 6,7-dimethyl-8-ribityllumazine synthase OS=Dehalococcoides sp. (strain BAV1) GN=ribH PE=3 SV=1

 Score = 94.7 bits (234), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 42/82 (51%), Positives = 61/82 (74%), Gaps = 1/82 (1%)

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

Query: 124 VVAQQLGKSGKYTAVLCIGAVV 145
           +VAQ+L KSG+Y AV+C+GAV+
Sbjct: 62  LVAQKLAKSGRYDAVVCLGAVI 83

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.

Dehalococcoides sp. (strain BAV1) (taxid: 216389)

EC: 2

EC: .

EC: 5

EC: .

EC: 1

EC: .

EC: 9

>sp|C3L2U0|RISB_CLOB6 6,7-dimethyl-8-ribityllumazine synthase OS=Clostridium botulinum (strain 657 / Type Ba4) GN=ribH PE=3 SV=1

 Score = 92.0 bits (227), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 36/72 (50%), Positives = 56/72 (77%)

Query: 74  EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSG 133
           EGL+  ++V+RFNE +T  LL G+++  K++  KE+NI+V WVPG+FEI V+A+++   G
Sbjct: 11  EGLKVGIIVSRFNEFITSKLLAGSIDCLKRHGAKEDNIEVCWVPGAFEIPVIAKKMASKG 70

Query: 134 KYTAVLCIGAVV 145
           KY AV+C+GAV+
Sbjct: 71  KYDAVICLGAVI 82

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 botulinum (strain 657 / Type Ba4) (taxid: 515621)

EC: 2

EC: .

EC: 5

EC: .

EC: 1

EC: .

EC: 9

>sp|B1IL45|RISB_CLOBK 6,7-dimethyl-8-ribityllumazine synthase OS=Clostridium botulinum (strain Okra / Type B1) GN=ribH PE=3 SV=1

 Score = 92.0 bits (227), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 36/72 (50%), Positives = 56/72 (77%)

Query: 74  EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSG 133
           EGL+  ++V+RFNE +T  LL G+++  K++  KE+NI+V WVPG+FEI V+A+++   G
Sbjct: 11  EGLKVGIIVSRFNEFITSKLLAGSIDCLKRHGAKEDNIEVCWVPGAFEIPVIAKKMASKG 70

Query: 134 KYTAVLCIGAVV 145
           KY AV+C+GAV+
Sbjct: 71  KYDAVICLGAVI 82

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 botulinum (strain Okra / Type B1) (taxid: 498213)

EC: 2

EC: .

EC: 5

EC: .

EC: 1

EC: .

EC: 9

>sp|B1KZ46|RISB_CLOBM 6,7-dimethyl-8-ribityllumazine synthase OS=Clostridium botulinum (strain Loch Maree / Type A3) GN=ribH PE=3 SV=1

 Score = 92.0 bits (227), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 36/72 (50%), Positives = 56/72 (77%)

Query: 74  EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSG 133
           EGL+  ++V+RFNE +T  LL G+++  K++  KE+NI+V WVPG+FEI V+A+++   G
Sbjct: 11  EGLKVGIIVSRFNEFITSKLLAGSIDCLKRHGAKEDNIEVCWVPGAFEIPVIAKKMASKG 70

Query: 134 KYTAVLCIGAVV 145
           KY AV+C+GAV+
Sbjct: 71  KYDAVICLGAVI 82

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 botulinum (strain Loch Maree / Type A3) (taxid: 498214)

EC: 2

EC: .

EC: 5

EC: .

EC: 1

EC: .

EC: 9

>sp|A7GH84|RISB_CLOBL 6,7-dimethyl-8-ribityllumazine synthase OS=Clostridium botulinum (strain Langeland / NCTC 10281 / Type F) GN=ribH PE=3 SV=1

 Score = 92.0 bits (227), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 36/72 (50%), Positives = 56/72 (77%)

Query: 74  EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSG 133
           EGL+  ++V+RFNE +T  LL G+++  K++  KE+NI+V WVPG+FEI V+A+++   G
Sbjct: 11  EGLKVGIIVSRFNEFITSKLLAGSIDCLKRHGAKEDNIEVCWVPGAFEIPVIAKKMASKG 70

Query: 134 KYTAVLCIGAVV 145
           KY AV+C+GAV+
Sbjct: 71  KYDAVICLGAVI 82

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 botulinum (strain Langeland / NCTC 10281 / Type F) (taxid: 441772)

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	145
225434247	222	PREDICTED: 6,7-dimethyl-8-ribityllumazin	0.882	0.576	0.711	2e-43
15224809	227	6,7-dimethyl-8-ribityllumazine synthase	0.896	0.572	0.684	3e-43
297824393	227	hypothetical protein ARALYDRAFT_903810 [	0.896	0.572	0.669	2e-41
296084377	181	unnamed protein product [Vitis vinifera]	0.731	0.585	0.785	2e-40
255581426	221	6,7-dimethyl-8-ribityllumazine synthase,	0.896	0.588	0.657	1e-39
224117846	221	predicted protein [Populus trichocarpa]	0.827	0.542	0.736	1e-39
388517513	228	unknown [Medicago truncatula]	0.993	0.631	0.525	3e-36
217071658	197	unknown [Medicago truncatula]	0.993	0.730	0.525	3e-36
224095325	180	predicted protein [Populus trichocarpa]	0.731	0.588	0.722	9e-36
5532608	225	6,7-dimethyl-8-ribityllumazine synthase	0.896	0.577	0.610	2e-35

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

 Score =  180 bits (456), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 96/135 (71%), Positives = 110/135 (81%), Gaps = 7/135 (5%)

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 KSGKYTAVLCIGAVV 145
           KS KY A+LCIGAV+
Sbjct: 134 KSKKYQAILCIGAVI 148

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 =  179 bits (454), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 89/130 (68%), Positives = 108/130 (83%)

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 TAVLCIGAVV 145
            AVLCIGAV+
Sbjct: 145 HAVLCIGAVI 154

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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 =  174 bits (440), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 87/130 (66%), Positives = 106/130 (81%)

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 TAVLCIGAVV 145
            AVLCIGAV+
Sbjct: 145 HAVLCIGAVI 154

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  170 bits (430), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 84/107 (78%), Positives = 95/107 (88%), Gaps = 1/107 (0%)

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

Query: 99  ETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVV 145
           ETFK+YSVKEE+IDVVWVPGSFEIGVVA++LGKS KY A+LCIGAV+
Sbjct: 61  ETFKRYSVKEEDIDVVWVPGSFEIGVVAERLGKSKKYQAILCIGAVI 107

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 =  167 bits (424), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 92/140 (65%), Positives = 112/140 (80%), Gaps = 10/140 (7%)

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 AQQLGKSGKYTAVLCIGAVV 145
           A++LGKS KY A+LCIGAVV
Sbjct: 129 AERLGKSRKYHAILCIGAVV 148

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  167 bits (423), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 92/125 (73%), Positives = 105/125 (84%), Gaps = 5/125 (4%)

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 IGAVV 145
           IGAVV
Sbjct: 144 IGAVV 148

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 =  156 bits (394), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 82/156 (52%), Positives = 109/156 (69%), Gaps = 12/156 (7%)

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 NIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVV 145
           ++DVVWVPG FEIG  A +LGKSGKY AV+CIGAV+
Sbjct: 120 DVDVVWVPGCFEIGAAATRLGKSGKYHAVICIGAVI 155

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|217071658|gb|ACJ84189.1| unknown [Medicago truncatula]

 Score =  155 bits (393), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 82/156 (52%), Positives = 109/156 (69%), Gaps = 12/156 (7%)

Query: 1   MALNLKTT--------IHHSP---LASSSRQFINGFSPKPTSMSFSRSSSLKGFGTQIAI 49
           MAL++ T         +HH P   +A+ +  F    +PK T+ S S S S++    +   
Sbjct: 1   MALSVSTDCFLPALGFVHHHPQHRIAAPTNFFNLQKAPK-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 NIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVV 145
           ++DVVWVPG FEIG  A +LGKSGKY AV+CIGAV+
Sbjct: 120 DVDVVWVPGCFEIGAAATRLGKSGKYHAVICIGAVI 155

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 =  154 bits (390), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 78/108 (72%), Positives = 91/108 (84%), Gaps = 2/108 (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  LETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVV 145
           + TFKKYSVKE+ IDVVWVPGSFEIG+VA++LGKSGKY AV+CIGAVV
Sbjct: 61  VATFKKYSVKED-IDVVWVPGSFEIGIVAERLGKSGKYNAVVCIGAVV 107

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  153 bits (387), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 83/136 (61%), Positives = 100/136 (73%), Gaps = 6/136 (4%)

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 GKSGKYTAVLCIGAVV 145
           GKS KY A+LCIGAV+
Sbjct: 136 GKSQKYQAILCIGAVI 151

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	145
TAIR|locus:2051739	227	COS1 "AT2G44050" [Arabidopsis	0.986	0.629	0.641	1.1e-41
TIGR_CMR|DET_1187	155	DET_1187 "6,7-dimethyl-8-ribit	0.558	0.522	0.512	6.5e-19
TIGR_CMR|BA_4334	153	BA_4334 "6,7-dimethyl-8-ribity	0.489	0.464	0.507	3.7e-16
TIGR_CMR|GSU_1691	155	GSU_1691 "6,7-dimethyl-8-ribit	0.558	0.522	0.463	1.4e-14
TIGR_CMR|CHY_1472	152	CHY_1472 "6,7-dimethyl-8-ribit	0.489	0.467	0.458	1.8e-14
UNIPROTKB|P61714	156	ribE "RibE" [Escherichia coli	0.475	0.442	0.485	3.8e-14
TIGR_CMR|CBU_0648	151	CBU_0648 "6,7-dimethyl-8-ribit	0.475	0.456	0.449	5e-12
TIGR_CMR|CPS_1531	154	CPS_1531 "6,7-dimethyl-8-ribit	0.496	0.467	0.397	5e-12
TIGR_CMR|SO_3466	158	SO_3466 "6,7-dimethyl-8-ribity	0.475	0.436	0.428	5e-12
TIGR_CMR|CJE_0432	154	CJE_0432 "6,7-dimethyl-8-ribit	0.551	0.519	0.362	6.4e-12

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

 Score = 442 (160.7 bits), Expect = 1.1e-41, P = 1.1e-41
 Identities = 93/145 (64%), Positives = 113/145 (77%)

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 EIGVVAQQLGKSGKYTAVLCIGAVV 145
             EIGVVAQ LGKSGK+ AVLCIGAV+
Sbjct:   130 EIGVVAQNLGKSGKFHAVLCIGAVI 154

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

 Score = 227 (85.0 bits), Expect = 6.5e-19, P = 6.5e-19
 Identities = 42/82 (51%), Positives = 61/82 (74%)

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

Query:   124 VVAQQLGKSGKYTAVLCIGAVV 145
             +VAQ+L KSG+Y AV+C+GAV+
Sbjct:    62 LVAQKLAKSGRYDAVICLGAVI 83

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

GO:0009231 "riboflavin biosynthetic process" evidence=ISS

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

 Score = 201 (75.8 bits), Expect = 3.7e-16, P = 3.7e-16
 Identities = 36/71 (50%), Positives = 53/71 (74%)

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

Query:   135 YTAVLCIGAVV 145
             Y AV+ +G V+
Sbjct:    71 YDAVITLGTVI 81

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 = 186 (70.5 bits), Expect = 1.4e-14, P = 1.4e-14
 Identities = 38/82 (46%), Positives = 56/82 (68%)

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

Query:   124 VVAQQLGKSGKYTAVLCIGAVV 145
             + AQ+L + G Y AV+C+GAV+
Sbjct:    62 LTAQKLVQKGNYDAVICLGAVI 83

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 = 185 (70.2 bits), Expect = 1.8e-14, P = 1.8e-14
 Identities = 33/72 (45%), Positives = 53/72 (73%)

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

Query:   134 KYTAVLCIGAVV 145
              Y A++C+GAV+
Sbjct:    71 -YDAIICLGAVI 81

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 = 182 (69.1 bits), Expect = 3.8e-14, P = 3.8e-14
 Identities = 34/70 (48%), Positives = 49/70 (70%)

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

Query:   136 TAVLCIGAVV 145
              AV+ +G V+
Sbjct:    74 DAVIALGTVI 83

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|CBU_0648 CBU_0648 "6,7-dimethyl-8-ribityllumazine synthase" [Coxiella burnetii RSA 493 (taxid:227377)]

 Score = 162 (62.1 bits), Expect = 5.0e-12, P = 5.0e-12
 Identities = 31/69 (44%), Positives = 47/69 (68%)

Query:    77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYT 136
             + A+VV++FN  VT+ LL G L+   +  V+   I  VWVPG+ EI ++A++L KS  Y 
Sbjct:     7 KLAIVVSQFNRAVTEKLLNGVLQRLTELGVQANQIKTVWVPGAVEIPLLAKRLAKSKHYQ 66

Query:   137 AVLCIGAVV 145
             AV+C+GAV+
Sbjct:    67 AVVCLGAVI 75

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

GO:0009231 "riboflavin biosynthetic process" evidence=ISS

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

 Score = 162 (62.1 bits), Expect = 5.0e-12, P = 5.0e-12
 Identities = 29/73 (39%), Positives = 54/73 (73%)

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 GKYTAVLCIGAVV 145
             G+  A++ IGAV+
Sbjct:    71 GEADAIIAIGAVI 83

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 = 162 (62.1 bits), Expect = 5.0e-12, P = 5.0e-12
 Identities = 30/70 (42%), Positives = 51/70 (72%)

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

Query:   136 TAVLCIGAVV 145
               ++ +GAV+
Sbjct:    74 DGIIALGAVI 83

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

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 = 161 (61.7 bits), Expect = 6.4e-12, P = 6.4e-12
 Identities = 29/80 (36%), Positives = 52/80 (65%)

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

Query:   126 AQQLGKSGKYTAVLCIGAVV 145
              ++  +S K+ A+ C+GAV+
Sbjct:    64 LKKAIESKKFDAICCVGAVI 83

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

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
4th Layer	2.5.1.9	0.914
3rd Layer	2.5.1	0.921

---

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	145
PLN02404	141	PLN02404, PLN02404, 6,7-dimethyl-8-ribityllumazine	4e-43
PRK00061	154	PRK00061, ribH, 6,7-dimethyl-8-ribityllumazine syn	2e-32
cd09209	133	cd09209, Lumazine_synthase-I, lumazine synthase (6	1e-31
pfam00885	144	pfam00885, DMRL_synthase, 6,7-dimethyl-8-ribityllu	2e-30
COG0054	152	COG0054, RibH, Riboflavin synthase beta-chain [Coe	8e-28
TIGR00114	138	TIGR00114, lumazine-synth, 6,7-dimethyl-8-ribityll	6e-22
PRK12419	158	PRK12419, PRK12419, riboflavin synthase subunit be	1e-08
cd08371	129	cd08371, Lumazine_synthase-like, lumazine synthase	2e-08
cd09208	137	cd09208, Lumazine_synthase-II, lumazine synthase (	2e-07
cd09211	131	cd09211, Lumazine_synthase_archaeal, lumazine synt	4e-07

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

 Score =  138 bits (350), Expect = 4e-43
 Identities = 61/76 (80%), Positives = 68/76 (89%)

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

Query: 130 GKSGKYTAVLCIGAVV 145
            KSGKY A+LCIGAV+
Sbjct: 62  AKSGKYDAILCIGAVI 77

Length = 141

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

 Score =  112 bits (282), Expect = 2e-32
 Identities = 42/72 (58%), Positives = 57/72 (79%)

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

Query: 134 KYTAVLCIGAVV 145
           KY AV+ +GAV+
Sbjct: 71  KYDAVIALGAVI 82

Length = 154

>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 =  109 bits (275), Expect = 1e-31
 Identities = 39/68 (57%), Positives = 54/68 (79%)

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

Query: 138 VLCIGAVV 145
           ++ +G V+
Sbjct: 61  IIALGCVI 68

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

 Score =  106 bits (267), Expect = 2e-30
 Identities = 41/72 (56%), Positives = 56/72 (77%)

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

Query: 134 KYTAVLCIGAVV 145
           +Y AV+ +GAV+
Sbjct: 62  RYDAVVALGAVI 73

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 =   99 bits (250), Expect = 8e-28
 Identities = 38/72 (52%), Positives = 56/72 (77%)

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

Query: 134 KYTAVLCIGAVV 145
           KY AV+ +GAV+
Sbjct: 71  KYDAVVALGAVI 82

Length = 152

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

 Score = 84.7 bits (210), Expect = 6e-22
 Identities = 31/70 (44%), Positives = 52/70 (74%)

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

Query: 136 TAVLCIGAVV 145
            AV+ +G V+
Sbjct: 61  DAVIALGTVI 70

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|237096 PRK12419, PRK12419, riboflavin synthase subunit beta; Provisional

 Score = 50.8 bits (122), Expect = 1e-08
 Identities = 21/72 (29%), Positives = 35/72 (48%)

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

Query: 134 KYTAVLCIGAVV 145
           +Y A++    VV
Sbjct: 69  RYAAIVAAALVV 80

Length = 158

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

 Score = 49.3 bits (118), Expect = 2e-08
 Identities = 24/68 (35%), Positives = 38/68 (55%), Gaps = 1/68 (1%)

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

Query: 138 VLCIGAVV 145
           V+ IG V+
Sbjct: 60  VVAIGVVI 67

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|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 = 46.6 bits (111), Expect = 2e-07
 Identities = 19/70 (27%), Positives = 36/70 (51%)

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

Query: 136 TAVLCIGAVV 145
            A++    VV
Sbjct: 61  AAIVGAALVV 70

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

>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 = 45.8 bits (109), Expect = 4e-07
 Identities = 24/69 (34%), Positives = 38/69 (55%), Gaps = 6/69 (8%)

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

Query: 137 AVLCIGAVV 145
           AV+ +GAV+
Sbjct: 58  AVVTLGAVI 66

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	145
PRK12419	158	riboflavin synthase subunit beta; Provisional	99.96
PLN02404	141	6,7-dimethyl-8-ribityllumazine synthase	99.96
COG0054	152	RibH Riboflavin synthase beta-chain [Coenzyme meta	99.96
TIGR00114	138	lumazine-synth 6,7-dimethyl-8-ribityllumazine synt	99.95
PRK00061	154	ribH 6,7-dimethyl-8-ribityllumazine synthase; Prov	99.95
PF00885	144	DMRL_synthase: 6,7-dimethyl-8-ribityllumazine synt	99.94
KOG3243	158	consensus 6,7-dimethyl-8-ribityllumazine synthase	99.93
PRK06455	155	riboflavin synthase; Provisional	99.87
TIGR01506	151	ribC_arch riboflavin synthase. This archaeal prote	99.77
COG1731	154	Archaeal riboflavin synthase [Coenzyme metabolism]	98.65
PRK11041	309	DNA-binding transcriptional regulator CytR; Provis	95.73
PF04392	294	ABC_sub_bind: ABC transporter substrate binding pr	95.46
cd06270	268	PBP1_GalS_like Ligand binding domain of DNA transc	94.7
cd06271	268	PBP1_AglR_RafR_like Ligand-binding domain of DNA t	94.66
cd01536	267	PBP1_ABC_sugar_binding_like Periplasmic sugar-bind	94.44
cd01537	264	PBP1_Repressors_Sugar_Binding_like Ligand-binding	94.41
cd06297	269	PBP1_LacI_like_12 Ligand-binding domain of unchara	94.14
cd06305	273	PBP1_methylthioribose_binding_like Methylthioribos	94.12
PF13377	160	Peripla_BP_3: Periplasmic binding protein-like dom	93.95
cd06292	273	PBP1_LacI_like_10 Ligand-binding domain of unchara	93.92
TIGR01481	329	ccpA catabolite control protein A. Catabolite cont	93.82
cd01541	273	PBP1_AraR Ligand-binding domain of DNA transcripti	93.79
cd06284	267	PBP1_LacI_like_6 Ligand-binding domain of an uncha	93.65
cd01391	269	Periplasmic_Binding_Protein_Type_1 Type 1 periplas	93.49
cd06310	273	PBP1_ABC_sugar_binding_like_2 Periplasmic sugar-bi	93.36
cd06281	269	PBP1_LacI_like_5 Ligand-binding domain of uncharac	93.33
cd01575	268	PBP1_GntR Ligand-binding domain of DNA transcripti	93.32
cd06320	275	PBP1_allose_binding Periplasmic allose-binding dom	93.16
cd06317	275	PBP1_ABC_sugar_binding_like_8 Periplasmic sugar-bi	93.12
cd06296	270	PBP1_CatR_like Ligand-binding domain of a LacI-lik	93.11
cd06301	272	PBP1_rhizopine_binding_like Periplasmic binding pr	93.06
cd06293	269	PBP1_LacI_like_11 Ligand-binding domain of unchara	93.05
cd06319	277	PBP1_ABC_sugar_binding_like_10 Periplasmic sugar-b	93.03
cd06273	268	PBP1_GntR_like_1 This group includes the ligand-bi	92.81
PRK09492	315	treR trehalose repressor; Provisional	92.75
cd06316	294	PBP1_ABC_sugar_binding_like_7 Periplasmic sugar-bi	92.71
cd01545	270	PBP1_SalR Ligand-binding domain of DNA transcripti	92.69
cd06286	260	PBP1_CcpB_like Ligand-binding domain of a novel tr	92.62
cd06291	265	PBP1_Qymf_like Ligand binding domain of the lacI-l	92.61
cd06318	282	PBP1_ABC_sugar_binding_like_9 Periplasmic sugar-bi	92.57
cd06280	263	PBP1_LacI_like_4 Ligand-binding domain of uncharac	92.55
PRK10423	327	transcriptional repressor RbsR; Provisional	92.55
cd06315	280	PBP1_ABC_sugar_binding_like_6 Periplasmic sugar-bi	92.5
cd06290	265	PBP1_LacI_like_9 Ligand-binding domain of uncharac	92.48
cd06267	264	PBP1_LacI_sugar_binding_like Ligand binding domain	92.41
cd01574	264	PBP1_LacI Ligand-binding domain of DNA transcripti	92.01
cd01538	288	PBP1_ABC_xylose_binding Periplasmic xylose-binding	91.98
cd06298	268	PBP1_CcpA_like Ligand-binding domain of the catabo	91.92
cd06300	272	PBP1_ABC_sugar_binding_like_1 Periplasmic sugar-bi	91.85
cd01542	259	PBP1_TreR_like Ligand-binding domain of DNA transc	91.81
cd06277	268	PBP1_LacI_like_1 Ligand-binding domain of uncharac	91.69
cd06275	269	PBP1_PurR Ligand-binding domain of purine represso	91.63
PF00532	279	Peripla_BP_1: Periplasmic binding proteins and sug	91.39
PRK14987	331	gluconate operon transcriptional regulator; Provis	91.38
cd06267	264	PBP1_LacI_sugar_binding_like Ligand binding domain	91.32
cd06283	267	PBP1_RegR_EndR_KdgR_like Ligand-binding domain of	91.27
PRK10014	342	DNA-binding transcriptional repressor MalI; Provis	91.12
cd01539	303	PBP1_GGBP Periplasmic glucose/galactose-binding pr	91.07
cd06278	266	PBP1_LacI_like_2 Ligand-binding domain of uncharac	91.04
cd06282	266	PBP1_GntR_like_2 Ligand-binding domain of putative	91.0
PRK10703	341	DNA-binding transcriptional repressor PurR; Provis	90.97
cd06306	268	PBP1_TorT-like TorT-like proteins, a periplasmic b	90.95
cd06307	275	PBP1_uncharacterized_sugar_binding Periplasmic sug	90.94
cd06323	268	PBP1_ribose_binding Periplasmic sugar-binding doma	90.84
PRK09701	311	D-allose transporter subunit; Provisional	90.83
cd06299	265	PBP1_LacI_like_13 Ligand-binding domain of DNA-bin	90.82
PRK11303	328	DNA-binding transcriptional regulator FruR; Provis	90.71
cd06274	264	PBP1_FruR Ligand binding domain of DNA transcripti	90.65
cd06272	261	PBP1_hexuronate_repressor_like Ligand-binding doma	90.65
cd06271	268	PBP1_AglR_RafR_like Ligand-binding domain of DNA t	90.64
TIGR02405	311	trehalos_R_Ecol trehalose operon repressor, proteo	90.6
cd06354	265	PBP1_BmpA_PnrA_like Periplasmic binding domain of	90.57
cd06304	260	PBP1_BmpA_like Periplasmic binding component of a	90.52
TIGR02417	327	fruct_sucro_rep D-fructose-responsive transcriptio	90.48
PRK10355	330	xylF D-xylose transporter subunit XylF; Provisiona	90.45
cd06289	268	PBP1_MalI_like Ligand-binding domain of MalI, a tr	90.45
TIGR02955	295	TMAO_TorT TMAO reductase system periplasmic protei	90.42
cd06279	283	PBP1_LacI_like_3 Ligand-binding domain of uncharac	90.19
cd06295	275	PBP1_CelR Ligand binding domain of a transcription	90.16
cd06302	298	PBP1_LsrB_Quorum_Sensing Periplasmic binding domai	90.03
cd06308	270	PBP1_sensor_kinase_like Periplasmic binding domain	90.01
PF00532	279	Peripla_BP_1: Periplasmic binding proteins and sug	89.92
cd06293	269	PBP1_LacI_like_11 Ligand-binding domain of unchara	89.85
cd06321	271	PBP1_ABC_sugar_binding_like_11 Periplasmic sugar-b	89.4
cd06294	270	PBP1_ycjW_transcription_regulator_like Ligand-bind	89.32
PRK10727	343	DNA-binding transcriptional regulator GalR; Provis	89.31
TIGR02634	302	xylF D-xylose ABC transporter, substrate-binding p	89.24
cd06299	265	PBP1_LacI_like_13 Ligand-binding domain of DNA-bin	89.22
cd06285	265	PBP1_LacI_like_7 Ligand-binding domain of uncharac	88.98
PRK10936	343	TMAO reductase system periplasmic protein TorT; Pr	88.93
cd06322	267	PBP1_ABC_sugar_binding_like_12 Periplasmic sugar-b	88.68
cd06307	275	PBP1_uncharacterized_sugar_binding Periplasmic sug	88.67
cd06273	268	PBP1_GntR_like_1 This group includes the ligand-bi	88.62
cd06275	269	PBP1_PurR Ligand-binding domain of purine represso	88.56
PF13407	257	Peripla_BP_4: Periplasmic binding protein domain;	88.38
cd06312	271	PBP1_ABC_sugar_binding_like_4 Periplasmic sugar-bi	88.19
cd06270	268	PBP1_GalS_like Ligand binding domain of DNA transc	88.16
cd01540	289	PBP1_arabinose_binding Periplasmic L-arabinose-bin	87.96
PRK10014	342	DNA-binding transcriptional repressor MalI; Provis	87.88
cd06309	273	PBP1_YtfQ_like Periplasmic binding domain of ABC-t	87.76
cd06284	267	PBP1_LacI_like_6 Ligand-binding domain of an uncha	87.76
cd01544	270	PBP1_GalR Ligand-binding domain of DNA transcripti	87.52
PRK15408	336	autoinducer 2-binding protein lsrB; Provisional	87.34
PF00465	366	Fe-ADH: Iron-containing alcohol dehydrogenase ; In	87.25
cd06288	269	PBP1_sucrose_transcription_regulator Ligand-bindin	87.24
cd06294	270	PBP1_ycjW_transcription_regulator_like Ligand-bind	87.24
cd06325	281	PBP1_ABC_uncharacterized_transporter Type I peripl	87.13
cd06287	269	PBP1_LacI_like_8 Ligand-binding domain of uncharac	86.96
PRK10401	346	DNA-binding transcriptional regulator GalS; Provis	86.9
cd06298	268	PBP1_CcpA_like Ligand-binding domain of the catabo	86.82
PRK10653	295	D-ribose transporter subunit RbsB; Provisional	86.62
PF03358	152	FMN_red: NADPH-dependent FMN reductase; InterPro:	86.49
cd06289	268	PBP1_MalI_like Ligand-binding domain of MalI, a tr	85.32
PRK10727	343	DNA-binding transcriptional regulator GalR; Provis	85.26
PRK09526	342	lacI lac repressor; Reviewed	85.09
PRK10703	341	DNA-binding transcriptional repressor PurR; Provis	85.05
PRK10401	346	DNA-binding transcriptional regulator GalS; Provis	84.81
PRK11041	309	DNA-binding transcriptional regulator CytR; Provis	84.67
cd06281	269	PBP1_LacI_like_5 Ligand-binding domain of uncharac	84.67
cd01575	268	PBP1_GntR Ligand-binding domain of DNA transcripti	84.6
COG0715	335	TauA ABC-type nitrate/sulfonate/bicarbonate transp	83.96
cd06285	265	PBP1_LacI_like_7 Ligand-binding domain of uncharac	83.95
PF09861	204	DUF2088: Domain of unknown function (DUF2088); Int	83.88
cd08170	351	GlyDH Glycerol dehydrogenases (GlyDH) catalyzes ox	83.81
cd08183	374	Fe-ADH2 Iron-containing alcohol dehydrogenases-lik	83.58
cd06292	273	PBP1_LacI_like_10 Ligand-binding domain of unchara	83.56
PF02662	124	FlpD: Methyl-viologen-reducing hydrogenase, delta	83.39
cd01537	264	PBP1_Repressors_Sugar_Binding_like Ligand-binding	83.39
cd06311	274	PBP1_ABC_sugar_binding_like_3 Periplasmic sugar-bi	83.34
cd06274	264	PBP1_FruR Ligand binding domain of DNA transcripti	83.2
cd06295	275	PBP1_CelR Ligand binding domain of a transcription	82.9
PRK10423	327	transcriptional repressor RbsR; Provisional	82.71
COG1609	333	PurR Transcriptional regulators [Transcription]	82.6
cd06319	277	PBP1_ABC_sugar_binding_like_10 Periplasmic sugar-b	82.43
cd06272	261	PBP1_hexuronate_repressor_like Ligand-binding doma	82.14
cd06303	280	PBP1_LuxPQ_Quorum_Sensing Periplasmic binding prot	82.08
cd06286	260	PBP1_CcpB_like Ligand-binding domain of a novel tr	82.02
PF09084	216	NMT1: NMT1/THI5 like; InterPro: IPR015168 This ent	81.86
cd06324	305	PBP1_ABC_sugar_binding_like_13 Periplasmic sugar-b	81.75
cd06290	265	PBP1_LacI_like_9 Ligand-binding domain of uncharac	81.68
PRK15395	330	methyl-galactoside ABC transporter galactose-bindi	81.21
cd06314	271	PBP1_tmGBP Periplasmic sugar-binding domain of The	81.08
cd06278	266	PBP1_LacI_like_2 Ligand-binding domain of uncharac	80.9
cd06341	341	PBP1_ABC_ligand_binding_like_7 Type I periplasmic	80.82
cd06297	269	PBP1_LacI_like_12 Ligand-binding domain of unchara	80.72
cd06291	265	PBP1_Qymf_like Ligand binding domain of the lacI-l	80.51
cd06306	268	PBP1_TorT-like TorT-like proteins, a periplasmic b	80.45
cd06339	336	PBP1_YraM_LppC_lipoprotein_like Periplasmic bindin	80.4
COG1609	333	PurR Transcriptional regulators [Transcription]	80.25
cd06282	266	PBP1_GntR_like_2 Ligand-binding domain of putative	80.01

>PRK12419 riboflavin synthase subunit beta; Provisional

Probab=99.96  E-value=3.4e-29  Score=197.36  Aligned_cols=77  Identities=27%  Similarity=0.398  Sum_probs=73.7

Q ss_pred             ccCCCCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeeeeC
Q 032216           69 FLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVV  145 (145)
Q Consensus        69 ~l~~~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~VI  145 (145)
                      +.++.+++|||||+||||++||++|++||+++|+++|+.+++|+++|||||||||+++++|+++++|||||||||||
T Consensus         4 ~~~~~~~~riaIV~srfn~~It~~Ll~gA~~~l~~~G~~~~~i~v~~VPGA~EiP~~a~~l~~~~~yDaiIaLG~VI   80 (158)
T PRK12419          4 SPRFATPQRIAFIQARWHADIVDQARKGFVAEIAARGGAASQVDIFDVPGAFEIPLHAQTLAKTGRYAAIVAAALVV   80 (158)
T ss_pred             CCCCCCCCEEEEEEecCCHHHHHHHHHHHHHHHHHcCCCccceEEEECCcHHHHHHHHHHHHhcCCCCEEEEEEEEE
Confidence            34567889999999999999999999999999999999999999999999999999999999999999999999997

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

Probab=99.96  E-value=3.7e-29  Score=193.83  Aligned_cols=75  Identities=80%  Similarity=1.242  Sum_probs=72.5

Q ss_pred             CCCCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeeeeC
Q 032216           71 TKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVV  145 (145)
Q Consensus        71 ~~~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~VI  145 (145)
                      .+++++|||||+||||++|+++|++||+++|+++|+.+++|+++|||||||||+++|+|+++++|||||||||||
T Consensus         3 ~~~~~~ri~IV~s~fn~~I~~~Ll~ga~~~l~~~gv~~~~i~v~~VPGa~EiP~a~~~l~~s~~~DavIaLG~VI   77 (141)
T PLN02404          3 LDGEGLRFGVVVARFNEIITKNLLEGALETFKRYSVKEENIDVVWVPGSFEIPVVAQRLAKSGKYDAILCIGAVI   77 (141)
T ss_pred             cCCCCCEEEEEEecCcHHHHHHHHHHHHHHHHHcCCCccceEEEEcCcHHHHHHHHHHHHhcCCCCEEEEEEEEE
Confidence            357789999999999999999999999999999999999999999999999999999999999999999999997

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

Probab=99.96  E-value=7.5e-29  Score=194.73  Aligned_cols=82  Identities=49%  Similarity=0.826  Sum_probs=77.4

Q ss_pred             hhhhccccCCCCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEee
Q 032216           63 VRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        63 ~~~~~g~l~~~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG  142 (145)
                      |+.+++.+. .++.|||||++|||++|+++|++||+++|+++|+..+||+++|||||||||+++++|+++++||||||||
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            455677774 7889999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeC
Q 032216          143 AVV  145 (145)
Q Consensus       143 ~VI  145 (145)
                      |||
T Consensus        80 ~VI   82 (152)
T COG0054          80 AVI   82 (152)
T ss_pred             eEE
Confidence            998

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

Probab=99.95  E-value=4.1e-28  Score=186.96  Aligned_cols=70  Identities=43%  Similarity=0.920  Sum_probs=68.6

Q ss_pred             CEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeeeeC
Q 032216           76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVV  145 (145)
Q Consensus        76 lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~VI  145 (145)
                      +|||||+||||++|+++|++||+++|+++|+.+++|+++||||+||||+++|+|+++++|||||||||||
T Consensus         1 ~ri~IV~s~~n~~i~~~L~~ga~~~l~~~g~~~~~i~v~~VPGa~EiP~a~~~l~~~~~~DavI~LG~VI   70 (138)
T TIGR00114         1 VRVGIVIARFNRDITDMLLKGAIDALKRLGAEVDNIDVIWVPGAFELPLAVKKLAETGKYDAVIALGCVI   70 (138)
T ss_pred             CEEEEEEecCCHHHHHHHHHHHHHHHHHcCCCccceEEEECCcHHHHHHHHHHHHhcCCCCEEEEEeeEE
Confidence            5999999999999999999999999999999999999999999999999999999999999999999997

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

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

Probab=99.95  E-value=1e-27  Score=187.40  Aligned_cols=79  Identities=56%  Similarity=0.925  Sum_probs=74.2

Q ss_pred             hccccCCCCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeeeeC
Q 032216           66 LTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVV  145 (145)
Q Consensus        66 ~~g~l~~~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~VI  145 (145)
                      +++.+. .++.|||||+||||++|++.|++||+++|+++|+.+++++++||||+||||+++|+|+++++|||||||||||
T Consensus         4 ~~~~~~-~~~~riaIV~s~~n~~i~~~l~~ga~~~l~~~gv~~~~i~v~~VPGa~EiP~a~~~l~~~~~~DavIalG~VI   82 (154)
T PRK00061          4 IEGNLV-AKGLRIGIVVARFNDFITDALLEGALDALKRHGVSEENIDVVRVPGAFEIPLAAKKLAESGKYDAVIALGAVI   82 (154)
T ss_pred             cCCCcC-CCCCEEEEEEecCcHHHHHHHHHHHHHHHHHcCCCccceEEEECCCHHHHHHHHHHHHHcCCCCEEEEEeeEE
Confidence            445554 6788999999999999999999999999999999999999999999999999999999999999999999997

>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=99.94  E-value=5.4e-27  Score=181.02  Aligned_cols=72  Identities=54%  Similarity=0.916  Sum_probs=70.2

Q ss_pred             CCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeeeeC
Q 032216           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVV  145 (145)
Q Consensus        74 ~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~VI  145 (145)
                      +++|||||+||||++|+++|+++|+++|+++|+.+++|++++|||+||||+++|+|+++++|||||||||||
T Consensus         2 ~~~ri~IV~s~~n~~i~~~ll~~a~~~l~~~g~~~~~i~~~~VPGa~ElP~a~~~l~~~~~~Davi~lG~VI   73 (144)
T PF00885_consen    2 SGLRIAIVVSRFNEEITDRLLEGALEELKRHGVAEENIEVIRVPGAFELPLAAKRLAESGRYDAVIALGCVI   73 (144)
T ss_dssp             TTEEEEEEEESTTHHHHHHHHHHHHHHHHHTTTTGGCEEEEEESSGGGHHHHHHHHHHCSTESEEEEEEEEE
T ss_pred             CCCEEEEEEEeccHHHHHHHHHHHHHHHHHcCCCccceEEEEcCCHHHHHHHHHHHhcccCccEEEEecccc
Confidence            468999999999999999999999999999999999999999999999999999999999999999999997

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=99.93  E-value=3.7e-26  Score=178.35  Aligned_cols=87  Identities=64%  Similarity=1.058  Sum_probs=83.3

Q ss_pred             hhhhhhhhccccCCCCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEE
Q 032216           59 QTEAVRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAV  138 (145)
Q Consensus        59 ~~~a~~~~~g~l~~~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAV  138 (145)
                      |++++++-++++-+++++||+||++|||+.+++.|++||++++++++|.++||++.||||+||||+.+|.+.++++||+|
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            45677888888889999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeeeeC
Q 032216          139 LCIGAVV  145 (145)
Q Consensus       139 IaLG~VI  145 (145)
                      ||||++|
T Consensus        81 i~IGvlI   87 (158)
T KOG3243|consen   81 ICIGVLI   87 (158)
T ss_pred             EEEEEEE
Confidence            9999987

>PRK06455 riboflavin synthase; Provisional

Probab=99.87  E-value=4.8e-22  Score=156.71  Aligned_cols=66  Identities=18%  Similarity=0.279  Sum_probs=62.0

Q ss_pred             CEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeeeeC
Q 032216           76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVV  145 (145)
Q Consensus        76 lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~VI  145 (145)
                      +|||||+|+||++   .|++||+++|+++| ...+|++++|||+||||+++|+|+++++||||||||||+
T Consensus         2 ~kigIV~s~fn~~---~L~~gAi~~L~~~g-~~~~I~v~~VPGa~ELP~aakkL~~~~~yDaVIaLG~VG   67 (155)
T PRK06455          2 MKIGIADTTFARV---DMGSAAIDELRKLD-PSAKIIRYTVPGIKDLPVAAKKLIEEEGCDIVMALGMPG   67 (155)
T ss_pred             cEEEEEEEecchH---HHHHHHHHHHHhcC-CCCceEEEECCCHHHHHHHHHHHHhcCCCCEEEEeccee
Confidence            6999999999997   69999999999998 556899999999999999999999999999999999984

>TIGR01506 ribC_arch riboflavin synthase

Probab=99.77  E-value=5e-19  Score=139.00  Aligned_cols=65  Identities=20%  Similarity=0.228  Sum_probs=60.1

Q ss_pred             EEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeeeeC
Q 032216           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVV  145 (145)
Q Consensus        77 RIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~VI  145 (145)
                      ||+|+.+.|-+.   .|.+||+++|+++| ...+|++++|||+||||+++|+|+++++|||||||||||
T Consensus         1 ~~~~~~ttf~~~---~M~~gA~~~L~~~g-~g~~i~v~~VPGa~EiP~aak~l~~~~~~DaVIaLG~VI   65 (151)
T TIGR01506         1 KVGIADTTFARY---DMGGAAIDELRKHT-AGIKIIRRTVPGIKDLPVAAKKLLEEEGCEMVITLGWVG   65 (151)
T ss_pred             Ccceecchhhhh---hHHHHHHHHHHhcC-CCCeEEEEECCcHhHHHHHHHHHHhcCCCCEEEEeceEE
Confidence            589999999998   89999999999966 345699999999999999999999999999999999997

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.

>COG1731 Archaeal riboflavin synthase [Coenzyme metabolism]

Probab=98.65  E-value=4.6e-08  Score=77.04  Aligned_cols=65  Identities=22%  Similarity=0.251  Sum_probs=58.9

Q ss_pred             CEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeeee
Q 032216           76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAV  144 (145)
Q Consensus        76 lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~V  144 (145)
                      .+|||+.+.|-+.   .|-.-|+++|+++--. ..|..++|||.-++|+++++|++...+|+||+||.+
T Consensus         2 ~kvGiaDTTFaRv---dMg~vai~~lk~~~~~-~~i~R~TVPGIKdlpvaakrLieeeGCd~Vi~lG~~   66 (154)
T COG1731           2 TKVGIADTTFARV---DMGSVAIDELKKLLPG-IKIKRYTVPGIKDLPVAAKRLIEEEGCDIVIALGWV   66 (154)
T ss_pred             ceeeeeccceeee---cchHHHHHHHHhhCCC-CceEEeeCCCcccChHHHHHHHHhcCCcEEEEccCc
Confidence            4899999999987   7999999999988543 468999999999999999999999999999999986

>PRK11041 DNA-binding transcriptional regulator CytR; Provisional

Probab=95.73  E-value=0.058  Score=42.91  Aligned_cols=69  Identities=12%  Similarity=0.059  Sum_probs=50.0

Q ss_pred             CCCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeee
Q 032216           72 KNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        72 ~~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~  143 (145)
                      .++..+||+|...+.......|++|+.++++++|..   +.+.+.....|....+-+.+.+.++||||..++
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            345579999999888778888999999999999973   555444444444444333344578999999865

>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=95.46  E-value=0.12  Score=42.47  Aligned_cols=66  Identities=14%  Similarity=0.214  Sum_probs=42.7

Q ss_pred             EEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHH--hhcCCCcEEEEeee
Q 032216           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQL--GKSGKYTAVLCIGA  143 (145)
Q Consensus        77 RIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~L--a~s~~yDAVIaLG~  143 (145)
                      ||||++.--|+.+.+ ..+|+++.|++.|..++++++..-..--+...+.+.+  +...++|.||++|.
T Consensus         1 ~v~i~~~~~~~~~~~-~~~gf~~~L~~~g~~~~~~~~~~~~a~~d~~~~~~~~~~l~~~~~DlIi~~gt   68 (294)
T PF04392_consen    1 KVGILQFISHPALDD-IVRGFKDGLKELGYDEKNVEIEYKNAEGDPEKLRQIARKLKAQKPDLIIAIGT   68 (294)
T ss_dssp             EEEEEESS--HHHHH-HHHHHHHHHHHTT--CCCEEEEEEE-TT-HHHHHHHHHHHCCTS-SEEEEESH
T ss_pred             CeEEEEEeccHHHHH-HHHHHHHHHHHcCCccccEEEEEecCCCCHHHHHHHHHHHhcCCCCEEEEeCc
Confidence            789999988888655 6899999999999987677765444444444333322  23579999999983

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.

>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=94.70  E-value=0.15  Score=39.55  Aligned_cols=60  Identities=17%  Similarity=0.181  Sum_probs=42.9

Q ss_pred             EEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH---HHHHHhhcCCCcEEEEeee
Q 032216           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        78 IaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl---aak~La~s~~yDAVIaLG~  143 (145)
                      ||+|...++...-..+.+|..++++++|+.   +.+  +++-++...   .++.+ .++++||||+.++
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            788998888888888999999999999974   333  333343322   22333 3578999999875

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

>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=94.66  E-value=0.16  Score=39.04  Aligned_cols=63  Identities=17%  Similarity=0.116  Sum_probs=43.9

Q ss_pred             EEEEEee----ecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeee
Q 032216           78 FALVVAR----FNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        78 IaIVvAr----fN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~  143 (145)
                      ||+|..+    |+......|++|..+.++++|+.   +.+......-+---.+.++..++++||+|..++
T Consensus         2 igvi~p~~~~~~~~~~~~~~~~~i~~~~~~~g~~---~~~~~~~~~~~~~~~~~~~~~~~~vdgiii~~~   68 (268)
T cd06271           2 IGLVLPTGEREEGDPFFAEFLSGLSEALAEHGYD---LVLLPVDPDEDPLEVYRRLVESGLVDGVIISRT   68 (268)
T ss_pred             eEEEeCCcccccCCccHHHHHHHHHHHHHHCCce---EEEecCCCcHHHHHHHHHHHHcCCCCEEEEecC
Confidence            5777766    56666778999999999999974   566655544333334555555678999998654

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

>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=94.44  E-value=0.21  Score=37.88  Aligned_cols=63  Identities=16%  Similarity=0.122  Sum_probs=43.3

Q ss_pred             EEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchH-HHHHHHHhhcCCCcEEEEeee
Q 032216           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEI-GVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        77 RIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfEL-Plaak~La~s~~yDAVIaLG~  143 (145)
                      |||+|...+....-..+++|+.+.++++|+.   +.++...+.-+- --.+++|... ++||||..++
T Consensus         1 ~ig~i~p~~~~~~~~~~~~~~~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~l~~~-~vdgvi~~~~   64 (267)
T cd01536           1 KIGLVVPSLNNPFWQAMNKGAEAAAKELGVE---LIVLDAQNDVSKQIQQIEDLIAQ-GVDGIIISPV   64 (267)
T ss_pred             CEEEEeccccCHHHHHHHHHHHHHHHhcCce---EEEECCCCCHHHHHHHHHHHHHc-CCCEEEEeCC
Confidence            6899998887777788999999999998863   444444432221 1334455544 8999997653

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

>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=94.41  E-value=0.26  Score=37.00  Aligned_cols=63  Identities=10%  Similarity=0.056  Sum_probs=44.4

Q ss_pred             EEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccc-hHHHHHHHHhhcCCCcEEEEeee
Q 032216           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSF-EIGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        77 RIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAf-ELPlaak~La~s~~yDAVIaLG~  143 (145)
                      |||+|....+......+.+|+.+.++++|+.   +.+.+..+.. +.--.++++.+ .++|++|+.++
T Consensus         1 ~ig~v~~~~~~~~~~~~~~g~~~~~~~~g~~---l~~~~~~~~~~~~~~~~~~~~~-~~~d~ii~~~~   64 (264)
T cd01537           1 TIGVLVPDLDNPFFAQVLKGIEEAAKAAGYQ---VLLANSQNDAEKQLSALENLIA-RGVDGIIIAPS   64 (264)
T ss_pred             CeEEEEcCCCChHHHHHHHHHHHHHHHcCCe---EEEEeCCCCHHHHHHHHHHHHH-cCCCEEEEecC
Confidence            5788887766666778999999999998873   5555554433 23445566654 47999998765

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

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

Probab=94.14  E-value=0.3  Score=38.39  Aligned_cols=63  Identities=8%  Similarity=0.001  Sum_probs=44.7

Q ss_pred             EEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeee
Q 032216           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        78 IaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~  143 (145)
                      ||+|+..+.......|++|..++++++|..   +.+......-+..-.+.+++.+.++||||..++
T Consensus         2 Igvi~p~~~~~~~~~~~~~i~~~~~~~gy~---~~~~~~~~~~~~~~~~~~~l~~~~vdgvi~~~~   64 (269)
T cd06297           2 ISVLLPVVATEFYRRLLEGIEGALLEQRYD---LALFPLLSLARLKRYLESTTLAYLTDGLLLASY   64 (269)
T ss_pred             EEEEeCCCcChhHHHHHHHHHHHHHHCCCE---EEEEeCCCcHHHHHHHHHHHHhcCCCEEEEecC
Confidence            788898887777888999999999999974   445443332233334444455678999998764

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.

>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=94.12  E-value=0.24  Score=38.30  Aligned_cols=60  Identities=17%  Similarity=0.041  Sum_probs=42.5

Q ss_pred             EEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHH---HHhhcCCCcEEEEee
Q 032216           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQ---QLGKSGKYTAVLCIG  142 (145)
Q Consensus        77 RIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak---~La~s~~yDAVIaLG  142 (145)
                      |||+|...+.......+++|..++++++|+.   +.+  ++..++.....+   .+. +.++||+|...
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            5889998888778888999999999999973   444  344455443333   233 45899999864

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.

>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=93.95  E-value=0.29  Score=35.26  Aligned_cols=66  Identities=23%  Similarity=0.183  Sum_probs=47.0

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHH-HhhcCCCcEEEEe
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQ-LGKSGKYTAVLCI  141 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~-La~s~~yDAVIaL  141 (145)
                      -.||+++...-+.......++|+.+.++++|+... ...+...+..+-...... ++++.+.|||||-
T Consensus         9 ~r~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~l~~~~pdaii~~   75 (160)
T PF13377_consen    9 HRRIAFIGGPPNSSVSRERLEGFREALKEHGIEFE-ELIFFSDDDSEDAREAQLLWLRRLRPDAIICS   75 (160)
T ss_dssp             -SSEEEEESSTTSHHHHHHHHHHHHHHHHTTSEEE-GEEEEESSSHHHHHHHHHHHHHTCSSSEEEES
T ss_pred             CCeEEEEecCCCChhHHHHHHHHHHHHHHCCCCCC-eeEeecCCcchhHHHHHHHHHhcCCCcEEEEc
Confidence            45899999888888899999999999999999744 334444444444443332 3454578999994

...

>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=93.92  E-value=0.31  Score=37.80  Aligned_cols=62  Identities=11%  Similarity=0.082  Sum_probs=43.4

Q ss_pred             EEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHH-HHHHhhcCCCcEEEEeee
Q 032216           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVV-AQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        78 IaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPla-ak~La~s~~yDAVIaLG~  143 (145)
                      ||+|...+.......+++|..+.++++|..   +.+..--..-|...- ++.|. +.++||+|.+++
T Consensus         2 Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~i~~l~-~~~vdgiIi~~~   64 (273)
T cd06292           2 VGLLVPELSNPIFPAFAEAIEAALAQYGYT---VLLCNTYRGGVSEADYVEDLL-ARGVRGVVFISS   64 (273)
T ss_pred             EEEEeCCCcCchHHHHHHHHHHHHHHCCCE---EEEEeCCCChHHHHHHHHHHH-HcCCCEEEEeCC
Confidence            789999888888888999999999999974   444433333343333 34444 468999998764

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=93.82  E-value=0.41  Score=38.64  Aligned_cols=67  Identities=13%  Similarity=0.157  Sum_probs=47.3

Q ss_pred             CCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHH-HHHHhhcCCCcEEEEeee
Q 032216           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVV-AQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        73 ~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPla-ak~La~s~~yDAVIaLG~  143 (145)
                      .+...||++...+....-..+++|+.+.++++|..   +.+.......+.-.. ++.+ ...++||||..+.
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            34568999998887677778999999999999973   555544544443332 2333 4578999998764

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.

