Citrus Sinensis ID: 045172

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------
Protein Sequence
RFYNNDKLVNHFRQIHEGEQKKRSNQIESARGKVRVLLVGNYSIKMEKNKMAASAILTPKVGYGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDMSDGALKRIANAFFSWSDLLMGK
Secondary Structure (PSIPRED)
ccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHcEEEEEEEcccccHHHHHHHHHHHHHHccccEEEEEEEccccHHHHHHHHHHccccEEEEEccccHHHHHHHHccccHHHHHccc
Secondary Structure Prediction (SSPRO)
ccccHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHcccEEEEcccccHHHHHHHHHHHHHHHHHccccEEEEEEcccHHHHHHHHHHHccccEEEEEccccccHHcEccEEEcHHHHHccc
Coil and Loop (DISEMBL)
RFYNNDKLVNHFRQIHEGEQKKRSNQIESARGKVRVLLVGNYSIKMEKNKMAASailtpkvgygfADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDMSDGALKRIANAFFSWSDLLMGK
Flexible Loop (DISEMBL)
rfynndklvnhfrqihegeqkkrsnqiesargkvrVLLVGNYSIKMEKNKMAASAILTPKVGYGFADELKRAWFWVRMVLvkpqdadvLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDMSDGALKRIANAffswsdllmgk
Low Complexity Region (SEG)
RFYNNDKLVNHFRQIHEGEQKKRSNQIESARGKVRVLLVGNYSIKMEKNKMAASAILTPKVGYGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLvvvsddsdfvevfQEATLRWLKMVVVGDMSDGALKRIANAFFSWSDLLMGK
Disordered region (IsUnstruct)
********************************KVRVLLVGNYSIKMEKNKMAASAILTPKVGYGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDMSDGALKRIANAFFSWSDLL***
Disordered Region (DISOPRED)
****NDKLVNHFRQIHE*************************SIKMEKNKMAASAILTPKVGYGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDMSDGALKRIANAFFSWSDLLMG*
Disordered Region (DISEMBL)
RFYNNDKLVNHFRQIHEGEQKKRSNQIESARGKVRVLLVGNYSIKMEKNKMAASAILTPKVGYGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDMSDGALKRIANAFFSWSDLLMGK
Disordered Region (DISPRO)
RFYNNDKLVNHFRQIHEGEQKKRSNQIESARGKVRVLLVGNYSIKMEKNKMAASAILTPKVGYGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDMSDGALKRIANAFFSWSDLLM**
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
RFYNNDKLVNHFRQIHEGEQKKRSNQIESARGKVRVLLVGNYSIKMEKNKMAASAILTPKVGYGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDMSDGALKRIANAFFSWSDLLMGK
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

No hits with e-value below 0.001 by BLAST

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	157
224074705	300	predicted protein [Populus trichocarpa]	0.993	0.52	0.698	2e-56
255537067	375	nucleic acid binding protein, putative [	1.0	0.418	0.687	3e-55
255537065	294	nucleic acid binding protein, putative [	1.0	0.534	0.687	1e-54
357462889	411	hypothetical protein MTR_3g084750 [Medic	1.0	0.381	0.651	5e-52
356538069	393	PREDICTED: uncharacterized protein LOC10	1.0	0.399	0.643	1e-51
356569166	356	PREDICTED: uncharacterized protein LOC10	1.0	0.441	0.624	3e-50
449494370	368	PREDICTED: uncharacterized LOC101211196	0.993	0.423	0.634	2e-49
449460491	367	PREDICTED: uncharacterized protein LOC10	0.987	0.422	0.628	2e-47
297809527	365	zinc finger family protein [Arabidopsis	1.0	0.430	0.573	8e-46
15234485	364	C2H2 type zinc finger protein [Arabidops	1.0	0.431	0.566	4e-45

>gi|224074705|ref|XP_002304433.1| predicted protein [Populus trichocarpa] gi|222841865|gb|EEE79412.1| predicted protein [Populus trichocarpa]

 Score =  223 bits (569), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 109/156 (69%), Positives = 129/156 (82%)

Query: 2   FYNNDKLVNHFRQIHEGEQKKRSNQIESARGKVRVLLVGNYSIKMEKNKMAASAILTPKV 61
           FYNN+K +NHF+QIHE EQ+KR NQIESARGK RV+LVG Y++KM+K K AA  ILTPKV
Sbjct: 51  FYNNEKFINHFKQIHEREQQKRLNQIESARGKRRVMLVGKYAMKMQKYKNAARDILTPKV 110

Query: 62  GYGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQE 121
           GYG ADELKRA FWVR VL KPQ ADV L+++MV M+DKRR  C V+VSDDSDFV V +E
Sbjct: 111 GYGLADELKRAGFWVRTVLDKPQAADVALKDHMVDMMDKRRAECFVLVSDDSDFVHVLKE 170

Query: 122 ATLRWLKMVVVGDMSDGALKRIANAFFSWSDLLMGK 157
           A  R LK VVVGD++DGALKR+A+A FSW ++LMGK
Sbjct: 171 AKSRCLKTVVVGDVNDGALKRVADAGFSWQEILMGK 206

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255537067|ref|XP_002509600.1| nucleic acid binding protein, putative [Ricinus communis] gi|223549499|gb|EEF50987.1| nucleic acid binding protein, putative [Ricinus communis]

 Score =  219 bits (558), Expect = 3e-55,   Method: Compositional matrix adjust.
 Identities = 108/157 (68%), Positives = 128/157 (81%)

Query: 1   RFYNNDKLVNHFRQIHEGEQKKRSNQIESARGKVRVLLVGNYSIKMEKNKMAASAILTPK 60
           RFYNN+KL+NHF+QIHE EQ+KR NQIESARGK RV LV  Y++KM+K K AA  +LTPK
Sbjct: 135 RFYNNEKLINHFKQIHEREQQKRLNQIESARGKRRVNLVAKYAMKMQKYKNAARDVLTPK 194

Query: 61  VGYGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQ 120
           VGYG ADELKRA FWV  V  KPQ ADV LR ++V M+DKRR  CLV+VSDDSDFV V +
Sbjct: 195 VGYGLADELKRAGFWVTTVSDKPQAADVALREHIVDMMDKRRAECLVLVSDDSDFVGVLK 254

Query: 121 EATLRWLKMVVVGDMSDGALKRIANAFFSWSDLLMGK 157
           EA LR +K VVVGD++DGALKR+A+A FSW ++LMGK
Sbjct: 255 EAKLRCVKTVVVGDINDGALKRVADAEFSWQEILMGK 291

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255537065|ref|XP_002509599.1| nucleic acid binding protein, putative [Ricinus communis] gi|223549498|gb|EEF50986.1| nucleic acid binding protein, putative [Ricinus communis]

 Score =  217 bits (553), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 108/157 (68%), Positives = 128/157 (81%)

Query: 1   RFYNNDKLVNHFRQIHEGEQKKRSNQIESARGKVRVLLVGNYSIKMEKNKMAASAILTPK 60
           RFYNN+KL+NHF+QIHE EQ+KR NQIESARGK RV LV  Y++KM+K K AA  +LTPK
Sbjct: 54  RFYNNEKLINHFKQIHEREQQKRLNQIESARGKRRVNLVAKYAMKMQKYKNAARDVLTPK 113

Query: 61  VGYGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQ 120
           VGYG ADELKRA FWV  V  KPQ ADV LR ++V M+DKRR  CLV+VSDDSDFV V +
Sbjct: 114 VGYGLADELKRAGFWVTTVSDKPQAADVALREHIVDMMDKRRAECLVLVSDDSDFVGVLK 173

Query: 121 EATLRWLKMVVVGDMSDGALKRIANAFFSWSDLLMGK 157
           EA LR +K VVVGD++DGALKR+A+A FSW ++LMGK
Sbjct: 174 EAKLRCVKTVVVGDINDGALKRVADAEFSWQEILMGK 210

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357462889|ref|XP_003601726.1| hypothetical protein MTR_3g084750 [Medicago truncatula] gi|355490774|gb|AES71977.1| hypothetical protein MTR_3g084750 [Medicago truncatula]

 Score =  208 bits (530), Expect = 5e-52,   Method: Compositional matrix adjust.
 Identities = 103/158 (65%), Positives = 125/158 (79%), Gaps = 1/158 (0%)

Query: 1   RFYNNDKLVNHFRQIHEGEQKKRSNQIESARGKVRVLLVGNYSIKMEKNKMAASAILTPK 60
           +FY N+KLVNHF+Q+HE E  KR N+IESARG  +V LVG Y++KMEK K AASA+LTPK
Sbjct: 181 KFYTNEKLVNHFKQLHEREHAKRLNRIESARGSRKVKLVGQYAMKMEKYKKAASAVLTPK 240

Query: 61  VGYGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQ 120
           VGYG ADELKRA FWV+ VL +PQ AD+ L+ +MV M+D RR  CLV+VSDDSDFV+V +
Sbjct: 241 VGYGLADELKRAGFWVQTVLDRPQAADIALQKHMVDMMDHRRVECLVLVSDDSDFVDVIK 300

Query: 121 EATLRWLKMVVVGDM-SDGALKRIANAFFSWSDLLMGK 157
           EA LR LK VV+GD  SDG LKR A+  FSW ++LMGK
Sbjct: 301 EAKLRCLKTVVIGDFSSDGVLKRTADTAFSWEEILMGK 338

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356538069|ref|XP_003537527.1| PREDICTED: uncharacterized protein LOC100785257 [Glycine max]

 Score =  207 bits (527), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 101/157 (64%), Positives = 121/157 (77%)

Query: 1   RFYNNDKLVNHFRQIHEGEQKKRSNQIESARGKVRVLLVGNYSIKMEKNKMAASAILTPK 60
           +FY NDKLVNHF+Q+HE E  KR NQIESARG  RV LV  YS+KMEK K AAS ILTPK
Sbjct: 145 KFYTNDKLVNHFKQLHESEHTKRMNQIESARGSRRVKLVAKYSMKMEKYKKAASDILTPK 204

Query: 61  VGYGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQ 120
           VGYG ADELKRA FWVR V  KPQ AD  L++++V ++D RR  C+V+VSDDSDFV+V  
Sbjct: 205 VGYGLADELKRAGFWVRTVSDKPQAADQALQSHIVDIMDHRRVECVVLVSDDSDFVDVIN 264

Query: 121 EATLRWLKMVVVGDMSDGALKRIANAFFSWSDLLMGK 157
           EA +R LK VV+GD+ +G LKR A+  FSW ++LMGK
Sbjct: 265 EAKMRCLKTVVIGDIDEGFLKRTADTAFSWEEILMGK 301

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356569166|ref|XP_003552776.1| PREDICTED: uncharacterized protein LOC100789840 [Glycine max]

 Score =  202 bits (514), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 98/157 (62%), Positives = 121/157 (77%)

Query: 1   RFYNNDKLVNHFRQIHEGEQKKRSNQIESARGKVRVLLVGNYSIKMEKNKMAASAILTPK 60
           +F+ NDKLVNHF+Q+HE E  KR NQIES+RG  RV LV  YS+KMEK K AAS ILTPK
Sbjct: 150 KFHTNDKLVNHFKQLHEREHAKRMNQIESSRGSRRVKLVAKYSMKMEKYKKAASDILTPK 209

Query: 61  VGYGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQ 120
           VGYG ADEL+RA FWV+ V  KPQ AD  L++++V ++D RR  C+V+VSDDSDFV+V  
Sbjct: 210 VGYGLADELRRAGFWVQTVSDKPQAADQALQSHIVDIMDHRRVECVVLVSDDSDFVDVIN 269

Query: 121 EATLRWLKMVVVGDMSDGALKRIANAFFSWSDLLMGK 157
           EA +R LK VV+GD+ DG LKR A+  FSW ++LMGK
Sbjct: 270 EAKMRCLKTVVIGDIDDGFLKRTADTAFSWEEILMGK 306

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449494370|ref|XP_004159528.1| PREDICTED: uncharacterized LOC101211196 [Cucumis sativus]

 Score =  200 bits (509), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 99/156 (63%), Positives = 122/156 (78%)

Query: 2   FYNNDKLVNHFRQIHEGEQKKRSNQIESARGKVRVLLVGNYSIKMEKNKMAASAILTPKV 61
           FY N+KLVNHF+QIHE E KKR NQIESA+G  RV LV  YS+K++K K AA  +LTP+V
Sbjct: 128 FYTNEKLVNHFKQIHESEHKKRLNQIESAKGSRRVKLVAKYSMKIQKYKNAARDVLTPEV 187

Query: 62  GYGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQE 121
           GYG ADELKRA F+V+ V  KP+ ADV LRN MV ++D+R+  CLV+VSDDSDFV V +E
Sbjct: 188 GYGLADELKRAGFFVKTVSDKPEAADVELRNDMVEIMDRRKAECLVLVSDDSDFVNVLKE 247

Query: 122 ATLRWLKMVVVGDMSDGALKRIANAFFSWSDLLMGK 157
           A LR L+ VVVGD++DG LKR A+  FSW ++LMGK
Sbjct: 248 AKLRCLRTVVVGDLNDGPLKRNADTGFSWQEILMGK 283

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449460491|ref|XP_004147979.1| PREDICTED: uncharacterized protein LOC101211196 [Cucumis sativus]

 Score =  193 bits (491), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 98/156 (62%), Positives = 121/156 (77%), Gaps = 1/156 (0%)

Query: 2   FYNNDKLVNHFRQIHEGEQKKRSNQIESARGKVRVLLVGNYSIKMEKNKMAASAILTPKV 61
           FY N+KLVNHF+QIHE E KKR NQIESA+G  RV LV  YS+K++K K AA  +L P+V
Sbjct: 128 FYTNEKLVNHFKQIHESEHKKRLNQIESAKGSRRVKLVAKYSMKIQKYKNAARDVL-PEV 186

Query: 62  GYGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQE 121
           GYG ADELKRA F+V+ V  KP+ ADV LRN MV ++D+R+  CLV+VSDDSDFV V +E
Sbjct: 187 GYGLADELKRAGFFVKTVSDKPEAADVELRNDMVEIMDRRKAECLVLVSDDSDFVNVLKE 246

Query: 122 ATLRWLKMVVVGDMSDGALKRIANAFFSWSDLLMGK 157
           A LR L+ VVVGD++DG LKR A+  FSW ++LMGK
Sbjct: 247 AKLRCLRTVVVGDLNDGPLKRNADTGFSWQEILMGK 282

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297809527|ref|XP_002872647.1| zinc finger family protein [Arabidopsis lyrata subsp. lyrata] gi|297318484|gb|EFH48906.1| zinc finger family protein [Arabidopsis lyrata subsp. lyrata]

 Score =  188 bits (477), Expect = 8e-46,   Method: Compositional matrix adjust.
 Identities = 90/157 (57%), Positives = 118/157 (75%)

Query: 1   RFYNNDKLVNHFRQIHEGEQKKRSNQIESARGKVRVLLVGNYSIKMEKNKMAASAILTPK 60
           RFY N+KL+NHF+QIHE E +KR  QIES++G  RV LV  YS+K+EK K AA  ILTPK
Sbjct: 123 RFYTNEKLINHFKQIHETENQKRMRQIESSKGHQRVRLVAKYSMKIEKYKRAARNILTPK 182

Query: 61  VGYGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQ 120
            GYG ADELKRA FWV+MV  KP+ AD  L+ ++V M+DKR   C+V+VSDDSD+  +  
Sbjct: 183 EGYGLADELKRAGFWVKMVSDKPEAADKALKEHLVDMMDKREVECVVLVSDDSDYAGILW 242

Query: 121 EATLRWLKMVVVGDMSDGALKRIANAFFSWSDLLMGK 157
           EA  R L+ VV+GD ++GALKR+A+  +SW +++MGK
Sbjct: 243 EAKERCLRTVVIGDSNEGALKRVADVAYSWKEVVMGK 279

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15234485|ref|NP_192961.1| C2H2 type zinc finger protein [Arabidopsis thaliana] gi|5281035|emb|CAB45971.1| hypothetical proteins [Arabidopsis thaliana] gi|7267925|emb|CAB78267.1| hypothetical proteins [Arabidopsis thaliana] gi|26452877|dbj|BAC43517.1| unknown protein [Arabidopsis thaliana] gi|28973009|gb|AAO63829.1| unknown protein [Arabidopsis thaliana] gi|332657707|gb|AEE83107.1| C2H2 type zinc finger protein [Arabidopsis thaliana]

 Score =  186 bits (471), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 89/157 (56%), Positives = 116/157 (73%)

Query: 1   RFYNNDKLVNHFRQIHEGEQKKRSNQIESARGKVRVLLVGNYSIKMEKNKMAASAILTPK 60
           RFY N+KL+NHF+QIHE E +KR  QIES++G  RV LV  YS+K+EK K AA  +LTPK
Sbjct: 125 RFYTNEKLINHFKQIHETENQKRMRQIESSKGHRRVRLVAKYSMKIEKYKRAARNVLTPK 184

Query: 61  VGYGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQ 120
            GYG ADELKRA FWV+MV  KP  AD  L+ ++V ++DKR   C+V+VSDDSDF  +  
Sbjct: 185 EGYGLADELKRAGFWVKMVSDKPDAADKALKEHLVEVMDKREVECVVLVSDDSDFAGILW 244

Query: 121 EATLRWLKMVVVGDMSDGALKRIANAFFSWSDLLMGK 157
           EA  R L+ VV+GD ++GALKR+A+  +SW ++ MGK
Sbjct: 245 EAKERCLRTVVIGDSNEGALKRVADVAYSWKEVTMGK 281

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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	157
TAIR|locus:2139119	364	AT4G12240 "AT4G12240" [Arabido	1.0	0.431	0.515	9.9e-39
TAIR|locus:2173038	396	AT5G52010 "AT5G52010" [Arabido	0.955	0.378	0.363	1.3e-14

TAIR|locus:2139119 AT4G12240 "AT4G12240" [Arabidopsis thaliana (taxid:3702)]

 Score = 414 (150.8 bits), Expect = 9.9e-39, P = 9.9e-39
 Identities = 81/157 (51%), Positives = 106/157 (67%)

Query:     1 RFYNNDKLVNHFRQIHEGEQKKRSNQIESARGKVRVLLVGNYSIKMEKNKMAASAILTPK 60
             RFY N+KL+NHF+QIHE E +KR  QIES++G  RV LV  YS+K+EK K AA  +LTPK
Sbjct:   125 RFYTNEKLINHFKQIHETENQKRMRQIESSKGHRRVRLVAKYSMKIEKYKRAARNVLTPK 184

Query:    61 VGYGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLXXXXXXXXXXXXXQ 120
              GYG ADELKRA FWV+MV  KP  AD  L+ ++V ++DKR   C+              
Sbjct:   185 EGYGLADELKRAGFWVKMVSDKPDAADKALKEHLVEVMDKREVECVVLVSDDSDFAGILW 244

Query:   121 EATLRWLKMVVVGDMSDGALKRIANAFFSWSDLLMGK 157
             EA  R L+ VV+GD ++GALKR+A+  +SW ++ MGK
Sbjct:   245 EAKERCLRTVVIGDSNEGALKRVADVAYSWKEVTMGK 281

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0005622 "intracellular" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA;ISS

GO:0009507 "chloroplast" evidence=ISM

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0006355 "regulation of transcription, DNA-dependent" evidence=TAS

GO:0005739 "mitochondrion" evidence=IDA

TAIR|locus:2173038 AT5G52010 "AT5G52010" [Arabidopsis thaliana (taxid:3702)]

 Score = 192 (72.6 bits), Expect = 1.3e-14, P = 1.3e-14
 Identities = 56/154 (36%), Positives = 78/154 (50%)

Query:     5 NDKLVNHFRQIHEGEQKKRSNQIESARGKVRVLLVGNYSIKMEKNKMAASAILTPKVGYG 64
             N  L  HF+Q+HE E++K+ N++ S +GK R      Y    EK   AA ++LTPKVGYG
Sbjct:   164 NLDLKKHFKQLHERERQKKVNRMRSLKGKKRQKFKERYVSGNEKYNEAARSLLTPKVGYG 223

Query:    65 FADELKRAWFWVRMVLVKPQDAD-VLLRNYMVAMVDKRRFGCLXXXXXXXXXXXXXQEAT 123
                EL+RA  +V+ V  KPQ AD  + R    +M   R    L             ++A 
Sbjct:   224 LEAELRRAGVYVKTVEDKPQAADWAVKRQIQHSMT--RGIDWLVLVSDDKDFSDMLRKAR 281

Query:   124 LRWLKMVVVGDMSDGALKRIANAFFSWSDLLMGK 157
                L  +VV DM D AL R A+ +  WS +  G+
Sbjct:   282 EADLGTLVVSDM-DRALGRHADLWVPWSGVEKGE 314


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.324   0.136   0.411    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      157       144   0.00091  102 3  11 22  0.39    31
                                                     30  0.48    33


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  2
  No. of states in DFA:  572 (61 KB)
  Total size of DFA:  142 KB (2088 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  11.88u 0.10s 11.98t   Elapsed:  00:00:01
  Total cpu time:  11.88u 0.10s 11.98t   Elapsed:  00:00:01
  Start:  Sat May 11 04:40:40 2013   End:  Sat May 11 04:40:41 2013

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0005622 "intracellular" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA;ISS

GO:0009507 "chloroplast" evidence=ISM

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0006355 "regulation of transcription, DNA-dependent" evidence=TAS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

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	157
cd06167	151	cd06167, LabA_like, LabA_like proteins	2e-06

>gnl|CDD|199895 cd06167, LabA_like, LabA_like proteins

 Score = 44.4 bits (105), Expect = 2e-06
 Identities = 28/106 (26%), Positives = 43/106 (40%), Gaps = 6/106 (5%)

Query: 52  AASAILTPKVGYGFADELKRAWFWVRMVL-----VKPQDADVLLRNYMVAMVDKRRFGCL 106
             +A   P     F + L+R  F V  V       + +  DV L    + +  +RR   +
Sbjct: 47  YNTARPDPSSPDRFQEALRRLGFEVIRVPRLRGKGEEKGVDVALALDALELAYERRIDTI 106

Query: 107 VVVSDDSDFVEVFQEATLRWLKMVVVGDMSDGALKRIANAFFSWSD 152
           V+VS DSDFV + +       K V+V      A   + NA   + D
Sbjct: 107 VLVSGDSDFVPLLERL-RERGKRVIVVGFRRSASSALKNAADEFID 151

A well conserved group of domains found in all three kingdoms of life, with no defined function. LabA, a member from Synechococcus elongatus PCC 7942, has been shown to play a role in cyanobacterial circadian timing. It is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system. In particular, LabA seems necessary for KaiC-dependent repression of gene expression. Another member is the N-terminal domain of limkain b1, a human autoantigen associated with cytoplasmic vesicles. Curiously, a gene labeled NicB from Pseudomonas putida S16, which is described as a putative NADH-dependent hydroxylase involved in the microbial degradation of nicotine also falls in the LabA_like family. LabA_like domains exhibit some similarity to the NYN domain, a distant relative of the PIN-domain nucleases. Length = 151

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	157
cd06167	149	LabA_like LabA_like proteins. A well conserved gro	99.5
TIGR00288	160	conserved hypothetical protein TIGR00288. This fam	99.48
PF01936	146	NYN: NYN domain; InterPro: IPR021139 This highly c	99.43
COG1432	181	Uncharacterized conserved protein [Function unknow	98.45
cd01545	270	PBP1_SalR Ligand-binding domain of DNA transcripti	96.24
cd05013	139	SIS_RpiR RpiR-like protein. RpiR contains a SIS (S	96.22
cd06305	273	PBP1_methylthioribose_binding_like Methylthioribos	96.0
cd01542	259	PBP1_TreR_like Ligand-binding domain of DNA transc	95.66
cd05014	128	SIS_Kpsf KpsF-like protein. KpsF is an arabinose-5	95.62
cd06295	275	PBP1_CelR Ligand binding domain of a transcription	95.6
TIGR02634	302	xylF D-xylose ABC transporter, substrate-binding p	95.59
cd06312	271	PBP1_ABC_sugar_binding_like_4 Periplasmic sugar-bi	95.57
PF13407	257	Peripla_BP_4: Periplasmic binding protein domain;	95.38
cd06318	282	PBP1_ABC_sugar_binding_like_9 Periplasmic sugar-bi	95.29
cd06324	305	PBP1_ABC_sugar_binding_like_13 Periplasmic sugar-b	95.25
PRK15482	285	transcriptional regulator MurR; Provisional	95.12
cd06303	280	PBP1_LuxPQ_Quorum_Sensing Periplasmic binding prot	95.12
cd06270	268	PBP1_GalS_like Ligand binding domain of DNA transc	95.05
cd06282	266	PBP1_GntR_like_2 Ligand-binding domain of putative	95.01
PRK15408	336	autoinducer 2-binding protein lsrB; Provisional	94.94
cd06281	269	PBP1_LacI_like_5 Ligand-binding domain of uncharac	94.91
cd06306	268	PBP1_TorT-like TorT-like proteins, a periplasmic b	94.91
cd06316	294	PBP1_ABC_sugar_binding_like_7 Periplasmic sugar-bi	94.79
cd06302	298	PBP1_LsrB_Quorum_Sensing Periplasmic binding domai	94.74
cd06294	270	PBP1_ycjW_transcription_regulator_like Ligand-bind	94.74
PF01380	131	SIS: SIS domain SIS domain web page.; InterPro: IP	94.71
cd06313	272	PBP1_ABC_sugar_binding_like_5 Periplasmic sugar-bi	94.66
cd01539	303	PBP1_GGBP Periplasmic glucose/galactose-binding pr	94.65
cd01540	289	PBP1_arabinose_binding Periplasmic L-arabinose-bin	94.6
cd06299	265	PBP1_LacI_like_13 Ligand-binding domain of DNA-bin	94.57
PRK10653	295	D-ribose transporter subunit RbsB; Provisional	94.51
PF00532	279	Peripla_BP_1: Periplasmic binding proteins and sug	94.51
cd01541	273	PBP1_AraR Ligand-binding domain of DNA transcripti	94.49
cd06322	267	PBP1_ABC_sugar_binding_like_12 Periplasmic sugar-b	94.47
cd06314	271	PBP1_tmGBP Periplasmic sugar-binding domain of The	94.45
cd06320	275	PBP1_allose_binding Periplasmic allose-binding dom	94.42
cd01538	288	PBP1_ABC_xylose_binding Periplasmic xylose-binding	94.42
TIGR02637	302	RhaS rhamnose ABC transporter, rhamnose-binding pr	94.4
cd06289	268	PBP1_MalI_like Ligand-binding domain of MalI, a tr	94.27
cd06323	268	PBP1_ribose_binding Periplasmic sugar-binding doma	94.2
PRK10014	342	DNA-binding transcriptional repressor MalI; Provis	94.17
cd05008	126	SIS_GlmS_GlmD_1 SIS (Sugar ISomerase) domain repea	94.15
cd06310	273	PBP1_ABC_sugar_binding_like_2 Periplasmic sugar-bi	94.15
cd06317	275	PBP1_ABC_sugar_binding_like_8 Periplasmic sugar-bi	94.09
cd06308	270	PBP1_sensor_kinase_like Periplasmic binding domain	93.98
cd06273	268	PBP1_GntR_like_1 This group includes the ligand-bi	93.98
cd06315	280	PBP1_ABC_sugar_binding_like_6 Periplasmic sugar-bi	93.94
cd06285	265	PBP1_LacI_like_7 Ligand-binding domain of uncharac	93.93
cd06292	273	PBP1_LacI_like_10 Ligand-binding domain of unchara	93.91
cd06301	272	PBP1_rhizopine_binding_like Periplasmic binding pr	93.8
cd06296	270	PBP1_CatR_like Ligand-binding domain of a LacI-lik	93.8
cd06321	271	PBP1_ABC_sugar_binding_like_11 Periplasmic sugar-b	93.78
cd06311	274	PBP1_ABC_sugar_binding_like_3 Periplasmic sugar-bi	93.71
cd01575	268	PBP1_GntR Ligand-binding domain of DNA transcripti	93.62
cd05005	179	SIS_PHI Hexulose-6-phosphate isomerase (PHI). PHI	93.57
cd06277	268	PBP1_LacI_like_1 Ligand-binding domain of uncharac	93.56
cd06298	268	PBP1_CcpA_like Ligand-binding domain of the catabo	93.55
cd06278	266	PBP1_LacI_like_2 Ligand-binding domain of uncharac	93.52
cd06319	277	PBP1_ABC_sugar_binding_like_10 Periplasmic sugar-b	93.5
TIGR02417	327	fruct_sucro_rep D-fructose-responsive transcriptio	93.45
PRK09552	219	mtnX 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosp	93.38
PRK10355	330	xylF D-xylose transporter subunit XylF; Provisiona	93.38
PRK09701	311	D-allose transporter subunit; Provisional	93.36
cd06309	273	PBP1_YtfQ_like Periplasmic binding domain of ABC-t	93.35
cd06271	268	PBP1_AglR_RafR_like Ligand-binding domain of DNA t	93.1
PRK11557	278	putative DNA-binding transcriptional regulator; Pr	93.06
TIGR03590	279	PseG pseudaminic acid biosynthesis-associated prot	92.77
cd06297	269	PBP1_LacI_like_12 Ligand-binding domain of unchara	92.74
TIGR01512	536	ATPase-IB2_Cd heavy metal-(Cd/Co/Hg/Pb/Zn)-translo	92.68
cd06283	267	PBP1_RegR_EndR_KdgR_like Ligand-binding domain of	92.65
PRK10936	343	TMAO reductase system periplasmic protein TorT; Pr	92.6
PRK14987	331	gluconate operon transcriptional regulator; Provis	92.56
cd06293	269	PBP1_LacI_like_11 Ligand-binding domain of unchara	92.45
cd06274	264	PBP1_FruR Ligand binding domain of DNA transcripti	92.32
cd05710	120	SIS_1 A subgroup of the SIS domain. SIS (Sugar ISo	92.25
TIGR00441	154	gmhA phosphoheptose isomerase. Involved in lipopol	92.08
TIGR01525	556	ATPase-IB_hvy heavy metal translocating P-type ATP	91.98
TIGR03127	179	RuMP_HxlB 6-phospho 3-hexuloisomerase. Members of	91.82
PRK11303	328	DNA-binding transcriptional regulator FruR; Provis	91.82
cd06300	272	PBP1_ABC_sugar_binding_like_1 Periplasmic sugar-bi	91.79
TIGR01664	166	DNA-3'-Pase DNA 3'-phosphatase. The central phosph	91.73
cd01536	267	PBP1_ABC_sugar_binding_like Periplasmic sugar-bind	91.38
cd06267	264	PBP1_LacI_sugar_binding_like Ligand binding domain	91.29
cd01574	264	PBP1_LacI Ligand-binding domain of DNA transcripti	91.23
PRK12342	254	hypothetical protein; Provisional	91.22
cd06307	275	PBP1_uncharacterized_sugar_binding Periplasmic sug	91.15
cd06291	265	PBP1_Qymf_like Ligand binding domain of the lacI-l	91.13
cd06290	265	PBP1_LacI_like_9 Ligand-binding domain of uncharac	91.11
PRK11337	292	DNA-binding transcriptional repressor RpiR; Provis	91.09
cd05006	177	SIS_GmhA Phosphoheptose isomerase is a member of t	90.8
TIGR02955	295	TMAO_TorT TMAO reductase system periplasmic protei	90.67
PRK13937	188	phosphoheptose isomerase; Provisional	90.61
cd01537	264	PBP1_Repressors_Sugar_Binding_like Ligand-binding	90.52
PRK15395	330	methyl-galactoside ABC transporter galactose-bindi	90.4
COG1609	333	PurR Transcriptional regulators [Transcription]	90.22
PF00702	215	Hydrolase: haloacid dehalogenase-like hydrolase; I	90.18
TIGR01481	329	ccpA catabolite control protein A. Catabolite cont	89.99
TIGR01511	562	ATPase-IB1_Cu copper-(or silver)-translocating P-t	89.83
cd06284	267	PBP1_LacI_like_6 Ligand-binding domain of an uncha	89.82
TIGR02137	203	HSK-PSP phosphoserine phosphatase/homoserine phosp	89.66
TIGR01491	201	HAD-SF-IB-PSPlk HAD-superfamily, subfamily-IB PSPa	89.63
cd06279	283	PBP1_LacI_like_3 Ligand-binding domain of uncharac	89.52
PRK13936	197	phosphoheptose isomerase; Provisional	89.26
TIGR01522	884	ATPase-IIA2_Ca golgi membrane calcium-translocatin	89.16
cd06360	336	PBP1_alkylbenzenes_like Type I periplasmic binding	88.81
cd06347	334	PBP1_ABC_ligand_binding_like_12 Type I periplasmic	88.72
TIGR00393	268	kpsF KpsF/GutQ family protein. This model describe	88.69
cd06361	403	PBP1_GPC6A_like Ligand-binding domain of the promi	88.54
cd06280	263	PBP1_LacI_like_4 Ligand-binding domain of uncharac	88.54
COG1737	281	RpiR Transcriptional regulators [Transcription]	88.49
cd06275	269	PBP1_PurR Ligand-binding domain of purine represso	88.44
cd06272	261	PBP1_hexuronate_repressor_like Ligand-binding doma	88.36
PRK00414	192	gmhA phosphoheptose isomerase; Reviewed	88.28
TIGR01490	202	HAD-SF-IB-hyp1 HAD-superfamily subfamily IB hydrol	87.98
PRK10423	327	transcriptional repressor RbsR; Provisional	87.94
cd06342	334	PBP1_ABC_LIVBP_like Type I periplasmic ligand-bind	87.06
cd06304	260	PBP1_BmpA_like Periplasmic binding component of a	87.03
PRK10703	341	DNA-binding transcriptional repressor PurR; Provis	86.92
COG0546	220	Gph Predicted phosphatases [General function predi	86.87
cd06286	260	PBP1_CcpB_like Ligand-binding domain of a novel tr	86.42
TIGR00147	293	lipid kinase, YegS/Rv2252/BmrU family. The E. coli	86.34
cd06330	346	PBP1_Arsenic_SBP_like Periplasmic solute-binding d	86.29
COG0560	212	SerB Phosphoserine phosphatase [Amino acid transpo	86.25
TIGR01489	188	DKMTPPase-SF 2,3-diketo-5-methylthio-1-phosphopent	86.1
PRK10671	834	copA copper exporting ATPase; Provisional	86.03
PF04123	344	DUF373: Domain of unknown function (DUF373); Inter	85.99
PRK07239	381	bifunctional uroporphyrinogen-III synthetase/respo	85.82
cd04509	299	PBP1_ABC_transporter_GCPR_C_like Family C of G-pro	85.79
PF02310	121	B12-binding: B12 binding domain; InterPro: IPR0061	85.63
cd01391	269	Periplasmic_Binding_Protein_Type_1 Type 1 periplas	85.56
COG1879	322	RbsB ABC-type sugar transport system, periplasmic	85.56
PRK14101	638	bifunctional glucokinase/RpiR family transcription	85.43
PRK13938	196	phosphoheptose isomerase; Provisional	85.33
PRK09484	183	3-deoxy-D-manno-octulosonate 8-phosphate phosphata	85.3
cd06276	247	PBP1_FucR_like Ligand-binding domain of a transcri	85.26
PRK02947	246	hypothetical protein; Provisional	85.21
cd06268	298	PBP1_ABC_transporter_LIVBP_like Periplasmic bindin	85.1
TIGR03333	214	salvage_mtnX 2-hydroxy-3-keto-5-methylthiopentenyl	85.07
PRK11543	321	gutQ D-arabinose 5-phosphate isomerase; Provisiona	85.04
PRK13582	205	thrH phosphoserine phosphatase; Provisional	84.76
PF15608	100	PELOTA_1: PELOTA RNA binding domain	84.56
PRK10892	326	D-arabinose 5-phosphate isomerase; Provisional	84.51
cd06337	357	PBP1_ABC_ligand_binding_like_4 Type I periplasmic	84.46
cd06354	265	PBP1_BmpA_PnrA_like Periplasmic binding domain of	84.38
PRK11302	284	DNA-binding transcriptional regulator HexR; Provis	84.2
cd08189	374	Fe-ADH5 Iron-containing alcohol dehydrogenases-lik	83.63
cd06346	312	PBP1_ABC_ligand_binding_like_11 Type I periplasmic	83.62
cd06288	269	PBP1_sucrose_transcription_regulator Ligand-bindin	83.6
TIGR02726	169	phenyl_P_delta phenylphosphate carboxylase, delta	83.59
cd08185	380	Fe-ADH1 Iron-containing alcohol dehydrogenases-lik	83.54
cd06269	298	PBP1_glutamate_receptors_like Family C G-protein c	83.46
cd06375	458	PBP1_mGluR_groupII Ligand binding domain of the gr	83.28
PLN02770	248	haloacid dehalogenase-like hydrolase family protei	83.21
cd06287	269	PBP1_LacI_like_8 Ligand-binding domain of uncharac	83.11
cd08188	377	Fe-ADH4 Iron-containing alcohol dehydrogenases-lik	82.72
cd06350	348	PBP1_GPCR_family_C_like Ligand-binding domain of m	82.56
cd06335	347	PBP1_ABC_ligand_binding_like_2 Type I periplasmic	82.53
PRK05441	299	murQ N-acetylmuramic acid-6-phosphate etherase; Re	82.52
TIGR00274	291	N-acetylmuramic acid 6-phosphate etherase. This pr	82.46
TIGR01422	253	phosphonatase phosphonoacetaldehyde hydrolase. Thi	82.33
PRK09860	383	putative alcohol dehydrogenase; Provisional	81.97
cd06333	312	PBP1_ABC-type_HAAT_like Type I periplasmic binding	81.84
PF02602	231	HEM4: Uroporphyrinogen-III synthase HemD; InterPro	81.76
cd06338	345	PBP1_ABC_ligand_binding_like_5 Type I periplasmic	81.69
cd05007	257	SIS_Etherase N-acetylmuramic acid 6-phosphate ethe	81.37
PRK13222	226	phosphoglycolate phosphatase; Provisional	81.1
cd06340	347	PBP1_ABC_ligand_binding_like_6 Type I periplasmic	80.93
cd06363	410	PBP1_Taste_receptor Ligand-binding domain of the T	80.92
cd06332	333	PBP1_aromatic_compounds_like Type I periplasmic bi	80.87
TIGR01261	161	hisB_Nterm histidinol-phosphatase. This model desc	80.75
cd05017	119	SIS_PGI_PMI_1 The members of this protein family c	80.39

>cd06167 LabA_like LabA_like proteins

Probab=99.50  E-value=1.3e-13  Score=102.71  Aligned_cols=87  Identities=30%  Similarity=0.370  Sum_probs=79.3

Q ss_pred             CCcHHHHHhhceEEEEec-----CCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC--
Q 045172           63 YGFADELKRAWFWVRMVL-----VKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM--  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~-----dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~--  135 (157)
                      -.+..+|++.||.|..++     ..++++|++|..+|++.+..++++++||||.|+||+++++.+|++|.+++|+|-.  
T Consensus        55 ~~~~~~L~~~g~~~~~~~~~~~~~~~~~~D~~l~~d~~~~~~~~~~d~ivLvSgD~Df~~~i~~lr~~G~~V~v~~~~~~  134 (149)
T cd06167          55 RGFLDALRRLGFEPIQKPLRTRGSGKKGVDVALAIDALELAYKRRIDTIVLVSGDSDFVPLVERLRELGKRVIVVGFEAK  134 (149)
T ss_pred             HHHHHHHHHCCcEEEEEcceecCCcccCccHHHHHHHHHHhhhcCCCEEEEEECCccHHHHHHHHHHcCCEEEEEccCcc
Confidence            456789999999999998     4568999999999999999889999999999999999999999999999999986  


Q ss_pred             CchHHHhhhhcccc
Q 045172          136 SDGALKRIANAFFS  149 (157)
Q Consensus       136 ~~~~L~r~AD~~fs  149 (157)
                      ...+|.+.||-+++
T Consensus       135 ~s~~L~~~~d~f~~  148 (149)
T cd06167         135 TSRELRKAADRFID  148 (149)
T ss_pred             ChHHHHHhCCcccc
Confidence            66899999996654

A well conserved group of bacterial proteins with no defined function. LabA, a member from Synechococcus elongatus PCC 7942, has been shown to play a role in cyanobacterial circadian timing. It is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system. In particular, LabA seems necessary for KaiC-dependent repression of gene expression.

>TIGR00288 conserved hypothetical protein TIGR00288

Probab=99.48  E-value=1.1e-13  Score=111.02  Aligned_cols=86  Identities=19%  Similarity=0.246  Sum_probs=76.9

Q ss_pred             CcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC--CchHHH
Q 045172           64 GFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM--SDGALK  141 (157)
Q Consensus        64 gla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~--~~~~L~  141 (157)
                      +|...|++.||.+..+.   .+.|++|.-++|+++++..+|++||||.|+||++++..+||+|.+++|||-.  ++.+|.
T Consensus        70 ~l~~~l~~~Gf~pv~~k---G~~Dv~laIDame~~~~~~iD~~vLvSgD~DF~~Lv~~lre~G~~V~v~g~~~~ts~~L~  146 (160)
T TIGR00288        70 KLIEAVVNQGFEPIIVA---GDVDVRMAVEAMELIYNPNIDAVALVTRDADFLPVINKAKENGKETIVIGAEPGFSTALQ  146 (160)
T ss_pred             HHHHHHHHCCceEEEec---CcccHHHHHHHHHHhccCCCCEEEEEeccHhHHHHHHHHHHCCCEEEEEeCCCCChHHHH
Confidence            35678999999987653   3999999999999998899999999999999999999999999999999943  778999


Q ss_pred             hhhhcccchhh
Q 045172          142 RIANAFFSWSD  152 (157)
Q Consensus       142 r~AD~~fsW~e  152 (157)
                      +.||-|+.-.|
T Consensus       147 ~acd~FI~L~~  157 (160)
T TIGR00288       147 NSADIAIILGE  157 (160)
T ss_pred             HhcCeEEeCCC
Confidence            99999986543

This family of orthologs is restricted to but universal among the completed archaeal genomes so far. Eubacterial proteins showing at least local homology include slr1870 from Synechocystis PCC6803 and two proteins from Aquifex aeolicusr, none of which is characterized.

>PF01936 NYN: NYN domain; InterPro: IPR021139 This highly conserved domain has no known function

Probab=99.43  E-value=6.4e-13  Score=97.15  Aligned_cols=86  Identities=30%  Similarity=0.408  Sum_probs=62.0

Q ss_pred             cHHHHHhhceEEEEecC------CCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEc--CCC
Q 045172           65 FADELKRAWFWVRMVLV------KPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVG--DMS  136 (157)
Q Consensus        65 la~eLrRAGv~V~~V~d------kpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVG--d~~  136 (157)
                      +-..|++.|+.|..++.      ..+++|+.|..+|++.+.+...+.+||||.|+||+++++.++++|.++.|+|  +..
T Consensus        52 ~~~~L~~~g~~v~~~~~~~~~~~~k~~~D~~l~~d~~~~~~~~~~d~ivLvSgD~Df~~~v~~l~~~g~~V~v~~~~~~~  131 (146)
T PF01936_consen   52 FQEALQRAGIKVRHFPLRKRGGGGKKGVDVALAVDILELAYENPPDTIVLVSGDSDFAPLVRKLRERGKRVIVVGAEDSA  131 (146)
T ss_dssp             HHHHHHHHT-EEEE------S---S---HHHHHHHHHHHG--GG-SEEEEE---GGGHHHHHHHHHH--EEEEEE-GGGS
T ss_pred             HHHHHHhCeeeEEeeecccccccccCCcHHHHHHHHHHHhhccCCCEEEEEECcHHHHHHHHHHHHcCCEEEEEEeCCCC
Confidence            45678999999988865      5679999999999999977778999999999999999999999999999999  336


Q ss_pred             chHHHhhhhcccch
Q 045172          137 DGALKRIANAFFSW  150 (157)
Q Consensus       137 ~~~L~r~AD~~fsW  150 (157)
                      ..+|.+.||-+++-
T Consensus       132 s~~L~~~ad~f~~~  145 (146)
T PF01936_consen  132 SEALRSAADEFISI  145 (146)
T ss_dssp             -HHHHHHSSEEEE-
T ss_pred             CHHHHHhcCEEEeC
Confidence            79999999998863

However it contains many conserved aspartates, suggesting an enzymatic function such as an endonuclease or glycosyl hydrolase.; PDB: 2QIP_A.

>COG1432 Uncharacterized conserved protein [Function unknown]

Probab=98.45  E-value=9.6e-07  Score=70.76  Aligned_cols=88  Identities=23%  Similarity=0.279  Sum_probs=73.2

Q ss_pred             cHHHHHhhceEEEEecCCCc--------cHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC-
Q 045172           65 FADELKRAWFWVRMVLVKPQ--------DADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM-  135 (157)
Q Consensus        65 la~eLrRAGv~V~~V~dkpq--------AAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~-  135 (157)
                      +-.+++.-|+-|.+.+-++-        .=|+-+--+|+..+++-.+|++||||-|.||.++++.|+++|.+|+|+|-+ 
T Consensus        65 ~~~~~~~~g~~v~~~~~~~~~~~~~~k~~vDv~la~D~~~l~~~~~~D~ivl~SgD~DF~p~v~~~~~~G~rv~v~~~~~  144 (181)
T COG1432          65 NEYELRSDGFTVVTSNLDGFTDLRITKGDVDVELAVDAMELADKKNVDTIVLFSGDGDFIPLVEAARDKGKRVEVAGIEP  144 (181)
T ss_pred             cHHHHhhcCcEEEeccccccCcccccccCcchhhHHHHHHhhcccCCCEEEEEcCCccHHHHHHHHHHcCCEEEEEecCC
Confidence            33488888888888654222        347888889999998889999999999999999999999999999999987 


Q ss_pred             -CchHHHhhhhcccchhh
Q 045172          136 -SDGALKRIANAFFSWSD  152 (157)
Q Consensus       136 -~~~~L~r~AD~~fsW~e  152 (157)
                       +..+|++.||-+..-..
T Consensus       145 ~~s~~L~~~aD~~i~L~~  162 (181)
T COG1432         145 MTSSDLRNAADYYIDLKS  162 (181)
T ss_pred             cCHHHHHHhhcceEEchh
Confidence             56899999998875443

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

Probab=96.24  E-value=0.019  Score=44.62  Aligned_cols=71  Identities=13%  Similarity=0.101  Sum_probs=55.2

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      +|+..+++..|+.+.++......+  .....+.+.+...++|.+++++.+.+..++++.+.+.|...|+||-.
T Consensus        19 ~gi~~~~~~~g~~~~~~~~~~~~~--~~~~~~~~~l~~~~vdgiii~~~~~~~~~~~~~~~~~~ipvv~i~~~   89 (270)
T cd01545          19 LGALDACRDTGYQLVIEPCDSGSP--DLAERVRALLQRSRVDGVILTPPLSDNPELLDLLDEAGVPYVRIAPG   89 (270)
T ss_pred             HHHHHHHHhCCCeEEEEeCCCCch--HHHHHHHHHHHHCCCCEEEEeCCCCCccHHHHHHHhcCCCEEEEecC
Confidence            688889999999988874433322  26667777666789999999987655678899999999999999854

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

>cd05013 SIS_RpiR RpiR-like protein

Probab=96.22  E-value=0.035  Score=39.34  Aligned_cols=77  Identities=19%  Similarity=0.138  Sum_probs=54.7

Q ss_pred             cHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCC---cchHHHHHHHHHcCCeEEEEcCCCchHHH
Q 045172           65 FADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDD---SDFVEVFQEATLRWLKMVVVGDMSDGALK  141 (157)
Q Consensus        65 la~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDD---sDF~~~lr~Arer~l~tVVVGd~~~~~L~  141 (157)
                      ++.-|.+.|..+..+++-      .........+  ..-+|++++|-.   .+..++++.|+++|.++|+|.+.....+.
T Consensus        31 ~~~~l~~~~~~~~~~~~~------~~~~~~~~~~--~~~~~~i~iS~~g~~~~~~~~~~~a~~~g~~iv~iT~~~~~~l~  102 (139)
T cd05013          31 LAYKLLRLGKPVVLLSDP------HLQLMSAANL--TPGDVVIAISFSGETKETVEAAEIAKERGAKVIAITDSANSPLA  102 (139)
T ss_pred             HHHHHHHcCCceEEecCH------HHHHHHHHcC--CCCCEEEEEeCCCCCHHHHHHHHHHHHcCCeEEEEcCCCCChhH
Confidence            455677888888886441      1111222223  234889999854   44777889999999999999998778999


Q ss_pred             hhhhcccc
Q 045172          142 RIANAFFS  149 (157)
Q Consensus       142 r~AD~~fs  149 (157)
                      +.+|..|.
T Consensus       103 ~~~d~~i~  110 (139)
T cd05013         103 KLADIVLL  110 (139)
T ss_pred             HhcCEEEE
Confidence            99998774

RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate isomerases that catalyze the reversible reactions of ribose 5-phosphate into ribulose 5-phosphate.

>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=96.00  E-value=0.043  Score=42.85  Aligned_cols=70  Identities=9%  Similarity=-0.035  Sum_probs=53.5

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcc-hHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSD-FVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsD-F~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++..|+.+..+....   |.....+.++.+...++|.|++.+.+++ ..++++.+.++|+..|.++..
T Consensus        19 ~gi~~~~~~~g~~~~~~~~~~---~~~~~~~~l~~~~~~~vdgii~~~~~~~~~~~~i~~~~~~~ipvV~~~~~   89 (273)
T cd06305          19 AGTKAEAEALGGDLRVYDAGG---DDAKQADQIDQAIAQKVDAIIIQHGRAEVLKPWVKRALDAGIPVVAFDVD   89 (273)
T ss_pred             HHHHHHHHHcCCEEEEECCCC---CHHHHHHHHHHHHHcCCCEEEEecCChhhhHHHHHHHHHcCCCEEEecCC
Confidence            467889999999998875433   3344445555555789999999876654 578899999999999999875

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.

>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=95.66  E-value=0.068  Score=41.39  Aligned_cols=69  Identities=10%  Similarity=0.103  Sum_probs=51.5

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++..|+.+........   .+-...+.+.+.+.++|++++++.+.+ ..+++.+++.|..+|++|..
T Consensus        19 ~gi~~~~~~~g~~~~~~~~~~~---~~~~~~~i~~l~~~~~dgii~~~~~~~-~~~~~~~~~~~ipvv~~~~~   87 (259)
T cd01542          19 KGILAALYENGYQMLLMNTNFS---IEKEIEALELLARQKVDGIILLATTIT-DEHREAIKKLNVPVVVVGQD   87 (259)
T ss_pred             HHHHHHHHHCCCEEEEEeCCCC---HHHHHHHHHHHHhcCCCEEEEeCCCCC-HHHHHHHhcCCCCEEEEecc
Confidence            6788899999999988755443   233333334444789999999987644 57888889999999999865

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

>cd05014 SIS_Kpsf KpsF-like protein

Probab=95.62  E-value=0.022  Score=41.04  Aligned_cols=78  Identities=10%  Similarity=0.157  Sum_probs=55.8

Q ss_pred             cHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcC---CcchHHHHHHHHHcCCeEEEEcCCCchHHH
Q 045172           65 FADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSD---DSDFVEVFQEATLRWLKMVVVGDMSDGALK  141 (157)
Q Consensus        65 la~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSD---DsDF~~~lr~Arer~l~tVVVGd~~~~~L~  141 (157)
                      ++..|.+.|..+....+.-     .+. +....+  ..=|+++++|-   ..+..++++.|+++|.++|+|-+..+..|.
T Consensus        18 ~~~~l~~~g~~~~~~~~~~-----~~~-~~~~~~--~~~d~vi~iS~sG~t~~~~~~~~~a~~~g~~vi~iT~~~~s~la   89 (128)
T cd05014          18 IAATLSSTGTPAFFLHPTE-----ALH-GDLGMV--TPGDVVIAISNSGETDELLNLLPHLKRRGAPIIAITGNPNSTLA   89 (128)
T ss_pred             HHHHhhcCCCceEEcccch-----hhc-cccCcC--CCCCEEEEEeCCCCCHHHHHHHHHHHHCCCeEEEEeCCCCCchh
Confidence            3445567788887764321     111 111112  23488999984   478999999999999999999998778999


Q ss_pred             hhhhcccch
Q 045172          142 RIANAFFSW  150 (157)
Q Consensus       142 r~AD~~fsW  150 (157)
                      +.||..|..
T Consensus        90 ~~ad~~l~~   98 (128)
T cd05014          90 KLSDVVLDL   98 (128)
T ss_pred             hhCCEEEEC
Confidence            999998865

KpsF is an arabinose-5-phosphate isomerase which contains SIS (Sugar ISomerase) domains. SIS domains are found in many phosphosugar isomerases and phosphosugar binding proteins. KpsF catalyzes the reversible reaction of ribulose 5-phosphate to arabinose 5-phosphate. This is the second step in the CMP-Kdo biosynthesis pathway.

>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=95.60  E-value=0.062  Score=42.23  Aligned_cols=66  Identities=18%  Similarity=0.280  Sum_probs=50.2

Q ss_pred             CcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           64 GFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        64 gla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      |+..+++..|+.+..+.-.++  +   ...+.+++...++|++++++.+.+ ...++.+.+.|..+|++|-.
T Consensus        31 gi~~~~~~~g~~~~v~~~~~~--~---~~~~~~~l~~~~~dgiii~~~~~~-~~~~~~~~~~~ipvV~~~~~   96 (275)
T cd06295          31 GIADALAERGYDLLLSFVSSP--D---RDWLARYLASGRADGVILIGQHDQ-DPLPERLAETGLPFVVWGRP   96 (275)
T ss_pred             HHHHHHHHcCCEEEEEeCCch--h---HHHHHHHHHhCCCCEEEEeCCCCC-hHHHHHHHhCCCCEEEECCc
Confidence            567889999999888755444  1   245556665689999999987654 56789999999999999754

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

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

Probab=95.59  E-value=0.071  Score=43.81  Aligned_cols=69  Identities=14%  Similarity=0.100  Sum_probs=55.5

Q ss_pred             CcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcc-hHHHHHHHHHcCCeEEEEcCC
Q 045172           64 GFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSD-FVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        64 gla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsD-F~~~lr~Arer~l~tVVVGd~  135 (157)
                      |+..+++..|+.+.+.+..   .|.+...++.+.|.+.++|+|++++.+++ ..+.++.+++.|...|+++..
T Consensus        19 ~i~~~a~~~g~~v~~~~~~---~~~~~q~~~i~~l~~~~vDgIIi~~~~~~~~~~~l~~~~~~~iPvV~~d~~   88 (302)
T TIGR02634        19 IFVAAAESLGAKVFVQSAN---GNEAKQISQIENLIARGVDVLVIIPQNGQVLSNAVQEAKDEGIKVVAYDRL   88 (302)
T ss_pred             HHHHHHHhcCCEEEEEeCC---CCHHHHHHHHHHHHHcCCCEEEEeCCChhHHHHHHHHHHHCCCeEEEecCc
Confidence            7788999999999776432   24555666777777899999999998765 578999999999999999765

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.

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

Probab=95.57  E-value=0.073  Score=42.00  Aligned_cols=71  Identities=15%  Similarity=0.039  Sum_probs=53.7

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcc-hHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSD-FVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsD-F~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+-.+++..|+.|.+.....  .|..-...+++.|...++|.+++++.+.+ +.+.++.++++|..+|+++..
T Consensus        20 ~g~~~~~~~~g~~v~~~~~~~--~~~~~~~~~i~~l~~~~vdgiii~~~~~~~~~~~l~~~~~~~ipvV~~~~~   91 (271)
T cd06312          20 NGAEDAAKDLGVDVEYRGPET--FDVADMARLIEAAIAAKPDGIVVTIPDPDALDPAIKRAVAAGIPVISFNAG   91 (271)
T ss_pred             HHHHHHHHHhCCEEEEECCCC--CCHHHHHHHHHHHHHhCCCEEEEeCCChHHhHHHHHHHHHCCCeEEEeCCC
Confidence            477788888999998875433  23344445555555789999999997765 678899999999999999864

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.

>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=95.38  E-value=0.093  Score=40.95  Aligned_cols=70  Identities=13%  Similarity=0.103  Sum_probs=52.8

Q ss_pred             CCcHHHHHhhceEEEEe-cCCCccHHHHHHHHHHHHhhccCcceEEEEcCCc-chHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMV-LVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDS-DFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V-~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDs-DF~~~lr~Arer~l~tVVVGd~  135 (157)
                      -|+..+++..|+.+.++ +.....  ..-...+.+++ +.++|+|++.+-|+ ...++++++.+.|+.+|.+...
T Consensus        18 ~g~~~~a~~~g~~~~~~~~~~~d~--~~q~~~i~~~i-~~~~d~Iiv~~~~~~~~~~~l~~~~~~gIpvv~~d~~   89 (257)
T PF13407_consen   18 KGAKAAAKELGYEVEIVFDAQNDP--EEQIEQIEQAI-SQGVDGIIVSPVDPDSLAPFLEKAKAAGIPVVTVDSD   89 (257)
T ss_dssp             HHHHHHHHHHTCEEEEEEESTTTH--HHHHHHHHHHH-HTTESEEEEESSSTTTTHHHHHHHHHTTSEEEEESST
T ss_pred             HHHHHHHHHcCCEEEEeCCCCCCH--HHHHHHHHHHH-HhcCCEEEecCCCHHHHHHHHHHHhhcCceEEEEecc
Confidence            46778899999999997 333331  33334455555 79999999996665 6889999999999999998765

...

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

Probab=95.29  E-value=0.11  Score=40.76  Aligned_cols=70  Identities=16%  Similarity=0.061  Sum_probs=52.4

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcc-hHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSD-FVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsD-F~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++++-|+.|.+.....   |.+......+.+-..++|+|++.+.+++ +.+.++.+.+.|...|+++..
T Consensus        19 ~~i~~~~~~~g~~v~~~~~~~---~~~~~~~~i~~~~~~~~Dgiii~~~~~~~~~~~i~~~~~~~iPvV~~~~~   89 (282)
T cd06318          19 EAAKAHAKALGYELISTDAQG---DLTKQIADVEDLLTRGVNVLIINPVDPEGLVPAVAAAKAAGVPVVVVDSS   89 (282)
T ss_pred             HHHHHHHHHcCCEEEEEcCCC---CHHHHHHHHHHHHHcCCCEEEEecCCccchHHHHHHHHHCCCCEEEecCC
Confidence            588899999999987764332   3333344455455799999999876654 357889999999999999864

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.

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

Probab=95.25  E-value=0.085  Score=43.06  Aligned_cols=70  Identities=13%  Similarity=0.059  Sum_probs=53.5

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhcc--CcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKR--RFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r--~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++..|+.+..+....   |..-...+.+.+.+.  ++|+|++.+.++....+++.+.++|+.+|+++..
T Consensus        20 ~gi~~~~~~~g~~v~~~~~~~---~~~~~~~~i~~~~~~~~~vdgiIi~~~~~~~~~~~~~~~~~giPvV~~~~~   91 (305)
T cd06324          20 RFMQAAADDLGIELEVLYAER---DRFLMLQQARTILQRPDKPDALIFTNEKSVAPELLRLAEGAGVKLFLVNSG   91 (305)
T ss_pred             HHHHHHHHhcCCeEEEEeCCC---CHHHHHHHHHHHHHhccCCCEEEEcCCccchHHHHHHHHhCCCeEEEEecC
Confidence            578888999999998874322   344444555555578  9999999876655677899999999999999864

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.