>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=93.79  E-value=0.39  Score=37.36  Aligned_cols=61  Identities=5%  Similarity=0.049  Sum_probs=43.1

Q ss_pred             EEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH-HHHHHhhcCCCcEEEEee
Q 032216           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV-VAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        78 IaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl-aak~La~s~~yDAVIaLG  142 (145)
                      ||+|...++...-..+++|+.++++++|..   +.+.....-.+... +++.|. +.++||+|..+
T Consensus         2 igvv~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~i~~l~-~~~vdgii~~~   63 (273)
T cd01541           2 IGVITTYISDYIFPSIIRGIESVLSEKGYS---LLLASTNNDPERERKCLENML-SQGIDGLIIEP   63 (273)
T ss_pred             eEEEeCCccchhHHHHHHHHHHHHHHcCCE---EEEEeCCCCHHHHHHHHHHHH-HcCCCEEEEec
Confidence            788999999888889999999999999974   54544433333332 233443 46899999753

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

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

Probab=93.65  E-value=0.34  Score=37.12  Aligned_cols=63  Identities=8%  Similarity=0.023  Sum_probs=42.8

Q ss_pred             EEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeee
Q 032216           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        78 IaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~  143 (145)
                      |++|...|+......+.+|..++++++|..   +.+......-+.-..+-..+.+.++||+|..++
T Consensus         2 i~~v~~~~~~~~~~~~~~~i~~~~~~~g~~---~~~~~~~~~~~~~~~~~~~~~~~~vdgiii~~~   64 (267)
T cd06284           2 ILVLVPDIANPFFSEILKGIEDEAREAGYG---VLLGDTRSDPEREQEYLDLLRRKQADGIILLDG   64 (267)
T ss_pred             EEEEECCCCCccHHHHHHHHHHHHHHcCCe---EEEecCCCChHHHHHHHHHHHHcCCCEEEEecC
Confidence            788888888888888999999999999873   444433222222222223445678999998654

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.

>cd01391 Periplasmic_Binding_Protein_Type_1 Type 1 periplasmic binding fold superfamily

Probab=93.49  E-value=0.39  Score=35.24  Aligned_cols=63  Identities=8%  Similarity=0.076  Sum_probs=42.3

Q ss_pred             EEEEEEeee-cHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccch--HH-HHHHHHhhcCCCcEEEEeee
Q 032216           77 RFALVVARF-NELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE--IG-VVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        77 RIaIVvArf-N~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfE--LP-laak~La~s~~yDAVIaLG~  143 (145)
                      |||++...+ +......+.+|+.+.+++.|.   ++++..+....+  -. -++++++ ..++|++|..++
T Consensus         1 ~Ig~i~~~~~~~~~~~~~~~~~~~~~~~~g~---~~~~~~~~~~~~~~~~~~~~~~~~-~~~~d~ii~~~~   67 (269)
T cd01391           1 KIGVLLPLSGSAPFGAQLLAGIELAAEEIGR---GLEVILADSQSDPERALEALRDLI-QQGVDGIIGPPS   67 (269)
T ss_pred             CceEEeecCCCcHHHHHHHHHHHHHHHHhCC---ceEEEEecCCCCHHHHHHHHHHHH-HcCCCEEEecCC
Confidence            578888877 677778888999999988422   245555555554  22 3334444 458999998775

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

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

Probab=93.36  E-value=0.38  Score=37.32  Aligned_cols=62  Identities=16%  Similarity=0.071  Sum_probs=40.9

Q ss_pred             EEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHH---HHHHhhcCCCcEEEEee
Q 032216           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVV---AQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        77 RIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPla---ak~La~s~~yDAVIaLG  142 (145)
                      |||+|+.++.......+.+|+.+.++++|..   +.++......+.--.   ++.+ .+.++||||..+
T Consensus         1 ~Igvi~~~~~~~~~~~~~~g~~~~~~~~g~~---~~~~~~~~~~~~~~~~~~i~~l-~~~~vdgvii~~   65 (273)
T cd06310           1 KIALVPKGTTSDFWQAVKAGAEAAAKELGVK---VTFQGPASETDVAGQVNLLENA-IARGPDAILLAP   65 (273)
T ss_pred             CeEEEecCCCcHHHHHHHHHHHHHHHHcCCE---EEEecCccCCCHHHHHHHHHHH-HHhCCCEEEEcC
Confidence            7999999886666678999999999999974   333322112232222   2333 345899999865

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.

>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=93.33  E-value=0.42  Score=37.25  Aligned_cols=64  Identities=8%  Similarity=0.062  Sum_probs=41.3

Q ss_pred             EEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeee
Q 032216           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        77 RIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~  143 (145)
                      .||+|...+....-..|++|..+.++++|..   +.+..-....+--..+-..+.+.++||||..++
T Consensus         1 ~Igvv~~~~~~~~~~~~~~~i~~~a~~~g~~---~~~~~~~~~~~~~~~~i~~l~~~~vdgii~~~~   64 (269)
T cd06281           1 TIGCLVSDITNPLLAQLFSGAEDRLRAAGYS---LLIANSLNDPERELEILRSFEQRRMDGIIIAPG   64 (269)
T ss_pred             CEEEEecCCccccHHHHHHHHHHHHHHcCCE---EEEEeCCCChHHHHHHHHHHHHcCCCEEEEecC
Confidence            3788888887677778999999999999873   333322222332222222234568999998764

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.

>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=93.32  E-value=0.53  Score=36.08  Aligned_cols=62  Identities=16%  Similarity=0.121  Sum_probs=41.1

Q ss_pred             EEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH-HHHHHhhcCCCcEEEEeee
Q 032216           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV-VAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        78 IaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl-aak~La~s~~yDAVIaLG~  143 (145)
                      ||+|+..+....-..+.+|..++++++|..   +.+......-+--. .++.+ .+.++||||..++
T Consensus         2 Ig~i~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~~~~l-~~~~vdgiii~~~   64 (268)
T cd01575           2 VAVLVPSLSNSVFADVLQGISDVLEAAGYQ---LLLGNTGYSPEREEELLRTL-LSRRPAGLILTGL   64 (268)
T ss_pred             EEEEeCCCcchhHHHHHHHHHHHHHHcCCE---EEEecCCCCchhHHHHHHHH-HHcCCCEEEEeCC
Confidence            788888887777788999999999999873   43433222222211 23333 3568999998774

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,

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

Probab=93.16  E-value=0.47  Score=36.97  Aligned_cols=62  Identities=19%  Similarity=0.266  Sum_probs=42.7

Q ss_pred             EEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH---HHHHHhhcCCCcEEEEee
Q 032216           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        77 RIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl---aak~La~s~~yDAVIaLG  142 (145)
                      |||+|...+.......|++|+.+.++++|..   +.+...++.-+.-.   +++++. +.++||+|..+
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            6899999888888889999999999999974   55554443322211   223333 35799988654

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.

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

Probab=93.12  E-value=0.55  Score=36.27  Aligned_cols=61  Identities=8%  Similarity=0.013  Sum_probs=43.5

Q ss_pred             EEEEEeee-cHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHH--hhcCCCcEEEEeee
Q 032216           78 FALVVARF-NELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQL--GKSGKYTAVLCIGA  143 (145)
Q Consensus        78 IaIVvArf-N~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~L--a~s~~yDAVIaLG~  143 (145)
                      ||+|...+ +......+++|+.++++++|+.   +.+  .+..++.....+.+  +.+.++||+|..++
T Consensus         2 i~vi~p~~~~~~~~~~~~~g~~~~~~~~g~~---~~~--~~~~~~~~~~~~~~~~l~~~~vdgiii~~~   65 (275)
T cd06317           2 IGYTQNNVGSHSYQTTYNKAFQAAAEEDGVE---VIV--LDANGDVARQAAQVEDLIAQKVDGIILWPT   65 (275)
T ss_pred             eEEEecccCCCHHHHHHHHHHHHHHHhcCCE---EEE--EcCCcCHHHHHHHHHHHHHcCCCEEEEecC
Confidence            78888888 7778889999999999999863   333  45555555444432  23457999988764

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.

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

Probab=93.11  E-value=0.42  Score=36.89  Aligned_cols=62  Identities=11%  Similarity=0.081  Sum_probs=43.6

Q ss_pred             EEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH-HHHHHHhhcCCCcEEEEeee
Q 032216           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        78 IaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP-laak~La~s~~yDAVIaLG~  143 (145)
                      ||||...++......+.+|..+.++++|+.   +.+....+.-|-- -+++.+. ++++||+|...+
T Consensus         2 i~vi~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~i~~l~-~~~~dgiii~~~   64 (270)
T cd06296           2 IGLVFPDLDSPWASEVLRGVEEAAAAAGYD---VVLSESGRRTSPERQWVERLS-ARRTDGVILVTP   64 (270)
T ss_pred             eEEEECCCCCccHHHHHHHHHHHHHHcCCe---EEEecCCCchHHHHHHHHHHH-HcCCCEEEEecC
Confidence            688888888777888999999999998873   5666555544322 3344443 468999987643

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.

>cd06301 PBP1_rhizopine_binding_like Periplasmic binding proteins specific to rhizopines

Probab=93.06  E-value=0.45  Score=36.87  Aligned_cols=61  Identities=13%  Similarity=0.209  Sum_probs=40.4

Q ss_pred             EEEEEEeeecHHHHHHHHHHHHHHHHH-CCCCCCCeEEEEecccchHHHH---HHHHhhcCCCcEEEEeee
Q 032216           77 RFALVVARFNELVTKLLLEGALETFKK-YSVKEENIDVVWVPGSFEIGVV---AQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        77 RIaIVvArfN~~It~~LleGA~~~L~~-~Gv~~e~I~vv~VPGAfELPla---ak~La~s~~yDAVIaLG~  143 (145)
                      |||+|...++...-..+.+|+.+.+++ +|+     +++...+..+.--.   ++.+. +.++||+|..++
T Consensus         1 ~igvi~~~~~~~~~~~~~~gi~~~~~~~~~~-----~~~~~~~~~~~~~~~~~i~~l~-~~~vdgiii~~~   65 (272)
T cd06301           1 KIGVSMANFDDNFLTLLRNAMKEHAKVLGGV-----ELQFEDAKNDVATQLSQVENFI-AQGVDAIIVVPV   65 (272)
T ss_pred             CeeEeecccCCHHHHHHHHHHHHHHHHcCCc-----EEEEeCCCCCHHHHHHHHHHHH-HcCCCEEEEecC
Confidence            688999888877788899999999998 775     33333443322222   22333 457999987653

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.

>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=93.05  E-value=0.43  Score=37.07  Aligned_cols=64  Identities=9%  Similarity=0.041  Sum_probs=43.0

Q ss_pred             EEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeee
Q 032216           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        77 RIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~  143 (145)
                      .||+|...+....-..+++|+.++++++|..   +.+....+..+--...-+.+.+.++||+|..++
T Consensus         1 ~Ig~i~~~~~~~~~~~~~~gi~~~~~~~gy~---v~~~~~~~~~~~~~~~i~~~~~~~~dgiii~~~   64 (269)
T cd06293           1 TIGLVVPDIANPFFAELADAVEEEADARGLS---LVLCATRNRPERELTYLRWLDTNHVDGLIFVTN   64 (269)
T ss_pred             CEEEEeCCCCCCcHHHHHHHHHHHHHHCCCE---EEEEeCCCCHHHHHHHHHHHHHCCCCEEEEeCC
Confidence            3788888877666677999999999999974   555544433332222222344678999998764

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.

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

Probab=93.03  E-value=0.5  Score=36.62  Aligned_cols=62  Identities=8%  Similarity=-0.038  Sum_probs=41.0

Q ss_pred             EEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccch-HHHHHHHHhhcCCCcEEEEee
Q 032216           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE-IGVVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        77 RIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfE-LPlaak~La~s~~yDAVIaLG  142 (145)
                      |||+|...+....-..+.+|+.+.++++|+.   +.++.-.+.-+ ---+++.+. ..++||||..+
T Consensus         1 ~i~vi~~~~~~~~~~~~~~~i~~~~~~~g~~---~~~~~~~~~~~~~~~~i~~~~-~~~~dgiii~~   63 (277)
T cd06319           1 QIAYIVSDLRIPFWQIMGRGVKSKAKALGYD---AVELSAENSAKKELENLRTAI-DKGVSGIIISP   63 (277)
T ss_pred             CeEEEeCCCCchHHHHHHHHHHHHHHhcCCe---EEEecCCCCHHHHHHHHHHHH-hcCCCEEEEcC
Confidence            5888888888778888999999999999863   33332232221 112334443 46799998655

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.

>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=92.81  E-value=0.55  Score=36.22  Aligned_cols=62  Identities=13%  Similarity=0.112  Sum_probs=41.8

Q ss_pred             EEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH-HHHHHHhhcCCCcEEEEeee
Q 032216           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        78 IaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP-laak~La~s~~yDAVIaLG~  143 (145)
                      ||+|...++...-..++++..++++++|..   +.+..-....|.- -.++.|. +.++||+|..++
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            788888887777788999999999999963   4443333323322 2234444 457999998764

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

>PRK09492 treR trehalose repressor; Provisional

Probab=92.75  E-value=0.66  Score=37.20  Aligned_cols=66  Identities=15%  Similarity=0.068  Sum_probs=43.7

Q ss_pred             CCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH-HHHHHhhcCCCcEEEEee
Q 032216           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV-VAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        73 ~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl-aak~La~s~~yDAVIaLG  142 (145)
                      .+...||+|...+....-..++++..+++.++|..   +.+.......+.-. .++. +.+.++||+|..+
T Consensus        60 ~~~~~Ig~i~~~~~~~~~~~~~~~i~~~~~~~gy~---~~~~~~~~~~~~~~~~~~~-l~~~~vdgiIi~~  126 (315)
T PRK09492         60 QSDKVVGIIVSRLDSLSENQAVRTMLPAFYEQGYD---PIIMESQFSPEKVNEHLGV-LKRRNVDGVILFG  126 (315)
T ss_pred             CCCCeEEEEecCCcCcccHHHHHHHHHHHHHcCCe---EEEEecCCChHHHHHHHHH-HHhcCCCEEEEeC
Confidence            34458999999876666677999999999999974   43333322222221 2233 3457899999876

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

Probab=92.71  E-value=0.61  Score=37.14  Aligned_cols=62  Identities=16%  Similarity=0.220  Sum_probs=42.8

Q ss_pred             EEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHH--hhcCCCcEEEEee
Q 032216           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQL--GKSGKYTAVLCIG  142 (145)
Q Consensus        77 RIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~L--a~s~~yDAVIaLG  142 (145)
                      |||+|+..++......+.+|..++++++|+.   +.++ -++-++.....+.+  +..+++||||..+
T Consensus         1 ~i~~i~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~-~~~~~~~~~~~~~l~~~~~~~~dgiii~~   64 (294)
T cd06316           1 KAAIVMHTSGSDWSNAQVRGAKDEFAKLGIE---VVAT-TDAQFDPAKQVADIETTISQKPDIIISIP   64 (294)
T ss_pred             CeEEEecCCCChHHHHHHHHHHHHHHHcCCE---EEEe-cCCCCCHHHHHHHHHHHHHhCCCEEEEcC
Confidence            6899999888778888999999999999973   3222 24444444333332  2246799998755

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.

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

Probab=92.69  E-value=0.67  Score=35.68  Aligned_cols=63  Identities=10%  Similarity=0.058  Sum_probs=41.1

Q ss_pred             EEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccch-HHHHHHHHhhcCCCcEEEEeee
Q 032216           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE-IGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        78 IaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfE-LPlaak~La~s~~yDAVIaLG~  143 (145)
                      |+++....+...-..+.+|+.+.++++|+.   +.+.+..+..+ .-..+.+++.+.++||+|...+
T Consensus         2 I~vi~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~~~~~l~~~~vdgiii~~~   65 (270)
T cd01545           2 IGLLYDNPSPGYVSEIQLGALDACRDTGYQ---LVIEPCDSGSPDLAERVRALLQRSRVDGVILTPP   65 (270)
T ss_pred             EEEEEcCCCcccHHHHHHHHHHHHHhCCCe---EEEEeCCCCchHHHHHHHHHHHHCCCCEEEEeCC
Confidence            677777766666677888888988888863   55555554333 2223333344578999987643

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

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

Probab=92.62  E-value=0.71  Score=35.55  Aligned_cols=63  Identities=14%  Similarity=0.083  Sum_probs=41.4

Q ss_pred             EEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeee
Q 032216           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        78 IaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~  143 (145)
                      ||++...++......|.+|+.+.++++|..   +.+......-+-....-..+.+.++||||..++
T Consensus         2 i~~i~~~~~~~~~~~i~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~i~~l~~~~vdgiii~~~   64 (260)
T cd06286           2 IGVVLPYINHPYFSQLVDGIEKAALKHGYK---VVLLQTNYDKEKELEYLELLKTKQVDGLILCSR   64 (260)
T ss_pred             EEEEeCCCCCchHHHHHHHHHHHHHHcCCE---EEEEeCCCChHHHHHHHHHHHHcCCCEEEEeCC
Confidence            788888888877888999999999999863   444333222222222222234568999998764

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.

>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=92.61  E-value=0.69  Score=35.71  Aligned_cols=62  Identities=10%  Similarity=0.014  Sum_probs=42.3

Q ss_pred             EEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccch-HHHHHHHHhhcCCCcEEEEeee
Q 032216           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE-IGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        78 IaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfE-LPlaak~La~s~~yDAVIaLG~  143 (145)
                      ||+|...+.......+.+|+.++++++|..   +.+....+.-+ .--.++. +...++||||..++
T Consensus         2 I~vi~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~i~~-~~~~~~dgiii~~~   64 (265)
T cd06291           2 IGLIVPTISNPFFSELARAVEKELYKKGYK---LILCNSDNDPEKEREYLEM-LRQNQVDGIIAGTH   64 (265)
T ss_pred             EEEEECCCCChhHHHHHHHHHHHHHHCCCe---EEEecCCccHHHHHHHHHH-HHHcCCCEEEEecC
Confidence            789998888888889999999999999974   44433332222 1122233 34568999998763

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

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

Probab=92.57  E-value=0.65  Score=36.21  Aligned_cols=62  Identities=11%  Similarity=0.059  Sum_probs=40.6

Q ss_pred             EEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH-HHHHHhhcCCCcEEEEee
Q 032216           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV-VAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        77 RIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl-aak~La~s~~yDAVIaLG  142 (145)
                      |||+|+..+....-..+.+|..++++++|+.   +.+...-+..+-.. .++.+ .+.++||||..+
T Consensus         1 ~igv~~~~~~~~~~~~~~~~i~~~~~~~g~~---v~~~~~~~~~~~~~~~i~~~-~~~~~Dgiii~~   63 (282)
T cd06318           1 KIGFSQYTLNSPFFAALTEAAKAHAKALGYE---LISTDAQGDLTKQIADVEDL-LTRGVNVLIINP   63 (282)
T ss_pred             CeeEEeccccCHHHHHHHHHHHHHHHHcCCE---EEEEcCCCCHHHHHHHHHHH-HHcCCCEEEEec
Confidence            5888888888777888999999999999873   33332222222221 23333 356899998754

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.

>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=92.55  E-value=0.66  Score=35.98  Aligned_cols=63  Identities=11%  Similarity=0.078  Sum_probs=42.2

Q ss_pred             EEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeee
Q 032216           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        78 IaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~  143 (145)
                      ||++...|....-..|+++..++++++|..   +.+......-+--..+-..+.+.++||+|..++
T Consensus         2 Ig~i~p~~~~~~~~~~~~~i~~~~~~~g~~---~~~~~~~~~~~~~~~~i~~l~~~~~dgiii~~~   64 (263)
T cd06280           2 VGLIVADIRNPFFTAVSRAVEDAAYRAGLR---VILCNTDEDPEKEAMYLELMEEERVTGVIFAPT   64 (263)
T ss_pred             EEEEecccccccHHHHHHHHHHHHHHCCCE---EEEEeCCCCHHHHHHHHHHHHhCCCCEEEEeCC
Confidence            788998888777788999999999999974   444332222222222223344668999998764

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.

>PRK10423 transcriptional repressor RbsR; Provisional

Probab=92.55  E-value=0.63  Score=37.40  Aligned_cols=67  Identities=9%  Similarity=0.063  Sum_probs=45.6

Q ss_pred             CCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH-HHHHHHhhcCCCcEEEEeee
Q 032216           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        73 ~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP-laak~La~s~~yDAVIaLG~  143 (145)
                      .+...||+|+..+....-..+++|..+.+.++|..   +.+....+..+-- -.++.| .+.++||||..+.
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            34568999998776555667999999999999974   4454444444332 233444 3568999998763

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

Probab=92.50  E-value=0.61  Score=37.07  Aligned_cols=63  Identities=16%  Similarity=0.028  Sum_probs=43.1

Q ss_pred             EEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH-HHHHHHhhcCCCcEEEEeee
Q 032216           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        77 RIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP-laak~La~s~~yDAVIaLG~  143 (145)
                      +||+|...++......+++|..++++++|..   +.+....+.-+-- -.++. +.+.++||||..+.
T Consensus         2 ~ig~i~~~~~~~~~~~~~~gi~~~a~~~gy~---~~~~~~~~~~~~~~~~i~~-l~~~~vdgiil~~~   65 (280)
T cd06315           2 NIIFVASDLKNGGILGVGEGVREAAKAIGWN---LRILDGRGSEAGQAAALNQ-AIALKPDGIVLGGV   65 (280)
T ss_pred             eEEEEecccCCcHHHHHHHHHHHHHHHcCcE---EEEECCCCCHHHHHHHHHH-HHHcCCCEEEEcCC
Confidence            6899999998888889999999999999973   3333222222211 12233 34578999998764

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.

>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=92.48  E-value=0.77  Score=35.47  Aligned_cols=60  Identities=15%  Similarity=0.238  Sum_probs=39.9

Q ss_pred             EEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH---HHHHHHhhcCCCcEEEEeee
Q 032216           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        78 IaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP---laak~La~s~~yDAVIaLG~  143 (145)
                      ||+|+..++...-..+.+|..+.++++|..   +.+  .+.-.+-.   -.++.+ .+.++||+|..++
T Consensus         2 i~vi~~~~~~~~~~~~~~gi~~~~~~~gy~---~~~--~~~~~~~~~~~~~i~~l-~~~~~dgiii~~~   64 (265)
T cd06290           2 IGVLTQDFASPFYGRILKGMERGLNGSGYS---PII--ATGHWNQSRELEALELL-KSRRVDALILLGG   64 (265)
T ss_pred             EEEEECCCCCchHHHHHHHHHHHHHHCCCE---EEE--EeCCCCHHHHHHHHHHH-HHCCCCEEEEeCC
Confidence            788888888777788999999999999863   333  33333322   112223 4567999998764

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.

>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=92.41  E-value=1  Score=33.86  Aligned_cols=68  Identities=19%  Similarity=0.052  Sum_probs=44.6

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccch-HHHHHHHHh-hcCCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE-IGVVAQQLG-KSGKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfE-LPlaak~La-~s~~yDAVIaLG  142 (145)
                      ..||+++...-+....+...+|..+.++++|...+...+...+...+ ..-.++.++ +..+.|+|+|.+
T Consensus       116 ~~~i~~i~~~~~~~~~~~r~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~i~~~~  185 (264)
T cd06267         116 HRRIAFIGGPPDLSTARERLEGYREALEEAGIPLDEELIVEGDFSEESGYEAARELLASGERPTAIFAAN  185 (264)
T ss_pred             CceEEEecCCCccchHHHHHHHHHHHHHHcCCCCCcceEEecccchhhHHHHHHHHHhcCCCCcEEEEcC
Confidence            46999998877766677788999999999996433333433333322 233344444 445699999864

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.

>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=92.01  E-value=0.98  Score=34.74  Aligned_cols=62  Identities=8%  Similarity=0.047  Sum_probs=41.9

Q ss_pred             EEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccc-hHH-HHHHHHhhcCCCcEEEEeee
Q 032216           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSF-EIG-VVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        78 IaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAf-ELP-laak~La~s~~yDAVIaLG~  143 (145)
                      ||+|...++......+++|+.+.++++|..   +.+......- +-. -.++.+ .+.++||+|..++
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            788888888777788999999999999874   4444333221 111 122333 4568999998764

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

>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=91.98  E-value=0.86  Score=36.35  Aligned_cols=63  Identities=8%  Similarity=-0.065  Sum_probs=41.3

Q ss_pred             EEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH-HHHHHHhhcCCCcEEEEeee
Q 032216           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        77 RIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP-laak~La~s~~yDAVIaLG~  143 (145)
                      .||+|+..+-...-..+++|..++++++|+.   +.++.-.+.-|-. -.++.+. ..++||||..++
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            3788888877777788999999999998874   4443333222322 2233333 468999987653

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.

>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=91.92  E-value=1  Score=34.57  Aligned_cols=61  Identities=10%  Similarity=0.127  Sum_probs=42.0

Q ss_pred             EEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHH---HHHHhhcCCCcEEEEeee
Q 032216           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVV---AQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        77 RIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPla---ak~La~s~~yDAVIaLG~  143 (145)
                      .||+|...++...-..+.+|..+.++++|..   +.++  +...+..-.   ++.+. ..++||||..++
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            3788998888878888999999999999873   4443  333333322   23333 468999998764

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.

>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=91.85  E-value=0.89  Score=35.35  Aligned_cols=63  Identities=6%  Similarity=0.007  Sum_probs=43.0

Q ss_pred             EEEEEEeeecHHHHHHHHHHHHHHHHHC---CCCCCCeEEEEecccchHHHHHHHH--hhcCCCcEEEEee
Q 032216           77 RFALVVARFNELVTKLLLEGALETFKKY---SVKEENIDVVWVPGSFEIGVVAQQL--GKSGKYTAVLCIG  142 (145)
Q Consensus        77 RIaIVvArfN~~It~~LleGA~~~L~~~---Gv~~e~I~vv~VPGAfELPlaak~L--a~s~~yDAVIaLG  142 (145)
                      |||+|...+.......|.+|..+.++++   |.   +++++..+...+-....+.+  +.+.++||||..+
T Consensus         1 ~Ig~i~~~~~~~~~~~~~~~i~~~~~~~~~~g~---~~~l~i~~~~~~~~~~~~~~~~~~~~~vdgiIi~~   68 (272)
T cd06300           1 KIGLSNSYAGNTWRAQMLDEFKAQAKELKKAGL---ISEFIVTSADGDVAQQIADIRNLIAQGVDAIIINP   68 (272)
T ss_pred             CeEEeccccCChHHHHHHHHHHHHHHhhhccCC---eeEEEEecCCCCHHHHHHHHHHHHHcCCCEEEEeC
Confidence            6888888877777778889999998888   75   24455555555544433332  1235899998865

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.

>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=91.81  E-value=1.1  Score=34.39  Aligned_cols=60  Identities=15%  Similarity=0.290  Sum_probs=41.3

Q ss_pred             EEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchH---HHHHHHHhhcCCCcEEEEeee
Q 032216           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEI---GVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        78 IaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfEL---Plaak~La~s~~yDAVIaLG~  143 (145)
                      ||+|...|.......+++|..++++++|+.   +.+  .+...+-   --.+++|. +.++||+|..+.
T Consensus         2 igvv~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~--~~~~~~~~~~~~~i~~l~-~~~~dgii~~~~   64 (259)
T cd01542           2 IGVIVPRLDSFSTSRTVKGILAALYENGYQ---MLL--MNTNFSIEKEIEALELLA-RQKVDGIILLAT   64 (259)
T ss_pred             eEEEecCCccchHHHHHHHHHHHHHHCCCE---EEE--EeCCCCHHHHHHHHHHHH-hcCCCEEEEeCC
Confidence            688888888878888999999999999974   333  3333321   12234443 478999998753

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

>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=91.69  E-value=0.93  Score=35.17  Aligned_cols=63  Identities=16%  Similarity=0.223  Sum_probs=39.2

Q ss_pred             EEEEEee---ecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeee
Q 032216           78 FALVVAR---FNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        78 IaIVvAr---fN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~  143 (145)
                      ||+++..   +....-..+.+|..+.++++|..   +.+......-+--..+...+.+.++||||..++
T Consensus         2 vgv~~~~~~~~~~~~~~~~~~~i~~~~~~~g~~---~~~~~~~~~~~~~~~~~~~l~~~~vdgiii~~~   67 (268)
T cd06277           2 IGLIASKRILNSPAFYSEIYRAIEEEAKKYGYN---LILKFVSDEDEEEFELPSFLEDGKVDGIILLGG   67 (268)
T ss_pred             eEEEEeccccccCCcHHHHHHHHHHHHHHcCCE---EEEEeCCCChHHHHHHHHHHHHCCCCEEEEeCC
Confidence            7788877   56666677889999999998873   444443322222222222234578999997653

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.

>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=91.63  E-value=1.1  Score=34.59  Aligned_cols=62  Identities=10%  Similarity=0.098  Sum_probs=40.8

Q ss_pred             EEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccch-HHHHHHHHhhcCCCcEEEEeee
Q 032216           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE-IGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        78 IaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfE-LPlaak~La~s~~yDAVIaLG~  143 (145)
                      ||+|...+.......+++|..++++++|..   +.+.......+ .--.++.+. ..++||||..++
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            788888887777778889999999998873   44443332222 222334443 468899998764

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

>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=91.39  E-value=0.7  Score=37.89  Aligned_cols=66  Identities=18%  Similarity=0.269  Sum_probs=47.7

Q ss_pred             CCCE-EEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH---HHHHHhhcC-CCcEEEEe
Q 032216           74 EGLR-FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGKSG-KYTAVLCI  141 (145)
Q Consensus        74 ~~lR-IaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl---aak~La~s~-~yDAVIaL  141 (145)
                      ...| |+++...=+......-++|..+.|+++|...+...+.  -|.+..+-   ++++|++++ .+|||+|.
T Consensus       117 Gh~~~I~~i~~~~~~~~~~~R~~Gy~~Al~~~Gl~~~~~~i~--~~~~~~~~g~~~~~~ll~~~p~idai~~~  187 (279)
T PF00532_consen  117 GHRRPIAFIGGPEDSSTSRERLQGYRDALKEAGLPIDEEWIF--EGDFDYESGYEAARELLESHPDIDAIFCA  187 (279)
T ss_dssp             TCCSTEEEEEESTTTHHHHHHHHHHHHHHHHTTSCEEEEEEE--ESSSSHHHHHHHHHHHHHTSTT-SEEEES
T ss_pred             ccCCeEEEEecCcchHHHHHHHHHHHHHHHHcCCCCCccccc--ccCCCHHHHHHHHHHHHhhCCCCEEEEEe
Confidence            3468 9999998887788888899999999999953333333  35666663   345666655 68899985

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 ....

>PRK14987 gluconate operon transcriptional regulator; Provisional

Probab=91.38  E-value=1.1  Score=36.46  Aligned_cols=65  Identities=8%  Similarity=-0.010  Sum_probs=43.5

Q ss_pred             CCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccc--hHHHHHHHHhhcCCCcEEEEeee
Q 032216           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSF--EIGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        74 ~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAf--ELPlaak~La~s~~yDAVIaLG~  143 (145)
                      ....||+|...+....-..+++|+.++++++|..   +.+......-  |.. .++.+ .+.++||||..++
T Consensus        62 ~~~~Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~-~~~~~-~~~~vdgiI~~~~  128 (331)
T PRK14987         62 TSRAIGVLLPSLTNQVFAEVLRGIESVTDAHGYQ---TMLAHYGYKPEMEQE-RLESM-LSWNIDGLILTER  128 (331)
T ss_pred             CCCEEEEEeCCCcchhHHHHHHHHHHHHHHCCCE---EEEecCCCCHHHHHH-HHHHH-HhcCCCEEEEcCC
Confidence            4458999998887767778999999999999973   3333222121  222 22333 4578999998764

>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=91.32  E-value=1.3  Score=33.37  Aligned_cols=61  Identities=11%  Similarity=0.089  Sum_probs=43.1

Q ss_pred             EEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccch---HHHHHHHHhhcCCCcEEEEeee
Q 032216           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE---IGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        77 RIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfE---LPlaak~La~s~~yDAVIaLG~  143 (145)
                      +||+|...++......+.+|+.+.++++|+.   +.  ..+..++   .--+++.+. ..++||||..+.
T Consensus         1 ~i~~v~~~~~~~~~~~~~~g~~~~~~~~g~~---~~--~~~~~~~~~~~~~~~~~~~-~~~~d~iii~~~   64 (264)
T cd06267           1 TIGVIVPDISNPFFAELLRGIEEAAREAGYS---VL--LCNSDEDPEKEREALELLL-SRRVDGIILAPS   64 (264)
T ss_pred             CEEEEECCCCCHHHHHHHHHHHHHHHHcCCE---EE--EEcCCCCHHHHHHHHHHHH-HcCcCEEEEecC
Confidence            4788888888888888999999999998863   33  3444454   223344454 458999998653

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.

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

Probab=91.27  E-value=1  Score=34.44  Aligned_cols=60  Identities=12%  Similarity=0.129  Sum_probs=39.8

Q ss_pred             EEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH---HHHHHhhcCCCcEEEEeee
Q 032216           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        78 IaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl---aak~La~s~~yDAVIaLG~  143 (145)
                      ||+|...|.......+.+|+.++++++|..   +.+..  ..++-+.   .++.+. +.++||||..+.
T Consensus         2 igvi~~~~~~~~~~~~~~~i~~~a~~~g~~---~~~~~--~~~~~~~~~~~~~~l~-~~~~dgiii~~~   64 (267)
T cd06283           2 IGVIVADITNPFSSLVLKGIEDVCRAHGYQ---VLVCN--SDNDPEKEKEYLESLL-AYQVDGLIVNPT   64 (267)
T ss_pred             EEEEecCCccccHHHHHHHHHHHHHHcCCE---EEEEc--CCCCHHHHHHHHHHHH-HcCcCEEEEeCC
Confidence            678888887777778999999999998863   43333  3333332   233333 468899987653

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

>PRK10014 DNA-binding transcriptional repressor MalI; Provisional

Probab=91.12  E-value=1.6  Score=35.40  Aligned_cols=67  Identities=15%  Similarity=0.063  Sum_probs=45.1

Q ss_pred             CCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccch-HHHHHHHHhhcCCCcEEEEeee
Q 032216           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE-IGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        73 ~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfE-LPlaak~La~s~~yDAVIaLG~  143 (145)
                      .....||++...|....-..+.+|..+.++++|..   +.+.......| ..-.++.|. ..++||||..+.
T Consensus        62 ~~~~~Igvv~~~~~~~~~~~i~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~l~-~~~vdgiIi~~~  129 (342)
T PRK10014         62 GQSGVIGLIVRDLSAPFYAELTAGLTEALEAQGRM---VFLLQGGKDGEQLAQRFSTLL-NQGVDGVVIAGA  129 (342)
T ss_pred             CCCCEEEEEeCCCccchHHHHHHHHHHHHHHcCCE---EEEEeCCCCHHHHHHHHHHHH-hCCCCEEEEeCC
Confidence            44568999999887777778999999999999963   33333222222 223334443 467999998753

>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=91.07  E-value=1.1  Score=36.40  Aligned_cols=60  Identities=7%  Similarity=0.040  Sum_probs=40.4

Q ss_pred             EEEEEEeeecHHHHHHHHHHHHHHHHH--CCCCCCCeEEEEecccchH--H-HHHHHHhhcCCCcEEEEee
Q 032216           77 RFALVVARFNELVTKLLLEGALETFKK--YSVKEENIDVVWVPGSFEI--G-VVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        77 RIaIVvArfN~~It~~LleGA~~~L~~--~Gv~~e~I~vv~VPGAfEL--P-laak~La~s~~yDAVIaLG  142 (145)
                      |||+|+.+++...-..+++|..+++++  +|+     ++...++..+.  - -.++.+ ...++||||..+
T Consensus         1 ~Igviv~~~~~~~~~~~~~gi~~~a~~~~~g~-----~~~~~~~~~~~~~q~~~i~~l-~~~~vdgiii~~   65 (303)
T cd01539           1 KIGVFLYKFDDTFISLVRKNLEDIQKENGGKV-----EFTFYDAKNNQSTQNEQIDTA-LAKGVDLLAVNL   65 (303)
T ss_pred             CeEEEeeCCCChHHHHHHHHHHHHHHhhCCCe-----eEEEecCCCCHHHHHHHHHHH-HHcCCCEEEEec
Confidence            689999998888888899999999998  554     33434443322  2 223333 345899998764

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.

>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=91.04  E-value=1.1  Score=34.26  Aligned_cols=62  Identities=15%  Similarity=0.143  Sum_probs=42.0

Q ss_pred             EEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeee
Q 032216           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        78 IaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~  143 (145)
                      ||++...+....-..+.+|..+.++++|..   +.++.....-+.--.++.+. +.++||+|..++
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            678888887777778889999999999974   44544443223333444444 467999997654

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.

>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=91.00  E-value=1.3  Score=33.80  Aligned_cols=59  Identities=8%  Similarity=0.108  Sum_probs=36.8

Q ss_pred             EEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH---HHHHHhhcCCCcEEEEee
Q 032216           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        78 IaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl---aak~La~s~~yDAVIaLG  142 (145)
                      ||+|...+....-..+.+|+.+.++++|..   +.+...  .++-..   +++.| .+.++||||...
T Consensus         2 igvv~~~~~~~~~~~~~~~i~~~~~~~g~~---~~~~~~--~~~~~~~~~~~~~l-~~~~vdgiii~~   63 (266)
T cd06282           2 VGVVLPSLANPVFAECVQGIQEEARAAGYS---LLLATT--DYDAEREADAVETL-LRQRVDGLILTV   63 (266)
T ss_pred             eEEEeCCCCcchHHHHHHHHHHHHHHCCCE---EEEeeC--CCCHHHHHHHHHHH-HhcCCCEEEEec
Confidence            678887776666667888888888888863   444332  233222   22333 346789988653

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

>PRK10703 DNA-binding transcriptional repressor PurR; Provisional

Probab=90.97  E-value=1.3  Score=36.08  Aligned_cols=67  Identities=7%  Similarity=-0.004  Sum_probs=45.1

Q ss_pred             CCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEee
Q 032216           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        73 ~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG  142 (145)
                      .+...||++...+....-..+++|..++++++|..   +.+..-.+..+--.-.-..+...++||||..+
T Consensus        57 ~~~~~i~vi~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~i~~l~~~~vdgiii~~  123 (341)
T PRK10703         57 NHTKSIGLLATSSEAPYFAEIIEAVEKNCYQKGYT---LILCNAWNNLEKQRAYLSMLAQKRVDGLLVMC  123 (341)
T ss_pred             CCCCeEEEEeCCCCCchHHHHHHHHHHHHHHCCCE---EEEEeCCCCHHHHHHHHHHHHHcCCCEEEEec
Confidence            34468999999887777778999999999999974   44443333333222222223456899999765

>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=90.95  E-value=1.1  Score=35.37  Aligned_cols=62  Identities=11%  Similarity=0.109  Sum_probs=42.2

Q ss_pred             EEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecc--cch-HHHHHHHHhhcCCCcEEEEee
Q 032216           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPG--SFE-IGVVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        77 RIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPG--AfE-LPlaak~La~s~~yDAVIaLG  142 (145)
                      |||+|+.+++......++.|..++++++|+.   +.+....+  ..+ .--.++.+. +.++||||..+
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            6899999988888888999999999999973   43332211  111 112344444 45899999764

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.

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

Probab=90.94  E-value=1.4  Score=34.44  Aligned_cols=64  Identities=11%  Similarity=0.138  Sum_probs=43.0

Q ss_pred             EEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHH--hhcCCCcEEEEee
Q 032216           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQL--GKSGKYTAVLCIG  142 (145)
Q Consensus        77 RIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~L--a~s~~yDAVIaLG  142 (145)
                      |||+|+..++......+++++.++++++|...-.+ ..+.+..++-....+.+  +.+ ++||+|..+
T Consensus         1 ~ig~v~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~-~~~~~~~~~~~~~~~~i~~~~~-~vdgiii~~   66 (275)
T cd06307           1 RLGFLLPKGSNAFYRELAAALEAAAAAFPDARIRV-RIHFVESFDPAALAAALLRLGA-RSDGVALVA   66 (275)
T ss_pred             CeEEEeCCCCChHHHHHHHHHHHHHhhhhccCceE-EEEEccCCCHHHHHHHHHHHHh-cCCEEEEeC
Confidence            68999999988888999999999999998752222 22223333333333332  234 899999865

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=90.84  E-value=1.1  Score=34.42  Aligned_cols=59  Identities=17%  Similarity=0.179  Sum_probs=39.1

Q ss_pred             EEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH---HHHHHhhcCCCcEEEEee
Q 032216           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        78 IaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl---aak~La~s~~yDAVIaLG  142 (145)
                      ||+|...+.......+.+++.+.++++|+.   +.+  .+...+..-   +++.+ .+.++||||..+
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            688888888888888999999999998863   433  333332221   22222 345799988754

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.

>PRK09701 D-allose transporter subunit; Provisional

Probab=90.83  E-value=1.4  Score=35.99  Aligned_cols=66  Identities=14%  Similarity=0.170  Sum_probs=47.9

Q ss_pred             CCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHH--hhcCCCcEEEEee
Q 032216           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQL--GKSGKYTAVLCIG  142 (145)
Q Consensus        74 ~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~L--a~s~~yDAVIaLG  142 (145)
                      ....||+|+..+....-..+.+|+.++++++|+.   +.++..|+..+..-..+.+  +...++||||..+
T Consensus        23 ~~~~Igvi~~~~~~~f~~~~~~gi~~~a~~~g~~---v~~~~~~~~~~~~~~~~~i~~l~~~~vDgiIi~~   90 (311)
T PRK09701         23 AAAEYAVVLKTLSNPFWVDMKKGIEDEAKTLGVS---VDIFASPSEGDFQSQLQLFEDLSNKNYKGIAFAP   90 (311)
T ss_pred             cCCeEEEEeCCCCCHHHHHHHHHHHHHHHHcCCe---EEEecCCCCCCHHHHHHHHHHHHHcCCCEEEEeC
Confidence            3459999998888777788999999999999974   4455457666665433332  2346799999865

>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=90.82  E-value=1.2  Score=34.25  Aligned_cols=60  Identities=5%  Similarity=-0.033  Sum_probs=38.0

Q ss_pred             EEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHH---HHHHhhcCCCcEEEEeee
Q 032216           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVV---AQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        78 IaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPla---ak~La~s~~yDAVIaLG~  143 (145)
                      ||+|...+....-..+.+|..++++++|+.   +.++  +...+-.--   ++. +...++||||..+.
T Consensus         2 igvv~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~~--~~~~~~~~~~~~~~~-l~~~~vdgiIi~~~   64 (265)
T cd06299           2 IGVIVPDIRNPYFASLATAIQDAASAAGYS---TIIG--NSDENPETENRYLDN-LLSQRVDGIIVVPH   64 (265)
T ss_pred             EEEEecCCCCccHHHHHHHHHHHHHHcCCE---EEEE--eCCCCHHHHHHHHHH-HHhcCCCEEEEcCC
Confidence            678887765555567889999999988863   4433  333333222   222 33568999998753

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

>PRK11303 DNA-binding transcriptional regulator FruR; Provisional

Probab=90.71  E-value=1.5  Score=35.35  Aligned_cols=66  Identities=6%  Similarity=0.036  Sum_probs=42.6

Q ss_pred             CCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH-HHHHHHhhcCCCcEEEEeee
Q 032216           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        74 ~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP-laak~La~s~~yDAVIaLG~  143 (145)
                      +...||+|...|....-..+++|..++++++|..   +.+...-...+-- -.++.| ...++||||.++.
T Consensus        60 ~~~~Igvv~~~~~~~~~~~l~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~~~~l-~~~~vdgiIi~~~  126 (328)
T PRK11303         60 RTRSIGLIIPDLENTSYARIAKYLERQARQRGYQ---LLIACSDDQPDNEMRCAEHL-LQRQVDALIVSTS  126 (328)
T ss_pred             CCceEEEEeCCCCCchHHHHHHHHHHHHHHcCCE---EEEEeCCCCHHHHHHHHHHH-HHcCCCEEEEcCC
Confidence            4457999998776555667999999999999974   4443321111211 123333 3568999998764

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

Probab=90.65  E-value=1.5  Score=33.99  Aligned_cols=62  Identities=8%  Similarity=0.104  Sum_probs=36.4

Q ss_pred             EEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH-HHHHHhhcCCCcEEEEeee
Q 032216           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV-VAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        78 IaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl-aak~La~s~~yDAVIaLG~  143 (145)
                      ||+++..|-...-..|.++..+.++++|..   +.+...-+.-+--. .++.+ .+.++||||..++
T Consensus         2 igvi~~~~~~~~~~~~~~~~~~~~~~~g~~---~~~~~~~~~~~~~~~~i~~l-~~~~vdgiii~~~   64 (264)
T cd06274           2 IGLIIPDLENRSFARIAKRLEALARERGYQ---LLIACSDDDPETERETVETL-IARQVDALIVAGS   64 (264)
T ss_pred             EEEEeccccCchHHHHHHHHHHHHHHCCCE---EEEEeCCCCHHHHHHHHHHH-HHcCCCEEEEcCC
Confidence            677777766666677888888888888763   44443322211111 12222 3457888887653

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

>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=90.65  E-value=1.3  Score=34.14  Aligned_cols=59  Identities=17%  Similarity=0.303  Sum_probs=42.2

Q ss_pred             EEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeee
Q 032216           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        78 IaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~  143 (145)
                      ||+|..++.......+++|..+.++++|..   +.+...+ ..+  -..+. +.+.++||||..++
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            788888888888888999999999999863   5555554 211  12233 45568999998764

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

>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=90.64  E-value=1.9  Score=33.03  Aligned_cols=68  Identities=18%  Similarity=0.080  Sum_probs=43.8

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH-HHHHHhhc-CCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV-VAQQLGKS-GKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl-aak~La~s-~~yDAVIaLG  142 (145)
                      ..||+++..+-+......-.+|..+.++++|+......+..-+...+-.. +++++++. .++|||+|.+
T Consensus       120 ~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~  189 (268)
T cd06271         120 HRRIALLNPPEDLTFAQHRRAGYRRALAEAGLPLDPALIVSGDMTEEGGYAAAAELLALPDRPTAIVCSS  189 (268)
T ss_pred             CCcEEEecCccccchHHHHHHHHHHHHHHhCCCCCCceEEeCCCChHHHHHHHHHHHhCCCCCCEEEEcC
Confidence            46899998665544445567999999999998643333444343443322 34455444 4699999975

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

>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial

Probab=90.60  E-value=1.7  Score=35.13  Aligned_cols=67  Identities=15%  Similarity=0.108  Sum_probs=43.5

Q ss_pred             CCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH-HHHHHHhhcCCCcEEEEeee
Q 032216           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        73 ~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP-laak~La~s~~yDAVIaLG~  143 (145)
                      .....||++...+.......++++..+.+.++|..   +.+.......|-- -..+. +.+.++||+|.++.
T Consensus        57 ~~~~~Ig~i~~~~~~~~~~~~~~~i~~~~~~~gy~---~~i~~~~~~~~~~~~~~~~-l~~~~vdGvIi~~~  124 (311)
T TIGR02405        57 GSDKVVAVIVSRLDSPSENLAVSGMLPVFYTAGYD---PIIMESQFSPQLTNEHLSV-LQKRNVDGVILFGF  124 (311)
T ss_pred             CCCCEEEEEeCCcccccHHHHHHHHHHHHHHCCCe---EEEecCCCChHHHHHHHHH-HHhcCCCEEEEeCC
Confidence            34457999998776556667899999999999974   3333222222211 22333 34568999998863

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

>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=90.57  E-value=1.7  Score=34.48  Aligned_cols=63  Identities=17%  Similarity=0.182  Sum_probs=40.0

Q ss_pred             EEEEEEee---ecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeee
Q 032216           77 RFALVVAR---FNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        77 RIaIVvAr---fN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~  143 (145)
                      |||+|..+   +....-..+++|..++++++|+.   +.+...-..-+.--.++.| ..+++||||.+++
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            68888877   55566667999999999999974   3333221111111223333 4578999998764

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.

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

Probab=90.52  E-value=1.6  Score=34.28  Aligned_cols=63  Identities=19%  Similarity=0.186  Sum_probs=37.8

Q ss_pred             EEEEEEee--ecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeee
Q 032216           77 RFALVVAR--FNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        77 RIaIVvAr--fN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~  143 (145)
                      |||+|...  +....-..|++|..+.++++|+.   +.+......-+.--..+.| ...++||||..+.
T Consensus         1 ~Igvi~~~~~~~~~f~~~l~~gi~~~~~~~gy~---~~~~~~~~~~~~~~~~~~l-~~~~vdgiii~~~   65 (260)
T cd06304           1 KVALVYDGGGGDKSFNQSAYEGLEKAEKELGVE---VKYVESVEDADYEPNLRQL-AAQGYDLIFGVGF   65 (260)
T ss_pred             CEEEEecCCCCcchHHHHHHHHHHHHHHhcCce---EEEEecCCHHHHHHHHHHH-HHcCCCEEEECCc
Confidence            68888874  44555667888888888888873   4444333111111223333 3457899987653

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.

>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor

Probab=90.48  E-value=1.5  Score=35.37  Aligned_cols=67  Identities=9%  Similarity=0.126  Sum_probs=44.7

Q ss_pred             CCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH-HHHHHHhhcCCCcEEEEeee
Q 032216           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        73 ~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP-laak~La~s~~yDAVIaLG~  143 (145)
                      .....||++...+....-..++++..++++++|..   +.+......-+-- -.++.+ .+.++||+|..+.
T Consensus        58 ~~~~~Igvi~~~~~~~~~~~~~~~i~~~~~~~gy~---~~i~~~~~~~~~~~~~~~~l-~~~~vdgiIi~~~  125 (327)
T TIGR02417        58 GRSRTIGLVIPDLENYSYARIAKELEQQCREAGYQ---LLIACSDDNPDQEKVVIENL-LARQVDALIVASC  125 (327)
T ss_pred             CCCceEEEEeCCCCCccHHHHHHHHHHHHHHCCCE---EEEEeCCCCHHHHHHHHHHH-HHcCCCEEEEeCC
Confidence            34468999998877666778999999999999974   4444433322211 223333 3568999998753

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.

>PRK10355 xylF D-xylose transporter subunit XylF; Provisional

Probab=90.45  E-value=1.7  Score=36.40  Aligned_cols=65  Identities=5%  Similarity=-0.049  Sum_probs=47.9

Q ss_pred             CCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH---HHHHHhhcCCCcEEEEeee
Q 032216           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        73 ~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl---aak~La~s~~yDAVIaLG~  143 (145)
                      .+..+||+|....+..--..+++|..++++++|+.     +..+++..+-.-   .++.+. +.++||+|..++
T Consensus        23 ~~~~~Ig~i~~~~~~~f~~~~~~gi~~~a~~~g~~-----l~i~~~~~~~~~~~~~i~~l~-~~~vDGiIi~~~   90 (330)
T PRK10355         23 AKEVKIGMAIDDLRLERWQKDRDIFVKKAESLGAK-----VFVQSANGNEETQMSQIENMI-NRGVDVLVIIPY   90 (330)
T ss_pred             CCCceEEEEecCCCchHHHHHHHHHHHHHHHcCCE-----EEEECCCCCHHHHHHHHHHHH-HcCCCEEEEeCC
Confidence            45779999999998888899999999999999973     344555544322   233343 468999998764

>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=90.45  E-value=1.5  Score=33.63  Aligned_cols=60  Identities=10%  Similarity=0.118  Sum_probs=39.9

Q ss_pred             EEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH---HHHHHHhhcCCCcEEEEeee
Q 032216           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        78 IaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP---laak~La~s~~yDAVIaLG~  143 (145)
                      ||+|...|....-..+++|+.+.++++|+.   +  +..++..+.-   -.++.+. +.++||+|..++
T Consensus         2 I~vi~~~~~~~~~~~~~~g~~~~a~~~g~~---~--~~~~~~~~~~~~~~~i~~~~-~~~vdgiii~~~   64 (268)
T cd06289           2 IGLVINDLTNPFFAELAAGLEEVLEEAGYT---V--FLANSGEDVERQEQLLSTML-EHGVAGIILCPA   64 (268)
T ss_pred             EEEEecCCCcchHHHHHHHHHHHHHHcCCe---E--EEecCCCChHHHHHHHHHHH-HcCCCEEEEeCC
Confidence            678887777666777899999999998863   3  3344433321   2233343 468999998764

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.

>TIGR02955 TMAO_TorT TMAO reductase system periplasmic protein TorT

Probab=90.42  E-value=1.3  Score=35.56  Aligned_cols=62  Identities=18%  Similarity=0.130  Sum_probs=40.6

Q ss_pred             EEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH---HHHHHHhhcCCCcEEEEee
Q 032216           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        77 RIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP---laak~La~s~~yDAVIaLG  142 (145)
                      ||++|+..++...-..+.+|+.++++++|+.   +.+....+-.+..   -.++.+ .+.++||||..+
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            5888888887777778889999999988873   4444333212211   233333 357899998754

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.

>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=90.19  E-value=1.6  Score=34.54  Aligned_cols=59  Identities=22%  Similarity=0.308  Sum_probs=40.2

Q ss_pred             EEEEEee-----ecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeee
Q 032216           78 FALVVAR-----FNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        78 IaIVvAr-----fN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~  143 (145)
                      ||+|+..     |.......+++|..+.++++|..   +.+  ++..+|.. ..+ .+...++||+|..++
T Consensus         2 igvi~p~~~~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~--~~~~~~~~-~~~-~~~~~~~dgiii~~~   65 (283)
T cd06279           2 VGVVLTDSLSYAFSDPVASQFLAGVAEVLDAAGVN---LLL--LPASSEDS-DSA-LVVSALVDGFIVYGV   65 (283)
T ss_pred             EEEEeCCcccccccCccHHHHHHHHHHHHHHCCCE---EEE--ecCccHHH-HHH-HHHhcCCCEEEEeCC
Confidence            6777777     66666777999999999999973   333  34434432 222 344678999998764

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.

>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=90.16  E-value=2  Score=33.38  Aligned_cols=63  Identities=25%  Similarity=0.354  Sum_probs=41.7

Q ss_pred             CEEEEEEee-------ecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeee
Q 032216           76 LRFALVVAR-------FNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        76 lRIaIVvAr-------fN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~  143 (145)
                      ..|||++.+       +....-..+++|+.+.++++|+.   +.++..... +...+.+.+ .+.++||||..++
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            468888864       34445566889999999999974   555544333 444444433 4578999998764

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

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

Probab=90.03  E-value=1.9  Score=34.69  Aligned_cols=61  Identities=18%  Similarity=0.143  Sum_probs=42.8

Q ss_pred             EEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEE-ecccchHHHHHHHHh--hcCCCcEEEEee
Q 032216           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVW-VPGSFEIGVVAQQLG--KSGKYTAVLCIG  142 (145)
Q Consensus        77 RIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~-VPGAfELPlaak~La--~s~~yDAVIaLG  142 (145)
                      +|++|...++...-..+++|+.++++++|+.     +.. .+.-.+-....+.+-  .+.++||||..+
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            5788887777666777999999999998863     443 366565554444332  245799999875

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

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

Probab=90.01  E-value=1.8  Score=33.71  Aligned_cols=61  Identities=3%  Similarity=0.027  Sum_probs=35.2

Q ss_pred             EEEEEEeeecHHHHHHHHHHHHHHHHHC-CCCCCCeEEEEecccc--hHHHHHHHHhhcCCCcEEEEee
Q 032216           77 RFALVVARFNELVTKLLLEGALETFKKY-SVKEENIDVVWVPGSF--EIGVVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        77 RIaIVvArfN~~It~~LleGA~~~L~~~-Gv~~e~I~vv~VPGAf--ELPlaak~La~s~~yDAVIaLG  142 (145)
                      +||+++..|.......++++..+.+.++ |+.   +.+...++..  |.... +.+. ..++||||..+
T Consensus         1 ~ig~~~~~~~~~~~~~~~~~i~~~~~~~~g~~---~~~~~~~~~~~~~~~~i-~~~~-~~~vdgiii~~   64 (270)
T cd06308           1 VIGFSQCNLADPWRAAMNDEIQREASNYPDVE---LIIADAADDNSKQVADI-ENFI-RQGVDLLIISP   64 (270)
T ss_pred             CEEEEeeCCCCHHHHHHHHHHHHHHHhcCCcE---EEEEcCCCCHHHHHHHH-HHHH-HhCCCEEEEec
Confidence            4677777666666667777777777775 653   4444444443  22222 2222 35678777654

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.

>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=89.92  E-value=2.1  Score=35.09  Aligned_cols=64  Identities=6%  Similarity=0.059  Sum_probs=51.9

Q ss_pred             CEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeee
Q 032216           76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        76 lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~  143 (145)
                      ..||+|+.......-..++.|..++++++|..   +-+....+.-|.--.++.| .+.++||+|..+.
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            37999999998777788999999999999984   6777888888887555544 5679999998753

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 ....

>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=89.85  E-value=1.6  Score=33.92  Aligned_cols=69  Identities=20%  Similarity=0.107  Sum_probs=41.6

Q ss_pred             CCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH-HHHHHHhhc-CCCcEEEEee
Q 032216           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKS-GKYTAVLCIG  142 (145)
Q Consensus        74 ~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP-laak~La~s-~~yDAVIaLG  142 (145)
                      ...||+++...=+......-.+|.++.++++|.......+.+..-.+|-. -.++++.++ .++|||+|-.
T Consensus       115 G~~~i~~i~~~~~~~~~~~R~~Gf~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~  185 (269)
T cd06293         115 GHRRIAFVGGPDALISARERYAGYREALAEAHIPEVPEYVCFGDYTREFGRAAAAQLLARGDPPTAIFAAS  185 (269)
T ss_pred             CCceEEEEecCcccccHHHHHHHHHHHHHHcCCCCChheEEecCCCHHHHHHHHHHHHcCCCCCCEEEEcC
Confidence            34699999765443333344699999999999864433443333333322 133444443 5689999864

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.

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

Probab=89.40  E-value=1.6  Score=33.86  Aligned_cols=63  Identities=17%  Similarity=0.215  Sum_probs=40.6

Q ss_pred             EEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHH--hhcCCCcEEEEee
Q 032216           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQL--GKSGKYTAVLCIG  142 (145)
Q Consensus        77 RIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~L--a~s~~yDAVIaLG  142 (145)
                      +||+|+..+....-..|.+|..++++++|.   +..++..++..+.....+.+  +...++||+|..+
T Consensus         1 ~Ig~v~~~~~~~~~~~~~~gi~~~~~~~~~---~~~~~~~~~~~~~~~~~~~i~~~~~~~~dgiIi~~   65 (271)
T cd06321           1 KIGVSVGDLGNPFFVALAKGAEAAAKKLNP---GVKVTVVSADYDLNKQVSQIDNFIAAKVDLILLNA   65 (271)
T ss_pred             CeEEEecccCCHHHHHHHHHHHHHHHHhCC---CeEEEEccCCCCHHHHHHHHHHHHHhCCCEEEEeC
Confidence            478888887777777888999999998542   24455555555443332222  2346789988754

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.

>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=89.32  E-value=1.6  Score=33.57  Aligned_cols=62  Identities=10%  Similarity=0.074  Sum_probs=35.6

Q ss_pred             EEEEEee-----ecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEee
Q 032216           78 FALVVAR-----FNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        78 IaIVvAr-----fN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG  142 (145)
                      ||+++..     |.......+.+++.+.++++|..   +.+..-.+.-+---.+..++.++++||||..+
T Consensus         2 igli~p~~~~~~~~~~~~~~~~~~~~~~~~~~g~~---~~~~~~~~~~~~~~~~~~~~~~~~~dgiii~~   68 (270)
T cd06294           2 IGVVLPPSADEAFQNPFFIEVLRGISAVANENGYD---ISLATGKNEEELLEEVKKMIQQKRVDGFILLY   68 (270)
T ss_pred             EEEEeCCccccCcCCCCHHHHHHHHHHHHHHCCCE---EEEecCCCcHHHHHHHHHHHHHcCcCEEEEec
Confidence            4555543     44455567888888888888863   43333222222223344445567788888754

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.

>PRK10727 DNA-binding transcriptional regulator GalR; Provisional

Probab=89.31  E-value=2.3  Score=34.80  Aligned_cols=67  Identities=9%  Similarity=-0.049  Sum_probs=44.7

Q ss_pred             CCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH-HHHHHHhhcCCCcEEEEeee
Q 032216           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        73 ~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP-laak~La~s~~yDAVIaLG~  143 (145)
                      .....||+|...+....-..|++|+.++++++|..   +.+.......|-- -.++.|. +.++||+|..+.
T Consensus        57 ~~~~~Igvi~~~~~~~f~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~i~~l~-~~~vdgiIi~~~  124 (343)
T PRK10727         57 QSTETVGLVVGDVSDPFFGAMVKAVEQVAYHTGNF---LLIGNGYHNEQKERQAIEQLI-RHRCAALVVHAK  124 (343)
T ss_pred             CCCCeEEEEeCCCCcchHHHHHHHHHHHHHHcCCE---EEEEeCCCCHHHHHHHHHHHH-hcCCCEEEEecC
Confidence            34457999998887667778999999999999973   4333333322221 2234443 568999998753

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

Probab=89.24  E-value=1.6  Score=35.56  Aligned_cols=61  Identities=7%  Similarity=-0.070  Sum_probs=33.8

Q ss_pred             EEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH-HHHHHhhcCCCcEEEEee
Q 032216           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV-VAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        78 IaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl-aak~La~s~~yDAVIaLG  142 (145)
                      ||++..+++...-+.+.++..++++++|+.   +.+....+..+.-. .++. +...++||||..+
T Consensus         1 ig~~~~~~~~~~~~~~~~~i~~~a~~~g~~---v~~~~~~~~~~~q~~~i~~-l~~~~vDgIIi~~   62 (302)
T TIGR02634         1 IGVSIDDLRLERWQKDRDIFVAAAESLGAK---VFVQSANGNEAKQISQIEN-LIARGVDVLVIIP   62 (302)
T ss_pred             CeeecCccchhhHHHHHHHHHHHHHhcCCE---EEEEeCCCCHHHHHHHHHH-HHHcCCCEEEEeC
Confidence            466777777777777777777777777763   33332222222111 1122 2345677777654

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.

>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=89.22  E-value=2  Score=33.09  Aligned_cols=66  Identities=17%  Similarity=0.162  Sum_probs=42.6

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchH--H-HHHHHHhhcCCCcEEEEeee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEI--G-VVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfEL--P-laak~La~s~~yDAVIaLG~  143 (145)
                      ..||+++...-+....+.-.+|..+.++++|...+...+  .+|.+..  . -.++.+.+++ +|||+|.+.
T Consensus       116 ~~~I~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~-~~av~~~~d  184 (265)
T cd06299         116 HKKIGYISGPQDTSTGRERLEAFRQACASLGLEVNEDLV--VLGGYSQESGYAGATKLLDQG-ATAIIAGDS  184 (265)
T ss_pred             CCcEEEEeCCCCcccHHHHHHHHHHHHHHCCCCCChHhE--EecCcchHHHHHHHHHHHcCC-CCEEEEcCc
Confidence            459999987766556667779999999999974222222  2344332  1 1334455544 999999754

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

>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=88.98  E-value=2.2  Score=33.01  Aligned_cols=60  Identities=13%  Similarity=0.078  Sum_probs=40.7

Q ss_pred             EEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHH---HHHHhhcCCCcEEEEeee
Q 032216           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVV---AQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        78 IaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPla---ak~La~s~~yDAVIaLG~  143 (145)
                      ||+|...|....-..+++|..+.++++|..   +.+  .++..+....   ++. +.+.++||||..++
T Consensus         2 igvi~p~~~~~~~~~~~~gi~~~~~~~~~~---~~~--~~~~~~~~~~~~~i~~-l~~~~~dgiii~~~   64 (265)
T cd06285           2 IGVLVPRLTDTVMATMYEGIEEAAAERGYS---TFV--ANTGDNPDAQRRAIEM-LLDRRVDGLILGDA   64 (265)
T ss_pred             EEEEeCCCCCccHHHHHHHHHHHHHHCCCE---EEE--EeCCCCHHHHHHHHHH-HHHcCCCEEEEecC
Confidence            788888887777788999999999999974   433  3333333221   222 34578999997654

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.

>PRK10936 TMAO reductase system periplasmic protein TorT; Provisional

Probab=88.93  E-value=2.6  Score=35.13  Aligned_cols=64  Identities=14%  Similarity=0.101  Sum_probs=46.4

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccch---HHHHHHHHhhcCCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE---IGVVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfE---LPlaak~La~s~~yDAVIaLG  142 (145)
                      ..+||+|...++......+.+|..++++++|+.   +.+...++..+   .--.++.+. ..++||||..+
T Consensus        46 t~~Igvv~p~~~~~f~~~~~~gi~~aa~~~G~~---l~i~~~~~~~~~~~q~~~i~~l~-~~~vdgIIl~~  112 (343)
T PRK10936         46 AWKLCALYPHLKDSYWLSVNYGMVEEAKRLGVD---LKVLEAGGYYNLAKQQQQLEQCV-AWGADAILLGA  112 (343)
T ss_pred             CeEEEEEecCCCchHHHHHHHHHHHHHHHhCCE---EEEEcCCCCCCHHHHHHHHHHHH-HhCCCEEEEeC
Confidence            569999998887777888999999999999973   55555544343   223344444 45799999865

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

Probab=88.68  E-value=2.5  Score=32.67  Aligned_cols=62  Identities=13%  Similarity=0.042  Sum_probs=36.8

Q ss_pred             EEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHH-HHHHhhcCCCcEEEEeee
Q 032216           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVV-AQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        78 IaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPla-ak~La~s~~yDAVIaLG~  143 (145)
                      ||+|....-......+++|+.+.++++|+.   +.+....+..+.-.. ++.+ .+.++||+|..++
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            566666666667777888888888888863   333332222221111 2223 3457899887653

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.

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

Probab=88.67  E-value=2  Score=33.50  Aligned_cols=68  Identities=6%  Similarity=-0.118  Sum_probs=42.1

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchH-HHHHHHHhh-cCCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEI-GVVAQQLGK-SGKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfEL-Plaak~La~-s~~yDAVIaLG  142 (145)
                      ..||+++..+-+....+.-.+|..+.++++|...+...+...+..+|- --.++++++ ..++|||+|-+
T Consensus       125 ~~~i~~i~~~~~~~~~~~R~~gf~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~  194 (275)
T cd06307         125 PGKVAVLAGSHRFRGHEEREMGFRSVLREEFPGLRVLETLEGLDDPARAYEATRKLLARHPDLVGIYNAG  194 (275)
T ss_pred             CCeEEEEecCCCCcchHHHHHHHHHHHHhhCCCcEEEeeccCCCChHHHHHHHHHHHHhCCCceEEEECC
Confidence            359999988766455667789999999998864221222222323322 124445543 45799999865

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.

>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=88.62  E-value=1.5  Score=33.87  Aligned_cols=67  Identities=18%  Similarity=0.152  Sum_probs=42.3

Q ss_pred             CCEEEEEEeee-cHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchH--HHHHHHHhh-cCCCcEEEEee
Q 032216           75 GLRFALVVARF-NELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEI--GVVAQQLGK-SGKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArf-N~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfEL--Plaak~La~-s~~yDAVIaLG  142 (145)
                      ..||+++...- +....+.-.+|..+.|+++|+......++..+..++-  ..+ +.+++ ..++|||+|.+
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            45999997543 2122345679999999999976444445555555542  333 34443 45799999865

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

>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=88.56  E-value=1.2  Score=34.31  Aligned_cols=69  Identities=17%  Similarity=0.079  Sum_probs=43.5

Q ss_pred             CCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH-HHHHHhhc-CCCcEEEEee
Q 032216           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV-VAQQLGKS-GKYTAVLCIG  142 (145)
Q Consensus        74 ~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl-aak~La~s-~~yDAVIaLG  142 (145)
                      ...||+++.++-+....+.-.+|..+.++++|+......++.-...++-.. .++.+.++ .++|||+|-.
T Consensus       116 G~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~  186 (269)
T cd06275         116 GHRRIGCITGPLEKAPAQQRLAGFRRAMAEAGLPVNPGWIVEGDFECEGGYEAMQRLLAQPKRPTAVFCGN  186 (269)
T ss_pred             CCceEEEEeCCCCCccHHHHHHHHHHHHHHcCCCCCHHHhccCCCChHHHHHHHHHHHcCCCCCcEEEECC
Confidence            346999998776666666667999999999997533222222233333322 34455544 4799999854

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

>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=88.38  E-value=2  Score=33.13  Aligned_cols=60  Identities=12%  Similarity=0.207  Sum_probs=45.7

Q ss_pred             EEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHh--hcCCCcEEEEe
Q 032216           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLG--KSGKYTAVLCI  141 (145)
Q Consensus        78 IaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La--~s~~yDAVIaL  141 (145)
                      ||+|........-..+.+|+.+.++++|..   +.++ .++-+...-..+.+-  -+.++||||..
T Consensus         1 I~vi~~~~~~~~~~~~~~g~~~~a~~~g~~---~~~~-~~~~~d~~~q~~~i~~~i~~~~d~Iiv~   62 (257)
T PF13407_consen    1 IGVIVPSMDNPFWQQVIKGAKAAAKELGYE---VEIV-FDAQNDPEEQIEQIEQAISQGVDGIIVS   62 (257)
T ss_dssp             EEEEESSSSSHHHHHHHHHHHHHHHHHTCE---EEEE-EESTTTHHHHHHHHHHHHHTTESEEEEE
T ss_pred             cEEEeCCCCCHHHHHHHHHHHHHHHHcCCE---EEEe-CCCCCCHHHHHHHHHHHHHhcCCEEEec
Confidence            688888888889999999999999999973   3332 588777776655542  24579999964

...

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

Probab=88.19  E-value=1.8  Score=33.77  Aligned_cols=61  Identities=15%  Similarity=0.158  Sum_probs=37.9

Q ss_pred             EEEEEEeee-cHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHH---HHHhhcCCCcEEEEee
Q 032216           77 RFALVVARF-NELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVA---QQLGKSGKYTAVLCIG  142 (145)
Q Consensus        77 RIaIVvArf-N~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaa---k~La~s~~yDAVIaLG  142 (145)
                      |||+|...+ .......+.+|..+.++++|+.   +.+....+ ++..-..   ++|. ..++||+|..+
T Consensus         1 ~i~~i~~~~~~~~~~~~~~~g~~~~~~~~g~~---v~~~~~~~-~~~~~~~~~i~~l~-~~~vdgiii~~   65 (271)
T cd06312           1 KIAFVTHGPAGDPFWTVVKNGAEDAAKDLGVD---VEYRGPET-FDVADMARLIEAAI-AAKPDGIVVTI   65 (271)
T ss_pred             CEEEecCCCCCCcHHHHHHHHHHHHHHHhCCE---EEEECCCC-CCHHHHHHHHHHHH-HhCCCEEEEeC
Confidence            577888777 5666677888888888888863   44433333 2433222   2333 34788888765

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=88.16  E-value=2.9  Score=32.43  Aligned_cols=68  Identities=18%  Similarity=0.284  Sum_probs=41.7

Q ss_pred             CCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH---HHHHHhhc-CCCcEEEEeee
Q 032216           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGKS-GKYTAVLCIGA  143 (145)
Q Consensus        74 ~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl---aak~La~s-~~yDAVIaLG~  143 (145)
                      ...||+++...........=.+|+++.++++|+..+...+.  ++.++..-   +++.++++ .++|||+|.+.
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            35689999876543334444589999999999864333333  33343322   33344444 46899999753

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

>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=87.96  E-value=1.8  Score=33.95  Aligned_cols=62  Identities=13%  Similarity=0.062  Sum_probs=37.8

Q ss_pred             EEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEee
Q 032216           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        77 RIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG  142 (145)
                      +||+|...........+.+|+.++++++|+.   +.++.....=+.=-.++.+. ..++||||..+
T Consensus         1 ~Ig~v~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~i~~~~-~~~~dgiii~~   62 (289)
T cd01540           1 KIGFIVKQPEEPWFQTEWKFAKKAAKEKGFT---VVKIDVPDGEKVLSAIDNLG-AQGAKGFVICV   62 (289)
T ss_pred             CeeeecCCCCCcHHHHHHHHHHHHHHHcCCE---EEEccCCCHHHHHHHHHHHH-HcCCCEEEEcc
Confidence            5788887766555667889999999998874   43332221101111223333 46789998765

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

>PRK10014 DNA-binding transcriptional repressor MalI; Provisional

Probab=87.88  E-value=2.1  Score=34.75  Aligned_cols=68  Identities=18%  Similarity=0.137  Sum_probs=42.3

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH-HHHHHhhc-CCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV-VAQQLGKS-GKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl-aak~La~s-~~yDAVIaLG  142 (145)
                      ..||+++...-+..-...-.+|..+.|+++|+..+...++..+...+-.+ +++.+++. .++|||+|..
T Consensus       182 ~~~I~~i~g~~~~~~~~~R~~Gf~~al~~~g~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~n  251 (342)
T PRK10014        182 HQRIAWLGGQSSSLTRAERVGGYCATLLKFGLPFHSEWVLECTSSQKQAAEAITALLRHNPTISAVVCYN  251 (342)
T ss_pred             CCEEEEEcCCcccccHHHHHHHHHHHHHHcCCCCCcceEecCCCChHHHHHHHHHHHcCCCCCCEEEECC
Confidence            45999997654433334456899999999998644333334444444332 33445443 4799999964

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

Probab=87.76  E-value=2.2  Score=33.29  Aligned_cols=61  Identities=3%  Similarity=-0.090  Sum_probs=33.6

Q ss_pred             EEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH-HHHHHHhhcCCCcEEEEee
Q 032216           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        78 IaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP-laak~La~s~~yDAVIaLG  142 (145)
                      ||+|.-.+....-..++++..+.++++|+.   +.+....+.-|.= -.++.|. +.++||||..+
T Consensus         2 ~g~~~~~~~~~~~~~~~~~~~~~a~~~g~~---~~~~~~~~~~~~~~~~i~~l~-~~~vdgiIi~~   63 (273)
T cd06309           2 VGFSQVGAESPWRTAETKSIKDAAEKRGFD---LKFADAQQKQENQISAIRSFI-AQGVDVIILAP   63 (273)
T ss_pred             eeeccCCCCCHHHHHHHHHHHHHHHhcCCE---EEEeCCCCCHHHHHHHHHHHH-HcCCCEEEEcC
Confidence            556666555555566777778888877763   3333322222211 1233333 35688887654

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.

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

Probab=87.76  E-value=3.5  Score=31.52  Aligned_cols=68  Identities=21%  Similarity=0.226  Sum_probs=40.8

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH-HHHHHHh-hcCCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLG-KSGKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP-laak~La-~s~~yDAVIaLG  142 (145)
                      ..||+++...-+....+.-.+|+.+.++++|+......+...+..+|-. -.++.++ +..+.|||+|..
T Consensus       115 ~~~i~~l~~~~~~~~~~~r~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~  184 (267)
T cd06284         115 HRRIALITGPRDNPLARDRLEGYRQALAEAGLPADEELIQEGDFSLESGYAAARRLLALPDRPTAIFCFS  184 (267)
T ss_pred             CceEEEEcCCccchhHHHHHHHHHHHHHHcCCCCCcceEEeCCCChHHHHHHHHHHHhCCCCCcEEEEcC
Confidence            4589999775444455666799999999999653322222222233321 1233444 344789999864

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.

>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=87.52  E-value=1.8  Score=33.89  Aligned_cols=55  Identities=11%  Similarity=0.160  Sum_probs=37.7

Q ss_pred             EEEEEEe-----eecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEee
Q 032216           77 RFALVVA-----RFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        77 RIaIVvA-----rfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG  142 (145)
                      |||+|..     .+....-..+++|..+.++++|+.   +.+..-++.  ..      ....++||+|..+
T Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~~~~~~~--~~------~~~~~vdgii~~~   60 (270)
T cd01544           1 RIAIVQWYSEEEELDDPYYLSIRLGIEKRAQELGIE---LTKFFRDDD--LL------EILEDVDGIIAIG   60 (270)
T ss_pred             CeEEEEeccccccccCccHHHHHHHHHHHHHHcCCE---EEEEeccch--hH------HhccCcCEEEEec
Confidence            6888888     455566677889999999999974   444433321  11      1356899999875

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

>PRK15408 autoinducer 2-binding protein lsrB; Provisional

Probab=87.34  E-value=4.1  Score=34.60  Aligned_cols=65  Identities=15%  Similarity=0.072  Sum_probs=45.9

Q ss_pred             CCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHH---HHHhhcCCCcEEEEee
Q 032216           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVA---QQLGKSGKYTAVLCIG  142 (145)
Q Consensus        73 ~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaa---k~La~s~~yDAVIaLG  142 (145)
                      ..+.+|++|...-+...-..+.+|+.+.++++|+.   +. +..|...+..--+   +.+. +.++||||...
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            45679999998776666668999999999999974   32 3357655544333   3333 46899999864

>PF00465 Fe-ADH: Iron-containing alcohol dehydrogenase ; InterPro: IPR001670 Alcohol dehydrogenase (1

Probab=87.25  E-value=1.8  Score=36.89  Aligned_cols=61  Identities=18%  Similarity=0.205  Sum_probs=41.2

Q ss_pred             EEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEE-eccc--chHHHHHHHHhhcCCCcEEEEee
Q 032216           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVW-VPGS--FEIGVVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        77 RIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~-VPGA--fELPlaak~La~s~~yDAVIaLG  142 (145)
                      |+.||..+.  .-...+.+...+.|++.|+.   +.++. +++-  +|-=..+-..++..++|.||++|
T Consensus        23 r~lvVt~~~--~~~~~~~~~v~~~L~~~~i~---~~~~~~~~~~p~~~~v~~~~~~~~~~~~D~IIaiG   86 (366)
T PF00465_consen   23 RVLVVTDPS--LSKSGLVDRVLDALEEAGIE---VQVFDGVGPNPTLEDVDEAAEQARKFGADCIIAIG   86 (366)
T ss_dssp             EEEEEEEHH--HHHHTHHHHHHHHHHHTTCE---EEEEEEESSS-BHHHHHHHHHHHHHTTSSEEEEEE
T ss_pred             CEEEEECch--HHhCccHHHHHHHHhhCceE---EEEEecCCCCCcHHHHHHHHHHHHhcCCCEEEEcC
Confidence            999999882  22223778888899999985   44444 4443  33333344456678999999998

1.1.1 from EC) (ADH) catalyzes the reversible oxidation of ethanol to acetaldehyde with the concomitant reduction of NAD. Currently three, structurally and catalytically, different types of alcohol dehydrogenases are known: Zinc-containing 'long-chain' alcohol dehydrogenases. Insect-type, or 'short-chain' alcohol dehydrogenases. Iron-containing alcohol dehydrogenases. Iron-containing ADH's have been found in yeast (gene ADH4) [], as well as in Zymomonas mobilis (gene adhB) []. These two iron-containing ADH's are closely related to the following enzymes: Escherichia coli propanediol oxidoreductase (1.1.1.77 from EC) (gene fucO) [], an enzyme involved in the metabolism of fucose and which also seems to contain ferrous ion(s). Clostridium acetobutylicum NADPH- and NADH-dependent butanol dehydrogenases (1.1.1 from EC) (genes adh1, bdhA and bdhB) [], an enzyme which has activity using butanol and ethanol as substrates. E. coli adhE [], an iron-dependent enzyme which harbor three different activities: alcohol dehydrogenase, acetaldehyde dehydrogenase (acetylating) (1.2.1.10 from EC) and pyruvate-formate-lyase deactivase. Bacterial glycerol dehydrogenase (1.1.1.6 from EC) (gene gldA or dhaD) []. Clostridium kluyveri NAD-dependent 4-hydroxybutyrate dehydrogenase (4hbd) (1.1.1.61 from EC). Citrobacter freundii and Klebsiella pneumoniae 1,3-propanediol dehydrogenase (1.1.1.202 from EC) (gene dhaT). Bacillus methanolicus NAD-dependent methanol dehydrogenase (1.1.1.244 from EC) []. E. coli and Salmonella typhimurium ethanolamine utilization protein eutG. E. coli hypothetical protein yiaY. ; GO: 0016491 oxidoreductase activity, 0046872 metal ion binding, 0055114 oxidation-reduction process; PDB: 1RRM_A 2BL4_A 2BI4_A 3BFJ_R 1KQ3_A 1JQ5_A 1JPU_A 1JQA_A 3JZD_A 3UHJ_A ....

>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=87.24  E-value=3.1  Score=31.94  Aligned_cols=62  Identities=11%  Similarity=0.093  Sum_probs=38.2

Q ss_pred             EEEEEeee-cHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccc-hHHHHHHHHhhcCCCcEEEEeee
Q 032216           78 FALVVARF-NELVTKLLLEGALETFKKYSVKEENIDVVWVPGSF-EIGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        78 IaIVvArf-N~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAf-ELPlaak~La~s~~yDAVIaLG~  143 (145)
                      ||+|.... ....-..+.+|..+.++++|+.   +.++.....- +.--.++.+ .+.++||+|..++
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 5566667888888888888863   4333322222 112223333 3568899988764

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.

>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=87.24  E-value=4.4  Score=31.14  Aligned_cols=66  Identities=17%  Similarity=0.176  Sum_probs=40.7

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH---HHHHHhhc-CCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGKS-GKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl---aak~La~s-~~yDAVIaLG  142 (145)
                      ..||+++.+.-+......-.+|..+.++++|.......+  +++-++.--   ++..++++ .++|||+|.+
T Consensus       122 ~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~  191 (270)
T cd06294         122 HKKIAFVGGDLDLEVTQDRLQGYKQALEDHGIPDRNEVI--ISLDFSEEGGYKALKKLLEQHPRPTAIVATD  191 (270)
T ss_pred             CccEEEecCCcccHHHHHHHHHHHHHHHHcCCCCCcceE--EecCCchHHHHHHHHHHHhCCCCCCEEEECC
Confidence            459999987666444455679999999999974222222  234343211   22334444 4699999964

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.

>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=87.13  E-value=3  Score=32.35  Aligned_cols=65  Identities=11%  Similarity=0.170  Sum_probs=42.6

Q ss_pred             EEEEEEeeecHHHHHHHHHHHHHHHHHCCCC-CCCeEEEEecccchHHH---HHHHHhhcCCCcEEEEeee
Q 032216           77 RFALVVARFNELVTKLLLEGALETFKKYSVK-EENIDVVWVPGSFEIGV---VAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        77 RIaIVvArfN~~It~~LleGA~~~L~~~Gv~-~e~I~vv~VPGAfELPl---aak~La~s~~yDAVIaLG~  143 (145)
                      ||||+.. ++......+++|..+++.++|.. ..++.++......+-.-   .++++. ++++|+||.++.
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 77767778999999999999862 12355544444333322   233443 468999998764

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.

>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=86.96  E-value=2.7  Score=33.48  Aligned_cols=64  Identities=13%  Similarity=-0.073  Sum_probs=40.7

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH---HHHHHhhc-CCCcEEEEe
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGKS-GKYTAVLCI  141 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl---aak~La~s-~~yDAVIaL  141 (145)
                      ..||+++.+.-+......-.+|..+.++++|+...   .+.+.+.++..-   +++++++. .++|||+|-
T Consensus       118 ~~~I~~i~~~~~~~~~~~R~~gf~~a~~~~g~~~~---~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~  185 (269)
T cd06287         118 ARQIALIVGSARRNSYLEAEAAYRAFAAEHGMPPV---VLRVDEAGGEEAGYAACAQLLAQHPDLDALCVP  185 (269)
T ss_pred             CCcEEEEeCCcccccHHHHHHHHHHHHHHcCCCcc---eeEecCCCChHHHHHHHHHHHhCCCCCCEEEEc
Confidence            45899997654433344566899999999998643   233444444322   33445543 468999985

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.

>PRK10401 DNA-binding transcriptional regulator GalS; Provisional

Probab=86.90  E-value=3.6  Score=33.67  Aligned_cols=67  Identities=9%  Similarity=-0.041  Sum_probs=43.4

Q ss_pred             CCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccch-HHHHHHHHhhcCCCcEEEEeee
Q 032216           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE-IGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        73 ~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfE-LPlaak~La~s~~yDAVIaLG~  143 (145)
                      .....||++...+....-..|++|..+.++++|..   +.+.......+ .--.++.+ .+.++||+|..+.
T Consensus        57 ~~~~~Igvi~~~~~~~f~~~l~~gi~~~~~~~gy~---~~~~~~~~~~~~~~~~i~~l-~~~~vdGiIi~~~  124 (346)
T PRK10401         57 QVSDTIGVVVMDVSDAFFGALVKAVDLVAQQHQKY---VLIGNSYHEAEKERHAIEVL-IRQRCNALIVHSK  124 (346)
T ss_pred             CCCCEEEEEeCCCCCccHHHHHHHHHHHHHHCCCE---EEEEcCCCChHHHHHHHHHH-HhcCCCEEEEeCC
Confidence            34457999998876666677999999999999973   33332222211 11233444 3568999998763

>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=86.82  E-value=2.3  Score=32.62  Aligned_cols=69  Identities=17%  Similarity=0.201  Sum_probs=41.1

Q ss_pred             CCCEEEEEEeeec-HHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH-HHHHHhhcCCCcEEEEee
Q 032216           74 EGLRFALVVARFN-ELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV-VAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        74 ~~lRIaIVvArfN-~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl-aak~La~s~~yDAVIaLG  142 (145)
                      ...||+++...=+ ....+.-.+|..+.++++|+..+...+.......|--. +++++.++.++|||+|-+
T Consensus       115 g~~~i~~l~~~~~~~~~~~~r~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ai~~~~  185 (268)
T cd06298         115 GHKKIAFISGPLEDSINGDERLAGYKEALSEANIEFDESLIFEGDYTYESGYELAEELLEDGKPTAAFVTD  185 (268)
T ss_pred             CCceEEEEeCCcccccchhHHHHHHHHHHHHcCCCCCHHHeEeCCCChhHHHHHHHHHhcCCCCCEEEEcC
Confidence            3468999975433 23344567999999999997532222222223334332 334555544499999864

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.

>PRK10653 D-ribose transporter subunit RbsB; Provisional

Probab=86.62  E-value=4.2  Score=32.51  Aligned_cols=65  Identities=20%  Similarity=0.065  Sum_probs=43.5

Q ss_pred             CCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccc-hHHHHHHHHhhcCCCcEEEEee
Q 032216           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSF-EIGVVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        74 ~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAf-ELPlaak~La~s~~yDAVIaLG  142 (145)
                      ....||++...+.......++++..++++++|+.   +.+....+.- +---.++.+. ..++||+|..+
T Consensus        25 ~~~~I~vi~~~~~~~f~~~~~~~i~~~~~~~G~~---~~~~~~~~d~~~~~~~~~~l~-~~~~dgiii~~   90 (295)
T PRK10653         25 AKDTIALVVSTLNNPFFVSLKDGAQKEADKLGYN---LVVLDSQNNPAKELANVQDLT-VRGTKILLINP   90 (295)
T ss_pred             cCCeEEEEecCCCChHHHHHHHHHHHHHHHcCCe---EEEecCCCCHHHHHHHHHHHH-HcCCCEEEEcC
Confidence            4558999999888888889999999999999974   4343332211 1112333333 45899988654

>PF03358 FMN_red: NADPH-dependent FMN reductase; InterPro: IPR005025 NADPH-dependent FMN reductase (1

Probab=86.49  E-value=1.4  Score=32.25  Aligned_cols=45  Identities=11%  Similarity=0.201  Sum_probs=36.4

Q ss_pred             CEEEEEEeeec-HHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH
Q 032216           76 LRFALVVARFN-ELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV  124 (145)
Q Consensus        76 lRIaIVvArfN-~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl  124 (145)
                      |||+||.+.-+ +-.++.|.+.+.+.|++.|++   ++++++..- .+|.
T Consensus         1 Mkilii~gS~r~~~~t~~l~~~~~~~l~~~g~e---~~~i~l~~~-~~p~   46 (152)
T PF03358_consen    1 MKILIINGSPRKNSNTRKLAEAVAEQLEEAGAE---VEVIDLADY-PLPC   46 (152)
T ss_dssp             -EEEEEESSSSTTSHHHHHHHHHHHHHHHTTEE---EEEEECTTS-HCHH
T ss_pred             CEEEEEECcCCCCCHHHHHHHHHHHHHHHcCCE---EEEEecccc-chhh
Confidence            68999999885 788999999999999999874   777776655 6774

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 ....

>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=85.32  E-value=4.3  Score=31.06  Aligned_cols=68  Identities=19%  Similarity=0.110  Sum_probs=41.4

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccch-HHHHHHHHhhc-CCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE-IGVVAQQLGKS-GKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfE-LPlaak~La~s-~~yDAVIaLG  142 (145)
                      ..||+++...-+....+.-.+|+.+.++++|.......++..+...| .--.++.++++ .++|||+|.+
T Consensus       117 ~~~i~~l~~~~~~~~~~~r~~gf~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~i~~~~  186 (268)
T cd06289         117 HRRIAFIGGLEDSSTRRERLAGYRAALAEAGLPFDSELVVEGPPSRQGGAEAVAQLLDLPPRPTAIVCFN  186 (268)
T ss_pred             CCCEEEecCCccccchHHHHHHHHHHHHHcCCCCCchhEEecCcchhhHHHHHHHHHcCCCCCCEEEEcC
Confidence            45899887654434455677999999999996433222332232222 22334455544 5799999875

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.

>PRK10727 DNA-binding transcriptional regulator GalR; Provisional

Probab=85.26  E-value=3.1  Score=34.06  Aligned_cols=66  Identities=15%  Similarity=0.171  Sum_probs=41.0

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH---HHHHHHhhc-CCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGKS-GKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP---laak~La~s-~~yDAVIaLG  142 (145)
                      ..||+++...-+......=.+|+.+.|+++|+..+...+  ..|.++.-   -+++.+++. .++|||+|..
T Consensus       176 ~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~gi~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~n  245 (343)
T PRK10727        176 HTRIGYLCSNHSISDAEDRLQGYYDALAESGIPANDRLV--TFGEPDESGGEQAMTELLGRGRNFTAVACYN  245 (343)
T ss_pred             CccEEEEeCCccccchHHHHHHHHHHHHHCCCCCChhhE--EeCCCChhHHHHHHHHHHhCCCCCCEEEEcC
Confidence            468999976554333344559999999999986432222  23544432   234555544 4689999953

>PRK09526 lacI lac repressor; Reviewed

Probab=85.09  E-value=5.2  Score=32.44  Aligned_cols=64  Identities=9%  Similarity=0.106  Sum_probs=43.2

Q ss_pred             CCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeccc-c-hHHHHHHHHhhcCCCcEEEEe
Q 032216           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGS-F-EIGVVAQQLGKSGKYTAVLCI  141 (145)
Q Consensus        74 ~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGA-f-ELPlaak~La~s~~yDAVIaL  141 (145)
                      +...||+|...++...-..|++|..++++++|+.   +.+...... . +.--.++.| .+.++||||..
T Consensus        62 ~~~~Igvv~~~~~~~~~~~~~~gi~~~a~~~g~~---~~i~~~~~~~~~~~~~~l~~l-~~~~vdGiii~  127 (342)
T PRK09526         62 QSLTIGLATTSLALHAPSQIAAAIKSRADQLGYS---VVISMVERSGVEACQAAVNEL-LAQRVSGVIIN  127 (342)
T ss_pred             CCceEEEEeCCCCcccHHHHHHHHHHHHHHCCCE---EEEEeCCCChHHHHHHHHHHH-HhcCCCEEEEe
Confidence            4457999998877665678999999999999974   555444321 1 112334444 35789999975

>PRK10703 DNA-binding transcriptional repressor PurR; Provisional

Probab=85.05  E-value=2.8  Score=34.04  Aligned_cols=66  Identities=21%  Similarity=0.255  Sum_probs=42.0

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH---HHHHHhh-cCCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGK-SGKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl---aak~La~-s~~yDAVIaLG  142 (145)
                      ..||++|.+.-+....+.-.+|+.+.|+++|+......+  ..+.++..-   .++.+.+ ..++|||+|.+
T Consensus       178 ~~~i~~i~~~~~~~~~~~R~~Gf~~~l~~~gi~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~n  247 (341)
T PRK10703        178 HRDIGVIPGPLERNTGAGRLAGFMKAMEEANIKVPEEWI--VQGDFEPESGYEAMQQILSQKHRPTAVFCGG  247 (341)
T ss_pred             CCcEEEEeCCccccchHHHHHHHHHHHHHcCCCCChHHe--EeCCCCHHHHHHHHHHHHhCCCCCCEEEECC
Confidence            458999977655555566679999999999986332222  244444322   2334443 35789999964

>PRK10401 DNA-binding transcriptional regulator GalS; Provisional

Probab=84.81  E-value=3  Score=34.13  Aligned_cols=67  Identities=13%  Similarity=0.058  Sum_probs=41.9

Q ss_pred             CCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccc--hHHH-HHHHHhhc-CCCcEEEEee
Q 032216           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSF--EIGV-VAQQLGKS-GKYTAVLCIG  142 (145)
Q Consensus        74 ~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAf--ELPl-aak~La~s-~~yDAVIaLG  142 (145)
                      ...||++|.+.-+....+.-.+|..+.|+++|+......+  ..|.+  |-.+ ++++++++ .++|||+|..
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            3469999976554444455669999999999986332222  23433  3222 34455544 4689999964

>PRK11041 DNA-binding transcriptional regulator CytR; Provisional

Probab=84.67  E-value=3.2  Score=32.94  Aligned_cols=66  Identities=18%  Similarity=0.249  Sum_probs=42.1

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccch--H-HHHHHHHhhc-CCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE--I-GVVAQQLGKS-GKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfE--L-Plaak~La~s-~~yDAVIaLG  142 (145)
                      ..||+++....+....+.-.+|..+.++++|+..+...+  +.|-++  - --++++++++ .++|||+|.+
T Consensus       152 ~~~I~~l~~~~~~~~~~~R~~Gf~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~  221 (309)
T PRK11041        152 HKRIACIAGPEEMPLCHYRLQGYVQALRRCGITVDPQYI--ARGDFTFEAGAKALKQLLDLPQPPTAVFCHS  221 (309)
T ss_pred             CceEEEEeCCccccchHHHHHHHHHHHHHcCCCCCHHHe--EeCCCCHHHHHHHHHHHHcCCCCCCEEEEcC
Confidence            359999987665555556789999999999985322112  233332  2 2344555554 3699999864

>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=84.67  E-value=2.3  Score=33.03  Aligned_cols=67  Identities=21%  Similarity=0.129  Sum_probs=40.3

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccch--HHHHHHHHhhcCCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE--IGVVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfE--LPlaak~La~s~~yDAVIaLG  142 (145)
                      ..||+++.++.+......-.+|..+.++++|+......+... +.++  ...+.+.|.+..++|||+|.+
T Consensus       116 ~~~i~~l~~~~~~~~~~~R~~Gf~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~l~~~~~~~ai~~~~  184 (269)
T cd06281         116 HRRIALVGGGSNTRPGRERLEGYKAAFAAAGLPPDPALVRLS-TPAASGFDATRALLALPDRPTAIIAGG  184 (269)
T ss_pred             CcEEEEecCccccccHHHHHHHHHHHHHHcCCCCCHHHeecC-cHHHHHHHHHHHHHcCCCCCcEEEEcC
Confidence            458999988766555556779999999999975321112221 1122  122333333445799999864

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.

>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=84.60  E-value=4.4  Score=30.98  Aligned_cols=69  Identities=20%  Similarity=0.269  Sum_probs=43.0

Q ss_pred             CCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH-HHHHHHhhc-CCCcEEEEee
Q 032216           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKS-GKYTAVLCIG  142 (145)
Q Consensus        74 ~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP-laak~La~s-~~yDAVIaLG  142 (145)
                      ...||+++...-+......-.+|..+.|+++|...+.+.....+-.++-. -+++.++++ .+.|||+|..
T Consensus       115 g~~~i~~i~~~~~~~~~~~r~~gf~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~  185 (268)
T cd01575         115 GYRRIGFLGARMDDTRAQQRLEGFRAALRAAGLDPPLVVTTPEPSSFALGRELLAELLARWPDLDAVFCSN  185 (268)
T ss_pred             CCCcEEEecCCCCcccHHHHHHHHHHHHHHcCCCCCceeEeccCCCHHHHHHHHHHHHhCCCCCCEEEECC
Confidence            34589999877653344456699999999999854333333233233322 244555544 5799999864

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,

>COG0715 TauA ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]

Probab=83.96  E-value=4.7  Score=32.96  Aligned_cols=58  Identities=14%  Similarity=0.265  Sum_probs=41.5

Q ss_pred             cCCCCCCEEEEEEeee-cHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEE
Q 032216           70 LTKNEGLRFALVVARF-NELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVL  139 (145)
Q Consensus        70 l~~~~~lRIaIVvArf-N~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVI  139 (145)
                      +.+.+++|||+..... ...    |+   ...|++.|+.++++.++.+|.+ +++   + .+..++.||++
T Consensus       131 ~adlkGk~vg~~~~~~~~~~----~l---~~~L~~~Gl~~~dv~~v~~~~~-~~~---~-al~~g~vda~~  189 (335)
T COG0715         131 VADLKGKKVGVPFGGSTSDF----LL---RYALAKAGLDPDDVELVNLPPA-DAV---A-ALAAGQVDAFV  189 (335)
T ss_pred             ccCCCCceEEEeCCCchHHH----HH---HHHHHHcCCCcccceEEeeCcH-HHH---H-HHhcCCcceEE
Confidence            3467889999998875 444    33   3457789999999999999988 222   2 23468999854

>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=83.95  E-value=3.8  Score=31.68  Aligned_cols=67  Identities=16%  Similarity=0.178  Sum_probs=42.1

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH---HHHHHhh-cCCCcEEEEeee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGK-SGKYTAVLCIGA  143 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl---aak~La~-s~~yDAVIaLG~  143 (145)
                      ..||+++...-+....+.-.+|.++.++++|+.-+...+.  .+.++..-   +++.+++ ..++|||+|.+.
T Consensus       114 ~~~i~~i~~~~~~~~~~~R~~Gf~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~d  184 (265)
T cd06285         114 HRRIAVLAGPDYASTARDRLAGFRAALAEAGIEVPPERIV--YSGFDIEGGEAAAEKLLRSDSPPTAIFAVND  184 (265)
T ss_pred             CccEEEEeCCcccccHHHHHHHHHHHHHHcCCCCChhhEE--eCCCCHHHHHHHHHHHHcCCCCCCEEEEcCc
Confidence            4589999876554445556799999999999853222222  23334332   3344443 346899999753

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.

>PF09861 DUF2088: Domain of unknown function (DUF2088); InterPro: IPR018657 This domain, found in various hypothetical proteins, has no known function

Probab=83.88  E-value=2.4  Score=34.52  Aligned_cols=45  Identities=33%  Similarity=0.544  Sum_probs=32.8

Q ss_pred             CCCEEEEEE---eeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccc
Q 032216           74 EGLRFALVV---ARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSF  120 (145)
Q Consensus        74 ~~lRIaIVv---ArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAf  120 (145)
                      .+.||+||+   +|...  .+.|+...+++|++.|+.+++|.++---|.-
T Consensus        53 ~~~~V~Ivv~D~TRp~p--~~~il~~ll~~L~~~Gv~~~~i~ii~A~G~H  100 (204)
T PF09861_consen   53 PGKRVAIVVDDITRPTP--SDLILPALLEELEEAGVKDEDITIIIALGTH  100 (204)
T ss_dssp             T-SEEEEEEE-TTS-----HHHHHHHHHHHHHT-T-TT-EEEEEEE-TTS
T ss_pred             CCCeEEEEeCCCCCCCC--HHHHHHHHHHHHHhcCCCccCEEEEEeCCCC
Confidence            458999999   77743  3789999999999999999999999888884

; PDB: 2YJG_B.

>cd08170 GlyDH Glycerol dehydrogenases (GlyDH) catalyzes oxidation of glycerol to dihydroxyacetone in glycerol dissmilation

Probab=83.81  E-value=6.4  Score=33.48  Aligned_cols=62  Identities=15%  Similarity=0.178  Sum_probs=40.8

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHH--HHHhhcCCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVA--QQLGKSGKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaa--k~La~s~~yDAVIaLG  142 (145)
                      +.|+.||..+.-..   .+.+...+.|+++|+.   +....++|--....+-  -.+++..++|.||++|
T Consensus        22 ~~r~livt~~~~~~---~~~~~v~~~L~~~~i~---~~~~~~~~~p~~~~v~~~~~~~~~~~~D~IIavG   85 (351)
T cd08170          22 GKRALIIADEFVLD---LVGAKIEESLAAAGID---ARFEVFGGECTRAEIERLAEIARDNGADVVIGIG   85 (351)
T ss_pred             CCeEEEEECHHHHH---HHHHHHHHHHHhCCCe---EEEEEeCCcCCHHHHHHHHHHHhhcCCCEEEEec
Confidence            35888888654333   6777888888888874   3344566643333332  2345677999999998

Glycerol dehydrogenases (GlyDH) is a key enzyme in the glycerol dissimilation pathway . In anaerobic conditions, many microorganisms utilize glycerol as a source of carbon through coupled oxidative and reductive pathways. One of the pathways involves the oxidation of glycerol to dihydroxyacetone with the reduction of NAD+ to NADH catalyzed by glycerol dehydrogenases. Dihydroxyacetone is then phosphorylated by dihydroxyacetone kinase and enters the glycolytic pathway for further degradation. The activity of GlyDH is zinc-dependent. The zinc ion plays a role in stabilizing an alkoxide intermediate at the active site.

>cd08183 Fe-ADH2 Iron-containing alcohol dehydrogenases-like

Probab=83.58  E-value=5.4  Score=34.43  Aligned_cols=60  Identities=22%  Similarity=0.262  Sum_probs=38.3

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeccc--chHHHHHHHHhhcCCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGS--FEIGVVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGA--fELPlaak~La~s~~yDAVIaLG  142 (145)
                      +.|+.||..+.-.     ..+...+.|++.|++   +.++.+++-  +|.=.-+-.+++..++|.||++|
T Consensus        22 ~~r~livtd~~~~-----~~~~v~~~L~~~g~~---~~~~~~~~~p~~~~v~~~~~~~~~~~~D~IIaiG   83 (374)
T cd08183          22 GRRVLLVTGASSL-----RAAWLIEALRAAGIE---VTHVVVAGEPSVELVDAAVAEARNAGCDVVIAIG   83 (374)
T ss_pred             CCcEEEEECCchH-----HHHHHHHHHHHcCCe---EEEecCCCCcCHHHHHHHHHHHHhcCCCEEEEec
Confidence            3589899876443     556677788888874   445545442  22222223345667999999998

Iron-containing alcohol dehydrogenases (Fe-ADH). Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions. The protein structure represents a dehydroquinate synthase-like fold and is a member of the iron-activated alcohol dehydrogenase-like family. They are distinct from other alcohol dehydrogenases which contains different protein domain. Proteins of this family have not been characterized. Their specific function is unknown. They are mainly found in bacteria.

>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=83.56  E-value=4.2  Score=31.48  Aligned_cols=65  Identities=17%  Similarity=0.174  Sum_probs=39.4

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH---HHHHHhhcCCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl---aak~La~s~~yDAVIaLG  142 (145)
                      ..||+++...-...-...=.+|..+.++++|+......+  +++-+....   +++++++.+ +|||+|..
T Consensus       122 ~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~i--~~~~~~~~~~~~~~~~~l~~~-~~ai~~~~  189 (273)
T cd06292         122 HRRIGFASGPGRTVPRRRKIAGFRAALEEAGLEPPEALV--ARGMFSVEGGQAAAVELLGSG-PTAIVAAS  189 (273)
T ss_pred             CceEEEEeCCcccccHHHHHHHHHHHHHHcCCCCChhhe--EeCCCCHHHHHHHHHHHhcCC-CCEEEEcC
Confidence            458999976543223334458999999999975332222  234444322   344555444 99999864

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.