>PRK15482 transcriptional regulator MurR; Provisional

Probab=95.12  E-value=0.095  Score=43.56  Aligned_cols=95  Identities=13%  Similarity=0.154  Sum_probs=66.0

Q ss_pred             hHHHHHHHHhhcCcccC--CC----------cHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCC-
Q 045172           46 MEKNKMAASAILTPKVG--YG----------FADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDD-  112 (157)
Q Consensus        46 ~~kY~~Aar~~l~pkvg--yg----------la~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDD-  112 (157)
                      .+.+++++..+...+.-  ||          ++--|.+.|..|....|..      +...+...+ +.+ |+++++|-. 
T Consensus       122 ~~~l~~~~~~i~~A~~I~i~G~G~S~~~A~~l~~~l~~~g~~~~~~~d~~------~~~~~~~~~-~~~-Dv~i~iS~sg  193 (285)
T PRK15482        122 YARLQKIIEVISKAPFIQITGLGGSALVGRDLSFKLMKIGYRVACEADTH------VQATVSQAL-KKG-DVQIAISYSG  193 (285)
T ss_pred             HHHHHHHHHHHHhCCeeEEEEeChhHHHHHHHHHHHHhCCCeeEEeccHh------HHHHHHhcC-CCC-CEEEEEeCCC
Confidence            45677777766555422  22          2344667898888755332      222223333 333 899999954 


Q ss_pred             --cchHHHHHHHHHcCCeEEEEcCCCchHHHhhhhccc
Q 045172          113 --SDFVEVFQEATLRWLKMVVVGDMSDGALKRIANAFF  148 (157)
Q Consensus       113 --sDF~~~lr~Arer~l~tVVVGd~~~~~L~r~AD~~f  148 (157)
                        .+-..+++.|+++|+++|.|-|.....|.+.||.-|
T Consensus       194 ~t~~~~~~~~~a~~~g~~iI~IT~~~~s~la~~ad~~l  231 (285)
T PRK15482        194 SKKEIVLCAEAARKQGATVIAITSLADSPLRRLAHFTL  231 (285)
T ss_pred             CCHHHHHHHHHHHHCCCEEEEEeCCCCCchHHhCCEEE
Confidence              677788999999999999999997789999999887

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

Probab=95.12  E-value=0.086  Score=42.18  Aligned_cols=72  Identities=10%  Similarity=0.113  Sum_probs=49.6

Q ss_pred             CCcHHHHHhhceEEEEec--CCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVL--VKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~--dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++..|+.+...+  ..++ .|..-.....+.+..+++|.|++.+++....+.++.+.+.+...|+++|.
T Consensus        20 ~~i~~~~~~~g~~~~~~~~~~~~~-~~~~~~~~~i~~l~~~~vDgiIv~~~~~~~~~~~~~l~~~~~p~V~i~~~   93 (280)
T cd06303          20 ASFTARLEELNIPYELTQFSSRPG-IDHRLQSQQLNEALQSKPDYLIFTLDSLRHRKLIERVLASGKTKIILQNI   93 (280)
T ss_pred             HHHHHHHHHcCCcEEEEEeccCcc-cCHHHHHHHHHHHHHcCCCEEEEcCCchhhHHHHHHHHhCCCCeEEEeCC
Confidence            478899999998877653  2221 12233334444444799999999876655678888888888888888663

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

>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=95.05  E-value=0.13  Score=40.20  Aligned_cols=69  Identities=12%  Similarity=0.082  Sum_probs=52.1

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++..|+.+..+....   |.....++.+.+.++++|++++++.+.+- ..++.+.+.|...|+++..
T Consensus        19 ~g~~~~a~~~g~~~~~~~~~~---~~~~~~~~i~~~~~~~vdgii~~~~~~~~-~~~~~~~~~~ipvV~~~~~   87 (268)
T cd06270          19 SGVESVARKAGKHLIITAGHH---SAEKEREAIEFLLERRCDALILHSKALSD-DELIELAAQVPPLVLINRH   87 (268)
T ss_pred             HHHHHHHHHCCCEEEEEeCCC---chHHHHHHHHHHHHcCCCEEEEecCCCCH-HHHHHHhhCCCCEEEEecc
Confidence            577888999999999875433   34555666666668999999998854332 2388899999999999864

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

>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=95.01  E-value=0.15  Score=39.44  Aligned_cols=70  Identities=11%  Similarity=0.093  Sum_probs=51.1

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++..|+.|.......+.   .-...+.+.+-..++|.+++.+.+.+...+++.+++.|..+|+++..
T Consensus        19 ~~i~~~~~~~g~~~~~~~~~~~~---~~~~~~~~~l~~~~vdgiii~~~~~~~~~~~~~~~~~~ipvV~~~~~   88 (266)
T cd06282          19 QGIQEEARAAGYSLLLATTDYDA---EREADAVETLLRQRVDGLILTVADAATSPALDLLDAERVPYVLAYND   88 (266)
T ss_pred             HHHHHHHHHCCCEEEEeeCCCCH---HHHHHHHHHHHhcCCCEEEEecCCCCchHHHHHHhhCCCCEEEEecc
Confidence            46778889999999987554332   22223333344689999999887766567889999999999999754

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

>PRK15408 autoinducer 2-binding protein lsrB; Provisional

Probab=94.94  E-value=0.11  Score=44.60  Aligned_cols=71  Identities=14%  Similarity=0.136  Sum_probs=53.9

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcc-hHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSD-FVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsD-F~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+.+..|+.|...  .|...|.+-+..+++.|-.+++|.||+++-|++ +.+.+++|+++|..+|.+...
T Consensus        43 ~Gi~~aa~~~G~~v~~~--~~~~~d~~~q~~~i~~li~~~vdgIiv~~~d~~al~~~l~~a~~~gIpVV~~d~~  114 (336)
T PRK15408         43 NGAKEAGKELGVDVTYD--GPTEPSVSGQVQLINNFVNQGYNAIIVSAVSPDGLCPALKRAMQRGVKVLTWDSD  114 (336)
T ss_pred             HHHHHHHHHhCCEEEEE--CCCCCCHHHHHHHHHHHHHcCCCEEEEecCCHHHHHHHHHHHHHCCCeEEEeCCC
Confidence            47778889999999763  244445555555555555899999999885544 689999999999999999765

>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=94.91  E-value=0.16  Score=39.94  Aligned_cols=71  Identities=14%  Similarity=0.124  Sum_probs=50.9

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDMS  136 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~~  136 (157)
                      .|+..+++..|+.|-.....-+   ..-...+.+.|...+++++++++.+.+-..+++.++++|...|+++...
T Consensus        19 ~~i~~~a~~~g~~~~~~~~~~~---~~~~~~~i~~l~~~~vdgii~~~~~~~~~~~~~~~~~~~ipvV~i~~~~   89 (269)
T cd06281          19 SGAEDRLRAAGYSLLIANSLND---PERELEILRSFEQRRMDGIIIAPGDERDPELVDALASLDLPIVLLDRDM   89 (269)
T ss_pred             HHHHHHHHHcCCEEEEEeCCCC---hHHHHHHHHHHHHcCCCEEEEecCCCCcHHHHHHHHhCCCCEEEEeccc
Confidence            4678889999999876533222   2223333344446899999999876665678889999999999998653

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.

>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=94.91  E-value=0.15  Score=40.49  Aligned_cols=72  Identities=8%  Similarity=0.076  Sum_probs=51.5

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++..|+.+-+...... .|.....+.++.+.+.++|.|++++-+.+....+..++..|..+|+++..
T Consensus        19 ~gi~~~a~~~g~~~~~~~~~~~-~~~~~~~~~i~~~~~~~vdgiI~~~~~~~~~~~~~~~~~~giPvV~~~~~   90 (268)
T cd06306          19 YGMVEEAKRLGVSLKLLEAGGY-PNLAKQIAQLEDCAAWGADAILLGAVSPDGLNEILQQVAASIPVIALVND   90 (268)
T ss_pred             HHHHHHHHHcCCEEEEecCCCC-CCHHHHHHHHHHHHHcCCCEEEEcCCChhhHHHHHHHHHCCCCEEEeccC
Confidence            5788999999999988743211 12223334444444789999999987776544678899999999999754

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.

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

Probab=94.79  E-value=0.12  Score=41.41  Aligned_cols=71  Identities=11%  Similarity=0.077  Sum_probs=52.1

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcc-hHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSD-FVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsD-F~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++..|+.+..+.....  |.....++++.+...++|.||+.+.|.+ ..+++..++++|...|.++..
T Consensus        19 ~gi~~~a~~~g~~~~~~~~~~~--~~~~~~~~l~~~~~~~~dgiii~~~~~~~~~~~i~~~~~~~iPvV~~~~~   90 (294)
T cd06316          19 RGAKDEFAKLGIEVVATTDAQF--DPAKQVADIETTISQKPDIIISIPVDPVSTAAAYKKVAEAGIKLVFMDNV   90 (294)
T ss_pred             HHHHHHHHHcCCEEEEecCCCC--CHHHHHHHHHHHHHhCCCEEEEcCCCchhhhHHHHHHHHcCCcEEEecCC
Confidence            5778899999999876644332  2333334444444789999999887765 478899999999999999875

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.

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

Probab=94.74  E-value=0.18  Score=41.03  Aligned_cols=70  Identities=16%  Similarity=0.100  Sum_probs=53.2

Q ss_pred             CCcHHHHHhhceEEEEe-cCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcc-hHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMV-LVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSD-FVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V-~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsD-F~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++.+.|+.|..+ +...+   .....++.+.+...++|.|++++-+++ +.++++.+++.|..+|.|+..
T Consensus        19 ~gi~~~a~~~g~~v~~~~~~~~d---~~~~~~~i~~~~~~~~DgiIi~~~~~~~~~~~~~~~~~~~iPvV~v~~~   90 (298)
T cd06302          19 EGAKEAAKELGVDAIYVGPTTAD---AAGQVQIIEDLIAQGVDAIAVVPNDPDALEPVLKKAREAGIKVVTHDSD   90 (298)
T ss_pred             HHHHHHHHHhCCeEEEECCCCCC---HHHHHHHHHHHHhcCCCEEEEecCCHHHHHHHHHHHHHCCCeEEEEcCC
Confidence            57888999999999876 43333   333345555554789999999986655 778899999999999999864

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

>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=94.74  E-value=0.17  Score=39.30  Aligned_cols=69  Identities=12%  Similarity=0.175  Sum_probs=51.2

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++..|+.+..... ..  +......+.+.+...++|+|++++.+.+ ..+++.+.+.|..+|.++..
T Consensus        24 ~~~~~~~~~~g~~~~~~~~-~~--~~~~~~~~~~~~~~~~~dgiii~~~~~~-~~~~~~~~~~~ipvV~~~~~   92 (270)
T cd06294          24 RGISAVANENGYDISLATG-KN--EEELLEEVKKMIQQKRVDGFILLYSRED-DPIIDYLKEEKFPFVVIGKP   92 (270)
T ss_pred             HHHHHHHHHCCCEEEEecC-CC--cHHHHHHHHHHHHHcCcCEEEEecCcCC-cHHHHHHHhcCCCEEEECCC
Confidence            5778889999999876532 22  2334556666665677999999975544 57788999999999999864

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.

>PF01380 SIS: SIS domain SIS domain web page

Probab=94.71  E-value=0.074  Score=37.89  Aligned_cols=47  Identities=17%  Similarity=0.316  Sum_probs=40.0

Q ss_pred             CcceEEEEcC---CcchHHHHHHHHHcCCeEEEEcCCCchHHHhhhhccc
Q 045172          102 RFGCLVVVSD---DSDFVEVFQEATLRWLKMVVVGDMSDGALKRIANAFF  148 (157)
Q Consensus       102 ~v~clvLVSD---DsDF~~~lr~Arer~l~tVVVGd~~~~~L~r~AD~~f  148 (157)
                      .-+|++++|-   ..+..+.++.|+++|.++|+|-+..+..+.+.||.-|
T Consensus        53 ~~d~vi~is~sg~~~~~~~~~~~ak~~g~~vi~iT~~~~~~l~~~ad~~l  102 (131)
T PF01380_consen   53 PDDLVIIISYSGETRELIELLRFAKERGAPVILITSNSESPLARLADIVL  102 (131)
T ss_dssp             TTEEEEEEESSSTTHHHHHHHHHHHHTTSEEEEEESSTTSHHHHHSSEEE
T ss_pred             ccceeEeeeccccchhhhhhhHHHHhcCCeEEEEeCCCCCchhhhCCEEE
Confidence            4489999994   3466778899999999999999987789999999877

; InterPro: IPR001347 The SIS (Sugar ISomerase) domain is a phosphosugar-binding domain [] found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars possibly by binding to the end-product of the pathway.; GO: 0005529 sugar binding, 0005975 carbohydrate metabolic process; PDB: 3TBF_C 2V4M_A 2ZJ4_A 2ZJ3_A 3FKJ_A 3ODP_A 3EUA_H 1VIV_A 1M3S_B 1TZB_A ....

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

Probab=94.66  E-value=0.16  Score=40.54  Aligned_cols=70  Identities=11%  Similarity=0.016  Sum_probs=53.0

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcc-hHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSD-FVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsD-F~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++..|+.+.......+   ..-..+..+.+..+++|.|++.+.|++ ..+.++.+.+.|..+|+++..
T Consensus        19 ~gi~~~~~~~G~~~~~~~~~~d---~~~~~~~i~~~~~~~vdgiii~~~~~~~~~~~i~~~~~~~iPvV~~~~~   89 (272)
T cd06313          19 QAADEAGKLLGVDVTWYGGALD---AVKQVAAIENMASQGWDFIAVDPLGIGTLTEAVQKAIARGIPVIDMGTL   89 (272)
T ss_pred             HHHHHHHHHcCCEEEEecCCCC---HHHHHHHHHHHHHcCCCEEEEcCCChHHhHHHHHHHHHCCCcEEEeCCC
Confidence            5778889999999998754433   333334444444799999999987766 467889999999999999864

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

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

Probab=94.65  E-value=0.2  Score=40.96  Aligned_cols=70  Identities=13%  Similarity=0.034  Sum_probs=53.7

Q ss_pred             CCcHHHHHh--hceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcc-hHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKR--AWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSD-FVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrR--AGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsD-F~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++..  .|+.+...+..   .|.+-+...++.+...+++.|++.+.|++ +.+.++.|++.|..+|.++..
T Consensus        19 ~gi~~~a~~~~~g~~~~~~~~~---~~~~~q~~~i~~l~~~~vdgiii~~~~~~~~~~~~~~~~~~giPvV~~~~~   91 (303)
T cd01539          19 KNLEDIQKENGGKVEFTFYDAK---NNQSTQNEQIDTALAKGVDLLAVNLVDPTAAQTVINKAKQKNIPVIFFNRE   91 (303)
T ss_pred             HHHHHHHHhhCCCeeEEEecCC---CCHHHHHHHHHHHHHcCCCEEEEecCchhhHHHHHHHHHHCCCCEEEeCCC
Confidence            477788888  88888776432   34555566666555889999999887766 678999999999999999754

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.

>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=94.60  E-value=0.18  Score=39.98  Aligned_cols=69  Identities=16%  Similarity=0.082  Sum_probs=49.7

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcch-HHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDF-VEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF-~~~lr~Arer~l~tVVVGd~  135 (157)
                      -|+..+++..|+.+..+... +. +. ....+..++ ..++|.|++.+.|++. .++++.+.+.|..+|+++..
T Consensus        19 ~gi~~~~~~~g~~~~~~~~~-~~-~~-~~~~i~~~~-~~~~dgiii~~~~~~~~~~~~~~~~~~~iPvV~~~~~   88 (289)
T cd01540          19 KFAKKAAKEKGFTVVKIDVP-DG-EK-VLSAIDNLG-AQGAKGFVICVPDVKLGPAIVAKAKAYNMKVVAVDDR   88 (289)
T ss_pred             HHHHHHHHHcCCEEEEccCC-CH-HH-HHHHHHHHH-HcCCCEEEEccCchhhhHHHHHHHHhCCCeEEEecCC
Confidence            36778889999998876332 32 21 223333344 6899999999988765 45789999999999999854

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

>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=94.57  E-value=0.17  Score=39.26  Aligned_cols=69  Identities=14%  Similarity=0.125  Sum_probs=51.6

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++++.|+.|.+++.. .  |..-...+.+.+.+.++|.|++.+.+.+- ..++.++++|..+|++|..
T Consensus        19 ~gi~~~~~~~g~~~~~~~~~-~--~~~~~~~~~~~l~~~~vdgiIi~~~~~~~-~~~~~l~~~~ipvV~~~~~   87 (265)
T cd06299          19 TAIQDAASAAGYSTIIGNSD-E--NPETENRYLDNLLSQRVDGIIVVPHEQSA-EQLEDLLKRGIPVVFVDRE   87 (265)
T ss_pred             HHHHHHHHHcCCEEEEEeCC-C--CHHHHHHHHHHHHhcCCCEEEEcCCCCCh-HHHHHHHhCCCCEEEEecc
Confidence            47888899999999987542 1  23333444555558899999998876553 5689999999999999875

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

>PRK10653 D-ribose transporter subunit RbsB; Provisional

Probab=94.51  E-value=0.18  Score=40.76  Aligned_cols=70  Identities=13%  Similarity=0.033  Sum_probs=52.9

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcch-HHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDF-VEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF-~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++++.|+.+-......+   ..-.....+.+...+++.+++.+.+++. ...+..+.+.|+.+|.++..
T Consensus        46 ~~i~~~~~~~G~~~~~~~~~~d---~~~~~~~~~~l~~~~~dgiii~~~~~~~~~~~l~~~~~~~ipvV~~~~~  116 (295)
T PRK10653         46 DGAQKEADKLGYNLVVLDSQNN---PAKELANVQDLTVRGTKILLINPTDSDAVGNAVKMANQANIPVITLDRG  116 (295)
T ss_pred             HHHHHHHHHcCCeEEEecCCCC---HHHHHHHHHHHHHcCCCEEEEcCCChHHHHHHHHHHHHCCCCEEEEccC
Confidence            6888999999999987644333   2333444444547899999999877655 57899999999999999864

>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=94.51  E-value=0.17  Score=41.87  Aligned_cols=68  Identities=12%  Similarity=0.185  Sum_probs=54.1

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++++.||.+-......+ .|  .. +.+++|.++++|.|++.|...++..+.+.++. +.-.|+++..
T Consensus        21 ~gIe~~a~~~Gy~l~l~~t~~~-~~--~e-~~i~~l~~~~vDGiI~~s~~~~~~~l~~~~~~-~iPvV~~~~~   88 (279)
T PF00532_consen   21 RGIEQEAREHGYQLLLCNTGDD-EE--KE-EYIELLLQRRVDGIILASSENDDEELRRLIKS-GIPVVLIDRY   88 (279)
T ss_dssp             HHHHHHHHHTTCEEEEEEETTT-HH--HH-HHHHHHHHTTSSEEEEESSSCTCHHHHHHHHT-TSEEEEESS-
T ss_pred             HHHHHHHHHcCCEEEEecCCCc-hH--HH-HHHHHHHhcCCCEEEEecccCChHHHHHHHHc-CCCEEEEEec
Confidence            5788999999999988655544 22  22 55556668999999999999998888888877 9999999987

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 ....

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

Probab=94.49  E-value=0.23  Score=38.93  Aligned_cols=70  Identities=9%  Similarity=0.091  Sum_probs=50.1

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcc----hHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSD----FVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsD----F~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++..|+.+-+.... ..  .....+..+.|-..++|++++.+.+++    ..+.++.+.+.|..+|.++..
T Consensus        19 ~gi~~~~~~~g~~~~~~~~~-~~--~~~~~~~i~~l~~~~vdgii~~~~~~~~~~~~~~~~~~~~~~~ipvV~~~~~   92 (273)
T cd01541          19 RGIESVLSEKGYSLLLASTN-ND--PERERKCLENMLSQGIDGLIIEPTKSALPNPNIDLYLKLEKLGIPYVFINAS   92 (273)
T ss_pred             HHHHHHHHHcCCEEEEEeCC-CC--HHHHHHHHHHHHHcCCCEEEEeccccccccccHHHHHHHHHCCCCEEEEecC
Confidence            57889999999999765432 22  223333444444789999999876543    457889999999999999854

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

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

Probab=94.47  E-value=0.23  Score=38.74  Aligned_cols=71  Identities=13%  Similarity=0.099  Sum_probs=52.1

Q ss_pred             CCCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcc-hHHHHHHHHHcCCeEEEEcCC
Q 045172           62 GYGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSD-FVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        62 gygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsD-F~~~lr~Arer~l~tVVVGd~  135 (157)
                      -.|+..+++..|+.+.+.....   |........+.+.++++|++++.+.+++ +.+.++.+++.|..+|.++..
T Consensus        18 ~~~i~~~~~~~g~~~~i~~~~~---~~~~~~~~~~~~~~~~vdgiii~~~~~~~~~~~~~~~~~~~ipvV~~~~~   89 (267)
T cd06322          18 ANAMKEEAKKQKVNLIVSIANQ---DLNKQLSDVEDFITKKVDAIVLSPVDSKGIRAAIAKAKKAGIPVITVDIA   89 (267)
T ss_pred             HHHHHHHHHhcCCEEEEecCCC---CHHHHHHHHHHHHHcCCCEEEEcCCChhhhHHHHHHHHHCCCCEEEEccc
Confidence            3678889999999997643222   3334444444444789999999876654 678899999999999999754

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.

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

Probab=94.45  E-value=0.17  Score=39.98  Aligned_cols=73  Identities=12%  Similarity=0.075  Sum_probs=54.1

Q ss_pred             ccCCCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcc-hHHHHHHHHHcCCeEEEEcCC
Q 045172           60 KVGYGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSD-FVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        60 kvgygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsD-F~~~lr~Arer~l~tVVVGd~  135 (157)
                      .+..|+..++++.|+.+..+.+..  .|........+.+..+++|.+++.+.+.+ ..++++.+.+ +..+|.+|..
T Consensus        15 ~~~~gi~~~~~~~g~~~~~~~~~~--~~~~~~~~~i~~l~~~~vDgiIi~~~~~~~~~~~l~~~~~-~ipvV~~~~~   88 (271)
T cd06314          15 IAEAGVKAAGKELGVDVEFVVPQQ--GTVNAQLRMLEDLIAEGVDGIAISPIDPKAVIPALNKAAA-GIKLITTDSD   88 (271)
T ss_pred             HHHHHHHHHHHHcCCeEEEeCCCC--CCHHHHHHHHHHHHhcCCCEEEEecCChhHhHHHHHHHhc-CCCEEEecCC
Confidence            345788999999999998874222  13333445555555899999999987654 5688999988 9999999864

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).

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

Probab=94.42  E-value=0.17  Score=39.83  Aligned_cols=73  Identities=15%  Similarity=0.140  Sum_probs=52.0

Q ss_pred             CCCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcc-hHHHHHHHHHcCCeEEEEcCC
Q 045172           62 GYGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSD-FVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        62 gygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsD-F~~~lr~Arer~l~tVVVGd~  135 (157)
                      ..|+..+++..|+.+..+..- ...|......+.+.+-..+++++|+++.+++ ....+..+++.|..+|.+|..
T Consensus        18 ~~gi~~~~~~~g~~~~~~~~~-~~~~~~~~~~~i~~l~~~~vdgiIi~~~~~~~~~~~~~~~~~~~iPvV~~~~~   91 (275)
T cd06320          18 KEGYENEAKKLGVSVDIQAAP-SEGDQQGQLSIAENMINKGYKGLLFSPISDVNLVPAVERAKKKGIPVVNVNDK   91 (275)
T ss_pred             HHHHHHHHHHhCCeEEEEccC-CCCCHHHHHHHHHHHHHhCCCEEEECCCChHHhHHHHHHHHHCCCeEEEECCC
Confidence            368889999999998876321 1112333344555554689999999876654 457789999999999999864

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.

>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=94.42  E-value=0.25  Score=39.76  Aligned_cols=70  Identities=11%  Similarity=0.065  Sum_probs=53.0

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcc-hHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSD-FVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsD-F~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++..|+.+.++....+   ..-...+.+.+...++|.|++++.+++ ..+.++.+++.|..+|+++..
T Consensus        19 ~gi~~~a~~~g~~~~~~~~~~~---~~~~~~~i~~~~~~~vdgiii~~~~~~~~~~~l~~l~~~~ipvV~~~~~   89 (288)
T cd01538          19 PNFEAALKELGAEVIVQNANGD---PAKQISQIENMIAKGVDVLVIAPVDGEALASAVEKAADAGIPVIAYDRL   89 (288)
T ss_pred             HHHHHHHHHcCCEEEEECCCCC---HHHHHHHHHHHHHcCCCEEEEecCChhhHHHHHHHHHHCCCCEEEECCC
Confidence            5888999999999998755332   222334444444789999999986655 578999999999999999765

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.

>TIGR02637 RhaS rhamnose ABC transporter, rhamnose-binding protein

Probab=94.40  E-value=0.17  Score=40.86  Aligned_cols=71  Identities=14%  Similarity=0.091  Sum_probs=50.0

Q ss_pred             CCcHHHHHhhceEEEEec-CCCccHHHHHHHHHHHHhhccCcceEEEEcCCcc-hHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVL-VKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSD-FVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~-dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsD-F~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++.+.|++.-++. ...  .|.+-+...++.+-..++|.||+++-|++ ....++.|+++|+.+|+++..
T Consensus        18 ~gi~~~a~~~g~~~~i~~~~~~--~d~~~q~~~i~~l~~~~vdgiIi~~~~~~~~~~~l~~~~~~giPvV~~~~~   90 (302)
T TIGR02637        18 KGAEEAAKELGSVYIIYTGPTG--TTAEGQIEVVNSLIAQKVDAIAISANDPDALVPALKKAMKRGIKVVTWDSG   90 (302)
T ss_pred             HHHHHHHHHhCCeeEEEECCCC--CCHHHHHHHHHHHHHcCCCEEEEeCCChHHHHHHHHHHHHCCCEEEEeCCC
Confidence            478888999995433332 222  23344445556665799999999987654 567899999999999999854

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

>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=94.27  E-value=0.3  Score=37.79  Aligned_cols=70  Identities=11%  Similarity=0.149  Sum_probs=51.1

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++++.|+.+...+...   |......+.+.+.+.++|.+++++.+++-.+.++.+.+.|+.+|.++..
T Consensus        19 ~g~~~~a~~~g~~~~~~~~~~---~~~~~~~~i~~~~~~~vdgiii~~~~~~~~~~~~~~~~~~ipvV~~~~~   88 (268)
T cd06289          19 AGLEEVLEEAGYTVFLANSGE---DVERQEQLLSTMLEHGVAGIILCPAAGTSPDLLKRLAESGIPVVLVARE   88 (268)
T ss_pred             HHHHHHHHHcCCeEEEecCCC---ChHHHHHHHHHHHHcCCCEEEEeCCCCccHHHHHHHHhcCCCEEEEecc
Confidence            466778888899887654332   2344455555565789999999986654345889999999999999754

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.

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

Probab=94.20  E-value=0.29  Score=37.79  Aligned_cols=70  Identities=13%  Similarity=0.100  Sum_probs=50.9

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcch-HHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDF-VEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF-~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++..|+.+.+.+...+.   .-...+.+.+...+++.+++++.+++. .+.++.+++.|+..|.++..
T Consensus        19 ~~i~~~~~~~g~~v~~~~~~~~~---~~~~~~~~~~~~~~~dgii~~~~~~~~~~~~l~~l~~~~ipvv~~~~~   89 (268)
T cd06323          19 DGAQKEAKELGYELTVLDAQNDA---AKQLNDIEDLITRGVDAIIINPTDSDAVVPAVKAANEAGIPVFTIDRE   89 (268)
T ss_pred             HHHHHHHHHcCceEEecCCCCCH---HHHHHHHHHHHHcCCCEEEEcCCChHHHHHHHHHHHHCCCcEEEEccC
Confidence            47888999999999876554332   222233333336789999999877665 36789999999999999875

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.

>PRK10014 DNA-binding transcriptional repressor MalI; Provisional

Probab=94.17  E-value=0.28  Score=40.18  Aligned_cols=70  Identities=9%  Similarity=-0.004  Sum_probs=52.3

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++...|+.+-++...+.   ..-.....+.|.+.++|.|++++.+......+..+++.|+.+|.++..
T Consensus        84 ~gi~~~a~~~g~~~~~~~~~~~---~~~~~~~~~~l~~~~vdgiIi~~~~~~~~~~~~~l~~~~iPvV~~~~~  153 (342)
T PRK10014         84 AGLTEALEAQGRMVFLLQGGKD---GEQLAQRFSTLLNQGVDGVVIAGAAGSSDDLREMAEEKGIPVVFASRA  153 (342)
T ss_pred             HHHHHHHHHcCCEEEEEeCCCC---HHHHHHHHHHHHhCCCCEEEEeCCCCCcHHHHHHHhhcCCCEEEEecC
Confidence            4677889999998877654433   222334455555789999999987666678899999999999999764

>cd05008 SIS_GlmS_GlmD_1 SIS (Sugar ISomerase) domain repeat 1 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD)

Probab=94.15  E-value=0.11  Score=37.27  Aligned_cols=75  Identities=15%  Similarity=0.124  Sum_probs=51.3

Q ss_pred             cHHHHHhhc-eEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCC---cchHHHHHHHHHcCCeEEEEcCCCchHH
Q 045172           65 FADELKRAW-FWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDD---SDFVEVFQEATLRWLKMVVVGDMSDGAL  140 (157)
Q Consensus        65 la~eLrRAG-v~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDD---sDF~~~lr~Arer~l~tVVVGd~~~~~L  140 (157)
                      ++.-|.+.| ..+...+  |.  +...  . ...+  ..-|+++.+|-.   .+-.++++.|+++|.++|.|-+..+..|
T Consensus        17 ~~~~l~~~~~~~~~~~~--~~--~~~~--~-~~~~--~~~d~~I~iS~sG~t~e~~~~~~~a~~~g~~vi~iT~~~~s~l   87 (126)
T cd05008          17 AKYLLERLAGIPVEVEA--AS--EFRY--R-RPLL--DEDTLVIAISQSGETADTLAALRLAKEKGAKTVAITNVVGSTL   87 (126)
T ss_pred             HHHHHHHhcCCceEEEe--hh--Hhhh--c-CCCC--CCCcEEEEEeCCcCCHHHHHHHHHHHHcCCeEEEEECCCCChH
Confidence            445567776 7777654  22  1111  1 1112  345778888854   4566778899999999999999877899


Q ss_pred             Hhhhhccc
Q 045172          141 KRIANAFF  148 (157)
Q Consensus       141 ~r~AD~~f  148 (157)
                      .+.||..|
T Consensus        88 a~~ad~~l   95 (126)
T cd05008          88 AREADYVL   95 (126)
T ss_pred             HHhCCEEE
Confidence            99999887

The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal glutaminase domain and two C-terminal SIS domains and catalyzes the first step in hexosamine metabolism, converting fructose 6-phosphate into glucosamine 6-phosphate using glutamine as nitrogen source. The glutaminase domain hydrolyzes glutamine to glutamate and ammonia. Ammonia is transferred through a channel to the isomerase domain for glucosamine 6-phosphate synthesis. The end product of the pathway is N-acetylglucosamine, which plays multiple roles in eukaryotic cells including being a building block of bacterial and fungal cell walls. In the absence of glutamine, GlmS catalyzes the isomerization of fructose 6-phosphate into glucose 6- phosphate (PGI-like activity). Glucosamine-6-phosphate deaminase (GlmD) cont

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

Probab=94.15  E-value=0.26  Score=38.57  Aligned_cols=72  Identities=15%  Similarity=0.103  Sum_probs=52.9

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcc-hHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSD-FVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsD-F~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++..|+.+..+.... .-|.+....+.+.+...++|.+++++.+.+ ..++++.+++.|...|.++..
T Consensus        19 ~g~~~~~~~~g~~~~~~~~~~-~~~~~~~~~~i~~l~~~~vdgvii~~~~~~~~~~~l~~~~~~~ipvV~~~~~   91 (273)
T cd06310          19 AGAEAAAKELGVKVTFQGPAS-ETDVAGQVNLLENAIARGPDAILLAPTDAKALVPPLKEAKDAGIPVVLIDSG   91 (273)
T ss_pred             HHHHHHHHHcCCEEEEecCcc-CCCHHHHHHHHHHHHHhCCCEEEEcCCChhhhHHHHHHHHHCCCCEEEecCC
Confidence            678899999999999874211 123444555565555789999999875543 357889999999999999764

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.

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

Probab=94.09  E-value=0.33  Score=37.76  Aligned_cols=70  Identities=11%  Similarity=0.091  Sum_probs=51.2

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcch-HHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDF-VEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF-~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++.+.|+.+.+.+.. .  |.......++.+...++|.+++.+.+++. .+.++.++++|..+|.++..
T Consensus        20 ~g~~~~~~~~g~~~~~~~~~-~--~~~~~~~~~~~l~~~~vdgiii~~~~~~~~~~~l~~~~~~~iPvV~~~~~   90 (275)
T cd06317          20 KAFQAAAEEDGVEVIVLDAN-G--DVARQAAQVEDLIAQKVDGIILWPTDGQAYIPGLRKAKQAGIPVVITNSN   90 (275)
T ss_pred             HHHHHHHHhcCCEEEEEcCC-c--CHHHHHHHHHHHHHcCCCEEEEecCCccccHHHHHHHHHCCCcEEEeCCC
Confidence            46777888899999887543 2  23333344444446899999999877664 68889999999999999764

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.

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

Probab=93.98  E-value=0.34  Score=38.08  Aligned_cols=70  Identities=9%  Similarity=0.058  Sum_probs=50.3

Q ss_pred             CCcHHHHHhh-ceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcc-hHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRA-WFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSD-FVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRA-Gv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsD-F~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++.+. |+.+.+... +...+  -...+++.+.+.++|.|++++.+++ +.+.+..+.+.|+..|+++..
T Consensus        19 ~~i~~~~~~~~g~~~~~~~~-~~~~~--~~~~~i~~~~~~~vdgiii~~~~~~~~~~~~~~~~~~~ipvV~~~~~   90 (270)
T cd06308          19 DEIQREASNYPDVELIIADA-ADDNS--KQVADIENFIRQGVDLLIISPNEAAPLTPVVEEAYRAGIPVILLDRK   90 (270)
T ss_pred             HHHHHHHHhcCCcEEEEEcC-CCCHH--HHHHHHHHHHHhCCCEEEEecCchhhchHHHHHHHHCCCCEEEeCCC
Confidence            5778888885 998877533 33222  2223334444789999999987754 578889999999999999864

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.

>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=93.98  E-value=0.36  Score=37.53  Aligned_cols=69  Identities=12%  Similarity=0.041  Sum_probs=51.3

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++..|+.+-...+.-   |......+.+.+.+.++|++++++.++. ..+++.+.+.|+..|.++..
T Consensus        19 ~~i~~~~~~~g~~~~~~~~~~---~~~~~~~~~~~l~~~~vdgiii~~~~~~-~~~~~~l~~~~iPvv~~~~~   87 (268)
T cd06273          19 QAFQETLAAHGYTLLVASSGY---DLDREYAQARKLLERGVDGLALIGLDHS-PALLDLLARRGVPYVATWNY   87 (268)
T ss_pred             HHHHHHHHHCCCEEEEecCCC---CHHHHHHHHHHHHhcCCCEEEEeCCCCC-HHHHHHHHhCCCCEEEEcCC
Confidence            578999999999988754332   2333445555555789999999877653 57788999999999999864

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

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

Probab=93.94  E-value=0.27  Score=39.38  Aligned_cols=70  Identities=11%  Similarity=0.008  Sum_probs=51.0

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcc-hHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSD-FVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsD-F~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++...|+.+-......+.++   .....+.+..+++|+|+|++.+.+ ..+.+..+++.+...|+++..
T Consensus        20 ~gi~~~a~~~gy~~~~~~~~~~~~~---~~~~i~~l~~~~vdgiil~~~~~~~~~~~~~~~~~~~iPvV~~d~~   90 (280)
T cd06315          20 EGVREAAKAIGWNLRILDGRGSEAG---QAAALNQAIALKPDGIVLGGVDAAELQAELELAQKAGIPVVGWHAG   90 (280)
T ss_pred             HHHHHHHHHcCcEEEEECCCCCHHH---HHHHHHHHHHcCCCEEEEcCCCHHHHHHHHHHHHHCCCCEEEecCC
Confidence            5778899999999877644333222   234444455799999999987755 356778888899999999864

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

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

Probab=93.93  E-value=0.35  Score=37.79  Aligned_cols=69  Identities=17%  Similarity=0.133  Sum_probs=53.3

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      +|+..+++..|+.+.+.+..   .|......+.+.+...++|.+++.+.+++ ...++.+.+.|..+|+++..
T Consensus        19 ~gi~~~~~~~~~~~~~~~~~---~~~~~~~~~i~~l~~~~~dgiii~~~~~~-~~~~~~~~~~~iPvv~~~~~   87 (265)
T cd06285          19 EGIEEAAAERGYSTFVANTG---DNPDAQRRAIEMLLDRRVDGLILGDARSD-DHFLDELTRRGVPFVLVLRH   87 (265)
T ss_pred             HHHHHHHHHCCCEEEEEeCC---CCHHHHHHHHHHHHHcCCCEEEEecCCCC-hHHHHHHHHcCCCEEEEccC
Confidence            68899999999998664332   24455666777777899999999875544 35689999999999999875

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.

>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=93.91  E-value=0.34  Score=37.88  Aligned_cols=70  Identities=14%  Similarity=0.018  Sum_probs=51.4

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCc----chHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDS----DFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDs----DF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++++.|+.+.+.+...+   ......+.+.+..+++|++++.+...    .....+..+.++|..+|.||-.
T Consensus        19 ~gi~~~~~~~g~~~~~~~~~~~---~~~~~~~i~~l~~~~vdgiIi~~~~~~~~~~~~~~i~~~~~~~ipvV~i~~~   92 (273)
T cd06292          19 EAIEAALAQYGYTVLLCNTYRG---GVSEADYVEDLLARGVRGVVFISSLHADTHADHSHYERLAERGLPVVLVNGR   92 (273)
T ss_pred             HHHHHHHHHCCCEEEEEeCCCC---hHHHHHHHHHHHHcCCCEEEEeCCCCCcccchhHHHHHHHhCCCCEEEEcCC
Confidence            5888999999999877544332   34445566666689999999986332    2345678889999999999854

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.

>cd06301 PBP1_rhizopine_binding_like Periplasmic binding proteins specific to rhizopines

Probab=93.80  E-value=0.47  Score=37.11  Aligned_cols=70  Identities=14%  Similarity=0.091  Sum_probs=52.7

Q ss_pred             CCcHHHHHh-hceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcch-HHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKR-AWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDF-VEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrR-AGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF-~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++. .|+.+..... ..  |..-...+.+.+.+.++|.+++.+.+++. .++++.+.+.|..+|.++..
T Consensus        19 ~gi~~~~~~~~~~~~~~~~~-~~--~~~~~~~~i~~l~~~~vdgiii~~~~~~~~~~~~~~l~~~~iPvv~~~~~   90 (272)
T cd06301          19 NAMKEHAKVLGGVELQFEDA-KN--DVATQLSQVENFIAQGVDAIIVVPVDTAATAPIVKAANAAGIPLVYVNRR   90 (272)
T ss_pred             HHHHHHHHHcCCcEEEEeCC-CC--CHHHHHHHHHHHHHcCCCEEEEecCchhhhHHHHHHHHHCCCeEEEecCC
Confidence            578888999 8999988543 22  23344444544457899999999887764 57889999999999999875

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.

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

Probab=93.80  E-value=0.32  Score=37.91  Aligned_cols=69  Identities=14%  Similarity=0.078  Sum_probs=50.8

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++..|+.+.......+.   .....+.+.+-..++|.|++++.+.+ ...++.+.+.++.+|.|+-.
T Consensus        19 ~gi~~~~~~~g~~~~~~~~~~~~---~~~~~~i~~l~~~~~dgiii~~~~~~-~~~~~~~~~~~ipvV~i~~~   87 (270)
T cd06296          19 RGVEEAAAAAGYDVVLSESGRRT---SPERQWVERLSARRTDGVILVTPELT-SAQRAALRRTGIPFVVVDPA   87 (270)
T ss_pred             HHHHHHHHHcCCeEEEecCCCch---HHHHHHHHHHHHcCCCEEEEecCCCC-hHHHHHHhcCCCCEEEEecc
Confidence            57888999999999876544332   23334444444789999999887654 36789999999999999854

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.

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

Probab=93.78  E-value=0.41  Score=37.56  Aligned_cols=71  Identities=13%  Similarity=0.053  Sum_probs=51.8

Q ss_pred             CCcHHHHHh--hceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcc-hHHHHHHHHHcCCeEEEEcCCC
Q 045172           63 YGFADELKR--AWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSD-FVEVFQEATLRWLKMVVVGDMS  136 (157)
Q Consensus        63 ygla~eLrR--AGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsD-F~~~lr~Arer~l~tVVVGd~~  136 (157)
                      .|+..+++.  .|+.+.++....+   ..-...+.+.+...++|.|++.+.|++ ..+.++.+.+.|...|+++...
T Consensus        19 ~gi~~~~~~~~~~~~~~~~~~~~~---~~~~~~~i~~~~~~~~dgiIi~~~~~~~~~~~i~~~~~~~ipvv~~~~~~   92 (271)
T cd06321          19 KGAEAAAKKLNPGVKVTVVSADYD---LNKQVSQIDNFIAAKVDLILLNAVDSKGIAPAVKRAQAAGIVVVAVDVAA   92 (271)
T ss_pred             HHHHHHHHHhCCCeEEEEccCCCC---HHHHHHHHHHHHHhCCCEEEEeCCChhHhHHHHHHHHHCCCeEEEecCCC
Confidence            578888899  8888877644332   223334444445789999999886654 5788899999999999998753

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.

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

Probab=93.71  E-value=0.54  Score=37.04  Aligned_cols=70  Identities=17%  Similarity=0.127  Sum_probs=50.2

Q ss_pred             CCcHHHHHhh-----ceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcc-hHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRA-----WFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSD-FVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRA-----Gv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsD-F~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++++.     |+.+......-   |..-..++.+.+-..++|.|++++.|++ +...++.|.++|..+|.++..
T Consensus        19 ~gi~~~a~~~~~~~~g~~~~~~~~~~---~~~~~~~~~~~l~~~~vDgiii~~~~~~~~~~~i~~~~~~gIpvV~~d~~   94 (274)
T cd06311          19 WHAQAAAKKLEAAYPDVEFILVTASN---DTEQQNAQQDLLINRKIDALVILPFESAPLTQPVAKAKKAGIFVVVVDRG   94 (274)
T ss_pred             HHHHHHHHHhhhhCCCeEEEEEcCCC---CHHHHHHHHHHHHHcCCCEEEEeCCCchhhHHHHHHHHHCCCeEEEEcCC
Confidence            3566667776     67777754332   2334456666554789999999986644 678899999999999999764

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.

>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=93.62  E-value=0.44  Score=36.85  Aligned_cols=69  Identities=14%  Similarity=0.069  Sum_probs=50.3

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++...|+.+.+....-+.   .-...+.+.+...++|.+++++.+.+ ...+..+.+.|+..|++++.
T Consensus        19 ~gi~~~~~~~g~~~~~~~~~~~~---~~~~~~~~~l~~~~vdgiii~~~~~~-~~~~~~~~~~~ipvv~~~~~   87 (268)
T cd01575          19 QGISDVLEAAGYQLLLGNTGYSP---EREEELLRTLLSRRPAGLILTGLEHT-ERTRQLLRAAGIPVVEIMDL   87 (268)
T ss_pred             HHHHHHHHHcCCEEEEecCCCCc---hhHHHHHHHHHHcCCCEEEEeCCCCC-HHHHHHHHhcCCCEEEEecC
Confidence            47788999999998876542222   22334444444789999999987655 56778888899999999875

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,

>cd05005 SIS_PHI Hexulose-6-phosphate isomerase (PHI)

Probab=93.57  E-value=0.13  Score=39.96  Aligned_cols=71  Identities=20%  Similarity=0.168  Sum_probs=54.4

Q ss_pred             HHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCC---cchHHHHHHHHHcCCeEEEEcCCCchHHHh
Q 045172           66 ADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDD---SDFVEVFQEATLRWLKMVVVGDMSDGALKR  142 (157)
Q Consensus        66 a~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDD---sDF~~~lr~Arer~l~tVVVGd~~~~~L~r  142 (157)
                      +..|.+.|..|..++|- .          ...+  ..=|+++.+|-.   .+...+++.|+++|+++|.|-+.....|.+
T Consensus        52 ~~~l~~~g~~~~~~~~~-~----------~~~~--~~~D~vI~iS~sG~t~~~i~~~~~ak~~g~~iI~IT~~~~s~la~  118 (179)
T cd05005          52 AMRLMHLGLNVYVVGET-T----------TPAI--GPGDLLIAISGSGETSSVVNAAEKAKKAGAKVVLITSNPDSPLAK  118 (179)
T ss_pred             HHHHHhCCCeEEEeCCC-C----------CCCC--CCCCEEEEEcCCCCcHHHHHHHHHHHHCCCeEEEEECCCCCchHH
Confidence            34577889988887652 1          0112  345888888854   677889999999999999999987789999


Q ss_pred             hhhcccc
Q 045172          143 IANAFFS  149 (157)
Q Consensus       143 ~AD~~fs  149 (157)
                      .||..|.
T Consensus       119 ~ad~~l~  125 (179)
T cd05005         119 LADVVVV  125 (179)
T ss_pred             hCCEEEE
Confidence            9998874

PHI is a member of the SIS (Sugar ISomerase domain) superfamily. In the ribulose monophosphate pathway of formaldehyde fixation, hexulose-6-phosphate synthase catalyzes the condensation of ribulose-5-phosphate with formadelhyde to become hexulose-6-phosphate, which is then isomerized to fructose-6-phosphate by PHI.

>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=93.56  E-value=0.43  Score=37.33  Aligned_cols=68  Identities=13%  Similarity=0.175  Sum_probs=50.5

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++..|+.+.+...-.+.   .-...+.+.+...++|.|++.+.+++  ..++.++++|..+|+++..
T Consensus        22 ~~i~~~~~~~g~~~~~~~~~~~~---~~~~~~~~~l~~~~vdgiii~~~~~~--~~~~~l~~~~ipvV~~~~~   89 (268)
T cd06277          22 RAIEEEAKKYGYNLILKFVSDED---EEEFELPSFLEDGKVDGIILLGGIST--EYIKEIKELGIPFVLVDHY   89 (268)
T ss_pred             HHHHHHHHHcCCEEEEEeCCCCh---HHHHHHHHHHHHCCCCEEEEeCCCCh--HHHHHHhhcCCCEEEEccC
Confidence            46788899999998877544443   22334444444789999999997654  4589999999999999865

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.

>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=93.55  E-value=0.45  Score=36.91  Aligned_cols=68  Identities=9%  Similarity=0.022  Sum_probs=47.8

Q ss_pred             CcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           64 GFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        64 gla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      |+..++++.|+.+..++...+   ..-...+.+.+...++|.+++.+.+.+ .++++.+.+.|...|+++..
T Consensus        20 ~~~~~~~~~g~~~~~~~~~~~---~~~~~~~i~~l~~~~vdgiii~~~~~~-~~~~~~l~~~~ipvV~~~~~   87 (268)
T cd06298          20 GIDDIATMYKYNIILSNSDND---KEKELKVLNNLLAKQVDGIIFMGGKIS-EEHREEFKRSPTPVVLAGSV   87 (268)
T ss_pred             HHHHHHHHcCCeEEEEeCCCC---HHHHHHHHHHHHHhcCCEEEEeCCCCc-HHHHHHHhcCCCCEEEEccc
Confidence            567788889999988754322   222233444444689999999875433 46888888899999999864

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.

>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=93.52  E-value=0.43  Score=36.84  Aligned_cols=68  Identities=12%  Similarity=0.197  Sum_probs=49.7

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++..|+.+..+....+. |.  ...+..++ ..++|.+++++.+.+ ..+++.+.+.|...|.++..
T Consensus        19 ~~i~~~~~~~g~~~~~~~~~~~~-~~--~~~i~~~~-~~~vdgiii~~~~~~-~~~~~~~~~~~ipvV~~~~~   86 (266)
T cd06278          19 EALSRALQARGYQPLLINTDDDE-DL--DAALRQLL-QYRVDGVIVTSGTLS-SELAEECRRNGIPVVLINRY   86 (266)
T ss_pred             HHHHHHHHHCCCeEEEEcCCCCH-HH--HHHHHHHH-HcCCCEEEEecCCCC-HHHHHHHhhcCCCEEEECCc
Confidence            46788999999999887654432 32  23333334 789999999976644 25588899999999999865

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=93.50  E-value=0.44  Score=37.23  Aligned_cols=70  Identities=10%  Similarity=0.032  Sum_probs=50.4

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcch-HHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDF-VEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF-~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++++.|+.+..+... ...  .-...+.+.+...++|.+++.+.+++. ..+++.+.+.|..+|+++..
T Consensus        19 ~~i~~~~~~~g~~~~~~~~~-~~~--~~~~~~i~~~~~~~~dgiii~~~~~~~~~~~l~~~~~~~ipvV~~~~~   89 (277)
T cd06319          19 RGVKSKAKALGYDAVELSAE-NSA--KKELENLRTAIDKGVSGIIISPTNSSAAVTLLKLAAQAKIPVVIADIG   89 (277)
T ss_pred             HHHHHHHHhcCCeEEEecCC-CCH--HHHHHHHHHHHhcCCCEEEEcCCchhhhHHHHHHHHHCCCCEEEEecC
Confidence            57788899999999876443 222  222233333336899999998888763 57899999999999999754

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.

>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor

Probab=93.45  E-value=0.45  Score=38.82  Aligned_cols=70  Identities=11%  Similarity=0.060  Sum_probs=50.0

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++...|+.+-......+   ..-.....+.+..+++|+|++.+.+.+..+.+..+.+.|..+|+++-.
T Consensus        80 ~~i~~~~~~~gy~~~i~~~~~~---~~~~~~~~~~l~~~~vdgiIi~~~~~~~~~~~~~l~~~~iPvV~~~~~  149 (327)
T TIGR02417        80 KELEQQCREAGYQLLIACSDDN---PDQEKVVIENLLARQVDALIVASCMPPEDAYYQKLQNEGLPVVALDRS  149 (327)
T ss_pred             HHHHHHHHHCCCEEEEEeCCCC---HHHHHHHHHHHHHcCCCEEEEeCCCCCChHHHHHHHhcCCCEEEEccc
Confidence            3788889999999977644322   222334445455789999999886653456778888899999999854

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.

>PRK09552 mtnX 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate phosphatase; Reviewed

Probab=93.38  E-value=0.23  Score=39.46  Aligned_cols=99  Identities=16%  Similarity=0.061  Sum_probs=57.7

Q ss_pred             HHHHHHHHhhcCcccC-CCcHHHHHhhceEEEEecCCCcc-HHHHHHHHHHHHhhccCcceEE-EEcCC--------c--
Q 045172           47 EKNKMAASAILTPKVG-YGFADELKRAWFWVRMVLVKPQD-ADVLLRNYMVAMVDKRRFGCLV-VVSDD--------S--  113 (157)
Q Consensus        47 ~kY~~Aar~~l~pkvg-ygla~eLrRAGv~V~~V~dkpqA-AD~AL~~~~~~~~~~r~v~clv-LVSDD--------s--  113 (157)
                      +.+.+...+.+.|.-| ..+-..|++.|+.+-.||+++.. ++..|...    +..-.+-|.- .++++        +  
T Consensus        63 ~~~~~~~~~~~~l~pG~~e~l~~l~~~g~~~~IvS~~~~~~i~~il~~~----~~~~~i~~n~~~~~~~~~~~~kp~p~~  138 (219)
T PRK09552         63 EEIIQFLLETAEIREGFHEFVQFVKENNIPFYVVSGGMDFFVYPLLQGL----IPKEQIYCNGSDFSGEYITITWPHPCD  138 (219)
T ss_pred             HHHHHHHHhCCCcCcCHHHHHHHHHHcCCeEEEECCCcHHHHHHHHHHh----CCcCcEEEeEEEecCCeeEEeccCCcc
Confidence            4444544455566666 56778899999999999999972 22222222    1110111101 12221        1  


Q ss_pred             ---------chHHHHHHHHHcCCeEEEEcCC-CchHHHhhhhcccc
Q 045172          114 ---------DFVEVFQEATLRWLKMVVVGDM-SDGALKRIANAFFS  149 (157)
Q Consensus       114 ---------DF~~~lr~Arer~l~tVVVGd~-~~~~L~r~AD~~fs  149 (157)
                               ....+++......-.+|.|||+ +|-...+.||+.|.
T Consensus       139 ~~~~~~~~~~K~~~l~~~~~~~~~~i~iGDs~~Di~aa~~Ag~~~a  184 (219)
T PRK09552        139 EHCQNHCGCCKPSLIRKLSDTNDFHIVIGDSITDLEAAKQADKVFA  184 (219)
T ss_pred             ccccccCCCchHHHHHHhccCCCCEEEEeCCHHHHHHHHHCCccee
Confidence                     1356666655555679999999 66666778887653

>PRK10355 xylF D-xylose transporter subunit XylF; Provisional

Probab=93.38  E-value=0.47  Score=40.08  Aligned_cols=69  Identities=14%  Similarity=0.104  Sum_probs=53.2

Q ss_pred             CcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcc-hHHHHHHHHHcCCeEEEEcCC
Q 045172           64 GFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSD-FVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        64 gla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsD-F~~~lr~Arer~l~tVVVGd~  135 (157)
                      |+-.++...|+.+.++....+   .....++.+.+.++++|.|++++.+++ +.+.++.+.+++..+|+++..
T Consensus        46 gi~~~a~~~g~~l~i~~~~~~---~~~~~~~i~~l~~~~vDGiIi~~~~~~~~~~~l~~~~~~~iPvV~id~~  115 (330)
T PRK10355         46 IFVKKAESLGAKVFVQSANGN---EETQMSQIENMINRGVDVLVIIPYNGQVLSNVIKEAKQEGIKVLAYDRM  115 (330)
T ss_pred             HHHHHHHHcCCEEEEECCCCC---HHHHHHHHHHHHHcCCCEEEEeCCChhhHHHHHHHHHHCCCeEEEECCC
Confidence            667788889999998754333   344445555555789999999987654 678899999999999999764

>PRK09701 D-allose transporter subunit; Provisional

Probab=93.36  E-value=0.4  Score=39.59  Aligned_cols=72  Identities=15%  Similarity=0.156  Sum_probs=51.9

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcc-hHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSD-FVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsD-F~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++..|+.+.++. .|...|..-.....+.+..+++|.|++.+.+++ =.+.+..+.+.|+.+|+++..
T Consensus        44 ~gi~~~a~~~g~~v~~~~-~~~~~~~~~~~~~i~~l~~~~vDgiIi~~~~~~~~~~~l~~~~~~giPvV~~~~~  116 (311)
T PRK09701         44 KGIEDEAKTLGVSVDIFA-SPSEGDFQSQLQLFEDLSNKNYKGIAFAPLSSVNLVMPVARAWKKGIYLVNLDEK  116 (311)
T ss_pred             HHHHHHHHHcCCeEEEec-CCCCCCHHHHHHHHHHHHHcCCCEEEEeCCChHHHHHHHHHHHHCCCcEEEeCCC
Confidence            678889999999998863 222223444455555555789999999886654 235577888999999999865

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

Probab=93.35  E-value=0.42  Score=37.62  Aligned_cols=70  Identities=9%  Similarity=0.067  Sum_probs=52.0

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcc-hHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSD-FVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsD-F~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++..|+.+......-+   ..-.....+.+-..++|.+++.+.+++ +.+.++.+.+.|..+|+++..
T Consensus        19 ~~~~~~a~~~g~~~~~~~~~~~---~~~~~~~i~~l~~~~vdgiIi~~~~~~~~~~~i~~~~~~~iPvV~~~~~   89 (273)
T cd06309          19 KSIKDAAEKRGFDLKFADAQQK---QENQISAIRSFIAQGVDVIILAPVVETGWDPVLKEAKAAGIPVILVDRG   89 (273)
T ss_pred             HHHHHHHHhcCCEEEEeCCCCC---HHHHHHHHHHHHHcCCCEEEEcCCccccchHHHHHHHHCCCCEEEEecC
Confidence            4778889999999998654332   333333343344689999999887765 578899999999999999864

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.

>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=93.10  E-value=0.5  Score=36.51  Aligned_cols=69  Identities=13%  Similarity=0.116  Sum_probs=49.3

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++..|+.+.......+   ......+.+++...++|++++.+.+.+ ...+..+.+.+..+|+++..
T Consensus        23 ~~i~~~~~~~g~~~~~~~~~~~---~~~~~~~~~~~~~~~vdgiii~~~~~~-~~~~~~~~~~~ipvV~~~~~   91 (268)
T cd06271          23 SGLSEALAEHGYDLVLLPVDPD---EDPLEVYRRLVESGLVDGVIISRTRPD-DPRVALLLERGFPFVTHGRT   91 (268)
T ss_pred             HHHHHHHHHCCceEEEecCCCc---HHHHHHHHHHHHcCCCCEEEEecCCCC-ChHHHHHHhcCCCEEEECCc
Confidence            4778899999999888654333   223344555555578999999876544 34567888899999999764

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

>PRK11557 putative DNA-binding transcriptional regulator; Provisional

Probab=93.06  E-value=0.42  Score=39.31  Aligned_cols=96  Identities=16%  Similarity=0.036  Sum_probs=64.2

Q ss_pred             hhHHHHHHHHhhcCcccC----CC--------cHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCC
Q 045172           45 KMEKNKMAASAILTPKVG----YG--------FADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDD  112 (157)
Q Consensus        45 k~~kY~~Aar~~l~pkvg----yg--------la~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDD  112 (157)
                      ..++.++++..+...+--    .|        ++--|.+.|..+...+|.      .........+  ..=|+++.+|-.
T Consensus       114 ~~~~l~~~~~~i~~a~~I~i~G~G~s~~~A~~~~~~l~~~g~~~~~~~d~------~~~~~~~~~~--~~~Dv~I~iS~s  185 (278)
T PRK11557        114 SEEKLHECVTMLRSARRIILTGIGASGLVAQNFAWKLMKIGINAVAERDM------HALLATVQAL--SPDDLLLAISYS  185 (278)
T ss_pred             CHHHHHHHHHHHhcCCeEEEEecChhHHHHHHHHHHHhhCCCeEEEcCCh------HHHHHHHHhC--CCCCEEEEEcCC
Confidence            346677777766555432    22        234467889888764332      2222223333  234677777743


Q ss_pred             ---cchHHHHHHHHHcCCeEEEEcCCCchHHHhhhhccc
Q 045172          113 ---SDFVEVFQEATLRWLKMVVVGDMSDGALKRIANAFF  148 (157)
Q Consensus       113 ---sDF~~~lr~Arer~l~tVVVGd~~~~~L~r~AD~~f  148 (157)
                         .+...+++.|+++|.++|+|-|.....+.+.||.-|
T Consensus       186 g~~~~~~~~~~~ak~~ga~iI~IT~~~~s~la~~ad~~l  224 (278)
T PRK11557        186 GERRELNLAADEALRVGAKVLAITGFTPNALQQRASHCL  224 (278)
T ss_pred             CCCHHHHHHHHHHHHcCCCEEEEcCCCCCchHHhCCEEE
Confidence               455678999999999999999987789999999877

>TIGR03590 PseG pseudaminic acid biosynthesis-associated protein PseG

Probab=92.77  E-value=0.52  Score=39.40  Aligned_cols=75  Identities=19%  Similarity=0.203  Sum_probs=43.5

Q ss_pred             HHHHhhceEEEEecCCCc-cHHHHHHHHHHHHhhccCcceEEEEcCCcchH-HHHHHHHHcCCeEEEEcCCCchHHHhhh
Q 045172           67 DELKRAWFWVRMVLVKPQ-DADVLLRNYMVAMVDKRRFGCLVVVSDDSDFV-EVFQEATLRWLKMVVVGDMSDGALKRIA  144 (157)
Q Consensus        67 ~eLrRAGv~V~~V~dkpq-AAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~-~~lr~Arer~l~tVVVGd~~~~~L~r~A  144 (157)
                      +.|+.+|+.|..+++... ..|.+   .+.+.+...+.|++  |.|.-+|. ...+..++.+.++++|-|..++..  .|
T Consensus        47 ~~i~~~g~~v~~~~~~~~~~~d~~---~~~~~l~~~~~d~v--V~D~y~~~~~~~~~~k~~~~~l~~iDD~~~~~~--~~  119 (279)
T TIGR03590        47 DLLLSAGFPVYELPDESSRYDDAL---ELINLLEEEKFDIL--IVDHYGLDADWEKLIKEFGRKILVIDDLADRPH--DC  119 (279)
T ss_pred             HHHHHcCCeEEEecCCCchhhhHH---HHHHHHHhcCCCEE--EEcCCCCCHHHHHHHHHhCCeEEEEecCCCCCc--CC
Confidence            455566666665554332 11222   24444544456644  55655544 344556678999999999854444  88


Q ss_pred             hccc
Q 045172          145 NAFF  148 (157)
Q Consensus       145 D~~f  148 (157)
                      |+.|
T Consensus       120 D~vi  123 (279)
T TIGR03590       120 DLLL  123 (279)
T ss_pred             CEEE
Confidence            9887

This protein is found in association with enzymes involved in the biosynthesis of pseudaminic acid, a component of polysaccharide in certain Pseudomonas strains as well as a modification of flagellin in Campylobacter and Hellicobacter. The role of this protein is unclear, although it may participate in N-acetylation in conjunction with, or in the absence of PseH (TIGR03585) as it often scores above the trusted cutoff to pfam00583 representing a family of acetyltransferases.

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

Probab=92.74  E-value=0.64  Score=36.83  Aligned_cols=69  Identities=13%  Similarity=0.068  Sum_probs=49.8

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++.+.|+.+-+......   ......+...+...++|++++.+.+.+ .+.++.+++.|..+|+++..
T Consensus        19 ~~i~~~~~~~gy~~~~~~~~~~---~~~~~~~~~~l~~~~vdgvi~~~~~~~-~~~~~~l~~~~iPvv~~~~~   87 (269)
T cd06297          19 EGIEGALLEQRYDLALFPLLSL---ARLKRYLESTTLAYLTDGLLLASYDLT-ERLAERRLPTERPVVLVDAE   87 (269)
T ss_pred             HHHHHHHHHCCCEEEEEeCCCc---HHHHHHHHHHHHhcCCCEEEEecCccC-hHHHHHHhhcCCCEEEEccC
Confidence            5888899999999888643322   122223333344789999999997766 46778889999999999864

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.