>PF02662 FlpD: Methyl-viologen-reducing hydrogenase, delta subunit; InterPro: IPR003813 Methyl-viologen-reducing hydrogenase (MVH) is one of the enzymes involved in methanogenesis and coded in the mth-flp-mvh-mrt cluster of methane genes in Methanothermobacter thermautotrophicus (Methanobacterium thermoformicicum) []

Probab=83.39  E-value=4.3  Score=30.51  Aligned_cols=35  Identities=20%  Similarity=0.376  Sum_probs=29.0

Q ss_pred             CCCeEEEEec--ccchHHHHHHHHhhcCCCcEEEEeeee
Q 032216          108 EENIDVVWVP--GSFEIGVVAQQLGKSGKYTAVLCIGAV  144 (145)
Q Consensus       108 ~e~I~vv~VP--GAfELPlaak~La~s~~yDAVIaLG~V  144 (145)
                      +.++.+++||  |..+.-++++.|.  ...|+|+.+||-
T Consensus        26 p~~vriIrvpC~Grv~~~~il~Af~--~GADGV~V~gC~   62 (124)
T PF02662_consen   26 PPNVRIIRVPCSGRVDPEFILRAFE--KGADGVLVAGCH   62 (124)
T ss_pred             CCCeEEEEccCCCccCHHHHHHHHH--cCCCEEEEeCCC
Confidence            4578999998  7788888888876  369999999983

No specific functions have been assigned to the delta subunit.; GO: 0015948 methanogenesis, 0055114 oxidation-reduction process

>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=83.39  E-value=4.1  Score=30.47  Aligned_cols=67  Identities=16%  Similarity=0.047  Sum_probs=41.3

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccc-hHHHHHHHHhhc-CCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSF-EIGVVAQQLGKS-GKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAf-ELPlaak~La~s-~~yDAVIaLG  142 (145)
                      ..||+++...-+....+...+|..+.++++| ..+.+.++...... +.--.++.+.+. .+.|+++|.+
T Consensus       118 ~~~i~~i~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~i~~~~  186 (264)
T cd01537         118 HRRIALLAGPLGSSTARERVAGFKDALKEAG-PIEIVLVQEGDWDAEKGYQAAEELLTAHPDPTAIFAAN  186 (264)
T ss_pred             CCcEEEEECCCCCCcHHHHHHHHHHHHHHcC-CcChhhhccCCCCHHHHHHHHHHHHhcCCCCCEEEEcC
Confidence            4699999876554556678899999999998 21222333333222 222334444444 4599999875

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

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

Probab=83.34  E-value=6.4  Score=30.67  Aligned_cols=65  Identities=15%  Similarity=0.097  Sum_probs=35.0

Q ss_pred             EEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHH--HHHHhhcCCCcEEEEee
Q 032216           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVV--AQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        78 IaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPla--ak~La~s~~yDAVIaLG  142 (145)
                      ||++...+.......|++|+.++++++|-...+++++...+..+-...  ....+...++||||..+
T Consensus         2 Ig~i~~~~~~~f~~~~~~gi~~~a~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~l~~~~vDgiii~~   68 (274)
T cd06311           2 IGVSIPAADHGWTAGIVWHAQAAAKKLEAAYPDVEFILVTASNDTEQQNAQQDLLINRKIDALVILP   68 (274)
T ss_pred             eeeeccCCCCcHHHHHHHHHHHHHHHhhhhCCCeEEEEEcCCCCHHHHHHHHHHHHHcCCCEEEEeC
Confidence            566666655555666777777777776422123455555554332211  11112345678887654

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.

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

Probab=83.20  E-value=7.7  Score=29.95  Aligned_cols=68  Identities=10%  Similarity=-0.093  Sum_probs=42.1

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH-HHHHHhhc--CCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV-VAQQLGKS--GKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl-aak~La~s--~~yDAVIaLG  142 (145)
                      ..||+++.+.-.......-.+|..+.++++|+..+...+...+-..|-.. +++.++++  .++|||+|.+
T Consensus       116 ~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~ai~~~~  186 (264)
T cd06274         116 PEEVLFLGGLPELSPSRERLAGFRQALADAGLPVQPDWIYAEGYSPESGYQLMAELLARLGRLPRALFTTS  186 (264)
T ss_pred             CCcEEEEeCCCcccchHHHHHHHHHHHHHcCCCCCcceeecCCCChHHHHHHHHHHHccCCCCCcEEEEcC
Confidence            45999998765544455667999999999997533333333332333221 23444444  4699999965

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

>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=82.90  E-value=5  Score=31.22  Aligned_cols=68  Identities=18%  Similarity=0.059  Sum_probs=41.4

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH-HHHHHHhh-cCCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGK-SGKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP-laak~La~-s~~yDAVIaLG  142 (145)
                      ..+|+++...-.......-.+|..+.++++|.......+...+..++-- -.++.+++ ..++|||+|.+
T Consensus       125 ~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~  194 (275)
T cd06295         125 RRRIAFLGGPQDMPEGEERLEGYREALAEAGLPLDPRLVAPGDFTEESGRAAMRALLERGPDFDAVFAAS  194 (275)
T ss_pred             CCeEEEEcCCCCcchhHHHHHHHHHHHHHcCCCCChhhEEeccCCHHHHHHHHHHHHhCCCCCCEEEECC
Confidence            4589998765442344566799999999999654333333333333321 23334443 35799999875

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

>PRK10423 transcriptional repressor RbsR; Provisional

Probab=82.71  E-value=6.5  Score=31.56  Aligned_cols=67  Identities=24%  Similarity=0.199  Sum_probs=42.3

Q ss_pred             CCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH---HHHHHHhhc-CCCcEEEEee
Q 032216           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGKS-GKYTAVLCIG  142 (145)
Q Consensus        74 ~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP---laak~La~s-~~yDAVIaLG  142 (145)
                      ...||+++.+.-+......-.+|..+.|+++|+....  .+...+.++.-   -+++++++. .++|||+|..
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            3469999976554444455679999999999975322  12234555432   234455544 4689999964

>COG1609 PurR Transcriptional regulators [Transcription]

Probab=82.60  E-value=5.7  Score=33.67  Aligned_cols=67  Identities=12%  Similarity=0.064  Sum_probs=47.9

Q ss_pred             CCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEee
Q 032216           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        73 ~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG  142 (145)
                      .+..-||+|...+....-..+++|..+.+.++|..   +.+......-|---.+.....+.++||||.+|
T Consensus        56 ~~s~~Ig~i~p~~~~~~~~~i~~gi~~~~~~~gy~---~~l~~~~~~~~~e~~~~~~l~~~~vdGiIi~~  122 (333)
T COG1609          56 GRTKTIGLVVPDITNPFFAEILKGIEEAAREAGYS---LLLANTDDDPEKEREYLETLLQKRVDGLILLG  122 (333)
T ss_pred             CCCCEEEEEeCCCCCchHHHHHHHHHHHHHHcCCE---EEEECCCCCHHHHHHHHHHHHHcCCCEEEEec
Confidence            34456899988777667777999999999999983   44444444334444444455678999999987

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

Probab=82.43  E-value=8.4  Score=29.80  Aligned_cols=65  Identities=12%  Similarity=0.063  Sum_probs=40.5

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccch--HH-HHHHHHhhc-CCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE--IG-VVAQQLGKS-GKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfE--LP-laak~La~s-~~yDAVIaLG  142 (145)
                      ..||+++...-+......-++|+.+.++++|..   +..+...+.+.  .. -+++.++++ .++|+|+|.+
T Consensus       125 ~~~i~~i~~~~~~~~~~~r~~gf~~~l~~~~~~---~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~  193 (277)
T cd06319         125 DGKVGMVAIPQKRKNGQKRTKGFKEAMKEAGCD---LAGIRQQKDFSYQETFDYTNDLLTANPDIRAIWLQG  193 (277)
T ss_pred             CCcEEEEeccCCCccHHHHHHHHHHHHHhcCCc---eEeeccCCCCCHHHHHHHHHHHHHhCCCCCEEEECC
Confidence            458999975443334456789999999999975   22223334443  22 223445543 5689999875

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.

>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=82.14  E-value=3.5  Score=31.78  Aligned_cols=68  Identities=21%  Similarity=0.118  Sum_probs=41.1

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH-HHHHHHhhc-CCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKS-GKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP-laak~La~s-~~yDAVIaLG  142 (145)
                      ..||+++...-.....+.-.+|..+.++++|+......+...+..+|-. -++++++++ .++|||+|..
T Consensus       111 ~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~  180 (261)
T cd06272         111 HKKIAYIGDLSLDRRQRKRFKGFLETCDENGISISDSHIDVDGLSAEGGDNAAKKLLKESDLPTAIICGS  180 (261)
T ss_pred             chhEEEeecccccccHHHHHHHHHHHHHHcCCCCCHHHeeeCCCCHHHHHHHHHHHHcCCCCCCEEEECC
Confidence            4589999765442233445699999999999742222233344444432 244555544 4699999864

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

>cd06303 PBP1_LuxPQ_Quorum_Sensing Periplasmic binding protein (LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from Vibrio harveyi and its close homologs

Probab=82.08  E-value=11  Score=29.76  Aligned_cols=60  Identities=3%  Similarity=0.019  Sum_probs=35.2

Q ss_pred             EEEEEEeee--cHHHHHHHHHHHHHHHHHCCCCCCCeEEEEe-cc-----cchHHHHHHHHhhcCCCcEEEEee
Q 032216           77 RFALVVARF--NELVTKLLLEGALETFKKYSVKEENIDVVWV-PG-----SFEIGVVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        77 RIaIVvArf--N~~It~~LleGA~~~L~~~Gv~~e~I~vv~V-PG-----AfELPlaak~La~s~~yDAVIaLG  142 (145)
                      |||+|....  |... ..++++..++++++|+.   +.+..+ ++     ..|.. .++.| .+.++||||..+
T Consensus         1 ~Igvi~~~~~~~~~~-~~~~~~i~~~~~~~g~~---~~~~~~~~~~~~~~~~~~~-~i~~l-~~~~vDgiIv~~   68 (280)
T cd06303           1 KIAVIYPGQQISDYW-VRNIASFTARLEELNIP---YELTQFSSRPGIDHRLQSQ-QLNEA-LQSKPDYLIFTL   68 (280)
T ss_pred             CeeEEecCccHHHHH-HHHHHHHHHHHHHcCCc---EEEEEeccCcccCHHHHHH-HHHHH-HHcCCCEEEEcC
Confidence            578888775  4443 56888888888888863   333322 22     12221 22333 346788888754

Periplasmic binding protein (LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from Vibrio harveyi and its close homologs from other bacteria. The members of this group are highly homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transport of many sugar based solutes in bacteria and archaea, and that are members of the type I periplasmic binding protein superfamily. The Vibrio harveyi AI-2 receptor consists of two polypeptides, LuxP and LuxQ: LuxP is a periplasmic binding protein that binds AI-2 by clamping it between two domains, LuxQ is an integral membrane protein belonging to the two-component sensor kinase family. Unlike AI-2 bound to the LsrB receptor in Salmonella typhimurium, the Vibrio harveyi AI-2 signaling molecule has an unusual furanosyl borate

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

Probab=82.02  E-value=6.2  Score=30.33  Aligned_cols=69  Identities=13%  Similarity=0.058  Sum_probs=42.2

Q ss_pred             CCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccch-HHHHHHHHhhc-CCCcEEEEee
Q 032216           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE-IGVVAQQLGKS-GKYTAVLCIG  142 (145)
Q Consensus        74 ~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfE-LPlaak~La~s-~~yDAVIaLG  142 (145)
                      ...||+++...=+......-.+|..+.|+++|.......+++-+-.++ .--+++.+++. .++|||+|..
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            356999997654434455667999999999997533322333222321 12344555544 5799999863

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.

>PF09084 NMT1: NMT1/THI5 like; InterPro: IPR015168 This entry is found in the NMT1 and THI5 proteins

Probab=81.86  E-value=2.6  Score=32.01  Aligned_cols=58  Identities=21%  Similarity=0.259  Sum_probs=36.9

Q ss_pred             CCCCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEE
Q 032216           71 TKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLC  140 (145)
Q Consensus        71 ~~~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIa  140 (145)
                      .+.+++||++........    ++   ...|+++|+..++++.+.+++ .+   ..+. +.+++.|++++
T Consensus        89 ~DLkGK~i~v~~~s~~~~----~~---~~~l~~~g~~~~~v~~v~~~~-~~---~~~a-l~~g~vDa~~~  146 (216)
T PF09084_consen   89 ADLKGKKIGVSRGSSSEY----FL---RALLKKNGIDPDDVKIVNLGP-PE---LAQA-LLSGQVDAAIL  146 (216)
T ss_dssp             GGGTTSEEEESTTSHHHH----HH---HHHHHHTTT-GGGSEEEES-H-HH---HHHH-HHTTSSSEEEE
T ss_pred             HHhCCCEEEEecCcchhH----HH---HHHHHHhccccccceeeeeeh-hh---hhhh-hhcCCCCEEEE
Confidence            356788999766434333    22   245788999999999887764 23   3332 34689999884

These proteins are proposed to be required for the biosynthesis of the pyrimidine moiety of thiamine [, , ]. They are regulated by thiamine []. ; PDB: 2X26_A 3E4R_A 3KSJ_A 3KSX_A 3UIF_A 4DDD_A 1US4_A 1US5_A 3IX1_B 2X7P_A ....

>cd06324 PBP1_ABC_sugar_binding_like_13 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems

Probab=81.75  E-value=6.9  Score=31.59  Aligned_cols=29  Identities=3%  Similarity=-0.079  Sum_probs=18.7

Q ss_pred             EEEEEeee-cHHHHHHHHHHHHHHHHHCCC
Q 032216           78 FALVVARF-NELVTKLLLEGALETFKKYSV  106 (145)
Q Consensus        78 IaIVvArf-N~~It~~LleGA~~~L~~~Gv  106 (145)
                      ||++...+ ....-..+++++.++++++|+
T Consensus         2 Igvi~~~~~~~~~~~~~~~gi~~~~~~~g~   31 (305)
T cd06324           2 VVFLNPGKSDEPFWNSVARFMQAAADDLGI   31 (305)
T ss_pred             eEEecCCCCCCcHHHHHHHHHHHHHHhcCC
Confidence            56666666 444445677777777777776

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 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.

>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=81.68  E-value=5.7  Score=30.60  Aligned_cols=66  Identities=17%  Similarity=0.170  Sum_probs=43.0

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchH---HHHHHHHhhc-CCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEI---GVVAQQLGKS-GKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfEL---Plaak~La~s-~~yDAVIaLG  142 (145)
                      ..||+++...-+......-.+|..+.+.++|+......  .+++.++.   --++++++++ .++|||+|..
T Consensus       115 ~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~l~~~~~~~aii~~~  184 (265)
T cd06290         115 HRRIAHITGPRGHIDARDRLAGYRKALEEAGLEVQPDL--IVQGDFEEESGLEAVEELLQRGPDFTAIFAAN  184 (265)
T ss_pred             CCeEEEEeCccccchhhHHHHHHHHHHHHcCCCCCHHH--EEecCCCHHHHHHHHHHHHcCCCCCCEEEEcC
Confidence            46999998765555555677999999999987533221  23444432   1245556554 4689999864

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.

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

Probab=81.21  E-value=14  Score=30.70  Aligned_cols=65  Identities=6%  Similarity=0.031  Sum_probs=43.3

Q ss_pred             CCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH---HHHHHhhcCCCcEEEEee
Q 032216           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        73 ~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl---aak~La~s~~yDAVIaLG  142 (145)
                      .++.+||+|...+-...-..+++|..+.++++|.    ..++.+++.++--.   .++.| .+.++||+|..+
T Consensus        22 ~~~~~Igvv~~~~~~~f~~~~~~gi~~~a~~~g~----~~~~~~~~~~~~~~~~~~i~~l-~~~~vdgiIi~~   89 (330)
T PRK15395         22 AADTRIGVTIYKYDDNFMSVVRKAIEKDAKAAPD----VQLLMNDSQNDQSKQNDQIDVL-LAKGVKALAINL   89 (330)
T ss_pred             cCCceEEEEEecCcchHHHHHHHHHHHHHHhcCC----eEEEEecCCCCHHHHHHHHHHH-HHcCCCEEEEec
Confidence            4567899999877666677899999999999863    23444444443332   22333 356899999864

>cd06314 PBP1_tmGBP Periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and its close homologs

Probab=81.08  E-value=8.5  Score=30.00  Aligned_cols=61  Identities=15%  Similarity=0.061  Sum_probs=34.4

Q ss_pred             EEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH--HHHHHHhhcCCCcEEEEee
Q 032216           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG--VVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        77 RIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP--laak~La~s~~yDAVIaLG  142 (145)
                      +||+|. .+....-..++.|..++++++|+.   +.++ .+..++.-  .-.-+.+.+.++||+|...
T Consensus         1 ~i~~v~-~~~~~~~~~~~~gi~~~~~~~g~~---~~~~-~~~~~~~~~~~~~i~~l~~~~vDgiIi~~   63 (271)
T cd06314           1 TIAVVT-NGASPFWKIAEAGVKAAGKELGVD---VEFV-VPQQGTVNAQLRMLEDLIAEGVDGIAISP   63 (271)
T ss_pred             CeEEEc-CCCcHHHHHHHHHHHHHHHHcCCe---EEEe-CCCCCCHHHHHHHHHHHHhcCCCEEEEec
Confidence            467666 344555667888888888888863   3333 12222222  1111223456888888764

Periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and its close homologs from other bacteria. They are a member of the type I periplasmic binding protein superfamily which consists of two domains connected by a three-stranded hinge. TmGBP is specific for glucose and its binding pocket is buried at the interface of the two domains. TmGBP also exhibits high thermostability and the highest structural similarity to E. coli glucose binding protein (ecGBP).

>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=80.90  E-value=4.5  Score=30.93  Aligned_cols=64  Identities=16%  Similarity=0.161  Sum_probs=42.5

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccch---HHHHHHHHhh-cCCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE---IGVVAQQLGK-SGKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfE---LPlaak~La~-s~~yDAVIaLG  142 (145)
                      ..||+++..+-+....+.-.+|..+.++++|..   +... +.+.++   .--.++.+.+ ..++|||+|.+
T Consensus       115 ~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~---~~~~-~~~~~~~~~~~~~~~~~l~~~~~~~~i~~~~  182 (266)
T cd06278         115 CRRIAFIGGPADTSTSRERERGFRDALAAAGVP---VVVE-EAGDYSYEGGYEAARRLLASRPRPDAIFCAN  182 (266)
T ss_pred             CceEEEEcCCCcccchHHHHHHHHHHHHHcCCC---hhhh-ccCCCCHHHHHHHHHHHHhcCCCCCEEEEcC
Confidence            459999998877767777889999999999875   2111 223332   2233344444 35799999865

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.

>cd06341 PBP1_ABC_ligand_binding_like_7 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions

Probab=80.82  E-value=10  Score=30.86  Aligned_cols=65  Identities=17%  Similarity=0.096  Sum_probs=45.5

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG  142 (145)
                      ..|++++...-+ ...+.+.++..+.++++|+..... ...-|+.-+.--.++++.+ .+.|+|++.+
T Consensus       132 ~~~~~~i~~~~~-~~g~~~~~~~~~~~~~~G~~v~~~-~~~~~~~~d~~~~~~~i~~-~~pdaV~~~~  196 (341)
T cd06341         132 GTRAVALVTALS-AAVSAAAALLARSLAAAGVSVAGI-VVITATAPDPTPQAQQAAA-AGADAIITVL  196 (341)
T ss_pred             CcEEEEEEeCCc-HHHHHHHHHHHHHHHHcCCccccc-cccCCCCCCHHHHHHHHHh-cCCCEEEEec
Confidence            569998876533 356678899999999999863222 2223566788667777754 4799998765

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

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

Probab=80.72  E-value=8.8  Score=30.06  Aligned_cols=68  Identities=15%  Similarity=-0.038  Sum_probs=41.9

Q ss_pred             CCEEEEEEeeecHH------HHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH-HHHHHHhhc-CCCcEEEEee
Q 032216           75 GLRFALVVARFNEL------VTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKS-GKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~------It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP-laak~La~s-~~yDAVIaLG  142 (145)
                      ..||+++.......      ..+.-++|..+.++++|+......+....=.++-. -++++++++ .++|||+|-.
T Consensus       113 ~~~i~~i~~~~~~~~~~~~~~~~~R~~gf~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~  188 (269)
T cd06297         113 PGRIGAITVEEEPDRAFRRTVFAERRAGFQQALKDAGRPFSPDLLAITDHSEEGGRLAMRHLLEKASPPLAVFASA  188 (269)
T ss_pred             CCceEEEeCccccccccccccHHHHHHHHHHHHHHcCCCCChhhEEeCCCChhhHHHHHHHHHcCCCCCcEEEEcC
Confidence            35899997765444      45566799999999999863321222222122222 244555544 5689999864

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.

>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=80.51  E-value=9.8  Score=29.29  Aligned_cols=65  Identities=17%  Similarity=0.133  Sum_probs=40.9

Q ss_pred             CCEEEEEEeeec-HHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH---HHHHHHh-hcCCCcEEEEee
Q 032216           75 GLRFALVVARFN-ELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLG-KSGKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN-~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP---laak~La-~s~~yDAVIaLG  142 (145)
                      ..||+++...-+ ......-.+|..+.|+++|...+.+   ..++.++..   -.+++++ +..+.|||+|.+
T Consensus       112 ~~~i~~i~~~~~~~~~~~~r~~gf~~~l~~~~~~~~~~---~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~  181 (265)
T cd06291         112 CKHIAHIGGPNNTVSPTNLRYEGFLDVLKENGLEVRII---EIQENFDDAEKKEEIKELLEEYPDIDGIFASN  181 (265)
T ss_pred             CcEEEEEccCcccccchHHHHHHHHHHHHHcCCCCChh---eeeccccchHHHHHHHHHHhCCCCCCEEEECC
Confidence            458999987665 3555566799999999999864322   233434322   1333444 345689999853

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

>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=80.45  E-value=7.3  Score=30.60  Aligned_cols=64  Identities=6%  Similarity=-0.005  Sum_probs=40.9

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH-HHHHHhhc-CCCcEEEE
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV-VAQQLGKS-GKYTAVLC  140 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl-aak~La~s-~~yDAVIa  140 (145)
                      ..||+++...-+...+..-.+|..+.++++|+..  ..+......+|-.. +++.++++ .++|+|+|
T Consensus       125 ~~~i~~l~g~~~~~~~~~R~~g~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~l~~~~~~~~i~~  190 (268)
T cd06306         125 PAKVAWFPGPKGAGWVKAVEKGFRDALAGSAIEI--SAIKYGDTGKEVQRKLVEEALEAHPDIDYIVG  190 (268)
T ss_pred             CceEEEEeCCCCCchHHHHHHHHHHHHhhcCcEE--eeeccCCccHHHHHHHHHHHHHhCCCcCEEee
Confidence            3699999877666566777899999999988742  11222223333332 33444543 57899986

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.

>cd06339 PBP1_YraM_LppC_lipoprotein_like Periplasmic binding component of lipoprotein LppC, an immunodominant antigen

Probab=80.40  E-value=11  Score=31.29  Aligned_cols=64  Identities=6%  Similarity=0.067  Sum_probs=47.8

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEE-ecccchHHHHHHHHhhc--------------------C
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVW-VPGSFEIGVVAQQLGKS--------------------G  133 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~-VPGAfELPlaak~La~s--------------------~  133 (145)
                      ..||+|+..  |....+.+.++..+.+++.|+..  +...+ -||.-+.--.++++...                    .
T Consensus       124 ~k~vaii~~--~~~~g~~~~~~f~~~~~~~G~~v--v~~~~~~~~~~d~~~~i~~i~~~~~~~~~~~~~~~~~~~~~~~~  199 (336)
T cd06339         124 KRRPLVLAP--DGAYGQRVADAFRQAWQQLGGTV--VAIESYDPSPTDLSDAIRRLLGVDDSEQRIAQLKSLESEPRRRQ  199 (336)
T ss_pred             ccceEEEec--CChHHHHHHHHHHHHHHHcCCce--eeeEecCCCHHHHHHHHHHHhccccchhhhhhhhhcccCccccC
Confidence            468999986  45667889999999999999852  33333 35888887778777654                    3


Q ss_pred             CCcEEEEee
Q 032216          134 KYTAVLCIG  142 (145)
Q Consensus       134 ~yDAVIaLG  142 (145)
                      +.|+|+.++
T Consensus       200 ~~d~v~~~~  208 (336)
T cd06339         200 DIDAIDAVA  208 (336)
T ss_pred             CCCcEEEEe
Confidence            789998865

This subgroup includes periplasmic binding component of lipoprotein LppC, an immunodominant antigen, whose molecular function is not characterized. Members of this subgroup are predicted to be involved in transport of lipid compounds, and they are sequence similar to the family of ABC-type hydrophobic amino acid transporters (HAAT).

>COG1609 PurR Transcriptional regulators [Transcription]

Probab=80.25  E-value=7.9  Score=32.82  Aligned_cols=67  Identities=19%  Similarity=0.217  Sum_probs=44.8

Q ss_pred             CCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH---HHHHHHhhc-CC-CcEEEEe
Q 032216           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGKS-GK-YTAVLCI  141 (145)
Q Consensus        73 ~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP---laak~La~s-~~-yDAVIaL  141 (145)
                      ....||+++...-+......=++|.++.|+++|+...  ....++|.|..-   -++++++.. .+ .|||+|.
T Consensus       173 ~G~~~i~~i~~~~~~~~~~~R~~Gf~~al~~~~~~~~--~~~i~~~~~~~~~g~~~~~~ll~~~~~~ptAif~~  244 (333)
T COG1609         173 LGHRRIAFIGGPLDSSASRERLEGYRAALREAGLPIN--PEWIVEGDFSEESGYEAAERLLARGEPRPTAIFCA  244 (333)
T ss_pred             CCCceEEEEeCCCccccHhHHHHHHHHHHHHCCCCCC--cceEEecCCChHHHHHHHHHHHhcCCCCCcEEEEc
Confidence            3356899999996544545557999999999999742  334455665333   233445543 34 9999985

>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=80.01  E-value=5.6  Score=30.38  Aligned_cols=66  Identities=15%  Similarity=0.136  Sum_probs=40.1

Q ss_pred             CCEEEEEEeee-cHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccc-hHHHHHHHHhhc-CCCcEEEEee
Q 032216           75 GLRFALVVARF-NELVTKLLLEGALETFKKYSVKEENIDVVWVPGSF-EIGVVAQQLGKS-GKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArf-N~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAf-ELPlaak~La~s-~~yDAVIaLG  142 (145)
                      ..||+++.++- |....+.-.+|..+.|+++|+....  .+..+-.. +..-.+..++++ .+.|||+|.+
T Consensus       116 ~~~i~~i~~~~~~~~~~~~r~~gf~~~l~~~~~~~~~--~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~  184 (266)
T cd06282         116 HRRIAMLAGRLAASDRARQRYAGYRAAMRAAGLAPLP--PVEIPFNTAALPSALLALLTAHPAPTAIFCSN  184 (266)
T ss_pred             cccEEEeccccccCchHHHHHHHHHHHHHHcCCCCCc--cccCCCcHHHHHHHHHHHhcCCCCCCEEEECC
Confidence            45899997653 3334555679999999999985222  22333221 122334444444 4789999864

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	145
1c2y_A	156	Crystal Structures Of A Pentameric Fungal And An Ic		2e-28
1vsw_A	153	Crystal Structure Of Lumazine Synthase From Bacillu		2e-17
3mk3_A	156	Crystal Structure Of Lumazine Synthase From Salmone		5e-14
1rvv_A	154	SynthaseRIBOFLAVIN SYNTHASE COMPLEX OF BACILLUS SUB		3e-13
1hqk_A	154	Crystal Structure Analysis Of Lumazine Synthase Fro		2e-11
2a57_A	159	Structure Of 6,7-dimthyl-8-ribityllumazine Synthase		5e-06
1kz4_A	159	Mutant Enzyme W63y Lumazine Synthase From S.pombe L		5e-06
1kz6_A	159	Mutant Enzyme W63y/l119f Lumazine Synthase From S.p		5e-06
1kyv_A	159	Lumazine Synthase From S.pombe Bound To Riboflavin		8e-06
1kz9_A	159	Mutant Enzyme L119f Lumazine Synthase From S.pombe		8e-06
4gef_A	179	Product Complex Of Lumazine Synthase From Candida G		1e-05
2jfb_A	164	3d Structure Of Lumazine Synthase From Candida Albi		2e-05
1kz1_A	159	Mutant Enzyme W27g Lumazine Synthase From S.pombe L		3e-05
1c41_A	200	Crystal Structures Of A Pentameric Fungal And An Ic		4e-05
1ejb_A	168	Lumazine Synthase From Saccharomyces Cerevisiae Len		3e-04

>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 =  120 bits (302), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 55/83 (66%), Positives = 70/83 (84%), Gaps = 1/83 (1%)
Query: 63  VRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEI 122
           +  L G++TK +  RFA+VVARFNE VT+ L+EGAL+TFKKYSV E+ IDVVWVPG++E+
Sbjct: 1   MNELEGYVTKAQSFRFAIVVARFNEFVTRRLMEGALDTFKKYSVNED-IDVVWVPGAYEL 59
Query: 123 GVVAQQLGKSGKYTAVLCIGAVV 145
           GV AQ LGKSGKY A++C+GAVV
Sbjct: 60  GVTAQALGKSGKYHAIVCLGAVV 82

>pdb|1VSW|A Chain A, Crystal Structure Of Lumazine Synthase From Bacillus Anthracis Length = 153

Iteration: 1
 Score = 84.7 bits (208), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 39/81 (48%), Positives = 56/81 (69%), Gaps = 5/81 (6%)
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 VAQQLGKSGKYTAVLCIGAVV 145
           +A+++  SGKY AV+ +G V+
Sbjct: 61  IAKKMANSGKYDAVITLGTVI 81

>pdb|3MK3|A Chain A, Crystal Structure Of Lumazine Synthase From Salmonella Typhimurium Lt2 Length = 156

Iteration: 1
 Score = 73.2 bits (178), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 31/70 (44%), Positives = 49/70 (70%), Gaps = 1/70 (1%)
Query: 77  RFALVVARFNELVTKLLLEGALETFKKYS-VKEENIDVVWVPGSFEIGVVAQQLGKSGKY 135
           R A+ +ARFN+ +   LL+GA++   +   VK++NI VVWVPG++E+ +  + L KSGKY
Sbjct: 14  RVAITIARFNQFINDSLLDGAVDALTRIGQVKDDNITVVWVPGAYELPLATEALAKSGKY 73
Query: 136 TAVLCIGAVV 145
            AV+ +G V+
Sbjct: 74  DAVVALGTVI 83

>pdb|1RVV|A Chain A, SynthaseRIBOFLAVIN SYNTHASE COMPLEX OF BACILLUS SUBTILIS Length = 154

Iteration: 1
 Score = 70.9 bits (172), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 29/71 (40%), Positives = 47/71 (66%)
Query: 75  GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGK 134
           GL+  +VV RFN+ +T  LL GA +   ++ V   +IDV WVPG+FEI   A+++ ++ K
Sbjct: 12  GLKIGIVVGRFNDFITSKLLSGAEDALLRHGVDTNDIDVAWVPGAFEIPFAAKKMAETKK 71
Query: 135 YTAVLCIGAVV 145
           Y A++ +G V+
Sbjct: 72  YDAIITLGTVI 82

>pdb|1HQK|A Chain A, Crystal Structure Analysis Of Lumazine Synthase From Aquifex Aeolicus Length = 154

Iteration: 1
 Score = 64.7 bits (156), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 30/72 (41%), Positives = 47/72 (65%)
Query: 74  EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSG 133
           EGLRF +V +RFN  +   L+EGA++   ++  +EE+I +V VPGS+EI V A +L +  
Sbjct: 11  EGLRFGIVASRFNHALVDRLVEGAIDCIVRHGGREEDITLVRVPGSWEIPVAAGELARKE 70
Query: 134 KYTAVLCIGAVV 145
              AV+ IG ++
Sbjct: 71  DIDAVIAIGVLI 82

>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 = 46.6 bits (109), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 29/75 (38%), Positives = 44/75 (58%), Gaps = 1/75 (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 KSGKYTAVLCIGAVV 145
               Y AV+ IG ++
Sbjct: 74  ARNTYDAVIGIGVLI 88

>pdb|1KZ4|A Chain A, Mutant Enzyme W63y Lumazine Synthase From S.pombe Length = 159

Iteration: 1
 Score = 46.6 bits (109), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 29/75 (38%), Positives = 44/75 (58%), Gaps = 1/75 (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 KSGKYTAVLCIGAVV 145
               Y AV+ IG ++
Sbjct: 74  ARNTYDAVIGIGVLI 88

>pdb|1KZ6|A Chain A, Mutant Enzyme W63y/l119f Lumazine Synthase From S.pombe Length = 159

Iteration: 1
 Score = 46.6 bits (109), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 29/75 (38%), Positives = 44/75 (58%), Gaps = 1/75 (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 KSGKYTAVLCIGAVV 145
               Y AV+ IG ++
Sbjct: 74  ARNTYDAVIGIGVLI 88

>pdb|1KYV|A Chain A, Lumazine Synthase From S.pombe Bound To Riboflavin Length = 159

Iteration: 1
 Score = 45.8 bits (107), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 29/75 (38%), Positives = 44/75 (58%), Gaps = 1/75 (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 KSGKYTAVLCIGAVV 145
               Y AV+ IG ++
Sbjct: 74  ARNTYDAVIGIGVLI 88

>pdb|1KZ9|A Chain A, Mutant Enzyme L119f Lumazine Synthase From S.pombe Length = 159

Iteration: 1
 Score = 45.8 bits (107), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 29/75 (38%), Positives = 44/75 (58%), Gaps = 1/75 (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 KSGKYTAVLCIGAVV 145
               Y AV+ IG ++
Sbjct: 74  ARNTYDAVIGIGVLI 88

>pdb|4GEF|A Chain A, Product Complex Of Lumazine Synthase From Candida Glabrata Length = 179

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 21/47 (44%), Positives = 31/47 (65%)
Query: 76  LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEI 122
           LR  ++ AR+N ++   L++GA++      VKEENI V  VPGSFE+
Sbjct: 29  LRVGIIHARWNRVIIDALVKGAIDRMLSLGVKEENIIVETVPGSFEL 75

>pdb|2JFB|A Chain A, 3d Structure Of Lumazine Synthase From Candida Albicans Length = 164

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/63 (39%), Positives = 39/63 (61%), Gaps = 2/63 (3%)
Query: 62  AVRHLTGFLTKNEG--LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGS 119
           AV+ L     K +G  LR  ++ AR+N  +   L+ GA++  +++ VKEENI +  VPGS
Sbjct: 2   AVKGLGEVDQKYDGSKLRIGILHARWNRKIIDALVAGAVKRLQEFGVKEENIIIETVPGS 61
Query: 120 FEI 122
           FE+
Sbjct: 62  FEL 64

>pdb|1KZ1|A Chain A, Mutant Enzyme W27g Lumazine Synthase From S.pombe Length = 159

Iteration: 1
 Score = 44.3 bits (103), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 29/75 (38%), Positives = 43/75 (57%), Gaps = 1/75 (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 KSGKYTAVLCIGAVV 145
               Y AV+ IG ++
Sbjct: 74  ARNTYDAVIGIGVLI 88

>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 = 43.9 bits (102), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 23/54 (42%), Positives = 31/54 (57%)
Query: 76  LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQL 129
           LR  +V AR+NE + + LL G         VKE NI V  VPGS+E+ +  Q+L
Sbjct: 16  LRIGIVHARWNETIIEPLLAGTKAKLLACGVKESNIVVQSVPGSWELPIAVQRL 69

>pdb|1EJB|A Chain A, Lumazine Synthase From Saccharomyces Cerevisiae Length = 168

Iteration: 1
 Score = 40.4 bits (93), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 17/47 (36%), Positives = 30/47 (63%)
Query: 76  LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEI 122
           +R  ++ AR+N ++   L++GA+E      V+E NI +  VPGS+E+
Sbjct: 17  IRVGIIHARWNRVIIDALVKGAIERMASLGVEENNIIIETVPGSYEL 63

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	145
1rvv_A	154	Riboflavin synthase; transferase, flavoprotein; HE	6e-37
1hqk_A	154	6,7-dimethyl-8-ribityllumazine synthase; analysi s	2e-36
1c2y_A	156	Protein (lumazine synthase); riboflavin biosynthes	3e-36
1di0_A	158	Lumazine synthase; transferase; 2.70A {Brucella ab	7e-35
3nq4_A	156	6,7-dimethyl-8-ribityllumazine synthase; 30MER, ic	8e-35
1kz1_A	159	6,7-dimethyl-8-ribityllumazine synthase; riboflavi	2e-34
2obx_A	157	DMRL synthase 1, 6,7-dimethyl-8-ribityllumazine sy	2e-34
1ejb_A	168	Lumazine synthase; analysis, inhibitor complex, vi	5e-32
2c92_A	160	6,7-dimethyl-8-ribityllumazine synthase; transfera	3e-28
1c41_A	200	Lumazine synthase; riboflavin biosynthesis, transf	2e-25
2i0f_A	157	6,7-dimethyl-8-ribityllumazine synthase 1; lumazin	3e-25
2b99_A	156	Riboflavin synthase; lumazine riboflavin, transfer	5e-08

>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 =  123 bits (310), Expect = 6e-37
 Identities = 31/83 (37%), Positives = 51/83 (61%), Gaps = 1/83 (1%)

Query: 63  VRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEI 122
           +  + G L    GL+  +VV RFN+ +T  LL GA +   ++ V   +IDV WVPG+FEI
Sbjct: 1   MNIIQGNLV-GTGLKIGIVVGRFNDFITSKLLSGAEDALLRHGVDTNDIDVAWVPGAFEI 59

Query: 123 GVVAQQLGKSGKYTAVLCIGAVV 145
              A+++ ++ KY A++ +G V+
Sbjct: 60  PFAAKKMAETKKYDAIITLGTVI 82

>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 =  121 bits (306), Expect = 2e-36
 Identities = 33/83 (39%), Positives = 52/83 (62%), Gaps = 1/83 (1%)

Query: 63  VRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEI 122
           ++   G LT  EGLRF +V +RFN  +   L+EGA++   ++  +EE+I +V VPGS+EI
Sbjct: 1   MQIYEGKLT-AEGLRFGIVASRFNHALVDRLVEGAIDCIVRHGGREEDITLVRVPGSWEI 59

Query: 123 GVVAQQLGKSGKYTAVLCIGAVV 145
            V A +L +     AV+ IG ++
Sbjct: 60  PVAAGELARKEDIDAVIAIGVLI 82

>1c2y_A Protein (lumazine synthase); riboflavin biosynthesis, transferase; HET: LMZ; 3.30A {Spinacia oleracea} SCOP: c.16.1.1 Length = 156

 Score =  121 bits (305), Expect = 3e-36
 Identities = 55/83 (66%), Positives = 70/83 (84%), Gaps = 1/83 (1%)

Query: 63  VRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEI 122
           +  L G++TK +  RFA+VVARFNE VT+ L+EGAL+TFKKYSV E +IDVVWVPG++E+
Sbjct: 1   MNELEGYVTKAQSFRFAIVVARFNEFVTRRLMEGALDTFKKYSVNE-DIDVVWVPGAYEL 59

Query: 123 GVVAQQLGKSGKYTAVLCIGAVV 145
           GV AQ LGKSGKY A++C+GAVV
Sbjct: 60  GVTAQALGKSGKYHAIVCLGAVV 82

>1di0_A Lumazine synthase; transferase; 2.70A {Brucella abortus} SCOP: c.16.1.1 PDB: 1t13_A* 1xn1_A Length = 158

 Score =  117 bits (296), Expect = 7e-35
 Identities = 14/72 (19%), Positives = 35/72 (48%)

Query: 74  EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSG 133
              + A + AR++  +     +  +      +     +++  VPG++EI + A+ L ++G
Sbjct: 9   TSFKIAFIQARWHADIVDEARKSFVAELAAKTGGSVEVEIFDVPGAYEIPLHAKTLARTG 68

Query: 134 KYTAVLCIGAVV 145
           +Y A++    V+
Sbjct: 69  RYAAIVGAAFVI 80

>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 =  117 bits (296), Expect = 8e-35
 Identities = 31/84 (36%), Positives = 52/84 (61%), Gaps = 2/84 (2%)

Query: 63  VRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKY-SVKEENIDVVWVPGSFE 121
           +  +   +      R A+ +ARFN+ +   LL+GA++   +   VK++NI VVWVPG++E
Sbjct: 1   MNIIKANVA-APDARVAITIARFNQFINDSLLDGAVDALTRIGQVKDDNITVVWVPGAYE 59

Query: 122 IGVVAQQLGKSGKYTAVLCIGAVV 145
           + +  + L KSGKY AV+ +G V+
Sbjct: 60  LPLATEALAKSGKYDAVVALGTVI 83

>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 =  116 bits (293), Expect = 2e-34
 Identities = 28/73 (38%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 74  EGLRFALVVARFNELVTKLLLEGALETF-KKYSVKEENIDVVWVPGSFEIGVVAQQLGKS 132
             LR  +V AR N    + L++GA+ET  +K+ VK ENID+  VPGS+E+    +     
Sbjct: 16  PELRILIVHARGNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSWELPQGIRASIAR 75

Query: 133 GKYTAVLCIGAVV 145
             Y AV+ IG ++
Sbjct: 76  NTYDAVIGIGVLI 88

>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 =  116 bits (293), Expect = 2e-34
 Identities = 22/72 (30%), Positives = 36/72 (50%)

Query: 74  EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSG 133
           E +R A+V AR++  +    +                +DV  VPG++EI + A+ L ++G
Sbjct: 10  ETVRIAVVRARWHADIVDQCVSAFEAEMADIGGDRFAVDVFDVPGAYEIPLHARTLAETG 69

Query: 134 KYTAVLCIGAVV 145
           +Y AVL    VV
Sbjct: 70  RYGAVLGTAFVV 81

>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 =  110 bits (278), Expect = 5e-32
 Identities = 20/77 (25%), Positives = 38/77 (49%), Gaps = 5/77 (6%)

Query: 74  EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQL---- 129
             +R  ++ AR+N ++   L++GA+E      V+E NI +  VPGS+E+    ++     
Sbjct: 15  SKIRVGIIHARWNRVIIDALVKGAIERMASLGVEENNIIIETVPGSYELPWGTKRFVDRQ 74

Query: 130 -GKSGKYTAVLCIGAVV 145
                    V+ IG ++
Sbjct: 75  AKLGKPLDVVIPIGVLI 91

>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 =  101 bits (253), Expect = 3e-28
 Identities = 23/72 (31%), Positives = 42/72 (58%), Gaps = 4/72 (5%)

Query: 74  EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSG 133
            G+R A+V + ++  +   LL+GA +      +  ++  VV V G+ EI VVAQ+L ++ 
Sbjct: 16  SGVRLAIVASSWHGKICDALLDGARKVAAGCGL--DDPTVVRVLGAIEIPVVAQELARN- 72

Query: 134 KYTAVLCIGAVV 145
            + AV+ +G V+
Sbjct: 73  -HDAVVALGVVI 83

>1c41_A Lumazine synthase; riboflavin biosynthesis, transferase; HET: LMZ; 3.10A {Magnaporthe grisea} SCOP: c.16.1.1 Length = 200

 Score = 94.9 bits (236), Expect = 2e-25
 Identities = 27/108 (25%), Positives = 41/108 (37%), Gaps = 36/108 (33%)

Query: 74  EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQL---- 129
             LR  +V AR+NE + + LL G         VKE NI V  VPGS+E+ +  Q+L    
Sbjct: 14  SALRIGIVHARWNETIIEPLLAGTKAKLLACGVKESNIVVQSVPGSWELPIAVQRLYSAS 73

Query: 130 --------------------------------GKSGKYTAVLCIGAVV 145
                                             +G + A++ IG ++
Sbjct: 74  QLQTPSSGPSLSAGDLLGSSTTDLTALPTTTASSTGPFDALIAIGVLI 121

>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 = 93.0 bits (232), Expect = 3e-25
 Identities = 19/77 (24%), Positives = 30/77 (38%), Gaps = 8/77 (10%)

Query: 74  EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSG 133
           +     +V ARF + +   LL+GA     +        DVV VPG+ EI           
Sbjct: 11  DAPHLLIVEARFYDDLADALLDGAKAALDEAGA---TYDVVTVPGALEIPATISFALDGA 67

Query: 134 -----KYTAVLCIGAVV 145
                +Y   + +G V+
Sbjct: 68  DNGGTEYDGFVALGTVI 84

>2b99_A Riboflavin synthase; lumazine riboflavin, transferase; HET: RDL; 2.22A {Methanocaldococcus jannaschii} PDB: 2b98_A* Length = 156

 Score = 48.4 bits (115), Expect = 5e-08
 Identities = 13/70 (18%), Positives = 27/70 (38%), Gaps = 4/70 (5%)

Query: 75  GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGK 134
             +  +V   F  +    +   A++  K+ S     I    VPG  ++ V  ++L +   
Sbjct: 2   TKKVGIVDTTFARVD---MASIAIKKLKELSPNI-KIIRKTVPGIKDLPVACKKLLEEEG 57

Query: 135 YTAVLCIGAV 144
              V+ +G  
Sbjct: 58  CDIVMALGMP 67

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	145
3nq4_A	156	6,7-dimethyl-8-ribityllumazine synthase; 30MER, ic	99.96
1c2y_A	156	Protein (lumazine synthase); riboflavin biosynthes	99.96
1hqk_A	154	6,7-dimethyl-8-ribityllumazine synthase; analysi s	99.96
1rvv_A	154	Riboflavin synthase; transferase, flavoprotein; HE	99.96
1di0_A	158	Lumazine synthase; transferase; 2.70A {Brucella ab	99.96
2obx_A	157	DMRL synthase 1, 6,7-dimethyl-8-ribityllumazine sy	99.96
1kz1_A	159	6,7-dimethyl-8-ribityllumazine synthase; riboflavi	99.95
1ejb_A	168	Lumazine synthase; analysis, inhibitor complex, vi	99.95
2i0f_A	157	6,7-dimethyl-8-ribityllumazine synthase 1; lumazin	99.94
2c92_A	160	6,7-dimethyl-8-ribityllumazine synthase; transfera	99.94
1c41_A	200	Lumazine synthase; riboflavin biosynthesis, transf	99.87
2b99_A	156	Riboflavin synthase; lumazine riboflavin, transfer	99.9
3e61_A	277	Putative transcriptional repressor of ribose OPER;	96.19
3l6u_A	293	ABC-type sugar transport system periplasmic compo;	96.13
3egc_A	291	Putative ribose operon repressor; structural genom	96.13
3k4h_A	292	Putative transcriptional regulator; structural gen	96.02
3jy6_A	276	Transcriptional regulator, LACI family; NYSGXRC, P	95.99
3hs3_A	277	Ribose operon repressor; PSI-II, NYSGXRC, periplas	95.67
3kke_A	303	LACI family transcriptional regulator; structural	95.66
3o74_A	272	Fructose transport system repressor FRUR; dual tra	95.65
3l49_A	291	ABC sugar (ribose) transporter, periplasmic substr	95.46
3k9c_A	289	Transcriptional regulator, LACI family protein; PS	95.45
3o1i_D	304	Periplasmic protein TORT; ligand free, two compone	95.33
3gv0_A	288	Transcriptional regulator, LACI family; transcript	95.19
3huu_A	305	Transcription regulator like protein; PSI-II, NYSG	95.17
3tb6_A	298	Arabinose metabolism transcriptional repressor; tr	95.15
3c3k_A	285	Alanine racemase; structural genomics, protein str	95.14
3miz_A	301	Putative transcriptional regulator protein, LACI f	94.95
3qk7_A	294	Transcriptional regulators; structural genomics, N	94.94
3brq_A	296	HTH-type transcriptional regulator ASCG; transcrip	94.63
1dbq_A	289	Purine repressor; transcription regulation, DNA-bi	94.59
2iks_A	293	DNA-binding transcriptional dual regulator; escher	94.56
2rgy_A	290	Transcriptional regulator, LACI family; 11011J, NY	94.51
3ksm_A	276	ABC-type sugar transport system, periplasmic COMP;	94.46
3uug_A	330	Multiple sugar-binding periplasmic receptor CHVE;	94.42
3hcw_A	295	Maltose operon transcriptional repressor; RNA-bind	94.39
3m9w_A	313	D-xylose-binding periplasmic protein; xylose bindi	94.38
2fep_A	289	Catabolite control protein A; CCPA, transcriptiona	94.37
3lkv_A	302	Uncharacterized conserved domain protein; ATPase b	94.34
3d8u_A	275	PURR transcriptional regulator; APC91343.1, vibrio	94.33
3g85_A	289	Transcriptional regulator (LACI family); transcrip	94.32
3jvd_A	333	Transcriptional regulators; structural genomics, P	94.26
1byk_A	255	Protein (trehalose operon repressor); LACI family,	94.2
3dbi_A	338	Sugar-binding transcriptional regulator, LACI FAM;	94.09
3h75_A	350	Periplasmic sugar-binding domain protein; protein	93.91
2fn9_A	290	Ribose ABC transporter, periplasmic ribose-bindin;	93.86
2o20_A	332	Catabolite control protein A; CCPA, transcriptiona	93.84
3clk_A	290	Transcription regulator; 11017J, PSI-II, NYSGXRC,	93.79
3e3m_A	355	Transcriptional regulator, LACI family; structural	93.75
3ctp_A	330	Periplasmic binding protein/LACI transcriptional;	93.71
3gbv_A	304	Putative LACI-family transcriptional regulator; NY	93.64
3rot_A	297	ABC sugar transporter, periplasmic sugar binding;	93.62
2fqx_A	318	Membrane lipoprotein TMPC; ABC transport system, l	93.59
3bil_A	348	Probable LACI-family transcriptional regulator; st	93.55
3h5o_A	339	Transcriptional regulator GNTR; transcription regu	93.5
3kjx_A	344	Transcriptional regulator, LACI family; LACL famil	93.39
2qu7_A	288	Putative transcriptional regulator; structural gen	93.19
8abp_A	306	L-arabinose-binding protein; binding proteins; HET	93.17
2rjo_A	332	Twin-arginine translocation pathway signal protei;	92.93
3qk7_A	294	Transcriptional regulators; structural genomics, N	92.88
2vk2_A	306	YTFQ, ABC transporter periplasmic-binding protein	92.88
2fvy_A	309	D-galactose-binding periplasmic protein; periplasm	92.84
2hsg_A	332	Glucose-resistance amylase regulator; CCPA, transc	92.81
3g1w_A	305	Sugar ABC transporter; sugar-binding protein, baci	92.78
3gyb_A	280	Transcriptional regulators (LACI-family transcript	92.78
1qpz_A	340	PURA, protein (purine nucleotide synthesis repress	92.65
3lft_A	295	Uncharacterized protein; ABC, ATPase, cassette, L-	92.54
3brs_A	289	Periplasmic binding protein/LACI transcriptional;	92.3
2qh8_A	302	Uncharacterized protein; conserved domain protein,	92.2
3hs3_A	277	Ribose operon repressor; PSI-II, NYSGXRC, periplas	91.97
2dri_A	271	D-ribose-binding protein; sugar transport; HET: RI	91.92
3tb6_A	298	Arabinose metabolism transcriptional repressor; tr	91.78
3k4h_A	292	Putative transcriptional regulator; structural gen	91.58
3d8u_A	275	PURR transcriptional regulator; APC91343.1, vibrio	91.52
2x7x_A	325	Sensor protein; transferase, sensor histidine kina	91.34
3miz_A	301	Putative transcriptional regulator protein, LACI f	91.25
3e61_A	277	Putative transcriptional repressor of ribose OPER;	91.16
3lft_A	295	Uncharacterized protein; ABC, ATPase, cassette, L-	91.04
2ioy_A	283	Periplasmic sugar-binding protein; ribose binding	90.79
3bbl_A	287	Regulatory protein of LACI family; protein structu	90.68
3g85_A	289	Transcriptional regulator (LACI family); transcrip	90.57
3cs3_A	277	Sugar-binding transcriptional regulator, LACI FAM;	90.49
1jye_A	349	Lactose operon repressor; gene regulation, protein	90.16
1gud_A	288	ALBP, D-allose-binding periplasmic protein; peripl	90.1
2qu7_A	288	Putative transcriptional regulator; structural gen	90.05
1pea_A	385	Amidase operon; gene regulator, receptor, binding	90.03
2h0a_A	276	TTHA0807, transcriptional regulator; repressor, st	89.78
3gbv_A	304	Putative LACI-family transcriptional regulator; NY	89.58
3kke_A	303	LACI family transcriptional regulator; structural	89.54
3d02_A	303	Putative LACI-type transcriptional regulator; peri	89.37
2qh8_A	302	Uncharacterized protein; conserved domain protein,	89.26
3hcw_A	295	Maltose operon transcriptional repressor; RNA-bind	89.15
3h5o_A	339	Transcriptional regulator GNTR; transcription regu	88.96
3bbl_A	287	Regulatory protein of LACI family; protein structu	88.64
2rgy_A	290	Transcriptional regulator, LACI family; 11011J, NY	88.56
3brq_A	296	HTH-type transcriptional regulator ASCG; transcrip	88.25
3dbi_A	338	Sugar-binding transcriptional regulator, LACI FAM;	88.12
2hsg_A	332	Glucose-resistance amylase regulator; CCPA, transc	87.84
2h3h_A	313	Sugar ABC transporter, periplasmic sugar-binding p	87.54
3gv0_A	288	Transcriptional regulator, LACI family; transcript	87.45
3jvd_A	333	Transcriptional regulators; structural genomics, P	87.39
2fvy_A	309	D-galactose-binding periplasmic protein; periplasm	87.31
3huu_A	305	Transcription regulator like protein; PSI-II, NYSG	87.09
2fep_A	289	Catabolite control protein A; CCPA, transcriptiona	87.06
2o20_A	332	Catabolite control protein A; CCPA, transcriptiona	87.03
2iks_A	293	DNA-binding transcriptional dual regulator; escher	86.83
1tjy_A	316	Sugar transport protein; protein-ligand complex, s	86.57
2h0a_A	276	TTHA0807, transcriptional regulator; repressor, st	86.55
1usg_A	346	Leucine-specific binding protein; leucine-binding	86.33
3o74_A	272	Fructose transport system repressor FRUR; dual tra	86.18
3lop_A	364	Substrate binding periplasmic protein; protein str	86.11
3rot_A	297	ABC sugar transporter, periplasmic sugar binding;	86.08
3c3k_A	285	Alanine racemase; structural genomics, protein str	85.95
3egc_A	291	Putative ribose operon repressor; structural genom	85.95
3ipc_A	356	ABC transporter, substrate binding protein (amino;	85.87
1jx6_A	342	LUXP protein; protein-ligand complex, signaling pr	85.51
3cs3_A	277	Sugar-binding transcriptional regulator, LACI FAM;	85.47
1qpz_A	340	PURA, protein (purine nucleotide synthesis repress	85.44
3snr_A	362	Extracellular ligand-binding receptor; structural	85.39
1dbq_A	289	Purine repressor; transcription regulation, DNA-bi	84.43
2hqb_A	296	Transcriptional activator of COMK gene; berkeley s	84.27
3gyb_A	280	Transcriptional regulators (LACI-family transcript	84.08
3kjx_A	344	Transcriptional regulator, LACI family; LACL famil	83.96
3hut_A	358	Putative branched-chain amino acid ABC transporter	83.93
4b4k_A	181	N5-carboxyaminoimidazole ribonucleotide mutase; is	83.9
3sg0_A	386	Extracellular ligand-binding receptor; structural	83.71
3g1w_A	305	Sugar ABC transporter; sugar-binding protein, baci	83.69
3h75_A	350	Periplasmic sugar-binding domain protein; protein	83.68
4evq_A	375	Putative ABC transporter subunit, substrate-bindi	83.61
3clk_A	290	Transcription regulator; 11017J, PSI-II, NYSGXRC,	83.08
4fe7_A	412	Xylose operon regulatory protein; HTH_ARAC, helix-	82.88
3k9c_A	289	Transcriptional regulator, LACI family protein; PS	82.77
3e3m_A	355	Transcriptional regulator, LACI family; structural	82.52
4eyg_A	368	Twin-arginine translocation pathway signal; PSI-bi	82.21
2h3h_A	313	Sugar ABC transporter, periplasmic sugar-binding p	81.8
3rpe_A	218	MDAB, modulator of drug activity B; structural gen	81.47
1jye_A	349	Lactose operon repressor; gene regulation, protein	81.46
3ksm_A	276	ABC-type sugar transport system, periplasmic COMP;	81.43
3okf_A	390	3-dehydroquinate synthase; structural genomics, ce	81.41
3l6u_A	293	ABC-type sugar transport system periplasmic compo;	81.01
3brs_A	289	Periplasmic binding protein/LACI transcriptional;	80.94
3i09_A	375	Periplasmic branched-chain amino acid-binding Pro;	80.54
2dri_A	271	D-ribose-binding protein; sugar transport; HET: RI	80.53
3ox4_A	383	Alcohol dehydrogenase 2; iron, NAD, oxidoreductase	80.44
3ors_A	163	N5-carboxyaminoimidazole ribonucleotide mutase; is	80.21
3h5t_A	366	Transcriptional regulator, LACI family; DNA-depend	80.2

>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=99.96  E-value=2.3e-30  Score=202.26  Aligned_cols=82  Identities=38%  Similarity=0.780  Sum_probs=78.2

Q ss_pred             hhhhccccCCCCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCC-CCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEe
Q 032216           63 VRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYS-VKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCI  141 (145)
Q Consensus        63 ~~~~~g~l~~~~~lRIaIVvArfN~~It~~LleGA~~~L~~~G-v~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaL  141 (145)
                      |+.++|++. ++++|||||+||||++|+++|++||+++|+++| +++++|+++||||+||||+++|+|+++++|||||||
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            456788885 889999999999999999999999999999999 999999999999999999999999999999999999


Q ss_pred             eeeC
Q 032216          142 GAVV  145 (145)
Q Consensus       142 G~VI  145 (145)
                      ||||
T Consensus        80 G~VI   83 (156)
T 3nq4_A           80 GTVI   83 (156)
T ss_dssp             EEEE
T ss_pred             eeee
Confidence            9997

>1c2y_A Protein (lumazine synthase); riboflavin biosynthesis, transferase; HET: LMZ; 3.30A {Spinacia oleracea} SCOP: c.16.1.1

Probab=99.96  E-value=5.2e-30  Score=200.17  Aligned_cols=81  Identities=68%  Similarity=1.187  Sum_probs=75.9

Q ss_pred             hhhccccCCCCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeee
Q 032216           64 RHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        64 ~~~~g~l~~~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~  143 (145)
                      +.++|.+++++++|||||+||||++|+++|++||+++|+++|++ ++|+++|||||||||+++|+|+++++|||||||||
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            34567765578899999999999999999999999999999998 89999999999999999999999999999999999


Q ss_pred             eC
Q 032216          144 VV  145 (145)
Q Consensus       144 VI  145 (145)
                      ||
T Consensus        81 VI   82 (156)
T 1c2y_A           81 VV   82 (156)
T ss_dssp             CC
T ss_pred             cc
Confidence            98

>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=99.96  E-value=4.5e-30  Score=199.89  Aligned_cols=80  Identities=40%  Similarity=0.669  Sum_probs=75.5

Q ss_pred             hhccccCCCCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeeee
Q 032216           65 HLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAV  144 (145)
Q Consensus        65 ~~~g~l~~~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~V  144 (145)
                      .++|.+ +++++|||||+||||++|+++|++||+++|+++|+++++|+++|||||||||+++|+|+++++||||||||||
T Consensus         3 ~~~g~~-~~~~~ri~IV~arfn~~I~~~Ll~ga~~~l~~~gv~~~~i~v~~VPGafEiP~aa~~la~~~~yDavIalG~V   81 (154)
T 1hqk_A            3 IYEGKL-TAEGLRFGIVASRFNHALVDRLVEGAIDCIVRHGGREEDITLVRVPGSWEIPVAAGELARKEDIDAVIAIGVL   81 (154)
T ss_dssp             EECCCS-CCTTCCEEEEEECTTHHHHHHHHHHHHHHHHHTTCCGGGEEEEEESSGGGHHHHHHHHHTCTTCCEEEEEEEE
T ss_pred             cccCCc-CCCCCEEEEEEeeCcHHHHHHHHHHHHHHHHHcCCCccceEEEECCcHHHHHHHHHHHHhcCCCCEEEEeeee
Confidence            356665 4788999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             C
Q 032216          145 V  145 (145)
Q Consensus       145 I  145 (145)
                      |
T Consensus        82 I   82 (154)
T 1hqk_A           82 I   82 (154)
T ss_dssp             E
T ss_pred             e
Confidence            7

>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=99.96  E-value=4.7e-30  Score=199.92  Aligned_cols=80  Identities=39%  Similarity=0.770  Sum_probs=75.5

Q ss_pred             hhccccCCCCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeeee
Q 032216           65 HLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAV  144 (145)
Q Consensus        65 ~~~g~l~~~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~V  144 (145)
                      .++|.+ +++++|||||+||||++|+++|++||+++|+++|+++++|+++|||||||||+++|+|+++++||||||||||
T Consensus         3 ~~~g~~-~~~~~ri~IV~arfn~~I~~~Ll~ga~~~l~~~gv~~~~i~v~~VPGafEiP~aa~~la~~~~yDavIaLG~V   81 (154)
T 1rvv_A            3 IIQGNL-VGTGLKIGIVVGRFNDFITSKLLSGAEDALLRHGVDTNDIDVAWVPGAFEIPFAAKKMAETKKYDAIITLGTV   81 (154)
T ss_dssp             EECCCS-CCTTCCEEEEEESTTHHHHHHHHHHHHHHHHHTTCCGGGEEEEEESSGGGHHHHHHHHHHTSCCSEEEEEEEE
T ss_pred             cccCCc-CCCCCEEEEEEEeCcHHHHHHHHHHHHHHHHHcCCCccceEEEECCcHHHHHHHHHHHHhcCCCCEEEEeeee
Confidence            355665 4788999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             C
Q 032216          145 V  145 (145)
Q Consensus       145 I  145 (145)
                      |
T Consensus        82 I   82 (154)
T 1rvv_A           82 I   82 (154)
T ss_dssp             E
T ss_pred             e
Confidence            7

>1di0_A Lumazine synthase; transferase; 2.70A {Brucella abortus} SCOP: c.16.1.1 PDB: 1t13_A* 1xn1_A

Probab=99.96  E-value=2.2e-29  Score=196.74  Aligned_cols=74  Identities=19%  Similarity=0.399  Sum_probs=70.7

Q ss_pred             CCCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeeeeC
Q 032216           72 KNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVV  145 (145)
Q Consensus        72 ~~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~VI  145 (145)
                      +++++|||||+||||++|+++|++||+++|+++|+++++|+++||||+||||+++|+|+++++|||||||||||
T Consensus         7 ~~~~~ri~IV~arfn~~I~~~Ll~gA~~~l~~~gv~~~~i~v~~VPGafEiP~aa~~la~~~~yDavIaLG~VI   80 (158)
T 1di0_A            7 NKTSFKIAFIQARWHADIVDEARKSFVAELAAKTGGSVEVEIFDVPGAYEIPLHAKTLARTGRYAAIVGAAFVI   80 (158)
T ss_dssp             --CCEEEEEEEECTTHHHHHHHHHHHHHHHHHHHTTSEEEEEEEESSGGGHHHHHHHHHHTSCCSEEEEEEECC
T ss_pred             CCCCCEEEEEEEeCcHHHHHHHHHHHHHHHHHcCCCccceEEEECCcHHHHHHHHHHHHhcCCCCEEEEeeccc
Confidence            46789999999999999999999999999999999988999999999999999999999999999999999998

>2obx_A DMRL synthase 1, 6,7-dimethyl-8-ribityllumazine synthase 1, riboflavin S; alpha-beta, transferase; HET: INI; 2.53A {Mesorhizobium loti}

Probab=99.96  E-value=2.2e-29  Score=196.50  Aligned_cols=74  Identities=30%  Similarity=0.408  Sum_probs=72.0

Q ss_pred             CCCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeeeeC
Q 032216           72 KNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVV  145 (145)
Q Consensus        72 ~~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~VI  145 (145)
                      +++++|||||+||||++|+++|++||+++|+++|+++++|+++||||+||||+++|+|+++++|||||||||||
T Consensus         8 ~~~~~ri~IV~arfn~~I~~~Ll~gA~~~l~~~Gv~~~~i~v~~VPGafEiP~aa~~la~~~~yDavIaLG~VI   81 (157)
T 2obx_A            8 DYETVRIAVVRARWHADIVDQCVSAFEAEMADIGGDRFAVDVFDVPGAYEIPLHARTLAETGRYGAVLGTAFVV   81 (157)
T ss_dssp             SCCCEEEEEEEECTTHHHHHHHHHHHHHHHHHHHTTSEEEEEEEESSGGGHHHHHHHHHHHTCCSEEEEEEECC
T ss_pred             CCCCCEEEEEEeeCcHHHHHHHHHHHHHHHHHcCCCccceEEEECCcHHHHHHHHHHHHhcCCCCEEEEeeccc
Confidence            57789999999999999999999999999999999988999999999999999999999999999999999998

>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=99.95  E-value=6.5e-29  Score=194.55  Aligned_cols=74  Identities=38%  Similarity=0.463  Sum_probs=71.7

Q ss_pred             CCCCCEEEEEEeeecHHHHHHHHHHHHHHHHH-CCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeeeeC
Q 032216           72 KNEGLRFALVVARFNELVTKLLLEGALETFKK-YSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVV  145 (145)
Q Consensus        72 ~~~~lRIaIVvArfN~~It~~LleGA~~~L~~-~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~VI  145 (145)
                      +++++|||||+||||++|+++|++||+++|++ +|+++++|+++||||+||||+++|+|+++++|||||||||||
T Consensus        14 ~~~~~riaIV~arfn~~I~~~Ll~ga~~~l~~~~Gv~~~~i~v~~VPGafEiP~aa~~la~~~~yDavIaLG~VI   88 (159)
T 1kz1_A           14 KGPELRILIVHARGNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSWELPQGIRASIARNTYDAVIGIGVLI   88 (159)
T ss_dssp             CCTTCCEEEEECCTTHHHHHHHHHHHHHHHHHHHCCCGGGEEEEECSSGGGHHHHHHHHHHHSCCSEEEEEEEEE
T ss_pred             CCCCCEEEEEEeeCcHHHHHHHHHHHHHHHHHHcCCCccceEEEECCcHHHHHHHHHHHHhcCCCCEEEEecccc
Confidence            46789999999999999999999999999999 999999999999999999999999999999999999999997

>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=99.95  E-value=2.2e-28  Score=192.85  Aligned_cols=74  Identities=27%  Similarity=0.493  Sum_probs=71.1

Q ss_pred             CCCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhh-----cCCCcEEEEeeeeC
Q 032216           72 KNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGK-----SGKYTAVLCIGAVV  145 (145)
Q Consensus        72 ~~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~-----s~~yDAVIaLG~VI  145 (145)
                      +++++|||||+||||++|+++|++||+++|+++|+.+++|+++||||+||||+++|+|++     +++|||||||||||
T Consensus        13 ~~~~~ri~IV~arfn~~I~~~Ll~gA~~~L~~~Gv~~~~i~v~~VPGafEiP~aak~la~~~~~~~~~yDavIaLG~VI   91 (168)
T 1ejb_A           13 DGSKIRVGIIHARWNRVIIDALVKGAIERMASLGVEENNIIIETVPGSYELPWGTKRFVDRQAKLGKPLDVVIPIGVLI   91 (168)
T ss_dssp             CCTTCCEEEEECCTTHHHHHHHHHHHHHHHHHTTCCGGGEEEEECSSGGGHHHHHHHHHHHHHHTTCCCSEEEEEEEEE
T ss_pred             CCCCCEEEEEEEeCcHHHHHHHHHHHHHHHHHcCCCccceEEEECCcHHHHHHHHHHHHhhccccCCCcCEEEEecccc
Confidence            457799999999999999999999999999999999999999999999999999999998     78999999999997

>2i0f_A 6,7-dimethyl-8-ribityllumazine synthase 1; lumazine synthase RIBH1, transferase; 2.22A {Brucella abortus} PDB: 2f59_A 2o6h_A*

Probab=99.94  E-value=6.2e-27  Score=182.80  Aligned_cols=68  Identities=28%  Similarity=0.448  Sum_probs=65.7

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhc-----CCCcEEEEeeeeC
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKS-----GKYTAVLCIGAVV  145 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s-----~~yDAVIaLG~VI  145 (145)
                      ++|||||+||||++|+++|++||+++|+++|   ++|+++|||||||||+++|+|+++     ++|||||||||||
T Consensus        12 ~~ri~IV~arfn~~I~~~Ll~gA~~~l~~~G---~~i~v~~VPGafEiP~aa~~la~~~~~~~~~yDavIaLG~VI   84 (157)
T 2i0f_A           12 APHLLIVEARFYDDLADALLDGAKAALDEAG---ATYDVVTVPGALEIPATISFALDGADNGGTEYDGFVALGTVI   84 (157)
T ss_dssp             CCEEEEEEECSSHHHHHHHHHHHHHHHHHTT---CEEEEEEESSGGGHHHHHHHHHHHHHTTCCCCSEEEEEEEEE
T ss_pred             CcEEEEEEEeCcHHHHHHHHHHHHHHHHHcC---CCeEEEECCcHHHHHHHHHHHHhhccccCCCCCEEEEeeeee
Confidence            4899999999999999999999999999999   489999999999999999999998     9999999999997

>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=99.94  E-value=1.5e-26  Score=181.19  Aligned_cols=70  Identities=33%  Similarity=0.525  Sum_probs=66.7

Q ss_pred             CCCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeeeeC
Q 032216           72 KNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVV  145 (145)
Q Consensus        72 ~~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~VI  145 (145)
                      +++++|||||+||||++|+++|++||+++|+++|++  +|+++||||+||||+++|+|++  +|||||||||||
T Consensus        14 ~~~~~ri~IV~arfn~~I~~~Ll~gA~~~l~~~G~~--~i~v~~VPGafEiP~aak~la~--~yDavIaLG~VI   83 (160)
T 2c92_A           14 DASGVRLAIVASSWHGKICDALLDGARKVAAGCGLD--DPTVVRVLGAIEIPVVAQELAR--NHDAVVALGVVI   83 (160)
T ss_dssp             CCTTCCEEEEEECSSHHHHHHHHHHHHHHHHHTTCS--CCEEEEESSGGGHHHHHHHHHT--SCSEEEEEEEEE
T ss_pred             CCCCCEEEEEEEeCcHHHHHHHHHHHHHHHHHcCCC--ceEEEECCcHHHHHHHHHHHHh--cCCEEEEEeeee
Confidence            467899999999999999999999999999999986  8999999999999999999996  599999999997

>1c41_A Lumazine synthase; riboflavin biosynthesis, transferase; HET: LMZ; 3.10A {Magnaporthe grisea} SCOP: c.16.1.1

Probab=99.87  E-value=1.8e-27  Score=192.49  Aligned_cols=74  Identities=36%  Similarity=0.596  Sum_probs=70.7

Q ss_pred             CCCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhh--------------------
Q 032216           72 KNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGK--------------------  131 (145)
Q Consensus        72 ~~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~--------------------  131 (145)
                      +++++|||||++|||++|+++|++||+++|+++|+.+++|++++|||+||||+++|+|++                    
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            457899999999999999999999999999999999999999999999999999999997                    


Q ss_pred             ----------------cCCCcEEEEeeeeC
Q 032216          132 ----------------SGKYTAVLCIGAVV  145 (145)
Q Consensus       132 ----------------s~~yDAVIaLG~VI  145 (145)
                                      +++|||||||||||
T Consensus        92 ~~~~~~~~~~~~~~~~~~~~DAVIaLG~VI  121 (200)
T 1c41_A           92 SSTTDLTALPTTTASSTGPFDALIAIGVLI  121 (200)
Confidence                            57899999999997

>2b99_A Riboflavin synthase; lumazine riboflavin, transferase; HET: RDL; 2.22A {Methanocaldococcus jannaschii} PDB: 2b98_A*

Probab=99.90  E-value=1.5e-24  Score=169.59  Aligned_cols=65  Identities=20%  Similarity=0.227  Sum_probs=62.2

Q ss_pred             CEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeeee
Q 032216           76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAV  144 (145)
Q Consensus        76 lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~V  144 (145)
                      +|||||+||||+   +.|++||+++|+++|+.++ |+++|||||||||+++|+|+++++||||||||||
T Consensus         3 ~ri~IV~arfn~---~~Ll~gA~~~L~~~G~~~~-i~~~~VPGafEiP~aak~la~~~~yDavIaLG~V   67 (156)
T 2b99_A            3 KKVGIVDTTFAR---VDMASIAIKKLKELSPNIK-IIRKTVPGIKDLPVACKKLLEEEGCDIVMALGMP   67 (156)
T ss_dssp             CEEEEEEESSCS---SCCHHHHHHHHHHHCTTCE-EEEEEESSGGGHHHHHHHHHHHSCCSEEEEEECC
T ss_pred             cEEEEEEEecch---HHHHHHHHHHHHHcCCCCe-EEEEECCcHHHHHHHHHHHHhcCCCCEEEEeccc
Confidence            699999999999   8999999999999999865 8889999999999999999999999999999997

>3e61_A Putative transcriptional repressor of ribose OPER; structural genomics, DNA-binding, transcripti regulation, PSI-2; 2.00A {Staphylococcus saprophyticus subsp}

Probab=96.19  E-value=0.02  Score=43.26  Aligned_cols=67  Identities=7%  Similarity=-0.003  Sum_probs=49.9

Q ss_pred             CCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEee
Q 032216           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        73 ~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG  142 (145)
                      .+..+||++...+.......+++|+.+.++++|+.   +.+....+..+--...-+.+.+.++||||..+
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            45568999999988888889999999999999984   66777777655554443444567899999865

>3l6u_A ABC-type sugar transport system periplasmic compo; structural genomics, nysgrc, target 11006S, PSI-2, protein S initiative; 1.90A {Exiguobacterium sibiricum}

Probab=96.13  E-value=0.025  Score=42.91  Aligned_cols=68  Identities=9%  Similarity=-0.092  Sum_probs=48.2

Q ss_pred             CCCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH-HHHHHhhcCCCcEEEEeee
Q 032216           72 KNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV-VAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        72 ~~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl-aak~La~s~~yDAVIaLG~  143 (145)
                      ..+..+||++...+.......+++|+.+.++++|+.   +.+....+..+-.. .++.+. +.++||||..+.
T Consensus         5 ~~~~~~Ig~i~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~l~-~~~vdgiI~~~~   73 (293)
T 3l6u_A            5 SPKRNIVGFTIVNDKHEFAQRLINAFKAEAKANKYE---ALVATSQNSRISEREQILEFV-HLKVDAIFITTL   73 (293)
T ss_dssp             ----CEEEEEESCSCSHHHHHHHHHHHHHHHHTTCE---EEEEECSSCHHHHHHHHHHHH-HTTCSEEEEECS
T ss_pred             CCCCcEEEEEEecCCcHHHHHHHHHHHHHHHHcCCE---EEEECCCCCHHHHHHHHHHHH-HcCCCEEEEecC
Confidence            355679999999998888889999999999999983   55555554444332 233343 578999998764

>3egc_A Putative ribose operon repressor; structural genomics, unknown function, DNA-binding, transcri transcription regulation, PSI-2; 2.35A {Burkholderia thailandensis}

Probab=96.13  E-value=0.025  Score=43.16  Aligned_cols=69  Identities=6%  Similarity=-0.030  Sum_probs=51.7

Q ss_pred             CCCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeee
Q 032216           72 KNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        72 ~~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~  143 (145)
                      .++..+||++...........+++|+.+.++++|+.   +.++...+..|-....-..+.+.++||||..+.
T Consensus         5 ~~~~~~Igvv~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~l~~~~vdgiIi~~~   73 (291)
T 3egc_A            5 SKRSNVVGLIVSDIENVFFAEVASGVESEARHKGYS---VLLANTAEDIVREREAVGQFFERRVDGLILAPS   73 (291)
T ss_dssp             --CCCEEEEEESCTTSHHHHHHHHHHHHHHHHTTCE---EEEEECTTCHHHHHHHHHHHHHTTCSEEEECCC
T ss_pred             cCCCcEEEEEECCCcchHHHHHHHHHHHHHHHCCCE---EEEEeCCCCHHHHHHHHHHHHHCCCCEEEEeCC
Confidence            355679999999888888888999999999999973   666766666555443333445679999998764

>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=96.02  E-value=0.012  Score=44.58  Aligned_cols=69  Identities=9%  Similarity=0.004  Sum_probs=49.1

Q ss_pred             CCCCCEEEEEEee-----ecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeee
Q 032216           72 KNEGLRFALVVAR-----FNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        72 ~~~~lRIaIVvAr-----fN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~  143 (145)
                      ..+..+||+|...     ++......+++|+.++++++|+.   +.+......-|.-..+-+.+.+.++||||.++.
T Consensus         5 ~~~~~~Igvi~~~~~~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~~~~~~vdgiIi~~~   78 (292)
T 3k4h_A            5 NQTTKTLGLVMPSSASKAFQNPFFPEVIRGISSFAHVEGYA---LYMSTGETEEEIFNGVVKMVQGRQIGGIILLYS   78 (292)
T ss_dssp             --CCCEEEEECSSCHHHHTTSTHHHHHHHHHHHHHHHTTCE---EEECCCCSHHHHHHHHHHHHHTTCCCEEEESCC
T ss_pred             cCCCCEEEEEecCCccccccCHHHHHHHHHHHHHHHHcCCE---EEEEeCCCCHHHHHHHHHHHHcCCCCEEEEeCC
Confidence            3556799999999     77777788999999999999973   444444444444333444455789999998764

>3jy6_A Transcriptional regulator, LACI family; NYSGXRC, PSI-II, protein S initiative, structural genomics; 1.97A {Lactobacillus brevis}

Probab=95.99  E-value=0.037  Score=41.95  Aligned_cols=68  Identities=10%  Similarity=0.059  Sum_probs=52.3

Q ss_pred             CCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeee
Q 032216           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        73 ~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~  143 (145)
                      ++..+||+|...+.......+++|..+.++++|+.   +.+....+..+-....-+.+.+.++||||..+.
T Consensus         5 ~~s~~Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~~~~l~~~~vdgiIi~~~   72 (276)
T 3jy6_A            5 QSSKLIAVIVANIDDYFSTELFKGISSILESRGYI---GVLFDANADIEREKTLLRAIGSRGFDGLILQSF   72 (276)
T ss_dssp             CCCCEEEEEESCTTSHHHHHHHHHHHHHHHTTTCE---EEEEECTTCHHHHHHHHHHHHTTTCSEEEEESS
T ss_pred             CCCcEEEEEeCCCCchHHHHHHHHHHHHHHHCCCE---EEEEeCCCCHHHHHHHHHHHHhCCCCEEEEecC
Confidence            45679999999998888889999999999999973   666666665554443333445679999998864

>3hs3_A Ribose operon repressor; PSI-II, NYSGXRC, periplasmic binding protein, structural genomics, protein structure initiative; 1.60A {Lactobacillus acidophilus}

Probab=95.67  E-value=0.046  Score=41.67  Aligned_cols=68  Identities=7%  Similarity=0.069  Sum_probs=48.6

Q ss_pred             CCCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCC-eEEEEecccchHHHHHHHHhhcCCCcEEEEee
Q 032216           72 KNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEEN-IDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        72 ~~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~-I~vv~VPGAfELPlaak~La~s~~yDAVIaLG  142 (145)
                      ..+..+||++...+....-..+++|+.++++++|+   + +.+....+..+-....-..+.+.++||||..+
T Consensus         7 ~~~~~~Igvi~~~~~~~~~~~~~~gi~~~a~~~g~---~~~~~~~~~~~~~~~~~~~~~l~~~~vdgiIi~~   75 (277)
T 3hs3_A            7 QKKSKMIGIIIPDLNNRFYAQIIDGIQEVIQKEGY---TALISFSTNSDVKKYQNAIINFENNNVDGIITSA   75 (277)
T ss_dssp             -CCCCEEEEEESCTTSHHHHHHHHHHHHHHHHTTC---EEEEEECSSCCHHHHHHHHHHHHHTTCSEEEEEC
T ss_pred             cCCCCEEEEEeCCCCChhHHHHHHHHHHHHHHCCC---CEEEEEeCCCChHHHHHHHHHHHhCCCCEEEEcc
Confidence            35567999999998888888899999999999997   3 44444444444443333334567999999864

>3kke_A LACI family transcriptional regulator; structural genomics, DNA-binding, transcription regulation, PSI-2; 2.20A {Mycobacterium smegmatis str}

Probab=95.66  E-value=0.038  Score=42.71  Aligned_cols=68  Identities=15%  Similarity=0.072  Sum_probs=50.8

Q ss_pred             CCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeee
Q 032216           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        73 ~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~  143 (145)
                      .+..+||+|...+....-..+++|+.++++++|+.   +.+....+.-|-....-+.+...++||||..+.
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            44568999999888777788999999999999984   677777776666554444455789999998764

>3o74_A Fructose transport system repressor FRUR; dual transcriptional regulator, DNA, transcription; 2.00A {Pseudomonas putida} PDB: 3o75_A*

Probab=95.65  E-value=0.054  Score=40.47  Aligned_cols=65  Identities=6%  Similarity=0.027  Sum_probs=49.5

Q ss_pred             CEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeee
Q 032216           76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        76 lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~  143 (145)
                      .+||++...++......+++|+.+.++++|..   +.++...+..|-....-+.+.+.++||||..+.
T Consensus         3 ~~Igvi~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~l~~~~vdgiIi~~~   67 (272)
T 3o74_A            3 RTLGFILPDLENPSYARIAKQLEQGARARGYQ---LLIASSDDQPDSERQLQQLFRARRCDALFVASC   67 (272)
T ss_dssp             CEEEEEESCTTCHHHHHHHHHHHHHHHHTTCE---EEEEECTTCHHHHHHHHHHHHHTTCSEEEECCC
T ss_pred             eEEEEEeCCCcChhHHHHHHHHHHHHHHCCCE---EEEEeCCCCHHHHHHHHHHHHHcCCCEEEEecC
Confidence            58999999998888889999999999999984   666666665554433333344578999998764

>3l49_A ABC sugar (ribose) transporter, periplasmic substrate-binding subunit; sugar binding/transporter, structural genomics, PSI; HET: UNL; 2.30A {Rhodobacter sphaeroides}

Probab=95.46  E-value=0.062  Score=40.64  Aligned_cols=66  Identities=11%  Similarity=-0.029  Sum_probs=47.4

Q ss_pred             CCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH-HHHHHhhcCCCcEEEEee
Q 032216           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV-VAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        73 ~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl-aak~La~s~~yDAVIaLG  142 (145)
                      .+..+||+|...++......+++|+.+.++++|+.   +.+....+..+--. .++.+ ...++||||..+
T Consensus         3 ~~~~~Ig~i~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~l-~~~~vdgiIi~~   69 (291)
T 3l49_A            3 LEGKTIGITAIGTDHDWDLKAYQAQIAEIERLGGT---AIALDAGRNDQTQVSQIQTL-IAQKPDAIIEQL   69 (291)
T ss_dssp             CTTCEEEEEESCCSSHHHHHHHHHHHHHHHHTTCE---EEEEECTTCHHHHHHHHHHH-HHHCCSEEEEES
T ss_pred             CCCcEEEEEeCCCCChHHHHHHHHHHHHHHHcCCE---EEEEcCCCCHHHHHHHHHHH-HHcCCCEEEEeC
Confidence            34569999999988888889999999999999973   55555444433222 22333 346899999765

>3k9c_A Transcriptional regulator, LACI family protein; PSI-II, 11026W, structural genomics, PR structure initiative; 2.14A {Rhodococcus jostii}

Probab=95.45  E-value=0.063  Score=41.19  Aligned_cols=67  Identities=15%  Similarity=0.138  Sum_probs=48.5

Q ss_pred             CCCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeee
Q 032216           72 KNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        72 ~~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~  143 (145)
                      .++..+||+|. .++...-..+++|+.+.++++|+.   +.+....+.-+---.++.| .+.++||||..+.
T Consensus         9 ~~~~~~Igvi~-~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~l-~~~~vdgiIi~~~   75 (289)
T 3k9c_A            9 QASSRLLGVVF-ELQQPFHGDLVEQIYAAATRRGYD---VMLSAVAPSRAEKVAVQAL-MRERCEAAILLGT   75 (289)
T ss_dssp             ----CEEEEEE-ETTCHHHHHHHHHHHHHHHHTTCE---EEEEEEBTTBCHHHHHHHH-TTTTEEEEEEETC
T ss_pred             cCCCCEEEEEE-ecCCchHHHHHHHHHHHHHHCCCE---EEEEeCCCCHHHHHHHHHH-HhCCCCEEEEECC
Confidence            34556899999 888778888999999999999974   6666666655533344445 4578999998764

>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=95.33  E-value=0.045  Score=41.58  Aligned_cols=67  Identities=9%  Similarity=-0.018  Sum_probs=48.1

Q ss_pred             CCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecc--cchHHH-HHHHHhhcCCCcEEEEeee
Q 032216           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPG--SFEIGV-VAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        73 ~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPG--AfELPl-aak~La~s~~yDAVIaLG~  143 (145)
                      ++..+||+|....+...-..+++|+.+.++++|+.   +.++...+  ..+--. .++.+. +.++||||..+.
T Consensus         3 ~~~~~Igvi~~~~~~~~~~~~~~g~~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~~~~~-~~~vdgiii~~~   72 (304)
T 3o1i_D            3 GSDEKICAIYPHLKDSYWLSVNYGMVSEAEKQGVN---LRVLEAGGYPNKSRQEQQLALCT-QWGANAIILGTV   72 (304)
T ss_dssp             --CCEEEEEESCSCSHHHHHHHHHHHHHHHHHTCE---EEEEECSSTTCHHHHHHHHHHHH-HHTCSEEEECCS
T ss_pred             CCCcEEEEEeCCCCCcHHHHHHHHHHHHHHHcCCe---EEEEcCCCCCCHHHHHHHHHHHH-HcCCCEEEEeCC
Confidence            45679999999998888889999999999999983   66666665  333332 223333 468999998753

>3gv0_A Transcriptional regulator, LACI family; transcription regulator, PSI-II, structural genomics structure initiative; 2.35A {Agrobacterium tumefaciens str}

Probab=95.19  E-value=0.022  Score=43.60  Aligned_cols=69  Identities=16%  Similarity=0.043  Sum_probs=48.2

Q ss_pred             CCCCCEEEEEEeeecH--HHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeee
Q 032216           72 KNEGLRFALVVARFNE--LVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        72 ~~~~lRIaIVvArfN~--~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~  143 (145)
                      .++..+||+|...++.  .....+++|+.+.++++|..   +.+....+.-+-...+..++.+.++||||..+.
T Consensus         5 ~~~s~~Igvv~~~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~l~~~~vdgiIi~~~   75 (288)
T 3gv0_A            5 TGKTNVIALVLSVDEELMGFTSQMVFGITEVLSTTQYH---LVVTPHIHAKDSMVPIRYILETGSADGVIISKI   75 (288)
T ss_dssp             --CCCEEEEECBCCCCSSCHHHHHHHHHHHHHTTSSCE---EEECCBSSGGGTTHHHHHHHHHTCCSEEEEESC
T ss_pred             cCCCCEEEEEecCCccccHHHHHHHHHHHHHHHHcCCE---EEEecCCcchhHHHHHHHHHHcCCccEEEEecC
Confidence            3556789999997653  45667999999999999973   555555544444444555566789999998763

>3huu_A Transcription regulator like protein; PSI-II, NYSGXRC, LAC I, STR genomics, protein structure initiative; 1.95A {Staphylococcus haemolyticus}

Probab=95.17  E-value=0.035  Score=42.82  Aligned_cols=68  Identities=10%  Similarity=0.049  Sum_probs=49.4

Q ss_pred             CCCCEEEEEEee-----ecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeee
Q 032216           73 NEGLRFALVVAR-----FNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        73 ~~~lRIaIVvAr-----fN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~  143 (145)
                      .+..+||+|...     +....-..+++|+.++++++|..   +.+....+.-|-....-+.+.+.++||||.++.
T Consensus        20 ~~~~~Igvi~~~~~~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~l~~~~vdgiIi~~~   92 (305)
T 3huu_A           20 NKTLTIGLIQKSSAPEIRQNPFNSDVLNGINQACNVRGYS---TRMTVSENSGDLYHEVKTMIQSKSVDGFILLYS   92 (305)
T ss_dssp             -CCCEEEEECSCCSHHHHTSHHHHHHHHHHHHHHHHHTCE---EEECCCSSHHHHHHHHHHHHHTTCCSEEEESSC
T ss_pred             CCCCEEEEEeCCCccccccCcHHHHHHHHHHHHHHHCCCE---EEEEeCCCChHHHHHHHHHHHhCCCCEEEEeCC
Confidence            445689999998     77777778999999999999973   555555554444444444456789999998764

>3tb6_A Arabinose metabolism transcriptional repressor; transcription regulation, arabinose binding, DNA binding Pro; HET: ARB; 2.21A {Bacillus subtilis}

Probab=95.15  E-value=0.062  Score=40.54  Aligned_cols=65  Identities=3%  Similarity=-0.023  Sum_probs=49.6

Q ss_pred             CEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeee
Q 032216           76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        76 lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~  143 (145)
                      .+||+|...+.......+++|..++++++|+.   +.++...+..|-....-+.+.+.++||||..++
T Consensus        16 ~~Igvi~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~l~~~~vdgiIi~~~   80 (298)
T 3tb6_A           16 KTIGVLTTYISDYIFPSIIRGIESYLSEQGYS---MLLTSTNNNPDNERRGLENLLSQHIDGLIVEPT   80 (298)
T ss_dssp             CEEEEEESCSSSTTHHHHHHHHHHHHHHTTCE---EEEEECTTCHHHHHHHHHHHHHTCCSEEEECCS
T ss_pred             ceEEEEeCCCCchHHHHHHHHHHHHHHHCCCE---EEEEeCCCChHHHHHHHHHHHHCCCCEEEEecc
Confidence            68999999988878888999999999999983   666666665554443333334679999998764

>3c3k_A Alanine racemase; structural genomics, protein structure initiative, NEW YORK research center for structural genomics, nysgxrc; 1.99A {Actinobacillus succinogenes}

Probab=95.14  E-value=0.092  Score=40.05  Aligned_cols=67  Identities=12%  Similarity=0.109  Sum_probs=45.7

Q ss_pred             CCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH-HHHHHHhhcCCCcEEEEeee
Q 032216           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        73 ~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP-laak~La~s~~yDAVIaLG~  143 (145)
                      ++..+||++...+....-..+++|+.+.++++|..   +.+....+..+-- -.++.+. +.++||||..+.
T Consensus         6 ~~~~~Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~~~~l~-~~~vdgiI~~~~   73 (285)
T 3c3k_A            6 AKTGMLLVMVSNIANPFCAAVVKGIEKTAEKNGYR---ILLCNTESDLARSRSCLTLLS-GKMVDGVITMDA   73 (285)
T ss_dssp             -CCCEEEEEESCTTSHHHHHHHHHHHHHHHHTTCE---EEEEECTTCHHHHHHHTHHHH-TTCCSEEEECCC
T ss_pred             CCCCEEEEEeCCCCCchHHHHHHHHHHHHHHcCCE---EEEEeCCCCHHHHHHHHHHHH-hCCCCEEEEeCC
Confidence            45668999999887777888999999999999973   4444433322211 1233343 578999998753

>3miz_A Putative transcriptional regulator protein, LACI family; LACL family, protein structure initiative II (PSI II), NYSGXRC, structural genomics; 1.91A {Rhizobium etli}

Probab=94.95  E-value=0.045  Score=42.02  Aligned_cols=69  Identities=14%  Similarity=0.100  Sum_probs=48.1

Q ss_pred             CCCCCEEEEEEeeecHHHHH-HHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeee
Q 032216           72 KNEGLRFALVVARFNELVTK-LLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        72 ~~~~lRIaIVvArfN~~It~-~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~  143 (145)
                      ..+..+||+|...+....-. .+++|+.+.++++|+.   +.+....+..|-....-+.+.+.++||||..+.
T Consensus        10 ~~~s~~Igvi~~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~l~~~~vdGiIi~~~   79 (301)
T 3miz_A           10 SSRSNTFGIITDYVSTTPYSVDIVRGIQDWANANGKT---ILIANTGGSSEREVEIWKMFQSHRIDGVLYVTM   79 (301)
T ss_dssp             --CCCEEEEEESSTTTCCSCHHHHHHHHHHHHHTTCE---EEEEECTTCHHHHHHHHHHHHHTTCSEEEEEEE
T ss_pred             hCCCCEEEEEeCCCcCcccHHHHHHHHHHHHHHCCCE---EEEEeCCCChHHHHHHHHHHHhCCCCEEEEecC
Confidence            34556899999877644444 7899999999999974   666666665555444333445679999998764

>3qk7_A Transcriptional regulators; structural genomics, NEW YORK structural genomix research CO NYSGXRC, PSI-2, protein structur initiative; 2.70A {Yersinia pestis}

Probab=94.94  E-value=0.066  Score=41.17  Aligned_cols=67  Identities=10%  Similarity=-0.061  Sum_probs=47.5

Q ss_pred             CCCCEEEEEEe----eecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeee
Q 032216           73 NEGLRFALVVA----RFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        73 ~~~lRIaIVvA----rfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~  143 (145)
                      ++..+||+|..    .+....-..+++|+.+.++++|..   +.+..... -+-...+.+++.+.++||||..+.
T Consensus         4 ~~s~~Igvi~~~~~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~-~~~~~~~~~~l~~~~vdGiIi~~~   74 (294)
T 3qk7_A            4 GRTDAIALAYPSRPRVLNNSTFLEMISWIGIELGKRGLD---LLLIPDEP-GEKYQSLIHLVETRRVDALIVAHT   74 (294)
T ss_dssp             -CCCEEEEEEESCSGGGSCHHHHHHHHHHHHHHHHTTCE---EEEEEECT-TCCCHHHHHHHHHTCCSEEEECSC
T ss_pred             CccceEEEEecCCCccccChhHHHHHHHHHHHHHHCCCE---EEEEeCCC-hhhHHHHHHHHHcCCCCEEEEeCC
Confidence            45568999998    677667778999999999999974   55655544 222233334445679999998764

>3brq_A HTH-type transcriptional regulator ASCG; transcriptional repressor structure escherichia coli, struct genomics, PSI-2; HET: FRU; 2.00A {Escherichia coli}

Probab=94.63  E-value=0.1  Score=39.23  Aligned_cols=67  Identities=16%  Similarity=0.039  Sum_probs=42.9

Q ss_pred             CCCCEEEEEEee--ecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH-HHHHHHhhcCCCcEEEEeee
Q 032216           73 NEGLRFALVVAR--FNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        73 ~~~lRIaIVvAr--fN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP-laak~La~s~~yDAVIaLG~  143 (145)
                      .+..+||++...  +.......+++|+.+.++++|..   +.+....+..|-- -.++.+. +.++||||..+.
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            445689999988  77667778999999999999973   4444333222211 2334444 468999998763

>1dbq_A Purine repressor; transcription regulation, DNA-binding regulatory protein; 2.20A {Escherichia coli} SCOP: c.93.1.1 PDB: 1jhz_A

Probab=94.59  E-value=0.13  Score=38.88  Aligned_cols=67  Identities=7%  Similarity=0.023  Sum_probs=44.2

Q ss_pred             CCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH-HHHHHHhhcCCCcEEEEeee
Q 032216           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        73 ~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP-laak~La~s~~yDAVIaLG~  143 (145)
                      ++..+||++...+.......+++|+.+.++++|..   +.+....+..|-- -.++.+. +.++||||..+.
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            45568999998887777788999999999999973   4444333322221 1234443 568999998753

>2iks_A DNA-binding transcriptional dual regulator; escherichia coli structural genomics, PSI-2, protein structure initiative; 1.85A {Escherichia coli}

Probab=94.56  E-value=0.18  Score=38.49  Aligned_cols=67  Identities=6%  Similarity=0.006  Sum_probs=46.0

Q ss_pred             CCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchH-HHHHHHHhhcCCCcEEEEeee
Q 032216           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEI-GVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        73 ~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfEL-Plaak~La~s~~yDAVIaLG~  143 (145)
                      .+..+||++...+....-..+++|+.+.++++|+.   +.+....+..+- --.++.+. +.++||||..+.
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            45568999999887777788999999999999973   444433332221 12234444 468999998763

>2rgy_A Transcriptional regulator, LACI family; 11011J, NYSGXRC, transctiptional regulator, SUG binding protein, structural genomics, PSI-2; 2.05A {Burkholderia phymatum}

Probab=94.51  E-value=0.1  Score=39.91  Aligned_cols=67  Identities=13%  Similarity=-0.009  Sum_probs=46.2

Q ss_pred             CCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH----HHHHHhhcCCCcEEEEeee
Q 032216           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV----VAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        73 ~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl----aak~La~s~~yDAVIaLG~  143 (145)
                      ++..+||++...+....-..+++|+.++++++|..   +.+....+..+--.    .++.+. +.++||||..+.
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            45568999998887777778999999999999973   44444433333222    344444 568999998763

>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=94.46  E-value=0.054  Score=40.39  Aligned_cols=64  Identities=11%  Similarity=-0.021  Sum_probs=46.4

Q ss_pred             CEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH---HHHHHhhcCCCcEEEEee
Q 032216           76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        76 lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl---aak~La~s~~yDAVIaLG  142 (145)
                      .|||+|...........+++|+.+.++++|+.   +.+.......+..-   .++.+.+.+++||||..+
T Consensus         1 ~~Ig~i~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~~~i~~l~~~~~vdgii~~~   67 (276)
T 3ksm_A            1 PKLLLVLKGDSNAYWRQVYLGAQKAADEAGVT---LLHRSTKDDGDIAGQIQILSYHLSQAPPDALILAP   67 (276)
T ss_dssp             CEEEEECSCSSSTHHHHHHHHHHHHHHHHTCE---EEECCCSSTTCHHHHHHHHHHHHHHSCCSEEEECC
T ss_pred             CeEEEEeCCCCChHHHHHHHHHHHHHHHcCCE---EEEECCCCCCCHHHHHHHHHHHHHhCCCCEEEEeC
Confidence            48999999888888888999999999999973   44444333343332   445566555599999876

>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=94.42  E-value=0.11  Score=40.01  Aligned_cols=66  Identities=3%  Similarity=-0.037  Sum_probs=46.7

Q ss_pred             CCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH-HHHHHhhcCCCcEEEEeee
Q 032216           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV-VAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        74 ~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl-aak~La~s~~yDAVIaLG~  143 (145)
                      +..+||+|........-..+++|+.+.++++|+.   +.+....+..+--. .++.+.+ .++||||..+.
T Consensus         2 ~~~~Igvi~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~i~~~~~-~~vdgiIi~~~   68 (330)
T 3uug_A            2 DKGSVGIAMPTKSSARWIDDGNNIVKQLQEAGYK---TDLQYADDDIPNQLSQIENMVT-KGVKVLVIASI   68 (330)
T ss_dssp             CCCEEEEEECCSSSTHHHHHHHHHHHHHHHTTCE---EEEEECTTCHHHHHHHHHHHHH-HTCSEEEECCS
T ss_pred             CCcEEEEEeCCCcchHHHHHHHHHHHHHHHcCCE---EEEeeCCCCHHHHHHHHHHHHH-cCCCEEEEEcC
Confidence            4568999999987667777999999999999973   55665444443332 2333433 57999998753

>3hcw_A Maltose operon transcriptional repressor; RNA-binding, PSI-2, NYSGXRC, STRU genomics, protein structure initiative; 2.20A {Staphylococcus aureus subsp}

Probab=94.39  E-value=0.076  Score=40.82  Aligned_cols=68  Identities=13%  Similarity=0.010  Sum_probs=47.1

Q ss_pred             CCCCEEEEEEe-----eecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeee
Q 032216           73 NEGLRFALVVA-----RFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        73 ~~~lRIaIVvA-----rfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~  143 (145)
                      .+..+||+|..     .+....-..+++|+.++++++|..   +.+....+..|....+-+.+.+.++||||..+.
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            44568999993     444555667999999999999973   445544444444444444456789999998763

>3m9w_A D-xylose-binding periplasmic protein; xylose binding protein, conformational changes, SUGA protein; 2.15A {Escherichia coli} PDB: 3m9x_A* 3ma0_A*

Probab=94.38  E-value=0.094  Score=40.43  Aligned_cols=66  Identities=8%  Similarity=-0.044  Sum_probs=45.3

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~  143 (145)
                      ..+||+|...+....-..+++|+.++++++|+.   +.+....+.-+--...-+.+.+.++||||..+.
T Consensus         2 ~~~Igvi~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~i~~l~~~~vdgiIi~~~   67 (313)
T 3m9w_A            2 EVKIGMAIDDLRLERWQKDRDIFVKKAESLGAK---VFVQSANGNEETQMSQIENMINRGVDVLVIIPY   67 (313)
T ss_dssp             -CEEEEEESCCSSSTTHHHHHHHHHHHHHTSCE---EEEEECTTCHHHHHHHHHHHHHTTCSEEEEECS
T ss_pred             CcEEEEEeCCCCChHHHHHHHHHHHHHHHcCCE---EEEECCCCCHHHHHHHHHHHHHcCCCEEEEeCC
Confidence            358999998876666677999999999999973   555555544443332222233568999998763

>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=94.37  E-value=0.18  Score=38.64  Aligned_cols=67  Identities=9%  Similarity=0.152  Sum_probs=45.8

Q ss_pred             CCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH-HHHHHHhhcCCCcEEEEeee
Q 032216           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        73 ~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP-laak~La~s~~yDAVIaLG~  143 (145)
                      ++..+||+|+..+....-..+++|+.++++++|..   +.+....+..+-- -.++.+. +.++||||..+.
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            45568999999888777888999999999999973   4444433332221 1233443 568999998763

>3lkv_A Uncharacterized conserved domain protein; ATPase binding cassette, PSI, MCSG, structural genomics, Pro structure initiative; HET: PHE; 2.20A {Vibrio cholerae}

Probab=94.34  E-value=0.32  Score=38.45  Aligned_cols=69  Identities=14%  Similarity=0.129  Sum_probs=48.8

Q ss_pred             CCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCC-CCeEE--EEecccc-hHHHHHHHHhhcCCCcEEEEeee
Q 032216           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKE-ENIDV--VWVPGSF-EIGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        73 ~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~-e~I~v--v~VPGAf-ELPlaak~La~s~~yDAVIaLG~  143 (145)
                      ++..||||+.---|..+ |...+|.++.|++.|..+ +|+++  .+--|-. .+.-.+++|. +.++|.||++|.
T Consensus         6 ~~~~~igi~q~~~hp~l-d~~~~G~~~~L~~~G~~~g~nv~~~~~~a~gd~~~~~~~~~~l~-~~~~DlIiai~t   78 (302)
T 3lkv_A            6 AKTAKVAVSQIVEHPAL-DATRQGLLDGLKAKGYEEGKNLEFDYKTAQGNPAIAVQIARQFV-GENPDVLVGIAT   78 (302)
T ss_dssp             -CCEEEEEEESCCCHHH-HHHHHHHHHHHHHTTCCBTTTEEEEEEECTTCHHHHHHHHHHHH-TTCCSEEEEESH
T ss_pred             cCCceEEEEEeecChhH-HHHHHHHHHHHHhhCcccCCcEEEEEEeCCCCHHHHHHHHHHHH-hcCCcEEEEcCC
Confidence            56779999987778776 678999999999999753 34544  4445532 2344455555 468999999873

>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=94.33  E-value=0.12  Score=38.71  Aligned_cols=65  Identities=14%  Similarity=0.171  Sum_probs=44.5

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH-HHHHHhhcCCCcEEEEeee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV-VAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl-aak~La~s~~yDAVIaLG~  143 (145)
                      ..+||+|...+.......+++|+.+.++++|..   +.+....+..+--. .++.+ .+.++||||..+.
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            358999999887777778999999999999974   33443333332222 23334 3578999998763

>3g85_A Transcriptional regulator (LACI family); transcription regulator, PSI-II, structural genomics structure initiative; 1.84A {Clostridium acetobutylicum atcc 824}

Probab=94.32  E-value=0.037  Score=41.97  Aligned_cols=69  Identities=14%  Similarity=0.167  Sum_probs=45.9