>TIGR01512 ATPase-IB2_Cd heavy metal-(Cd/Co/Hg/Pb/Zn)-translocating P-type ATPase

Probab=92.68  E-value=0.26  Score=45.15  Aligned_cols=79  Identities=16%  Similarity=0.092  Sum_probs=52.6

Q ss_pred             HHHHHhhce-EEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC-CchHHHhh
Q 045172           66 ADELKRAWF-WVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM-SDGALKRI  143 (157)
Q Consensus        66 a~eLrRAGv-~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~-~~~~L~r~  143 (157)
                      -.+|+++|+ .+-.++.+|+..=.       ..+...|++-+.--....+=..+++.....+-.++.|||+ +|-.-.+.
T Consensus       371 i~~L~~~Gi~~v~vvTgd~~~~a~-------~i~~~lgi~~~f~~~~p~~K~~~i~~l~~~~~~v~~vGDg~nD~~al~~  443 (536)
T TIGR01512       371 IAELKALGIEKVVMLTGDRRAVAE-------RVARELGIDEVHAELLPEDKLEIVKELREKYGPVAMVGDGINDAPALAA  443 (536)
T ss_pred             HHHHHHcCCCcEEEEcCCCHHHHH-------HHHHHcCChhhhhccCcHHHHHHHHHHHhcCCEEEEEeCCHHHHHHHHh
Confidence            457888888 88888887772111       1112234432211111224466888888888899999999 87788899


Q ss_pred             hhcccchh
Q 045172          144 ANAFFSWS  151 (157)
Q Consensus       144 AD~~fsW~  151 (157)
                      ||+.++|.
T Consensus       444 A~vgia~g  451 (536)
T TIGR01512       444 ADVGIAMG  451 (536)
T ss_pred             CCEEEEeC
Confidence            99999996

.

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

Probab=92.65  E-value=0.78  Score=35.41  Aligned_cols=69  Identities=13%  Similarity=0.074  Sum_probs=48.7

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++..|+.+.+......   ........+.+.+.++|++++.+.+.+- ..++.+.+.|...|+++..
T Consensus        19 ~~i~~~a~~~g~~~~~~~~~~~---~~~~~~~~~~l~~~~~dgiii~~~~~~~-~~l~~~~~~~ipvV~~~~~   87 (267)
T cd06283          19 KGIEDVCRAHGYQVLVCNSDND---PEKEKEYLESLLAYQVDGLIVNPTGNNK-ELYQRLAKNGKPVVLVDRK   87 (267)
T ss_pred             HHHHHHHHHcCCEEEEEcCCCC---HHHHHHHHHHHHHcCcCEEEEeCCCCCh-HHHHHHhcCCCCEEEEcCC
Confidence            3677778888988876544332   2333344444447899999998866553 4578889999999999875

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

>PRK10936 TMAO reductase system periplasmic protein TorT; Provisional

Probab=92.60  E-value=0.48  Score=39.94  Aligned_cols=71  Identities=10%  Similarity=0.081  Sum_probs=49.9

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcc-hHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSD-FVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsD-F~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++..|+.+......++ .|..-.....+.+-++++|.|++++.+++ +.+.+ .+++.|+.+|.+++.
T Consensus        66 ~gi~~aa~~~G~~l~i~~~~~~-~~~~~q~~~i~~l~~~~vdgIIl~~~~~~~~~~~l-~~~~~giPvV~~~~~  137 (343)
T PRK10936         66 YGMVEEAKRLGVDLKVLEAGGY-YNLAKQQQQLEQCVAWGADAILLGAVTPDGLNPDL-ELQAANIPVIALVNG  137 (343)
T ss_pred             HHHHHHHHHhCCEEEEEcCCCC-CCHHHHHHHHHHHHHhCCCEEEEeCCChHHhHHHH-HHHHCCCCEEEecCC
Confidence            4788899999999888643211 12233334455555899999999987655 44667 889999999988654

>PRK14987 gluconate operon transcriptional regulator; Provisional

Probab=92.56  E-value=0.77  Score=37.62  Aligned_cols=69  Identities=6%  Similarity=-0.003  Sum_probs=48.6

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++...|+.+-..+...+   ........+.+...++|.+++++.+.+ .+.++.+.+.|..+|+++|.
T Consensus        83 ~gi~~~~~~~g~~~~~~~~~~~---~~~~~~~~~~~~~~~vdgiI~~~~~~~-~~~~~~l~~~~iPvV~~~~~  151 (331)
T PRK14987         83 RGIESVTDAHGYQTMLAHYGYK---PEMEQERLESMLSWNIDGLILTERTHT-PRTLKMIEVAGIPVVELMDS  151 (331)
T ss_pred             HHHHHHHHHCCCEEEEecCCCC---HHHHHHHHHHHHhcCCCEEEEcCCCCC-HHHHHHHHhCCCCEEEEecC
Confidence            5788899999998876543322   222234445455789999999874433 57788888999999988764

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

Probab=92.45  E-value=0.92  Score=35.52  Aligned_cols=69  Identities=10%  Similarity=0.075  Sum_probs=49.9

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++++.|+.|.......   |..-...+.+.+...++|++++++.+.+.. .++.+...+..+|+|+..
T Consensus        19 ~gi~~~~~~~gy~v~~~~~~~---~~~~~~~~i~~~~~~~~dgiii~~~~~~~~-~~~~~~~~~~pvV~i~~~   87 (269)
T cd06293          19 DAVEEEADARGLSLVLCATRN---RPERELTYLRWLDTNHVDGLIFVTNRPDDG-ALAKLINSYGNIVLVDED   87 (269)
T ss_pred             HHHHHHHHHCCCEEEEEeCCC---CHHHHHHHHHHHHHCCCCEEEEeCCCCCHH-HHHHHHhcCCCEEEECCC
Confidence            578889999999997764332   334455566666689999999998665544 345566779999999964

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

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

Probab=92.32  E-value=0.72  Score=35.99  Aligned_cols=69  Identities=10%  Similarity=0.002  Sum_probs=48.5

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++..|+.+....-..   |..-...+.+.+.++++|.+++++.+.+-.. ++.+++.|..+|+++-.
T Consensus        19 ~~~~~~~~~~g~~~~~~~~~~---~~~~~~~~i~~l~~~~vdgiii~~~~~~~~~-~~~~~~~~ipvV~~~~~   87 (264)
T cd06274          19 KRLEALARERGYQLLIACSDD---DPETERETVETLIARQVDALIVAGSLPPDDP-YYLCQKAGLPVVALDRP   87 (264)
T ss_pred             HHHHHHHHHCCCEEEEEeCCC---CHHHHHHHHHHHHHcCCCEEEEcCCCCchHH-HHHHHhcCCCEEEecCc
Confidence            466778889999886653322   2233334555555899999999987654333 77889999999999765

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

>cd05710 SIS_1 A subgroup of the SIS domain

Probab=92.25  E-value=0.31  Score=35.86  Aligned_cols=45  Identities=16%  Similarity=0.217  Sum_probs=39.0

Q ss_pred             ceEEEEcCC---cchHHHHHHHHHcCCeEEEEcCCCchHHHhhhhccc
Q 045172          104 GCLVVVSDD---SDFVEVFQEATLRWLKMVVVGDMSDGALKRIANAFF  148 (157)
Q Consensus       104 ~clvLVSDD---sDF~~~lr~Arer~l~tVVVGd~~~~~L~r~AD~~f  148 (157)
                      |+++.+|-.   .+-.+.++.|+++|.+++.|-+..+..|.+.||..|
T Consensus        49 dl~I~iS~SG~t~~~~~~~~~a~~~g~~vi~iT~~~~s~la~~ad~~l   96 (120)
T cd05710          49 SVVILASHSGNTKETVAAAKFAKEKGATVIGLTDDEDSPLAKLADYVI   96 (120)
T ss_pred             cEEEEEeCCCCChHHHHHHHHHHHcCCeEEEEECCCCCcHHHhCCEEE
Confidence            888888854   677788899999999999999987789999999876

SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars.

>TIGR00441 gmhA phosphoheptose isomerase

Probab=92.08  E-value=0.27  Score=37.81  Aligned_cols=49  Identities=12%  Similarity=0.240  Sum_probs=40.5

Q ss_pred             cCcceEEEEcCC---cchHHHHHHHHHcCCeEEEEcCCCchHHHhhhhcccc
Q 045172          101 RRFGCLVVVSDD---SDFVEVFQEATLRWLKMVVVGDMSDGALKRIANAFFS  149 (157)
Q Consensus       101 r~v~clvLVSDD---sDF~~~lr~Arer~l~tVVVGd~~~~~L~r~AD~~fs  149 (157)
                      ..=|+++++|-.   .+-.++++.|+++|++++.|-+.....|.+.||.-|.
T Consensus        78 ~~~D~~i~iS~sG~t~~~~~~~~~a~~~g~~ii~iT~~~~s~l~~~ad~~l~  129 (154)
T TIGR00441        78 QKGDVLLGISTSGNSKNVLKAIEAAKDKGMKTITLAGKDGGKMAGLADIELR  129 (154)
T ss_pred             CCCCEEEEEcCCCCCHHHHHHHHHHHHCCCEEEEEeCCCCCchhhhCCEEEE
Confidence            344889999955   5566788999999999999998877899999998773

Involved in lipopolysaccharide biosynthesis it may have a role in virulence in Haemophilus ducreyi.

>TIGR01525 ATPase-IB_hvy heavy metal translocating P-type ATPase

Probab=91.98  E-value=0.47  Score=43.49  Aligned_cols=79  Identities=16%  Similarity=0.055  Sum_probs=53.2

Q ss_pred             HHHHHhhc-eEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC-CchHHHhh
Q 045172           66 ADELKRAW-FWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM-SDGALKRI  143 (157)
Q Consensus        66 a~eLrRAG-v~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~-~~~~L~r~  143 (157)
                      -.+|+..| +.+-+++.+|+..=.+       ++...|++.+.--....|=..+++.+...+-.++.|||+ +|-.-.+.
T Consensus       393 l~~L~~~g~i~v~ivTgd~~~~a~~-------i~~~lgi~~~f~~~~p~~K~~~v~~l~~~~~~v~~vGDg~nD~~al~~  465 (556)
T TIGR01525       393 IAALKRAGGIKLVMLTGDNRSAAEA-------VAAELGIDEVHAELLPEDKLAIVKELQEEGGVVAMVGDGINDAPALAA  465 (556)
T ss_pred             HHHHHHcCCCeEEEEeCCCHHHHHH-------HHHHhCCCeeeccCCHHHHHHHHHHHHHcCCEEEEEECChhHHHHHhh
Confidence            45678889 9999998888732122       223345543322112223346777777788899999999 77677789


Q ss_pred             hhcccchh
Q 045172          144 ANAFFSWS  151 (157)
Q Consensus       144 AD~~fsW~  151 (157)
                      ||+.+.|.
T Consensus       466 A~vgia~g  473 (556)
T TIGR01525       466 ADVGIAMG  473 (556)
T ss_pred             CCEeEEeC
Confidence            99999986

This alignment encompasses two equivalog models for the copper and cadmium-type heavy metal transporting P-type ATPases (TIGR01511 and TIGR01512) as well as those species which score ambiguously between both models. For more comments and references, see the files on TIGR01511 and 01512.

>TIGR03127 RuMP_HxlB 6-phospho 3-hexuloisomerase

Probab=91.82  E-value=0.33  Score=37.49  Aligned_cols=69  Identities=16%  Similarity=0.167  Sum_probs=52.6

Q ss_pred             HHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCC---cchHHHHHHHHHcCCeEEEEcCCCchHHHhh
Q 045172           67 DELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDD---SDFVEVFQEATLRWLKMVVVGDMSDGALKRI  143 (157)
Q Consensus        67 ~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDD---sDF~~~lr~Arer~l~tVVVGd~~~~~L~r~  143 (157)
                      .-|.+.|..+..+++--           ...+  ..=|+++++|-.   .+-.++++.|+++|.+++.|-+.....|.+.
T Consensus        50 ~~l~~~g~~~~~~~~~~-----------~~~~--~~~Dv~I~iS~sG~t~~~i~~~~~ak~~g~~ii~IT~~~~s~la~~  116 (179)
T TIGR03127        50 MRLMHLGFNVYVVGETT-----------TPSI--KKGDLLIAISGSGETESLVTVAKKAKEIGATVAAITTNPESTLGKL  116 (179)
T ss_pred             HHHHhCCCeEEEeCCcc-----------cCCC--CCCCEEEEEeCCCCcHHHHHHHHHHHHCCCeEEEEECCCCCchHHh
Confidence            34678899998876521           1122  234888888854   6677889999999999999988767899999


Q ss_pred             hhccc
Q 045172          144 ANAFF  148 (157)
Q Consensus       144 AD~~f  148 (157)
                      ||.-|
T Consensus       117 ad~~l  121 (179)
T TIGR03127       117 ADVVV  121 (179)
T ss_pred             CCEEE
Confidence            99876

Members of this protein family are 6-phospho 3-hexuloisomerase (PHI), or the PHI domain of a fusion protein. This enzyme is part of the ribulose monophosphate (RuMP) pathway, which in one direction removes the toxic metabolite formaldehyde by assimilation into fructose-6-phosphate. In the other direction, in species lacking a complete pentose phosphate pathway, the RuMP pathway yields ribulose-5-phosphate, necessary for nucleotide biosynthesis, at the cost of also yielding formaldehyde. These latter species tend usually have a formaldehyde-activating enzyme to attach formaldehyde to the C1 carrier tetrahydromethanopterin.

>PRK11303 DNA-binding transcriptional regulator FruR; Provisional

Probab=91.82  E-value=0.94  Score=36.86  Aligned_cols=70  Identities=9%  Similarity=0.015  Sum_probs=49.2

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++..|+.+-.......   ..-...+.+.+...++|++++.+.+.+-.+.++.+.+.|..+|.||..
T Consensus        81 ~gi~~~~~~~g~~~~~~~~~~~---~~~~~~~~~~l~~~~vdgiIi~~~~~~~~~~~~~l~~~~iPvV~v~~~  150 (328)
T PRK11303         81 KYLERQARQRGYQLLIACSDDQ---PDNEMRCAEHLLQRQVDALIVSTSLPPEHPFYQRLQNDGLPIIALDRA  150 (328)
T ss_pred             HHHHHHHHHcCCEEEEEeCCCC---HHHHHHHHHHHHHcCCCEEEEcCCCCCChHHHHHHHhcCCCEEEECCC
Confidence            3788889999999877542211   222234455555789999999876544456788888899999999864

>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=91.79  E-value=1.4  Score=34.48  Aligned_cols=70  Identities=11%  Similarity=0.058  Sum_probs=47.1

Q ss_pred             CCcHHHHHhh---ceEE--EEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCc-chHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRA---WFWV--RMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDS-DFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRA---Gv~V--~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDs-DF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++++.   |+.+  ... +..+.  ........+.+...++|.+++.+-|+ .+.+.+..+.++|...|+++..
T Consensus        19 ~~i~~~~~~~~~~g~~~~l~i~-~~~~~--~~~~~~~~~~~~~~~vdgiIi~~~~~~~~~~~l~~~~~~~iPvv~~~~~   94 (272)
T cd06300          19 DEFKAQAKELKKAGLISEFIVT-SADGD--VAQQIADIRNLIAQGVDAIIINPASPTALNPVIEEACEAGIPVVSFDGT   94 (272)
T ss_pred             HHHHHHHHhhhccCCeeEEEEe-cCCCC--HHHHHHHHHHHHHcCCCEEEEeCCChhhhHHHHHHHHHCCCeEEEEecC
Confidence            4666777777   9844  443 33332  22233344444468999999988664 4778899999999999998754

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.

>TIGR01664 DNA-3'-Pase DNA 3'-phosphatase

Probab=91.73  E-value=1.5  Score=34.40  Aligned_cols=88  Identities=13%  Similarity=0.161  Sum_probs=57.8

Q ss_pred             cHHHHHhhceEEEEecCCCccH-----HHHHHHHHHHHhhccCcceEEEEcCCcc-h----HHHHHHHHH-cC-----Ce
Q 045172           65 FADELKRAWFWVRMVLVKPQDA-----DVLLRNYMVAMVDKRRFGCLVVVSDDSD-F----VEVFQEATL-RW-----LK  128 (157)
Q Consensus        65 la~eLrRAGv~V~~V~dkpqAA-----D~AL~~~~~~~~~~r~v~clvLVSDDsD-F----~~~lr~Are-r~-----l~  128 (157)
                      +=..|+.+|+.+=.++.+|..+     ..++...+...+...|++..+.++.+.. .    .+++..+.+ -|     =.
T Consensus        50 ~L~~Lk~~G~~l~I~TN~~~~~~~~~~~~~~~~~i~~~l~~~gl~~~~ii~~~~~~~~KP~p~~~~~~~~~~~~~~~~~~  129 (166)
T TIGR01664        50 KLQELDDEGYKIVIFTNQSGIGRGKLSAESFKNKIEAFLEKLKVPIQVLAATHAGLYRKPMTGMWEYLQSQYNSPIKMTR  129 (166)
T ss_pred             HHHHHHHCCCEEEEEeCCcccccCcccHHHHHHHHHHHHHHcCCCEEEEEecCCCCCCCCccHHHHHHHHHcCCCCCchh
Confidence            3457788999999999998742     2345556666777777765444443332 2    345555555 34     24


Q ss_pred             EEEEcCCC---------chHHHhhhhcccchhh
Q 045172          129 MVVVGDMS---------DGALKRIANAFFSWSD  152 (157)
Q Consensus       129 tVVVGd~~---------~~~L~r~AD~~fsW~e  152 (157)
                      ++.|||..         |-.-.+.|-+-|=|.+
T Consensus       130 ~v~VGD~~~~~~~~~~~Di~aA~~aGi~~~~~~  162 (166)
T TIGR01664       130 SFYVGDAAGRKLDFSDADIKFAKNLGLEFKYPE  162 (166)
T ss_pred             cEEEECCCCCCCCCchhHHHHHHHCCCCcCChH
Confidence            99999974         6677777877777764

The central phosphatase domain is a member of the IIIA subfamily (TIGR01662) of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. As is common in this superfamily, the enzyme is magnesium dependent. A difference between this enzyme and other HAD-superfamily phosphatases is in the third conserved catalytic motif which usually contains two conserved aspartate residues believed to be involved in binding the magnesium ion. Here, the second aspartate is usually replaced by an arginine residue which may indicate an interaction with the phosphate backbone of the substrate. Alternatively, there is an additional conserved aspartate downstream of the ususal site which may indicate slightly different fold in this region.

>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=91.38  E-value=1.5  Score=33.58  Aligned_cols=71  Identities=10%  Similarity=0.050  Sum_probs=49.3

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchH-HHHHHHHHcCCeEEEEcCCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFV-EVFQEATLRWLKMVVVGDMS  136 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~-~~lr~Arer~l~tVVVGd~~  136 (157)
                      .|+..++...|+.+.++....+. +.. ...+.+++ ..+++.+++++.+++.. +++..+++.+...|.++...
T Consensus        19 ~~~~~~a~~~g~~~~~~~~~~~~-~~~-~~~~~~l~-~~~vdgvi~~~~~~~~~~~~~~~l~~~~ip~V~~~~~~   90 (267)
T cd01536          19 KGAEAAAKELGVELIVLDAQNDV-SKQ-IQQIEDLI-AQGVDGIIISPVDSAALTPALKKANAAGIPVVTVDSDI   90 (267)
T ss_pred             HHHHHHHHhcCceEEEECCCCCH-HHH-HHHHHHHH-HcCCCEEEEeCCCchhHHHHHHHHHHCCCcEEEecCCC
Confidence            35566677789999887654432 221 13333444 57999999998776654 58899999999999998753

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

>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=91.29  E-value=1.5  Score=33.26  Aligned_cols=70  Identities=13%  Similarity=0.102  Sum_probs=49.7

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDMS  136 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~~  136 (157)
                      .|+..+++..|+.+.......+   ..-...+.+.+-+++++++++...++.=.. ++.+.+.|+..|.++...
T Consensus        19 ~g~~~~~~~~g~~~~~~~~~~~---~~~~~~~~~~~~~~~~d~iii~~~~~~~~~-~~~~~~~~ipvv~~~~~~   88 (264)
T cd06267          19 RGIEEAAREAGYSVLLCNSDED---PEKEREALELLLSRRVDGIILAPSRLDDEL-LEELAALGIPVVLVDRPL   88 (264)
T ss_pred             HHHHHHHHHcCCEEEEEcCCCC---HHHHHHHHHHHHHcCcCEEEEecCCcchHH-HHHHHHcCCCEEEecccc
Confidence            4667777788988887755433   232333333333789999999888766555 888999999999998763

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=91.23  E-value=1.2  Score=34.63  Aligned_cols=71  Identities=14%  Similarity=0.024  Sum_probs=49.8

Q ss_pred             CCCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           62 GYGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        62 gygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      ..|+..++++-|+.+........  |........+.+.+.++|++++.+.+.+=.. +..+.+.|..+|++|..
T Consensus        18 ~~gi~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~l~~~~vdgiii~~~~~~~~~-~~~~~~~~ipvv~~~~~   88 (264)
T cd01574          18 LAAIESAAREAGYAVTLSMLAEA--DEEALRAAVRRLLAQRVDGVIVNAPLDDADA-ALAAAPADVPVVFVDGS   88 (264)
T ss_pred             HHHHHHHHHHCCCeEEEEeCCCC--chHHHHHHHHHHHhcCCCEEEEeCCCCChHH-HHHHHhcCCCEEEEecc
Confidence            46888899999999887644322  2344555566565789999999865433233 45567899999999875

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

>PRK12342 hypothetical protein; Provisional

Probab=91.22  E-value=1.3  Score=37.95  Aligned_cols=67  Identities=16%  Similarity=0.076  Sum_probs=51.1

Q ss_pred             HHHHHhhceEEEEecCCCccHHHH-HHHHHHHHhhccCcceEEEEcCC----cch---HHHHHHHHH-cCCeEEEEcCCC
Q 045172           66 ADELKRAWFWVRMVLVKPQDADVL-LRNYMVAMVDKRRFGCLVVVSDD----SDF---VEVFQEATL-RWLKMVVVGDMS  136 (157)
Q Consensus        66 a~eLrRAGv~V~~V~dkpqAAD~A-L~~~~~~~~~~r~v~clvLVSDD----sDF---~~~lr~Are-r~l~tVVVGd~~  136 (157)
                      |-.||+.|-.|-.++..|..|+.+ |+++++    ..|+|-.|||||+    +|-   +.+|..+-+ .+..-|+.|..+
T Consensus        44 AlrLk~~g~~Vtvls~Gp~~a~~~~l~r~al----amGaD~avli~d~~~~g~D~~ata~~La~~i~~~~~DLVl~G~~s  119 (254)
T PRK12342         44 ASQLATDGDEIAALTVGGSLLQNSKVRKDVL----SRGPHSLYLVQDAQLEHALPLDTAKALAAAIEKIGFDLLLFGEGS  119 (254)
T ss_pred             HHHHhhcCCEEEEEEeCCChHhHHHHHHHHH----HcCCCEEEEEecCccCCCCHHHHHHHHHHHHHHhCCCEEEEcCCc
Confidence            556676788999999999877666 666665    5799999999988    566   566655544 478889999873

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

Probab=91.15  E-value=0.63  Score=36.68  Aligned_cols=72  Identities=8%  Similarity=-0.129  Sum_probs=49.7

Q ss_pred             CCcHHHHHhhceEEEEec-CCCccHHHHHHHHHHHHhhccCcceEEEEcCCcc-hHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVL-VKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSD-FVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~-dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsD-F~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++..|+.+-.+. .-+..-|.....+..+.+.. ++|.+++++.+++ +.+.++.+.+.|...|+++..
T Consensus        19 ~~i~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~i~~~~~-~vdgiii~~~~~~~~~~~i~~~~~~~ipvV~~~~~   92 (275)
T cd06307          19 AALEAAAAAFPDARIRVRIHFVESFDPAALAAALLRLGA-RSDGVALVAPDHPQVRAAVARLAAAGVPVVTLVSD   92 (275)
T ss_pred             HHHHHHHhhhhccCceEEEEEccCCCHHHHHHHHHHHHh-cCCEEEEeCCCcHHHHHHHHHHHHCCCcEEEEeCC
Confidence            477788899887544432 11222233444555566656 9999999987754 468899999999999998753

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.

>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=91.13  E-value=0.98  Score=35.15  Aligned_cols=66  Identities=9%  Similarity=0.062  Sum_probs=46.7

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++..|+.+........ +  .-...+.+.+-..+++++++.+.|++    ++.+++.|..+|.++..
T Consensus        19 ~gi~~~~~~~g~~~~~~~~~~~-~--~~~~~~i~~~~~~~~dgiii~~~~~~----~~~~~~~gipvv~~~~~   84 (265)
T cd06291          19 RAVEKELYKKGYKLILCNSDND-P--EKEREYLEMLRQNQVDGIIAGTHNLG----IEEYENIDLPIVSFDRY   84 (265)
T ss_pred             HHHHHHHHHCCCeEEEecCCcc-H--HHHHHHHHHHHHcCCCEEEEecCCcC----HHHHhcCCCCEEEEeCC
Confidence            5778899999998876543322 2  22234444455789999999998766    34777889999999875

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

>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=91.11  E-value=1.3  Score=34.44  Aligned_cols=68  Identities=13%  Similarity=0.127  Sum_probs=49.6

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++..|+.+-..+..   .|..-...+.+.+.+.++|.+++++.+.+- +.+...+ .+...|++|-.
T Consensus        19 ~gi~~~~~~~gy~~~~~~~~---~~~~~~~~~i~~l~~~~~dgiii~~~~~~~-~~~~~~~-~~iPvV~i~~~   86 (265)
T cd06290          19 KGMERGLNGSGYSPIIATGH---WNQSRELEALELLKSRRVDALILLGGDLPE-EEILALA-EEIPVLAVGRR   86 (265)
T ss_pred             HHHHHHHHHCCCEEEEEeCC---CCHHHHHHHHHHHHHCCCCEEEEeCCCCCh-HHHHHHh-cCCCEEEECCC
Confidence            57888999999998776543   345566677777778999999999865443 3344444 58999999864

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.

>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional

Probab=91.09  E-value=0.86  Score=37.84  Aligned_cols=94  Identities=16%  Similarity=0.181  Sum_probs=62.9

Q ss_pred             HHHHHHHHhhcCccc----CCC--------cHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcC---
Q 045172           47 EKNKMAASAILTPKV----GYG--------FADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSD---  111 (157)
Q Consensus        47 ~kY~~Aar~~l~pkv----gyg--------la~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSD---  111 (157)
                      +..++++..+...+.    |.|        ++--|.|.|+.+..++|..      ........+  ..=|+++++|-   
T Consensus       128 ~~l~~~~~~i~~A~~I~i~G~G~S~~~A~~l~~~l~~~g~~~~~~~d~~------~~~~~~~~~--~~~Dl~I~iS~sG~  199 (292)
T PRK11337        128 DEFHRAARFFYQARQRDLYGAGGSAAIARDVQHKFLRIGVRCQAYDDAH------IMLMSAALL--QEGDVVLVVSHSGR  199 (292)
T ss_pred             HHHHHHHHHHHcCCeEEEEEecHHHHHHHHHHHHHhhCCCeEEEcCCHH------HHHHHHhcC--CCCCEEEEEeCCCC
Confidence            556666665555432    222        3345678898887764421      111111112  34477888875   


Q ss_pred             CcchHHHHHHHHHcCCeEEEEcCCCchHHHhhhhccc
Q 045172          112 DSDFVEVFQEATLRWLKMVVVGDMSDGALKRIANAFF  148 (157)
Q Consensus       112 DsDF~~~lr~Arer~l~tVVVGd~~~~~L~r~AD~~f  148 (157)
                      ..+..++++.|+++|.++|+|-+.....|.+.||.-|
T Consensus       200 t~~~~~~~~~ak~~g~~ii~IT~~~~s~la~~ad~~l  236 (292)
T PRK11337        200 TSDVIEAVELAKKNGAKIICITNSYHSPIAKLADYVI  236 (292)
T ss_pred             CHHHHHHHHHHHHCCCeEEEEeCCCCChhHHhCCEEE
Confidence            3678889999999999999999987789999999877

>cd05006 SIS_GmhA Phosphoheptose isomerase is a member of the SIS (Sugar ISomerase) superfamily

Probab=90.80  E-value=0.45  Score=36.85  Aligned_cols=47  Identities=17%  Similarity=0.248  Sum_probs=39.2

Q ss_pred             cceEEEEcC---CcchHHHHHHHHHcCCeEEEEcCCCchHHHhhhhcccc
Q 045172          103 FGCLVVVSD---DSDFVEVFQEATLRWLKMVVVGDMSDGALKRIANAFFS  149 (157)
Q Consensus       103 v~clvLVSD---DsDF~~~lr~Arer~l~tVVVGd~~~~~L~r~AD~~fs  149 (157)
                      =|+++++|-   ..+-..+++.|+++|++||.|-+.....|.+.||..|.
T Consensus       102 ~Dv~I~iS~SG~t~~~i~~~~~ak~~Ga~vI~IT~~~~s~La~~aD~~l~  151 (177)
T cd05006         102 GDVLIGISTSGNSPNVLKALEAAKERGMKTIALTGRDGGKLLELADIEIH  151 (177)
T ss_pred             CCEEEEEeCCCCCHHHHHHHHHHHHCCCEEEEEeCCCCCchhhhCCEEEE
Confidence            377888874   35677888999999999999988867889999999874

Phosphoheptose isomerase catalyzes the isomerization of sedoheptulose 7-phosphate into D-glycero-D-mannoheptose 7-phosphate. This is the first step of the biosynthesis of gram-negative bacteria inner core lipopolysaccharide precursor, L-glycero-D-mannoheptose (Gmh).

>TIGR02955 TMAO_TorT TMAO reductase system periplasmic protein TorT

Probab=90.67  E-value=1.2  Score=36.11  Aligned_cols=69  Identities=6%  Similarity=0.094  Sum_probs=46.4

Q ss_pred             CCcHHHHHhhceEEEEecCC--CccHHHHHHHHHHHHhhccCcceEEEEcCC-cchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVK--PQDADVLLRNYMVAMVDKRRFGCLVVVSDD-SDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dk--pqAAD~AL~~~~~~~~~~r~v~clvLVSDD-sDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++..|+.+......  ++   ..-.....+.+.++++|.|++++.+ +.+.+.+..+ +.|..+|++++.
T Consensus        19 ~gi~~~a~~~g~~v~~~~~~~~~~---~~~~~~~i~~l~~~~vDgiIi~~~~~~~~~~~l~~~-~~~iPvV~~~~~   90 (295)
T TIGR02955        19 YGMVEQAKHLGVELKVLEAGGYPN---LDKQLAQIEQCKSWGADAILLGTVSPEALNHDLAQL-TKSIPVFALVNQ   90 (295)
T ss_pred             HHHHHHHHHhCCEEEEEcCCCCCC---HHHHHHHHHHHHHcCCCEEEEecCChhhhhHHHHHH-hcCCCEEEEecC
Confidence            47778899999999876432  22   2222234445558999999999754 4446777766 469999888543

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.

>PRK13937 phosphoheptose isomerase; Provisional

Probab=90.61  E-value=0.5  Score=37.57  Aligned_cols=48  Identities=13%  Similarity=0.230  Sum_probs=40.4

Q ss_pred             CcceEEEEc---CCcchHHHHHHHHHcCCeEEEEcCCCchHHHhhhhcccc
Q 045172          102 RFGCLVVVS---DDSDFVEVFQEATLRWLKMVVVGDMSDGALKRIANAFFS  149 (157)
Q Consensus       102 ~v~clvLVS---DDsDF~~~lr~Arer~l~tVVVGd~~~~~L~r~AD~~fs  149 (157)
                      .=|+++.+|   ...+-.++++.|+++|.+||.|-+..+..|.+.||..+.
T Consensus       106 ~~Dl~i~iS~sG~t~~~~~~~~~ak~~g~~~I~iT~~~~s~L~~~ad~~l~  156 (188)
T PRK13937        106 PGDVLIGISTSGNSPNVLAALEKARELGMKTIGLTGRDGGKMKELCDHLLI  156 (188)
T ss_pred             CCCEEEEEeCCCCcHHHHHHHHHHHHCCCeEEEEeCCCCChhHHhCCEEEE
Confidence            338888888   456778899999999999999987767899999998774

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

Probab=90.52  E-value=2  Score=32.42  Aligned_cols=71  Identities=13%  Similarity=0.135  Sum_probs=50.0

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDMS  136 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~~  136 (157)
                      .|+..+++..|+.+....+.... | .....+..++ +.+++++|+.+.+......+..+.+.++.+|.++...
T Consensus        19 ~g~~~~~~~~g~~l~~~~~~~~~-~-~~~~~~~~~~-~~~~d~ii~~~~~~~~~~~~~~l~~~~ip~v~~~~~~   89 (264)
T cd01537          19 KGIEEAAKAAGYQVLLANSQNDA-E-KQLSALENLI-ARGVDGIIIAPSDLTAPTIVKLARKAGIPVVLVDRDI   89 (264)
T ss_pred             HHHHHHHHHcCCeEEEEeCCCCH-H-HHHHHHHHHH-HcCCCEEEEecCCCcchhHHHHhhhcCCCEEEeccCC
Confidence            45666677788888877655432 1 2233344444 6799999998877666557899999999999998764

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

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

Probab=90.40  E-value=1.6  Score=36.63  Aligned_cols=70  Identities=14%  Similarity=0.043  Sum_probs=47.3

Q ss_pred             CCcHHHHHhhc-eEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcch-HHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAW-FWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDF-VEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAG-v~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF-~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++...| +.+.++... ..  ........+.+..+++|.|+|+.-|+++ .+.++.+++.|..+|+|+..
T Consensus        44 ~gi~~~a~~~g~~~~~~~~~~-~~--~~~~~~~i~~l~~~~vdgiIi~~~~~~~~~~~l~~l~~~giPvV~vd~~  115 (330)
T PRK15395         44 KAIEKDAKAAPDVQLLMNDSQ-ND--QSKQNDQIDVLLAKGVKALAINLVDPAAAPTVIEKARGQDVPVVFFNKE  115 (330)
T ss_pred             HHHHHHHHhcCCeEEEEecCC-CC--HHHHHHHHHHHHHcCCCEEEEeccCHHHHHHHHHHHHHCCCcEEEEcCC
Confidence            46677888885 566553322 12  2233334444557899999998655553 45789999999999999874

>COG1609 PurR Transcriptional regulators [Transcription]

Probab=90.22  E-value=1.6  Score=37.49  Aligned_cols=70  Identities=10%  Similarity=0.133  Sum_probs=51.6

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDMS  136 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~~  136 (157)
                      -|+..++...|+.+-...-..   |....+.+.+.+..+++|.|++.+ -.+=......+.+.+..+|+||...
T Consensus        78 ~gi~~~~~~~gy~~~l~~~~~---~~~~e~~~~~~l~~~~vdGiIi~~-~~~~~~~~~~l~~~~~P~V~i~~~~  147 (333)
T COG1609          78 KGIEEAAREAGYSLLLANTDD---DPEKEREYLETLLQKRVDGLILLG-ERPNDSLLELLAAAGIPVVVIDRSP  147 (333)
T ss_pred             HHHHHHHHHcCCEEEEECCCC---CHHHHHHHHHHHHHcCCCEEEEec-CCCCHHHHHHHHhcCCCEEEEeCCC
Confidence            378899999999999875554   345556666667789999999998 2222334455566699999999863

>PF00702 Hydrolase: haloacid dehalogenase-like hydrolase; InterPro: IPR005834 This group of hydrolase enzymes is structurally different from the alpha/beta hydrolase family (abhydrolase)

Probab=90.18  E-value=0.95  Score=34.21  Aligned_cols=73  Identities=19%  Similarity=0.165  Sum_probs=44.2

Q ss_pred             cHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCC--c----chHHHHHHHHHcCCeEEEEcCC-Cc
Q 045172           65 FADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDD--S----DFVEVFQEATLRWLKMVVVGDM-SD  137 (157)
Q Consensus        65 la~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDD--s----DF~~~lr~Arer~l~tVVVGd~-~~  137 (157)
                      +-.+|+.+|+.+.+++.-+..       -+...+...|++..+..+..  +    -|..+++.....+-.++.|||+ +|
T Consensus       135 ~l~~L~~~Gi~~~i~TGD~~~-------~a~~~~~~lgi~~~~v~a~~~~kP~~k~~~~~i~~l~~~~~~v~~vGDg~nD  207 (215)
T PF00702_consen  135 ALQELKEAGIKVAILTGDNES-------TASAIAKQLGIFDSIVFARVIGKPEPKIFLRIIKELQVKPGEVAMVGDGVND  207 (215)
T ss_dssp             HHHHHHHTTEEEEEEESSEHH-------HHHHHHHHTTSCSEEEEESHETTTHHHHHHHHHHHHTCTGGGEEEEESSGGH
T ss_pred             hhhhhhccCcceeeeeccccc-------cccccccccccccccccccccccccchhHHHHHHHHhcCCCEEEEEccCHHH
Confidence            345788899998888754431       11222234677554444443  2    4677888877545599999999 54


Q ss_pred             hHHHhhh
Q 045172          138 GALKRIA  144 (157)
Q Consensus       138 ~~L~r~A  144 (157)
                      -.-.+.|
T Consensus       208 ~~al~~A  214 (215)
T PF00702_consen  208 APALKAA  214 (215)
T ss_dssp             HHHHHHS
T ss_pred             HHHHHhC
Confidence            3333333

This group includes L-2-haloacid dehalogenase, epoxide hydrolases and phosphatases. The structure consists of two domains. One is an inserted four helix bundle, which is the least well conserved region of the alignment, between residues 16 and 96 of HAD1_PSESP. The rest of the fold is composed of the core alpha/beta domain.; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 1TE2_A 3NAL_A 3NAM_A 3NAN_A 3A1D_B 3J09_A 3J08_A 2B8E_C 3A1E_A 2VOY_J ....

>TIGR01481 ccpA catabolite control protein A

Probab=89.99  E-value=2  Score=35.01  Aligned_cols=69  Identities=7%  Similarity=0.053  Sum_probs=47.1

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++...|+.+.+.....+   ........+.+...++|.+++++.+.+ ..++..+.+.|..+|.++..
T Consensus        79 ~~i~~~~~~~g~~~~i~~~~~~---~~~~~~~~~~l~~~~vdGiIi~~~~~~-~~~~~~l~~~~iPvV~~~~~  147 (329)
T TIGR01481        79 RGIEDIATMYKYNIILSNSDED---PEKEVQVLNTLLSKQVDGIIFMGGTIT-EKLREEFSRSPVPVVLAGTV  147 (329)
T ss_pred             HHHHHHHHHcCCEEEEEeCCCC---HHHHHHHHHHHHhCCCCEEEEeCCCCC-hHHHHHHHhcCCCEEEEecC
Confidence            4677888889999877543322   222334444455789999999875433 34567777889999999864

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.

>TIGR01511 ATPase-IB1_Cu copper-(or silver)-translocating P-type ATPase

Probab=89.83  E-value=1.1  Score=41.36  Aligned_cols=77  Identities=17%  Similarity=0.066  Sum_probs=53.8

Q ss_pred             HHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC-CchHHHhhhh
Q 045172           67 DELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM-SDGALKRIAN  145 (157)
Q Consensus        67 ~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~-~~~~L~r~AD  145 (157)
                      .+|++.|+.+-+++.+++.       .+...+...|++++.-+ ...+=..+++...+.+-+++.|||+ +|-..-+.||
T Consensus       415 ~~Lk~~Gi~v~ilSgd~~~-------~a~~ia~~lgi~~~~~~-~p~~K~~~v~~l~~~~~~v~~VGDg~nD~~al~~A~  486 (562)
T TIGR01511       415 QALKRRGIEPVMLTGDNRK-------TAKAVAKELGINVRAEV-LPDDKAALIKELQEKGRVVAMVGDGINDAPALAQAD  486 (562)
T ss_pred             HHHHHcCCeEEEEcCCCHH-------HHHHHHHHcCCcEEccC-ChHHHHHHHHHHHHcCCEEEEEeCCCccHHHHhhCC
Confidence            4688889888888888772       12222233466633222 1235577888888888899999999 8777788899


Q ss_pred             cccchh
Q 045172          146 AFFSWS  151 (157)
Q Consensus       146 ~~fsW~  151 (157)
                      +.+.|.
T Consensus       487 vgia~g  492 (562)
T TIGR01511       487 VGIAIG  492 (562)
T ss_pred             EEEEeC
Confidence            998886

One member from Halobacterium is annotated as "molybdenum-binding protein" although no evidence can be found for this classification.

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

Probab=89.82  E-value=1.9  Score=33.22  Aligned_cols=68  Identities=12%  Similarity=0.148  Sum_probs=47.4

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      +|+..+++..|+.+.++...-   |......+++.+...++|.+++.+.+.+-. +++ +.+.|...|++++.
T Consensus        19 ~~i~~~~~~~g~~~~~~~~~~---~~~~~~~~~~~~~~~~vdgiii~~~~~~~~-~~~-~~~~~ipvv~~~~~   86 (267)
T cd06284          19 KGIEDEAREAGYGVLLGDTRS---DPEREQEYLDLLRRKQADGIILLDGSLPPT-ALT-ALAKLPPIVQACEY   86 (267)
T ss_pred             HHHHHHHHHcCCeEEEecCCC---ChHHHHHHHHHHHHcCCCEEEEecCCCCHH-HHH-HHhcCCCEEEEecc
Confidence            678888999999997764332   234444555566578999999987665433 333 44679999999865

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.

>TIGR02137 HSK-PSP phosphoserine phosphatase/homoserine phosphotransferase bifunctional protein

Probab=89.66  E-value=2  Score=34.74  Aligned_cols=78  Identities=17%  Similarity=0.173  Sum_probs=49.4

Q ss_pred             CcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcc-eEE--EEcCC------------cchHHHHHHHHHcCCe
Q 045172           64 GFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFG-CLV--VVSDD------------SDFVEVFQEATLRWLK  128 (157)
Q Consensus        64 gla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~-clv--LVSDD------------sDF~~~lr~Arer~l~  128 (157)
                      .+-..|++.| .+-.||.+++.    ....+.+   ..|++ .++  |..++            .+=..+++...+.|..
T Consensus        75 ell~~lk~~~-~~~IVS~~~~~----~~~~il~---~lgi~~~~an~l~~~~~g~~tG~~~~~~~~K~~~l~~l~~~~~~  146 (203)
T TIGR02137        75 EFVDWLRERF-QVVILSDTFYE----FSQPLMR---QLGFPTLLCHKLEIDDSDRVVGYQLRQKDPKRQSVIAFKSLYYR  146 (203)
T ss_pred             HHHHHHHhCC-eEEEEeCChHH----HHHHHHH---HcCCchhhceeeEEecCCeeECeeecCcchHHHHHHHHHhhCCC
Confidence            4556677765 88888999882    2222222   23443 222  33333            2233457777778889


Q ss_pred             EEEEcCC-CchHHHhhhhcccc
Q 045172          129 MVVVGDM-SDGALKRIANAFFS  149 (157)
Q Consensus       129 tVVVGd~-~~~~L~r~AD~~fs  149 (157)
                      ++.|||+ +|-.+.+.||..+-
T Consensus       147 ~v~vGDs~nDl~ml~~Ag~~ia  168 (203)
T TIGR02137       147 VIAAGDSYNDTTMLSEAHAGIL  168 (203)
T ss_pred             EEEEeCCHHHHHHHHhCCCCEE
Confidence            9999999 77788888887663

This enzyme is a member of the haloacid dehalogenase (HAD) superfamily, specifically part of subfamily IB by virtue of the presence of an alpha helical domain in between motifs I and II of the HAD domain . The closest homologs to this family are monofunctional phosphoserine phosphatases (TIGR00338).

>TIGR01491 HAD-SF-IB-PSPlk HAD-superfamily, subfamily-IB PSPase-like hydrolase, archaeal

Probab=89.63  E-value=2.5  Score=32.02  Aligned_cols=92  Identities=14%  Similarity=-0.018  Sum_probs=52.0

Q ss_pred             HHHHHHhhcCcccC-CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcce---EEEEcCCcc----------
Q 045172           49 NKMAASAILTPKVG-YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGC---LVVVSDDSD----------  114 (157)
Q Consensus        49 Y~~Aar~~l~pkvg-ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~c---lvLVSDDsD----------  114 (157)
                      ++....+ +.|.-| --+-..|++.|+.+-.||..+.    .+...+.+.   .|++.   -.+.+++..          
T Consensus        72 ~~~~~~~-~~~~~g~~e~l~~l~~~g~~~~IvS~~~~----~~~~~~l~~---~g~~~~~~~~~~~~~~g~~~p~~~~~~  143 (201)
T TIGR01491        72 VEEIFKE-ISLRDYAEELVRWLKEKGLKTAIVSGGIM----CLAKKVAEK---LNPDYVYSNELVFDEKGFIQPDGIVRV  143 (201)
T ss_pred             HHHHHHh-CCCCccHHHHHHHHHHCCCEEEEEeCCcH----HHHHHHHHH---hCCCeEEEEEEEEcCCCeEecceeeEE
Confidence            4443333 344444 3456788899999999999875    233333332   24432   233444321          


Q ss_pred             ----hHHHHHHHHH-cCC---eEEEEcCC-CchHHHhhhhccc
Q 045172          115 ----FVEVFQEATL-RWL---KMVVVGDM-SDGALKRIANAFF  148 (157)
Q Consensus       115 ----F~~~lr~Are-r~l---~tVVVGd~-~~~~L~r~AD~~f  148 (157)
                          -..+++.+.+ .|+   .++.|||+ +|-.....|+..|
T Consensus       144 ~~~~k~~~~~~~~~~~~~~~~~~i~iGDs~~D~~~a~~ag~~~  186 (201)
T TIGR01491       144 TFDNKGEAVERLKRELNPSLTETVAVGDSKNDLPMFEVADISI  186 (201)
T ss_pred             ccccHHHHHHHHHHHhCCCHHHEEEEcCCHhHHHHHHhcCCeE
Confidence                1235555444 454   58999999 6556666666644

This hypothetical equivalog is a member of the IB subfamily (TIGR01488) of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The sequences modelled by this alignment are all from archaeal species. The phylogenetically closest group of sequences to these are phosphoserine phosphatases (TIGR00338). There are no known archaeal phosphoserine phosphatases, and no archaea fall within TIGR00338. It is likely, then, that This model represents the archaeal branch of the PSPase equivalog.

>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=89.52  E-value=1.7  Score=34.64  Aligned_cols=65  Identities=20%  Similarity=0.108  Sum_probs=48.2

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++..|+.+..++...   +..    +.+.+...++|.+++.+.+.. ...++.+++.|...|.++..
T Consensus        24 ~gi~~~a~~~g~~~~~~~~~~---~~~----~~~~~~~~~~dgiii~~~~~~-~~~~~~~~~~~ipvV~~~~~   88 (283)
T cd06279          24 AGVAEVLDAAGVNLLLLPASS---EDS----DSALVVSALVDGFIVYGVPRD-DPLVAALLRRGLPVVVVDQP   88 (283)
T ss_pred             HHHHHHHHHCCCEEEEecCcc---HHH----HHHHHHhcCCCEEEEeCCCCC-hHHHHHHHHcCCCEEEEecC
Confidence            578899999999998876543   222    223334789999999886533 36789999999999999765

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.

>PRK13936 phosphoheptose isomerase; Provisional

Probab=89.26  E-value=0.72  Score=37.08  Aligned_cols=47  Identities=15%  Similarity=0.258  Sum_probs=39.1

Q ss_pred             CcceEEEEcCC---cchHHHHHHHHHcCCeEEEEcCCCchHHHhh---hhccc
Q 045172          102 RFGCLVVVSDD---SDFVEVFQEATLRWLKMVVVGDMSDGALKRI---ANAFF  148 (157)
Q Consensus       102 ~v~clvLVSDD---sDF~~~lr~Arer~l~tVVVGd~~~~~L~r~---AD~~f  148 (157)
                      .=|+++++|-.   .+-.++++.|+++|+++|.|.+.....|.+.   ||..|
T Consensus       111 ~~Dv~i~iS~sG~t~~~~~~~~~ak~~g~~iI~IT~~~~s~l~~l~~~ad~~l  163 (197)
T PRK13936        111 PGDVLLAISTSGNSANVIQAIQAAHEREMHVVALTGRDGGKMASLLLPEDVEI  163 (197)
T ss_pred             CCCEEEEEeCCCCcHHHHHHHHHHHHCCCeEEEEECCCCChhhhhhccCCEEE
Confidence            44999999955   6778899999999999999999766778874   88776

>TIGR01522 ATPase-IIA2_Ca golgi membrane calcium-translocating P-type ATPase

Probab=89.16  E-value=1.6  Score=42.68  Aligned_cols=39  Identities=13%  Similarity=0.134  Sum_probs=33.0

Q ss_pred             cchHHHHHHHHHcCCeEEEEcCC-CchHHHhhhhcccchh
Q 045172          113 SDFVEVFQEATLRWLKMVVVGDM-SDGALKRIANAFFSWS  151 (157)
Q Consensus       113 sDF~~~lr~Arer~l~tVVVGd~-~~~~L~r~AD~~fsW~  151 (157)
                      .+=..+++..++.|-.+..|||+ +|-.--+.||++++|.
T Consensus       604 ~~K~~iv~~lq~~g~~v~mvGDGvND~pAl~~AdVGia~g  643 (884)
T TIGR01522       604 EHKMKIVKALQKRGDVVAMTGDGVNDAPALKLADIGVAMG  643 (884)
T ss_pred             HHHHHHHHHHHHCCCEEEEECCCcccHHHHHhCCeeEecC
Confidence            34577889999999999999999 7766668999999984

The calcium P-type ATPases have been characterized as Type IIA based on a phylogenetic analysis which distinguishes this group from the Type IIB PMCA calcium pump modelled by TIGR01517. A separate analysis divides Type IIA into sub-types, SERCA and PMR1 the former of which is modelled by TIGR01116.

>cd06360 PBP1_alkylbenzenes_like Type I periplasmic binding component of active transport systems that are predicted be involved in anaerobic biodegradation of alkylbenzenes such as toluene and ethylbenzene

Probab=88.81  E-value=1.7  Score=35.23  Aligned_cols=69  Identities=16%  Similarity=0.177  Sum_probs=50.4

Q ss_pred             CcHHHHHhhceEEEEe-cCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCC--eEEEEcCC
Q 045172           64 GFADELKRAWFWVRMV-LVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWL--KMVVVGDM  135 (157)
Q Consensus        64 gla~eLrRAGv~V~~V-~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l--~tVVVGd~  135 (157)
                      ++...|+.+|+.|... .-.+.+.|.+  ..+..+. ..+.|.|++.+..++...+++.+++.|+  +..++|-+
T Consensus       153 ~~~~~~~~~G~~v~~~~~~~~~~~d~~--~~v~~~~-~~~pd~v~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~  224 (336)
T cd06360         153 GFKEAFTEAGGKIVKELWVPFGTSDFA--SYLAQIP-DDVPDAVFVFFAGGDAIKFVKQYDAAGLKAKIPLIGSG  224 (336)
T ss_pred             HHHHHHHHcCCEEEEEEecCCCCcchH--HHHHHHH-hcCCCEEEEecccccHHHHHHHHHHcCCccCCeEEecc
Confidence            3556788889887543 3334566654  3444445 5789999999999999999999999999  66677643

This group includes the type I periplasmic binding component of active transport systems that are predicted be involved in anaerobic biodegradation of alkylbenzenes such as toluene and ethylbenzene; their substrate specificity is not well characterized, however.

>cd06347 PBP1_ABC_ligand_binding_like_12 Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions

Probab=88.72  E-value=1.2  Score=35.95  Aligned_cols=67  Identities=10%  Similarity=0.113  Sum_probs=48.4

Q ss_pred             cHHHHHhhceEEEEe-cCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcC
Q 045172           65 FADELKRAWFWVRMV-LVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGD  134 (157)
Q Consensus        65 la~eLrRAGv~V~~V-~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd  134 (157)
                      +..+|..+|+.|-.+ .-.+...|  ....+.++. ..+.+.+++.+...+...+++.+++.|++..++|-
T Consensus       156 ~~~~~~~~g~~v~~~~~~~~~~~d--~~~~~~~~~-~~~~d~i~~~~~~~~~~~~~~~~~~~g~~~~i~~~  223 (334)
T cd06347         156 FKEAFKKLGGEIVAEETFNAGDTD--FSAQLTKIK-AKNPDVIFLPGYYTEVGLIAKQARELGIKVPILGG  223 (334)
T ss_pred             HHHHHHHcCCEEEEEEEecCCCCc--HHHHHHHHH-hcCCCEEEEcCchhhHHHHHHHHHHcCCCCcEEec
Confidence            445666788766543 22344445  445555555 57999999999999999999999999998877763

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 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); however its ligand specificity has not been determined experimentally.

>TIGR00393 kpsF KpsF/GutQ family protein

Probab=88.69  E-value=0.63  Score=37.68  Aligned_cols=78  Identities=9%  Similarity=0.042  Sum_probs=53.8

Q ss_pred             cHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCC---cchHHHHHHHHHcCCeEEEEcCCCchHHH
Q 045172           65 FADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDD---SDFVEVFQEATLRWLKMVVVGDMSDGALK  141 (157)
Q Consensus        65 la~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDD---sDF~~~lr~Arer~l~tVVVGd~~~~~L~  141 (157)
                      ++--|-+.|..+..+++      ......+...+  ..=|+++.+|-.   .+-..+++.|+++|++++.|-+.....|.
T Consensus        18 ~~~~l~~~g~~~~~~~~------~~~~~~~~~~~--~~~d~~i~iS~sG~t~~~~~~~~~a~~~g~~ii~iT~~~~s~l~   89 (268)
T TIGR00393        18 IVATFASTGTPSFFLHP------TEAMHGDLGMV--EPNDVVLMISYSGESLELLNLIPHLKRLSHKIIAFTGSPNSSLA   89 (268)
T ss_pred             HHHHHHhcCCceEEeCH------hHHhhcccCCC--CCCCEEEEEeCCCCCHHHHHHHHHHHHcCCcEEEEECCCCCccc
Confidence            34445677777776543      11111010112  233889999865   66778899999999999999998778999


Q ss_pred             hhhhcccch
Q 045172          142 RIANAFFSW  150 (157)
Q Consensus       142 r~AD~~fsW  150 (157)
                      ..||..|..
T Consensus        90 ~~~d~~l~~   98 (268)
T TIGR00393        90 RAADYVLDI   98 (268)
T ss_pred             ccCCEEEEc
Confidence            999999865

This model describes a number of closely related proteins with the phosphosugar-binding domain SIS (Sugar ISomerase) followed by two copies of the CBS (named after Cystathionine Beta Synthase) domain. One is GutQ, a protein of the glucitol operon. Another is KpsF, a virulence factor involved in capsular polysialic acid biosynthesis in some pathogenic strains of E. coli.

>cd06361 PBP1_GPC6A_like Ligand-binding domain of the promiscuous L-alpha-amino acid receptor GPRC6A which is a broad-spectrum amino acid-sensing receptor

Probab=88.54  E-value=2.6  Score=36.92  Aligned_cols=71  Identities=11%  Similarity=0.125  Sum_probs=50.4

Q ss_pred             cHHHHHhhceEEEE---ecCCCccH--HHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           65 FADELKRAWFWVRM---VLVKPQDA--DVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        65 la~eLrRAGv~V~~---V~dkpqAA--D~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      +..++++.|+-|-.   ++..+...  +......+...+...+.+.+++.++..+-..+++.|++.|++.+.||-.
T Consensus       192 f~~~~~~~GicIa~~e~~~~~~~~~~~~~~~~~~~~~~ik~~~a~vVvv~~~~~~~~~l~~~a~~~g~~~~wigs~  267 (403)
T cd06361         192 FIIQAEANGVCIAFKEILPASLSDNTKLNRIIRTTEKIIEENKVNVIVVFARQFHVFLLFNKAIERNINKVWIASD  267 (403)
T ss_pred             HHHHHHHCCeEEEEEEEecCccCcchhHHHHHHHHHHHHhcCCCeEEEEEeChHHHHHHHHHHHHhCCCeEEEEEC
Confidence            55788889987743   33332211  1123333344344678999999999999999999999999998888855

This family includes the ligand-binding domain of the promiscuous L-alpha-amino acid receptor GPRC6A which is a broad-spectrum amino acid-sensing receptor, and its fish homolog, the 5.24 chemoreceptor. GPRC6A is a member of the family C of G-protein-coupled receptors that transduce extracellular signals into G-protein activation and ultimately into cellular responses.

>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=88.54  E-value=2.8  Score=32.75  Aligned_cols=68  Identities=9%  Similarity=0.092  Sum_probs=46.6

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      -|+..+++..|+.+.......+   ......+.+.+-..++|+|++++.+.+.. .. .+...|..+|.|+..
T Consensus        19 ~~i~~~~~~~g~~~~~~~~~~~---~~~~~~~i~~l~~~~~dgiii~~~~~~~~-~~-~~~~~~iPvV~~~~~   86 (263)
T cd06280          19 RAVEDAAYRAGLRVILCNTDED---PEKEAMYLELMEEERVTGVIFAPTRATLR-RL-AELRLSFPVVLIDRA   86 (263)
T ss_pred             HHHHHHHHHCCCEEEEEeCCCC---HHHHHHHHHHHHhCCCCEEEEeCCCCCch-HH-HHHhcCCCEEEECCC
Confidence            3677889999999977654433   23333444445478899999999665543 33 456679999999865

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.

>COG1737 RpiR Transcriptional regulators [Transcription]

Probab=88.49  E-value=1.3  Score=37.32  Aligned_cols=96  Identities=22%  Similarity=0.204  Sum_probs=66.9

Q ss_pred             hhHHHHHHHHhhcCccc----CCC--------cHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCC
Q 045172           45 KMEKNKMAASAILTPKV----GYG--------FADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDD  112 (157)
Q Consensus        45 k~~kY~~Aar~~l~pkv----gyg--------la~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDD  112 (157)
                      .++..++|+.-+...+.    |.|        ++--|-|-|+.|..++|....      . |  ++...+-+++|++-+-
T Consensus       116 ~~~~l~~av~~L~~A~rI~~~G~g~S~~vA~~~~~~l~~ig~~~~~~~d~~~~------~-~--~~~~~~~~Dv~i~iS~  186 (281)
T COG1737         116 DEEALERAVELLAKARRIYFFGLGSSGLVASDLAYKLMRIGLNVVALSDTHGQ------L-M--QLALLTPGDVVIAISF  186 (281)
T ss_pred             CHHHHHHHHHHHHcCCeEEEEEechhHHHHHHHHHHHHHcCCceeEecchHHH------H-H--HHHhCCCCCEEEEEeC
Confidence            45566677776666661    222        234567889999998876551      1 1  2224556656655555


Q ss_pred             cch----HHHHHHHHHcCCeEEEEcCCCchHHHhhhhcccc
Q 045172          113 SDF----VEVFQEATLRWLKMVVVGDMSDGALKRIANAFFS  149 (157)
Q Consensus       113 sDF----~~~lr~Arer~l~tVVVGd~~~~~L~r~AD~~fs  149 (157)
                      |..    ..+++.|+++|+++|.|=|.....|.+.||..+.
T Consensus       187 sG~t~e~i~~a~~ak~~ga~vIaiT~~~~spla~~Ad~~L~  227 (281)
T COG1737         187 SGYTREIVEAAELAKERGAKVIAITDSADSPLAKLADIVLL  227 (281)
T ss_pred             CCCcHHHHHHHHHHHHCCCcEEEEcCCCCCchhhhhceEEe
Confidence            544    5678999999999999999977899999999874

>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=88.44  E-value=3  Score=32.41  Aligned_cols=70  Identities=17%  Similarity=0.133  Sum_probs=45.1

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++...|+.+.++...-   |.+....+++.+..+++|.+++.+-+.+-..+-......|..+|+||..
T Consensus        19 ~gi~~~~~~~g~~~~~~~~~~---~~~~~~~~i~~l~~~~vdgiii~~~~~~~~~~~~l~~~~~ipvV~i~~~   88 (269)
T cd06275          19 RGVEQYCYRQGYNLILCNTEG---DPERQRSYLRMLAQKRVDGLLVMCSEYDQPLLAMLERYRHIPMVVMDWG   88 (269)
T ss_pred             HHHHHHHHHcCCEEEEEeCCC---ChHHHHHHHHHHHHcCCCEEEEecCCCChHHHHHHHhcCCCCEEEEecc
Confidence            467778888899887754322   2334444444555789999999886655322222233468999999865

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

>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=88.36  E-value=2.5  Score=32.91  Aligned_cols=65  Identities=8%  Similarity=0.134  Sum_probs=46.1

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++.+.|+.+......++       ....+.+.+.++|++++++.+.+ ...++.+++.|..+|.+|..
T Consensus        19 ~gi~~~~~~~g~~~~~~~~~~~-------~~~~~~l~~~~vdgii~~~~~~~-~~~~~~~~~~~ipvV~~~~~   83 (261)
T cd06272          19 TGINQAISKNGYNMNVSITPSL-------AEAEDLFKENRFDGVIIFGESAS-DVEYLYKIKLAIPVVSYGVD   83 (261)
T ss_pred             HHHHHHHHHcCCEEEEEecccH-------HHHHHHHHHcCcCEEEEeCCCCC-hHHHHHHHHcCCCEEEEccc
Confidence            4778889999998887643211       12233344789999999976543 33568888999999999875

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

>PRK00414 gmhA phosphoheptose isomerase; Reviewed

Probab=88.28  E-value=0.94  Score=36.43  Aligned_cols=48  Identities=15%  Similarity=0.284  Sum_probs=40.8

Q ss_pred             cCcceEEEEcCC---cchHHHHHHHHHcCCeEEEEcCCCchHHHhhhhccc
Q 045172          101 RRFGCLVVVSDD---SDFVEVFQEATLRWLKMVVVGDMSDGALKRIANAFF  148 (157)
Q Consensus       101 r~v~clvLVSDD---sDF~~~lr~Arer~l~tVVVGd~~~~~L~r~AD~~f  148 (157)
                      ..=|+++.+|..   .+-..+++.|+++|++||.|-...+..|.+.||.-+
T Consensus       110 ~~~Dv~I~iS~SG~t~~~i~~~~~ak~~g~~iI~iT~~~~s~l~~~ad~~l  160 (192)
T PRK00414        110 REGDVLLGISTSGNSGNIIKAIEAARAKGMKVITLTGKDGGKMAGLADIEI  160 (192)
T ss_pred             CCCCEEEEEeCCCCCHHHHHHHHHHHHCCCeEEEEeCCCCChhHHhCCEEE
Confidence            455888889854   677788999999999999998877789999999876

>TIGR01490 HAD-SF-IB-hyp1 HAD-superfamily subfamily IB hydrolase, TIGR01490

Probab=87.98  E-value=4.4  Score=31.05  Aligned_cols=75  Identities=12%  Similarity=0.080  Sum_probs=43.9

Q ss_pred             HHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEE---EEc-CCcchH--------------H-HHHHHHHcCC
Q 045172           67 DELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLV---VVS-DDSDFV--------------E-VFQEATLRWL  127 (157)
Q Consensus        67 ~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clv---LVS-DDsDF~--------------~-~lr~Arer~l  127 (157)
                      ..|++.|+.|-.|+..|+   . +.+.+.+.   .|++.++   ++. +|--|+              . +.+.+.+.++
T Consensus        97 ~~l~~~g~~v~ivS~s~~---~-~v~~~~~~---lg~~~~~~~~l~~~~~g~~~g~~~~~~~~g~~K~~~l~~~~~~~~~  169 (202)
T TIGR01490        97 RWHKAEGHTIVLVSASLT---I-LVKPLARI---LGIDNAIGTRLEESEDGIYTGNIDGNNCKGEGKVHALAELLAEEQI  169 (202)
T ss_pred             HHHHHCCCEEEEEeCCcH---H-HHHHHHHH---cCCcceEecceEEcCCCEEeCCccCCCCCChHHHHHHHHHHHHcCC
Confidence            445788999999999997   2 22223322   3555332   333 431121              2 3344455676


Q ss_pred             ---eEEEEcCC-CchHHHhhhhccc
Q 045172          128 ---KMVVVGDM-SDGALKRIANAFF  148 (157)
Q Consensus       128 ---~tVVVGd~-~~~~L~r~AD~~f  148 (157)
                         .++.|||+ +|-.+.+.|+..+
T Consensus       170 ~~~~~~~~gDs~~D~~~~~~a~~~~  194 (202)
T TIGR01490       170 DLKDSYAYGDSISDLPLLSLVGHPY  194 (202)
T ss_pred             CHHHcEeeeCCcccHHHHHhCCCcE
Confidence               58899999 6666666666543

A subset of these sequences, including the Caulobacter crescentus CicA protein, cluster together and may represent a separate equivalog.