Q ss_pred             CCCCCEEEEEEe-eecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeee
Q 032216           72 KNEGLRFALVVA-RFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        72 ~~~~lRIaIVvA-rfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~  143 (145)
                      ..+..+||++.. .+.......+++|+.++++++|..   +.++...+..+--...-+.+.+.++||||..+.
T Consensus         8 ~~~~~~Igvi~~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~l~~~~vdgiIi~~~   77 (289)
T 3g85_A            8 SQSKPTIALYWSSDISVNIISRFLRGLQSKLAKQNYN---YNVVICPYKTDCLHLEKGISKENSFDAAIIANI   77 (289)
T ss_dssp             ---CCEEEEEEETTSCGGGHHHHHHHHHHHHHHTTTC---SEEEEEEECTTCGGGCGGGSTTTCCSEEEESSC
T ss_pred             cCCCceEEEEeccccchHHHHHHHHHHHHHHHHcCCe---EEEEecCCCchhHHHHHHHHhccCCCEEEEecC
Confidence            355678999998 677777778999999999999985   455544443322111222334679999998764

>3jvd_A Transcriptional regulators; structural genomics, PSI-2, sugar binding protein, transcrip regulation, protein structure initiative; 2.30A {Corynebacterium glutamicum}

Probab=94.26  E-value=0.11  Score=41.00  Aligned_cols=67  Identities=9%  Similarity=0.014  Sum_probs=48.3

Q ss_pred             CCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeee
Q 032216           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        73 ~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~  143 (145)
                      .+..+||++...+....-..+++|+.+.++++|..   +.+....+ -|-....-..+...++||||..+.
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            44568999999988778888999999999999974   66666665 444333333334568999998753

>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=94.20  E-value=0.24  Score=36.86  Aligned_cols=64  Identities=19%  Similarity=0.156  Sum_probs=44.2

Q ss_pred             CEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH-HHHHHhhcCCCcEEEEeee
Q 032216           76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV-VAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        76 lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl-aak~La~s~~yDAVIaLG~  143 (145)
                      .+||+|........-..+++|..+.++++|..   +.+....+..+--. .++.+ .+.++||||..++
T Consensus         3 ~~Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~~~~l-~~~~vdgiI~~~~   67 (255)
T 1byk_A            3 KVVAIIVTRLDSLSENLAVQTMLPAFYEQGYD---PIMMESQFSPQLVAEHLGVL-KRRNIDGVVLFGF   67 (255)
T ss_dssp             CEEEEEESCTTCHHHHHHHHHHHHHHHHHTCE---EEEEECTTCHHHHHHHHHHH-HTTTCCEEEEECC
T ss_pred             CEEEEEeCCCCCccHHHHHHHHHHHHHHcCCE---EEEEeCCCcHHHHHHHHHHH-HhcCCCEEEEecC
Confidence            47999998877777778999999999999973   44444333222222 23333 4578999998764

>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=94.09  E-value=0.19  Score=39.37  Aligned_cols=66  Identities=17%  Similarity=0.052  Sum_probs=47.4

Q ss_pred             CCCCEEEEEEee--ecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH-HHHHHhhcCCCcEEEEee
Q 032216           73 NEGLRFALVVAR--FNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV-VAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        73 ~~~lRIaIVvAr--fN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl-aak~La~s~~yDAVIaLG  142 (145)
                      .+..+||++...  +....-..+++|+.++++++|+.   +.+....+..|--. .++.| ...++||||..+
T Consensus        59 ~~~~~Igvi~~~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~l-~~~~vdgiIi~~  127 (338)
T 3dbi_A           59 KSTQTLGLVVTNTLYHGIYFSELLFHAARMAEEKGRQ---LLLADGKHSAEEERQAIQYL-LDLRCDAIMIYP  127 (338)
T ss_dssp             -CCSEEEEEECTTTTSTTHHHHHHHHHHHHHHHTTCE---EEEEECTTSHHHHHHHHHHH-HHTTCSEEEECC
T ss_pred             CCCCEEEEEecCCcccChhHHHHHHHHHHHHHHCCCE---EEEEeCCCChHHHHHHHHHH-HhCCCCEEEEeC
Confidence            456789999998  77667778999999999999973   55555544444433 33444 356899999875

>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=93.91  E-value=0.27  Score=38.63  Aligned_cols=65  Identities=5%  Similarity=-0.032  Sum_probs=48.2

Q ss_pred             CCEEEEEEeeecH-HHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH-HHHHHHhhc-CCCcEEEEee
Q 032216           75 GLRFALVVARFNE-LVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKS-GKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~-~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP-laak~La~s-~~yDAVIaLG  142 (145)
                      ..+||+|...+.. ..-..+.+|+.+.++++|+.   +.+....+..+-- -.++.+.++ .++||||..+
T Consensus         3 ~~~Ig~i~p~~~~~~f~~~~~~g~~~~a~~~g~~---~~~~~~~~~~~~~~~~i~~~i~~~~~vDgiIi~~   70 (350)
T 3h75_A            3 LTSVVFLNPGNSTETFWVSYSQFMQAAARDLGLD---LRILYAERDPQNTLQQARELFQGRDKPDYLMLVN   70 (350)
T ss_dssp             CCEEEEEECSCTTCHHHHHHHHHHHHHHHHHTCE---EEEEECTTCHHHHHHHHHHHHHSSSCCSEEEEEC
T ss_pred             CCEEEEECCCCCCChHHHHHHHHHHHHHHHcCCe---EEEEECCCCHHHHHHHHHHHHhcCCCCCEEEEeC
Confidence            4699999998865 67788999999999999983   5666555544432 234556665 7999999875

>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=93.86  E-value=0.26  Score=37.25  Aligned_cols=64  Identities=13%  Similarity=0.100  Sum_probs=44.1

Q ss_pred             CEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH-HHHHHHhhcCCCcEEEEeee
Q 032216           76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        76 lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP-laak~La~s~~yDAVIaLG~  143 (145)
                      .+||++...+.......+++|+.+.++++|..   +.+....+..+-- -.++.+. +.++||||..+.
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            48999998887777778999999999999973   4444433332222 2234444 468999998653

>2o20_A Catabolite control protein A; CCPA, transcriptional regulator, helix-turn-helix, transcrip; 1.90A {Lactococcus lactis}

Probab=93.84  E-value=0.26  Score=38.58  Aligned_cols=67  Identities=9%  Similarity=0.129  Sum_probs=46.4

Q ss_pred             CCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH-HHHHHHhhcCCCcEEEEeee
Q 032216           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        73 ~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP-laak~La~s~~yDAVIaLG~  143 (145)
                      .+..+||++...+....-..+++|..+.++++|..   +.+....+..+-- -.++.+. ..++||||..+.
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            45568999998887777778999999999999973   5455444333221 2334444 468999998763

>3clk_A Transcription regulator; 11017J, PSI-II, NYSGXRC, dimer, structural genomics, protein structure initiative; 2.08A {Lactobacillus plantarum WCFS1}

Probab=93.79  E-value=0.11  Score=39.70  Aligned_cols=67  Identities=15%  Similarity=0.067  Sum_probs=42.0

Q ss_pred             CCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEE-EecccchHH-HHHHHHhhcCCCcEEEEeee
Q 032216           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVV-WVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        73 ~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv-~VPGAfELP-laak~La~s~~yDAVIaLG~  143 (145)
                      .+..+||++...+.......+++|+.+.++++|+.   +.+. ...+..|-- -.++.+. +.++||||..+.
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            45568999998887777778999999999999973   4333 222222211 1234443 568999998763

>3e3m_A Transcriptional regulator, LACI family; structural genomics, DNA-binding, plasmid, transcription regulation, PSI-2; 1.60A {Silicibacter pomeroyi}

Probab=93.75  E-value=0.27  Score=38.95  Aligned_cols=67  Identities=9%  Similarity=0.018  Sum_probs=46.8

Q ss_pred             CCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHH-HHHHhhcCCCcEEEEeee
Q 032216           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVV-AQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        73 ~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPla-ak~La~s~~yDAVIaLG~  143 (145)
                      .+...||++...+....-..+++|..+.++++|..   +.+....+..|--.. ++.| ...++||||..+.
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            44568999999888777788999999999999984   555555444443322 2333 3568999998763

>3ctp_A Periplasmic binding protein/LACI transcriptional; structural genomics, protein structure initiative; HET: XLF; 1.41A {Alkaliphilus metalliredigens}

Probab=93.71  E-value=0.27  Score=38.40  Aligned_cols=66  Identities=11%  Similarity=0.039  Sum_probs=44.9

Q ss_pred             CCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH-HHHHHHhhcCCCcEEEEeee
Q 032216           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        73 ~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP-laak~La~s~~yDAVIaLG~  143 (145)
                      .+..+||++...+....-..+++|+.+.++++|..   +.+....+..|-- -.++.|. +.++|||| .+.
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            44568999998877666778999999999999973   5555444333322 2234444 46899999 763

>3gbv_A Putative LACI-family transcriptional regulator; NYSGXRC, PSI-II, 11231J, structur genomics, protein structure initiative; 2.20A {Bacteroides fragilis}

Probab=93.64  E-value=0.21  Score=37.71  Aligned_cols=68  Identities=13%  Similarity=0.185  Sum_probs=46.2

Q ss_pred             CCCCCEEEEEEeee-cHHHHHHHHHHHHHHHHHC-CCCCCCeEEEEec-ccchHHH---HHHHHhhcCCCcEEEEeee
Q 032216           72 KNEGLRFALVVARF-NELVTKLLLEGALETFKKY-SVKEENIDVVWVP-GSFEIGV---VAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        72 ~~~~lRIaIVvArf-N~~It~~LleGA~~~L~~~-Gv~~e~I~vv~VP-GAfELPl---aak~La~s~~yDAVIaLG~  143 (145)
                      ..+..+||++...+ ....-..+++|+.+.++++ |..   +.+.... ...+..-   .++.+ ...++||||..+.
T Consensus         5 ~~~~~~Igvi~~~~~~~~~~~~~~~gi~~~a~~~~g~~---~~~~~~~~~~~~~~~~~~~i~~l-~~~~vdgiii~~~   78 (304)
T 3gbv_A            5 SNKKYTFACLLPKHLEGEYWTDVQKGIREAVTTYSDFN---ISANITHYDPYDYNSFVATSQAV-IEEQPDGVMFAPT   78 (304)
T ss_dssp             --CCEEEEEEEECCCTTSHHHHHHHHHHHHHHHTGGGC---EEEEEEEECSSCHHHHHHHHHHH-HTTCCSEEEECCS
T ss_pred             cCCcceEEEEecCCCCchHHHHHHHHHHHHHHHHHhCC---eEEEEEcCCCCCHHHHHHHHHHH-HhcCCCEEEECCC
Confidence            35667999999998 6667778999999999999 763   5665542 2222222   23333 4579999998764

>3rot_A ABC sugar transporter, periplasmic sugar binding; nysgrc, PSI-biology, structural genomics; 1.91A {Legionella pneumophila subsp}

Probab=93.62  E-value=0.17  Score=38.83  Aligned_cols=65  Identities=11%  Similarity=0.098  Sum_probs=44.7

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEec--ccchHHH-HHHHHhhcCCCcEEEEeee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVP--GSFEIGV-VAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VP--GAfELPl-aak~La~s~~yDAVIaLG~  143 (145)
                      ..+||+|....+......+++|+.+.++++|+.   +.+....  +..+--. .++.+. ..++||||..+.
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            569999999987777888999999999999974   4444333  2222222 233333 467999997653

>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=93.59  E-value=0.31  Score=38.82  Aligned_cols=66  Identities=12%  Similarity=0.122  Sum_probs=44.3

Q ss_pred             CCCEEEEEEe--eecH-HHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeee
Q 032216           74 EGLRFALVVA--RFNE-LVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        74 ~~lRIaIVvA--rfN~-~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~  143 (145)
                      +..+||+|..  ..++ .....+.+|..+.++++|+.   +.++.....-+.--.++.|++ .++|+||+.|.
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            4579999996  5554 56677889999999999974   444333222222234666664 57999999863

>3bil_A Probable LACI-family transcriptional regulator; structural genomics, unknown function, PSI-2, protein structure initiative; 2.50A {Corynebacterium glutamicum atcc 13032}

Probab=93.55  E-value=0.23  Score=39.41  Aligned_cols=67  Identities=9%  Similarity=0.048  Sum_probs=45.0

Q ss_pred             CCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH-HHHHHhhcCCCcEEEEeee
Q 032216           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV-VAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        73 ~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl-aak~La~s~~yDAVIaLG~  143 (145)
                      .+..+||+|...+....-..+++|+.+.++++|..   +.+....+..|--. .++.|. ..++||||..+.
T Consensus        64 ~~s~~Igvi~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~l~-~~~vdgiI~~~~  131 (348)
T 3bil_A           64 SRSNTIGVIVPSLINHYFAAMVTEIQSTASKAGLA---TIITNSNEDATTMSGSLEFLT-SHGVDGIICVPN  131 (348)
T ss_dssp             ----CEEEEESCSSSHHHHHHHHHHHHHHHHTTCC---EEEEECTTCHHHHHHHHHHHH-HTTCSCEEECCC
T ss_pred             CCCCEEEEEeCCCCCcHHHHHHHHHHHHHHHcCCE---EEEEeCCCCHHHHHHHHHHHH-hCCCCEEEEeCC
Confidence            34457999998887777778999999999999984   55555444333222 234443 568999998763

>3h5o_A Transcriptional regulator GNTR; transcription regulator, GNTR,chromobacterium violaceum, PSI, SGX, DNA-binding; 2.30A {Chromobacterium violaceum}

Probab=93.50  E-value=0.2  Score=39.29  Aligned_cols=68  Identities=9%  Similarity=-0.030  Sum_probs=46.7

Q ss_pred             CCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeee
Q 032216           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        73 ~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~  143 (145)
                      .+...||++...+....-..+++|+.+.+.++|..   +.+....+..+--...-+.+...++||||..+.
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            44568999998877666677999999999999974   555555555444433323334679999998763

>3kjx_A Transcriptional regulator, LACI family; LACL family, protein structure initiative II(PSI II), NYSGXRC, structural genomics; 2.33A {Silicibacter pomeroyi}

Probab=93.39  E-value=0.24  Score=39.00  Aligned_cols=68  Identities=15%  Similarity=0.070  Sum_probs=47.3

Q ss_pred             CCCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHH-HHHHhhcCCCcEEEEeee
Q 032216           72 KNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVV-AQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        72 ~~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPla-ak~La~s~~yDAVIaLG~  143 (145)
                      ..+..+||++...+....-..+++|+.++++++|+.   +.+....+..|--.. ++.+ .+.++||||..+.
T Consensus        65 ~~~~~~Ig~i~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~i~~l-~~~~vdGiIi~~~  133 (344)
T 3kjx_A           65 SNRVNLVAVIIPSLSNMVFPEVLTGINQVLEDTELQ---PVVGVTDYLPEKEEKVLYEM-LSWRPSGVIIAGL  133 (344)
T ss_dssp             TSCCSEEEEEESCSSSSSHHHHHHHHHHHHTSSSSE---EEEEECTTCHHHHHHHHHHH-HTTCCSEEEEECS
T ss_pred             cCCCCEEEEEeCCCCcHHHHHHHHHHHHHHHHCCCE---EEEEeCCCCHHHHHHHHHHH-HhCCCCEEEEECC
Confidence            345568999998877666678999999999999974   555554444443322 2333 4578999998763

>2qu7_A Putative transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 2.30A {Staphylococcus saprophyticus subsp}

Probab=93.19  E-value=0.2  Score=37.99  Aligned_cols=66  Identities=11%  Similarity=0.078  Sum_probs=43.8

Q ss_pred             CCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH-HHHHHHhhcCCCcEEEEeee
Q 032216           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        73 ~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP-laak~La~s~~yDAVIaLG~  143 (145)
                      ++..+||++... ....-..+++|+.+.++++|+.   +.+....+..|-- -.++.+. +.++||||..+.
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            445689999988 6566677999999999999973   4444433332221 2334444 468999998753

>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=93.17  E-value=0.26  Score=37.45  Aligned_cols=64  Identities=13%  Similarity=-0.007  Sum_probs=43.8

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH-HHHHHHhhcCCCcEEEEeee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP-laak~La~s~~yDAVIaLG~  143 (145)
                      ..+||++........-..+++|+.++++++|+.   +.++.. +.-+-- -.++.+.+ .++||||..+.
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            468999999887777788999999999999973   433332 222211 22344444 46999998753

>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=92.93  E-value=0.33  Score=37.84  Aligned_cols=68  Identities=13%  Similarity=-0.033  Sum_probs=46.7

Q ss_pred             CCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH-HHHHHHhhcC-CCcEEEEeee
Q 032216           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSG-KYTAVLCIGA  143 (145)
Q Consensus        73 ~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP-laak~La~s~-~yDAVIaLG~  143 (145)
                      ++..+||+|...+....-..+++|+.+.++++|+.   +.+....+..+-- -.++.+.+.+ ++||||..+.
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            34568999999887777788999999999999984   5555444333322 2344455433 2999998753

>3qk7_A Transcriptional regulators; structural genomics, NEW YORK structural genomix research CO NYSGXRC, PSI-2, protein structur initiative; 2.70A {Yersinia pestis}

Probab=92.88  E-value=0.57  Score=35.84  Aligned_cols=68  Identities=16%  Similarity=0.010  Sum_probs=46.2

Q ss_pred             CCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH-HHHHHHhhc-CCCcEEEEe
Q 032216           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKS-GKYTAVLCI  141 (145)
Q Consensus        74 ~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP-laak~La~s-~~yDAVIaL  141 (145)
                      ...||+++....+....+.-.+|..+.|+++|+..+...++...-..|-- -+++++++. .++|||+|.
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            34599999988776666666899999999999874443344444333332 234555554 689999985

>2vk2_A YTFQ, ABC transporter periplasmic-binding protein YTFQ; transport protein, galactofuranose; HET: GZL; 1.20A {Escherichia coli}

Probab=92.88  E-value=0.29  Score=37.63  Aligned_cols=65  Identities=8%  Similarity=-0.081  Sum_probs=44.9

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH-HHHHHHhhcCCCcEEEEeee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP-laak~La~s~~yDAVIaLG~  143 (145)
                      ..+||++...........+++|+.++++++|+.   +.+....+..+-- -.++.|. +.++||||..+.
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   4444433322221 2234444 457999998753

>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=92.84  E-value=0.39  Score=36.42  Aligned_cols=63  Identities=6%  Similarity=-0.055  Sum_probs=42.8

Q ss_pred             CEEEEEEeeecHHHHHHHHHHHHHHHHHCCC-CCCCeEEEEecccchHH-HHHHHHhhcCCCcEEEEee
Q 032216           76 LRFALVVARFNELVTKLLLEGALETFKKYSV-KEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        76 lRIaIVvArfN~~It~~LleGA~~~L~~~Gv-~~e~I~vv~VPGAfELP-laak~La~s~~yDAVIaLG  142 (145)
                      .+||+|...+.......+++|+.+.++++|. .   +.+....+..+-- -.++.+. +.++||||..+
T Consensus         3 ~~Igvi~~~~~~~~~~~~~~gi~~~a~~~g~~~---~~~~~~~~~~~~~~~~~~~~~-~~~vdgiii~~   67 (309)
T 2fvy_A            3 TRIGVTIYKYDDNFMSVVRKAIEQDAKAAPDVQ---LLMNDSQNDQSKQNDQIDVLL-AKGVKALAINL   67 (309)
T ss_dssp             EEEEEEESCTTSHHHHHHHHHHHHHHHTCTTEE---EEEEECTTCHHHHHHHHHHHH-HTTCSEEEECC
T ss_pred             cEEEEEeccCCcHHHHHHHHHHHHHHHhcCCeE---EEEecCCCCHHHHHHHHHHHH-HcCCCEEEEeC
Confidence            4799999888777778899999999999995 3   4444333322221 1233343 46899999865

>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=92.81  E-value=0.21  Score=39.05  Aligned_cols=67  Identities=6%  Similarity=0.136  Sum_probs=43.1

Q ss_pred             CCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH-HHHHHhhcCCCcEEEEeee
Q 032216           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV-VAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        73 ~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl-aak~La~s~~yDAVIaLG~  143 (145)
                      .+..+||++...+....-..+++|+.+.++++|..   +.+....+..+--. .++.+ ...++||||..+.
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            45568999998876666777999999999999973   44444333222221 23333 3578999998763

>3g1w_A Sugar ABC transporter; sugar-binding protein, bacillus halod target 11229F, transport protein, structural genomics; 2.02A {Bacillus halodurans c-125}

Probab=92.78  E-value=0.17  Score=38.57  Aligned_cols=64  Identities=11%  Similarity=0.077  Sum_probs=44.1

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH---HHHHHhhcCCCcEEEEeee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl---aak~La~s~~yDAVIaLG~  143 (145)
                      +.+|++|........-..+++|+.+.++++|+.   +.++ .+...+.--   .++.+. ..++||||..++
T Consensus         4 ~~~I~~i~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~-~~~~~~~~~~~~~i~~l~-~~~vdgiIi~~~   70 (305)
T 3g1w_A            4 NETYMMITFQSGMDYWKRCLKGFEDAAQALNVT---VEYR-GAAQYDIQEQITVLEQAI-AKNPAGIAISAI   70 (305)
T ss_dssp             -CEEEEEESSTTSTHHHHHHHHHHHHHHHHTCE---EEEE-ECSSSCHHHHHHHHHHHH-HHCCSEEEECCS
T ss_pred             CceEEEEEccCCChHHHHHHHHHHHHHHHcCCE---EEEe-CCCcCCHHHHHHHHHHHH-HhCCCEEEEcCC
Confidence            569999999988888888999999999999973   3332 233333222   223333 468999998763

>3gyb_A Transcriptional regulators (LACI-family transcriptional regulatory protein); protein structure initiative II(PSI II), nysgxrc; 1.60A {Corynebacterium glutamicum}

Probab=92.78  E-value=0.069  Score=40.29  Aligned_cols=65  Identities=9%  Similarity=0.070  Sum_probs=45.2

Q ss_pred             CCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH-HHHHHHhhcCCCcEEEEeee
Q 032216           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        73 ~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP-laak~La~s~~yDAVIaLG~  143 (145)
                      ++..+||++...++...-..+++|+.++++++|+.   +.++... ..|-- -.++.| .+.++|||| ++.
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            44568999998888777788999999999999973   4454444 22211 123333 467999999 764

>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=92.65  E-value=0.56  Score=36.77  Aligned_cols=67  Identities=7%  Similarity=0.023  Sum_probs=45.7

Q ss_pred             CCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH-HHHHHHhhcCCCcEEEEeee
Q 032216           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        73 ~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP-laak~La~s~~yDAVIaLG~  143 (145)
                      .+..+||++...+....-..+++|+.+.++++|..   +.+....+..|-- -.++.|. ..++||||..+.
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            44568999998877777778999999999999973   4444333332221 1234443 568999998763

>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=92.54  E-value=0.69  Score=35.61  Aligned_cols=65  Identities=12%  Similarity=0.202  Sum_probs=41.6

Q ss_pred             CEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEE--EecccchH-HHHHHHHhhcCCCcEEEEee
Q 032216           76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVV--WVPGSFEI-GVVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        76 lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv--~VPGAfEL-Plaak~La~s~~yDAVIaLG  142 (145)
                      .+||||.. .+...-..+++|..+.|.++|....++.+.  ..-+..|- .-.+++| .+.++|+||++|
T Consensus         3 ~~Igvi~~-~~~p~~~~i~~gi~~~l~~~gy~g~~v~l~~~~~~~~~~~~~~~~~~l-~~~~vDgII~~~   70 (295)
T 3lft_A            3 AKIGVLQF-VSHPSLDLIYKGIQDGLAEEGYKDDQVKIDFMNSEGDQSKVATMSKQL-VANGNDLVVGIA   70 (295)
T ss_dssp             EEEEEEEC-SCCHHHHHHHHHHHHHHHHTTCCGGGEEEEEEECTTCHHHHHHHHHHH-TTSSCSEEEEES
T ss_pred             eEEEEEEc-cCChhHHHHHHHHHHHHHHcCCCCCceEEEEecCCCCHHHHHHHHHHH-HhcCCCEEEECC
Confidence            47998843 443444568999999999999832355443  33343332 2233444 467999999986

>3brs_A Periplasmic binding protein/LACI transcriptional; structural genomics, protein structure initiative; 2.00A {Clostridium phytofermentans}

Probab=92.30  E-value=0.26  Score=37.11  Aligned_cols=66  Identities=15%  Similarity=0.193  Sum_probs=43.2

Q ss_pred             CCCEEEEEEeeec--HHHHHHHHHHHHHHHHHCCCCCCCeEEEEec--ccchH-HHHHHHHhhcCCCcEEEEeee
Q 032216           74 EGLRFALVVARFN--ELVTKLLLEGALETFKKYSVKEENIDVVWVP--GSFEI-GVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        74 ~~lRIaIVvArfN--~~It~~LleGA~~~L~~~Gv~~e~I~vv~VP--GAfEL-Plaak~La~s~~yDAVIaLG~  143 (145)
                      +..+||+|...+.  ...-..+++|+.+.++++|..   +.++...  +..+- --.++.+. +.++||||..+.
T Consensus         4 ~~~~Ig~v~~~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~~~l~-~~~vdgii~~~~   74 (289)
T 3brs_A            4 KQYYMICIPKVLDDSSDFWSVLVEGAQMAAKEYEIK---LEFMAPEKEEDYLVQNELIEEAI-KRKPDVILLAAA   74 (289)
T ss_dssp             -CCEEEEECSCCCSSSHHHHHHHHHHHHHHHHHTCE---EEECCCSSTTCHHHHHHHHHHHH-HTCCSEEEECCS
T ss_pred             CCcEEEEEeCCCCCCchHHHHHHHHHHHHHHHcCCE---EEEecCCCCCCHHHHHHHHHHHH-HhCCCEEEEeCC
Confidence            4568999998876  666777999999999999973   3333221  22221 12344444 468999998753

>3hs3_A Ribose operon repressor; PSI-II, NYSGXRC, periplasmic binding protein, structural genomics, protein structure initiative; 1.60A {Lactobacillus acidophilus}

Probab=91.97  E-value=0.65  Score=35.19  Aligned_cols=64  Identities=9%  Similarity=0.001  Sum_probs=47.4

Q ss_pred             CCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhc-CCCcEEEEe
Q 032216           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKS-GKYTAVLCI  141 (145)
Q Consensus        74 ~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s-~~yDAVIaL  141 (145)
                      ...||+++...-+....+.-.+|..+.|+++|+..+  .. ...|.++ --+++.++++ .++|||+|.
T Consensus       121 G~~~I~~i~~~~~~~~~~~R~~Gf~~~l~~~g~~~~--~~-~~~~~~~-~~~~~~~l~~~~~~~ai~~~  185 (277)
T 3hs3_A          121 KIEKVLIQHWPLSLPTIRERIEAMTAEASKLKIDYL--LE-ETPENNP-YISAQSALNKSNQFDAIITV  185 (277)
T ss_dssp             TCCEEEEEESCTTSHHHHHHHHHHHHHHHHTTCEEE--EE-ECCSSCH-HHHHHHHHHTGGGCSEEECS
T ss_pred             CCCEEEEEeCCCcCccHHHHHHHHHHHHHHCCCCCC--CC-CccCCch-HHHHHHHHcCCCCCCEEEEC
Confidence            345999999887666666777999999999998522  12 5678888 5555666654 689999985

>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=91.92  E-value=0.63  Score=35.08  Aligned_cols=63  Identities=21%  Similarity=0.098  Sum_probs=42.7

Q ss_pred             CEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH-HHHHHhhcCCCcEEEEee
Q 032216           76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV-VAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        76 lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl-aak~La~s~~yDAVIaLG  142 (145)
                      .+||++...++...-..+++|+.++++++|..   +.+....+..+--. .++.+. +.++||+|..+
T Consensus         2 ~~Igvi~~~~~~~f~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~i~~l~-~~~vdgiIi~~   65 (271)
T 2dri_A            2 DTIALVVSTLNNPFFVSLKDGAQKEADKLGYN---LVVLDSQNNPAKELANVQDLT-VRGTKILLINP   65 (271)
T ss_dssp             CEEEEEESCSSSHHHHHHHHHHHHHHHHHTCE---EEEEECTTCHHHHHHHHHHHT-TTTEEEEEECC
T ss_pred             cEEEEEecCCCCHHHHHHHHHHHHHHHHcCcE---EEEeCCCCCHHHHHHHHHHHH-HcCCCEEEEeC
Confidence            47999999887777778999999999999973   44443333322221 223333 56899999754

>3tb6_A Arabinose metabolism transcriptional repressor; transcription regulation, arabinose binding, DNA binding Pro; HET: ARB; 2.21A {Bacillus subtilis}

Probab=91.78  E-value=0.61  Score=34.99  Aligned_cols=67  Identities=12%  Similarity=0.037  Sum_probs=43.5

Q ss_pred             CCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccch---HHHHHHHHh-hcCC--CcEEEEe
Q 032216           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE---IGVVAQQLG-KSGK--YTAVLCI  141 (145)
Q Consensus        74 ~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfE---LPlaak~La-~s~~--yDAVIaL  141 (145)
                      ...||+++...-+ .....-.+|..+.|+++|+..+...++..+...+   .--+++.++ +..+  +|||+|.
T Consensus       136 G~~~i~~i~~~~~-~~~~~R~~gf~~~l~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~ai~~~  208 (298)
T 3tb6_A          136 GHTHMMGIFKADD-TQGVKRMNGFIQAHRERELFPSPDMIVTFTTEEKESKLLEKVKATLEKNSKHMPTAILCY  208 (298)
T ss_dssp             TCCSEEEEEESSS-HHHHHHHHHHHHHHHHTTCCCCGGGEEEECHHHHTTHHHHHHHHHHHHTTTSCCSEEECS
T ss_pred             CCCcEEEEcCCCC-ccHHHHHHHHHHHHHHcCCCCCcceEEEecccchhhhHHHHHHHHHhcCCCCCCeEEEEe
Confidence            3458999987766 4444557999999999998755444454443322   123344444 4455  9999985

>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=91.58  E-value=0.82  Score=34.38  Aligned_cols=67  Identities=19%  Similarity=0.115  Sum_probs=44.9

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH-HHHHHHhhc-CCCcEEEEe
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKS-GKYTAVLCI  141 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP-laak~La~s-~~yDAVIaL  141 (145)
                      ..||+++....+....+.-.+|..+.|+++|...+...++..+...|-- -+++.++++ .++|||+|.
T Consensus       131 ~~~i~~i~~~~~~~~~~~R~~gf~~~l~~~g~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~  199 (292)
T 3k4h_A          131 HKQIAFIGGGSDLLVTRDRLAGMSDALKLADIVLPKEYILHFDFSRESGQQAVEELMGLQQPPTAIMAT  199 (292)
T ss_dssp             CCCEEEEESCTTBHHHHHHHHHHHHHHHHTTCCCCGGGEEECCSSHHHHHHHHHHHHTSSSCCSEEEES
T ss_pred             CceEEEEeCcccchhHHHHHHHHHHHHHHcCCCCChheEEecCCCHHHHHHHHHHHHcCCCCCcEEEEc
Confidence            3499999988776666666899999999999864433344333333322 234445544 589999985

>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=91.52  E-value=0.59  Score=34.86  Aligned_cols=66  Identities=12%  Similarity=0.045  Sum_probs=44.1

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH---HHHHHhhc-CCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGKS-GKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl---aak~La~s-~~yDAVIaLG  142 (145)
                      ..||+++...-+......-.+|..+.|+++|+..+..  +..+|.+...-   +++.+++. .++|||+|..
T Consensus       120 ~~~i~~i~~~~~~~~~~~R~~gf~~~l~~~g~~~~~~--~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~  189 (275)
T 3d8u_A          120 FKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTPDHF--LTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSH  189 (275)
T ss_dssp             CCCEEEEECSCSSHHHHHHHHHHHHHHHHTTCCCCCE--EECSSCCCHHHHHHHHHHHHTTCTTCCEEEESS
T ss_pred             CCeEEEEcCCCCCchHHHHHHHHHHHHHHcCCCCCcc--EEEeCCCChhHHHHHHHHHHhCCCCCCEEEEcC
Confidence            4599999987655555566799999999999864332  22356554432   23445544 5799999863

>2x7x_A Sensor protein; transferase, sensor histidine kinase; HET: FRU; 2.64A {Bacteroides thetaiotaomicron}

Probab=91.34  E-value=0.66  Score=36.11  Aligned_cols=66  Identities=6%  Similarity=0.023  Sum_probs=41.8

Q ss_pred             CCCCEEEEEEeeecHHHHHHHHHHHHHHHHHC-CCCCCCeEEEEecccchHH-HHHHHHhhcCCCcEEEEeee
Q 032216           73 NEGLRFALVVARFNELVTKLLLEGALETFKKY-SVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        73 ~~~lRIaIVvArfN~~It~~LleGA~~~L~~~-Gv~~e~I~vv~VPGAfELP-laak~La~s~~yDAVIaLG~  143 (145)
                      ++..+||++... ....-..+++|+.+.++++ |+.   +.+....+..+-- -.++.+. +.++||||..+.
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            345689999877 5555567889999999888 763   4444444333222 2334444 467999998653

>3miz_A Putative transcriptional regulator protein, LACI family; LACL family, protein structure initiative II (PSI II), NYSGXRC, structural genomics; 1.91A {Rhizobium etli}

Probab=91.25  E-value=0.39  Score=36.70  Aligned_cols=68  Identities=18%  Similarity=0.136  Sum_probs=46.1

Q ss_pred             CCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEe---cccchH---HHHHHHHhhc-CCCcEEEEe
Q 032216           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWV---PGSFEI---GVVAQQLGKS-GKYTAVLCI  141 (145)
Q Consensus        74 ~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~V---PGAfEL---Plaak~La~s-~~yDAVIaL  141 (145)
                      ...||+++....+....+.-.+|..+.|+++|+..+...++..   +-..|-   .-+++++++. .++|||+|.
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            3459999998877666667789999999999987544444433   222221   1345555544 589999985

>3e61_A Putative transcriptional repressor of ribose OPER; structural genomics, DNA-binding, transcripti regulation, PSI-2; 2.00A {Staphylococcus saprophyticus subsp}

Probab=91.16  E-value=0.48  Score=35.52  Aligned_cols=65  Identities=9%  Similarity=0.065  Sum_probs=46.4

Q ss_pred             CCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEee
Q 032216           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        74 ~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG  142 (145)
                      ...||+++...-+....+.-.+|..+.|+++|+.   +.. ..++.+...-+.+.|.+..++|||+|..
T Consensus       121 G~~~i~~i~~~~~~~~~~~R~~gf~~~l~~~~~~---~~~-~~~~~~~~~~~~~~l~~~~~~~ai~~~~  185 (277)
T 3e61_A          121 KGKNVLIVHENLLIDAFHQRVQGIKYILDQQRID---YKM-LEATLLDNDKKFIDLIKELSIDSIICSN  185 (277)
T ss_dssp             TCCSEEEEESCTTSHHHHHHHHHHHHHHHC---C---EEE-EEGGGGGSHHHHHHHHHHHTCCEEEESS
T ss_pred             CCCeEEEEeCCCCCccHHHHHHHHHHHHHHcCCC---ccc-eecCCCCHHHHHHHhhcCCCCCEEEECC
Confidence            3458999998876666677789999999999985   333 5677777666666666667899999863

>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=91.04  E-value=1.5  Score=33.61  Aligned_cols=73  Identities=14%  Similarity=0.139  Sum_probs=51.1

Q ss_pred             hhhhhhccccCCCCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEE
Q 032216           61 EAVRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLC  140 (145)
Q Consensus        61 ~a~~~~~g~l~~~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIa  140 (145)
                      .+++++...++  ...|||++...-+. -....++|..+.|+++|+.   +...++...-|..-++++|.  .++|||+|
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            34455544332  23599999987543 3556779999999999985   44556666667777888876  47999998


Q ss_pred             e
Q 032216          141 I  141 (145)
Q Consensus       141 L  141 (145)
                      .
T Consensus       193 ~  193 (295)
T 3lft_A          193 P  193 (295)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2ioy_A Periplasmic sugar-binding protein; ribose binding protein, thermophilic proteins; HET: RIP; 1.90A {Thermoanaerobacter tengcongensis}

Probab=90.79  E-value=0.86  Score=34.53  Aligned_cols=63  Identities=22%  Similarity=0.101  Sum_probs=42.2

Q ss_pred             CEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH-HHHHHHhhcCCCcEEEEee
Q 032216           76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        76 lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP-laak~La~s~~yDAVIaLG  142 (145)
                      .+||++........-..+++|+.++++++|+.   +.+....+..+-- -.++.+. +.++||||..+
T Consensus         2 ~~Igvi~~~~~~~f~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~i~~l~-~~~vdgiIi~~   65 (283)
T 2ioy_A            2 KTIGLVISTLNNPFFVTLKNGAEEKAKELGYK---IIVEDSQNDSSKELSNVEDLI-QQKVDVLLINP   65 (283)
T ss_dssp             CEEEEEESCSSSHHHHHHHHHHHHHHHHHTCE---EEEEECTTCHHHHHHHHHHHH-HTTCSEEEECC
T ss_pred             eEEEEEecCCCCHHHHHHHHHHHHHHHhcCcE---EEEecCCCCHHHHHHHHHHHH-HcCCCEEEEeC
Confidence            37899998887777778999999999999973   4333322222221 1234444 56899999765

>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=0.2  Score=38.22  Aligned_cols=65  Identities=5%  Similarity=-0.023  Sum_probs=41.9

Q ss_pred             CCEEEEEEee-e---cHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchH-HHHHHHHhhcCCCcEEEEeee
Q 032216           75 GLRFALVVAR-F---NELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEI-GVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        75 ~lRIaIVvAr-f---N~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfEL-Plaak~La~s~~yDAVIaLG~  143 (145)
                      ..+||+|... +   ....-..+++|+.+.++++|..   +.+....+.-+- --.++.+ .+.++||||..+.
T Consensus         4 s~~Ig~i~~~~~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~l-~~~~vdgiIi~~~   73 (287)
T 3bbl_A            4 SFMIGYSWTQTEPGQVNHILDQFLSSMVREAGAVNYF---VLPFPFSEDRSQIDIYRDLI-RSGNVDGFVLSSI   73 (287)
T ss_dssp             CCEEEECCCCCCTTCSCCTHHHHHHHHHHHHHHTTCE---EEECCCCSSTTCCHHHHHHH-HTTCCSEEEECSC
T ss_pred             eeEEEEEecccccccCChhHHHHHHHHHHHHHHcCCE---EEEEeCCCchHHHHHHHHHH-HcCCCCEEEEeec
Confidence            4589999887 6   5555667999999999999973   333322222211 1223444 3578999998753

>3g85_A Transcriptional regulator (LACI family); transcription regulator, PSI-II, structural genomics structure initiative; 1.84A {Clostridium acetobutylicum atcc 824}

Probab=90.57  E-value=0.46  Score=35.86  Aligned_cols=68  Identities=21%  Similarity=0.157  Sum_probs=45.6

Q ss_pred             CCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH-HHHHHhhc-CCCcEEEEe
Q 032216           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV-VAQQLGKS-GKYTAVLCI  141 (145)
Q Consensus        74 ~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl-aak~La~s-~~yDAVIaL  141 (145)
                      ...||+++...-+....+.-.+|..+.|+++|+..+...++..+-..|--+ +++++++. .++|||+|.
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            346899999887766666677999999999998644333443333333322 34555544 579999985

>3cs3_A Sugar-binding transcriptional regulator, LACI FAM; structural genomics, sugar-binding transcriptional regulator structure initiative; 2.40A {Enterococcus faecalis}

Probab=90.49  E-value=0.22  Score=37.62  Aligned_cols=61  Identities=11%  Similarity=0.071  Sum_probs=41.9

Q ss_pred             CCCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEee
Q 032216           72 KNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        72 ~~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG  142 (145)
                      ..+..+||+|...+.......+++|+.+.++++|..   +.++...+..|.-      .+ -++||||..+
T Consensus         5 ~~~~~~Igvi~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~------~~-~~vdgiI~~~   65 (277)
T 3cs3_A            5 RRQTNIIGVYLADYGGSFYGELLEGIKKGLALFDYE---MIVCSGKKSHLFI------PE-KMVDGAIILD   65 (277)
T ss_dssp             CCCCCEEEEEECSSCTTTHHHHHHHHHHHHHTTTCE---EEEEESTTTTTCC------CT-TTCSEEEEEC
T ss_pred             ccCCcEEEEEecCCCChhHHHHHHHHHHHHHHCCCe---EEEEeCCCCHHHH------hh-ccccEEEEec
Confidence            355678999999887777778999999999999973   4444443322210      00 1788888765

>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=90.16  E-value=1.2  Score=35.19  Aligned_cols=66  Identities=11%  Similarity=0.118  Sum_probs=43.4

Q ss_pred             CCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEeccc-chH-HHHHHHHhhcCCCcEEEEee
Q 032216           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGS-FEI-GVVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        73 ~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGA-fEL-Plaak~La~s~~yDAVIaLG  142 (145)
                      .....||++........-..+++|+.++++++|+.   +.+...... .|- --.++.+. ..++||||..+
T Consensus        59 ~~~~~Igvi~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~l~~l~-~~~vdGiIi~~  126 (349)
T 1jye_A           59 KQSLLIGVATSSLALHAPSQIVAAILSRADQLGAS---VVVSMVERSGVEACKTAVHNLL-AQRVSGLIINY  126 (349)
T ss_dssp             ---CEEEEEESCTTSHHHHHHHHHHHHHHHHTTCE---EEEEECCSSSHHHHHHHHHHHH-TTTCSCEEEES
T ss_pred             CCCCEEEEEeCCCCcccHHHHHHHHHHHHHHcCCE---EEEEeCCCCcHHHHHHHHHHHH-HCCCCEEEEec
Confidence            34568999998876556677999999999999974   555444332 222 22344444 56899999874

>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=90.10  E-value=1.3  Score=33.68  Aligned_cols=63  Identities=14%  Similarity=0.230  Sum_probs=42.7

Q ss_pred             CEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH---HHHHHhhcCCCcEEEEee
Q 032216           76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        76 lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl---aak~La~s~~yDAVIaLG  142 (145)
                      .+||+|........-..+++|+.++++++|+.   +.+...+...+.-.   .++.+. +.++||||..+
T Consensus         2 ~~Igvi~~~~~~~f~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~~~~~-~~~vdgiIi~~   67 (288)
T 1gud_A            2 AEYAVVLKTLSNPFWVDMKKGIEDEAKTLGVS---VDIFASPSEGDFQSQLQLFEDLS-NKNYKGIAFAP   67 (288)
T ss_dssp             CEEEEEESCSSSHHHHHHHHHHHHHHHHHTCC---EEEEECSSTTCHHHHHHHHHHHH-TSSEEEEEECC
T ss_pred             cEEEEEeCCCCchHHHHHHHHHHHHHHHcCCE---EEEeCCCCCCCHHHHHHHHHHHH-HcCCCEEEEeC
Confidence            47999998877777778999999999999974   54544223232222   223343 46799999765

>2qu7_A Putative transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 2.30A {Staphylococcus saprophyticus subsp}

Probab=90.05  E-value=1  Score=33.99  Aligned_cols=67  Identities=10%  Similarity=0.060  Sum_probs=43.7

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccc----hHH---HHHHHHhhcCCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSF----EIG---VVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAf----ELP---laak~La~s~~yDAVIaLG  142 (145)
                      ..||+++...-+......-.+|..+.|+++|+..+...++..+|.|    ...   -+++.+++. ++|||+|..
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            4699999987554455566799999999999753221122115666    332   234555555 899999864

>1pea_A Amidase operon; gene regulator, receptor, binding protein; 2.10A {Pseudomonas aeruginosa} SCOP: c.93.1.1 PDB: 1qo0_A 1qnl_A

Probab=90.03  E-value=1.3  Score=35.11  Aligned_cols=63  Identities=6%  Similarity=0.152  Sum_probs=44.6

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEec---ccchHHHHHHHHhhcCCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVP---GSFEIGVVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VP---GAfELPlaak~La~s~~yDAVIaLG  142 (145)
                      ..||++|...  ........++..+.|+++|+..  ....++|   |..+.--+++++.+. +.|+|+|.+
T Consensus       140 ~~~ia~i~~~--~~~~~~~~~~~~~~l~~~G~~v--~~~~~~~~~~~~~d~~~~~~~l~~~-~pdaI~~~~  205 (385)
T 1pea_A          140 GERVVFIGSD--YIYPRESNHVMRHLYRQHGGTV--LEEIYIPLYPSDDDLQRAVERIYQA-RADVVFSTV  205 (385)
T ss_dssp             CSEEEEEEES--SHHHHHHHHHHHHHHHHTTCEE--EEEEEECSSCCHHHHHHHHHHHHHH-TCSEEEEEC
T ss_pred             CcEEEEEeCC--ChHHHHHHHHHHHHHHHcCCEE--EEEEeecCCCCcchHHHHHHHHHHC-CCCEEEEec
Confidence            4699999874  4556778899999999999741  1223444   766665666776543 789999864

>2h0a_A TTHA0807, transcriptional regulator; repressor, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.80A {Thermus thermophilus}

Probab=89.78  E-value=0.25  Score=36.98  Aligned_cols=63  Identities=5%  Similarity=-0.011  Sum_probs=38.4

Q ss_pred             EEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchH-HHHHHHHhhcCCCcEEEEeee
Q 032216           77 RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEI-GVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        77 RIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfEL-Plaak~La~s~~yDAVIaLG~  143 (145)
                      .||++...+....-..+++|+.+.++++|..   +.+....+..+- --.++.+. +.++||||..+.
T Consensus         1 ~Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~~~~~~l~-~~~vdgiI~~~~   64 (276)
T 2h0a_A            1 TVSVLLPFVATEFYRRLVEGIEGVLLEQRYD---LALFPILSLARLKRYLENTTL-AYLTDGLILASY   64 (276)
T ss_dssp             CEEEEECCSCCHHHHHHHHHHHHHHGGGTCE---EEECCCCSCCCCC----------CCCSEEEEESC
T ss_pred             CEEEEECCCCCHHHHHHHHHHHHHHHHCCCE---EEEEeCCCchhhHHHHHHHHH-hCCCCEEEEecC
Confidence            3789998887777778999999999999973   333322222111 11234443 468999998763

>3gbv_A Putative LACI-family transcriptional regulator; NYSGXRC, PSI-II, 11231J, structur genomics, protein structure initiative; 2.20A {Bacteroides fragilis}

Probab=89.58  E-value=1.4  Score=33.13  Aligned_cols=68  Identities=1%  Similarity=-0.138  Sum_probs=42.2

Q ss_pred             CCEEEEEEee----ecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccch-HHHHHHHHhh-cCCCcEEEEee
Q 032216           75 GLRFALVVAR----FNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE-IGVVAQQLGK-SGKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvAr----fN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfE-LPlaak~La~-s~~yDAVIaLG  142 (145)
                      ..||+++...    -.....+.-.+|..+.|+++|...+...+..-....| ---+++.+++ ..++|||+|..
T Consensus       135 ~~~i~~i~~~~~g~~~~~~~~~R~~gf~~~l~~~g~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~  208 (304)
T 3gbv_A          135 DREIVIFRKIHEGVIGSNQQESREIGFRQYMQEHHPACNILELNLHADLNIEDSRMLDDFFREHPDVKHGITFN  208 (304)
T ss_dssp             CSEEEEEEEEBTTBCCCHHHHHHHHHHHHHHHHHCTTSEEEEEEEESSCSSCHHHHHHHHHHHCTTCCEEEESS
T ss_pred             CCeEEEEEecccCCccchhHHHHHHHHHHHHHhhCCCcEEEEeeecCCCHHHHHHHHHHHHHhCCCeEEEEEcC
Confidence            3699999844    2334555667999999999998643232322222222 2234455554 45899999863

>3kke_A LACI family transcriptional regulator; structural genomics, DNA-binding, transcription regulation, PSI-2; 2.20A {Mycobacterium smegmatis str}

Probab=89.54  E-value=1.2  Score=34.13  Aligned_cols=68  Identities=22%  Similarity=0.102  Sum_probs=45.4

Q ss_pred             CCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH-HHHHH-----hh-cCCCcEEEEe
Q 032216           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV-VAQQL-----GK-SGKYTAVLCI  141 (145)
Q Consensus        74 ~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl-aak~L-----a~-s~~yDAVIaL  141 (145)
                      ...||+++....+....+.-.+|..+.|+++|+..+...+.......|--+ +++.+     ++ ..++|||+|.
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            345999999887766666777999999999998644333333333333222 34555     54 4579999985

>3d02_A Putative LACI-type transcriptional regulator; periplasmic sugar-binding protein, structura genomics; HET: MSE GOL; 1.30A {Klebsiella pneumoniae subsp}

Probab=89.37  E-value=0.78  Score=34.70  Aligned_cols=64  Identities=13%  Similarity=0.055  Sum_probs=42.9

Q ss_pred             CCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH---HHHHHhhcCCCcEEEEee
Q 032216           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        74 ~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl---aak~La~s~~yDAVIaLG  142 (145)
                      +..+||++........-..+++|+.+.++++|+.   +.+ ..+...+.--   .++.+. ..++||||..+
T Consensus         3 ~~~~Ig~i~~~~~~~~~~~~~~g~~~~~~~~g~~---~~~-~~~~~~~~~~~~~~~~~l~-~~~vdgiii~~   69 (303)
T 3d02_A            3 AEKTVVNISKVDGMPWFNRMGEGVVQAGKEFNLN---ASQ-VGPSSTDAPQQVKIIEDLI-ARKVDAITIVP   69 (303)
T ss_dssp             -CEEEEEECSCSSCHHHHHHHHHHHHHHHHTTEE---EEE-ECCSSSCHHHHHHHHHHHH-HTTCSEEEECC
T ss_pred             CceEEEEEeccCCChHHHHHHHHHHHHHHHcCCE---EEE-ECCCCCCHHHHHHHHHHHH-HcCCCEEEEec
Confidence            3568999998777777778999999999999863   222 2344333222   234444 46899999765

>3hcw_A Maltose operon transcriptional repressor; RNA-binding, PSI-2, NYSGXRC, STRU genomics, protein structure initiative; 2.20A {Staphylococcus aureus subsp}

Probab=89.15  E-value=1.7  Score=33.22  Aligned_cols=66  Identities=12%  Similarity=0.124  Sum_probs=43.7

Q ss_pred             CCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH-HHHHHhhc----CCCcEEEEee
Q 032216           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV-VAQQLGKS----GKYTAVLCIG  142 (145)
Q Consensus        74 ~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl-aak~La~s----~~yDAVIaLG  142 (145)
                      ...||+++...-+....+.-.+|..+.|+++|+.   +.++...-..|--+ +++.+++.    .++|||+|..
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            3459999998776666666789999999999985   33333332333222 34555543    2799999853

>3h5o_A Transcriptional regulator GNTR; transcription regulator, GNTR,chromobacterium violaceum, PSI, SGX, DNA-binding; 2.30A {Chromobacterium violaceum}

Probab=88.96  E-value=1.4  Score=34.41  Aligned_cols=66  Identities=14%  Similarity=0.240  Sum_probs=44.4

Q ss_pred             CCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH---HHHHHhh-cCCCcEEEEe
Q 032216           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGK-SGKYTAVLCI  141 (145)
Q Consensus        74 ~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl---aak~La~-s~~yDAVIaL  141 (145)
                      ...||+++....+.... .-.+|..+.|+++|....+...+ .++.+..-.   +++.+++ ..++|||+|.
T Consensus       177 G~~~I~~i~~~~~~~~~-~R~~Gf~~al~~~g~~~~~~~~~-~~~~~~~~~~~~~~~~ll~~~~~~~ai~~~  246 (339)
T 3h5o_A          177 GKRRIGFLGAQLDERVM-KRLDGYRAALDAADCRDAGLEWL-DPQPSSMQMGADMLDRALAERPDCDALFCC  246 (339)
T ss_dssp             TCCSEEEEEESCCHHHH-HHHHHHHHHHHHTTCCCGGGEEE-ECSCCCHHHHHHHHHHHHHHCTTCCEEEES
T ss_pred             CCCeEEEEeCCCCccHH-HHHHHHHHHHHHCCCCCCChheE-ecCCCCHHHHHHHHHHHHcCCCCCcEEEEC
Confidence            34689999988765544 45699999999999843334433 466664432   3444544 4589999985