>PRK10423 transcriptional repressor RbsR; Provisional

Probab=87.94  E-value=3  Score=33.82  Aligned_cols=69  Identities=7%  Similarity=-0.023  Sum_probs=43.7

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGD  134 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd  134 (157)
                      .|+..++.+.|+.+.......+   ..-..++.+.+...++|.+++.+.+.+....-...+..++.+|.||.
T Consensus        76 ~gi~~~~~~~g~~~~~~~~~~~---~~~~~~~~~~l~~~~vdGiI~~~~~~~~~~~~~l~~~~~iPvV~i~~  144 (327)
T PRK10423         76 RGVERSCFERGYSLVLCNTEGD---EQRMNRNLETLMQKRVDGLLLLCTETHQPSREIMQRYPSVPTVMMDW  144 (327)
T ss_pred             HHHHHHHHHcCCEEEEEeCCCC---HHHHHHHHHHHHHcCCCEEEEeCCCcchhhHHHHHhcCCCCEEEECC
Confidence            4778899999998876543322   22233444445578999999998665543221111235889999975

>cd06342 PBP1_ABC_LIVBP_like Type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine)

Probab=87.06  E-value=2.1  Score=34.64  Aligned_cols=67  Identities=12%  Similarity=-0.052  Sum_probs=48.0

Q ss_pred             HHHHHhhceEEEEec-CCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           66 ADELKRAWFWVRMVL-VKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        66 a~eLrRAGv~V~~V~-dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      ...|++.|+.|-... -.|.+.|..  ..+..+. ..+.+.+++.+...+...+++.+++.|+...++|..
T Consensus       156 ~~~~~~~g~~v~~~~~~~~~~~d~~--~~l~~i~-~~~~~~vi~~~~~~~~~~~~~~~~~~g~~~~~~~~~  223 (334)
T cd06342         156 KKALKAAGGKVVAREGTTDGATDFS--AILTKIK-AANPDAVFFGGYYPEAGPLVRQMRQLGLKAPFMGGD  223 (334)
T ss_pred             HHHHHHcCCEEEEEecCCCCCccHH--HHHHHHH-hcCCCEEEEcCcchhHHHHHHHHHHcCCCCcEEecC
Confidence            355666788666543 333455642  2233333 578999999999999999999999999998888764

This subgroup includes the type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine). This subgroup also includes a leucine-specific binding protein (or LivK), which is very similar in sequence and structure to leucine-isoleucine-valine binding protein (LIVBP). ABC-type active transport systems are transmembrane proteins that function in the transport of diverse sets of substrates across extra- and intracellular membranes, including carbohydrates, amino acids, inorganic ions, dipeptides and oligopeptides, metabolic products, lipids and sterols, and heme, to name a few.

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

Probab=87.03  E-value=3.2  Score=32.86  Aligned_cols=68  Identities=12%  Similarity=-0.040  Sum_probs=44.8

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHc-CCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLR-WLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer-~l~tVVVGd~  135 (157)
                      .|+..+++..|+.+...... .   ..-..++.+.+..+++|.|++++.+.+ ..++..+.+. +...|+++..
T Consensus        21 ~gi~~~~~~~gy~~~~~~~~-~---~~~~~~~~~~l~~~~vdgiii~~~~~~-~~~~~~~~~~~~ipvv~~~~~   89 (260)
T cd06304          21 EGLEKAEKELGVEVKYVESV-E---DADYEPNLRQLAAQGYDLIFGVGFGFM-DAVEKVAKEYPDVKFAIIDGV   89 (260)
T ss_pred             HHHHHHHHhcCceEEEEecC-C---HHHHHHHHHHHHHcCCCEEEECCcchh-HHHHHHHHHCCCCEEEEecCc
Confidence            46778889999998875332 2   223345666666789999999875533 2333444443 7888998865

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.

>PRK10703 DNA-binding transcriptional repressor PurR; Provisional

Probab=86.92  E-value=4  Score=33.47  Aligned_cols=69  Identities=12%  Similarity=0.094  Sum_probs=49.4

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHH-cCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATL-RWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Are-r~l~tVVVGd~  135 (157)
                      .|+..++...|+.+.+.+.. .  |..-...+.+.+..+++|+|++++.+. ..+.++.+.+ .|+.+|.++..
T Consensus        79 ~gi~~~~~~~g~~~~~~~~~-~--~~~~~~~~i~~l~~~~vdgiii~~~~~-~~~~~~~l~~~~~iPvV~~d~~  148 (341)
T PRK10703         79 EAVEKNCYQKGYTLILCNAW-N--NLEKQRAYLSMLAQKRVDGLLVMCSEY-PEPLLAMLEEYRHIPMVVMDWG  148 (341)
T ss_pred             HHHHHHHHHCCCEEEEEeCC-C--CHHHHHHHHHHHHHcCCCEEEEecCCC-CHHHHHHHHhcCCCCEEEEecc
Confidence            57888899999988876432 1  233344555555578999999987543 3467788888 89999999754

>COG0546 Gph Predicted phosphatases [General function prediction only]

Probab=86.87  E-value=1.4  Score=35.18  Aligned_cols=83  Identities=27%  Similarity=0.333  Sum_probs=54.6

Q ss_pred             CCcHHHHHhhceEEEEecCCCc-cHHHHHHHHHHHHhhccCcceEEEEc-CC-----cchHHHHHHHHHcCCe---EEEE
Q 045172           63 YGFADELKRAWFWVRMVLVKPQ-DADVLLRNYMVAMVDKRRFGCLVVVS-DD-----SDFVEVFQEATLRWLK---MVVV  132 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpq-AAD~AL~~~~~~~~~~r~v~clvLVS-DD-----sDF~~~lr~Arer~l~---tVVV  132 (157)
                      +.+-.+|+.+|+..=.|+.||+ .++..|..+-..-    -+++  .++ |+     +|-..++..+.+.|+.   ++.|
T Consensus        95 ~e~L~~L~~~g~~l~i~T~k~~~~~~~~l~~~gl~~----~F~~--i~g~~~~~~~KP~P~~l~~~~~~~~~~~~~~l~V  168 (220)
T COG0546          95 KELLAALKSAGYKLGIVTNKPERELDILLKALGLAD----YFDV--IVGGDDVPPPKPDPEPLLLLLEKLGLDPEEALMV  168 (220)
T ss_pred             HHHHHHHHhCCCeEEEEeCCcHHHHHHHHHHhCCcc----ccce--EEcCCCCCCCCcCHHHHHHHHHHhCCChhheEEE
Confidence            5566789999999999999998 4444444322211    1222  333 32     3456788888888887   8999


Q ss_pred             cCC-CchHHHhhhh---cccchh
Q 045172          133 GDM-SDGALKRIAN---AFFSWS  151 (157)
Q Consensus       133 Gd~-~~~~L~r~AD---~~fsW~  151 (157)
                      ||+ .|-.-.++|.   +.+.|.
T Consensus       169 GDs~~Di~aA~~Ag~~~v~v~~g  191 (220)
T COG0546         169 GDSLNDILAAKAAGVPAVGVTWG  191 (220)
T ss_pred             CCCHHHHHHHHHcCCCEEEEECC
Confidence            999 5555566665   445664

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

Probab=86.42  E-value=3.5  Score=32.00  Aligned_cols=68  Identities=15%  Similarity=0.161  Sum_probs=45.0

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      -|+..+++..|+.+......-   |..-...+.+.+.+.++|++++.+.+.+ .+.++.+.+.+ .+|+|+..
T Consensus        19 ~gi~~~~~~~g~~~~~~~~~~---~~~~~~~~i~~l~~~~vdgiii~~~~~~-~~~~~~~~~~~-pvv~~~~~   86 (260)
T cd06286          19 DGIEKAALKHGYKVVLLQTNY---DKEKELEYLELLKTKQVDGLILCSREND-WEVIEPYTKYG-PIVLCEEY   86 (260)
T ss_pred             HHHHHHHHHcCCEEEEEeCCC---ChHHHHHHHHHHHHcCCCEEEEeCCCCC-HHHHHHHhcCC-CEEEEecc
Confidence            467788888899887754321   1222223444444789999999886544 35677777877 88888764

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.

>TIGR00147 lipid kinase, YegS/Rv2252/BmrU family

Probab=86.34  E-value=3.2  Score=34.38  Aligned_cols=22  Identities=14%  Similarity=0.166  Sum_probs=11.8

Q ss_pred             CcceEEEEcCCcchHHHHHHHH
Q 045172          102 RFGCLVVVSDDSDFVEVFQEAT  123 (157)
Q Consensus       102 ~v~clvLVSDDsDF~~~lr~Ar  123 (157)
                      +.+++|.+.-|=-+..+++.+.
T Consensus        57 ~~d~ivv~GGDGTl~~v~~~l~   78 (293)
T TIGR00147        57 GVDTVIAGGGDGTINEVVNALI   78 (293)
T ss_pred             CCCEEEEECCCChHHHHHHHHh
Confidence            4555555555555555555443

The E. coli member of this family, YegS has been purified and shown to have phosphatidylglycerol kinase activity. The member from M. tuberculosis, Rv2252, has diacylglycerol kinase activity. BmrU from B. subtilis is in an operon with multidrug efflux transporter Bmr, but is uncharacterized.

>cd06330 PBP1_Arsenic_SBP_like Periplasmic solute-binding domain of active transport proteins

Probab=86.29  E-value=1.6  Score=35.87  Aligned_cols=66  Identities=24%  Similarity=0.182  Sum_probs=44.5

Q ss_pred             cHHHHHhhceEEEEecC---CCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCC--eEEEEc
Q 045172           65 FADELKRAWFWVRMVLV---KPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWL--KMVVVG  133 (157)
Q Consensus        65 la~eLrRAGv~V~~V~d---kpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l--~tVVVG  133 (157)
                      +...|+++|.-+.+|..   .+...|  ....+.+++ ..+.+.+++++...+...+++.+++.|+  ...++|
T Consensus       158 ~~~~~~~~g~~~~~v~~~~~~~~~~d--~~~~v~~i~-~~~~d~ii~~~~~~~~~~~~~~~~~~g~~~~~~~~~  228 (346)
T cd06330         158 FKAALKRLRPDVEVVSEQWPKLGAPD--YGSEITALL-AAKPDAIFSSLWGGDLVTFVRQANARGLFDGTTVVL  228 (346)
T ss_pred             HHHHHHHhCCCCeecccccCCCCCcc--cHHHHHHHH-hcCCCEEEEecccccHHHHHHHHHhcCcccCceEEe
Confidence            45667777654455432   223333  334445555 6889999999989999999999999999  434443

Periplasmic solute-binding domain of active transport proteins found in bacteria and Archaea that is predicted to be involved in the efflux of toxic compounds. Members of this subgroup include proteins from Herminiimonas arsenicoxydans, which is resistant to arsenic and various heavy metals such as cadmium and zinc. Moreover, they show significant sequence similarity to the cluster of AmiC and active transport systems for short-chain amides and urea (FmdDEF), and thus are likely to exhibit a ligand-binding mode similar to that of the amide sensor protein AmiC from Pseudomonas aeruginosa.

>COG0560 SerB Phosphoserine phosphatase [Amino acid transport and metabolism]

Probab=86.25  E-value=2.6  Score=34.48  Aligned_cols=98  Identities=15%  Similarity=0.017  Sum_probs=62.1

Q ss_pred             HHHHHHhhcCcccC-CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHH----------
Q 045172           49 NKMAASAILTPKVG-YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVE----------  117 (157)
Q Consensus        49 Y~~Aar~~l~pkvg-ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~----------  117 (157)
                      -++...+.++...| -.|...|+.+|..|-.||..|.    -+-+.+.+.+--..+-+.+|..+|--|++          
T Consensus        68 v~~~~~~~~~l~~ga~elv~~lk~~G~~v~iiSgg~~----~lv~~ia~~lg~d~~~an~l~~~dG~ltG~v~g~~~~~~  143 (212)
T COG0560          68 LEEVREEFLRLTPGAEELVAALKAAGAKVVIISGGFT----FLVEPIAERLGIDYVVANELEIDDGKLTGRVVGPICDGE  143 (212)
T ss_pred             HHHHHHhcCcCCccHHHHHHHHHHCCCEEEEEcCChH----HHHHHHHHHhCCchheeeEEEEeCCEEeceeeeeecCcc
Confidence            33444443333333 5678899999999999999998    44444544442112234445555411333          


Q ss_pred             -----HHHHHHHcCCe---EEEEcCC-CchHHHhhhhcccch
Q 045172          118 -----VFQEATLRWLK---MVVVGDM-SDGALKRIANAFFSW  150 (157)
Q Consensus       118 -----~lr~Arer~l~---tVVVGd~-~~~~L~r~AD~~fsW  150 (157)
                           +.+.+.+.|..   |+-+||+ +|-.+-+.|+..+-+
T Consensus       144 ~K~~~l~~~~~~~g~~~~~~~a~gDs~nDlpml~~ag~~ia~  185 (212)
T COG0560         144 GKAKALRELAAELGIPLEETVAYGDSANDLPMLEAAGLPIAV  185 (212)
T ss_pred             hHHHHHHHHHHHcCCCHHHeEEEcCchhhHHHHHhCCCCeEe
Confidence                 44777888997   9999999 777777777766543

>TIGR01489 DKMTPPase-SF 2,3-diketo-5-methylthio-1-phosphopentane phosphatase

Probab=86.10  E-value=2.2  Score=31.85  Aligned_cols=83  Identities=13%  Similarity=0.107  Sum_probs=48.9

Q ss_pred             CcccC-CCcHHHHHhhceEEEEecCCCcc-HHHHHHHHHHHHhhccCcceE--EEEcC---------------------C
Q 045172           58 TPKVG-YGFADELKRAWFWVRMVLVKPQD-ADVLLRNYMVAMVDKRRFGCL--VVVSD---------------------D  112 (157)
Q Consensus        58 ~pkvg-ygla~eLrRAGv~V~~V~dkpqA-AD~AL~~~~~~~~~~r~v~cl--vLVSD---------------------D  112 (157)
                      .|.-| ..+-..|+..|+.+-.+|..+.. .+..+.        ..+++-+  ..+|.                     +
T Consensus        72 ~l~~g~~~ll~~l~~~g~~~~i~S~~~~~~~~~~l~--------~~~l~~~f~~i~~~~~~~~~~g~~~~~~~~~~~~~~  143 (188)
T TIGR01489        72 PIDPGFKEFIAFIKEHGIDFIVISDGNDFFIDPVLE--------GIGEKDVFIEIYSNPASFDNDGRHIVWPHHCHGCCS  143 (188)
T ss_pred             CCCccHHHHHHHHHHcCCcEEEEeCCcHHHHHHHHH--------HcCChhheeEEeccCceECCCCcEEEecCCCCccCc
Confidence            34333 44557788899999999988762 222221        1222111  12221                     1


Q ss_pred             cc----hHHHHHHHHHc-CCeEEEEcCC-CchHHHhhhhccc
Q 045172          113 SD----FVEVFQEATLR-WLKMVVVGDM-SDGALKRIANAFF  148 (157)
Q Consensus       113 sD----F~~~lr~Arer-~l~tVVVGd~-~~~~L~r~AD~~f  148 (157)
                      +.    =..+++...+. .-+++.|||+ +|-.-.+.||+-|
T Consensus       144 ~~~g~~K~~~~~~~~~~~~~~~i~iGD~~~D~~aa~~~d~~~  185 (188)
T TIGR01489       144 CPCGCCKGKVIHKLSEPKYQHIIYIGDGVTDVCPAKLSDVVF  185 (188)
T ss_pred             CCCCCCHHHHHHHHHhhcCceEEEECCCcchhchHhcCCccc
Confidence            11    13477777776 8889999999 6655666788765

Note that SP|P53981 from S. cerevisiae, a member of this family, is annotated as a "probable membrane protein" due to a predicted transmembrane helix. The region in question contains the second of the three conserved HAD superfamily catalytic motifs and thus, considering the fold of the HAD catalytic domain, is unlikely to be a transmembrane region in fact.

>PRK10671 copA copper exporting ATPase; Provisional

Probab=86.03  E-value=2.2  Score=41.17  Aligned_cols=78  Identities=12%  Similarity=0.081  Sum_probs=47.9

Q ss_pred             HHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC-CchHHHhhhh
Q 045172           67 DELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM-SDGALKRIAN  145 (157)
Q Consensus        67 ~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~-~~~~L~r~AD  145 (157)
                      .+|+..|+.+-+++.+++..=.+       .+...|++-+.--....+=..+++.....+-.++.|||+ +|-..-+.||
T Consensus       660 ~~L~~~gi~v~~~Tgd~~~~a~~-------ia~~lgi~~~~~~~~p~~K~~~i~~l~~~~~~v~~vGDg~nD~~al~~Ag  732 (834)
T PRK10671        660 QRLHKAGYRLVMLTGDNPTTANA-------IAKEAGIDEVIAGVLPDGKAEAIKRLQSQGRQVAMVGDGINDAPALAQAD  732 (834)
T ss_pred             HHHHHCCCeEEEEcCCCHHHHHH-------HHHHcCCCEEEeCCCHHHHHHHHHHHhhcCCEEEEEeCCHHHHHHHHhCC
Confidence            45667777776666555521111       112234432221112223455677777788889999999 8888889999


Q ss_pred             cccchh
Q 045172          146 AFFSWS  151 (157)
Q Consensus       146 ~~fsW~  151 (157)
                      +.+.|.
T Consensus       733 vgia~g  738 (834)
T PRK10671        733 VGIAMG  738 (834)
T ss_pred             eeEEec
Confidence            998885

>PF04123 DUF373: Domain of unknown function (DUF373); InterPro: IPR007254 This archaeal family of unknown function is predicted to be an integral membrane protein with six transmembrane regions

Probab=85.99  E-value=3.4  Score=37.12  Aligned_cols=72  Identities=26%  Similarity=0.206  Sum_probs=55.7

Q ss_pred             CCcHHHHHhhc--eEEEEecCCCc---cHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHH----cCCeEEEEc
Q 045172           63 YGFADELKRAW--FWVRMVLVKPQ---DADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATL----RWLKMVVVG  133 (157)
Q Consensus        63 ygla~eLrRAG--v~V~~V~dkpq---AAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Are----r~l~tVVVG  133 (157)
                      .-+.+||++-|  |.|=+|+.-|.   .||..+.+++-++++..+.+..++|||-.+=..++---+.    .+++-|||=
T Consensus        54 vkiydeL~~~GedveVA~VsG~~~~~v~ad~~I~~qld~vl~~~~~~~~i~VsDGaeDE~vlPiIqSr~~V~sV~RVVVk  133 (344)
T PF04123_consen   54 VKIYDELKAEGEDVEVAVVSGSPDVGVEADRKIAEQLDEVLSKFDPDSAIVVSDGAEDERVLPIIQSRVPVDSVKRVVVK  133 (344)
T ss_pred             HHHHHHHHhcCCCeEEEEEECCCCCchhhHHHHHHHHHHHHHhCCCCEEEEEecChhhhhhhHhhhccCceEEEEEEEEE
Confidence            45779999999  55666766666   7999999999999999999999999997765555444433    567777774


Q ss_pred             C
Q 045172          134 D  134 (157)
Q Consensus       134 d  134 (157)
                      =
T Consensus       134 Q  134 (344)
T PF04123_consen  134 Q  134 (344)
T ss_pred             c
Confidence            3

>PRK07239 bifunctional uroporphyrinogen-III synthetase/response regulator domain protein; Validated

Probab=85.82  E-value=2.5  Score=36.73  Aligned_cols=82  Identities=20%  Similarity=0.165  Sum_probs=52.2

Q ss_pred             cccCCCcHHHHHhhceEEEEecC---CCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHH-----------H
Q 045172           59 PKVGYGFADELKRAWFWVRMVLV---KPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEAT-----------L  124 (157)
Q Consensus        59 pkvgygla~eLrRAGv~V~~V~d---kpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Ar-----------e  124 (157)
                      |.-+..|+..|+..|..|-.+|.   .|-..+-++...+.+.. ....||||+.|-+. ...++..++           -
T Consensus        19 ~~~a~~la~~L~~~G~~~~~~P~i~i~~~~~~~~~~~~~~~l~-~~~~d~vvfTS~ng-v~~~~~~l~~~~~~~~~~~~l   96 (381)
T PRK07239         19 ARRAEELAALLERRGARVVHAPALRIVPLADDDELRAATRALI-AAPPDIVVATTGIG-FRGWVEAADGWGLADELLEAL   96 (381)
T ss_pred             cCCHHHHHHHHHHcCCeEEEecCEEEecCCCcHHHHHHHHHHH-cCCCCEEEEeChHH-HHHHHHHHHHcCChHHHHHHH
Confidence            44446788999999999887632   22222223333333333 35799999999776 333333322           2


Q ss_pred             cCCeEEEEcCCCchHHHh
Q 045172          125 RWLKMVVVGDMSDGALKR  142 (157)
Q Consensus       125 r~l~tVVVGd~~~~~L~r  142 (157)
                      .+++.+.||..|..+|..
T Consensus        97 ~~~~i~aVG~~Ta~aL~~  114 (381)
T PRK07239         97 SSARLLARGPKATGAIRA  114 (381)
T ss_pred             cCCeEEEECccHHHHHHH
Confidence            578899999998777774

>cd04509 PBP1_ABC_transporter_GCPR_C_like Family C of G-protein coupled receptors and their close homologs, the type I periplasmic-binding proteins of ATP-binding cassette transporter-like systems

Probab=85.79  E-value=2.5  Score=32.43  Aligned_cols=68  Identities=13%  Similarity=0.093  Sum_probs=44.3

Q ss_pred             CcHHHHHhhceEEEEecCC-CccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCC--eEEEEcC
Q 045172           64 GFADELKRAWFWVRMVLVK-PQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWL--KMVVVGD  134 (157)
Q Consensus        64 gla~eLrRAGv~V~~V~dk-pqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l--~tVVVGd  134 (157)
                      ++...++.+|+.+..+..- +...|.  ...+.++. ..+.+.+++.++.++...+++.+++.|+  ...+||-
T Consensus       155 ~~~~~~~~~g~~i~~~~~~~~~~~~~--~~~~~~l~-~~~~~~v~~~~~~~~~~~~~~~~~~~g~~~~~~~i~~  225 (299)
T cd04509         155 AFKAAFKKKGGTVVGEEYYPLGTTDF--TSLLQKLK-AAKPDVIVLCGSGEDAATILKQAAEAGLTGGYPILGI  225 (299)
T ss_pred             HHHHHHHHcCCEEEEEecCCCCCccH--HHHHHHHH-hcCCCEEEEcccchHHHHHHHHHHHcCCCCCCcEEec
Confidence            4556777888766543222 222332  22233333 4567888888888999999999999999  6666663

This CD includes members of the family C of G-protein coupled receptors and their close homologs, the type I periplasmic-binding proteins of ATP-binding cassette transporter-like systems. The family C GPCR includes glutamate/glycine-gated ion channels such as the NMDA receptor, G-protein-coupled receptors, metabotropic glutamate, GABA-B, calcium sensing, phermone receptors, and atrial natriuretic peptide-guanylate cyclase receptors. The glutamate receptors that form cation-selective ion channels, iGluR, can be classified into three different subgroups according to their binding-affinity for the agonists NMDA (N-methyl-D-asparate), AMPA (alpha-amino-3-dihydro-5-methyl-3-oxo-4-isoxazolepropionic acid), and kainate. L-glutamate is a major neurotransmitter in the brain of vertebrates and acts th

>PF02310 B12-binding: B12 binding domain; InterPro: IPR006158 The cobalamin (vitamin B12) binding domain can bind two different forms of the cobalamin cofactor, with cobalt bonded either to a methyl group (methylcobalamin) or to 5'-deoxyadenosine (adenosylcobalamin)

Probab=85.63  E-value=7.5  Score=27.53  Aligned_cols=67  Identities=18%  Similarity=0.091  Sum_probs=42.3

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEc-CCcchHHHHHHHH---HcCCe-EEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVS-DDSDFVEVFQEAT---LRWLK-MVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVS-DDsDF~~~lr~Ar---er~l~-tVVVGd~  135 (157)
                      .-+++.|+++|+.|..+..-...      .++.+.+...+.|.+++-+ ..+.+..+.+.++   +.+-. .+++|..
T Consensus        18 ~~la~~l~~~G~~v~~~d~~~~~------~~l~~~~~~~~pd~V~iS~~~~~~~~~~~~l~~~~k~~~p~~~iv~GG~   89 (121)
T PF02310_consen   18 LYLAAYLRKAGHEVDILDANVPP------EELVEALRAERPDVVGISVSMTPNLPEAKRLARAIKERNPNIPIVVGGP   89 (121)
T ss_dssp             HHHHHHHHHTTBEEEEEESSB-H------HHHHHHHHHTTCSEEEEEESSSTHHHHHHHHHHHHHTTCTTSEEEEEES
T ss_pred             HHHHHHHHHCCCeEEEECCCCCH------HHHHHHHhcCCCcEEEEEccCcCcHHHHHHHHHHHHhcCCCCEEEEECC
Confidence            44789999999999987322211      5555656567888877766 5666655555554   44332 5556655

Cobalamin-binding domains are mainly found in two families of enzymes present in animals and prokaryotes, which perform distinct kinds of reactions at the cobalt-carbon bond. Enzymes that require methylcobalamin carry out methyl transfer reactions. Enzymes that require adenosylcobalamin catalyse reactions in which the first step is the cleavage of adenosylcobalamin to form cob(II)alamin and the 5'-deoxyadenosyl radical, and thus act as radical generators. In both types of enzymes the B12-binding domain uses a histidine to bind the cobalt atom of cobalamin cofactors. This histidine is embedded in a DXHXXG sequence, the most conserved primary sequence motif of the domain [, , ]. Proteins containing the cobalamin-binding domain include: Animal and prokaryotic methionine synthase (2.1.1.13 from EC), which catalyse the transfer of a methyl group from methyl-cobalamin to homocysteine, yielding enzyme-bound cob(I)alamin and methionine. Animal and prokaryotic methylmalonyl-CoA mutase (5.4.99.2 from EC), which are involved in the degradation of several amino acids, odd-chain fatty acids and cholesterol via propionyl-CoA to the tricarboxylic acid cycle. Prokaryotic lysine 5,6-aminomutase (5.4.3.4 from EC). Prokaryotic glutamate mutase (5.4.99.1 from EC) []. Prokaryotic methyleneglutarate mutase (5.4.99.4 from EC). Prokaryotic isobutyryl-CoA mutase (5.4.99.13 from EC). The core structure of the cobalamin-binding domain is characterised by a five-stranded alpha/beta (Rossmann) fold, which consists of 5 parallel beta-sheets surrounded by 4-5 alpha helices in three layers (alpha/beta/alpha) []. Upon binding cobalamin, important elements of the binding site appear to become structured, including an alpha-helix that forms on one side of the cleft accommodating the nucleotide 'tail' of the cofactor. In cobalamin, the cobalt atom can be either free (dmb-off) or bound to dimethylbenzimidazole (dmb-on) according to the pH. When bound to the cobalamin-binding domain, the dimethylbenzimidazole ligand is replaced by the active histidine (His-on) of the DXHXXG motif. The replacement of dimethylbenzimidazole by histidine allows switching between the catalytic and activation cycles []. In methionine synthase the cobalamin cofactor is sandwiched between the cobalamin-binding domain and an approximately 90 residues N-terminal domain forming a helical bundle comprising two pairs of antiparallel helices []. In methionine synthase, there is a second, adjacent domain involved in cobalamin binding that forms a 4-helical bundle cap (IPR003759 from INTERPRO); in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain (IPR004223 from INTERPRO) [].; GO: 0031419 cobalamin binding, 0046872 metal ion binding; PDB: 1Y80_A 3BUL_A 1K7Y_A 1BMT_A 3IV9_A 1K98_A 3IVA_A 3KP1_A 3KOW_A 3KOZ_A ....

>cd01391 Periplasmic_Binding_Protein_Type_1 Type 1 periplasmic binding fold superfamily

Probab=85.56  E-value=6.3  Score=29.06  Aligned_cols=71  Identities=8%  Similarity=0.048  Sum_probs=47.9

Q ss_pred             CCcHHHHHh--hceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCCC
Q 045172           63 YGFADELKR--AWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDMS  136 (157)
Q Consensus        63 ygla~eLrR--AGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~~  136 (157)
                      .|+...+..  .|+.+.++.......+  ....+.++. ..+++.+++.+.+..-..++..+.+.++.+|.++-..
T Consensus        20 ~~~~~~~~~~g~~~~~~~~~~~~~~~~--~~~~~~~~~-~~~~d~ii~~~~~~~~~~~~~~~~~~~ip~v~~~~~~   92 (269)
T cd01391          20 AGIELAAEEIGRGLEVILADSQSDPER--ALEALRDLI-QQGVDGIIGPPSSSSALAVVELAAAAGIPVVSLDATA   92 (269)
T ss_pred             HHHHHHHHHhCCceEEEEecCCCCHHH--HHHHHHHHH-HcCCCEEEecCCCHHHHHHHHHHHHcCCcEEEecCCC
Confidence            355556666  6777776654433212  222233333 5699999999888776668999999999999998763

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

>COG1879 RbsB ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]

Probab=85.56  E-value=2.5  Score=34.90  Aligned_cols=69  Identities=13%  Similarity=0.127  Sum_probs=49.2

Q ss_pred             CCcHHHHHhhce--EEEEecCCCccHHHHHHH-HHHHHhhccCcceEEEEcCCc-chHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWF--WVRMVLVKPQDADVLLRN-YMVAMVDKRRFGCLVVVSDDS-DFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv--~V~~V~dkpqAAD~AL~~-~~~~~~~~r~v~clvLVSDDs-DF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+-.+-+..|+  .+...+..+   |.+-+. ++.+++ .+++|.|++..-|+ -+.+.+++|.++|..+|.+-..
T Consensus        53 ~g~~~~a~~~g~~~~~~~~~~~~---d~~~Q~~~i~~~i-a~~~daIiv~~~d~~~~~~~v~~a~~aGIpVv~~d~~  125 (322)
T COG1879          53 KGAEAAAKKLGVVVAVVIADAQN---DVAKQIAQIEDLI-AQGVDAIIINPVDPDALTPAVKKAKAAGIPVVTVDSD  125 (322)
T ss_pred             HHHHHHHHHcCCcEEEEeccccc---ChHHHHHHHHHHH-HcCCCEEEEcCCChhhhHHHHHHHHHCCCcEEEEecC
Confidence            567788888895  444433333   344444 334444 79999999986555 6999999999999999998776

>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional

Probab=85.43  E-value=3.1  Score=38.97  Aligned_cols=96  Identities=15%  Similarity=0.139  Sum_probs=64.7

Q ss_pred             hhHHHHHHHHhhcCccc----CCC--------cHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCC
Q 045172           45 KMEKNKMAASAILTPKV----GYG--------FADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDD  112 (157)
Q Consensus        45 k~~kY~~Aar~~l~pkv----gyg--------la~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDD  112 (157)
                      ..+.+++++..+...+.    |.|        +...|.+.|+.+....|      ..+.......+  ..=|+++++|-.
T Consensus       454 d~~~l~~aa~~L~~a~rI~i~G~G~S~~~A~~~~~~l~~lg~~~~~~~d------~~~~~~~~~~l--~~~DvvI~iS~s  525 (638)
T PRK14101        454 NFEHVEQAIDILNNARRIEFYGLGNSNIVAQDAHYKFFRFGIPTIAYGD------LYMQAASAALL--GKGDVIVAVSKS  525 (638)
T ss_pred             CHHHHHHHHHHHhcCCEEEEEEccHHHHHHHHHHHHHhcCCceEEEcCC------HHHHHHHHhcC--CCCCEEEEEeCC
Confidence            34567777777766554    223        23356778888776543      22322222233  233889999864


Q ss_pred             ---cchHHHHHHHHHcCCeEEEEcCCCchHHHhhhhcccc
Q 045172          113 ---SDFVEVFQEATLRWLKMVVVGDMSDGALKRIANAFFS  149 (157)
Q Consensus       113 ---sDF~~~lr~Arer~l~tVVVGd~~~~~L~r~AD~~fs  149 (157)
                         .+-..+++.|+++|+++|.|-|. ...|.+.||.-|.
T Consensus       526 G~t~e~i~~~~~Ak~~Ga~vIaIT~~-~spLa~~aD~~L~  564 (638)
T PRK14101        526 GRAPELLRVLDVAMQAGAKVIAITSS-NTPLAKRATVALE  564 (638)
T ss_pred             CCCHHHHHHHHHHHHCCCeEEEEcCC-CChhHhhCCEEEE
Confidence               45677888999999999999996 6889999998773

>PRK13938 phosphoheptose isomerase; Provisional

Probab=85.33  E-value=1.3  Score=36.16  Aligned_cols=49  Identities=16%  Similarity=0.139  Sum_probs=39.7

Q ss_pred             CcceEEEEcCC---cchHHHHHHHHHcCCeEEEEcCCCchHHHhhhhcccch
Q 045172          102 RFGCLVVVSDD---SDFVEVFQEATLRWLKMVVVGDMSDGALKRIANAFFSW  150 (157)
Q Consensus       102 ~v~clvLVSDD---sDF~~~lr~Arer~l~tVVVGd~~~~~L~r~AD~~fsW  150 (157)
                      .=|+++.+|-.   .+-..+++.|+++|+++|.|.+..+..|.+.||.-|..
T Consensus       113 ~~DllI~iS~SG~t~~vi~a~~~Ak~~G~~vI~iT~~~~s~La~~aD~~l~v  164 (196)
T PRK13938        113 PGDTLFAISTSGNSMSVLRAAKTARELGVTVVAMTGESGGQLAEFADFLINV  164 (196)
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHCCCEEEEEeCCCCChhhhhCCEEEEe
Confidence            33788888875   34457788999999999999998778999999987743

>PRK09484 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase; Provisional

Probab=85.30  E-value=3.3  Score=32.49  Aligned_cols=77  Identities=14%  Similarity=0.153  Sum_probs=41.7

Q ss_pred             ccCCCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHH-HHHcCC---eEEEEcCC
Q 045172           60 KVGYGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQE-ATLRWL---KMVVVGDM  135 (157)
Q Consensus        60 kvgygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~-Arer~l---~tVVVGd~  135 (157)
                      +.|+|+ ..|+..|+.+-.++.+|..   ... .   .+...|++-+.- +.+ +..+.++. +.+.|+   .++.|||+
T Consensus        52 ~d~~~i-~~L~~~Gi~v~I~T~~~~~---~v~-~---~l~~lgl~~~f~-g~~-~k~~~l~~~~~~~gl~~~ev~~VGDs  121 (183)
T PRK09484         52 RDGYGI-RCLLTSGIEVAIITGRKSK---LVE-D---RMTTLGITHLYQ-GQS-NKLIAFSDLLEKLAIAPEQVAYIGDD  121 (183)
T ss_pred             cchHHH-HHHHHCCCEEEEEeCCCcH---HHH-H---HHHHcCCceeec-CCC-cHHHHHHHHHHHhCCCHHHEEEECCC
Confidence            334555 4577899999999988872   111 1   222334443221 333 33344444 444665   58888888


Q ss_pred             -CchHHHhhhhc
Q 045172          136 -SDGALKRIANA  146 (157)
Q Consensus       136 -~~~~L~r~AD~  146 (157)
                       +|-...+.|.+
T Consensus       122 ~~D~~~a~~aG~  133 (183)
T PRK09484        122 LIDWPVMEKVGL  133 (183)
T ss_pred             HHHHHHHHHCCC
Confidence             54444444443

>cd06276 PBP1_FucR_like Ligand-binding domain of a transcription repressor, FucR, which functions as a molecular sensor of L-fucose availability

Probab=85.26  E-value=4.1  Score=32.50  Aligned_cols=67  Identities=13%  Similarity=0.181  Sum_probs=44.5

Q ss_pred             CCcHHHHHhhc-eEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAW-FWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAG-v~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      -|+...|...| +.+-+....+   |  ....+..++ .+++|.++++|...+=......+.+.+..+|++|..
T Consensus        18 ~~i~~~l~~~g~~~l~~~~~~~---~--~~~~~~~~~-~~~vdGvIi~~~~~~~~~~~~~~~~~~~PvV~i~~~   85 (247)
T cd06276          18 NSFVNTLGKNAQVDLYFHHYNE---D--LFKNIISNT-KGKYSGYVVMPHFKNEIQYFLLKKIPKEKLLILDHS   85 (247)
T ss_pred             HHHHHHHHhcCcEEEEEEcCch---H--HHHHHHHHH-hcCCCEEEEecCCCCcHHHHHHhccCCCCEEEEcCc
Confidence            47888999999 7776654443   2  223445555 689999999986422111344445578899999975

Ligand-binding domain of a transcription repressor, FucR, which functions as a molecular sensor of L-fucose availability. FcuR acts as an inducer of fucRRIAK and as a corepressor of another locus that regulates production of fucosylated glycans. FcuR and its close homologs in this group are 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 t

>PRK02947 hypothetical protein; Provisional

Probab=85.21  E-value=1.5  Score=36.53  Aligned_cols=48  Identities=27%  Similarity=0.317  Sum_probs=39.7

Q ss_pred             cCcceEEEEcCC---cchHHHHHHHHHcCCeEEEEcCCC-----------chHHHhhhhccc
Q 045172          101 RRFGCLVVVSDD---SDFVEVFQEATLRWLKMVVVGDMS-----------DGALKRIANAFF  148 (157)
Q Consensus       101 r~v~clvLVSDD---sDF~~~lr~Arer~l~tVVVGd~~-----------~~~L~r~AD~~f  148 (157)
                      ..=|+++++|-.   .+-.++++.|+++|.++|.|-+..           ...|.+.||.-+
T Consensus       105 ~~~Dv~i~iS~sG~t~~~i~~~~~a~~~g~~vI~iT~~~~s~~~~~~h~~gs~l~~~ad~~l  166 (246)
T PRK02947        105 RPGDVLIVVSNSGRNPVPIEMALEAKERGAKVIAVTSLAYSASVASRHSSGKRLAEVADVVL  166 (246)
T ss_pred             CCCCEEEEEeCCCCCHHHHHHHHHHHHCCCEEEEEcCCcccccccccCCCcCchhHhCCEEE
Confidence            344899999954   677788999999999999999874           268999999877

>cd06268 PBP1_ABC_transporter_LIVBP_like Periplasmic binding domain of ATP-binding cassette transporter-like systems that belong to the type I periplasmic binding fold protein superfamily

Probab=85.10  E-value=2.9  Score=32.03  Aligned_cols=69  Identities=17%  Similarity=0.138  Sum_probs=45.6

Q ss_pred             CcHHHHHhhceEEEEecCC-CccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           64 GFADELKRAWFWVRMVLVK-PQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        64 gla~eLrRAGv~V~~V~dk-pqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      ++...+++.|+.+.....- +...|  ....+.+++ ..+.+.+++.++..+...+++.+++.|+...++|-.
T Consensus       154 ~~~~~~~~~g~~i~~~~~~~~~~~~--~~~~~~~l~-~~~~~~vi~~~~~~~~~~~~~~~~~~g~~~~~~~~~  223 (298)
T cd06268         154 AFREALKKLGGEVVAEETYPPGATD--FSPLIAKLK-AAGPDAVFLAGYGGDAALFLKQAREAGLKVPIVGGD  223 (298)
T ss_pred             HHHHHHHHcCCEEEEEeccCCCCcc--HHHHHHHHH-hcCCCEEEEccccchHHHHHHHHHHcCCCCcEEecC
Confidence            3455677778655433222 22233  233444444 567899999999899999999999999876676643

Periplasmic binding domain of ATP-binding cassette transporter-like systems that belong to the type I periplasmic binding fold protein superfamily. They are mostly present in archaea and eubacteria, and are primarily involved in scavenging solutes from the environment. ABC-type transporters couple ATP hydrolysis with the uptake and efflux of a wide range of substrates across bacterial membranes, including amino acids, peptides, lipids and sterols, and various drugs. These systems are comprised of transmembrane domains, nucleotide binding domains, and in most bacterial uptake systems, periplasmic binding proteins (PBPs) which transfer the ligand to the extracellular gate of the transmembrane domains. These PBPs bind their substrates selectively and with high affinity. Members of this group include ABC

>TIGR03333 salvage_mtnX 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate phosphatase

Probab=85.07  E-value=7.5  Score=30.79  Aligned_cols=98  Identities=12%  Similarity=0.046  Sum_probs=57.7

Q ss_pred             HHHHHHHHhhcCcccC-CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhh-ccCcceE-EEEcCC--------cc-
Q 045172           47 EKNKMAASAILTPKVG-YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVD-KRRFGCL-VVVSDD--------SD-  114 (157)
Q Consensus        47 ~kY~~Aar~~l~pkvg-ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~-~r~v~cl-vLVSDD--------sD-  114 (157)
                      +.+.+.+.+-+.+.-| ..+-..|++.|+.+-.||+++..    .+..+.+-+. ...+-|- ..++++        ++ 
T Consensus        59 ~~~~~~~~~~~~l~pg~~e~l~~l~~~g~~~~IvS~~~~~----~i~~il~~~~~~~~i~~n~~~~~~~~~~~~~p~~~~  134 (214)
T TIGR03333        59 EEITSFVLETAEIREGFREFVAFINEHGIPFYVISGGMDF----FVYPLLEGIVEKDRIYCNEADFSNEYIHIDWPHPCD  134 (214)
T ss_pred             HHHHHHHHhcCcccccHHHHHHHHHHCCCeEEEECCCcHH----HHHHHHHhhCCcccEEeceeEeeCCeeEEeCCCCCc
Confidence            3555544443445445 56677788889999999999871    2222222220 1112110 122221        11 


Q ss_pred             ----------hHHHHHHHHHcCCeEEEEcCC-CchHHHhhhhccc
Q 045172          115 ----------FVEVFQEATLRWLKMVVVGDM-SDGALKRIANAFF  148 (157)
Q Consensus       115 ----------F~~~lr~Arer~l~tVVVGd~-~~~~L~r~AD~~f  148 (157)
                                -..+++......=+++.|||+ +|-...+.||+.|
T Consensus       135 ~~~~~~cg~~K~~~l~~~~~~~~~~i~iGDg~~D~~~a~~Ad~~~  179 (214)
T TIGR03333       135 GTCQNQCGCCKPSLIRKLSEPNDYHIVIGDSVTDVEAAKQSDLCF  179 (214)
T ss_pred             cccccCCCCCHHHHHHHHhhcCCcEEEEeCCHHHHHHHHhCCeeE
Confidence                      246777666666789999999 7777778888876

Members of this family are the methionine salvage enzyme MnxX, a member of the HAD-superfamily hydrolases, subfamily IB (see TIGR01488). Members are found in Bacillus subtilis and related species, paired with MtnW (TIGR03332). In most species that recycle methionine from methylthioadenosine, the single protein MtnC replaces the MtnW/MtnX pair. In B. subtilis, mtnX was first known as ykrX.

>PRK11543 gutQ D-arabinose 5-phosphate isomerase; Provisional

Probab=85.04  E-value=1.7  Score=36.42  Aligned_cols=75  Identities=11%  Similarity=0.037  Sum_probs=51.8

Q ss_pred             HHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCC---cchHHHHHHHHHcCCeEEEEcCCCchHHHh
Q 045172           66 ADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDD---SDFVEVFQEATLRWLKMVVVGDMSDGALKR  142 (157)
Q Consensus        66 a~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDD---sDF~~~lr~Arer~l~tVVVGd~~~~~L~r  142 (157)
                      +.-|-+.|..+..+.+-     ..+..++  .. -..=|+++.+|-.   .+-.++++.|+++|.++|.|-+.....|.+
T Consensus        61 ~~~l~~~g~~~~~~~~~-----~~~~~~~--~~-~~~~d~~i~iS~sG~t~~~~~~~~~ak~~g~~vI~iT~~~~s~la~  132 (321)
T PRK11543         61 AATLASTGTPAFFVHPA-----EALHGDL--GM-IESRDVMLFISYSGGAKELDLIIPRLEDKSIALLAMTGKPTSPLGL  132 (321)
T ss_pred             HHHHHcCCCceeecChH-----HHhhCCc--Cc-cCCCCEEEEEeCCCCcHHHHHHHHHHHHcCCeEEEEECCCCChhHH
Confidence            44567788888776431     1111111  11 1233788888865   566778889999999999999986789999


Q ss_pred             hhhccc
Q 045172          143 IANAFF  148 (157)
Q Consensus       143 ~AD~~f  148 (157)
                      .||.-|
T Consensus       133 ~ad~~l  138 (321)
T PRK11543        133 AAKAVL  138 (321)
T ss_pred             hCCEEE
Confidence            999977

>PRK13582 thrH phosphoserine phosphatase; Provisional

Probab=84.76  E-value=3.3  Score=31.81  Aligned_cols=86  Identities=15%  Similarity=0.181  Sum_probs=50.7

Q ss_pred             cCcccC-CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcce----EE-------EEc----CCcchHHHHH
Q 045172           57 LTPKVG-YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGC----LV-------VVS----DDSDFVEVFQ  120 (157)
Q Consensus        57 l~pkvg-ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~c----lv-------LVS----DDsDF~~~lr  120 (157)
                      ++|--| .-+-..|+.+ +.+-.||.++..    ....+.+   ..|++.    .+       ++.    ........++
T Consensus        67 ~~~~pg~~e~L~~L~~~-~~~~IvS~~~~~----~~~~~l~---~~gl~~~f~~~~~~~~~~~i~~~~~~~p~~k~~~l~  138 (205)
T PRK13582         67 LDPLPGAVEFLDWLRER-FQVVILSDTFYE----FAGPLMR---QLGWPTLFCHSLEVDEDGMITGYDLRQPDGKRQAVK  138 (205)
T ss_pred             CCCCCCHHHHHHHHHhc-CCEEEEeCCcHH----HHHHHHH---HcCCchhhcceEEECCCCeEECccccccchHHHHHH
Confidence            344444 3566778888 888889999982    1122222   223221    11       111    1134556777


Q ss_pred             HHHHcCCeEEEEcCC-CchHHHhhhhcccch
Q 045172          121 EATLRWLKMVVVGDM-SDGALKRIANAFFSW  150 (157)
Q Consensus       121 ~Arer~l~tVVVGd~-~~~~L~r~AD~~fsW  150 (157)
                      .....+-.+|.|||+ +|-...+.|++.+.|
T Consensus       139 ~~~~~~~~~v~iGDs~~D~~~~~aa~~~v~~  169 (205)
T PRK13582        139 ALKSLGYRVIAAGDSYNDTTMLGEADAGILF  169 (205)
T ss_pred             HHHHhCCeEEEEeCCHHHHHHHHhCCCCEEE
Confidence            777788899999999 554567777766543

>PF15608 PELOTA_1: PELOTA RNA binding domain

Probab=84.56  E-value=2.9  Score=31.85  Aligned_cols=42  Identities=24%  Similarity=0.258  Sum_probs=36.7

Q ss_pred             HHHHHhhccCcceEEEEc--CCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           93 YMVAMVDKRRFGCLVVVS--DDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        93 ~~~~~~~~r~v~clvLVS--DDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .++.++. |+++|-+||-  ||+|-..++.+|.++|+...+++|.
T Consensus        46 EaTRvLL-RRvP~~vLVr~~~~pd~~Hl~~LA~ekgVpVe~~~d~   89 (100)
T PF15608_consen   46 EATRVLL-RRVPWKVLVRDPDDPDLAHLLLLAEEKGVPVEVYPDL   89 (100)
T ss_pred             HHHHHHH-hcCCCEEEECCCCCccHHHHHHHHHHcCCcEEEeCCC
Confidence            4556664 8999999996  6789999999999999999999997

>PRK10892 D-arabinose 5-phosphate isomerase; Provisional

Probab=84.51  E-value=1.3  Score=37.34  Aligned_cols=76  Identities=11%  Similarity=0.142  Sum_probs=54.2

Q ss_pred             cHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCC---cchHHHHHHHHHcCCeEEEEcCCCchHHH
Q 045172           65 FADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDD---SDFVEVFQEATLRWLKMVVVGDMSDGALK  141 (157)
Q Consensus        65 la~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDD---sDF~~~lr~Arer~l~tVVVGd~~~~~L~  141 (157)
                      ++.-|-+.|..+..+.+.    +..  ......+  ..-|+++.+|-.   .+-.++++.|+++|++||.|-+.....|.
T Consensus        65 ~~~~l~~~g~~~~~~~~~----~~~--~~~~~~~--~~~d~~I~iS~sG~t~~~~~~~~~ak~~g~~vi~iT~~~~s~la  136 (326)
T PRK10892         65 MAATFASTGTPSFFVHPG----EAA--HGDLGMV--TPQDVVIAISNSGESSEILALIPVLKRLHVPLICITGRPESSMA  136 (326)
T ss_pred             HHHHHhcCCceeEEeChH----Hhh--ccccccC--CCCCEEEEEeCCCCCHHHHHHHHHHHHCCCcEEEEECCCCCccc
Confidence            344566788888775321    111  1111222  233788899864   77888999999999999999999778999


Q ss_pred             hhhhccc
Q 045172          142 RIANAFF  148 (157)
Q Consensus       142 r~AD~~f  148 (157)
                      +.||..|
T Consensus       137 ~~ad~~l  143 (326)
T PRK10892        137 RAADIHL  143 (326)
T ss_pred             ccCCEEE
Confidence            9999988

>cd06337 PBP1_ABC_ligand_binding_like_4 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=84.46  E-value=2.5  Score=35.62  Aligned_cols=64  Identities=16%  Similarity=0.136  Sum_probs=46.0

Q ss_pred             HHHHhhceEEE-EecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEc
Q 045172           67 DELKRAWFWVR-MVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVG  133 (157)
Q Consensus        67 ~eLrRAGv~V~-~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVG  133 (157)
                      .+|++.|+.|- .+.-.|..+|..  ..+..+. ..+.|+|++.+..+|.+.+++.+++.|+..-+++
T Consensus       170 ~~~~~~G~~vv~~~~~~~~~~D~~--~~v~~ik-~a~pD~v~~~~~~~~~~~~~~~~~~~G~~~~~~~  234 (357)
T cd06337         170 AALADAGYKLVDPGRFEPGTDDFS--SQINAFK-REGVDIVTGFAIPPDFATFWRQAAQAGFKPKIVT  234 (357)
T ss_pred             HHHHhCCcEEecccccCCCCCcHH--HHHHHHH-hcCCCEEEeCCCccHHHHHHHHHHHCCCCCCeEE
Confidence            45667888764 334455677744  2233333 6889999999999999999999999999754443

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.

>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=84.38  E-value=4.6  Score=32.34  Aligned_cols=68  Identities=16%  Similarity=0.053  Sum_probs=45.1

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHc-CCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLR-WLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer-~l~tVVVGd~  135 (157)
                      .|+..++++.|+.+..++.. ...+   ..+..+.+.+.++|.+++.+-..+ ..+...+++. +...|++|..
T Consensus        22 ~gi~~~~~~~gy~~~i~~~~-~~~~---~~~~i~~l~~~~vdgiI~~~~~~~-~~~~~~~~~~~~~PiV~i~~~   90 (265)
T cd06354          22 EGLERAAKELGIEYKYVESK-SDAD---YEPNLEQLADAGYDLIVGVGFLLA-DALKEVAKQYPDQKFAIIDAV   90 (265)
T ss_pred             HHHHHHHHHcCCeEEEEecC-CHHH---HHHHHHHHHhCCCCEEEEcCcchH-HHHHHHHHHCCCCEEEEEecc
Confidence            47788999999999887443 2222   234455555899999999863311 1344444543 8899999864

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.

>PRK11302 DNA-binding transcriptional regulator HexR; Provisional

Probab=84.20  E-value=1.9  Score=35.36  Aligned_cols=95  Identities=17%  Similarity=0.132  Sum_probs=58.0

Q ss_pred             hHHHHHHHHhhcCccc----CCC----cHHH----HHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCC-
Q 045172           46 MEKNKMAASAILTPKV----GYG----FADE----LKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDD-  112 (157)
Q Consensus        46 ~~kY~~Aar~~l~pkv----gyg----la~e----LrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDD-  112 (157)
                      .+..++++..+...+-    |.|    +|.+    |-|-|+.+....|      ..........+  ..=|+++++|-. 
T Consensus       115 ~~~i~~~~~~i~~a~~I~i~G~G~S~~~a~~~~~~l~~~g~~~~~~~~------~~~~~~~~~~~--~~~D~vI~iS~sG  186 (284)
T PRK11302        115 PSAINRAVDLLTQAKKISFFGLGASAAVAHDAQNKFFRFNVPVVYFDD------IVMQRMSCMNS--SDGDVVVLISHTG  186 (284)
T ss_pred             HHHHHHHHHHHHcCCeEEEEEcchHHHHHHHHHHHHHhcCCceEecCC------HHHHHHHHHhC--CCCCEEEEEeCCC
Confidence            4556666666655442    222    2322    5567776665432      21111111111  233777777654 


Q ss_pred             --cchHHHHHHHHHcCCeEEEEcCCCchHHHhhhhcccc
Q 045172          113 --SDFVEVFQEATLRWLKMVVVGDMSDGALKRIANAFFS  149 (157)
Q Consensus       113 --sDF~~~lr~Arer~l~tVVVGd~~~~~L~r~AD~~fs  149 (157)
                        .+...+++.|+++|+++|+|.+ ....|.+.||.-|.
T Consensus       187 ~t~~~~~~~~~ak~~g~~vI~IT~-~~s~l~~~ad~~l~  224 (284)
T PRK11302        187 RTKSLVELAQLARENGATVIAITS-AGSPLAREATLALT  224 (284)
T ss_pred             CCHHHHHHHHHHHHcCCeEEEECC-CCChhHHhCCEEEe
Confidence              4566788999999999999998 46789999998773

>cd08189 Fe-ADH5 Iron-containing alcohol dehydrogenases-like

Probab=83.63  E-value=5.5  Score=34.77  Aligned_cols=78  Identities=13%  Similarity=0.011  Sum_probs=53.5

Q ss_pred             cHHHHHhhce-EEEEecCCCccHHHHHHHHHHHHhhccCcceEEE--EcCCcchH---HHHHHHHHcCCeEEE-EcCCCc
Q 045172           65 FADELKRAWF-WVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVV--VSDDSDFV---EVFQEATLRWLKMVV-VGDMSD  137 (157)
Q Consensus        65 la~eLrRAGv-~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvL--VSDDsDF~---~~lr~Arer~l~tVV-VGd~~~  137 (157)
                      |..+|++-|. .|-.|.|+- ..+..+...+.+.+...|+++.+.  |-.++.+.   .++..+++.+...|| ||.++.
T Consensus        17 l~~~l~~~g~~~~lvvt~~~-~~~~g~~~~v~~~L~~~g~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~d~IIaiGGGS~   95 (374)
T cd08189          17 LPAAISQLGVKKVLIVTDKG-LVKLGLLDKVLEALEGAGIEYAVYDGVPPDPTIENVEAGLALYRENGCDAILAVGGGSV   95 (374)
T ss_pred             HHHHHHhcCCCeEEEEeCcc-hhhcccHHHHHHHHHhcCCeEEEeCCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCccH
Confidence            6778888774 566667743 444556677888887778876654  33345554   777888888998888 999865


Q ss_pred             hHHHhh
Q 045172          138 GALKRI  143 (157)
Q Consensus       138 ~~L~r~  143 (157)
                      ......
T Consensus        96 ~D~aK~  101 (374)
T cd08189          96 IDCAKA  101 (374)
T ss_pred             HHHHHH
Confidence            555544

Iron-containing alcohol dehydrogenase-like. 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 belongs to the alcohol dehydrogenase-like superfamily. 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.

>cd06346 PBP1_ABC_ligand_binding_like_11 Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions

Probab=83.62  E-value=4.3  Score=33.25  Aligned_cols=75  Identities=15%  Similarity=-0.002  Sum_probs=52.8

Q ss_pred             hcCcccCCC------cHHHHHhhceEEEE-ecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCe
Q 045172           56 ILTPKVGYG------FADELKRAWFWVRM-VLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLK  128 (157)
Q Consensus        56 ~l~pkvgyg------la~eLrRAGv~V~~-V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~  128 (157)
                      ++.+...||      +...+++.|+.|-. ..-.|...|..  ..+..+. ..+.|.|++.+...+-+.+++.+++.|+.
T Consensus       142 il~~~~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~~d~~--~~v~~l~-~~~pd~v~~~~~~~~~~~~~~~~~~~G~~  218 (312)
T cd06346         142 TTYINNDYGVGLADAFTKAFEALGGTVTNVVAHEEGKSSYS--SEVAAAA-AGGPDALVVIGYPETGSGILRSAYEQGLF  218 (312)
T ss_pred             EEEccCchhhHHHHHHHHHHHHcCCEEEEEEeeCCCCCCHH--HHHHHHH-hcCCCEEEEecccchHHHHHHHHHHcCCC
Confidence            344555555      44677788987643 34445566655  4555555 57899999999999999999999999997


Q ss_pred             EEEEc
Q 045172          129 MVVVG  133 (157)
Q Consensus       129 tVVVG  133 (157)
                      .-++|
T Consensus       219 ~~~~~  223 (312)
T cd06346         219 DKFLL  223 (312)
T ss_pred             CceEe
Confidence            54554

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 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); however its ligand specificity has not been determined experimentally.

>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=83.60  E-value=7.2  Score=30.20  Aligned_cols=68  Identities=15%  Similarity=0.080  Sum_probs=45.9

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++..|+.+.+.+...++   .......+.+...++|.+++.+.+++=.  ...+.+.+...|+++..
T Consensus        20 ~~i~~~~~~~g~~~~~~~~~~~~---~~~~~~~~~l~~~~~dgiii~~~~~~~~--~~~~~~~~ipvv~~~~~   87 (269)
T cd06288          20 LGAQDAAREHGYLLLVVNTGGDD---ELEAEAVEALLDHRVDGIIYATMYHREV--TLPPELLSVPTVLLNCY   87 (269)
T ss_pred             HHHHHHHHHCCCEEEEEeCCCCH---HHHHHHHHHHHHcCCCEEEEecCCCChh--HHHHHhcCCCEEEEecc
Confidence            36677888899998887655543   2233444445578999999998654422  22346689999999864

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.