>3bbl_A Regulatory protein of LACI family; protein structure initiative II, PSI-II, NYSGXRC, transcript regulator, periplasmic binding protein; 2.35A {Chloroflexus aggregans}

Probab=88.64  E-value=1.7  Score=32.94  Aligned_cols=66  Identities=20%  Similarity=0.178  Sum_probs=43.1

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH---HHHHHHhh-c-C-CCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGK-S-G-KYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP---laak~La~-s-~-~yDAVIaLG  142 (145)
                      ..||+++...-+......-.+|..+.|+++|+..+...++  +|.|...   -+++.+++ . . ++|||+|..
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            4599999877554455566799999999999763322233  4544433   23455655 4 4 799999853

>2rgy_A Transcriptional regulator, LACI family; 11011J, NYSGXRC, transctiptional regulator, SUG binding protein, structural genomics, PSI-2; 2.05A {Burkholderia phymatum}

Probab=88.56  E-value=1.7  Score=32.97  Aligned_cols=65  Identities=14%  Similarity=0.313  Sum_probs=42.3

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH---HHHHHhh-cCCCcEEEEe
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGK-SGKYTAVLCI  141 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl---aak~La~-s~~yDAVIaL  141 (145)
                      ..||+++...-.......-.+|..+.|+++|+..+...++  +|.|...-   +++.+++ ..++|||+|.
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            4599999887544444556799999999999763322233  45554332   2344554 4589999985

>3brq_A HTH-type transcriptional regulator ASCG; transcriptional repressor structure escherichia coli, struct genomics, PSI-2; HET: FRU; 2.00A {Escherichia coli}

Probab=88.25  E-value=0.94  Score=33.92  Aligned_cols=66  Identities=11%  Similarity=0.151  Sum_probs=42.2

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH---HHHHHHhhc-CCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGKS-GKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP---laak~La~s-~~yDAVIaLG  142 (145)
                      ..||+++...-+....+.-.+|..+.|+++|+..+...+  .+|.+...   -+++.+++. .++|||+|..
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            458999987654444556679999999999976332222  35555433   234455543 5799999864

>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=88.12  E-value=1.3  Score=34.55  Aligned_cols=66  Identities=11%  Similarity=0.160  Sum_probs=45.5

Q ss_pred             CCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH---HHHHHh-hcCCCcEEEEe
Q 032216           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLG-KSGKYTAVLCI  141 (145)
Q Consensus        74 ~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl---aak~La-~s~~yDAVIaL  141 (145)
                      ...||+++....+....+.-.+|..+.|+++|+..+...+  ++|.|...-   +++.++ +..++|||+|.
T Consensus       180 G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~g~~~~~~~~--~~~~~~~~~~~~~~~~ll~~~~~~~ai~~~  249 (338)
T 3dbi_A          180 GHQEIAFLTGSMDSPTSIERLAGYKDALAQHGIALNEKLI--ANGKWTPASGAEGVEMLLERGAKFSALVAS  249 (338)
T ss_dssp             TCCSEEEECCCTTCHHHHHHHHHHHHHHHHTTCCCCGGGE--ECCCSSHHHHHHHHHHHHHTTCCCSEEEES
T ss_pred             CCCEEEEEeCCCCCccHHHHHHHHHHHHHHCCCCCCcceE--EeCCCCHHHHHHHHHHHHcCCCCCeEEEEC
Confidence            3468999988766666666789999999999986443323  345554432   344455 44689999985

>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=87.84  E-value=1.3  Score=34.42  Aligned_cols=65  Identities=14%  Similarity=0.172  Sum_probs=43.2

Q ss_pred             CCEEEEEEeee-cHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH---HHHHHHhhc-CCCcEEEEe
Q 032216           75 GLRFALVVARF-NELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGKS-GKYTAVLCI  141 (145)
Q Consensus        75 ~lRIaIVvArf-N~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP---laak~La~s-~~yDAVIaL  141 (145)
                      ..||+++...- +....+.-.+|..+.|+++|+..+...++  +|.|...   -+++.+++. .++|||+|.
T Consensus       177 ~~~I~~i~~~~~~~~~~~~R~~Gf~~al~~~g~~~~~~~~~--~~~~~~~~~~~~~~~ll~~~~~~~ai~~~  246 (332)
T 2hsg_A          177 HKNIAFVSGTLEEPINHAKKVKGYKRALTESGLPVRDSYIV--EGDYTYDSGIEAVEKLLEEDEKPTAIFVG  246 (332)
T ss_dssp             CSCEEEEESCTTSHHHHTTHHHHHHHHHHTTTCCCCGGGEE--ECCSSHHHHHHHHHHHHHSSSCCSEEEES
T ss_pred             CCEEEEEeCCcccCccHHHHHHHHHHHHHHcCCCCChheEE--eCCCCHHHHHHHHHHHHcCCCCCeEEEEC
Confidence            46999999875 54555566799999999999863322233  4545433   234555554 479999985

>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=87.54  E-value=1.4  Score=33.82  Aligned_cols=62  Identities=11%  Similarity=0.113  Sum_probs=42.7

Q ss_pred             CEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH---HHHHHhhcCCCcEEEEeee
Q 032216           76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        76 lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl---aak~La~s~~yDAVIaLG~  143 (145)
                      .+||+|...+.. .-..+++|+.+.++++|+.   +.+. .+...+..-   .++.+. ..++||||..+.
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            479999988877 7788999999999999973   3333 243333322   334444 468999998653

>3gv0_A Transcriptional regulator, LACI family; transcription regulator, PSI-II, structural genomics structure initiative; 2.35A {Agrobacterium tumefaciens str}

Probab=87.45  E-value=0.77  Score=34.88  Aligned_cols=67  Identities=18%  Similarity=0.169  Sum_probs=44.2

Q ss_pred             CCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH---HHHHHHhhc-CCCcEEEEee
Q 032216           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGKS-GKYTAVLCIG  142 (145)
Q Consensus        74 ~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP---laak~La~s-~~yDAVIaLG  142 (145)
                      ...||+++...-+....+.-.+|..+.|+++|+..+...+  +++.++.-   -+++.+++. .++|||+|..
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            3459999988766555566679999999999985332222  34444432   234555544 5799999853

>3jvd_A Transcriptional regulators; structural genomics, PSI-2, sugar binding protein, transcrip regulation, protein structure initiative; 2.30A {Corynebacterium glutamicum}

Probab=87.39  E-value=2.1  Score=33.58  Aligned_cols=63  Identities=19%  Similarity=0.244  Sum_probs=43.6

Q ss_pred             CCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEec-ccchHHH---HHHHHhhcCCCcEEEEee
Q 032216           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVP-GSFEIGV---VAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        74 ~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VP-GAfELPl---aak~La~s~~yDAVIaLG  142 (145)
                      ...||+++...-+....+.=.+|..+.|+++|+.      ..++ |.|...-   +++.+++..++|||+|..
T Consensus       173 G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~g~~------~~~~~~~~~~~~~~~~~~~ll~~~~~~ai~~~n  239 (333)
T 3jvd_A          173 SGMNIAALVGEESLSTTQERMRGISHAASIYGAE------VTFHFGHYSVESGEEMAQVVFNNGLPDALIVAS  239 (333)
T ss_dssp             SSCEEEEEESCTTSHHHHHHHHHHHHHHHHTTCE------EEEEECCSSHHHHHHHHHHHHHTCCCSEEEECC
T ss_pred             CCCeEEEEeCCCCCccHHHHHHHHHHHHHHCCCC------EEEecCCCCHHHHHHHHHHHhcCCCCcEEEECC
Confidence            4569999998866555666679999999999974      2233 5554432   345555554499999863

>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=87.31  E-value=2.3  Score=32.04  Aligned_cols=65  Identities=9%  Similarity=0.089  Sum_probs=42.5

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH---HHHHHHhhc-C--CCcEEEEe
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGKS-G--KYTAVLCI  141 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP---laak~La~s-~--~yDAVIaL  141 (145)
                      ..||+++...-.......-.+|..+.|+++|...+..  ..+.|.++..   -+++.++++ .  ++|||+|.
T Consensus       140 ~~~i~~i~~~~~~~~~~~R~~gf~~~l~~~g~~~~~~--~~~~~~~~~~~~~~~~~~~l~~~~~~~~~ai~~~  210 (309)
T 2fvy_A          140 QIQFVLLKGEPGHPDAEARTTYVIKELNDKGIKTEQL--QLDTAMWDTAQAKDKMDAWLSGPNANKIEVVIAN  210 (309)
T ss_dssp             SEEEEEEECSTTCHHHHHHHHHHHHHHHHTTCCEEEE--EEEECTTCHHHHHHHHHHHHTSTTGGGCCEEEES
T ss_pred             ceEEEEEEcCCCCccHHHHHHHHHHHHHhcCCceEEE--EEecCCCCHHHHHHHHHHHHHhCCCCCccEEEEC
Confidence            3589999876554455666799999999999752212  1234555443   234556655 3  79999985

>3huu_A Transcription regulator like protein; PSI-II, NYSGXRC, LAC I, STR genomics, protein structure initiative; 1.95A {Staphylococcus haemolyticus}

Probab=87.09  E-value=1.4  Score=33.76  Aligned_cols=64  Identities=11%  Similarity=-0.058  Sum_probs=41.9

Q ss_pred             CCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchH-HHHHHHH-hh-cCCCcEEEEe
Q 032216           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEI-GVVAQQL-GK-SGKYTAVLCI  141 (145)
Q Consensus        74 ~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfEL-Plaak~L-a~-s~~yDAVIaL  141 (145)
                      ...||+++....+....+.-.+|..+.|+++|+..+.    .+.|.|.- --+++++ ++ ..++|||+|.
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            3458999998877666666789999999999986432    24565553 1123344 44 4689999985

>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=87.06  E-value=2  Score=32.72  Aligned_cols=65  Identities=18%  Similarity=0.165  Sum_probs=43.6

Q ss_pred             CCEEEEEEeee-cHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH---HHHHHHhhc-CCCcEEEEe
Q 032216           75 GLRFALVVARF-NELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGKS-GKYTAVLCI  141 (145)
Q Consensus        75 ~lRIaIVvArf-N~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP---laak~La~s-~~yDAVIaL  141 (145)
                      ..||+++...- +......-.+|.++.|+++|+..+...++  +|.|...   -+++.+++. .++|||+|.
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            46999999876 55555666799999999999864322233  4555433   234555554 579999986

>2o20_A Catabolite control protein A; CCPA, transcriptional regulator, helix-turn-helix, transcrip; 1.90A {Lactococcus lactis}

Probab=87.03  E-value=1.5  Score=34.16  Aligned_cols=65  Identities=12%  Similarity=0.190  Sum_probs=43.2

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH---HHHHHHhhcCCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP---laak~La~s~~yDAVIaLG  142 (145)
                      ..||+++...-+......-.+|..+.|+++|+..+...+  .+|.|...   -+++.+++. ++|||+|..
T Consensus       180 ~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~g~~~~~~~~--~~~~~~~~~~~~~~~~ll~~-~~~ai~~~~  247 (332)
T 2o20_A          180 NKKIAYIMGSLKDVENTERMVGYQEALLEANIEFDENLV--FEGNYSYEQGKALAERLLER-GATSAVVSH  247 (332)
T ss_dssp             CSSEEEECSCTTSHHHHHHHHHHHHHHHHTTCCCCGGGE--ECSCCSHHHHHHHHHHHHHT-TCCEEEESC
T ss_pred             CCeEEEEeCCcccccHHHHHHHHHHHHHHcCCCCChhhE--EeCCCCHHHHHHHHHHHhcc-CCCEEEECC
Confidence            458999987754444455579999999999986332222  35555433   234556666 899999853

>2iks_A DNA-binding transcriptional dual regulator; escherichia coli structural genomics, PSI-2, protein structure initiative; 1.85A {Escherichia coli}

Probab=86.83  E-value=2.1  Score=32.48  Aligned_cols=65  Identities=12%  Similarity=0.045  Sum_probs=43.0

Q ss_pred             CCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH---HHHHHhhc-CCCcEEEEee
Q 032216           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGKS-GKYTAVLCIG  142 (145)
Q Consensus        74 ~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl---aak~La~s-~~yDAVIaLG  142 (145)
                      ...||+++...-+....+.-.+|..+.|+++|..   ...+ .+|.|+..-   +++.+++. .++|||+|..
T Consensus       137 G~~~I~~i~~~~~~~~~~~R~~Gf~~~l~~~g~~---~~~~-~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~  205 (293)
T 2iks_A          137 PAETVLYLGALPELSVSFLREQGFRTAWKDDPRE---VHFL-YANSYEREAAAQLFEKWLETHPMPQALFTTS  205 (293)
T ss_dssp             CCSSEEEEEECTTSHHHHHHHHHHHHHHTTCCCC---EEEE-EESSSCHHHHHHHHHHHTTTSCCCSEEEESS
T ss_pred             CCCEEEEEecCcccccHHHHHHHHHHHHHHcCCC---ccEE-EcCCCChhhHHHHHHHHHhcCCCCCEEEECC
Confidence            3469999988755444556679999999999972   3322 356555432   34455544 4799999863

>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=86.57  E-value=2.3  Score=33.06  Aligned_cols=62  Identities=18%  Similarity=0.143  Sum_probs=43.5

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEe-cccchHHHH---HHHHhhcCCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWV-PGSFEIGVV---AQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~V-PGAfELPla---ak~La~s~~yDAVIaLG  142 (145)
                      ..+||++........-..+.+|+.+.++++|+     ++... |...+..-.   ++.|. +.++|+||..+
T Consensus         3 ~~~Igvi~~~~~~~~~~~~~~g~~~~~~~~g~-----~~~~~~~~~~d~~~q~~~i~~li-~~~vdgiii~~   68 (316)
T 1tjy_A            3 AERIAFIPKLVGVGFFTSGGNGAQEAGKALGI-----DVTYDGPTEPSVSGQVQLVNNFV-NQGYDAIIVSA   68 (316)
T ss_dssp             CCEEEEECSSSSSHHHHHHHHHHHHHHHHHTC-----EEEECCCSSCCHHHHHHHHHHHH-HTTCSEEEECC
T ss_pred             CCEEEEEeCCCCChHHHHHHHHHHHHHHHhCC-----EEEEECCCCCCHHHHHHHHHHHH-HcCCCEEEEeC
Confidence            45899999887766777899999999999996     33333 554544433   34444 46899998754

>2h0a_A TTHA0807, transcriptional regulator; repressor, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.80A {Thermus thermophilus}

Probab=86.55  E-value=1.6  Score=32.47  Aligned_cols=68  Identities=16%  Similarity=0.035  Sum_probs=40.9

Q ss_pred             CCEEEEEEeee-c---HHHHH-HHHHHHHHHHHHCCCCCCCeEEEEecccchHHH-HHHHHhhc-CCCcEEEEee
Q 032216           75 GLRFALVVARF-N---ELVTK-LLLEGALETFKKYSVKEENIDVVWVPGSFEIGV-VAQQLGKS-GKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArf-N---~~It~-~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl-aak~La~s-~~yDAVIaLG  142 (145)
                      ..||+++...- .   ..... .-.+|..+.|+++|+..+...++..+-..|--. +++.++++ .++|||+|..
T Consensus       114 ~~~i~~i~~~~~~~~~~~~~~~~R~~gf~~~l~~~g~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~  188 (276)
T 2h0a_A          114 GPIFAIAVEEEPDRAFRRTVFAERMAGFQEALKEAGRPFSPDRLYITRHSQEGGRLALRHFLEKASPPLNVFAGA  188 (276)
T ss_dssp             SCEEEEEECCSCCC---CCHHHHHHHHHHHHHHHTTCCCCGGGEEEECSSHHHHHHHHHHHHTTCCSSEEEECSS
T ss_pred             CCeEEEEecCcccccccchhHHHHHHHHHHHHHHcCCCCChHHeeecCCChHHHHHHHHHHHhCCCCCCEEEECC
Confidence            45999998765 3   33344 456999999999998633222333222233222 34555544 4799999853

>1usg_A Leucine-specific binding protein; leucine-binding protein, X-RAY crystallography, protein structure, ABC transport systems, transport protein; 1.53A {Escherichia coli} SCOP: c.93.1.1 PDB: 1usi_A* 1usk_A 2lbp_A 1z15_A 1z16_A 1z17_A 1z18_A 2liv_A

Probab=86.33  E-value=2.1  Score=32.75  Aligned_cols=63  Identities=14%  Similarity=0.136  Sum_probs=44.8

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEe-cccchHHHHHHHHhhcCCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWV-PGSFEIGVVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~V-PGAfELPlaak~La~s~~yDAVIaLG  142 (145)
                      ..||+++...  ......+.++..+.|+++|+..  ...... +|..+.--+++++.+ .+.|+|++.+
T Consensus       138 ~~~i~~i~~~--~~~~~~~~~~~~~~l~~~g~~v--~~~~~~~~~~~d~~~~~~~l~~-~~~d~i~~~~  201 (346)
T 1usg_A          138 PQRIAIIHDK--QQYGEGLARSVQDGLKAANANV--VFFDGITAGEKDFSALIARLKK-ENIDFVYYGG  201 (346)
T ss_dssp             CSSEEEEECS--SHHHHHHHHHHHHHHHHTTCCE--EEEEECCTTCCCCHHHHHHHHH-TTCCEEEEES
T ss_pred             CCeEEEEECC--CchHHHHHHHHHHHHHHcCCEE--EEEeccCCCCcCHHHHHHHHHh-cCCCEEEEcC
Confidence            4699999874  4566778899999999999851  122233 576666566677764 4789999875

>3o74_A Fructose transport system repressor FRUR; dual transcriptional regulator, DNA, transcription; 2.00A {Pseudomonas putida} PDB: 3o75_A*

Probab=86.18  E-value=1.3  Score=32.76  Aligned_cols=65  Identities=22%  Similarity=0.170  Sum_probs=43.3

Q ss_pred             CCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH---HHHHHHhh-cC-CCcEEEEee
Q 032216           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGK-SG-KYTAVLCIG  142 (145)
Q Consensus        74 ~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP---laak~La~-s~-~yDAVIaLG  142 (145)
                      ...||+++...-+....+.-.+|+.+.|+++|+.   +.. ...+.+...   -+++++++ .. ++|||+|..
T Consensus       119 G~~~i~~i~~~~~~~~~~~R~~gf~~~l~~~~~~---~~~-~~~~~~~~~~~~~~~~~~l~~~~~~~~ai~~~~  188 (272)
T 3o74_A          119 APRSIALIGARPELSVSQARAGGFDEALQGYTGE---VRR-YQGEAFSRECGQRLMQQLIDDLGGLPDALVTTS  188 (272)
T ss_dssp             CCSEEEEEEECTTSHHHHHHHHHHHHHTTTCCSE---EEE-EEESSSSHHHHHHHHHHHHHHHTSCCSEEEESS
T ss_pred             CCcEEEEEecCCCCccHHHHHHHHHHHHHHcCCC---hhe-eecCCCCHHHHHHHHHHHHhcCCCCCcEEEEeC
Confidence            3469999998776666667779999999999974   222 234444333   23344444 45 699999853

>3lop_A Substrate binding periplasmic protein; protein structure initiative II(PSI II), NYSGXRC, structural genomics; 1.55A {Ralstonia solanacearum}

Probab=86.11  E-value=3.9  Score=31.84  Aligned_cols=64  Identities=13%  Similarity=0.142  Sum_probs=46.4

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG  142 (145)
                      ..||++|..  +......+.++..+.|+++|+... .....-+|..+.--.++++.+ .+.|+|++.+
T Consensus       141 ~~~iaii~~--~~~~g~~~~~~~~~~~~~~G~~v~-~~~~~~~~~~d~~~~~~~l~~-~~~d~v~~~~  204 (364)
T 3lop_A          141 VTRIGVLYQ--EDALGKEAITGVERTLKAHALAIT-AMASYPRNTANVGPAVDKLLA-ADVQAIFLGA  204 (364)
T ss_dssp             CCCEEEEEE--TTHHHHHHHHHHHHHHHTTTCCCS-EEEEECTTSCCCHHHHHHHHH-SCCSEEEEES
T ss_pred             CceEEEEEe--CchhhHHHHHHHHHHHHHcCCcEE-EEEEecCCCccHHHHHHHHHh-CCCCEEEEec
Confidence            469999986  445677889999999999998622 233345677776666777654 5789999865

>3rot_A ABC sugar transporter, periplasmic sugar binding; nysgrc, PSI-biology, structural genomics; 1.91A {Legionella pneumophila subsp}

Probab=86.08  E-value=4.8  Score=30.53  Aligned_cols=62  Identities=5%  Similarity=0.011  Sum_probs=41.4

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH---HHHHH-HhhcCCCcEEEEe
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQ-LGKSGKYTAVLCI  141 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP---laak~-La~s~~yDAVIaL  141 (145)
                      ..||+++...-.......-.+|+++.|+++|+.   +  ..+.+.+.-.   -+++. |.+..++|||+|.
T Consensus       130 ~~~i~~i~g~~~~~~~~~R~~Gf~~~l~~~g~~---~--~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~  195 (297)
T 3rot_A          130 AKRALVLNPQPGHIGLEKRAYGIKTILQDKGIF---F--EELDVGTDPNQVQSRVKSYFKIHPETNIIFCL  195 (297)
T ss_dssp             CCEEEEEESCTTCHHHHHHHHHHHHHHHHTTCE---E--EEEECCSCHHHHHHHHHHHHHHCTTCCEEEES
T ss_pred             CceEEEEeCCCCcHHHHHHHHHHHHHHHhcCCe---E--EEeecCCChHHHHHHHHHHHHhCCCCCEEEEc
Confidence            569999988766666666789999999999874   2  2233333322   22334 3345679999985

>3c3k_A Alanine racemase; structural genomics, protein structure initiative, NEW YORK research center for structural genomics, nysgxrc; 1.99A {Actinobacillus succinogenes}

Probab=85.95  E-value=3.5  Score=31.14  Aligned_cols=65  Identities=18%  Similarity=0.078  Sum_probs=42.0

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH-HHHHH--Hhhc-CCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG-VVAQQ--LGKS-GKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP-laak~--La~s-~~yDAVIaLG  142 (145)
                      ..||+++...-+......-.+|..+.|+++|+..+   ++..+...|-- -+++.  +++. .++|||+|..
T Consensus       124 ~~~I~~i~~~~~~~~~~~R~~gf~~~l~~~g~~~~---~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~  192 (285)
T 3c3k_A          124 KKRIALINHDLAYQYAQHRESGYLNRLKFHGLDYS---RISYAENLDYMAGKLATFSLLKSAVKPDAIFAIS  192 (285)
T ss_dssp             CCCEEEEECCTTSHHHHHHHHHHHHHHHHHTCCCC---EEEECSSSSHHHHHHHHHHHHSSSSCCSEEEESS
T ss_pred             CCeEEEEeCCCccccHHHHHHHHHHHHHHcCCCce---EeecCCChHHHHHHHHHHHHHcCCCCCeEEEECC
Confidence            46899998865444455567999999999998633   33323233322 23455  5554 4799999863

>3egc_A Putative ribose operon repressor; structural genomics, unknown function, DNA-binding, transcri transcription regulation, PSI-2; 2.35A {Burkholderia thailandensis}

Probab=85.95  E-value=1.2  Score=33.57  Aligned_cols=67  Identities=13%  Similarity=0.089  Sum_probs=42.4

Q ss_pred             CCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH---HHHHHHh-hcCCCcEEEEee
Q 032216           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLG-KSGKYTAVLCIG  142 (145)
Q Consensus        74 ~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP---laak~La-~s~~yDAVIaLG  142 (145)
                      ...||+++...-+......-.+|..+.|+++|+..+...+  +.|.++.-   -+++.++ +..++|||+|..
T Consensus       124 G~~~i~~i~~~~~~~~~~~R~~gf~~~l~~~g~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~  194 (291)
T 3egc_A          124 GHTRIGAIVGSAGLMTSRERLKGFRAAMSAAGLPVRQEWI--AAGGVRADNGRDGAIKVLTGADRPTALLTSS  194 (291)
T ss_dssp             TCCSEEEECSCTTSHHHHHHHHHHHHHHHHTTCCCCGGGE--EC------CCHHHHHHHHTC-CCCSEEEESS
T ss_pred             CCCEEEEEeCCCCCcCHHHHHHHHHHHHHHcCCCCCHHHe--EeCCCChhHHHHHHHHHHhCCCCCcEEEECC
Confidence            3458999998876666777789999999999986432222  23433322   2345555 456899999863

>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=85.87  E-value=3.2  Score=32.02  Aligned_cols=64  Identities=9%  Similarity=0.066  Sum_probs=46.5

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG  142 (145)
                      ..||++|..  +......+.++..+.|+++|+... .....-+|..+.--.++++.+ .+.|+|++.+
T Consensus       138 ~~~iaii~~--~~~~~~~~~~~~~~~l~~~g~~v~-~~~~~~~~~~d~~~~~~~l~~-~~~d~v~~~~  201 (356)
T 3ipc_A          138 DAKVAIIHD--KTPYGQGLADETKKAANAAGVTEV-MYEGVNVGDKDFSALISKMKE-AGVSIIYWGG  201 (356)
T ss_dssp             TCCEEEEEC--SSHHHHHHHHHHHHHHHHTTCCCS-EEEECCTTCCCCHHHHHHHHH-TTCCEEEEES
T ss_pred             CCEEEEEeC--CChHHHHHHHHHHHHHHHcCCEEE-EEEeeCCCCCCHHHHHHHHHh-cCCCEEEEcc
Confidence            459999987  556677899999999999998632 222334677777777777654 5789998654

>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=85.51  E-value=3.8  Score=31.69  Aligned_cols=65  Identities=6%  Similarity=-0.040  Sum_probs=42.4

Q ss_pred             CCCCEEEEEEee-ecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecc----cchH-HHHHHHHhhcCCCcEEEEe
Q 032216           73 NEGLRFALVVAR-FNELVTKLLLEGALETFKKYSVKEENIDVVWVPG----SFEI-GVVAQQLGKSGKYTAVLCI  141 (145)
Q Consensus        73 ~~~lRIaIVvAr-fN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPG----AfEL-Plaak~La~s~~yDAVIaL  141 (145)
                      .+..+||++... .....-..+++|+.+.++++|..   +.+.....    ..+- --.++.+. +.++||||..
T Consensus        41 ~~~~~Igvi~~~~~~~~~~~~~~~gi~~~a~~~g~~---~~~~~~~~~~~~~~~~~~~~i~~l~-~~~vdgiIi~  111 (342)
T 1jx6_A           41 QRPIKISVVYPGQQVSDYWVRNIASFEKRLYKLNIN---YQLNQVFTRPNADIKQQSLSLMEAL-KSKSDYLIFT  111 (342)
T ss_dssp             SSCEEEEEEECCCSSCCHHHHHHHHHHHHHHHTTCC---EEEEEEECCTTCCHHHHHHHHHHHH-HTTCSEEEEC
T ss_pred             CCceEEEEEecCCcccHHHHHHHHHHHHHHHHcCCe---EEEEecCCCCccCHHHHHHHHHHHH-hcCCCEEEEe
Confidence            445689999987 55555567899999999999974   55543222    2221 12344444 3579999973

>3cs3_A Sugar-binding transcriptional regulator, LACI FAM; structural genomics, sugar-binding transcriptional regulator structure initiative; 2.40A {Enterococcus faecalis}

Probab=85.47  E-value=2.8  Score=31.48  Aligned_cols=63  Identities=10%  Similarity=0.188  Sum_probs=42.5

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH---HHHHHHhhc--CCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGKS--GKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP---laak~La~s--~~yDAVIaLG  142 (145)
                      ..||+++...-+......-.+|..+.|+++|+.   +++  +.|.|+..   -+++.++++  .++|||+|..
T Consensus       118 ~~~i~~i~~~~~~~~~~~R~~gf~~~l~~~g~~---~~~--~~~~~~~~~~~~~~~~~l~~~~~~~~ai~~~~  185 (277)
T 3cs3_A          118 SKKVLLLSGPEKGYDSQERLAVSTRELTRFGIP---YEI--IQGDFTEPSGYAAAKKILSQPQTEPVDVFAFN  185 (277)
T ss_dssp             CSCEEEEECCTTSHHHHHHHHHHHHHHHHTTCC---EEE--EECCSSHHHHHHHHHHHTTSCCCSSEEEEESS
T ss_pred             CceEEEEeCCccCccHHHHHHHHHHHHHHcCCC---eeE--EeCCCChhHHHHHHHHHHhcCCCCCcEEEEcC
Confidence            468999987755445556679999999999975   332  34555433   234555554  5799999863

>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=85.44  E-value=1.5  Score=34.26  Aligned_cols=66  Identities=21%  Similarity=0.252  Sum_probs=43.2

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH---HHHHHhhc-CCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGKS-GKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl---aak~La~s-~~yDAVIaLG  142 (145)
                      ..||+++...-+....+.-.+|..+.|+++|+..+...+  .+|.|+..-   +++.+++. .++|||+|..
T Consensus       177 ~~~I~~i~g~~~~~~~~~R~~Gf~~al~~~g~~~~~~~~--~~~~~~~~~~~~~~~~ll~~~~~~~ai~~~n  246 (340)
T 1qpz_A          177 HREIGVIPGPLERNTGAGRLAGFMKAMEEAMIKVPESWI--VQGDFEPESGYRAMQQILSQPHRPTAVFCGG  246 (340)
T ss_dssp             CCCEEEECCCTTSHHHHHHHHHHHHHHHHTTCCCCGGGB--CCCCSSHHHHHHHHHHHHTSSSCCSEEEESS
T ss_pred             CCEEEEEeCCCccccHHHHHHHHHHHHHHCCCCCChhhe--EeCCCCHHHHHHHHHHHHcCCCCCcEEEECC
Confidence            458999987655444455679999999999986332212  355554432   34555554 5799999863

>1dbq_A Purine repressor; transcription regulation, DNA-binding regulatory protein; 2.20A {Escherichia coli} SCOP: c.93.1.1 PDB: 1jhz_A

Probab=84.43  E-value=1.1  Score=33.69  Aligned_cols=66  Identities=21%  Similarity=0.222  Sum_probs=39.9

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH---HHHHHHhhc-CCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGKS-GKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP---laak~La~s-~~yDAVIaLG  142 (145)
                      ..||+++...-+....+.-.+|..+.|+++|+..+...  .++|.|+..   -+++.+++. .++|||+|..
T Consensus       126 ~~~i~~i~~~~~~~~~~~R~~g~~~~l~~~g~~~~~~~--~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~  195 (289)
T 1dbq_A          126 HREIGVIPGPLERNTGAGRLAGFMKAMEEAMIKVPESW--IVQGDFEPESGYRAMQQILSQPHRPTAVFCGG  195 (289)
T ss_dssp             CCSEEEECCC------CHHHHHHHHHHHHTTCCCCGGG--BCCCCSSHHHHHHHHHHHHTSSSCCSEEEESC
T ss_pred             CCeEEEEecCCccccHHHHHHHHHHHHHHCCCCCChHH--eEeCCCCHHHHHHHHHHHHhCCCCCCEEEECC
Confidence            45999998765444455567999999999997533221  235555432   234455544 5899999864

>2hqb_A Transcriptional activator of COMK gene; berkeley structure genomics center target 1957B, structural genomics, PSI; 2.70A {Bacillus halodurans}

Probab=84.27  E-value=1.4  Score=34.50  Aligned_cols=65  Identities=17%  Similarity=0.162  Sum_probs=37.5

Q ss_pred             CCCCEEEEEEee-ecH-HHHHHHHHHHHHHHHHCCCCCCCeEEEE-ecc-cchHHHHHHHHhhcCCCcEEEEee
Q 032216           73 NEGLRFALVVAR-FNE-LVTKLLLEGALETFKKYSVKEENIDVVW-VPG-SFEIGVVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        73 ~~~lRIaIVvAr-fN~-~It~~LleGA~~~L~~~Gv~~e~I~vv~-VPG-AfELPlaak~La~s~~yDAVIaLG  142 (145)
                      ++..+||+|+.. .++ .....+.+|..+.++++|+.   +.++. .+. .-|. -.++.|+ +.++|+||+.|
T Consensus         3 ~~~~~Ig~v~~~~~~d~~f~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~~~-~~l~~l~-~~~vdgIi~~~   71 (296)
T 2hqb_A            3 GGGGMVGLLVEDTIDDQGWNRKAYEGLLNIHSNLDVD---VVLEEGVNSEQKAH-RRIKELV-DGGVNLIFGHG   71 (296)
T ss_dssp             ---CEEEEECCCC----CCTHHHHHHHHHHHHHSCCE---EEEECCCCSHHHHH-HHHHHHH-HTTCCEEEECS
T ss_pred             CCCcEEEEEECCCCCCCcHHHHHHHHHHHHHHHhCCe---EEEEeCCCCHHHHH-HHHHHHH-HCCCCEEEEcC
Confidence            345689998852 333 44556888888999999973   33321 121 2222 2455555 45799999876

>3gyb_A Transcriptional regulators (LACI-family transcriptional regulatory protein); protein structure initiative II(PSI II), nysgxrc; 1.60A {Corynebacterium glutamicum}

Probab=84.08  E-value=2.9  Score=31.17  Aligned_cols=63  Identities=11%  Similarity=-0.083  Sum_probs=44.4

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHH---HHHHh-hcCCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVV---AQQLG-KSGKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPla---ak~La-~s~~yDAVIaLG  142 (145)
                      ..||+++...-..  ...-.+|..+.|+++|....   ..++++.++..-+   ++.++ +..++|||+|..
T Consensus       118 ~~~i~~i~~~~~~--~~~R~~gf~~~l~~~~~~~~---~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~  184 (280)
T 3gyb_A          118 HTHIAHLRVGSGA--GLRRFESFEATMRAHGLEPL---SNDYLGPAVEHAGYTETLALLKEHPEVTAIFSSN  184 (280)
T ss_dssp             CCSEEEECCSSHH--HHHHHHHHHHHHHHTTCCCE---ECCCCSCCCHHHHHHHHHHHHHHCTTCCEEEESS
T ss_pred             CCeEEEEeCCCch--HHHHHHHHHHHHHHcCcCCC---cccccCCCCHHHHHHHHHHHHhCCCCCCEEEECC
Confidence            4589999987766  66677999999999998632   2236777665433   34444 446899999853

>3kjx_A Transcriptional regulator, LACI family; LACL family, protein structure initiative II(PSI II), NYSGXRC, structural genomics; 2.33A {Silicibacter pomeroyi}

Probab=83.96  E-value=2.5  Score=33.08  Aligned_cols=65  Identities=15%  Similarity=0.182  Sum_probs=42.6

Q ss_pred             CCEEEEEEeeec-HHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH---HHHHHhh-cCCCcEEEEe
Q 032216           75 GLRFALVVARFN-ELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGK-SGKYTAVLCI  141 (145)
Q Consensus        75 ~lRIaIVvArfN-~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl---aak~La~-s~~yDAVIaL  141 (145)
                      ..||+++....+ ....+.=.+|..+.|+++|+..+...+  .+|.+..--   +++.+++ ..++|||+|.
T Consensus       185 ~~~I~~i~~~~~~~~~~~~R~~Gf~~al~~~g~~~~~~~~--~~~~~~~~~~~~~~~~ll~~~~~~~ai~~~  254 (344)
T 3kjx_A          185 YRRIGFMGTKMPLDYRARKRFEGFTEVLGKNGVEIEDREF--YSGGSALAKGREMTQAMLERSPDLDFLYYS  254 (344)
T ss_dssp             CCSCCEEESSTTTCHHHHHHHHHHHHHHHHTTCCCSCEEE--CSSCCCHHHHHHHHHHHHHHSTTCCEEEES
T ss_pred             CCeEEEEecCcccCccHHHHHHHHHHHHHHcCCCCChheE--EeCCCCHHHHHHHHHHHHhcCCCCCEEEEC
Confidence            358999998761 234444569999999999987543333  445554432   3444544 4589999985

>3hut_A Putative branched-chain amino acid ABC transporter; extracellular ligand-binding receptor,transport protein; 1.93A {Rhodospirillum rubrum atcc 11170}

Probab=83.93  E-value=3  Score=32.19  Aligned_cols=65  Identities=9%  Similarity=-0.052  Sum_probs=46.3

Q ss_pred             CCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEee
Q 032216           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        74 ~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG  142 (145)
                      ...||++|.  -+......+.++..+.|+++|+... -....-+|..+.--.++++.+ .+.|+|++.+
T Consensus       138 g~~~ia~i~--~~~~~~~~~~~~~~~~l~~~g~~v~-~~~~~~~~~~~~~~~~~~l~~-~~~d~i~~~~  202 (358)
T 3hut_A          138 GFTSVAVIG--VTTDWGLSSAQAFRKAFELRGGAVV-VNEEVPPGNRRFDDVIDEIED-EAPQAIYLAM  202 (358)
T ss_dssp             TCCEEEEEE--ESSHHHHHHHHHHHHHHHHTTCEEE-EEEEECTTCCCCHHHHHHHHH-HCCSEEEEES
T ss_pred             CCCEEEEEe--cCcHHHHHHHHHHHHHHHHcCCEEE-EEEecCCCCccHHHHHHHHHh-cCCCEEEEcc
Confidence            346999997  3556678899999999999998521 122334577777667777754 4689999865

>4b4k_A N5-carboxyaminoimidazole ribonucleotide mutase; isomerase; 2.50A {Bacillus anthracis}

Probab=83.90  E-value=4.8  Score=31.92  Aligned_cols=68  Identities=4%  Similarity=0.106  Sum_probs=47.8

Q ss_pred             ccccCCCCCCE--EEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhh---cCCCcEEEEe
Q 032216           67 TGFLTKNEGLR--FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGK---SGKYTAVLCI  141 (145)
Q Consensus        67 ~g~l~~~~~lR--IaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~---s~~yDAVIaL  141 (145)
                      ++-++.+..+|  |+||.+.--+.   .-.+.|.+.|++.|+.    ..++|-+|--.|--+..+++   ..+++.|||.
T Consensus        12 s~~~p~~~~mkp~V~IimGS~SD~---~v~~~a~~~L~~~gI~----~e~~V~SAHRtp~~l~~~~~~a~~~g~~ViIa~   84 (181)
T 4b4k_A           12 SGLVPRGSHMKSLVGVIMGSTSDW---ETMKYACDILDELNIP----YEKKVVSAHRTPDYMFEYAETARERGLKVIIAG   84 (181)
T ss_dssp             ----------CCSEEEEESSGGGH---HHHHHHHHHHHHTTCC----EEEEECCTTTSHHHHHHHHHHTTTTTCCEEEEE
T ss_pred             cccccCCCCCCccEEEEECCHhHH---HHHHHHHHHHHHcCCC----eeEEEEccccChHHHHHHHHHHHhcCceEEEEe
Confidence            34445555555  99999888877   5678999999999996    45789999999987777653   4578988875

>3sg0_A Extracellular ligand-binding receptor; structural genomics, PSI-biology; HET: 173; 1.20A {Rhodopseudomonas palustris} PDB: 4dqd_A*

Probab=83.71  E-value=3.3  Score=32.07  Aligned_cols=65  Identities=8%  Similarity=-0.020  Sum_probs=47.1

Q ss_pred             CCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEee
Q 032216           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        74 ~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG  142 (145)
                      ...||++|..  +....+.+.++..+.|+++|+.... .....+|..+.--.++++.+ .+.|+|++.+
T Consensus       158 g~~~ia~i~~--~~~~~~~~~~~~~~~l~~~g~~v~~-~~~~~~~~~d~~~~~~~~~~-~~~dav~~~~  222 (386)
T 3sg0_A          158 GAKKVGYIGF--SDAYGEGYYKVLAAAAPKLGFELTT-HEVYARSDASVTGQVLKIIA-TKPDAVFIAS  222 (386)
T ss_dssp             TCCEEEEEEE--SSHHHHHHHHHHHHHHHHHTCEECC-CEEECTTCSCCHHHHHHHHH-TCCSEEEEEC
T ss_pred             CCCEEEEEec--CchHHHHHHHHHHHHHHHcCCEEEE-EEeeCCCCCcHHHHHHHHHh-cCCCEEEEec
Confidence            3469999954  5667788999999999999975221 23345677777666777654 5789998865

>3g1w_A Sugar ABC transporter; sugar-binding protein, bacillus halod target 11229F, transport protein, structural genomics; 2.02A {Bacillus halodurans c-125}

Probab=83.69  E-value=3.6  Score=31.11  Aligned_cols=75  Identities=19%  Similarity=0.122  Sum_probs=46.6

Q ss_pred             hhhhhhccccCCCCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEE-ecccchHHH---HHHHHhh-cCCC
Q 032216           61 EAVRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVW-VPGSFEIGV---VAQQLGK-SGKY  135 (145)
Q Consensus        61 ~a~~~~~g~l~~~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~-VPGAfELPl---aak~La~-s~~y  135 (145)
                      .|++++-..+  ....||+++...-+ .....-.+|..+.|+++|..   ++..+ ..|.+..--   +++.+++ ..++
T Consensus       115 ~~~~~l~~~~--~g~~~i~~i~~~~~-~~~~~R~~gf~~~l~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  188 (305)
T 3g1w_A          115 NAAYKMAELL--DGEGEVAVITLPNQ-LNHQERTTGFKETLEAEFPA---IEVIAVEDGRGDSLHSRRVAHQLLEDYPNL  188 (305)
T ss_dssp             HHHHHHHHHT--TTCEEEEEEECTTC-HHHHHHHHHHHHHHHHHCTT---EEEEEEEECTTCHHHHHHHHHHHHHHCTTE
T ss_pred             HHHHHHHHHh--CCCcEEEEEeCCCc-ccHHHHHHHHHHHHHhhCCC---CEEEEEecCCCCHHHHHHHHHHHHHhCCCc
Confidence            3445544433  13458999987644 45566679999999999875   33332 245554332   3344444 4589


Q ss_pred             cEEEEe
Q 032216          136 TAVLCI  141 (145)
Q Consensus       136 DAVIaL  141 (145)
                      |||+|.
T Consensus       189 ~ai~~~  194 (305)
T 3g1w_A          189 AGIFAT  194 (305)
T ss_dssp             EEEEES
T ss_pred             eEEEEC
Confidence            999985

>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=83.68  E-value=4.6  Score=31.51  Aligned_cols=64  Identities=16%  Similarity=0.022  Sum_probs=44.2

Q ss_pred             CEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHH---HHHHh-hcCCCcEEEEee
Q 032216           76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVV---AQQLG-KSGKYTAVLCIG  142 (145)
Q Consensus        76 lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPla---ak~La-~s~~yDAVIaLG  142 (145)
                      .||+++...-.....+.-.+|..+.|+++|.. +  ....++|.+...-+   ++.++ +..++|||+|..
T Consensus       146 ~~i~~i~g~~~~~~~~~R~~Gf~~~l~~~~~~-~--~~~~~~~~~~~~~~~~~~~~~L~~~~~~~aI~~~~  213 (350)
T 3h75_A          146 IELLAFSGLKVTPAAQLRERGLRRALAEHPQV-H--LRQLVYGEWNRERAYRQAQQLLKRYPKTQLVWSAN  213 (350)
T ss_dssp             EEEEEEESCTTSHHHHHHHHHHHHHHHHCTTE-E--EEEEEECTTCHHHHHHHHHHHHHHCTTEEEEEESS
T ss_pred             ceEEEEeCCCCCHHHHHHHHHHHHHHHHCCCe-E--EEEEeeCCCcHHHHHHHHHHHHHhCCCcCEEEECC
Confidence            69999998766666667789999999999862 2  22345666655433   33344 446799999864

>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=83.61  E-value=3.6  Score=31.86  Aligned_cols=65  Identities=11%  Similarity=-0.028  Sum_probs=45.5

Q ss_pred             CCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEee
Q 032216           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        74 ~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG  142 (145)
                      ...||++|..  +........++..+.|+++|+... -....-+|..+.--.++++.+ .+.|+|++.+
T Consensus       150 g~~~ia~i~~--~~~~~~~~~~~~~~~l~~~G~~v~-~~~~~~~~~~d~~~~~~~l~~-~~~dai~~~~  214 (375)
T 4evq_A          150 GLKKAVTVTW--KYAAGEEMVSGFKKSFTAGKGEVV-KDITIAFPDVEFQSALAEIAS-LKPDCVYAFF  214 (375)
T ss_dssp             TCCEEEEEEE--SSHHHHHHHHHHHHHHHHTTCEEE-EEEEECTTCCCCHHHHHHHHH-HCCSEEEEEC
T ss_pred             CCcEEEEEec--CchHHHHHHHHHHHHHHHcCCeEE-EEEecCCCCccHHHHHHHHHh-cCCCEEEEec
Confidence            3469999974  455677889999999999998411 122234576666666777654 3689999854

>3clk_A Transcription regulator; 11017J, PSI-II, NYSGXRC, dimer, structural genomics, protein structure initiative; 2.08A {Lactobacillus plantarum WCFS1}

Probab=83.08  E-value=1.5  Score=33.20  Aligned_cols=66  Identities=12%  Similarity=0.194  Sum_probs=42.5

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH---HHHHHhhcCCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl---aak~La~s~~yDAVIaLG  142 (145)
                      ..||+++...-+......-.+|..+.|+++|+..+...+  ++|.|...-   +++.+++..++|||+|..
T Consensus       125 ~~~i~~i~~~~~~~~~~~R~~gf~~~l~~~g~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~ai~~~~  193 (290)
T 3clk_A          125 HRQIGIAGIDQYPYTGRKRLAGYKKALKEANIAINQEWI--KPGDYSYTSGEQAMKAFGKNTDLTGIIAAS  193 (290)
T ss_dssp             CCSEEEESCCCCTTTHHHHHHHHHHHHHHTTCCCCGGGE--ECCCSSHHHHHHHHHHHCTTCCCSEEEESS
T ss_pred             CCEEEEEeCCCCCcchHHHHHHHHHHHHHcCCCCCcceE--EcCCCChhhHHHHHHHHhccCCCcEEEECC
Confidence            458999987644444445679999999999976332212  356554442   334444445799999863

>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=82.88  E-value=2.9  Score=34.04  Aligned_cols=60  Identities=15%  Similarity=0.134  Sum_probs=39.0

Q ss_pred             CCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEE
Q 032216           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLC  140 (145)
Q Consensus        73 ~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIa  140 (145)
                      ++..+||+|.. .+...-..+++|+.+.++++|..   +.+......-+.   ++.+ .+.++||||.
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            45568999996 66666667999999999999974   566654443332   3333 4568999986

>3k9c_A Transcriptional regulator, LACI family protein; PSI-II, 11026W, structural genomics, PR structure initiative; 2.14A {Rhodococcus jostii}

Probab=82.77  E-value=2.3  Score=32.30  Aligned_cols=63  Identities=14%  Similarity=-0.005  Sum_probs=44.2

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH---HHHHHhh-cCCCcEEEEe
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGK-SGKYTAVLCI  141 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl---aak~La~-s~~yDAVIaL  141 (145)
                      ..||+++....+. ..+.-.+|..+.|+++|...+.   ..++|.++.--   +++++++ ..++|||+|.
T Consensus       126 ~~~I~~i~~~~~~-~~~~R~~Gf~~al~~~g~~~~~---~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~  192 (289)
T 3k9c_A          126 HRNIAHIDGADAP-GGADRRAGFLAAMDRHGLSASA---TVVTGGTTETEGAEGMHTLLEMPTPPTAVVAF  192 (289)
T ss_dssp             CCSEEEECCTTST-THHHHHHHHHHHHHHTTCGGGE---EEECCCSSHHHHHHHHHHHHTSSSCCSEEEES
T ss_pred             CCcEEEEeCCCCc-cHHHHHHHHHHHHHHCCCCCCc---cEEECCCCHHHHHHHHHHHHcCCCCCCEEEEC
Confidence            4589999987766 4556679999999999986322   34566665543   3444554 4589999985

>3e3m_A Transcriptional regulator, LACI family; structural genomics, DNA-binding, plasmid, transcription regulation, PSI-2; 1.60A {Silicibacter pomeroyi}

Probab=82.52  E-value=1.7  Score=34.32  Aligned_cols=67  Identities=6%  Similarity=0.105  Sum_probs=43.0

Q ss_pred             CCCEEEEEEeeecHHH-HHHHHHHHHHHHHHCCCCCCCeEEEEecccchHH---HHHHHHhh-cCCCcEEEEe
Q 032216           74 EGLRFALVVARFNELV-TKLLLEGALETFKKYSVKEENIDVVWVPGSFEIG---VVAQQLGK-SGKYTAVLCI  141 (145)
Q Consensus        74 ~~lRIaIVvArfN~~I-t~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELP---laak~La~-s~~yDAVIaL  141 (145)
                      ...||+++....+... .+.-.+|..+.|+++|+..+.. +....+.+..-   -+++++++ ..++|||+|.
T Consensus       186 G~r~I~~i~~~~~~~~~~~~R~~Gf~~al~~~g~~~~~~-~~~~~~~~~~~~~~~~~~~ll~~~~~~~ai~~~  257 (355)
T 3e3m_A          186 GFRKIVFLGEKDDDWTRGAARRAGFKRAMREAGLNPDQE-IRLGAPPLSIEDGVAAAELILQEYPDTDCIFCV  257 (355)
T ss_dssp             TCCSEEEEEESSCTTSHHHHHHHHHHHHHHHTTSCSCCE-EEESCSSCCHHHHHHHHHHHHHHCTTCCEEEES
T ss_pred             CCCeEEEEccCcccChhHHHHHHHHHHHHHHCCcCCCcc-EEEecCCCCHHHHHHHHHHHHcCCCCCcEEEEC
Confidence            3459999998655432 4455799999999999875432 33334444322   23344444 4689999985

>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=82.21  E-value=5.4  Score=30.81  Aligned_cols=63  Identities=13%  Similarity=0.010  Sum_probs=44.8

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEe-cccchHHHHHHHHhhcCCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWV-PGSFEIGVVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~V-PGAfELPlaak~La~s~~yDAVIaLG  142 (145)
                      ..||++|..  +......+.++..+.|+++|+.  -+....+ +|..+.--.++++.+ .+.|+|++.+
T Consensus       139 ~~~ia~i~~--~~~~g~~~~~~~~~~l~~~g~~--v~~~~~~~~~~~d~~~~~~~l~~-~~~d~v~~~~  202 (368)
T 4eyg_A          139 IKKVATLTS--DYAPGNDALAFFKERFTAGGGE--IVEEIKVPLANPDFAPFLQRMKD-AKPDAMFVFV  202 (368)
T ss_dssp             CCEEEEEEE--SSHHHHHHHHHHHHHHHHTTCE--EEEEEEECSSSCCCHHHHHHHHH-HCCSEEEEEC
T ss_pred             CCEEEEEec--CchHhHHHHHHHHHHHHHcCCE--EEEEEeCCCCCCcHHHHHHHHHh-cCCCEEEEec
Confidence            469999984  5556777889999999999974  2223333 466666666777654 4689999854

>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=81.80  E-value=6  Score=30.23  Aligned_cols=64  Identities=8%  Similarity=0.063  Sum_probs=41.5

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH---HHHHHhh-cCCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGK-SGKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl---aak~La~-s~~yDAVIaLG  142 (145)
                      ..||+++...-+....+.-.+|..+.|++.|+..  ..  ...+.++..-   +++.+++ ..++|||+|..
T Consensus       123 ~~~I~~i~~~~~~~~~~~R~~gf~~~l~~~g~~~--~~--~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~  190 (313)
T 2h3h_A          123 KGKVVIGTGSLTAMNSLQRIQGFKDAIKDSEIEI--VD--ILNDEEDGARAVSLAEAALNAHPDLDAFFGVY  190 (313)
T ss_dssp             CSEEEEEESCSSCHHHHHHHHHHHHHHTTSSCEE--EE--EEECSSCHHHHHHHHHHHHHHCTTCCEEEECS
T ss_pred             CCEEEEEECCCCCccHHHHHHHHHHHhcCCCCEE--EE--eecCCCCHHHHHHHHHHHHHHCcCceEEEEcC
Confidence            4599999987554455566799999999988741  12  2345454332   3344444 45799999863

>3rpe_A MDAB, modulator of drug activity B; structural genomics, center for structural genomics of infec diseases, csgid, flavodoxin-like fold; HET: FAD; 1.10A {Yersinia pestis}