>TIGR02726 phenyl_P_delta phenylphosphate carboxylase, delta subunit

Probab=83.59  E-value=7.7  Score=30.89  Aligned_cols=78  Identities=13%  Similarity=-0.009  Sum_probs=45.7

Q ss_pred             cCCCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCC---eEEEEcCC-C
Q 045172           61 VGYGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWL---KMVVVGDM-S  136 (157)
Q Consensus        61 vgygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l---~tVVVGd~-~  136 (157)
                      .|+|+ .+|++.|+.+-.++.+|+.    ....   .+...|+..+.-..- ++-..+...+..-|+   .++.|||+ +
T Consensus        39 D~~~~-~~L~~~Gi~laIiT~k~~~----~~~~---~l~~lgi~~~f~~~k-pkp~~~~~~~~~l~~~~~ev~~iGD~~n  109 (169)
T TIGR02726        39 DGMGV-IVLQLCGIDVAIITSKKSG----AVRH---RAEELKIKRFHEGIK-KKTEPYAQMLEEMNISDAEVCYVGDDLV  109 (169)
T ss_pred             hHHHH-HHHHHCCCEEEEEECCCcH----HHHH---HHHHCCCcEEEecCC-CCHHHHHHHHHHcCcCHHHEEEECCCHH
Confidence            34444 4789999999999999982    2222   233456654444332 222344444444555   59999998 5


Q ss_pred             chHHHhhhhcc
Q 045172          137 DGALKRIANAF  147 (157)
Q Consensus       137 ~~~L~r~AD~~  147 (157)
                      |-...+.|.+.
T Consensus       110 Di~~~~~ag~~  120 (169)
T TIGR02726       110 DLSMMKRVGLA  120 (169)
T ss_pred             HHHHHHHCCCe
Confidence            54455555443

Members of this protein family are the alpha subunit of phenylphosphate carboxylase. Phenol (methyl-benzene) is converted to phenylphosphate, then para-carboxylated by this four-subunit enzyme, with the release of phosphate, to 4-hydroxybenzoate. The enzyme contains neither biotin nor thiamin pyrophosphate. This delta subunit belongs to HAD family hydrolases.

>cd08185 Fe-ADH1 Iron-containing alcohol dehydrogenases-like

Probab=83.54  E-value=7.7  Score=33.87  Aligned_cols=79  Identities=13%  Similarity=0.047  Sum_probs=56.5

Q ss_pred             cHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEE--EcCCcchH---HHHHHHHHcCCeEEE-EcCCCch
Q 045172           65 FADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVV--VSDDSDFV---EVFQEATLRWLKMVV-VGDMSDG  138 (157)
Q Consensus        65 la~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvL--VSDDsDF~---~~lr~Arer~l~tVV-VGd~~~~  138 (157)
                      |..++++.|=.|-.|.|+-......+..++.+.+...|+++.+.  |..++.+.   ++++.+|+.+...|| ||.++..
T Consensus        17 l~~~~~~~g~r~livt~~~~~~~~g~~~~v~~~L~~~~~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IiavGGGS~i   96 (380)
T cd08185          17 LGEEALKPGKKALIVTGNGSSKKTGYLDRVIELLKQAGVEVVVFDKVEPNPTTTTVMEGAALAREEGCDFVVGLGGGSSM   96 (380)
T ss_pred             HHHHHHhcCCeEEEEeCCCchhhccHHHHHHHHHHHcCCeEEEeCCccCCCCHHHHHHHHHHHHHcCCCEEEEeCCccHH
Confidence            55677776766777787654334678888999997778887665  55566666   566788888998888 9998654


Q ss_pred             HHHhh
Q 045172          139 ALKRI  143 (157)
Q Consensus       139 ~L~r~  143 (157)
                      .....
T Consensus        97 D~aK~  101 (380)
T cd08185          97 DTAKA  101 (380)
T ss_pred             HHHHH
Confidence            44444

Iron-containing alcohol dehydrogenases-like (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 fold and is a member of the iron-containing alcohol dehydrogenase-like family. They are distinct from other alcohol dehydrogenases which contain different protein domains. Proteins of this family have not been characterized. Their specific function is unknown. They are present in bacteria and archaea.

>cd06269 PBP1_glutamate_receptors_like Family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases such as the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein (LIVBP)-like domain of the ionotropic glutamate receptors

Probab=83.46  E-value=8.7  Score=29.52  Aligned_cols=69  Identities=19%  Similarity=0.271  Sum_probs=46.2

Q ss_pred             cHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCC---eEEEEcCC
Q 045172           65 FADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWL---KMVVVGDM  135 (157)
Q Consensus        65 la~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l---~tVVVGd~  135 (157)
                      +...++..|+.|..+..-|... ......+.++. ..+.+.+++.+...+...+++.|++.|+   ..+++.+.
T Consensus       160 ~~~~~~~~~~~v~~~~~~~~~~-~~~~~~l~~l~-~~~~~viv~~~~~~~~~~~l~~a~~~g~~~~~~~i~~~~  231 (298)
T cd06269         160 LEEELEKNGICVAFVESIPDGS-EDIRRLLKELK-SSTARVIVVFSSEEDALRLLEEAVELGMMTGYHWIITDL  231 (298)
T ss_pred             HHHHHHHCCeeEEEEEEcCCCH-HHHHHHHHHHH-hcCCcEEEEEechHHHHHHHHHHHHcCCCCCeEEEEECh
Confidence            3445556788888776655432 22333333333 4566888888888999999999999988   66666665

This CD represents the ligand-binding domain of the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases such as the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein (LIVBP)-like domain of the ionotropic glutamate receptors, all of which are structurally similar and related to the periplasmic-binding fold type I family. The family C GPCRs consist of metabotropic glutamate receptor (mGluR) receptors, a calcium-sensing receptor (CaSR), gamma-aminobutyric receptors (GABAb), the promiscuous L-alpha-amino acid receptor GPR6A, families of taste and pheromone receptors, and orphan receptors. Truncated splicing va

>cd06375 PBP1_mGluR_groupII Ligand binding domain of the group II metabotropic glutamate receptor

Probab=83.28  E-value=5.1  Score=35.70  Aligned_cols=66  Identities=12%  Similarity=0.085  Sum_probs=46.0

Q ss_pred             HHHHhhceEEEE---ecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcC
Q 045172           67 DELKRAWFWVRM---VLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGD  134 (157)
Q Consensus        67 ~eLrRAGv~V~~---V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd  134 (157)
                      .++++.|+-|-.   ++..|...|.  ...+.++....+.+.||+.+...+...+++.|++.|+..+.||-
T Consensus       196 ~~~~~~gi~i~~~~~i~~~~~~~d~--~~~l~~l~~~~~a~vVvl~~~~~~~~~ll~~a~~~g~~~~wigs  264 (458)
T cd06375         196 QEARLRNICIATSEKVGRSADRKSY--DSVIRKLLQKPNARVVVLFTRSEDARELLAAAKRLNASFTWVAS  264 (458)
T ss_pred             HHHHHCCeeEEEEEEecCCCCHHHH--HHHHHHHhccCCCEEEEEecChHHHHHHHHHHHHcCCcEEEEEe
Confidence            557778977643   4444444343  33333333235889999999999999999999999999766754

Ligand binding domain of the group II metabotropic glutamate receptor, a family that contains mGlu2R and mGlu3R, all of which inhibit adenylyl cyclase. The metabotropic glutamate receptor is a member of the family C of G-protein-coupled receptors that transduce extracellular signals into G-protein activation and ultimately into intracellular responses. The mGluRs are classified into three groups which comprise eight subtypes

>PLN02770 haloacid dehalogenase-like hydrolase family protein

Probab=83.21  E-value=11  Score=30.78  Aligned_cols=39  Identities=21%  Similarity=0.147  Sum_probs=26.7

Q ss_pred             hHHHHHHHHhhcCcccC-CCcHHHHHhhceEEEEecCCCc
Q 045172           46 MEKNKMAASAILTPKVG-YGFADELKRAWFWVRMVLVKPQ   84 (157)
Q Consensus        46 ~~kY~~Aar~~l~pkvg-ygla~eLrRAGv~V~~V~dkpq   84 (157)
                      ...|+......+.|--| ..+-..|+..|+.+=.++.++.
T Consensus        96 ~~~y~~~~~~~~~l~pgv~e~L~~L~~~g~~l~I~Tn~~~  135 (248)
T PLN02770         96 EALFRKLASEQLKPLNGLYKLKKWIEDRGLKRAAVTNAPR  135 (248)
T ss_pred             HHHHHHHHHhcCCcCccHHHHHHHHHHcCCeEEEEeCCCH
Confidence            34455544444555555 5566678889999999999986

>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=83.11  E-value=3.4  Score=33.29  Aligned_cols=63  Identities=13%  Similarity=0.049  Sum_probs=46.5

Q ss_pred             CCCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           62 GYGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        62 gygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      -.|+..+++..|+.+-+.+...+ .+         .+...++|.+++++.+.+- +.++.+.+.+..+|+||..
T Consensus        26 ~~~i~~~~~~~gy~~~~~~~~~~-~~---------~l~~~~vdgiIi~~~~~~~-~~~~~l~~~~iPvV~i~~~   88 (269)
T cd06287          26 AAAAAESALERGLALCLVPPHEA-DS---------PLDALDIDGAILVEPMADD-PQVARLRQRGIPVVSIGRP   88 (269)
T ss_pred             HHHHHHHHHHCCCEEEEEeCCCc-hh---------hhhccCcCeEEEecCCCCC-HHHHHHHHcCCCEEEeCCC
Confidence            36888999999999988754321 11         2336799999999865443 5667778889999999864

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.

>cd08188 Fe-ADH4 Iron-containing alcohol dehydrogenases-like

Probab=82.72  E-value=6  Score=34.68  Aligned_cols=88  Identities=15%  Similarity=0.091  Sum_probs=56.3

Q ss_pred             HhhcCcccCCC------cHHHHHhhce-EEEEecCCCccHHHHHHHHHHHHhhccCcceEEE--EcCCcchHH---HHHH
Q 045172           54 SAILTPKVGYG------FADELKRAWF-WVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVV--VSDDSDFVE---VFQE  121 (157)
Q Consensus        54 r~~l~pkvgyg------la~eLrRAGv-~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvL--VSDDsDF~~---~lr~  121 (157)
                      |...+|++-||      +..+|++-|. .|-.|.| +...+..+..++.+.+...|+++.+.  |..++....   .+..
T Consensus         2 ~~~~~~~i~~G~g~l~~l~~~l~~~g~~~~livt~-~~~~~~~~~~~v~~~L~~~~~~~~~~~~v~~~p~~~~v~~~~~~   80 (377)
T cd08188           2 RKFVAPEIIFGRGALKLAGRYARRLGAKKVLLVSD-PGVIKAGWVDRVIESLEEAGLEYVVFSDVSPNPRDEEVMAGAEL   80 (377)
T ss_pred             CCccCCceEECcCHHHHHHHHHHHcCCCeEEEEeC-cchhhCccHHHHHHHHHHcCCeEEEeCCCCCCCCHHHHHHHHHH
Confidence            45567777665      4456666663 4455666 44445556777888887778877654  445566654   4677


Q ss_pred             HHHcCCeEEE-EcCCCchHHHh
Q 045172          122 ATLRWLKMVV-VGDMSDGALKR  142 (157)
Q Consensus       122 Arer~l~tVV-VGd~~~~~L~r  142 (157)
                      +++.+...|| ||.++......
T Consensus        81 ~~~~~~d~IIaiGGGsviD~AK  102 (377)
T cd08188          81 YLENGCDVIIAVGGGSPIDCAK  102 (377)
T ss_pred             HHhcCCCEEEEeCCchHHHHHH
Confidence            7887777666 88886544443

Iron-containing alcohol dehydrogenase-like. 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 belonged to the alcohol dehydrogenase-like superfamily. They are distinct from other alcohol dehydrogenases which contain different protein domains. Proteins of this family have not been characterized. Their specific function is unknown.

>cd06350 PBP1_GPCR_family_C_like Ligand-binding domain of membrane-bound glutamate receptors that mediate excitatory transmission on the cellular surface through initial binding of glutamate and are categorized into ionotropic glutamate receptors (iGluRs) and metabotropic glutamate receptors (mGluRs)

Probab=82.56  E-value=7.2  Score=31.90  Aligned_cols=67  Identities=19%  Similarity=0.311  Sum_probs=44.5

Q ss_pred             HHHHHhhceEEEEecCCCc---cHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCC--eEEEEcCC
Q 045172           66 ADELKRAWFWVRMVLVKPQ---DADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWL--KMVVVGDM  135 (157)
Q Consensus        66 a~eLrRAGv~V~~V~dkpq---AAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l--~tVVVGd~  135 (157)
                      ..+++..|+-|-....-|.   ..|  +...+..+. ..+.+.+++.+...|...+++.|++.|+  ..++++++
T Consensus       181 ~~~~~~~gi~v~~~~~~~~~~~~~d--~~~~l~~l~-~~~~~vvv~~~~~~~~~~~~~~a~~~g~~~~~~i~~~~  252 (348)
T cd06350         181 EEELEKNGICIAFVEAIPPSSTEED--IKRILKKLK-SSTARVIVVFGDEDDALRLFCEAYKLGMTGKYWIISTD  252 (348)
T ss_pred             HHHHHHCCCcEEEEEEccCCCcHHH--HHHHHHHHH-hCCCcEEEEEeCcHHHHHHHHHHHHhCCCCeEEEEEcc
Confidence            3456667766654332232   344  334444444 5677999999999999999999999998  34455554

Ligand-binding domain of membrane-bound glutamate receptors that mediate excitatory transmission on the cellular surface through initial binding of glutamate and are categorized into ionotropic glutamate receptors (iGluRs) and metabotropic glutamate receptors (mGluRs). The metabotropic glutamate receptors (mGluR) are key receptors in the modulation of excitatory synaptic transmission in the central nervous system. The mGluRs are coupled to G proteins and are thus distinct from the iGluRs which internally contain ligand-gated ion channels. The mGluR structure is divided into three regions: the extracellular region, the seven-spanning transmembrane region and the cytoplasmic region. The extr

>cd06335 PBP1_ABC_ligand_binding_like_2 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=82.53  E-value=3.3  Score=34.53  Aligned_cols=67  Identities=9%  Similarity=0.067  Sum_probs=49.4

Q ss_pred             cHHHHHhhceEEEEec-CCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcC
Q 045172           65 FADELKRAWFWVRMVL-VKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGD  134 (157)
Q Consensus        65 la~eLrRAGv~V~~V~-dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd  134 (157)
                      +..+|++.|+.|-.+. -.|.+.|.  ...+.++. +.+.+.|++.+...+++.+++.+++.|++.-++|.
T Consensus       158 ~~~~~~~~G~~v~~~~~~~~~~~d~--s~~i~~i~-~~~~d~v~~~~~~~~~~~~~~~~~~~g~~~~~~~~  225 (347)
T cd06335         158 LTAALAARGLKPVAVEWFNWGDKDM--TAQLLRAK-AAGADAIIIVGNGPEGAQIANGMAKLGWKVPIISH  225 (347)
T ss_pred             HHHHHHHcCCeeEEEeeecCCCccH--HHHHHHHH-hCCCCEEEEEecChHHHHHHHHHHHcCCCCcEecc
Confidence            3467788898865432 22345554  35555555 57899999999999999999999999998766663

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.

>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed

Probab=82.52  E-value=2.4  Score=36.63  Aligned_cols=49  Identities=10%  Similarity=0.024  Sum_probs=41.8

Q ss_pred             CcceEEEEcCC---cchHHHHHHHHHcCCeEEEEcCCCchHHHhhhhcccch
Q 045172          102 RFGCLVVVSDD---SDFVEVFQEATLRWLKMVVVGDMSDGALKRIANAFFSW  150 (157)
Q Consensus       102 ~v~clvLVSDD---sDF~~~lr~Arer~l~tVVVGd~~~~~L~r~AD~~fsW  150 (157)
                      .=|++|.+|-.   .+..+.++.|+++|.+||.|-...+..|.+.||.-+..
T Consensus       131 ~~DvvI~IS~SG~T~~vi~al~~Ak~~Ga~tI~IT~~~~s~La~~aD~~I~~  182 (299)
T PRK05441        131 AKDVVVGIAASGRTPYVIGALEYARERGALTIGISCNPGSPLSKEADIAIEV  182 (299)
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHHHCCCeEEEEECCCCChhhHhCCEEEEc
Confidence            34899999865   67888999999999999999988678999999998743

>TIGR00274 N-acetylmuramic acid 6-phosphate etherase

Probab=82.46  E-value=2.4  Score=36.65  Aligned_cols=49  Identities=12%  Similarity=0.016  Sum_probs=41.3

Q ss_pred             CcceEEEEcCC---cchHHHHHHHHHcCCeEEEEcCCCchHHHhhhhcccch
Q 045172          102 RFGCLVVVSDD---SDFVEVFQEATLRWLKMVVVGDMSDGALKRIANAFFSW  150 (157)
Q Consensus       102 ~v~clvLVSDD---sDF~~~lr~Arer~l~tVVVGd~~~~~L~r~AD~~fsW  150 (157)
                      .=|++|.+|-.   .+..++++.|+++|.+|+.|.......|.+.||+.+..
T Consensus       126 ~~DvvI~IS~SG~T~~vi~al~~Ak~~Ga~tIaIT~~~~s~La~~aD~~I~~  177 (291)
T TIGR00274       126 KNDVVVGIAASGRTPYVIAGLQYARSLGALTISIACNPKSAASEIADIAIET  177 (291)
T ss_pred             CCCEEEEEeCCCCcHHHHHHHHHHHHCCCeEEEEECCCCChhHHhCCEEEec
Confidence            34999999965   56678899999999999999887667899999998854

This protein, MurQ, is involved in recycling components of the bacterial murein sacculus turned over during cell growth. The cell wall metabolite anhydro-N-acetylmuramic acid (anhMurNAc) is converted by a kinase, AnmK, to MurNAc-phosphate, then converted to N-acetylglucosamine-phosphate by this etherase, called MurQ. This family of proteins is similar to the C-terminal half of a number of vertebrate glucokinase regulator proteins and contains a Prosite pattern which is shared by this group of proteins in a region of local similarity.

>TIGR01422 phosphonatase phosphonoacetaldehyde hydrolase

Probab=82.33  E-value=18  Score=29.02  Aligned_cols=74  Identities=15%  Similarity=0.060  Sum_probs=42.7

Q ss_pred             cCcccC-CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccC--cceEEEEcCCc-----chHHHHHHHHHcCCe
Q 045172           57 LTPKVG-YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRR--FGCLVVVSDDS-----DFVEVFQEATLRWLK  128 (157)
Q Consensus        57 l~pkvg-ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~--v~clvLVSDDs-----DF~~~lr~Arer~l~  128 (157)
                      +.|--| ..+-..|+..|+.+=.++.+|..    ....+++.+.-.+  ++ .|+.||+.     +=..+++.++.-|+.
T Consensus        98 ~~~~pg~~e~L~~L~~~g~~l~IvT~~~~~----~~~~~l~~~gl~~~f~d-~ii~~~~~~~~KP~p~~~~~a~~~l~~~  172 (253)
T TIGR01422        98 SSPIPGVIEVIAYLRARGIKIGSTTGYTRE----MMDVVAPEAALQGYRPD-YNVTTDDVPAGRPAPWMALKNAIELGVY  172 (253)
T ss_pred             CccCCCHHHHHHHHHHCCCeEEEECCCcHH----HHHHHHHHHHhcCCCCc-eEEccccCCCCCCCHHHHHHHHHHcCCC
Confidence            445444 45667888899999999999862    2222332221112  13 33445442     323445555666763


Q ss_pred             ----EEEEcCC
Q 045172          129 ----MVVVGDM  135 (157)
Q Consensus       129 ----tVVVGd~  135 (157)
                          +++|||+
T Consensus       173 ~~~~~l~IGDs  183 (253)
T TIGR01422       173 DVAACVKVGDT  183 (253)
T ss_pred             CchheEEECCc
Confidence                8999998

This enzyme is a member of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases (pfam00702), and contains a modified version of the conserved catalytic motifs of that superfamily: the first motif is usually DxDx(T/V), here it is DxAxT, and in the third motif the normal conserved lysine is instead an arginine. Additionally, the enzyme contains a unique conserved catalytic lysine (B. cereus pos. 53) which is involved in the binding and activation of the substrate through the formation of a Schiff base. The substrate of this enzyme is the product of 2-aminoethylphosphonate (AEP) transaminase, phosphonoacetaldehyde. This degradation pathway for AEP may be related to its toxic properties which are utilized by microorganisms as a chemical warfare agent.

>PRK09860 putative alcohol dehydrogenase; Provisional

Probab=81.97  E-value=6.5  Score=34.70  Aligned_cols=77  Identities=8%  Similarity=-0.007  Sum_probs=53.5

Q ss_pred             cHHHHHhhce-EEEEecCCCccHHHHHHHHHHHHhhccCcceEEE--EcCCcchH---HHHHHHHHcCCeEEE-EcCCCc
Q 045172           65 FADELKRAWF-WVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVV--VSDDSDFV---EVFQEATLRWLKMVV-VGDMSD  137 (157)
Q Consensus        65 la~eLrRAGv-~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvL--VSDDsDF~---~~lr~Arer~l~tVV-VGd~~~  137 (157)
                      |..++++-|. .|-.|.| +......+..++.+.+...|+++.+.  |..++.+.   ..++.+|+.+...|| ||.++.
T Consensus        22 l~~~~~~~g~~~~livt~-~~~~~~g~~~~v~~~L~~~~i~~~~f~~v~~np~~~~v~~~~~~~~~~~~D~IiaiGGGS~  100 (383)
T PRK09860         22 AMNMMADYGFTRTLIVTD-NMLTKLGMAGDVQKALEERNIFSVIYDGTQPNPTTENVAAGLKLLKENNCDSVISLGGGSP  100 (383)
T ss_pred             HHHHHHhcCCCEEEEEcC-cchhhCccHHHHHHHHHHcCCeEEEeCCCCCCcCHHHHHHHHHHHHHcCCCEEEEeCCchH
Confidence            5677888784 5556677 44444667778899887788876544  54466666   667788889999888 999865


Q ss_pred             hHHHh
Q 045172          138 GALKR  142 (157)
Q Consensus       138 ~~L~r  142 (157)
                      -....
T Consensus       101 iD~AK  105 (383)
T PRK09860        101 HDCAK  105 (383)
T ss_pred             HHHHH
Confidence            43333

>cd06333 PBP1_ABC-type_HAAT_like Type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids

Probab=81.84  E-value=3.6  Score=33.31  Aligned_cols=68  Identities=7%  Similarity=-0.069  Sum_probs=46.9

Q ss_pred             CcHHHHHhhceEEEEecC-CCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcC
Q 045172           64 GFADELKRAWFWVRMVLV-KPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGD  134 (157)
Q Consensus        64 gla~eLrRAGv~V~~V~d-kpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd  134 (157)
                      ++...+++.|+.+-.... .+.+.|  ....+.+.+ ..+.|+|++.+++.+-..+++.+++.|++.=++|-
T Consensus       152 ~~~~~~~~~G~~v~~~~~~~~~~~d--~~~~~~~l~-~~~pdaIi~~~~~~~~~~~~~~l~~~g~~~p~~~~  220 (312)
T cd06333         152 ELKALAPKYGIEVVADERYGRTDTS--VTAQLLKIR-AARPDAVLIWGSGTPAALPAKNLRERGYKGPIYQT  220 (312)
T ss_pred             HHHHHHHHcCCEEEEEEeeCCCCcC--HHHHHHHHH-hCCCCEEEEecCCcHHHHHHHHHHHcCCCCCEEee
Confidence            345667777876543222 233444  344566666 46789999999998888899999999998766643

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

>PF02602 HEM4: Uroporphyrinogen-III synthase HemD; InterPro: IPR003754 Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway []

Probab=81.76  E-value=0.92  Score=35.64  Aligned_cols=77  Identities=19%  Similarity=0.239  Sum_probs=53.1

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHH-----HcCCeEEEEcCCCc
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEAT-----LRWLKMVVVGDMSD  137 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Ar-----er~l~tVVVGd~~~  137 (157)
                      ..|...|+.+|+.|..+.-=-. .......++.+.+....++++++-|. +-+..+++...     -.++..++||..+-
T Consensus       130 ~~l~~~L~~~g~~v~~~~vY~~-~~~~~~~~~~~~l~~~~~~~v~ftS~-~~~~~~~~~~~~~~~~~~~~~~~~ig~~ta  207 (231)
T PF02602_consen  130 PDLPEKLREAGIEVTEVIVYET-PPEELSPELKEALDRGEIDAVVFTSP-SAVRAFLELLKKNGALLKRVPIVAIGPRTA  207 (231)
T ss_dssp             HHHHHHHHHTTEEEEEEECEEE-EEHHHHHHHHHHHHHTTTSEEEESSH-HHHHHHHHHSSGHHHHHTTSEEEESSHHHH
T ss_pred             HHHHHHHHHCCCeEEEEEEeec-ccccchHHHHHHHHcCCCCEEEECCH-HHHHHHHHHhHhhhhhhhCCEEEEECHHHH
Confidence            3478899999999988744333 44557778888886667777666555 44555555544     57899999998864


Q ss_pred             hHHH
Q 045172          138 GALK  141 (157)
Q Consensus       138 ~~L~  141 (157)
                      .++.
T Consensus       208 ~~l~  211 (231)
T PF02602_consen  208 KALR  211 (231)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5544

The end-product, uroporphyrinogen III, is used to synthesise a number of important molecules, including vitamin B12, haem, sirohaem, chlorophyll, coenzyme F430 and phytochromobilin []. The first stage in tetrapyrrole synthesis is the synthesis of 5-aminoaevulinic acid ALA via two possible routes: (1) condensation of succinyl CoA and glycine (C4 pathway) using ALA synthase (2.3.1.37 from EC), or (2) decarboxylation of glutamate (C5 pathway) via three different enzymes, glutamyl-tRNA synthetase (6.1.1.17 from EC) to charge a tRNA with glutamate, glutamyl-tRNA reductase (1.2.1.70 from EC) to reduce glutamyl-tRNA to glutamate-1-semialdehyde (GSA), and GSA aminotransferase (5.4.3.8 from EC) to catalyse a transamination reaction to produce ALA. The second stage is to convert ALA to uroporphyrinogen III, the first macrocyclic tetrapyrrolic structure in the pathway. This is achieved by the action of three enzymes in one common pathway: porphobilinogen (PBG) synthase (or ALA dehydratase, 4.2.1.24 from EC) to condense two ALA molecules to generate porphobilinogen; hydroxymethylbilane synthase (or PBG deaminase, 2.5.1.61 from EC) to polymerise four PBG molecules into preuroporphyrinogen (tetrapyrrole structure); and uroporphyrinogen III synthase (4.2.1.75 from EC) to link two pyrrole units together (rings A and D) to yield uroporphyrinogen III. Uroporphyrinogen III is the first branch point of the pathway. To synthesise cobalamin (vitamin B12), sirohaem, and coenzyme F430, uroporphyrinogen III needs to be converted into precorrin-2 by the action of uroporphyrinogen III methyltransferase (2.1.1.107 from EC). To synthesise haem and chlorophyll, uroporphyrinogen III needs to be decarboxylated into coproporphyrinogen III by the action of uroporphyrinogen III decarboxylase (4.1.1.37 from EC) []. This entry represents uroporphyrinogen III synthase (4.2.1.75 from EC) which functions during the second stage of tetrapyrrole biosynthesis. This enzyme catalyses the inversion of the final pyrrole unit (ring D) of the linear tetrapyrrole molecule, linking it to the first pyrrole unit (ring A), thereby generating a large macrocyclic structure called uroporphyrinogen III []. The enzyme folds into two alpha/beta domains connected by a beta-ladder, the active site being located between the two domains []. Congenital erythropoietic porphyria (CEP) is an autosomal recessive inborn error of metabolism that results from the markedly deficient activity of uroporphyrinogen III synthase []. ; GO: 0004852 uroporphyrinogen-III synthase activity, 0033014 tetrapyrrole biosynthetic process; PDB: 1WD7_B 1WCX_A 1WCW_A 3D8R_A 3D8T_B 3D8S_A 3D8N_A 3RE1_A 3MW8_A 3P9Z_A ....

>cd06338 PBP1_ABC_ligand_binding_like_5 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=81.69  E-value=4.6  Score=33.09  Aligned_cols=64  Identities=14%  Similarity=0.016  Sum_probs=45.7

Q ss_pred             HHHHHhhceEEEEe-cCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEE
Q 045172           66 ADELKRAWFWVRMV-LVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVV  132 (157)
Q Consensus        66 a~eLrRAGv~V~~V-~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVV  132 (157)
                      ...|++.|+.|-.. .-.|+..|..  ..+.++. ..+.|.+++.+.+.++..+++.+++.|++.-++
T Consensus       162 ~~~~~~~g~~v~~~~~~~~~~~d~~--~~v~~l~-~~~~d~i~~~~~~~~~~~~~~~~~~~g~~~~~~  226 (345)
T cd06338         162 REKAEAAGLEVVYDETYPPGTADLS--PLISKAK-AAGPDAVVVAGHFPDAVLLVRQMKELGYNPKAL  226 (345)
T ss_pred             HHHHHHcCCEEEEEeccCCCccchH--HHHHHHH-hcCCCEEEECCcchhHHHHHHHHHHcCCCCCEE
Confidence            34678889887542 3334555633  3444444 688999999999999999999999999874333

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. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT); however their ligand specificity has not been determined experimentally.

>cd05007 SIS_Etherase N-acetylmuramic acid 6-phosphate etherase

Probab=81.37  E-value=3  Score=35.13  Aligned_cols=48  Identities=8%  Similarity=0.070  Sum_probs=40.7

Q ss_pred             CcceEEEEcCC---cchHHHHHHHHHcCCeEEEEcCCCchHHHhhhhcccc
Q 045172          102 RFGCLVVVSDD---SDFVEVFQEATLRWLKMVVVGDMSDGALKRIANAFFS  149 (157)
Q Consensus       102 ~v~clvLVSDD---sDF~~~lr~Arer~l~tVVVGd~~~~~L~r~AD~~fs  149 (157)
                      .=|+++.+|-.   ++..+.++.|+++|.+||.|.......|.+.||.-+.
T Consensus       118 ~~DvvI~IS~SG~T~~vi~al~~Ak~~Ga~~I~It~~~~s~L~~~aD~~I~  168 (257)
T cd05007         118 ERDVVIGIAASGRTPYVLGALRYARARGALTIGIACNPGSPLLQLADIAIA  168 (257)
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHHHCCCeEEEEECCCCChhHHhCCEEEE
Confidence            44899999864   6788889999999999999988767899999998773

Members of this family contain the SIS (Sugar ISomerase) domain. The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. The bacterial cell wall sugar N-acetylmuramic acid carries a unique D-lactyl ether substituent at the C3 position. The etherase catalyzes the cleavage of the lactyl ether bond of N-acetylmuramic acid 6-phosphate.

>PRK13222 phosphoglycolate phosphatase; Provisional

Probab=81.10  E-value=10  Score=29.26  Aligned_cols=85  Identities=22%  Similarity=0.216  Sum_probs=44.5

Q ss_pred             cCcccC-CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhh-ccCcceEEEEcCC-----cc---hHHHHHHHHHcC
Q 045172           57 LTPKVG-YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVD-KRRFGCLVVVSDD-----SD---FVEVFQEATLRW  126 (157)
Q Consensus        57 l~pkvg-ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~-~r~v~clvLVSDD-----sD---F~~~lr~Arer~  126 (157)
                      ..|--| ..+-..|+..|+.+-+++..+..    ...++.+.+. ..-+++ ++-+++     ++   |..+++......
T Consensus        92 ~~~~~g~~~~l~~l~~~g~~~~i~S~~~~~----~~~~~l~~~~l~~~f~~-~~~~~~~~~~kp~~~~~~~~~~~~~~~~  166 (226)
T PRK13222         92 SRLYPGVKETLAALKAAGYPLAVVTNKPTP----FVAPLLEALGIADYFSV-VIGGDSLPNKKPDPAPLLLACEKLGLDP  166 (226)
T ss_pred             CccCCCHHHHHHHHHHCCCeEEEEeCCCHH----HHHHHHHHcCCccCccE-EEcCCCCCCCCcChHHHHHHHHHcCCCh
Confidence            334444 45666778889999999988752    2223333221 112343 222222     12   333333333333


Q ss_pred             CeEEEEcCC-CchHHHhhhhc
Q 045172          127 LKMVVVGDM-SDGALKRIANA  146 (157)
Q Consensus       127 l~tVVVGd~-~~~~L~r~AD~  146 (157)
                      -++++|||+ ++-...+.|++
T Consensus       167 ~~~i~igD~~~Di~~a~~~g~  187 (226)
T PRK13222        167 EEMLFVGDSRNDIQAARAAGC  187 (226)
T ss_pred             hheEEECCCHHHHHHHHHCCC
Confidence            468999998 55555555655

>cd06340 PBP1_ABC_ligand_binding_like_6 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=80.93  E-value=4  Score=34.00  Aligned_cols=71  Identities=10%  Similarity=0.110  Sum_probs=49.8

Q ss_pred             hcCcccCCCc------HHHHHhhceEEEEecCCC-ccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCe
Q 045172           56 ILTPKVGYGF------ADELKRAWFWVRMVLVKP-QDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLK  128 (157)
Q Consensus        56 ~l~pkvgygl------a~eLrRAGv~V~~V~dkp-qAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~  128 (157)
                      ++.+...||-      ...++++|+.|-.+..-| .+.|..  .++.++. ..+.|.|++....++...+++.+++.|+.
T Consensus       149 ~l~~~~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~~d~~--~~i~~l~-~~~~d~v~~~~~~~~~~~~~~~~~~~G~~  225 (347)
T cd06340         149 LVHEDTEFGTSVAEAIKKFAKERGFEIVEDISYPANARDLT--SEVLKLK-AANPDAILPASYTNDAILLVRTMKEQRVE  225 (347)
T ss_pred             EEecCchHhHHHHHHHHHHHHHcCCEEEEeeccCCCCcchH--HHHHHHH-hcCCCEEEEcccchhHHHHHHHHHHcCCC
Confidence            4445445552      346888998886543333 344443  3444444 57899999999999999999999999996


Q ss_pred             E
Q 045172          129 M  129 (157)
Q Consensus       129 t  129 (157)
                      .
T Consensus       226 ~  226 (347)
T cd06340         226 P  226 (347)
T ss_pred             C
Confidence            4

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. 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); however their ligand specificity has not been determined experimentally.

>cd06363 PBP1_Taste_receptor Ligand-binding domain of the T1R taste receptor

Probab=80.92  E-value=7.5  Score=33.54  Aligned_cols=69  Identities=12%  Similarity=0.187  Sum_probs=47.0

Q ss_pred             cHHHHHhhceEEEEecCCC--ccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCC-eEEEEcC
Q 045172           65 FADELKRAWFWVRMVLVKP--QDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWL-KMVVVGD  134 (157)
Q Consensus        65 la~eLrRAGv~V~~V~dkp--qAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l-~tVVVGd  134 (157)
                      +..+|++.|+-|-...--|  +..+......+.++. ..+.+.|++.++.++-..+++.|++.|+ ..+.||.
T Consensus       196 ~~~~l~~~gi~i~~~~~~~~~~~~~~d~~~~l~~i~-~~~~dvIil~~~~~~~~~il~qa~~~g~~~~~~i~~  267 (410)
T cd06363         196 FSELIANTGICIAYQGLIPLDTDPETDYQQILKQIN-QTKVNVIVVFASRQPAEAFFNSVIQQNLTGKVWIAS  267 (410)
T ss_pred             HHHHHHHCCeEEEEEEEecCCCchHHHHHHHHHHHh-cCCCeEEEEEcChHHHHHHHHHHHhcCCCCCEEEEe
Confidence            3467888897664322111  112334445555555 6789999999999999999999999999 4444553

Ligand-binding domain of the T1R taste receptor. The T1R is a member of the family C receptors within the G-protein coupled receptor superfamily, which also includes the metabotropic glutamate receptors, GABAb receptors, the calcium-sensing receptor (CaSR), the V2R pheromone receptors, and a small group of uncharacterized orphan receptors.

>cd06332 PBP1_aromatic_compounds_like Type I periplasmic binding proteins of active transport systems that are predicted to be involved in transport of aromatic compounds such as 2-nitrobenzoic acid and alkylbenzenes

Probab=80.87  E-value=5.5  Score=32.07  Aligned_cols=59  Identities=14%  Similarity=0.022  Sum_probs=42.1

Q ss_pred             ceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCC--eEEEEcC
Q 045172           73 WFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWL--KMVVVGD  134 (157)
Q Consensus        73 Gv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l--~tVVVGd  134 (157)
                      |..|......+...|.+  ..+..+. .-+.|.|++.++..+-..+++.+++.|+  +.-++|-
T Consensus       160 ~~~~~~~~~~~~~~d~~--~~i~~l~-~~~~d~i~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~  220 (333)
T cd06332         160 GEVVEEVYTPLGQLDFS--AELAQIR-AAKPDAVFVFLPGGMAVNFVKQYDQAGLKKKIPLYGP  220 (333)
T ss_pred             EEEeeEEecCCCCcchH--HHHHHHH-hcCCCEEEEecccchHHHHHHHHHHcCcccCCceecc
Confidence            55555545555666654  2344433 6788999999888999999999999999  7656664

This group includes the type I periplasmic binding proteins of active transport systems that are predicted to be involved in transport of aromatic compounds such as 2-nitrobenzoic acid and alkylbenzenes; their substrate specificities are not well characterized, however. Members also exhibit close similarity to active transport systems for short chain amides and/or urea found in bacteria and archaea.

>TIGR01261 hisB_Nterm histidinol-phosphatase

Probab=80.75  E-value=8.4  Score=30.12  Aligned_cols=87  Identities=21%  Similarity=0.210  Sum_probs=54.1

Q ss_pred             cCcccC-CCcHHHHHhhceEEEEecCCC--------ccHHHHHHHHHHHHhhccCcceE--EEEc-----CCcch----H
Q 045172           57 LTPKVG-YGFADELKRAWFWVRMVLVKP--------QDADVLLRNYMVAMVDKRRFGCL--VVVS-----DDSDF----V  116 (157)
Q Consensus        57 l~pkvg-ygla~eLrRAGv~V~~V~dkp--------qAAD~AL~~~~~~~~~~r~v~cl--vLVS-----DDsDF----~  116 (157)
                      +.|--| ..+-..|+..|+.+=.|+.++        .+...+....+.+++...|+. |  +.+|     ++...    .
T Consensus        28 ~~~~pgv~e~L~~L~~~g~~l~IvSN~~g~~~~~~~~~~~~~~~~~~~~~l~~~gl~-fd~ii~~~~~~~~~~~~~KP~~  106 (161)
T TIGR01261        28 LRFEKGVIPALLKLKKAGYKFVMVTNQDGLGTPSFPQADFDGPHNLMLQIFRSQGII-FDDVLICPHFPDDNCDCRKPKI  106 (161)
T ss_pred             eeECCCHHHHHHHHHHCCCeEEEEeCCccccCCcCCHHHHHHHHHHHHHHHHHCCCc-eeEEEECCCCCCCCCCCCCCCH
Confidence            455555 566788999999999999875        233344556677777777887 4  4455     44222    3


Q ss_pred             HHHHHHHH-cCC---eEEEEcCC-CchHHHhhh
Q 045172          117 EVFQEATL-RWL---KMVVVGDM-SDGALKRIA  144 (157)
Q Consensus       117 ~~lr~Are-r~l---~tVVVGd~-~~~~L~r~A  144 (157)
                      +++..+-+ -|+   .++.|||+ +|-...+.|
T Consensus       107 ~~~~~~~~~~~~~~~e~l~IGD~~~Di~~A~~a  139 (161)
T TIGR01261       107 KLLEPYLKKNLIDKARSYVIGDRETDMQLAENL  139 (161)
T ss_pred             HHHHHHHHHcCCCHHHeEEEeCCHHHHHHHHHC
Confidence            45555544 443   48999998 433334433

This model describes histidinol phosphatase. All known examples in the scope of this model are bifunctional proteins with a histidinol phosphatase domain followed by an imidazoleglycerol-phosphate dehydratase domain. These enzymatic domains catalyze the ninth and seventh steps, respectively, of histidine biosynthesis.

>cd05017 SIS_PGI_PMI_1 The members of this protein family contain the SIS (Sugar ISomerase) domain and have both the phosphoglucose isomerase (PGI) and the phosphomannose isomerase (PMI) functions

Probab=80.39  E-value=4.2  Score=29.61  Aligned_cols=42  Identities=24%  Similarity=0.271  Sum_probs=32.7

Q ss_pred             CcceEEEEcC---CcchHHHHHHHHHcCCeEEEEcCCCchHHHhhhh
Q 045172          102 RFGCLVVVSD---DSDFVEVFQEATLRWLKMVVVGDMSDGALKRIAN  145 (157)
Q Consensus       102 ~v~clvLVSD---DsDF~~~lr~Arer~l~tVVVGd~~~~~L~r~AD  145 (157)
                      .-|+++.+|-   ..+-.+.++.|+++|.++|+|-+.  +.|...||
T Consensus        43 ~~dl~I~iS~SG~t~e~i~~~~~a~~~g~~iI~IT~~--~~l~~~~~   87 (119)
T cd05017          43 RKTLVIAVSYSGNTEETLSAVEQAKERGAKIVAITSG--GKLLEMAR   87 (119)
T ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEeCC--chHHHHHH
Confidence            4478888884   456778888999999999998754  35888887

These functions catalyze the reversible reactions of glucose 6-phosphate to fructose 6-phosphate, and mannose 6-phosphate to fructose 6-phosphate, respectively at an equal rate. This protein contains two SIS domains. This alignment is based on the first SIS domain.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	157
2qip_A	165	Protein of unknown function VPA0982; APC85975, vib	99.46
3jy6_A	276	Transcriptional regulator, LACI family; NYSGXRC, P	95.76
3gbv_A	304	Putative LACI-family transcriptional regulator; NY	95.43
3o74_A	272	Fructose transport system repressor FRUR; dual tra	95.33
3l6u_A	293	ABC-type sugar transport system periplasmic compo;	95.31
3sho_A	187	Transcriptional regulator, RPIR family; structural	95.2
3m9w_A	313	D-xylose-binding periplasmic protein; xylose bindi	95.13
3tb6_A	298	Arabinose metabolism transcriptional repressor; tr	95.09
3g1w_A	305	Sugar ABC transporter; sugar-binding protein, baci	95.07
3l49_A	291	ABC sugar (ribose) transporter, periplasmic substr	95.04
3h75_A	350	Periplasmic sugar-binding domain protein; protein	95.0
1gud_A	288	ALBP, D-allose-binding periplasmic protein; peripl	94.99
8abp_A	306	L-arabinose-binding protein; binding proteins; HET	94.91
3ksm_A	276	ABC-type sugar transport system, periplasmic COMP;	94.84
2fn9_A	290	Ribose ABC transporter, periplasmic ribose-bindin;	94.81
1tjy_A	316	Sugar transport protein; protein-ligand complex, s	94.75
2dri_A	271	D-ribose-binding protein; sugar transport; HET: RI	94.7
3huu_A	305	Transcription regulator like protein; PSI-II, NYSG	94.7
3dbi_A	338	Sugar-binding transcriptional regulator, LACI FAM;	94.68
3k4h_A	292	Putative transcriptional regulator; structural gen	94.63
3uug_A	330	Multiple sugar-binding periplasmic receptor CHVE;	94.56
2fep_A	289	Catabolite control protein A; CCPA, transcriptiona	94.49
2h3h_A	313	Sugar ABC transporter, periplasmic sugar-binding p	94.42
3e3m_A	355	Transcriptional regulator, LACI family; structural	94.38
2vk2_A	306	YTFQ, ABC transporter periplasmic-binding protein	94.37
3hcw_A	295	Maltose operon transcriptional repressor; RNA-bind	94.37
3d8u_A	275	PURR transcriptional regulator; APC91343.1, vibrio	94.22
2ioy_A	283	Periplasmic sugar-binding protein; ribose binding	94.2
2rgy_A	290	Transcriptional regulator, LACI family; 11011J, NY	94.03
3egc_A	291	Putative ribose operon repressor; structural genom	93.96
3kjx_A	344	Transcriptional regulator, LACI family; LACL famil	93.87
2fvy_A	309	D-galactose-binding periplasmic protein; periplasm	93.85
3h5o_A	339	Transcriptional regulator GNTR; transcription regu	93.78
3brq_A	296	HTH-type transcriptional regulator ASCG; transcrip	93.76
3rot_A	297	ABC sugar transporter, periplasmic sugar binding;	93.73
1jx6_A	342	LUXP protein; protein-ligand complex, signaling pr	93.68
3kke_A	303	LACI family transcriptional regulator; structural	93.59
2rjo_A	332	Twin-arginine translocation pathway signal protei;	93.32
3d02_A	303	Putative LACI-type transcriptional regulator; peri	93.11
2o20_A	332	Catabolite control protein A; CCPA, transcriptiona	93.1
2l82_A	162	Designed protein OR32; structural genomics, northe	92.95
3c3k_A	285	Alanine racemase; structural genomics, protein str	92.89
3mmz_A	176	Putative HAD family hydrolase; structural genomics	92.88
3gv0_A	288	Transcriptional regulator, LACI family; transcript	92.85
3e61_A	277	Putative transcriptional repressor of ribose OPER;	92.76
2iks_A	293	DNA-binding transcriptional dual regulator; escher	92.7
3bil_A	348	Probable LACI-family transcriptional regulator; st	92.67
3qk7_A	294	Transcriptional regulators; structural genomics, N	92.65
1tk9_A	188	Phosphoheptose isomerase 1; lipopolysaccharide bio	92.38
2hsg_A	332	Glucose-resistance amylase regulator; CCPA, transc	92.37
3o1i_D	304	Periplasmic protein TORT; ligand free, two compone	92.27
3bbl_A	287	Regulatory protein of LACI family; protein structu	92.26
3k9c_A	289	Transcriptional regulator, LACI family protein; PS	92.26
2xbl_A	198	Phosphoheptose isomerase; capsule; HET: M7P PGE PG	92.16
2x7x_A	325	Sensor protein; transferase, sensor histidine kina	92.01
3clk_A	290	Transcription regulator; 11017J, PSI-II, NYSGXRC,	91.87
1dbq_A	289	Purine repressor; transcription regulation, DNA-bi	91.85
2yj3_A	263	Copper-transporting ATPase; hydrolase, P-type ATPa	91.1
3brs_A	289	Periplasmic binding protein/LACI transcriptional;	91.59
3l8h_A	179	Putative haloacid dehalogenase-like hydrolase; HAD	91.44
1m3s_A	186	Hypothetical protein YCKF; structural genomics, PS	91.05
1x92_A	199	APC5045, phosphoheptose isomerase; midwest centre	90.97
1jeo_A	180	MJ1247, hypothetical protein MJ1247; RUMP pathway,	90.74
2i2w_A	212	Phosphoheptose isomerase; lipopolysaccharide biosy	90.63
1vim_A	200	Hypothetical protein AF1796; structural genomics,	90.62
3fxa_A	201	SIS domain protein; structural genomics, joint cen	90.18
2xhz_A	183	KDSD, YRBH, arabinose 5-phosphate isomerase; lipop	89.96
2yva_A	196	DNAA initiator-associating protein DIAA; intermole	89.81
3j08_A	645	COPA, copper-exporting P-type ATPase A; copper tra	89.81
3miz_A	301	Putative transcriptional regulator protein, LACI f	89.78
3skx_A	280	Copper-exporting P-type ATPase B; P1B-ATPase, ATP	89.68
3e8m_A	164	Acylneuraminate cytidylyltransferase; 2-keto-3-deo	89.66
3ij5_A	211	3-deoxy-D-manno-octulosonate 8-phosphate phosphat;	89.64
3a1c_A	287	Probable copper-exporting P-type ATPase A; ATP-bin	89.38
3etn_A	220	Putative phosphosugar isomerase involved in capsu	89.23
3n07_A	195	3-deoxy-D-manno-octulosonate 8-phosphate phosphat;	89.16
3trj_A	201	Phosphoheptose isomerase; lipopolysaccharide biosy	88.84
3hs3_A	277	Ribose operon repressor; PSI-II, NYSGXRC, periplas	88.74
1qpz_A	340	PURA, protein (purine nucleotide synthesis repress	88.48
2h0a_A	276	TTHA0807, transcriptional regulator; repressor, st	88.2
1pea_A	385	Amidase operon; gene regulator, receptor, binding	87.74
3rfu_A	736	Copper efflux ATPase; alpha helical, CPC, CXXC, AT	87.49
3ewi_A	168	N-acylneuraminate cytidylyltransferase; beta barre	87.35
1jye_A	349	Lactose operon repressor; gene regulation, protein	86.35
2l69_A	134	Rossmann 2X3 fold protein; structural genomics, no	85.96
3mn1_A	189	Probable YRBI family phosphatase; structural genom	85.9
3n1u_A	191	Hydrolase, HAD superfamily, subfamily III A; struc	85.57
1usg_A	346	Leucine-specific binding protein; leucine-binding	84.73
4evq_A	375	Putative ABC transporter subunit, substrate-bindi	84.58
2qu7_A	288	Putative transcriptional regulator; structural gen	84.26
3cvj_A	243	Putative phosphoheptose isomerase; rossman fold, 3	84.24
3h5t_A	366	Transcriptional regulator, LACI family; DNA-depend	84.0
4ex6_A	237	ALNB; modified rossman fold, phosphatase, magnesiu	83.99
1nri_A	306	Hypothetical protein HI0754; structural genomics,	83.77
2zj3_A	375	Glucosamine--fructose-6-phosphate aminotransferase	83.28
3j09_A	723	COPA, copper-exporting P-type ATPase A; copper tra	82.7
1j5x_A	342	Glucosamine-6-phosphate deaminase; structural geno	82.63
1rku_A	206	Homoserine kinase; phosphoserine phosphatase, phos	82.52
2hqb_A	296	Transcriptional activator of COMK gene; berkeley s	82.47
3td9_A	366	Branched chain amino acid ABC transporter, peripl	82.37
3gyb_A	280	Transcriptional regulators (LACI-family transcript	82.37
3i09_A	375	Periplasmic branched-chain amino acid-binding Pro;	82.31
3ipc_A	356	ABC transporter, substrate binding protein (amino;	82.22
2a3n_A	355	Putative glucosamine-fructose-6-phosphate aminotr;	81.89
2r8e_A	188	3-deoxy-D-manno-octulosonate 8-phosphate phosphata	81.81
3ic5_A	118	Putative saccharopine dehydrogenase; structural ge	81.52
1byk_A	255	Protein (trehalose operon repressor); LACI family,	81.41
2p9j_A	162	Hypothetical protein AQ2171; secsg, riken, PSI, st	81.23
3lkb_A	392	Probable branched-chain amino acid ABC transporter	80.99
1k1e_A	180	Deoxy-D-mannose-octulosonate 8-phosphate phosphat;	80.73
3kbb_A	216	Phosphorylated carbohydrates phosphatase TM_1254;	80.3
2fqx_A	318	Membrane lipoprotein TMPC; ABC transport system, l	80.08

>2qip_A Protein of unknown function VPA0982; APC85975, vibrio parahaemolyticus RIMD 2210633, STR genomics, PSI-2, protein structure initiative; 1.48A {Vibrio parahaemolyticus}

Probab=99.46  E-value=2e-13  Score=104.46  Aligned_cols=88  Identities=23%  Similarity=0.228  Sum_probs=77.1

Q ss_pred             cHHHHHhhceEEEEecC-------CCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHc-CCeEEEEcCC-
Q 045172           65 FADELKRAWFWVRMVLV-------KPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLR-WLKMVVVGDM-  135 (157)
Q Consensus        65 la~eLrRAGv~V~~V~d-------kpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer-~l~tVVVGd~-  135 (157)
                      +..+|++.||.|.+.|-       ..++.|++|.-+|++..  ..+|++||||.|+||+++++.+|++ |.+++|+|-. 
T Consensus        66 ~~~~L~~~g~~v~~~p~~~~~~~~~k~~~Dv~laiD~~~~a--~~~d~~vLvSgD~DF~plv~~lr~~~G~~V~v~g~~~  143 (165)
T 2qip_A           66 FHHILRGVGFEVMLKPYIQRRDGSAKGDWDVGITLDAIEIA--PDVDRVILVSGDGDFSLLVERIQQRYNKKVTVYGVPR  143 (165)
T ss_dssp             HHHHHHHHTCEEEECCCCCCSSCCCSCCCHHHHHHHHHHHG--GGCSEEEEECCCGGGHHHHHHHHHHHCCEEEEEECGG
T ss_pred             HHHHHHHCCcEEEEEeeeeccCCccCCCccHHHHHHHHHhh--ccCCEEEEEECChhHHHHHHHHHHHcCcEEEEEeCCC
Confidence            34688899999987653       34699999999999986  6899999999999999999999998 9999999964 


Q ss_pred             -CchHHHhhhhcccchhhhh
Q 045172          136 -SDGALKRIANAFFSWSDLL  154 (157)
Q Consensus       136 -~~~~L~r~AD~~fsW~ev~  154 (157)
                       ++.+|.+.||-|++++++.
T Consensus       144 ~~s~~L~~~ad~fi~l~~~~  163 (165)
T 2qip_A          144 LTSQTLIDCADNFVAIDDDF  163 (165)
T ss_dssp             GSCHHHHHHSSEEEECSGGG
T ss_pred             cChHHHHHhCCEEEecchhh
Confidence             5689999999999998764

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

Probab=95.76  E-value=0.045  Score=41.79  Aligned_cols=68  Identities=15%  Similarity=0.157  Sum_probs=54.5

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++.+.|+.+.......+   ......+.+.+..+++|.|++.+.+.  ...++.+.+.|..+|+||..
T Consensus        27 ~gi~~~~~~~g~~~~~~~~~~~---~~~~~~~~~~l~~~~vdgiIi~~~~~--~~~~~~l~~~~iPvV~i~~~   94 (276)
T 3jy6_A           27 KGISSILESRGYIGVLFDANAD---IEREKTLLRAIGSRGFDGLILQSFSN--PQTVQEILHQQMPVVSVDRE   94 (276)
T ss_dssp             HHHHHHHHTTTCEEEEEECTTC---HHHHHHHHHHHHTTTCSEEEEESSCC--HHHHHHHHTTSSCEEEESCC
T ss_pred             HHHHHHHHHCCCEEEEEeCCCC---HHHHHHHHHHHHhCCCCEEEEecCCc--HHHHHHHHHCCCCEEEEecc
Confidence            4678889999999988765544   33344555555589999999999888  88999999999999999876

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

Probab=95.43  E-value=0.031  Score=42.68  Aligned_cols=73  Identities=5%  Similarity=-0.077  Sum_probs=54.0

Q ss_pred             CCcHHHHHhh-ceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcc-hHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRA-WFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSD-FVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRA-Gv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsD-F~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++.. |+.+.+..-.....|..-...+.+.+..+++|.|++.+.+++ +.+.++.+.+.|..+|+|+..
T Consensus        29 ~gi~~~a~~~~g~~~~~~~~~~~~~~~~~~~~~i~~l~~~~vdgiii~~~~~~~~~~~~~~~~~~~iPvV~~~~~  103 (304)
T 3gbv_A           29 KGIREAVTTYSDFNISANITHYDPYDYNSFVATSQAVIEEQPDGVMFAPTVPQYTKGFTDALNELGIPYIYIDSQ  103 (304)
T ss_dssp             HHHHHHHHHTGGGCEEEEEEEECSSCHHHHHHHHHHHHTTCCSEEEECCSSGGGTHHHHHHHHHHTCCEEEESSC
T ss_pred             HHHHHHHHHHHhCCeEEEEEcCCCCCHHHHHHHHHHHHhcCCCEEEECCCChHHHHHHHHHHHHCCCeEEEEeCC
Confidence            4677788888 888877542222233444445555555899999999988774 788999999999999999976

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

Probab=95.33  E-value=0.046  Score=41.15  Aligned_cols=71  Identities=11%  Similarity=0.054  Sum_probs=54.3

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDMS  136 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~~  136 (157)
                      .|+..++++.|+.+.......+   ..-.....+.+.++++|.+++.+.++.-.+.++.+.+.|..+|+++...
T Consensus        22 ~gi~~~a~~~g~~~~~~~~~~~---~~~~~~~~~~l~~~~vdgiIi~~~~~~~~~~~~~~~~~~iPvV~~~~~~   92 (272)
T 3o74_A           22 KQLEQGARARGYQLLIASSDDQ---PDSERQLQQLFRARRCDALFVASCLPPEDDSYRELQDKGLPVIAIDRRL   92 (272)
T ss_dssp             HHHHHHHHHTTCEEEEEECTTC---HHHHHHHHHHHHHTTCSEEEECCCCCSSCCHHHHHHHTTCCEEEESSCC
T ss_pred             HHHHHHHHHCCCEEEEEeCCCC---HHHHHHHHHHHHHcCCCEEEEecCccccHHHHHHHHHcCCCEEEEccCC
Confidence            4677888999999988765433   3334455555557899999999877545778889999999999998763

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

Probab=95.31  E-value=0.082  Score=40.33  Aligned_cols=71  Identities=10%  Similarity=0.068  Sum_probs=52.6

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCC-cchHHHHHHHHHcCCeEEEEcCCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDD-SDFVEVFQEATLRWLKMVVVGDMS  136 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDD-sDF~~~lr~Arer~l~tVVVGd~~  136 (157)
                      .|+..++++.|+.+.......+   ..-.....+.+..+++|.|++.+.+ +++..+++.+.+.|..+|+++...
T Consensus        28 ~gi~~~a~~~g~~~~~~~~~~~---~~~~~~~~~~l~~~~vdgiI~~~~~~~~~~~~~~~~~~~~iPvV~~~~~~   99 (293)
T 3l6u_A           28 NAFKAEAKANKYEALVATSQNS---RISEREQILEFVHLKVDAIFITTLDDVYIGSAIEEAKKAGIPVFAIDRMI   99 (293)
T ss_dssp             HHHHHHHHHTTCEEEEEECSSC---HHHHHHHHHHHHHTTCSEEEEECSCTTTTHHHHHHHHHTTCCEEEESSCC
T ss_pred             HHHHHHHHHcCCEEEEECCCCC---HHHHHHHHHHHHHcCCCEEEEecCChHHHHHHHHHHHHcCCCEEEecCCC
Confidence            4677889999999988755433   2333334444447999999998654 455689999999999999998763

>3sho_A Transcriptional regulator, RPIR family; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; 1.80A {Sphaerobacter thermophilus}

Probab=95.20  E-value=0.1  Score=38.53  Aligned_cols=78  Identities=18%  Similarity=0.121  Sum_probs=54.1

Q ss_pred             cHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCC---cchHHHHHHHHHcCCeEEEEcCCCchHHH
Q 045172           65 FADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDD---SDFVEVFQEATLRWLKMVVVGDMSDGALK  141 (157)
Q Consensus        65 la~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDD---sDF~~~lr~Arer~l~tVVVGd~~~~~L~  141 (157)
                      ++..|.+.|..|..+++.+.  +.  . .....+  ..=|+++++|-.   .+-..+++.|+++|.++|.|-+.....|.
T Consensus        57 ~~~~l~~~g~~~~~~~~~~~--~~--~-~~~~~~--~~~d~~i~iS~sG~t~~~~~~~~~ak~~g~~vi~IT~~~~s~l~  129 (187)
T 3sho_A           57 LGHGLNSLGIRTTVLTEGGS--TL--T-ITLANL--RPTDLMIGVSVWRYLRDTVAALAGAAERGVPTMALTDSSVSPPA  129 (187)
T ss_dssp             HHHHHHHTTCCEEEECCCTH--HH--H-HHHHTC--CTTEEEEEECCSSCCHHHHHHHHHHHHTTCCEEEEESCTTSHHH
T ss_pred             HHHHHHhcCCCEEEecCCch--hH--H-HHHhcC--CCCCEEEEEeCCCCCHHHHHHHHHHHHCCCCEEEEeCCCCCcch
Confidence            45567889999999873332  11  1 112222  223677777764   35567788999999999999998678999


Q ss_pred             hhhhcccc
Q 045172          142 RIANAFFS  149 (157)
Q Consensus       142 r~AD~~fs  149 (157)
                      +.||..+.
T Consensus       130 ~~ad~~l~  137 (187)
T 3sho_A          130 RIADHVLV  137 (187)
T ss_dssp             HHCSEEEE
T ss_pred             hhCcEEEE
Confidence            99998773

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

Probab=95.13  E-value=0.11  Score=40.41  Aligned_cols=71  Identities=14%  Similarity=0.082  Sum_probs=54.4

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcc-hHHHHHHHHHcCCeEEEEcCCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSD-FVEVFQEATLRWLKMVVVGDMS  136 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsD-F~~~lr~Arer~l~tVVVGd~~  136 (157)
                      .|+..+++..|+.+.......   |......+++.+-.+++|.|++.+.+++ +.+.++.+.+.|+.+|+++...
T Consensus        22 ~gi~~~a~~~g~~~~~~~~~~---~~~~~~~~i~~l~~~~vdgiIi~~~~~~~~~~~~~~~~~~~iPvV~~~~~~   93 (313)
T 3m9w_A           22 DIFVKKAESLGAKVFVQSANG---NEETQMSQIENMINRGVDVLVIIPYNGQVLSNVVKEAKQEGIKVLAYDRMI   93 (313)
T ss_dssp             HHHHHHHHHTSCEEEEEECTT---CHHHHHHHHHHHHHTTCSEEEEECSSTTSCHHHHHHHHTTTCEEEEESSCC
T ss_pred             HHHHHHHHHcCCEEEEECCCC---CHHHHHHHHHHHHHcCCCEEEEeCCChhhhHHHHHHHHHCCCeEEEECCcC
Confidence            467888999999998865432   3344445555555799999999987654 5889999999999999998763

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

Probab=95.09  E-value=0.091  Score=39.91  Aligned_cols=70  Identities=7%  Similarity=0.028  Sum_probs=53.5

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCc----chHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDS----DFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDs----DF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++++.|+.+........   ..-.....+.+..+++|.|++.+.++    .-.++++.+.+.|..+|+++..
T Consensus        35 ~gi~~~a~~~g~~~~~~~~~~~---~~~~~~~~~~l~~~~vdgiIi~~~~~~~~~~~~~~~~~~~~~~iPvV~~~~~  108 (298)
T 3tb6_A           35 RGIESYLSEQGYSMLLTSTNNN---PDNERRGLENLLSQHIDGLIVEPTKSALQTPNIGYYLNLEKNGIPFAMINAS  108 (298)
T ss_dssp             HHHHHHHHHTTCEEEEEECTTC---HHHHHHHHHHHHHTCCSEEEECCSSTTSCCTTHHHHHHHHHTTCCEEEESSC
T ss_pred             HHHHHHHHHCCCEEEEEeCCCC---hHHHHHHHHHHHHCCCCEEEEecccccccCCcHHHHHHHHhcCCCEEEEecC
Confidence            4778899999999988754433   33344555555579999999998765    3457899999999999999876

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

Probab=95.07  E-value=0.071  Score=41.03  Aligned_cols=72  Identities=11%  Similarity=0.088  Sum_probs=53.5

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCc-chHHHHHHHHHcCCeEEEEcCCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDS-DFVEVFQEATLRWLKMVVVGDMS  136 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDs-DF~~~lr~Arer~l~tVVVGd~~  136 (157)
                      .|+..+++..|+.+..+.+...  |..-.....+.+..+++|.|++.+-++ .+.+.++.+.+.|..+|+++...
T Consensus        24 ~gi~~~a~~~g~~~~~~~~~~~--~~~~~~~~i~~l~~~~vdgiIi~~~~~~~~~~~~~~~~~~~iPvV~~~~~~   96 (305)
T 3g1w_A           24 KGFEDAAQALNVTVEYRGAAQY--DIQEQITVLEQAIAKNPAGIAISAIDPVELTDTINKAVDAGIPIVLFDSGA   96 (305)
T ss_dssp             HHHHHHHHHHTCEEEEEECSSS--CHHHHHHHHHHHHHHCCSEEEECCSSTTTTHHHHHHHHHTTCCEEEESSCC
T ss_pred             HHHHHHHHHcCCEEEEeCCCcC--CHHHHHHHHHHHHHhCCCEEEEcCCCHHHHHHHHHHHHHCCCcEEEECCCC
Confidence            4678889999999987432222  334444555555578999999987555 47889999999999999998763

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

Probab=95.04  E-value=0.079  Score=40.36  Aligned_cols=71  Identities=6%  Similarity=-0.094  Sum_probs=54.1

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCc-chHHHHHHHHHcCCeEEEEcCCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDS-DFVEVFQEATLRWLKMVVVGDMS  136 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDs-DF~~~lr~Arer~l~tVVVGd~~  136 (157)
                      .|+..++++.|+.+.......+   ..-...+.+.+..+++|.|++.+.++ ...+.++.+.+.|..+|+++...
T Consensus        25 ~gi~~~a~~~g~~~~~~~~~~~---~~~~~~~~~~l~~~~vdgiIi~~~~~~~~~~~~~~~~~~~iPvV~~~~~~   96 (291)
T 3l49_A           25 QAQIAEIERLGGTAIALDAGRN---DQTQVSQIQTLIAQKPDAIIEQLGNLDVLNPWLQKINDAGIPLFTVDTAT   96 (291)
T ss_dssp             HHHHHHHHHTTCEEEEEECTTC---HHHHHHHHHHHHHHCCSEEEEESSCHHHHHHHHHHHHHTTCCEEEESCCC
T ss_pred             HHHHHHHHHcCCEEEEEcCCCC---HHHHHHHHHHHHHcCCCEEEEeCCChhhhHHHHHHHHHCCCcEEEecCCC
Confidence            4677889999999988754433   33344445555578999999998774 56789999999999999998764

>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=95.00  E-value=0.1  Score=41.42  Aligned_cols=71  Identities=7%  Similarity=0.030  Sum_probs=53.5

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHH-HHHHHHhhc-cCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLR-NYMVAMVDK-RRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDMS  136 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~-~~~~~~~~~-r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~~  136 (157)
                      .|+..+++..|+.+..+....+   ..-. ..+.+++.. .++|.|+++++++....+++.+.+.|..+|.|+...
T Consensus        24 ~g~~~~a~~~g~~~~~~~~~~~---~~~~~~~i~~~i~~~~~vDgiIi~~~~~~~~~~~~~~~~~giPvV~~~~~~   96 (350)
T 3h75_A           24 QFMQAAARDLGLDLRILYAERD---PQNTLQQARELFQGRDKPDYLMLVNEQYVAPQILRLSQGSGIKLFIVNSPL   96 (350)
T ss_dssp             HHHHHHHHHHTCEEEEEECTTC---HHHHHHHHHHHHHSSSCCSEEEEECCSSHHHHHHHHHTTSCCEEEEEESCC
T ss_pred             HHHHHHHHHcCCeEEEEECCCC---HHHHHHHHHHHHhcCCCCCEEEEeCchhhHHHHHHHHHhCCCcEEEEcCCC
Confidence            4677888899999988754433   3333 334445532 599999999877778889999999999999999763

>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=94.99  E-value=0.074  Score=41.08  Aligned_cols=72  Identities=15%  Similarity=0.151  Sum_probs=51.6

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcc-hHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSD-FVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsD-F~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++..|+.+..... +...|.......++.+..+++|.|++.+.+++ +.+.++.+.+.|..+|+++..
T Consensus        21 ~gi~~~a~~~g~~~~~~~~-~~~~~~~~~~~~~~~~~~~~vdgiIi~~~~~~~~~~~~~~~~~~~iPvV~~~~~   93 (288)
T 1gud_A           21 KGIEDEAKTLGVSVDIFAS-PSEGDFQSQLQLFEDLSNKNYKGIAFAPLSSVNLVMPVARAWKKGIYLVNLDEK   93 (288)
T ss_dssp             HHHHHHHHHHTCCEEEEEC-SSTTCHHHHHHHHHHHHTSSEEEEEECCSSSSTTHHHHHHHHHTTCEEEEESSC
T ss_pred             HHHHHHHHHcCCEEEEeCC-CCCCCHHHHHHHHHHHHHcCCCEEEEeCCChHHHHHHHHHHHHCCCeEEEECCC
Confidence            4778889999998877541 11123334444455444789999999876654 567889999999999999865

>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=94.91  E-value=0.12  Score=39.56  Aligned_cols=68  Identities=18%  Similarity=0.046  Sum_probs=51.3

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcc-hHHHHHHHHHcCCeEEEEcC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSD-FVEVFQEATLRWLKMVVVGD  134 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsD-F~~~lr~Arer~l~tVVVGd  134 (157)
                      .|+..+++..|+.+..... .   |..-....++.+-.+++|.|++.+.|++ ....++.+.+.|+.+|+++.
T Consensus        22 ~gi~~~a~~~g~~~~~~~~-~---~~~~~~~~i~~l~~~~vdgiii~~~~~~~~~~~~~~~~~~~iPvV~~~~   90 (306)
T 8abp_A           22 KFADKAGKDLGFEVIKIAV-P---DGEKTLNAIDSLAASGAKGFVICTPDPKLGSAIVAKARGYDMKVIAVDD   90 (306)
T ss_dssp             HHHHHHHHHHTEEEEEEEC-C---SHHHHHHHHHHHHHTTCCEEEEECSCGGGHHHHHHHHHHTTCEEEEESS
T ss_pred             HHHHHHHHHcCCEEEEeCC-C---CHHHHHHHHHHHHHcCCCEEEEeCCCchhhHHHHHHHHHCCCcEEEeCC
Confidence            4677888899999977644 2   3444444444444789999999987765 45679999999999999994

>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=94.84  E-value=0.11  Score=38.97  Aligned_cols=73  Identities=14%  Similarity=0.114  Sum_probs=53.5

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccC-cceEEEEcCCc-chHHHHHHHHHcCCeEEEEcCCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRR-FGCLVVVSDDS-DFVEVFQEATLRWLKMVVVGDMS  136 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~-v~clvLVSDDs-DF~~~lr~Arer~l~tVVVGd~~  136 (157)
                      .|+..++++.|+.+..+... ...|..-.....+.+-.++ +|.|++.+-++ ...+.++.+.+.|..+|+++...
T Consensus        20 ~gi~~~~~~~g~~~~~~~~~-~~~~~~~~~~~i~~l~~~~~vdgii~~~~~~~~~~~~~~~~~~~~ipvV~~~~~~   94 (276)
T 3ksm_A           20 LGAQKAADEAGVTLLHRSTK-DDGDIAGQIQILSYHLSQAPPDALILAPNSAEDLTPSVAQYRARNIPVLVVDSDL   94 (276)
T ss_dssp             HHHHHHHHHHTCEEEECCCS-STTCHHHHHHHHHHHHHHSCCSEEEECCSSTTTTHHHHHHHHHTTCCEEEESSCC
T ss_pred             HHHHHHHHHcCCEEEEECCC-CCCCHHHHHHHHHHHHHhCCCCEEEEeCCCHHHHHHHHHHHHHCCCcEEEEecCC
Confidence            46778888999999876421 2234444444555554788 99999998654 57789999999999999998763

>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=94.81  E-value=0.14  Score=38.99  Aligned_cols=70  Identities=6%  Similarity=0.003  Sum_probs=50.3

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCc-chHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDS-DFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDs-DF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++...|+.+.+.....   |......+.+.+..+++|.|++.+.++ ++.+.++.+.+.|..+|+++..
T Consensus        22 ~gi~~~~~~~g~~~~~~~~~~---~~~~~~~~~~~l~~~~vdgiI~~~~~~~~~~~~~~~~~~~~iPvV~~~~~   92 (290)
T 2fn9_A           22 ETAKQRAEQLGYEATIFDSQN---DTAKESAHFDAIIAAGYDAIIFNPTDADGSIANVKRAKEAGIPVFCVDRG   92 (290)
T ss_dssp             HHHHHHHHHTTCEEEEEECTT---CHHHHHHHHHHHHHTTCSEEEECCSCTTTTHHHHHHHHHTTCCEEEESSC
T ss_pred             HHHHHHHHHcCCEEEEeCCCC---CHHHHHHHHHHHHHcCCCEEEEecCChHHHHHHHHHHHHCCCeEEEEecC
Confidence            467778888899887754322   233333444444478999999987654 4668899999999999999865

>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=94.75  E-value=0.086  Score=41.62  Aligned_cols=71  Identities=15%  Similarity=0.125  Sum_probs=51.5

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcc-hHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSD-FVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsD-F~~~lr~Arer~l~tVVVGd~  135 (157)
                      -|+..+++..|+.+....  |...|.+-.....+.|-.+++|.||+.+-|++ ...+++.|++.|+.+|.++..
T Consensus        23 ~g~~~~~~~~g~~~~~~~--~~~~d~~~q~~~i~~li~~~vdgiii~~~~~~~~~~~~~~a~~~gipvV~~d~~   94 (316)
T 1tjy_A           23 NGAQEAGKALGIDVTYDG--PTEPSVSGQVQLVNNFVNQGYDAIIVSAVSPDGLCPALKRAMQRGVKILTWDSD   94 (316)
T ss_dssp             HHHHHHHHHHTCEEEECC--CSSCCHHHHHHHHHHHHHTTCSEEEECCSSSSTTHHHHHHHHHTTCEEEEESSC
T ss_pred             HHHHHHHHHhCCEEEEEC--CCCCCHHHHHHHHHHHHHcCCCEEEEeCCCHHHHHHHHHHHHHCcCEEEEecCC
Confidence            466777888898887642  22234444444454444799999999987765 578999999999999999754

>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=94.70  E-value=0.13  Score=39.29  Aligned_cols=70  Identities=13%  Similarity=0.057  Sum_probs=50.9

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcc-hHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSD-FVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsD-F~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++..|+.+........   ..-....++.+..+++|.|++.+.+++ ....++.+++.|+.+|+++..
T Consensus        21 ~gi~~~~~~~g~~~~~~~~~~~---~~~~~~~i~~l~~~~vdgiIi~~~~~~~~~~~~~~~~~~~iPvV~i~~~   91 (271)
T 2dri_A           21 DGAQKEADKLGYNLVVLDSQNN---PAKELANVQDLTVRGTKILLINPTDSDAVGNAVKMANQANIPVITLDRQ   91 (271)
T ss_dssp             HHHHHHHHHHTCEEEEEECTTC---HHHHHHHHHHHTTTTEEEEEECCSSTTTTHHHHHHHHHTTCCEEEESSC
T ss_pred             HHHHHHHHHcCcEEEEeCCCCC---HHHHHHHHHHHHHcCCCEEEEeCCChHHHHHHHHHHHHCCCcEEEecCC
Confidence            5778889999998877543222   233344445555789999999876544 457889999999999999865

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

Probab=94.70  E-value=0.075  Score=41.27  Aligned_cols=69  Identities=12%  Similarity=0.108  Sum_probs=53.3

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++++.|+.+.......   |......+.+.+..+++|.|++++.+.+ .+.++.+.+.|..+|+||..
T Consensus        47 ~gi~~~a~~~g~~~~~~~~~~---~~~~~~~~~~~l~~~~vdgiIi~~~~~~-~~~~~~l~~~~iPvV~i~~~  115 (305)
T 3huu_A           47 NGINQACNVRGYSTRMTVSEN---SGDLYHEVKTMIQSKSVDGFILLYSLKD-DPIEHLLNEFKVPYLIVGKS  115 (305)
T ss_dssp             HHHHHHHHHHTCEEEECCCSS---HHHHHHHHHHHHHTTCCSEEEESSCBTT-CHHHHHHHHTTCCEEEESCC
T ss_pred             HHHHHHHHHCCCEEEEEeCCC---ChHHHHHHHHHHHhCCCCEEEEeCCcCC-cHHHHHHHHcCCCEEEECCC
Confidence            477889999999998865433   3444556667776899999999875543 27888899999999999876

>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=94.68  E-value=0.13  Score=40.58  Aligned_cols=70  Identities=7%  Similarity=-0.073  Sum_probs=54.0

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++...|+.+.......+   ........+.+..+++|.|++.+.+.+-..+...+.+.+..+|+++..
T Consensus        83 ~gi~~~a~~~g~~~~~~~~~~~---~~~~~~~~~~l~~~~vdgiIi~~~~~~~~~~~~~~~~~~iPvV~~~~~  152 (338)
T 3dbi_A           83 FHAARMAEEKGRQLLLADGKHS---AEEERQAIQYLLDLRCDAIMIYPRFLSVDEIDDIIDAHSQPIMVLNRR  152 (338)
T ss_dssp             HHHHHHHHHTTCEEEEEECTTS---HHHHHHHHHHHHHTTCSEEEECCSSSCHHHHHHHHHHCSSCEEEESSC
T ss_pred             HHHHHHHHHCCCEEEEEeCCCC---hHHHHHHHHHHHhCCCCEEEEeCCCCChHHHHHHHHcCCCCEEEEcCC
Confidence            4778899999999988764333   333344455555799999999998877777888899999999999875

>3k4h_A Putative transcriptional regulator; structural genomics, protein structure INI NEW YORK structural genomix research consortium; HET: MAL; 2.80A {Bacillus cytotoxicus nvh 391-98}

Probab=94.63  E-value=0.082  Score=40.28  Aligned_cols=69  Identities=16%  Similarity=0.200  Sum_probs=52.8

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++.+.|+.+.......   |......+.+.+..+++|.|++++.+.+ ...++.+.+.|..+|+|+..
T Consensus        33 ~gi~~~a~~~g~~~~~~~~~~---~~~~~~~~~~~~~~~~vdgiIi~~~~~~-~~~~~~l~~~~iPvV~~~~~  101 (292)
T 3k4h_A           33 RGISSFAHVEGYALYMSTGET---EEEIFNGVVKMVQGRQIGGIILLYSREN-DRIIQYLHEQNFPFVLIGKP  101 (292)
T ss_dssp             HHHHHHHHHTTCEEEECCCCS---HHHHHHHHHHHHHTTCCCEEEESCCBTT-CHHHHHHHHTTCCEEEESCC
T ss_pred             HHHHHHHHHcCCEEEEEeCCC---CHHHHHHHHHHHHcCCCCEEEEeCCCCC-hHHHHHHHHCCCCEEEECCC
Confidence            477889999999998764433   3444556666666899999999875543 37888999999999999876

>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=94.56  E-value=0.1  Score=40.67  Aligned_cols=71  Identities=14%  Similarity=0.192  Sum_probs=53.7

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCc-chHHHHHHHHHcCCeEEEEcCCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDS-DFVEVFQEATLRWLKMVVVGDMS  136 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDs-DF~~~lr~Arer~l~tVVVGd~~  136 (157)
                      .|+..+++..|+.+.......   |..-....++.+-.+++|.|++.+-++ ...+.++.+.+.|..+|+|+...
T Consensus        23 ~gi~~~a~~~g~~~~~~~~~~---~~~~~~~~i~~~~~~~vdgiIi~~~~~~~~~~~~~~~~~~giPvV~~~~~~   94 (330)
T 3uug_A           23 NNIVKQLQEAGYKTDLQYADD---DIPNQLSQIENMVTKGVKVLVIASIDGTTLSDVLKQAGEQGIKVIAYDRLI   94 (330)
T ss_dssp             HHHHHHHHHTTCEEEEEECTT---CHHHHHHHHHHHHHHTCSEEEECCSSGGGGHHHHHHHHHTTCEEEEESSCC
T ss_pred             HHHHHHHHHcCCEEEEeeCCC---CHHHHHHHHHHHHHcCCCEEEEEcCCchhHHHHHHHHHHCCCCEEEECCCC
Confidence            467788899999988875332   233334444444478999999998776 57889999999999999998763

>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=94.49  E-value=0.16  Score=39.19  Aligned_cols=69  Identities=9%  Similarity=0.047  Sum_probs=49.8

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++++.|+.+.......   |..-...+.+.+..+++|.|++.+.+.+ .+.++.+.+.|..+|+++..
T Consensus        36 ~gi~~~a~~~g~~~~~~~~~~---~~~~~~~~~~~l~~~~vdgiIi~~~~~~-~~~~~~l~~~~iPvV~~~~~  104 (289)
T 2fep_A           36 RGIEDIATMYKYNIILSNSDQ---NMEKELHLLNTMLGKQVDGIVFMGGNIT-DEHVAEFKRSPVPIVLAASV  104 (289)
T ss_dssp             HHHHHHHHHTTCEEEEEECTT---CHHHHHHHHHHHHHTTCSEEEECCSCCC-HHHHHHHHHSSSCEEEESCC
T ss_pred             HHHHHHHHHcCCEEEEEeCCC---CHHHHHHHHHHHHhCCCCEEEEecCCCC-HHHHHHHHhcCCCEEEEccc
Confidence            577888889999887754332   2333344445554789999999886544 56788888999999999875

>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=94.42  E-value=0.13  Score=40.03  Aligned_cols=71  Identities=10%  Similarity=0.070  Sum_probs=50.2

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCc-chHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDS-DFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDs-DF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++..|+.+..+...  ..|..-...+.+.+..+++|.|++.+.++ .+...++.+.+.|..+|+++..
T Consensus        20 ~gi~~~~~~~g~~~~~~~~~--~~~~~~~~~~i~~l~~~~vdgiIi~~~~~~~~~~~~~~~~~~~iPvV~~~~~   91 (313)
T 2h3h_A           20 QGVKAAGKALGVDTKFFVPQ--KEDINAQLQMLESFIAEGVNGIAIAPSDPTAVIPTIKKALEMGIPVVTLDTD   91 (313)
T ss_dssp             HHHHHHHHHHTCEEEEECCS--SSCHHHHHHHHHHHHHTTCSEEEECCSSTTTTHHHHHHHHHTTCCEEEESSC
T ss_pred             HHHHHHHHHcCCEEEEECCC--CCCHHHHHHHHHHHHHcCCCEEEEeCCChHHHHHHHHHHHHCCCeEEEeCCC
Confidence            46677788889988775321  22333333444444468999999987655 4678899999999999999865

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

Probab=94.38  E-value=0.2  Score=40.00  Aligned_cols=69  Identities=12%  Similarity=0.074  Sum_probs=51.7

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++.+.|+.+........   ..-...+.+.+..+++|.|++.+.+.+ ...+..+.+.|+.+|+|++.
T Consensus        90 ~gi~~~a~~~g~~~~~~~~~~~---~~~~~~~~~~l~~~~vdGiI~~~~~~~-~~~~~~l~~~~iPvV~i~~~  158 (355)
T 3e3m_A           90 QSLTDVLEQGGLQLLLGYTAYS---PEREEQLVETMLRRRPEAMVLSYDGHT-EQTIRLLQRASIPIVEIWEK  158 (355)
T ss_dssp             HHHHHHHHHTTCEEEEEECTTC---HHHHHHHHHHHHHTCCSEEEEECSCCC-HHHHHHHHHCCSCEEEESSC
T ss_pred             HHHHHHHHHCCCEEEEEeCCCC---hHHHHHHHHHHHhCCCCEEEEeCCCCC-HHHHHHHHhCCCCEEEECCc
Confidence            4788999999999987643322   223344555555799999999987655 36788899999999999875

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

Probab=94.37  E-value=0.14  Score=39.78  Aligned_cols=70  Identities=7%  Similarity=-0.017  Sum_probs=50.7

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcc-hHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSD-FVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsD-F~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++..|+.+........   ..-.....+.+..+++|.|++.+.+++ ..+.++.+.+.|..+|+++..
T Consensus        22 ~gi~~~a~~~g~~l~~~~~~~~---~~~~~~~i~~l~~~~vdgiIi~~~~~~~~~~~~~~~~~~~iPvV~~~~~   92 (306)
T 2vk2_A           22 NVAKSEAEKRGITLKIADGQQK---QENQIKAVRSFVAQGVDAIFIAPVVATGWEPVLKEAKDAEIPVFLLDRS   92 (306)
T ss_dssp             HHHHHHHHHHTCEEEEEECTTC---HHHHHHHHHHHHHHTCSEEEECCSSSSSCHHHHHHHHHTTCCEEEESSC
T ss_pred             HHHHHHHHHcCCEEEEeCCCCC---HHHHHHHHHHHHHcCCCEEEEeCCChhhHHHHHHHHHHCCCCEEEecCC
Confidence            4677888899999887643322   233333444444789999999887654 578899999999999999865

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

Probab=94.37  E-value=0.1  Score=40.44  Aligned_cols=69  Identities=10%  Similarity=0.159  Sum_probs=52.6

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++.+.|+.+.......   |......+.+.+..+++|.|++++.+.+ ..+++.+.+.|..+|+||..
T Consensus        32 ~gi~~~a~~~g~~~~~~~~~~---~~~~~~~~~~~l~~~~vdGiI~~~~~~~-~~~~~~l~~~~iPvV~i~~~  100 (295)
T 3hcw_A           32 LGISETCNQHGYGTQTTVSNN---MNDLMDEVYKMIKQRMVDAFILLYSKEN-DPIKQMLIDESMPFIVIGKP  100 (295)
T ss_dssp             HHHHHHHHTTTCEEEECCCCS---HHHHHHHHHHHHHTTCCSEEEESCCCTT-CHHHHHHHHTTCCEEEESCC
T ss_pred             HHHHHHHHHCCCEEEEEcCCC---ChHHHHHHHHHHHhCCcCEEEEcCcccC-hHHHHHHHhCCCCEEEECCC
Confidence            567889999999997754332   3445556667776899999999865543 26788889999999999976

>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=94.22  E-value=0.14  Score=38.71  Aligned_cols=69  Identities=9%  Similarity=0.103  Sum_probs=49.9

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++.+.|+.+.......   |........+.+..+++|.|++.+.+.+ ..+++.+.+.|..+|+++..
T Consensus        23 ~gi~~~~~~~g~~~~~~~~~~---~~~~~~~~~~~l~~~~vdgii~~~~~~~-~~~~~~l~~~~iPvV~~~~~   91 (275)
T 3d8u_A           23 PSFQQALNKAGYQLLLGYSDY---SIEQEEKLLSTFLESRPAGVVLFGSEHS-QRTHQLLEASNTPVLEIAEL   91 (275)
T ss_dssp             HHHHHHHHHTSCEECCEECTT---CHHHHHHHHHHHHTSCCCCEEEESSCCC-HHHHHHHHHHTCCEEEESSS
T ss_pred             HHHHHHHHHCCCEEEEEcCCC---CHHHHHHHHHHHHhcCCCEEEEeCCCCC-HHHHHHHHhCCCCEEEEeec
Confidence            577788889999887654332   2333344455555799999999886654 47788888999999999865

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

Probab=94.20  E-value=0.2  Score=38.47  Aligned_cols=70  Identities=13%  Similarity=0.115  Sum_probs=49.5

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCc-chHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDS-DFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDs-DF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++..|+.+-......+   ..-....++.+..+++|.|++.+.++ +..+.++.+.+.|..+|+++..
T Consensus        21 ~gi~~~~~~~g~~~~~~~~~~~---~~~~~~~i~~l~~~~vdgiIi~~~~~~~~~~~~~~~~~~~iPvV~~~~~   91 (283)
T 2ioy_A           21 NGAEEKAKELGYKIIVEDSQND---SSKELSNVEDLIQQKVDVLLINPVDSDAVVTAIKEANSKNIPVITIDRS   91 (283)
T ss_dssp             HHHHHHHHHHTCEEEEEECTTC---HHHHHHHHHHHHHTTCSEEEECCSSTTTTHHHHHHHHHTTCCEEEESSC
T ss_pred             HHHHHHHHhcCcEEEEecCCCC---HHHHHHHHHHHHHcCCCEEEEeCCchhhhHHHHHHHHHCCCeEEEecCC
Confidence            4677888999999877643332   22223333333378999999987654 4567889999999999999864

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

Probab=94.03  E-value=0.12  Score=39.89  Aligned_cols=69  Identities=22%  Similarity=0.106  Sum_probs=49.0

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHH---HHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNY---MVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~---~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++++.|+.+.......+..   -...   +.+.+..+++|.|++.+.+.+ .+.++.+++.|..+|+++..
T Consensus        28 ~gi~~~a~~~g~~~~~~~~~~~~~---~~~~~~~~~~~l~~~~vdgiIi~~~~~~-~~~~~~l~~~~iPvV~~~~~   99 (290)
T 2rgy_A           28 KQTDLELRAVHRHVVVATGCGEST---PREQALEAVRFLIGRDCDGVVVISHDLH-DEDLDELHRMHPKMVFLNRA   99 (290)
T ss_dssp             HHHHHHHHHTTCEEEEECCCSSSC---HHHHHHHHHHHHHHTTCSEEEECCSSSC-HHHHHHHHHHCSSEEEESSC
T ss_pred             HHHHHHHHHCCCEEEEEeCCCchh---hhhhHHHHHHHHHhcCccEEEEecCCCC-HHHHHHHhhcCCCEEEEccc
Confidence            477788889999887654332211   1222   334444789999999987766 57788888899999999875

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

Probab=93.96  E-value=0.081  Score=40.55  Aligned_cols=70  Identities=13%  Similarity=0.151  Sum_probs=53.8

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDMS  136 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~~  136 (157)
                      .|+..++++.|+.+........   ..-...+.+.+..+++|.|++.+.+. ....++.+.+.|..+|+++...
T Consensus        28 ~gi~~~a~~~g~~~~~~~~~~~---~~~~~~~~~~l~~~~vdgiIi~~~~~-~~~~~~~~~~~~iPvV~~~~~~   97 (291)
T 3egc_A           28 SGVESEARHKGYSVLLANTAED---IVREREAVGQFFERRVDGLILAPSEG-EHDYLRTELPKTFPIVAVNREL   97 (291)
T ss_dssp             HHHHHHHHHTTCEEEEEECTTC---HHHHHHHHHHHHHTTCSEEEECCCSS-CCHHHHHSSCTTSCEEEESSCC
T ss_pred             HHHHHHHHHCCCEEEEEeCCCC---HHHHHHHHHHHHHCCCCEEEEeCCCC-ChHHHHHhhccCCCEEEEeccc
Confidence            4677889999999988754333   33345555555579999999998776 5678888999999999999764

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

Probab=93.87  E-value=0.2  Score=39.78  Aligned_cols=68  Identities=7%  Similarity=-0.068  Sum_probs=50.3

Q ss_pred             CcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           64 GFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        64 gla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      |+..++.+.|+.+........   ..-...+.+.+..+++|.|++++.+.+- ..++.+.+.|+.+|++||.
T Consensus        89 gi~~~a~~~g~~~~~~~~~~~---~~~~~~~i~~l~~~~vdGiIi~~~~~~~-~~~~~l~~~~iPvV~i~~~  156 (344)
T 3kjx_A           89 GINQVLEDTELQPVVGVTDYL---PEKEEKVLYEMLSWRPSGVIIAGLEHSE-AARAMLDAAGIPVVEIMDS  156 (344)
T ss_dssp             HHHHHHTSSSSEEEEEECTTC---HHHHHHHHHHHHTTCCSEEEEECSCCCH-HHHHHHHHCSSCEEEEEEC
T ss_pred             HHHHHHHHCCCEEEEEeCCCC---HHHHHHHHHHHHhCCCCEEEEECCCCCH-HHHHHHHhCCCCEEEEeCC
Confidence            788889999999876543322   2233444555557999999999766543 6788899999999999875

>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=93.85  E-value=0.19  Score=38.41  Aligned_cols=70  Identities=14%  Similarity=0.016  Sum_probs=50.5

Q ss_pred             CCcHHHHHhhce-EEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcc-hHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWF-WVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSD-FVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv-~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsD-F~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++.+.|+ .+.......   |.......++.+..+++|.|++.+.+.+ ...+++.+.+.|..+|+++..
T Consensus        22 ~gi~~~a~~~g~~~~~~~~~~~---~~~~~~~~~~~~~~~~vdgiii~~~~~~~~~~~~~~~~~~~iPvV~~~~~   93 (309)
T 2fvy_A           22 KAIEQDAKAAPDVQLLMNDSQN---DQSKQNDQIDVLLAKGVKALAINLVDPAAAGTVIEKARGQNVPVVFFNKE   93 (309)
T ss_dssp             HHHHHHHHTCTTEEEEEEECTT---CHHHHHHHHHHHHHTTCSEEEECCSSGGGHHHHHHHHHTTTCCEEEESSC
T ss_pred             HHHHHHHHhcCCeEEEEecCCC---CHHHHHHHHHHHHHcCCCEEEEeCCCcchhHHHHHHHHHCCCcEEEecCC
Confidence            467778888896 676653321   3334444555555789999999887665 467899999999999999875

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

Probab=93.78  E-value=0.25  Score=39.11  Aligned_cols=69  Identities=10%  Similarity=-0.032  Sum_probs=51.1

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++.+.|+.+.......+   ..-...+.+.+..+++|.|++.+.+.+- .++..+.+.|..+|++++.
T Consensus        82 ~gi~~~a~~~g~~~~~~~~~~~---~~~~~~~~~~l~~~~vdGiIi~~~~~~~-~~~~~l~~~~iPvV~~~~~  150 (339)
T 3h5o_A           82 TGIETVLDAAGYQMLIGNSHYD---AGQELQLLRAYLQHRPDGVLITGLSHAE-PFERILSQHALPVVYMMDL  150 (339)
T ss_dssp             HHHHHHHHHTTCEEEEEECTTC---HHHHHHHHHHHHTTCCSEEEEECSCCCT-THHHHHHHTTCCEEEEESC
T ss_pred             HHHHHHHHHCCCEEEEEeCCCC---hHHHHHHHHHHHcCCCCEEEEeCCCCCH-HHHHHHhcCCCCEEEEeec
Confidence            3778899999999987654333   2333445555558999999999855443 6788889999999999875

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

Probab=93.76  E-value=0.34  Score=36.63  Aligned_cols=69  Identities=7%  Similarity=-0.037  Sum_probs=48.8

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHH-cCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATL-RWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Are-r~l~tVVVGd~  135 (157)
                      .|+..++...|+.+.......+   ..-.....+.+..+++|.|++.+.+.+ ...+..+.+ .|..+|+++..
T Consensus        41 ~gi~~~~~~~g~~~~~~~~~~~---~~~~~~~~~~l~~~~vdgii~~~~~~~-~~~~~~l~~~~~iPvV~~~~~  110 (296)
T 3brq_A           41 FHAARMAEEKGRQLLLADGKHS---AEEERQAIQYLLDLRCDAIMIYPRFLS-VDEIDDIIDAHSQPIMVLNRR  110 (296)
T ss_dssp             HHHHHHHHHTTCEEEEECCTTS---HHHHHHHHHHHHHTTCSEEEEECSSSC-HHHHHHHHHTCSSCEEEESCC
T ss_pred             HHHHHHHHHCCCEEEEEeCCCC---HHHHHHHHHHHHhcCCCEEEEecCCCC-hHHHHHHHhcCCCCEEEEccc
Confidence            4677788889998887654332   233334444444789999999876654 366788888 89999999865

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

Probab=93.73  E-value=0.19  Score=38.89  Aligned_cols=73  Identities=10%  Similarity=0.026  Sum_probs=53.0

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCc-chHHHHHHHHHcCCeEEEEcCCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDS-DFVEVFQEATLRWLKMVVVGDMS  136 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDs-DF~~~lr~Arer~l~tVVVGd~~  136 (157)
                      .|+..+++..|+.+...... +..|..-.....+.+..+++|+|++.+.++ .+...++.+++.|..+|.++...
T Consensus        23 ~gi~~~a~~~g~~~~~~~~~-~~~~~~~~~~~i~~l~~~~vdgiii~~~~~~~~~~~~~~~~~~giPvV~~~~~~   96 (297)
T 3rot_A           23 QGAKKAAEELKVDLQILAPP-GANDVPKQVQFIESALATYPSGIATTIPSDTAFSKSLQRANKLNIPVIAVDTRP   96 (297)
T ss_dssp             HHHHHHHHHHTCEEEEECCS-SSCCHHHHHHHHHHHHHTCCSEEEECCCCSSTTHHHHHHHHHHTCCEEEESCCC
T ss_pred             HHHHHHHHHhCcEEEEECCC-CcCCHHHHHHHHHHHHHcCCCEEEEeCCCHHHHHHHHHHHHHCCCCEEEEcCCC
Confidence            57778888999999876522 112333444445444478999999987554 46889999999999999998763

>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=93.68  E-value=0.16  Score=39.98  Aligned_cols=72  Identities=11%  Similarity=0.151  Sum_probs=48.3

Q ss_pred             CCcHHHHHhhceEEEEe--cCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMV--LVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V--~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++.+.|+.+...  ...++ .|..-.....+.+..+++|.|++.++.......++.+.+.|..+|++.|.
T Consensus        64 ~gi~~~a~~~g~~~~~~~~~~~~~-~~~~~~~~~i~~l~~~~vdgiIi~~~~~~~~~~~~~~~~~~ip~V~~~~~  137 (342)
T 1jx6_A           64 ASFEKRLYKLNINYQLNQVFTRPN-ADIKQQSLSLMEALKSKSDYLIFTLDTTRHRKFVEHVLDSTNTKLILQNI  137 (342)
T ss_dssp             HHHHHHHHHTTCCEEEEEEECCTT-CCHHHHHHHHHHHHHTTCSEEEECCSSSTTHHHHHHHHHHCSCEEEEETC
T ss_pred             HHHHHHHHHcCCeEEEEecCCCCc-cCHHHHHHHHHHHHhcCCCEEEEeCChHhHHHHHHHHHHcCCCEEEEecC
Confidence            37888999999877665  22210 12333334444444789999999544444578899999999999988554

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

Probab=93.59  E-value=0.18  Score=39.19  Aligned_cols=70  Identities=7%  Similarity=-0.044  Sum_probs=51.4

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDMS  136 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~~  136 (157)
                      .|+..++.+.|+.+........   ..-...+.+.+..+++|.|++.+.+.+-.+.+..+.+ |+.+|+||...
T Consensus        35 ~gi~~~a~~~g~~~~~~~~~~~---~~~~~~~~~~l~~~~vdgiI~~~~~~~~~~~~~~l~~-~iPvV~i~~~~  104 (303)
T 3kke_A           35 SGVQMAASGHSTDVLLGQIDAP---PRGTQQLSRLVSEGRVDGVLLQRREDFDDDMLAAVLE-GVPAVTINSRV  104 (303)
T ss_dssp             HHHHHHHHHTTCCEEEEECCST---THHHHHHHHHHHSCSSSEEEECCCTTCCHHHHHHHHT-TSCEEEESCCC
T ss_pred             HHHHHHHHHCCCEEEEEeCCCC---hHHHHHHHHHHHhCCCcEEEEecCCCCcHHHHHHHhC-CCCEEEECCcC
Confidence            4778889999999988755443   2233455555668999999999876653327788888 99999998764

>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=93.32  E-value=0.24  Score=38.97  Aligned_cols=70  Identities=9%  Similarity=-0.123  Sum_probs=50.7

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccC--cceEEEEcCCcc-hHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRR--FGCLVVVSDDSD-FVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~--v~clvLVSDDsD-F~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++++.|+.+.......   |..-....++.+..++  +|.|++.+.+++ ..++++.+.+.|+.+|+++..
T Consensus        25 ~gi~~~a~~~g~~l~~~~~~~---~~~~~~~~i~~l~~~~~~vdgiIi~~~~~~~~~~~~~~~~~~~iPvV~~~~~   97 (332)
T 2rjo_A           25 KGAQSFAKSVGLPYVPLTTEG---SSEKGIADIRALLQKTGGNLVLNVDPNDSADARVIVEACSKAGAYVTTIWNK   97 (332)
T ss_dssp             HHHHHHHHHHTCCEEEEECTT---CHHHHHHHHHHHHHHTTTCEEEEECCSSHHHHHHHHHHHHHHTCEEEEESCC
T ss_pred             HHHHHHHHHcCCEEEEecCCC---CHHHHHHHHHHHHHCCCCCCEEEEeCCCHHHHHHHHHHHHHCCCeEEEECCC
Confidence            567788888999887764332   2333344444444678  999999887654 457889999999999999875

>3d02_A Putative LACI-type transcriptional regulator; periplasmic sugar-binding protein, structura genomics; HET: MSE GOL; 1.30A {Klebsiella pneumoniae subsp}

Probab=93.11  E-value=0.28  Score=37.46  Aligned_cols=71  Identities=14%  Similarity=0.125  Sum_probs=48.8

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcc-hHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSD-FVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsD-F~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++..|+.+..+.+..  .|..-.....+.+..+++|.|++.+.+++ ...+++.+.+.|+.+|.++..
T Consensus        24 ~g~~~~~~~~g~~~~~~~~~~--~~~~~~~~~~~~l~~~~vdgiii~~~~~~~~~~~~~~~~~~~ipvV~~~~~   95 (303)
T 3d02_A           24 EGVVQAGKEFNLNASQVGPSS--TDAPQQVKIIEDLIARKVDAITIVPNDANVLEPVFKKARDAGIVVLTNESP   95 (303)
T ss_dssp             HHHHHHHHHTTEEEEEECCSS--SCHHHHHHHHHHHHHTTCSEEEECCSCHHHHHHHHHHHHHTTCEEEEESCT
T ss_pred             HHHHHHHHHcCCEEEEECCCC--CCHHHHHHHHHHHHHcCCCEEEEecCChHHHHHHHHHHHHCCCeEEEEecC
Confidence            467778888899887543221  12233333344444689999999887654 457889999999999999764

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

Probab=93.10  E-value=0.35  Score=38.18  Aligned_cols=69  Identities=12%  Similarity=0.094  Sum_probs=49.2

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++...|+.+.......+   ..-.....+.+..+++|.|++.+.+.+ .+.+..+.+.|..+|+++..
T Consensus        83 ~gi~~~~~~~g~~~~~~~~~~~---~~~~~~~~~~l~~~~vdgiI~~~~~~~-~~~~~~l~~~~iPvV~~~~~  151 (332)
T 2o20_A           83 RGVDDIASMYKYNMILANSDND---VEKEEKVLETFLSKQVDGIVYMGSSLD-EKIRTSLKNSRTPVVLVGTI  151 (332)
T ss_dssp             HHHHHHHHHTTCEEEEEECTTC---HHHHHHHHHHHHHTTCSEEEECSSCCC-HHHHHHHHHHCCCEEEESCC
T ss_pred             HHHHHHHHHcCCEEEEEECCCC---hHHHHHHHHHHHhCCCCEEEEeCCCCC-HHHHHHHHhCCCCEEEEccc
Confidence            4778889999999887644332   233334444444789999999885443 45677788899999999865

>2l82_A Designed protein OR32; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, de novo protein; NMR {Artificial gene}

Probab=92.95  E-value=0.32  Score=37.88  Aligned_cols=77  Identities=21%  Similarity=0.180  Sum_probs=53.1

Q ss_pred             HHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcC-Ccc-hHHHHHHHHHcCCeEEEEcCCCchHHHhhhh
Q 045172           68 ELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSD-DSD-FVEVFQEATLRWLKMVVVGDMSDGALKRIAN  145 (157)
Q Consensus        68 eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSD-DsD-F~~~lr~Arer~l~tVVVGd~~~~~L~r~AD  145 (157)
                      |....||-|+||+||..--  --++.+++--  -.+|.+|+|+- |.. ..+++.+|+|+|+.+.||=+..+..-+.-|.
T Consensus        47 efekqgvdvrtvedkedfr--enireiwery--pqldvvvivttddkewikdfieeakergvevfvvynnkdddrrkeaq  122 (162)
T 2l82_A           47 EFEKQGVDVRTVEDKEDFR--ENIREIWERY--PQLDVVVIVTTDDKEWIKDFIEEAKERGVEVFVVYNNKDDDRRKEAQ  122 (162)
T ss_dssp             HHHTTTCEEEECCSHHHHH--HHHHHHHHHC--TTCCEEEEEECCCHHHHHHHHHHHHHTTCEEEEEEECSCHHHHHHHH
T ss_pred             HHHHcCCceeeeccHHHHH--HHHHHHHHhC--CCCcEEEEEecCcHHHHHHHHHHHHhcCcEEEEEecCCCchhHHHHH
Confidence            5667899999999986521  1234455443  35677777764 444 3578999999999999998875555555565


Q ss_pred             ccc
Q 045172          146 AFF  148 (157)
Q Consensus       146 ~~f  148 (157)
                      .-|
T Consensus       123 qef  125 (162)
T 2l82_A          123 QEF  125 (162)
T ss_dssp             HHH
T ss_pred             HHh
Confidence            544

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

Probab=92.89  E-value=0.3  Score=37.47  Aligned_cols=68  Identities=7%  Similarity=0.139  Sum_probs=48.0

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++..|+.+.......   |..-...+.+.+..+++|.|++.+.+.+ .+.+..+. .|..+|+++..
T Consensus        28 ~gi~~~~~~~g~~~~~~~~~~---~~~~~~~~~~~l~~~~vdgiI~~~~~~~-~~~~~~l~-~~iPvV~~~~~   95 (285)
T 3c3k_A           28 KGIEKTAEKNGYRILLCNTES---DLARSRSCLTLLSGKMVDGVITMDALSE-LPELQNII-GAFPWVQCAEY   95 (285)
T ss_dssp             HHHHHHHHHTTCEEEEEECTT---CHHHHHHHTHHHHTTCCSEEEECCCGGG-HHHHHHHH-TTSSEEEESSC
T ss_pred             HHHHHHHHHcCCEEEEEeCCC---CHHHHHHHHHHHHhCCCCEEEEeCCCCC-hHHHHHHh-cCCCEEEEccc
Confidence            467788888999987765332   2333344455555789999999875543 35677777 99999999865

>3mmz_A Putative HAD family hydrolase; structural genomics, protein structure initiative, NEW YORK structural genomix research consortium; 1.84A {Streptomyces avermitilis}

Probab=92.88  E-value=0.38  Score=35.47  Aligned_cols=76  Identities=9%  Similarity=-0.010  Sum_probs=48.0

Q ss_pred             cHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHH-HHcC---CeEEEEcCC-CchH
Q 045172           65 FADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEA-TLRW---LKMVVVGDM-SDGA  139 (157)
Q Consensus        65 la~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~A-rer~---l~tVVVGd~-~~~~  139 (157)
                      +-.+|+..|+.+-.++.+|..    ..+.+   +...|++  +.-+..+. ...++.+ .+-|   -.+++|||+ +|-.
T Consensus        47 ~l~~L~~~g~~~~i~T~~~~~----~~~~~---~~~lgi~--~~~~~~~k-~~~l~~~~~~~~~~~~~~~~vGD~~nD~~  116 (176)
T 3mmz_A           47 GIAALRKSGLTMLILSTEQNP----VVAAR---ARKLKIP--VLHGIDRK-DLALKQWCEEQGIAPERVLYVGNDVNDLP  116 (176)
T ss_dssp             HHHHHHHTTCEEEEEESSCCH----HHHHH---HHHHTCC--EEESCSCH-HHHHHHHHHHHTCCGGGEEEEECSGGGHH
T ss_pred             HHHHHHHCCCeEEEEECcChH----HHHHH---HHHcCCe--eEeCCCCh-HHHHHHHHHHcCCCHHHEEEEcCCHHHHH
Confidence            457899999999999988872    11222   2344677  33333333 4444444 4444   468999999 7767


Q ss_pred             HHhhhhcccch
Q 045172          140 LKRIANAFFSW  150 (157)
Q Consensus       140 L~r~AD~~fsW  150 (157)
                      ..+.|++.+-+
T Consensus       117 ~~~~ag~~v~~  127 (176)
T 3mmz_A          117 CFALVGWPVAV  127 (176)
T ss_dssp             HHHHSSEEEEC
T ss_pred             HHHHCCCeEEC
Confidence            77777766644

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

Probab=92.85  E-value=0.24  Score=38.10  Aligned_cols=69  Identities=9%  Similarity=0.093  Sum_probs=49.6

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++++.|+.+...........   ...+.+++..+++|.|++++.+.+ .+.++.+.+.|..+|+++..
T Consensus        30 ~gi~~~a~~~g~~~~~~~~~~~~~~---~~~~~~~l~~~~vdgiIi~~~~~~-~~~~~~l~~~~iPvV~i~~~   98 (288)
T 3gv0_A           30 FGITEVLSTTQYHLVVTPHIHAKDS---MVPIRYILETGSADGVIISKIEPN-DPRVRFMTERNMPFVTHGRS   98 (288)
T ss_dssp             HHHHHHHTTSSCEEEECCBSSGGGT---THHHHHHHHHTCCSEEEEESCCTT-CHHHHHHHHTTCCEEEESCC
T ss_pred             HHHHHHHHHcCCEEEEecCCcchhH---HHHHHHHHHcCCccEEEEecCCCC-cHHHHHHhhCCCCEEEECCc
Confidence            4778889999999988754333222   233444455789999999875533 26788899999999999975

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

Probab=92.76  E-value=0.29  Score=37.02  Aligned_cols=68  Identities=9%  Similarity=0.052  Sum_probs=50.5

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHH-HHHHcCCeEEEEcCCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQ-EATLRWLKMVVVGDMS  136 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr-~Arer~l~tVVVGd~~  136 (157)
                      .|+..++...|+.+.......+   ......+.+.+..+++|+|++.+.+   .+.++ .+.+.|..+|++|...
T Consensus        28 ~gi~~~~~~~g~~~~~~~~~~~---~~~~~~~~~~l~~~~~dgiIi~~~~---~~~~~~~l~~~~iPvV~~~~~~   96 (277)
T 3e61_A           28 RGVEDVALAHGYQVLIGNSDND---IKKAQGYLATFVSHNCTGMISTAFN---ENIIENTLTDHHIPFVFIDRIN   96 (277)
T ss_dssp             HHHHHHHHHTTCCEEEEECTTC---HHHHHHHHHHHHHTTCSEEEECGGG---HHHHHHHHHHC-CCEEEGGGCC
T ss_pred             HHHHHHHHHCCCEEEEEeCCCC---HHHHHHHHHHHHhCCCCEEEEecCC---hHHHHHHHHcCCCCEEEEeccC
Confidence            5678889999999887655443   3444555555558999999999844   45678 8899999999998873

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

Probab=92.70  E-value=0.19  Score=38.64  Aligned_cols=70  Identities=6%  Similarity=0.000  Sum_probs=49.4

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++++.|+.+.......   |..-...+.+.+..+++|.|++++.+++=..++..+.+.|..+|+++..
T Consensus        40 ~gi~~~~~~~g~~~~~~~~~~---~~~~~~~~~~~l~~~~vdgii~~~~~~~~~~~~~~~~~~~iPvV~~~~~  109 (293)
T 2iks_A           40 NYLERQARQRGYQLLIACSED---QPDNEMRCIEHLLQRQVDAIIVSTSLPPEHPFYQRWANDPFPIVALDRA  109 (293)
T ss_dssp             HHHHHHHHHTTCEEEEEECTT---CHHHHHHHHHHHHHTTCSEEEECCSSCTTCHHHHTTTTSSSCEEEEESC
T ss_pred             HHHHHHHHHCCCEEEEEcCCC---CHHHHHHHHHHHHHcCCCEEEEeCCCCCcHHHHHHHHhCCCCEEEECCc
Confidence            477788889999888764332   2333334444444789999999876543245778888899999999865

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

Probab=92.67  E-value=0.28  Score=39.29  Aligned_cols=69  Identities=7%  Similarity=0.071  Sum_probs=49.2

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++...|+.+.......   |..-...+.+.+..+++|.|++.+.+.+ .+.++.+.+.|+.+|+++..
T Consensus        86 ~gi~~~a~~~g~~~~~~~~~~---~~~~~~~~~~~l~~~~vdgiI~~~~~~~-~~~~~~l~~~~iPvV~i~~~  154 (348)
T 3bil_A           86 TEIQSTASKAGLATIITNSNE---DATTMSGSLEFLTSHGVDGIICVPNEEC-ANQLEDLQKQGMPVVLVDRE  154 (348)
T ss_dssp             HHHHHHHHHTTCCEEEEECTT---CHHHHHHHHHHHHHTTCSCEEECCCGGG-HHHHHHHHHC-CCEEEESSC
T ss_pred             HHHHHHHHHcCCEEEEEeCCC---CHHHHHHHHHHHHhCCCCEEEEeCCCCC-hHHHHHHHhCCCCEEEEccc
Confidence            477788899999887764332   2333344455555789999999876654 46788888899999999865

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

Probab=92.65  E-value=0.23  Score=38.39  Aligned_cols=68  Identities=15%  Similarity=0.183  Sum_probs=50.0

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++.+.|+.+..........    ...+.+.+..+++|.|++.+.+.+- ..++.+.+.|+.+|+|+..
T Consensus        30 ~gi~~~a~~~g~~~~~~~~~~~~~----~~~~~~~l~~~~vdGiIi~~~~~~~-~~~~~l~~~~iPvV~~~~~   97 (294)
T 3qk7_A           30 SWIGIELGKRGLDLLLIPDEPGEK----YQSLIHLVETRRVDALIVAHTQPED-FRLQYLQKQNFPFLALGRS   97 (294)
T ss_dssp             HHHHHHHHHTTCEEEEEEECTTCC----CHHHHHHHHHTCCSEEEECSCCSSC-HHHHHHHHTTCCEEEESCC
T ss_pred             HHHHHHHHHCCCEEEEEeCCChhh----HHHHHHHHHcCCCCEEEEeCCCCCh-HHHHHHHhCCCCEEEECCC
Confidence            467888999999988874332111    2334455557899999999876543 7888999999999999875

>1tk9_A Phosphoheptose isomerase 1; lipopolysaccharide biosynthesis, structural genomics, NYSGXRC, LPC1_camje, PSI, protein structure initiative; 2.10A {Campylobacter jejuni} SCOP: c.80.1.3

Probab=92.38  E-value=0.12  Score=38.13  Aligned_cols=47  Identities=11%  Similarity=0.208  Sum_probs=39.2

Q ss_pred             CcceEEEEcC---CcchHHHHHHHHHcCCeEEEEcCCCchHHHhhhhccc
Q 045172          102 RFGCLVVVSD---DSDFVEVFQEATLRWLKMVVVGDMSDGALKRIANAFF  148 (157)
Q Consensus       102 ~v~clvLVSD---DsDF~~~lr~Arer~l~tVVVGd~~~~~L~r~AD~~f  148 (157)
                      .=|+++++|-   ..+-.++++.|+++|.++|.|-+..+..|.+.||..|
T Consensus       110 ~~Dvvi~iS~sG~t~~~~~~~~~ak~~g~~vi~iT~~~~s~L~~~ad~~l  159 (188)
T 1tk9_A          110 EKDVLIGISTSGKSPNVLEALKKAKELNMLCLGLSGKGGGMMNKLCDHNL  159 (188)
T ss_dssp             TTCEEEEECSSSCCHHHHHHHHHHHHTTCEEEEEEEGGGTTHHHHCSEEE
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHHHCCCEEEEEeCCCCcchHHcCCEEE
Confidence            4488888886   4567788899999999999998876678999999876

>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=92.37  E-value=0.33  Score=38.16  Aligned_cols=69  Identities=9%  Similarity=0.050  Sum_probs=51.0

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++...|+.+.......   |......+.+.+..+++|.|++.+.+.+ .+.+..+.+.|..+|+++..
T Consensus        80 ~gi~~~a~~~g~~~~~~~~~~---~~~~~~~~~~~l~~~~vdgiI~~~~~~~-~~~~~~l~~~~iPvV~~~~~  148 (332)
T 2hsg_A           80 RGIEDIATMYKYNIILSNSDQ---NQDKELHLLNNMLGKQVDGIIFMSGNVT-EEHVEELKKSPVPVVLAASI  148 (332)
T ss_dssp             HHHHHHHHHHTCEEEEEECCS---HHHHHHHHHHHTSCCSSCCEEECCSSCC-HHHHHHHTTSSSCEEEESCC
T ss_pred             HHHHHHHHHcCCEEEEEeCCC---ChHHHHHHHHHHHhCCCcEEEEecCCCC-HHHHHHHHhCCCCEEEEccc
Confidence            467788899999988764322   3444455566665799999999886554 36788888899999999865

>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=92.27  E-value=0.14  Score=39.04  Aligned_cols=71  Identities=8%  Similarity=0.100  Sum_probs=50.8

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcc-hHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSD-FVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsD-F~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++..|+.+....... ..|..-.....+.+..+++|.|++.+-+++ +...++.+. .|+.+|+++..
T Consensus        25 ~g~~~~a~~~g~~~~~~~~~~-~~~~~~~~~~~~~~~~~~vdgiii~~~~~~~~~~~~~~~~-~~iPvV~~~~~   96 (304)
T 3o1i_D           25 YGMVSEAEKQGVNLRVLEAGG-YPNKSRQEQQLALCTQWGANAIILGTVDPHAYEHNLKSWV-GNTPVFATVNQ   96 (304)
T ss_dssp             HHHHHHHHHHTCEEEEEECSS-TTCHHHHHHHHHHHHHHTCSEEEECCSSTTSSTTTHHHHT-TTSCEEECSSC
T ss_pred             HHHHHHHHHcCCeEEEEcCCC-CCCHHHHHHHHHHHHHcCCCEEEEeCCChhHHHHHHHHHc-CCCCEEEecCC
Confidence            467788889999988865443 123444444455444789999999876654 456788888 99999999655

>3bbl_A Regulatory protein of LACI family; protein structure initiative II, PSI-II, NYSGXRC, transcript regulator, periplasmic binding protein; 2.35A {Chloroflexus aggregans}

Probab=92.26  E-value=0.16  Score=39.05  Aligned_cols=69  Identities=10%  Similarity=0.015  Sum_probs=47.1

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++..|+.+.......+   ..-...+.+.+..+++|.|++.+.+.+ ...++.+.+.|..+|+++..
T Consensus        28 ~gi~~~a~~~g~~~~~~~~~~~---~~~~~~~~~~l~~~~vdgiIi~~~~~~-~~~~~~l~~~~iPvV~~~~~   96 (287)
T 3bbl_A           28 SSMVREAGAVNYFVLPFPFSED---RSQIDIYRDLIRSGNVDGFVLSSINYN-DPRVQFLLKQKFPFVAFGRS   96 (287)
T ss_dssp             HHHHHHHHHTTCEEEECCCCSS---TTCCHHHHHHHHTTCCSEEEECSCCTT-CHHHHHHHHTTCCEEEESCC
T ss_pred             HHHHHHHHHcCCEEEEEeCCCc---hHHHHHHHHHHHcCCCCEEEEeecCCC-cHHHHHHHhcCCCEEEECCc
Confidence            4677888899998877542211   111122334444789999999876543 26788888899999999865

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

Probab=92.26  E-value=0.42  Score=36.84  Aligned_cols=67  Identities=15%  Similarity=0.130  Sum_probs=47.9

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++++.|+.+..........    .....+.+..+++|.|++.+.+.+- ..++.+.+ |..+|+|+..
T Consensus        31 ~gi~~~a~~~g~~~~~~~~~~~~~----~~~~~~~l~~~~vdgiIi~~~~~~~-~~~~~~~~-~iPvV~i~~~   97 (289)
T 3k9c_A           31 EQIYAAATRRGYDVMLSAVAPSRA----EKVAVQALMRERCEAAILLGTRFDT-DELGALAD-RVPALVVARA   97 (289)
T ss_dssp             HHHHHHHHHTTCEEEEEEEBTTBC----HHHHHHHHTTTTEEEEEEETCCCCH-HHHHHHHT-TSCEEEESSC
T ss_pred             HHHHHHHHHCCCEEEEEeCCCCHH----HHHHHHHHHhCCCCEEEEECCCCCH-HHHHHHHc-CCCEEEEcCC
Confidence            467889999999888764333221    2233333447999999999876654 67777777 9999999976

>2xbl_A Phosphoheptose isomerase; capsule; HET: M7P PGE PG4; 1.62A {Burkholderia pseudomallei} PDB: 2x3y_A

Probab=92.16  E-value=0.21  Score=37.07  Aligned_cols=47  Identities=15%  Similarity=0.271  Sum_probs=39.0

Q ss_pred             CcceEEEEcCC---cchHHHHHHHHHcCCeEEEEcCCCchHHHhhhhccc
Q 045172          102 RFGCLVVVSDD---SDFVEVFQEATLRWLKMVVVGDMSDGALKRIANAFF  148 (157)
Q Consensus       102 ~v~clvLVSDD---sDF~~~lr~Arer~l~tVVVGd~~~~~L~r~AD~~f  148 (157)
                      .=|+++++|-.   .+-..+++.|+++|.++|.|-+..+..|.+.||..|
T Consensus       116 ~~d~vI~iS~SG~t~~~~~~~~~ak~~g~~vI~IT~~~~s~L~~~ad~~l  165 (198)
T 2xbl_A          116 EGDVLIGYSTSGKSPNILAAFREAKAKGMTCVGFTGNRGGEMRELCDLLL  165 (198)
T ss_dssp             TTCEEEEECSSSCCHHHHHHHHHHHHTTCEEEEEECSCCCTHHHHCSEEE
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHHHCCCeEEEEECCCCCcHHHhCCEEE
Confidence            45788888864   356778889999999999999986688999999876

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

Probab=92.01  E-value=0.46  Score=37.32  Aligned_cols=70  Identities=11%  Similarity=0.052  Sum_probs=48.7

Q ss_pred             CCcHHHHHhh-ceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcc-hHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRA-WFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSD-FVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRA-Gv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsD-F~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++... |+.+.......   |.......++.+..+++|.|++.+.+.+ +.+.++.+.+.|+.+|+++..
T Consensus        25 ~gi~~~a~~~~g~~l~i~~~~~---~~~~~~~~i~~l~~~~vdgiIi~~~~~~~~~~~~~~~~~~~iPvV~~~~~   96 (325)
T 2x7x_A           25 DEILREAMFYNGVSVEIRSAGD---DNSKQAEDVHYFMDEGVDLLIISANEAAPMTPIVEEAYQKGIPVILVDRK   96 (325)
T ss_dssp             HHHHHHHTTSSSCEEEEEECTT---CHHHHHHHHHHHHHTTCSEEEECCSSHHHHHHHHHHHHHTTCCEEEESSC
T ss_pred             HHHHHHHHHcCCcEEEEeCCCC---CHHHHHHHHHHHHHcCCCEEEEeCCCHHHHHHHHHHHHHCCCeEEEeCCC
Confidence            4666777777 88887654322   2233333444444689999999876654 467888899999999999865

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

Probab=91.87  E-value=0.16  Score=38.95  Aligned_cols=69  Identities=9%  Similarity=-0.040  Sum_probs=41.5

Q ss_pred             CCcHHHHHhhceEEEEe-cCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMV-LVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V-~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++++.|+.+... ....+   ..-...+.+.+..+++|.|++.+.+.+ ...++.+.+.|..+|+++..
T Consensus        28 ~gi~~~a~~~g~~~~~~~~~~~~---~~~~~~~~~~l~~~~vdgiI~~~~~~~-~~~~~~l~~~~iPvV~~~~~   97 (290)
T 3clk_A           28 DGIQEEAHKNGYNLIIVYSGSAD---PEEQKHALLTAIERPVMGILLLSIALT-DDNLQLLQSSDVPYCFLSMG   97 (290)
T ss_dssp             HHHHHHHHTTTCEEEEEC-------------CHHHHHHSSCCSEEEEESCC-----CHHHHHCC--CEEEESCC
T ss_pred             HHHHHHHHHcCCeEEEEeCCCCC---HHHHHHHHHHHHhcCCCEEEEecccCC-HHHHHHHHhCCCCEEEEcCC
Confidence            46778888899988776 33222   222233444444789999999876543 35677788899999999875