Probab=81.47  E-value=4.8  Score=31.70  Aligned_cols=59  Identities=8%  Similarity=0.070  Sum_probs=46.1

Q ss_pred             CEEEEEEeeec-----HHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEE
Q 032216           76 LRFALVVARFN-----ELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLC  140 (145)
Q Consensus        76 lRIaIVvArfN-----~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIa  140 (145)
                      +||.||.+-=+     ...+..|++.+.+.|++.|.   +++++++...+++.-..+++.   ..|+||-
T Consensus        26 ~kiLiI~gsp~~~~s~~s~n~~L~~~~~~~l~~~g~---ev~~~dL~~~~Dv~~~~~~l~---~aD~iv~   89 (218)
T 3rpe_A           26 SNVLIINAMKEFAHSKGALNLTLTNVAADFLRESGH---QVKITTVDQGYDIESEIENYL---WADTIIY   89 (218)
T ss_dssp             CCEEEEECCCCBTTBCSHHHHHHHHHHHHHHHHTTC---CEEEEEGGGCCCHHHHHHHHH---HCSEEEE
T ss_pred             cceEEEEeCCCcccCCChHHHHHHHHHHHHHhhCCC---EEEEEECCCccCHHHHHHHHH---hCCEEEE
Confidence            58999987653     47888999999999998886   478888887788776666665   6788774

>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=81.46  E-value=8.7  Score=30.15  Aligned_cols=64  Identities=16%  Similarity=0.146  Sum_probs=42.4

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH---HHHHHhhc-CCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGKS-GKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl---aak~La~s-~~yDAVIaLG  142 (145)
                      ..||+++....+......=.+|..+.|+++|+...  .+  .+|.|...-   +++.+++. .++|||+|..
T Consensus       179 ~~~I~~i~g~~~~~~~~~R~~Gf~~al~~~gi~~~--~~--~~~~~~~~~~~~~~~~ll~~~~~~~ai~~~n  246 (349)
T 1jye_A          179 HQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPI--AE--REGDWSAMSGFQQTMQMLNEGIVPTAMLVAN  246 (349)
T ss_dssp             CCSEEEEECCTTSHHHHHHHHHHHHHHHHTTCCCS--EE--EECCSSHHHHHHHHHHHHHTTCCCSEEEESS
T ss_pred             CCEEEEEeCCCCCccHHHHHHHHHHHHHHcCCCcc--cc--ccCCCChHHHHHHHHHHHhCCCCCCEEEECC
Confidence            45899999876544455567999999999998532  22  345554332   33444444 5799999863

>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=81.43  E-value=2  Score=31.73  Aligned_cols=77  Identities=19%  Similarity=0.140  Sum_probs=48.1

Q ss_pred             hhhhhhccccCCCCCCEEEEEEeeecHHHHHHHHHHHHHHHHHC-CCCCCCeEEEEecccchHHHH---HHHHhh-cCCC
Q 032216           61 EAVRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKY-SVKEENIDVVWVPGSFEIGVV---AQQLGK-SGKY  135 (145)
Q Consensus        61 ~a~~~~~g~l~~~~~lRIaIVvArfN~~It~~LleGA~~~L~~~-Gv~~e~I~vv~VPGAfELPla---ak~La~-s~~y  135 (145)
                      .+++++-..+......||+++...-+......-.+|..+.|+++ |+.   +. ..+.+.+...-+   ++.+++ ..++
T Consensus       113 ~~~~~l~~~~~~~G~~~i~~i~~~~~~~~~~~R~~gf~~~l~~~~~~~---~~-~~~~~~~~~~~~~~~~~~~l~~~~~~  188 (276)
T 3ksm_A          113 LAARALLATLDLSKERNIALLRLRAGNASTDQREQGFLDVLRKHDKIR---II-AAPYAGDDRGAARSEMLRLLKETPTI  188 (276)
T ss_dssp             HHHHHHHHHSCTTSCEEEEECBCCTTCHHHHHHHHHHHHHHTTCTTEE---EE-ECCBCCSSHHHHHHHHHHHHHHCSCC
T ss_pred             HHHHHHHHhcCcCCCceEEEEEcCCCchhHHHHHHHHHHHHHhCCCcE---EE-EEecCCCcHHHHHHHHHHHHHhCCCc
Confidence            34455433321114569999988766666667789999999988 653   21 234566655433   344444 4589


Q ss_pred             cEEEEe
Q 032216          136 TAVLCI  141 (145)
Q Consensus       136 DAVIaL  141 (145)
                      |||+|.
T Consensus       189 ~ai~~~  194 (276)
T 3ksm_A          189 DGLFTP  194 (276)
T ss_dssp             CEEECC
T ss_pred             eEEEEC
Confidence            999985

>3okf_A 3-dehydroquinate synthase; structural genomics, center for structural genomics of infec diseases, csgid, NAD, lyase; HET: NAD; 2.50A {Vibrio cholerae o1 biovar eltor}

Probab=81.41  E-value=8.5  Score=32.95  Aligned_cols=63  Identities=11%  Similarity=0.170  Sum_probs=40.2

Q ss_pred             CCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecc-----cchHHHHHHHHhhcCCC---cEEEEee
Q 032216           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPG-----SFEIGVVAQQLGKSGKY---TAVLCIG  142 (145)
Q Consensus        74 ~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPG-----AfELPlaak~La~s~~y---DAVIaLG  142 (145)
                      .+.|+.||..+.-..   ...+...+.|++.|+.   +.++.+|+     .+|-=..+-..+...++   |.||++|
T Consensus        61 ~~~rvlIVtd~~v~~---~~~~~v~~~L~~~g~~---~~~~~~~~gE~~kt~~~v~~~~~~l~~~~~~R~d~IIAvG  131 (390)
T 3okf_A           61 AKQKVVIVTNHTVAP---LYAPAIISLLDHIGCQ---HALLELPDGEQYKTLETFNTVMSFLLEHNYSRDVVVIALG  131 (390)
T ss_dssp             TTCEEEEEEETTTHH---HHHHHHHHHHHHHTCE---EEEEEECSSGGGCBHHHHHHHHHHHHHTTCCTTCEEEEEE
T ss_pred             CCCEEEEEECCcHHH---HHHHHHHHHHHHcCCe---EEEEEECCCcCCchHHHHHHHHHHHHhcCCCcCcEEEEEC
Confidence            456899988765443   3667777888888874   56667787     33333333223334444   8999998

>3l6u_A ABC-type sugar transport system periplasmic compo; structural genomics, nysgrc, target 11006S, PSI-2, protein S initiative; 1.90A {Exiguobacterium sibiricum}

Probab=81.01  E-value=4.6  Score=30.22  Aligned_cols=61  Identities=20%  Similarity=0.214  Sum_probs=42.1

Q ss_pred             EEEEEEeeecHHHHHHHHHHHHHHHHHC-CCCCCCeEEEEecccchHHHH---HHHHhh-cCCCcEEEEe
Q 032216           77 RFALVVARFNELVTKLLLEGALETFKKY-SVKEENIDVVWVPGSFEIGVV---AQQLGK-SGKYTAVLCI  141 (145)
Q Consensus        77 RIaIVvArfN~~It~~LleGA~~~L~~~-Gv~~e~I~vv~VPGAfELPla---ak~La~-s~~yDAVIaL  141 (145)
                      ||+++...-+......-.+|..+.|+++ |+.   +.. ...|.+...-+   ++.+++ ..++|||+|.
T Consensus       137 ~i~~i~g~~~~~~~~~R~~gf~~~l~~~~g~~---~~~-~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~  202 (293)
T 3l6u_A          137 RIVEITGTANVYTTNERHRGFLKGIENEPTLS---IVD-SVSGNYDPVTSERVMRQVIDSGIPFDAVYCH  202 (293)
T ss_dssp             EEEEEECSTTCHHHHHHHHHHHHHHTTCTTEE---EEE-EEECTTCHHHHHHHHHHHHHTTCCCSEEEES
T ss_pred             eEEEEECCCCCchHHHHHHHHHHHHHhCCCcE---Eee-eccCCCCHHHHHHHHHHHHHhCCCCCEEEEC
Confidence            9999997766666677789999999998 763   221 24565554433   344444 4689999986

>3brs_A Periplasmic binding protein/LACI transcriptional; structural genomics, protein structure initiative; 2.00A {Clostridium phytofermentans}

Probab=80.94  E-value=4.7  Score=30.12  Aligned_cols=64  Identities=11%  Similarity=-0.052  Sum_probs=41.5

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH---HHHHHhh-cCCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGK-SGKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl---aak~La~-s~~yDAVIaLG  142 (145)
                      ..||+++...-+....+.-.+|..+.++++|..   +.. .++|.+...-   +++.+++ ..++|||+|..
T Consensus       131 ~~~i~~i~~~~~~~~~~~R~~gf~~~l~~~g~~---~~~-~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~  198 (289)
T 3brs_A          131 SGKIGVISFVKNSKTAMDREEGLKIGLSDDSNK---IEA-IYYCDSNYDKAYDGTVELLTKYPDISVMVGLN  198 (289)
T ss_dssp             SCEEEEEESCTTSHHHHHHHHHHHHHHGGGGGG---EEE-EEECTTCHHHHHHHHHHHHHHCTTEEEEEESS
T ss_pred             CceEEEEECCCCCccHHHHHHHHHHHHHhCCCc---EEe-eecCCCCHHHHHHHHHHHHHhCCCceEEEECC
Confidence            469999987755455566679999999999863   221 2345443322   2344444 45799999863

>3i09_A Periplasmic branched-chain amino acid-binding Pro; type I periplasmic binding protein, structural genomics, JOI for structural genomics; HET: MSE CIT; 1.80A {Burkholderia mallei}

Probab=80.54  E-value=7.5  Score=30.34  Aligned_cols=64  Identities=14%  Similarity=0.050  Sum_probs=45.3

Q ss_pred             CCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEe-cccchHHHHHHHHhhcCCCcEEEEee
Q 032216           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWV-PGSFEIGVVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        74 ~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~V-PGAfELPlaak~La~s~~yDAVIaLG  142 (145)
                      ...||++|..  |....+.+.++..+.|+++|+.  -+....+ +|..+.--.++++.+ .+.|+|++.+
T Consensus       139 g~~~vaii~~--~~~~g~~~~~~~~~~~~~~G~~--v~~~~~~~~~~~d~~~~l~~i~~-~~~d~v~~~~  203 (375)
T 3i09_A          139 GGKTWFFLTA--DYAFGKALEKNTADVVKANGGK--VLGEVRHPLSASDFSSFLLQAQS-SKAQILGLAN  203 (375)
T ss_dssp             TCCEEEEEEE--SSHHHHHHHHHHHHHHHHTTCE--EEEEEEECTTCSCCHHHHHHHHH-TCCSEEEEEC
T ss_pred             CCceEEEEec--ccHHHHHHHHHHHHHHHHcCCE--EeeeeeCCCCCccHHHHHHHHHh-CCCCEEEEec
Confidence            3569999965  4556778999999999999974  2223333 477776666666653 5789998754

>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=80.53  E-value=7.5  Score=29.03  Aligned_cols=62  Identities=15%  Similarity=0.039  Sum_probs=40.8

Q ss_pred             CEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHH---HHHHHhh-cCCCcEEEEe
Q 032216           76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGV---VAQQLGK-SGKYTAVLCI  141 (145)
Q Consensus        76 lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPl---aak~La~-s~~yDAVIaL  141 (145)
                      .||+++...-+......=.+|..+.|+++|+.   +.. ..+|.|+..-   +++.+++ ..++|||+|.
T Consensus       124 ~~I~~i~g~~~~~~~~~R~~Gf~~al~~~g~~---~~~-~~~~~~~~~~~~~~~~~ll~~~~~~~ai~~~  189 (271)
T 2dri_A          124 AKVIELQGIAGTSAARERGEGFQQAVAAHKFN---VLA-SQPADFDRIKGLNVMQNLLTAHPDVQAVFAQ  189 (271)
T ss_dssp             CEEEEEECCTTCHHHHHHHHHHHHHHHHHTCE---EEE-EEECTTCHHHHHHHHHHHHHHCTTCCEEEES
T ss_pred             CeEEEEECCCCCccHhHHHHHHHHHHhcCCCE---EEE-ecCCCCCHHHHHHHHHHHHHhCCCccEEEEC
Confidence            59999987654444455569999999999874   221 2456554442   3344444 4579999985

>3ox4_A Alcohol dehydrogenase 2; iron, NAD, oxidoreductase; HET: NAD; 2.00A {Zymomonas mobilis} PDB: 3owo_A*

Probab=80.44  E-value=3.8  Score=34.25  Aligned_cols=62  Identities=13%  Similarity=0.111  Sum_probs=38.6

Q ss_pred             CCEEEEEEeeecHHHHHH-HHHHHHHHHHHCCCCCCCeEEE-EecccchHH--HHHHHHhhcCCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKL-LLEGALETFKKYSVKEENIDVV-WVPGSFEIG--VVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~-LleGA~~~L~~~Gv~~e~I~vv-~VPGAfELP--laak~La~s~~yDAVIaLG  142 (145)
                      ..|+.||..+   .+.+. +.+...+.|++.|+.   +.++ .|.+-=.+-  ..+-.+++..++|.||++|
T Consensus        31 ~~~~liVtd~---~~~~~g~~~~v~~~L~~~gi~---~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IIavG   96 (383)
T 3ox4_A           31 FKNALIVSDA---FMNKSGVVKQVADLLKAQGIN---SAVYDGVMPNPTVTAVLEGLKILKDNNSDFVISLG   96 (383)
T ss_dssp             CCEEEEEEEH---HHHHTTHHHHHHHHHHTTTCE---EEEEEEECSSCBHHHHHHHHHHHHHHTCSEEEEEE
T ss_pred             CCEEEEEECC---chhhCchHHHHHHHHHHcCCe---EEEECCccCCCCHHHHHHHHHHHHhcCcCEEEEeC
Confidence            3588888875   24443 678888899988874   3333 233322222  2233344566899999998

>3ors_A N5-carboxyaminoimidazole ribonucleotide mutase; isomerase, isomerase,biosynthetic protein; 1.45A {Staphylococcus aureus subsp}

Probab=80.21  E-value=8  Score=30.04  Aligned_cols=61  Identities=5%  Similarity=0.125  Sum_probs=50.1

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhh---cCCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGK---SGKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~---s~~yDAVIaLG  142 (145)
                      ..+|+||.+.--+.   .-.+.|.+.|++.|+.    ..++|-|+.-.|--...+++   ...++.||+..
T Consensus         3 ~~~V~Iimgs~SD~---~v~~~a~~~l~~~gi~----~ev~V~SaHR~p~~~~~~~~~a~~~g~~ViIa~A   66 (163)
T 3ors_A            3 AMKVAVIMGSSSDW---KIMQESCNMLDYFEIP----YEKQVVSAHRTPKMMVQFASEARERGINIIIAGA   66 (163)
T ss_dssp             CCCEEEEESCGGGH---HHHHHHHHHHHHTTCC----EEEEECCTTTSHHHHHHHHHHTTTTTCCEEEEEE
T ss_pred             CCeEEEEECcHHHH---HHHHHHHHHHHHcCCC----EEEEEECCcCCHHHHHHHHHHHHhCCCcEEEEEC
Confidence            35899999998877   5668899999999996    45689999999999888864   35689888764

>3h5t_A Transcriptional regulator, LACI family; DNA-dependent, protein structure initiative II(PSI II), NYSGXRC, 11232D), structural genomics; 2.53A {Corynebacterium glutamicum}

Probab=80.20  E-value=2.6  Score=33.26  Aligned_cols=66  Identities=14%  Similarity=0.183  Sum_probs=40.8

Q ss_pred             CCCCEEEEEEee-----ecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccch-HHHHHHHHhhcCCCcEEEEeee
Q 032216           73 NEGLRFALVVAR-----FNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE-IGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        73 ~~~lRIaIVvAr-----fN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfE-LPlaak~La~s~~yDAVIaLG~  143 (145)
                      .+...||+|...     |....-..+++|+.++++  |.   ++.++.....-+ -....-..+...++||||.++.
T Consensus        66 ~~s~~Igvi~~~~~~~~~~~~~~~~~~~gi~~~a~--g~---~~~~~~~~~~~~~~~~~~~~~l~~~~vdGiIi~~~  137 (366)
T 3h5t_A           66 RRAGAIGVLLTEDLTYAFEDMASVDFLAGVAQAAG--DT---QLTLIPASPASSVDHVSAQQLVNNAAVDGVVIYSV  137 (366)
T ss_dssp             --CCEEEEEESSCTTHHHHSHHHHHHHHHHHHHSS--SC---EEEEEECCCCTTCCHHHHHHHHHTCCCSCEEEESC
T ss_pred             CCCCEEEEEecCCccccccCHHHHHHHHHHHHHHh--hC---CEEEEEcCCCccHHHHHHHHHHHhCCCCEEEEecC
Confidence            445679999987     544555678899988877  54   355665543321 1122223344679999998764

---

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	145
d1c2ya_	155	c.16.1.1 (A:) Lumazine synthase {Spinach (Spinacia	5e-19
d1c41a_	195	c.16.1.1 (A:) Lumazine synthase {Rice blast fungus	7e-19
d1nqua_	154	c.16.1.1 (A:) Lumazine synthase {Aquifex aeolicus	6e-17
d1ejba_	168	c.16.1.1 (A:) Lumazine synthase {Baker's yeast (Sa	7e-17
d1kz1a_	150	c.16.1.1 (A:) Lumazine synthase {Fission yeast (Sc	3e-16
d1rvv1_	154	c.16.1.1 (1:) Lumazine synthase {Bacillus subtilis	4e-16
d1di0a_	148	c.16.1.1 (A:) Lumazine synthase {Brucella abortus	6e-16

>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 = 76.2 bits (187), Expect = 5e-19
 Identities = 54/83 (65%), Positives = 69/83 (83%), Gaps = 1/83 (1%)

Query: 63  VRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEI 122
           +  L G++TK +  RFA+VVARFNE VT+ L+EGAL+TFKKYSV E+  DVVWVPG++E+
Sbjct: 1   MNELEGYVTKAQSFRFAIVVARFNEFVTRRLMEGALDTFKKYSVNEDI-DVVWVPGAYEL 59

Query: 123 GVVAQQLGKSGKYTAVLCIGAVV 145
           GV AQ LGKSGKY A++C+GAVV
Sbjct: 60  GVTAQALGKSGKYHAIVCLGAVV 82

>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 = 76.7 bits (188), Expect = 7e-19
 Identities = 23/64 (35%), Positives = 33/64 (51%)

Query: 74  EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSG 133
             LR  +V AR+NE + + LL G         VKE NI V  VPGS+E+ +  Q+L  + 
Sbjct: 10  SALRIGIVHARWNETIIEPLLAGTKAKLLACGVKESNIVVQSVPGSWELPIAVQRLYSAS 69

Query: 134 KYTA 137
           +   
Sbjct: 70  QLQT 73

>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 = 70.4 bits (172), Expect = 6e-17
 Identities = 30/72 (41%), Positives = 47/72 (65%)

Query: 74  EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSG 133
           EGLRF +V +RFN  +   L+EGA++   ++  +EE+I +V VPGS+EI V A +L +  
Sbjct: 11  EGLRFGIVASRFNHALVDRLVEGAIDCIVRHGGREEDITLVRVPGSWEIPVAAGELARKE 70

Query: 134 KYTAVLCIGAVV 145
              AV+ IG ++
Sbjct: 71  DIDAVIAIGVLI 82

>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 = 70.8 bits (173), Expect = 7e-17
 Identities = 20/77 (25%), Positives = 38/77 (49%), Gaps = 5/77 (6%)

Query: 74  EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQL---- 129
             +R  ++ AR+N ++   L++GA+E      V+E NI +  VPGS+E+    ++     
Sbjct: 15  SKIRVGIIHARWNRVIIDALVKGAIERMASLGVEENNIIIETVPGSYELPWGTKRFVDRQ 74

Query: 130 -GKSGKYTAVLCIGAVV 145
                    V+ IG ++
Sbjct: 75  AKLGKPLDVVIPIGVLI 91

>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 = 68.5 bits (167), Expect = 3e-16
 Identities = 28/73 (38%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 74  EGLRFALVVARFNELVTKLLLEGALETF-KKYSVKEENIDVVWVPGSFEIGVVAQQLGKS 132
             LR  +V AR N    + L++GA+ET  +K+ VK ENID+  VPGS+E+    +     
Sbjct: 8   PELRILIVHARGNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSWELPQGIRASIAR 67

Query: 133 GKYTAVLCIGAVV 145
             Y AV+ IG ++
Sbjct: 68  NTYDAVIGIGVLI 80

>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 = 68.1 bits (166), Expect = 4e-16
 Identities = 29/72 (40%), Positives = 47/72 (65%)

Query: 74  EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSG 133
            GL+  +VV RFN+ +T  LL GA +   ++ V   +IDV WVPG+FEI   A+++ ++ 
Sbjct: 11  TGLKIGIVVGRFNDFITSKLLSGAEDALLRHGVDTNDIDVAWVPGAFEIPFAAKKMAETK 70

Query: 134 KYTAVLCIGAVV 145
           KY A++ +G V+
Sbjct: 71  KYDAIITLGTVI 82

>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 = 67.7 bits (165), Expect = 6e-16
 Identities = 14/71 (19%), Positives = 35/71 (49%)

Query: 75  GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGK 134
             + A + AR++  +     +  +      +     +++  VPG++EI + A+ L ++G+
Sbjct: 2   SFKIAFIQARWHADIVDEARKSFVAELAAKTGGSVEVEIFDVPGAYEIPLHAKTLARTGR 61

Query: 135 YTAVLCIGAVV 145
           Y A++    V+
Sbjct: 62  YAAIVGAAFVI 72

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	145
d1rvv1_	154	Lumazine synthase {Bacillus subtilis [TaxId: 1423]	99.95
d1nqua_	154	Lumazine synthase {Aquifex aeolicus [TaxId: 63363]	99.95
d1c2ya_	155	Lumazine synthase {Spinach (Spinacia oleracea) [Ta	99.95
d1di0a_	148	Lumazine synthase {Brucella abortus [TaxId: 235]}	99.94
d1ejba_	168	Lumazine synthase {Baker's yeast (Saccharomyces ce	99.94
d1kz1a_	150	Lumazine synthase {Fission yeast (Schizosaccharomy	99.93
d1c41a_	195	Lumazine synthase {Rice blast fungus (Magnaporthe	99.92
d1dbqa_	282	Purine repressor (PurR), C-terminal domain {Escher	95.86
d1tjya_	316	AI-2 receptor LsrB {Salmonella typhi [TaxId: 90370	94.77
d2nzug1	275	Glucose-resistance amylase regulator CcpA, C-termi	94.63
d1guda_	288	D-allose-binding protein {Escherichia coli [TaxId:	93.97
d1byka_	255	Trehalose repressor, C-terminal domain {Escherichi	93.18
d8abpa_	305	L-arabinose-binding protein {Escherichia coli [Tax	91.13
d2dria_	271	D-ribose-binding protein {Escherichia coli, strain	89.36
d1jyea_	271	Lac-repressor (lacR) core (C-terminal domain) {Esc	88.84
d2fvya1	305	Galactose/glucose-binding protein {Escherichia col	88.68
d1jyea_	271	Lac-repressor (lacR) core (C-terminal domain) {Esc	87.9
d1vlja_	398	NADH-dependent butanol dehydrogenase A (TM0820) {T	86.64
d2f7wa1	173	MogA {Shewanella oneidensis [TaxId: 70863]}	84.39
d1o2da_	359	Alcohol dehydrogenase TM0920 {Thermotoga maritima	82.25
d2qwxa1	230	Quinone reductase type 2 (menadione reductase) {Hu	81.76
d1rrma_	385	Lactaldehyde reductase FucO {Escherichia coli [Tax	80.46

>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=99.95  E-value=5.2e-29  Score=191.77  Aligned_cols=82  Identities=38%  Similarity=0.765  Sum_probs=78.5

Q ss_pred             hhhhccccCCCCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEee
Q 032216           63 VRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        63 ~~~~~g~l~~~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG  142 (145)
                      |+.++|.+. ++++||+||+|+||++|+++|++||+++|+++|+..++|++++||||||||+++++++++++||||||||
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            566788884 8999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeC
Q 032216          143 AVV  145 (145)
Q Consensus       143 ~VI  145 (145)
                      |||
T Consensus        80 ~VI   82 (154)
T d1rvv1_          80 TVI   82 (154)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            997

>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=99.95  E-value=1.1e-28  Score=189.96  Aligned_cols=82  Identities=40%  Similarity=0.675  Sum_probs=78.3

Q ss_pred             hhhhccccCCCCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEee
Q 032216           63 VRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        63 ~~~~~g~l~~~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG  142 (145)
                      |+.++|.+. ++++||+||+|+||++|+++|++||+++|+++|+..++|++++||||||||+++++++++++||||||||
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            566788884 8999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeC
Q 032216          143 AVV  145 (145)
Q Consensus       143 ~VI  145 (145)
                      |||
T Consensus        80 ~VI   82 (154)
T d1nqua_          80 VLI   82 (154)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            997

>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=99.95  E-value=1.9e-28  Score=188.90  Aligned_cols=82  Identities=67%  Similarity=1.179  Sum_probs=78.2

Q ss_pred             hhhhccccCCCCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEee
Q 032216           63 VRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        63 ~~~~~g~l~~~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG  142 (145)
                      |+.++|++++.+++|||||+|+||++|+++|++||+++|+++|++ ++++++|||||||||+++++|+++++||||||||
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 6799999999999999999999999999999999


Q ss_pred             eeC
Q 032216          143 AVV  145 (145)
Q Consensus       143 ~VI  145 (145)
                      |||
T Consensus        80 ~VI   82 (155)
T d1c2ya_          80 AVV   82 (155)
T ss_dssp             ECC
T ss_pred             EEE
Confidence            998

>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=99.94  E-value=2.9e-27  Score=180.81  Aligned_cols=72  Identities=19%  Similarity=0.402  Sum_probs=69.7

Q ss_pred             CCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeeeeC
Q 032216           74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVV  145 (145)
Q Consensus        74 ~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~VI  145 (145)
                      +++||+||+|+||++|+++|+++|+++|.++|+..++|+++|||||||||+++++|+++++|||||||||||
T Consensus         1 ss~rI~IV~s~~n~~i~~~ll~~a~~~l~~~g~~~~~i~~~~VPGa~EiP~aa~~l~~~~~~daiI~lG~VI   72 (148)
T d1di0a_           1 TSFKIAFIQARWHADIVDEARKSFVAELAAKTGGSVEVEIFDVPGAYEIPLHAKTLARTGRYAAIVGAAFVI   72 (148)
T ss_dssp             CCEEEEEEEECTTHHHHHHHHHHHHHHHHHHHTTSEEEEEEEESSGGGHHHHHHHHHHTSCCSEEEEEEECC
T ss_pred             CCCEEEEEEeeCCHHHHHHHHHHHHHHHHHcCCCcceeEEEEcCChhhhHHHHHHHHhhcccCeEEEEEEEe
Confidence            368999999999999999999999999999999989999999999999999999999999999999999997

>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=99.94  E-value=5.1e-27  Score=182.85  Aligned_cols=75  Identities=27%  Similarity=0.478  Sum_probs=71.3

Q ss_pred             CCCCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhh-----cCCCcEEEEeeeeC
Q 032216           71 TKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGK-----SGKYTAVLCIGAVV  145 (145)
Q Consensus        71 ~~~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~-----s~~yDAVIaLG~VI  145 (145)
                      .+++++||+||+|+||++|+++|++||+++|+++|+..++|+++|||||||||+++++|++     +++|||||||||||
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            3678999999999999999999999999999999999999999999999999999999985     47899999999997

>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=99.93  E-value=1.6e-26  Score=177.08  Aligned_cols=74  Identities=39%  Similarity=0.472  Sum_probs=70.4

Q ss_pred             CCCCCEEEEEEeeecHHHHHHHHHHHHHHHH-HCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeeeeC
Q 032216           72 KNEGLRFALVVARFNELVTKLLLEGALETFK-KYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGAVV  145 (145)
Q Consensus        72 ~~~~lRIaIVvArfN~~It~~LleGA~~~L~-~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~VI  145 (145)
                      +++++||+||+|+||++|+++|++||+++|+ +.|+..++|++++||||||||+++++++++++|||||||||||
T Consensus         6 ~~~~~rI~IV~s~~n~~i~~~L~~ga~~~l~~~~~~~~~~i~v~~VPGa~EiP~~~~~~~~~~~~D~iIalG~VI   80 (150)
T d1kz1a_           6 KGPELRILIVHARGNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSWELPQGIRASIARNTYDAVIGIGVLI   80 (150)
T ss_dssp             CCTTCCEEEEECCTTHHHHHHHHHHHHHHHHHHHCCCGGGEEEEECSSGGGHHHHHHHHHHHSCCSEEEEEEEEE
T ss_pred             CCCCCEEEEEEccCCHHHHHHHHHHHHHHHHHhcCCCccccEEEEeCCHHHHHHHHHHHHhccccceEEEEEEEe
Confidence            4788999999999999999999999999996 4689999999999999999999999999999999999999997

>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=99.92  E-value=8.9e-26  Score=180.17  Aligned_cols=74  Identities=36%  Similarity=0.616  Sum_probs=70.2

Q ss_pred             CCCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHH----------------------
Q 032216           72 KNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQL----------------------  129 (145)
Q Consensus        72 ~~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~L----------------------  129 (145)
                      +++++||+||+|+||++|++.|++||+++|+++|+.+++|++++||||||||+++|+|                      
T Consensus         8 d~s~lrI~IV~s~~n~~I~d~Ll~ga~~~L~~~Gv~~~~i~v~~VPGa~ElP~a~~~l~~~~~~~~~~~~~~~~~~~~~~   87 (195)
T d1c41a_           8 DGSALRIGIVHARWNETIIEPLLAGTKAKLLACGVKESNIVVQSVPGSWELPIAVQRLYSASQLQTPSSGPSLSAGDLLG   87 (195)
T ss_dssp             CCSSCCEEEEEECTTHHHHHHHHHHHHHHHHHTTCCGGGEEEEEESSTTHHHHHHHHHHHHHHHC---------------
T ss_pred             CCCCCEEEEEEccCCHHHHHHHHHHHHHHHHHcCCCcccCeEEECCcHHHHHHHHHHHHhhccccccccccccccccccc
Confidence            6889999999999999999999999999999999999999999999999999999998                      


Q ss_pred             --------------hhcCCCcEEEEeeeeC
Q 032216          130 --------------GKSGKYTAVLCIGAVV  145 (145)
Q Consensus       130 --------------a~s~~yDAVIaLG~VI  145 (145)
                                    +++++|||||||||||
T Consensus        88 ~~~~~~~~~~~~~~a~~~~yDaiIaLG~VI  117 (195)
T d1c41a_          88 SSTTDLTALPTTTASSTGPFDALIAIGVLI  117 (195)
T ss_dssp             ---------------CCSCCSEEEEEEEEE
T ss_pred             cccccccchhhhhhhhcCCccEEEEEEEEE
Confidence                          3567899999999997

>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=95.86  E-value=0.014  Score=42.11  Aligned_cols=65  Identities=6%  Similarity=-0.026  Sum_probs=49.2

Q ss_pred             CEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeee
Q 032216           76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        76 lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~  143 (145)
                      +.||+|+..++...-..+++|..++++++|+   ++.++...+..|.=.-+-..+.+.++||+|.++.
T Consensus         1 ktIg~i~~~~~~pf~~~~~~gi~~~~~~~gy---~~~~~~~~~d~~~~~~~~~~l~~~~vdgiIi~~~   65 (282)
T d1dbqa_           1 KSIGLLATSSEAAYFAEIIEAVEKNCFQKGY---TLILGNAWNNLEKQRAYLSMMAQKRVDGLLVMCS   65 (282)
T ss_dssp             CEEEEEESCTTSHHHHHHHHHHHHHHHHHTC---EEEEEECTTCHHHHHHHHHHHHHTTCSEEEEECS
T ss_pred             CEEEEEeCCCCCHHHHHHHHHHHHHHHHcCC---EEEEEeCCCCHHHHHHHHHHHHhcCCCEEeeecc
Confidence            3799999999988888899999999999998   3666666666664333333335678999987653

>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=94.77  E-value=0.032  Score=40.30  Aligned_cols=65  Identities=15%  Similarity=0.060  Sum_probs=48.2

Q ss_pred             CCCCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHH---HhhcCCCcEEEEee
Q 032216           73 NEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQ---LGKSGKYTAVLCIG  142 (145)
Q Consensus        73 ~~~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~---La~s~~yDAVIaLG  142 (145)
                      ++..|||+|+...+...-..+.+|+.++++++|+.   + ++..|+-.+..--.+.   ++ ..++|+||...
T Consensus         1 G~~~kI~~i~~~~~npf~~~~~~g~~~~a~~~G~~---v-~~~~~~~~d~~~q~~~i~~~i-~~~~dgIIi~~   68 (316)
T d1tjya_           1 GSAERIAFIPKLVGVGFFTSGGNGAQEAGKALGID---V-TYDGPTEPSVSGQVQLVNNFV-NQGYDAIIVSA   68 (316)
T ss_dssp             CCCCEEEEECSSSSSHHHHHHHHHHHHHHHHHTCE---E-EECCCSSCCHHHHHHHHHHHH-HTTCSEEEECC
T ss_pred             CCCCEEEEEeCCCCCHHHHHHHHHHHHHHHHcCCE---E-EEEECCCCCHHHHHHHHHHHH-hcCCCeeeecc
Confidence            35689999999999888889999999999999973   2 2234665665443333   33 46899999764

>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=94.63  E-value=0.068  Score=38.38  Aligned_cols=65  Identities=6%  Similarity=0.057  Sum_probs=46.6

Q ss_pred             CEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeee
Q 032216           76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        76 lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~  143 (145)
                      .-||+|+...+...-..+++|+.++++++|+.   ..++...+.-|.=..+-..+.+.++||+|..++
T Consensus         4 ~tIgvvvp~l~~~f~~~~~~gi~~~~~~~g~~---~~~~~~~~~~~~e~~~i~~~~~~~vdgii~~~~   68 (275)
T d2nzug1           4 TTVGVIIPDISNIFYAELARGIEDIATMYKYN---IILSNSDQNQDKELHLLNNMLGKQVDGIIFMSG   68 (275)
T ss_dssp             SEEEEEESCTTSHHHHHHHHHHHHHHHHTTCE---EEEEECTTCHHHHHHHHHHHHTTCCSEEEECCS
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHHHcCCE---EEEEECCCCHHHHHHHHHHHHhcCCceeecccc
Confidence            35999999887777788999999999999983   555555555443222222234578999998875

>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=93.97  E-value=0.1  Score=37.60  Aligned_cols=64  Identities=14%  Similarity=0.177  Sum_probs=49.9

Q ss_pred             CEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHH--hhcCCCcEEEEee
Q 032216           76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQL--GKSGKYTAVLCIG  142 (145)
Q Consensus        76 lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~L--a~s~~yDAVIaLG  142 (145)
                      .++|+|+...+...-..+.+|+.+.++++|+   ++.++..++-.+...-.+.+  +...++||||..+
T Consensus         2 ~~~a~i~~~~~npff~~i~~g~~~~a~~~g~---~~~i~~~~~~~d~~~q~~~i~~~i~~~~DgIi~~~   67 (288)
T d1guda_           2 AEYAVVLKTLSNPFWVDMKKGIEDEAKTLGV---SVDIFASPSEGDFQSQLQLFEDLSNKNYKGIAFAP   67 (288)
T ss_dssp             CEEEEEESCSSSHHHHHHHHHHHHHHHHHTC---CEEEEECSSTTCHHHHHHHHHHHHTSSEEEEEECC
T ss_pred             cEEEEEeCCCCCHHHHHHHHHHHHHHHHcCC---EEEEEecCCCCCHHHHHHHHHHHHhcCCCEEEEec
Confidence            3799999999988888899999999999997   47777778777766543333  2356799998753

>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=93.18  E-value=0.2  Score=36.16  Aligned_cols=66  Identities=17%  Similarity=0.121  Sum_probs=48.4

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEeee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG~  143 (145)
                      +.-|||++.+........+++|..+.++++|..   +.++..-..-|.-.-.-..+.+.++||||..++
T Consensus         2 ~k~Igvi~p~~~~~~~~~~~~~i~~~~~~~Gy~---~~~~~s~~d~~~~~~~i~~l~~~~vdgiIi~~~   67 (255)
T d1byka_           2 DKVVAIIVTRLDSLSENLAVQTMLPAFYEQGYD---PIMMESQFSPQLVAEHLGVLKRRNIDGVVLFGF   67 (255)
T ss_dssp             CCEEEEEESCTTCHHHHHHHHHHHHHHHHHTCE---EEEEECTTCHHHHHHHHHHHHTTTCCEEEEECC
T ss_pred             CCEEEEEeCCCCCHHHHHHHHHHHHHHHHcCCE---EEEEeCCCCHHHHHHHHHHHHhccccceeeccc
Confidence            457999998877777778999999999999974   555555555554443333345678999998763

>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=91.13  E-value=0.26  Score=35.76  Aligned_cols=64  Identities=13%  Similarity=0.032  Sum_probs=44.6

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHHhhcCCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~La~s~~yDAVIaLG  142 (145)
                      ++|||+|+..-+...-..+.+|+.++++++|+.   +........=+---.++.+. +.++||||...
T Consensus         1 ~~kIg~v~~~~~~p~~~~~~~g~~~aa~~~G~~---~i~~~~~d~~~q~~~i~~li-~~~vDgiIi~~   64 (305)
T d8abpa_           1 NLKLGFLVKQPEEPWFQTEWKFADKAGKDLGFE---VIKIAVPDGEKTLNAIDSLA-ASGAKGFVICT   64 (305)
T ss_dssp             CEEEEEEESCTTSHHHHHHHHHHHHHHHHHTEE---EEEEECCSHHHHHHHHHHHH-HTTCCEEEEEC
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHHHHcCCE---EEEEcCCCHHHHHHHHHHHH-HcCCCEEEEcc
Confidence            479999999999888888999999999999984   43333322212222333444 46899999764

>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=89.36  E-value=0.57  Score=32.83  Aligned_cols=59  Identities=17%  Similarity=0.072  Sum_probs=40.9

Q ss_pred             EEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHHHHH--hhcCCCcEEEEe
Q 032216           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQL--GKSGKYTAVLCI  141 (145)
Q Consensus        78 IaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaak~L--a~s~~yDAVIaL  141 (145)
                      ||+|+...++..-..+++|+.++++++|+.   +.  ..+...+.....+.+  +...++|++|..
T Consensus         4 Igvvvp~~~~~f~~~~~~gi~~~a~~~g~~---~~--i~~~~~~~~~~~~~i~~~~~~~~d~ii~~   64 (271)
T d2dria_           4 IALVVSTLNNPFFVSLKDGAQKEADKLGYN---LV--VLDSQNNPAKELANVQDLTVRGTKILLIN   64 (271)
T ss_dssp             EEEEESCSSSHHHHHHHHHHHHHHHHHTCE---EE--EEECTTCHHHHHHHHHHHTTTTEEEEEEC
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHHHHcCCE---EE--EEeCCCCHHHHHHHHHHHHhcCCcccccc
Confidence            899999987777778999999999999973   43  344545443333222  124678988864

>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=88.84  E-value=0.77  Score=33.20  Aligned_cols=62  Identities=8%  Similarity=0.081  Sum_probs=46.7

Q ss_pred             EEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEec--ccchHHHHHHHHhhcCCCcEEEEeee
Q 032216           78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVP--GSFEIGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        78 IaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VP--GAfELPlaak~La~s~~yDAVIaLG~  143 (145)
                      ||++.+........+++++..++++++|+.   +.+...-  +.-+..-.++.|.++ ++||||..+.
T Consensus         3 igv~~~~l~~~~~~~i~~~i~~~a~~~Gy~---v~v~~~~~~~~~~~~~~l~~l~~~-~vdgiIl~~~   66 (271)
T d1jyea_           3 IGVATSSLALHAPSQIVAAILSRADQLGAS---VVVSMVERSGVEACKTAVHNLLAQ-RVSGLIINYP   66 (271)
T ss_dssp             EEEEESCTTSHHHHHHHHHHHHHHHHTTCE---EEEEECCSSSHHHHHHHHHHHHTT-TCSCEEEESC
T ss_pred             EEEEeCCCCChHHHHHHHHHHHHHHHcCCE---EEEEECCCCCHHHHHHHHHHHHhc-CCCEEEeccc
Confidence            799999999999999999999999999984   4444332  223455667777654 7999997653

>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=88.68  E-value=0.91  Score=32.21  Aligned_cols=62  Identities=6%  Similarity=0.018  Sum_probs=43.3

Q ss_pred             CEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHHH---HHHhhcCCCcEEEEee
Q 032216           76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVA---QQLGKSGKYTAVLCIG  142 (145)
Q Consensus        76 lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPlaa---k~La~s~~yDAVIaLG  142 (145)
                      .|||+++...+...-..+.+|+.+++++++.    ++++...+....--..   +.|.. .++||||...
T Consensus         2 ~kIgv~~~~~~~~f~~~i~~gi~~~a~~~~~----~~l~~~~~~~~~~~q~~~i~~li~-~~vDgiii~~   66 (305)
T d2fvya1           2 TRIGVTIYKYDDNFMSVVRKAIEQDAKAAPD----VQLLMNDSQNDQSKQNDQIDVLLA-KGVKALAINL   66 (305)
T ss_dssp             EEEEEEESCTTSHHHHHHHHHHHHHHHTCTT----EEEEEEECTTCHHHHHHHHHHHHH-TTCSEEEECC
T ss_pred             cEEEEEeCCCCCHHHHHHHHHHHHHHHHcCC----cEEEEEcCCCCHHHHHHHHHHHHH-cCCCEEEeec
Confidence            5999999999998888999999999987731    3444444444443333   33443 5799998653

>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=87.90  E-value=0.72  Score=33.36  Aligned_cols=66  Identities=18%  Similarity=0.102  Sum_probs=44.7

Q ss_pred             CCEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccchHHHH-H-HHHhhcCCCcEEEEee
Q 032216           75 GLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVV-A-QQLGKSGKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfELPla-a-k~La~s~~yDAVIaLG  142 (145)
                      ..||++|...-+....+.-.+|+.+.+++++....  .....+...+--+- + +.+.+..++|||+|..
T Consensus       118 ~~~i~~i~~~~~~~~~~~R~~g~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~ai~~~~  185 (271)
T d1jyea_         118 HQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPI--AEREGDWSAMSGFQQTMQMLNEGIVPTAMLVAN  185 (271)
T ss_dssp             CCSEEEEECCTTSHHHHHHHHHHHHHHHHTTCCCS--EEEECCSSHHHHHHHHHHHHHTTCCCSEEEESS
T ss_pred             cccccccccccccchHHhhhHHHHHHhhhcccccc--ceeccccccccccchhhhhhhcccccchhhccc
Confidence            34899999887777788888999999999998632  33334433332222 2 2244556799999865

>d1vlja_ e.22.1.2 (A:) NADH-dependent butanol dehydrogenase A (TM0820) {Thermotoga maritima [TaxId: 2336]}

class: Multi-domain proteins (alpha and beta)
fold: Dehydroquinate synthase-like
superfamily: Dehydroquinate synthase-like
family: Iron-containing alcohol dehydrogenase
domain: NADH-dependent butanol dehydrogenase A (TM0820)
species: Thermotoga maritima [TaxId: 2336]

Probab=86.64  E-value=0.6  Score=36.97  Aligned_cols=62  Identities=18%  Similarity=0.146  Sum_probs=41.3

Q ss_pred             CCEEEEEEee--ecHHHHHHHHHHHHHHHHHCCCCCCCeEEEE-ecc--cchHHHHHHHHhhcCCCcEEEEee
Q 032216           75 GLRFALVVAR--FNELVTKLLLEGALETFKKYSVKEENIDVVW-VPG--SFEIGVVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvAr--fN~~It~~LleGA~~~L~~~Gv~~e~I~vv~-VPG--AfELPlaak~La~s~~yDAVIaLG  142 (145)
                      ..|+.||+++  |+..   .+.+..++.|++.|+.   +.++. +.+  .+|--.-+...++..++|.||++|
T Consensus        34 ~~rvliVt~~~~~~~~---g~~~~l~~~L~~~gi~---~~~f~~v~~~pt~~~v~~~~~~~~~~~~D~IIavG  100 (398)
T d1vlja_          34 IRKVLFLYGGGSIKKN---GVYDQVVDSLKKHGIE---WVEVSGVKPNPVLSKVHEAVEVAKKEKVEAVLGVG  100 (398)
T ss_dssp             CCEEEEEECSSHHHHS---SHHHHHHHHHHHTTCE---EEEECCCCSSCBHHHHHHHHHHHHHTTCSEEEEEE
T ss_pred             CCeEEEEECCcHHHHh---hHHHHHHHHHHhcCCe---EEEEcCccCCCCHHHHHHHhhhcccccCceEEecC
Confidence            3589999876  5543   3456667788888884   33332 322  355555555666778999999998

>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=84.39  E-value=0.47  Score=33.71  Aligned_cols=69  Identities=10%  Similarity=0.166  Sum_probs=45.7

Q ss_pred             CCEEEEEEee---ecHHHHHHHHHHHHHHHHHCCCCCCCeEEEEecccch-HHHHHHHHhhcCCCcEEEEeee
Q 032216           75 GLRFALVVAR---FNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFE-IGVVAQQLGKSGKYTAVLCIGA  143 (145)
Q Consensus        75 ~lRIaIVvAr---fN~~It~~LleGA~~~L~~~Gv~~e~I~vv~VPGAfE-LPlaak~La~s~~yDAVIaLG~  143 (145)
                      ..|||||+.-   ++..+.|.--....+.|.+.|.....+...-||--.| |=-++++++.+.+||-|++-|-
T Consensus         2 ~~rv~IitvsD~~~~G~~~D~~gp~l~~~L~~~G~~~~~v~~~ivpDd~~~I~~~l~~~~~~~~~dlIittGG   74 (173)
T d2f7wa1           2 KAKIGIVTVSDRASAGIYEDISGKAIIDTLNDYLTSEWEPIYQVIPDEQDVIETTLIKMADEQDCCLIVTTGG   74 (173)
T ss_dssp             CEEEEEEEECHHHHHCCSCCHHHHHHHHHHHHHBCSCEEEEEEEECSCHHHHHHHHHHHHHTSCEEEEEEESC
T ss_pred             CCEEEEEEeCCCCcCCCccCCCHHHHHHHHHHhCCCceEEEEEEcCCcHHHHHHHhhhhhhcccccEEEEecc
Confidence            5699998853   3333334555666778888898633233334887764 4455677877889999999873

>d1o2da_ e.22.1.2 (A:) Alcohol dehydrogenase TM0920 {Thermotoga maritima [TaxId: 2336]}

class: Multi-domain proteins (alpha and beta)
fold: Dehydroquinate synthase-like
superfamily: Dehydroquinate synthase-like
family: Iron-containing alcohol dehydrogenase
domain: Alcohol dehydrogenase TM0920
species: Thermotoga maritima [TaxId: 2336]

Probab=82.25  E-value=1.5  Score=34.19  Aligned_cols=62  Identities=15%  Similarity=0.192  Sum_probs=39.1

Q ss_pred             CCEEEEEEee--ecHHHHHHHHHHHHHHHHHCCCCCCCeEEE-Eeccc--chHHHHHHHHhhcCCCcEEEEee
Q 032216           75 GLRFALVVAR--FNELVTKLLLEGALETFKKYSVKEENIDVV-WVPGS--FEIGVVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        75 ~lRIaIVvAr--fN~~It~~LleGA~~~L~~~Gv~~e~I~vv-~VPGA--fELPlaak~La~s~~yDAVIaLG  142 (145)
                      +.|+.||..+  +...   ..++...+.|++.|+.   +.++ .|.+-  +|-=.-+...++..++|.||++|
T Consensus        28 g~k~liV~~~~~~~~~---g~~~~v~~~L~~~~i~---~~~f~~v~~~p~~~~v~~~~~~~~~~~~D~IIavG   94 (359)
T d1o2da_          28 GKRALVVTGKSSSKKN---GSLDDLKKLLDETEIS---YEIFDEVEENPSFDNVMKAVERYRNDSFDFVVGLG   94 (359)
T ss_dssp             CSEEEEEEESSGGGTS---SHHHHHHHHHHHTTCE---EEEEEEECSSCBHHHHHHHHHHHTTSCCSEEEEEE
T ss_pred             CCeEEEEEcCcHHHHh---hHHHHHHHHHHHcCCe---EEEEcCccCCCCHHHHHHhhhhccccCCceEEecc
Confidence            4699999875  3332   2445566778888874   3343 35443  33333344456778999999998

>d2qwxa1 c.23.5.3 (A:1-230) Quinone reductase type 2 (menadione reductase) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: Flavoproteins
family: Quinone reductase
domain: Quinone reductase type 2 (menadione reductase)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.76  E-value=0.98  Score=32.41  Aligned_cols=40  Identities=15%  Similarity=0.177  Sum_probs=33.1

Q ss_pred             CCCEEEEEEeeec-HHHHHHHHHHHHHHHHHCCCCCCCeEEEEe
Q 032216           74 EGLRFALVVARFN-ELVTKLLLEGALETFKKYSVKEENIDVVWV  116 (145)
Q Consensus        74 ~~lRIaIVvArfN-~~It~~LleGA~~~L~~~Gv~~e~I~vv~V  116 (145)
                      .+|||.||.+--+ +-.+..|++.+++.|++.|.+   +++++.
T Consensus         1 ~~mKiLiI~ghp~~~S~t~~l~~~~~~~~~~~g~e---v~~~dL   41 (230)
T d2qwxa1           1 AGKKVLIVYAHQEPKSFNGSLKNVAVDELSRQGCT---VTVSDL   41 (230)
T ss_dssp             CCCEEEEEECCSCTTSHHHHHHHHHHHHHHHTTCE---EEEEET
T ss_pred             CCCEEEEEEeCCCCccHHHHHHHHHHHHHHhCCCE---EEEEEc
Confidence            4799999998777 558899999999999999973   666654

>d1rrma_ e.22.1.2 (A:) Lactaldehyde reductase FucO {Escherichia coli [TaxId: 562]}

class: Multi-domain proteins (alpha and beta)
fold: Dehydroquinate synthase-like
superfamily: Dehydroquinate synthase-like
family: Iron-containing alcohol dehydrogenase
domain: Lactaldehyde reductase FucO
species: Escherichia coli [TaxId: 562]

Probab=80.46  E-value=0.79  Score=35.93  Aligned_cols=62  Identities=6%  Similarity=-0.010  Sum_probs=42.9

Q ss_pred             CEEEEEEeeecHHHHHHHHHHHHHHHHHCCCCCCCeEEE-Eecc--cchHHHHHHHHhhcCCCcEEEEee
Q 032216           76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVV-WVPG--SFEIGVVAQQLGKSGKYTAVLCIG  142 (145)
Q Consensus        76 lRIaIVvArfN~~It~~LleGA~~~L~~~Gv~~e~I~vv-~VPG--AfELPlaak~La~s~~yDAVIaLG  142 (145)
                      .|+.||..+.-..  ..+++.-++.|++.|+.   +.++ .|++  .+|-=..+..+++..++|.||++|
T Consensus        31 k~~Livt~~~~~~--~g~~~~v~~~L~~~gi~---~~vf~~v~~~p~~~~v~~~~~~~~~~~~D~IiaiG   95 (385)
T d1rrma_          31 QKALIVTDKTLVQ--CGVVAKVTDKMDAAGLA---WAIYDGVVPNPTITVVKEGLGVFQNSGADYLIAIG   95 (385)
T ss_dssp             CEEEEECBHHHHH--TTHHHHHHHHHHHTTCE---EEEECBCCSSCBHHHHHHHHHHHHHHTCSEEEEEE
T ss_pred             CEEEEEECcchhh--CcHHHHHHHHHHHcCCe---EEEEcCccCCCCHHHHHHHhhhhhccCCCEEEecC
Confidence            5888888765322  24677788889999984   4444 4665  445555555566778999999998