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

Probab=91.85  E-value=0.89  Score=34.42  Aligned_cols=69  Identities=12%  Similarity=0.078  Sum_probs=46.5

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHH-cCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATL-RWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Are-r~l~tVVVGd~  135 (157)
                      .|+..++++.|+.+.......   |..-...+.+.+...++|.|++.+.+.+ ..++..+.+ .|+.+|+++..
T Consensus        27 ~gi~~~~~~~g~~~~~~~~~~---~~~~~~~~~~~l~~~~vdgii~~~~~~~-~~~~~~l~~~~~iPvV~~~~~   96 (289)
T 1dbq_A           27 EAVEKNCFQKGYTLILGNAWN---NLEKQRAYLSMMAQKRVDGLLVMCSEYP-EPLLAMLEEYRHIPMVVMDWG   96 (289)
T ss_dssp             HHHHHHHHHHTCEEEEEECTT---CHHHHHHHHHHHHHTTCSEEEEECSCCC-HHHHHHHHHTTTSCEEEEECS
T ss_pred             HHHHHHHHHcCCeEEEEcCCC---ChHHHHHHHHHHHhCCCCEEEEEeccCC-HHHHHHHHhccCCCEEEEccC
Confidence            467778888999887764432   2333444455544789999999876653 234555555 79999999865

>2yj3_A Copper-transporting ATPase; hydrolase, P-type ATPase, COPB, heavy metal translocation; 2.20A {Sulfolobus solfataricus} PDB: 2iye_A 2yj6_A* 2yj5_A* 2yj4_A*

Probab=91.10  E-value=0.031  Score=44.15  Aligned_cols=81  Identities=14%  Similarity=0.164  Sum_probs=54.7

Q ss_pred             CcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC-CchHHHh
Q 045172           64 GFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM-SDGALKR  142 (157)
Q Consensus        64 gla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~-~~~~L~r  142 (157)
                      .+-.+|+..|+.+-+++.+|...       +...+...|++.++-..-..+|..+++.....+-.++.|||+ +|-.-.+
T Consensus       143 ~~l~~L~~~g~~~~i~T~~~~~~-------~~~~~~~~gl~~~f~~~~p~~k~~~~~~l~~~~~~~~~VGD~~~D~~aa~  215 (263)
T 2yj3_A          143 DYLEKLKNEGLKIIILSGDKEDK-------VKELSKELNIQEYYSNLSPEDKVRIIEKLKQNGNKVLMIGDGVNDAAALA  215 (263)
Confidence            44567899999999998887722       111222234432211111457888888888877889999999 6666778


Q ss_pred             hhhcccchh
Q 045172          143 IANAFFSWS  151 (157)
Q Consensus       143 ~AD~~fsW~  151 (157)
                      .|++.+.|.
T Consensus       216 ~Agv~va~g  224 (263)
T 2yj3_A          216 LADVSVAMG  224 (263)
Confidence            888888885

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

Probab=91.59  E-value=0.29  Score=37.12  Aligned_cols=72  Identities=15%  Similarity=0.177  Sum_probs=50.1

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCc-chHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDS-DFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDs-DF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++++.|+.+..+... ...|..-.....+.+..+++|.|++.+.++ ++.+.++.+.+.|..+|+++..
T Consensus        27 ~gi~~~a~~~g~~~~~~~~~-~~~~~~~~~~~~~~l~~~~vdgii~~~~~~~~~~~~~~~~~~~~iPvV~~~~~   99 (289)
T 3brs_A           27 EGAQMAAKEYEIKLEFMAPE-KEEDYLVQNELIEEAIKRKPDVILLAAADYEKTYDAAKEIKDAGIKLIVIDSG   99 (289)
T ss_dssp             HHHHHHHHHHTCEEEECCCS-STTCHHHHHHHHHHHHHTCCSEEEECCSCTTTTHHHHTTTGGGTCEEEEESSC
T ss_pred             HHHHHHHHHcCCEEEEecCC-CCCCHHHHHHHHHHHHHhCCCEEEEeCCChHHhHHHHHHHHHCCCcEEEECCC
Confidence            47778889999988876431 012223333344444478999999987554 4567888899999999999865

>3l8h_A Putative haloacid dehalogenase-like hydrolase; HAD superfamily, GMHB, D-glycero-D-manno-heptose-1, 7-bispho phosphatase; HET: FX1; 1.68A {Bordetella bronchiseptica}

Probab=91.44  E-value=0.94  Score=32.28  Aligned_cols=82  Identities=15%  Similarity=0.019  Sum_probs=45.3

Q ss_pred             CcHHHHHhhceEEEEecCCCcc-------HH-HHHHHHHHHHhhccC--cceEEEE----cCCcch-----HHHHHHHHH
Q 045172           64 GFADELKRAWFWVRMVLVKPQD-------AD-VLLRNYMVAMVDKRR--FGCLVVV----SDDSDF-----VEVFQEATL  124 (157)
Q Consensus        64 gla~eLrRAGv~V~~V~dkpqA-------AD-~AL~~~~~~~~~~r~--v~clvLV----SDDsDF-----~~~lr~Are  124 (157)
                      .+-.+|++.|+.+-.++..|..       .+ .++...+...+...|  ++.++..    |++...     .-+...+++
T Consensus        34 ~~l~~L~~~g~~~~i~Tn~~~~~~~~~~~~~~~~~~~~~~~~l~~~g~~~~~~~~~~~~~~~~~~~~KP~~~~~~~~~~~  113 (179)
T 3l8h_A           34 QAIARLTQADWTVVLATNQSGLARGLFDTATLNAIHDKMHRALAQMGGVVDAIFMCPHGPDDGCACRKPLPGMYRDIARR  113 (179)
T ss_dssp             HHHHHHHHTTCEEEEEEECTTTTTTSSCHHHHHHHHHHHHHHHHHTTCCCCEEEEECCCTTSCCSSSTTSSHHHHHHHHH
T ss_pred             HHHHHHHHCCCEEEEEECCCccccCcCCHHHHHHHHHHHHHHHHhCCCceeEEEEcCCCCCCCCCCCCCCHHHHHHHHHH
Confidence            3456788889999888888751       11 122344555555566  6665532    344321     223333333


Q ss_pred             cCC---eEEEEcCC-CchHHHhhhh
Q 045172          125 RWL---KMVVVGDM-SDGALKRIAN  145 (157)
Q Consensus       125 r~l---~tVVVGd~-~~~~L~r~AD  145 (157)
                      -|+   .+++|||+ +|-.-.+.|-
T Consensus       114 ~~~~~~~~~~vGD~~~Di~~a~~aG  138 (179)
T 3l8h_A          114 YDVDLAGVPAVGDSLRDLQAAAQAG  138 (179)
T ss_dssp             HTCCCTTCEEEESSHHHHHHHHHHT
T ss_pred             cCCCHHHEEEECCCHHHHHHHHHCC
Confidence            454   58888888 4444445554

>1m3s_A Hypothetical protein YCKF; structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; 1.95A {Bacillus subtilis} SCOP: c.80.1.3 PDB: 1viv_A

Probab=91.05  E-value=0.63  Score=34.28  Aligned_cols=71  Identities=11%  Similarity=0.053  Sum_probs=51.0

Q ss_pred             cHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCc---chHHHHHHHHHcCCeEEEEcCCCchHHH
Q 045172           65 FADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDS---DFVEVFQEATLRWLKMVVVGDMSDGALK  141 (157)
Q Consensus        65 la~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDs---DF~~~lr~Arer~l~tVVVGd~~~~~L~  141 (157)
                      ++..|.+.|+.+..+++- .          ...+  ..=|+++++|-.-   +-..+++.|+++|.++|.|-+..+..|.
T Consensus        55 ~~~~l~~~g~~~~~~~~~-~----------~~~~--~~~d~vI~iS~sG~t~~~~~~~~~ak~~g~~vi~IT~~~~s~l~  121 (186)
T 1m3s_A           55 FAMRLMHMGFNAHIVGEI-L----------TPPL--AEGDLVIIGSGSGETKSLIHTAAKAKSLHGIVAALTINPESSIG  121 (186)
T ss_dssp             HHHHHHHTTCCEEETTST-T----------CCCC--CTTCEEEEECSSSCCHHHHHHHHHHHHTTCEEEEEESCTTSHHH
T ss_pred             HHHHHHhcCCeEEEeCcc-c----------ccCC--CCCCEEEEEcCCCCcHHHHHHHHHHHHCCCEEEEEECCCCCchH
Confidence            345677899988887543 1          0111  2336777777543   4566788899999999999998667899


Q ss_pred             hhhhccc
Q 045172          142 RIANAFF  148 (157)
Q Consensus       142 r~AD~~f  148 (157)
                      +.||..+
T Consensus       122 ~~ad~~l  128 (186)
T 1m3s_A          122 KQADLII  128 (186)
T ss_dssp             HHCSEEE
T ss_pred             HhCCEEE
Confidence            9999876

>1x92_A APC5045, phosphoheptose isomerase; midwest centre for structural genomics, SIS domain, A/B protein, lipopolysaccharide biosynthesis, PSI; HET: M7P; 2.30A {Pseudomonas aeruginosa} SCOP: c.80.1.3 PDB: 3bjz_A

Probab=90.97  E-value=0.35  Score=36.13  Aligned_cols=47  Identities=15%  Similarity=0.237  Sum_probs=38.8

Q ss_pred             CcceEEEEcCC---cchHHHHHHHHHcCCeEEEEcCCCchHHHhh---hhccc
Q 045172          102 RFGCLVVVSDD---SDFVEVFQEATLRWLKMVVVGDMSDGALKRI---ANAFF  148 (157)
Q Consensus       102 ~v~clvLVSDD---sDF~~~lr~Arer~l~tVVVGd~~~~~L~r~---AD~~f  148 (157)
                      .=|+++++|-.   .+-.++++.|+++|.+||.|-+.....|.+.   ||..|
T Consensus       113 ~~DvvI~iS~SG~t~~~i~~~~~ak~~g~~vI~IT~~~~s~La~~~~~ad~~l  165 (199)
T 1x92_A          113 PGDVLLAISTSGNSANVIQAIQAAHDREMLVVALTGRDGGGMASLLLPEDVEI  165 (199)
T ss_dssp             TTCEEEEECSSSCCHHHHHHHHHHHHTTCEEEEEECTTCHHHHHHCCTTCEEE
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHHHCCCEEEEEECCCCCcHHhccccCCEEE
Confidence            44777777754   4567788999999999999999877899999   99876

>1jeo_A MJ1247, hypothetical protein MJ1247; RUMP pathway, phosphosugar, 3-hexulose-6-phosphate isomerase structural genomics; HET: CME CIT; 2.00A {Methanocaldococcus jannaschii} SCOP: c.80.1.3

Probab=90.74  E-value=0.3  Score=35.83  Aligned_cols=70  Identities=14%  Similarity=0.081  Sum_probs=50.3

Q ss_pred             cHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCc---chHHHHHHHHHcCCeEEEEcCCCchHHH
Q 045172           65 FADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDS---DFVEVFQEATLRWLKMVVVGDMSDGALK  141 (157)
Q Consensus        65 la~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDs---DF~~~lr~Arer~l~tVVVGd~~~~~L~  141 (157)
                      ++..|.+.|..|..++|- .          ...+  ..=|+++++|-.-   +...+++.|+++|.++|.|-+..+. |.
T Consensus        58 ~~~~l~~~g~~~~~~~~~-~----------~~~~--~~~d~vi~iS~sG~t~~~~~~~~~ak~~g~~vi~IT~~~~s-l~  123 (180)
T 1jeo_A           58 FAMRLMHLGFKSYFVGET-T----------TPSY--EKDDLLILISGSGRTESVLTVAKKAKNINNNIIAIVCECGN-VV  123 (180)
T ss_dssp             HHHHHHHTTCCEEETTST-T----------CCCC--CTTCEEEEEESSSCCHHHHHHHHHHHTTCSCEEEEESSCCG-GG
T ss_pred             HHHHHHHcCCeEEEeCCC-c----------cccC--CCCCEEEEEeCCCCcHHHHHHHHHHHHCCCcEEEEeCCCCh-HH
Confidence            345567889999887542 1          0111  2337788888654   4566788899999999999998667 99


Q ss_pred             hhhhccc
Q 045172          142 RIANAFF  148 (157)
Q Consensus       142 r~AD~~f  148 (157)
                      +.||..+
T Consensus       124 ~~ad~~l  130 (180)
T 1jeo_A          124 EFADLTI  130 (180)
T ss_dssp             GGCSEEE
T ss_pred             HhCCEEE
Confidence            9999876

>2i2w_A Phosphoheptose isomerase; lipopolysaccharide biosynthesis; 1.95A {Escherichia coli} PDB: 2i22_A 1x94_A

Probab=90.63  E-value=0.24  Score=37.95  Aligned_cols=79  Identities=13%  Similarity=0.153  Sum_probs=51.9

Q ss_pred             HHhhceEEEEecCCCcc----H----HHHHHHHHHHHhhccCcceEEEEcCC---cchHHHHHHHHHcCCeEEEEcCCCc
Q 045172           69 LKRAWFWVRMVLVKPQD----A----DVLLRNYMVAMVDKRRFGCLVVVSDD---SDFVEVFQEATLRWLKMVVVGDMSD  137 (157)
Q Consensus        69 LrRAGv~V~~V~dkpqA----A----D~AL~~~~~~~~~~r~v~clvLVSDD---sDF~~~lr~Arer~l~tVVVGd~~~  137 (157)
                      +.+.|+.+..++|....    .    +..++......+  ..=|+++++|-.   .+-.++++.|+++|.+||.|-+..+
T Consensus        92 ~~~~g~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~--~~~DvvI~iS~SG~t~~~i~~~~~ak~~G~~vIaIT~~~~  169 (212)
T 2i2w_A           92 ENRPGYPAIAISDVSHISCVGNDFGFNDIFSRYVEAVG--REGDVLLGISTSGNSANVIKAIAAAREKGMKVITLTGKDG  169 (212)
T ss_dssp             TTSSSCSEEECCCTTCGGGGSCCCSCSSHHHHHHHHHC--CTTCEEEEECSSSCCHHHHHHHHHHHHHTCEEEEEEETTC
T ss_pred             ccCCCCeEEecCChHHhhHhhccCCHHHHHHHHHHhcC--CCCCEEEEEECCCCCHHHHHHHHHHHHCCCeEEEEECCCC
Confidence            34578888776633210    0    011222222223  345788888754   4567788899999999999999867


Q ss_pred             hHHHhhhhcccc
Q 045172          138 GALKRIANAFFS  149 (157)
Q Consensus       138 ~~L~r~AD~~fs  149 (157)
                      ..|.+.||.-|.
T Consensus       170 s~La~~aD~~l~  181 (212)
T 2i2w_A          170 GKMAGTADIEIR  181 (212)
T ss_dssp             GGGTTCSSEEEE
T ss_pred             CchHHhCCEEEE
Confidence            889999998763

>1vim_A Hypothetical protein AF1796; structural genomics, unknown function; 1.36A {Archaeoglobus fulgidus} SCOP: c.80.1.3

Probab=90.62  E-value=0.33  Score=36.92  Aligned_cols=71  Identities=23%  Similarity=0.214  Sum_probs=52.3

Q ss_pred             cHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCC---cchHHHHHHHHHcCCeEEEEcCCCchHHH
Q 045172           65 FADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDD---SDFVEVFQEATLRWLKMVVVGDMSDGALK  141 (157)
Q Consensus        65 la~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDD---sDF~~~lr~Arer~l~tVVVGd~~~~~L~  141 (157)
                      ++..|.+.|..|..++|- .+          ..+  ..=|+++++|-.   .+-.++++.|+++|+++|.|-+.....|.
T Consensus        65 ~~~~l~~~g~~~~~~~~~-~~----------~~~--~~~DvvI~iS~SG~t~~~i~~~~~ak~~g~~vI~IT~~~~s~La  131 (200)
T 1vim_A           65 FAMRLMHLGYTVYVVGET-VT----------PRI--TDQDVLVGISGSGETTSVVNISKKAKDIGSKLVAVTGKRDSSLA  131 (200)
T ss_dssp             HHHHHHHTTCCEEETTST-TC----------CCC--CTTCEEEEECSSSCCHHHHHHHHHHHHHTCEEEEEESCTTSHHH
T ss_pred             HHHHHHhcCCeEEEeCCc-cc----------cCC--CCCCEEEEEeCCCCcHHHHHHHHHHHHCCCeEEEEECCCCChHH
Confidence            344677889988887542 10          011  233788888854   45677888999999999999998678999


Q ss_pred             hhhhccc
Q 045172          142 RIANAFF  148 (157)
Q Consensus       142 r~AD~~f  148 (157)
                      +.||..|
T Consensus       132 ~~ad~~l  138 (200)
T 1vim_A          132 KMADVVM  138 (200)
T ss_dssp             HHCSEEE
T ss_pred             HhCCEEE
Confidence            9999877

>3fxa_A SIS domain protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE; 1.60A {Listeria monocytogenes str}

Probab=90.18  E-value=0.25  Score=37.16  Aligned_cols=76  Identities=11%  Similarity=0.192  Sum_probs=51.3

Q ss_pred             HHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCc---chHHHHHHHHHcCCeEEEEcCCCchHHHh
Q 045172           66 ADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDS---DFVEVFQEATLRWLKMVVVGDMSDGALKR  142 (157)
Q Consensus        66 a~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDs---DF~~~lr~Arer~l~tVVVGd~~~~~L~r  142 (157)
                      +..|.+.|..+..+++    .+  ........+  ..=|+++++|-.-   +-..+++.|+++|.++|.|-+.....|.+
T Consensus        64 ~~~l~~~g~~~~~~~~----~~--~~~~~~~~~--~~~dvvI~iS~sG~t~~~~~~~~~ak~~g~~vi~IT~~~~s~l~~  135 (201)
T 3fxa_A           64 VHSFNCIERPAVFLTP----SD--AVHGTLGVL--QKEDILILISKGGNTGELLNLIPACKTKGSTLIGVTENPDSVIAK  135 (201)
T ss_dssp             HHHHHHTTCCEEECCH----HH--HTTTGGGGC--CTTCEEEEECSSSCCHHHHTTHHHHHHHTCEEEEEESCTTSHHHH
T ss_pred             HHHHHhcCCcEEEeCc----hH--HHhhhhhcC--CCCCEEEEEeCCCCCHHHHHHHHHHHHcCCeEEEEECCCCChhHH
Confidence            3457788998888643    11  110001112  1227888887653   45567789999999999999987789999


Q ss_pred             hhhcccc
Q 045172          143 IANAFFS  149 (157)
Q Consensus       143 ~AD~~fs  149 (157)
                      .||..+.
T Consensus       136 ~ad~~l~  142 (201)
T 3fxa_A          136 EADIFFP  142 (201)
T ss_dssp             HCSEEEE
T ss_pred             hCCEEEE
Confidence            9998873

>2xhz_A KDSD, YRBH, arabinose 5-phosphate isomerase; lipopolysaccharide biogenesis; 2.60A {Escherichia coli}

Probab=89.96  E-value=0.41  Score=35.11  Aligned_cols=76  Identities=7%  Similarity=0.089  Sum_probs=52.1

Q ss_pred             cHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhc-cCcceEEEEcCCc---chHHHHHHHHHcCCeEEEEcCCCchHH
Q 045172           65 FADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDK-RRFGCLVVVSDDS---DFVEVFQEATLRWLKMVVVGDMSDGAL  140 (157)
Q Consensus        65 la~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~-r~v~clvLVSDDs---DF~~~lr~Arer~l~tVVVGd~~~~~L  140 (157)
                      ++..|.+.|..+..+++-    + .+    ...+.. ..=|+++++|-.-   +-.++++.|+++|.++|.|-+..+..|
T Consensus        67 ~~~~l~~~g~~~~~~~~~----~-~~----~~~~~~~~~~d~vI~iS~sG~t~~~~~~~~~ak~~g~~vi~IT~~~~s~l  137 (183)
T 2xhz_A           67 MAATFASTGTPSFFVHPG----E-AA----HGDLGMVTPQDVVIAISNSGESSEITALIPVLKRLHVPLICITGRPESSM  137 (183)
T ss_dssp             HHHHHHTTTCCEEECCTT----H-HH----HHTSTTCCTTCEEEEECSSSCCHHHHHHHHHHHTTTCCEEEEESCTTSHH
T ss_pred             HHHHHHhcCceEEEeCch----H-Hh----hhhhccCCCCCEEEEEeCCCCCHHHHHHHHHHHHCCCCEEEEECCCCChh
Confidence            345677889988887532    1 11    111111 2337888888643   456677889999999999999867899


Q ss_pred             Hhhhhcccc
Q 045172          141 KRIANAFFS  149 (157)
Q Consensus       141 ~r~AD~~fs  149 (157)
                      .+.||..+.
T Consensus       138 a~~ad~~l~  146 (183)
T 2xhz_A          138 ARAADVHLC  146 (183)
T ss_dssp             HHHSSEEEE
T ss_pred             HHhCCEEEE
Confidence            999998763

>2yva_A DNAA initiator-associating protein DIAA; intermolecular disulfide bonding, putative phosphosugar BIND protein, DNAA binding protein; 1.85A {Escherichia coli}

Probab=89.81  E-value=0.51  Score=35.08  Aligned_cols=47  Identities=19%  Similarity=0.279  Sum_probs=38.1

Q ss_pred             CcceEEEEcCC---cchHHHHHHHHHcCCeEEEEcCCCchHHHhh---hhccc
Q 045172          102 RFGCLVVVSDD---SDFVEVFQEATLRWLKMVVVGDMSDGALKRI---ANAFF  148 (157)
Q Consensus       102 ~v~clvLVSDD---sDF~~~lr~Arer~l~tVVVGd~~~~~L~r~---AD~~f  148 (157)
                      .=|+++.+|-.   .+-.++++.|+++|.+||.|-+.....|.+.   ||..+
T Consensus       109 ~~DvvI~iS~SG~t~~~i~~~~~ak~~g~~vI~IT~~~~s~la~~~~~ad~~l  161 (196)
T 2yva_A          109 AGDVLLAISTRGNSRDIVKAVEAAVTRDMTIVALTGYDGGELAGLLGPQDVEI  161 (196)
T ss_dssp             TTCEEEEECSSSCCHHHHHHHHHHHHTTCEEEEEECTTCHHHHTTCCTTSEEE
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHHHCCCEEEEEeCCCCchhhhcccCCCEEE
Confidence            44777777754   4567788899999999999999866889998   88866

>3j08_A COPA, copper-exporting P-type ATPase A; copper transporter, adenosine triphosph archaeal proteins, cation transport proteins; 10.00A {Archaeoglobus fulgidus}

Probab=89.81  E-value=0.66  Score=42.13  Aligned_cols=77  Identities=17%  Similarity=0.084  Sum_probs=58.7

Q ss_pred             HHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC-CchHHHhhhh
Q 045172           67 DELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM-SDGALKRIAN  145 (157)
Q Consensus        67 ~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~-~~~~L~r~AD  145 (157)
                      .+|+++|+.|-+++..+...       +...+...|++.++.-....+=..+++...+. -.++.|||+ +|-.--+.||
T Consensus       467 ~~L~~~Gi~v~~~TGd~~~~-------a~~ia~~lgi~~~~~~~~P~~K~~~v~~l~~~-~~v~~vGDg~ND~~al~~A~  538 (645)
T 3j08_A          467 QELKRMGIKVGMITGDNWRS-------AEAISRELNLDLVIAEVLPHQKSEEVKKLQAK-EVVAFVGDGINDAPALAQAD  538 (645)
T ss_dssp             HHHHHTTCEEEEECSSCHHH-------HHHHHHHHTCSEEECSCCTTCHHHHHHHHTTT-CCEEEEECSSSCHHHHHHSS
T ss_pred             HHHHHCCCEEEEEeCCCHHH-------HHHHHHHcCCCEEEEeCCHHhHHHHHHHHhhC-CeEEEEeCCHhHHHHHHhCC
Confidence            56889999999998887622       22233456787777666677888889888887 778999999 8877778899


Q ss_pred             cccchh
Q 045172          146 AFFSWS  151 (157)
Q Consensus       146 ~~fsW~  151 (157)
                      +.+.+.
T Consensus       539 vgiamg  544 (645)
T 3j08_A          539 LGIAVG  544 (645)
T ss_dssp             EEEEEC
T ss_pred             EEEEeC
Confidence            988774

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

Probab=89.78  E-value=0.13  Score=39.73  Aligned_cols=68  Identities=12%  Similarity=-0.041  Sum_probs=50.2

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++++.|+.+........   ..-...+.+.+..+++|.|++.+.+.+=  .+..+.+.|+.+|+||..
T Consensus        34 ~gi~~~a~~~g~~~~~~~~~~~---~~~~~~~~~~l~~~~vdGiIi~~~~~~~--~~~~~~~~~iPvV~~~~~  101 (301)
T 3miz_A           34 RGIQDWANANGKTILIANTGGS---SEREVEIWKMFQSHRIDGVLYVTMYRRI--VDPESGDVSIPTVMINCR  101 (301)
T ss_dssp             HHHHHHHHHTTCEEEEEECTTC---HHHHHHHHHHHHHTTCSEEEEEEEEEEE--CCCCCTTCCCCEEEEEEE
T ss_pred             HHHHHHHHHCCCEEEEEeCCCC---hHHHHHHHHHHHhCCCCEEEEecCCccH--HHHHHHhCCCCEEEECCC
Confidence            4578899999999988654322   3334455556668999999998865443  677788899999999865

>3skx_A Copper-exporting P-type ATPase B; P1B-ATPase, ATP binding domain, copper(II) transporter, MEMB protein, hydrolase; 1.59A {Archaeoglobus fulgidus} PDB: 3sky_A*

Probab=89.68  E-value=1.1  Score=33.61  Aligned_cols=79  Identities=13%  Similarity=0.069  Sum_probs=49.3

Q ss_pred             cHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC-CchHHHhh
Q 045172           65 FADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM-SDGALKRI  143 (157)
Q Consensus        65 la~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~-~~~~L~r~  143 (157)
                      +-.+|+..|+.+-.++.+|...    ...+.   ...|++..+-..-.++=+..++..-+.. .+++|||+ +|-...+.
T Consensus       152 ~l~~l~~~g~~~~i~T~~~~~~----~~~~~---~~~gl~~~f~~~~~~~k~~~~k~~~~~~-~~~~vGD~~nDi~~~~~  223 (280)
T 3skx_A          152 AISKLKAIGIKCMMLTGDNRFV----AKWVA---EELGLDDYFAEVLPHEKAEKVKEVQQKY-VTAMVGDGVNDAPALAQ  223 (280)
T ss_dssp             HHHHHHHTTCEEEEECSSCHHH----HHHHH---HHHTCSEEECSCCGGGHHHHHHHHHTTS-CEEEEECTTTTHHHHHH
T ss_pred             HHHHHHHCCCEEEEEeCCCHHH----HHHHH---HHcCChhHhHhcCHHHHHHHHHHHHhcC-CEEEEeCCchhHHHHHh
Confidence            3457888899999998888621    12222   2335543332222234445555555543 88999999 77777888


Q ss_pred             hhcccchh
Q 045172          144 ANAFFSWS  151 (157)
Q Consensus       144 AD~~fsW~  151 (157)
                      |++.+.|.
T Consensus       224 Ag~~va~~  231 (280)
T 3skx_A          224 ADVGIAIG  231 (280)
T ss_dssp             SSEEEECS
T ss_pred             CCceEEec
Confidence            88877774

>3e8m_A Acylneuraminate cytidylyltransferase; 2-keto-3-deoxynononic acid 9-phosphate phosphohydrolase, nucleotidyltransferase; HET: PEG PG4 EDO PGE; 1.10A {Bacteroides thetaiotaomicron} PDB: 3e84_A 3e81_A*

Probab=89.66  E-value=1.2  Score=31.54  Aligned_cols=75  Identities=9%  Similarity=-0.038  Sum_probs=43.2

Q ss_pred             HHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCC---eEEEEcCC-CchHHH
Q 045172           66 ADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWL---KMVVVGDM-SDGALK  141 (157)
Q Consensus        66 a~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l---~tVVVGd~-~~~~L~  141 (157)
                      -..|++.|+.+-.++..|..       .+...+...|++.++-.. -++-..+...+++-|+   .+++|||+ +|-...
T Consensus        40 l~~l~~~g~~~~i~T~~~~~-------~~~~~~~~~gl~~~~~~~-kpk~~~~~~~~~~~~~~~~~~~~vGD~~~Di~~~  111 (164)
T 3e8m_A           40 IFWAHNKGIPVGILTGEKTE-------IVRRRAEKLKVDYLFQGV-VDKLSAAEELCNELGINLEQVAYIGDDLNDAKLL  111 (164)
T ss_dssp             HHHHHHTTCCEEEECSSCCH-------HHHHHHHHTTCSEEECSC-SCHHHHHHHHHHHHTCCGGGEEEECCSGGGHHHH
T ss_pred             HHHHHHCCCEEEEEeCCChH-------HHHHHHHHcCCCEeeccc-CChHHHHHHHHHHcCCCHHHEEEECCCHHHHHHH
Confidence            57789999999999998861       122222344665433222 2222233333333443   68888888 665666


Q ss_pred             hhhhccc
Q 045172          142 RIANAFF  148 (157)
Q Consensus       142 r~AD~~f  148 (157)
                      +.|++.+
T Consensus       112 ~~ag~~~  118 (164)
T 3e8m_A          112 KRVGIAG  118 (164)
T ss_dssp             TTSSEEE
T ss_pred             HHCCCeE
Confidence            6666554

>3ij5_A 3-deoxy-D-manno-octulosonate 8-phosphate phosphat; IDP022 hydrolase, lipopolysaccharide biosynthesis, magnesium, STRU genomics; 1.95A {Yersinia pestis}

Probab=89.64  E-value=0.93  Score=35.10  Aligned_cols=75  Identities=13%  Similarity=-0.026  Sum_probs=47.0

Q ss_pred             cHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHH-cC---CeEEEEcCC-CchH
Q 045172           65 FADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATL-RW---LKMVVVGDM-SDGA  139 (157)
Q Consensus        65 la~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Are-r~---l~tVVVGd~-~~~~  139 (157)
                      +-.+|+.+|+.+-.++.+|..    ....   .+...|++.++-..  .+=.++++.+.+ -|   -.+++|||+ +|-.
T Consensus        84 ~L~~L~~~G~~l~I~T~~~~~----~~~~---~l~~lgi~~~f~~~--k~K~~~l~~~~~~lg~~~~~~~~vGDs~nDi~  154 (211)
T 3ij5_A           84 GIRCLITSDIDVAIITGRRAK----LLED---RANTLGITHLYQGQ--SDKLVAYHELLATLQCQPEQVAYIGDDLIDWP  154 (211)
T ss_dssp             HHHHHHHTTCEEEEECSSCCH----HHHH---HHHHHTCCEEECSC--SSHHHHHHHHHHHHTCCGGGEEEEECSGGGHH
T ss_pred             HHHHHHHCCCEEEEEeCCCHH----HHHH---HHHHcCCchhhccc--CChHHHHHHHHHHcCcCcceEEEEcCCHHHHH
Confidence            447899999999999999872    1122   22334665433322  233455555544 34   468999999 6666


Q ss_pred             HHhhhhccc
Q 045172          140 LKRIANAFF  148 (157)
Q Consensus       140 L~r~AD~~f  148 (157)
                      ..+.|++.+
T Consensus       155 ~~~~ag~~~  163 (211)
T 3ij5_A          155 VMAQVGLSV  163 (211)
T ss_dssp             HHTTSSEEE
T ss_pred             HHHHCCCEE
Confidence            677777654

>3a1c_A Probable copper-exporting P-type ATPase A; ATP-binding, cell membrane, copper transport, hydrolase, ION transport, magnesium, membrane; HET: ACP; 1.85A {Archaeoglobus fulgidus} PDB: 3a1d_A* 3a1e_A* 2b8e_A 2voy_J 2voy_I

Probab=89.38  E-value=1  Score=35.39  Aligned_cols=79  Identities=15%  Similarity=0.065  Sum_probs=49.7

Q ss_pred             cHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC-CchHHHhh
Q 045172           65 FADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM-SDGALKRI  143 (157)
Q Consensus        65 la~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~-~~~~L~r~  143 (157)
                      +-..|+..|+.+-.++..|...    ...+.   ...|++.++-..-..+....++..... -.+++|||+ +|-...+.
T Consensus       171 ~l~~L~~~g~~~~i~T~~~~~~----~~~~l---~~~gl~~~f~~i~~~~K~~~~~~l~~~-~~~~~vGDs~~Di~~a~~  242 (287)
T 3a1c_A          171 AVQELKRMGIKVGMITGDNWRS----AEAIS---RELNLDLVIAEVLPHQKSEEVKKLQAK-EVVAFVGDGINDAPALAQ  242 (287)
T ss_dssp             HHHHHHHTTCEEEEECSSCHHH----HHHHH---HHHTCSEEECSCCTTCHHHHHHHHTTT-CCEEEEECTTTCHHHHHH
T ss_pred             HHHHHHHCCCeEEEEeCCCHHH----HHHHH---HHhCCceeeeecChHHHHHHHHHHhcC-CeEEEEECCHHHHHHHHH
Confidence            4457888999999999998731    12222   223554332111123566666666655 679999999 66667777


Q ss_pred             hhcccchh
Q 045172          144 ANAFFSWS  151 (157)
Q Consensus       144 AD~~fsW~  151 (157)
                      |++.+.|.
T Consensus       243 ag~~v~~~  250 (287)
T 3a1c_A          243 ADLGIAVG  250 (287)
T ss_dssp             SSEEEEEC
T ss_pred             CCeeEEeC
Confidence            88776663

>3etn_A Putative phosphosugar isomerase involved in capsu formation; YP_209877.1; HET: MSE CMK; 1.70A {Bacteroides fragilis nctc 9343}

Probab=89.23  E-value=0.53  Score=36.55  Aligned_cols=77  Identities=17%  Similarity=0.160  Sum_probs=54.1

Q ss_pred             cHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCC---cchHHHHHHHHH--cCCeEEEEcCCCchH
Q 045172           65 FADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDD---SDFVEVFQEATL--RWLKMVVVGDMSDGA  139 (157)
Q Consensus        65 la~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDD---sDF~~~lr~Are--r~l~tVVVGd~~~~~  139 (157)
                      ++..|.+.|+.+..+++.-...      .....+  ..=|+++++|-.   .+-..+++.|++  +|.++|.|-+.....
T Consensus        77 ~~~~l~~lg~~~~~~~~~~~~~------~~~~~~--~~~DlvI~iS~SG~t~~~i~~~~~ak~~~~Ga~vI~IT~~~~s~  148 (220)
T 3etn_A           77 IATTFCSTGIPSVFLHPSEAQH------GDLGIL--QENDLLLLISNSGKTREIVELTQLAHNLNPGLKFIVITGNPDSP  148 (220)
T ss_dssp             HHHHHHHTTCCEEECCTTGGGB------TGGGGC--CTTCEEEEECSSSCCHHHHHHHHHHHHHCTTCEEEEEESCTTSH
T ss_pred             HHHHHHhcCCcEEEeCCHHHHH------hhhccC--CCCCEEEEEcCCCCCHHHHHHHHHHHhcCCCCeEEEEECCCCCh
Confidence            4556889999998875432100      001112  223778887754   456678899999  999999999987789


Q ss_pred             HHhhhhcccc
Q 045172          140 LKRIANAFFS  149 (157)
Q Consensus       140 L~r~AD~~fs  149 (157)
                      |.+.||..+.
T Consensus       149 La~~aD~~l~  158 (220)
T 3etn_A          149 LASESDVCLS  158 (220)
T ss_dssp             HHHHSSEEEE
T ss_pred             hHHhCCEEEE
Confidence            9999998774

>3n07_A 3-deoxy-D-manno-octulosonate 8-phosphate phosphat; structural genomics, phosphatase, PSI-2, protein structure initiative; HET: MSE; 1.76A {Vibrio cholerae}

Probab=89.16  E-value=1.3  Score=33.79  Aligned_cols=75  Identities=8%  Similarity=0.006  Sum_probs=46.1

Q ss_pred             HHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCC---eEEEEcCC-CchHHH
Q 045172           66 ADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWL---KMVVVGDM-SDGALK  141 (157)
Q Consensus        66 a~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l---~tVVVGd~-~~~~L~  141 (157)
                      -..|+.+|+.+-.++.+|..       .+...+...|++.++--. .+.-..+...+.+-|+   .+++|||+ +|-...
T Consensus        61 l~~L~~~G~~~~ivT~~~~~-------~~~~~l~~lgi~~~~~~~-k~k~~~~~~~~~~~~~~~~~~~~vGD~~nDi~~~  132 (195)
T 3n07_A           61 VKALMNAGIEIAIITGRRSQ-------IVENRMKALGISLIYQGQ-DDKVQAYYDICQKLAIAPEQTGYIGDDLIDWPVM  132 (195)
T ss_dssp             HHHHHHTTCEEEEECSSCCH-------HHHHHHHHTTCCEEECSC-SSHHHHHHHHHHHHCCCGGGEEEEESSGGGHHHH
T ss_pred             HHHHHHCCCEEEEEECcCHH-------HHHHHHHHcCCcEEeeCC-CCcHHHHHHHHHHhCCCHHHEEEEcCCHHHHHHH
Confidence            36789999999999998872       112222345665443222 3333444444455565   68999999 666666


Q ss_pred             hhhhccc
Q 045172          142 RIANAFF  148 (157)
Q Consensus       142 r~AD~~f  148 (157)
                      +.|++.+
T Consensus       133 ~~ag~~v  139 (195)
T 3n07_A          133 EKVALRV  139 (195)
T ss_dssp             TTSSEEE
T ss_pred             HHCCCEE
Confidence            6666554

>3trj_A Phosphoheptose isomerase; lipopolysaccharide biosynthesis; 2.80A {Francisella tularensis subsp}

Probab=88.84  E-value=0.44  Score=36.69  Aligned_cols=48  Identities=19%  Similarity=0.259  Sum_probs=39.8

Q ss_pred             cCcceEEEEcCC---cchHHHHHHHHHcCCeEEEEcCCCchHHHhhh---hccc
Q 045172          101 RRFGCLVVVSDD---SDFVEVFQEATLRWLKMVVVGDMSDGALKRIA---NAFF  148 (157)
Q Consensus       101 r~v~clvLVSDD---sDF~~~lr~Arer~l~tVVVGd~~~~~L~r~A---D~~f  148 (157)
                      ..=|+++.+|-.   .+-..+++.|+++|.++|.|-+.....|.+.|   |..+
T Consensus       113 ~~~Dvvi~iS~SG~t~~~~~~~~~ak~~g~~vi~iT~~~~s~la~~a~~~d~~l  166 (201)
T 3trj_A          113 NEDDILLVITTSGDSENILSAVEEAHDLEMKVIALTGGSGGALQNMYNTDDIEL  166 (201)
T ss_dssp             CTTCEEEEECSSSCCHHHHHHHHHHHHTTCEEEEEEETTCCGGGGTCCTTCEEE
T ss_pred             CCCCEEEEEeCCCCCHHHHHHHHHHHHCCCcEEEEECCCCCHHHHhhccCCEEE
Confidence            345888888864   56778889999999999999887668999999   9866

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

Probab=88.74  E-value=0.24  Score=37.92  Aligned_cols=64  Identities=5%  Similarity=0.021  Sum_probs=46.7

Q ss_pred             CCcHHHHHhhceE-EEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFW-VRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~-V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++++.|+. +........   ..-...+.+.+..+++|.|++.+      +.+..+.+.|..+|+++..
T Consensus        30 ~gi~~~a~~~g~~~~~~~~~~~~---~~~~~~~~~~l~~~~vdgiIi~~------~~~~~~~~~~iPvV~~~~~   94 (277)
T 3hs3_A           30 DGIQEVIQKEGYTALISFSTNSD---VKKYQNAIINFENNNVDGIITSA------FTIPPNFHLNTPLVMYDSA   94 (277)
T ss_dssp             HHHHHHHHHTTCEEEEEECSSCC---HHHHHHHHHHHHHTTCSEEEEEC------CCCCTTCCCSSCEEEESCC
T ss_pred             HHHHHHHHHCCCCEEEEEeCCCC---hHHHHHHHHHHHhCCCCEEEEcc------hHHHHHHhCCCCEEEEccc
Confidence            4678889999999 766544433   33345555556689999999998      2355677889999999875

>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=88.48  E-value=1.8  Score=34.17  Aligned_cols=69  Identities=12%  Similarity=0.071  Sum_probs=45.5

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHH-cCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATL-RWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Are-r~l~tVVVGd~  135 (157)
                      .|+..++...|+.+.......+   ..-.....+.+..+++|.|++.+.+.+ ..++....+ .|..+|+++..
T Consensus        78 ~gi~~~a~~~g~~~~~~~~~~~---~~~~~~~~~~l~~~~vdgiI~~~~~~~-~~~~~~l~~~~~iPvV~~~~~  147 (340)
T 1qpz_A           78 EAVEKNCFQKGYTLILGNAWNN---LEKQRAYLSMMAQKRVDGLLVMCSEYP-EPLLAMLEEYRHIPMVVMDWG  147 (340)
T ss_dssp             HHHHHHHHHTTCEEEEEECTTC---HHHHHHHHHHHHHTTCSEEEECCSCCC-HHHHHHHHTTTTSCEEEEEES
T ss_pred             HHHHHHHHHcCCEEEEEeCCCC---HHHHHHHHHHHHcCCCCEEEEeCCCCC-hHHHHHHHhhCCCCEEEEecc
Confidence            4778888999999877543322   233334444544789999999876543 133444444 79999999865

>2h0a_A TTHA0807, transcriptional regulator; repressor, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.80A {Thermus thermophilus}

Probab=88.20  E-value=0.16  Score=38.39  Aligned_cols=70  Identities=11%  Similarity=0.019  Sum_probs=40.3

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDMS  136 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~~  136 (157)
                      .|+..++++.|+.+.......+...   .....+.+..+++|.+++.+.+.+ ...++.+++.|..+|+++...
T Consensus        19 ~gi~~~~~~~g~~~~~~~~~~~~~~---~~~~~~~l~~~~vdgiI~~~~~~~-~~~~~~~~~~~iPvV~~~~~~   88 (276)
T 2h0a_A           19 EGIEGVLLEQRYDLALFPILSLARL---KRYLENTTLAYLTDGLILASYDLT-ERFEEGRLPTERPVVLVDAQN   88 (276)
T ss_dssp             HHHHHHHGGGTCEEEECCCCSCCCC---C---------CCCSEEEEESCCCC-------CCSCSSCEEEESSCC
T ss_pred             HHHHHHHHHCCCEEEEEeCCCchhh---HHHHHHHHHhCCCCEEEEecCCCC-HHHHHHHhhcCCCEEEEeccC
Confidence            5777888999998877643322111   122333333689999999876654 367788888999999998753

>1pea_A Amidase operon; gene regulator, receptor, binding protein; 2.10A {Pseudomonas aeruginosa} SCOP: c.93.1.1 PDB: 1qo0_A 1qnl_A

Probab=87.74  E-value=0.9  Score=36.34  Aligned_cols=69  Identities=10%  Similarity=0.054  Sum_probs=46.8

Q ss_pred             CcHHHHHhhceEEEE---ecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCe---EEEEcCC
Q 045172           64 GFADELKRAWFWVRM---VLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLK---MVVVGDM  135 (157)
Q Consensus        64 gla~eLrRAGv~V~~---V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~---tVVVGd~  135 (157)
                      |+...|+++|..|..   ++..+...|..  ..+.+++ ..+.+.|++.+++.+-..+++.+++.|++   ..++|..
T Consensus       159 ~~~~~l~~~G~~v~~~~~~~~~~~~~d~~--~~~~~l~-~~~pdaI~~~~~~~~a~~~~~~~~~~G~~~~~~~~~~~~  233 (385)
T 1pea_A          159 VMRHLYRQHGGTVLEEIYIPLYPSDDDLQ--RAVERIY-QARADVVFSTVVGTGTAELYRAIARRYGDGRRPPIASLT  233 (385)
T ss_dssp             HHHHHHHHTTCEEEEEEEECSSCCHHHHH--HHHHHHH-HHTCSEEEEECCTHHHHHHHHHHHHHHCSSCCCCEEESS
T ss_pred             HHHHHHHHcCCEEEEEEeecCCCCcchHH--HHHHHHH-HCCCCEEEEecccccHHHHHHHHHHcCCCcCCceEEecc
Confidence            345677788876542   33223444543  3444444 45899999998888999999999999988   4456654

>3rfu_A Copper efflux ATPase; alpha helical, CPC, CXXC, ATP-binding, hydrolase, ION transp magnesium, Cu+, membrane, metal-binding; 3.20A {Legionella pneumophila subsp}

Probab=87.49  E-value=0.79  Score=42.66  Aligned_cols=77  Identities=16%  Similarity=0.063  Sum_probs=54.9

Q ss_pred             HHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC-CchHHHhhhh
Q 045172           67 DELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM-SDGALKRIAN  145 (157)
Q Consensus        67 ~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~-~~~~L~r~AD  145 (157)
                      .+|+++|+.|-+++..+...       +...+...|++.++.-....|=..+++..++.|-.+..|||+ +|-.--+.||
T Consensus       564 ~~L~~~Gi~v~mlTGd~~~~-------a~~ia~~lgi~~v~a~~~P~~K~~~v~~l~~~g~~V~~vGDG~ND~paL~~Ad  636 (736)
T 3rfu_A          564 LELQQSGIEIVMLTGDSKRT-------AEAVAGTLGIKKVVAEIMPEDKSRIVSELKDKGLIVAMAGDGVNDAPALAKAD  636 (736)
T ss_dssp             HHHHHHTCEEEEECSSCHHH-------HHHHHHHHTCCCEECSCCHHHHHHHHHHHHHHSCCEEEEECSSTTHHHHHHSS
T ss_pred             HHHHHCCCeEEEECCCCHHH-------HHHHHHHcCCCEEEEecCHHHHHHHHHHHHhcCCEEEEEECChHhHHHHHhCC
Confidence            46788888888887766521       122233456766555455567788999999999999999999 7766667788


Q ss_pred             cccch
Q 045172          146 AFFSW  150 (157)
Q Consensus       146 ~~fsW  150 (157)
                      +.+.-
T Consensus       637 vGIAm  641 (736)
T 3rfu_A          637 IGIAM  641 (736)
T ss_dssp             EEEEE
T ss_pred             EEEEe
Confidence            87643

>3ewi_A N-acylneuraminate cytidylyltransferase; beta barrel, HAD-like, rossmannoid fold, nucleotidyltransferase, nucleus; 1.90A {Mus musculus}

Probab=87.35  E-value=1.5  Score=32.90  Aligned_cols=73  Identities=18%  Similarity=0.082  Sum_probs=47.0

Q ss_pred             HHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCC---eEEEEcCC-CchHHHh
Q 045172           67 DELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWL---KMVVVGDM-SDGALKR  142 (157)
Q Consensus        67 ~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l---~tVVVGd~-~~~~L~r  142 (157)
                      .+|++.|+.+-.++.+ ..+...+     +.+ ..+++  +.....+.-..+...+.+.|+   .++.|||+ +|-...+
T Consensus        46 ~~Lk~~Gi~~~I~Tg~-~~~~~~l-----~~l-~lgi~--~~~g~~~K~~~l~~~~~~~gi~~~~~~~vGD~~nDi~~~~  116 (168)
T 3ewi_A           46 SLLKKSGIEVRLISER-ACSKQTL-----SAL-KLDCK--TEVSVSDKLATVDEWRKEMGLCWKEVAYLGNEVSDEECLK  116 (168)
T ss_dssp             HHHHHTTCEEEEECSS-CCCHHHH-----HTT-CCCCC--EECSCSCHHHHHHHHHHHTTCCGGGEEEECCSGGGHHHHH
T ss_pred             HHHHHCCCEEEEEeCc-HHHHHHH-----HHh-CCCcE--EEECCCChHHHHHHHHHHcCcChHHEEEEeCCHhHHHHHH
Confidence            6899999999999988 4333222     222 45777  334444444455555555665   68999999 7666666


Q ss_pred             hhhccc
Q 045172          143 IANAFF  148 (157)
Q Consensus       143 ~AD~~f  148 (157)
                      .|.+.+
T Consensus       117 ~ag~~~  122 (168)
T 3ewi_A          117 RVGLSA  122 (168)
T ss_dssp             HSSEEE
T ss_pred             HCCCEE
Confidence            666654

>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=86.35  E-value=1.9  Score=34.31  Aligned_cols=71  Identities=13%  Similarity=-0.010  Sum_probs=44.2

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++...|+.+........  |........+.+..+++|.|++++...+-..+...+...|..+|+++..
T Consensus        81 ~gi~~~a~~~g~~~~~~~~~~~--~~~~~~~~l~~l~~~~vdGiIi~~~~~~~~~~~~~~~~~~iPvV~i~~~  151 (349)
T 1jye_A           81 AAILSRADQLGASVVVSMVERS--GVEACKTAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVS  151 (349)
T ss_dssp             HHHHHHHHHTTCEEEEEECCSS--SHHHHHHHHHHHHTTTCSCEEEESCCCHHHHHHHHHHTTTSCEEESSSC
T ss_pred             HHHHHHHHHcCCEEEEEeCCCC--cHHHHHHHHHHHHHCCCCEEEEecCCCChhHHHHHHhhCCCCEEEEccc
Confidence            4778889999998877543221  1122223334444789999999843222223445566789999999753

>2l69_A Rossmann 2X3 fold protein; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Artificial gene}

Probab=85.96  E-value=2  Score=32.54  Aligned_cols=63  Identities=29%  Similarity=0.394  Sum_probs=48.6

Q ss_pred             cHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHH-HHHHHHHcCCeEEEE
Q 045172           65 FADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVE-VFQEATLRWLKMVVV  132 (157)
Q Consensus        65 la~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~-~lr~Arer~l~tVVV  132 (157)
                      +-+.++..||.|+||.. ||    -|+..+.+...+.+..-+|+|-||.++++ .+|+.+.-|..+.+|
T Consensus        18 fkdiikkngfkvrtvrs-pq----elkdsieelvkkynativvvvvddkewaekairfvkslgaqvlii   81 (134)
T 2l69_A           18 FKDIIKKNGFKVRTVRS-PQ----ELKDSIEELVKKYNATIVVVVVDDKEWAEKAIRFVKSLGAQVLII   81 (134)
T ss_dssp             HHHHHHHTTCEEEEECS-HH----HHHHHHHHHTTCCCCEEEEEECSSHHHHHHHHHHHHHHCCCCEEE
T ss_pred             HHHHHHhcCceEEEecC-HH----HHHHHHHHHHHHhCCeEEEEEEccHHHHHHHHHHHHhcCCeEEEE
Confidence            34678999999999854 65    57788888887888888888999988875 567777777776544

>3mn1_A Probable YRBI family phosphatase; structural genomics, PSI, protein structure initiative, NYSG phosphatase; 1.80A {Pseudomonas syringae PV} PDB: 3nrj_A

Probab=85.90  E-value=2.3  Score=31.57  Aligned_cols=75  Identities=11%  Similarity=-0.044  Sum_probs=42.3

Q ss_pred             cHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHH-cC---CeEEEEcCC-CchH
Q 045172           65 FADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATL-RW---LKMVVVGDM-SDGA  139 (157)
Q Consensus        65 la~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Are-r~---l~tVVVGd~-~~~~  139 (157)
                      +-.+|+..|+.+-.++.+|...       +...+...|++-++-..  .+=.+.++.+.+ -|   -.+++|||+ +|-.
T Consensus        54 ~l~~L~~~g~~~~i~T~~~~~~-------~~~~~~~lgl~~~f~~~--~~K~~~~~~~~~~~g~~~~~~~~vGD~~nDi~  124 (189)
T 3mn1_A           54 GIKMLIASGVTTAIISGRKTAI-------VERRAKSLGIEHLFQGR--EDKLVVLDKLLAELQLGYEQVAYLGDDLPDLP  124 (189)
T ss_dssp             HHHHHHHTTCEEEEECSSCCHH-------HHHHHHHHTCSEEECSC--SCHHHHHHHHHHHHTCCGGGEEEEECSGGGHH
T ss_pred             HHHHHHHCCCEEEEEECcChHH-------HHHHHHHcCCHHHhcCc--CChHHHHHHHHHHcCCChhHEEEECCCHHHHH
Confidence            4578999999999999998721       11122233554322111  111244444433 34   358888888 6656


Q ss_pred             HHhhhhccc
Q 045172          140 LKRIANAFF  148 (157)
Q Consensus       140 L~r~AD~~f  148 (157)
                      ..+.|++.+
T Consensus       125 ~~~~ag~~~  133 (189)
T 3mn1_A          125 VIRRVGLGM  133 (189)
T ss_dssp             HHHHSSEEE
T ss_pred             HHHHCCCeE
Confidence            666666655

>3n1u_A Hydrolase, HAD superfamily, subfamily III A; structural genomics, PSI-2; 1.80A {Legionella pneumophila} SCOP: c.108.1.0

Probab=85.57  E-value=2.9  Score=31.17  Aligned_cols=75  Identities=11%  Similarity=-0.040  Sum_probs=40.6

Q ss_pred             HHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCC---eEEEEcCC-CchHHH
Q 045172           66 ADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWL---KMVVVGDM-SDGALK  141 (157)
Q Consensus        66 a~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l---~tVVVGd~-~~~~L~  141 (157)
                      -..|+..|+.+-.++..|..   .+    ...+...|++.++-.. -+.-..+.+.++.-|+   .+++|||+ +|-...
T Consensus        55 l~~L~~~g~~~~ivTn~~~~---~~----~~~l~~lgl~~~~~~~-kpk~~~~~~~~~~~~~~~~~~~~vGD~~~Di~~~  126 (191)
T 3n1u_A           55 LKLLMAAGIQVAIITTAQNA---VV----DHRMEQLGITHYYKGQ-VDKRSAYQHLKKTLGLNDDEFAYIGDDLPDLPLI  126 (191)
T ss_dssp             HHHHHHTTCEEEEECSCCSH---HH----HHHHHHHTCCEEECSC-SSCHHHHHHHHHHHTCCGGGEEEEECSGGGHHHH
T ss_pred             HHHHHHCCCeEEEEeCcChH---HH----HHHHHHcCCccceeCC-CChHHHHHHHHHHhCCCHHHEEEECCCHHHHHHH
Confidence            46789999999999988862   11    1122233554322111 1222333333333454   58888887 555555


Q ss_pred             hhhhccc
Q 045172          142 RIANAFF  148 (157)
Q Consensus       142 r~AD~~f  148 (157)
                      +.|++.+
T Consensus       127 ~~ag~~~  133 (191)
T 3n1u_A          127 QQVGLGV  133 (191)
T ss_dssp             HHSSEEE
T ss_pred             HHCCCEE
Confidence            5555544

>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=84.73  E-value=1  Score=34.83  Aligned_cols=68  Identities=16%  Similarity=0.123  Sum_probs=45.0

Q ss_pred             CcHHHHHhhceEEEEe-cCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcC
Q 045172           64 GFADELKRAWFWVRMV-LVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGD  134 (157)
Q Consensus        64 gla~eLrRAGv~V~~V-~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd  134 (157)
                      |+..+|++.|..|... .-.+...|..  ..+.+++ ..+.+.|++.+++.+...+++.+++.|++.-++|-
T Consensus       157 ~~~~~l~~~g~~v~~~~~~~~~~~d~~--~~~~~l~-~~~~d~i~~~~~~~~a~~~~~~~~~~g~~~~~~~~  225 (346)
T 1usg_A          157 SVQDGLKAANANVVFFDGITAGEKDFS--ALIARLK-KENIDFVYYGGYYPEMGQMLRQARSVGLKTQFMGP  225 (346)
T ss_dssp             HHHHHHHHTTCCEEEEEECCTTCCCCH--HHHHHHH-HTTCCEEEEESCHHHHHHHHHHHHHTTCCCEEEEC
T ss_pred             HHHHHHHHcCCEEEEEeccCCCCcCHH--HHHHHHH-hcCCCEEEEcCcchHHHHHHHHHHHcCCCCeEEec
Confidence            3456677888765431 2122223332  2334444 46889999999889999999999999998766663

>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=84.58  E-value=0.9  Score=35.64  Aligned_cols=69  Identities=10%  Similarity=0.117  Sum_probs=45.9

Q ss_pred             CcHHHHHhhceEEE-EecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           64 GFADELKRAWFWVR-MVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        64 gla~eLrRAGv~V~-~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      |+..+|+.+|..|- ...-.+...|..  ..+..+. ..+.+.|++.+.|.+-..+++.+++.|++.-++|.+
T Consensus       170 ~~~~~l~~~G~~v~~~~~~~~~~~d~~--~~~~~l~-~~~~dai~~~~~~~~a~~~~~~~~~~g~~vp~~~~~  239 (375)
T 4evq_A          170 GFKKSFTAGKGEVVKDITIAFPDVEFQ--SALAEIA-SLKPDCVYAFFSGGGALKFIKDYAAANLGIPLWGPG  239 (375)
T ss_dssp             HHHHHHHHTTCEEEEEEEECTTCCCCH--HHHHHHH-HHCCSEEEEECCTHHHHHHHHHHHHTTCCCCEEEEG
T ss_pred             HHHHHHHHcCCeEEEEEecCCCCccHH--HHHHHHH-hcCCCEEEEecCcchHHHHHHHHHHcCCCceEEecC
Confidence            45567788887653 222122223322  2223333 458899999899999999999999999998888753

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

Probab=84.26  E-value=0.76  Score=35.01  Aligned_cols=67  Identities=9%  Similarity=0.138  Sum_probs=44.8

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++.+.|+.+.......   |......+.+.+..+++|.|++.+.+.+- ..++.+  .|..+|+++..
T Consensus        27 ~gi~~~~~~~g~~~~~~~~~~---~~~~~~~~~~~l~~~~vdgiI~~~~~~~~-~~~~~l--~~iPvV~~~~~   93 (288)
T 2qu7_A           27 TEISHECQKHHLHVAVASSEE---NEDKQQDLIETFVSQNVSAIILVPVKSKF-QMKREW--LKIPIMTLDRE   93 (288)
T ss_dssp             HHHHHHHGGGTCEEEEEECTT---CHHHHHHHHHHHHHTTEEEEEECCSSSCC-CCCGGG--GGSCEEEESCC
T ss_pred             HHHHHHHHHCCCEEEEEeCCC---CHHHHHHHHHHHHHcCccEEEEecCCCCh-HHHHHh--cCCCEEEEecc
Confidence            467778888999887765433   23333444555447899999998765431 334444  78999999865

>3cvj_A Putative phosphoheptose isomerase; rossman fold, 3-layer (ABA) sandwich, structural genomics, J center for structural genomics, JCSG; HET: MSE; 2.00A {Bacillus halodurans c-125}

Probab=84.24  E-value=0.51  Score=36.72  Aligned_cols=46  Identities=17%  Similarity=0.202  Sum_probs=36.9

Q ss_pred             cceEEEEcCC---cchHHHHHHHHHcCCeEEEEcCCCch-----------HHHhhhhccc
Q 045172          103 FGCLVVVSDD---SDFVEVFQEATLRWLKMVVVGDMSDG-----------ALKRIANAFF  148 (157)
Q Consensus       103 v~clvLVSDD---sDF~~~lr~Arer~l~tVVVGd~~~~-----------~L~r~AD~~f  148 (157)
                      =|+++++|-.   .+-.++++.|+++|++||.|-+....           .|.+.||+.|
T Consensus       109 ~Dv~I~iS~SG~t~~~i~~~~~Ak~~G~~vI~IT~~~~s~~~~~~~~~g~~La~~aD~~l  168 (243)
T 3cvj_A          109 KDVIMIISNSGRNTVPVEMAIESRNIGAKVIAMTSMKHSQKVTSRHKSGKKLYEYADVVL  168 (243)
T ss_dssp             TCEEEEECSSCCSHHHHHHHHHHHHHTCEEEEEECHHHHHHSCCCSTTSCCGGGGCSEEE
T ss_pred             CCEEEEEeCCCCCHHHHHHHHHHHHCCCEEEEEeCCcccccccccCCCcCcHHHhCCEEE
Confidence            3788888754   56778889999999999999886323           7999999877

>3h5t_A Transcriptional regulator, LACI family; DNA-dependent, protein structure initiative II(PSI II), NYSGXRC, 11232D), structural genomics; 2.53A {Corynebacterium glutamicum}

Probab=84.00  E-value=1.1  Score=35.67  Aligned_cols=67  Identities=13%  Similarity=0.075  Sum_probs=45.1

Q ss_pred             CcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           64 GFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        64 gla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      |+..++.  |+.+..+...++..+  -...+.+.+..+++|.|++++.+.+ ...+..+.+.|+.+|+||..
T Consensus        94 gi~~~a~--g~~~~~~~~~~~~~~--~~~~~~~~l~~~~vdGiIi~~~~~~-~~~~~~l~~~~iPvV~i~~~  160 (366)
T 3h5t_A           94 GVAQAAG--DTQLTLIPASPASSV--DHVSAQQLVNNAAVDGVVIYSVAKG-DPHIDAIRARGLPAVIADQP  160 (366)
T ss_dssp             HHHHHSS--SCEEEEEECCCCTTC--CHHHHHHHHHTCCCSCEEEESCCTT-CHHHHHHHHHTCCEEEESSC
T ss_pred             HHHHHHh--hCCEEEEEcCCCccH--HHHHHHHHHHhCCCCEEEEecCCCC-hHHHHHHHHCCCCEEEECCc
Confidence            5556666  888777654443221  1233445555899999999876433 36778888899999999875

>4ex6_A ALNB; modified rossman fold, phosphatase, magnesium binding, hydro; 1.25A {Streptomyces SP} PDB: 4ex7_A

Probab=83.99  E-value=6.1  Score=28.52  Aligned_cols=22  Identities=27%  Similarity=0.178  Sum_probs=17.8

Q ss_pred             CCcHHHHHhhceEEEEecCCCc
Q 045172           63 YGFADELKRAWFWVRMVLVKPQ   84 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpq   84 (157)
                      ..+-.+|+..|+.+-.++..+.
T Consensus       110 ~~~l~~l~~~g~~~~i~s~~~~  131 (237)
T 4ex6_A          110 LEGLDRLSAAGFRLAMATSKVE  131 (237)
T ss_dssp             HHHHHHHHHTTEEEEEECSSCH
T ss_pred             HHHHHHHHhCCCcEEEEcCCCh
Confidence            3456778889999999998876

>1nri_A Hypothetical protein HI0754; structural genomics, haemophilus influ PSI, protein structure initiative, midwest center for struc genomics; 1.90A {Haemophilus influenzae} SCOP: c.80.1.3

Probab=83.77  E-value=1.2  Score=36.44  Aligned_cols=49  Identities=12%  Similarity=0.066  Sum_probs=40.4

Q ss_pred             CcceEEEEcCC---cchHHHHHHHHHcCCeEEEEcCCCchHHHhhhhcccch
Q 045172          102 RFGCLVVVSDD---SDFVEVFQEATLRWLKMVVVGDMSDGALKRIANAFFSW  150 (157)
Q Consensus       102 ~v~clvLVSDD---sDF~~~lr~Arer~l~tVVVGd~~~~~L~r~AD~~fsW  150 (157)
                      .=|++|.+|-.   .+-.++++.|+++|.+||.|.+.....|.+.||..|.-
T Consensus       140 ~~DvvI~IS~SG~T~~vi~al~~Ak~~Ga~~IaIT~~~~S~La~~AD~~I~~  191 (306)
T 1nri_A          140 KNDVLVGIAASGRTPYVIAGLQYAKSLGALTISIASNPKSEMAEIADIAIET  191 (306)
T ss_dssp             TTSEEEEECTTSCCHHHHHHHHHHHHHTCEEEEEESSTTCHHHHHSSEEEEC
T ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEECCCCChHHHhCCEEEEc
Confidence            34888888754   45678899999999999999998678999999988743

>2zj3_A Glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1; glucosamine-6-phosphate synthase, aldose/ketose isomerase, rossmann-like fold; HET: G6P; 1.90A {Homo sapiens} PDB: 2zj4_A* 2v4m_A*

Probab=83.28  E-value=1.4  Score=36.96  Aligned_cols=46  Identities=11%  Similarity=0.052  Sum_probs=37.8

Q ss_pred             ceEEEEcCC---cchHHHHHHHHHcCCeEEEEcCCCchHHHhhhhcccc
Q 045172          104 GCLVVVSDD---SDFVEVFQEATLRWLKMVVVGDMSDGALKRIANAFFS  149 (157)
Q Consensus       104 ~clvLVSDD---sDF~~~lr~Arer~l~tVVVGd~~~~~L~r~AD~~fs  149 (157)
                      |++|.+|-.   .|-..+++.|+++|.+||.|-+..+..|.+.||..|.
T Consensus       109 dlvI~iS~SG~T~e~l~a~~~Ak~~Ga~~iaIT~~~~S~La~~ad~~l~  157 (375)
T 2zj3_A          109 DVCFFLSQSGETADTLMGLRYCKERGALTVGITNTVGSSISRETDCGVH  157 (375)
T ss_dssp             EEEEEEESSSCCHHHHHHHHHHHHTTCEEEEEESCTTCHHHHHSSEEEE
T ss_pred             CEEEEEeCCCCCHHHHHHHHHHHHcCCcEEEEECCCCChHHHhCCEeee
Confidence            677777753   4566788999999999999999867899999998763

>3j09_A COPA, copper-exporting P-type ATPase A; copper transporter, adenosine triphosph archaeal proteins, cation transport proteins; 10.00A {Archaeoglobus fulgidus}

Probab=82.70  E-value=2.8  Score=38.46  Aligned_cols=77  Identities=17%  Similarity=0.084  Sum_probs=53.6

Q ss_pred             HHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC-CchHHHhhhh
Q 045172           67 DELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM-SDGALKRIAN  145 (157)
Q Consensus        67 ~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~-~~~~L~r~AD  145 (157)
                      ..|+++|+.|-+++..+...       +.......|++.++.=....+=..+++..++. -.+..|||+ +|-.--+.||
T Consensus       545 ~~l~~~Gi~v~~~TGd~~~~-------a~~ia~~lgi~~~~~~~~P~~K~~~v~~l~~~-~~v~~vGDg~ND~~al~~A~  616 (723)
T 3j09_A          545 QELKRMGIKVGMITGDNWRS-------AEAISRELNLDLVIAEVLPHQKSEEVKKLQAK-EVVAFVGDGINDAPALAQAD  616 (723)
T ss_dssp             HHHHHTTCEEEEECSSCHHH-------HHHHHHHHTCSEEECSCCTTCHHHHHHHHTTT-CCEEEEECSSTTHHHHHHSS
T ss_pred             HHHHHCCCEEEEECCCCHHH-------HHHHHHHcCCcEEEccCCHHHHHHHHHHHhcC-CeEEEEECChhhHHHHhhCC
Confidence            46788888888887766521       12223345776665555556778888888777 678999999 8766677899


Q ss_pred             cccchh
Q 045172          146 AFFSWS  151 (157)
Q Consensus       146 ~~fsW~  151 (157)
                      +.+...
T Consensus       617 vgiamg  622 (723)
T 3j09_A          617 LGIAVG  622 (723)
T ss_dssp             EEEECC
T ss_pred             EEEEeC
Confidence            887653

>1j5x_A Glucosamine-6-phosphate deaminase; structural genomics, TM0813, glucosamine-6-phosphate deamina PSI, protein structure initiative; 1.80A {Thermotoga maritima} SCOP: c.80.1.1

Probab=82.63  E-value=1.5  Score=36.37  Aligned_cols=75  Identities=8%  Similarity=0.034  Sum_probs=49.8

Q ss_pred             HHHHHh-hceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCC---cchHHHHHHHHHcCCeEEEEcCCCchHHH
Q 045172           66 ADELKR-AWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDD---SDFVEVFQEATLRWLKMVVVGDMSDGALK  141 (157)
Q Consensus        66 a~eLrR-AGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDD---sDF~~~lr~Arer~l~tVVVGd~~~~~L~  141 (157)
                      +.-|.+ .|+.|..+.+    .+.   .+....+ ..+-|+++.+|-.   .|-..+++.|+++|.+++.|-+..+..|.
T Consensus        71 ~~~l~~~~g~~v~~~~~----~~~---~~~~~~~-~~~~dlvI~iS~SG~T~e~l~a~~~ak~~Ga~vIaIT~~~~S~La  142 (342)
T 1j5x_A           71 SYYFERVLKIRTKAIPA----GEV---AFQKIPD-LEERGLAFLFSRTGNTTEVLLANDVLKKRNHRTIGITIEEESRLA  142 (342)
T ss_dssp             HHHHHHHHCCEEEEEEH----HHH---HTTCSCC-CCSSEEEEEECSSSCCHHHHHHHHHHHHTTEEEEEEESCTTSHHH
T ss_pred             HHHHHHhhCCeEEEECc----hHH---HhcCccc-CCCCeEEEEEcCCCCCHHHHHHHHHHHHCCCCEEEEECCCCCHHH
Confidence            445667 8988887642    111   0000001 1111677777753   46677889999999999999988678999


Q ss_pred             hhhhccc
Q 045172          142 RIANAFF  148 (157)
Q Consensus       142 r~AD~~f  148 (157)
                      +.||..+
T Consensus       143 ~~ad~~l  149 (342)
T 1j5x_A          143 KESDLPL  149 (342)
T ss_dssp             HHSSEEE
T ss_pred             HhcCEEE
Confidence            9999866

>1rku_A Homoserine kinase; phosphoserine phosphatase, phosphoserine:homoserine phosphotransferase, THRH, phosphoserine phosphoryl donor; 1.47A {Pseudomonas aeruginosa} SCOP: c.108.1.11 PDB: 1rkv_A

Probab=82.52  E-value=6  Score=28.28  Aligned_cols=78  Identities=17%  Similarity=0.174  Sum_probs=47.2

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcc-eEE--EEc-CCc-----------chHHHHHHHHHcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFG-CLV--VVS-DDS-----------DFVEVFQEATLRWL  127 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~-clv--LVS-DDs-----------DF~~~lr~Arer~l  127 (157)
                      -.+-.+|++. +.+-.++..|..    ....+.+   ..|++ +++  +++ ++.           .|...++......-
T Consensus        75 ~~~l~~l~~~-~~~~i~s~~~~~----~~~~~l~---~~gl~~~f~~~~~~~~~~~~~~~~~p~p~~~~~~l~~l~~~~~  146 (206)
T 1rku_A           75 VEFVDWLRER-FQVVILSDTFYE----FSQPLMR---QLGFPTLLCHKLEIDDSDRVVGYQLRQKDPKRQSVIAFKSLYY  146 (206)
T ss_dssp             HHHHHHHHTT-SEEEEEEEEEHH----HHHHHHH---HTTCCCEEEEEEEECTTSCEEEEECCSSSHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHhc-CcEEEEECChHH----HHHHHHH---HcCCcceecceeEEcCCceEEeeecCCCchHHHHHHHHHhcCC
Confidence            3445667777 888888888751    2222332   33443 332  333 343           37777777776777


Q ss_pred             eEEEEcCC-CchHHHhhhhccc
Q 045172          128 KMVVVGDM-SDGALKRIANAFF  148 (157)
Q Consensus       128 ~tVVVGd~-~~~~L~r~AD~~f  148 (157)
                      .+++|||+ +|-...+.|...+
T Consensus       147 ~~~~iGD~~~Di~~a~~aG~~~  168 (206)
T 1rku_A          147 RVIAAGDSYNDTTMLSEAHAGI  168 (206)
T ss_dssp             EEEEEECSSTTHHHHHHSSEEE
T ss_pred             EEEEEeCChhhHHHHHhcCccE
Confidence            89999999 5555555665543

>2hqb_A Transcriptional activator of COMK gene; berkeley structure genomics center target 1957B, structural genomics, PSI; 2.70A {Bacillus halodurans}

Probab=82.47  E-value=2.5  Score=33.37  Aligned_cols=67  Identities=9%  Similarity=-0.024  Sum_probs=42.2

Q ss_pred             CcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHH-HHHHH-cCCeEEEEcCC
Q 045172           64 GFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVF-QEATL-RWLKMVVVGDM  135 (157)
Q Consensus        64 gla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~l-r~Are-r~l~tVVVGd~  135 (157)
                      |+...++..|+.+..++..+..+|.   ...++.+-.+++|.|+++|.  .+.+.+ ..+.+ .++.+|+|+..
T Consensus        28 gi~~~~~~~g~~~~~~~~~~~~~~~---~~~l~~l~~~~vdgIi~~~~--~~~~~~~~~~~~~p~~p~v~id~~   96 (296)
T 2hqb_A           28 GLLNIHSNLDVDVVLEEGVNSEQKA---HRRIKELVDGGVNLIFGHGH--AFAEYFSTIHNQYPDVHFVSFNGE   96 (296)
T ss_dssp             HHHHHHHHSCCEEEEECCCCSHHHH---HHHHHHHHHTTCCEEEECST--HHHHHHHTTTTSCTTSEEEEESCC
T ss_pred             HHHHHHHHhCCeEEEEeCCCCHHHH---HHHHHHHHHCCCCEEEEcCH--hHHHHHHHHHHHCCCCEEEEEecC
Confidence            5667788889998877544443332   23344444789999999873  333333 33333 27889999764

>3td9_A Branched chain amino acid ABC transporter, peripl amino acid-binding protein; leucine binding, structural genomics; HET: MSE PHE; 1.90A {Thermotoga maritima}

Probab=82.37  E-value=0.73  Score=36.27  Aligned_cols=69  Identities=9%  Similarity=0.035  Sum_probs=47.5

Q ss_pred             CcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           64 GFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        64 gla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      ++...|+++|+.|....-.+...|..  ..+..+. ..+.+.|++.+.+.+...+++.+++.|++.-++|-.
T Consensus       169 ~~~~~~~~~G~~v~~~~~~~~~~d~~--~~~~~l~-~~~~d~v~~~~~~~~a~~~~~~~~~~g~~~~~~~~~  237 (366)
T 3td9_A          169 FFINKFTELGGQVKRVFFRSGDQDFS--AQLSVAM-SFNPDAIYITGYYPEIALISRQARQLGFTGYILAGD  237 (366)
T ss_dssp             HHHHHHHHTTCEEEEEEECTTCCCCH--HHHHHHH-HTCCSEEEECSCHHHHHHHHHHHHHTTCCSEEEECG
T ss_pred             HHHHHHHHCCCEEEEEEeCCCCccHH--HHHHHHH-hcCCCEEEEccchhHHHHHHHHHHHcCCCceEEeeC
Confidence            45567788887664432122233322  2233334 578999999899999999999999999998888753

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

Probab=82.37  E-value=0.59  Score=35.37  Aligned_cols=65  Identities=9%  Similarity=0.063  Sum_probs=40.7

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDMS  136 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~~  136 (157)
                      .|+..++++.|+.+..+... ...   -...+.+.+..+++|.|+ ++.+.+ ...+..   .|..+|+++...
T Consensus        25 ~gi~~~a~~~g~~~~~~~~~-~~~---~~~~~~~~l~~~~vdgiI-~~~~~~-~~~~~~---~~iPvV~~~~~~   89 (280)
T 3gyb_A           25 QSLSDVLTPKGYRLSVIDSL-TSQ---AGTDPITSALSMRPDGII-IAQDIP-DFTVPD---SLPPFVIAGTRI   89 (280)
T ss_dssp             HHHHHHHGGGTCEEEEECSS-SSC---SSSCHHHHHHTTCCSEEE-EESCC------------CCCEEEESCCC
T ss_pred             HHHHHHHHHCCCEEEEEeCC-Cch---HHHHHHHHHHhCCCCEEE-ecCCCC-hhhHhh---cCCCEEEECCCC
Confidence            46788899999999887554 211   122233334479999999 877766 344444   899999998764

>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=82.31  E-value=1.3  Score=35.08  Aligned_cols=68  Identities=13%  Similarity=0.002  Sum_probs=46.3

Q ss_pred             cHHHHHhhceEEEEe-cCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeE--EEEcCC
Q 045172           65 FADELKRAWFWVRMV-LVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKM--VVVGDM  135 (157)
Q Consensus        65 la~eLrRAGv~V~~V-~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~t--VVVGd~  135 (157)
                      +...|+++|..|-.. .-.+...|..  ..+..+. ..+.+.|++.++..+...+++.+++.|++.  .++|..
T Consensus       160 ~~~~~~~~G~~v~~~~~~~~~~~d~~--~~l~~i~-~~~~d~v~~~~~~~~~~~~~~~~~~~g~~~~~~i~g~~  230 (375)
T 3i09_A          160 TADVVKANGGKVLGEVRHPLSASDFS--SFLLQAQ-SSKAQILGLANAGGDTVNAIKAAKEFGITKTMKLAALL  230 (375)
T ss_dssp             HHHHHHHTTCEEEEEEEECTTCSCCH--HHHHHHH-HTCCSEEEEECCHHHHHHHHHHHHHTTGGGTCEEEESS
T ss_pred             HHHHHHHcCCEEeeeeeCCCCCccHH--HHHHHHH-hCCCCEEEEecCchhHHHHHHHHHHcCCCcCceEEecc
Confidence            455777888776422 2222333422  2333334 578999999998889999999999999987  578765

>3ipc_A ABC transporter, substrate binding protein (amino; venus flytrap domain, transport protein; 1.30A {Agrobacterium tumefaciens} PDB: 3ip5_A 3ip6_A 3ip7_A 3ip9_A 3ipa_A

Probab=82.22  E-value=1.1  Score=35.04  Aligned_cols=69  Identities=13%  Similarity=-0.040  Sum_probs=45.9

Q ss_pred             CcHHHHHhhceEEE-EecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           64 GFADELKRAWFWVR-MVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        64 gla~eLrRAGv~V~-~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      |+..+|+.+|+.|- ...-.+...|..  ..+..+. ..+.+.+++.+.+.+...+++.+++.|++.-++|..
T Consensus       157 ~~~~~l~~~g~~v~~~~~~~~~~~d~~--~~~~~l~-~~~~d~v~~~~~~~~a~~~~~~~~~~g~~~~~~~~~  226 (356)
T 3ipc_A          157 ETKKAANAAGVTEVMYEGVNVGDKDFS--ALISKMK-EAGVSIIYWGGLHTEAGLIIRQAADQGLKAKLVSGD  226 (356)
T ss_dssp             HHHHHHHHTTCCCSEEEECCTTCCCCH--HHHHHHH-HTTCCEEEEESCHHHHHHHHHHHHHHTCCCEEEECG
T ss_pred             HHHHHHHHcCCEEEEEEeeCCCCCCHH--HHHHHHH-hcCCCEEEEccCchHHHHHHHHHHHCCCCCcEEEec
Confidence            45566777787542 222223333322  1222333 578999999999999999999999999998887743

>2a3n_A Putative glucosamine-fructose-6-phosphate aminotr; structural genomics, joint center for structural genomics; HET: MSE; 1.23A {Salmonella typhimurium}

Probab=81.89  E-value=1.8  Score=35.87  Aligned_cols=45  Identities=13%  Similarity=0.229  Sum_probs=36.7

Q ss_pred             ceEEEEcCC---cchHHHHHHHHHcCCeEEEEcCCCchHHHhhhhccc
Q 045172          104 GCLVVVSDD---SDFVEVFQEATLRWLKMVVVGDMSDGALKRIANAFF  148 (157)
Q Consensus       104 ~clvLVSDD---sDF~~~lr~Arer~l~tVVVGd~~~~~L~r~AD~~f  148 (157)
                      |+++.+|-.   .|-..+++.|+++|.+||.|-+..+..|.+.||.-+
T Consensus       104 dlvI~iS~SG~t~e~~~a~~~ak~~Ga~vi~IT~~~~S~La~~ad~~l  151 (355)
T 2a3n_A          104 SVVITLSKSGDTKESVAIAEWCKAQGIRVVAITKNADSPLAQAATWHI  151 (355)
T ss_dssp             CEEEEECSSSCCHHHHHHHHHHHHTTCEEEEEESCTTSHHHHTCSEEE
T ss_pred             CEEEEEeCCCCCHHHHHHHHHHHHCCCeEEEEECCCCChhhHhCCEEE
Confidence            666667653   456778889999999999999986789999999866

>2r8e_A 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase; YRBI, divalent metal, HAD superfamily, KDO 8-P, hydrolase; 1.40A {Escherichia coli O6} PDB: 2r8x_A 2r8y_A 2r8z_A 3hyc_A 3i6b_A*

Probab=81.81  E-value=5.9  Score=29.07  Aligned_cols=77  Identities=10%  Similarity=-0.056  Sum_probs=45.5

Q ss_pred             cHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHH-cCC---eEEEEcCC-CchH
Q 045172           65 FADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATL-RWL---KMVVVGDM-SDGA  139 (157)
Q Consensus        65 la~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Are-r~l---~tVVVGd~-~~~~  139 (157)
                      +-.+|+++|+.+-.++..|...    ...+.   ...|++-++  +....-...++.+.+ -|+   .++.|||+ +|-.
T Consensus        61 ~l~~L~~~g~~v~ivT~~~~~~----~~~~l---~~lgl~~~~--~~~kpk~~~~~~~~~~~g~~~~~~~~iGD~~~Di~  131 (188)
T 2r8e_A           61 GIRCALTSDIEVAIITGRKAKL----VEDRC---ATLGITHLY--QGQSNKLIAFSDLLEKLAIAPENVAYVGDDLIDWP  131 (188)
T ss_dssp             HHHHHHTTTCEEEEECSSCCHH----HHHHH---HHHTCCEEE--CSCSCSHHHHHHHHHHHTCCGGGEEEEESSGGGHH
T ss_pred             HHHHHHHCCCeEEEEeCCChHH----HHHHH---HHcCCceee--cCCCCCHHHHHHHHHHcCCCHHHEEEECCCHHHHH
Confidence            3567899999999999988731    12222   233555332  222333445554444 453   68899998 6666


Q ss_pred             HHhhhhcccch
Q 045172          140 LKRIANAFFSW  150 (157)
Q Consensus       140 L~r~AD~~fsW  150 (157)
                      ..+.|.+.+-|
T Consensus       132 ~a~~ag~~~~~  142 (188)
T 2r8e_A          132 VMEKVGLSVAV  142 (188)
T ss_dssp             HHTTSSEEEEC
T ss_pred             HHHHCCCEEEe
Confidence            66666665544

>3ic5_A Putative saccharopine dehydrogenase; structural genomics, APC63807.2, N-terminal domain, saccharo dehydrogenase, PSI-2; HET: MSE; 2.08A {Ruegeria pomeroyi}

Probab=81.52  E-value=3.3  Score=27.09  Aligned_cols=71  Identities=11%  Similarity=-0.050  Sum_probs=49.1

Q ss_pred             CCcHHHHHhhc-eEEEEecCCCccHHHHH-------------HHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCe
Q 045172           63 YGFADELKRAW-FWVRMVLVKPQDADVLL-------------RNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLK  128 (157)
Q Consensus        63 ygla~eLrRAG-v~V~~V~dkpqAAD~AL-------------~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~  128 (157)
                      ..++..|.+.| +.|..+...|+.++...             ...+.+.+  .++|.++..........++..+.+.|.+
T Consensus        18 ~~~~~~l~~~g~~~v~~~~r~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~--~~~d~vi~~~~~~~~~~~~~~~~~~g~~   95 (118)
T 3ic5_A           18 QMIAALLKTSSNYSVTVADHDLAALAVLNRMGVATKQVDAKDEAGLAKAL--GGFDAVISAAPFFLTPIIAKAAKAAGAH   95 (118)
T ss_dssp             HHHHHHHHHCSSEEEEEEESCHHHHHHHHTTTCEEEECCTTCHHHHHHHT--TTCSEEEECSCGGGHHHHHHHHHHTTCE
T ss_pred             HHHHHHHHhCCCceEEEEeCCHHHHHHHHhCCCcEEEecCCCHHHHHHHH--cCCCEEEECCCchhhHHHHHHHHHhCCC
Confidence            45677888888 77777665555433322             12333444  3788888887766678899999999999


Q ss_pred             EEEEcCC
Q 045172          129 MVVVGDM  135 (157)
Q Consensus       129 tVVVGd~  135 (157)
                      .+.+++.
T Consensus        96 ~~~~~~~  102 (118)
T 3ic5_A           96 YFDLTED  102 (118)
T ss_dssp             EECCCSC
T ss_pred             EEEecCc
Confidence            9888765

>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=81.41  E-value=2.4  Score=31.54  Aligned_cols=66  Identities=9%  Similarity=-0.032  Sum_probs=43.6

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCC-cchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDD-SDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDD-sDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++.+.|+.+.......+   ..-.....+.+..+++|.+++.+.+ .+. +   ...+.+..+|+++..
T Consensus        22 ~gi~~~~~~~g~~~~~~~~~~~---~~~~~~~~~~l~~~~vdgiI~~~~~~~~~-~---~l~~~~~pvV~~~~~   88 (255)
T 1byk_A           22 QTMLPAFYEQGYDPIMMESQFS---PQLVAEHLGVLKRRNIDGVVLFGFTGITE-E---MLAHWQSSLVLLARD   88 (255)
T ss_dssp             HHHHHHHHHHTCEEEEEECTTC---HHHHHHHHHHHHTTTCCEEEEECCTTCCT-T---TSGGGSSSEEEESSC
T ss_pred             HHHHHHHHHcCCEEEEEeCCCc---HHHHHHHHHHHHhcCCCEEEEecCccccH-H---HHHhcCCCEEEEccc
Confidence            5778889999999887654333   2223344455557899999998743 332 2   234568888988764

>2p9j_A Hypothetical protein AQ2171; secsg, riken, PSI, structural GENO protein structure initiative, southeast collaboratory for S genomics; 2.40A {Aquifex aeolicus}

Probab=81.23  E-value=9.4  Score=26.66  Aligned_cols=19  Identities=5%  Similarity=0.013  Sum_probs=11.8

Q ss_pred             HHHHHhhceEEEEecCCCc
Q 045172           66 ADELKRAWFWVRMVLVKPQ   84 (157)
Q Consensus        66 a~eLrRAGv~V~~V~dkpq   84 (157)
                      -.+|++.|+.+-.++..|.
T Consensus        45 l~~l~~~g~~~~i~T~~~~   63 (162)
T 2p9j_A           45 IKLLQKMGITLAVISGRDS   63 (162)
T ss_dssp             HHHHHTTTCEEEEEESCCC
T ss_pred             HHHHHHCCCEEEEEeCCCc
Confidence            3456666766666666654

>3lkb_A Probable branched-chain amino acid ABC transporter, amino acid binding protein; branched amino acid, PSI-II, NYSGXRC, structural genomics; 2.40A {Thermus thermophilus}

Probab=80.99  E-value=1.1  Score=35.68  Aligned_cols=69  Identities=13%  Similarity=0.064  Sum_probs=47.6

Q ss_pred             CcHHHHHhhceEEEEe-cCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           64 GFADELKRAWFWVRMV-LVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        64 gla~eLrRAGv~V~~V-~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      |+...|+++|+.|... .-.+...|..  ..+..+. ..+.+.|++.+.+.+...+++.+++.|++.-++|..
T Consensus       162 ~~~~~l~~~G~~v~~~~~~~~~~~d~~--~~~~~l~-~~~~dav~~~~~~~~a~~~~~~~~~~g~~~~~~~~~  231 (392)
T 3lkb_A          162 DARKAARELGLQIVDVQEVGSGNLDNT--ALLKRFE-QAGVEYVVHQNVAGPVANILKDAKRLGLKMRHLGAH  231 (392)
T ss_dssp             HHHHHHHHHTCEEEEEEECCTTCCCCH--HHHHHHH-HTTCCEEEEESCHHHHHHHHHHHHHTTCCCEEEECG
T ss_pred             HHHHHHHHcCCeEEEEEeeCCCCcCHH--HHHHHHH-hcCCCEEEEecCcchHHHHHHHHHHcCCCceEEEec
Confidence            4566788888866432 2222333321  2233333 578999999999999999999999999998888754

>1k1e_A Deoxy-D-mannose-octulosonate 8-phosphate phosphat; structural genomics, KDO 8-P phosphatase, structure function project, S2F; HET: MES; 1.67A {Haemophilus influenzae RD} SCOP: c.108.1.5 PDB: 1j8d_A*

Probab=80.73  E-value=8  Score=28.05  Aligned_cols=75  Identities=11%  Similarity=-0.038  Sum_probs=38.4

Q ss_pred             cHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHH-HcCC---eEEEEcCC-CchH
Q 045172           65 FADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEAT-LRWL---KMVVVGDM-SDGA  139 (157)
Q Consensus        65 la~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Ar-er~l---~tVVVGd~-~~~~  139 (157)
                      +-.+|++.|+.+-.++..|...   + ..   .+...|++.++  +...+=...++.+. +.|+   .++.|||+ +|-.
T Consensus        43 ~l~~L~~~G~~~~i~Tg~~~~~---~-~~---~~~~lgl~~~~--~~~k~k~~~~~~~~~~~~~~~~~~~~vGD~~~Di~  113 (180)
T 1k1e_A           43 GIKMLMDADIQVAVLSGRDSPI---L-RR---RIADLGIKLFF--LGKLEKETACFDLMKQAGVTAEQTAYIGDDSVDLP  113 (180)
T ss_dssp             HHHHHHHTTCEEEEEESCCCHH---H-HH---HHHHHTCCEEE--ESCSCHHHHHHHHHHHHTCCGGGEEEEECSGGGHH
T ss_pred             HHHHHHHCCCeEEEEeCCCcHH---H-HH---HHHHcCCceee--cCCCCcHHHHHHHHHHcCCCHHHEEEECCCHHHHH
Confidence            3457888899888888887621   1 11   22223454433  22222233433333 3353   56777777 4444


Q ss_pred             HHhhhhccc
Q 045172          140 LKRIANAFF  148 (157)
Q Consensus       140 L~r~AD~~f  148 (157)
                      ..+.|++.+
T Consensus       114 ~~~~ag~~~  122 (180)
T 1k1e_A          114 AFAACGTSF  122 (180)
T ss_dssp             HHHHSSEEE
T ss_pred             HHHHcCCeE
Confidence            455555444

>3kbb_A Phosphorylated carbohydrates phosphatase TM_1254; hydrolase, arbohydrate metabolism, COBA magnesium, manganese, metal-binding, nickel; HET: MSE GOL; 1.74A {Thermotoga maritima MSB8}

Probab=80.30  E-value=6.5  Score=28.21  Aligned_cols=38  Identities=21%  Similarity=0.215  Sum_probs=26.6

Q ss_pred             HHHHHHHHhhcCcccC-CCcHHHHHhhceEEEEecCCCc
Q 045172           47 EKNKMAASAILTPKVG-YGFADELKRAWFWVRMVLVKPQ   84 (157)
Q Consensus        47 ~kY~~Aar~~l~pkvg-ygla~eLrRAGv~V~~V~dkpq   84 (157)
                      +.|.....+...|--| ..+-..|+..|+.+-.++..|.
T Consensus        73 ~~~~~~~~~~~~~~pg~~~~l~~L~~~g~~~~i~tn~~~  111 (216)
T 3kbb_A           73 EEKKRVFSELLKENPGVREALEFVKSKRIKLALATSTPQ  111 (216)
T ss_dssp             HHHHHHHHHHCCBCTTHHHHHHHHHHTTCEEEEECSSCH
T ss_pred             HHHHHHHHHhcccCccHHHHHHHHHHcCCCcccccCCcH
Confidence            3444455555566555 5667788999999999988876

>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=80.08  E-value=6.8  Score=31.26  Aligned_cols=66  Identities=17%  Similarity=0.199  Sum_probs=42.3

Q ss_pred             CcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHH-HHHHHHH-cCCeEEEEcCC
Q 045172           64 GFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVE-VFQEATL-RWLKMVVVGDM  135 (157)
Q Consensus        64 gla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~-~lr~Are-r~l~tVVVGd~  135 (157)
                      |+...++..|+.+..+....+ +|.  ...+..++ .+++|.|+++|..  +.+ +...+.+ .++.+|+|+..
T Consensus        28 Gi~~~~~~~g~~~~~~~~~~~-~~~--~~~l~~l~-~~~~dgIi~~~~~--~~~~~~~~a~~~p~~p~v~id~~   95 (318)
T 2fqx_A           28 GISRFAQENNAKCKYVTASTD-AEY--VPSLSAFA-DENMGLVVACGSF--LVEAVIETSARFPKQKFLVIDAV   95 (318)
T ss_dssp             HHHHHHHHTTCEEEEEECCSG-GGH--HHHHHHHH-HTTCSEEEEESTT--THHHHHHHHHHCTTSCEEEESSC
T ss_pred             HHHHHHHHhCCeEEEEeCCCH-HHH--HHHHHHHH-HcCCCEEEECChh--HHHHHHHHHHHCCCCEEEEEcCc
Confidence            566677888998887654332 443  23333444 7899999999743  233 4444544 38999999864

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	157
d1dbqa_	282	Purine repressor (PurR), C-terminal domain {Escher	95.86
d2dria_	271	D-ribose-binding protein {Escherichia coli, strain	95.27
d1jyea_	271	Lac-repressor (lacR) core (C-terminal domain) {Esc	94.64
d8abpa_	305	L-arabinose-binding protein {Escherichia coli [Tax	94.45
d2feaa1	226	2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate	93.94
d1tjya_	316	AI-2 receptor LsrB {Salmonella typhi [TaxId: 90370	93.77
d2b8ea1	135	Cation-transporting ATPase {Archaeon Archaeoglobus	93.24
d1guda_	288	D-allose-binding protein {Escherichia coli [TaxId:	92.82
d2fvya1	305	Galactose/glucose-binding protein {Escherichia col	91.28
d1vima_	192	Hypothetical protein AF1796 {Archaeon Archaeoglobu	90.49
d1m3sa_	186	Hypothetical protein YckF {Bacillus subtilis [TaxI	90.07
d1jx6a_	338	Quorum-sensing signal (autoinducer-2) binding prot	88.9
d2nzug1	275	Glucose-resistance amylase regulator CcpA, C-termi	88.69
d1r8ja2	135	N-terminal domain of the circadian clock protein K	88.63
d1u7pa_	164	Magnesium-dependent phosphatase-1, Mdp1 {Mouse (Mu	88.05
d2bona1	295	Lipid kinase YegS {Escherichia coli [TaxId: 562]}	87.82
d1byka_	255	Trehalose repressor, C-terminal domain {Escherichi	85.55
d1swva_	257	Phosphonoacetaldehyde hydrolase {Bacillus cereus [	81.68

>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=0.019  Score=41.68  Aligned_cols=70  Identities=11%  Similarity=0.032  Sum_probs=54.3

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      -|+..++++.|+.+.+.+...+   ......+.+.+..++++.+++++.+.+-..+...+...++..|++|..
T Consensus        20 ~gi~~~~~~~gy~~~~~~~~~d---~~~~~~~~~~l~~~~vdgiIi~~~~~~~~~~~~~~~~~~iPvV~~~~~   89 (282)
T d1dbqa_          20 EAVEKNCFQKGYTLILGNAWNN---LEKQRAYLSMMAQKRVDGLLVMCSEYPEPLLAMLEEYRHIPMVVMDWG   89 (282)
T ss_dssp             HHHHHHHHHHTCEEEEEECTTC---HHHHHHHHHHHHHTTCSEEEEECSCCCHHHHHHHHHTTTSCEEEEECS
T ss_pred             HHHHHHHHHcCCEEEEEeCCCC---HHHHHHHHHHHHhcCCCEEeeecccccchhhhhHHhhcCCCceEEEec
Confidence            4778899999999988765544   555667777777899999999887776555556666689999999865

>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=95.27  E-value=0.035  Score=39.80  Aligned_cols=70  Identities=10%  Similarity=0.035  Sum_probs=55.4

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCC-cchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDD-SDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDD-sDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+-.++++.|+.+.+....   .|.+...+..+.+-.+|++++++.+.| ..+.+.++.+++.|...|+++..
T Consensus        21 ~gi~~~a~~~g~~~~i~~~~---~~~~~~~~~i~~~~~~~~d~ii~~~~~~~~~~~~~~~~~~~~ipvV~~~~~   91 (271)
T d2dria_          21 DGAQKEADKLGYNLVVLDSQ---NNPAKELANVQDLTVRGTKILLINPTDSDAVGNAVKMANQANIPVITLDRQ   91 (271)
T ss_dssp             HHHHHHHHHHTCEEEEEECT---TCHHHHHHHHHHHTTTTEEEEEECCSSTTTTHHHHHHHHHTTCCEEEESSC
T ss_pred             HHHHHHHHHcCCEEEEEeCC---CCHHHHHHHHHHHHhcCCcccccccccccchHHHHHHHhhcceeEEEeccc
Confidence            58889999999999876432   355655555555558999999999765 55789999999999999999864

>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=94.64  E-value=0.034  Score=41.28  Aligned_cols=71  Identities=10%  Similarity=0.022  Sum_probs=50.9

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++.+||.|-+....-..+ ......+..++ .+++|.|+|-++..+...+..++.+.++.+|.+|-.
T Consensus        20 ~~i~~~a~~~Gy~v~v~~~~~~~~-~~~~~~l~~l~-~~~vdgiIl~~~~~~~~~~~~~~~~~~iPvV~~d~~   90 (271)
T d1jyea_          20 AAILSRADQLGASVVVSMVERSGV-EACKTAVHNLL-AQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVS   90 (271)
T ss_dssp             HHHHHHHHHTTCEEEEEECCSSSH-HHHHHHHHHHH-TTTCSCEEEESCCCHHHHHHHHHHTTTSCEEESSSC
T ss_pred             HHHHHHHHHcCCEEEEEECCCCCH-HHHHHHHHHHH-hcCCCEEEeccccCchhHHHHHHHhcCCCeeeeecc
Confidence            577889999999996643221111 22333344444 789999998877777788889999999999998653

>d8abpa_ c.93.1.1 (A:) L-arabinose-binding protein {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like I
superfamily: Periplasmic binding protein-like I
family: L-arabinose binding protein-like
domain: L-arabinose-binding protein
species: Escherichia coli [TaxId: 562]

Probab=94.45  E-value=0.099  Score=38.48  Aligned_cols=67  Identities=18%  Similarity=0.057  Sum_probs=50.8

Q ss_pred             CcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcc-hHHHHHHHHHcCCeEEEEcC
Q 045172           64 GFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSD-FVEVFQEATLRWLKMVVVGD  134 (157)
Q Consensus        64 gla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsD-F~~~lr~Arer~l~tVVVGd  134 (157)
                      |.-.+.+..|+.+..+.. .   |..-+...++.+-.+++|.|++++-|++ +..+++.|++.|..+|.++.
T Consensus        22 g~~~aa~~~G~~~i~~~~-~---d~~~q~~~i~~li~~~vDgiIi~~~~~~~~~~~~~~a~~~giPVV~~d~   89 (305)
T d8abpa_          22 FADKAGKDLGFEVIKIAV-P---DGEKTLNAIDSLAASGAKGFVICTPDPKLGSAIVAKARGYDMKVIAVDD   89 (305)
T ss_dssp             HHHHHHHHHTEEEEEEEC-C---SHHHHHHHHHHHHHTTCCEEEEECSCGGGHHHHHHHHHHTTCEEEEESS
T ss_pred             HHHHHHHHcCCEEEEEcC-C---CHHHHHHHHHHHHHcCCCEEEEccccccccHHHHHHHHhcCCCEEEEcC
Confidence            445567788998855432 2   4555566666666899999999987665 67899999999999999964

>d2feaa1 c.108.1.20 (A:2-227) 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate phosphatase MtnX {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: HAD-like
superfamily: HAD-like
family: MtnX-like
domain: 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate phosphatase MtnX
species: Bacillus subtilis [TaxId: 1423]

Probab=93.94  E-value=0.048  Score=38.58  Aligned_cols=101  Identities=13%  Similarity=0.113  Sum_probs=64.0

Q ss_pred             hhHHHHHHHHhhcCcccC-CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHh-hccCcceEEEEcCCcch-------
Q 045172           45 KMEKNKMAASAILTPKVG-YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMV-DKRRFGCLVVVSDDSDF-------  115 (157)
Q Consensus        45 k~~kY~~Aar~~l~pkvg-ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~-~~r~v~clvLVSDDsDF-------  115 (157)
                      ..+.|.....+.+++.-| ..+-..|+..|+.+-.|+.++.    ...+.+.+-+ ..--+-|-.++.++.++       
T Consensus        62 ~~~~~~~~~~~~~~l~pg~~~~l~~L~~~g~~~~ivS~~~~----~~i~~~l~~l~~~~~~~an~~~~~~~~~~~~~~~~  137 (226)
T d2feaa1          62 LKEEITSFVLEDAKIREGFREFVAFINEHEIPFYVISGGMD----FFVYPLLEGIVEKDRIYCNHASFDNDYIHIDWPHS  137 (226)
T ss_dssp             GHHHHHHHHHHHCCBCTTHHHHHHHHHHHTCCEEEEEEEEH----HHHHHHHTTTSCGGGEEEEEEECSSSBCEEECTTC
T ss_pred             cHHHHHHHHHhccchhHHHHHHHHHHHhcccccccCCcchh----hhHHHHHHHcCCccceeeeeEEEeCCcceeccccc
Confidence            344455555556666555 5567779999999999998876    2333333221 01122343455554433       


Q ss_pred             -------------HHHHHHHHHcCCeEEEEcCC-CchHHHhhhhcccc
Q 045172          116 -------------VEVFQEATLRWLKMVVVGDM-SDGALKRIANAFFS  149 (157)
Q Consensus       116 -------------~~~lr~Arer~l~tVVVGd~-~~~~L~r~AD~~fs  149 (157)
                                   ..+++......-.++.|||+ +|-.-.+.||+.|.
T Consensus       138 ~~~~~~~~k~~~~~~~~~~~~~~~~~~i~iGDs~~Dl~~a~~A~~~~a  185 (226)
T d2feaa1         138 CKGTCSNQCGCCKPSVIHELSEPNQYIIMIGDSVTDVEAAKLSDLCFA  185 (226)
T ss_dssp             CCTTCCSCCSSCHHHHHHHHCCTTCEEEEEECCGGGHHHHHTCSEEEE
T ss_pred             cccccccCCHHHHHHHHHHhcCCCceEEEEeCchhhHHHHHHCCEEEE
Confidence                         46677777777799999999 76666778898763

>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=93.77  E-value=0.095  Score=37.92  Aligned_cols=71  Identities=14%  Similarity=0.104  Sum_probs=54.4

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCc-chHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDS-DFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDs-DF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++..||.|..+.  |.-.|.+-+...++.+-..++|.||+...|+ .+...++.|.+.|..+|++...
T Consensus        23 ~g~~~~a~~~G~~v~~~~--~~~~d~~~q~~~i~~~i~~~~dgIIi~~~~~~~~~~~~~~a~~~gi~vv~~d~~   94 (316)
T d1tjya_          23 NGAQEAGKALGIDVTYDG--PTEPSVSGQVQLVNNFVNQGYDAIIVSAVSPDGLCPALKRAMQRGVKILTWDSD   94 (316)
T ss_dssp             HHHHHHHHHHTCEEEECC--CSSCCHHHHHHHHHHHHHTTCSEEEECCSSSSTTHHHHHHHHHTTCEEEEESSC
T ss_pred             HHHHHHHHHcCCEEEEEE--CCCCCHHHHHHHHHHHHhcCCCeeeecccccchhhhhhhhhhcccccceecccc
Confidence            577888999999887652  2224566666666665589999999987665 5788999999999999998765

>d2b8ea1 c.108.1.7 (A:416-434,A:548-663) Cation-transporting ATPase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: HAD-like
superfamily: HAD-like
family: Meta-cation ATPase, catalytic domain P
domain: Cation-transporting ATPase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=93.24  E-value=0.075  Score=37.84  Aligned_cols=76  Identities=18%  Similarity=0.109  Sum_probs=51.6

Q ss_pred             HHHHHhhceEEEEecCCCc-cHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC-CchHHHhh
Q 045172           66 ADELKRAWFWVRMVLVKPQ-DADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM-SDGALKRI  143 (157)
Q Consensus        66 a~eLrRAGv~V~~V~dkpq-AAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~-~~~~L~r~  143 (157)
                      -.+|+++|+.|.+++.-.+ .|.        ......|++.+.-=+...+=..+++..+..+ .+.+|||+ +|-..-+.
T Consensus        30 I~~L~~~Gi~v~ilTGD~~~~a~--------~ia~~lgI~~v~~~~~p~~k~~~v~~~q~~~-~v~~vGDg~nD~~aL~~  100 (135)
T d2b8ea1          30 VQELKRMGIKVGMITGDNWRSAE--------AISRELNLDLVIAEVLPHQKSEEVKKLQAKE-VVAFVGDGINDAPALAQ  100 (135)
T ss_dssp             HHHHHHTTCEEEEECSSCHHHHH--------HHHHHHTCSEEECSCCHHHHHHHHHHHTTTS-CEEEEECSSSSHHHHHH
T ss_pred             HHHHHHcCCEEEEEcCcchhhhh--------HHHhhhhhhhhccccchhHHHHHHHHHHcCC-EEEEEeCCCCcHHHHHh
Confidence            4579999999999965444 221        2223457876665455555566676666554 78899999 77777778


Q ss_pred             hhcccch
Q 045172          144 ANAFFSW  150 (157)
Q Consensus       144 AD~~fsW  150 (157)
                      ||+.++.
T Consensus       101 Advgia~  107 (135)
T d2b8ea1         101 ADLGIAV  107 (135)
T ss_dssp             SSEEEEE
T ss_pred             CCeeeec
Confidence            8988864

>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=92.82  E-value=0.16  Score=36.88  Aligned_cols=72  Identities=13%  Similarity=0.118  Sum_probs=54.5

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCC-cchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDD-SDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDD-sDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+-.+++..|+.+..+....+ .|.+...+..+.+-++++|.|++.+-+ .+....+++|.+.|...|.+...
T Consensus        21 ~g~~~~a~~~g~~~~i~~~~~~-~d~~~q~~~i~~~i~~~~DgIi~~~~~~~~~~~~l~~~~~~gipvv~~d~~   93 (288)
T d1guda_          21 KGIEDEAKTLGVSVDIFASPSE-GDFQSQLQLFEDLSNKNYKGIAFAPLSSVNLVMPVARAWKKGIYLVNLDEK   93 (288)
T ss_dssp             HHHHHHHHHHTCCEEEEECSST-TCHHHHHHHHHHHHTSSEEEEEECCSSSSTTHHHHHHHHHTTCEEEEESSC
T ss_pred             HHHHHHHHHcCCEEEEEecCCC-CCHHHHHHHHHHHHhcCCCEEEEecCCcchhhHHHHHHHhCCCeEEEeCCC
Confidence            4777889999999998643222 455655555555448999999998654 56788999999999999998765

>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=91.28  E-value=0.35  Score=34.78  Aligned_cols=70  Identities=14%  Similarity=0.053  Sum_probs=52.0

Q ss_pred             CCcHHHHHhh-ceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEc-CCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRA-WFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVS-DDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRA-Gv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVS-DDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..+++.. |+-+......   .|.+-+...++.+-++++|.|++.. +...+...+..+++.|..+|++...
T Consensus        21 ~gi~~~a~~~~~~~l~~~~~~---~~~~~q~~~i~~li~~~vDgiii~~~~~~~~~~~~~~~~~~~ipvv~~~~~   92 (305)
T d2fvya1          21 KAIEQDAKAAPDVQLLMNDSQ---NDQSKQNDQIDVLLAKGVKALAINLVDPAAAGTVIEKARGQNVPVVFFNKE   92 (305)
T ss_dssp             HHHHHHHHTCTTEEEEEEECT---TCHHHHHHHHHHHHHTTCSEEEECCSSGGGHHHHHHHHHTTTCCEEEESSC
T ss_pred             HHHHHHHHHcCCcEEEEEcCC---CCHHHHHHHHHHHHHcCCCEEEeecccccccHHHHHHHHhcCCceeeeeec
Confidence            4566777765 7777665322   2566666665555579999999885 5678899999999999999999765

>d1vima_ c.80.1.3 (A:) Hypothetical protein AF1796 {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: SIS domain
superfamily: SIS domain
family: mono-SIS domain
domain: Hypothetical protein AF1796
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=90.49  E-value=0.16  Score=36.99  Aligned_cols=70  Identities=21%  Similarity=0.183  Sum_probs=51.0

Q ss_pred             HHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCC---cchHHHHHHHHHcCCeEEEEcCCCchHHHh
Q 045172           66 ADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDD---SDFVEVFQEATLRWLKMVVVGDMSDGALKR  142 (157)
Q Consensus        66 a~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDD---sDF~~~lr~Arer~l~tVVVGd~~~~~L~r  142 (157)
                      +..|.+-|..|..+++-- ++          .+ + .=|+++++|-.   .+-.++++.|+++|.++|.|=+.....|.+
T Consensus        59 ~~~l~~lg~~~~~~~~~~-~~----------~i-~-~~Dl~i~iS~sG~t~~~i~~~~~ak~~g~~vI~IT~~~~s~l~~  125 (192)
T d1vima_          59 AMRLMHLGYTVYVVGETV-TP----------RI-T-DQDVLVGISGSGETTSVVNISKKAKDIGSKLVAVTGKRDSSLAK  125 (192)
T ss_dssp             HHHHHHTTCCEEETTSTT-CC----------CC-C-TTCEEEEECSSSCCHHHHHHHHHHHHHTCEEEEEESCTTSHHHH
T ss_pred             hhhhcccccccccccccc-cc----------cc-c-ccccceeccccccchhhHHHHHHHHhhcccceeeeecccccccc
Confidence            445778898888876521 11          12 1 23788888744   556778889999999999997776689999


Q ss_pred             hhhccc
Q 045172          143 IANAFF  148 (157)
Q Consensus       143 ~AD~~f  148 (157)
                      .||..|
T Consensus       126 ~ad~~l  131 (192)
T d1vima_         126 MADVVM  131 (192)
T ss_dssp             HCSEEE
T ss_pred             ccceEE
Confidence            999887

>d1m3sa_ c.80.1.3 (A:) Hypothetical protein YckF {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: SIS domain
superfamily: SIS domain
family: mono-SIS domain
domain: Hypothetical protein YckF
species: Bacillus subtilis [TaxId: 1423]

Probab=90.07  E-value=0.2  Score=36.28  Aligned_cols=70  Identities=10%  Similarity=0.019  Sum_probs=51.2

Q ss_pred             HHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCC---cchHHHHHHHHHcCCeEEEEcCCCchHHHh
Q 045172           66 ADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDD---SDFVEVFQEATLRWLKMVVVGDMSDGALKR  142 (157)
Q Consensus        66 a~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDD---sDF~~~lr~Arer~l~tVVVGd~~~~~L~r  142 (157)
                      +..|.+-|+.+-.+.|- .+          ..+  ..=||++.+|-.   .+-.++++.|+++|.++|.|-+.....|.+
T Consensus        56 ~~~l~~lg~~~~~~~d~-~~----------~~~--~~~Dl~I~iS~sG~t~~~i~~~~~ak~~g~~iI~IT~~~~s~La~  122 (186)
T d1m3sa_          56 AMRLMHMGFNAHIVGEI-LT----------PPL--AEGDLVIIGSGSGETKSLIHTAAKAKSLHGIVAALTINPESSIGK  122 (186)
T ss_dssp             HHHHHHTTCCEEETTST-TC----------CCC--CTTCEEEEECSSSCCHHHHHHHHHHHHTTCEEEEEESCTTSHHHH
T ss_pred             HHHHHhccCCCCcCChh-hc----------ccC--CCCCEEEEecCccchhhhHHHHHHHHHCCCCEEEEecCCCchhhH
Confidence            44578899988887552 10          012  223788888865   355678899999999999997776789999


Q ss_pred             hhhccc
Q 045172          143 IANAFF  148 (157)
Q Consensus       143 ~AD~~f  148 (157)
                      .||..+
T Consensus       123 ~ad~~i  128 (186)
T d1m3sa_         123 QADLII  128 (186)
T ss_dssp             HCSEEE
T ss_pred             hCCEEE
Confidence            999776

>d1jx6a_ c.93.1.1 (A:) Quorum-sensing signal (autoinducer-2) binding protein LuxP {Vibrio harveyi [TaxId: 669]}

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: Quorum-sensing signal (autoinducer-2) binding protein LuxP
species: Vibrio harveyi [TaxId: 669]

Probab=88.90  E-value=0.61  Score=35.02  Aligned_cols=71  Identities=14%  Similarity=0.171  Sum_probs=49.0

Q ss_pred             CCcHHHHHhhceE--EEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHH-HcCCeEEEEcC
Q 045172           63 YGFADELKRAWFW--VRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEAT-LRWLKMVVVGD  134 (157)
Q Consensus        63 ygla~eLrRAGv~--V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Ar-er~l~tVVVGd  134 (157)
                      .|+..++...|+.  +.++...++ .|.+......+.+-..++|.||+.+++++....+..+. +.+..+|+++-
T Consensus        61 ~~~~~~~~~~g~~~~i~~~~~~s~-~d~~~q~~~i~~~i~~~vDgIIi~~~~~~~~~~i~~~~~~~~ipvv~~~~  134 (338)
T d1jx6a_          61 ASFEKRLYKLNINYQLNQVFTRPN-ADIKQQSLSLMEALKSKSDYLIFTLDTTRHRKFVEHVLDSTNTKLILQNI  134 (338)
T ss_dssp             HHHHHHHHHTTCCEEEEEEECCTT-CCHHHHHHHHHHHHHTTCSEEEECCSSSTTHHHHHHHHHHCSCEEEEETC
T ss_pred             HHHHHHHHHcCCcEEEEEEecCCC-CCHHHHHHHHHHHHhcCCCEEEEecCcccchHHHHHHHHhCCCeEEEEcc
Confidence            4678889999954  444443333 55666666555555899999999998888887665554 46677776653

>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=88.69  E-value=1.3  Score=31.49  Aligned_cols=69  Identities=9%  Similarity=0.043  Sum_probs=50.5

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDM  135 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~  135 (157)
                      .|+..++++.|+.+.+..-.-.   ......+.+.+..+++|.+++++...+ ......+++.+...|.++..
T Consensus        23 ~gi~~~~~~~g~~~~~~~~~~~---~~~e~~~i~~~~~~~vdgii~~~~~~~-~~~~~~l~~~~~pvv~~~~~   91 (275)
T d2nzug1          23 RGIEDIATMYKYNIILSNSDQN---QDKELHLLNNMLGKQVDGIIFMSGNVT-EEHVEELKKSPVPVVLAASI   91 (275)
T ss_dssp             HHHHHHHHHTTCEEEEEECTTC---HHHHHHHHHHHHTTCCSEEEECCSCCC-HHHHHHHHHCSSCEEEESCC
T ss_pred             HHHHHHHHHcCCEEEEEECCCC---HHHHHHHHHHHHhcCCceeeccccchh-hHHHHHHhhccccccccccc
Confidence            5789999999999987644332   344455566555799999998875544 34457788899999999865

>d1r8ja2 c.23.1.5 (A:1-135) N-terminal domain of the circadian clock protein KaiA {Synechococcus elongatus [TaxId: 32046]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: N-terminal domain of the circadian clock protein KaiA
domain: N-terminal domain of the circadian clock protein KaiA
species: Synechococcus elongatus [TaxId: 32046]

Probab=88.63  E-value=0.34  Score=35.52  Aligned_cols=36  Identities=28%  Similarity=0.577  Sum_probs=32.0

Q ss_pred             ccCcceEEEEcCCcchHHHHHHHHHcC--CeEEEEcCC
Q 045172          100 KRRFGCLVVVSDDSDFVEVFQEATLRW--LKMVVVGDM  135 (157)
Q Consensus       100 ~r~v~clvLVSDDsDF~~~lr~Arer~--l~tVVVGd~  135 (157)
                      +..|||||||.++.+...+.....++|  +-+||||+.
T Consensus        48 ~e~iDcLVl~~~~~~l~~l~~qL~~~GlLlPaViv~~~   85 (135)
T d1r8ja2          48 RDQIDCLILVAANPSFRAVVQQLCFEGVVVPAIVVGDR   85 (135)
T ss_dssp             TTSCSEEEEETTSTTHHHHHHHHHHTTCCCCEEEESCC
T ss_pred             cccCCEEEEEecCCccHHHHHHHHhcCccccEEEEecC
Confidence            456999999999999999999999988  579999975

>d1u7pa_ c.108.1.17 (A:) Magnesium-dependent phosphatase-1, Mdp1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: HAD-like
superfamily: HAD-like
family: Magnesium-dependent phosphatase-1, Mdp1
domain: Magnesium-dependent phosphatase-1, Mdp1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=88.05  E-value=1  Score=30.98  Aligned_cols=21  Identities=10%  Similarity=-0.091  Sum_probs=15.9

Q ss_pred             CcHHHHHhhceEEEEecCCCc
Q 045172           64 GFADELKRAWFWVRMVLVKPQ   84 (157)
Q Consensus        64 gla~eLrRAGv~V~~V~dkpq   84 (157)
                      .+-.+|+..|+.+-.+|.+++
T Consensus        53 e~L~~L~~~G~~~~v~S~~~~   73 (164)
T d1u7pa_          53 EVLGRLQSLGVPVAAASRTSE   73 (164)
T ss_dssp             HHHHHHHHTTCCEEEEECCSC
T ss_pred             HHHHHHHHCCCcEEEEecccc
Confidence            455778888888888887766

>d2bona1 e.52.1.2 (A:5-299) Lipid kinase YegS {Escherichia coli [TaxId: 562]}

class: Multi-domain proteins (alpha and beta)
fold: NAD kinase/diacylglycerol kinase-like
superfamily: NAD kinase/diacylglycerol kinase-like
family: Diacylglycerol kinase-like
domain: Lipid kinase YegS
species: Escherichia coli [TaxId: 562]

Probab=87.82  E-value=0.34  Score=36.72  Aligned_cols=58  Identities=17%  Similarity=0.233  Sum_probs=45.2

Q ss_pred             HHHHHHHhhccCcceEEEEcCCc-chHHHHHHHHHcCCeEEEEcCCCchHHHhhhhcccc
Q 045172           91 RNYMVAMVDKRRFGCLVVVSDDS-DFVEVFQEATLRWLKMVVVGDMSDGALKRIANAFFS  149 (157)
Q Consensus        91 ~~~~~~~~~~r~v~clvLVSDDs-DF~~~lr~Arer~l~tVVVGd~~~~~L~r~AD~~fs  149 (157)
                      .+++.+.+...|+++-+.+|... |-.++++.|.+.+..+|||+.+ |+.+...++..+.
T Consensus        17 ~~~~~~~l~~~g~~~~v~~T~~~g~a~~~~~~~~~~~~d~Ivv~GG-DGTv~ev~~gl~~   75 (295)
T d2bona1          17 LREAIMLLREEGMTIHVRVTWEKGDAARYVEEARKFGVATVIAGGG-DGTINEVSTALIQ   75 (295)
T ss_dssp             HHHHHHHHHTTTCCEEEEECCSTTHHHHHHHHHHHHTCSEEEEEES-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCEEEEEEcCCcchHHHHHHHHHhcCCCEEEEECC-CcHHHHHHHHHHh
Confidence            35677788788899977777664 7888889888888888888777 6778777766543

>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=85.55  E-value=0.72  Score=33.37  Aligned_cols=68  Identities=9%  Similarity=-0.035  Sum_probs=49.7

Q ss_pred             CCcHHHHHhhceEEEEecCCCccHHHHHHHHHHHHhhccCcceEEEEcCCcchHHHHHHHHHcCCeEEEEcCCC
Q 045172           63 YGFADELKRAWFWVRMVLVKPQDADVLLRNYMVAMVDKRRFGCLVVVSDDSDFVEVFQEATLRWLKMVVVGDMS  136 (157)
Q Consensus        63 ygla~eLrRAGv~V~~V~dkpqAAD~AL~~~~~~~~~~r~v~clvLVSDDsDF~~~lr~Arer~l~tVVVGd~~  136 (157)
                      .|+..+|+..||.+-++.-..+   ........+.+.++++|.+++.+.+.+-..   .+...+...|+||...
T Consensus        22 ~~i~~~~~~~Gy~~~~~~s~~d---~~~~~~~i~~l~~~~vdgiIi~~~~~~~~~---~~~~~~~p~v~i~~~~   89 (255)
T d1byka_          22 QTMLPAFYEQGYDPIMMESQFS---PQLVAEHLGVLKRRNIDGVVLFGFTGITEE---MLAHWQSSLVLLARDA   89 (255)
T ss_dssp             HHHHHHHHHHTCEEEEEECTTC---HHHHHHHHHHHHTTTCCEEEEECCTTCCTT---TSGGGSSSEEEESSCC
T ss_pred             HHHHHHHHHcCCEEEEEeCCCC---HHHHHHHHHHHHhccccceeeccccchHHH---HHHHcCCCEEEeccCC
Confidence            5789999999999988754433   334444556666899999999977665543   4456788999998764

>d1swva_ c.108.1.3 (A:) Phosphonoacetaldehyde hydrolase {Bacillus cereus [TaxId: 1396]}

class: Alpha and beta proteins (a/b)
fold: HAD-like
superfamily: HAD-like
family: Phosphonoacetaldehyde hydrolase-like
domain: Phosphonoacetaldehyde hydrolase
species: Bacillus cereus [TaxId: 1396]

Probab=81.68  E-value=5.1  Score=28.14  Aligned_cols=40  Identities=10%  Similarity=-0.094  Sum_probs=27.9

Q ss_pred             hhHHHHHHHHhhcCcccC-CCcHHHHHhhceEEEEecCCCc
Q 045172           45 KMEKNKMAASAILTPKVG-YGFADELKRAWFWVRMVLVKPQ   84 (157)
Q Consensus        45 k~~kY~~Aar~~l~pkvg-ygla~eLrRAGv~V~~V~dkpq   84 (157)
                      ..+.|.+.......|--| -.+-.+|+..|+.+=.++..|.
T Consensus        86 ~~~~~~~~~~~~~~~~~g~~~~L~~Lk~~g~~i~i~Tn~~~  126 (257)
T d1swva_          86 FEEILFAILPRYASPINGVKEVIASLRERGIKIGSTTGYTR  126 (257)
T ss_dssp             HHHHHHHHGGGGCCBCTTHHHHHHHHHHTTCEEEEBCSSCH
T ss_pred             HHHHHHHHhhccCccCCcHHHHHHHHHhcccceeecCCCch
Confidence            445566665555555555 4566778889999999988876